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Lobbing a grenade into the Tetrapod Evolution picture

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A year ago, Nature published an educational booklet with the title 15 Evolutionary gems (as a resource for the Darwin Bicentennial). Number 2 gem is Tiktaalik a well-preserved fish that has been widely acclaimed as documenting the transition from fish to tetrapod. Tiktaalik was an elpistostegalian fish: a large, shallow-water dwelling carnivore with tetrapod affinities yet possessing fins. Unfortunately, until Tiktaalik, most elpistostegids remains were poorly preserved fragments.

“In 2006, Edward Daeschler and his colleagues described spectacularly well preserved fossils of an elpistostegid known as Tiktaalik that allow us to build up a good picture of an aquatic predator with distinct similarities to tetrapods – from its flexible neck, to its very limb-like fin structure. The discovery and painstaking analysis of Tiktaalik illuminates the stage before tetrapods evolved, and shows how the fossil record throws up surprises, albeit ones that are entirely compatible with evolutionary thinking.”

Just when everyone thought that a consensus had emerged, a new fossil find is reported – throwing everything into the melting pot (again!). Trackways of an unknown tetrapod have been recovered from rocks dated 10 million years earlier than Tiktaalik. The authors say that the trackways occur in rocks that: “can be securely assigned to the lower-middle Eifelian, corresponding to an age of approximately 395 million years”. At a stroke, this rules out not only Tiktaalik as a tetrapod ancestor, but also all known representatives of the elpistostegids. The arrival of tetrapods is now considered to be 20 million years earlier than previously thought and these tetrapods must now be regarded as coexisting with the elpistostegids. Once again, the fossil record has thrown up a big surprise, but this one is not “entirely compatible with evolutionary thinking”. It is a find that was not predicted and it does not fit at all into the emerging consensus.

“Now, however, Niedzwiedzki et al. lob a grenade into that picture. They report the stunning discovery of tetrapod trackways with distinct digit imprints from Zachemie, Poland, that are unambiguously dated to the lowermost Eifelian (397 Myr ago). This site (an old quarry) has yielded a dozen trackways made by several individuals that ranged from about 0.5 to 2.5 metres in total length, and numerous isolated footprints found on fragments of scree. The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr.” (Janvier & Clement, 2010)

The Nature Editor’s summary explained: “The finds suggests that the elpistostegids that we know were late-surviving relics rather than direct transitional forms, and they highlight just how little we know of the earliest history of land vertebrates.” Henry Gee, one of the Nature editors, wrote in a blog:

“What does it all mean?
It means that the neatly gift-wrapped correlation between stratigraphy and phylogeny, in which elpistostegids represent a transitional form in the swift evolution of tetrapods in the mid-Frasnian, is a cruel illusion. If – as the Polish footprints show – tetrapods already existed in the Eifelian, then an enormous evolutionary void has opened beneath our feet.”

For more, go here:
Lobbing a grenade into the Tetrapod Evolution picture
http://www.arn.org/blogs/index.php/literature/2010/01/09/lobbing_a_grenade_into_the_tetrapod_evol

Additional note: The Henry Gee quote is interesting for the words “elpistostegids represent a transitional form”. In some circles, transitional forms are ‘out’ because Darwinism presupposes gradualism and every form is no more and no less transitional than any other form. Gee reminds us that in the editorial office of Nature, it is still legitimate to refer to old-fashioned transitional forms!

Comments
vjtorley at 408, When Dr. Dembski wrote his article on “Specification” in 2004, detailed probabilistic calculations were not yet available. In any case, calculating the probability of a bacterial flagellum emerging by undirected processes would have been too difficult. How, then, was he able to claim unequivocally that those probabilities are "exceedingly small"?Mustela Nivalis
January 29, 2010
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vjtorley at 409, Next, you write: "[Dembski's] analogy with a housing contractor and the list of supposed requirements assume that evolutionary mechanisms are looking for a particular outcome. This is sometimes referred to as the 'Lottery Winner' fallacy" I can assure you that neither Dembski nor Meyer commits any such fallacy. From your posts here you seem intelligent and likable, so I'd like to take your assurance. Unfortunately, I've read the material as well, and I think my assessment is reasonable based on what Dembski has written. The housing contractor was simply an illustration of the probabilistic hurdles confronting any undirected mechanism that is supposed to produce irreducibly complex biochemical machines. Dembski listed seven: availability of ingredients; synchronization; localization; interfering cross-reactions; interface compatibility; order of assembly; and configuration. No matter what kind of irreducibly complex structure you’re making, these hurdles need to be overcome. Dembski fails to consider the fact that these issues may be addressed by building on earlier versions. That is, he fails to take into account known evolutionary mechanisms. He also appears to assume a particular result, leading me to raise the Lottery Winner Fallacy. I should add that Dr. Dembski is a qualified mathematician. It’s hardly likely that he’d be making a high school blunder. This is just an argument from authority. Based on what Dembski wrote, I don't believe my understanding is unreasonable. As Nakashima points out, Dembski could eliminate the confusion by simply publishing his calculations.Mustela Nivalis
January 29, 2010
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vjtorley at 408, And what of the alternative mechanisms you propose? "If you want to find true counter-examples, look for reasoning and math that assumes f(t+1) = f(t) + variation + selection, in other words, an iterated function system. Look for the use of the Price equation or Holland’s Schema Theorem. But I have to warn you, I have never seen an ID theorist reason using these tools to show the inadequacy of evolution." Iteration won’t work as an account of how specified information originates. Polymerization, yes; specificity, no. Could you please explain your reasoning? It will probably require a precise, mathematical definition of "specified information" in order to prove your point.Mustela Nivalis
January 29, 2010
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Mr VJtorley, With respect to abiogenesis, I think the relevant issues are: 1 - are there abiotic pathways to the creation of RNA monomers, amino acids, and phospholipid bilayers? This gets a qualifed yes, but more work is necessary. 2 - Can these chemicals accumulate in the same environment (which may involve transport from the environment where they are synthesized)? Also a qualified yes. 3 - Is there any direct interaction of AAs and RNA chains in the absence of a translation system? Cases: 3.a - no interactions. Still a need to find a translation system. 3.b - complete and permanent binding. Need to find a way to keep them separated and a translation system. 3.c - temporary binding. AAs and RNA bind due to mechanical (shape) and or chemical (charge distribution) reasons. Goldilocks would be so happy! Cases: 3.c.i - random bindings. RNAs show no preferences for any AA over any other AA. Still need to find a source of specificity. 3.c.ii - preferential binding. RNA shows at least probabilistic prefernces for some AAs over other AAs. What Yarus, et al are showing is that case 3.c.ii corresponds to the real world. The laws of physics and chemistry drive the existence and general layout of the genetic code. As I said earlier, mutualism between proteins and the RNAs that template them is necessary. Is this realistic? A typical evolutionary rate based argument says yes. Assume there is some distribution of mutualism among RNA/protein pairs. Some pairs are actually antagonistic - the protein attacks the RNA that is its template. Some pairs are neutral - they don't interact at all after separation. Some are positively mutualistic - the protein helps the RNA as an enzyme, protects it from degradation in some way, or the RNA helps the protein fold into some shape that itself lasts longer. Across this distribution - if it exists at all - over time the mutualistic pairs will dominate.Nakashima
