Home » Darwinism, Evolution, Intelligent Design » Doug Axe now replies to James Shapiro: Can we let the science decide?

Doug Axe now replies to James Shapiro: Can we let the science decide?

Readers will recall James Shapiro, author of Evolution: A View from the 21st Century. Bill Dembski asked him, based on his observations, Why aren’t you a design theorist?

Which, in the context, is somewhat like asking, “Well, if you agree with me about how badly things are run down at City Hall, will you join Citizens for Municipal Reform?”

Well, Shapiro replied, giving his objections, and now Biologic Institute’s Doug Axe has replied to Shapiro here:

I think we all agree that science should be the arbiter here. Naturalism and ID both make testable claims about how things happen in the real world, so it ought to be possible to evaluate these positions by evaluating their respective claims.

If crutches are devices for propping up lame positions, then I completely agree that they should go, but let’s be careful to call a crutch a crutch. As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

Shapiro is looking for a no-Darwin but no-intelligence  solution. Does it exist?

Also, Axe’s senior scientist Ann Gauger offer some thoughts on Dembski’s questions here.

0 to 60 quick, on Shapiro:

Antibiotic resistance: The non-Darwin truth

“Four kinds of rapid, multi-character evolutionary changes Darwin could not have imagined”

“Key non-Darwinian Evolutionary Scientists in the 20th Century”

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154 Responses to Doug Axe now replies to James Shapiro: Can we let the science decide?

  1. Douglas Axe:

    As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not. [Emphasis added]

    Another case of an ID proponent appealing to the supernatural. I show that Dembski does the same thing here and here.

    Could we drop the “ID isn’t religious” pretense?

  2. Only if we could drop “Darwinism isn’t religious” pretense.

  3. ‘Darwinism’ doesn’t appeal to the supernatural.

  4. Yeah, I often wonder why the ID people fight so hard for the pretence that ID is not religious. Why does it matter to them? Why try and construct a science around a religious belief?

  5. 5

    Supernatural does not necessarily = religious. A religious interpretation is one of many possible interpretations of an assumed supernatural event. As in the religious interpretations of t=0. Arguing that a specific creator triggered the big bang is religious. However, recognizing t=0 as outside the laws of nature, i.e. supernatural by definition, is within the scientific framework.

  6. “Darwinism” isn’t a religion, on any definition of religion that I know of.

    It’s a scientific theory.

  7. Darwinism isn’t a scientific theory based on any definition of science nor theory that I know of.

  8. champignon- ARTIFICIAL not supernatural-> natural is being contrasted with artificial.

  9. Really?

    So, how come Shubin knew exactly where to dig to find Tiktaalik?

    Just a guess was it?

    I’d suspect the probably of that being a guess would be over the UPB and therefore it must be design!

    I’ve got no way of substantiating that, it’s just a “feeling”. Nonetheless it’s true! I just know it.

  10. 10

    Joe,
    So what is the most parsimonious explanation then?

    Given that you already said you actually believe the designer is in fact an alien race that colonized earth and that we in fact are those aliens I have to wonder if the tent can survive getting any bigger?

    In fact, I think I see it blowing away!

    So, Joe, if the designer is aliens where did they come from? They evolved did they? Or what?

    ROFL.

  11. By “naturalistic solution,” Axe is clearly referring to the (supposedly) intelligence-free forces of nature, in and of themselves.

    The origin of Stonehenge is also said to preclude any naturalistic solution. Does that mean Stonehenge is the product of the supernatural? Of course not.

    As kairosfocus has repeatedly pointed out, the distinction here isn’t between natural and supernatural, but natural (created by nature) and artificial (created by intelligence).

    The brilliant Doug Axe recognizes that the origin of life, and, subsequently, the entire domain of biology, falls under the latter: artificiality.

    You three, Liz, Nick, etc., refuse to recognize it, not because of an absence of evidence or convincing arguments, but because you have a dogmatic, religious-like commitment to a design-free worldview.

    Your entire purpose here is to concoct as many excuses as possible to justify this rejection, without admitting your true motivations: It dumps all over your preferred worldview.

    What you want us to believe: “I reject I.D. because it’s not scientific! There’s no evidence for it! It’s unfalsifiable!”

    What we actually know: “I reject I.D. because I absolutely hate the implications of life being designed!”

    I assure you, no one’s being fooled.

  12. What is/are your definition(s) of science and of theory?

  13. 13

    jammer,

    the distinction here isn’t between natural and supernatural, but natural (created by nature) and artificial (created by intelligence)

    So, jammer, you would presumably then agree that the distinct structures that enable protein molecules to perform their specific tasks inside cells were created by aliens who visited the earth a very long time ago?

    After all, if they are natural and created by intelligent action the only option you have is that it was done by aliens. Very long lived aliens who act in ways that exactly mimic what we would call evolution. And who never, ever, pass innovations over clades.

    The brilliant Doug Axe recognizes that the origin of life, and, subsequently, the entire domain of biology, falls under the latter: artificiality.

    Do you think the aliens still come to visit? That perhaps they visited recently in human history? That some of the stories about the golden city are really true?

    If it’s not space aliens then what is it? It can’t be a supernatural deity, that option is not even on the table if natural (created by nature) and artificial (created by intelligence) is all there is.

    Do you and Joe believe in the same aliens, out of interest? Or are there sub-groupings there also?

    Where did the aliens come from by the way? Did they evolve originally?

  14. 14

    “I reject I.D. because I absolutely hate the implications of life being designed!”

    What exactly are those implications then? If we are designed by a material intelligent much like us then what comfort does that give the theists exactly? It’s not a very good designer. Almost autistic I’d say. Sure, the fine detail work is great, but putting the food down the same pipe as the air? Please! And looking downstairs, a similar basic error was made!

    the distinction here isn’t between natural and supernatural, but natural (created by nature) and artificial (created by intelligence).

    So the implication is that we were designed by aliens who may or may not be (crop circles?) still around. How do you feel about that, exactly? Does it worry you? Does it make you anxious?

  15. Darwinism is a scientific hypothesis formulated in the ignorance of the mid-19th century. It’s since been falsified by nearly every single branch of biology.

    Unfortunately, somewhere in between the time it arrived on the scene and the present day, it evolved into less of a scientific hypothesis and more of an atheistic religion. It purported to explain the huge design of life, absent an actual designer?exactly what atheists needed for “intellectual fulfillment.”

    This is the real reason why the various forms of “blind watchmaker” evolution are so ardently defended. Not to protect science, but to protect that illusion of “intellectual fulfillment.”

    It’s no coincidence that a high percentage of Darwinism’s most notable defenders are atheist: Richard Dawkins, Jerry Coyne, Eugenics Scott, P.Z. Myers… The list could go on for ages.

    Sure, there are some confused theists who support Darwinism for various reasons (they’ve been taught it as fact for so long, they give in to peer-pressure, they have financial commitments, etc.), but the percentage of atheists amongst Darwin defenders cannot be ignored, nor can it be written off as coincidence.

    So, yes, Darwinism is clearly a religion, and yes, every single overzealous defender of Darwinism should be labeled a religious fanatic. As someone who doesn’t subscribe to any religion, I can say with nary an ounce of doubt that the average Darwinist is far more fanatical than the average Christian.

  16. champignon:

    Another case of an ID proponent appealing to the supernatural. I show that Dembski does the same thing here and here.

    Could we drop the “ID isn’t religious” pretense?

    Axe has shown using results that he reached experimentally in his field (cell biochemistry) that a Darwinian or other naturalistic explanation for the biochemical mechanisms in the cell is so improbable as to be virtually impossible. This is a scientific result.

    It is you that draws the conclusion that he is appealing to the supernatural. He has not done that. He has merely demonstrated the inadequacy of the existing scientific theory.

    If you believe that the only possible explanation for what Axe has shown to be true using the scientific method is that there is a supernatural cause for the existence of living things, then I suggest you re-evaluate your materialism.

  17. ‘Can we let the science decide?’

    The perfect rejoinder, Mr Dembski. It is regrettable that elementary didacticism should occasionally be necessary, but Mother Nature, alas, is a sham and it is important to insist on it.

  18. Peter:

    So what is the most parsimonious explanation then?

    One design.

    Given that you already said you actually believe the designer is in fact an alien race that colonized earth and that we in fact are those aliens I have to wonder if the tent can survive getting any bigger?

    Actually I said I am OK with the notion that we are decendents from an other-world civilization.

    So, Joe, if the designer is aliens where did they come from?

    can’t say until we can study them, duh.

  19. Peter:

    So, how come Shubin knew exactly where to dig to find Tiktaalik?

    According to Shubin he wouldn’t have been looking there had he known about the data that came after his discovery. ya see he said he was looking where he did because he thought tetrapods didn’t exist yet- however they did. He was looking in the worng strata for the transition he said he was looking for. Read “Your Inner Fish” chapter 1.

  20. Elizabeth,

    I use the standard and accepted definitions of both science and theory.

  21. I use the standard and accepted definitions of both science and theory.

    Which are…?

  22. According to Shubin he wouldn’t have been looking there had he known about the data that came after his discovery. ya see he said he was looking where he did because he thought tetrapods didn’t exist yet- however they did. He was looking in the worng strata for the transition he said he was looking for. Read “Your Inner Fish” chapter 1.

    I’ve read it. It doesn’t say that.

    You are making the “why are there still monkeys?” mistake.

  23. Bruce,

    If the facts preclude a naturalistic explanation, as Axe believes, then what is left? A non-naturalistic (aka supernatural) explanation.

    Or are you claiming that there is such a thing as a non-naturalistic, non-supernatural explanation?

  24. Axe has shown using results that he reached experimentally in his field (cell biochemistry) that a Darwinian or other naturalistic explanation for the biochemical mechanisms in the cell is so improbable as to be virtually impossible. This is a scientific result.

    Depends what you mean by “a scientific result”. There have been plenty of criticisms of his probability calculations.

  25. I have it and it says it:

    Shubin said- SHUBIN SAID- he was looking where he did because he had data that put the transition from fish to tetrapods between 385- 365 million years ago.:

    Chapter 1 of “Your Inner Fish” tells us why:

    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    However new data has tetrapods appearing over 390 million years ago, meaning his data was out-dated and is wrong.

  26. I use the standard and accepted definitions of both science and theory.

    Which are…?

    Buy a dictionary or a vowel- what is wrong with you people?

  27. I’m not claiming anything other than that Axe’s scientific research has demonstrated that Darwinism in particular and a naturalistic explanation of life in general is untenable.

    You’re drawing the conclusions. I think that if you conclude that this implies that life has a supernatural cause, you should have the courage of your convictions and abandon your commitment to a materialistic philosophy.

  28. Yes, and Axe has answered them. He’s way too smart to make a mistake in his probability calculations in a paper prepared for publication.

  29. It’s not the calculations; it’s the narrowness of the sampled population.

  30. Mr Griffin,

    You seem to be someone who has more answers than questions, so I thought you might shed some light on some observable (and very interesting) physical dynamics. If it’s not too much of an imposition, would you mind being interuped just for a moment in order to address such an issue, in earnest of course?

    All life on this planet stems from a formal system where two material objects have a purely relational coordination to one another, yet they do not interact, and both must be in place for the system to function. Can you shed some light on the (apparently) obvious origin of such a system?

  31. Upright,

    While Mr. Griffin ponders your question, perhaps you could answer the question Nick Matzke posed to you three days ago, which you have been avoiding ever since:

    if a gene is duplicated, and one copy get modified such that it has a different specificity or function, has the amount of information in the genome increased?

  32. Which came first, the chicken or the egg?

  33. Petrushka,

    What you don’t get about the proponents of ID is those of them who are scientists are very, very smart. Michael Behe, Jonathan Wells, Stephen Meyer, William Dembski, and particularly Douglas Axe would never be so stupid or careless as to make rookie mistakes in the application of probability theory or statistics in a published paper. Not gonna happen.

  34. True, but materialistic naturalism (and Darwinism as an epitome of it) willfully ignores certain obvious information and control related things. This has been repeated so many times… If Darwinist explanations were adequate 150 years ago in the absence of knowledge in some specific areas of the theory of information and biochemistry, now it is no longer enough.

    Before Darwin, scientists were quite happy with something that ‘appealed to the supernatural’. If we ask ourselves what did Darwin actially, did he show something rigorously? The answer is, no. He hypothesised and philosophised. While some may be happy with what he wrote, others are free to question it. It does not stand scrutiny. Trouble is it is not accepted by a majority today. Well, as we know from the history of science, things do change. People are always angree at something which questions their position. At one point, Georg Ohm’s colleagues ridiculed his work on electricity calling him all sorts of names. Where are they now?

  35. Joe, it is no use. We know empirically how people from the other camp can twist definitions they said were taken from a dictionary.

  36. No, it means that he was correct, for correct reasons, in his prediction that he would find tetrapods in that stratum in that place.

    We know know that other tetrapods also lived earlier. But his prediction was not that “the first tetrapods will be found in Greenland” but that “tetrapods showing transitional characteristics are likely to be found in Greenland”.

    And he was absolutely correct.

  37. I mean “transitional” of course in the sense of “showing features of both earlier and later organisms, not as in “animals that are both descended from Silurian fish and directly ancestral to all modern tetrapods”.

  38. I would just say that IMO Shapiro can go on with his cognitive attitude, and go on making good science. Unless he can really show a “third way” (and I don’t think he can), all he does is definitely in favour of ID.

    That’s very fine with me. It’s important to have people who make good ID research outside of ID.

  39. So why can’t you produce the definitions you are using?

    How else are we to know which of several dictionary definitions is the one you mean?

