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It’s all about information, Professor Feser

Over at his blog, Professor Edward Feser has been writing a multi-part critique of Professor Alex Rosenberg’s bestselling book, The Atheist’s Guide to Reality: Enjoying Life without Illusions. Rosenberg is an unabashed defender of scientism, an all-out reductionist who doesn’t believe in a “self”, doesn’t believe we have thoughts that are genuinely about anything, and doesn’t believe in free will or morality. Instead, he advocates what he calls “nice nihilism.” In the last line of his book, Rosenberg advises his readers to “Take a Prozac or your favorite serotonin reuptake inhibitor, and keep taking them till they kick in.”

Edward Feser has done an excellent job of demolishing Rosenberg’s arguments, and if readers want to peruse his posts from start to finish, they can read them all here:

Part One
Part Two
Part Three
Part Four
Part Five
Part Six

Professor Rosenberg’s argument that Darwinism is incompatible with God

In his latest installment, Professor Feser takes aim at an argument put forward by Rosenberg, that Darwinism is incompatible with the idea that God is omniscient. In his reply to Rosenberg, Feser also takes a swipe at Intelligent Design, about which I’ll have more to say below. In the meantime, let’s have a look at Rosenberg’s argument against theistic evolution.

Rosenberg argues as follows: Darwinian processes, being non-teleological, do not aim at the generation of any particular kind of species, including the human species. What’s more, these processes contain a built-in element of irreducible randomness: variation. Mutations are random, and no one could have known in advance that evolution would go the way it did. Therefore if God had used such processes as a means of creating us, He could not have known that they would be successful, and therefore He would not be omniscient.

In his response, Feser criticizes Professor Rosenberg’s argument on several grounds, arguing that:

(i) belief in the God of classical theism does not logically entail that the emergence of the human race was an event planned by Him (i.e. God might have intentionally made the cosmos, but we might have been an accident);

(ii) God may have intended that the universe should contain rational beings (who possess the ability to reason by virtue of their having immortal souls) without intending that these beings should be human beings, with the kind of body that Homo sapiens possesses – hence our bodies may be the result of an accidental process;

(iii) if you believe in the multiverse (which Feser doesn’t but Rosenberg does), it is perfectly consistent to hold that while the evolution of Homo sapiens may have been improbable in any particular universe, nevertheless it would have been inevitable within some universe; and

(iv) in any case, the probabilistic nature of Darwinian processes does not rule out divine intervention.

Professor Feser’s big beef with Rosenberg’s argument: Divine causality is of a different order from that of natural causes

But Professor Feser’s chief objection to Rosenberg’s anti-theistic argument is that it ignores the distinction between Divine and creaturely causality. At this point, Feser takes pains to distinguish his intellectual position from that of the Intelligent Design movement. He remarks: “What Aristotelian-Thomistic critics of ID fundamentally object to is ID’s overly anthropomorphic conception of God and its implicit confusion of primary and secondary causality.” (I should point out in passing that Intelligent Design is a scientific program, and as such, it makes no claim to identify the Designer. Nevertheless, many Intelligent Design proponents would be happy to refer to this Designer as God.)

God, argues Feser, is like the author of a book. Intelligent natural agents (e.g. human beings) are the characters in the story, while sub-intelligent agents correspond to the everyday processes described within the story. The key point here is that God is outside the book that He creates and maintains in existence (i.e. the cosmos), while we are inside it. God’s causality is therefore of an entirely different order from that of creatures. To say that God intervened in the history of life in order to guarantee that Homo sapiens would emerge (as Rosenberg seems to think that believers in God-guided evolution are bound to believe) is tantamount to treating God like one of the characters in His own story. In Feser’s words, it “is like saying that the author of a novel has to ‘intervene’ in the story at key points, keeping events from going the way they otherwise would in order to make sure that they turn out the way he needs them to for the story to work.” In reality, authors don’t need to intervene into their stories to obtain the outcomes they want, and neither need we suppose that God intervened in the history of life on Earth, so as to guarantee the emergence of human beings.

Feser then argues that things in the world derive their being and causal power from God, just as the characters in a story only exist and alter the course of events within the story because the author of the story wrote it in a way that allows them to do so. For this reason, Feser has no philosophical problem with the notion of Darwinian processes being sufficient to generate life, or biological species such as Homo sapiens. Causal agents possesss whatever powers God wants them to have, and their (secondary) causality is genuine, and perfectly compatible with the (primary) causality of God, their Creator. Just as “it would be absurd to suggest that in a science fiction novel in which such-and-such a species evolves, it is not really Darwinian processes that generate the species, but rather the author of the story who does so and merely made it seem as if Darwinian processes had done it,” so too, “it is absurd to suggest that if God creates a world in which human beings come about by natural selection, He would have to intervene in order to make the Darwinian processes come out the way He wants them to, in which case they would not be truly Darwinian.”

The problem isn’t one of insufficient causal power in Nature; it’s all about information

When I read this passage, I thought, “Aha! Now I see why Professor Feser thinks Intelligent Design proponents have got the wrong end of the stick. Now I see why he thinks we are committed to belief in a tinkering Deity who has to intervene in the natural order in order to change it.” For Feser inadvertently revealed two very interesting things in his thought-provoking post.

The first thing that Professor Feser inadvertently revealed was that he thinks that the difficulty that Intelligent Design proponents have with Darwinian evolution has to do with power – in particular, the causal powers of natural agents. As an Aristotelian-Thomist, Feser sees no difficulty in principle with God granting natural agents whatever causal powers He wishes, so long as they are not powers that only a Creator could possess. Why could not God therefore give mud the power to evolve into microbes, and thence into biological species such as Homo sapiens?

But the problem that Intelligent Design advocates have with this scenario has nothing to do with the powers of causal agents. Rather, it’s all about information: complex specified information, to be precise. By definition, any pattern in Nature that is highly improbable (from a naturalistic perspective) but is nevertheless capable of being described in a few words, instantiates complex specified information (CSI). So the philosophical question we need to address here is not: could God give mud the power to evolve into microbes and thence into the body of a man, but rather: could God give mud the complex specified information required for it to evolve into microbes and thence into the body of a man?

The answer to this question, as Edward Feser should be aware from having read Professor Michael Behe’s book, The Edge of Evolution (Free Press, 2007, pp. 238-239), is that Intelligent Design theory is perfectly compatible with such front-loading scenarios. Indeed, Behe argues that God might have fine-tuned the initial conditions of the universe at the Big Bang, in such a way that life’s subsequent evolution – and presumably that of human beings – was inevitable, without the need for any subsequent acts of God.

A second possibility is that God added complex specified information to the universe at some point (or points) subsequent to the Big Bang – e.g. at the dawn of life, or the Cambrian explosion – thereby guaranteeing the results He intended.

A third possibility is that the universe contains hidden laws, as yet unknown to science, which are very detailed, highly elaborate and specific, unlike the simple laws of physics that we know. On this scenario, complex specified information belongs to the very warp and woof of the universe: it’s a built-in feature, requiring no initial fine-tuning.

Personally, my own inclination is to plump for the second scenario, and say that we live in a cosmos which is made to be manipulated: it’s an inherently incomplete, open system, and the “gaps” are a vital part of Nature, just as the holes are a vital feature of Swiss cheese. I see no reason to believe in the existence of hidden, information-rich laws of the cosmos, especially when all the laws we know are low in information content; moreover, as Dr. Stephen Meyer has pointed out in his book, Signature in the Cell, all the scientific evidence we have points against the idea of “biochemical predestination”: simple chemicals do not naturally arrange themselves into complex information-bearing molecules such as DNA. I also think that front-loading the universe at the Big Bang would have required such an incredibly exquisite amount of fine-tuning on God’s part that it would have been much simpler for Him to “inject” complex specified information into the cosmos at a later date, when it was required. (When I say “at a later date”, I mean “later” from our time-bound perspective, of course, as the God of classical theism is timeless.) However, this is just my opinion. I could be wrong.

Complex specified information has to come from somewhere

One thing I’m quite sure of, though: not even God could make a universe without finely-tuned initial conditions and without information-rich laws, that was still capable of generating life without any need for a special act of God (or what Intelligent Design critics derogatorily refer to as “Divine intervention”, “manipulation” or “tinkering”). The reason why this couldn’t happen is that complex specified information doesn’t come from nowhere. It needs a source. And this brings me to the second point that Professor Feser inadvertently revealed in his post: he seems to think that information can just appear in the cosmos wherever God wants it to appear, without God having to perform any specific act that generates it.

This is where the book metaphor leads Feser astray, I believe. The author of a book doesn’t have to specify exactly how the events in his/her story unfold. All stories written by human authors are under-specified, in terms of both the states of affairs they describe – e.g. what’s the color of the house at 6 Privet Drive, next door to Harry Potter’s house? – and in terms of the processes occurring within the story – e.g. how exactly do magic wands do their work in Harry Potter? What law is involved? J. K. Rowling doesn’t tell us these things, and I don’t think most of her readers care, anyway.

But here’s the thing: God can’t afford to be vague about such matters. He’s not just writing a story; He’s making a world. Everything that He brings about in this world, He has to specify in some way: what happens, and how does it happen?

One way in which God could bring about a result He desires is by specifying the initial conditions in sufficient detail, such that the result is guaranteed to arise, given the ordinary course of events.

A second way for God to bring about a result He wants is for Him to specify the exact processes generating the result, in such detail that its subsequent production is bound to occur. (On this scenario, God brings about His desired effect through the operation of deterministic laws.)

A third way for God to produce a desired effect is for Him to make use of processes that do not infallibly yield a set result – i.e. probabilistic occurrences, which take place in accordance with indeterministic laws, and which involve a certain element of what we call randomness. In this case, God would not only have to specify the probabilistic processes He intends to make use of, but also specify the particular outcome He desires these processes to generate. (This could be accomplished by God without Him having to bias the probabilities of the processes in any way: all that is needed is top-down causation, which leaves the micro-level probabilistic processes intact but imposes an additional macro-level constraint on the outcome. For a description of how this would work, see my recent post, Is free will dead?)

Finally, God may refuse to specify any natural process or set of initial conditions that could help to generate the result He desires, and instead, simply specify the precise spatio-temporal point in the history of the cosmos.at which the result will occur. That’s what we call an act of God, and in such a case, the result is said to be brought about purely by God’s will, which acts as an immediate efficient cause generating the effect.

But whatever the way in which God chooses to bring about the result He desires, He must make a choice. He cannot simply specify the effect He desires, without specifying its cause – whether it be His Will acting immediately on Nature to bring about a desired effect, or some natural process and/or set of conditions operating in a manner that tends to generate the effect. Whatever God does, God has to do somehow.

But couldn’t God make evolution occur as a result of a probabilistic process?

Let’s go back to the third way available to God for generating a desired result: namely, working through probabilistic processes. What does Intelligent Design theory have to say about this Divine modus operandi? Basically, what it says is that it is impossible for God to remain hidden, if He chooses this way of acting, and if the desired effect is both improbable (in the normal course of events) and capable of being described very briefly – in other words, rich in complex specified information. For even if the micro-level probabilities are in no way affected by His agency, the macro-level effect constitutes a pattern in Nature which we can recognize as the work of an intelligent agent, since it is rich in CSI.

Professor Feser, working from his authorial metaphor for God, seems to have overlooked this point. The human author of a story can simply write: “Y occurred, as a freakish but statistically possible result of process X.” Here, the author simply specifies the result he/she intends (effect Y) and the process responsible (probabilistic process X, which, as luck would have it, produced Y). Because the effect in the story (Y) is both the result of a natural process (X) occurring in the story, and the result (on a higher level) of the author’s will, it appears that nothing more needs to be said. Feser seems to think that the same holds true for effects brought about by God, working through probabilistic processes: they are both the work of Nature and the work of God. Hence, he believes, nothing prevents God from producing life by a Darwinistic process, if He so chooses.

Not so fast, say Intelligent Design proponents. Probabilistic processes have no inherent tendency to generate outcomes that can be concisely described in language. If an outcome that can be described in a very concise manner is generated by a probabilistic process, and if the likelihood of the outcome is sufficiently low, then it is simply wrong to put this down to the work of Nature. The real work here is done by God, the Intelligent Agent Who specified the outcome in question. It’s fundamentally wrong to give any credit to the natural probabilistic process for the result obtained, in a case like this: for even if God works through such a process, the process itself has no tendency to aim for concisely describable outcomes. God-guided evolution is therefore by definition non-Darwinian. Contrary to Feser, it is not absurd for Intelligent Design proponents to argue that when “such-and-such a species evolves, it is not really Darwinian processes that generate the species,” since Darwinian processes are inherently incapable of generating large amounts of complex specific information, and when we trace the evolution of any species back far enough, we will find that large amounts of complex specific information had to be generated.

Putting it another way: not even God could make an unintelligent natural process with a built-in tendency to hone in on outcomes having a short verbal description. Such a feat is logically impossible, because it would be tantamount to making an unintelligent process capable of making linguistic choices – which is absurd, because language is a hallmark of intelligent agents. Not even God can accomplish that which is logically imposible.

I hope Professor Feser now recognizes what the real point at issue is between Darwinism and Intelligent Design theory. I hope he also realizes that Intelligent Design is not committed to an anthropomorphic Deity, or to any particular Divine modus operandi. ID proponents are well aware of the distinction between primary and secondary causality; we just don’t think it’s very useful in addressing the problem of where the complex specified information in Nature came from. The problem here is not one of finding a primary (or secondary) cause that can generate the information, but rather one of finding an intelligent agent that can do so. Lastly, ID proponents do not think of God as a “tinkerer who cleverly intervenes in a natural order that could in principle have carried on without him,” for the simple reason that Intelligent Design is a scientific program concerned with the detection of patterns in Nature that are the result of intelligent agency, and not a metaphysical program concerned with the being of Nature as such. Metaphysical arguments that Nature depends for its being on God are all well and good, but they’re not scientific arguments as such. For this reason, these metaphysical arguments fall outside the province of Intelligent Design, although they are highly regarded by some ID proponents.

Is Variation Random?

Finally, I’d like to challenge the claim made by Professor Rosenberg and other Darwinists that biological variation is random. Stephen Talbott has skilfully dismantled this claim in a highly original article in The New Atlantis, entitled, Evolution and the Illusion of Randomness. Talbott takes aim at the oft-heard claim, popularized by Richard Dawkins and Daniel Dennett, that Nature operates with no purpose in mind, and that evolution is the outcome of random variation, culled by the non-random but mindless mechanism of natural selection. Talbott’s scientific arguments against Dawkins and Dennett are devastating, and he makes a convincing scientific case that mutation is anything but random in real life; that the genomes of organisms respond to environmental changes in a highly co-ordinated and purposeful fashion; and that even the most minimal definition of random variation – i.e. the commonly held view that the chance that a specific mutation will occur is not affected by how useful that mutation would be – crumbles upon inspection, as the whole concept of “usefulness” or “fitness” turns out to be irretrievably obscure. At the end of his article, Talbott summarizes his case:

Here, then, is what the advocates of evolutionary mindlessness and meaninglessness would have us overlook. We must overlook, first of all, the fact that organisms are masterful participants in, and revisers of, their own genomes, taking a leading position in the most intricate, subtle, and intentional genomic “dance” one could possibly imagine. And then we must overlook the way the organism responds intelligently, and in accord with its own purposes, to whatever it encounters in its environment, including the environment of its own body, and including what we may prefer to view as “accidents.” Then, too, we are asked to ignore not only the living, reproducing creatures whose intensely directed lives provide the only basis we have ever known for the dynamic processes of evolution, but also all the meaning of the larger environment in which these creatures participate — an environment compounded of all the infinitely complex ecological interactions that play out in significant balances, imbalances, competition, cooperation, symbioses, and all the rest, yielding the marvelously varied and interwoven living communities we find in savannah and rainforest, desert and meadow, stream and ocean, mountain and valley. And then, finally, we must be sure to pay no heed to the fact that the fitness, against which we have assumed our notion of randomness could be defined, is one of the most obscure, ill-formed concepts in all of science.

Overlooking all this, we are supposed to see — somewhere — blind, mindless, random, purposeless automatisms at the ultimate explanatory root of all genetic variation leading to evolutionary change….

This “something random” … is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” A faith that fills the ever-shrinking gaps in our knowledge of the organism with a potent meaninglessness capable of transforming everything else into an illusion is a faith that could benefit from some minimal grounding. Otherwise, we can hardly avoid suspecting that the importance of randomness in the minds of the faithful is due to its being the only presumed scrap of a weapon in a compulsive struggle to deny all the obvious meaning of our lives.

My response to Rosenberg

I would like to briefly respond to Professor Rosenberg’s argument that belief in God is incompatible with Darwinism. He is right about one thing: not even God can use randomness to bring about highly specific results, without “injecting” the complex specified information that guarantees the production of the result in question. If you’re a thoroughgoing Darwinist who believes that evolutionary variation is inherently random and that Nature is a closed system, then there’s no way for God to do His work. However, on an empirical level, I see no reason to believe that evolutionary variation is inherently random: Talbott’s article, from which I quoted above, cites evidence that the effects of environmental change on an organism’s genome are highly co-ordinated by the organism itself. What’s more, recent scientific evidence that even the multiverse must have had a beginning, and that even the multiverse must have been exquisitely fine-tuned, points very strongly to the fact that Nature is not a closed system. (See my article, Vilenkin’s verdict: “All the evidence we have says that the universe had a beginning”, which also contains links to my recent posts on cosmological fine-tuning.) And of course, Professor Feser has done an excellent job of expounding the metaphysical arguments showing that Nature is not self-sufficient, but requires a Cause.

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258 Responses to It’s all about information, Professor Feser

  1. By definition, any pattern in Nature that is highly improbable (from a naturalistic perspective) but is nevertheless capable of being described in a few words, instantiates complex specified information (CSI).

    You should talk to Gpuccio about this.  He defines dFCSI in terms of not being capable of being defined in a few words!

  2. Hi markf,

    Are you the world’s fastest reader or what? That couldn’t have taken you more than a minute or two. I’m impressed.

    Anyway, I’m just using Professor Dembski’s definition of CSI in The Design of Life, which stipulates two conditions: (i) the pattern in question identifies a highly improbable event; (ii) the pattern is easily described.

    If gpuccio wishes to comment, he is more than welcome to do so.

  3. The article by Stephen Talbott quoted above is a must read and the fourth installment of an excellent work. It very much goes on line with Shapiro´s “natural genetic engineer” approach to evolutionary change. This approach represents a shift on reigning paradigm. In fact, if variation is a consequence of purposeful programmed molecular reactions to environment changes, then this variation should be expected to occur in all (or most) individuals of a group at the same time,(when experimenting similar environmental conditions) since all of them are bound to identical genetic (and epigenetic) prescriptive information. In this case, natural selection would not have any role to plays in the process. New mutants do not need to compete with organisms belonging to the “original species” in order to spread new traits among the population.
    Bye-bye Darwin.

  4. Dr Torley, It appears, from recent developments in quantum mechanics, that atheistic materialist are in far more of a bind than just explaining an absolute transcendent origin for the universe (or even multiverse per Vilenkin). This is because it is now shown that material particles are not the self sustaining entities that materialists presupposed them to be. Material particles are now shown to be dependent on a ‘non-local’, beyond space and time, cause in order to explain their continued existence within space time.

    i.e. Quantum Mechanics has now been extended by Anton Zeilinger, and team, to falsify local realism (reductive materialism) without even using quantum entanglement to do it:

    ‘Quantum Magic’ Without Any ‘Spooky Action at a Distance’ – June 2011
    Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically.
    http://www.sciencedaily.com/re.....111942.htm

    Falsification of Local Realism without using Quantum Entanglement – Anton Zeilinger
    http://vimeo.com/34168474

    Thus Dr. Torley, my question is, ‘If atheistic materialist have such a breakdown in logic trying to dodge the absolute transcendent origin of the universe, what in blue blazes are they going to do when they realize that they have to dodge a transcendent cause for each and every material particle’s continued existence in the universe? ,,,

    Verses and music:

    Revelation 4:11
    “You are worthy, our Lord and God, to receive glory and honor and power, for you created all things, and by your will they were created and have their being.”

    I Timothy 1:17
    Now to the King eternal, immortal, invisible, the only God, be honor and glory for ever and ever. Amen.

    Unto The King Eternal – music
    http://www.youtube.com/watch?v=mLPYRhOQcCU

  5. vjtorley,

    Haven’t you already applied Dembski’s algorithm to a gene duplication event in the post “on-the-non-evolution-of-irreducible-complexity-how-arthur-hunt-fails-to-refute-behe” in comment 282 and were forced to conclude that this mechanism could create CSI?

  6. I didn’t read it all – just skipped down to the bit about information. Perhaps you can see why CSI, FSCI and dFSCI are not as clearly defined as some in the ID community suppose.

    Dembski does indeed define CSI in terms of low Kolgomorov complexity which more or less corresponds to being able to be defined in a few words. He does this in several places. But when I refer to this in debate I frequently get told that this is not the relevant definition and gpuccio quite explicitly rejects it, at least in the case of DNA, as he feels that a low Kolgomorov complexity is a sign that the pattern could have arisen through necessity e.g. through gene duplication.

  7. VJT:

    Well said.

    KF

    PS: Despite the usual talking points that no it is not clear it is meaningless etc, we can define FSCI in an equation: Chi_500 = Ip*S – 500, bits beyond the solar system threshold. And, the definition of S = 1, can take in K-compressibility as one way to look at it. Indeed, last March-April, Dr Torley did just that in answering the issues raised at that time. The expression just given builds on that.

  8. Hi felipe,

    I had the same reaction as you when I read Talbott’s latest article in The New Atlantis. He does sound an awful lot like James Shapiro, when he suggests that organisms respond intelligently to environmental changes. It’ll be interesting to see if the “powers that be” allow American high school students to be exposed to Shapiro’s non-Darwinian model of evolution. Shapiro’s model is useful to the ID movement, because it highlights the sheer brilliance of the cell’s modus operandi. Anything that’s capable of engineering its own response to environmental change immediately invites the further question: who or what made it?

  9. Shapiro’s model is not “non-Darwinian”.

    As for the cell’s responses to environmental signals, that’s not even controversial. We know it happens.

    Not only that, but we know it happens in response to our own thoughts, i.e. is an “intelligent” response.

    This is completely non-controversial, and I certainly hope it is taught in schools. It should be a basic component of health education, for a start.

  10. Hi markf,

    Just a quick comment. Low Kolgomorov complexity in itself is not a guarantee of high CSI, as you are doubtless aware. The probabilistic complexity must also be high – that is, the outcome must be highly improbable, as a result of non-foresighted processes. If gene duplication is an occurrence that you would ascribe to necessity, then that would automatically preclude the existence of high probabilistic complexity in duplicated genes – which means that CSI is also low.

  11. I understand that to have high complex specified information (not CSI per se, which also includes a term representing the alpha cutoff), a pattern has to have high Shannon Entropy as well as high Kolmogorov compressiblity.

    That’s already problematic, because we can’t easily calculate the compressibility.

    The bigger problem, however, is that even if we could, there’s no reason in principle to think that such a pattern had to be intelligently designed (i.e designed by a purposeful agent). Nonlinear stochastic systems are perfectly capable of doing just that, and Darwinian evolution is exactly such a system.

    The only prerequisite (and it is an important one) are entities that self-replicate with heritable variance in reproductive success.

  12. The article by Stephen Talbott quoted above is a must read …

    When I saw the reference in the main post of this thread, I assumed that Talbott simply misunderstood “random” which is a common problem among critics of evolution.

    Now that you have mentioned Talbott, and suggested that his article is a “must read”, I decided to read it.

    It turns out that Talbott simply misunderstood “random” as is so common among critics of evolution.

  13. It’ll be interesting to see if the “powers that be” allow American high school students to be exposed to Shapiro’s non-Darwinian model of evolution.

    Whether Shapiro’s view is “non-Darwinian” depends on what one means by “Darwinian.”

    Shapiro’s ideas probably won’t make it into standard high school text books any time soon. At the level of high school texts, we would expect only an over-simplified account anyway.

    If an individual teacher happens to be familiar with Shapiro’s work, and attempts to discuss that in class, it is unlikely that there would be any objection raised. That presumes that it is discussed in a scientific manner.

  14. Hi Elizabeth,

    I have to respectfully disagree with your claim that Shapiro’s model is not “non-Darwinian.” In a talk entitled, Revisiting Evolution in the 21st Century (October 3, 2010), he tells his audience that “Genome change is a cell-regulated process, not a series of accidents.” He goes on to list six “Key non-Darwinian Evolutionary Scientists in the 20th Century.” He then presents a slide entitled, “Four kinds of rapid, multi-character changes Darwin could not have imagined” – including “natural genetic engineering.” His second-last slide is entitled, “Searching Genome Space by Natural Genetic Engineering: More Ef?cient than a Random Walk Guided by Gradual Selection.” I have to say that doesn’t sound too Darwinian to me. It sounds like he is proposing a new and more efficient evolutionary mechanism.

    On his last slide, “A 21st Century View of Evolution”, he writes that “Macroevolution [is] triggered by cell fusions & interspeci?c hybridizations (WGDs) leading to massive episodes of horizontal transfer, genome rearrangements.” Hmm. Whatever happened to the Darwinian principle that “Nature does not make leaps“?

    Shapiro made his views about macroevolution very plain at a talk given on January 22, 2010 in Ramsey Auditorium at Fermi National Accelerator Laboratory. Paul Nelson blogged about it here :

    During the Q & A, a man sitting just behind me asked — with unmistakable agitation — why Shapiro had frequently used the word “macroevolution.” The questioner protested that macroevolution was a concept dreamed up by creationists, so how could Shapiro use the term? Was Shapiro intending to “repurpose” macroevolution for his own ends?

    Shapiro respectfully, but forcefully, disagreed. Macroevolution is not simply microevolution plus time. “Macroevolution,” he argued, “refers to when we have a major change in the nature of the organism. When a chordate changes into a vertebrate, that’s macroevolution. When one kind of plant changes into a flowering plant and the genome doubles at the same time, that’s what I would consider a macroevolutionary change.”

    By contrast, Shapiro continued, “when a butterfly changes the pigment on its wings so it doesn’t get predated when it’s sitting on a city wall, that’s microevolution. That’s a small change. So I think the two changes can be distinguished from each other.”

    “These are sudden events,” he concluded. “They can’t occur over many cell generations or many organism generations. They must occur within a single generation. Big changes can happen suddenly. How that all works, we don’t know yet. But we have to recognize that it must work suddenly and try and figure out what are the control processes and how does the complexity of the living cell allow these things to happen.”

    Vertebrates appeared within a single generation? Flowering plants (Darwin’s “abominable mystery”) appeared within a single generation? I think Darwin would be turning in his grave.

    I do agree with you about one thing, Elizabeth. Shapiro’s views should indeed be a basic component of education in schools. They’ll serve to open up people’s minds.

  15. Hi Neil,

    Would you care to explain in what sense you believe evolutionary variation to be random? I’d be interested to hear your response.

  16. The only prerequisite (and it is an important one) are entities that self-replicate with heritable variance in reproductive success.

    It needs more than that. It needs the variance to be able to produce something new, ie something that was not present in the original.

    The effects of low-impact mutations in digital organisms

    Chase W. Nelson and John C. Sanford

    Theoretical Biology and Medical Modelling, 2011, 8:9 | doi:10.1186/1742-4682-8-9

    Abstract:

    Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.

    Results:

    When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida’s default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.

    Conclusions:

    Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

  17. paragwinn,

    Gene duplications rely on existing information that needs to be accounted for first.

    This has been pointed out hundreds, if not thousands, of times, yet evos still persist.

  18. Well, in the sense that Darwin had no conception at all even of genes, sure, he’s not a Darwinian.

    I think he’s overstating his case though, if he actually uses “non-Darwinian” in that sense (and if he does, then I take it back – Margulis expressly called herself a Darwinist, just not a “neo-Darwinist” and I thought Shapiro had said the same”.

    To my knowledge, Shapiro has proposed nothing that is not compatible with basic Darwinian theory, although plenty that is not compatible with some “neo-Darwinian” theories.

    He talks about “the evolution of evolvability”, which is essentially Darwinian evolution at between-population level rather than within-population level. So if that is “non-Darwinian” I agree. But it seems rather hard on poor old Darwin!

    But are you saying that Shapiro is suggesting that “Vertebrates appeared within a single generation? Flowering plants (Darwin’s “abominable mystery”) appeared within a single generation?”

    If so, do you have a citation? Because, if so, I have misread Shapiro, and I talk back everything :)

    But it that’s what he’s saying, then it’s definitely not ready for prime time!

  19. Sorry, I didn’t read to the end of your quote of Shapiro.

    Do you have a reference to an actual paper where he says this?

    Oh, and “no big leaps” is not a fundamental Darwinian principle. It’s just that given the fundamental Darwinian principle, big leaps would seem unlikely.

    Evo-devo shows that biggish leaps can happen, though, because small changes in regulatory genes can scale up to big phenotypic changes.

  20. “Random” is a truly terrible word in this context! It should be banned! It’s an invitation to inadvertent equivocation.

  21. Right, well, let me rephrase that (I thought it was clear, but perhaps it isn’t):

    What is required is self-replication with variance and where that variance is reflected in differential reproductive success of the phenotype.

    Not so succinct, but perhaps less ambiguous.

  22. Hi bornagain77,

    Thank you for your post. It is very interesting to see that science itself is now pointing towards the conclusion that particles have a non-local cause of their existence.

  23. I agree Elizabeth let’s try to clear up some of the ambiguity surrounding the word ‘random’; I wrote a little piece on ‘randomness’ a short while back:

    Blackholes – The neo-Darwinian ‘god of entropic randomness’ which can create all things (at least according to them)

    Being the helpful guy I am, always trying to help atheists out when I get a chance, I’ve been trying to piece together a experiment that would prove once and for all, for everyone to see, that RANDOM variation plus undirected natural selection can produce functional proteins just as atheists adamantly claim (even though no one has ever seen RANDOM processes do this). Now I just about got the RANDOM part of the experiment down for the atheists! I’ve searched for the maximum source of randomness that I could find in the universe, (since the ‘god of randomness’ is who atheists adamantly claim for their creator), and I think I’ve found their god for them;

    First:

    Thermodynamics – 3.1 Entropy
    Excerpt:
    Entropy – A measure of the amount of randomness
    or disorder in a system.
    http://www.saskschools.ca/curr.....rgy3_1.htm

    Thus, the more entropy a system has the more randomness it will generate for our experiment to find a RANDOM functional protein. And if we ask, ‘what is the maximum source of entropy, i.e. RANDOMNESS, in the universe?’, we find this:

    Entropy of the Universe – Hugh Ross – May 2010
    Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.
    http://www.reasons.org/entropy-universe

    “But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.”
    Roger Penrose – How Special Was The Big Bang?

    Plus for a added bonus for atheists, being the helpful guy that I am, I found that if we find a massive magnetized blackhole we might just start to overcome the homochirality problem, which is a huge problem against finding functional proteins, as well:

    Homochirality and Darwin: part 2 – Robert Sheldon – May 2010
    Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn’t imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos?
    http://procrustes.blogtownhall.com/page3

    But of course there is the extreme logistics problem with actually transporting the atheists to the massive magnetized blackholes to actually do the experiments, so that they may try to actually RANDOMLY generate a functional protein just as they claim can be done. Not to mention the minor problem of someone trying to survive being stretched into as a piece of spaghetti, by the extreme warping of space-time, near the blackhole.

    What Would Happen If You Fell into a Black Hole? – video
    http://www.youtube.com/watch?v=gLMiJQXsmkc

    ,,Not to mention trying to survive the extremely high temperatures surrounding the event horizon of the black hole:,,

    Scientists gear up to take a picture of a black hole – January 2012
    Excerpt: “Swirling around the black hole like water circling the drain in a bathtub, the matter compresses and the resulting friction turns it into plasma heated to a billion degrees or more, causing it to ‘glow’ – and radiate energy that we can detect here on Earth.”
    http://www.physorg.com/news/20.....-hole.html

    But what the hey, it is just a little sacrifice for ‘science’ right!?! At least atheists will have the maximum source of randomness in the universe to work with in their experiments!!! But there is another problem I probably need to tell atheists about before they pack up and go off to the massive magnetized blackholes in order to prove to the world that their ‘god of randomness’ can create all things,

    “Gain in entropy always means loss of information, and nothing more.”
    Gilbert Newton Lewis – Eminent Chemist

    “Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…”
    Tom Siegfried, Dallas Morning News, 5/14/90 – Quotes attributed to Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin in the article

    But what the hey, atheists haven’t needed any stinking equations to sell their theory to a gullible public so far have they!?!

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

    I even have a inspirational quote for the future experiment of our space traveling atheists;

    GILBERT NEWTON LEWIS: AMERICAN CHEMIST (1875-1946)
    “I have attempted to give you a glimpse…of what there may be of soul in chemistry. But it may have been in vain. Perchance the chemist is already damned and the guardian the blackest. But if the chemist has lost his soul, he will not have lost his courage and as he descends into the inferno, sees the rows of glowing furnaces and sniffs the homey fumes of brimstone, he will call out-: ‘Asmodeus, hand me a test-tube.’”(1) Gilbert Newton Lewis
    http://www.woodrow.org/teachers/ci/1992/Lewis.html

    And I even have a inspirational song for their experiment;

    Creed – Six Feet
    http://www.youtube.com/v/aQ9Gr.....autoplay=1

  24. I’m seriously wondering if that’s a transcription error, actually. Or if there’s missing context.

    Either way, I’d want to see something more than a transcript from a Q&A before it went into the school science curriculum :)

  25. What is required is self-replication with variance and where that variance is reflected in differential reproductive success of the phenotype.

    Still not good enough to do anything. If one family of humans out-reproduces another family, so what?

    “Look that family has 8 people and this family has 7. Do you know what that means?”

    “Yes, there are 15 people in those two families.”

  26. Hi Elizabeth,

    I’m not aware of evidence that such a mechanism naturally tends to generate outcomes that possess high Kolmogorov compressibility as well as high Shannon complexity. Would you care to cite what you consider to be your best examples?

    (If you’re talking about Tierra or Avida, I can’t really help you, as I don’t know enough about them, and what I’ve seen online is simply too opaque to convince me to change my mind. Joe’s citation above makes me highly suspicious of Avida. I just wish someone could write a 200-line program in Pascal that could do what’s claimed for these programs.)

    What I’d be more interested in seeing from you is a general argument that the mechanisms you describe tend to increase Kolmogorov compressibility as well as Shannon complexity.

  27. Well, before I answer, can you tell me how you would compute the Kolmogorov Compressibility, of, say, a DNA sequence? The Shannon Entropy of any DNA sequence, will of course, equal approximately 2 bits per nucleotide, so the total Shannon information will equal approximately 2*L where L is the length of the sequence.

    But how would you estimate the Kolmogorov compressibility?

  28. Hi Elizabeth,

    If you’d like a paper where Shapiro says that vertebrates and flowering plants appeared within a single generation, then here’s one:
    http://www.mobilednajournal.com/content/1/1/4
    (“Mobile DNA and evolution in the 21st century”, in Mobile DNA 2010, 1:4 doi:10.1186/1759-8753-1-4, published 25 January 2010). An excerpt:

    Genome doublings have been documented in yeasts [116,117], ciliated protozoa [118] and plants [119]. There is even evidence of a genome tripling at the base of the angiosperm radiation (in a letter to J D Hooker, 22 July 1879, Darwin described the rapid rise and early diversification within the angiosperms as ‘an abominable mystery’ [120]) [121]. In animals, the most important WGD [whole genome doubling - VJT] events have been found at the base of the vertebrate lineage, where two successive events gave rise first to all vertebrates and then to jawed vertebrates [122]. This 2R double WGD event was originally postulated by Ohno in his 1970 book on the essential role of duplications in evolution [123]. Later in vertebrate evolution, there was another WGD event at the origin of teleost fish [122,124]. Characteristic of transitions marked by WGD events are the rapid formation of a cluster of related species, as in Paramecium [118], or the appearance of major innovations, as with the vertebrate skeleton [125] and jaw [122]. WGD is yet another evolutionary process outside the Darwinist perspective that occurs suddenly (that is, within a single generation) and simultaneously affects multiple phenotypic characters [126]. It is especially significant to note that a genome doubling means that the dispersed coding elements for complex circuits are duplicated and the two duplicate circuits can then undergo independent modifications as distinct entities [127]. (Emphases mine – VJT.)

    “Within a single generation.” “Outside the Darwinist perspective.” “Gave rise first to all vertebrates and then to jawed vertebrates.” Convinced?

    Yeah, I definitely think American high school kids should hear about this guy’s views. Plus he has a Ph.D. in genetics.

  29. Hi Kairosfocus,

    Thank you for your kind comments. I’d like to mention your own articles on the subject of FSCI, for Uncommon Descent, especially these:

    How to calculate Chi_500, a log-reduced, simplified form of the Dembski Chi-metric for CSI

    ID Foundations, 11: Borel’s Infinite Monkeys analysis and the significance of the log reduced Chi metric, Chi_500 = I*S – 500

  30. In any case, a simple sorting system will do the trick. My favorite example is Chesil Beach, on the south coast of England, which is an 18 mile pebble beach along the length of which the pebbles are beautifully sorted from almost sand at the West end, to boulders at the east.

    Clearly the sequence of pebble sizes has high Shannon Information (each pebble is of different size and there are a huge number of different sizes) and yet the sequence can be very simply described (“from sand size in the West to boulder size 18 miles to the East”).

    It is, equally clearly, not intelligently designed.

    Yet clearly there is some algorithm at work that results in the small pebbles being deposited at one end and large at the other, with such consistency that local tradition says that fishermen landing at night could tell where they were by rolling the pebbles in their palms to estimate the size.

    So the beach is informative.

    Why does it not have Complex (high Shannon) Specified (high compressibility) Information (meaningful to lost fishermen at night)?

    (I’m sure there’s an answer, but I’d like to hear it :))

  31. Elizabeth,

    You are confusing the arrangement of things to create meaning with the assignment of meaning to something.

    In your example the fisherman can tell where they are by the size of the pebbles. But if some other cause-and-effect process deposited recognizable rocks or caused unique erosions along the way they could just as easily assign the same meaning to those.

    In both your example and this one, neither the pebbles nor the rocks contain meaningful, functional information. That meaning is assigned or that information is created by observing that rocks of a certain size are found at a certain location, or that a certain formation is found at a certain place, and creating that association.

    Reduced to its simplest form, suggesting that they contain functional information is similar to suggesting that raindrops striking one’s face contain functional information regarding the current weather. They don’t. They follow natural laws, and intelligent agents assign information to them.

  32. Hi Elizabeth:

    1. The Kolmogorov compressibility for a DNA sequence would be very high, especially if it’s complete – e.g. “Complete DNA sequence for a human being.” (That’s a generic description, of course; if you wanted a description that would specify each and every base, you might say: “Complete DNA sequence for Tom Jones.” To be complete, you’d have to specify the time as well, as our DNA is continually changing due to cell mutations.)

    2. Regarding your beach example: the sorted pebbles have high Kolmogorov compressibility, but low Shannon complexity. If they were sorted randomly, they’d have high Shannon complexity. Since they’re sorted in order, they have low Shannon complexity, which means they don’t require an intelligent designer.

    What would impress me far more is a sequence of pebbles encoding the first 100 digits of pi by virtue of their sizes (0 for the smallest, 9 for the biggest): high Shannon complexity and high Kolmogorov compressibility.

  33. Would you care to explain in what sense you believe evolutionary variation to be random?

    I mean it in the sense that Talbott attributes to Futuyma. Clearly, Talbott thinks that’s cheating.

    When people hear “random” they tend to think of what a mathematician would call “random with a uniform distribution.” But that “uniform distribution” part is not at all implied by “random.” Elizabeth is right, that the term “random” tends to confuse.

    There are problem solving techniques that are known as “Monte Carlo methods.” They use randomness, but they use it cleverly. I suspect that Shapiro would probably see mutations as something like a Monte Carlo method at work.

    I have not read Rosenberg’s book, so I can only go on what I glean from Feser’s review. And that, admittedly, might be unfair to Rosenberg. That said, it seems possible that Rosenberg has overlooked the possibility of Monte Carlo methods being used.

  34. I am not confused. If anyone is, it’s Dembski. I’m simply pointing out a problem with his definition of CSI.

    One of his favorite examples is the dealing of cards: would you suspect skulduggery (aka “design”) more if someone dealt:

    A♥ 2♥ 3♥ 4♥ 5♥ 6♥ 7♥ 8♥ 9♥ J♥ Q♥ K♥

    than if they dealt:

    J♦ K♥ 3♣ 5♣ A♠ 8♥ 9♦ J♣ Q♥ 3♠ A♦ 5♣

    Dembski says you would: that the first pattern suggests design, because it is much more compressible, for the same amount of Shannon Complexity (the two sequences are equiprobable) because the first is one of a small, rare subset of highly compressible sequences (“All the hearts from Ace to King”)

    That’s no different from my beach, that I can see.

    And my take is that in a sense he is absolutely right: both that hand of cards and Chesil beach demand an explanation – clearly some algorithm is at work in both cases.

    Dembski’s mistake, IMO, is to infer that the explanation must always be “a designer”. Not all algorithms are produced by designers. Some emerge spontaneously from non-linear systems, as on Chesil beach.

  35. Hi Elizabeth:

    1. The Kolmogorov compressibility for a DNA sequence would be very high, especially if it’s complete – e.g. “Complete DNA sequence for a human being.” (That’s a generic description, of course; if you wanted a description that would specify each and every base, you might say: “Complete DNA sequence for Tom Jones.” To be complete, you’d have to specify the time as well, as our DNA is continually changing due to cell mutations.)

    OK (although I dispute that actually – as Dennis Noble makes clear, human DNA does not alone contain the specification for a human being – did you ever play that lecture?).

    2. Regarding your beach example: the sorted pebbles have high Kolmogorov compressibility, but low Shannon complexity. If they were sorted randomly, they’d have high Shannon complexity. Since they’re sorted in order, they have low Shannon complexity, which means they don’t require an intelligent designer.

    No, the sort order is irrelevant. It has a lot of Shannon information because there are lots of different pebble sizes, and therefore needs a lot of bits to code each item. In other words it has a large “alphabet”.

    To take a simplified example: let’s say you had 1000 pebble sizes, of which the smallest had diameter 1 mm, and the largest had diameter 1000 i.e. a substantial boulder, in 1 mm increments.

    And some blind process picked 10000 pebbles at random and put it next to the last. That sequence of diameters would have approximately 13.2877 bits of information per pebble, i.e per item in the sequence.

    And it would be essentially imcompressible (there might be the odd fortuitous shortcut), because there is, by definition, no way of predicting the next pebble from the last.

    Now rearrange those pebbles in precise size order. There is no increase or decrease in Shannon information. However there is a huge increase in compressibility.

    Shannon information doesn’t care what order the items are arranged in, it only cares how many ways there are of arranging the items. In other words, how “improbable” is any one sequence, given the size of the alphabet (which in this case is very large – it is much smaller, of course, for DNA). Notoriously, a recording of white noise contains as much Shannon Information as a recording of Sir Winston Churchill’s speeches.

    What would impress me far more is a sequence of pebbles encoding the first 100 digits of pi by virtue of their sizes (0 for the smallest, 9 for the biggest): high Shannon complexity and high Kolmogorov compressibility.

    But I’m not trying to impress you. I’m trying to show that even an extremely unimpressive arrangement (actually Chesil beach is awesome, but apart from that) has the same CSI, as far as I can tell, by Dembski’s metric, as the first 100 digits of pi. More, actually, because it’s longer, and it’s got a bigger alphabet.

  36. Elizabeth,

    One needs to be dealt MULTIPLE hands of the same thing in order to infer design.

  37. Dembski is quite willing to invoke Bayesian reasoning for card games or for election rigging, but unwilling to apply it to evolution.

    The trick is deciding when to invoke known kinds of causes (such as cheaters) as probable causes of events that affect the causal candidates.

    The problem for ID is that the known causes of genomic change produce the observed kinds of genomes (nested hierarchies, vestigial genomic elements, and so forth), whereas known designers do much much more horizontal transfer, and much more cleanup. You hardly ever see tillers on automobiles or wing warping on airplanes. In fact, if you have a collection of computers you can see the gradual change in expansion slots and the gradual elimination of obsolete kinds of slots.

    In living things the genes for legs continue on in snakes and whales. Rather than being removed from the genome, they just get disabled.

    I realize this is not proof of anything, but it contributes to a Bayesian inference. The same kind of inference that leads you to suspect cheating when certain kinds of hands get dealt in card games.

  38. The problem for ID is that the known causes of genomic change produce the observed kinds of genomes (nested hierarchies, vestigial genomic elements, and so forth)

    You’re begging the question. We have no way of knowing that the “known causes of genomic change” produce such observed genomes as those of orbital web-weaving spiders, dolphins, or venus flytraps. We don’t know that they have, we don’t know why they would, and we certainly don’t know whether they could. How convenient to skip over all that doesn’t fit to the parts that do.

    It’s a bit like predicting precipitation and calling it confirmed when Buicks start falling from the sky. It’s a confirmation as long you carefully decide which minor details to ignore.

  39. Elizabeth,

    One needs to be dealt MULTIPLE hands of the same thing in order to infer design.

    Not according to that paper by Dembski.

    And in any case, my beach would still count, because it’s been there for centuries, and while the actual pebbles are always changing, the order of sizes remains the same.

    What are the odds of that happening, if there were not some underlying algorithm at work?

    Tiny. That’s why we can infer an underlying algorithm, even though we don’t yet know exactly what it is.

    So Dembski is exactly half right, IMO. CSI does signify that something interesting is going on. It just doesn’t signify what he thinks it signifies (well, actually he even gets that half right too – he says it signifies a selection process: something with “the power and facility to choose between options” – it’s just that that something doesn’t need to be an agent with foresight, as it turns out. Even a blind algorithm can sort pebbles).

  40. Hi vj,

    The Kolmogorov compressibility for a DNA sequence would be very high, especially if it’s complete – e.g. “Complete DNA sequence for a human being.” (That’s a generic description, of course; if you wanted a description that would specify each and every base, you might say: “Complete DNA sequence for Tom Jones.”

    That’s not what Kolmogorov complexity is, and even if it were, it simply doesn’t work. As I pointed out on another thread:

    …I’m afraid your [Kolmogorov] criterion still leads to absurdities. “Created the universe” is adjudged more plausible than “created a new rhododendron hybrid”, and “rose from the dead” is on par with “made a coin disappear”.

    You are assuming that the length of a natural language description is a proxy for Kolmogorov complexity, but it is not. Kolmogorov complexity is algorithmic complexity, and as such it has meaning only relative to a specified algorithmic description language.

    You can get wildly different answers depending on your choice of description language. In a description language where there are only four characters (A,C,G,T) representing the nucleotides, and no means of designating repetition, it takes a very long string to specify the DNA sequence of vjtorley. In a description language where ‘X’ is defined as the actual sequence of nucleotides in vjtorley’s DNA, it takes only one character: X.

    To lessen the dependence of Kolmogorov complexity on the choice of description language, a common practice is to specify complexity relative to a universal Turing machine. In other words, the Kolmogorov complexity is represented as the concatenation of two strings: the first string is a program which enables the UTM to process strings written in the chosen description language, and the second string is the actual description in that language.

    If you do this, the complexity of Tom Jones’ DNA sequence is much, much higher than “Complete DNA sequence for Tom Jones”.

  41. You’re begging the question. We have no way of knowing that the “known causes of genomic change” produce such observed genomes as those of orbital web-weaving spiders, dolphins, or venus flytraps.

    It is your prerogative to be hyperskeptical about extrapolating from observed processes, and it is mine to point out that you have no alternative.

    The first thing Darwin does in “Origin” is devote a third of the book to demonstrating the power of selection to modify plants and animals. I think you could only make your assertion by ignoring 150 years of biology.

  42. What are the odds of that happening, if there were not some underlying algorithm at work?

    Gravity- also CSI is not compressible via an algorithm.

  43. 43

    Thank you, Petrushka. Whenever someone trots out the old ’150 years of biology’ rather than any specific example of anything you know there’s not much behind it.

    It is your prerogative to be hyperskeptical about extrapolating from observed processes, and it is mine to point out that you have no alternative.

    As I’ve explained more than once, extrapolation is a logically valid concept. It does not follow that absolutely any reasoning, however faulty, becomes valid when you call it an extrapolation. Your extrapolation is unwarranted. Calling that “hyperskepticism” is pointless rhetoric. I could call you “hypergullible” but I’d much rather stick to the evidence.