January 27, 2010
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Mr Vjtorley, Thank you for your response. Yes, I did notice the structuring of your message, parallel to Dr Meyer's book. In fact, my message @396 also notes that the first several of those quotes appear in the chance hypothesis section, and give them a pass. It's the one that are not in the chance hypothesis section that are problematic, of which I noted three. (This next section of your message is not directly about the tornado problem, but I will comment.) I'll pass over the summary of the first two sections (chance and self organization) since I don't have any strong objections to Meyer's presentation or your summary. Of the three problems re the RNA world that you quote: Problem 3 - Yes, the lack of a plausible historical pathway will only be resolved through more research. Problem 4 - Dr Meyer is wrong here to not discuss Yarus and the stereochemical hypothesis, since it is the answer to this question. (The big question of the entire book.) Problem 5 - Criticising the fact that scientists work with abstractions and models is a bit silly. One lab scientist working on an experiment will apply stronger mutagens and selection pressures to see if they get any response from the chemicals in a liter of water than are necessary for the same results to occur in an entire ocean in millions of years. You write: In short, Dr. Meyer looked at the most promising non-random hypotheses for the origin of life, and found them wanting: they all failed to account for the origin of specified information that is found in living things. Sadly no, as I point out above in relation to problem 4. I agree that the Schema Theorem and Price's Equation are properly applied to already living systems. In the context of abiogenesis, fitness simply means using feedstocks faster than the next molecule. But they do apply to biological situations, and we still see "tornado" reasoning applied outside of abiogenesis, for example in irreducible complexity. It is heartening to hear that between 2004 and 2008, some calculations were completed, however I note that you don't quote them. That is the point. Quoting an abiogenesis calculation by Dr Meyer does not support a claim to an irreducible complexity argument about new functions arising in already living systems. Until we see those calculations to which Dr Dembski refers, we won't know whether they use "tornado" reasoning or not. Your final quote of Dr Meyer is problematic. As you yourself note, assuming the 250 proteins need to form independently is "tornado" reasoning. In addition, where did that 10^-164 number come from? Looking back, we see that it came from Axe's work quoted in ...drumroll please... chance hypothesis section. As a matter of fact, not just the number comes from the chance hypothesis section, the whole quote does. You are summarizing Dr Meyer's reasoning by quoting pure tornado calculations. Finally, you make a challenge to point out the mechanisms by which a functional protein could encourage the creation of another protein with another function. Off the top of my head, I can think of two. Both rely on the idea that protein chains would form by individual amino acids sticking to RNA chains and then being connected. Further, the proteins that match the RNA strand must have a mutualistic relationship, they must somehow help each other survive. The first method is that the underlying RNA chains break and reform in different sequences and combinations. As a result new protein sequences will form. As with exaptation in cells, exchanging sequences of RNA is reusing a part that are already contributing to some function, so this is a faster kind of functional exploration than single base mutations. The other method relies on the idea that the early templating process of AA on RNA was not exact. Today one triplet of RNA codes for only one AA, with the help of the whole tRNA system. But earlier, I think Yarus' research shows it was more probabilistic. Therefore, one RNA sequence mapped to several proteins. Templating and ligation didn't just produce one protein, it created a whole cloud of different proteins at different probabilities.Nakashima
January 27, 2010
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Mr Zeph, I'm also interested in the "edge of evolution", "what evolution can't do", etc. in order to understand the limits of a tool. To continue your car analogy, tires a helpful, but they have warnings "don't inflate to more than X pressure". Knowing the same limits to evolution lets you use the tool effectively, for example by giving you sizing parapmeters - if your problem solution candidates are k bits long, use a population size of 1.4*k to get convergence near the global optimum in k generations. However, I'm the wrong person to ask about why chance is highlighted so often. Perhaps it is just human nature to highlight differences.Nakashima
January 27, 2010
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Mustela Nivalis (#394) Thank you for your post. I'd like to respond to two points you raised regarding Dr. Dembski's argument for intelligent design. First, you write:
I haven't seen an attempt by Dembski to calculate CSI for a real biological artifact with reference to how particular physical, chemical, and evolutionary mechanisms affect the calculations.
I sympathize with your frustration. However, with regard to origin-of-life scenarios, none of the self-organization hypotheses proposed to date contain any detailed probabilistic calculations for the mechanisms they put forward. Without these, detailed CSI calculations of the kind you request are impossible. Next, you write:
[Dembski's] analogy with a housing contractor and the list of supposed requirements assume that evolutionary mechanisms are looking for a particular outcome. This is sometimes referred to as the "Lottery Winner" fallacy...
I can assure you that neither Dembski nor Meyer commits any such fallacy. The housing contractor was simply an illustration of the probabilistic hurdles confronting any undirected mechanism that is supposed to produce irreducibly complex biochemical machines. Dembski listed seven: availability of ingredients; synchronization; localization; interfering cross-reactions; interface compatibility; order of assembly; and configuration. No matter what kind of irreducibly complex structure you're making, these hurdles need to be overcome. I should add that Dr. Dembski is a qualified mathematician. It's hardly likely that he'd be making a high school blunder. The same goes for Dr. Meyer's book, Signature in the Cell. On page 210, Meyer refers to the likelihood of producing "any functional protein whatsoever", and later on he writes:
The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebiotic soup is no better than 1 chance in 10^164...