    Here is Merriam-Webster:

    Definition of SCIENCE
    1
    : the state of knowing : knowledge as distinguished from ignorance or misunderstanding
    2
    a : a department of systematized knowledge as an object of study [the science of theology] b : something (as a sport or technique) that may be studied or learned like systematized knowledge [have it down to a science]
    3
    a : knowledge or a system of knowledge covering general truths or the operation of general laws especially as obtained and tested through scientific method b : such knowledge or such a system of knowledge concerned with the physical world and its phenomena : natural science
    4
    : a system or method reconciling practical ends with scientific laws [cooking is both a science and an art]
    5
    capitalized : christian science

    Definition of THEORY
    1
    : the analysis of a set of facts in their relation to one another
    2
    : abstract thought : speculation
    3
    : the general or abstract principles of a body of fact, a science, or an art [music theory]
    4
    a : a belief, policy, or procedure proposed or followed as the basis of action [her method is based on the theory that all children want to learn] b : an ideal or hypothetical set of facts, principles, or circumstances —often used in the phrase in theory [in theory, we have always advocated freedom for all]
    5
    : a plausible or scientifically acceptable general principle or body of principles offered to explain phenomena [the wave theory of light]
    6
    a : a hypothesis assumed for the sake of argument or investigation b : an unproved assumption : conjecture c : a body of theorems presenting a concise systematic view of a subject [theory of equations]

    Which of these do you regard as “standard”?

  40. But his research completely undermines ID’s central thesis! It suggests that the design processes that give rise to functional organisms are intrinsic, not the result of external design and implementation.

  41. 41

    Here’s my questions to atheists:

    1. At what point would you accept that the universe or nature had a supernatural first cause, or would you always just hope/believe that one day, perhaps long after you’re gone, an answer will be found that supports a materialistic explanation? Isn’t that FAITH?? For example, let’s say GOD created the universe, how would you ever realize THAT if you continue to reject that possibility from the start? You say the supernatural is not science, but you accept other things that cannot be verified by our scientific methods, such as the belief that all life is the sole product of darwinian evolution. Even uber-darwinist Jerry Coyne admitted:

    In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history’s inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike “harder” scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.
    Of Vice and Men The New Republic April 3 2000 p.27

    Yet darwinian evolution is beyond reproach. Why? How is your faith in it, different from my faith in a creator? (Aside from the fact logical deduction of the evidence points to a creator)

    2. Why is ANY possibility allowed, EXCEPT God? Extraterrestrials, a multiverse, etc are both allowed to be promoted as ‘science’ yet there’s no evidence for either. There’s also no evidence our ‘scientific’ methods would be able to determine an extraterrestrial or a multiverse, yet both are put forward as possibilities…but not GOD. Why?

    Thank you

  42. Elizabeth:

    It may suggest that, but it will never be scientifically supported, because there is no “third way” (just my opinion :) ). The research remains valid, and it supports ID. Shapiro is just looking desperately for a way out of the simple fact that all he knows and all he finds supports ID. But he will not find that way. In the meantime, as he is a good and honest scientist, his research is contributing both data and concepts that are certainly useful.

    By the way, could you explain simply what you (or Shapiro) really mean by “intrinsic design process”? Just curious.

  43. No, he is not “looking desperately”.

    And by “intrinsic design process” I mean the evolutionary algorithm itself – the tendency of things that replicate with heritable variance in reproductive success to adapt to their environment. Shapiro essentially is talking about that algorithm at population level – the evolution of evolvability. Which you could state as the tendency of populations that are maximally adaptive (have optimal rates and types of variance production for instance, or optimal epigenetic mechanisms) to persist over time, resulting in extant populations being those consisting of organisms who have heritable mechanisms that tend to result in successful population adaptation.

    It’s an extension of the Darwinian system, not an alternative to it.

  44. Dr Liddle,

    This is equivalent to the untenable position of emerging formalism and semantics. Unguided evolution can at best modify what it’s given. It has no capacity to produce sufficient novelty. There is no ‘magic’ inside RV + NS. Emergence is just a rhetorical device. Nothing of the sort has ever been detected in nature (apart from life, which is the point in question, and complex enough artefacts).

    In nature, there are no algorithms, nor ever can be. Simply because physical reality is inert to utility.

    Algorithm is a formal process which assumes a formal language, semantics and a way to steer system states towards improving utility (i.e. control). Algorithms therefore cannot explain the emergence of semantics.

  45. Spot on.

  46. Pick any one (from each word) and tell us how Darwinism fits it.

    Good luck…

  47. I answered Nick’s question. Eiethr respond to that or bug off.

  48. Elizabeth you are confused. He was NOT looking for tetrapods. He said he was looking for the TRANSITION between fish and tetrapods which occured much earlier than the strata he found Tiktaalik.

    And yes his prediction was that the transition between fish and tetrapods would be found in strata after fish and BEFORE tetrapods. That is what Shubin said.

    It is stupid to go looking for evidence of a transition many millions of years AFTER the transition took place.

    Also “transitional foem” boils down to nothing more than “it looks like a transitional to me”.

    Also given the new data there would be no reason to look for the transition where he did.

    But obvioulsy you cannot grasp any of that.

  49. Shubin:
    Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.- Neil Subin pages 9-10

    Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.

    What part of that don’t you understand? The problem is the transition took place millions of years earlier. So no he shouldn’t be looking for evidence of the transition between fish and tetrapods in rocks about 375 million years old. The transition took place before that.

    IOW you evos don’t know what you are talking about and it shows.

  50. 2.2.1.

    Champignon,

    Could I also add my two pence. I hope UprightBiped will allow me to intervene.

    I think that the answer to your question is ‘yes’. A simpler example is a random correction of an error (such as a double negation, one after the other, or a sequence of two mutations where the second cancels the first). These are examples where an increase of information happens by chance. However, acknowledging that this can happen is not the same as acknowledging that this is the way functional information emerges. Do you think that the two are equivalent:

    1) I can walk;
    2) Since I can physically walk, I can walk to the Moon?

    Empirically, we can see that whenever there is a high enough quantity of functional info, it is as a result of intelligent agency. As has been noted, this is not a logical necessity proof, but an empirical observation based on data available today.

    Empirically, as soon as we detect formal function, control, semantics, we are looking at artefacts. In other words, one can engage in all sort of Darwinian explanations but by far probabilistically the best (in terms of Newton, Occam and Bayes) will be choice contingency (design).

  51. I think it was the egg. I believe you think so too (correct me if I am wrong). And so?

  52. Dr Liddle,

    This is equivalent to the untenable position of emerging formalism and semantics. Unguided evolution can at best modify what it’s given. It has no capacity to produce sufficient novelty. There is no ‘magic’ inside RV + NS.

    There doesn’t have to be “magic” to produce novelty. And I simply dispute your other assertions!

    Emergence is just a rhetorical device. Nothing of the sort has ever been detected in nature (apart from life, which is the point in question, and complex enough artefacts).

    It’s certainly a word, and so, in that sense, is a “rhetorical device”. I’d say, rather, that it is a useful concept, and if we describe it simply as properties of a whole that are not possessed by its parts, then it is “detected” in nature all the time. We would be unable to make sense of the world were it not so.

    In nature, there are no algorithms, nor ever can be. Simply because physical reality is inert to utility.

    This makes no sense to me. Clearly there are only things called “algorithms” if there are people to call things “algorithms”. “Algorithm” in other words is an attribute we assign to systems with certain properties that we call “algorithmic”. And there are many processes in nature that display those properties, I would argue, not all of them even organic. Any sorting systems is “algorithmic”. And evolutionary processes certainly are, because we can actually model them as computer algorithms!

    Algorithm is a formal process which assumes a formal language, semantics and a way to steer system states towards improving utility (i.e. control). Algorithms therefore cannot explain the emergence of semantics.

    Well, the expression of an algorithm may require a semantic language (at least at high level). But the essence of an algorithmic process, surely, is that what happens next is contingent on what happened before – the “if…then” statement in a computer algorithm. But it doesn’t have be expressed symbolically, it can just occur. “WHILE stones exist IF stone weight > W AND velocity < V, THEN drop stone, ELSE roll it back” is just a human-language way of expressing the intrinsic rule by which, for example, stones along a beach may be systematically graded small to large.

    Chesil Beach

  53. Also “transitional foem” boils down to nothing more than “it looks like a transitional to me”.

    No, it doesn’t. That’s probably why you’ve misunderstood Shubin.

  54. Yes it does- just look at the criteria for “transitional form”.

    And you have no idea what Shubin said- you obviously have reading comprehension issues.

  55. And what are the criteria for “transitional form” Joe?

  56. Yet darwinian evolution is beyond reproach. Why? How is your faith in it, different from my faith in a creator?

    The darwinian paradigm is based upon actions that we can see having an effect on the very entities in which we are interested – biological organisms. The competition of replicators in a finite world is almost axiomatic – of course if more organisms are born than can possibly survive, there will be concentration of fitter variants. Whether this simple fact can or cannot have led to current organismal diversity is a challenge to one’s conceptions of plausibility, and one cannot put one’s own conceptions as superior to another’s, in either direction. Still … I have absolutely no trouble with conceiving the process in action, sweeping right through barriers that others perceive – and all too often, these perceptions are quite clearly rooted in a misperception of what evolution actually says. Trying to deal with those misperceptions wins one no friends, since one is dealing with something rather central to the opponent’s worldview***, rather than someone keen to learn more.

    Evolution has the satisfying character that no causes are introduced that we cannot observe in action, or model based upon known principles. If you think that the proposition is implausible, fair enough. But it requires no faith to consider history to have unrolled according to principles we can investigate now, any more than it requires faith to consider it plausible that the Normans came from France rather than from outer space. And the better one understands the fundamentals of the process, the better placed one is to evaluate its plausibility.

    The design inference, however, requires introduction of an exceptional cause. We can see design in action, among entities that are the end result of some historic process. We use that inference to pass that same quality back into the historic process itself. And that, to me, requires the leap of faith – faith I do not possess, that an entity capable of such interference can even have existed, let alone performed the interactions necessary to overcome the assumed barriers to complexity. The same applies to space aliens as to deities.

    *** And, as an aside, I do wish people would stop asserting that somehow atheists have some fundamental need, ideological or whatever, to see evolution as true. Their confidence in it (faith, if you will) is rational, and would be overthrown by rational considerations. That’s not to say that alternatives are irrational, but analogies that other people find convincing are not convincing to me. My ‘commitment’ to atheism is about equivalent to my commitment to not supporting a particular, or any, football team. I’m just not that interested. It needs no support from biology.

  57. Geez you just can’t do anything for yourself- It has to look like a transitional form, meaning is has characteristics of the alleged ancestor and the alleged descenents:

    Fossils or organisms that show the intermediate states between an ancestral form and that of its descendants are referred to as transitional forms.- UBerkley

    That means it looks like a transitional form.

  58. Misposted reply to Blue Savannah at 6!

  59. OK so according to Shubin he was NOT looking for a transitional form, rather he was looking for evidence of the transition which HE said would be between two data points-> fish and no tetrapods and fish and tetrapods.

    Unfortunately Tiktaalik was found in strata in which both fish and tetrapods existed.

  60. Dr Liddle,

    What “just occurs” (borrowing your terminology) cannot be shown to prefer one scenario over another to achieve a goal. Agent-based choice between naturally occurring scenarios is the only thing that can cause control to happen.

    I define control as a formally describable process that drives a system through a sequence of states towards improved utility (function). Empirically, control per se always requires a layer on top of physical reality. Particular mechanisms of control are necessarily instantiated into physicality, but physicality alone cannot be sufficient to understand the semantics of information. There are simply no observations which would give grounds to the belief that control can crystallise from chaos. So control is irreducible to physicality.

    Think of the TCP/IP stack of protocols for communication between computers. Control is first defined conceptually at the top (application layer) and then realised all the way down to network layer and finally to physical layer of electric/optic circuitry. Semantics is given by the encoding/decoding protocols, i.e. via a non-physical entity. In no way is it possible to think of anything like a scenario where the meaning of communication can emerge at the level of voltage jumps in the connecting cable. We note on massive observation that meaning or control cannot crystallise.

    Agent-based choice is at the heart of any algorithm. Why is control inherent in what “just occurs” in the cell or complex artefacts and, at the same time, not inherent in what “just occurs” in other scenarios? When you answer this question for yourself, you will see that formalism or semantics cannot emerge in “just-occurring” scenarios but always need agency. Whenever we are able to detect formal function, the detection is an empirically warranted pointer of design.

  61. Elizabeth:

    And by “intrinsic design process” I mean the evolutionary algorithm itself – the tendency of things that replicate with heritable variance in reproductive success to adapt to their environment. Shapiro essentially is talking about that algorithm at population level – the evolution of evolvability. Which you could state as the tendency of populations that are maximally adaptive (have optimal rates and types of variance production for instance, or optimal epigenetic mechanisms) to persist over time, resulting in extant populations being those consisting of organisms who have heritable mechanisms that tend to result in successful population adaptation.

    Wow! When you start that way, I have only two options: either become aggressive and spend a lot of time trying to show you, without succeeding, that what you are saying is senseless, or leave you at your opinions.

    As today we suceeded in agreeing on one thing, I will take the second option :)

  62. The most parsimonious explanation is: “I don’t know.” Everything else is playing the Texas Shaprshooter fallacy over billions of years of rock strata. And it’s not simply that the historical narrative of Evolution is a creation myth. It’s a creation myth that rests its laurels on ad-hoc hypothesizing and positivism as its proof that it is the One-True-Truth behind the creation of man.

    If you want parsimonious religious frameworks then there are plenty to choose from that have far better apologetics in place than Darwinism. If you want parsimonious scientific theories, then get back to me when we start performing experiments on the lab-table.

  63. 63

    Thank you for your reply Chas.