    No alternative? Saying that I don’t know and neither do you is an alternative. It’s really good one. Please tell me that you don’t teach science in any way, shape, or form. Lesson one: When someone uses the word “extrapolate,” you have no alternative but to believe everything they tell you. No one ever offers an unwarranted extrapolation. (Let me guess – it’s up to me to explain why it is not warranted.)

    The first thing Darwin does in “Origin” is devote a third of the book to demonstrating the power of selection to modify plants and animals.

    If the substance of evidence were measured in ‘book fractions,’ well, I still don’t know if I’d be impressed. Is one third good? But it’s not, and I’m not. That you are speaks many fractions of volumes.

  44. OK, thanks for that. Interesting.

    However, I remain of my view: Shapiro is not challenging the fundamental Darwinian algorithm, merely the size of certain steps.

    He could be right.

    And sure, high school kids should hear about his views. What would be very misleading though, would be to present them as a challenge to the basic theory of evolution (that heritable variation in reproductive success in the current environment leads to adaptive change), because it doesn’t. It merely provides a(nother) causal mechanism for genetic variation.

    But I think this is mostly a terminological issue. Shapiro seems to call himself (or class himself as) an “evolutionist”. He explicitly puts forward a new theory of variance generation. He writes, at the end of that paper:

    This 21st century scenario assumes a major role for the kind of cellular sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel Prize address [1]. Such a cognitive component is absent from conventional evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgeable about cellular response and control networks. This 21st century view of evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions. It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties. In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science.

    As I said, he is talking about the evolution of evolvability.

    And as I have also been saying for years, he is regarding evolutionary processes as an intelligent system.

    In that sense – and in that sense only – I am an ID advocate, and always have been.

    And I think Dembski inadvertently hit on a real truth when he noted the “pattern that signifies design” although I think he defined it badly. He also, correctly, inferred that the key component of a “designer” is the capacity to select what works (“choose between options”).

    What he didn’t see is that this description applies to evolutionary processes, which are therefore, by his own logic, capable of design. In other words, the “designer” in question is intrinsic to the biosphere itself. It’s a bootstrapped system.

    Shapiro, although I’m not convinced he’s right about some things, is taken seriously because he’s potentially shedding important light on just how “intelligent” that evolutionary process became.

  45. as to this comment:

    They use randomness, but they use it cleverly.

    HMMM???? Would you accept Intelligent Design if its name were changed to Clever Design? What if we changed it to Clever Evolution instead, would you then accept it?

    notes:

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

  46. bornagain77:

    Would you accept Intelligent Design if its name were changed to Clever Design? What if we changed it to Clever Evolution instead, would you then accept it?

    I don’t particularly care about the name. I am not offended by the idea of intelligent design, if one is talking about intelligence within biological systems redesigning themselves. The objection is to the idea of an external designer, for which no evidence has been presented.

    I’m not certain, but I think Elizabeth Liddle has also expressed agreement with the idea of intelligence within biological systems, and self-design. And that seems to be Shapiro’s view.

    In any case, the argument about names misses the point. The basic problem with ID is its use of politics to try to force ID into the classroom. Call off the politicians, and work on the science. If there is enough good science forthcoming, then scientists will become interested.

  47. And Mr. Rickert, exactly how is this ‘self design’ accomplished? Do you have any evidence of even one molecular machine being ‘self designed’ by the ‘intelligence’ within the cell?

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    Perhaps you have an example of one these following molecular machines being ‘self designed’ by a cell?

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
    http://www.metacafe.com/watch/3994630

    The ATP Synthase Enzyme – exquisite motor necessary for first life – video
    http://www.youtube.com/watch?v=W3KxU63gcF4

    Powering the Cell: Mitochondria – video
    http://www.youtube.com/watch?v=RrS2uROUjK4

    Molecular Machine – Nuclear Pore Complex – Stephen C. Meyer – video
    http://www.metacafe.com/watch/4261990

    Programming of Life – Protein Synthesis – video
    http://www.youtube.com/user/Pr.....5Z3afBdxB0

    Kinesin Linear Motor – Video
    http://www.youtube.com/watch?v=kOeJwQ0OXc4

    DNA – Replication, Wrapping & Mitosis
    http://vimeo.com/33882804

    or if you can’t find an example of ‘self design’ for one of those molecular machines there are several more here that you can look for examples for:

    The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell:
    Molecular Machines in the Cell -
    http://www.discovery.org/a/14791

    and after you get done producing any evidence whatsoever that cells can ‘self design’ any molecular machine from scratch, then you can work on refuting this falsification of neo-Darwinism:

    Falsification Of Neo-Darwinism by ‘non-local’ Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

  48. Vincent:

    It’s useless arguing with Elizabeth about vocabulary. She has her mind made up what “Darwinian” means, and she is not going to budge.

    Over the past few months, Elizabeth and I carried on a running battle, on two or more threads, about the meaning of “Darwinian.” First I argued that Margulis and Shapiro were anti-Darwinian. Then she denied it. Then I asked her to look at the sources I had already provided. She appeared to have looked at some, not all, of the sources I provided (I can’t tell because she never quoted specific passages and analyzed them). Then she said, well, they are anti-neo-Darwinian (though she had previously denied knowing what neo-Darwinian meant, on the grounds that everyone used it so confusingly), but not anti-Darwinian. Then I showed her a passage in Shapiro where he rejected an element common to both neo-Darwinism and original Darwinism. No reply. I linked her to a Discovery series of columns where Dembski and Shapiro speak in their own words. No reply to Shapiro’s specific words. So let me try one more time, from another of the Dembski-Shapiro-Gauger-Axe exchanges. Shapiro:

    “Proteins evolve largely by shuffling and accreting functional subregions called “domains,” not through the Darwinian modifications of individual amino acids (Doolittle and Bork 1993). Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains.”

    Source:

    http://www.evolutionnews.org/2.....55351.html

    So in one short passage, he twice indicates a disagreement with the “Darwinian” view. But adding one more passage of Shapiro, or Margulis, or any other evolutionary biologist, won’t do any good. Elizabeth has decided what “Darwinian” means, and that everyone should use the word “Darwinian” in her way — even professional evolutionary biologists like Shapiro.

    Given a choice between using terms the way the professional evolutionary biologists do, and the way a neuroscientist with a hobby of reading up on evolutionary biology does, it seems to me that the choice is clear. There will be less confusion if we follow the language used by the evolutionary biologists themselves.

    Elizabeth is free to use words any way she likes; but she had no authority to offer her private definition of “Darwinian” as *the* definition of “Darwinian.” So I would advise everyone here to simply ignore her when she raises these quarrels over words. If she doesn’t like the way professional evolutionary biologists use words, she can take the argument to them and try to reform the language of the field. As for me, I’m quite content to use the language that has become intelligible to most scientists and lay interpreters of science for the last 100 years or so. And I’m pleased to see that most ID proponents have taken the same line.

    T.

  49. “It’s useless arguing with Elizabeth about vocabulary. She has her mind made up what “Darwinian” means, and she is not going to budge.”

    Well, what does “Darwinian” mean?

    In a historical sense, genes aren’t Darwinian. Neither is chromatin (1910). Transposons later (1960), HGT later, endosymbiosis, etc etc…

    The question you’ve got to be asking is whether the authors and quotes you’ve fallen in love with support ID or evolutionary biology.

    Saying something discovered recently is post-Darwinian is a hilarious given, in a historical sense. Taking that as support for ID is just terribly sad.

  50. Elizabeth (2.1.1.1.5):

    You quote a paragraph from Shapiro, and in your discussion of it inform us that Shapiro considers himself “an evolutionist.” That is supposed to be news to us? Please, we are not in kindergarten.

    Or is your point that he doesn’t use the language of Darwinism and non-Darwinism, but only the language of “evolutionism”? Well, I’ve already demonstrated that to be untrue. He uses all of these terms.

    Newsflash: When he speaks in your quoted paragraph of “conventional evolutionary theory” and “19th and 20th century evolutionists” he is speaking of Darwinians and neo-Darwinians, as his language elsewhere makes clear. So if you want to interpret Shapiro in terms of his own vocabulary and intentions, instead of imposing your own vocabulary and intentions upon him, you will call him a non-Darwinian evolutionist. Or, if you are so sure of yourself as to say that Shapiro has misunderstood what “Darwinian” means, at the very least, you should say that he is an evolutionist who understands himself to be non-Darwinian.

    Note that Shapiro does not, in the paragraph you quote, call evolutionary processes “an intelligent system.” He says: “evolution by natural genetic engineering has the capacity to generate complex novelties.” The words “intelligent system” is your gloss upon his words. He might agree with your gloss, or he might not; it’s certainly not obviously there in what he said. If you specify a certain definition of “intelligent” you might be able to squeeze it out of his words there; but there’s no evidence what I’ve read of him that he thinks there is any “intelligence” (as the word is normally used) operating in the evolutionary process. Certainly he thinks that it can mimic the results typically achieved only by intelligent agents. If that’s all you mean, there is no argument, but all evolutionary theorists say that, so it’s nothing specific to Shapiro, and is a platitude.

    Again, only obscurity results from playing with the normal meaning of words. To the average educated reader, “intelligence” is associated with consciousness or mind; and you certainly don’t think that any consciousness or mind is directing evolution, either from the outside or the inside, so your language makes your argument murky. Whether you just don’t see that it makes your argument murky, or whether you are trying to playfully test us, to see whether we will detect the ambiguity you are relying upon, or fall prey to it, I don’t know, because I have no conception of your motives. But the effect of your usage of the notion of “intelligent systems” is to create confusion and non-communication, rather than to produce clarity and a sharper picture of where you disagree and agree with ID.

    And by the way, I know of no ID proponent who is saying that Shapiro should be taught in biology class as refuting “evolution.” Again, if you would follow our terminology, no such confusion on your part would arise. Shapiro, as a non-Darwinian evolutionist, is valuable because hearing about him would inform ninth-grade American students that the “consensus science” of the 20th century (which Eugenie Scott and the NCSE still want taught in the 21st) may be seriously flawed, because evolution may take place in a way that is *significantly different* from what was previously thought. It would be very good for young, impressionable 14-year-olds to be made aware that loud shouting about the immense creative capacity of random mutations plus natural selection does not make that crude model of evolution true, and that empirical investigations are now suggesting that it may have to be seriously modified. Anything that weans students off the worship of consensus and majority is good for their scientific education — and their general education.

    T.

  51. And Mr. Rickert, exactly how is this ‘self design’ accomplished? Do you have any evidence of even one molecular machine being ‘self designed’ by the ‘intelligence’ within the cell?

    It won’t be design by the cell. It will be design by the population, using random variation and natural selection keep the population well adapted.

  52. Dr Rec:

    Where, on any thread on this site, have I ever said that because there have been post-Darwinian discoveries in evolutionary biology, therefore ID is true? You won’t find any such argument from me.

    Where have I said that Margulis or Shapiro support ID? You’ll never find such statements from me. Unlike some people who post here, I read texts carefully before I report on the views on their authors.

    What I have said is that Elizabeth should stop using language which (intentionally or not) obscures just how much disagreement there is between some of the leading evolutionary biologists of the past few years and the standard Darwinian view of evolutionary mechanism.

    The fact is that the general educated public, the sort of middle-class people who watch NOVA science specials and read National Geographic and teach high school and edit mainstream magazines and newspapers and run public TV networks and practice dentistry and law and proctology, still think of random mutations being filtered by natural selection as the primary motor of evolution. But if people like Shapiro, Margulis, Newman, etc., are right, this picture of evolution is wrong. And that means the experts, the consensus, whatever you want to call it, may have been wrong. It’s very important for the public to see that the experts can be wrong. And it’s very important for the public to realize that the ideal portrait of science — this body of people in white coats with scrupulous integrity who always sacrifice their egos and their career ambitions to the evidence and the truth — is mythological. Scientists are just as prone to defend set ideas as anyone else, and sometimes more so, if the incentives (grant money, tenure, hiring, etc.) favor the status quo. The public has to be aware that scientists (like all academics) can be quite political, quite manipulative, and quite unfair to challengers to their beliefs.

    Given a choice between a public that accepts ID, but accepts it uncritically, and a public which rejects ID, but also rejects Darwinism because it has a critical mind and doesn’t kowtow to authority, I would far rather have the latter. I don’t want ID as a conclusion pushed in the schools; I want the views of Richard Dawkins and Jerry Coyne and Richard Lewontin and Ernst Mayr taught much more in the schools, and analyzed and criticized in tiny detail in the schools, so that students can see just how shaky those views are. And anything that helps that process along — such as learning a little about the criticisms of people like Shapiro and Margulis and Newman — should be welcomed. I want students to have a shot at wrestling with competing arguments and practising arriving at the truth on their own, as opposed to being indocrinated in what the leading evolutionary biologists believed 40 years ago and what the mediocre evolutionary biologists still believe now.

    T.

  53. You can use Darwinian any way you like as long as you make it clear what you mean.

    I spent ages trying to establish what various people meant by “neo Darwinian” and gave up. I quoted Margulis as saying she was a a Darwinian but not a neo-Darwinian, and normally use those words now in the sense in which she gave.

    If Shapiro says he is not a “Darwinian” but nonetheless an “evolutionist” then he is not using the word in the same sense as Margulis.

    Whatever.

    If Shapiro is not a Darwinian, nor am I.

    Definitions are descriptive, not prescriptive. What is not on, however, is to define the word in one sense, then argue against it in another. That is “equivocation”. If “Darwinism” is being defeated, and what is meant by “Darwinism” is some aspect of evolutionary theory that Darwin didn’t consider, or argued against, or argued for (Lamarckism, for instance) then, sure, it’s being defeated.

    It seems a little unfair on Darwin, though, whose basic insight (and that of Wallace) that heritable variation and natural selection together would result in adaptation is what a great many people think of as “Darwinian”.

    It’s the basis of evolutionary algorithms, and underpins evolutionary biology, including the work of Shapiro and Margulis.

    Give it another name if you like, but it’s in no danger of defeat.

    And when campaigning against the alleged evils of “Darwinism” be sure to say what you mean.

    Timaeus, you seem to have this bizarre view that I am trying to wield “authority” here, despite the fact that I have repeated disavowed any such claim or intentions.

    I don’t care how people use words as long as they are clear what they mean.

    And if Shapiro uses the word Darwinian in a different sense to the way I do (and, I’d argue, the way most people do) that is absolutely fine, and I retract my claim that he is a “Darwinian” in his sense of the word.

    The reason I fuss about definitions is to avoid equivocation, not to lay down the law about how words should be used. That’s why I often ask for operational definitions, for instance, of the word “random” which is used in all kinds of sense here, from “equiprobable” to “non-intentional” to “drawn from a probability distribution” to “stochastic”. I don’t care which, as long as it’s clear.

  54. If “Darwinism” means “what Darwin said” then every single biologist in the world rejects Darwin.

    Of course there is disagreement among evolutionary biologists. If there weren’t, we would have made no progress over the last 150 years, and the progress has been extraordinary.

    But the basic idea of heritable variation and natural selection that Darwin proposed as the mechanism of adaptation still lies at the heart of evolutionary theory. What Shapiro and Margulis have done (and many others) is delve into the origins of heritable variation, something about which Darwin had no idea (at one point he favored some kind of Lamarckian scenario).

    So to say that Shapiro and Margulis, whatever they call themselves (and Margulis called herself a Darwinian) are opposed to this aspect of Darwinian theory is simply wrong.

    They do “still think of …mutations being filtered by natural selection as the primary motor of evolution” (well Margulis until her death). The word random (which I replaced by ellipses above) wasn’t actually used by Darwin, and, as I keep saying, means very little, or rather too much.

    Neither Margulis nor Shapiro think that variation is generated by a designer. If “random” means “not generated by a designer” then Margulis and Shapiro sign up to your statement. If it means “drawn from a flat distribution” or “drawn from a distribution that itself did not evolve” then they don’t.

    And nor do I, and nor, I suggest does any living biologist. Nor anyone who got as far as meiosis in high school biology.

  55. Okie Dokie Mr. Rickert, please show me just one example of any of the molecular machines I listed being designed from scratch by any population of cells? Shoot, I’ll give you the whole universe, please show me ANYWHERE in the universe that any machine has come about without a mind bringing it into existence.

  56. And to be fair Mr. Rickert to the scientific method, here is an example of mind bringing a machine into existence;

    Game on! A bioinformatician confronts Intelligent Design – VJT – January 2012
    Excerpt: The moment one constructs a device to carry into practise a crude idea he finds himself unavoidably engrossed with the details and defects of the apparatus. As he goes on improving and reconstructing, his force of concentration diminishes and he loses sight of the great underlying principle. Results may be obtained but always at the sacrifice of quality.
    My method is different. I do not rush into actual work. When I get an idea I start at once building it up in my imagination. I change the construction, make improvements and operate the device in my mind. It is absolutely immaterial to me whether I run my turbine in thought or test it in my shop. I even note if it is out of balance. There is no difference whatever, the results are the same. In this way I am able to rapidly develop and perfect a conception without touching anything. When I have gone so far as to embody in the invention every possible improvement I can think of and see no fault anywhere, I put into concrete form this final product of my brain. Invariably my device works as I conceived that it should, and the experiment comes out exactly as I planned it. In twenty years there has not been a single exception. Why should it be otherwise? Engineering, electrical and mechanical, is positive in results. There is scarcely a subject that cannot be mathematically treated and the effects calculated or the results determined beforehand from the available theoretical and practical data. The carrying out into practise of a crude idea as is being generally done is, I hold, nothing but a waste of energy, money and time. – Nikola Tesla
    http://www.uncommondescent.com.....nt-design/

    Further notes:

    The Mind Is Not The Brain – Scientific Evidence – Rupert Sheldrake – video (with Referenced Notes)
    http://vimeo.com/33479544

    Moreover, the argument for God from consciousness can be framed like this:

    1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ of material reality.
    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even central, position within material reality.
    4. Therefore, consciousness is found to precede material reality.

    Psalm 33:13-15
    The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007
    http://henry.pha.jhu.edu/aspect.html

    “Descartes said ‘I think, therefore I am.’ My bet is that God replied, ‘I am, therefore think.’”
    Art Battson – Access Research Group

    Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer – video – (Notes in description)
    http://vimeo.com/32145998

    Verse and Poem set to Music:

    Acts 17:28
    ‘For in him we live and move and have our being.’ As some of your own poets have said, ‘We are his offspring.’

    There Is More – Poem – video
    http://www.metacafe.com/watch/4102086/

  57. Elizabeth:

    I never said at any point that Margulis or Shapiro thought that variation is generated by a designer. Why don’t you listen to what I say, instead of projecting? Did you even read my reply to Dr. Rec above, before you reacted to it? Can you not see where I denied the belief you are now alleging? Is this how carefully you read Darwin, Margulis, Behe, Dembski, etc.?

    Margulis’s view was that massive recombinations of genomes were a much more important driver of major evolutionary change than what are normally called “mutations” by conventional evolutionary biologists. If you had read the articles I linked you to on another thread, you would know that.

    Elizabeth, you say you are asking for clarity about people’s definitions, but you are one of the main producers of non-clarity here. You have been ferociously arguing that Shapiro and Margulis are perfectly “Darwinian.” This creates endless confusion.

    Shapiro and Margulis both have very serious disagreements with what is broadly called “Darwinian” theory by most evolutionary biologists. Your attempt to include them as “Darwinian” obscures that. You are trying to downplay the differences that they are very clearly and loudly trying to emphasize. No, they are *not* just adding one or two new mechanisms to the repertoire of evolutionary mechanisms. They are saying that the mainstream of 20th-century evolutionary biology was *wrong* in what it took to be the main driving force of evolution. You can disagree with their criticisms of mainstream evolutionary thought if you like, but don’t try to make out that they don’t have these criticisms, and don’t try to make out that they aren’t major criticisms. If either Margulis or Shapiro is right, then the picture of evolution most commonly held by educated lay people — the one promoted (in various ways) by Mayr, Simpson, Dobzhansky, Dawkins, Miller, Scott, Gould, and others — is seriously misleading. And Margulis explicitly says — in the reference which I gave you and you apparently ignored — that the ID people are *right* in their criticism of the conventional picture.

    As I said before, Elizabeth, you can use words any way you want. But when you use words that obscure the situation, that mask important theoretical differences, your usage is bad. I think you should fall into line with the usage I’ve already explained to you at great length, the usage common to Shapiro, Coyne, Dawkins, Mayr, Simpson, Behe, Dembski, etc. Otherwise you simply obstruct the conversation rather than contribute to it. I don’t expect you to listen to this advice, but there it is.

    And it would be nice if you would admit error on specific points, e.g., you said that Shapiro criticizes only “neo-Darwinism” and not just “Darwinian” theory. I gave you an explicit quotation above to the contrary. The proper answer, Elizabeth, is “I was wrong, and retract my assertion about Shapiro’s view.” See if you can choke those words out of your throat. It would look good on you.

    T.

  58. And you are ignoring the fact that both of these “criticisms” of “Darwinism” are well within the mainstream of empiricism. They present testable conjectures that do not assume any mysterious interventions.

    Since they involve knowledge beyond what was available to Darwin, they cannot be anti-Darwinian. At most they are extensions of theory. At worst they are simply wrong. The fact that they can potentially be demonstrated right or wrong places them within the mainstream.

  59. For those interested in an interpretation of Shapiro’s thought by someone who knows Shapiro personally and is also well-versed in the field, I would recommend the book review by Adam Wilkins here:

    http://gbe.oxfordjournals.org/.....l.pdf+html

    Wilkins disagrees with some of Shapiro’s major points, but he confirms my analysis of where Shapiro departs in crucial ways from the mainstream of 20th-century evolutionary theory (which Wilkins characterizes as “Darwinian,” p. 2). Wilkins does not soft-pedal the differences, because he knows they are important. And at the end of the review, he notes that there is a swelling chorus of voices against the mainstream. And he there vindicates my perception that the population geneticists are frequently the “old guard” and those coming in from other angles (including molecular biology) are often the challengers. I’ve said that here before.

    It’s heartening for me to know that an evolutionary biologist who disagrees with me about the causes of evolution agrees that I have the right perception — the same perception as the trained professionals — of what the debate is about.

    T.

  60. I’m not accusing you of anything Timaeus, please stop regarding my posts as imperious pronouncements and corrections! That’s kairosfocus’s job ;)

    And I did, in fact, retract my claim about Shapiro, and fully accept that he did, in fact, characterise the view he rejects as “Darwinian. I will happily retract it again. He seems to call himself an “evolutionist”.

    Margulis, on the other hand differentiated between “Darwinian” and “neo-Darwinian” and accepted the former label.

    As I said, I don’t mind what labels people use, as long as it’s clear, and I am happy to clarify my own use.

    Shapiro and Margulis both have very serious disagreements with what is broadly called “Darwinian” theory by most evolutionary biologists.

    Well, we can disagree about what “Most evolutionary biologists” call “Darwinian”, but there’s no point: let’s see what they disagree with:

    YNo, they are *not* just adding one or two new mechanisms to the repertoire of evolutionary mechanisms. They are saying that the mainstream of 20th-century evolutionary biology was *wrong* in what it took to be the main driving force of evolution.

    Well, I would agree, as would most modern biologists, that in the early days there was too much emphasis on selection, none on drift, and not enough on the mechanisms of variance generation, nor on population-level selection (selection of populations). That has radically changed. Most people don’t call themselves “non-Darwinian” as a result; for some reason Shapiro does.

    You can disagree with their criticisms of mainstream evolutionary thought if you like, but don’t try to make out that they don’t have these criticisms, and don’t try to make out that they aren’t major criticisms.

    I don’t disagree with their criticisms; I don’t make out they don’t have them; however I do not think they are major criticisms of Darwin’s original theory of heritable variance in reproductive success as the mechanism of adaptation of populations to their environment. What they have both done, of course, is something that Darwin didn’t not even attempt to do, which is to work on the mechanisms of variance generation.

    If either Margulis or Shapiro is right, then the picture of evolution most commonly held by educated lay people — the one promoted (in various ways) by Mayr, Simpson, Dobzhansky, Dawkins, Miller, Scott, Gould, and others — is seriously misleading.

    I don’t think so, although clearly several of those (including Dawkins I might say) are out of date. For me, one of the biggest breakthroughs in evolutionary science in recent times has been the domain of “evo-devo”, again in the area of variance generation.

    But no “Darwinist” could ever claim that natural selection alone can result in adaptive evolution (it would be a koan anyway – you can’t have selection without a range to select from) any more than any “Darwinist” could claim that variance alone can result in adaptive evolution (and impossible anyway, given that we know that some variants are incompatible with life).

    So while there might have been changes of emphasis over the years, I don’t see that Shapiro is offering anything not implicit in what has gone before.

    And Margulis explicitly says — in the reference which I gave you and you apparently ignored — that the ID people are *right* in their criticism of the conventional picture.

    And I have often made the same point myself. In fact my very first post at UD made precisely that point: rhat the identification of patterns in biology do indicate that something rather special and design-y is going on. And what I like about both Margulis and Shapiro (especially Shapiro) is that he regards evolutionary processes as an intelligent system. So do I. I work with intelligent systems, and my job is trying to find out how they work. Saying that biological organisms aren’t “intelligently” designed, in one sense, is clearly wrong. They are. And the designing intelligence is one that works in many ways very like our own, with the minor difference (and it really is minor) that it has no future goals, it is entirely reactive, and does not simulate possible outcomes in order to choose the next path. It’s a feeler, not a seer – it has “tactile” intelligence rather than sighted intelligence, as someone recently posted (can’t remember who).

    As I said before, Elizabeth, you can use words any way you want. But when you use words that obscure the situation, that mask important theoretical differences, your usage is bad.

    Obviously I don’t want to mask important theoretical differences, but I do want to point out where those are absent. And I will use language to the best of my ability to make my points. If I am unclear, please just ask. I am always willing to clarify.

    I think you should fall into line with the usage I’ve already explained to you at great length, the usage common to Shapiro, Coyne, Dawkins, Mayr, Simpson, Behe, Dembski, etc. Otherwise you simply obstruct the conversation rather than contribute to it. I don’t expect you to listen to this advice, but there it is.

    Well, I’ll listen, but as I dsipute the premise that all these people use the same terms in the same way, no, I won’t take it, because I can’t. However, I will try to make it clearer in future precisely what I mean by a term in any usage of it.

    PS: searching for my retraction I see that it was implicit in this post:

    http://www.uncommondescent.com.....ent-417678

    taken in subsequent context, but not explicit.

    I unreservedly retract any claim I made that implied that Shapiro did not reject the description “Darwinian”. It seems he did.

    My view is that that’s a little unfair on Darwin, but he’s entitled to his idiolect :) In my view, Shapiro view of evolution owes one heck of a lot to Darwin.

  61. Hi Elizabeth,

    Thank you for your posts (1.1.2.1.10 and 1.1.2.1.11). You were quite right about one thing: the sort order is irrelevant to computations of Shannon complexity. Mea culpa. However, I believe you were mistaken when you wrote:

    Shannon information doesn’t care what order the items are arranged in, it only cares how many ways there are of arranging the items.

    This is fine if all arrangements are equiprobable. But what if they’re not? In your case (Chesil beach), there is a natural biasing factor at work, causing the pebbles to be sorted in descending order of size. This means that a random sequence of pebbles would be far more surprising than a sequence of equal length, in which the size of the pebbles was in descending order. Hence it would contain more Shannon information. Likewise English text is considered to be fairly low in entropy because it is largely predictable: the only letters that can appear after “abl”, for instance, are “a”, “e”, “i”, “o”, “u” and “y”, and of these, “e” and “y” are by far the most common.

    Now compare Professor Dembski’s card case with Chesil beach. The point is that the cards, unlike the beach, contain no built-in bias favoring lower values. Hence each possible arrangement of cards is equally improbable and thus contains the same amount of Shannon information. The probability of getting all spades in ascending order in a hand of 13 cards is extremely low; and the Kolmogorov compressibility of the sequence is high. That points to agency. On the other hand, the probability of getting sand grains sorted roughly by size on Chesil beach is not that low, given the causal factors at work. So the parallel breaks down.

    Another problem with your example is that your verbal description (which is supposed to roughly correspond to Kolmogorov complexity) doesn’t specify any particular arrangement of pebbles. It merely describes a generic feature of that arrangement: namely, that the pebbles tend to descend in order of size. If you wanted to describe a particular sequence of pebbles, however, you would need quite a lot of space to do so, unless it were a sequence in which the pebbles along the beach descended in perfect order of size – which is extremely unlikely to be the case. If they did, I’d suspect intelligent agency was at work:)

    So Professor Dembski’s point that high Kolmogorov complexity combined with high improbability is a hallmark of intelligent agency, remains a valid one.

    champignon:

    Thank you for your clarification regarding Kolmogorov complexity and algorithms. You are right, of course. The length of a verbal descriptions is language-dependent. Algorithms are a better way to go if you want an objective mathematical figure. Upon reflection, I agree that Tom Jones’ DNA will be difficult to reproduce via an algorithm, because of the very large number of mutational steps from the first living cell to Tom Jones.

    However, it occurs to me that a point raised by mathematician Gregory Chaitin, in a talk I wrote a post about recently, is of relevance here. The key point relates to three ways of obtaining the Busy Beaver (BB) function of a given number N:

    Exhaustive search reaches fitness BB(N) in time 2^N.
    Intelligent Design reaches fitness BB(N) in time N. (That’s the fastest possible regime.)
    Random evolution reaches fitness BB(N) in time between N^2 and N^3.

    Chaitin added:

    But I told a friend of mine … about this result. He doesn’t like Darwinian evolution, and he told me, “Well, you can look at this the other way if you want. This is actually much too slow to justify Darwinian evolution on planet Earth. And if you think about it, he’s right… If you make an estimate, the human genome is something on the order of a gigabyte of bits. So it’s … let’s say a billion bits – actually 6 x 10^9 bits, I think it is, roughly – … so we’re looking at programs up to about that size [here he pointed to N^2 on the slide] in bits, and N is about of the order of a billion, 10^9, and the time, he said … that’s a very big number, and you would need this to be linear, for this to have happened on planet Earth, because if you take something of the order of 10^9 and you square it or you cube it, well … forget it. There isn’t enough time in the history of the Earth … Even though it’s fast theoretically, it’s too slow to work. He said, “You really need something more or less linear.” And he has a point….

    So there we are. Something of the order of 10^9 looks like the answer to your question.

  62. Petrushka (5.1.1.1.1):

    I said nothing against empiricism and nothing in favor of mysterious interventions. You, like so many critics of ID, appear to have a reading comprehension problem, inferring positions that your debating partners are not advancing.

    Your view that Shapiro and Margulis are merely extending Darwinian theory, rather than fundamentally challenging key aspects of it, shows a lack of understanding of the subject matter. Please read Shapiro’s book, and then read the review I discussed immediately above. There will be a quiz.

    T.

  63. Hi Elizabeth,

    OK, let’s clear up the issue of whether Shapiro is a Darwinian or not, once and for all. What is the essence of Darwinism? According to you, it’s this: “heritable variation and natural selection together would result in adaptation.” So randomness doesn’t come into it, according to you. Fair enough; Darwin himself vacillated somewhat on this question, apparently.

    Now let’s see what Adam S. Wilkins has to say about the difference between Shapiro’s definition of evolution and yours (which you claim to be the bare essence of Darwinism), in his review of Shapiro’s book, Evolution: a view from the 21st century. He writes:

    My final disagreement with Jim [Shapiro]’s general argument concerns a truly fundamental point, however: the dismissal of natural selection as a shaping force in evolution. Thus, it is stated, at the very start of the book (top of p. 1): “Innovation, not selection, is the critical issue in evolutionary change. Without variation and novelty, selection has nothing to act upon.” While all evolutionists would agree whole-heartedly with the second sentence, most would reject the first. The matter of selection is then virtually ignored until the final section of the book. There we read, as one of nine bullet-points that summarize the core message: “The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. Selection operates as a purifying but not creative force [emphasis added].” (Bold emphases mine – VJT.)

    Do you think Charles Darwin would have agreed with the statement: “Innovation, not selection, is the critical issue in evolutionary change”?

  64. Petrushka,

    You are missing the point. Countless individuals, yourself included, have argued the obvious, inevitable creative ability of darwinian mechanisms. Now “mainstream science” is questioning them.

    This is not specifically about ID, which is what I suppose you are alluding to with ‘mysterious interventions.’

    It is a clearer indication of what others have already admitted, that while many agree that some process of evolution is taking place, the mechanisms are pretty much up in the air. The implicit acknowledgement that the traditionally accepted mechanisms (you know, the ones they drum into students’ heads) are inadequate at least as significant as the new ones tentatively proposed. You can pretend that doesn’t validate what skeptics have been saying about RM+NS just about forever, but you’d be in denial. You’re trying to turn the page on the fundamentals of evolution without admitting that those who questioned those fundamentals were right. No one likes to hear ‘I told you so.’

    That much has nothing to do with ID, because many people have been pointing out that RM+NS is a vacuous explanation long before anyone formulated ID. (Many of them were children.)

    There is of course an ID implication. Acknowledging that we don’t know what causes produced an effect undermines the unscientific rhetoric that rules out any intelligently designed mechanism. Unless, that is, evolution is defined as the nebulous theory of ‘change over time by mechanisms that are unspecified except we know for darned sure they weren’t intelligent.’

  65. Hi bornagain77 and Neil Rickert,

    I have to say, bornagain77, I was absolutely blown away by the talk given by Rupert Sheldrake on http://vimeo.com/33479544 . It’s a must-see. Anyone who still thinks the mind is the brain after watching that video is defying the known facts.

    Neil Rickert, you think Futuyma’s definition of random – i.e. that the chance that a specific mutation will occur is not affected by how useful that mutation would be – is a defensible one. I would agree that it is, if the notion of “fitness” or “usefulness” can be made rigorous. Talbott thinks it can’t. After reading his article, I think he at least makes a case that needs to be answered.

    Regarding intelligent evolution, you claim that the notion of “biological systems redesigning themselves” is not a problematic one, and that no evidence of an external designer has been presented. Adam Wilkins, in his review of Shapiro’s book, evidently disagreed with you. Commenting on Shapiro’s claims that “Innovation, not selection, is the critical issue in evolutionary change” and that “Selection operates as a purifying but not creative force”, which tend to belittle the importance of natural selection in evolution, Wilkins writes:

    The arguments from paleontological evidence for the importance of natural selection largely concern the observed long-term trends of morphological change, which are visible in many lineages. It is hard to imagine what else but natural selection could be responsible for such trends, unless one invokes supernatural or mystical forces such as the long-popular but ultimately discredited force of “orthogenesis”…

    Finally, with respect to this issue of selection, one might add that, in terms of Jim [Shapiro]’s particular thesis, it is hard to understand how cells could have the very capacities for “natural genetic engineering” attributed to them without those capacities having been evolved, in some manner and over long evolutionary spans, by natural selection. The evolution of such capabilities, favouring the process of “evolvability” (the capacity to give rise to new properties), is a fascinating subject, mentioned explicitly though only briefly in the book, and deserves more attention than it has traditionally received. Again, the only alternative for the origination of these capabilities, if one discards natural selection as the generative agent, is some supra-natural force, a position that I am certain is not being advocated here. (Bold emphases mine – VJT.)

    In other words, Wilkins thinks “intelligent evolution” won’t work, and that only an intelligent designer could make it work. True intelligence is far-sighted, looking to the distant future. That’s how it achieves its spectacular results. But Shapiro’s self-designing cells can’t achieve those results – unless they’re packed with information at the start (front-loaded) by an external Designer, who has a long-term aim in mind and who anticipates the obstacles that will occur in the process of reaching it. All that Shapiro’s cells can look to is the immediate future; hence they’re not really intelligent.

  66. Hi Elizabeth,

    Re whether or not Shapiro is Darwinian, please see my remarks above, at http://www.uncommondescent.com.....ent-417905 . In particular, I’d be interested to hear your answer to my question: Do you think Charles Darwin would have agreed with the statement: “Innovation, not selection, is the critical issue in evolutionary change”? That’s what Shapiro wrote.

    By the way, I suggest you have a look at the talk by Rupert Sheldrake at http://vimeo.com/33479544 , which bornagain77 kindly linked to. It’ll shatter your belief in materialism. Mind-blowing stuff.

  67. Sorry Elizabeth,

    That comment of mine didn’t come out quite where I wanted it:

    http://www.uncommondescent.com.....ent-417909

  68. Thanks for the retraction, Elizabeth. It was not explicit before.

    Of course all evolutionary biologists owe *something* to Darwin. Newton owed a fair bit to Galileo, too, but his disagreements with Galileo, where they existed, were major. And Einstein owed something to Newton, but his disagreements, where they existed, were non-trivial. For that matter, Galileo owed something important to Aristotle, but his criticism of Aristotle was of central import for physical theory. Shapiro and Margulis are not merely updating or tweaking what is normally called “Darwinian” theory (a term which no one in the field limits to only the exact views held by Darwin); they are suggesting a major reorientation about how major novelties in form arise.

    When Margulis said that John Maynard Smith didn’t understand evolution (!), she was throwing down a gauntlet, and if you grasp that, then any defensive quibbles about her saying “neo-Darwinian” rather than “Darwinian” seem quite silly. Smith and the other leaders of mainstream 20th-century biology conceived of themselves as faithful to the original insights of Darwin (while correcting his obvious factual errors), and hence as authentically “Darwinian.” It’s precisely the *inadequacy* of that “corrected but faithful” Darwinian position that Shapiro and Margulis and others are now criticizing. So no matter how you play around with the terms, the result is the same: Darwin’s detailed science is hopelessly outdated, and the improved Darwinian evolutionary science of Smith, Mayr, Dobzhansky, etc. is the target of the critics I’m speaking of.

    If you are going to try to shoehorn Margulis and Shapiro into the “Darwinian” camp, then all that one can say is that “Darwinian” theory is extremely broad; indeed, if they fit into it, it would be hard to see any difference between Darwinian theory and evolutionary theory generally. But that is a ludicrous result, since the whole point of Darwinian theory was to provide a particular mechanism for evolution; it has to be distinguishable from non-Darwinian theories, e.g., Lamarck’s, Denton’s. If Darwinian theory is (as you seem to think) essentially nothing more than variation plus inheritable change, then every evolutionary theory is Darwinian.

    Once again I refer you to the Wilkins review of Shapiro, cited below. If the distinctions Wilkins makes do not convince you of the importance of the point I am making, I am sure that nothing further that I can say will do so.

    T.

  69. It’s a feeler, not a seer – it has “tactile” intelligence rather than sighted intelligence, as someone recently posted (can’t remember who).

    I’ll take the credit, but I doubt I’m the first to use the metaphor. For some reason the word “blind” suggested Braille and the way blind people examine things.

    Blind people are certainly intelligent, but their vision is limited to what is within reach. If they have to explore a space, they can do it, but not as quickly as a sighted person.

    For the same reason and in the same way, tactile evolution can explore the same space as a system with “foresight.” It just takes longer and is more wasteful.

  70. 5.1.1.2: “I’m not accusing you of anything Timaeus,”

    Actually, Elizabeth, you did implicitly accuse me of something. In a post addressed to me, and disputing some of my claims, you opened a paragraph with:

    “Neither Margulis nor Shapiro think that variation is generated by a designer.”

    How else was I to take that remark, but as a statement of what you thought I believed about Margulis and Shapiro?

    My argument that Shapiro and Margulis each had a fundamental disagreement with Darwinian theory in no way implied that I thought that either of them believed in a designer.

    Hence my “indignation” when you seemed to impute that view to me.

    And of course, if you glance at the attacks from Dr Rec and Petrushka above, you will see that they, too, have imputed to me views that I have not advanced. That’s par for the course around here, so you perhaps shouldn’t be surprised that I thought you were doing the same thing.

    T.

  71. First, you told Petrushka…

    I said nothing against empiricism and nothing in favor of mysterious interventions. You, like so many critics of ID, appear to have a reading comprehension problem, inferring positions that your debating partners are not advancing.

    and then, to Elizabeth…

    And of course, if you glance at the attacks from Dr Rec and Petrushka above, you will see that they, too, have imputed to me views that I have not advanced. That’s par for the course around here, so you perhaps shouldn’t be surprised that I thought you were doing the same thing.

    In other words, ID critics aren’t allowed to assume what one ID advocate implied based on what other ID advocates make explicit. But you’re allowed to assume what one ID critic implied based on what other ID critics made explicit.

  72. And the designing intelligence is one that works in many ways very like our own, with the minor difference (and it really is minor) that it has no future goals, it is entirely reactive, and does not simulate possible outcomes in order to choose the next path. It’s a feeler, not a seer – it has “tactile” intelligence rather than sighted intelligence, as someone recently posted (can’t remember who).

    Except that as far as we know, evolution neither has nor can behave in any such manner. The capabilities of evolutionary processes are what they are and what they were yesterday. Calling them “intelligent” sheds no light on whether or not they did any such thing to merit that designation. That is precisely the question you are begging.

    It also seems rather circular to call such mechanisms “intelligent” because of the seemingly intelligent outputs attributed to them while asserting that they are capable of producing such results because of their intelligence.

    I’m sure you’ll argue that it’s not circular. But given the current lack of evidence that any evolutionary process (GAs included) can act with the intelligence attributed to them, that’s exactly what it is.

  73. vjtorley:

    Neil Rickert, you think Futuyma’s definition of random – i.e. that the chance that a specific mutation will occur is not affected by how useful that mutation would be – is a defensible one.

    I see it as good enough. One does not need a precise definition here.

    I look at evolution as a learning system. A population of organisms lives in a changing environment. The climate changes, the food sources change, the predators that threaten the population change. If the population is to survive, it must adapt to those ever-changing conditions. The best way to adapt is to correctly predict the future. But, assuming that such prediction is not possible, the next best alternative is to maintain sufficient variation within the population, so that it is likely that some of the variants will survive and propagate whatever traits they have that aid their survival. That is something like a Monte Carlo method, making good use of randomness.

    If changes at some locations on the genome usually have fatal effects, then it would not be useful to have a lot of variation at those locations. If changes at other locations have, in past generations, been particularly useful, then it would make sense to have more variation at those locations. So we wouldn’t expect the amount of variation to be constant across the entire genome. It seems to me that a system would evolve toward producing the variation at locations in the genome where it has proved most useful in the past.

    It seems to me that what we see fits that kind of learning strategy very well.

    I would agree that it is, if the notion of “fitness” or “usefulness” can be made rigorous. Talbott thinks it can’t.

    That’s where I think my view differs a little from that of traditional Darwinism.

    I want to define “niche” very narrowly, whereas it is usually taken fairly broadly. When I use a narrow definition of niche, then we have to see a population as occupying a range of niches, rather than a single niche. To give an example, some humans occupy the carpenter niche, some the banker niche, some the educator niche, etc.

    From that perspective, fitness would be fitness of a particular organism to a specific niche. What matters to the population as a whole is a kind of average fitness taken over the population for a range of niches. So fitness would be a function of niche and organism, and the average fitness would be a kind of integral of that fitness function over the entire population with respect to the range of niches that are occupied. That makes fitness a bit complex.

    In any case, from that way of looking at things, a population is best served by broadening its range of niches where possible, even if that results in a small reduction of average fitness. A population does not need to be optimal for its range of niches. Suboptimal is fine, as long as there is sufficient fitness that it can maintain the population size.

    The use of random mutation is a way for a population to attempt to broaden its range of niches. It can be thought of as a way of exploring niche space.

  74. 74

    The best way to adapt is to correctly predict the future. But, assuming that such prediction is not possible, the next best alternative is to maintain sufficient variation within the population, so that it is likely that some of the variants will survive and propagate whatever traits they have that aid their survival.

    You are saying that living things cannot predict the future, and so they exercise foresight instead, having on hand what they will likely need. Predicting the future and foresight aren’t exactly the same thing, but you’re still attributing foresight to evolution.

    It’s essentially the same thing as saying that a person can’t predict the future, so he exercises foresight by saving money to be prepared for unexpected events. You’re still describing an intelligent behavior, more intelligent even than some people.

  75. Hi Elizabeth,

    OK, let’s clear up the issue of whether Shapiro is a Darwinian or not, once and for all. What is the essence of Darwinism? According to you, it’s this: “heritable variation and natural selection together would result in adaptation.” So randomness doesn’t come into it, according to you. Fair enough; Darwin himself vacillated somewhat on this question, apparently.

    “Randomness” is a word I try to avoid, as it has so many meanings.

    Now let’s see what Adam S. Wilkins has to say about the difference between Shapiro’s definition of evolution and yours (which you claim to be the bare essence of Darwinism), in his review of Shapiro’s book, Evolution: a view from the 21st century. He writes:

    My final disagreement with Jim [Shapiro]’s the dismissal of natural selection as a shaping force in evolution. Thus, it is stated, at the very start of the book (top of p. 1): “Innovation, not selection, is the critical issue in evolutionary change. Without variation and novelty, selection has nothing to act upon.” While all evolutionists would agree whole-heartedly with the second sentence, most would reject the first. The matter of selection is then virtually ignored until the final section of the book. There we read, as one of nine bullet-points that summarize the core message: “The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. Selection operates as a purifying but not creative force [emphasis added].” (Bold emphases mine – VJT.)

    Do you think Charles Darwin would have agreed with the statement: “Innovation, not selection, is the critical issue in evolutionary change”?

    Yes, I think he would have disagreed with it, and so do I. I think that comment of Shapiro’s is rather silly. The two concepts are not separable. Selection isn’t something you “add” to variation to get evolution. To get evolution you need variance generation, and as long as that variance generation includes variance in reproductive success, then you have both. If it doesn’t, then no amount of novelty is going to result in adaptatation.

    But of course Shapiro is absolutely right to emphasise the importance of the mechanisms (and the evolving of those mechanisms) of heritable variance generation in understanding evolutionary processes. What is silly, IMO, is apparently forgetting that heritable variance in reproductive success is all natural selection is.

  76. I’ve read the book, and I’ve quoted extensively from it. I’ve read the review.

    My own take is that the apparent controversy is the result of incautious writing. It reminds me of the quip that a manuscript is both good and original, but the parts that are original are not good, and the parts that are good are not original. That’s too harsh, but it’s my impression.

    It’s really rather difficult to come up with original critiques of evolution. For the first 80 years after “Origin” there was no widespread agreement at all about any part of Darwin’s theory. There were disagreements about saltation and about natural selection, not to mention disagreements about Lamarkian variation.

    So to write as if Shapiro has an original and unique perspective is to ignore history. Evolvability is an old idea. He has brought considerable expertise to the task of defining it and presenting it as something that can be rigorously studied, but it is not his original idea.

    One of the things ignored by Shapiro and described in the review is that the mechanisms that Shapiro calls “engineering” had to evolve by less efficient processes. that is Why Koonin — who takes a similar stance — emphasizes that most evolutionary inventions occurred in microbes and spread quickly by horizontal transfer.

    Unlike ID advocates, Shapiro invokes no external designer. He simply leaves unaddressed the origin of the mechanisms he describes.

  77. It is not circular to describe a system that learns intelligent.

    Learning via feedback can be described independently of labels.

  78. 78

    Oh, my bad. I didn’t realize that it learns. When you put it that way I suppose it must be intelligent. Nothing circular here.

  79. Actually, Elizabeth, you did implicitly accuse me of something. In a post addressed to me, and disputing some of my claims, you opened a paragraph with:

    “Neither Margulis nor Shapiro think that variation is generated by a designer.”

    How else was I to take that remark, but as a statement of what you thought I believed about Margulis and Shapiro?

    As a statement of what I believed about Margulis and Shapiro!

    Seriously, I’m not the Maggie Smith character you seem to think I am :)

  80. *pricks up ears at the word “learns”*

    Who are you responding to, where, Scott?

  81. Ah, here :)

    Yes, Scott, GAs are learning algorithms. They are awesome learning algorithms, so much so that we use them to model learning as well as to model evolution.

    And, to learn with, of course :)

  82. ScottAndrews2:

    You are saying that living things cannot predict the future, and so they exercise foresight instead, having on hand what they will likely need.

    I’m not sure where you are getting that “foresight”. It is not anything that I have suggested. Randomness does not depend on foresight.

    Perhaps you are seeing a claim of foresight in my comment about the value of maintaining some variation within the population. But standard Darwinian reasoning would say that if populations that maintain variation do better, then they will win the natural selection game. No actual foresight is required.

  83. lastyearon:

    I had an independent reason for my inference, based entirely on the internal logic of Elizabeth’s letter. I set forth that reason, and it had nothing to do with what other posters here said. I had already written my reply to Elizabeth up, when I remembered what the other posters had done, and I threw in the remark you are complaining about as an afterthought, so it doesn’t affect my core statement.