Here, he is clearly referring to the odds of getting one protein that can perform any kind of function at all, not the odds of getting a protein which performs a particular function. Dr. Meyer continues:
If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or 1 in 10^41,000. This kind of number allows a great deal of quibbling about the accuracy of various estimates without altering the conclusion.
Here, once again, Dr. Meyer is not referring to any particular functions performed by the proteins in question. His argument hinges on the simple fact that the most basic viable cell requires 250 proteins. That's all. Dembski and Wells' latest book, The Design of Life, refers to the same data relating to proteins. Once again, we have no "Lottery Winner" fallacy here. Unless Darwinists can put forward a mechanism and demonstrate that it dramatically shortens the odds, the hypothesis of abiogenesis is in deep, deep trouble.vjtorley
January 27, 2010
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Mr. Nakashima (#396) Thank you for your post. With the greatest respect, you seem to have missed the point of the quotations I cited from Dr. Stephen Meyer's book, Signature in the Cell. You wrote:
With respect to Signature in the Cell, Dr Meyer quotes a number of calculations, some of which you have highlighted... Bringing these quotations together does not dispel the notion that ID theorists frequently use the idea and mathematical equivalent of Dr Hoyle's memorable phrase... Bolding Dr Fred Hoyle's original tornado-in-a-junkyard calculation is not going to convince anyone that ID does not routinely use tornado-in-a-junkyard argumentation... To summarize, if you see the phrase "random process... by chance" then you are not dealing with chance and selection. If you see "number of trials" you are not dealing with selection and contingency, you are dealing with independent trials. If you see "the probability of X is A, so the probability of N*X is A^N" you are dealing independent trials, not selection, variation, exaptation, history, or contingency on the laws of chemistry and physics. All of the above are versions of “if it happened at all, it happened all at once" aka tornado-in-a-junkyard.
If you look back at my post on Dr. Meyer (#391) you will see that it is divided into three main parts. The first part does deal with pure chance. Indeed, I myself described it as such: Evaluating the “pure chance” hypothesis for the origin of life. That's where the bold quotes you cited came from. The point of this section was purely to show that random processes alone don't have a snowball's chance in Hades of generating life. Comparisons with Hoyle were entirely apt here; the difference being that in the 27 years since he wrote, the probability calculations have improved for the "pure chance" scenario. Evidently, the probability of life originating by pure chance isn't 10~-40,000, as Hoyle thought. It's 10~-41,000 - give or take. The next section in my post (#391) was entitled, Evaluating the self-organization hypothesis for the origin of life. In this section, Meyer carefully considered non-random mechanisms that had been proposed for the origin of life, including Kauffman's self-organization theory and several other related hypotheses. After examining them carefully, Meyer's found them wanting:
...I realized that self-organizational models either failed to solve the problem of the origin of specified information, or they “solved” the problem at the expense of introducing other, unexplained sources of information. ...In my view, these models either begged the question or invoked a logical contradiction. Proposals that merely transfer the information elsewhere necessarily fail because they assume the existence of the very entity – specified information – they are trying to explain. And new laws will never explain the origin of information, because the processes that laws describe necessarily lack the complexity that informative sequences require.
I think that's clear enough. Don't you? Finally, Meyer addressed the RNA world. He listed five reasons why he thought it wouldn't work. I quoted the three most important ones:
Problem 3: An RNA-based Translation and Coding System Is Implausible RNA-world advocates offer no plausible explanation for how primitive self-replicating RNA molecules might have evolved into modern cells that rely on a variety of proteins to process genetic information and regulate metabolism... Problem 4: The RNA World Doesn’t Explain the Origin of Genetic Information Page 315 [A]s Gerald Joyce and Leslie Orgel note, for a single-stranded RNA catalyst to produce an RNA identical to itself, (i.e. to self-replicate), it must find an appropriate RNA molecule nearby to function as a template, since a single-stranded RNA cannot function as both replicase and template. Moreover, as they observe, this RNA template would have to be the precise complement of the replicase. Problem 5: Ribozyme Engineering Does Not Simulate Undirected Chemical Evolution Ribozyme engineers tend to overlook the role that their own intelligence has played in enhancing the functional capacities of their RNA catalysts. The way the engineers use their intelligence to assist the process of directed evolution would have had no parallel in a prebiotic setting, at least one in which only undirected processes drove chemical evolution forward.
In short, Dr. Meyer looked at the most promising non-random hypotheses for the origin of life, and found them wanting: they all failed to account for the origin of specified information that is found in living things. The failure here was not isolated to this or that hypothesis: it was a pervasive failure, suggesting that scientists seeking to account for the origin of life had taken a fundamentally wrong-headed approach. I should like to add that Dr. Meyer has been investigating the problem of the origin of life since the mid-1980s, and his book has received high praise from several professors in related disciplines, such as chemistry and biology. You can verify this yourself at his Website: http://www.signatureinthecell.com/quotes.php .His book was also extensively reviewed by experts in the fields he discusses, before it was published. To accuse Dr. Meyer of attacking a strawman, and of having fundamentally misconstrued contemporary scientific approaches to the origin of life striked me as implausible to the n-th degree. And what of the alternative mechanisms you propose?
If you want to find true counter-examples, look for reasoning and math that assumes f(t+1) = f(t) + variation + selection, in other words, an iterated function system. Look for the use of the Price equation or Holland's Schema Theorem. But I have to warn you, I have never seen an ID theorist reason using these tools to show the inadequacy of evolution.
Iteration won't work as an account of how specified information originates. Polymerization, yes; specificity, no. Let's see what Wikipedia has to say about the equation and theorem you discuss.
Holland's schema theorem Holland's schema theorem is widely taken to be the foundation for explanations of the power of genetic algorithms... Using the established methods and genetic operators of genetic algorithms, the schema theorem states that short, low-order, schemata with above-average fitness increase exponentially in successive generations. Price equation The Price equation (also known as Price's equation) is a covariance equation which is a mathematical description of evolution and natural selection. The Price equation was derived by George R. Price, working in London to rederive W.D. Hamilton's work on kin selection... Suppose there is a population of n individuals over which the amount of a particular characteristic varies... Index each group with i so that the number of members in the group is n_i and the value of the characteristic shared among all members of the group is z_i. Now assume that having z_i of the characteristic is associated with having a fitness w_i where the product w_i * n_i represents the number of offspring in the next generation. Note that this is really a difference equation relating the average value of a characteristic in one generation to the average value of the characteristic in the very next generation.