    But it requires no faith to consider history to have unrolled according to principles we can investigate now, any more than it requires faith to consider it plausible that the Normans came from France rather than from outer space. And the better one understands the fundamentals of the process, the better placed one is to evaluate its plausibility.

    It DOES require faith Chas, because you’re talking about a historical science, not an empirical one. Like I showed in my original post, even Jerry Coyne admits that. Darwinism is a worldview, a religion if you will, not a scientific theory. When ANYTHING and EVERYTHING is attributed to it no matter how contradictory to previous predictions and claims, that proves the ‘theory’ is UNfalsifiable.

    Now, if you wish to believe in it, that’s your right. I firmly believe God gave us free will (contrary to atheists’ claims that we have no free will) and that you have the right to believe as you choose. The problem is, you are not promoting a scientific theory, but rather your materialistic faith.

    As I asked before, at what point would you ever concede there MUST be a supernatural first cause for nature/the natural? If you say never, then you are ignoring the known scientific principles we have, in exchange for faith that one day, all the mysteries will be explained by purely naturalistic means.

    The design inference, however, requires introduction of an exceptional cause. We can see design in action, among entities that are the end result of some historic process. We use that inference to pass that same quality back into the historic process itself. And that, to me, requires the leap of faith – faith I do not possess, that an entity capable of such interference can even have existed, let alone performed the interactions necessary to overcome the assumed barriers to complexity. The same applies to space aliens as to deities.

    Tell that to seti and the other ‘scientific’ journals that allow e’t's to be postulated, but not GOD. ;-)

    But to get back to the point, what you’re doing is saying GOD wouldn’t do this or that, ergo God can’t exist. That’s not a logical position my friend. Why couldn’t the GOD of the Bible exist and do what the Bible claims He did/does?
    Only GOD, someone outside the laws of physics, could be the cause of them. God is eternal, and UNcaused…that’s why He’s GOD. Just because you may not be able to fully comprehend Him (none of us can) doesn’t mean His existence is improbable. Only GOD could be the intelligent agent behind the complex genetic code.

    The living cell is a complex, biological machine that rivals computer OS in terms of information. If you wouldn’t believe the information in Windows 7 came into existence by itself, why would you believe the information in a living cell did? We can use the same experience and knowledge that tell us the information in Windows 7 had an intelligent creator, to deduce the information in the living cell had a creator. All I’m asking is that you use the same logic and intelligence that tells you the faces on Mt Rushmore were not caused by erosion slowly over time, to realize the living cell is not the product of blind, random chance.

    And, as an aside, I do wish people would stop asserting that somehow atheists have some fundamental need, ideological or whatever, to see evolution as true. Their confidence in it (faith, if you will) is rational, and would be overthrown by rational considerations.

    I have to disagree. It was Richard Dawkins who said:

    An atheist before Darwin could have said, following Hume: “I have no explanation for complex biological design. All I know is that God isn’t a good explanation, so we must wait and hope that somebody comes up with a better one.” I can’t help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.
    – Richard Dawkins, The Blind Watchmaker (1986), page 6

    Atheists NEED darwinism, which is why they fight so hard to prevent it form being criticized, and having dissenting opinions heard.

    Take care

  64. “Only GOD could be the intelligent agent behind the complex genetic code.”

    I think there’s an ixnay on admitting the Godnay is the Designernay herenay….

    Hilariously to those of us amused each time someone tries to argue ID isn’t a flimsy creationist front, against historical, current funding and logical considerations.

    Your politicians even call it “intelligent design creationism”

  65. Elizabeth, you wrote:

    “But his research completely undermines ID’s central thesis! It suggests that the design processes that give rise to functional organisms are intrinsic, not the result of external design and implementation.”

    Who told you that “ID’s central thesis” is about *external* design and implementation? Or did you just infer it, based on your dipping into bits of ID writing and lots of critical writing against ID?

    Bill Dembski has spoken on more than one occasion of two possibilities: immanent design processes and extrinsic ones. He has said he personally finds the extrinsic one more probable, but has made a point of including the immanent one under the ID concept. Also, in Michael Denton, the only “external” imposition is at the time of the Big Bang; after that, evolution takes place entirely in accord with the immanent potentiality of nature. Michael Behe has acknowledged that such a possibility falls under the rubric of ID as well.

    I am *not* arguing that Shapiro counts as an ID theorist. I am merely point out a misconception that you are promoting about ID. I think you had better check out what ID people say about themselves before deciding what “ID’s central thesis” is. It *isn’t* “biological design is externally imposed.”

    T.

  66. I think there’s an ixnay on admitting the Godnay is the Designernay herenay….

    Hilariously to those of us amused each time someone tries to argue ID isn’t a flimsy creationist front, against historical, current funding and logical considerations.

    Your politicians even call it “intelligent design creationism”

    You would have an argument IF I were an I.D proponent, but I’m not that vague. I’m a Young earth CREATIONIST, and have disagreed with some of the articles I’ve seen on here. If I.D and creationism were the same, why would there be disagreements??? The great thing is, unlike darwinists, creationists and I.D proponents allow other opinions to be heard.

  67. Elizabeth, you wrote:

    “It’s an extension of the Darwinian system, not an alternative to it.”

    Let’s see now. James Shapiro is a full-time evolutionary biologist. He publishes in that field, and, I presume, keeps up with the technical literature in that field, goes to conferences in that field, discusses the broader implications of his work with colleagues in that field, etc. His own description of his work is as a challenge to major elements of the classical neo-Darwinian system (Modern Synthesis).

    Elizabeth is a neuroscientist. She publishes in that field, and presumably, requires many hours per month to keep up with the technical literature in that field, go to conferences in that field, etc. This leaves her with little time to read the technical literature that James Shapiro reads, little time to write the articles that James Shapiro writes, and little time to go to the conferences on evolutionary biology that James Shapiro attends.

    So, we have a claim that a neuroscientist who reads about evolutionary biology on the side understands the implications of an evolutionary biologist’s work better than he himself does? He erroneously supposes himself to be challenging the neo-Darwinian synthesis, but she correctly discerns that he is merely extending it?

    Is it usual practice for a scientist in field A to claim to have understood the meaning of the work of a scientist in field B better than the scientist in field B understands it himself?

    Just asking.

    T.

  68. Timaeus

    Seems like according to your account ID is compatible with Darwinism. Is that true?

  69. ‘Darwinism’ is an ideology. Is there really any honest dispute about this?

    What kind of PoS is on tap here?

  70. Blue-Savannah

    You raise a good point. If we only accept methodological naturalism how are we ever going to know about a supernatural being or event? My personal answer is that it has to be by direct experience – revelation or whatever. It cannot be through science for reasons that Lizzie has explained. A good scientist, when he or she cannot find a natural explanation of anything, says “I don’t know why – but let’s keep on trying to find out”.

  71. markf:

    Huh? I have no idea how you could have drawn that conclusion from anything that I wrote. I said that ID is compatible with immanent design. Darwinism is the denial of all design (all real design, I mean, as opposed to simulated design).

    Are you possibly confusing “Darwinism” (a mechanism explaining evolution) with evolution itself (a process of change in species)? Of course ID is compatible with “evolution.” Again, the most obvious example is Denton. ID’s beef is against the Darwinian mechanism, not against evolution. Many ID proponents endorse evolution — Behe, O’Leary, Sternberg, StephenB — they just think the Darwinian explanation of evolution is hopelessly inadequate. (As do some prominent non-ID scientists, including Margulis and Shapiro.)

    T.

  72. It DOES require faith Chas, because you’re talking about a historical science, not an empirical one.

    The processes of evolution can be empirically verified right now. They boil down to birth and death in a finite world. They lead to emergent consequences, deeply investigated, and these are, quite reasonably, inferred to have operated whenever birth-and-death-in-a-finite-world has occurred. It requires no faith in something else. In the specific historic matter of how life got to its present state, we are not privileged to evaluate any proposition directly. But speaking strictly for myself, I do not perceive this as a matter of faith. Faith requires the introduction of additional causes, not empirically observable. The observation of designing entities in the present is not equivalent to the observation of processes emergent upon birth and death in a finite world.

    Darwinism is a worldview, a religion if you will, not a scientific theory.

    Well, I will just have to disagree. This ‘religion’ thing is pushed to death, and if it helps you to rationalise why people may think differently on the data, please yourself. But it requires no belief in an external entity, higher intelligence, moral code, ritual, static text by revelation or any of the trappings one would conventionally ascribe to a religion. All we are left is the vague metaphorical usage of “something pursued with enthusiasm”. Whatever!

    Now, if you wish to believe in it, that’s your right. I firmly believe God gave us free will (contrary to atheists’ claims that we have no free will) and that you have the right to believe as you choose. The problem is, you are not promoting a scientific theory, but rather your materialistic faith.

    Yes, the familiar phase 2 of the argument. I’m afraid not. The theory is deeply embedded within biology, but it requires nothing more, as I say, than birth and death in a finite world. I can operate that process in a lab, or a mathematical model, or a computer, or investigate it in the wild, and see what consequences it has. They are evolutionary consequences. We can extrapolate out: IF the simple process I outlined is at the back of it, what would we expect to see in the world? The marks of heredity. If birth and death are all there was, we would expect to see organisms related at the fundamental, genetic level. And we do. This COULD have been falsified. We could have found anything. But we didn’t; we found common descent.

    Now I know you may rail against common descent, but the evidence is overwhelming. I am not trying to persuade you of that fact, but to say that I am persuaded of it. So, when you talk of ‘choice’, and ‘free will’ one only has a choice to believe in something if all options are equally consistent. I have no choice, with the mountain of confirmatory evidence I have from studying biology, but to conclude that the data points nowhere but common descent.

    As I asked before, at what point would you ever concede there MUST be a supernatural first cause for nature/the natural? If you say never, then you are ignoring the known scientific principles we have, in exchange for faith that one day, all the mysteries will be explained by purely naturalistic means.

    No, because “never” could also apply to a natural first cause. We may never know how it all started. I only concede the supernatural when I get some direct evidence that there is such a thing.

    Tell that to seti and the other ‘scientific’ journals that allow e’t’s to be postulated, but not GOD. ;-)

    Postulating ET’s and ascribing in them the powers to cross vast distances of interstellar space, armed with the tools of biological design, and some means of suspending known physics while they create their creations, are two completely different things. I can actually buy the supernatural more readily than I can buy hyper-intelligent aliens as a cause. Trekkies need to get some sense of scale!

    But to get back to the point, what you’re doing is saying GOD wouldn’t do this or that, ergo God can’t exist.

    No, I’m saying I have no idea if God even exists. I’m not arguing him out of the picture; that would be absurd. To talk about limitations would require me to accept the basic fact of his existence, and I am afraid, in all conscience, I do not have any reason to do so. People tell me he exists – but then people tell me a lot of things!

    Atheists NEED darwinism, which is why they fight so hard to prevent it form being criticized, and having dissenting opinions heard.

    So, I tell you I don’t, but you know better. Fair enough. As I say, it is one way for you to rationalise why people think differently from you. I was an atheist before I knew anything of biology. I didn’t seize upon it to confirm my godless ways; I studied it, found it fascinating, and know why biologists are so robust in their defence of it. God (if he exists) has presented this vast mountain of evidence before me, and I am supposed to pretend I cannot see what I can see, just to get on the right side of him?

    I am a skeptic in all things – including science. I don’t accept anything just because people tell me to, including evolution.

  73. Timaeus:

    Not sure what you mean by “immanent design”. Is that different from “intrinsic”?

    But if ID’s thesis is not “external design” by which I mean design by some agent other than the system itself, then what’s wrong with Darwinian theory? That’s exactly what Darwin’s theory is: that populations of self-replicators that replicate with heritable variance in reproductive success within the current enviroment form an intrinsic design system.

    But I will await your definition of “immanent”.

    However, if all an IDist is alleging is that “ID” means that the universe capable of producing life was brought into being by a creator God, then it doesn’t conflict with Darwinian theory at all. In fact, that would be the position of most “theistic evolutionists”, so derided so regularly on this (ID) blog, and certainly not the view of those (Dembski, Meyer, Behe, Wells) who argue that Darwinian theory (essentially, intrinsic design) cannot account for what we observe.

    I do wish you’d drop these snide speculations about my reading, btw. I have read many papers by Dembski, and also critiques of them.

    I haven’t “dipped” into them. I’ve read them, really very thoroughly.

  74. Like mathematicians and philsophers claiming such about biologists, for example? ;)

    Timaeus, please re-read what you wrote, carefully. Both Shapiro and Margulis rejected what they called the “neo-Darwinian synthesis”.

    Neither rejected Darwinism, and, indeed, Margulis called herself a Darwinist, explicitly (don’t know about Shapiro). But whatever Shapiro calls himself, his position is not non-Darwinian. What it is not is “neo-Darwinian”. tbh, I don’t think there’s a “neo-Darwinian” biologist left. It was a “synthesis” announced in 1959. A huge amount has been learned since then – not least being the whole domain of “evo-devo”.

    But also, symbiosis, and population-level selection, which Margulis and Shapiro, respectively, have championed.

    I think it is really important that this word “neo-Darwinism” is either defined precisely each time it is used, or dropped. The idea that it always means “everything Darwinist biologists believe today” is simply wrong. In Shapiro and Margulis’ cases, it means a very specific, and outdated, view of how Darwinian evolution works.

  75. I am a skeptic in all things – including science. I don’t accept anything just because people tell me to, including evolution.

    Well, that’s a good start.