    Still, I can be generous to you and concede that ID proponents do from time to time make unfavorable assumptions about what their opponents mean. Yet civilized people can get over that. I had a great dialogue recently with aiguy, whose motives I at first distrusted. That happened because we each cut the other some slack and listened. We ended up finding a surprising degree of common ground. But what am I supposed to do when the same small group of people here, time after time, on thread after thread, keeps trotting out the “ID means miracles” trope, even after everyone here (a) denies it, and (b) explains at great length, on multiple threads, why miracles are not necessary for ID? Do you expect me to believe that these people are sincere debaters? Similarly, the “Who designed the designer?” argument has been refuted scores of times, but people who know that still keep bringing it up. Should I impute high motives to people who employ sophistry like that?

    Sincere debaters, who are after truth rather than simply blood sport, don’t behave in that way. They either try to refute the point, or they concede the point. Or they say: “I’m not sure. You’ve given me food for thought. Give me a couple of weeks to chew on that one, and I’ll get back to you.” They *don’t* just go silent, and then make the same argument again on another thread in hopes that no one will notice that their argument has already been refuted elsewhere.

    More than one person here has said false things about Michael Denton, and then, when exposed by someone who has actually read Denton’s works, has retreated, to say the same false things a few days or weeks later on another thread. More than one person here has said false things about Michael Behe, been shown direct quotations that refute the charge, and conducted himself in the same way. Once a pattern like that develops, one tends to get a reflex activity when a new poster makes an argument identical in form that bad-mouths Behe or Denton or Meyer or Dembski etc. One tends to assume that the distortion or the sophistical reasoning is deliberate.

    I make a point of *not* saying false things about Shapiro, Miller, Dawkins, Margulis, etc. I may occasionally make an error in interpretation, but I don’t make stuff up, I don’t literature bluff about stuff I haven’t read, and when shown I’m wrong, I don’t use the same argument again elsewhere. So I think I’ve earned trust, even from those who disagree with me. That’s more than I can say for many Darwinists who post here and elsewhere on the internet. Misrepresentation seems to be their game.

    You want more trust? Earn it. Let’s hear some Darwinists here repudiate some false things that other Darwinists here have said about Behe; let’s hear a Darwinist here admit that the phrase “intelligent design creationism” is deliberately demagogical when used by the NCSE in political contexts. Let’s hear some Darwinists here say that federal judges are incompetent to settle questions of science and theology (as they would have said if the Dover Trial had gone the other way). Let’s hear Nick Matzke just once, in years of posting here, admit he has made an error of any kind, or grant a substantive point to anyone, or state even one thing he has learned from reading an ID book. (Is every single word on every single page of every ID book false and deceptive? Does Nick Matzke know more about biology, biochemistry, probability theory, philosophy of science, etc., than every ID proponent on the planet? Unlikely.) And when someone says: Shapiro criticizes Darwinian mechanisms, let’s hear just one Darwinian here say, clearly and unambiguously: “You’re right; he does,” instead of replying “There’s no way Shapiro supports ID,” which is a non sequitur and is (I believe) generally devised to change the topic from the legitimate, non-religious, scientific criticism of Darwinism.

    The Darwinians who post here tend to be (with a few notable exceptions, like Allan MacNeill) dogmatic, doctrinaire, baiting, filled with rehearsed arguments from Panda’s Thumb, and obviously anti-religious in motivation. Doesn’t give us much trust to go on, does it? How about some dialogue that suggests: “I don’t know whether unguided mechanisms were sufficient to achieve this result, or whether some intelligent guidance or planning was required. Let’s search the answer out together.” Any chance we will get that tone from you, lastyearon? Or Petrushka? When I start seeing that dialogical approach, as opposed to the “dig in your heels and don’t grant those ID people an inch or they’ll take a mile” approach, I’ll start to be much more charitable in the way I read arguments here that at first glance seem dishonest, bluffing, sarcastic, motive-mongering, New Atheist chest-thumping, etc.

    T.

  84. 84

    I commented on this but put it in the wrong place.

    It is not circular to describe a system that learns intelligent.

    Your argument that it isn’t circular is a bit circular. It’s intelligent because it learns. How do we know it learns? Because it’s intelligent.

    Or were you just begging the question – reasserting that evolution “learned” how to do everything? How does that work? If you reassert your conclusion enough times do you get a trip to Mexico, or at least a toaster?

    Yes, Scott, GAs are learning algorithms.

    That really tells us nothing at all. Perhaps we’re equivocating on “learning.” Goldfish learn. That doesn’t mean they design immune systems. Chess programs are intelligent. But all they do is play chess.

    You can add the adjective “intelligent” to your idea of what you believe evolutionary processes have accomplished or can accomplish. I’ll go along. If it did any of those things, then it is a form of intelligence.

    So now we’ve added an adjective. What bearing does that have on the underlying question of whether or not it did or can do these things that we have agreed to call “intelligent?”

  85. I missed commenting on this part in my earlier response.

    vjtorley writes:

    Adam Wilkins, in his review of Shapiro’s book, evidently disagreed with you. Commenting on Shapiro’s claims that “Innovation, not selection, is the critical issue in evolutionary change” and that “Selection operates as a purifying but not creative force”, which tend to belittle the importance of natural selection in evolution,

    I tend to agree with Shapiro on that. But it is really two different ways of describing the same thing.

    We have an ever changing environment and an ever changing population. The two interact. We can give a description in which the environment is taken as the main actor. And that would be the traditional “natural selection” account. Or we can give a description where the population is taken as the main actor.

    We could step back from either, and just say that there’s an interaction. But our language allows us to be more specific in our description if we present it with one of the two being the main actor.

    Given two choices of main actor, which should we choose? One choice describes the environment (in the form of natural selection) as an intentional actor. And everyone understands that the intentionality is false. The other choice is to describe the population as an intentional actor. And maybe the intentionality is false there, too. However, everything about biology suggests some degree of intentionality, so I’m not sure that the intentionality is false. It seems to me that it can be fully accounted for in the behavior of the homestatic processes that we find in biological systems. Presenting the population as the main actor should draw our attention more to the natural feedback cycles that exist within biological systems. So I prefer that form of explanation.

  86. Yes, you intended it as a statement of what you believed, but you wrote it in the context of a refutation of my points. Most of your replies to me are of the form: “You are wrong because …” (repeat n times in n paragraphs, as needed). So I took it that you were refuting something that you thought I believed.

    I’m not browbeating you, just explaining how I read it. A suggestion: You could have written: “I know you haven’t said this, but some people here seem to believe that Margulis and Shapiro think … and that is wrong.”

    Which Maggie Smith character? She played hundreds of characters! Though I did see her as Lady MacBeth once, and, now that I think about it, …

    :-) (nyuk, nyuk) :-) JUST JOKIN’ :-)

  87. Petrushka:

    I agree with what you say about the early history of Darwin’s theory. But Shapiro, Margulis and other modern critics are reacting not to early versions of the theory but to the Modern Synthesis of about 75 years ago, which dominated evolutionary theory for most of the next 50 years and still is the core ingredient in mainstream evolutionary theory, around which other putative mechanisms tend to crystallize.

    Almost no idea in science or philosophy or theology or anything else is entirely original, so I have no problem admitting that Shapiro’s theory has earlier analogues. The point is not that he is entirely novel; the point is that his view attacks core positions of the Modern Synthesis. I don’t think this is contestable, on any honest reading of his work.

    I am not here trying to establish that Shapiro is right; I have been trying to rebut people who say he is Darwinian; that is a misleading description, to say the least.

    I agree that Shapiro invokes no designer; I’ve said that several times, and I don’t know why people keep thinking they need to tell me what I’ve already said I agree with.

    T.

  88. OK, we agree on some things.

    I have trouble getting excited about challenges to “Darwinism” that do not include what I consider the non-negotiable difference between evolution and ID, and that would be in the predictability of need and solutions to need.

    I think evolution is what it is because the future in a chaotic system is not predictable in detail over large periods of time.

    I think evolution is what it is because protein folding and coding sequences are inherently unpredictable. I’ve looked as some very recent papers on sequence prediction, and the best methods appear to involve GAs, methods that mimic biological evolution.

    So evolution proceeds by producing variations at a rate consistent with population survival. I’m aware of the claims of genetic entropy and meltdown, but I don’t see it happening. Measurements of mutations in the vicinity of Chernobyl indicate a rate three times “normal,” and yet populations are thriving.

    Natural selection is a kind of negative feedback. Negative feedback is a powerful way of stabilizing a dynamic system. All audio amplifiers use it to prevent runaway oscillation.

    Living populations combine feedback with the ability to remember the changes responsible for any improved function. The system doesn’t guarantee perpetual survival. Populations go extinct. But so far as we know, it guarantees the survival of life itself, because so many variations exist that they do not all go extinct.

  89. Thanks for the retraction, Elizabeth. It was not explicit before.

    Of course all evolutionary biologists owe *something* to Darwin. Newton owed a fair bit to Galileo, too, but his disagreements with Galileo, where they existed, were major. And Einstein owed something to Newton, but his disagreements, where they existed, were non-trivial. For that matter, Galileo owed something important to Aristotle, but his criticism of Aristotle was of central import for physical theory. Shapiro and Margulis are not merely updating or tweaking what is normally called “Darwinian” theory (a term which no one in the field limits to only the exact views held by Darwin); they are suggesting a major reorientation about how major novelties in form arise.

    Well, it’s obviously a “major reorientation” from Darwin, because Darwin had no idea how any novelty arose.

    When Margulis said that John Maynard Smith didn’t understand evolution (!), she was throwing down a gauntlet, and if you grasp that, then any defensive quibbles about her saying “neo-Darwinian” rather than “Darwinian” seem quite silly.

    To you, perhaps, but obviously not to her, because she was very explicit about claiming to be a Darwinian, not a neo-Darwinian.

    Smith and the other leaders of mainstream 20th-century biology conceived of themselves as faithful to the original insights of Darwin (while correcting his obvious factual errors), and hence as authentically “Darwinian.” It’s precisely the *inadequacy* of that “corrected but faithful” Darwinian position that Shapiro and Margulis and others are now criticizing. So no matter how you play around with the terms, the result is the same: Darwin’s detailed science is hopelessly outdated, and the improved Darwinian evolutionary science of Smith, Mayr, Dobzhansky, etc. is the target of the critics I’m speaking of.

    Of course Darwin is outdated. Of course Smith, Mayr, Dobzhansky are outdated. Evolutionary biology is a continuously developing field. But no-one has yet thrown out Darwin’s basic principle (give it another name if you don’t want to call it – Wallacian, perhaps) that heritable variance in reproductive success leads to the adaptation of populations to their environment. That principle remains fundamental to evolutionary biology.

    If you are going to try to shoehorn Margulis and Shapiro into the “Darwinian” camp, then all that one can say is that “Darwinian” theory is extremely broad; indeed, if they fit into it,it would be hard to see any difference between Darwinian theory and evolutionary theory generally.

    No, it would simply mean that what unites the field is the fundamental principle that heritable variance in reproductive success leads to adaptive evolution, no matter what the arguments about the generation of that variance, or the level at which “reproductive success” is measured (between cells; between organisms; between populations).

    But that is a ludicrous result, since the whole point of Darwinian theory was to provide a particular mechanism for evolution; it has to be distinguishable from non-Darwinian theories, e.g., Lamarck’s, Denton’s. If Darwinian theory is (as you seem to think) essentially nothing more than variation plus inheritable change, then every evolutionary theory is Darwinian.

    Yes, it was: the mechanism of heritable variance in reproductive success. And, sure, I think most evolutionary theories are Darwinian. It’s so obvious that it must happen, that even Creationists invoke it to explain the divergence of baramins post-flood. Within evolutionary theories that invoke the Darwinian mechanism, obviously people differ in how they think it works, and we are now much more aware of the role of drift, and of regulatory genes, and “evo-devo”, as well as Margulis’ drift theory, and population-level selection (as with Shapiro), and the biochemistry of DNA sequence shuffling.

    None of this was known to Darwin, or even Gould. The concept of drift seems to escape Dawkins.

    But it doesn’t make these theories “non-Darwinian” in the sense that I am using the term. The basic Darwinian mechanism is still invoked.

    What does separate some of these theories of course, is the idea that some external designer created the variants at key points, or adjusted the code. AFAIK, neither Shapiro or Margulis has proposed this.

    Once again I refer you to the Wilkins review of Shapiro, cited below. If the distinctions Wilkins makes do not convince you of the importance of the point I am making, I am sure that nothing further that I can say will do so.

    Well, I’ll wait until my own copy of Shapiro’s book arrives :)

  90. Petrushka:

    I’m no expert on the argument from genetic entropy. But before judging the concept, you should read John Sanford’s book if you haven’t already. He’s certainly a bona fide research geneticist, from an Ivy League school, with biological patents to boot, so presumably, though he may be wrong, he is not a scientific incompetent. From the little I understand of his position, his view is not that we do in fact observe genetic entropy, but that, on Darwinian premises, we should observe it, or at least more of it than we do, and therefore something non-Darwinian is going on to combat the entropy. If I have that right, the Chernobyl observations would not count against his view. But don’t rely on me; read what he says.

    I understand how natural selection is supposed to work. I don’t contest the plausibility of the notion, in the abstract. The problem is generating evolutionary novelty for natural selection to process. That’s where most of the criticism of the Modern Synthesis is coming from these days. (Though I gather that natural selection is taking some hits, too.)

    The future may not be predictable in detail but its general outlines may be predictable. We cannot predict the exact shape that water droplets will take in a cloud, but we can predict that they will form clouds. The question is whether evolution as a process could be designed ahead of time so as to be predictable in its general outlines. This is the view of Michael Denton, that it could be so designed. So it cannot predict the birth of Petruskha, but it can predict the emergence of some sort of humanoid or analogous-to-humanoid intelligence on a planet like earth. Here Denton differs from Gould quite a bit, and is closer to Conway Morris, though I think there are still important differences between them. But I suspect that Denton does not agree with you that evolution is a chaotic system. (It certainly must be, on any Darwinian-type model, but Denton thinks there are non-Darwinian possibilities.)

    I am not arguing here that Denton is right, but if he is right, then it is very clear that evolution and design are not the opposites that you are painting them. That is why ID proponent bristle when, having explained such things a hundred times on UD and just as often on Telic Thoughts and in TE venues and elsewhere, they hear over and over again the charge that ID demands miracles or interventions.

    As for Shapiro, the only thing I have claimed is that his view is not incompatible with ID. From an ID point of view, the design of the first cells still needs to be explained. Where did this marvel, with its powers of evolutionary self-engineering, get those powers? Shapiro does not answer that question. And that’s honest; he doesn’t know the answer. But until he can answer it, he cannot rule out a design origin for the very features of life on which his evolutionary theory leans.

  91. Hi Elizabeth,

    Re whether or not Shapiro is Darwinian, please see my remarks above, at http://www.uncommondescent.com…..ent-417905 . In particular, I’d be interested to hear your answer to my question: Do you think Charles Darwin would have agreed with the statement: “Innovation, not selection, is the critical issue in evolutionary change”? That’s what Shapiro wrote.

    Done :)

    By the way, I suggest you have a look at the talk by Rupert Sheldrake at http://vimeo.com/33479544 , which bornagain77 kindly linked to. It’ll shatter your belief in materialism. Mind-blowing stuff.

    Also done.

    I’m sorry vjtorley, but I find that talk deeply unimpressive. For a start, he sets up a complete straw man at the beginning with his account of mainstream vision science, as well as his description of consciousness studies. Throughout he makes transparent logical fallacies (just because lots of people report the experience of being watched doesn’t mean that lots of people can actually detect being watched), and makes sweeping statistical claims for allegedly replicated experiments (with infinitessimal combined p values) with no attempt to do any kind of meta-analysis, or correct for methodological flaws. I’ve read several empirical papers by Sheldrake, and his methodological technique is terrible.

    So he has several credibility mountains to climb for me: first I have to put aside his apparent ignorance of the science he is claiming to overturn; second, his apparent lack of understanding that the plural of anecdote is not “data” but “anecdotes” and that the reason for that is the word “response bias”; thirdly, the glib way he fails to address any alternative hypotheses for his findings; fourthly the way he repeatedly refers to his “morphic field” theory, despite the fact there is no evidence at all for the existence of such a field; and fifthly, his terrible track record in regard to methodological rigour, coupled with his apparent unawareness of any such problem in his own studies.

    It’s possible that there are sensory modalities that we are as yet unaware of (for example, many animals are able to detect the electromagnetic fields surrounding other living things; some animals can see outside our visible spectrum; dogs clearly have a sense that gives them a sense of the world much more akin to the sense we get from sight.

    And it’s even possible (I’m open to it) that there yet other modalities, about which we know nothing as yet. But he doesn’t demonstrate good evidence for it, and the fact that so much of his reasoning is clearly flawed makes me regard what alleged evidence he does cite with great skepticism.

    So my verdict is: “interesting, if true”.

  92. Elizabeth (5.1.1.2.8):

    I won’t cavil with you any longer about Margulis. I found you passages where Shapiro criticized “Darwinian” mechanisms, and I wouldn’t be surprised if I could find passages where Margulis uses the same term. But even if I can’t, the *theoretically viable* version of Darwinism from about 1930 to about 1980 (and in some places, up to the present) has been what is called The Modern Synthesis (or Modern Synthesis as core, dressed up with some ancillary mechanisms), and if you read the two pieces by Margulis that I pointed you to, you will not be able to deny that she has intellectual contempt for that form of Darwinism; she says explicitly that she regards it as incompetent to explain the origin of strikingly novel biological form. The direct quotations are abundant in the sources, and I’m not doing any more work for you; you will have to find them yourself. If you don’t agree with me that this is her attitude, then our disagreement will not be over Biology, but over the interpretation of clear English prose.

    As I said above, I think your definition of “Darwinian” is too broad, and encompasses too much to be a useful term of distinction. That the points you mention are “Darwinian” I have never contested; that they are a sufficient and complete definition of “Darwinian” I do not grant, as that is not the usage I have encountered in the writing of most full-time evolutionary biologists that I have read over the past 40+ years. Usually the word means somewhat more than your minimalist definition, and in past posts I have already tried to flesh that out. I have no more time to do it again. I will continue to use a more multi-pronged definition of Darwinian in the future, so if you do decide to debate with me, please don’t debate over the meaning of “Darwinian” any more; you know what I mean, so just translate it into your private evolutionary language, and respond to the substance rather than the vocabulary.

    I think it’s a pretty sad state of affairs that you’ve been arguing for days about what Shapiro thinks and haven’t yet started reading his brand-new book. And I know from your responses that you hadn’t read his comments on the Discovery site until I pointed them out to you. (Which has already forced you into one retraction which you could easily have avoided if you had read first and formed your opinion later.) When you started arguing about Shapiro, you had read, what, one journal article of his from what year? And you were prepared to debate with Vincent who had read his new book and many other things of his besides? Why do you enjoy this “read a short article and fly by the seat of your pants” style of intellectual exchange? What joy do you get out of it? Why not study your authors carefully first before venturing an opinion? That’s what you would be expected to do if you were publishing an article in an evolutionary biology journal. You’d be expected to know the relevant authors cold. So why are we subjected to “Lizzie at the Improv” when with a little patience you could supply us with an intellectual act that was well-rehearsed? :-)

    You can have the last word; I must break off here.

  93. I’ve been following Shapiro’s work for years, via his published papers, and I would normally place more credence on peer-reviewed papers than on books and articles/interviews.

    And I use my own critical faculties. I still don’t think that Shapiro’s work is anti-Darwinian in the sense I am using the term, whether or not Shapiro disagrees.

    And right now, I don’t know what he means when he says he is non-Darwinian. It doesn’t really matter – what matters is what his findings actually imply.

    And I remain of the view that it is simply incoherent to separate the concept of variance generation from the concept of natural selection. If there is heritable variance in reproductive success, by definition, there is natural selection. If there is no heritable variance, or if it does not sometimes result in differential reproductive success, then there will be no natural selection. Shapiro is proposing mechanisms whereby variance in reproductive success is generated, ergo he is not departing from Darwin’s algorithm whatever word you or he want to apply to his view.

    As for Margulis, we are not even in disagreement, as should have been clear by now, so I don’t know why you keep bringing it up.

    We both agree that she rejected “the modern synthesis”. She was badly treated I think, over her symbiosis idea, for which she is now highly regarded, but I still think she overstates the distance between her views and the rest of biology. Scientific research is a continuous process of revising previous theories, tweaking old models, and sometimes subjecting old assumptions to fairly radical revision.

    But to spin either Shapiro or Margulis’ work as the death-knell of Darwinism as though it moves science nearer to ID, is simply wrong, IMO. It’s simply the death-knell to some bits of evolutionary theory that are now replaced by less wrong bits.

    And so it will go on, till the sun fails.

  94. Hi Elizabeth,

    I don’t know if anyone continued the conversation with you about Chisel Beach. I looked it up and found this image:

    http://en.wikipedia.org/wiki/F.....l_Cove.jpg

    The shingles (pebbles) don’t appear to be as well ordered as you claimed. True, they are smaller at one end of the beach and gradually become larger until they reach the other end. But as the image would suggest, one will find disordered differences within any given space.

    My guess is that the constant motion of the water against the shingles pushes the smaller ones towards the further end of the beach.

    Now compare this to getting all the cards of one suit into precise order. What sort of physical force could accomplish that?

  95. You make harsh accusations. But you don’t provide any evidence to support them.

    In the last discussion you and I were involved in, you said this…

    the NCSE has steadily opposed the introduction of scientific criticisms of Darwinian evolution into the school curriculum. In fact, it has usually maintained that there are no scientific criticisms of Darwinian evolution, only religiously-motivated criticisms.

    Elizabeth asked you to cite a specific example, and you didn’t. Maybe you didn’t have the time to do the research. Maybe you know that an example of NCSE opposition to “scientific criticisms of Darwinian evolution” will make it clear that you are equivocating with the term “Darwinsm” in that context. It doesn’t matter.

    You make other accusations about people putting words in your mouth, when you do the exact same thing (per my earlier comment).

    You’re confronted with your errors and you don’t retract, (or make half-hearted attempts at apologies that really serve to vindicate yourself). And then you accuse others here of doing the same thing!

    Your accusations alone have no credibility. How ’bout you provide examples of the ones you made above. Whaddaya say?

  96. @Timaeus,

    First, that was one seriously overwrought rant.

    First, I recently just happened to be reading over on (UD Author) Cornelius Hunter’s blog, and saw this from Nick Matzke.

    Fair enough. I was wrong and I apologize. I think once you’ve agreed that historical science works in the case of the age of the earth, your arguments against inference in historical science in other cases are sunk, but that’s a different debate.

    To which, lest you suppose that was sarcastic or somehow not earnest, Hunter responded with this:

    Apology accepted and I forgive you wholeheartedly.

    That’s just from recent memory, a clear example discrediting your… overwroughtness, regarding Matzke, and a solid data point supporting what I claim is a problem that tilts the other way. UD has an execrable record on the part of its advocates of being incorrigible, not in matters of opinion and values, but in matters of fact. It’s a human problem that is not monopolized by either side, or any side, but the management here has a whole lot of evidence in the archives of this blog pointing intransigence and just plain refusal act like grown-ups in the face of correction and information about mistakes or screw ups.

    I know that won’t be settled here. But for the record, just by local recall, you have an example of Matzke being a stand up guy. If you can find me one post in all of kairosfocus’ posting here like the one I just happened to see a couple days ago from Matzke, let me know, and I will eat crow here and make a donation to the Discovery Institute in your name for $50.

    vjtorley deserves a tip of the hat as an exception, here, I should say. I don’t agree with much more of what he says that kairosfocus, but I know from reading him that he’s got the guts to stand up and be corrected, correcting himself or being corrected by others, at least some of the time (and that’s not slam, some of the time is a lot in these contexts, especially compared to his peers here).

    One way forward in these kinds of debates — and this is a really strong benefit of adopting the methods and culture of science — is that we aren’t limited to overwrought appeals on tone: we can actually do math, apply criteria scientifically, and look at the results. As one of the Republicans said, “this ain’t bean bag”. That doesn’t countenance ad hominems or incivility, but “tone alone” is a dead end. In science circles, the debates can be quite intense and brusque, but they are professional and productive insofar as they don’t reach comity by “playing nice”, but by DOING SCIENCE, and APPLYING OBJECTIVE TESTS, and PROVIDING FORMAL DETAILED MODELS that we all can examine.

    And that really is the failure of the ID movement overall, and a particularly damning aspect of the ID advocacy here at UncommonDescent.

    Someone who seeks constructive debates — truly constructive through hammering out precise terms, operational models, and the means to apply those models, doing real math with real evidence, with real results — is taken for a sucker here. No one — no one — either can or will engage on a level that admits of honorable and objective adjudication.

    In 1997 Stephen Hawking conceded defeat in what Leonard Susskind would call in a book he wrote about it “The Black Hole War”. The “Susskind-Hawking Battle”, as I knew it at the time, was a pitched debate that took a long time to solve, but the parties understood that “tone” doesn’t settle anything. Models, predictions and results do. Susskind won the dispute, and Hawking graciously and honorably conceded.

    The impoverishment of ID is its wallowing in culture war, despite any and all attempts and opportunities to put its ideas and claims to an objective, honorable test. Anyone who really would like to see a scientific dispute engaged and worked out here, even on small issues, is a chump at this blog, sad to say. That doesn’t mean critics (or ID advocates) can’t make good points, and articulate their positions well. But the merit-based methods, let the models, predictions, math, data and results decide from specific tests and models each produces and lets compete against each other are unable to get any purchase here.

    So, I understand some of your frustration, and agree that we can always aspire to more responsible and charitable discourse, but that’s a hollow, shallow appeal — that’s aiming really, really low — for a blog with a charter like this one claims for itself.

  97. lastyearon:

    You are right that it would have been better if I could cite one specific example for Elizabeth. But I couldn’t remember one state in particular — a number of names of states involved in evolution quarrels came into my head — Kansas, Texas, Louisiana, South Caroline and others — but I didn’t want to go by memory regarding which ones had introduced “scientific criticism” or “critical thought” legislation (as opposed to ID legislation, creationist legislation, teach the controversy legislation), so rather than guess, I referred Elizabeth to the same online sources that I had originally read, where all proposed state policies were analyzed and criticized to death. I simply did not have time to go searching Discovery and NCSE sites and re-read articles I had read months or years ago. But I indicated where the data could be found. It is as if I said that no metal had a melting point higher than 10,000 degrees Celsius, and couldn’t remember the particular boiling points of each metal, but know I looked them up in the Handbook of Chemistry and Physics.

    My claim was a broad negation, which could be falsified by producing even one case of the positive. I said that in every instance where States had passed or proposed critical analysis language or scientific criticism language bill, the NCSE had opposed the measure. I still believe that is true. If you or anyone else here can find a single counter-example, I will retract my statement and admit that sometimes the NCSE has sided with such policies. So the ball is in your court.

    I may have erred, but I did not lie. If you show me the error, I will retract.

    I don’t think it is a harsh accusation to say that people have said false things about Behe and Denton. It is a true accusation. If the truth is harsh, so be it. If people are going to tell lies, they are going to be criticized for it. They should be ashamed to lie, or even to fail to retract an honest error once it is pointed out to them. But I have found that in many cases the rage of the Darwinists overcomes shame.

    It doesn’t need to be this way. People could enter the debate about design versus non-design with open minds and charitable attitudes about the motives of others. Nothing would make me happier. I always try to start out that way myself. But sometimes the rage, the sarcasm, the visceral hatred of anything that might even indirectly make possible the existence of God (such as evidence of design in nature), gets to me and I get drawn into a lower level of debate. Have you never read some of the extreme things said by Mark Chu-Carroll, P. Z. Myers, etc.? Do you think ID proponents should have to take such vile insults lying down, and not defend themselves? Have you ever interceded and told these extremists they are out of line? If not, why not?

    Let me test you, lastyearon. I’ve promised here to retract if I am wrong about the NCSE. Do you promise, the next time someone says something false about ID or Behe or Discovery, and texts are produced, to show it is false, and the person who made the error will not retract, to jump in and urge the person to do so? Even if it is a big anti-ID star like Matzke? So if someone says that Behe is a creationist and it is demonstrated that he is an evolutionist, and the person won’t retract, you will side with the ID defender who has pointed out the error? Of if someone says that Behe requires miracles and a passage is given that shows he doesn’t, and the person won’t retract, you will again jump in and side against the Darwinist who is too stubborn to withdraw a false claim? If you will do that, I will greatly respect you.

  98. Eigenstate:

    It Matzke apologized and/or retracted an error, I salute him. I have never seen him do it here, or anywhere else. Maybe he has, but in my experience it is very atypical of his debating stance. Let’s hope the example you have given marks a change of attitude on his part. If it does, many ID proponents will respect him a lot more.

    Sure, ID supporters aren’t perfect. I would prefer that some of the ID people who post here did not post arguments the length of book chapters with a score of long quotations that no one has time to read. I would prefer it if accusations of immorality or wickedness were never levelled at someone just because he endorses Darwinism or finds some ID argument inadequate. I would prefer it if some people wouldn’t seem to argue as if Darwinism must be false as biology because it had some bad historical consequences for ethics or politics. I would prefer it if UD would get rid of any references to cultural renewal or combatting materialism and so on from its mission statement, and concentrate on design arguments and criticizing non-design positions scientifically and philosophically. (Which is not to say that ID people should cease to defend their personal philosophical and theological commitments here if atheism and materialism are thrown in their faces by commenters.) And I don’t like it when ID supporters here or anywhere argue that ID is against “evolution” or that belief in “evolution” is itself ungodly or wicked.

    I and others here have sometimes stood up against excesses from the ID camp. I remember admonishing a guy named “Ray” (I think that was the name) who tried to tie ID to Protestant fundamentalism and ended up bad-mouthing Catholics as having a false Christianity. And I remember having allies here on that point. And I’ve repeatedly said that “evolution” as such is neither bad science nor ungodly in its religious implications. So have many others here: Torley, Cudworth, nullasalus, StephenB … But I have no authority to control what anyone says here.

    I could go on. I could say nice things about Darwin. I think the man was largely wrong, but I think his *Origin* is a classic of argumentative literature that every scientist, philosopher and literary critic should read from cover to cover. And I think he was a great natural historian who by and large argued fairly and like a gentleman — unlike many of his modern defenders. I could even say nice things about Dawkins. He is a great science writer, and honest and up front rather than manipulative and scheming in these culture war debates. He is clueless in religion and philosophy, and embarrasses himself when he writes about them, but his *Blind Watchmaker* should be required reading for all camps. I also think that there have been reasonable, responsible ID critics, like biologist H. Allen Orr, physicist Stephen Barr, historian Ted Davis, and others, and that often Allen MacNeill has been a voice of moderation here. Such people don’t hit below the belt.

    You say ID wallows in the culture war. I see. And the columns of Jeffrey Shallit, Mark Chu-Carroll, P. Z. Myers, Jason Rosenhouse, Larry Moran, etc., *never* stoop so low as to do that? No Wikipedia editor has *ever* let his personal hatred of ID bias his editing? Michael Shermer is always completely objective in his assessments of ID? The people at Biologos are completly above culture-war motivations? Ken Miller is completely above them? Eugenie Scott? Nick Matzke? Abbie Smith? Is the culture war all ID’s fault, then?

    As for appealing to science and reason, and avoiding lengthy disputes about tone, I agree that would be ideal. The best way do to that is to lead by example, by not employing a tone that is unnecessarily aggressive, and focusing entirely on the argument. Behe and Meyer are perfect gentlemen in the way they write and speak in public. One may disagree strongly with their positions, but one cannot fault their manners. I don’t see any belligerence in their books or public addresses. I see appeals to data, to peer-reviewed literature, and so on. Can one say the same thing about some of the people I have named above? Does Behe call his opponents Darwinidiots, for example? Does he attempt to match Eugenie Scott’s deliberately polemical and baiting phrase “intelligent design creationism” by speaking of “Darwinatheism”? No, he argues from his knowledge of biochemical systems. And I have often held up the example of Denton, who avoids all culture-war squabbling and concentrates on explaining his scientific views. I have praised Shapiro, who criticizes Darwinian theory, but I have also just praised a review of Shapiro by Wilkins who disagrees with him. Both of them stick to the science. I’m happy with that. But a number of anti-ID people won’t follow that example.

    I don’t think we are disagreeing on principle here. I think we are disagreeing over who threw the first stone, or the most stones, or who struck the lowest blows, etc. The point is, how can we improve the situation? I’m willing to work with any atheist or TE who will renounce ad hominem comments and call his brethren on them when they make them. I’ll try do to the same at my end.

  99. Liz, I don’t understand your objections. Both Shapiro and Margulis disputed the MET claim that that the Darwinian mechanism can explain radical leaps in the fossil record or, for that matter, how new species emerge. That makes them non-Darwinists. What you have described (or tried to define) is evolution, the genus, not Darwinian evolution, the species. For the Darwinist (or neo-Darwinist), the mechanism explains everything–and I mean everything.

  100. The “Darwinian mechanism”, as I am using the term, is that heritable variance in reproductive success leads to adaptation.

    This, conceivably, can happen in leaps if a variant occurs that has greatly improved reproductive success.

    Both Shapiro and Margulis have proposed variance-generation mechanisms that could account for variants with large increases in reproductive success. So have the evo-devo people.

    What they both did was challenge the notion that all variants result from minor reshuffles to DNA. And evo-devo shows us that even minor reshuffles of DNA can result in major phenotypic changes, and thereby, potentially, major changes in reproductive success.

    Darwin didn’t even know about DNA. He didn’t know how variance was generated. We no know that there are not only mechanisms that explain minor variation, but also that explain major variation.

    And Shapiro, interestingly, adds to the basic Darwinian recipe, evolution at population level – the evolution of evolvability.

    If people don’t want to give Darwin the credit for this, fine. But in that case, don’t use “Darwinist” to describe modern evolutionary biologists, and perhaps news could stop writing headlines announcing the death of “Darwinism”. If Darwinism is the state of evolutionary biology post Watson and Crick then it’s long dead. Evolutionary theory is still thriving though.

  101. How is evolutionary theory “thriving” when it hasn’t been able to answer any of the tough questions pertaining to evolution?

  102. Elizabeth:

    As I promised, I will let you have the last word on Darwinism and Margulis and Shapiro; however, your bizarre comment on papers versus books is a new topic (actually harking back to an older discussion) that I cannot let pass.

    Your attitude here seems irrational. First of all, if an author writes several papers over a series of years, he or she may change his mind about some of them. The argument of a paper may since have been invalidated by someone else’s research, or even by the author’s own; or the author’s theoretical perspective may have changed due to conversations or readings during the intervening time. For this reason, if an author has written something newer that deals with the same topic as an older article, the newer item, whether paper or book, is going to be a more reliable indicator of what the author thinks *now*.

    Second, scientific papers are often of a very narrow focus, discussing this or that bit of experimental data, or this or that aspect of a mechanism. They often don’t indicate the full scope and coherence of an author’s thought, either because at the time of writing, the author’s thought still has not achieved its full scope and coherence, or because the author has chosen to contribute only a small and focused piece of his thought. A book, on the other hand, enables an author to look back over the accomplishment of several years and many papers, and bring together common themes into a coherent “big picture,” while abandoning errors and de-emphasizing work that doesn’t help to convey that big picture. It allows the author to arrange things in a way that is more orderly and systematic for the reader, and to make points afresh in sometimes more pointed and illuminating language. It allows the author more space to ruminate on wider implications and indulge in more historical context than there is normally room for in a short journal article. It allows for a richer and more reflective presentation.

    So Shapiro’s book, being brand-new, (a) where it differs from his earlier articles, supersedes them as a statement of his current thinking; and (b) where it agrees with his earlier articles, presents them in a broad synthetic form rather than as a series of isolated snapshots. If one wants to discuss Shapiro, especially in the context of a debate over “what Shapiro thinks,” it is more rational to rest more weight on a new book than on old articles. This is especially the case when it is obvious from the very title and theme of the book that he intends it as his grand current overview of the field.

    Thus, ID people have been eagerly digging away at the book ever since it came out, and eagerly reading the Dembski/Shapiro exchange on Discovery — which is even newer! And quite reasonably, they have taken their conception of “what Shapiro thinks now” from *these* sources. Makes good sense to me. And to argue against people who have read the newest version of an author’s thought, based on an older version of an author’s thought, strikes me as an odd procedure.

    For analogous reasons, by the way, it makes less sense to take Dembski’s thought from one or two isolated papers, and more sense to take it from larger synthetic works, i.e., books, where he has put together a large body of earlier work and honed it. Thus, to understand Dembski, one should look at, to start with, *No Free Lunch* (and, when it comes out, his projected revision of that work), and also the later *The Design of Life* which he co-wrote with Jonathan Wells. It is dangerous to infer that one has refuted Dembski because one has found a flaw in one article. Much of an author’s thought, as expressed in expansive book form, may remain of value even if his execution of a single argument or calculation leaves something to be desired.

    From numerous remarks you have made, and from remarks others have made here over the years, I get the strong sense that you and many ID critics are predominantly “article readers” rather than “book readers.” Often it appears that criticisms are based on a single journal article, or on a single chapter of a book, or (I am thinking here less of you than of others) on a blog column, or on a transcription of a radio interview, or on a summary from Wikipedia, or on reports of what an ID proponent believes (reports circulating on Panda’s Thumb or some equally unreliable source of objective reporting). In the meantime, defenders of the ID people in question have usually read all the ID person’s books as well as many or all of his journal articles, essay contributions to anthologies, and blog pieces, and have heard numerous podcasts, radio interviews, etc.

    Most of the internet critics of Michael Behe appear not to have read both of his books straight through. A surprising number of them have taken their view of Behe from Ken Miller’s summary and refutation of Behe regarding the single narrow issue of the flagellum, as if there is no need to read either Behe’s own explanation of the flagellum, or the rest of what Behe wrote. And even there, it often seems to be the case that Behe’s rejoinders to Miller have not been read. And many people have read only Denton’s first book, not his second, yet pronounce upon his thought nonetheless. Still others have condemned Meyer’s new book without having read it, based on hearsay. On other sites I have heard Jonathan Wells’s new book on junk DNA trashed by people who have not read it. To ID people, it goes without saying that if you want to know a thinker’s systematic thought, with all the pieces put together in an organic whole, you read (a) a book, not a single article; and (b) the latest book you can find. So ID people are book-readers.

    As a scholar, I was trained not to criticize the thought of a person until one had soaked oneself in it. If we are talking about something tiny, like a measurement or a historical fact, it is all right to criticize on a piecemeal basis, but if one is claiming to have refuted an entire position, it is necessary to really know the position that one is refuting, and rarely is a broad theoretical position adequately expressed in one specialist article or one popular article. So I was trained to read books, often long books. It’s just par for the course in humanities and social science scholarship. The natural sciences seem to be different, at least, the life sciences, if the way people trained in the life sciences argue against ID authors is any indication of their reading habits.

    Of course, in saying all of this, I have wandered away from any specific concern with your approach to Shapiro. My point is more general. I would like to have more assurance that you and other ID critics have read many long ID books, slowly and carefully. Often I don’t feel any such assurance, as passages from the books are rarely discussed. Or if they are discussed, a blogger or commenter will rant for paragraphs about an alleged scientific or mathematical error found on page 201 of a book, without even trying to show that this error is such that it invalidates the argument of even a chapter of the work, let alone the whole work, still less all of ID. Of course, to make the wider claim one would have to know intimately the argument of the larger work, and it’s precisely that which I often feel the critics do not know. And of course I am no longer speaking primarily to you, Elizabeth, but to anyone for whom the shoe fits. And now you can have the last word on the new subject!

    T.

  103. Yes, the natural sciences are different, Timaeus. My early career was in the humanities and I quite agree.

    But for science it is quite different, and peer-review a much more important filter and refiner. It’s a principle of empirical science papers that you should be able to provide sufficient detail to enable replication of your study by another investigator. It is also required that your conclusions are at least arguably supported by your data and your data analysis. And the review process does a pretty good job of ensuring that most papers are better in these respects than they were when they are first written.

    In addition, the space constraints of a paper mean that you are required to distil your question, evidence and argument into clear, succinct and unambiguous form (typically with introduction, method, results, conclusions) and so, even when papers are not peer-reviewed, I would prefer to read a paper than a book. And, to be honest, if an author can’t distill the essence of an argument into a paper, I’d be a bit skeptical of the argument.

    But, no matter. I’ve been wanting to read that book by Shapiro since it came out, and it’s winging its way from Amazon to me right now.

    Cheers

    Lizzie

  104. Oh, and I finally made it to the end of The Signature In The Cell. I though it was dreadful!

    And dreadfully prolix too! Give me a properly formatted, concise peer-reviewed paper any day!

  105. The shingles (pebbles) don’t appear to be as well ordered as you claimed. True, they are smaller at one end of the beach and gradually become larger until they reach the other end. But as the image would suggest, one will find disordered differences within any given space.

    Well, the pebble sizes are remarkably uniform in any given stretch of beach. But sure, there is some variation. The chances that they would have ended up that way without some kind of sorting mechanism is infinitesimal.

    My guess is that the constant motion of the water against the shingles pushes the smaller ones towards the further end of the beach.

    Something like that, although there seems to be a feedback loop whereby the size of the pebbles already on the beach affect which sizes are deposited there.

    <blockquote.Now compare this to getting all the cards of one suit into precise order. What sort of physical force could accomplish that?

    Human beings probably!

    I think you may have missed my point :)

  106. One cannot read everything, so one filters the choice of books by what is said about them. I tend to judge ID books by what their advocates say about them.

    I’ve read Dembski’s “Mere Creation” through. It’s a collection of essays by supposedly the best thinkers friendly to ID. I’ve recently read the Koonin and Shapiro books, as they were free and were promoted here.

    Before I invest time and money in a book, I’d like to see something from its friends and advocates that indicates it has something important to say. This seems to be the home of ID advocacy, so this is where I go to find the best reason to read ID books.

  107. I said that in every instance where States had passed or proposed critical analysis language or scientific criticism language bill, the NCSE had opposed the measure. I still believe that is true. If you or anyone else here can find a single counter-example, I will retract my statement and admit that sometimes the NCSE has sided with such policies.

    Show me an example of a State passing a “critical analysis” or “scientific criticism” bill that isn’t religiously motivated, and I will show you a bill that the NCSE doesn’t oppose.

    The very notion that the state should mandate that a certain theory be critically analyzed in class rests on the (religiously motivated) assumption that scientists and science teachers are hiding something about that theory.

    Eugenie Scott of the NCSE, on the religiously motivated nature of these types of bills

  108. Elizabeth:

    Some footnotes:

    1. I too thought Meyer’s book could have been considerably shortened without any loss of substance. On the other hand, you have to take into account the intended audience of the book, which was broader than the very small number of people who specialize in origin-of-life research. General introductory material is needed for that broader audience. Still, I think it could have been done in 200-300 pages, as opposed to 500.

    2. Your general principle about distilling the essence of an argument, while sensible in the appropriate contexts, if taken literally would mean that Darwin should not have written *The Origin of Species*, but should have published a journal article instead. (“If he can’t say it in 20 pages …”) That’s a ludicrous conclusion. Obviously arguments of large scope require longer treatment than arguments of small scope. If you are trying to prove that the TTSS has some proteins similar to those of the bacterial flagellum, you publish an article; if you are calling for a rethinking of evolutionary theory as a whole, you need a book-length treatment.

    So yes, an argument should always be stated as concisely as possible, but that does not mean that the article is always preferable to the book. What it means is that when books are necessary, they should be written as concisely as possible (e.g., if it can be said in 200 pages rather than 500, it should be said in 200 pages), and when articles are more appropriate, they should be written as concisely as possible (e.g., if they can be executed in 20 pages rather than 40, then 20 pages is how long they should be).

  109. 109

    I had a toy when I was a child. It was a plastic tube filled with plastic balls of various sizes. Along its interior were several barriers each having holes smaller than the previous. If you hold it one way and shake it, all the balls go to one end. If you turn it the other way and shake it the balls are separated by size.

    The mechanism is not a feedback loop but the result is the same. There’s just nothing particularly intelligent about it.

    The example of sorting cards is different, as they are identical with regard to any purely physical process. Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them. Natural laws can affect rocks of varying sizes but cannot act upon abstract symbols without some intentional input.

    You can print the digits 0-9 on paper, carve them out of wood, or whatever, and no natural process will sort them.

    Your example of pebbles leads right back to the difference between physical attributes and symbolic information. One could argue that digits have no physical connection to what they represent because they were designed that way. But as has been shown repeatedly, there is no direct physical correlation between genetic information and the proteins it codes for and the behaviors it regulates. An intermediate protocol is required, just as one is required to read the words “eight pennies” and imagine or count out eight pennies.

  110. Petrushka:

    Here is my short list of crucial ID books, which I would recommend reading straight through: both of Behe’s books, both of Denton’s books (though his first book is not really a direct advocacy of design but more a critique of Darwinian theory), Dembski’s No Free Lunch, and Dembski and Wells’s The Design of Life. I think a couple of Meyer’s earlier articles are also essential; his book could be read by a combination of skimming and close reading.

    In no way am I arguing that everything in these books is excellent or unassailable. But they do give the broad outlines of the ID argument. And contrary to ID detractors, they aren’t about the Bible or creationism or theocracy or social renewal by combatting atheism and materialism. They are about science, and to some extent about the historical, methodological and philosophical background of science. If one is going to attack ID, one should attack it based on these writings, not on the basis of Dembski’s writings about Christianity or the church affiliation of ID proponents or culture war propaganda one has heard from the NCSE or Wikipedia or Panda’s Thumb or what the special witnesses for the plaintiffs said about ID at the Dover Trial or the book Of Pandas and People or what Phil Johnson wrote about materialism and the supernatural 15 years ago.

    As for the many books written by ID proponents about Christianity, they may have their own merits, but I don’t recommend them as expositions of ID theory, as they mix it up with extraneous matter.

    Of anthologies, the Ruse/Dembski collection is very helpful. (It also contains a not-often-enough read refutation by Behe of Ken Miller’s misrepresentation of Behe’s position on the flagellum.)

    Maybe this will reduce your reading load to a bare minimum. :-)

  111. Scott,

    The example of sorting cards is different, as they are identical with regard to any purely physical process.

    No. If they were physically identical, we (and machines) wouldn’t be able to see the difference between the 2 of spades and the queen of hearts.

  112. Despite its title, “Mere Creation” is about ID, not theology. It’s presented as the best exposition of the ID position in all its flavors, including Behe’s.

    I’ve read Behe’s defence of the Edge.

    I don’t think Behe is being ignored. I think the work of Lenski and Thornton is in direct response. Obviously this kind of research takes time. It’s modelling processes that take thousands of years in the wild.

    What I haven’t seen from the ID movement is a theory of design, something in response to Philip Johnson’s call. I mean a description of the process by which a designer would create the long fuvctional sequences that are supposedly beyond the reach of evolution.

    You can describe the steps by which architects and engineers proceed.

  113. Actually, if Darwin was alive now, he probably would have published Origin as a paper, and expanded it as a book. It’s ideas could certainly be distilled into a small space, and it’s part of its genius that the central idea can be distilled into a single sentence.

  114. Actually, if Darwin was alive now, he probably would have published Origin as a paper, and expanded it as a book. It’s ideas could certainly be distilled into a small space, and it’s part of its genius that his central idea can be distilled into a single sentence.

    My bigger point is that if Dembski, for instance, writes what he has claimed is his most rigorous and up to date treatment of CSI in a formal paper, but it can only be understood if you also read his other books and works, then his paper is not doing what it says on the tin. It should stand on its own. I think it does, and I think it is fundamentally flawed. I’m not going to withhold that judgement just because he has also written some books I have not read.

    Same with Shapiro. I have read a substantial number of his papers, including his recent review papers. If he has managed to miss some key point in those that can only be gleaned from his book then I’ll stick with the papers. Those have been peer reviewed.

    And from those papers I do not see that he is proposing anything that does not come under the heading: heritable variance in reproductive success, which I would say is the essence of Darwin’s algorithm.

  115. If one is going to attack ID, one should attack it based on these writings, not on the basis of Dembski’s writings about Christianity or the church affiliation of ID proponents or culture war propaganda one has heard from the NCSE or Wikipedia or Panda’s Thumb or what the special witnesses for the plaintiffs said about ID at the Dover Trial or the book Of Pandas and People or what Phil Johnson wrote about materialism and the supernatural 15 years ago.

    Just to make something clear: I don’t do any of these things, although I have read some critiques at Panda’s Thumb and TO.

    But I always try to go to primary sources, and wrt Dembski I’m going on his papers that are specifically about ID, including his papers with Robert Marks, but also “Specification: The Pattern That Signifies Design” which he has actually said supercedes his earlier writings.

    But when you say we shouldn’t judge ID on “what Phil Johnson wrote about materialism and the supernatural 15 years ago”, then could I also ask that people don’t judge evolutionary theory on what Gould wrote thirty years ago, or on what Darwin wrote 150 years ago?