This is all very well and good, but it doesn't tell us where this variation comes from. Moreover, "fitness" is a biological concept. Polypeptides are neither fit nor unfit, so it seems to me that Price's equation and Holland's schema theorem are of no help in explaining the origin of proteins, let alone the first living cell. Unless you can tell me why polypeptides that fold up nicely and do a job are more likely to have proliferated on the primordial Earth than polypeptides that don't, it seems to me that the two mathematical results you quote won't help explain abiogenesis. Finally, you claim that Dembski doesn't give detailed probabilistic calculations to support his case:
If Dr Dembski, or whoever had done the calculations that "always end up being exceedingly small" would publish those calculations, the critics would be quieted. Instead we get an analogy about house building, and not building a series of houses, either. So while Dr Dembski does say the calculations take selection into account, without seeing them there is still an opening for the critics.
When Dr. Dembski wrote his article on "Specification" in 2004, detailed probabilistic calculations were not yet available. In any case, calculating the probability of a bacterial flagellum emerging by undirected processes would have been too difficult. However, since then, it has become possible to calculate the likelihood of a functional protein emerging, and to arrive at a ballpark figure for the probability of life emerging, since the simplest cell requires hundreds of proteins. Dembski refers to these results in his 2008 book, The Design of Life. As Dr. Meyer puts it in Signature in the Cell:
If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10^164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or in in 10^41,000. This kind of number allows a great deal of quibbling about the accuracy of various estimates without altering the conclusion.
You may object that this is "tornado in a junkyard" reasoning again, as the calculation assumes that the proteins formed independently. So here's my challenge: show me a mechanism that would allow an already formed functional protein to increase the probability of another functional protein arising, while swimming around in the primordial soup, thereby raising the likelihood of life forming by undirected processes. I'm waiting.vjtorley
January 26, 2010
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I have a question for Nakashima and Mustela (and anybody else). Yeah, me again. Thanks to all the kind souls who have tolerated and responded. I'll get too busy with some other projects soon and need to drop back, promise. Reading around on this site, I seem to perceive a recurring propensity to briefly characterize the heart of Darwinian Evolution as "chance" or "randomness". Not in the most sophisticated arguments from ID proponents, tho even they sometimes slip into that kind of phrasing despite knowing better. I find interesting and legitimate the hypothesis that mutation + natural selection + conserved incremental cumulative functionality are insufficient to account for known complexity (tho I'm not decided either way). But forgetting selection and mentioning just chance sounds to me like skepticism that just draining the oil from your engine periodically could allow your car to operate for over 200K miles - and often forgetting to mention that the oil change proponents also expect the car to be refilled with clean new oil, probably the more important half of the operation. (The car would do better - for at least a while - with no oil change than with draining without refilling. Likewise, in DE, we'd survive better in the short run with zero mutations, absent any selection process to cull the results. Somewhere not far beyond this point, the analogy breaks down faster than the oil free car). The question: why is chance so often mentioned alone? Is this sort of like Einstein's famous quote about refusing to believe that God plays dice (quantum physics) - an intuitive repugnance or rejection of randomness (that entropic killer of all that is orderly and good) which puts "chance" at the top of the Most Wanted List of intellectual felons? Or do many ID folks basically not understand the core concepts of (neo) Darwinian Evolution? (Obviously *some* ID proponents understand it quite well, better than I as a non-biologist). Or is it a rhetorical ploy, building a strawman to tear down, even if they (should) know better? (Right now I'm not talking about full blown tornado/junkyard arguments, but just frequent casual references in the course of other arguements) I wish this was less prevalent. I'm tryinig to give ID a fair hearing (and am impressed with the best of its arguments, if not yet fully convinced). But it helps me follow along when I see that the ID proponent is not overtly distorting or demeaning DE, just trying to out-reason it fairly. Thoughts?Zeph
January 26, 2010
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Nakashima: I’m in violent agreement with you... Wow, I read that as violent disagreement, and started to compose a clarification, thinking I must have clumsily sounded like I was making a broader assertion than I intended. (smile) Your point that DNA fragments are sequentially read is well taken. It's a good thing that there are a lot of parallel and sometimes redundant genes, so a minor error in one location *often need not* affect full functioning elsewhere (tho of course it might). I continue to be amazed and delighted with the mechanisms of life, starting with DNA/RNA/proteins. Intel does a pretty good job too, but is adapted to a different purpose and environment. Er, designed for a different purpose, in this particular case.Zeph
January 26, 2010
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Zeph -Alas, I don’t see much interest yet in ID addressing “How” questions But it won't be ID doing the addressing. It would be someone in medicine or chemistry or astrophysics asking the question with ID in the rather distant background. And I think you and I are in agreement on much.tribune7
January 26, 2010
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tribune7: We are in alignment about many things. If you are studying nature you are going to look for natural causes. The problem that has occurred is the claim that the study of nature can reveal all truths, or if it can’t be found in the study of nature the truth is not important. As it happens, I personally do not believe the science explains everything. I think that science excels at the aspects of the universe which are naturalistic and subject to systematic study using the scientific method. Within that sphere, I think it does a good job. But I doubt that science will ever answer questions like "is there a God?" per se, because it's outside science's realm. ID wants to be accepted within the domain of things that Science excels at, using the logic and tools of science. To take another theory of creation, some say that the universe was created a few thousand years ago, complete with fossils and radioactive decay residues and everything - completely and seamlessly simulating all evidence of a long pre-history. Because of the way this is exposited, science can not weigh in on it on way or the other - it's not a scientific hypothesis. Whereas I think most people here recognize that at least parts of ID are legitimate scientific hypotheses (whether or not they consider those hypotheses validated). When scientists assume God did it and ask “how?” they are more productive than if assume chance did it and ask “how?” Well, I don't know if we're ready to assume the designer fits the full description English speakers ascribe to "God" :-), but we are in alignment that asking "How?" the designer did their work would be very interesting! Let's look for signs of a mechanism or the structure of its abilities and limits or any other discernalbe "how". If that free inquiry yields many scientific results, I will agree with your contention that breaking the dogma of DE has opened the door to expanding human knowledge. Maybe you are right, and asking "how" within the context of assuming ID will prove more fruitful than asking "how" within the context of assuming DE. The proof will be in the pudding. Alas, I don't see much interest yet in ID addressing "How" questions now that it has the freedom to do so, but it sounds like you'd like to see that happen too.Zeph