  76. Here’s my questions to atheists:

    1. At what point would you accept that the universe or nature had a supernatural first cause, or would you always just hope/believe that one day, perhaps long after you’re gone, an answer will be found that supports a materialistic explanation? Isn’t that FAITH?? For example, let’s say GOD created the universe, how would you ever realize THAT if you continue to reject that possibility from the start? You say the supernatural is not science, but you accept other things that cannot be verified by our scientific methods, such as the belief that all life is the sole product of darwinian evolution. Even uber-darwinist Jerry Coyne admitted:

    In science’s pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics. For evolutionary biology is a historical science, laden with history’s inevitable imponderables. We evolutionary biologists cannot generate a Cretaceous Park to observe exactly what killed the dinosaurs; and, unlike “harder” scientists, we usually cannot resolve issues with a simple experiment, such as adding tube A to tube B and noting the color of the mixture.
    Of Vice and Men The New Republic April 3 2000 p.27

    I do not think that the answer to whether God exists can be found through science – empirical evidence. I think there are logical reasons for rejecting the idea of God, but not empirical ones. Or rather, I think some ideas about God can be rejected empirically (a God who made the earth in 6 days, about 6,000 years ago, for instance), but the notion that something brought the world intentionally into existence seems to be not one that can, in principle, be answered empirically.

    Yet darwinian evolution is beyond reproach. Why? How is your faith in it, different from my faith in a creator? (Aside from the fact logical deduction of the evidence points to a creator)

    It isn’t beyond reproach. It’s simply a well-supported (by evidence) scientific theory. It’s far from complete, and may be wrong in important respects. Certainly Darwin himself was wrong on several counts.

    2. Why is ANY possibility allowed, EXCEPT God? Extraterrestrials, a multiverse, etc are both allowed to be promoted as ‘science’ yet there’s no evidence for either. There’s also no evidence our ‘scientific’ methods would be able to determine an extraterrestrial or a multiverse, yet both are put forward as possibilities…but not GOD. Why?

    All possiblities are “allowed” but only some are amenable to investigation. Depending on your definition of God (or your concept anyway), God is probably not amenable to scientific i.e. empirical investigation (from my own theological stance, a God that was amenable to empirical investigation wouldn’t be what I would call God – merely a previously unknown denizen of the world). The others are.

    Thank you

    You are welcome :) Good questions.

  77. Well, that’s a good start.

    Errr … not really. To dispense with it as an explanatory framework because of a set of pet problems such as avian lungs, flagella, whales, the genetic code, the mammalian jawbone, cytochrome b, the sea squirt, mostly pursued with variable degrees of ignorance of actual biology? … no, not good enough.

    Biology is huge, and it confirms common descent from tangled root to branch tip. Population principles and their consequences have also been deeply investigated. I don’t accept evolution because people tell me to, but because I can see the merit in the explanatory framework and the data. This, or that, detail may be lacking a current explanation. I have not read every single paper published. But I have read a lot. I am not aware of one that casts serious doubt on it (of course, this is because there is a conspiracy to suppress them!). So if you see my averred skepticism as a ‘foot-in-the-door’ for discard of the paradigm… nope. Give me a better one first.

  78. No DrREC, People get to say God is the designer. ID does not say that but people can. They come to that conclusion via other-than-science, even Behe said that.

    ID isn’t Creation- people who understand ID and Creation know there are huge differences- only the willfully ignorant conflate the two- that is the hillarious part.

    Intelligent Design Creationism only exists in the minds of the willfully ignorant- and here you are…

  79. Elizabeth:

    You’re wrong about the history of evolutionary theory — again. The Modern Synthesis is generally considered to have been worked out between about 1937 and 1947; the term The Modern Synthesis was actually in the title of a book in the mid-1940s.

    No significant ID proponent would ever make the equation between “neo-Darwinism” and “everything Darwinist biologists believe today.” That would indicate a massive vocabulary confusion. An ID proponent would use “Darwinist” for the original views of Darwin, or as a short form for “neo-Darwinist” where the context made the meaning clear, but would not muddle things by putting “neo-Darwinism” and “Darwinist” in a construction such as you have created.

    You are the only one who finds the term “neo-Darwinism” unclear, Elizabeth. All the other players in the game — all the real evolutionary biologists, as opposed to neurologists playing at being evolutionary biologists — know that it refers to the synthesis achieved by Mayr, Dobzhansky, Gaylord Simpson, Julian Huxley and their friends, and that it focused on random mutation plus natural selection. The ID people — at least, the more disciplined ID people — use the term in the same way. So do Shapiro and Margulis, when they criticize it. The fact that you don’t easily recognize the term, and find it confusing and misleading, suggests to me that you jumped into this subject (evolution/ID) fairly recently and are still trying get your head oriented to the history of the subject. And that’s fine, but at least you could take instruction from those who are more historically informed than you are, instead of trying to act like the expert on the relevant vocabulary.

    There may not be many “pure” neo-Darwinians left, but there are plenty of biologists left whose overall orientation to evolution is *primarily* neo-Darwinian. Ken Miller, Eugenie Scott, Richard Dawkins, the folks over at Biologos, etc. I would bet that if you surveyed most American high school biology textbooks the presentation of evolution there is also primarily neo-Darwinian. It is that orientation which ID people have been most extensively criticizing.

    Your last sentence continues to infect others with the confusion in your own vocabulary. You said “how Darwinian evolution works”; you should have said simply “how evolution works”. Otherwise, the context of your statement implies that the neo-Darwinian view of evolution is now outdated, but today we have a truer Darwinian view. But of course, the view among the leading evolutionary theorists of today is getting farther and farther away from anything that can reasonably be called “Darwinian.” And that’s a good thing, because both the Darwinian and neo-Darwinian models were extremely implausible. (Margulis’s view was not much better; there is more hope for the ideas of Shapiro and Newman and others.)

    T.

  80. Just a few points, I think worth making:

    Darwinism =/= atheism

    Darwinism =/= eugenics

    atheism =/= no free will

    atheism =/= amorality

    methodological naturalism =/= censorship of science

    methodological naturalism =/= no free will

    methodological naturalism =/= atheism

  81. Provine says Darwinism = atheism

    Scientists said darwinism = eugenics

    Provine said there isn’t any free will

  82. Well, if it was even earlier than 1959, that makes my point even more emphatically. It is out of date.

    You are the only one who finds the term “neo-Darwinism” unclear, Elizabeth. All the other players in the game — all the real evolutionary biologists, as opposed to neurologists playing at being evolutionary biologists — know that it refers to the synthesis achieved by Mayr, Dobzhansky, Gaylord Simpson, Julian Huxley and their friends, and that it focused on random mutation plus natural selection.

    Self-evidently it is unclear, Timaeus, because you yourself conflated my word “Darwinian system” with your/Shapiro’s word “neo-Darwinian system” in your very post!

    That is why I made the distinction.

    Darwin did not even propose a mechanism for variance-generation. At one point he went for Lamarck’s view.

    And saying “Darwinian” not “neo-Darwinian” when I mean “Darwinian” not “neo-Darwinian” should confuse no-one. And yet, weirdly, it confused you.

    But let me be absolutely clear: by Darwinian, as I have said, many times, so often that I should really store a keyboard shortcut for the phrase, the principle that when self-replicators replicate with heritable variance in reproductive success in a given environment, the population will adapt to that environment.

    That was Darwin’s great insight, it remains at the core of evolutionary theory, and is not denied or rejected by either Margulis or Shapiro.

    What Margulis challenged was the neo-Darwinist understanding of variance creation. What Shapiro challenges is the idea that variance creation is “random” (whatever that means, and I think to some extent Shapiro, and Margulis for that matter, is attacking a straw man).

    Margulis put forward the role of symbiosis as a generator of variance, and Shapiro talks about the evolution of evolvability. But that evolution of evolvability he attributes to the basic Darwinian algorithm, except applied at between-population level, rather than within-population level.

    But of course, the view among the leading evolutionary theorists of today is getting farther and farther away from anything that can reasonably be called “Darwinian.”

    I disagree, although I do agree that we have moved vastly further than the state of knowledge that Darwin possessed, obviously. He didn’t even know about genetics. And our undertanding of the concept of “species” has changed fairly radically.

    But his simple principle remains the foundation of evolutionary theory in a very profound sense.

    At any rate, if you disagree, please explain why.

    Oh, and Timaeus, evolutionary theory is highly relevant to my own field, for many reasons: because the mathematics of evolution is also the mathematics of cognition; because brains evolved; and because genes expression is vital to brain function.

    Also others, but those will do for starters.

  83. How can something that is untestable be relevant to any field?

    Mathematics of evolution? Please show us this math and how it pertains to say the evolution of the bacterial flagellum via darwinian mechanisms.

    Brains evolved? Yeah from the originally designed brains. And all “evolution” means in this context is “change”.

  84. Joe, it’s perfectly testable. That you refuse to accept this really isn’t my problem.

    And if you want to know the mathematics of evolution, read any paper on any evolutionary model, including genetic algorithms.

    And no, none of that will tell you how, or even whether, the bacterial flagellum evolved, and we will probably never know, exactly.

    All we ever have in science is testable hypotheses, and those tests can only ever support a hypothesis, not prove it.

    It’s models, all the way down.

  85. Elizabeth:

    I didn’t think “immanent” should be all that difficult a word for someone with your level of education. But what I meant was that the living organism contains the ability to remodel itself into new organisms, so that new organisms don’t have to be created from scratch by some outside intelligence. ID is compatible with either option — some outside intelligence literally manipulating matter to get new organs, systems, or creatures, or organisms evolving without new intelligent input from outside, because they have a sort of built-in program for self-development. Your statement indicated that you did not realize this. It indicated that you thought ID accepted only the externalist notion. I’m not asking you to agree with ID, Elizabeth, but I am asking you not to say incorrect things about it, and not to keep fighting when you are corrected by those who have been involved in ID longer than you have and know all the nuances of the various ID authors more intimately than you do.

    Many of us here at UD have read Michael Denton’s second book, and recognize in his thought a sort of “inbuilt intelligence” model, as opposed to, say, a view of direct creation, like of Paley, where the intelligence is clearly external, or an evolutionary model in which God or some other intelligence is always pushing and steering the process along, and therefore again inputting external intelligence. Shapiro’s seems to be another “inbuilt intelligence” model, though it appears to differ in detail from Denton’s.

    Classic neo-Darwinian theory, of course, involves no “intelligence” or “design” in the normal sense of those words at all; the whole point of it was to show that blind natural forces and contingent events could in the long run produce new arrangements that looked as if they were designed by an intelligence (but weren’t).

    You don’t need to tell us what the theistic evolutionists, hold, Elizabeth; we all know their positions, in excruciating detail and far better than you do. But in fact, to say that the universe was brought into being capable of producing life covers many more options than the Darwinian. Michael Denton (whose second book I’m convinced from your various remarks that you have not read) also has the universe capable of producing life, but not in a Darwinian or neo-Darwinian way. Shapiro’s scheme, insofar as he has developed it, is not primarily Darwinian or neo-Darwinian, either.

    You say you’ve read a few papers by Dembski. Why don’t you read *No Free Lunch*? Have you read both of Behe’s books? Have you read Meyer’s book? Which books of Wells have you read? How about The Design of Life by Dembski and Wells? And I’m not convinced you’ve read what you’ve read very thoroughly, because you keep misrepresenting or confusing what ID is about.

    As for your earlier comment, it’s perfectly acceptable for mathematicians and philosophers to criticize biologists when biologists make statements that fall partly into the territory of the mathematicians or philosophers, as has often been the case in evolutionary theorizing. It would be foolish, however, for a specialist in linear algebra to tell a specialist in probability theory that he had misunderstood Bayes’s Theorem. My point was that Shapiro doesn’t need your constructions of what does and does not count as “Darwinian” or “neo-Darwinian,” any more than the probability theorist needs the linear algebraist’s opinion about Bayes’s theorem. And if I have to choose whose vocabulary to use, Shapiro’s or yours, I’ll take his.

    T.

  86. No, it isn’t testable. If it was then I wouold still be an evolutionist and you would be telling us how to test it.

    Genetic algorithms don’t have anything to do with biological reality.

    As for testable hypotheses, well you can’t produce any of those either.

    So it isn’t that I refuse to accpet anything. It is that it is untestable. And nothing you can say, beyond telling us how to test it, will change that.

  87. Timaeus, please stop with the snidey remarks about my education.

    When I don’t know what someone means, I ask.

    Works have many definitions, and what I am asking for is not some canonical dictionary definition (which are not canonical anyway – they describe usage, they don’t prescribe it) but the sense in which YOU are using the word in THIS post.

    Your statement indicated that you did not realize this. It indicated that you thought ID accepted only the externalist notion.

    Yes. Because Darwinian evolution is an “internalist” notion, and IDists reject it.

    I’d like to see an ID paper that accepts the possibility of Darwinian evolution, or other “internalist” system as compatible with an Intelligent God. It seems to me, as I said, that this is precisely the position of theistic evolutionists, is it not?

    And I myself have been proposing “inbuilt intelligence” for years. I think that’s exactly what Darwinian evolution is.

    You don’t need to tell us what the theistic evolutionists, hold, Elizabeth; we all know their positions, in excruciating detail and far better than you do.

    Oh yeah? And how do you know that you know their position “in excruciating detail” or “far better than [I] do”?

    hmmm?

    After all I was one myself for half a century. Indeed, almost every theist I ever met or read in that time was a “theistic evolutionist”. And one thing I did find out is that it is a highly heterogeneous field.

    And I may well confused what ID is about. But that is at least in part (and I would suggest almost wholly) because ID is also a thoroughly heterogeneous and often intra-contradictory set of positions.

    And no, I don’t think I will tell you what I’ve read, right now. You tell me what you think I have wrong, and I will give you a citation for where I got it from.