    Science moves on. That’s one other good reasons for reading papers rather than books.

  116. 116

    Champignon,

    Do you really think I didn’t know that, and didn’t even wonder whether someone would point out the obvious just for the sake of meaningless, pointless contradiction? I considered specifying that they are identical except for the arrangement of the ink. I just really didn’t think it was necessary.

    That you singled that out indicates that you really don’t grasp the point. What natural laws do you think will affect cards with digits and symbols printed on them in such a way that it will sort them? I can just see the wheels turning trying to imagine something. That’s how it works, after all. Imagine something preposterous, then it becomes plausible, then it becomes probable, and eventually inevitable.

    Let me save you the trouble. What happens when I change my mind and decide that “3″ means XXXX and “4″ means XXX? Then how will those natural laws sort the cards?

    There are numerous lines of evidence pointing to design in biology. Some are circumstantial. Even those can be pretty good. But the instantiation and processing of semiotic information is a fingerprint of purposeful intelligence. It is a byproduct of imagination.

    You see it too. But you’ll argue against it anyway. No reason can contend with the will to oppose reason. I don’t mean that as harshly as it sounds. I’m sure that every person, myself included, allows themselves some little bit of insanity. I refuse to eat peas even though I know they’re good for me and won’t hurt me.

  117. But the instantiation and processing of semiotic information is a fingerprint of purposeful intelligence. It is a byproduct of imagination.

    The words purposeful and intelligence are just labels we attach to what chemistry does when certain complex arrangements occur.

    I grant that we don’t know how the arrangements first arose, but I would argue that the history of science is full of cases where complexity arises out of regular processes.

    I have cited Newton’s characterization of the solar system as impossibly complex and obviously the work of gods and angels. (Maybe it is, but it is also the result of regular processes.)

    Until ID at least comes up with a competitive process by which evolution is instantiated, a theory of design that explains how the designer overcomes the problem of time and large numbers, some form of evolution is the only player with chips on the table.

  118. Scott, the reason I mentioned the beach was not to argue that it was especially complex or required an especially fancy algorithm to create. In fact my point was that it did not.

    It came up because Dembski, in his paper: “Specification: the Pattern that signifies Intelligence” says that a pattern has CSI if it has a lot of Shannon information (Complexity) but is highly specified (high compressibility).

    I was pointing out that a sorted series has both of those attributes, and that sorted series occur naturally, for example at Chesil Beach.

    Yet we all readily agree that Chesil Beach is not the result of Intelligent Design.

    And so it seems to me that Dembski’s definition of CSI completely fails. It is not “the pattern that signifies intelligence”. It’s simply a pattern that signifies some kind of algorithmic process, not surprisingly, as the S part of the definition refers to the shortness of the shortest algorithm that can produce the sequence – the shorter, the less “random” according to Dembski, and therefore the more likely to be Designed, if the sequence also has high Shannon Information (“complexity”) i.e. is a sequence very unlikely to be thrown up by chance.

  119. Design detection is still a Bayesian process requiring knowledge of possible causes. Sorted pebbles suggest one cause on a beach, possibly another cause in a Japanese garden. (Same principle for card deals.)

    When design advocates manage to come up with a biological design process, a concrete methodology by which living things could be designed from scratch (or invented for the first time) then we can apply some reasoning to the question of which process best fits the data.

  120. Well, Dembski specifically rejects Bayesian inference for design IIRC.

    He’s very keen on Fisher.

    But I’d be interested if a Dembski fan – or anyone – would explain to me how Dembski’s CSI avoids classifying Chesil Beach as Intelligently Designed.

    Because it seems to me he’s made a very elementary mistake.

  121. It is interesting that Dembski favors Bayes when analyzing the possibility of cheating in elections, and ID advocates are fond of invoking Bayes when looking at card deals that would be useful to a gambler, but do not wish to apply the same logic to evolution.

    The reason is that the putative designer has no attributes or known abilities. There is nothing to compare to evolution except an imaginary entity.

    When you ask why a designer would do things a certain way — create malaria, for example — we are told the question is forbidden. Not part of design theory.

    But this is precisely the kind of information required for a Bayesian inference.

  122. Elizabeth (10.1.1.2.3):

    “Just to make something clear: I don’t do any of these things, although I have read some critiques at Panda’s Thumb and TO.”

    I know you don’t. I was making a comment about what other people do, in the context of my reply to Petrushka. I wasn’t accusing either you or Petrushka of what I was describing.

    “Science moves on. That’s one other good reasons for reading papers rather than books.”

    This doesn’t logically follow. What logically follows is that one should read the newest articles *and* the newest books, rather than books *or* articles containing views that have since been disproved or have been in some important way superseded. (Of course, I am not implying that every new view is automatically better than every old one, but I am, like you, speaking of the case where new knowledge has rendered an old view untenable.)

    For example, Shapiro’s brand-new *book* would be more useful to read than many old *articles* by Dobzhansky, because it incorporates recent knowledge that D. had no access to.

  123. It seems we agree on all this, Timaeus.

    Cool :)

  124. I find that reasonable, assuming the author characterizes his book as his latest and best thoughts.

    But when a new book comes out, my inclination to read it depends on the critical commentary. I’m particularly influenced by favorable commentary. If the favorable commentary doesn’t bring up anything new or interesting, I’m not likely to read the book.

    So I read the Shapiro and Koonin books. I’ve read a couple chapters of Behe. I’ve certainly learned things, but I haven’t seen anything that would tip the scales one way or another.

  125. 125

    I would argue that the history of science is full of cases where complexity arises out of regular processes.

    Then do. I think everyone already knows what everyone else would argue.

    Until ID at least comes up with a competitive process by which evolution is instantiated, a theory of design that explains how the designer overcomes the problem of time and large numbers, some form of evolution is the only player with chips on the table.

    What? A competitive process by which a competitive process is instantiated? Time is a problem? If having some form of explanation is the price of entry then why would you say that evolution has ‘chips on the table?’ You just ruled it out with your own criteria.

    You continually allude to some out-of-sight set of facts that you apparently don’t need to state.

    90% of your argument is some imaginary negative evidence against design, as if some magical, unspecified self-instantiation is a reasonable default until something else comes along. So far your positive evidence consists of GAs and the promise that they will get better. Your evidence against design consists first of ignoring or discounting examples of design, such as people designing an enzyme faster than a GA, along with the bizarre, reality-defying prognostication that they won’t get better. You know, because in the history of the world, people have never gotten better at designing stuff.

    I honestly don’t see any difference between your faithful defense of this dogma and any other religious conviction.

  126. 126

    Scott, the reason I mentioned the beach was not to argue that it was especially complex or required an especially fancy algorithm to create. In fact my point was that it did not.

    The process was not complex. Neither was the result. How does your example relate to anything?

  127. Elizabeth:

    If you think a guy with two Ph.D.s (one in math, one in philosophy) has made an elementary mistake in his own research field, and you have the mathematical knowledge to demonstrate the mistake, then why don’t you write up your argument formally and submit it as an article (I know you are a big fan of articles!) to a peer-reviewed journal of probability theory or design theory or the like, instead of airing it here or on other blog sites, among people who mostly aren’t competent to referee? If you are going to invest scores of hours arguing against Dembski’s position, why not do it where it counts?

  128. There have been very many critiques of Dembski’s math. None to my knowledge are published, because you don’t get papers published if they are critiques of non-published work.

    Most are much more detailed than mine, but mine seems a simple enough point that I’d have thought someone here (maybe even Dembski himself) could respond. Possibly gpuccio or kairosfocus, both of whom have developed their own versions of CSI.

    I’m no mathematician, but of course I am a data analyst, and use inferential statistics daily.

    And actually, there are plenty of mathematically competent people who post here who could chime in.

  129. Petrushka (10.1.2.2.2):

    To use your phrasing, what I haven’t seen from the Darwinian model of evolution is any hypothetical evolutionary pathway from non-flagellum to flagellum, or deer to whale, or the like. I’m not talking about a half-dozen intermediary fossil forms. I’m not talking about scattered observations that a few proteins here might be homologous to a few proteins there. I’m talking about a pathway of particular molecular/genetic changes, specifying what might have happened, in a plausible order, producing intermediate forms that would be selectable. There’s no stepwise account there, any more than there is in ID. Why should ID people have to enumerate all the things a designer might have done, when Darwinians think it’s unreasonable for them to have to produce full evolutionary pathways? Why the double standard?

    I’ll make you a deal; you publish a book with a full hypothetical Darwinian pathway to the first cardio-vascular system, and after I read your book, I will write a book detailing the hypothetical steps by which a designer could have effected the same thing. That seems fair to me.

  130. Scott,

    My interpretation of your statement…

    The example of sorting cards is different, as they are identical with regard to any purely physical process.

    …was that you meant what you said: that cards are identical with regard to any purely physical process.

    You are scolding me because I didn’t assume that you meant the opposite of what you wrote. If you want to be understood, say what you mean.

    And ironically, my interpretation of your statement was the most charitable one. If you didn’t mean that “cards are identical with regard to any purely physical process”, then the rest of your argument isn’t even wrong.

    Speaking of the rest of your argument, you wrote:

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

    This is obviously not true, even setting aside your problematic use of the word “awareness”. A computer can sort cards based on their symbolic meaning (“5 is less than 6, so the 5 of hearts goes before the 6 of hearts”), but it doesn’t need to do it this way. It can just as easily treat the cards as pure patterns with no meaning: “a card with pattern X goes before a card with pattern Y”. And this kind of sorting can be applied to, say, geometric patterns or postcard landscapes where there are no symbols at all.

    Another problem with your argument is that you are assuming that human intelligence is a nonphysical process. What is your evidence for this assumption?

  131. I’m not talking about a half-dozen intermediary fossil forms. I’m not talking about scattered observations that a few proteins here might be homologous to a few proteins there. I’m talking about a pathway of particular molecular/genetic changes, specifying what might have happened, in a plausible order, producing intermediate forms that would be selectable.

    Ah, the pathetic level of detail. I wouldn’t worry too much. It’s the kind of work that’s accumulating bit by bit, but you are safe for he near future. But comparative genomics is on the rise, and there will be more Thorntons looking to find pathways connecting cousins.

    It’s missing links redux.

  132. “old *articles* by Dobzhansky” – Timaeus

    Well, I’d highly recommend Dobzhansky’s text “Anthropology and the Natural Sciences – The Problem of Human Evolution” from 1963 in Current Anthropology, even for ‘people today.’ Much more anthropology is needed in the IDM, in this case healthy and provocative to read as written by a ‘creationist-evolutionist’.

    http://www.jstor.org/pss/2739837

    In fact, I’d take most things written by Marshall McLuhan (1911-1980) in the 1960s and 70s over William Dembski’s 1990s and 2000s contribution on the topic of ‘information.’ But hey, maybe I’m just being nostalgic. People are still catching up to McLuhan. Not sure if the same will be said of Dembski’s specification mathematics or his EF in 10 or 20 years.

    “The shock of recognition! In an electric information environment, minority groups can no longer be contained—ignored. Too many people know too much about each other. Our new environment compels commitment and participation. We have become irrevocably involved with, and responsible for, each other.” (1967)

    “If the work of the city is the remaking or translating of man into a more suitable form than his [sic] nomadic ancestors achieved, then might not our current translation of our entire lives into the spiritual form of information seem to make of the entire globe, and of the human family, a single consciousness?” (1964)

    “Today our science and method strive not towards a point of view but to discover how not to have a point of view, the method not of closure and perspective but of the open ‘field’ and the suspended judgment. Such is now the only viable method under electric conditions of simultaneous information movement and total human interdependence.” (1962)

  133. So he doesn’t accept the fossil and genetic evidence for common descent?

    And he gets angry when ID is “confused” with creationism.

    If it looks like a duck..

  134. 134

    Champignon,

    Wow, did I say “physical” when I meant “natural” in the sense of non-artificial, undirected? Good catch. Maybe you can find a spelling error while you’re ignoring the content.

    This is obviously not true, even setting aside your problematic use of the word “awareness”. A computer can sort cards based on their symbolic meaning (“5 is less than 6, so the 5 of hearts goes before the 6 of hearts”), but it doesn’t need to do it this way. It can just as easily treat the cards as pure patterns with no meaning: “a card with pattern X goes before a card with pattern Y”.

    Show me anything that will sort cards, virtual or physical, by number and suit, without someone telling it what value to assign to each? If you can find anything, anywhere that can tell that 4 < 5 < 6 < 8 < 9 without someone to tell it what each symbol represents, then you will have something of substance.

    If not, why even bring it up? Are you seriously arguing that a computer can find something intrinsic to the symbol "7" that associates it with the number or quantity seven?

    These arguments are pointless. I don't see what you hope to accomplish. The mere thought of disagreement does not refute logic.

  135. 135

    The words purposeful and intelligence are just labels we attach to what chemistry does when certain complex arrangements occur.

    Of course they are, if that’s what you want them to mean and you redefine them as such. While we’re at it, choreography is just a label I attach to the thing I make toast with. And war is just a label I attach to peace. When all else fails, redefine reality.

  136. Scott,

    Show me anything that will sort cards, virtual or physical, by number and suit, without someone telling it what value to assign to each? If you can find anything, anywhere that can tell that 4 < 5 < 6 < 8 < 9 without someone to tell it what each symbol represents, then you will have something of substance.

    You’re a programmer, right? Think about the problem for a while. If you can’t come up with an algorithm that sorts cards without assigning a value to each, let me know, and I’ll provide one.

  137. 137

    Champignon,

    I don’t even know how many decades back you have to go to find a programming language or framework that had not already assigned the value of 8 to 8. And if you go back any farther than that, then yes, you would have to assign the values.

    What about the concept that 10 < Jack < Queen < King? Did you even pause to think about where that comes from? Yes, I am a programmer. There are essentially two ways to do it.

    One is to write a function that compares two cards and returns an indicator of whether the first card is less than, equal to, or greater than the second card. That function contains such logic as:

    If Card A is a Queen and card B is a Jack, the result is “greater than.”

    It would be long, ugly function.

    Or you assign a numerical value to each card and use a numerical sort. Or you write a function that receives a card and returns a value by which to sort. Same thing.

    What a waste of time to spell out something so obvious. In which scenario does the computer “know” that a king is greater than a jack without being told? What intrinsic quality of “queen of spades” makes it greater than “jack of spades?”

    Meanwhile, any group of card players is free to decide that from now on, jack < king < queen. Those are the new rules. If, as you suggest, the initial arrangement is somehow emergent from natural law, then how did they change it?

    What you said is silly enough that most people would dismiss it without logically explaining why. But that’s what this is all about – taking something worthy of immediate dismissal and accommodating it, dignifying it with discussion. This is what I would do if my son told me that babies grew on trees or if I encountered someone who was hallucinating.

    So now I’ve given you several paragraphs explaining the obvious, that a computer cannot sort cards without someone first assigning value to them, maintaining the illusion that we’re having a rational discussion.

  138. I honestly don’t see any difference between your faithful defense of this dogma and any other religious conviction.

    I really can’t help you if you haven’t noticed the gradual retreat of anti-evolutionism over the last 150 years from it never happened, to it happened but only due to intervention, to it happened without intervention, but it was front loaded, to it happened without front loading, but the parameters of the universe were designed so it would happen.

    Most ID proponents fall into at least one of these categories.

    The same progression occurred with the age of the earth and universe. The same progression occurred with the nature of the solar system.

    It’s always a rear guard action.

    At the moment we have some instances of “impossible” three step mutation sequences involving intermediate loss of function. there will be more such instances. Right now they are declared rare. In ten years, not so rare.

    Eventually the rule of three will be the rule of four, or something like that.

  139. lastyearon:

    If you’re speaking about me, you should, in the interests of both politeness and clarity, identify me by something other than “he.”

    Your inference is completely unwarranted. I never said anything about not accepting common descent. I asked for a specification of some hypothetical molecular/genetic pathways between radically different forms, which is a different matter. This is a reasonable request when someone has asked for an equally specific set of steps from intelligent design proponents.

  140. Petrushka:

    You are the one who initially asked for “the pathetic level of detail.” I merely responded in kind.

  141. Hi Elizabeth,

    Re Chesil beach, please see my comment above:

    http://www.uncommondescent.com.....ent-417903

    Got to go. Bye.

  142. Scott,

    One is to write a function that compares two cards and returns an indicator of whether the first card is less than, equal to, or greater than the second card. That function contains such logic as:

    If Card A is a Queen and card B is a Jack, the result is “greater than.”

    Almost, but not quite. Not only does the program not need to use the comparison operators, it also does not need to designate cards as King or Jack or 7.

    All it needs to do is compare card images, look for the best match, and then apply the kind of sorting algorithm you described.

    For example, if one card matches pattern X, which happens to be an image of the King of Clubs, and another card matches pattern Y, which happens to be an image of the 9 of Clubs, then the card that matches pattern Y goes in front of the card that matches pattern X. Similar logic applies for every possible card pairing.

    Note that the program is not “aware” that it’s looking at an image of a card, that the card has symbols on it, that the meaning of one of the symbols is “King”, or that “King” comes after “9″. Yet it still sorts the cards into the correct order, which according to you should be impossible:

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

    Your statement is clearly false.

    Meanwhile, any group of card players is free to decide that from now on, jack < king < queen. Those are the new rules. If, as you suggest, the initial arrangement is somehow emergent from natural law, then how did they change it?

    Their brains did it, operating according to physical law. How do you think they did it? Do you think there was something nonphysical about it? If so, how did the nonphysical entity interact with the physical brain to cause the player suggesting the change to discuss it with the others?

  143. By the way, Elizabeth, Darwin *did* originally publish an “article” first in a “peer-review” context; he and Wallace submitted a joint paper which was read aloud to the Linnaean society. But it was the book-length treatment, with its massive documentation and extensive argumentation, which won over the world. Only historical specialists now could tell you what was in the paper, and it was hardly paid attention to when it was read at the meeting. So books do sometimes matter, regardless of what you may think.

    Did you write to the publisher or to Shapiro and ask if Shapiro’s new book was peer-reviewed? If not, how do you know that it wasn’t? In any case, that is irrelevant to what we were debating, which was what Shapiro currently thought, not whether or not his peers deemed those current thoughts to be any good. If you want to know a man’s current views, you read his current writings, not what he wrote five years ago. Vincent was arguing from Shapiro’s current views, and you were contradicting him (and me) without first learning what those views were; that was my complaint.

    On your other point, if Dembski wrote an article with a limited purpose, of course it should prove what it set out to prove, and if it doesn’t, you have the right to point that out. All that I am saying is that you can’t get the total thought of an author from one paper or even one book; you have to examine the whole corpus. No Free Lunch is a large book, and very extensive in scope; you can’t say that it failed in every respect if you haven’t read it. The only arguments you can say have failed are those you have read. And further, you can’t say that intelligent design fails because one paper by one of many ID authors fails. I hope we can agree on all of this, but in any case, I’d like to get off this thread. So long.

  144. Hi Elizabeth,

    Thank you for your posts (1.1.2.1.10 and 1.1.2.1.11). You were quite right about one thing: the sort order is irrelevant to computations of Shannon complexity. Mea culpa. However, I believe you were mistaken when you wrote:

    Shannon information doesn’t care what order the items are arranged in, it only cares how many ways there are of arranging the items.

    This is fine if all arrangements are equiprobable. But what if they’re not?

    Exactly! In other words, in order to do the calculation for the quantity Dembski calls CSI, the “pattern that signifies intelligence” you have to know the probability of the observed pattern under the null. And Dembski makes absolutely no attempt to even begin to calculate that. And that’s the gaping vacuum at the heart of ID – or at least at the heart of Dembski’s ID.

    In your case (Chesil beach), there is a natural biasing factor at work, causing the pebbles to be sorted in descending order of size.

    Right. There’s a “natural biasing factor”. And so what if, for organisms there is also a “natural biasing factor”? Which is precisely what Darwinian evolution theory proposes! In other words, you can’t infer intelligent design from CSI without calculating the probability under the null of Darwinian evolution!

    So Dembski is caught on the horns of a dilemma: either he assumes all sequences are equiprobable under the null, in which case Chesil beach has CSI, or he attempts to calculate the probability distribution of sequences under the null, in which case he has to calculate the non-flat distribution of sequences under all possible “natural” hypotheses, in which case his argument is entirely circular.

    Another problem with your example is that your verbal description (which is supposed to roughly correspond to Kolmogorov complexity) doesn’t specify any particular arrangement of pebbles. It merely describes a generic feature of that arrangement: namely, that the pebbles tend to descend in order of size. If you wanted to describe a particular sequence of pebbles, however, you would need quite a lot of space to do so, unless it were a sequence in which the pebbles along the beach descended in perfect order of size – which is extremely unlikely to be the case. If they did, I’d suspect intelligent agency was at work:)

    No, that doesn’t get you off the hook, because Dembski doesn’t require that the compressible sequence is the only compressible sequence, just one of the tiny proportion of sequences that are at least as compressible out of all possible sequences. And while the number of approximately linearly graded sequences there are on that beach, may be very large, it is an infinitessimal proportion of the total number of sequences of pebbles.

    So Professor Dembski’s point that high Kolmogorov complexity combined with high improbability is a hallmark of intelligent agency, remains a valid one.

    Nope :)

  145. Ah yes, he did didn’t he! Thanks for reminding me.

    Books aren’t peer-reviewed, Timaeus, in anything like the way papers are. Sometimes experts will be sought to give their views, but the publisher is interested in a book that will sell, not a journal that has reliable good-quality papers. Not that I’m knocking books, it’s just that in the pecking order, in the 21st century, peer-reviewed journals are the vehicle for dissemination of science. Not that peer-review is perfect, far from it, but it’s a first pass, and almost all papers go through a rigorous editing process in the light of peer review, and the reviewing process itself is highly formalised, with specific categories of issues that the reviewer has to comment on.

    But I agree, obviously, that you can’t get the whole thought of a writer from one article. On the other hand, if an author claims that his findings are X, in a book, and his papers, in the view of reader Y, do not indicate that his findings are X, X is not obliged to agree with the author that his findings are X. In other words, the beauty of scientific publishing is that papers are (or should be, if they get past peer-review) capable of being evaluated independently of the author’s own evaluation. The reader should be given enough information that she can come to a different conclusion from the data than the author did.

    My conclusion, from Shapiro’s paper, is that he is not proposing a mechanism for evolution that departs from what I mean by the “Darwinian” principle of heritable variance in reproductive success.

  146. No, I don’t think anyone is asking for anything like those specific steps from IDists, Timaeus.

    Just a hypothesis about how, in principle, the design process was implemented would be cool.

    Genomicus has stepped up to the plate with his frontloading hypothesis (although I think it is problematic wrt to testability) but it’s a rare thing to see.

  147. 147

    Champignon,

    Are you winding me up?

    For example, if one card matches pattern X, which happens to be an image of the King of Clubs, and another card matches pattern Y, which happens to be an image of the 9 of Clubs, then the card that matches pattern Y goes in front of the card that matches pattern X. Similar logic applies for every possible card pairing.

    It doesn’t matter if it starts with an image. Text processing can start with OCR. But how does it determine that the image of a king of clubs is “greater than” the image of the nine of clubs? Which one has more color? Which one is bigger? The king is still greater even if you print it real small and print the 9 real big. You can’t compare their values until you match the images to the cards. And then you’re not comparing the images. You’re comparing the cards. And how does it know that the king is greater than the nine? Because you tell it so. Unless you tell it that the nine is greater, and then it is.

    Note that the program is not “aware” that it’s looking at an image of a card

    Programs aren’t “aware” of anything. What does that have to do with anything? Given sufficient input, a program can identify a picture as being of a king of clubs, nine of clubs, a baseball, or a specific person. But the sort order between a king and a nine is whatever you or I say it is. So how do you think the computer can sort them without being told which is greater? That meaning is not intrinsic to the pictures, the arrangement of ink molecules, or the pronunciation of the words which varies from language to language.

    We’re using kings and nines as an example because only one is a number. But it doesn’t matter. A quantity of nine is greater than a quantity of five, but the expression 9 > 5 is only true if you assign a meaning to each symbol. Do you really think that any computer ever made the association between the symbol and the abstract concept or an actual quantity of something on its own?

    So would you care to explain again how a computer would sort them without input to specify what the symbols represent? Maybe you’re missing this because it’s built in to both hardware and software so that you no longer have to define it when writing new software. But somebody still had to do it.

    How do you think they did it? Do you think there was something nonphysical about it? If so, how did the nonphysical entity interact with the physical brain to cause the player suggesting the change to discuss it with the others?

    Sorry, I was so caught up in the inanity of explaining that the sort order of cards and of symbols is arbitrary and not an emergent property of the pictures on them or pictures of them that I forgot to answer this.

    What non-physical entity? I don’t think there is anything non-physical about it. I told you two posts ago that I meant “natural laws,” in the sense of undirected, not artificial. I said “physical laws” and that’s not what I meant. You pointed it out abundantly and I corrected my choice of words.

  148. Scott,

    Are you winding me up?

    No, I think you’re doing a fine job of that by yourself. Why do you bother coming here if you find it so painful to be corrected?

    You made this statement:

    The example of sorting cards is different, as they are identical with regard to any purely physical process.

    I showed you that your statement was wrong. You agreed that it was wrong, and yet you blasted me for not assuming that you meant the exact opposite of what you wrote!

    You also claimed:

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

    I provided a detailed example showing why that statement is also false. Your response was to sputter about “inanity” and to complain that I’m “winding you up”.

    It’s very simple, Scott. If you don’t want to be corrected, then either 1) don’t say anything, or 2) make sure that what you say is correct.

    We’ve agreed that the first of your two statements is wrong. Do you agree that the second one is wrong, also?

  149. So other than humans or computers, can anyone think of another way to get our cards sorted in the right suit and order?

  150. Elizabeth:

    You’ve twice now referred to Shapiro’s “paper” in the singular, as if your notion of his view of evolution was based on only one paper. But you have also a couple of times said that you have been following Shapiro’s ideas for some time, implying that you have based your ideas of him on more than one paper. Which is it?

    It would be pointless to get into a debate about what “peer review” means — we spent too long on what “Darwinian” means already. I’ve done peer-reviewing for an academic journal, and my usage of the term comes from my experience there. Reviewers in my experience are not given a checklist of any formal set of items that have to be covered (spark plugs, tires, wiper blades, hinges, oil, radiator fluid — sheeesh!); their job is to comment on the general competence of the author in the subject area, the general argumentative quality of the work, and its original contribution to scholarship. Reviewers may if they wish append detailed comments wherever they see fit, but that is not their main job. Their main job is to ascertain that the work is overall competent and original.

    It is my understanding that science book publishers often seek advice of this sort. So your unclearly expressed insinuation in your second paragraph, that in the case of books, the author evaluates his own work, whereas in the case of journal articles, others evaluate his work, is simply not true — not for any publisher that seeks outside advice from experts in the author’s field. If you don’t want to call that “peer review” then fine. My point was that you do not know for certain that this was not done in Shapiro’s case. For all you know, the manuscript may have been read and praised by the Regius Professor of Zoology at Cambridge or the Emeritus Professor or Evolutionary Biology at Harvard. If this would not be good enough for you, because some detailed formal process was not followed, then I think you have an irrational fetish about such processes. I suggest you read Frank Tipler’s essay on the history of peer review in the sciences.

  151. 151

    Champignon,

    The first point on which you “corrected” me was merely a choice of words. You drilled into that and ignored the content. I don’t see the point since I have no problem correcting a poor word choice. And yet for the third or fourth time you’re still harping on it.

    With regard to the example of a computer sorting cards, that’s why I wonder if you’re playing a joke on me. It’s easier to believe than that you’re serious.

    It’s okay. I like being right about as much as the next guy. I does get a little boring after a while. And if someone wants to wind me up by saying crazy stuff and watching me spout paragraphs of straight-faced responses, that’s fine too. I don’t take myself that seriously. And neither does anyone else.

    But you are scraping the bottom of the wrongness barrel. There must be plenty of computer programmers following this. Recognizing symbols is easy. There’s been commercial software that converts scanned documents to text for a long time. But if any programmer would like to suggest how software might arrange symbols such as digits, letters, or playing cards in order without intelligent input to specify the meaning of the symbols and either how they are sorted or relate them to values which can be sorted, I’d love to hear it.

    Am I not putting myself out on a limb? There are plenty of better programmers than me.

    Don’t forget that even the storage of the simplest values requires a degree of deliberate abstraction. It is impossible for the bits 1001 to represent nine unless someone determines that the first bit is 1, the second 2, the third 4, and the fourth 8. That even the most basic storage and manipulation of numbers requires that an intelligent agent assign values to bits makes it impossible for any process automated by a computer to act without the deliberate assignment of meaning to symbols.

    Your argument is denial of reality, as is your imagination that you have corrected me.

    I think we talk enough trash that when correction comes, it comes hard. I’m okay with that. If it’s too much then I’ll run off and hide in the woods, grow a big beard, and dwell among the bears and squirrels. But more likely I’ll just retreat into awkward silence for a spell and hopefully come back a little bit smarter.

    If I were really smart I’d stand on the shore waiting for the tide to go out rather than struggling in vain to push against it. But I’m not.

  152. Scott,

    Do you stand by the following statement, or do you wish to retract it?

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

  153. @Timaeus

    It Matzke apologized and/or retracted an error, I salute him. I have never seen him do it here, or anywhere else. Maybe he has, but in my experience it is very atypical of his debating stance. Let’s hope the example you have given marks a change of attitude on his part. If it does, many ID proponents will respect him a lot more.

    If??? The blog post in quesion was posted here at Uncommon Descent (see here). Hunter likes to drive UD traffic to his blog, so some of the comments end up over there, including Matzke’s apology. Maybe you didn’t see it in the post there, but I provided both the quote and the link to Matzke’s apology.

    As for “many ID proponents will respect him a lot more”, I think that is a fool’s errand for Nick, or any of the thoughtful and experienced critics here. Civil discourse is its own reward, and I value content-rich and non-personal exchanges just as something I expect from myself, by my own standards (or at least the part of the conversation I control), but any critic who is gaining the respect of ID proponents here should be alarmed. If that’s happening, you’re very likely to be broadly mistaken, a coward or both.

    ID isn’t young earth creationism, but the culture and advocacy dynamics are quite similar. YECs are more straightforward and honest with themselves and others about the kinds of positions they are defending, I’d say, but in any case, there has been a long procession of critics here (“Diffaxial”, “Nakashima”, “ROb”…) who’ve been polite and excrutiating careful not to step on the delicate egos and hair-trigger reflexes of the management and ID regulars here. There’s a very strong, solid case that “tone” appeals are a trick here. No amount of bending over backwards (to the point of self-humiliation in the case of some of those posters, dealing with the likes of Joe and KairosFocus, etc.) will earn any “respect” worthy of the term.

    Instead, it’s a way to dull an deflect criticism. Diffaxial, if you remember him, was positively withering, and yet, almost embarrassingly obsequious (made me cringe, any way). Didn’t help. “Tone” appeals are a trap. If you are critic, and you are going to press your case on science, math, data models, papers, and hold the ID folks to their claims in similar ways critics are used to be held accountable, no “tone” can help you. “Respect” in the sense that ID advocates see you as non-threatening is a “badge of dishonor”, if anything.

    Critics should (and I think largely do) post on the merits and with a focus on salient issues with the CONCEPTS of ID, and the logic and heuristics of ID with a tone that helps them make their point. That really is the most devastating way to deal with the ID advocates here. It’s not for “respect from IDers”. IDers, if they are paying attention, should be howling from the searing effects of real science and critical think and applied maths and all that being put their arguments. They SHOULD be, and often are, angry as hornets in a nest that got kicked over.

    You say ID wallows in the culture war. I see. And the columns of Jeffrey Shallit, Mark Chu-Carroll, P. Z. Myers, Jason Rosenhouse, Larry Moran, etc., *never* stoop so low as to do that? No Wikipedia editor has *ever* let his personal hatred of ID bias his editing? Michael Shermer is always completely objective in his assessments of ID? The people at Biologos are completly above culture-war motivations? Ken Miller is completely above them? Eugenie Scott? Nick Matzke? Abbie Smith? Is the culture war all ID’s fault, then?

    Of course not. I’m under no illusions about the nature of “war” as a two way or n-way engagement. P.Z. Myers can be brutal, over-the-top, outrageously offensive. But for all that, just to focus on Myers for the moment, Myers has strong redeeming qualities. He knows what he’s talking about. He’s proficient in knowledge building, he’s a scientist. He’s expert with the tools and methods of his profession.

    If I can agree that the science side of the war has plenty (or equal) share of culture war sins to admit to, the indictment of ID still stands, for it doesn’t have a P.Z. Myers, it is culture war from start to finish. There is no “proficiency” that redeems ID, no science, no applications that contribute to knowledge. Culture war is the pinnacle for UD and ID. That’s not the case for Jerry Coyne, or PZ Myers, or Larry Moran, or Nick Matzke. These other guys actually know what they’re talking about in their respective domains, and can demonstrate it all day long.

    A friend of mine who is quite pro-ID recently told me, in response to a comment I made like this in response to a similar question from him that “We have Stephen Meyer, and he doesn’t do the crap that Myers does!”.

    That pretty much sums up the ID delusion right there, I think. Myers, for all his shenanigans, respects the serious enterprise of knowledge building and science. Stephen Meyer is polite con man, an elite subversion tool for science and human knowledge. I’d take the uncouth antics of PZ, combined with the earnest and sober engagement with the hard problems of real biology over the execrable sophistry of Meyer any day, even if Meyer never so much as called a critic a “jerk”.

    That doesn’t excuse abuses and bad behavior on the science side of the war. But it does identify redeeming substance and serious commitments to knowledge and critical thinking that ID eschews, so far as I can see, after following the movement for years. Dembski and this blog are the apotheosis of this problem in ID. Mike Gene and the crew over at Telic Thoughts, by contrast, have the same problem, but here problem is thick and rife.

    Behe and Meyer are perfect gentlemen in the way they write and speak in public. One may disagree strongly with their positions, but one cannot fault their manners.

    Being polite and having good manners is not sufficient, as good as those behaviors may be. Ken Ham of Answers in Genesis has been quite self-deprecating and polite the couple times I’ve heard him speak in person, quite congenial and pleasant in Q&A sessions with the crowd. That doesn’t compensate for the heinous kinds of fraud Ken Ham tries to pull on the faithful who trust him (often very successfully). Meyer’s no different, and no better than that. Much smoother, I’ll grant, than Ham, who affects a more hill-billy vibe that works with the fundamentalist culture better, etc.

    Don’t get me wrong, I can and do appreciate being polite. But that does not redeem being a huckster, a con man. I’m quite happy having lots of posters in the “Joe/Joseph” or KairosFocus mode. They are pretty much self-refuting, and are less than harmless, unwitting aids for the critics. Meyer, though, takes a keen and careful look, but when you do tease his stuff apart, it’s a fairly potent bit of deception, equivocation, evasion. I can salute Meyer as an effective tool for the ID movement. But it’s using a sharp able mind to subvert, denigrate, and thwart knowledge, reason, and other noble uses of his considerable capabilities.

    I’ll leave off there. I’m tempted to tear into the objection about “intelligent design creationism”, which is a term I have at length come to see as both empirically grounded and somewhat charitable. But enough for now.

  154. 154

    No, I’d rephrase it. Computers aren’t aware. Programmers speak that way metaphorically, but I can see you getting ready to spring on my word choice again.

    I would say that if something can sort playing cards it must have some input (that’s where I used the word “awareness”) telling it which cards are greater to or lesser than others.

    In the case of a program that information could reside at one of several levels. Most modern programmers don’t have to specify the order of numerals. But the information is still there. Any mapping between a numeric value and the appearance of the digits must be specified. The mapping between numeric values and their stored representation also requires specification.

    I don’t see what’s so complicated. The meaning of the symbols on the cards, including the digits, is entirely arbitrary. They have no emergent property by which they can be sorted.

    Clearly you feel that you have something remarkable up your sleeve. It almost doesn’t matter because I’d have to scroll up past 50 posts to remember what the point about the cards was. It was the difference between sorting rocks by size and sorting cards. Size is a property of a rock. One is or is not bigger than the other. That a queen is greater than a jack or 7 is greater than 6 because they are chosen representations of numbers are both mental constructs. They are imagined properties. They are not emergent from any natural law. This is evident quite simply because the meaning of any symbol can be changed at will without requiring a change to the behavior of natural law.

    The only refutation to any of this is to deny free will, to determine that even our collective agreement on a set of symbols, which looks like imagination, is just a predictable set of chemical reactions across multiple organisms. Or we could just say that it’s predictable but impossible to model so it just looks like free will.

    I’m just not interested in that discussion. But at least I’ve provided you with the coherent counterargument you couldn’t find yourself. Don’t say I never gave you anything.

  155. Scott,

    No, I’d rephrase it.

    Thank you.

    Computers aren’t aware. Programmers speak that way metaphorically, but I can see you getting ready to spring on my word choice again.

    Says the person who sprang on me for using that word, even though I was only echoing you, and even though I put the word in quotes!

    I wrote:

    Note that the program is not “aware” that it’s looking at an image of a card…

    You pounced on me…

    Programs aren’t “aware” of anything. What does that have to do with anything?

    …totally forgetting that you had written this:

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them. [Emphasis mine]

    LOL.

    Scott, when you wind yourself up like that, you make silly mistakes. Try to relax a little.

  156. Scott:

    I would say that if something can sort playing cards it must have some input (that’s where I used the word “awareness”) telling it which cards are greater to or lesser than others.

    More precisely, there needs to be an ordering scheme for the algorithm to follow. This is not a quibble. The program can follow the ordering scheme without making use of the concepts “greater than” and “less than”. To reiterate:

    Note that the program [in my example] is not “aware” that it’s looking at an image of a card, that the card has symbols on it, that the meaning of one of the symbols is “King”, or that “King” comes after “9?. Yet it still sorts the cards into the correct order, which according to you should be impossible…

    You continue:

    I don’t see what’s so complicated. The meaning of the symbols on the cards, including the digits, is entirely arbitrary.

    Yes, in the sense that if we a) define a new set of symbols in one-to-one correspondence with the existing set, b) replace the old symbols on each card with their new counterparts, and c) replace the old symbols with the new symbols in our ordering rules, then if we order the cards by symbols, they will end up in the same order as before.

    They have no emergent property by which they can be sorted.

    Yes, if you mean that the ordering rules aren’t determined by the geometry of the symbols themselves.

    Clearly you feel that you have something remarkable up your sleeve. It almost doesn’t matter because I’d have to scroll up past 50 posts to remember what the point about the cards was.

    It would have gone a lot faster if you hadn’t been so resistant to admitting error.

    It was the difference between sorting rocks by size and sorting cards. Size is a property of a rock. One is or is not bigger than the other.

    Yes, unless they’re the same size.

    …the meaning of any symbol can be changed at will without requiring a change to the behavior of natural law.

    Yes. In other words, the mapping of a symbol to its referent is not an invariant under natural law.

    The only refutation to any of this is to deny free will…

    No. If you change the meaning of a symbol “at will”, it just means that you act in accordance with your will. It doesn’t mean that your will is free.

    I’m just not interested in that discussion. But at least I’ve provided you with the coherent counterargument you couldn’t find yourself. Don’t say I never gave you anything.

    You give crappy presents, Scott. :-)

  157. Here’s where I think you’re getting hung up, Scott. While the mapping of symbols to referents isn’t an invariant under natural law, that doesn’t mean that such mappings can’t be explained by natural law.

    In other words, if thinking is a physical process, then the difference between a person who uses one symbol-to-referent mapping and a person who uses a different mapping is simply a difference in brain states. Neither person’s brain states violate the laws of physics; they’re both compatible with natural law.

  158. It was a typo, Timaeus. Apologies. I meant “paper”, specifically these fairly recent ones:

    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    http://shapiro.bsd.uchicago.ed.....ileDNA.pdf

    http://shapiro.bsd.uchicago.ed.....ective.pdf

    And other more technical papers that I am fortunate enough to have access to via my library.

    Reviewers in my experience are not given a checklist of any formal set of items that have to be covered (spark plugs, tires, wiper blades, hinges, oil, radiator fluid — sheeesh!); their job is to comment on the general competence of the author in the subject area, the general argumentative quality of the work, and its original contribution to scholarship. Reviewers may if they wish append detailed comments wherever they see fit, but that is not their main job. Their main job is to ascertain that the work is overall competent and original.

    Well, it may be slightly different in the humanities (I have only occasionally reviewed in the humanities) but the list is usually a little more specific in the sciences, and generally includes the request that reviewers to comment on whether the conclusions are justified by the evidence.

    What is also possibly different is that in the sciences, even if a paper is eventually accepted, it frequently (usually, in my experience) goes back and forth a few times until the reviewers are satisfied that their criticisms have been met. This sometimes includes re-analysis of the data, sometimes the collection of new data, sometimes a revision of conclusions, sometimes a more thorough review of the literature. In other words it’s far more than just a vetting process, it’s actually part of the writing process.

    It is my understanding that science book publishers often seek advice of this sort. So your unclearly expressed insinuation in your second paragraph, that in the case of books, the author evaluates his own work, whereas in the case of journal articles, others evaluate his work, is simply not true — not for any publisher that seeks outside advice from experts in the author’s field. If you don’t want to call that “peer review” then fine. My point was that you do not know for certain that this was not done in Shapiro’s case. For all you know, the manuscript may have been read and praised by the Regius Professor of Zoology at Cambridge or the Emeritus Professor or Evolutionary Biology at Harvard. If this would not be good enough for you, because some detailed formal process was not followed, then I think you have an irrational fetish about such processes. I suggest you read Frank Tipler’s essay on the history of peer review in the sciences.

    I’m getting a little fed up of your “insinuations” Timaeus. I did not “insinuate” any such thing, I merely stated what is a fact, that the publishers of a book are interested in selling a specific piece of writing – that book, whereas publishers of a journal are interested in producing a journal that contains highly cited and consistently excellent scientific papers. The motivations are quite different, and this is reflected in two very different editorial approaches.

    I am not saying that Shapiro’s editors did not send his copy out to reviewers, they may well have done. More importantly, his publishers may have commissioned – or been enthusiastic about – Shapiro’s book because of Shapiro’s existing reputation as a highly regarded and copiously published scientist. It is not to denigrate an author because what he has produced is a book.

    My very simple point is that if you want to know what a scientist has actually found, or even, sometimes, what his view of the field is (review articles by eminent scientists are very useful) then peer-reviewed articles, as well as being more accessible, generally, are often a better way of finding out than reading a book. Or, at least, as good.

    But this argument is really very silly, because I have no problem in reading Shapiro’s book, and have wanted to for some time, and I’m hoping it arrives today.

    However, I’m very uninclined to read any more stuff by Meyer, or, indeed, by Behe, given what I have read so far, and by the few readily accessible public writings I have seen. I’ve read Darwin’s Black Box. I thought it was very silly.

  159. No, Bilbo, I can’t. As I said, you seem to have completely missed my point.

  160. Golly I must have a sticky s key or something!

    “I meant paperssssssss”

    oops.

  161. Elizabeth, what you seemed to be saying, in a rather murky way, was that in the case of books, the author is the judge of his own merits, whereas in the case of journal articles, the author’s merits are judged by others. And my point was that is false, or only true in cases where the publisher of the book does not ask for critical internal reviews of the manuscript before publishing it. I used the word “insinuated,” because it seemed you were trying to imply something without making a direct case for it. But if it was just a case of awkward wording, I retract the term.

    Yes, publishers are out to make money, but some publishers are *also* out to maintain a reputation as publishers of quality scientific books rather than trash. Such publishers will ask for expert criticism of manuscripts before accepting them. I don’t know if that was done in Shapiro’s case, but you don’t know that it wasn’t.

    You are right: this discussion has gone on way too long on a simple point. The simple point is that Shapiro is MEGA-interesting as an evolutionary theorist, and when someone is interesting, I don’t give a fig whether or not his books or even his articles have been peer-reviewed. I want to hear the argument. And as journal articles tend to be very dry and technical, focused on convincing specialists of one small point, whereas books are often broader in scope and aimed at bringing a wider-than-specialist audience on board, I’d far rather read a book than an article. But when I listen to you, I hear — “Oooh, a BOOK? I don’t normally trust (shudder!) BOOKS … but in this case I guess I could make an exception.” That’s just bizarre to me. And you are representing this hesitation as a healthy scientific tendency. But evolutionary biologists, and others interested in questions of evolution and design etc. — Dawkins, Miller, Coyne, Sean Carroll, H. Allen Orr, etc. — read books on evolution all the time, without worrying about catching the Cooties from something that’s not peer-reviewed. Sometimes, Elizabeth, you come across as a very strange person!

    I’m sorry that you found Darwin’s Black Box very silly. But as I said before, you approach evolutionary questions with the mind of a population geneticist. All the population geneticists object to Behe. To get the force of Behe, you have to think like a biochemist, and/or like an engineer. (Denton, for example, is a biochemist who employs kindred arguments, and many ID proponents are engineers.) This tension between approaches existed long before our time — it was present at the Wistar conference in 1966, and it will continue into the future, so you and I are not going to settle it here.

    In any case, I didn’t find Behe’s book “silly” at all. Imperfectly argued at points, certainly — what book isn’t? Certainly not silly. No good general answer to the theoretical problem he posed has yet been provided by the Darwinian [in my sense] camp. But don’t worry, Elizabeth, because in fifty years, the Darwinian camp will be gone, and thus Behe’s book, no longer having a target, will become irrelevant. You can take solace in that.

  162. You are right: this discussion has gone on way too long on a simple point. The simple point is that Shapiro is MEGA-interesting as an evolutionary theorist, and when someone is interesting, I don’t give a fig whether or not his books or even his articles have been peer-reviewed. I want to hear the argument.

    Me too. My only point in dispute was whether you have to read the books to understand the argument. My point, in the case of scientists, is that reading the papers is just as good, if not a better, way of understanding the argument. But if I’m impressed by a scientist’s papers, I’m especially interested in reading his/her books, hence my current Amazon order.

    If you took from my words some kind of fetishistic fear of catching cooties from books, you couldn’t be more wrong. And in fields in which I have no expertise (cosmology for instance!) I’d much rather read a book than a paper.

    I’m sorry that you found Darwin’s Black Box very silly. But as I said before, you approach evolutionary questions with the mind of a population geneticist. All the population geneticists object to Behe. To get the force of Behe, you have to think like a biochemist, and/or like an engineer.

    I dispute this. In any case, in background, I’m much closer to an engineer than to a population geneticist (I am most assuredly not a population geneticist).

    I think Behe’s argument is flawed in many ways, one of which being that he seems not to understand the role of drift, so he would benefit from considering population genetics a little more) but it is not the only flaw in his argument, it’s just one of the more egregious ones.

    No good general answer to the theoretical problem he posed has yet been provided by the Darwinian [in my sense] camp.

    I disagree. The theoretical problem he posed has been thoroughly dealt with (indeed, demonstrated to be not-a-problem). Specific challenges (how to account, step by step, for the evolution of certain allegedly IC biological features) have not been met, and never will be, to his satisfaction, because that would be like saying that Julius Caesar’s mother never existed on the grounds that we have no minute by minute account of her life. Some details of history are not discoverable post hoc; the data simply is not there.

    But we cannot assume from the lack of data that the event did not occur. And to demonstrate that it could have occurred, we need to demonstrate that, in principle, the theoretical problem can be over come.

    This has been done.

  163. The words purposeful and intelligence are just labels we attach to what chemistry does when certain complex arrangements occur

    Full stop. By the same logic, the word “Petrushka” as well as all he writes here on this blog are also just labels we attach to what chemistry does.

  164. We would love to see an evolutionary hypothesis pertaining to the “how”- as in how did any bacterial flagellum evolve via stochastic processes?

    Ya see Liz, your position doesn’t have any testable hypotheses and your complaining to the contrary doesn’t do any good.

  165. I think the whole argument boils down to what David Abel calls the The Formalism > Physicality (F > P) Principle. It is only intelligence that in practice can be shown to be able to assign a particular meaning to a particular configuration of matter. In practice it is only intelligence that can then choose between various configurations selecting those that are ‘good’ based on the assigned meaning and filtering out others as ‘bad’. Nature does not care about semantics. It can only provide constraints, not controls in the cybernetic sense. I.e. nature cannot itself organise processes that steer systems towards improved utility.

  166. 166

    Champignon,

    The program can follow the ordering scheme without making use of the concepts “greater than” and “less than”.

    You’re absolutely correct. Greater than and less than are just shorthand for the result of a comparison. It does not literally mean that the king is greater than the nine. It means that it is determined as having a higher sort order.

    But in real life, how do you think that programmers implement this? By specifying a set of rules for the comparison of every card to every other card? There might be cases where they actually do so. In those cases they are providing the program with the sort order.