January 26, 2010
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tribune7: There’s a subtlety your missing. Overturning a dogma that has become a dead-end would expand human knowledge more than any new science could. First off, I hope you have understood that I support challenging the DE orthodoxy on scientific grounds. I can see that evolutionists have circled the wagons and rigidified. (I actually think the ID debate would be far healthier if there were not battle scars from biblical creationism poisoning the trust and good will possibilities, but the world is as it is). So I say "go for it" - see if your viewpoint can win on scientific grounds. I'm intrigued as I say. BUT - I don't honestly see that biology is at any dead end because of some DE dogma. There is an assertion that they have not yet sufficiently explained macroevolution - but even many ID folks concede that microevolution has explanatory value. As I've said in another post, science is OK with marking something "not yet fully explained" for generations, so long as they meanwhile are producing useful results, incrementally chipping away. On the other hand - once the dogma if DE (I'm tired of writing out Darwinian Evolution) has been defeated and ID is free to demonstrate its scientific fruits - what will they be? If DE's explanation has lost traction by 2015, how will ID step in to continue to expand human knowledge from 2015 to 2025? I appear to be hearing that there's no interest, drive or perhaps ability for ID science to continue to expand human knowledge any further than "intelligent intervention of some kind happened". Now if you want a stagnant science to attack, try String Theory. The case for that being an intellectual dead end are far stronger than for DE and biology. The cosmologists need some radically new theories - but ones that can in turn be elaborated and tested. But that's another subject. For now, we're talking biology. And I'm genuinely curious what sorts of ongoing expansion of human knowledge you think will arise once the dragon of Darwin has been tamed and minds are free to expand on alternate hypotheses, including ID. What would be a possible example second finding from studying ID?Zeph
January 26, 2010
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Zeph --Continually expecting a material explanation – even if we don’t have it yet – has turned out to be a remarkably fertile intellectual approach. If you are studying nature you are going to look for natural causes. The problem that has occurred is the claim that the study of nature can reveal all truths, or if it can't be found in the study of nature the truth is not important. And some the greatest scientific discoveries have occurred almost in direct opposition to the expectation of a material cause. Think thermodynamics, biogenesis, The Big Bang. When scientists assume God did it and ask "how?" they are more productive than if assume chance did it and ask "how?"tribune7
January 26, 2010
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I talk mostly about scientific evidence, but I've been thinking about the "materialist" orientation of science. That particular obsession seems to particularly gall some ID proponents. I do not believe it arises from atheism or desire to deny spirit - indeed many of the leading proponents of science have been theists. I believe this material or natural orientation arises more as a heuristic of sorts, based on accumualated experience. Continually expecting a material explanation - even if we don't have it yet - has turned out to be a remarkably fertile intellectual approach. That is, people following that approach achieve more useful or valuable results, which leads to others adopting similar approaches. The alternative is in a broad sense, magic. Perhaps there is a better word, but this will do for now. As a plot device, the characteristic of magic is that it has no limits - except the limits the author wants for plot purposes. The magic in Harry Potter's universe follows no real structure, has little rhyme or reason. This is convenient for fiction - if you need a spell for changing a housecat into a dragon, such spells are possible. No explanation needed, "it just is". The real world isn't like that. There is an inherent structure of what can become what, restrictions like conservation of mass, or dynamics of loss vs gain of information. (These limitations are what ID advocates rely on when scientifically critiquing DE). We can invent similar magical explanations of the natural universe. We as humans have done so many times and in many ways. The brilliance of the scientific method is its dogged (even if at times time delayed) return to the test of the real world. I've heard reality defined as "that which stays around even if we stop believing in it". And that reality which doesn't bend to our norms and expectations and desires is the pole star to which science keeps returning, honing and burnishing (and breaking and rebuilding) its explanations. (If ID wins scientifically, it will be from using these tools). If the cause of leprosy is ascribed to supernatural means, then either we don't even bother trying to understand it better, or we come up with many conflicting and arbitrary treatments or propituations which basically don't work because they take their cues from theories and imaginings ungrounded in empiricism. If on the other hand we assume there are natural causes to be eventually discovered, through continuing to observe, hypothesize, and test against the real world - wow, time after time we wind up finding at least part of the answer. We might learn how to avoid spreading it, even before learning about microbes. Science does not have all the answers and probably never will; but it's approach in assuming there are materialistic or naturalistic answers has proven to be extremely fruitful compared to many other approaches. It has an ongoing and even accelerating success at explaining more and more, which is hard to argue with. The anti-DE part of ID is very much within that realm. So science is naturally biased against accepting something like "some non-natural intelligence intervened" because that becomes a show stopper, like a convenient magic spell to untangle plot crisis. The gap in knowledge is filled with an all purpose formless putty that admits no further exploration or illumination. It's like letting a geometry student just write on their paper "this lemma will lead to the desired theorum" in green ink whenever they come to a step for which they have no solution, and considering that sufficient explanation. Once you can do that, there's no point in working up as sweat looking for a more nuanced solution. But then, you don't develop the mathematics to build a bridge, because you didn't keep working to fill in the gaps of your earlier knowledge. So - even if ID is "true", it's understandable that science is going to have a hard time accepting it, so long as adopting its approach leads to intellectual dead ends. Suppose you are are a grad student looking into some adaptation of butterflies which is mysterious; why bother continuing to puzzle it out if you can just say "this was probably a manifestation of the designer because we have no naturalistic explanation", turn in your thesis, and get your degree? And teach your students to do the same. A nation whose "scientists" did that would be out-competed by a nation whose scientists doggedly assumed and sought a natural explanations even if it takes generations to find it. Maybe there are non-natural explanations for many daunting phenomena. But assuming otherwise and continuing to look has proven over time to be extemely adaptive. Even mysteries that have baffled scientists for generations sometimes unfold later, because they keep assuming there's a natural explanation. So scientists have developed a strong allergy to non-naturalistic answers as being "too pat" and "intellectually sterile, leading to no further insights". This is why I'd like to see ID actually take on learning more about the nature of the designer, the methods and nature of the interventions, etc. Become fruitful and the memes will multiply (even if such reproductive success doesn't explain the original memes :-)). Show that ID is not an immediate scientific dead end, with 90% of all it will ever in a thousand years deliver already known by 2010. A metascientific prediction would be: because it relies on non-natural interventions, ID is likely to be less fertile in the knowledge and insights it yields over time. That has historically been the experience of other conflicts between scientific naturalism and non-naturalistic hypotheses or approaches, so the natural prediction is that it will happen again with ID. This prediction is testable and falsifiable, but I don't claim it's directly scientific. I'd like to see that prediction proven wrong, by a robust ID science field which elaborates the details, debates the evidence, forms theories, challenges itself - and comes up with far more than one result.Zeph