  88. Well, there’s not much point in trading assertions, Joe.

    Obviously I think you are wrong, and you think I am, so we’ll just have to leave it there.

  89. Timeaus

    Here is why I think “immanent design” is compatible with Darwinism.

    I assume the point about immanent design is that the design happens up front – in Denton’s case at the Big Bang – and no afterwards. How are we to distinguish immanent design from continuing interventions by a designer? Take any variation in the genome from one generation to the next but before selection has acted on it. There are two options:

    1) It is clearly and implausibly oriented to provide some benefit for the organism.
    2) It isn’t. It appears unguided.

    Option 2 is the essence of Darwinism. Variation either provides no benefit or if it does provide a benefit then this variation can plausibly be accounted for by natural processes (the leap might a point mutation, or Margulis endosymbiosis, or Shapiro’s internal mechanisms – Darwin would not have known the difference).

    But in the case of 1 how do we tell the difference between immanent and continuing intervention? Without knowing the actual intervention mechanism the two are indistinguishable.

  90. Right- no more assertions, just tell us how to test it!

    Your silence betrays you, Elizabeth. Strange that you think it somehow saves you.

  91. Elizabeth (5.1.1.2.2):

    Your remarks about Margulis and Shapiro don’t tell me anything I didn’t already know.

    The problem here is your restricted use of the term “Darwinian.” Yes, the description you are giving is an important part of “Darwinian” thought. But it is incomplete, and that is where we are having so much problem with vocabulary. I could say that “London” is Picadilly Circus and Buckingham Palace and the Tower Bridge, on the ground that they are central spots and symbols of the city, but that leaves out Hyde Park and Trafalgar Square and Soho.

    You are speaking as if your definition is the only important part of Darwinian thought, and as if everything else can be scrapped, and the word “Darwinian” still used. Well, this is a matter of convention, but for many analysts of evolutionary theory, gradualism is a crucially important part of Darwinian theory (both Charles- and neo-). But gradualism was severely criticized by Gould, and also in a different way by Margulis, and of course by the ID people. Another important aspect of Darwinism was Darwin’s resolute anti-teleology — which carried over into neo-Darwinism. Now if you read Denton’s second book, you will see that Denton questions both the gradualism [in a certain way] and the anti-teleology; Denton clearly sees these things as very important to Darwinian thinking. And you will also see from his two books that he is very well versed in the history of evolutionary thinking, so it would be unwise to simply dismiss his vocabulary because you would like to use the word differently.

    As for your final statement, I’m sure I could find you ten young earth creationists with life science Ph.D.s who agree that gene expression is vital to brain function. That has nothing in itself to do with Darwinian theory or evolutionary theory at all. Of course, you can gratuitously add that the current gene expression system arose as a result of this or that evolutionary mechanism if you wish. Whatever makes you happy. And whether brains evolved or not, they work the way they work. If a mechanic is fixing my car, he doesn’t need to know that this particular Ford engine has an engineering lineage going back to the Model T; all he needs to know is how the parts work together. If I ever need brain surgery, all I care about is that the surgeon knows how all the parts of my brain and body work together; I couldn’t care less if he has never read a single article about the evolution of Neanderthal or Australopithecine brains. In fact, if I thought he spent more than a small fraction of his time reading things like that, I would be worried that he was too speculative, and not empirical enough, and would look for a different surgeon, one who preferred to devour articles on surgical techniques and post-operative medications and the functions (year 2012 AD, not year 200,000 BC) of the various regions of the brain.

    In any case, I wasn’t denying that you might have found some use for this or that idea from evolutionary biology in your own work; I was denying that you would be recognized by evolutionary biologists as a peer in that field. Yet you write with a tone of authority, as if you are lecturing us all on evolutionary theory. But why should we accept you as an an expert on contemporary evolutionary theory, when you have no academic achievements in that field? Especially when we see how carelessly you have misinterpreted ID notions; what guarantee do we have that your reading of evolutionary biologists is not equally careless? Maybe you should get an endorsement from Simon Conway Morris or someone on that level, e.g.: “Elizabeth is the greatest popular expositor of evolutionary theory currently living, and you can trust everything that she says.”

    T.

  92. Elizabeth,

    I see that you have a clueless evotard cheering section over on atbc. Unfortunately for them you cannot support your assertions so they have to make stuff up to try to “attack” me.

  93. Your remarks about Margulis and Shapiro don’t tell me anything I didn’t already know.

    Good, I’m glad we agree then.

    The problem here is your restricted use of the term “Darwinian.” Yes, the description you are giving is an important part of “Darwinian” thought.

    Yes, it is.

    But it is incomplete, and that is where we are having so much problem with vocabulary. I could say that “London” is Picadilly Circus and Buckingham Palace and the Tower Bridge, on the ground that they are central spots and symbols of the city, but that leaves out Hyde Park and Trafalgar Square and Soho.

    You are speaking as if your definition is the only important part of Darwinian thought, and as if everything else can be scrapped, and the word “Darwinian” still used. Well, this is a matter of convention, but for many analysts of evolutionary theory, gradualism is a crucially important part of Darwinian theory (both Charles- and neo-). But gradualism was severely criticized by Gould, and also in a different way by Margulis, and of course by the ID people. Another important aspect of Darwinism was Darwin’s resolute anti-teleology — which carried over into neo-Darwinism. Now if you read Denton’s second book, you will see that Denton questions both the gradualism [in a certain way] and the anti-teleology; Denton clearly sees these things as very important to Darwinian thinking. And you will also see from his two books that he is very well versed in the history of evolutionary thinking, so it would be unwise to simply dismiss his vocabulary because you would like to use the word differently.

    If, by “Darwinian” you mean “what Darwin thought” then, sure, it’s incomplete.

    But in my experience, it’s that key insight that is generally regarded as the essence of Darwinian theory. So in future I will make that clear whenever I use the word.

    Another shorthand is “RM+NS” but I don’t think that works as well, because Darwin didn’t propose “RM” he just proposed heritable variance. At one stage he didn’t even regard it as random. So I think my shorthand is better.

    As for your final statement, I’m sure I could find you ten young earth creationists with life science Ph.D.s who agree that gene expression is vital to brain function. That has nothing in itself to do with Darwinian theory or evolutionary theory at all.

    Yes, it has a huge amout to do with evolutionary theory, whether or not your 10 YECs have a view. Genes are the unit of inheritance, and gene expression is about how the genetic inheritance affects the phenotype, the unit of selection. That’s why evolutionary theory is relevant to my field.

    Of course, you can gratuitously add that the current gene expression system arose as a result of this or that evolutionary mechanism if you wish. Whatever makes you happy. And whether brains evolved or not, they work the way they work. If a mechanic is fixing my car, he doesn’t need to know that this particular Ford engine has an engineering lineage going back to the Model T; all he needs to know is how the parts work together.

    And finding out how the parts work together, in the absence of a user manual, often involves figuring out how those parts got there, and what earlier variants did in earlier models.

    If I ever need brain surgery, all I care about is that the surgeon knows how all the parts of my brain and body work together; I couldn’t care less if he has never read a single article about the evolution of Neanderthal or Australopithecine brains. In fact, if I thought he spent more than a small fraction of his time reading things like that, I would be worried that he was too speculative, and not empirical enough, and would look for a different surgeon, one who preferred to devour articles on surgical techniques and post-operative medications and the functions (year 2012 AD, not year 200,000 BC) of the various regions of the brain.

    That’s probably true of brain surgery. I’m not a brain surgeon (you will be relieve to know).

    In any case, I wasn’t denying that you might have found some use for this or that idea from evolutionary biology in your own work; I was denying that you would be recognized by evolutionary biologists as a peer in that field. Yet you write with a tone of authority, as if you are lecturing us all on evolutionary theory.

    Well, that’s unfortunate, and largely imaginary I suggest. I do not appeal to authority or put myself out as anybody special. I’m not. You are reading “tone” where it isn’t there. As I’ve said to you before, the great thing about the internet is that your arguments have to make sense. You can’t appeal to your own authority because nobody knows for sure who you are. You don’t know for sure who I am. I might be my cat.

    But why should we accept you as an an expert on contemporary evolutionary theory, when you have no academic achievements in that field?

    You shouldn’t.

    Especially when we see how carelessly you have misinterpreted ID notions;

    Well, I don’t think I have. But of course you are free to disagree. And make your rebuttal.

    what guarantee do we have that your reading of evolutionary biologists is not equally careless?

    None. But that doesn’t mean I am not entitled to say what I think they are saying.

    Maybe you should get an endorsement from Simon Conway Morris or someone on that level, e.g.: “Elizabeth is the greatest popular expositor of evolutionary theory currently living, and you can trust everything that she says.”

    Why should I? I’m not instructing you to accept my word. I’m simply expressing my view on the internet. I’m as fallible as anyone else.

    But obviously don’t think I’m wrong at the time I write, otherwise I wouldn’t write it! And I’m more than willing to concede (as I’ve indicated before) when I am persuaded that I am in error.

  94. Provine says Darwinism = atheism

    Is the same as? I would disagree.

    Scientists said darwinism = eugenics

    A kind of ‘natural’ eugenics, then maybe. Artificial selection is eugenics, which was Darwin’s jumping-off point. Guided human eugenics is a different kettle of ethical fish. It acts against the natural variation in the population more quickly than it can be replaced, and so seems like a crap road for a geneticist to wish to go down. No accounting for people, though. It does contain the ridiculous presumption from people like Fisher that the world only needs a load more specky intellectuals like them!

    Provine said there isn’t any free will

    I wonder what made him say that? :0)

  95. Joe: maybe Provine is wrong?

  96. Elizabeth (5.1.2.2.2):

    As you yourself point out, Elizabeth, words have different meanings for different groups of people. “Theistic evolutionist” has a sort of generic meaning, which probably covers what you used to be; but you made a little dig about the criticisms we here on UD make of theistic evolution, and *that particular form of theistic evolution* is an American development of the past 20 years, and we know it extremely well; some of our members here have been on the mats with TEs in numerous public venues. Many of us know all the nuances in the positions of Ken Miller, Karl Giberson, Darrel Falk, Dennis Venema, George Murphy, Francis Collins, Denis Lamoureux, etc. We have read scores of their essays, hundreds of their blog posts, and many of their books. If you aren’t deeply familiar with these authors, your comments on the subject will be of no use to us.

    The theistic evolutionists of whom I have been speaking are indeed Christian Darwinists, which for most ID people is a contradiction in terms, meaning, in effect, “teleological anti-teleologists.” ID people are not Christian Darwinists, because they are not Darwinists at all — as they understand the term.

    My comment about your ID reading was not for the sake of one-upmanship. I think that some of your confusions spring directly from not reading enough ID material, and not collating it all in your mind, noting similiarities and differences, resolving apparent internal contradictions by noting careful qualifications, etc. You seem to prefer attacking single statements or articles on a piecemeal basis. I have noticed that this is a common approach among science-trained people who debate evolution on the internet. Arts-trained people operate differently. They read broadly and deeply when learning a new position, before trying to refute it.

    My comment about your vocabulary was meant as a compliment, not as a dig. I was saying that you were bright, and given that you said you used to spend much time reflecting on religious questions and reading the likes of Aquinas, I was surprised you didn’t immediately translate “immanent” into some appropriate biological equivalent. In any case, I’ve now explained what I meant by it.

    We aren’t going to agree on the supposed intrinsic intelligence or design in Darwinism. I just refuse to use the word intelligent or design unless we are talking about conscious minds. There is no design in Darwinism; what arises, arises without any intelligent planning. You can use words any way you want to; but there is no point in your continuing to disagree with people here about intelligence and design in Darwinian biology when no one in this camp is going to use the words with your definitions. Banging your head against that wall will produce only a sore head.

    T.

  97. Joe, if eugenics is the deliberate policy of allowing some human beings to breed and not others (as it usually is) then Darwinism is not eugenics.

    Darwinism is about natural selection, not artificial selection.
    Darwinism is a scientific theory, not a policy
    Darwinism about how we, and all other species, came to be the way we are, not what we should do in order to becomes somethign else.

  98. Elizabeth,

    Artificial selection is what is allowing people who shpuldn’t breed to breed.

    And yes maybe Provine is wrong but the arguments he makes are better than anything you have ever posted.

  99. Artificial selection is what is allowing people who shpuldn’t breed to breed.

    What?

  100. Elizabeth,

    For one, modern medicine, including vaccines, have allowed some people to live when nature would have eliminated them.

  101. 101

    Joe,
    One of the ways that ID can differentiate itself from creationism is to distinctly say when the design event(s) happened.

    Was there just one, a long time ago, or does design happen all the time everywhere?

  102. 102

    Joe,

    One design.

    Typically you support your answer with reasoning.

    can’t say until we can study them, duh.

    And yet in another breath you say that ID is not about studying the designer and you can’t in fact study the designer.

    Make your mind up!

  103. Peter,

    Evos never support anything.

    And yet in another breath you say that ID is not about studying the designer and you can’t in fact study the designer.

    You are seriouly demented as I have never said that.

    ID is not about the designer. that does not mean no one can try to determine who/ what it was.

    And context is important and obvioulsy you are too stupid to understand the context of what I posted even though I was responding to you.

  104. ID diiferentiates itself from Creationism by the mere fact that ID does not rely on the Bible.

    That said what you asked is what science is for. Also your position doesn’t have any answers.

  105. Such as? I’d love to hear.

  106. 106

    http://pandasthumb.org/archive.....st-fa.html

    To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

    http://sfmatheson.blogspot.com.....se-to.html

    This does not mean that Axe and Gauger are incorrect in their hypothesis, namely that different proteins are separated by vast evolutionary wastelands that can only be traversed with the help of “design.” That may be the case. But the newly-published work in BIO-Complexity gets them no closer to establishing that hypothesis as reasonable or even likely.

    http://aghunt.wordpress.com/20.....-function/

    To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

    Obviously the quotes are just tasters, follow the links for the full detail. If, however, you choose to read the ID supporting point of view Darwinism has already been disconfirmed and they are just waiting for somebody to take away the remains!