    In most cases, however, this would be accomplished by assigning a numerical value to the card. (It depends entirely on the application.) Jack = 11, Queen = 12, and so forth. And then they are sorted by their numerical values.

    It really doesn’t matter. In either case the computer is provided with the sort order. Yes, the cards are physically different from each other, but that physical difference means nothing at all unless someone assigns meaning to the symbols depicted.

    The very simple point I’m arguing against is your assertion that a computer can sort cards without some reference to the symbolic meanings given them. It doesn’t matter if the computer calls it a King or assigns an arbitrary identifier to it. It cannot sort the cards without some form of input determining what order they should go in, because the sort order of the cards is not an emergent property of the cards.

    That leads back to biology, what you seem to be trying to lead this away from. The forms of proteins and the regulations of their growth are not an emergent property of genetic information. Neither is genetic information an emergent property of what it codes for.

    The illustration of the cards is quite simple and was not meant to be a 20-post diversion into hair-splitting over words. I would imagine someone debating whether the illustration is applicable. But within the context of the illustration itself, the point made with regard to the playing cards is clear unless you’re determined to be confused by it. I’m going to try not to pay attention to any more trifling over it. I don’t know if I’ll succeed. I’m clearly not smart enough to know when to stop explaining the same thing over and over, and in doing so providing even more fodder for hair-splitting.

  167. That leads back to biology, what you seem to be trying to lead this away from. The forms of proteins and the regulations of their growth are not an emergent property of genetic information.

    Does that mean you finally have a theory for mapping sequences to function (not retrospectively)? And function to utility in a a changing ecosystem?

    You can design a protein or a regulatory function at the sequence level without copying an existing sequence and testing modifications? Without using GAs or directed evolution?

    I think that without resorting to spookiness, the term emergent means that the properties of a combination cannot be predicted from the properties of the components. Unless you have uncovered a theory of biological design, I think that fits biochemistry.

  168. 168

    Champignon,

    In other words, if thinking is a physical process, then the difference between a person who uses one symbol-to-referent mapping and a person who uses a different mapping is simply a difference in brain states. Neither person’s brain states violate the laws of physics; they’re both compatible with natural law.

    I agree that all of it operates within natural law and that none of it violates any laws of physics. Otherwise I would have to think that something bizarre and supernatural occurs every time I imagine a shopping list, write it down, and then go to the store and retrieve the physical items corresponding to my abstraction.

    You are missing the enormous difference between saying that something is compatible with natural law and that it can be explained by it.

    No one disputes that when a computer processes data and displays or prints output in symbols, what takes place is purely electronic. No one knows what goes on in the brain, but I don’t doubt that it’s chemicals and electricity.

    I’m stopping here instead of typing my next sentence. That natural laws do not instantiate symbolic relationships and abstraction has been explained a dozen times over by people better at it than me, and even then every attempt was made to confuse or change the subject rather than refute it. I don’t expect anything different in this case.

  169. One of the characteristics of a language is that you can read it. That may seem trivial, but it’s not trivial or tautological in the case of the genetic code.

    It may be that the translation of a sequence into proteins or regulation is deterministic, but it can’t be a language in the usual sense unless you can parse it. If the dictionary for translation is the same length as the number of possible utterances, it’s not analogous to language or even to programming.

    Imagine a computer programming environment in which there are no lines of code, just an assemblage of DLLs that cannot be disassembled into component instructions. That seems to be the case with gpuccio’s protein domains. He claims they are irreducible.

    From my point of view, if this is the case, both design and evolution have the same problem — explaining how long sequences that are completely isolated from each other came into being.

    From my point of view the solution is not obvious, but the working hypothesis is obvious. The working hypothesis is that sequences are not isolated. They are connectable by cumulative change.

  170. 170

    Petrushka,

    You can design a protein or a regulatory function at the sequence level without copying an existing sequence and testing modifications? Without using GAs or directed evolution?

    No one has a theory. Yours is to say that somehow it evolved from something that somehow existed. I’ll counter it by saying that somehow it was designed. I believe that sentence matches the level of detail you’ve offered.

    Both are a great big stretch beyond anything we’ve observed. I don’t mind admitting that, while you cling to supposed demonstrations that don’t even remotely relate to what you extrapolate from them.

    As demonstrated by Thornton’s recent paper, efforts to demonstrate the ‘evolution of complexity’ amount to hyperbolic grasping at straws that insults readers’ intelligence. It’s nonsense at face value, and such sadly inflated ‘evidence’ reinforces that evaluation. I’d call it desperate if he didn’t have a choir to preach to. But it is pandering, pathetic, and insulting.

    I could generously supposed that it’s not representative of the evidence that persuades you (IOW maybe it’s not all crap) except that you’re just so proud of it. You know, ‘Come back when you’ve read and understood it’ and all that.

    I’ve addressed its merits. What I can’t make clear enough is that people should be offended by this contemptuous attempt to impress them with something shiny, like giving a lighter to half-naked savages. You don’t do it because the lighter is so impressive. You do it because you think they’re stupid.

  171. 171

    I forgot to mention that between the two, far more experimental research with regard to biological origins is done in favor of design. See the work of Szostak’s lab.

  172. Hi Elizabeth,

    Thank you for your post. Professor Dembski is well aware of the dilemma you raise:

    Right. There’s a “natural biasing factor” [in the case of the distribution of pebbles along Chesil beach - VJT]. And so what if, for organisms there is also a “natural biasing factor”? Which is precisely what Darwinian evolution theory proposes! In other words, you can’t infer intelligent design from CSI without calculating the probability under the null of Darwinian evolution!

    So Dembski is caught on the horns of a dilemma: either he assumes all sequences are equiprobable under the null, in which case Chesil beach has CSI, or he attempts to calculate the probability distribution of sequences under the null, in which case he has to calculate the non-flat distribution of sequences under all possible “natural” hypotheses, in which case his argument is entirely circular.

    In reply, I would like to point out that Professor Dembski is perfectly aware of the argument you raise, and he has already addressed it. As far back as 2003, he wrote, in his paper, Still Spinning Just Fine: A Response to Ken Miller :

    Why is intelligent design held to such a high standard when that standard is absent from the rest of the empirical sciences (nowhere else in the natural sciences is strict logical possibility/impossibility enforced, not even with the best established physical laws like the first and second laws of thermodynamics)?

    What’s behind this double-standard is a curious logic that propels evolutionary reasoning. I call it evolutionary logic or the logic of credulity. Evolutionary logic takes the form of a reductio ad absurdum. The absurdity is intelligent design or more generally any substantive teleology. For evolutionary biologists, to treat design or teleology as fundamental modes of explanation capable of accounting for the emergence of biological structures is totally unacceptable. Any valid argument that concludes design in such cases must therefore derive from faulty premises. Thus, in particular, any claim that entails, makes probable, or otherwise implicates design in the emergence of biological structures must be rejected. But evolutionary logic doesn’t stop there. Not only must any claim that supports design be rejected, but any claim that rules out design thereby demands assent and commands belief. Hence evolution’s logic of credulity — belief in an evolutionary claim is enjoined simply because it acts as a defeater to design and not because any actual evidence supports it…

    Bottom line: Calculate the probability of getting a flagellum by stochastic (and that includes Darwinian) means any way you like, but do calculate it. All such calculations to date have fallen well below my universal probability bound of 10^(-150). But for Miller all such calculations are besides the point because a Darwinian pathway, though completely unknown, most assuredly exists and, once made explicit, would produce probabilities above my universal probability bound. To be sure, if a Darwinian pathway exists, the probabilities associated with it would no longer trigger a design inference. But that’s just the point, isn’t it? Namely, whether such a pathway exists in the first place. Miller, it seems, wants me to calculate probabilities associated with indirect Darwinian pathways leading to the flagellum. But until such paths are made explicit, there’s no way to calculate the probabilities. This is all very convenient for Darwinism and allows Darwinists to insulate their theory from critique indefinitely.

    In other words, if you believe there is a natural biasing factor at work in Nature which makes Darwinian evolution possible, then please demonstrate its existence, and then we can perform probability calculations. Until then, the default assumption is that there is none. As far as the origin of life is concerned, Dr. Stephen Meyer has argued in Signature in the Cell that the hypothesis of “biochemical predestination” flies in the face of everything we know about DNA. There are no signi?cant differential af?nities between any of thefour bases in DNA and the binding sites along the sugar-phosphate backbone. The same type of N-glycosidic bond occurs between the base and the backboneregardless of which base attaches. All four bases are acceptable; none is chemically favored.

    The same logic applies to proteins as well. As Dr. Meyer puts it: “differing chemical af?nities do not explain themultiplicity of amino acid sequences existing in naturally occurring proteinsor the sequential arrangement of amino acids in any particular protein.”

    We may fairly conclude that at least as far as the origin of life is concerned, Dembski’s assumption that all sequences are equiprobable is a perfectly good null hypothesis.

  173. 173

    It may be that the translation of a sequence into proteins or regulation is deterministic, but it can’t be a language in the usual sense unless you can parse it.

    Are you suggesting that it cannot be parsed? That it’s not a language because it can’t be read? And yet somehow the same genes produce the same frog over and over. You can’t deny that the relationship exists and that it behaves consistently. But the crux of your argument is that it’s impossible to comprehend or predict.

    To say that what behaves with uniform consistency is unpredictable is the antithesis of science. You are literally arguing that what is unknown cannot be known. But only in this case. And they say ID is a science-stopper.

    If the dictionary for translation is the same length as the number of possible utterances, it’s not analogous to language or even to programming.

    This gets stranger and stranger. If the content of DNA could not be translated without a dictionary containing every possible combination then the mechanisms for protein synthesis would be physically massive.

    How can you argue that translation requires a dictionary of every possible sequence when every second it is being translated without such a dictionary? Here’s the DNA, here’s the protein produced as a result (plus whatever else it codes for.) Both are real and one results from the other. Where is this massive dictionary you speak of?

    Your argument is a surreal denial of the existence of the process you purport to explain. I must be dreaming or hallucinating. I need to come up for air.

  174. Hi Elizabeth,

    You raise several valid points in your criticisms of Sheldrake’s lack of rigor. So I think it’s best to focus on his most convincing evidence that the mind and brain are distinct: telephone telepathy. The best paper I’ve found on the subject is Do You Know Who is Calling? by
    Stefan Schmidt, Devi Erath, Viliana Ivanova and Harald Walac in The Open Psychology Journal, 2009, Volume 2, pp. 12-18. On the other hand, Dr. Chris French has a Youtube critique of Sheldrake’s experiments here: http://www.youtube.com/watch?v=9TWwjBFYRhc – although I don’t think it’s pertinent to Schmidt et al.’s paper.
    Anyway, that’s about all I know. I was personally impressed by the Nolan sisters, but I realize that the odds of the results occurring by chance aren’t anywhere near low enough to make the case compelling: http://deanradin.blogspot.com/.....pathy.html

    Many critics have found Sheldrake’s hypothesis of morphogenetic fields rather nebulous. I don’t think that’s altogether fair: Newton famously feigned no hypotheses about how gravity worked. A better criticism would be that the notion of a morphogenetic field needs to be described mathematically before it can be said to qualify as a bona fide formal cause of the kind that scientists can investigate. By the way, Ken Wilber has an interesting article on Sheldrake’s views, entitled, Sheldrake’s theory of morphogenesis .

  175. What Thornton has done is demonstrate a procedure for investigating connectability. That is what science does: devise testable hypotheses and test them.

    What alternative is there? I haven’t seen one from the ID camp.

  176. How can you argue that translation requires a dictionary of every possible sequence when every second it is being translated without such a dictionary? Here’s the DNA, here’s the protein produced as a result (plus whatever else it codes for.) Both are real and one results from the other. Where is this massive dictionary you speak of?

    Languages have words and syntax. Dictionaries define words and the rules of grammar define syntax.

    You do not have language dictionaries containing every possible sentence.

    What a theory of biological design would require (at a minimum) is a dictionary of words that is smaller than the list of possible sentences or paragraphs.

    Unless I misread gpuccio, the shortest word in DNA is the protein domain. I’m not convinced, but that’s the way I read his assertion.

    The problem is that the domain is a rather long sequence and unlikely to arise by pure chance. (Only a few thousand exist, so the invention is suitably rare.)

    Now there are several possible ways that domain sequences could arise.

    1. They could be designed by a being capable of seeing sequence spaces that are larger than the number of particles in the universe.

    2. There are smaller words and a grammar within the sequences that we haven’t yet discovered. (If so, the smaller words would be selectable.)

    3. The sequences could arise for some other reason as part of some other selectable structure.

    4. The sequences are simply the current version of sequences that have accumulated from shorter sequences.

    5. Something else.

    I don’t know which is correct, but I do know which conjectures can be investigated by science.

  177. There are reports of situations
    where a person intends to call another person and in the
    very moment when s/he wants to lift the receiver this other
    person calls in.

    I’ve had that happen. I lifted the receiver before the phone rang, and the person I was going to call was already on the line.

    I fail to see how that supports telepathy.

    Now if it had been the President or someone who had no prior contact with me, that would have been exciting.

  178. I’d like to point out that however much I disagree with gpuccio, I recognize the problems he presents as real problems, and I take the trouble to understand what he is saying and why it is important.

    I can’t really say the same for most ID advocates regarding evolution and the problems presented by ID.

    In general researchers in mainstream biology have already formulated the kinds of questions raised by critics of evolution, and research programs are in place (and have been in place for a long time) to address these questions. Most of the criticisms of evolution go back a century or two. Progress is dependent on the current state of technology and the tools available.

    None of these questions really cast doubt that evolution happened over billions of years, any more than questions about the origin of the moon cast doubt on the age of the solar system and its general history.

    If the current theory of moon formation is wrong, the default fallback explanation is not space aliens or magic.

  179. 179

    Petrushka,

    You allow for only one scenario that it includes intelligence, accept that it isn’t intelligent.

    They could be designed by a being capable of seeing sequence spaces that are larger than the number of particles in the universe.

    You have an odd way of phrasing one assumption within another, as in this case you defy countless examples of intelligent arrangement, including your own writing, which is not achieved by examining every possible sequence.

    Time and time again this argument is your linchpin, and yet it is predicated upon willful ignorance of the abundant demonstrations of how intelligence operates, and the assumption that what behaves predictably cannot be predicted.

    Your reasoning requires the acceptance of an irrational assumption. And the reward for doing so is that one then has a basis for accepting an even more irrational belief. It’s flawed to the core, and one irrationality begets the next.

    And then, confronted with the stark reality that people with no experience whatsoever do in fact learn to fold proteins, you retreat to the argument that they won’t get any better at it but the GAs they quickly surpassed will. As if this evidence has not already bowled over what was shaky logic to begin with.

    What you offer runs contrary to all of human experience, depends on acceptance of unwarranted and irrational assumptions, and is refuted by empirical evidence. And you you proceed from one point to the next anyway in an endless loop of denial. Curse my get-the-last-word-always-be-right impulse. I need to disconnect from this.

  180. Thank you for your post. Professor Dembski is well aware of the dilemma you raise:

    Right. There’s a “natural biasing factor” [in the case of the distribution of pebbles along Chesil beach - VJT]. And so what if, for organisms there is also a “natural biasing factor”? Which is precisely what Darwinian evolution theory proposes! In other words, you can’t infer intelligent design from CSI without calculating the probability under the null of Darwinian evolution!

    So Dembski is caught on the horns of a dilemma: either he assumes all sequences are equiprobable under the null, in which case Chesil beach has CSI, or he attempts to calculate the probability distribution of sequences under the null, in which case he has to calculate the non-flat distribution of sequences under all possible “natural” hypotheses, in which case his argument is entirely circular.

    In reply, I would like to point out that Professor Dembski is perfectly aware of the argument you raise, and he has already addressed it. As far back as 2003, he wrote, in his paper, Still Spinning Just Fine: A Response to Ken Miller :

    This is certainly not a response to the argument I raise. It is a response to Ken Miller’s objection to his argument about Irreducible Complexity, which it fails to meet, and in a minute I will go through and show you why. However, my objection to Dembski’s 2005 paper: Specification: the Pattern that Signifies Intelligence is much more basic that this.

    In that paper, Dembski proposes a metric for detecting intelligent design from a given pattern. He does not even mention Irreducible Complexity, although I think he things his metric subsumes it. And my point is that that metric is simply invalid, in its own terms.

    To put it simply, Dembski’s argument is that natural processes can produce “complex” patterns, which he defines as being patterns are one of a very large number of patterns that might be generated by some “chance” process, and the example he gives are series of coin tosses. Chance, he says, might give you a series of heads and tails, which we can represent as ones and zeros. Now, any one pattern is as likely as any other pattern, so 100 heads is no less likely that, say: 0 0 0 1 0 0 1 1 0 0 1 1 1 1 1 0 0 0 1 1 0 1 0 0 1 1 1 0 0 1 0 1 1 0 0 0 1 0 1 0 1 0 1 1 1 0 1 0 1 1 0 0 0 0 1 0 0 1 1 1 0 1 0 0 1 0 1 0 0 1 0 1 0 1 0 1 1 0 1 0 1 0 0 1 0 0 1 1 0 1 1 1 0 0 1 0 1 1 0 1,which I just generated randomly.

    So both are equally “complex” – have the same amount of Shannon information. However, he argues that the reason we would suspect skulduggery if someone tossed 100 heads is that 100 heads is one of a very small group subset of patterns of heads and tails that can be described as simply as “all heads”. “All tails” is another candidate. This subset of patterns he calls “specified” – not, note, “pre-specified”. Thus he proposes that without even knowing what a pattern was “supposed” to be, if it is both very complex (high Shannon) and very compressible (high Kolmogorov compressibility) that we can infer that something other than “chance” was responsible.

    Oddly, in that 2006 paper, he drops his “Explanatory Filter”, thinking it no longer necessary, apparently (you can probably find the announcement in here somewhere, there was a piece about it at Panda’s Thumb), and considering that CSI took care of both Chance and Necessity.

    Well, as you’ve just noted, it doesn’t. If a pattern has CSI (and although I haven’t calculated it, I’m fairly confident that Chesil Beach would come into the rejection region of Dembski’s null distribution), we know that it was not generated by a process that generates a flat distribution of patterns, i.e. in which all patterns are equiprobable (and few processes do). But that does NOT tell you the thing was created by intelligence. We all agree that Chesil Beach wasn’t, and indeed, there are many patterns in geology that exhibit vast amounts of CSI by Dembski’s metric, and no-one argues that they are intelligently designed (except in a remotely deist sort of way).

    So Dembski has dropped the ball. He always did need to reject patterns created by “necessity” before considering “chance”, in order to filter out patterns like Chesil Beach. CSI doesn’t do the job.

    But then we are back to all the original problems with Explanatory Filter. The EF tried to separate Chance from Necessity, and, pace Monod, this is not actually possible, because the two are not two kinds of causes, they are two ways of looking at one kind of cause. Something happens “of necessity” if it is not contingent on anything else. One could argue that no event, not even the sunrise, is contingent on nothing, but let’s for the moment imagine that some events are absolutely certain. And let’s give them a Necessity score of 1, which we could also write as a probability of 1. Now let’s make the event slightly more contingent – take a coin toss. If we toss a coin, there is a probability of almost 1 that it will land either face up or face down (presumably very occasionally a coin lands on its edge), which we will round to 1. However, there is only a .5 probability that it will land heads. So now we reduce our Necessity score to .5. And so on. In other words, “Necessity” is just the name we give to events that are contingent only on extremely unlikely other events, and “Chance” the name we give to events that are contingent on a vast number of extremely unlikely (individually) other events. Somewhere in between are events with a measurable probability distribution, and we call processes that are statistically predictable in the mass, but not predictable as individual events, “stochastic”.

    So Dembski was in fact absolutely right to abandon the EF in favour of CSI, but in so doing, he simply makes explicit what the problem that was implicit in the EF: perfectly natural stochastic processes can produce patterns that are highly compressible (what emerges is a tiny fraction of what could emerge from a process that produced a flat distribution), and yet have high complexity (be very unlikely to be generated by a flat-distribution-producing process).

    Therefore, all we can say, if a pattern exhibits CSI is that it was not produced by a process in which all permutations of the pattern elements are equiprobable. And so it does not allow us to distinguish Intelligent Design from stochastic natural processes (or non-stochastic ones, actually – the EF did at least allow us to do that).

    But it gets worse. We know that non-linear natural processes (stochastic or non-stochastic) can produce vastly complex patterns that have all the appearance of design. All the mathematics of chaos tell us that. And what Darwin proposed was a non-linear natural process.

    And so CSI simply cannot distinguish Design from Darwinian processes. You’d need something else. Hence “Irreducible Complexity”. Unfortunately that has problems too, and Dembski has not dealt with them:

    Why is intelligent design held to such a high standard when that standard is absent from the rest of the empirical sciences (nowhere else in the natural sciences is strict logical possibility/impossibility enforced, not even with the best established physical laws like the first and second laws of thermodynamics)?

    Interesting that Dembski seems to accept that the 2LoT is not violated by biological agents, but let that pass :)

    What’s behind this double-standard is a curious logic that propels evolutionary reasoning. I call it evolutionary logic or the logic of credulity. Evolutionary logic takes the form of a reductio ad absurdum. The absurdity is intelligent design or more generally any substantive teleology. For evolutionary biologists, to treat design or teleology as fundamental modes of explanation capable of accounting for the emergence of biological structures is totally unacceptable. Any valid argument that concludes design in such cases must therefore derive from faulty premises. Thus, in particular, any claim that entails, makes probable, or otherwise implicates design in the emergence of biological structures must be rejected. But evolutionary logic doesn’t stop there. Not only must any claim that supports design be rejected, but any claim that rules out design thereby demands assent and commands belief. Hence evolution’s logic of credulity — belief in an evolutionary claim is enjoined simply because it acts as a defeater to design and not because any actual evidence supports it…

    This is simply wrong. As Dawkins said in his interview with Ben Stein (which Dembski clearly misunderstands totally) there’s nothing intrinsically anathema about making a Design inference. And as he points out with SETI, scientists do the same thing, as do archaeologists, forensic scientists, and people in my business too (we regularly conduct statistical tests to see whether people are responding “above chance” i.e. intelligently). So I dismiss this rebuttal as the rebuttal of a straw man.

    Bottom line: Calculate the probability of getting a flagellum by stochastic (and that includes Darwinian) means any way you like, but do calculate it. All such calculations to date have fallen well below my universal probability bound of 10^(-150). But for Miller all such calculations are besides the point because a Darwinian pathway, though completely unknown, most assuredly exists and, once made explicit, would produce probabilities above my universal probability bound. To be sure, if a Darwinian pathway exists, the probabilities associated with it would no longer trigger a design inference. But that’s just the point, isn’t it? Namely, whether such a pathway exists in the first place. Miller, it seems, wants me to calculate probabilities associated with indirect Darwinian pathways leading to the flagellum. But until such paths are made explicit, there’s no way to calculate the probabilities. This is all very convenient for Darwinism and allows Darwinists to insulate their theory from critique indefinitely.

    No. Dembski has this backwards, by his own methodology. It was he who cast “natural” causes as the null, and insisted on Fisherian, not Bayesian, logic. And under his own chosen statistical method, it is up to him to show that the pattern in question could not be generated under that null. And I have just demonstrated that he cannot do this, and does not even attempt to. He regards “equiprobable” as the null, and natural non-linear stochastic processes (and many others) do no not produce equiprobable outcomes. He can’t have it both ways. Either he models the null properly, or he must cast natural processes as as H1.

    Behe, however does better. He claims that certain features cannot evolve (in other words he actually casts Darwinian evolution as H1). Unfortunately, however, he makes two errors. First of all, he posits a general principle which is easily falsifiable, and has been falsified: that “irreducibly complex” features cannot evolve by Darwinian processes, or, alternatively, by deeply IC pathways (he has presented both). This was famously falsified by Lenski’s AVIDA trials. Secondly, he sets up putative IC structures, and claims they, specifically, cannot have evolved, because they require too many improbable sequence changes to have happened simultaneously. This is simply a mistake. As with his general principle, he forgets drift (and also does not take into account the unknown number of possible comparable features that might have, but did not, evolve to do a similar job). If three genetic changes are required to bring about a reproductive advantage, they do not have to happen simultaneously, and the longer the first hangs around in the gene pool, the more individuals bearing that change there are in whom a second change may occur. So you do not reach an “Edge of Evolution” by multiplying the (im-)probability of each change, because you also have to factor in the probability of each change propagating substantially through the population (which is a bit tricky, but population geneticists can supply the necessary integral equations). And so he does not earn the result to “retain the null” of no Darwinian evolution; and even if he did, that is a weak conclusion, as it only rejects one specific hypothesis; it does not allow him to infer “Design” as the only one remaining.

    In other words, if you believe there is a natural biasing factor at work in Nature which makes Darwinian evolution possible, then please demonstrate its existence, and then we can perform probability calculations.

    A “natural biasing factor” is exactly what Darwin’s “natural selection” is. And we know that it happens because we can actually observe it in real time. But you can’t do probability calculations on it. They won’t demonstrate the truth of Darwinian evolution any more than they will demonstrate the truth of ID. It’s just not the right methodology for this questions.

    What you can do, is the good old tried-and-true method of generating specific hypotheses from your theory, and testing them, and then computing the probability of seeing those observations under your null. Or, using Bayesian stats if you prefer. But you need a specific hypothesis to test. That’s why the one potentially fruitful line of ID research IMO is something like the “front-loading” hypothesis, but it needs a heck of a lot more work. Your own brave attempt is also possible (and possibly related!) – the trouble is that a null finding would not either falsify Darwinism or ID. I can write a non-linear stochastic pattern generator that will produce lovely fractals, no two the same. However, if I store my random inputs, and find one I like, I can reproduce it exactly by specifying those inputs next time instead of drawing from my specified distributions.

    So I can “play God” as it were, and reliably produce the desired pattern, even though it is one perfectly generatable by my original non-linear stochastic pattern generator. There’s no way you could, post hoc, examine my pattern and say whether it was the one generated by the run in which I pre-specified the parameters, knowing what I’d get, and the one originally generated that I happened to like.

    And if God is omniscient, he doesn’t even have to go to the trouble of waiting until the one he likes comes up :)

    In other words – “theistic evolution” is perfectly viable. There’s nothing in Darwin’s theory (or modern evolutionary theory) that is inconsistent with a Designer God. More to the point, Darwin’s theory could explain every detail of every critter that ever lived, and still be “wrong” in the sense that “actually” God foresaw, planned, and intended the whole thing, just like me with my little pattern generator.

    Until then, the default assumption is that there is none. As far as the origin of life is concerned, Dr. Stephen Meyer has argued in Signature in the Cell that the hypothesis of “biochemical predestination” flies in the face of everything we know about DNA. There are no signi?cant differential af?nities between any of thefour bases in DNA and the binding sites along the sugar-phosphate backbone. The same type of N-glycosidic bond occurs between the base and the backboneregardless of which base attaches. All four bases are acceptable; none is chemically favored.

    This is just silly. Unless he thinks that every time a cell divides, or any biochemical process takes place, the molecules are actually being pushed around by little intelligent angels or something. Clearly the biochemistry works, even if where don’t know exactly how. And when we find out, then we will be in a better position to understand the origin of DNA. I mean it’s possible that it will remain forever a mystery, but you can’t infer design from a mystery. That’s argument from ignorance and a fallacy.

    The same logic applies to proteins as well. As Dr. Meyer puts it: “differing chemical af?nities do not explain themultiplicity of amino acid sequences existing in naturally occurring proteinsor the sequential arrangement of amino acids in any particular protein.”

    And my same objection applies.

    We may fairly conclude that at least as far as the origin of life is concerned, Dembski’s assumption that all sequences are equiprobable is a perfectly good null hypothesis.

    But we weren’t talking about OOL! And no, it isn’t a reasonable assumption. In fact one hypothesis is that the very earliest reproductively advantageous sequences were those that contained greater proportions of the more prevalent ingredients. In a soup of mainly carrots, quite a few peas and the odd mushroom, a peptide made mostly of carrots is going to reproduce more often than one made mostly of mushrooms. So it is at least likely that the first Darwinian-capable self-replicators were already a biased sample of the possible compounds floating around the primordial goo.

    OK, that took more time than I meant it to, and I gotta run, so I’m hoping there aren’t too many typos or (worse!) Freudian slips!

    Nice to talk to you as ever

    Lizzie

  181. You have an odd way of phrasing one assumption within another, as in this case you defy countless examples of intelligent arrangement, including your own writing, which is not achieved by examining every possible sequence.

    But that is exactly why I am trying to explain the difference between a language comprised of words and syntax and a language in which each and every utterance is separate and distinct, with no connection to other words or utterances.

    That is what I mean by a language in which there must be a dictionary entry for every possible sentence and paragraph.

    It is the claim of some ID advocates that function is comprised of islands, each of which is irreducible and each of which is isolated from other islands.

    It’s as if we claimed Hamlet is a single irreducible entity having no separable components, no grammar, no syntax, no way of being constructed except as a whole.

    If such were the case, I daresay we would all be mute.

    As I see language, there are numerous ways of expressing functional ideas, and it is possible to rank expressions as to quality. It is possible to say or write things and to revise and refine them.

    In short, statements can be evolved and refined. They can be brief, and brief statements can be expanded and extended. They can include superfluous elements that do not block function but which can be eliminated without harming function.

  182. And then, confronted with the stark reality that people with no experience whatsoever do in fact learn to fold proteins, you retreat to the argument that they won’t get any better at it but the GAs they quickly surpassed will.

    In your “stark reality” can these people distinguish between a sequence that folds and one that doesn’t fold?

    If you take a sequence known to fold and modify a couple of characters and ask them to fold it, what is likely to happen?

    If you give them a random sequence, what is likely to happen?

    These are not rhetorical questions. I don’t know the answers, and I’ll be happy to concede the point if you provide answers I don’t expect.

  183. It’s “complex” in Dembski’s sense, also “specified” in Dembski’s sense, so it has CSI.

    So Dembski’s metric doesn’t work.

  184. Scott:

    You’re absolutely correct. Greater than and less than are just shorthand for the result of a comparison. It does not literally mean that the king is greater than the nine. It means that it is determined as having a higher sort order.

    Good. Let’s see if we can build on this point of agreement.

    But in real life, how do you think that programmers implement this? By specifying a set of rules for the comparison of every card to every other card?

    No, of course not. But the point of this discussion isn’t to identify the best card-sorting implementation, it’s to determine whether your claim is correct: that sorting cannot be done without reference to meaning.

    In most cases, however, this would be accomplished by assigning a numerical value to the card. (It depends entirely on the application.) Jack = 11, Queen = 12, and so forth. And then they are sorted by their numerical values.

    An enumerated type would be even better, with the compiler doing the card-to-number mappings.

    In either case the computer is provided with the sort order.

    Yes, we agree on that.

    The very simple point I’m arguing against is your assertion that a computer can sort cards without some reference to the symbolic meanings given them. It doesn’t matter if the computer calls it a King or assigns an arbitrary identifier to it. It cannot sort the cards without some form of input determining what order they should go in, because the sort order of the cards is not an emergent property of the cards.

    This is the crux of the dispute, Scott, so please pay close attention. You are conflating meaning with sort order. Of course a program needs to know the sort order in order to sort cards correctly. That’s practically a tautology. But the program does not need to know the meaning of the symbols on the cards in order to sort them. As I explained earlier:

    Not only does the program not need to use the comparison operators, it also does not need to designate cards as King or Jack or 7.

    All it needs to do is compare card images, look for the best match, and then apply the kind of sorting algorithm you described.

    For example, if one card matches pattern X, which happens to be an image of the King of Clubs, and another card matches pattern Y, which happens to be an image of the 9 of Clubs, then the card that matches pattern Y goes in front of the card that matches pattern X. Similar logic applies for every possible card pairing. [Note that the sort order is specified: cards matching pattern Y go in front of cards matching pattern X. But the meaning of the symbols in patterns X and Y is not specified, and it doesn't need to be.]

    Note that the program is not “aware” that it’s looking at an image of a card, that the card has symbols on it, that the meaning of one of the symbols is “King”, or that “King” comes after “9?. Yet it still sorts the cards into the correct order, which according to you should be impossible…

    Here’s another example to help you see this. Imagine that a Martian comes to Earth and hires you to implement a card-sorting system for him. He gives you the full set of symbols that can appear on the cards, and he specifies the order into which those symbols should be sorted, but he doesn’t tell you what the symbols represent. They could be numbers, letters, Martian UPC codes, whatever.

    He gives you the sort order (“the squiggle with the horizontal line through it goes before the circle with the dot underneath it”, for example), but he doesn’t explain the significance of the sort order. Is the squiggle less than the circle, or greater than it? You don’t know. In fact, you don’t even know that they are numbers. They could be symbols for the successive monarchs of the Fluborgian dynasty, arranged chronologically. The sort order could even be meaningless — just an arbitrary convention that the Martians follow.

    Yet you can implement the sorting system, even though you (and your program) are clueless about the meanings of the symbols and the significance of the sort order. That is why I take issue with your claim:

    The very simple point I’m arguing against is your assertion that a computer can sort cards without some reference to the symbolic meanings given them.

    The take-home message:
    Sorting can be done purely syntactically, without any reference to meaning.

  185. Scott,

    The illustration of the cards is quite simple and was not meant to be a 20-post diversion into hair-splitting over words.

    It’s not “hair-splitting over words” when the word choice is crucial to the meaning of the sentence and the meaning of the sentence is crucial to the argument being made.

    Take responsibility for what you write, Scott.

  186. If a pattern has CSI (and although I haven’t calculated it, I’m fairly confident that Chesil Beach would come into the rejection region of Dembski’s null distribution), we know that it was not generated by a process that generates a flat distribution of patterns, i.e. in which all patterns are equiprobable (and few processes do). But that does NOT tell you the thing was created by intelligence. We all agree that Chesil Beach wasn’t, and indeed, there are many patterns in geology that exhibit vast amounts of CSI by Dembski’s metric, and no-one argues that they are intelligently designed (except in a remotely deist sort of way).

    Wrong, wrong, wrong- Thajt beach does not fit any example of CSI and there aren’t any examples in geology with CSI.

    You’ll just say anything.

    But then we are back to all the original problems with Explanatory Filter.

    the only “problem” with the EF would be the user.

    The EF tried to separate Chance from Necessity,

    that is false. After the first node necessity and chance are together.

    We know that non-linear natural processes (stochastic or non-stochastic) can produce vastly complex patterns that have all the appearance of design.

    Evidence please.

    And again as for the OoL well that is DIRCTLY linked to any subsequent evolution- if living organisms were designed then they were designed to evolve. Only if living organisms arose from non-living matter via stochastic processes would we infer evolution was entirely stochastic.

  187. Elizabeth (15.1.1.1.3):

    No, the theoretical problem not only hasn’t been disposed of, it hasn’t even been scratched. If you are referring to Ken Miller’s desperate remarks about the flagellum, they are based on a misunderstanding of Behe’s argument (which Behe has repeatedly corrected), and in any case they are entirely inadequate.

    As for your last paragraph, Behe never argued that ‘the event did not occur.’ (You’re confusing Behe with creationists.) He argues that it could not have occurred through Darwinian mechanisms [as he defines them] alone, and that design would be required as a genuine causal factor. (And this where your background in architecture stunningly fails to show up in your writing here; someone trained in architecture, of all people, might be expected to be sensitive to the very strong hints of design in biological systems. But you argue exactly as the design-blind population geneticists do.)

    The theoretical problem has not been overcome until a description has been provided regarding how a strikingly new organ, system, or organism could have been built. This requires proposing a series of hypothetical intermediates and giving a description of their genomes and their form and physiology, and showing how they would be likely to survive and thrive under selection. Population genetics equations tell us absolutely nothing at all about this, and it useless to keep waving them in ID people’s faces. Population genetics tells us how genes are spread throughout a population; it tells us nothing about how critters are built from genetic information and extra-genetic factors. If we ever do learn how a bacterium without a flagellum could evolve into a bacterium with one, it won’t be the population geneticists who show us how.

    I won’t respond to you again about Behe, until you publish a formal refutation of his arguments in a scientific journal or high-end generalist journal or a book. I want to see your reputation as a scientist put on the line, as Behe has put his on the line.

    Tim

  188. 188

    Champignon,

    You’re calling attention to my reference to the ‘meaning’ of the cards in a manner that completely misses the point changes absolutely nothing.

    Of course a program needs to know the sort order in order to sort cards correctly. That’s practically a tautology. But the program does not need to know the meaning of the symbols on the cards in order to sort them.

    When I spoke of the ‘meaning’ of the cards, their relative sort order is exactly what I was referring to. In the context of the discussion I don’t know what other meaning there is that we could be referring to.

    I don’t mind clarifying myself if I choose words carelessly and create confusion. But in this case it’s rather obvious that you get the message that the sort order must be specified. That’s the entire material point. If you didn’t understand what I was saying at all, fine. But you are repeating the message back to me, clearly, while trifling over my choice of words.

    How does what you’re saying change anything material to what I said? It doesn’t. The relative sort order between a king and a jack and a nine is meaning. It is information that is assigned to the card, not emergent from it.

    Therefore it follows that nothing can sort the cards without having the outcome of the comparison of any one card to any other card specified for it in some way.

    Let’s compare that to my very first statement over which you have quibbled.

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them. Natural laws can affect rocks of varying sizes but cannot act upon abstract symbols without some intentional input.

    To know that 5 < 9 < king is to ‘have awareness of the meaning of the symbols’ unless you are predisposed to claw at any possible hair-splitting semantic flaw. Frankly I doubt that anyone not inclined to so nitpick had the slightest trouble understanding the statement as written the very first time.

    Now the point has been stated yet again. How do you propose that anything might sort playing cards without receiving some information relating the image upon it to its sort order?

    I’ve followed through in this discussion, but what a waste of time. I actually find the substance of the debate interesting, so I’d rather not abandon it and trifle over the meaning of words that were pretty clear to start with.

    Such unnecessary trifling only raises an obstacle to meaningful debate. Why would I even attempt to connect this point to yet another knowing that you will ignore the content and feign a lack of comprehension? If drowning out the discussion was your objective, you have succeeded. At this point I’d rather let its bloated corpse float to the surface and drift away.

  189. Scott,

    I wrote:

    In other words, if thinking is a physical process, then the difference between a person who uses one symbol-to-referent mapping and a person who uses a different mapping is simply a difference in brain states. Neither person’s brain states violate the laws of physics; they’re both compatible with natural law.

    You replied:

    I agree that all of it operates within natural law and that none of it violates any laws of physics. Otherwise I would have to think that something bizarre and supernatural occurs every time I imagine a shopping list, write it down, and then go to the store and retrieve the physical items corresponding to my abstraction.

    Good. Another point of agreement.

    You are missing the enormous difference between saying that something is compatible with natural law and that it can be explained by it.

    Here’s where you lose me. On the one hand, you acknowledge that our brains operate strictly according to physical law. On the other hand, you seem to be arguing that when a brain picks an arbitrary mapping of symbols to referents, this somehow can’t be explained by physical law.

    Could you elaborate on what you’re claiming?

    Elsewhere you have pointed out that the laws of nature don’t mandate any single symbol-to-referent mapping. Other mappings are perfectly allowable under natural law. I agree wholeheartedly.

    But you seem to be arguing that if the laws of nature don’t mandate a single mapping, then they can’t explain any particular mapping.

  190. No, the theoretical problem not only hasn’t been disposed of, it hasn’t even been scratched. If you are referring to Ken Miller’s desperate remarks about the flagellum, they are based on a misunderstanding of Behe’s argument (which Behe has repeatedly corrected), and in any case they are entirely inadequate.

    No, I’m referring to a great deal of work that shows that “irreducibly complex” features can evolve by Darwinian (in my sense of the word) mechanisms, and by “irreducibly complex” pathways, the most notable being Lenski’s AVIDA studies.

    As for your last paragraph, Behe never argued that ‘the event did not occur.’ (You’re confusing Behe with creationists.)

    I meant the series of putative Darwinian intermediates.

    He argues that it could not have occurred through Darwinian mechanisms [as he defines them] alone, and that design would be required as a genuine causal factor. (And this where your background in architecture stunningly fails to show up in your writing here; someone trained in architecture, of all people, might be expected to be sensitive to the very strong hints of design in biological systems. But you argue exactly as the design-blind population geneticists do.)

    On the contrary, it is because I know quite a lot about design processes that I would say I understand how natural non-linear stochastic systems are capable designers. They work very much as we do, indeed, our brains are arguably natural non-linear stochastic design systems, with one big extra trick, which is forward modelling. It means we can take shortcuts, and make different kinds of errors.

    The theoretical problem has not been overcome until a description has been provided regarding how a strikingly new organ, system, or organism could have been built. This requires proposing a series of hypothetical intermediates and giving a description of their genomes and their form and physiology, and showing how they would be likely to survive and thrive under selection.

    I agree that Darwinian evolution does not account for a “new organism”. That is an OOL question. However, there are plenty of testable (and tested) hypotheses about how what you call “new” organs or systems” can arise, some of them very specific. We will never know for sure, however, for any one organism, because we simply do not have the data, and never will. What we can do instead is to model scenarios and generate more testable hypotheses. Meantime, it remains invalid to infer “Intelligent Designer” in lieu of a detailed natural explanation.

    Population genetics equations tell us absolutely nothing at all about this, and it useless to keep waving them in ID people’s faces. Population genetics tells us how genes are spread throughout a population; it tells us nothing about how critters are built from genetic information and extra-genetic factors.

    You are right that population genetics tells us nothing about how a phenotype relates to a genotype. For that you need other branches of biology, specifically developmental molecular biology. They are not lacking, and the explosion of GWAS has told us a great deal already.

    If we ever do learn how a bacterium without a flagellum could evolve into a bacterium with one, it won’t be the population geneticists who show us how.

    You are correct, although drift is an important aspect of the process. But you are right. You need biochemists and molecular biologists.

    I won’t respond to you again about Behe, until you publish a formal refutation of his arguments in a scientific journal or high-end generalist journal or a book. I want to see your reputation as a scientist put on the line, as Behe has put his on the line.

    Oh for goodness’ sake.

  191. Wrong, wrong, wrong- Thajt beach does not fit any example of CSI and there aren’t any examples in geology with CSI.

    You’ll just say anything.

    Well, let’s see your calcs, Joe.

    I might have a shot at an approximate answer myself.

  192. 192

    On the other hand, you seem to be arguing that when a brain picks an arbitrary mapping of symbols to referents, this somehow can’t be explained by physical law.

    It’s not just any particular mapping that natural laws do not explain. It is the very concept of relating a symbol to a reality. It is abstraction.

    It’s not that it is impossible for natural law to do so. I can’t declare anything absolutely impossible. (Have I used the word? I don’t recall. I don’t care.) But every abstraction or symbolic code used to functionally represent a physical entity (a functional entity, at that) for which the origin is known is the result of both purpose and forethought – the plan to store information distinctly from what it represents for later use.

    There are no known natural laws that behave in such a manner. Neither are any hypothesized. While insisting that natural laws have done such things, no one has even attempted to speculate on how they might have from any closer than 10,000 feet. The single most compelling reason to believe that it has ever happened is that perhaps someone told you that it did. That’s it.

    If you would have me set aside the observation that, with the exception of one of unknown origin, such arrangements only appear by intent, with what will I replace it? With something never known to have happened and not even an idea as to how it could or would have?

    Designed or not, biological origins are not observable to us. The only observations available to us indicate design. On the other side we have a claim which is supported by not a single observation since the beginning of recorded history.

    There is admittedly not a whole lot of clarity or detail on either side of the scale. But it is something weighed against nothing. What would you place on the other side of the scale?

  193. Scott,

    Your inability to admit error is leading you further into absurdity. You now claim that the sort order of a symbol is its meaning.

    To see how ridiculous that is, consider an imaginary dialogue between us:

    champignon: Scott, here is a list of words: dog, aardvark, cat. Please sort them into alphabetical order.

    Scott: OK. Aardvark, cat, dog.

    champignon: Thank you. What is the meaning of ‘cat’?

    Scott: It comes before ‘dog’.

    champignon: No, I asked for the meaning of cat.

    Scott: I told you. It comes before dog. That’s its meaning.

    champignon: WTF???

    Sort order and meaning are two different things.

    Your statement…

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

    …is just wrong.

    To know that 5 [is less than] 9 [is less than] king is to ‘have awareness of the meaning of the symbols’ unless you are predisposed to claw at any possible hair-splitting semantic flaw. [bracketed phrases needed because of a WordPress bug]

    For the nth time, the program does not need to know that it is looking at a 5 or a 9 or a king. It doesn’t need to know that 5 is less than 9 which is less than a king. All it needs to know is that a card that matches pattern X (which happens to be an image of the 5 of hearts) goes before a card that matches pattern Y (which happens to be an image of the king of hearts). It doesn’t understand that the numeral 5 represents the number 5, it doesn’t recognize the club symbol. Indeed, it doesn’t even know that there are symbols on the cards at all. How can it depend on an “awareness of the meaning of the symbols” if it doesn’t even know that there are symbols on the cards?

  194. Scott,

    It’s not just any particular mapping that natural laws do not explain. It is the very concept of relating a symbol to a reality.

    Relating symbols to referents is something that brains do. You’ve told me that you agree that brains operate according to physical law. If so, then in what sense does physical law fail to explain the mapping?

  195. Yes the Schmidt et al paper is quite interesting, although it renders Sheldrake something of a clock striking thirteen. Someone who repeats as well-established fact something that is clearly not replicated by conscientious researchers (e.g. his claim that telepathy is very common) doesn’t incline me to take anything he says without a very large pinch of salt.

    Schmidt et al found one anomaly though. This could be interesting. It could also be a fraud, and it could also be a result of non-blinding. The way forward would be to find people who do seem to be outliers and invite them to repeat the performance under conditions set out by people without any vested interest in their success (James Randi, for instance). As I said, I don’t rule out the possibility that something interesting is going on, but my priors are low, and the possibilities for false positives, huge.

    Many critics have found Sheldrake’s hypothesis of morphogenetic fields rather nebulous. I don’t think that’s altogether fair: Newton famously feigned no hypotheses about how gravity worked.

    And nobody yet knows. It’s just a law, not a theory.

    A better criticism would be that the notion of a morphogenetic field needs to be described mathematically before it can be said to qualify as a bona fide formal cause of the kind that scientists can investigate.

    Absolutely, it needs to be formulated as a predictive law, like gravity, and tested against data. There is no law, and no test. Sheldrake hand waves.

    By the way, Ken Wilber has an interesting article on Sheldrake’s views, entitled, Sheldrake’s theory of morphogenesis .

    Well, again, I’d have more faith in Wilber if he didn’t start off with a completely untrue set of statements!

    He writes:

    Perhaps the most persistent problem in developmental biology concerns morphogenesis, or the coming into being of form, because the actual form of an organism—its pattern, its shape, its spatiotemporal order—cannot be predicted or even accounted for in terms of its constituent material parts. To give the simplest example: a protein is a long chain of molecules that, based on the properties of the molecules themselves, could easily fold into any number of energetically equivalent forms, and yet, in living systems, they are always found folded in only one way. That is, one form is always selected from numerous equivalent possibilities, and yet, on the basis of mass and energy considerations, no one form should be preferable to any other. The same puzzle is found, a fortiori, in larger and more complex organic systems. No known physical laws can account for the form these systems take. So what does account for it?

    I take it that developmental cell biology isn’t his subject :)

  196. Elizabeth:

    Lenski’s work shows only the most meager results, and nothing that disproves Behe. Behe has followed Lenski’s work all along, and the work of Lenski’s students, and has commented on it regularly. Follow the Discovery web site, and this one, and search on Behe.

    All existing computer simulations of evolution abstract in one or more important ways from real-world situations. See the discussion of Doug Axe et al. in the article on the Stylus genome in the recent issue of Biocomplexity. (Ironically, those trying the hardest to make the simulations more like real-world biology are the ID proponents!) I’m unimpressed by computer models of evolution generally, and do not accept any conclusions drawn from them as valid. They merely provide an excuse for biologists to avoid describing in detail how the evolutionary process occurs in the real world. They mask a sea of ignorance about developmental processes, the function of the unaccounted-for DNA, selectable intermediate forms, etc., under the pretense of doing high-tech, rigorous science loaded up with the jargon of computer science.

    When Darwinists use the phrase “evolutionary algorithm,” which sounds so technical, so mathematical, and so professional, those without much knowledge of computer science retreat in fear and defer to the jargon-user, and the jargon-user’s biological ignorance about how evolution actually occurs goes undetected. But when asked to put into English prose a hypothetical chain of evolutionary intermediates and describe the molecular processes which could have produced each one, the Darwinists, unable to retreat behind weighty-sounding tech-talk, again and again reveal that the Emperor has no clothes.