January 26, 2010
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Zeph -- Your interest in ID is not in developing an fertile and intellectually vigorous new science which is ever expanding human knowledge like other sciences, but to provide more of a philosophical or sociological outcome. There's a subtlety your missing. Overturning a dogma that has become a dead-end would expand human knowledge more than any new science could. “One of the big problems with out culture, science and educational system is the insistence in attempting — pretending might be a better word — to provide empirical certainty where none exists. . . but isn’t that what ID is attempting as well? I can't speak for all ID proponents but the consensus to me seems to be that ID follows a scientific methodology which means it is and must remain potentially falsifiable. Its proponents in general appear to be just as firm in their belief that their hypothesis is certainly correct, as are their opponents Obviously, a sincere advocate will believe his position to be correct but I hope nobody here wants to hold ID as a dogma - i.e. we have the truth hence if you question us you must not be allowed tenure, be kept from publishing etc.tribune7
January 26, 2010
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tribune7: "The one useful thing I see ID as doing is refuting, conclusively, material accidentalism." OK, that's honest. Your interest in ID is not in developing an fertile and intellectually vigorous new science which is ever expanding human knowledge like other sciences, but to provide more of a philosophical or sociological outcome. To do that, the only result it needs is "some kind of non-natural intelligence was injected into the system at some point", and once that's conceded, there's no need to examine the issue any further. I have the impression that some people actually believe ID has the potential to become a science in itself. It is they who may be disappointed. Assume success. Once attacking Darwinism becomes beating a dead horse, there's no need for graduate students to study ID and hope to make a career in it - if the sum total of all it ever intends to reveal is that simple statement and stop there. The only useful conclusion of ID will have been "proven", so there's nothing left for ID to investigate or explicate. Meanwhile, the evolutionary biologists will continue to have a rich intellectual endeavor which continues to illuminate "micro-evolution" with all its fascinating twists and turns. There will be ongoing employment for practical or small scale evolutionists, even if they can explain only part of the picture (micro-evolution), because that part keeps expanding and deepening. It's a fertile science in its ability to explain more and more, even if it were never to explain everything. This reminds me of some people who dispute the validity of all macroeconomic models. If they succeeded in convincing everybody that there was no point to macroeconomics because the phenomena were too complex, the microeconomists would still be employed. (But there's no need to pay anybody to keep reproving that macroeconomics isn't correct, without elaborating on any alternative). I'm really interested in finding our best understanding of the scientific truth here, separated from religion, philosophy, and politics. "One of the big problems with out culture, science and educational system is the insistence in attempting — pretending might be a better word — to provide empirical certainty where none exists." Hmmm. I may be misunderstanding, but isn't that what ID is attempting as well? Its proponents in general appear to be just as firm in their belief that their hypothesis is certainly correct, as are their opponents. (The opponents have the advantage of numbers currently, but I'm talking about attitudes, and obviously many here wish to change that disparity - to have more ID believers than DE believers a decade hence). I'm not saying that ID is worse; just that it fits the same characterization - fulfilling a cultural need for alleged certainty rather than uncertainty. I appreciate your desire to avoid dogma, but I have doubts about the success with regard to ID, if it has only one simple conclusion and no internal debate or investigation of further details. (By the way, while I agree that science class isn't the place - I agree that "we want the citizenry to realize they have an individual responsibility for compassion and action independent of the state". I'd probably say independent of any particular religion or groups of religions as well. I'm not sure ID would actually lead to that, but I can sympathize with your goals).Zeph
January 26, 2010
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Zeph I’m not asking ID to come up with details on the cause of intelligence or who designed the designer, just more structure for how the process works or worked. I'd say that life came about via a "big design" is a fair analogy to claiming the universe came about via a big bang. :-) I’m asserting that the only people who need to “accept the observation” now are ID scientists. They are free already to produce fruitful results and begin elaborating signficant structure in the designer, And that they are. But it is certainly not inappropriate for them to defend the observation. Suppose a decade from now Darwinian evolution was totally discredited, and there was no longer any need to attack it. One of the big problems with out culture, science and educational system is the insistence in attempting -- pretending might be a better word -- to provide empirical certainty where none exists. This is evident in the way Darwinian evolution is treated as dogma even including attacks on heretics and such. I would not want ID to become a dogma. One of my big concerns regarding ID is that people will attempt to use it to prove God via science, which would be a very bad thing. Now, I think it would be very good for a nation to hold the existence of God -- the loving one of Judeo-Christianity -- as axiomatically true even if just for the hopefully obvious reasons that we want those who write and enforce society's laws to realize that there will be an ultimate accounting for injustice, and that we want the citizenry to realize they have an individual responsibility for compassion and action independent of the state, but science class isn't the place to teach this. The one useful thing I see ID as doing is refuting, conclusively, material accidentalism.tribune7
January 26, 2010