  107. “…does design happen all the time everywhere?”

    Oh yes, it is happenning as we speak. You and I are using our keybords to write specific sentences and record them using appropriate media. I just don’t see why science should be afraid of “design” as causation.

  108. 108

    Joe,
    When did the design get implemented Joe?

    A million years ago? 10 million
    6000 years ago?
    Yesterday? Right now?

    That said what you asked is what science is for. Also your position doesn’t have any answers.

    A transitional fossil was predicted at a particular location. A transitional fossil was found at the predicted location. Case closed!

    Here’s an answer for you Joe. You claim that ATP was designed. Here’s evidence that it evolved!

    http://www.nature.com/nature/j.....10724.html

    Many cellular processes are carried out by molecular ‘machines’—assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine—the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump—increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

    Whereas the ID “explanation” for how ATP came to be is “it was designed”

    Sure, you can write page after page (and you have) as to why it’s not possible it evolved but in fact you don’t have a word to say about how it did come to be. Yet “Darwinism” does.

    I know you’ll jump on this phrase “Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking”

    I’d only note that “weak evidence” (i.e. not strong) is better then no evidence at all (i.e. what ID can offer with regard to the origin of ATP). And the point of that article is to provide such strong evidence in any case.

    Can ID offer anything with a comparable level of detail as to the purported intelligent design of ATP?

  109. 109

    Eugene,
    That’s not what I meant and you know it!

    I just don’t see why science should be afraid of “design” as causation.

    It’s not afraid. When you have evidence for it, then science will examine that evidence! It’s as simple as that!

    So, today for the next hour only, I’m not going to be afraid of design as causation.

    Eugene S, please tell me how ID explains the origin of ATP via design!

    You can’t, of course. And that’s the point. When you can it will be listened to. Until then, well, publish or perish!

  110. 110

    Apparently, once again, there is no interest in discussing material evidence.

  111. Upright,

    Apparently, once again, you are avoiding Nick’s question. At least Eugene had the guts to admit that evolution can produce an increase in information.

  112. It’s a bit like asking which came first, males or females.

    Or which came first, the genetic code or the machinery that interprets it.

  113. 113

    Upright,
    Could I have a fer’instance?

  114. 114

    Champ, thank you for providing a link. I am perfectly happy to allow the previous exchange to speak for itself.

    Peter, I provided a link.

    I’ll check back later, cheers.

  115. Peter,

    “…well, publish or perish!”

    I can’t fully appreciate all the intricacies of English even though I have lived more than 10 years in the UK. But at the face of it, it sounds quite rude to me.

    On the material point, it is up to you, guys, to explain how symbolic information transfer, control and function are possible via chance and necessity.

    Up to the time of Darwin, to be a scientist one needed just to be a strong independent thinker without necessarily having to publish stuff anywhere. And even now it takes genius, independence of thought and courage to be a genuine one. I think that the main design proponents have those qualities in much bigger quantities than ordinary blokes who publish scores of papers a year and peer review the same stuff by their colleagues in like numbers. I am sure in 100 years’ time no one will even know who these mainstream personalities were (without calling names) but people will know who, say, Dembski or Abel were, for sure.

  116. I have no problem with God creating the universe, except that it doesn’t answer any questions about how things work. You still need science to figure out how stuff works.

    Science doesn’t answer big questions such as why there is something rather than nothing, but it can describe the solar system and enable us to explore it.

    It can probably never answer the historical question of how live originated, but it can study and describe how living things behave.

  117. 117

    Perhaps I should just start a list.

    :l

  118. markf:

    I’ve run out of time on this thread, so briefly:

    I’m confused by your exposition. The alternatives Elizabeth and I were discussing were (1) design imposed upon organic matter by an outside mind, i.e., a direct creation model, and (2) design that organic matter imposes upon itself by some set of intrinsic creative capabilities.

    You now seem to be throwing in a third possibility — continuous intervention — which we weren’t discussing. Why have you added this in?

    Regarding the two models were were discussing, my view is that position (2) above amounts to an indirect creation model. For how did these genius “self-engineering” cellular-protein-genome systems become such geniuses? They may have produced all species, but what is *their* origin? I’d argue that they must have been intelligently designed. So we would need an “external” designer to create these systems, after which they would operate as the “internal” designer of future evolutionary outcomes. The difference would be that the external designer would (in my view) have to be a conscious agent, whereas the internal self-engineering systme would not be a conscious agent, but would merely be a highly adaptive organic computer program (of a type far beyond what human engineering could produce today).

    This is why ID people are more sympathetic with Shapiro than with ND or Margulis; Shapiro’s view lends itself to an ID interpretation, even if Shapiro himself refuses to speculate about the origin of the self-engineering, self-evolving systems.

    If you want the empirical evidence which Shapiro uses to shoot down classical ND mechanisms and support his own, don’t guess and speculate; read what Shapiro has written. If you want to know how Denton’s system would operate differently from Darwin’s, and hence would yield different predictions, read Denton. Don’t rely on me to summarize for you. I might do it inaccurately, and in any case, I have no more time. If you are really interested, you won’t shirk the job.

    T.

  119. Timeaus

    I agree my comment was poorly expressed.  I have a little more time this morning. I will try to put it more carefully and clearly.

    Take your option (2):

    (2) design that organic matter imposes upon itself by some set of intrinsic creative capabilities

    My contention is that this is either compatible with Darwinism or indistinguishable from external design.

    First I assume you agree that evolution happens by a process of one organism being descended from one or two parents and the child being different from the parents.  I am not saying anything about the degree or mechanism of this variation at this point.

    There are two options for this variation. 

    A) There is a satisfactory unguided explanation of the variation.  By an unguided explanation I mean we can see a plausible route for how given the features of the parent the child could arise which is based on natural and understood processes.  For example, if the parent contained units of DNA that would be extremely useful to the child and all that was required was a simple shifting around of those units that would be plausible given the parent.  (Shapiro and Margulis both fall into this category).

    B) There is no satisfactory unguided explanation.  For example, in some inexplicable way the base pairs reorganise themselves in one go into a complicated structure that provides a whole new useful function for the child – such as a new appendage.

    In case (B), if  you are prepared to accept design as an explanation, then I cannot see that there is anything immanent about it.  There was nothing in the parent to make it happen.  If there had been it would have fallen under case (A).  Some external force must have caused the implausible leap.

    So immanent design must be case (A) – every child is descended by unguided processes from its parent(s) and anything that makes you think design arises from features of the parent.  So how far do you take this back?  We have said that every child is descended from the parent by unguided processes (or else we have an instance of external designer intervention). So we must go back at least to the origin of life and you seem to imply that Denton goes back to the Big Bang. So we can summarise immanent design as life evolved from the OOL (or before) through unguided processes and the design of life is a result of features of the first living things.

    But Darwin’s theory had nothing to say about the origin of life much the less the Big Bang (he speculated about OOL in informal letters but it was not part of his theory).  His was only a theory about how life evolved from the OOL onwards.  It can be summarised as life evolved from the OOL through unguided processes. It said nothing about the features of the first living things.

    Therefore immanent design is compatible with Darwinism. In fact it is a special case of Darwinism.

    I take your point about reading Michael Denton.  You have not yet convinced me it is worth it.  I wasted a fair amount of time spent reading Signature in the Cell because of similar taunts.  If someone can provide a convincing example of what is meant by immanent design I might change my mind.

  120. markf:

    Thanks for your restatement.

    First, “immanent design” was a phrase I made up on the spur of the moment, not one that is used generally by ID people, so don’t agonize over the precise phrase. I’ve explained what I meant by it — the organism has its own “intelligence,” so to speak, by which it can respond creatively to its environment by actually changing its own genetic makeup. It doesn’t have to
    wait until some cosmic ray or chemical strikes its DNA and makes an alteration that will just *happen* to be of some use. To some extent it makes its own opportunities.

    Now, as I’ve defined both Darwinism and neo-Darwinism at great length to Elizabeth, the idea that the organism could do such self-engineering is non-Darwinian. To the neo-Darwinists the notion is anathema, and as for Darwin, whose Origin I read with great care and great enjoyment a few years ago, the closest he came was in his flirtation with bits of Lamarckianism; but his overall scheme lay in a different direction from this. (I’m just giving the generally accepted reading of Darwin, here, nothing tricky or peculiar.)

    So, no matter how the discussion twists and turns, I am never going to accept the term “Darwinian” as a reasonable description of what Shapiro is arguing for. I don’t believe in uses of words which equate two things which are substantially different.

    Regarding your Point A, we are using the word “unguided” in two different senses, and this is what is causing the problem. I consider Shapiro’s model of evolution “guided,” not in the sense that God or some supernatural agent is steering the process, but in the sense that the organism has its destiny, to some extent, in its own hands. Think of those bumper car rides that little kids go on in the parks and carnivals. The kids have a range of freedom, allowing them to avoid certain collisions and to initiate others. I see the organism, in Shapiro’s model, as like that. It is self-guiding, to an extent, because it can control not only how it responds to its environment (as in Darwin), but can even remake itself. The self-guidance is not supernatural, nor is it “intelligent” in the sense that the organism is “thinking” how to handle its problems, but there is a feedback between environment and genetic material that does not exist in neo-Darwinism and was a most a minor ancillary to Darwin’s own view.

    Now Margulis’s view of evolution I *would* call unguided. She proposes that massive recombinations of genomes are relatively common and the major source of evolutionary novelty. But she gives no suggestion that these recombinations are any less accidental than the random mutations of neo-Darwinism. Her view of evolution, then, is equally “chancy”. Its only advantage over neo-Darwinism is that it can achieve large leaps in biological form very quickly, and therefore doesn’t face the problem of incrementalism with which the ID people (in agreement with her) have assaulted neo-Darwinism.

    Most of 20th-century evolutionary biology, whether it was neo-Darwinian or whether it laid more emphasis on “drift” or whether it threw in more radical notions such as those of Margulis, ultimately laid the creation of radically new biological form at the doorstep of “chance” — contingent events not dictated by any natural law. Natural selection could play its role only after “chance” produced the new forms. ID contests that any such modes of generating novel biological form, or all of them put together, could suffice to generate selectable traits sufficiently often to generate what we observe. I’m not going to argue that case here; I’m just making a general point to classify models of evolution.

    Shapiro’s view is quite different. Since, in his view, the interaction is two-way, with the initiation of organic change sometimes coming from the genome, but sometimes from the environment, and since there is an “intelligent” interface where the two sources of change can communicate, allowing the organism to make “decisions” (I need all the scare quotes because I don’t think that Shapiro believes that genomes or cells have intelligence or planning in the normal sense of those words), the whole question of probability becomes less important. If organisms have to wait for the right mutation, or the right combination of two, three, or more mutations, before they gain any selection advantage, then the sort of arguments that Behe and Dembski make become very important (even if Elizabeth believes that their numbers are wrong, their concern is in principle right); but if organisms can, to a significant extent, reorganize their own genetic material, evolution could happen much more quickly than the ND or other merely stochastic models would allow for.

    Using scare quotes again, to show that I realize the inaccuracy of these terms if we are trying to be historically strict, Shapiro’s view seems to be more “Lamarckian” than “Darwinian.” And ID arguments don’t apply against “Lamarckian” notions of evolution. Or at least, they would need to be radically reformulated in order to do so; the whole ID machine is tooled for the attack on neo-Darwinism.

    So ID can take two approaches to someone like Shapiro. It can take a skeptical approach, and deny that the evidence for self-engineering capacities is very great; in that case, Shapiro’s evolution would boil down to something like NDE with just a few extra bells and whistles, occasionally a bit faster but otherwise largely dependent upon external contingencies. Or, if the evidence for Shapiro’s view builds, and it looks as if organisms can reorganize their genomes in a serious way, in response to need, then ID can ask: “Where did organisms get this capacity?” After all, when human beings build computer systems that can respond to situations and make choices based on those situations, those computer systems are *designed*; they aren’t the product of chance. If the DNA-protein-cellular system, from the get-go, already has capacities for choice, including the choice of self-reorganization, and if, as it seems, these capacities go far beyond any system human engineers have so far devised, we have to ask how this *system* arose. Could it have arisen without the planning or design of an intelligence external to itself? Analogy from human experience would suggest, “No.” So ID proponents would then be able to congratulate Shapiro on his successful breaking of the Darwinian mold, but then argue that he should join the ID camp.

    Back to Denton. Because Denton takes the design beyond the design of the first living things back to the design of the fundamental particles and laws of nature, his view is more radical than Shapiro’s, and more ambitious. Denton is aware that his view is speculative and he doesn’t claim to have proved anything. However, the advantage of Denton’s view for those who cannot accept the notion of “intervention,” is that, unlike Shapiro, he doesn’t just stop at the question how life got its quasi-intelligent properties, leaving a door open for a miracle; he tries to show that no intervention would ever be necessary if you get the laws of nature right at the time of the Big Bang. This throws the intelligent design of the universe back to the beginning, and leaves the intelligent designer out of the picture after that. So if you believe in some sort of God as the brains behind nature and life, but don’t want him interfering in any way, Denton is the man for you. You get God, while getting rid of miracles — for some people, the best of both worlds, because it retains an intelligent source of nature, while freeing up natural science completely from religious restrictions of any kind, allowing it investigate literally any past event without invoking miracles. The only scientifically inexplicable event is then the absolute beginning in which nature itself was created — it is only there that intelligent design is tied to a particular creative action.