    When I referred to “new organism” I was not talking about OOL. A whale is a “new organism” in comparison with its putative artiodactyl ancestor. I say that no biologist living can explain how this new organism was produced by Darwinian means. And I don’t mean they are missing a few steps. I mean they are missing virtually all the steps, at both the molecular and physiological levels. Half a dozen fossils that look as if they might be intermediate forms is peanuts compared to the number of transitional forms that would be needed, and in any case no causal story for the transitions at the molecular level accompanies the fossils.

    Your comments on architecture and design show that we mean very different things by both architecture and design. I’ve known architects and they sound nothing at all like you. They show a balance between mathematical/technical intelligence and intuitive/aesthetic intelligence that is missing in your way of reasoning.

    As for my last remark, well, you asked for it. You called Behe’s book “silly.” With all due respect for your generally high intelligence, I honestly think that you are incapable of writing an extended refutation of Behe’s book that would withstand examination from a broad scientific audience (as opposed to the internet subculture of ID/evolution debaters). That’s my challenge. Take it or leave it. I’m indifferent as to what you do.

    I’m sure you feel the urge to do your tribal duty and rush to the defense of Lenski and of computer modelling of evolution. Do as you please; I won’t be responding. Not until that extended refutation of Behe appears in print.

    Adieu.

  197. I’m not sure why you keep telling me you won’t respond, because you mostly do :)

    I do find your manner rather odd.

    Lenski’s work shows only the most meager results, and nothing that disproves Behe. Behe has followed Lenski’s work all along, and the work of Lenski’s students, and has commented on it regularly. Follow the Discovery web site, and this one, and search on Behe.

    Well, I completely disagree. And yes, I have read some of Behe’s counter-rebuttals and found them quite inadequate.

    All existing computer simulations of evolution abstract in one or more important ways from real-world situations.

    That is irrelevant. We were talking about theory. AVIDA directly falsfies Behe’s theory. If Behe’s theory were correct, it should apply in computer models as well as in nature. It doesn’t.

    See the discussion of Doug Axe et al. in the article on the Stylus genome in the recent issue of Biocomplexity. (Ironically, those trying the hardest to make the simulations more like real-world biology are the ID proponents!)

    From as much as I’ve seen this does not appear to be true.

    I’m unimpressed by computer models of evolution generally, and do not accept any conclusions drawn from them as valid. They merely provide an excuse for biologists to avoid describing in detail how the evolutionary process occurs in the real world. They mask a sea of ignorance about developmental processes, the function of the unaccounted-for DNA, selectable intermediate forms, etc., under the pretense of doing high-tech, rigorous science loaded up with the jargon of computer science.

    And that is a blatant moving of goalposts. Behe laid out a theory. That theory was falsified by Lenski. To then come back and say, oh well, I really meant that you couldn’t account for something like a bacterial flagellum, is moving the goalposts. We don’t know whether a bacterial flagellum could have evolved or not, but Behe’s argument that it couldn’t has been falsified. See my response to vjtorley above for more details.

    When Darwinists use the phrase “evolutionary algorithm,” which sounds so technical, so mathematical, and so professional, those without much knowledge of computer science retreat in fear and defer to the jargon-user, and the jargon-user’s biological ignorance about how evolution actually occurs goes undetected.

    Well, that’s a silly reaction. It’s actually a dead simple algorithm, and you can demonstrate it in primary school sunflower-growing experiments.

    But when asked to put into English prose a hypothetical chain of evolutionary intermediates and describe the molecular processes which could have produced each one, the Darwinists, unable to retreat behind weighty-sounding tech-talk, again and again reveal that the Emperor has no clothes.

    Again, goalpost moving. The algorithm is simple. It is demosntrably extremely powerful (which is why it is used so widely to solve engineering problems, and why cognitive scientists use it to model learning, indeed to actually analyse patterns in data). It’s not that mathematical, but if you need an explanation, I’m sure I can give you one in lay language. But to jump from there to the issue of how a specific organism or feature evolved is massive goal-post moving. We do not claim to know how a single feature evolved. We cannot know, because to know that you would have to know not only every actual sequence change (as opposed to proposing one) but every environment in which the population inhabited during the relevant evolutionary period. Nonetheless, as you must know, Pallen and Matske put forward a nice theory for the evolution of the flagellum. I’m not sure if it generated any testable hypotheses (Nick will weigh in I hope, if he is around) or whether they have been tested. But it was a nice model.

    When I referred to “new organism” I was not talking about OOL. A whale is a “new organism” in comparison with its putative artiodactyl ancestor.

    Not really. Or rather, to assert so is to beg the question. The evidence instead suggests that there are no “new organisms” (or perhaps, if Margulis and/or Shapiro are right, very occasional big leaps), but rather that every organism is the offspring of a very similar parent.

    Obviously you may disagree, but you can’t really expect evolutionary theory to account for something that it posits did not occur!

    I say that no biologist living can explain how this new organism was produced by Darwinian means.

    Of course not. Rather, they explain that the “new organism” was no such thing.

    And I don’t mean they are missing a few steps. I mean they are missing virtually all the steps, at both the molecular and physiological levels.

    Well, not really, although clearly for any given transition the data is very much a sampling. But what we have is enough to place organisms on a clear nested hierarchy, and the molecular evidence has remarkable concordance with the morphological evidence, with a few extremely interesting and informative exceptions.

    Half a dozen fossils that look as if they might be intermediate forms is peanuts compared to the number of transitional forms that would be needed, and in any case no causal story for the transitions at the molecular level accompanies the fossils.

    Well, I can only suggest you read up a bit on palaeontology. For a start, all forms are “intermediate” in the sense you seem to be using of the term. Including you.

    Your comments on architecture and design show that we mean very different things by both architecture and design. I’ve known architects and they sound nothing at all like you. They show a balance between mathematical/technical intelligence and intuitive/aesthetic intelligence that is missing in your way of reasoning.

    Well, actually I think you are wrong. Obviously that is just my opinion, but there it is. I don’t claim to be anything special, as I’ve said, but I have reasonably good mathematical and technical intelligence (I was actually rather good at the structural engineering side), and I’m a fairly creative/intuitive artist, I think. Also scientist. That seems to be my strength, I’d say. I’m quite good at looking at things lots of ways round, and thinking up novel ways of analysing data, or indeed hypotheses. But whatever. You are entitled to your impression, of course. My suspicion, though, is that you are misled by your own preconceptions.

    As for my last remark, well, you asked for it. You called Behe’s book “silly.” With all due respect for your generally high intelligence, I honestly think that you are incapable of writing an extended refutation of Behe’s book that would withstand examination from a broad scientific audience (as opposed to the internet subculture of ID/evolution debaters). That’s my challenge. Take it or leave it. I’m indifferent as to what you do.

    Of course I’m not capable of it. I’m no biochemist. However, I do understand evolutionary algorithms, and I’m as capable as anyone at seeing a logical flaw in an argument. But I’m perfectly happy to leave it to those far more expert than me to do the debunking. They are not in short supply.

    I’m sure you feel the urge to do your tribal duty and rush to the defense of Lenski and of computer modelling of evolution. Do as you please; I won’t be responding. Not until that extended refutation of Behe appears in print.

    Now, really, Timaeus, this is too much. “Tribal duty” indeed.

    harrumph.

    That is just about the rudest thing anyone has ever said to me, and goes a long way to explaining why you think so little of my architectural abilities. If you are dismissing my posts as the outpourings of a “tribalist” then I’m not sure why you are even bothering to respond to them.

    I have my faults, but tribalism isn’t one of them. Again, I can’t prove it, but you’ve got me wrong. More seriously, jumping to the conclusion that those who disagree with you are merely defending their “tribe” is a sure way to ensure that you don’t actually learn anything.

    I don’t treat other people that way, and I don’t expect to be treated that way.

    So perhaps this time you really had better not respond. If you do, I shall have a large gin before I click on the link.

    *in high dudgeon*

    Lizzie

  198. Eigenstate (8.1.1.2.2):

    Thanks for the frank exchange. I’m not sure where to start.

    You write throughout your post as if there is some kind of war between ID and something you call “science.” This is the “warfare view” that pits “science” against “religion,” with the new twist that ID is now cast as the representative of “religion.” The warfare view of science and religion has been discredited among serious historians of science for decades. It survives only in popular culture and among those academics and scientists who read no history.

    Beyond this general point, warfare against science is a complete misrepresentation of the intentions of all the intellectually serious ID people. ID’s whole point is the ID/Darwinism conflict must be understood as science vs. science, not science vs. religion. What we have is two different groups of scientists and admirers of science, each interpreting nature differently. We have Dawkins, telling us that design in biological systems is only apparent design, and Behe, telling us it is real design. Both have Ph.D.s. Both have written dozens of peer-reviewed papers and/or scientific books. Both teach/have taught at secular universities (not Bible colleges or denominational colleges). What we have is two scientists who disagree about the implications of protein science, of irreducibly complex systems, etc.

    Behe never appeals to the Bible in any of his arguments; he cites only scientific literature. You can agree or disagree with Behe, but you can’t honestly find “science versus religion” in his writing. The same is true of design proponents such as Sternberg and Denton. There is no appeal to the Bible or theology in any of their writings. They write articles for peer-reviewed journals, and they study the scientific literature, and they criticize existing evolutionary theory on scientific grounds. The same is true of Axe, Gauger and others. There is no attack upon science from the point of view of religion here. There is only an attack on the neo-Darwinian conception of evolutionary change.

    This is true even of the ID proponents who are also creationists. Dembski and Wells, in their Design of Life book, make zero use of the Bible or the theological tradition. Meyer does not argue from the Bible in Signature in the Cell. Wells does not argue from it in his new book on junk DNA. I’ve never seen Nelson dismiss a scientific argument on the basis of the Bible.

    In short, I know of no place where ID makes any “religious” argument against “science.”

    I don’t know what to make of some of your remarks about politeness and respect. I see that you agree with me that politeness is a good thing in itself. You also make a point, which I accept, that politeness is no substitute for good science, good reasoning, etc. Who could disagree with that? But other parts of what you are saying, I’m having trouble following. Let me clarify my position: I wasn’t saying that anyone should seek being respected by UD commenters as a valuable goal in itself. I wasn’t suggesting that they should sacrifice self-respect in order to be thought of highly. I was saying:

    (1) You can firmly disagree with ID without being rude, obnoxious, stubborn, dogmatic, manipulative, deliberately misrepresenting people’s arguments, refusing to accept corrections when direct quotations stare you in the face,
    etc. Physicist Stephen Barr and evolutionary biologist H. Allen Orr disagree with ID, and they are gentlemen. Myers and Shallit and Moran disagree with ID, and they are Neanderthals. (I wouldn’t put Matzke in the
    same group as the Neanderthals. Matzke is generally polite. But he is incredibly stubborn and closed-minded when it comes to ID.)

    (2) It isn’t important to gain the respect of *everyone* in the opposing camp; it is important to gain the respect of *the most moderate and thoughtful members* of the opposing camp — if you hope to ever persuade them to your point of view. If *those* people think you are rude, or vulgar, or ideological, or stubborn, or condescending, or unfair in
    argument, or intellectually dishonest, or too proud to ever grant a point to them, you have lost the only potential converts that you have. So, for example, I couldn’t care less if I have the respect of Shallit or Myers;
    they are thugs, and I don’t care what thugs think of me. But I would be very glad to have the respect of H. Allen Orr or Stephen Barr or John Polkinghorne or any of the
    more thoughtful and reflective champions of Darwinian ideas. Precisely because they are thoughtful, there is hope of winning them over to ID, or at least of showing them that ID is a serious intellectual position, not
    religious fundamentalism.

    I’m not really interested in going over all the vagaries of the disputes of the various UD commenters you’ve mentioned. I don’t know the history of when each of them was banned, disciplined, put on moderation, etc. If you
    are harking back to four or five years ago, remember that the two head honchos who did most of the bannings back then are no longer here.

    I don’t think Myers has any redeeming qualities. I think he is an embarrassment to his university and that his manners and his ideological orientation to knowledge disgrace the very title Doctor of Philosophy (Ph.D.) He represents the vulgarization of the American professoriate more than anyone else I can think of, and his occupation of a professor’s chair is evidence of the decline of Western Civilization. If he is one of your role models for evolution/ID discussion, you and I are not going to see eye to eye.

  199. Elizabeth:

    Make that gin a double. It’s going to get worse. :-)

    You’re far too easily offended by a little verbal jousting. I said “tribal” with a friendly elbow and a wink. And even if I had meant it aggressively, ID proponents are accused of being things 100 times worse than “tribal” every day. And I haven’t seen you jumping in, here or elsewhere, to say that those denigrations and demonizations are inappropriate.

    As for much of the rest of your post, where you restate your knowledge in this or that area, I’m well aware that you have a high estimation of your own abilities — an estimation which applies, as far as I can tell from your words, not only to the only biological fields in which you have degrees and publications (neuroscience and psychology, I believe), but to evolutionary biology and many other areas of the life sciences and other sciences where you have neither degrees nor publications, but are mainly an autodidact.

    I am quite happy to acknowledge that you are a bright autodidact. I think you have a fine mind. But you can’t expect me to take seriously your claim to judge between Behe and Lenski, when both of them have spent many more years studying the relevant material than you have. Behe has three degrees in the life sciences as opposed to your one, and more than 35 peer-reviewed publications, outside of his work on ID. He reads the literature on Lenski and related material assiduously. You cannot possibly have read as much of this literature as Behe has — not if you are keeping up with your research and teaching obligations in neuroscience and psychology. So there is no reason for me or anyone else to assume that your decision for Lenski and against Behe is well-grounded. (Especially when I strongly suspect that you have misinterpreted what Behe means by “Darwinian” because of your minimalist definition of that term, which we have recently established.)

    As far as what you say about evolutionary algorithms, I would not trust it as far as I could throw it. Dembski and Marks have been researching and publishing (and in the case of Marks, teaching) in this area for 10 years, and you don’t have a peer-reviewed article in the field at all. You’re making an amateur judgment. You’ve never written a computer program that models biological evolution, or if you have, you’ve never submitted it to the scientific world for criticism. You know a *bit* about evolutionary biology and a *bit* about computer science, but you have degrees in neither. To do evolutionary algorithms *properly* one needs a lot of knowledge in both fields. That’s not a description of either your formal education or your research record, unless you are hiding something from us. Sorry to be blunt, but it’s true.

    This is not a personal attack. I find you a pleasant, friendly person, much more likeable than 99% of the internet Darwinists I deal with. And as I’ve said, I find you bright. You’re also quite a diverse and interesting person. But I also find you scientifically pretentious, as if you see yourself as a sort of modern Renaissance man, able to comment on a high level on almost anything that has anything to do with science generally and on almost anything in the life sciences in particular. I wish you would stop standing in judgment and rendering verdicts. It is this which bothers me, not that you disagree with me, or that you criticize ID, or anything like that.

    Finally, to be frank, it puts me off that you claim to be such a good research scientist, but spend so much time blogging. I’ve known many good scientists. A good research scientist is passionately committed to the life of research, and it occupies a huge proportion of the scientist’s time. In addition, scientists who are university teachers should be passionately committed to students, both in the classroom and after hours in the office and in grading and commenting constructively on their work in the office or at home. I think it is irresponsible for anyone to take a salary for teaching and research and spend more than a few hours a week wrangling about evolution on the internet. You could produce three or four scientific articles per year with the time you spend on internet debates with non-scientists and half-scientists. I don’t think serious scientists should be doing that. You don’t see top evolutionary biologists like Allen Orr, Sean Carroll, Eva Jablonka, etc. blogging and debating to the extent that you do. And those scientists who *do* blog and debate extensively — well, check out their record of recent publications in their fields, and compare it with their output before they ventured into culture-war polemics.

    Go ahead, tell me to mind my own business, but I have strong feelings about the duties of university faculty, and I think you are misusing your time. This is part of the cause of the friction you are feeling from me. I know many very fine scientists and scholars who, despite sterling academic records and substantial publications, never got university positions, and would kill to get one, and, if they got one, would never fritter away so much potential research time for the joys of internet blood sport.

    I say all of this because you have obviously detected that there is more in my posts than merely scientific disagreement. We have a basic disagreement in attitude, and I wanted to get that out in the open. If, given my feelings, you don’t want me to respond to your posts again, I will respect your wishes by not doing so. But I wanted you to see that my somewhat forceful responses to you are not arbitrary, but have a basis, and what that basis is.

    I continue to think of you personally in a friendly manner, despite my obvious criticisms of your debating habits and activities.

    T.

  200. @Timaeus#18,

    You write throughout your post as if there is some kind of war between ID and something you call “science.” This is the “warfare view” that pits “science” against “religion,” with the new twist that ID is now cast as the representative of “religion.” The warfare view of science and religion has been discredited among serious historians of science for decades. It survives only in popular culture and among those academics and scientists who read no history.

    I’m not suggesting that is a necessary condition; I was a Christian for decades, and for most of that a theistic evolutionist. While I no longer believe that’s a position that’s warranted or supported by the evidence around us, at the same time having spent much time and effort in that position, I understand that some forms of religion can be and are highly compatible with modern science, “overlays” that are careful to yield to and integrate scientific knowledge, and which provide metaphysical explanations and other meta-narratives that are beyond the epistemic reach of science. Young Earth Creationism cannot harmonize with science, in other words, but careful forms of theistic evolution can.

    In any case, that’s not my offering here. I’m thinking about the realpolitik of the debate in places like this blog. It really would be noble and interesting if ID were to offer a serious challenge to current science in such a way that progress could be made on the evidence, models, predictions, empirical tests — science is a powerful, peaceful, and robust way to settle disputes and competing conjectures. People with clashing ideas can honorably agree to “let the numbers tell the tale”, and “let the evidence from empirical tests decide”. I don’t see that as negating or nullifying all religion, and know that some religious frameworks can “wrap around” science without incurring fatal contradictions or self-falsification in doing so.

    But here, this is pure culture war, alas. I can, and many other critics have more ably than I, press for application of models, precise and operational definitions of terms, etc. But a review over years of posts here shows that such efforts just have to stand as futile attempts to engage. The IDers here won’t/can’t participate at that level.

    That said, I can tip my hat to Genomicus, who I see as making an earnest attempt at providing scientific predictions for his particular take on ID. The predictions as he has presented them are problematic, for reasons I detailed in my responses to him, but that should not diminish my appreciation of an earnest effort to “do the right thing” on this blog, where such is so rare.

    Beyond this general point, warfare against science is a complete misrepresentation of the intentions of all the intellectually serious ID people. ID’s whole point is the ID/Darwinism conflict must be understood as science vs. science, not science vs. religion. What we have is two different groups of scientists and admirers of science, each interpreting nature differently. We have Dawkins, telling us that design in biological systems is only apparent design, and Behe, telling us it is real design. Both have Ph.D.s. Both have written dozens of peer-reviewed papers and/or scientific books. Both teach/have taught at secular universities (not Bible colleges or denominational colleges). What we have is two scientists who disagree about the implications of protein science, of irreducibly complex systems, etc.

    Well, this is tough going, addressing this question. I do think there are intellectually serious ID people, but they are not the people I’ve seen you identify. A profound insight available from this blog (now a bit faded into past years, but still valid) is just how UNSERIOUS Bill Dembski is an an ID thinker. The “intellectual” offerings from Dembski are best understood to be just cynical tools of a shamed culture warrior, a man who personifies what the French would call the politics of ressentiment.

    Stephen Meyer has serious intellectual chops, I’ll grant. Dembski’s not any near in his class. I know you admire Meyer, and can see reasons for that, even from my point of view, but at the end of the day, Meyer is “lying for Jesus”, even (and especially) when he never mentions Jesus (thinking of Signature in the Cell, here, for example). Not only is the argument specious and self-serving in gerrymandering around the competition that his ideas really face from mainstream science (and of which he surely is aware), it’s extra unserious in that just adds baroque ornamentation to a profoundly unserious impulse — the God-of-the-Gaps reflex.

    Just by way of laying my cards on the table, that’s Meyer in “high horsepower” mode, advocating for intuition and superstition. I understand you (or others, if not you) will find that a form of “seriousness”, and I’m fine agreeing to disagree on that.

    Behe never appeals to the Bible in any of his arguments; he cites only scientific literature. You can agree or disagree with Behe, but you can’t honestly find “science versus religion” in his writing. The same is true of design proponents such as Sternberg and Denton. There is no appeal to the Bible or theology in any of their writings. They write articles for peer-reviewed journals, and they study the scientific literature, and they criticize existing evolutionary theory on scientific grounds. The same is true of Axe, Gauger and others. There is no attack upon science from the point of view of religion here. There is only an attack on the neo-Darwinian conception of evolutionary change.

    I agree with you on Behe and “science vs. religion” in his writing. I’ve read Darwin’s Black Box a couple times through now, but I’ve not read Edge of Evolution, so I’m fine stipulating that, but can only speak from reading the first book of his.

    And as for Axe, Gauger, Behe, Abel, et al, I have no problem with, or little problem — Sternberg’s goof was a kind of ‘religious sin’ as an editor, but I will concede your point, broadly speaking. I don’t see that as part of the ID movement, though. I am fully aware that ID partisans are eager to “penetrate” the peer reviewed literature for the intellectual currency that may afford them, so there will be cases like Biological Society of Washington where excepts to good practices occur, but generally, if ID thinkers can get their work through the healthy functioning turnstyles of respected secular journals, more power to ‘em. That’s just science at that point.

    The ID movement, and particularly this blog, is the “negative field” on background to anything like that. Just as a quick example, if Douglas Axe gets a major published this year that shows some failure in massive tests of E. Coli to evolve as predicted, that is what it is, scientifically, and more power to him. But there is a predictable and stark logic fail that will happen once Uncommon Descent gets wind of that: the failures, or changes needed for evolutionary theory don’t help Intelligent Design at all. Axe’s work may (this is all hypothetical, of course) dislodge some beam in the current theory. Scientifically, this is of no help to Intelligent Design; ID doesn’t win anything by forfeit or default. That’s not how science works.

    But that is how Uncommon Descent works. I understand various noises are made by the more thoughtful ID partisans of a science-ish nature. But if we did an audit of the last posts here in the last 3 years, the evidence would be overwhelming in support of the hypothesis that ID-at-UD is all about taking down evolution, and perceived fellow demons: materialism, socialism, neuroscience and heavy metal music. It’s not a serious claim to suggest this blog is about a scientific case FOR anything at all, intelligent design or otherwise. Axe’s (hypothetical) breakthrough would be celebrated as a major win for ID here, because the ethos here is not intellectually serious, but is just politically radioactive as part of the culture war between secular scientific and Supernatural Designer factions.

    This is true even of the ID proponents who are also creationists. Dembski and Wells, in their Design of Life book, make zero use of the Bible or the theological tradition. Meyer does not argue from the Bible in Signature in the Cell. Wells does not argue from it in his new book on junk DNA. I’ve never seen Nelson dismiss a scientific argument on the basis of the Bible.

    I have no trouble affirming all of that, and will go one further and stipulate that all of these men make a paragraph like that a “design objective” for their works.

    In short, I know of no place where ID makes any “religious” argument against “science.”

    This is not said as any kind of joke, but in all seriousness: you cannot say that with a straight face after reading this blog for more than a day or two.

    This is where it’s good to point out the basis for using the term “intelligent design creationism”. Not only is it apt on the merits — the designer/front loader satisfies the criteria for the “creator” for the vast majority of its subscribers — but importantly, ID uses the same “sciency mumbo jumbo” methods as the streams of creationism it sprang from. Paul Nelson can give the faithful plenty of sciency-sounding jargon that helps dissipate the cognitive dissonance of the religious believers. See? Science really does support my Christian faith! Is my God an awesome God or what???

    This is a path Henry Morris plowed for ID, and Ken Ham after him. The faithful *aren’t* critical or skeptical, and so “Meyer quality” sciency stuff, which I grant is WAY, WAY more sophisticated that the stuff Henry Morris pioneered this trope with, just gets a visceral, credulous acceptance. We have CSI now! The sign of intelligence, doncha know!

    This is apologetics in action. It needn’t say “God did it”. The audience already believes that, even if they are struggling at some level with the dissonance brought on by secular science. All they need is “jury nullification”, and that is what Meyer and Nelson and Behe provide. They are confronted by a “scientific jury” that discredits their superstitions. Meyer doesn’t need to mention Jesus or superstitions ONCE. All he has to do is nullify (in the eyes of the faithful) mainstream science, in sciency terms.

    That is the foundation of creationism, the apologetic basis for creation science, and now, here, intelligent design.

    More later, thanks for the feedback. I’m shocked at your last response to Dr. Liddle, and happy to continue, overall, but feel sheepish about this in light of such a childish reaction on your part to her, demanding she get a paper published in refutation of Behe (really? Did I really read that from you?) before you’ll deign to respond. I’ll chalk it up to momentary lapse of reason. But I do note that that bit of acting is the very kind of thing I understand to be beneath of all this, dialectically, here. You were doing a decent job of being a counterexample, but have nicely fit into my hypothesis, there. I’d rather have the counterexample confronting me, and you corresponding like a grown-up to Dr. Liddle, though. You are in very small company as an IDer in that regard, as it is.

  201. @Timaeus#18,

    I don’t know what to make of some of your remarks about politeness and respect. I see that you agree with me that politeness is a good thing in itself. You also make a point, which I accept, that politeness is no substitute for good science, good reasoning, etc. Who could disagree with that? But other parts of what you are saying, I’m having trouble following. Let me clarify my position: I wasn’t saying that anyone should seek being respected by UD commenters as a valuable goal in itself. I wasn’t suggesting that they should sacrifice self-respect in order to be thought of highly. I was saying:

    OK, I like this paragraph!

    (1) You can firmly disagree with ID without being rude, obnoxious, stubborn, dogmatic, manipulative, deliberately misrepresenting people’s arguments, refusing to accept corrections when direct quotations stare you in the face,
    etc. Physicist Stephen Barr and evolutionary biologist H. Allen Orr disagree with ID, and they are gentlemen. Myers and Shallit and Moran disagree with ID, and they are Neanderthals. (I wouldn’t put Matzke in the
    same group as the Neanderthals. Matzke is generally polite. But he is incredibly stubborn and closed-minded when it comes to ID.)

    I understand. I think the “elephant in the room” is that there is a line crossed where the “other side” (or possibly both, I guess) is not dealing in good faith. For example, Wells’ Icons is a “textbook case” of bad-faith apologetics, dishonest dealing on the subject of evolution. It’s not a matter of being just wrong on the merits; that really is not such a problem, and science doesn’t go anywhere if thinkers are not venturing hypotheses and models that are wrong, and sometimes spectacularly wrong. Rather, Wells is pulling a con-job, and it’s not hard to spot, or even to demonstrate, given you can get an audience that will listen long enough to digest the debunking of that work. Politeness is a worthy goal, but Wells is scoundrel, and debases the whole enterprise of science by bringing in the kind of malign polemics and cheap misdirections he does in his book.

    Being polite, as good as that is, is just playing the chump to Wells.

    Just by way of contrast, I think Michael Behe’s works are problematic, but have no problem understanding that Behe proceeds in good faith for the most part. His “defenses” routinely signal “goal post moving” to me, but even if that’s true, that’s a guy who deserves politeness and comity in engaging him, even if he’s thoroughly mistaken. I just point this out as a means of demonstrating that it’s not *intrinsic* to ID advocacy. Mike Gene is another example of a “good faith” ID proponent, even as I so strongly disagree with his (her?) ideas. William Dembski isn’t quite as bad as Wells, but he’s in the same “bad faith” tier. Not intellectually serious, earnest, accountable. And proud of it, to boot! “FU, mainstream science who has scorned me!.

    Ressentiment

    (2) It isn’t important to gain the respect of *everyone* in the opposing camp; it is important to gain the respect of *the most moderate and thoughtful members* of the opposing camp — if you hope to ever persuade them to your point of view.

    I can get behind this idea, for the most part. Uncommon Descent is, by far, the most cynical blog I’ve encountered in this respect, though. Or rather, the “pro-IDers” here are so thoroughly immoderate, and unthoughtful, and just plain ignorant [SERIOUSLY: elsewhere, right now, BA77 is defending the idea that evolution is a violation of the Second Law of Thermodynamics. Even worse, not ONE pro-IDer, who BA77 might listen to just a little bit, as opposed any critics who reply to him, has taken the opportunity to mitigate this kind of embarrassment… this gets pounced on to stop the humilation at young earth creationist forums, by YECs).

    That’s a generalization, and generalizations are necessarily false, to some degree, or they are not generalizations. But in many years of “touring” creationist/religious/fundamentalist sites on the web, this one has the most conspicuous dearth of moderate, thoughtful IDers to engage. It’s not a mystery, but an entirely predictable product of the choices Dembski made to manage and moderate this blog. It’s the “Free Republic Principle”, where the partisans in charge discourage moderation (“No Romney!”) and exalt immoderation and “red meat” partisanship (I could have used “Democratic Underground Principle”, too, I know, as that’s not just a right wing phenomenon, but the current “biorhythms” of American politics has the right wing in “frothing” mode right now).

    If *those* people think you are rude, or vulgar, or ideological, or stubborn, or condescending, or unfair in
    argument, or intellectually dishonest, or too proud to ever grant a point to them, you have lost the only potential converts that you have. So, for example, I couldn’t care less if I have the respect of Shallit or Myers;
    they are thugs, and I don’t care what thugs think of me.

    Right. I get that, truly. We can be on opposite sides, and both appreciate the symmetry of that sentiment, the “cuts both ways” dynamic. That’s pretty much the rub, though. Myers is more responsible and grown up than kairosfocus, though, and I don’t need to diminish the offenses of PZ to say that. Shallitt has way more respect for science, philosophy, inquiry, and intellectual discipline than Gil Dodgen does, and that stands, in my view, even being fully aware of Shallitt’s boorishness, etc.

    I would say you are the counterexample, if I had to name one here. You don’t have much competition, unfortunately, and as I said above, I can see the “spirit of kairosfocus” peeking out around the edges of your last couple posts to Dr. Liddle. I think I well may be seeing Timaeus conform to the culture that’s fostered here, and soon. I hope not.

    But I would be very glad to have the respect of H. Allen Orr or Stephen Barr or John Polkinghorne or any of the
    more thoughtful and reflective champions of Darwinian ideas. Precisely because they are thoughtful, there is hope of winning them over to ID, or at least of showing them that ID is a serious intellectual position, not
    religious fundamentalism.

    Understand and agree! I will insist on a key asymmetry here, though. PZ Myers, for all his “uncouthness”, can deliver, intellectually, when he wants to, or needs to. He’s a heavy-weight, or a heft medium-weight when it counts to the difficult work of intellectual performance and knowledge building. Dembski is a con man, though, a lightweight, a poser. He makes lots of social blunders, too, I note, but he doesn’t have the redeeming substance of actually being able to deliver where it really counts. That’s not a hard rule for ID advocates, as I said above. There are ID advocates who are serious, thoughtful, deserving of respectful dialog and discourse, even if I/we disagree vehemently on the merits of the argument. Uncommon Descent just doesn’t attract, seek or develop that. It’s an intellectual ghetto here, a place for the scorned and dissonance-discomfited to get a shot in the arm for their superstitions. That is Dembski’s legacy, here, a heritage of ressentiment.

    I’m not really interested in going over all the vagaries of the disputes of the various UD commenters you’ve mentioned. I don’t know the history of when each of them was banned, disciplined, put on moderation, etc. If you
    are harking back to four or five years ago, remember that the two head honchos who did most of the bannings back then are no longer here.

    I understand. The harsh truth is UD was better off under the management of DaveScot. That’s a damning realization if there ever was one. It’s way more “ghetto” now than it was then, intellectually. Dave was obnoxious and capricious, but could at least follow what he was reading, and just had a huge ego rather than the kind of pompous narcissism that controls the knobs here. vjtorley seems a decent guy, I have to point out, an exception to the rule. Fair’s fair.

    I don’t think Myers has any redeeming qualities. I think he is an embarrassment to his university and that his manners and his ideological orientation to knowledge disgrace the very title Doctor of Philosophy (Ph.D.) He represents the vulgarization of the American professoriate more than anyone else I can think of, and his occupation of a professor’s chair is evidence of the decline of Western Civilization. If he is one of your role models for evolution/ID discussion, you and I are not going to see eye to eye.
    OK, I understand, and I do disagree. I don’t think the science CAN be vulgarized or debased AS science, no matter how many Eucharist wafers Myers profanes. The science is what it is, and stands on its own. I don’t countenance antics like PZ’s wafer shenanigans, but that really is a trifle, a faux pas compared to the sustained and deliberate campaigns of debasing science and knowledge building waged by people like Dembski, Wells, and Meyers.

    Those are value judgments, I know. And I’m fine with clarity on each of our different value choices as the outcome of this.

  202. Very elegantly and cogently put, Eigenstate.

  203. Eigenstate:

    Thanks for your articulate and educated reply. Your earlier comments were quite aggressive, and I did not see the thoughtfulness underneath them until your latest recasting. I appreciate the effort.

    I can agree with most of what you say, though not always with the way you are framing things.

    You seem to be disappointed that UD does not live up to the standards that ID proclaims. Well, so am I. I think there is too much evolution-bashing here, and too much culture-war flak. (From all sides, not just the ID side.) But you are asking the impossible of an institution like this.

    Anyone can post comments on UD. We have people here with everything from Ph.D.s in biology down to high school diplomas in nothing in particular. Some people posting here know biology but not computer science; others know computer science but not biology. Some are scientists, some lawyers, some writers, some housewives. Some are undergraduates, some are retired professors. Some have read every book by every major ID proponent, some have read only a few blogs and bits of Behe or Johnson. Some are Christians, some Jews, some agnostic, some Deist, some devotees of Eastern religion. Of the Christians, some are Catholic and some fundamentalist.

    There is no entrance exam for being even a columnist on UD, let alone a commenter. You don’t have to prove you know anything about population genetics or computer programming or probability theory or even that you have read any of the books you are arguing vehemently for or against. The place is a free-for-all, where great knowledge and insight are mixed up with ignorance, stupidity, bluffing, and political agendas. And that applies to all camps who write here, not just the ID people.

    Compare this with, say, a scientific journal, where certain standards have to be met before an article is published, or an academic conference of scientists or scholars, where papers have to be accepted beforehand, and, when they are debated after being read, must be debated relevantly and politely, with no long digressions on people’s pet peeves.

    Or with a place like The Discovery Institute, which selects its Fellows according to its own criteria, and therefore can achieve some focus in its program, not trying to encompass every idiosyncratic viewpoint that one might hold on design and evolution.

    You can get a coherent ideal form of ID if you distill the highest and noblest claims of its most thoughtful advocates (whether they are housed at Discovery or elsewhere). You cannot expect that in a free-for-all, everyone is going to exemplify the ideal form of ID.

    This is true on every single blog site on the internet. I don’t think that Pharyngula or Panda’s Thumb or TalkOrigins come even close to exemplifying the gracious, gentlemanly habits of doing science that were practiced by Darwin and the folks of his age. Those places are filled with polemics, unfair arguments, cheap shots, literature bluffs, ad hominem remarks, mischaracterizations of one’s opponent, etc. All the very opposite of the spirit in which Darwin wrote The Origin of Species. So what should we do, throw out the theory of evolution because half the posters at those sites are bluffing, cocky, arrogant a–holes? And if you wouldn’t do that, why would you throw out ID, just because so many commenters on UD fail to live up to the noble ideal of ID science held out by Behe, etc.

    I would love it if this place, and all the sites I just mentioned, and Biologos, and other sites would all agree to just debate the science and the methods of science (with reference to the history and philsophy of science) and eschew all the culture-war business. But that isn’t going to happen. It’s like wishing that people all over the world would renounce war or that all religions or ethnic groups would agree to live harmony starting tomorrow.

    If anyone wants to read some “pure” ID, not tainted by all the culture-war business, I have already suggested how to find it. I gave a list of basic writings to Petrushka. In those writings there is no culture-war flak. There are scientific arguments. They may be good or bad, useful or useless. But they are what ID is about. (There are some columnists here also who do a fair job of presenting the core ideas of ID. I think a discerning reader can tell which ones, by the tone, the orderly presentation, the respect for empirical science, and the genuine concern for understanding nature that underlies the writing.)

    If anyone finds the presentation of ID here belligerent, confused, or ideological, they have two options:

    (1) Find the reasonable, moderate people here, whether columnists or commenters, who appear to have actually read ID writings carefully, and argue only with them, ignoring all the rest;

    (2) Forget about this place, and engage the actual ID leaders in debate.

    By (2) I don’t mean by “engaging” that some smart-ass grad student in say, virology (to choose a subject at random), should write a letter to Behe, saying “How can you publish such sophomore crap as science?” I mean entering upon a respectful conversation. This could be done privately with individual ID proponents who work in a field that one knows (e.g. biochemistry, computer science). It could be done, occasionally, through Discovery (see the politie Dembski/Shapiro/Axe/Gauger conversation there). It could be also be done in various media, e.g., Huffington Post, First Things, Scientific American, etc., if critics of ID would publish reviews of ID jobs that are not deliberate hatchet jobs, but constructively critical; the critics would find that the leading ID people would respond very positively to critics who gave them some credit for intelligence and honesty instead of treating them as scientific incompetents and liars.

    You made a remark about this statement:

    “In short, I know of no place where ID makes any “religious” argument against “science.” ”

    You said that I could not say that with a straight face in light of what is written on this site. But I said ID, not UD. By ID I mean the general argument for design, not the cultural activities of any people who happen to be defending ID at the moment. ID *per se* has no religious argument at all. ID proponents quite often do; but when they do this, they speak as lone wolves, not for ID as a theory.

    I think you are being less than charitable or even fair in your imputations of motives to Dembski, Nelson, Meyer, etc. I think imputing motives is a very difficult thing to carry off successfully. It’s better to focus on the argument.

    I’m not sure what else to say. I cannot speak for anyone else here but myself. I’m not management, just a guest like you. I disagree with some positions taken by UD columnists. I disagree with some positions taken by ID commenters here. But I’m not going to abandon ID for that, any more than someone would abandon a political party whose goals they supported because they didn’t like a couple of planks in the platform, and than someone would abandon his family because it contained a black sheep or two. I think that ID as a position is defensible. Not flawless — there isn’t an ID book I don’t have some criticism of, and I like some ID leaders’ position better than others’. But I think the position is defensible. And I think that the classic neo-Darwinian position has gaping weaknesses. What else can I do, but what I’m doing? Move over to Panda’s Thumb, and be personally reviled? Move over to Biologos, and be told I support bad science and heretical theology? Start my own blog, maybe, and get very little traffic to hear my ideas? I’m open to suggestions.

    My dispute with Elizabeth has a long history. I have corresponded with her for months now, and most of the time, I think, like a grown-up, as you put it. I have never refused to debate any of her points. The particular statement you objected to may have seemed like grandstanding, but that wasn’t its intention. I was responding to her (non-grown-up, in my opinion) denigration of Behe’s book as “silly” and challenging her to back up that claim to Behe and the scientific public rather than me and UD. I’ve since written a follow-up post which makes my motives more explicit. You can like it or hate it, but my differences with Elizabeth spring largely from personal style and have nothing at all to do with the nuts and bolts of ID. But any further discussion of this matter I will have with Elizabeth herself; or, if she so instructs me, I will leave off criticizing her in the future. But that has nothing to do with you and me. It’s up to you whether to continue on this thread.

    I hope I’ve listened and granted you all I can. If I don’t hear back, maybe we will meet on some other thread.

  204. Timaeus,

    Judging by the tone of your response, I could almost swear you’re a sock for Dr^3 Dembski.

  205. “This is not a personal attack.”

    Really?

    Timaeus, have you ever published in Nature? Have you ever gotten a top notch grant, or tenure at a R1 university? Then you have no right to critique anything Lenski writes. Or me, for that matter. So shut up. That is the tone of your post.

    Your entire post is a diatribe against one person who posts here, largely based on some (likely fictitious) claim to authority.

    Most interesting to me is the line that her time is to valuable to post here…which implies the other denizens of this blog who spend far more time posting tens of thousands of words at once…have time, perhaps not as valuable as hers? Are they useful idiots to you?

  206. @Timaeus#21,

    You seem to be disappointed that UD does not live up to the standards that ID proclaims. Well, so am I. I think there is too much evolution-bashing here, and too much culture-war flak. (From all sides, not just the ID side.) But you are asking the impossible of an institution like this.

    I agree, as it’s constituted and run. It didn’t have to be this way. Much of what you see here are just the natural consequences of the choices management has made. And really, for what the management is hungry for, UD is actually pretty successful (from their PoV), I think.

    Anyone can post comments on UD. We have people here with everything from Ph.D.s in biology down to high school diplomas in nothing in particular. Some people posting here know biology but not computer science; others know computer science but not biology. Some are scientists, some lawyers, some writers, some housewives. Some are undergraduates, some are retired professors. Some have read every book by every major ID proponent, some have read only a few blogs and bits of Behe or Johnson. Some are Christians, some Jews, some agnostic, some Deist, some devotees of Eastern religion. Of the Christians, some are Catholic and some fundamentalist.

    Understood. The management bears the responsibility, here, though. As much as I may shudder at the posting habits of the more trollish posters (hey Joe!), they are just the playing pieces on the board. This blog is designed to be what it is. Look at who edits and manages this blog. There is no other explanation for those choices than to effect just what you see and lament, here. Joe’s a device. So is kairosfocus, just like Denyse or DaveScot, implements toward a desired solution. The latter are just “official” devices.

    There is no entrance exam for being even a columnist on UD, let alone a commenter. You don’t have to prove you know anything about population genetics or computer programming or probability theory or even that you have read any of the books you are arguing vehemently for or against. The place is a free-for-all, where great knowledge and insight are mixed up with ignorance, stupidity, bluffing, and political agendas. And that applies to all camps who write here, not just the ID people.

    Again, the restaurant will necessarily reflect the choices and priorities of the management. You get the clientele and behavior you design for with those choices. Look at Telic Thoughts. Two stark contrasts are easily identified: 1) the pro-ID mods and management have some measure of responsibility in policing trolls, on BOTH sides, and 2) the mods and management actually make earnest efforts to LEAD, and promote edifying discussion.

    They can’t control what people say (beyond mod/censor capabilities). But they can set good examples, and people notice that and respect that and follow that. At UD, some of the worst offenders are the ones running the joint. There’s really no way to sugar-coat the realization that this blog is largely RUN by trolls. Again, there are exceptions, which I appreciate, but it bears comparison even with some of the more feverish young earth creationist forums: there, you get some crazy stuff and really bad behavior, but the “leading trolls” are not typically the people with the keys to the admin dashboard.

    Compare this with, say, a scientific journal, where certain standards have to be met before an article is published, or an academic conference of scientists or scholars, where papers have to be accepted beforehand, and, when they are debated after being read, must be debated relevantly and politely, with no long digressions on people’s pet peeves.

    Indeed. I understand this and agree with the comparison you are drawing. I just think you are overlooking the corrosive role of the management in the case of UD. Lots of “free-for-all” blogs are not like this.

    This is true on every single blog site on the internet. I don’t think that Pharyngula or Panda’s Thumb or TalkOrigins come even close to exemplifying the gracious, gentlemanly habits of doing science that were practiced by Darwin and the folks of his age. Those places are filled with polemics, unfair arguments, cheap shots, literature bluffs, ad hominem remarks, mischaracterizations of one’s opponent, etc. All the very opposite of the spirit in which Darwin wrote The Origin of Species. So what should we do, throw out the theory of evolution because half the posters at those sites are bluffing, cocky, arrogant a–holes? And if you wouldn’t do that, why would you throw out ID, just because so many commenters on UD fail to live up to the noble ideal of ID science held out by Behe, etc.

    I think we will “agree on symmetry” in the sense we both see the other side as being more problematic than our own. But I maintain that Panda’s Thumb, even if I stipulate a kind of “troll parity” (and I do not agree with that as a fact of the matter, just a hypothetical) with UD, still has both the authors/management and the “supporters” engaging in substantive intellectual discourse that UD just doesn’t provide, and not nearly so.

    I anticipate you won’t agree, but that is a stark asymmetry I identify.

    I would love it if this place, and all the sites I just mentioned, and Biologos, and other sites would all agree to just debate the science and the methods of science (with reference to the history and philosophy of science) and eschew all the culture-war business. But that isn’t going to happen. It’s like wishing that people all over the world would renounce war or that all religions or ethnic groups would agree to live harmony starting tomorrow.

    Perhaps. But this is one of those situations where “deliberate naïveté” and suspension of rational cynicism is in order. If we — you, me, other readers of good will here — don’t take it upon ourselves to focus on substance (doing the math, applying the models, giving precise definitions to our terms, assessing results objectively, etc.), then we really can’t complain about anyone else. I’m not naïve enough to think I can change any of this myself, but this is where “bottom up” works. Just police our own area, each of us, and that is a good thing. It can scale!

    If anyone wants to read some “pure” ID, not tainted by all the culture-war business, I have already suggested how to find it. I gave a list of basic writings to Petrushka. In those writings there is no culture-war flak. There are scientific arguments. They may be good or bad, useful or useless. But they are what ID is about. (There are some columnists here also who do a fair job of presenting the core ideas of ID. I think a discerning reader can tell which ones, by the tone, the orderly presentation, the respect for empirical science, and the genuine concern for understanding nature that underlies the writing.)

    OK, I do remember you offered a list, but if I recall correctly, you had Stephen Meyer AND Denton on it (apologies if I’m confusing your list with someone else’s). If so, I think we are at loggerheads, I’m afraid. Lauding Meyer’s decorum is to miss the big, bad problems in Signature in the Cell. It’s all the more problematic since by virtue of his obvious skills and eduction, he should know better than just about anyone to avoid doing what he does. I know we’ve covered that a bit… just sayin’.

    I don’t doubt that other books on your list fit nicely into what you are saying about being the “best of ID”, or “pure ID”, however. I’ll go have a look.

    Continued anon…

  207. @Timaeus#21,

    If anyone finds the presentation of ID here belligerent, confused, or ideological, they have two options:

    (1) Find the reasonable, moderate people here, whether columnists or commenters, who appear to have actually read ID writings carefully, and argue only with them, ignoring all the rest;

    (2) Forget about this place, and engage the actual ID leaders in debate.

    Those are two options, but not the only ones. There’s a pretty noble tradition (from my perspective) that’s evolved on this blog, over time, from the critics’ side. Because of UD’s self-serving and hypocritical “moderation” policies, critics who are high-powered intellectually, expert in relevant areas of discussion, and willing to speak up, will eventually get banned. It doesn’t matter how careful they are about tone or decorum. It’s the criticism itself that the management will not brook from a single, persistent critic over time.

    This has created a “stream” of critics, who do not (so far as I can tell) seek out the moderates and responsible IDers, here (neither do they avoid them, though), but instead just go to bat for rigorous scientific thinking. That’s not option (1) or (2), but it’s a pretty cool phenomenon. Paradoxically, that has made Uncommon Descent a much more valuable resource against creationism than TalkOrigins ever was. Some of the long threads where “Nakashima” really got into a groove, for example, are really extraordinarily good resources on these issues.

    The (3) option just uses the IDers as a foil (with good will available for those IDers who DO want to engage and debate on points). The UD grinders make an EXCELLENT backdrop for the case against ID, or at least the culture-war, vulgar sectors of the ID movement. I encourage all me friends to read UD regularly, it’s an effective “missionary outpost” for both science and atheism.

    And you don’t need to take that as particularly one-sided from me. If you go look up some of the ‘mega-threads’ that Nakashima and Diffaxial and ROb participated in, there ARE some pretty good representation from the other side, at points. It’s hard for me to point to other places on the internet where such “get down on it” debates really work themselves on out on ID-related issues, at length. Again, the paradox: UD is really valuable that way.

    In spite of itself, though!

    By (2) I don’t mean by “engaging” that some smart-ass grad student in say, virology (to choose a subject at random), should write a letter to Behe, saying “How can you publish such sophomore crap as science?” I mean entering upon a respectful conversation. This could be done privately with individual ID proponents who work in a field that one knows (e.g. biochemistry, computer science). It could be done, occasionally, through Discovery (see the politie Dembski/Shapiro/Axe/Gauger conversation there). It could be also be done in various media, e.g., Huffington Post, First Things, Scientific American, etc., if critics of ID would publish reviews of ID jobs that are not deliberate hatchet jobs, but constructively critical; the critics would find that the leading ID people would respond very positively to critics who gave them some credit for intelligence and honesty instead of treating them as scientific incompetents and liars.