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Tribune7: Zeph: Imagine that the Darwinists had just said “the diversity of life comes from accumulated gradual changes” and stopped there... No further details or structure or analysis of how or when... Tribune7: What are the details on the cause of The Big Bang? Is The Big Bang science? I notice a shift of "details or structure or analysis" to "details on the cause", which is quite different. I'm not asking ID to come up with details on the cause of intelligence or who designed the designer, just more structure for how the process works or worked. Note that there has been a tremendous amount of detailed analysis of the likely events and mechanisms during the Big Bang, as well as attempts to validate and test alternative details based on such evidence as differences in cosmic background radiation. The proponents decidedly didn't stop at "there was a big bang out of which everything expanded somehow" or it would not have been a branch of science. You see no value in new observations? It’s when the observation is accepted that expansion occurs. No, I do see value in new analyses, which is why I'm here. I'm intrigued by the intelligent design hypothesis and the critiques of Darwinian evolution associated with it. However, I'm asserting that the only people who need to "accept the observation" now are ID scientists. They are free already to produce fruitful results and begin elaborating signficant structure in the designer, the mechanism, etc so that the sum total of "results" is more than "somehow intelligence was probably introduced at some point or points", and defend those results to the same standard that they hold Darwinists to. THEN the world will really take notice! (And I'll be truly excited). It doesn't work to say "ID scientists are unable to elaborate any details whatsoever until mainstream science totally accepts their hypothesis". That's putting the cart before the horse. They need to believe in their hypothesis sufficiently to produce some real theories and content. Suppose a decade from now Darwinian evolution was totally discredited, and there was no longer any need to attack it. An ID textbook is being taught in school. It has one introductory "historical context" chapter detailing how ID proponents discredited Darwinnian evolution; sort of like a microbiology book with a brief nod to pre-germ theory notions before getting down to the real content. The remainder of the book would describe the results of ID science. Currently that rest of that book on ID science seems to be "somehow some kind of intelligence of unknown nature of was injected at some time or times in the past". No further details. No theories. No structure. No mechanisms. No progress on reducing any of the vagueness in that statement. No experimental validation of its own detailed elaborations (versus attacking Darwinism, which was completed in the intro chapter). Please understand that even somebody open minded and interested in alternate hypotheses has a hard time characterizing that textbook as describing even a new science. I'm hoping for more. I'm rooting for it, not against it. I would enjoy having a true science of ID with fruitful and exciting results, internal debates and schools of scientific thought, everexpanding scientific knowledge. As a newbie, at this point I'm struck by how little scientific fertility the ID hypothesis appears to have, and hoping that will change.Zeph
January 26, 2010
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Mr Vjtorley, With regard to your quotation from Dr Dembski, that matter would be settled if we looked at the work of which he says Yet even with the most generous allowance of legitimate advantages, the probabilities computed for the Darwinian mechanism to evolve irreducibly complex biochemical systems like the bacterial flagellum always end up being exceedingly small. If Dr Dembski, or whoever had done the calculations that "always end up being exceedingly small" would publish those calculations, the critics would be quieted. Instead we get an analogy about house building, and not building a series of houses, either. So while Dr Dembski does say the calculations take selection into account, without seeing them there is still an opening for the critics. With respect to Signature in the Cell, Dr Meyer quotes a number of calculations, some of which you have highlighted. Bolding Dr Fred Hoyle's original tornado-in-a-junkyard calculation is not going to convince anyone that ID does not routinely use tornado-in-a-junkyard argumentation. All of these phrases that you have bolded: "random process producing amino-acid chains of this length would stumble onto" "probability that a 150 amino-acid compound assembled by a random interaction" "The odds of getting even one functional protein of modest length (150 amino acids) by chance" "Axe’s experiments calculated the odds of finding a relatively short protein by chance alone." "odds of producing the proteins necessary to service a simple one-celled organism by chance" "If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10^164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or in in 10^41,000." Now, all of the above appear in the section on the chance hypothesis, so you can say that Meyer is quoting them correctly. Subsequent occurences cannot be treated as kindly. "He famously compared the problem of getting life to arise spontaneously from its constituent parts to the problem of getting a 747 airplane to come together from a tornado swirling through a junk yard..." Ooops. "As noted in Chapter 10, the probabilistic resources of the entire universe equal 10^139 trials" "reasonably expected to occur by chance" To summarize, if you see the phrase "random process ... by chance" then you are not dealing with chance and selection. If you see "number of trials" you are not dealing with selection and contingency, you are dealing with independent trials. If you see "the probability of X is A, so the probability of N*X is A^N" you are dealing independent trials, not selection, variation, exaptation, history, or contingency on the laws of chemistry and physics. All of the above are versions of "if it happened at all, it happened all at once" aka tornado-in-a-junkyard. Bringing these quotations together does not dispel the notion that ID theorists frequently use the idea and mathematical equivalent of Dr Hoyle's memorable phrase. You could go to papers by Kalinsky, Abel and others and get more examples. If you want to find true counter-examples, look for reasoning and math that assumes f(t+1) = f(t) + variation + selection, in other words, an iterated function system. Look for the use of the Price equation or Holland's Schema Theorem. But I have to warn you, I have never seen an ID theorist reason using these tools to show the inadequacy of evolution.Nakashima
January 25, 2010
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vjtorley, I intend to respond to your citations of Dunston, Chiu, et al. as time permits. I have some notes from when I first read those papers. Real world work is interfering with my web time, though, so it may be a day or two. Regards.Mustela Nivalis
January 25, 2010
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vjtorley at 385, Thanks for the detailed quote from Dembski -- it really helps to have the reference material as part of the discussion. One of the reasons I'm interested in getting a better understanding of CSI is because, as you note, Dembski does explicitly state that known evolutionary mechanisms must be taken into account if the measurement is to be meaningful in the real world. There are, however, two problems with his further discussion of the topic. The first is that he never, to my knowledge, actually discusses particular mechanisms. That is, I haven't seen an attempt by Dembski to calculate CSI for a real biological artifact with reference to how particular physical, chemical, and evolutionary mechanisms affect the calculation. Everything I've read is at a very high level, whereas the CSI, if it's there, will be in the details. The second problem is illustrated by the section you quoted. The analogy with a housing contractor and the list of supposed requirements assume that evolutionary mechanisms are looking for a particular outcome. This is sometimes referred to as the "Lottery Winner fallacy" and is, unfortunately, almost as prevalent in ID calculations as the uniform probability distribution. While any specific outcome might be unlikely, an outcome of some sort (a lottery winner or a viable organism) is far more probable. I do hope that Dembski or another ID researcher takes the CSI concept to the next level and calculates it for some real biological artifacts, keeping in mind Dembski's quite appropriate insistence that known evolutionary mechanisms be incorporated.Mustela Nivalis
January 25, 2010
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Zeph -- Imagine that the Darwinists had just said “the diversity of life comes from accumulated gradual changes” and stopped there. It would actually be correct. Diversity of life does come from accumulated gradual changes. The problem comes when it claims "all diversity of life" and "only through accumulated gradual changes" No further details or structure or analysis of how or when, What are the details on the cause of The Big Bang? Is The Big Bang science? and no desire or interest in going beyond championing & defending that one hypotheses You see no value in new observations? It's when the observation is accepted that expansion occurs.tribune7
January 25, 2010