    So Denton’s view compels the existence of God, but not the interfering God of revealed religion; Shapiro’s view is silent about God, but leaves open the possibility that God directly created these marvellous self-engineering cells (though Shapiro himself doesn’t appear to personally believe that). Both of them agree that once the cells are created, no miracles are needed to explain anything that happens later.

    I’ve given you this long explanation so that you can see exactly how, in my view, Shapiro and Denton differ from Darwinian thinking. In my view, you can only call either one a special case of “Darwinism” by overlooking very important differences, and the label “Darwinism” for either one would massively confuse anyone who was trying to understand how these writers think evolution works. If you choose to call either or both of them special cases of “Darwinism,” despite my analysis, I cannot stop you. But now you know why I wouldn’t use that term for either one of them, and so my obligation to explain myself is fully discharged.

    (I would add that Denton contrasts his own view with the Darwinian, and Shapiro contrasts his own view with at least the neo-Darwinian, so even if you don’t find my discussion helpful, it might be wise not to classify these people with a terminology they would not accept.)

    As for your Denton/Meyer comparison, all I can say to you is that I have read both books, very carefully, and there is no comparison. Meyer’s book has merit, but is much too long for its limited purpose, whereas Denton’s book (his second book, *Nature’s Destiny*, is the one I’m speaking of) is necessarily long because of the richness of detail of his discussion. And Denton’s book is such that its content (a vast but integrated tour through cosmology, geology, biochemistry, etc.) is intrinsically interesting, outside of any reference to evolution, design, etc. His broad grasp of nature is impressive and he infects the reader with a love for the dazzling intricacy and sophistication of the natural world. Reading Denton is like reading Dawkins’s *The Blind Watchmaker* or Sagan’s *Intelligent Life in the Universe*. I don’t see how anyone with any broad interest in natural science could fail to enjoy reading Denton’s book, even if they disagreed with his conclusions. There is no book by any Discovery fellow anything like it. That is not to denigrate the books of Dembski, Meyer, Behe, etc. It’s merely to indicate that Denton’s book, while “id” in the generic sense, is not “ID” in the sense of belonging to the institutional program of Discovery. Anyone taking any position in the culture wars could enjoy it and benefit from it. So if you want one of the most thoughtful book-length treatments of evolution to appear in the past 20 years, Denton will satisfy.

    But of course, if you have some sort of inbuilt hatred for any writer who would even consider the possibility than there might intelligent design anywhere in the universe, you will not want to read Denton, since you will reject his conclusions a priori. But such a position would reflect an atheist dogmatism, not a genuine scientific curiosity about nature.

    T.

  121. T – thanks for your lengthy reply. I think we will have to agree to disagree on the meaning of the word “Darwinian”. I have always found it to be a very ambiguous phrase which is bandied about without much thought – especially on Uncommon Descent – so I probably should not have used it myself.

    Of course I do not have an “inbuilt hatred for any writer who would even consider the possibility than there might intelligent design anywhere in the universe,“- else why would I have spent time reading Dembski and Meyer and Behe? I just need to decide where best to spend my time. I will make Denton my next ID book – which doesn’t mean I will read it soon. In return may I recommend “The Better Angels of our Nature” by Stephen Pinker – which has nothing to do with ID but is one of the most interesting and well argued non-fiction books I have read for a very long time. It is a must read if you are interested in the moral state of society today.

  122. Just a brief comment, Timaeus: Thanks for this clarification.

    It seems that the “immanent” intelligence to which you refer chiefly differs from my use by refering to intelligence intrinsic to the organism – I am talking about “intelligence” intrinsic to the population – the capacity of a population to optimise the phenotypes of its members to survive in any given environment. The interesting thing that Shapiro shows is that through between-population selection, this “intelligence” can be raised to a meta-level: populations whose members tend to produce variant offspring within a range likely to render the population more robust to environment change. This is not the same as “foresight” of course; more like making sure you have a large Swiss Army Knife with which to confront the unforeseen!

    A similar role has been proposed for epigenetic effects.

  123. 123

    “In return may I recommend “The Better Angels of our Nature” by Stephen Pinker – which has nothing to do with ID but is one of the most interesting and well argued non-fiction books I have read for a very long time.”

    Allow me to recommend against taking Pinker’s analysis seriously based on the following criticisms:

    http://bedejournal.blogspot.co.....evolt.html

    http://bedejournal.blogspot.co.....usade.html

    http://bedejournal.blogspot.co.....rates.html

  124. 124
  125. Obviously the quotes are just tasters

    They are indeed. Saying it might still happen by chance is unbeatable. It takes a different kind of mentality to accept that it might not just be by chance. But that of course is a no-no. I am not impressed. Anyway, thanks for the leads.

  126. Petrushka,

    That is a tard different kettle of fish. It’s strange that you don’t see the obvious distinction. I strongly believe that whenever there’s code, the coder must have come first. Rules that complex systems – such as biological machinery – obey are not the same as physical laws. Say, I have an electric switch on the wall. It is clear that its existence is not necessitated by the existence of Ohm’s law.

  127. Thanks, markf.

    I don’t deny that some ID proponents, especially those whose main claim to fame is their contribution to blog sites, have misused or ambiguously used the word “Darwinian.” They’ve also sometimes misused the word “evolution” as a synonym for “Darwinian evolution,” forgetting (or never aware) that there have been other explications of evolution: Lamarck’s, Bergson’s, Chardin’s, etc. I often have to criticize ID proponents who claim that ID is against “evolution,” pointing out to them that Michael Behe is against the Darwinian explanation but not against evolution itself.

    Most of the time, however, the major ID figures use terms like “Darwinian” and “evolution” fairly consistently, and quite often they explain what they mean by “evolution” or “Darwinian evolution” near the beginning of their books or papers.

    For myself, I’ve tried to follow the usage of mainstream writers. The meaning of “Darwinian” that I employ is one I absorbed from reading semipopular science works long before I ever heard of ID, TE, or the New Atheists. And in those books the “Darwinian” formulation of evolution was always: (1) changes — usually ascribed to “random mutations” — were filtered by natural selection; (2) over long periods of time, such changes could accumulate to produce new species, families, classes, phyla, etc.; (3) that this process was gradual, with no sudden leaps (say, from fish to reptile, or insectivore to primate), but only very small gradations, often invisible to inexperienced observers; (4) that the whole process was wholly natural, without any intervention, however slight, by supernatural action; (5) that neither the mutations nor the selection process had any end in mind, so that evolution had neither particular goals nor even a destined general direction — toward man or anything else. It is such a characterization of evolution that I absorbed very early on, as a young person obsessed with natural science who scoured school and public libraries for every book on cosmology, dinosaurs, evolution and other subjects, and who spent his pennies on paperbacks by Ph.D.s-turned science writers like Sagan, Asimov, etc. So when I first came across Behe several years ago (I had barely heard of ID at the time, and of the current edition of TE I as yet knew nothing), and he used the phrase “Darwinian evolution” or “Darwinian mechanisms” or the like, I immediately clicked with his usage, and had no adjustment to make. Similarly, when Denton contrasted his view of evolution with the “Darwinian,” the contrast struck me as obvious and justified, and I took it in stride.

    I’m certainly interested in moral questions, and some day I may give Pinker a look. My reading list is backed up several books at the moment, however.

    T.

  128. Thank you, Elizabeth. I’m glad if I was able to communicate my ideas to you more effectively, even if I achieved it only indirectly in trying to reply to markf.

    I want to study Shapiro more closely before I make anything beyond the general statements I’ve already made, so I can’t comment properly on your remark about populations in relation to his understanding.

    You are right that I am focusing on organisms, not populations. Before any genomic change can spread into a population, it has to occur in an individual organism. And I’ve always found the neo-Darwinian explanation of how useful genomic changes first arise in organisms to be highly suspect. But if Shapiro is right about the two-way interaction, and if such interaction is common rather than rare, then a much less improbable explanation of significant evolutionary change is available.

    I agree with you about the Swiss Army knife, but of course, Swiss Army knives are designed by intelligent agents who have in mind the broad types of things that soldiers, hikers, campers, travellers, etc. might need to do. The question is: how on earth did life first acquire this Swiss Army knife of self-engineering tools? Was it put together by a trial-and-error? Shapiro doesn’t claim to answer that question, and to be sure, he can do his evolutionary theorizing without answering it; but inquiring minds still cannot let that question rest.

    T.

  129. Dr.Rec,

    I think you need to brush up on your pig Latin , ” od-gay” not godnay

  130. blue_savannah

    If I.D and creationism were the same, why would there be disagreements???

    Do you agree with Old Earth Creationists completely or are there disagreements?

  131. Apologies for all caps

  132. Shapiro doesn’t claim to answer that question

    Well, my understanding from what I’ve read of his, he does – explains it by population-level selection.

    You can disagree, of course, but I think that’s his proposal :)

    Cheers

    Lizzie

  133. ‘Population’ in natural-physical (*read impersonal) science-speak

    Translates into

    ‘Community’ or ‘Society’

    in human-social science-speak.

    The latter is of course Home to choice, decision-making, purpose, plan, teleology, etc.

    Not the former.

    (Return to discussion after having pointed out the obvious.)

  134. You are free to believe anything, but it’s possible that chemistry can do things you haven’t dreamed of. It will be settled in the laboratory, not by philosophy.

  135. Elizabeth (16.1.2.1.1):

    You are not understanding my meaning.

    The “smart features” of the genome-cell system that I am talking about would have to have existed (in at least a 1.1 version) in the very first living cell, when there was no “population” to derive the features from. I don’t think Shapiro purports to explain the origin of the first cells, the first genomes, the protein-DNA system, etc.

    As a side remark, I think that you approach evolutionary models from the point of view of population geneticist, and I approach them from the point of view of an engineer, and I think this accounts for a number of confusions between us. We are trying to describe the same entities and processes, but we are using entirely different languages. This, incidentally, is a very old problem; it was present at the Wistar Conference of 1966, where some of the leading physicists and engineers in the world challenged the leading neo-Darwinians regarding the mathematical plausibility of their model, and it continues today, as ID people (who generally think like engineers) challenge current population geneticist types.

    I actually find it rather odd that a neuroscientist would think more like a population geneticist than like an engineer, especially a neuroscientist with background in architecture. I would think that such a person would be thinking more in terms of the complex interlocking of parts needed to build organs and systems, and the strict engineering constraints which would make most alterations deleterious, and most of the remaining alterations less efficient than existing arrangements. The type of arguments you are offering I would expect to hear from someone who taught genetics and evolution in a standard biology department, not from someone with your unique training. But hey, as it said in the Monty Python film, “WE’RE ALL INDIVIDUALS!”, and a neuroscientist/architect has the right to think like a population geneticist if she wants to, just as a philosopher has a right to think like an engineer if he wants to.

    T.

  136. You are not understanding my meaning.

    OK.

    The “smart features” of the genome-cell system that I am talking about would have to have existed (in at least a 1.1 version) in the very first living cell, when there was no “population” to derive the features from. I don’t think Shapiro purports to explain the origin of the first cells, the first genomes, the protein-DNA system, etc.

    No, he doesn’t, but I don’t think he shares your premise, either.

    As a side remark, I think that you approach evolutionary models from the point of view of population geneticist, and I approach them from the point of view of an engineer, and I think this accounts for a number of confusions between us. We are trying to describe the same entities and processes, but we are using entirely different languages. This, incidentally, is a very old problem; it was present at the Wistar Conference of 1966, where some of the leading physicists and engineers in the world challenged the leading neo-Darwinians regarding the mathematical plausibility of their model, and it continues today, as ID people (who generally think like engineers) challenge current population geneticist types.

    Well, I think that’s a false distinction, myself. Although I do see it frequently made, here.

    I actually find it rather odd that a neuroscientist would think more like a population geneticist than like an engineer, especially a neuroscientist with background in architecture. I would think that such a person would be thinking more in terms of the complex interlocking of parts needed to build organs and systems,

    As indeed I do, but that is not incompatible with “thinking like a population geneticist”, if indeed that’s what I do (I don’t think it’s a very good description myself). I’m very interested, obviously, in feedback loops, and indeed, in chaotic systems, and the systems I model (systems of neurons, for example) have a substantial family resemblance to evolutionary systems. Perhaps it’s time that engineers learned some populations genetics :) As in fact a lot of them have (hence GAs).

    and the strict engineering constraints which would make most alterations deleterious, and most of the remaining alterations less efficient than existing arrangements.

    That only matters if bad prototypes are costly. If they are cheap, it doesn’t matter how deleterious most alterations are as long as you a) keep producing the good ones and b) start producing beneficial ones when they come along. This is precisely why engineers need to think like population geneticists :)

    The type of arguments you are offering I would expect to hear from someone who taught genetics and evolution in a standard biology department, not from someone with your unique training. But hey, as it said in the Monty Python film, “WE’RE ALL INDIVIDUALS!”, and a neuroscientist/architect has the right to think like a population geneticist if she wants to, just as a philosopher has a right to think like an engineer if he wants to.

    Indeed. And don’t forget I have a musical training too :)

  137. Uhm – they all appear to come from the one blog.  They seem to part of a campaign rather than a genuine assessment of the book.  For example, one of the five blog items is dedicated to one line (the An Lushan revolt) in one of Pinker’s many tables.  The conclusion is the figure may be wrong.  Pinker says of the same table:

    These figures cannot of course be taken at face value. Some tendentiously blame the entire death toll of a famine or epidemic on a particular war, rebellion or tyrant. And some come from innumerate cultures that lacked modern techniques for counting and record keeping.