    I hear you, and understand the problem. I think there’s more “constructive criticism” out there than you think, and account for that delta by supposing that much of that constructive criticism does come with varying degrees of derision towards the ID proponents. That is not to excuse unwarranted derision, but sometimes, the derision is deserved, too. Either way, though, understand that ID, thanks is part to this very blog and our gracious host Dr. Dembski, has a badly damaged brand. It’s a fallacy to dismiss an ID proposal just because it comes under the auspices of a damaged brand, but let’s not kid ourselves about the expectations. It’s something IDers are going to have to expect to overcome.

    There is much constructive criticism to work with, if you don’t dismiss anything that comes ALSO with a sneer outright. It’s unfair at points, no doubt, but if you really ARE motived by the substance, you have a lot to work with if you can just get over the sneer. I have a lot of experience with this myself as a vocal atheist. In my family/community/circle of peers, there are lots of challenges that come from a theistic perspective. But it’s part and parcel of those contexts that they come wrapped in all manner of derision, bile, and outright hatred. I don’t like that anymore than you would, but I do claim to be interested in the substance, and so, letting that stuff just run right off my back is what works toward my goals.

    You made a remark about this statement:

    “In short, I know of no place where ID makes any “religious” argument against “science.” ”

    You said that I could not say that with a straight face in light of what is written on this site. But I said ID, not UD. By ID I mean the general argument for design, not the cultural activities of any people who happen to be defending ID at the moment. ID *per se* has no religious argument at all. ID proponents quite often do; but when they do this, they speak as lone wolves, not for ID as a theory.

    Fair enough, I accept that as an effective clarification away from my reaction.

    I don’t see any scientific argument for design in ANY of ID, and I claim to have looked, watched, read, searched. I don’t count arguments that “win by default” as a positive or scientific argument for ID, however, so I suspect that is why we will disagree on whether ID has an authentically scientific framework to advance. I don’t doubt that many suppose that design IS scientifically discoverable/determinable, but to date, nothing has gotten beyond a casual, informal, intuitive conviction along these lines. There are lots of examples to cite in support of this claim on this blog.

    I think you are being less than charitable or even fair in your imputations of motives to Dembski, Nelson, Meyer, etc. I think imputing motives is a very difficult thing to carry off successfully. It’s better to focus on the argument.

    I agree, in principle. But at some point, the consilience is just compelling in terms of the fraud. I don’t have to know Wells’ “heart” to understand his Icons to be an egregious crime against scientific thinking and good scholarship. Perhaps Wells is just stupendously incompetent or gullible. That’s an option, I guess. But one can’t look at that in a sober way and not see both the motive and the manifestation of a deliberate hack job. For the record, that happens from the science side, too. It just doesn’t tend to get the “leading minds of the movement” traction that Wells, for example, does. And also for the record, for all of Wells’ troubles, I don’t see all ID advocates as being similarly problematic. Behe’s mistaken, I think, but he’s not a con-man like Wells. That’s to Behe’s credit and Wells’ demerit. Every case is a different case.

    I’m not sure what else to say. I cannot speak for anyone else here but myself. I’m not management, just a guest like you. I disagree with some positions taken by UD columnists. I disagree with some positions taken by ID commenters here. But I’m not going to abandon ID for that, any more than someone would abandon a political party whose goals they supported because they didn’t like a couple of planks in the platform, and than someone would abandon his family because it contained a black sheep or two. I think that ID as a position is defensible. Not flawless — there isn’t an ID book I don’t have some criticism of, and I like some ID leaders’ position better than others’. But I think the position is defensible. And I think that the classic neo-Darwinian position has gaping weaknesses. What else can I do, but what I’m doing? Move over to Panda’s Thumb, and be personally reviled? Move over to Biologos, and be told I support bad science and heretical theology? Start my own blog, maybe, and get very little traffic to hear my ideas? I’m open to suggestions.

    I don’t have any magic wands to wave, here, unfortunately. But I can salute what I see as an earnest appeal to high-minded principles here from you, thanks. I won’t hold back on criticizing where I think it’s deserved. I also don’t want to overlook moments where good principles and good will are put into action. Kudos!

    If you are an earnest ID proponent (and I don’t doubt you are, now), you have a really remarkable opportunity. It should speak loudly to you that all this huffing and puffing here at UD about the scientific gravitas of ID is conspicuously missing application, actual development, or putting-to-the-test. If your understanding is right, there really are profound breakthroughs to be made along the path you are thinking.

    I don’t think the enterprise gets off the ground, at all. But it’s not a settled matter. If you are “the real deal”, it’s wide open, man. Get to really pushing the frontiers of ID as a serious, scientific, intellectual enterprise. You don’t have much competition. And you don’t have to be the “Newton of Information Theory”. Just making small, but real advances on the intellectual frontiers of ID would be highly interesting for everybody, and super gratifying for you!

    My dispute with Elizabeth has a long history. I have corresponded with her for months now, and most of the time, I think, like a grown-up, as you put it. I have never refused to debate any of her points. The particular statement you objected to may have seemed like grandstanding, but that wasn’t its intention. I was responding to her (non-grown-up, in my opinion) denigration of Behe’s book as “silly” and challenging her to back up that claim to Behe and the scientific public rather than me and UD. I’ve since written a follow-up post which makes my motives more explicit. You can like it or hate it, but my differences with Elizabeth spring largely from personal style and have nothing at all to do with the nuts and bolts of ID. But any further discussion of this matter I will have with Elizabeth herself; or, if she so instructs me, I will leave off criticizing her in the future. But that has nothing to do with you and me. It’s up to you whether to continue on this thread.

    I don’t know the back story, you’re right. It seemed quite incongruous, though. I had gone to read your exchange with aiguy_again (which was worthwhile, thanks to both!), and that snark toward Dr. Little just was quite a juxtaposition.

    But really, best to just cruise right by all that melodrama, and focus on the big concepts and issues. Do the math! So that’s is correction I can accept for myself, and can see my own contributions to the snark there, myself. Sorry.

    Plus, Dr. Liddle is more than able to take care of her own affairs. She doesn’t need the likes of me butting in, there.

    Thanks!

  208. Timaeus:

    No gin this morning, a stiff cup of coffee will have to do the trick.

    You’re far too easily offended by a little verbal jousting. I said “tribal” with a friendly elbow and a wink. And even if I had meant it aggressively, ID proponents are accused of being things 100 times worse than “tribal” every day. And I haven’t seen you jumping in, here or elsewhere, to say that those denigrations and demonizations are inappropriate.

    So the verb conjugates: “I joust; you are far too easily offended”, right? You didn’t suspect a little levity in my response? My “high dudgeon”? My gin tipple? At at least my joust was at my own expense, not yours. Seriously: no, my responses are not “tribal”. The reason I love science is because it’s the place where argument and evidence trump, in principle at least, tribal loyalties. It’s not perfect, but it’s the principle, and the incentives to overturn consensus are far greater than the incentives to prop it up. I remained a theist for half a century not out of tribal loyalty (indeed a changed tribes several times) but out of convictions, and abandoned it despite undoubted feelings of loyalty (and indeed grief) when I found myself persuaded by alternative arguments. So no, I am not tribal. And I repeat: if you dismiss as “tribal” posts that you disagree with you risk massively missing the points being made. As in this case.

    As for much of the rest of your post, where you restate your knowledge in this or that area, I’m well aware that you have a high estimation of your own abilities — an estimation which applies, as far as I can tell from your words, not only to the only biological fields in which you have degrees and publications (neuroscience and psychology, I believe), but to evolutionary biology and many other areas of the life sciences and other sciences where you have neither degrees nor publications, but are mainly an autodidact.

    No, I don’t have a particularly high estimation of my own abilities, but as you keep challenging my competence, I will respond with what I think is a fair and honest estimate. For some bizarre reason you seem to regard willingness to opine on the internet as some indicator of self-esteem, in my case but not in others. Why me? And what is so odd about it anyway? It’s not as though (as I’ve said many times) you can argue from authority on the internet anyway. If you disagree with me, make your argument. Simply accusing me of lacking the authority to hold my opinions is a cop-out, and irrelevant, seeing as I don’t claim that authority. I can’t. For all you know I might be a spotty eighteen year old in his mum’s basement.

    I am quite happy to acknowledge that you are a bright autodidact. I think you have a fine mind.

    Well, gee thanks.

    But you can’t expect me to take seriously your claim to judge between Behe and Lenski, when both of them have spent many more years studying the relevant material than you have. Behe has three degrees in the life sciences as opposed to your one, and more than 35 peer-reviewed publications, outside of his work on ID. He reads the literature on Lenski and related material assiduously. You cannot possibly have read as much of this literature as Behe has — not if you are keeping up with your research and teaching obligations in neuroscience and psychology. So there is no reason for me or anyone else to assume that your decision for Lenski and against Behe is well-grounded. (Especially when I strongly suspect that you have misinterpreted what Behe means by “Darwinian” because of your minimalist definition of that term, which we have recently established.)

    Yes, I can expect you to take it seriously. Not because I have credentials or authority, but because I am making an argument. If you disagree with it, post your rebuttal.

    If you are not competent to disagree with it, and must choose between me and Behe, then by all means choose Behe, but be aware that you are not selecting the better argument, but selecting the more credentialed exponent. Moreoever, examine your criteria when choosing between Behe and Lenski. Both are excellently credentialled – why choose Behe? Unless you are competent to critique both? And if you are competent to critique both, why not critique me?

    There’s nothing wrong with deferring to authority in fields in which one is not competent to judge. But it seems odd to argue that your opponent must be wrong because she lacks authority, if so. If you aren’t competent to judge, fine, but that’s your problem, not mine.

    As far as what you say about evolutionary algorithms, I would not trust it as far as I could throw it. Dembski and Marks have been researching and publishing (and in the case of Marks, teaching) in this area for 10 years, and you don’t have a peer-reviewed article in the field at all. You’re making an amateur judgment. You’ve never written a computer program that models biological evolution, or if you have, you’ve never submitted it to the scientific world for criticism. You know a *bit* about evolutionary biology and a *bit* about computer science, but you have degrees in neither. To do evolutionary algorithms *properly* one needs a lot of knowledge in both fields. That’s not a description of either your formal education or your research record, unless you are hiding something from us. Sorry to be blunt, but it’s true.

    How do you know it’s true? Because someone with lots of credentials told you? Don’t you see the problem here? Instead of tackling my arguments you are shooting at my (alleged) lack of expertise. About which you know, for sure, nothing. If I’ve said something wrong about evolutionary algorithms, point it out. But if all you are claiming is that I don’t have the credentials to know about evolutionary arguments, then your rebuttal is, simply, a fallacious argument from authority. And if you are arguing from authority, then please explain why Lenski, who clearly is adequately credentialed, is wrong, and Behe is right.

    As it happens I do write evolutionary algorithms, and have had one simple learning model published. But that is entirely irrelevant to my argument. My argument is, simply, that Behe claimed that either Irreducibly Complex functions(i.e. features that would fail to function if any part were removed) could not evolve by means of random variation and natural selection or that features could not evolve by deeply Irreducibly Complex pathways (quantified by the number of non-advantageous steps between the last advantageous step and the function in question). Lenski showed that neither of these claims were true, by demonstrating in a model which used random variation and natural selection to evolve, from a starting population of virtual organisms that could do nothing except reproduce, Irreducibly Complex functions (that would break if you removed any one part) by deeply Irreduciably Complex pathways (pathways that involved many non-advantageous steps and some substantially deleterious ones). In other words, he falsified Behe’s theory.

    This is not a personal attack. I find you a pleasant, friendly person, much more likeable than 99% of the internet Darwinists I deal with. And as I’ve said, I find you bright. You’re also quite a diverse and interesting person. But I also find you scientifically pretentious, as if you see yourself as a sort of modern Renaissance man, able to comment on a high level on almost anything that has anything to do with science generally and on almost anything in the life sciences in particular.

    Are you suggesting that anyone who comments on any field outside their own area of expertise is a “pretender”? How about Dembski, then, who has made a career out of inferring Design from biological structures without so much as a undergraduate degree in biology?

    Is it some kind of pretentious offense to form an opinion on anything in which you are not qualified, and express it? If so, how does anyone come to a view on either Intelligent Design or anything else (Darwinian evolution?) without higher degrees in biological sciences?

    I fully confess to being a bit of an intellectual magpie. I love science, and always have, despite having spent most of my life in the arts. I’m a jack-of-all-trades and master of none. I’m not especially proud of it, but it’s the way I seem to be built. I’m obviously smart enough to get a degree or two, but so are lots of people. I pretend nothing. And if I express an opinion, I expect it to be critiqued, not for me to be lambasted for lacking an authority I do not (indeed explicitly do not) claim.

    I wish you would stop standing in judgment and rendering verdicts. It is this which bothers me, not that you disagree with me, or that you criticize ID, or anything like that.

    I see someone standing in judgement and delivering verdicts here, Timaeus, and it isn’t me. I respectfully submit that you may be looking in the mirror. Whatever, what you are seeing is not what I am doing.

    Finally, to be frank, it puts me off that you claim to be such a good research scientist, but spend so much time blogging. I’ve known many good scientists. A good research scientist is passionately committed to the life of research, and it occupies a huge proportion of the scientist’s time. In addition, scientists who are university teachers should be passionately committed to students, both in the classroom and after hours in the office and in grading and commenting constructively on their work in the office or at home. I think it is irresponsible for anyone to take a salary for teaching and research and spend more than a few hours a week wrangling about evolution on the internet. You could produce three or four scientific articles per year with the time you spend on internet debates with non-scientists and half-scientists. I don’t think serious scientists should be doing that. You don’t see top evolutionary biologists like Allen Orr, Sean Carroll, Eva Jablonka, etc. blogging and debating to the extent that you do. And those scientists who *do* blog and debate extensively — well, check out their record of recent publications in their fields, and compare it with their output before they ventured into culture-war polemics.

    I’m sure I do spend too much time blogging. I certainly don’t spend enough time washing the dishes.

    Go ahead, tell me to mind my own business, but I have strong feelings about the duties of university faculty, and I think you are misusing your time. This is part of the cause of the friction you are feeling from me. I know many very fine scientists and scholars who, despite sterling academic records and substantial publications, never got university positions, and would kill to get one, and, if they got one, would never fritter away so much potential research time for the joys of internet blood sport.

    I say all of this because you have obviously detected that there is more in my posts than merely scientific disagreement. We have a basic disagreement in attitude, and I wanted to get that out in the open. If, given my feelings, you don’t want me to respond to your posts again, I will respect your wishes by not doing so. But I wanted you to see that my somewhat forceful responses to you are not arbitrary, but have a basis, and what that basis is.

    Yes, I will tell you to mind your own business (as I did once before). You are extrapolating beyond the range of your data. However, I am tickled by the spectacle of someone wasting time on the internet getting annoyed at someone else for wasting time on the internet, so I’ll forgive you.

    I continue to think of you personally in a friendly manner, despite my obvious criticisms of your debating habits and activities.

    Can I go now, sir?

  209. Elizabeth, just out of curiosity, what were these “alternative arguments” that persuaded you against theism and towards atheism?
    I’d be interested to hear your reasons.

  210. Just three points, Timaeus, on your interesting response to eigenstate:

    There is no entrance exam for being even a columnist on UD, let alone a commenter. You don’t have to prove you know anything about population genetics or computer programming or probability theory or even that you have read any of the books you are arguing vehemently for or against. The place is a free-for-all, where great knowledge and insight are mixed up with ignorance, stupidity, bluffing, and political agendas. And that applies to all camps who write here, not just the ID people.

    Exactly. And unlike Eigenstate, I think UD is far better than it was in this regard, in that dissenting views seem much more likely to be retained on the site, if not always welcomed! More to the point, this is why I like the internet – because credentials are not required, and anyone can say what they think and have the argument critiqued on its merits. That is the very point I was trying to make to you in my earlier response.

    By (2) I don’t mean by “engaging” that some smart-ass grad student in say, virology (to choose a subject at random), should write a letter to Behe, saying “How can you publish such sophomore crap as science?” I mean entering upon a respectful conversation.

    I take it you are thinking of Abbie Smith. She is indeed a smart-ass graduate student, and a feisty lady, but if you think that her argument with Behe amounts to “How can you publish such sophomore crap as science?” you were cut off at the pass by her rude words, and your credentialism. Her argument was substantive and devastating to Behe, and I have not seen an adequate response. It’s a shame that her style gave Behe an excuse to ignore the substance, but substance there most certainly was.

    My dispute with Elizabeth has a long history. I have corresponded with her for months now, and most of the time, I think, like a grown-up, as you put it. I have never refused to debate any of her points.

    Actually, I think you have. For some reason I get up your nose (and I understand, it happens) and as a result, it seems, all your responses to me have been about credentials and style, not substance. I’d be delighted to respond to substantive criticism of my actual arguments.

    But being told repeatedly that you will not respond to me (despite the fact that you do!) unless I am prepared to publish my critiques in some peer-reviewed journal (despite the fact that most peer-reviewed journals are simply not interested in critiques of non-peer-reviewed science), does, well, get up my nose.

    So let’s either declare a truce, or ignore each other from henceforth eh?

    Ball’s in your court.

    Peace

    Lizzie

  211. Well, it’s a long story, and the final jump turned out to be a very small one, but a world-rocking one nonetheless.

    Essentially it was the perception that the Hard Problem of Consciousness wasn’t actually Hard at all.

    In some ways, I retain my old theology, I just lost the “McGuffin” if you like. And my old theology was remarkably orthodox, in the sense that it was that of a theologian I very much respect, although he did not publish much in his lifetime (but I was privileged to hear many of his Sunday sermons), Herbert McCabe.

    Although in some ways, I may be even closer to McCabe’s view than I was then (he was a vigorous non-dualist) – just minus the McGuffin :)

  212. @Elizabeth 17.1.2.2.2
    Oh, okay. Thanks. Though Im not farmiliar with the term mcguffin. I googled it but i still dont understand what you mean by it.
    In any case, I wouldnt object to the possibility that we are nothing but brains since theism doesnt require any commitment to cartesian dualism and i dont see any conflict either way.

  213. Sorry!

    A McGuffin is a plot element that the narrative is hung on, but isn’t, in itself, important; what is important is the narrative itself.

    So to put it less telegraphically: a Creator God was the plot element I hung my theological narrative on, which included the idea that God is love, God is good, to do right is to do what an all-good, all-just God would require, that God is inspires us to do what is right, yet forgives us when we fail, and various other fairly orthodox attributes of God, including the idea that to give your life for your friends is the highest act of love, and that our duty and our joy is to love our neighbours as ourselves.

    Then I realised you didn’t need to have the Creator God part. Nor indeed the immortal soul part. The narrative still works.

  214. No, Elizabeth, you are wrong. That beach is in no way an example of CSI- you don’t know what you are talking about.

    As I said both CSI and the EF are only as good as the user.

  215. Bald assertion, Joe.

    Please calculate for me the CSI of that beach, and demonstrate that it falls below the UBP cutoff.

    And show your work :)

  216. Nothing to calculate. As I said you don’t know what you are talking about.

  217. What calcs, Liz?

  218. What, CSI isn’t calculable? It’s not a metric? Have you told Dembski about this?

  219. The CSI calcs.

    The equation is here:

    http://www.designinference.com.....cation.pdf

    The beach is 28 k long, and 160 m wide, and the stones are graded from pea size at the west end to fist size at the east end.

    If we assume a depth of shingle of about 400mm, and a standard deviation at any one point of 1 mm, that should be conservative, and allow us to calculate the number of permutations.

    I’ll post my answer if you post yours.

    See you at the finish :)

  220. CSI can be measured and it is a metric.

    You need to make a case that a calculation/ measurement is required and then you need to tell us why CSI would be the correct tool to use when dealing with your examples.

  221. Yup and you would use a hammer to tune a piano.

    The beach is 28 k long, and 160 m wide, and the stones are graded from pea size at the west end to fist size at the east end.

    Have you been there? Have you thoroughly investigated the site?

  222. Yes I have. It’s awesome.

    Here’s a webpage about it:

    http://www.chesilbeach.org/Chesil/

  223. Well, I’ve just discovered part of the problem:

    The Lenski I am talking about is the Lenski who has been growing bacteria in test tubes for the past 20 or 30 years and recording his results.

    The Lenski you are talking about is this one:

    “Lenski showed that neither of these claims were true, by demonstrating in a model which used random variation and natural selection to evolve, from a starting population of virtual organisms that could do nothing except reproduce,”

    Huh? “Virtual organisms?” I’m scratching my head. Bacteria reproducing in test tubes are not “virtual organisms.” Are we talking about the same Lenski?

    Either Lenski conducted two different kinds of investigations, one with computer models and virtual organisms, and one with real bacteria, or we are talking about two different Lenskis.

    If it is the former, I don’t ever recall Behe mentioning the part about virtual organisms. If Behe did discuss Lenski’s work on virtual organisms and I didn’t catch it, I apologize to you for misreading Behe and then being angry with you because of my misreading. If Behe didn’t, now you know that we were talking at cross purposes.

    My point was that none of the bacteria produced by Lenski destroyed Behe’s argument. The changes that Lenski did observe were mostly trivial, and even the changes that were non-trivial were still relatively small and well within what Behe’s argument would expect of Darwinian processes. Behe doesn’t argue that Darwinian processes can do *nothing* (indeed, he is less hard on them than Margulis is); he just thinks they can’t do the heavy lifting claimed for them.

    Whether any Lenski computer simulation using virtual organisms destroyed Behe’s argument, I cannot say, because I simply don’t know what computer simulation you are talking about.

    All of my objections to you about Lenski were based on my assumption that you were talking about the bacteria grown in the test tubes. As far as I know, bacteriology isn’t your field, so I couldn’t understand how you could be qualified to judge how much change in these critters would falsify Behe’s arguments.

    I have no idea what programming a “learning model” means. A model of *what* learning *what*? Of autistic children learning to count? Of adults learning a foreign language? Of rats learning how to select the door with the cheese? I can think of all kinds of “learning models” which wouldn’t have anything to do with the operation of biological evolution, even if “learning” is used in a broad sense which completely removes the subjective element I associate with the word.

    Is this “learning model” you have written published on-line? And if so, where? And if not, what journal is it in? (I presume, given your understanding of peer review, that you would never publish it in a book!) What volume and number and pages?

    As for the rest, maybe I’m getting old and cranky, but my attitude has changed from that of a couple of years ago. I used to enjoy the idea of “combat by proxy,” where the hobbyist disciples of ID people and the hobbyist disciples of the Darwinians would wage battle on the internet. I no longer do. Far too often, on both sides, the hobbyist disciples don’t get the arguments of their masters right, or haven’t even read them carefully. Far too often, the two sides can’t even agree on terms, like “Darwinian” or “learning” or “intelligence” or “intervention.” And of course, pseudonymity allows for irresponsible behavior on all sides. And finally, for the most part, the targets of all the debating — Miller and Ayala and Behe and Dembski and Wells and Denton and Sternberg — aren’t even reading what is said about them or their books on these blogs.

    I’d rather see direct criticism of the big players, written by people who use their real names, and published in places that have some literary and scientific standards (though not necessarily peer-reviewed academic journals). And I’d like to see the criticism substantiated by equations, diagrams, lab results, etc., produced by the critic, not regurgitated from the work of other researchers, or worse, from other blog sites. And I’d like to see the big boys (Miller, Behe, Dawkins, Dembski, etc.) reply to such criticisms.

    This is why I’m thinking of abandoning all internet conversations such as this. It’s a sink hole for time, and it produces no critical work that will ever be taken note of outside a circle of a few thousand hobbyists around the world. I’m not sure that all the debating on TalkOrigins, Biologos and here, in the long run, contributes anything to scientific knowledge, or amounts to anything more than a huge debate between Stooge fans about whether Shemp or Curly is superior.

    Twice now you have made the suggestion that you might not be the person you are representing yourself to be. I don’t mind pseudonymity — people have to protect themselves, especially ID people, who, unlike atheist Darwinists and theistic evolutionists, have lost jobs and careers in secular universities for their views. But I don’t like misrepresentation. If you *are* just a spotty teenager, or anything other than the professor with your name who has a web site at a British university, I’d like you to declare it now. I’m not asking you to divulge your real identity if you are someone else, but just to say if you are or are not the 59-year-old professor described on the web site. Obviously if you are not that professor, much of my criticism is misplaced, though I would not apologize for it, since I was deliberately misled by a false identity. If you are that professor, however, I stand by what I said. The field of that professor is such that the amount of time you are spending here and elsewhere debating evolutionary biology on the internet is in my opinion incompatible with doing a responsible job in the academic position for which a full-time salary is being paid. And now you can tell me to mind my own business for a third time. It’s the last time you’ll have to tell me.

    Yes, you may go now. I’m going, too.

    T.

  224. Elizabeth:

    I wasn’t initially thinking about anyone in particular, but it seems to me that Abbie Smith would be a good example of the generic case that I was talking about. And since you have raised her case, I will comment. You are missing the main point about the exchange between her and Behe. The main point is that her public behavior *did not warrant the dignity of a reply*. It would *not* be tolerated in any peer-reviewed journal, at any scientific conference, etc. (And “feisty” is not the word for her behavior; “obnoxious” is. Nor did her behavior warrant the term “lady,” for that matter.) By replying to an *enfant terrible*, one encourages *enfant terrible* behavior. That was why Behe was right not to reply to her for so long. In the end, he relented, and replied to her, but only because his friends urged him to, lest anyone should suppose he was unable to answer. That doesn’t change the fact that, in terms of the dignity of scientific culture, she wasn’t entitled to an answer until she first apologized to a man who was her senior both in age and in scientific accomplishment. If you disagree with me on this, we have very different ideas about how scientific culture and academic culture should operate, how students (including clever graduate students) should treat professors, and how younger people should treat older people. I won’t debate this, any more than I would debate the rightness of cannibalism or slavery.

    I do not know whether you have read Behe’s reply to Abbie Smith or not. If you have not, you should be able to find it here on UD, in the cache of Behe’s replies (formerly on Amazon) to his *Edge of Evolution* critics. I read both her criticism and Behe’s reply. (And of course I read the book thoroughly before reading either.)

    I don’t claim to be competent in virology, but it certainly didn’t seem to me that her critique was “devastating,” especially since, if you have read *The Edge of Evolution* (and you have admitted that you haven’t), Behe spent far less time discussing viruses (which was her field) than discussing malaria (which was his). He could be entirely wrong about viruses, and the main argument of the book could still be correct.

    How you could be sure that a reply to a book which you have not read is “devastating” is beyond me. I guess that Arts and Science people think differently. In the Arts we are expected to have read the books that we condemn, not to dismiss them on the basis of someone else’s criticism. I thought it was the same in Science, but perhaps I am misinformed. Please do instruct me on how scientists feel about secondhand dismissals.

    It is ridiculous for you to say, “all your responses to me have been about credentials and style, not substance.” You and I have debated for months now, and only recently have I focused on credentials and style. Before that, we discussed at length specific ideas of Behe, Shapiro, Margulis, etc., specific positions of various school boards and the NCSE, the history of evolutionary theory, and many other things. I prefer discussing substance to credentials and style. But you have constantly made remarks about your level of knowledge of various scientific subjects, at least some of which, according to your own biographical self-description, are not part of your training, and thus you raised in my mind the question of credentials. However, I don’t wish to make any bigger deal of credentials than I have already indicated, and I’m content to drop my complaint on that score as non-productive.

    I think we need to take a break for a while now. I’m glad you are going to read Shapiro’s book. I hope you will absorb the full force of what he understands himself to be doing. I think he’s a breath of fresh air to evolutionary thinking. If I were young enough to go back and study evolutionary biology at Chicago, I would try to do my graduate research under him rather than under Jerry Coyne.

    T.

  225. Well, I’ve just discovered part of the problem:

    The Lenski I am talking about is the Lenski who has been growing bacteria in test tubes for the past 20 or 30 years and recording his results.

    The Lenski you are talking about is this one:

    “Lenski showed that neither of these claims were true, by demonstrating in a model which used random variation and natural selection to evolve, from a starting population of virtual organisms that could do nothing except reproduce,”

    Huh? “Virtual organisms?” I’m scratching my head. Bacteria reproducing in test tubes are not “virtual organisms.” Are we talking about the same Lenski?

    Either Lenski conducted two different kinds of investigations, one with computer models and virtual organisms, and one with real bacteria, or we are talking about two different Lenskis.

    If it is the former, I don’t ever recall Behe mentioning the part about virtual organisms. If Behe did discuss Lenski’s work on virtual organisms and I didn’t catch it, I apologize to you for misreading Behe and then being angry with you because of my misreading. If Behe didn’t, now you know that we were talking at cross purposes.

    My point was that none of the bacteria produced by Lenski destroyed Behe’s argument. The changes that Lenski did observe were mostly trivial, and even the changes that were non-trivial were still relatively small and well within what Behe’s argument would expect of Darwinian processes. Behe doesn’t argue that Darwinian processes can do *nothing* (indeed, he is less hard on them than Margulis is); he just thinks they can’t do the heavy lifting claimed for them.

    Whether any Lenski computer simulation using virtual organisms destroyed Behe’s argument, I cannot say, because I simply don’t know what computer simulation you are talking about.

    All of my objections to you about Lenski were based on my assumption that you were talking about the bacteria grown in the test tubes. As far as I know, bacteriology isn’t your field, so I couldn’t understand how you could be qualified to judge how much change in these critters would falsify Behe’s arguments.

    Both Lenskis are the same man:

    http://myxo.css.msu.edu/ResearchInterests.html

    I have no idea what programming a “learning model” means. A model of *what* learning *what*? Of autistic children learning to count? Of adults learning a foreign language? Of rats learning how to select the door with the cheese? I can think of all kinds of “learning models” which wouldn’t have anything to do with the operation of biological evolution, even if “learning” is used in a broad sense which completely removes the subjective element I associate with the word.

    Is this “learning model” you have written published on-line? And if so, where? And if not, what journal is it in? (I presume, given your understanding of peer review, that you would never publish it in a book!) What volume and number and pages?

    It’s a simple learning model of inhibitory control, of relevance to children with ADHD. Learning models and evolutionary models are very similar, which is why I find the distinction between “evolutionary processes” and “intelligence” somewhat moot. Darwinian mechanisms are essentially, trial-and-error learning mechanisms.

    If you are really interested, the reference is here:

    http://www.ncbi.nlm.nih.gov/pubmed/19409540

    Yes, it is peer-reviewed. No, as I’ve said, I don’t have any problems with books. My husband published a very good book on the neuroscience of mental disorders. And I have the beginnings of a draft of a mind-brain book myself.

    As for the rest, maybe I’m getting old and cranky, but my attitude has changed from that of a couple of years ago. I used to enjoy the idea of “combat by proxy,” where the hobbyist disciples of ID people and the hobbyist disciples of the Darwinians would wage battle on the internet. I no longer do. Far too often, on both sides, the hobbyist disciples don’t get the arguments of their masters right, or haven’t even read them carefully. Far too often, the two sides can’t even agree on terms, like “Darwinian” or “learning” or “intelligence” or “intervention.”

    I agree that this is problem. It’s why I’m picky about definitions – not to prescribe them, but to establish what the user means by them. A huge amount of “talking past the other” arises from misunderstanding of the other’s usage, or from either inadvertent or even deliberate equivocation. That thicket of brambles needs to be cleared before real progress can be made in a discussion, but it often creates a lot of tension in the process.

    And of course, pseudonymity allows for irresponsible behavior on all sides. And finally, for the most part, the targets of all the debating — Miller and Ayala and Behe and Dembski and Wells and Denton and Sternberg — aren’t even reading what is said about them or their books on these blogs.

    Yes, that’s why I use my real name. Not to assert authority but because I want to be as straightforward as possible in a murky environment.

    I’d rather see direct criticism of the big players, written by people who use their real names, and published in places that have some literary and scientific standards (though not necessarily peer-reviewed academic journals). And I’d like to see the criticism substantiated by equations, diagrams, lab results, etc., produced by the critic, not regurgitated from the work of other researchers, or worse, from other blog sites. And I’d like to see the big boys (Miller, Behe, Dawkins, Dembski, etc.) reply to such criticisms.

    Yes indeed. There are certainly plenty of critiques out there, signed, and some replies. I don’t find the replies convincing, and often they have to be googled for. It would be good to gather them in one place. Perhaps I’ll start a list of links on my blog, and people can supplement it. It would be a useful resource.

    This is why I’m thinking of abandoning all internet conversations such as this. It’s a sink hole for time, and it produces no critical work that will ever be taken note of outside a circle of a few thousand hobbyists around the world. I’m not sure that all the debating on TalkOrigins, Biologos and here, in the long run, contributes anything to scientific knowledge, or amounts to anything more than a huge debate between Stooge fans about whether Shemp or Curly is superior.

    Ah, cheer up, it’s not that bad :) We are all learning here, right?

    Twice now you have made the suggestion that you might not be the person you are representing yourself to be. I don’t mind pseudonymity — people have to protect themselves, especially ID people, who, unlike atheist Darwinists and theistic evolutionists, have lost jobs and careers in secular universities for their views. But I don’t like misrepresentation. If you *are* just a spotty teenager, or anything other than the professor with your name who has a web site at a British university, I’d like you to declare it now.

    Well, I’m not a professor, but that is my real name, and I am an author on the paper I just linked to. I’m also, if you care, the same Elizabeth Liddle that pops up in most entries if you google Elizabeth Liddle viol, Elizabeth Liddle author, or, for my sins, Elizabeth Liddle exit polls. My point was simply that you only have my word here for that, and that on the internet, you cannot argue from authority, because you cannot prove authority – you have to argue on the merits of your argument. It’s why I like it :)

    I’m not asking you to divulge your real identity if you are someone else, but just to say if you are or are not the 59-year-old professor described on the web site. Obviously if you are not that professor, much of my criticism is misplaced, though I would not apologize for it, since I was deliberately misled by a false identity. If you are that professor, however, I stand by what I said. The field of that professor is such that the amount of time you are spending here and elsewhere debating evolutionary biology on the internet is in my opinion incompatible with doing a responsible job in the academic position for which a full-time salary is being paid. And now you can tell me to mind my own business for a third time. It’s the last time you’ll have to tell me.

    Well, that’s your judgement of course. However, the fact is that I do my job with such dedication that I am rarely away from my computer, and I use my time while my stuff is running to chatter about stuff on the internet. I’d be better getting some fresh air (although I do, generally, cycle to work) or cooking more nutritious food, or ironing the horrible pile of clothes in the basket, or washing the dishes. mea culpa. Or even buying some new clothes or having my hair cut, or playing my viol. But I like thinking, and the internet community has proven a great place for me to bat ideas around. I’d never have written that paper if I hadn’t learned about evolutionary models as learning algorithsm from, as it happens, long running thread at the old IIDB forum between a Behe fan and a GA expert, on Lenski’s AVIDA. It was a fascinating thread. The GA expert (aka RBH at Panda’s Thumb) downloaded AVIDA and did lots of test runs under different conditions. That’s why I know so much about AVIDA, and indeed, about Behe (who at one point engaged in dialogue with the IDist IIRC).

    Yes, you may go now. I’m going, too.

    Go well, and be well :)

    Lizzie

  226. How you could be sure that a reply to a book which you have not read is “devastating” is beyond me. I guess that Arts and Science people think differently. In the Arts we are expected to have read the books that we condemn, not to dismiss them on the basis of someone else’s criticism. I thought it was the same in Science, but perhaps I am misinformed. Please do instruct me on how scientists feel about secondhand dismissals.

    Because I was talking about a reply to an argument, not a reply to a book.

    Yes, that is different from the arts. Science is much more telegraphic, and if there’s an error, it’s an error, whether or not the other arguments are correct. In that sense it’s more like math.

    And I’m neither applauding nor condemning ERV’s manner. It’s certainly not my style, but again, if someone points out a math error in my work, then the manner in which it is done is irrelevant – what would matter to me would be whether it is in fact an error, not how rudely it was pointed out.

    As eigenstate says, that’s the great thing about science. Rudeness and incivility may be regrettable, but ultimately they are irrelevant. What matters is whether you are right. It probably makes us rather thickskinned actually. I don’t take offense very easily (contrary to your impression!) and often completely fail to notice ruderies if someone is making what seems to be a valid point. Or, an invalid one, for that matter – all I see see is the argument. The one thing that does bug me, though, is the accusation of dishonesty, or lack of integrity. That seems to undermine the whole basis of discourse. Not that you did it, but “tribal” came close :)

    As for whether you have debated me on substance: perhaps you have; if so I apologise (I am not very good at remembering who I’ve had exchanges with, I’m afraid).

    But let’s get this personal stuff out of the way, and if that means a break, then so be it. I really have got a rather large basketful of ironing that I am averting my gaze from. And then there’s that book….

    Cheers

    Lizzie

  227. Oh, and what is really very bizarre, and I must just point it out, that at no time have I every disagreed that Shapiro’s work is refreshing and exciting!

    Not only that, but I’ve said it’s an approach I’ve been advocating for some time. Which is why I’ve been following his papers – and why I ordered his book!!!!

  228. Sigh:

    I see the Chesil beach example that was cogently answered almost a year ago, has been recycled; as though this has not been long since dealt with more than adequately, and with the same interlocutor.

    The answer to it is simple: this is not a complex, specified — and especially functionally specified — result, it is a physically caused sorting by size known to be driven by the mechanical forces at work.

    In the Chi_500 simplified metric, we have low contingency under the circumstances, so Ip –> 0.

    Chi_500(chesil) = [~ 0]*S – 500 –> – 500,

    i.e. well clear of the zone in which one would infer design. (And that holds before we consider whether S is 1 or 0. S is a don’t care in this case. (FYI, for S to go to 1, we need high contingency AND confinement to a narrow, functional zone in the space of possibilities, e.g. text in this and other posts. There is no high contingency due to the mechanical action, and so S will be 0. Of course if someone comes to the beach and modifies it by imposing a different pattern with a fleet of dredges, that would be a different situation and would be artificially induced.])

    (That is, there is a mechanical reason why the stones are sorted by size from one end to the other, so that in the days of smugglers they could tell where they were along the beach at night by the size of the pebbles underfoot.)

    If one wishes to argue, the size of pebbles codes where you are on the beach, not so at all. The size of pebbles — thanks to the cluster of mechanical effects at work — is functionally [mathematical sense] tied to position along the beach. This is an effect driven by causal forces, not a code of symbols and rules.

    It is we who come along and turn this into a function that can be calibrated to distance along the beach. And, that is what would be informational, and of course is intelligently produced.

    GEM of TKI

  229. 229

    Champignon,

    Here goes my February 3rd resolution down the drain.

    Sort order and meaning are two different things.

    Thank you for boiling this down to its essence. I understand your argument more clearly now. But if this is where you would like me to admit to error, I must disappoint you.

    Sort order, when not derived purely from the physical properties of a thing, is meaning. It is certainly not the entire meaning of whatever is being sorted. But is absolutely is meaning. It is information attributed to a thing.

    Your example of sorting animal names makes no sense at all. When sorting alphabetically, the meaning of the words is irrelevant. But the “meaning,” or information assigned to the letters, that A comes before B which comes before C, is essential. That meaning is assigned, not in any way emergent.

    All it needs to know is that a card that matches pattern X (which happens to be an image of the 5 of hearts) goes before a card that matches pattern Y (which happens to be an image of the king of hearts). It doesn’t understand that the numeral 5 represents the number 5, it doesn’t recognize the club symbol. Indeed, it doesn’t even know that there are symbols on the cards at all.

    And how does it “know” the bolded point above without an input of information, the arbitrary assignment of that relationship? That is my point in its entirety, from the beginning of this discussion until now, and it has not changed. Having re-read my very first statement to that effect, I don’t see how it was unclear at all, even though you would have me polish it until you can see your reflection.

    And in your example above in which the computer has no information regarding the relationship between the symbols on the cards and yet somehow magically sorts them anyway, what happens when I replace 2, 3, 4, and 5 with II, III, IV, and “five?” Now how will it sort them without some new input assigning meaning to those symbols?

    Perhaps you’ve heard people say “Let’s make this interesting” to describe taking something trivial and making it more significant by betting money on it. The only way left I can see to make this interesting is to count how many more times you will feign inability to comprehend this very simple point rather than address it, or better, concede that it is correct. (Other options include giving up or finding something else in my post unrelated to the point to quibble over. I suppose we could count those too.)

  230. So you didn’t read my response to vjtorley, kf?

    Yes, there’s a mechanical reason why the stones are sorted.

    Exactly.

    Dembski’s CSI does not include a term for the process by which the pattern arose – not surprisingly, because the whole point of his metric is to enable us to determine the nature of that process by examining the pattern alone.

    Your own version may be superior, but it was Dembki’s metric I was using.

  231. That is one of several reasons why concepts like CSI can distinguish can distinguish between random sorting and non-random sorting, but cannot distinguish between natural processes and intervention.

    In particular, such metrics cannot distinguish between sortings made by a foresightful process and sortings made by cumulative selection.

    Which is why KF and gpuccio are careful to assert that functional sequences are isolated and cannot be reached by cumulative selection.

    But that is a different war, and it will be won or lost by troops on the ground, not by philosophy. The Lenskis and Thorntons and Szostaks and their compatriots will decide the issue of connectness.

  232. Despite claims to the contrary, the only process known for designing proteins and for discovering their folds is cumulative selection. In chemistry or in simulations, it’s cut and try.

  233. Elizabeth:

    Regarding the conversation higher up on the thread, if I understand you correctly, you are saying that you are not a full-time faculty member at the institution with which you are associated. If that is the case, then obviously you do not have the contractual or moral obligations of such a faculty member, and I apologize for accusing you of shirking those obligations. (But if this is the case, you could have saved me embarrassment and yourself further irritating criticism by clarifying this when I first made this accusation a while back. I would have apologized right away.)

    One more pass at the Abbie Smith affair:

    1. Of course an error is an error, regardless of what else is in a book. That’s true in the arts as well as in the natural sciences. But if Abbie Smith detected an error in Behe’s account of viruses, that does not make her reply “devastating.” The word “devastating” in these polemical contexts generally means “destroys the author’s thesis.” But one error in one small section of a book does not destroy the author’s thesis. At most her criticism was “devastating” to some remarks Behe made about viruses. But his thesis didn’t depend on what he said about viruses. So maybe what we are disagreeing about is merely the usage of the word “devastating.”

    2. You didn’t really answer my question, which was about whether scientists consider it appropriate to declare that the author of a book has been refuted when they have read only someone else’s criticism of the book, and have not checked the book itself to make sure that the critic has in fact fairly represented the argument of the book. Many apparently “devastating” arguments are no longer seen as such once the original writing is consulted; often a straw man rather than the real thing has been refuted. Arts people are trained to always go back to the primary source. In the case of Behe’s *Edge of Evolution*, you did not display this kind of training, so I was wondering if that was just a decision of your own (to trust the critic without checking the original), or whether scientists are habitually that academically careless.

    In addition, local circumstances would seem to have dictated that a check of the original was in order: the critic clearly was sarcastic, angry, and with a bee in her bonnet, indicating the possibility that she might have read Behe less than dispassionately; and the critic was someone still some months or possibly even years away from completing her doctoral work, and was criticizing a tenured professor with over 35 peer-reviewed papers in his field, which might indicate that the critic had insufficient experience to make a balanced judgment. Yet despite these warning lights to go back to read the original source, you simply accepted Smith’s presentation of Behe’s argument. My arts training tells me this is a faulty procedure. And I think a good number of scientists would agree with me that the original source should be checked before the critic’s statement is simply accepted.

    3. You still haven’t caught the point about behavior. If you say to a critic: “You are rude and obnoxious, but I am going to carefully read your criticism and respond to it just as if you were respectful”, you are taking away all the incentive for the rude and obnoxious critic to change her habits. But if you say: “You may or may not have some valid scientific criticisms in here, but I have no intention of reading them until you apologize for your opening insolence and commit to not speaking to me, or to any scientific colleague, in that manner again,” you have created a strong incentive for the behavior to change. The arrogant young would-be scientist will then realize that his or her projected brilliant scientific career is toast, unless he/she gets a handle on his/her ego and learns the art of civilized academic discourse. This is basic psychology, and as you have a Ph.D. in that subject, I’m surprised you wouldn’t have thought of this already.

    And by the way, even if one *says* that one is not going to read the paper of the insulting person, that does not mean that one cannot in fact read it (unbeknownst to that person) and thus benefit from any scientific criticisms or detections of error that it contains. The point is that, in order to achieve the desired alteration of anti-social behavior, one should not give any *public acknowledgment* that one has read it. The one thing that *enfants terribles* crave, above all, is attention; the thought that their brilliance is not getting any attention from their elders is the most horrifying thing in the world for them. Therefore, one must make them think that no one is paying the slightest bit of attention to them. Then, surprise, surprise, the *enfant terrible* behavior starts to go away.

    Finally, regarding this paragraph:

    “As for whether you have debated me on substance: perhaps you have; if so I apologise (I am not very good at remembering who I’ve had exchanges with, I’m afraid).”

    I find it rather insulting. I don’t mean it intends to insult, but it’s still insulting. I have a vivid memory of every single exchange we have had, and can even remember particular twists and turns of argument; yet apparently my careful comments to you, which often take a great deal of time and editing to produce, make little lasting impression on your mind. This is another good reason for abandoning this kind of forum; not only do Behe, Dembski, Miller, etc. not pay attention to anything that is said here; even some of the people addressing each other here forget what their opponents have said if it is more than a few days or weeks ago! If I don’t have any lasting influence upon someone like you, with whom I’ve probably exchanged thirty thousand words over the past six months, in close back-and-forth, point-by-point responses, it’s unlikely anything I say is going to affect the way Eugenie Scott or Bill Dembski conduct themselves.

    I think this covers everything, Elizabeth. Best wishes.

    T.

  234. Dr Liddle:

    Pardon, but had you read my own answer with intent to understand rather than to object you would have seen why a mechanical sort will not fit in with the functional form of CSI, and onwards why the same low contingency system will not have CSI in the general sense. That is part of why I took the matter in two bites, looking at the Ip and the S terms.

    For INFORMATION-carrying capacity to exist, there has to be high contingency, which is then manifested in a way that is locked down to a narrow and specific zone in the field of possibilities, all of that stuff about CASES E IN SPECIFIC ZONES T IN THE WIDER FIELD OF POSSIBILITIES W, as can be seen in NFL by a certain Wm A D.

    That is crucial.

    In short, until we arrive at high contingency, an entity is not in the zone where informational character is at stake.

    Only highly contingent objects storing 500 or more bits of information capacity need apply, and it is in that context that CSI THEN HELPS US DECIDE IF THE OUTCOME OBSERVED IN SUCH A HIGHLY CONTINGENT CASE IS BEST EXPLAINED ON CHANCE OR DESIGN.

    The way that is done is per inference to best explanation, given the balance of clusters of possible outcomes in the space of possible configs. 500 coins in no particular order, chance. 500 coins spelling out he first 73 ASCII characters of this post, design.

    The pebbles on Chesil beach under the circumstances precisely do not have that high contingency.

    They are thus not informational.

    And, I actually described a different possible case, where they could be made informational, with a fleet of dredges and barges. Which of course would be by intelligent design.

    G’day

    GEM of TKI

  235. Scott,

    How far will you go to avoid admitting error? This is actually kind of interesting. Your ego is backing you into ever tighter corners.

    You wrote:

    Sort order, when not derived purely from the physical properties of a thing, is meaning.

    I can generate a sort order for a set of symbols using a random number generator. According to you, the output of my random number generator is therefore part of the meaning of the symbols. Does that not strike you as absurd?

    It is certainly not the entire meaning of whatever is being sorted. But is absolutely is meaning. It is information attributed to a thing.

    The meaning of a symbol is what it represents. The sort order of a symbol is information about the symbol, but it is not the symbol’s meaning. The American flag is flying in front of the fire station at 6th and Main. That’s information about the symbol. ‘Flying in front of the fire station’ is assuredly not part of the flag’s meaning, however.

    And how does it “know” the bolded point above without an input of information, the arbitrary assignment of that relationship? That is my point in its entirety, from the beginning of this discussion until now, and it has not changed.

    I’ve never disagreed, and in fact I explicitly agreed way back here. You’re the one who has been stalling the discussion by refusing to correct your errors.

    So, do you finally agree that this statement of yours is incorrect?

    Anything that sorts them, human or otherwise, must have awareness of the meaning of the symbols printed on them.

    And can we finally move on to this point?

    Scott,

    It’s not just any particular mapping that natural laws do not explain. It is the very concept of relating a symbol to a reality.

    Relating symbols to referents is something that brains do. You’ve told me that you agree that brains operate according to physical law. If so, then in what sense does physical law fail to explain the mapping?

  236. Elizabeth:

    Regarding the conversation higher up on the thread, if I understand you correctly, you are saying that you are not a full-time faculty member at the institution with which you are associated. If that is the case, then obviously you do not have the contractual or moral obligations of such a faculty member, and I apologize for accusing you of shirking those obligations. (But if this is the case, you could have saved me embarrassment and yourself further irritating criticism by clarifying this when I first made this accusation a while back. I would have apologized right away.)