    The other blog posts are on much the same lines. Take one figure or fact and dispute it. This is a very broad book which includes an absolute mass of data and facts and some important and novel ideas.  If they can only find five items to dispute (and they are obviously trying very hard) then I think he is not in bad shape.  I cannot find anywhere on the blog a proper review of the book.  They don’t even summarise the conclusions – much less say if they agree.

    The other thing that stands out is they appear to see this as a dispute about religion.  Pinker is an atheist but this book is not about religion.  For example, he emphasises the large role communism had in violent deaths in the 20th century.  He does argue that for a really large body count you need an ideology – but who would dispute that?

  138. Elizabeth:

    On what Shapiro says, I would direct you to the following:

    http://www.evolutionnews.org/2.....55051.html

    And particularly to this exchange between Dembski and Shapiro:

    ************

    Dembski: “James, we met the first time at Wheaton College at a symposium in the spring of 1997 featuring principally you and Michael Behe along with Paul Nelson and David Hull. At the time, I asked you about the origin of such “natural genetic engineering” systems. As I recall, you indicated that this was not really the problem you were addressing. Have you thought any more about this problem? Specifically, how do such systems arise that can take over their evolution? And how much complexity do they require? Are you confident that non-teleological mechanisms can account for the rise of natural genetic engineering systems, and if so why?”

    Dembski (narrating) Shapiro’s reply was illuminating for what it failed to say:

    Shapiro: “I am not sure how to answer your question. All existing living organisms possess natural genetic engineering capabilities. So they must be pretty fundamental. Any self-organizing evolving system has to have the capacity to alter its information store. That’s what they do. Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cells.”

    Dembski (narration): Where do the fundamental biological structures that make natural genetic engineering possible come from in the first place? Shapiro punted on this question back then and continues to punt to this day.

    [Dembski, in his narration, then goes on to say that Shapiro maintains his agnosticism as of January 2012, and provides this:]

    Shapiro: “How did the first functional envelope-spanning complex originally arise in evolution? Although we can easily reject the supernatural solution ID advocates propose in response to this question, we also have to acknowledge that we still have no clear scientific answer to it.”

    *****************

    Elizabeth: It was these statements, and statements like them, that I had in mind. Now do you see that I was not making anything up, and what I meant?

    As for this comment:

    “That only matters if bad prototypes are costly. If they are cheap, it doesn’t matter how deleterious most alterations are as long as you a) keep producing the good ones and b) start producing beneficial ones when they come along. This is precisely why engineers need to think like population geneticists.”

    I don’t know what distinction you are making between “good” and “beneficial” in a and b above, but anyhow: the engineer would grant the point, but would say that the order of acquisition is important, because islands of functionality must be created between original form A and ultimate form B. Not all orders of acquisition, even of all the right parts, allow for this. If I have a bicycle with three speeds, and it has the capacity to admit the substitution of a five-speed system, I can ride my bicycle with only three speeds, until I acquire a five-speed system. But if someone gives me the chain and gears and other apparatus for a five-speed system, but no bicycle, I cannot ride at all until a bicycle comes along. I have to walk. That is no minor inconvenience. So if you tell me that, given five million years, eventually part A and part B will be found together, and then the creature will have a new function, I am going to ask: what will the creature do for five millions years with only part A, and what with only part B? And then you have to construct a scenario, plausible to the engineering mind, in which at least one order of acquisition (and I’m keeping it unrealistically simple, with only two parts) will give the creature some viable intermediate capability. The engineer does not object if such scenarios are hypothetical, if only they are plausible.

    Unfortunately, when asked for such detailed scenarios, 99% of population geneticists duck out, claiming that it’s utterly unreasonable to demand such a thing before accepting their model. They think the model should be accepted on the basis of their mathematical calculations alone, without any discussion of the physical/engineering problems that might arise when actual forms have to be dealt with. And so the standoff continues. Population genetics math is great — I don’t object to it. But it will never, never convince a Darwin skeptic by itself. It has to be supplemented by a discussion of the structure and function of the hypothetical intermediate organs, systems and organisms which must fall between A and B. And that is what Darwinians, neo-Darwinians, Darwinians + drifters, etc., rarely or never do.

    Yes, you have mentioned your musical training to us many times. And I think someone here pointed out to you that it does not show up in your unmusical thinking about religious matters. :-)

    T.

  139. You are quite rude, Timaeus!

    What do you mean by my “unmusical thinking about religious matters”?

    I have no idea.

    You seem far more interested in putting me into some box of your own making than actually communicating.

    harrumph.

    I’ll try and respond to content later.

  140. Timaeus has a tin ear for social interactions. Perhaps some musical training would help.

  141. Elizabeth:

    Did you not see the smiley face? And you have obviously forgotten the earlier exchange you had with someone here, which was the basis of the teasing remark.

    Since my attempt to relieve tension by joking flopped, I’ll assume a Puritan seriousness from here on in.

    T.

  142. Well, maybe. But I’d be just as happy if s/he’d actually say what s/he means.

    I can’t exactly offer a defence to an allegation like that.

    Perhaps I do have a tin ear for religion. Dunno. I don’t think so.

  143. Yes I saw the smiley face, Timaeus :)

    Did you not see my harrumph?

    No, I don’t remember the exchange, although I’ve exchanged musical thoughts with Gil before now. In fact I was playing his lovely Chopin on my computer only half an hour ago.

    Not that I can play Chopin. I can’t play keyboard at all.

    But I was a leetle bit cross about the continued digs at my (supposed) areas of expertise/lack of expertise.

    Hence the harrumph.

    Back to business: Not sure what you are trying to say about Shapiro. Dembski seems keen to point out what Shapiro is not saying.

    What do you think that Shapiro is saying? I have to say, he’s not the best communicator, but this paper is worth wading through, I think:

    http://shapiro.bsd.uchicago.ed.....5.Gene.pdf

    Anyway, no hard feelings :)

    Cheers

    Lizzie

  144. This is called being ‘religiously unmusical’ in technical terms, by Max Weber. He claimed the same (temperament) of himself, according to the ideology of ‘secularisation,’ aka ‘disenchantment.’ Nowadays, new theorists have arisen that challenge this supposedly ‘scientific’ thesis.

    My view is that ‘music’ is a ‘universal,’ i.e. not just an ‘evolutionary’ one but a ‘real one, which all human beings share. Religious music is one type, demonstrated in manifold ways (genres). There are of course other types as well, which perhaps Elizabeth is keen to celebrate.

    Waiting in line for Elizabeth to philosophise about ‘naturalism’ and its alternatives.

  145. Well, I’m not :(

    I loved my religion. Still do, in a way.

    And St John’s Gospel is still one of my favorite pieces of literature.

    Waiting in line for Elizabeth to philosophise about ‘naturalism’ and its alternatives.

    Well, you may wait awhile :) Unless you have a specific question? Or have I gone and lost track of one I owe you?

  146. Yes, well, old loves often die hard or live again.

    Agreeing about John’s power, though as more than just ‘literature.’

    The specific question was made here:
    http://www.uncommondescent.com.....th-liddle/

    Question/Section 9.1 It is made as clear as possible.

  147. Elizabeth:

    You ask: “What do you think that Shapiro is saying?”

    I’m confused. I gave you direct quotations from Shapiro. I think he is saying what he is saying there. He is saying that he has no theory about the origin of the self-engineering capacities of the cell. And that’s what I said (16.1.2.1) that Shapiro said in the original comment that you objected to (16.1.2.1.1). You expressed doubt that I had interpreted him aright, so I provided direct quotations.

    If you find his paper unclear, why don’t you read his new book? Probably every ID person I know has bought it and has read it or is in the process of reading it. It has technical parts aimed at evolutionary biologists, but parts of it are quite clear to the non-specialist with a basic general knowledge of evolutionary ideas.

    Here is an example of his writing, not on the point above about the origin of systems, but about the distinction between the new evolutionary biology and the mainstream evolutionary biology of the 20th century:

    “A shift from thinking about gradual selection of localized random changes to sudden genome restructuring by sensory network-influenced cell systems is a major conceptual change. It replaces the “invisible hands” of geological time and natural selection with cognitive networks and cellular functions for self-modification. The emphasis is systemic rather than atomistic and information-based rather than stochastic.” (145-146)

    I find that a rather elegant summary.

    He has similar lucid remarks on Darwin and neo-Darwinism on pp. 1-2. (And note that he ties them together, justifying my claim that he is critical of “Darwinian” thought more broadly, not just neo-Darwinism.)

    He seems to me to be an adequate communicator.

    I am nowhere near understanding all of his book yet, but his key claims seem to be clear enough. I don’t think I’ve misinterpreted those.

    I won’t discuss Shapiro any further at this point, until I know more about him. In the meantime, if you still disagree with my original statement, “Shapiro doesn’t claim to answer that question” (16.1.2.1 above) there is nothing more I can do about that. I’ve documented it in his own words.

    T.

  148. Agreed (re John).

    Thanks for the link.

  149. Well, he gives a theory in that paper I linked to.

    So we’ll have to agree to differ on that for now :)

    Apologies for the grumpy old lady stuff earlier.

    Peace.

    Lizzie

  150. Elizabeth:

    I don’t perceive that you owe me any apology. I made a joke without thinking that it might be taken less than affectionately. If we were old chums from school days, I think it would have been taken in good part, but given that I had irritated you earlier, I should have known enough not to venture the wisecrack. And I did press you a little hard on your internet persona. You had a right to show irritation, if that’s what you felt.

    Nonetheless, you have to know that irritation can be generated by many things; it can be generated by aggressive manners (which is what you felt from me), or it can be generated by polite manners coupled with an air of certainty about a wide range of scientific and intellectual subjects that no human can encompass in a lifetime, and that’s what I’ve often felt from you (whether you intend it or not). So I guess both of us gave way to irritation, only the reason for my irritation was probably not clearly visible to you and therefore it would have come across to you as ungrounded belligerence. Bad judgment on my part.

    I don’t know what the date of the paper is that you read, or what it was about. I assume that Bill Dembski’s quotation of Shapiro from January 2012 would represent Shapiro’s current view on the subject we were discussing. That’s all about Shapiro for now.

    T.

  151. Elizabeth Liddle:

    I don’t know if you still read UD, or get responses to threads via some kind of automatic feed, but if either is the case, I have an answer to your last post.

    I had written:

    “The question is: how on earth did life first acquire this Swiss Army knife of self-engineering tools? Was it put together by a trial-and-error? Shapiro doesn’t claim to answer that question”

    You answered:

    “Well, he gives a theory in that paper I linked to.”

    I just checked the paper you linked to, which was:

    http://shapiro.bsd.uchicago.ed.....5.Gene.pdf

    I have now read the article, and I see nowhere where he tries to answer the question which I posed. It thus appears that you have misunderstood either my question or Shapiro’s article.

    It would indeed have been surprising if Shapiro had presented an answer to such a fundamental question in 2004 and then, more than 7 years later, in 2012, denied (as he does, in the passage I quoted) that he had any clue how to answer the question. That is why I doubted from the beginning that you had interpreted the article correctly. And now, having looked at the article, I see that my doubts were quite warranted. He gave no origin for the capacity I identified, back then any more than he does now. He’s simply agnostic about it. And really he has to be, because the question cannot be answered without answering the question of the origin of cellular life itself.

  152. Timaeus,

    Why is it that true believers keep claiming there are things addressed in papers when the papers don’t actually address the things claimed? Is it a problem of reading comprehension? Faulty logic? Wishful thinking?

    With Nick Matzke I think it is just a literature bombing debate tactic. With Elizabeth it seems to be more of the wishful thinking. Interesting . . .

  153. Eric:

    I can’t explain, in Elizabeth’s case. Her motivations are an enigma shrouded in a mystery etc. She does seem to obsessed with reciting standard population genetics approaches to evolution, however. It’s almost as if, when she took up an interest in evolution — which I suspect was not early in her life, but relatively recently — she imbibed the standard approach from some textbooks or general books recommended to her, and learned their approach religiously. (Remember, her first two degrees were in music and architecture, so she may never have actually taken an undergraduate biology course, and population genetics wouldn’t be on the curriculum for a Ph.D. in cognitive psychology.) If that’s the case, she probably tries to make everything she reads about evolution somehow fit into her first understanding.

    In one of her comments above, she speaks of Shapiro as explaining things in terms of “between-population selection,” but in the article she cites, the word “population” occurs exactly once, and the phrase “between-population selection” not at all. And she couldn’t have got the idea from Shapiro’s book, because at the time she hadn’t read it yet. Maybe, in making that remark, she had some other articles by Shapiro in mind, but as far as the cited article goes, the phrase is purely her invention. It’s as if she is determined to see Shapiro, and all other evolutionary biologists, through a set of glasses tinted with a certain shade.

    ID people, on the other hand, read Shapiro, Margulis, etc. in accord with their own stated intentions, which are insurrectionist. Shapiro thinks that much of mainstream evolutionary thought is blatantly wrong. He’s shaking the foundations.

    That is why Coyne is so furious with Shapiro lately, and is insulting him and belittling him in public. If Shapiro were just offering another source of mutational novelty, Coyne wouldn’t be so angry. Coyne, who knows evolutionary theory far better than Elizabeth will ever know it, understands that Shapiro isn’t just adding another modification, which the mainstream theory can absorb with a little adjustment, but throwing down a gauntlet. All the ID people understand that, and Elizabeth doesn’t — which calls into question the depth of the understanding of evolutionary theory which she has acquired in her autodidactic wanderings through the field.

  154. >>>Champignon wrote on 1/18/12: “Darwinism’ doesn’t appeal to the supernatural.”

    That’s because it relies on mathematical miracles.

    Darwinists habitually stare sequence probabilities of 1/10^150 or less without batting an eyelash. If they can go THAT deeply into denial, it makes sense that they don’t feel the need to invoke a designing intelligence.

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