    I’m actually not going to answer this, Timaeus. If you really want to know more about me I’ll leave it to your google fu. I have told you no lies.

    As far as I am concerned, my credentials are irrelevant to my arguments. They must stand or fall on their merits.

    One more pass at the Abbie Smith affair:

    1. Of course an error is an error, regardless of what else is in a book. That’s true in the arts as well as in the natural sciences. But if Abbie Smith detected an error in Behe’s account of viruses, that does not make her reply “devastating.” The word “devastating” in these polemical contexts generally means “destroys the author’s thesis.” But one error in one small section of a book does not destroy the author’s thesis. At most her criticism was “devastating” to some remarks Behe made about viruses. But his thesis didn’t depend on what he said about viruses. So maybe what we are disagreeing about is merely the usage of the word “devastating.”

    Perhaps we are. But as I understood it, Behe had made an inference about the evolution a gene on the HIV virus that was falsified by Abbie Smith’s evidence. But I should probably have used “falsified” rather than “devastated”.

    2. You didn’t really answer my question, which was about whether scientists consider it appropriate to declare that the author of a book has been refuted when they have read only someone else’s criticism of the book, and have not checked the book itself to make sure that the critic has in fact fairly represented the argument of the book. Many apparently “devastating” arguments are no longer seen as such once the original writing is consulted; often a straw man rather than the real thing has been refuted. Arts people are trained to always go back to the primary source. In the case of Behe’s *Edge of Evolution*, you did not display this kind of training, so I was wondering if that was just a decision of your own (to trust the critic without checking the original), or whether scientists are habitually that academically careless.

    That is a fair comment. As Behe’s case is made in a book, not in a subscription journal, I do not have access to the primary source. I agree that it was possible that Smith misrepresented his argument. The same applies to the Chloroquine Complexity Cluster argument, which has been thoroughly critiqued. It is possible that those critics have misrepresented his argument too. I did assume that the actual substance of each claim had been fairly represented, but I agree that I am not in a position to check.

    In addition, local circumstances would seem to have dictated that a check of the original was in order: the critic clearly was sarcastic, angry, and with a bee in her bonnet, indicating the possibility that she might have read Behe less than dispassionately; and the critic was someone still some months or possibly even years away from completing her doctoral work, and was criticizing a tenured professor with over 35 peer-reviewed papers in his field, which might indicate that the critic had insufficient experience to make a balanced judgment. Yet despite these warning lights to go back to read the original source, you simply accepted Smith’s presentation of Behe’s argument. My arts training tells me this is a faulty procedure. And I think a good number of scientists would agree with me that the original source should be checked before the critic’s statement is simply accepted.

    Yes, I agree, that is a fair point. I do tend to assume that scientists are honest, however rude. That is not necessarily a safe assumption.

    3. You still haven’t caught the point about behavior. If you say to a critic: “You are rude and obnoxious, but I am going to carefully read your criticism and respond to it just as if you were respectful”, you are taking away all the incentive for the rude and obnoxious critic to change her habits. But if you say: “You may or may not have some valid scientific criticisms in here, but I have no intention of reading them until you apologize for your opening insolence and commit to not speaking to me, or to any scientific colleague, in that manner again,” you have created a strong incentive for the behavior to change. The arrogant young would-be scientist will then realize that his or her projected brilliant scientific career is toast, unless he/she gets a handle on his/her ego and learns the art of civilized academic discourse. This is basic psychology, and as you have a Ph.D. in that subject, I’m surprised you wouldn’t have thought of this already.

    I’m not sure whether to laugh or cry. I think I’ll laugh. You keep accusing me of not showing the expertise you’d expect from someone with my apparent credentials, yet you happily assume the competence to judge what someone with that expertise should think! But I’ll answer: yes, I know a little bit about behavioural training. Actually, it’s my field. But, firstly, there is more to behavioural training than rewarding good behaviour and penalising bad. Secondly, I don’t consider it my business to reform the behaviour of random internet tough guys! And thirdly, I confess, Abbie makes me laugh. oops.

    And by the way, even if one *says* that one is not going to read the paper of the insulting person, that does not mean that one cannot in fact read it (unbeknownst to that person) and thus benefit from any scientific criticisms or detections of error that it contains. The point is that, in order to achieve the desired alteration of anti-social behavior, one should not give any *public acknowledgment* that one has read it. The one thing that *enfants terribles* crave, above all, is attention; the thought that their brilliance is not getting any attention from their elders is the most horrifying thing in the world for them. Therefore, one must make them think that no one is paying the slightest bit of attention to them. Then, surprise, surprise, the *enfant terrible* behavior starts to go away.

    Yep. When my son was bullied at primary school, I suggested that if he didn’t react so spectacularly when provoked, the bullies would cease to get a reward, and gradually stop (behaviour goes to “extinction” heh – I told you learning was like evolution). I explained about “Skinnerian conditioning” in other words. He came home the next day and said: “Mum, that Skinnerific condition really works!”

    Finally, regarding this paragraph:

    “As for whether you have debated me on substance: perhaps you have; if so I apologise (I am not very good at remembering who I’ve had exchanges with, I’m afraid).”

    I find it rather insulting. I don’t mean it intends to insult, but it’s still insulting. I have a vivid memory of every single exchange we have had, and can even remember particular twists and turns of argument; yet apparently my careful comments to you, which often take a great deal of time and editing to produce, make little lasting impression on your mind. This is another good reason for abandoning this kind of forum; not only do Behe, Dembski, Miller, etc. not pay attention to anything that is said here; even some of the people addressing each other here forget what their opponents have said if it is more than a few days or weeks ago! If I don’t have any lasting influence upon someone like you, with whom I’ve probably exchanged thirty thousand words over the past six months, in close back-and-forth, point-by-point responses, it’s unlikely anything I say is going to affect the way Eugenie Scott or Bill Dembski conduct themselves.

    Yes, I realised it was potentially insulting, and I’m sorry. But you needn’t be insulted. I do have a good memory for these exchanges – what I don’t have a good memory for, and it’s at least partly my age, is the names of the people I was exchanging with. That’s partly a result of anonymity of course – if I can put a face and a background to a name, I’m more likely to remember which conversation was with whom. And I’ve had email exchanges with a few people, and remember which ones. And the other thing is (and it’s both a fault and a merit), is that I do, on the whole, tend to focus on substance, rather than tone (as I said) and that again biases me towards remembering what was said rather than by whom. Lastly, perhaps it’s worth considering that I stand out here rather more obviously than IDists stand out from each other! I’m obviously female, and not an IDist. That paints me in a fairly vivid colour (though I’m not the only Darwin Girl here, even not including the one that turned out to be a Darwin Boy :))

    So don’t be insulted. Remind me specifically of the conversations, and I’ll almost certainly remember them. I just don’t have names very firmly tagged to them. It’s the who, not the what, that fails to stick in my aging brain. Or email me :) You’d be very welcome to.

    I think this covers everything, Elizabeth. Best wishes.

    And to you, Timaeus.

    Peace.

    Lizzie

  237. Pet: we have very little experience with designing proteins [I suspect, across this century that will change], but a lot more in designing automated manufacturing and control tapes for such that use digital codes. Those highly specific, functional and complex codes that drive the primary form of AA sequences that fold and form proteins that work in life, as assembled in the ribosome, point rather strongly to design. Please answer the case in front of us, not the easily set up and knocked over strawman. KF

  238. kf, first of all, I was not critiquing your version of CSI, but Dembski’s, and showing that as defined in “Specification: the Pattern that Signifies Intelligence” CSI doesn’t work, because it doesn’t rule out something like Chesil Beach.

    But let’s take your own argument:

    For INFORMATION-carrying capacity to exist, there has to be high contingency, which is then manifested in a way that is locked down to a narrow and specific zone in the field of possibilities, all of that stuff about CASES E IN SPECIFIC ZONES T IN THE WIDER FIELD OF POSSIBILITIES W, as can be seen in NFL by a certain Wm A D.

    That is crucial.

    Well, define what you mean by “high contingency”.

    In short, until we arrive at high contingency, an entity is not in the zone where informational character is at stake.

    Well, I need your operational definition of “high contingency”.

    Only highly contingent objects storing 500 or more bits of information capacity need apply, and it is in that context that CSI THEN HELPS US DECIDE IF THE OUTCOME OBSERVED IN SUCH A HIGHLY CONTINGENT CASE IS BEST EXPLAINED ON CHANCE OR DESIGN.

    So it seems you have added another item to the filter, namely “high contingency”. I really do need this definition.

    The way that is done is per inference to best explanation, given the balance of clusters of possible outcomes in the space of possible configs. 500 coins in no particular order, chance. 500 coins spelling out he first 73 ASCII characters of this post, design.

    The pebbles on Chesil beach under the circumstances precisely do not have that high contingency.

    They are thus not informational.

    There are, I estimate, about 100 billion pebbles on Chesil beach. Of the possible ways of arranging those pebbles (let’s say to the nearest millimeter, with the pebbles ranging from 10mm diameter to 110mm), a tiny fraction will be graded in size from 10mm at the West end to 110 at the east. That is a very simply described pattern, and I suggest that the only other pattern that is equally simple of description is: graded from 10mm at the East end to 110 at the west. So we have a highly specified pattern, and a high Shannon information-full beach.

    It fulfills Dembski’s requirements for CSI. The pattern is also informative in two senses: one is that “semiotic agents” to use Dembski’s term, can orient themselves by it. The second is that the beach itself is constantly renewed, and the sizes of the pebbles already on the beach at least partly determine the sizes of the pebbles that will be deposited there by the next tide.

    Tell me why it does not have “high contingency”.

    Note, that I do not argue that the beach was designed, or even that this post wasn’t. I simply dispute that the CSI metric can distinguish between the two on the evidence of the pattern alone. I think it produces both false positives and false negatives.

    But I await your definition of “high contingency”.

    Cheers

    Lizzie

  239. 239

    Champignon,

    I can generate a sort order for a set of symbols using a random number generator. According to you, the output of my random number generator is therefore part of the meaning of the symbols. Does that not strike you as absurd?

    It’s not absurd. If you specify a sort order using a random number generator and match each symbol with a value, then you are assigning that meaning to the symbol. What part of that is confusing? It does not require that the sort order is the only meaning assigned to the symbol.

    I’m sorry if I’m not get getting this whole ‘backed into a corner’ vibe. What I’m saying makes perfect sense.

    ‘Flying in front of the fire station’ is assuredly not part of the flag’s meaning, however.

    Unless, that is, it is determined that flying a flag in front of the fire station does have meaning and it is done to convey that meaning.

    If you see the flag flying at half mast, does that mean anything to you? It means something to the person who flew it at half mast, and they expect that at least some people will recognize that meaning. The example you used to demonstrate what does not have meaning is actually a real example of something that literally can and does have meaning. Perhaps you should have thought about that longer.

    Although I’ve clarified the wording of my initial statement for the benefit of the one person challenged by it, I think that nearly anyone who read it understood it the first time.

    And can we finally move on to this point?

    Relating symbols to referents is something that brains do. You’ve told me that you agree that brains operate according to physical law. If so, then in what sense does physical law fail to explain the mapping?

    I’m happy to move on to your next question, as it implicitly concedes the point you’ve wasted so many posts quibbling over.

    You may find my answer to this question we’re ‘finally moving on to’ back at 12.1.1.2.30.

    Put about as simply as I can, physical laws do not explain everything that they permit or enable.

    A car enables a person to drive from A to B. If you park your car outside a store and it’s across the street when you come out, how will you explain that? Is ‘the car drove there’ an adequate explanation? It’s almost certainly true that the car drove there, and whoever drove it did so the same way anyone drives any car. But an explanation of how the car operates and how one drives it would not sufficiently explain how it got across the street. That is not the explanation you would want.

    Similarly, the operation of natural laws upon the molecules of one’s brain does not explain why one person writes a novel and another whistles Beethoven in the men’s room. And the operation of natural laws does not explain why some cultures selected the symbols “7″ and “XII” to represent the number or quantity seven. They do not explain that there is an abstract concept of “seven” which can be associated with any symbol.

    If you disagree then
    – use natural law to explain why the digits 0-9 represent numbers
    or
    – use natural law to explain any set of symbols
    or
    – offer even the vaguest hypothetical process by which a natural law might produce any set of hypothetical symbols.

    Keep in mind that in each case the symbols are not just a reflection, an effect of what they represent, but are used both to create and to receive abstract information. You know, just like when someone imagines 52 cards, prints them on paper or represents them within a simulation, and someone else understands their meaning, even if only in the limited sense of knowing in which order to sort them.

    I admit error all the time, even when I’m right. I’m married. But I won’t admit error when I’m right just because you ask me to.

  240. I’ve read several recent papers on predicting protein folding and see nothing that indicates that protein design can be simulated or modeled to the degree necessary to do biological design without doing actual chemistry. To the extent that we can model protein folding it requires annealing algorithms or genetic algorithms, which are evolutionary.

    Gpuccio suggests intelligent selection. It’s still a variety of evolution, and more importantly, it depends on the connectedness of the search space. The connectedness of functional space is the keystone issue. If function can be connected, there is no need to posit intervention.

    What you and GP have is an updated gaps argument. You have transferred the argument from bones to sequences, but it’s the same argument: no intermediate sequences.

    I will grant that it’s an interesting argument. Everyone admits it. Paleontologists have spent centuries addressing fossil gaps. The desire to fill the gaps is in obsession of mainstream biology. It’s not being ignored.

    And it’s not being ignored in the arena of molecular biology. But our technology for investigating genomes is about at the level of Leeuwenhoek’s microscope. My opinion is worth what you paid for it, but if it’s of any interest to you, I accept your challenge at face value and look forward to the future of research. We shall see as time goes by whether connectedness is supported by evidence.

  241. I’ve discussed this elsewhere, but got no response. The problem with calling DNA a code is that it gets confused with language.

    Language is comprised of words and syntax. A dictionary of words has fewer entries than a dictionary of all the possible sentences and paragraphs.

    We really don’t know if there is anything comparable in the genetic code. The closest thing seems to be protein domains. But they are already rather long. Using your argument, they are too long to have assembled purely by chance.

    If I make a typo in posting, most people can still read and understand what I say. An editor can usually correct it and recreate the intended sequence.

    Cells also have editors, but when errors get past them and passed on to the next generation, there is no way to recreate the intended sequence. Unlike paragraphs and sentences, there is no dictionary of subunits that partially convey the meaning. No way to tell which of hundreds or thousands of base pairs has been altered.

    It is the lack of subunits that makes both design and evolution difficult. The dictionary of functional units has the same number of entries as the dictionary of minimum length words. Every possible utterance in the genetic code has it’s own entry.

    Unless it is possible to build functional units incrementally and cumulatively. Unless functional space is connected.

  242. Dr Liddle:

    Pardon, but could you kindly read here, the very first ID Foundations post?

    (I refer you there to see that this is not anything novel; the very reason why we distinguish mechanical necessity leading to lawlike regularity of outcomes is that this is manifested in low contingency of outcomes. When we have high contingency of outcomes for an aspect of an object or process, under similar initial conditions we do not have similar outcomes. Nor is the case of sensitive dependence to initial conditions an objection: it is precisely because we are unable to get the similarity that this yields large differences across time to a dynamic system. That is, it is because of small or even imperceptible differences in initial conditions that are essentially chance driven that we get the much amplified variability of outcomes. Indeed I have argued — I believe to you — that this accounts for how a die behaves.)

    For an object to be of information-bearing potential, it has to have high contingency. For instance, a string of ASCII characters, c1-c2-c3 . . . cn has 128 possibilities per position. Only a very few of these, relatively speaking, will be an informational post in English responsive to this thread.

    So, when Dr Dembski spoke of something as informational, this long since implies high contingency. Complexity then points to a sufficiently large set of possibilities that it would be maximally unlikely and implausible to hit on E’s from separately and “simply” describable — the hint at K-complexity is intended — zones T within W where T is much smaller than W.

    What I find here is a conceptual gap that is revealing.

    And, after many, many months of back-forth on these very points. That suggests to me a presumption on your part that I and others did not know what we are talking about at all in addressing very basic points. It frankly suggests reading to dismiss rather than first to understand.

    Sorry if that sounds harsh, but this feels a lot like you have wasted a lot of our time. Let’s just say that the state space concept and the related phase space concept, are basic to a lot of physics and engineering disciplines. In fact, W is a stand-in for Omega, used by Boltzmann, as in s = k*log W. As Section A and Appendix 1 my always linked note discuss, that them leads to cross connexions between entropy, information and information-carrying capacity.

    Indeed, maybe we are looking at one reason why engineering and physics types tend to “see” the point of the design inference relatively easily.

    Do you now see why I have repeatedly talked about islands of function in large seas of non-functional configurations?

    The issue then is that the nodes of the EF identify, first whether there is or is not high contingency, and then what is the best explanation for a given, highly contingent outcome. And, quite some months ago, we have had an argument along just these lines, in a context where you misperceived the EF.

    At that point I highlighted essentially what I now am saying, and it is clear that you rejected it. So, it resurfaces.

    No, I am not idiosyncratically making up dubious ideas (your latest talking point, that takes on some peculiar colour here), we are here close to the holy grail that makes a lot of physics of the small work. And, for that matter this is close to ideas about samples and populations in statistics, INCLUDING the underlying rationale for Fisherian inference testing.

    Namely that an at random sample in a given set of opportunities to sample is most likely going to come from the bulk of a distribution, not special zones in its far skirts.

    But, if you have not been able to appreciate that the issue of high contingency is central to information bearing potential or capacity, then you have not grasped the core ideas that lie underneath the design inference. In short, your objections here are directed at not the real matter but a misimpression of it.

    I suggest that you may find it helpful to read the IOSE introduction page.

    GEM of TKI

  243. In that case my beach has high contingency. Even if we assume that the grading just needs to be to the nearest millimeter, that gives us about 100 “characters” between a 10 mm pebble and a 110 mm pebble.

    Let’s consider we have a bag of those pebbles and we draw a line of 500 of them. There are 100^500 possible arrangements of pebble sizes on that line.

    Of those, 100 arrangements are very simple – all the pebbles are the same size. Of linearly graded arrangements, we have from 2 to 100 pebble sizes (99) in equal gradations, so 99. If we allow for non-linear arrangements we have rather more (I’ll have to work it out), we have rather more, but the total will clearly come to a tiny fraction of 100^500.

    And that’s for a line of 500 pebbles. I’m talking about a beach of 100 billion pebbles.

    And, after many, many months of back-forth on these very points. That suggests to me a presumption on your part that I and others did not know what we are talking about at all in addressing very basic points. It frankly suggests reading to dismiss rather than first to understand.

    Well, no. It suggests that I understood exactly what you meant, but rather assumed there might be something more to it than that.

    It looks as though your CSI is exactly the same as Dembski’s and fails for exactly the same reason: it cannot distinguish between a long series of items from an alphabet (high Shannon information, or, in your words, “high contingency”) that has been generated by a simple algorithm (and therefore, by definition, high compressibility), and one generated by intelligence.

  244. Dr Liddle,

    We keep going in circles, pardon.

    recall, the EF looks per aspect. The aspect you presumably had in mind was the grading of pebble size from one end to the other. This is accounted for on chance plus necessity.

    Now, you are looking at the pebbles piled and thus in a large number of possible configs. For this aspect, the problem is low specificity. Within the broad ambit of a beach profile, particle location and orientation on packing together is not very specific. And, the function, if you want to call it that is not seriously determined by being in a narrow zone in the space of configs. S = 0.

    On Dembski’s summary, there is low specificity. Complex but not particularly specific, as Orgel spoke about crystal grains in granite. In short, not organised. Randomness, not organisation, dominates the aspect.

    And, all of this distinction has been on the table since 1973.

    you will note that the Shannon-type metric is a measure of info-carrying capacity of a code-system, not a measure of specified complexity. The Chi Metric, Durston’s Fits metric and the modified Chi_500 metric all address specificity, thus changing the Shannon metric. This is done in various ways but the simplest to see is functional specificity, requiring complex, information-rich organisation. Especially, when expressed in a code, and again especially a string.

    Which last happens to be the case with DNA. Proteins are manufactured in an automated unit based on those coded instructions.

    Using the case of Chi_500:

    Chi_500 = Ip*S – 500, bits beyond the solar system threshold.

    As pointed out, if there is not a high contingency similar to bit values in a string, then we do not have high contingency. And indeed, this is WLOG, as a networked, composite object can be reduced to a nodes and arcs list, with parts enumerated and orientation coded for. This is routinely done with CAD software.

    Specificity can be tested by injecting random noise and observing effects. English text with maybe 1 – 3% noise will be annoying, but readable — about one to two errors per average word. Much beyond this and chaos [ think of scanned Gutenberg books, about 95% reliability is needed, and it is annoying at that level]; we have sophisticated processing, but there are limits. Wiring diagrams are a LOT less noise tolerant as a rule. Don’t even THINK about making random changes to high power circuits.

    Overall, I get the impression that very little of what design thinkers have been saying, or its context, has been understood. I suspect much of that is because things that are unexceptional have been treated with selective hyperskepticism, leading to incoherence on standards of warrant.

    For instance, if one is in a very special and isolated zone T in a config space W, such that the available resources would strongly lead to the expectation that a chance and necessity based blind walk would be maximally unlikely to land in T, the best explanation for being in T is design.

    Nothing in that should be too hard to understand for anyone made to do a treasure hunt game with no clues on whether one is warmer or colder, just hit or miss, blindly.

    Actually, too, being reduced to such incoherence on what is demanded to accept a finding is a strong indicator that some rethinking is needed on the part of objectors to the design inference.

    Please, re-read to understand, rather than to toss out seemingly clever objections that seem rather to pivot on want of thorough understanding.

    GEM of TKI

  245. P: Still on strawman. Observe the system that makes the proteins and come back to us on how selection pressure on proteins drives DNA codes, several steps upstream. Intelligence routinely is able to find heuristics that break through seemingly impossible odds against chance based random walks. And the strong evidence is that the space is NOT connected in the large, though it may be connected in the small, just think about requisites of folding.As in islands, not continents of function. If you wish to assert such connexion in the large, show us empirically, kindly. KF

  246. Dr Liddle,

    We keep going in circles, pardon.

    recall, the EF looks per aspect. The aspect you presumably had in mind was the grading of pebble size from one end to the other. This is accounted for on chance plus necessity.

    Well, I don’t think it is.

    Now, you are looking at the pebbles piled and thus in a large number of possible configs. For this aspect, the problem is low specificity. Within the broad ambit of a beach profile, particle location and orientation on packing together is not very specific. And, the function, if you want to call it that is not seriously determined by being in a narrow zone in the space of configs. S = 0.

    None of that makes sense to me, kairosfocus. There are certainly a very large number of possible configurations of pebbles. Of those, there are a tiny proportion that are as simply described as “graded linearly in ascending size from west to east”. So the zone is very narrowly defined, and the “configuration space” is vast

    On Dembski’s summary, there is low specificity. Complex but not particularly specific, as Orgel spoke about crystal grains in granite. In short, not organised. Randomness, not organisation, dominates the aspect.

    No. On Dembski’s definition, the specification is extraordinarily precise. The pebbles are so finely graded that a fisherman, landing at night, can tell where he is by the size of the pebbles. In other words, the arrangement is not “random” at all. It is a highly ordered grading.

    And, all of this distinction has been on the table since 1973.

    you will note that the Shannon-type metric is a measure of info-carrying capacity of a code-system, not a measure of specified complexity. The Chi Metric, Durston’s Fits metric and the modified Chi_500 metric all address specificity, thus changing the Shannon metric.

    I am talking about Dembski’s measure of specified complexity, CSI. I am not talking about those other things, if they are different.

    This is done in various ways but the simplest to see is functional specificity, requiring complex, information-rich organisation. Especially, when expressed in a code, and again especially a string.

    Which last happens to be the case with DNA. Proteins are manufactured in an automated unit based on those coded instructions.

    Using the case of Chi_500:

    Chi_500 = Ip*S – 500, bits beyond the solar system threshold.

    As pointed out, if there is not a high contingency similar to bit values in a string, then we do not have high contingency. And indeed, this is WLOG, as a networked, composite object can be reduced to a nodes and arcs list, with parts enumerated and orientation coded for. This is routinely done with CAD software.

    Specificity can be tested by injecting random noise and observing effects. English text with maybe 1 – 3% noise will be annoying, but readable — about one to two errors per average word. Much beyond this and chaos [ think of scanned Gutenberg books, about 95% reliability is needed, and it is annoying at that level]; we have sophisticated processing, but there are limits. Wiring diagrams are a LOT less noise tolerant as a rule. Don’t even THINK about making random changes to high power circuits.

    Overall, I get the impression that very little of what design thinkers have been saying, or its context, has been understood. I suspect much of that is because things that are unexceptional have been treated with selective hyperskepticism, leading to incoherence on standards of warrant.

    For instance, if one is in a very special and isolated zone T in a config space W, such that the available resources would strongly lead to the expectation that a chance and necessity based blind walk would be maximally unlikely to land in T, the best explanation for being in T is design.

    Nothing in that should be too hard to understand for anyone made to do a treasure hunt game with no clues on whether one is warmer or colder, just hit or miss, blindly.

    Actually, too, being reduced to such incoherence on what is demanded to accept a finding is a strong indicator that some rethinking is needed on the part of objectors to the design inference.

    Please, re-read to understand, rather than to toss out seemingly clever objections that seem rather to pivot on want of thorough understanding.

    GEM of TKI

    Are you actually reading my posts, kf?

  247. Hi Elizabeth,

    Thanks for your post at 1.1.2.2.1. A few quick points in reply:

    (1) You write:

    A “natural biasing factor” is exactly what Darwin’s “natural selection” is. And we know that it happens because we can actually observe it in real time. But you can’t do probability calculations on it. They won’t demonstrate the truth of Darwinian evolution any more than they will demonstrate the truth of ID. It’s just not the right methodology for this question.

    I have several problems with this statement.

    First, we can indeed observe Darwinian evolution in real time, but it doesn’t follow from that that given a few billion years, changes of the magnitude of, say, the Cambrian explosion are likely to occur, or even possible. That’s an unwarranted extrapolation. We have good grounds for saying that evolution has occurred – e.g. our loss of the gene for producing vitamin C points to our kinship with the apes. But that tells us nothing of whether the process that led to the human body was a Darwinian one or not – or even whether it was a natural one or not. To demonstrate this, you really have to show it’s feasible, or reasonably likely to occur, where “reasonably likely” is defined as “having a probability of 10^(-120) or more, over a time span of a few billion years” – which I think is a pretty reasonable request. Normally in science, whenever you’re proposing a brand new mechanism for an object you’re designing (let’s say, a new car engine), you have to demonstrate its feasibility, and I think I’ve set the bar pretty low with my 10^(-120) probability hurdle. If you can’t clear that hurdle, then you might just as well say that fairies were responsible for human evolution, as I argued in my post, The 10^(-120) challenge, or: The fairies at the bottom of the garden .

    Second, Darwinians are wont to say that the demand for a probability calculation is an unreasonable request, because the events described happened so long ago. But if we’re going to establish how they happened, as opposed to whether they happened, then we do need to have a mechanism that’s been shown to work on the scale hypothesized. (My legs are good enough to let me do a long-jump of perhaps four meters, but they certainly won’t let me jump across the Grand Canyon – even in a billion years.)

    Third, Darwinians often balk at the distance between the two events whose probability pathway they are asked to calculate, and object that so many complicating factors could occur along the way that it’s impossible to do any realistic number-crunching. I say that’s baloney. Even when you give them all their desired ingredients and ask them to perform a relatively modest calculation for the probability of a structure evolving, they can’t do it.

    Two cases in point:

    (a) To this day, Darwinians refuse to even attempt to calculate the probability of functional proteins evolving from a primordial soup filled with amino acids. They don’t like the scenario of amino acids hooking up to form proteins, because they know perfectly well that it can’t realistically happen in the time available, as only an infinitesimal fraction of amino acid sequences are in any way functional. So they suggest a backdoor route: RNA formed, and gave rise to proteins and DNA. Fine; what’s the probability of a chain of RNA that’s big enough to make a protein, forming from nucleotides? Silence.

    (b) Darwinians have not yet attempted to calculate the probability of a bacterial flagellum forming from its precursors – which is remarkable, as I understand they’ve proposed some fairly detailed scenarios. Why the reluctance to calculate? Why the reluctance to even set upper and lower probability bounds for the likelihood of the process occurring over a period of four billion years? I find their coyness very curious.

    Fourth, you object that we can’t do probability calculations with ID either. That depends on what probability you want to calculate. If you are referring to the probability that the Designer would design DNA, or bacterial flagella, or any particular structure, then I agree. But if you are referring to the the probability that the Designer could design DNA, or bacterial flagella, if He set His mind to it, then that’s easy to calculate. So long as the structure is one that teams of human scientists can produce in a laboratory, and so long as the Designer is super-human, then the answer is 1.

    (2) Referring to Dr. Stephen Meyer’s objections to biochemical predestination (which were also voiced long before him, by biologists such as Professor Dean Kenyon), you write:

    Unless he thinks that every time a cell divides, or any biochemical process takes place, the molecules are actually being pushed around by little intelligent angels or something. Clearly the biochemistry works, even if where don’t know exactly how. And when we find out, then we will be in a better position to understand the origin of DNA.

    Well, we know that DNA replicates by natural means today, and we know that cells divide by processes not requiring intelligent guidance to make them work, but that doesn’t tell us whether the first DNA double helix (or, for that matter, the first cell) formed by non-foresighted natural processes or not. All the scientific investigations we’ve done so far suggest that the probability of DNA forming is extremely remote. Please don’t take my word for it: have a look at my recent post, The Big Picture: 56 minutes that may change your life , where you can hear chemistry Professor John C. Walton lecture on abiogenesis, or scroll down to view my summary of his lecture.

    (3) You raise a point of substance when you write:

    Dembski has this backwards, by his own methodology. It was he who cast “natural” causes as the null, and insisted on Fisherian, not Bayesian, logic. And under his own chosen statistical method, it is up to him to show that the pattern in question could not be generated under that null. And I have just demonstrated that he cannot do this, and does not even attempt to. He regards “equiprobable” as the null, and natural non-linear stochastic processes (and many others) do no not produce equiprobable outcomes. He can’t have it both ways. Either he models the null properly, or he must cast natural processes as as H1.

    I attempted to address the question of the null hypothesis in my post, Why there’s no such thing as a CSI Scanner, or: Reasonable and Unreasonable Demands Relating to Complex Specified Information and Of little green men and CSI-lite , back in March/April 2011. (You might want to have a look at those, by the way.) In the first post, I wrote:

    During the past couple of days, I’ve been struggling to formulate a good definition of “chance hypothesis”, because for some people, “chance”; means “totally random”, while for others it means “not directed by an intelligent agent possessing foresight of long-term results”; and hence “blind” (even if law-governed), as far as long-term results are concerned. In his essay, Professor Dembski is quite clear in his essay that he means to include Darwinian processes (which are not totally random, because natural selection implies non-random death) under the umbrella of “chance hypotheses”. So here’s how I envisage it. A chance hypothesis describes a process which does not require the input of information, either at the beginning of the process or during the process itself, in order to generate its result (in this case, a complex system). On this definition, Darwinian processes would qualify as a chance hypotheses, because they claim to be able to grow information, without the need for input from outside – whether by a front-loading or a tinkering Designer of life.

    CSI has already been calculated for some quite large real-life biological systems. In a post on the recent thread, On the calculation of CSI, I calculated the CSI in a bacterial flagellum, using a naive provisional estimate of the probability P(T|H). The numeric value of the CSI was calculated as being somewhere between 2126 and 3422. Since this is far in excess of 1, the cutoff point for a specification, I argued that the bacterial flagellum was very likely designed. Of course, a critic could fault the naive provisional estimate I used for the probability P(T|H). But my point was that the calculated CSI was so much greater than the minimum value needed to warrant a design inference that it was incumbent on the critic to provide an argument as to why the calculated CSI should be less than or equal to 1.

    Let me stress that I claim no expertise whatsoever on bacterial flagella or the origin of life. All I’m saying is: you’re welcome to suppose the existence of biasing factors in Nature that favor the production of these structures if you wish. And if you find them, they’ll dramatically lower the CSI estimate for these structures in the process.

    Does that mean that CSI estimates are completely uninformative? Not at all; it just means that they’re provisional and falsifiable – which is a good thing, not a bad thing, from a scientific perspective.

    (4) You also overlook the alleged improbability of producing a compressible structure (which may be overcome by natural biasing) with the improbability of naturally producing a code (which as far as I know has never been achieved naturally) or something that can perform a function (which is highly debatable, depending on how liberally you define “function”) write:

    Therefore, all we can say, if a pattern exhibits CSI is that it was not produced by a process in which all permutations of the pattern elements are equiprobable. And so it does not allow us to distinguish Intelligent Design from stochastic natural processes (or non-stochastic ones, actually – the EF did at least allow us to do that).

    But it gets worse. We know that non-linear natural processes (stochastic or non-stochastic) can produce vastly complex patterns that have all the appearance of design. All the mathematics of chaos tell us that. And what Darwin proposed was a non-linear natural process.

    The fact that Chesil beach, whose order is highly compressible, formed naturally, does not tell us whether the DNA code can do so. Not does it tell us whether new cell types can perform, or new biological structures capable of performing new functions. Sorting by size is not a particularly complicated thing for Nature to do.

    (5) Regarding Behe’s alleged requirement of three simultaneous mutations: I think that’s a mis-reading of what he says in The Edge of Evolution, just as “Hoyle’s fallacy” is based on a mythical mis-reading of what he wrote.

    Bye for now.

  248. Thanks for your reply. I’d like to address it, but it might be helpful to have your response to the rest of my post first.

    If not, I’ll try to respond in the morning.

    Cheers

    Lizzie

  249. <blockqIf you wish to assert such connexion in the large, show us empirically, kindly. KF

    The question of connectability will be decided by research like that being done by Thornton. The existence of alleles demonstrates that most coding sequences have functional and selectable variants within reach of a single mutation.

  250. 250

    KF: “The aspect you presumably had in mind was the grading of pebble size from one end to the other. This is accounted for on chance plus necessity.”

    Liz: “Well I don’t think it is”

    Science: “Lateral grading of beach sediments can be achieved by down drift and/or long shore drifting.”

    http://www.jstor.org/pss/4298523

    It appears the pebble gradients are accountable by chance and necessity.

    And the chance-necessity mechanism for the origin of the genetic code is___

  251. Scott,

    You posted your response in the wrong place, so I’m reproducing it here:

    Champignon,

    I can generate a sort order for a set of symbols using a random number generator. According to you, the output of my random number generator is therefore part of the meaning of the symbols. Does that not strike you as absurd?

    It’s not absurd. If you specify a sort order using a random number generator and match each symbol with a value, then you are assigning that meaning to the symbol. What part of that is confusing? It does not require that the sort order is the only meaning assigned to the symbol.

    I’m sorry if I’m not get getting this whole ‘backed into a corner’ vibe. What I’m saying makes perfect sense.

    ‘Flying in front of the fire station’ is assuredly not part of the flag’s meaning, however.

    Unless, that is, it is determined that flying a flag in front of the fire station does have meaning and it is done to convey that meaning.

    If you see the flag flying at half mast, does that mean anything to you? It means something to the person who flew it at half mast, and they expect that at least some people will recognize that meaning. The example you used to demonstrate what does not have meaning is actually a real example of something that literally can and does have meaning. Perhaps you should have thought about that longer.

    Although I’ve clarified the wording of my initial statement for the benefit of the one person challenged by it, I think that nearly anyone who read it understood it the first time.

    And can we finally move on to this point?

    Relating symbols to referents is something that brains do. You’ve told me that you agree that brains operate according to physical law. If so, then in what sense does physical law fail to explain the mapping?

    I’m happy to move on to your next question, as it implicitly concedes the point you’ve wasted so many posts quibbling over.

    You may find my answer to this question we’re ‘finally moving on to’ back at 12.1.1.2.30.

    Put about as simply as I can, physical laws do not explain everything that they permit or enable.

    A car enables a person to drive from A to B. If you park your car outside a store and it’s across the street when you come out, how will you explain that? Is ‘the car drove there’ an adequate explanation? It’s almost certainly true that the car drove there, and whoever drove it did so the same way anyone drives any car. But an explanation of how the car operates and how one drives it would not sufficiently explain how it got across the street. That is not the explanation you would want.

    Similarly, the operation of natural laws upon the molecules of one’s brain does not explain why one person writes a novel and another whistles Beethoven in the men’s room. And the operation of natural laws does not explain why some cultures selected the symbols “7? and “XII” to represent the number or quantity seven. They do not explain that there is an abstract concept of “seven” which can be associated with any symbol.

    If you disagree then
    – use natural law to explain why the digits 0-9 represent numbers
    or
    – use natural law to explain any set of symbols
    or
    – offer even the vaguest hypothetical process by which a natural law might produce any set of hypothetical symbols.

    Keep in mind that in each case the symbols are not just a reflection, an effect of what they represent, but are used both to create and to receive abstract information. You know, just like when someone imagines 52 cards, prints them on paper or represents them within a simulation, and someone else understands their meaning, even if only in the limited sense of knowing in which order to sort them.

    I admit error all the time, even when I’m right. I’m married. But I won’t admit error when I’m right just because you ask me to.

  252. Scott,

    You’re digging the hole deeper:

    If you specify a sort order using a random number generator and match each symbol with a value, then you are assigning that meaning to the symbol.

    I’ve already shown that you don’t have to match each symbol with a value in order to do a sort, and that the program doesn’t even need to know that there are symbols involved. In fact, there don’t even have to be symbols at all. A computer can sort abstract patterns that don’t symbolize anything. (And please don’t come up with some absurd rationalization like “a pattern always symbolizes itself”. A meaningless abstract pattern doesn’t symbolize anything; it just is.)

    I wrote:

    ‘Flying in front of the fire station’ is assuredly not part of the flag’s meaning, however.

    You replied:

    Unless, that is, it is determined that flying a flag in front of the fire station does have meaning and it is done to convey that meaning.

    No, because if flying the flag in front of the fire station symbolizes something different from what the flag by itself symbolizes, then it is a different symbol.

    If you see the flag flying at half mast, does that mean anything to you? It means something to the person who flew it at half mast, and they expect that at least some people will recognize that meaning.

    Of course. People use symbols to convey meaning. But a flag flying at half mast is a different symbol from the flag itself. A flag flying at half mast symbolizes a significant death or a tragedy. The flag itself does not symbolize either of these things.

    Similarly, the operation of natural laws upon the molecules of one’s brain does not explain why one person writes a novel and another whistles Beethoven in the men’s room.

    Why not? You’ve agreed that the brain operates according to physical law without supernatural intervention:

    I agree that all of it operates within natural law and that none of it violates any laws of physics. Otherwise I would have to think that something bizarre and supernatural occurs every time I imagine a shopping list, write it down, and then go to the store and retrieve the physical items corresponding to my abstraction.

    If making a shopping list just involves a succession of physical brain states evolving according to the laws of physics, why do you believe that the same thing can’t be happening when someone writes a novel or whistles Beethoven?

    I admit error all the time, even when I’m right. I’m married.

    When you think you’re right. I suspect your wife might agree with me on that. :-)

  253. Dr Liddle

    I just saw you jumping from one aspect to another, i.e. you are back to the size sorting aspect; you are jumping from one aspect to another, in a context where it is explicit — cf the EF diagrams you have been referred to over and over a gain over the past nigh on year — are on a per aspect basis. the complexity and specificity must address the SAME aspect of the object, process or phenomenon in question, or you are just confusing yourself.

    The whole point of scientific analysis is that we isolate relevant aspects of phenomena and address them analytically, and from that we build up an overall picture cumulatively.

    With a pendulum, we lock ourselves to a given length, a given swing arc, a given bob-mass, and see how we get a given period. then, systematically, we vary, and see the effects, and notice the mechanically necessary aspects that are showing by low contingency, once we set up a given set-up. Then we see how we have scatter around the ideal model, attributable to various random chance effects. Then also, we may see that there is a personal equation aspect, reflecting the experimenter’s own particular patterns of behaviour. And,we may have someone cooking results — Galileo did, he should have seen enough to note that he arc length does affect period, why in school labs we tell students not to swing more than about 6 degrees.)

    Please, this is not dubious stuff, to be resisted all along. You will end up in inconsistent standards of warrant very fast if you do that.

    Similarly, you will confuse yourself if you refuse to recognise the need to look per aspect.

    And, notice how I have used classic paradigm examples, in the implicit context that a lot of science works by paradigm examples and family resemblance, perhaps with elaborations on a case by case basis.

    The size-based sorting along the length of the beach is a case of mechanical ordering, and is of low contingency, so low information storing potential. That is one aspect.

    I addressed this, and you jumped to another aspect, as though there was not an isolation at work.

    I then noted that the precise pattern of location of pebbles in a vicinity (or even overall) and their alignment in space and relative to each other in contact is a different aspect. That has a lot of randomness in it driving complexity and high contingency.

    This aspect, is highly contingent but resists simple, compressed description that allows you to give the particular pattern. And, the patterns are non-specific, within a broad range, there is no difference between effects of configs. E.g., whether a given flat and oval shaped pebble, no xyzabc, is face up or face down makes but little difference to the functionality of a pile of pebbles shaped by waves. But that ability to be face up/down DOUBLES the number of possibilities for the beach as a whole. Let us say it has eight possible orientations, that gives us three more bits, i.e. we now have FOUR doublings of the number of possibilities for the beach as a whole, and yet whether the pebble is in the horizontal space, in positions 0 to 7, and face up or down, make little or no difference to the behaviour of the beach as a whole or in the pebble’s vicinity.

    (The whole obseerved universe put to work could not sort through all the possibilities of Chesil beach’s pebbles from birth to heat death. So, the arrangement possibilities like this are complex indeed, but hey are not specific, in senses (a) the sort of variability in question has no significant effect on any reasonably defined function, and (b) there is no way to compress and tighten the description from essentially enumerating the locations and orientations of all pebbles. That is, turn the beach into a pseudo-lottery. If you give any particular set of values from the huge config space, obviously it will be very unlikely that that particular config will turn up, but the thing here is that this is in effect a specification of a one-state zone T, and it will not be simply describable.)

    The lottery game tactic — as long since pointed out and it seems brushed aside — is a red herring. I suggest you re-read what Orgel and Wicken have to say, long before Dembski came on the scene; they are in the IOSE intro page that you have been so quick to dismiss. maybe you read, but not with intent to understand. This reminds me of trying to work through the long division algorithm with a young child who is full of objections and distractions.

    Remember, Dembski’s model and metric were designed in light of the issues highlighted by these men and the like.

    By being informational, it confines us to high contingency aspects, which are the only ones that can store lots of info, 500+ bits being in view, so W is beyond reasonable search resources. By looking at specificity of outcomes, that is simply and independently describable, i.e. comes from a special zone T in W, it locks out lotteries.

    the issue then becomes, with chance and necessity on one side and intelligence on the other, what best explains being in T from W? The search challenge makes C + N a most implausible explanation, for long since easily understandable reasons. Intelligence is routinely seen as allowing us to achieve this sort of outcome, as close to hand as text of posts in this thread.

    Can you at least acknowledge this empirical fact, of how intelligence routinely tosses up cases E in zones T in fields of possibilities W? And, how hard it is for a blind chance and necessity alternative to land you in such a zone T?

    What we have been discussing all along is an issue that pivots on high/low contingency AND on specificity in the sense just again pointed out. Functionality, especially that pivoting on digital code strings, is simply the easiest to directly see, and enables understanding the other cases that are reducible to that, once we see how we can represent a nodes-arcs topology as a structured set of digital strings.

    And, yes, GP’s dFSCI case is WLOG, once we genuinely are dealing with being in a narrow, separately and simply describable zone T from a W.

    Of course, all sorts of objections and obfuscations can be tossed out to cloud the issue and distract attention from the pivotal issue on the table. We see that going on all the time.

    That does not change the simple fact that it is all about complex, specific information, and especially functionally specific complex information and linked organisation on a Wicken wiring diagram.

    Yes, we can have difficulties, we can have hard cases, we can have puzzles and limitations, but he CSI concept and its derivatives are about something real and important.

    It is the consistent refusal to acknowledge this, that is so telling about what has gone wrong with the institutionally dominant evolutionary materialist paradigm in science.

    And, in the context that counts, functional objects that are dependent on a narrow set of configs, T, in a W, the log-reduced chi metric expression allows us to focus the issues:

    Chi_500 = Ip*S – 500, bits beyond . . .

    Is the matter informational/highly contingent? is it a matter of a law of necessity?

    Ip settles that.

    (BTW, that is in some respects a postponement of the design inference issue, as the cluster of laws of physics seems also to be contingent and functionally specific in their organisation, i.e. the issue then is pushed back to the design of the observed cosmos. But, that is a reasonable division of work.)

    Is the matter functionally specific? Does it come from a narrow zone T in W, such that wandering outside of T by injecting random noise or some other reasonable and observable test, will lead to breakdown of function? Is it hard to find the next zone of function once we have lost function?

    S accounts for these questions.

    if we have Ip exceeding 500 and S being 1, we then have cases where the inference is best explained on design.

    there are billions of test cases where we can separately know, and the inference is reliable. So there is an epistemic right to use it on inductive reliability.

    To counter this, we need credible counter-examples, which of course, have not been forthcoming, hence the sort of rhetoric-heavy, selectively hyperskeptical objections we keep on seeing.

    Please, let us not just go in circles of recycled, long since cogently answered — but evidently brushed aside — objections. That would point to closed minded ideologically driven a priori commitment (specifically to evolutionary materialism a la Lewontin) in the face of empirical evidence and linked reasonable analysis.

    GEM of TKI

  254. P: The question of isolation is to be addressed on the known challenge of isolation of protein fold domains, the known general pattern of functional specificity to achieve a given capacity, cases like the ATP synthase enzyme, which is a nanotech motor, and the like. At gross scale, we can look at cases like the origin of the avian type one way flow lung, from the bellows type lung. All these have long since been pointed out, and ducked or brushed aside rhetorically. Ideological lock-in of Lewontinian a priori evolutionary materialism and/or its fellow travellers, seems the most credible explanation. KF

  255. KF: “The aspect you presumably had in mind was the grading of pebble size from one end to the other. This is accounted for on chance plus necessity.”

    Liz: “Well I don’t think it is”

    Science: “Lateral grading of beach sediments can be achieved by down drift and/or long shore drifting.”

    http://www.jstor.org/pss/4298523

    It appears the pebble gradients are accountable by chance and necessity.

    And the chance-necessity mechanism for the origin of the genetic code is___

    I wasn’t clear. What I meant was that kf cannot dismiss the beach’s CSI because it is discounted by a “Chance and Necessity” explanation. Dembski’s (and, as far as I can understand it, kf’s) formula for calculating CSI does not have term that says: A pattern only has CSI if it is not caused by Chance or Necessity.

    That would be entirely circular. Dembski’s Fisherian test is that if the CSI of a pattern is beyond a certain value, then we can reject chance or necessity and conclude design.

    So kf is not being logical if he is arguing that, well, no, the beach doesn’t have CSI because it’s created by Chance and Necessity.

    The point of CSI is that it is supposed to tell us whether an object was created by Chance or Necessity, and, if not, by Design. To calculate the CSI by including a known cause in the calculation would render it useless.

    Not that I accept the Chance vs Necessity dichotomy. That’s another fundamental problem with Dembski’s argument, but perhaps it’s better to leave that for another time, seeing as in his 2006 formulation he dropped the distinction.

  256. Here is your error, kf:

    The size-based sorting along the length of the beach is a case of mechanical ordering, and is of low contingency, so low information storing potential. That is one aspect.

    You have, a priori, dismissed CSI for my beach because you happen to know (as I do) what caused the pattern.

    But you cannot insert a “cause of pattern” term into the CSI calculation because the whole point of the CSI calculation is to determine whether the cause of the pattern is Chance, Necessity of Design.

    So you are assuming your consequent.

  257. You have, a priori, dismissed CSI for my beach because you happen to know (as I do) what caused the pattern.

    CSI doesn’t even apply in the beach scenario.

    But you cannot insert a “cause of pattern” term into the CSI calculation because the whole point of the CSI calculation is to determine whether the cause of the pattern is Chance, Necessity of Design.

    Specified complexity, not CSI.

    You don’t use CSI for a beach Lizzie.

  258. Petrushka:

    Despite claims to the contrary, the only process known for designing proteins and for discovering their folds is cumulative selection. In chemistry or in simulations, it’s cut and try.

    The one BIG problem with that is cumulative selection has never constructed a protein from scratch, ie in the absence of any other protein(s).

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