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Jerry & tribune7, ID as part of the field of Design Detection? Hmmm. What I'm perceiving here is that what is called "ID" feels like a marriage of convenience between (1) tearing down Darwin scientifically, and (2) describing a competitive hypothesis, not very scientifically. I find the former (critique of Darwinism on scientific grounds) worthwhile in its own right, whether it winds up in the end discrediting Darwinism or revolutionizing it (or even being discredited itself). It's a good line of argument to pursue, and it fits within the framework of evolutionary biology (leaving aside whether the human proponents therein react well or not to it). But critiquing the Darwinian explanation is not really elaborating or developing any science of "intelligent design"; it's just creating enough space for an alternative approach like ID to compete for explanatory value. I'm finding more difficulty discerning much content to the alternative that ID is proposing. What I'm hearing is extremely vague and amorphic: support for a hypothesis that intelligent design was injected into the mixture. Nothing about the shape or scope of that intervention, nothing about the structure or frequency or style of the intervention, or the nature of the presumed designer. Imagine that the Darwinists had just said "the diversity of life comes from accumulated gradual changes" and stopped there. No further details or structure or analysis of how or when, and no desire or interest in going beyond championing & defending that one hypotheses as the sole "product" of Darwinian evolution as science. I wouldn't call that "a science", it's just a simple hypothesis (however well supported) in search of elaboration and development. Jerry, you do a very lucid job of describing the critique of established science alongside what is still accepted (at least by you) from that science. Thank you. But then when you start describing the alternative, for me the lucidity of your prose seems to recede, and you do things like blatently conflating intelligence and free will as if it were obvious that these are the same thing or completely linked. (If seeding oyster beds is intelligence, I can show you some very intelligent programs that do not appear to be exhibiting free will). That kind of thinking jumps the rails of science. I'm a very receptive audience for anything that ID can produce in the way of telling us something about the designer or the mechanism or the structure of the interventions. Like, suppose that using evidence and scientific analysis, ID could identify two strains of intelligent design with different styles, goals, or mechanisms. Or estimate the IQ of the designer, based on analysis of mistakes. THOSE would be fascinating, and would be an original contribution of merit to science. Certainly literary forensics can discover such things, so it's not setting the bar impossibly high. Is the ID hypothesis fruitful, or sterile, as an area of human research? Do you care to predict whether, in say the next ten years, ID will develop any structure beyond "some kind of intelligence intervened in some way once or many times"? One thing I'm wondering is whether this lack of even rudimentary elaboration of ID's hypothesis is due to "there's nothing to be discerned" (true intellectual sterility) or "it might offend some supporters who believe the designer is the Christian God" (adherence to a limiting but unspoken agenda). Suppose some ID researcher, analyzing signs of intelligence, asserted that there were two distinguishable styles of intervention. Scientifically, this might be a breakthrough of enormous impact. But for anybody who supports ID (rhetorically, finanically or emotionally) with the hope that it will validate their religious faith, this might be unsettling. Is this sign of Jesus vs Yahweh having different styles (where's the holy ghost?). Or is it the pagan God and Goddess? Yahweh and Satan? Theologically it would be a mess, and might result in that branch of ID being condemned from the pulpit as furiously as Darwin is. What's your sense? Is the ID movement intellectually free to pursue the evidence where ever it might lead, or are there orthodoxies which might constrain which ID research gets support from the ID community, depending on its conclusions?Zeph
January 25, 2010
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This post is on the same theme as my previous one: do the writings of ID proponents suffer from the tornado in a junkyard fallacy? Mustela Nivalis (326)
As it turns out, I actually have read all of your references in my search for a definition of CSI that ID proponents agree uniquely identifies design and that takes into account known physics, chemistry, and evolutionary mechanisms. Unfortunately, none of your referenced materials do that. Most suffer from the assumption of a uniform probability distribution (the tornado in a junkyard fallacy described by Aleta).
R0b (336)
You can scour ID works until doomsday and not find any CSI (or FSCI, or FCSI) analysis that allows for a possibility of Darwinian factors. Assuming tractability of such probability calculations, taking into account physical laws in addition to random mutations could significantly shrink CSI totals. As it is, uniform distributions form a singular basis for CSI claims, and applicability of such quantifications to biological organisms is doubtful.
In my previous post, I demonstrated that Dembski's writings on intelligent design do not suffer from the tornado in a junkyard fallacy. In this post, I argue that Dr. Meyer's latest book, Signature in the Cell does not suffer from this fallacy either. Meyer does take the time to evaluate and reject the "pure chance" hypothesis for the origin of life, but he then goes on to carefully examine a number of hypotheses that invoke a combination of chance and necessity - including the much-vaunted RNA-world hypothesis. The following extracts convey the flavor of his work, and give the lie to claims made by some Darwinists that Meyer is attacking a straw man in his book.
Evaluating the "pure chance" hypothesis for the origin of life Pages 210-213 [B]y taking what he knew about protein folding into acocunt, Axe estimated the ratio of (a) the number of 150-amino-acid sequences that produce any functional protein whatsoever to (b) the whole set of possible amino-acide sequences of that length. Axe's estimated ratio of 1 in 10^74 implied that the probability of producing any properly sequenced 150-amino-acid protein at random is also about 1 in 10^74. In other words, a random process producing amino-acid chains of this length would stumble onto a functional protein only about once in every 10^74 attempts... In June 2007, Axe had a chance to present his findings at a symposium commemorating the publication of the proceedings from the original Wistar symposium forty years earlier. In attendance at this symposium was MIT engineering professor Murray Eden... Axe's improved estimate of how rare functional proteins are within "sequence space" has now made it possible to calculate the probability that a 150 amino-acid compound assembled by a random interaction in a prebiotic soup would be a functional protein. This calculation can be made by multiplying the three independent probabilities by one another: the probability of incorporating only peptide bonds (1 in 10^45) , the probability of incorporating only left-handed amino acids (1 in 10^45), and the probability of achieving correct amino acid sequencing (using Axe's 1 in 10^74 estimate). Making that calculation (multiplying the separate probabilities by adding their exponents: 10^45+45+74) gives a dramatic answer. The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebiotic soup is no better than 1 chance in 10^164.....[T]he probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a singel specified particle among all the particles in the [observable- VJT] universe. And the probability is even worse than this for at least two reasons. First, Axe's experiments calculated the odds of finding a relatively short protein by chance alone. More typical proteins have hundreds of amino acids, and in many cases their function requires close association with other protein chains.... Second, as discussed, a minimally complex cell would require many more proteins than just one. Taking this into account only causes the improbability of generating the necessary proteins by chance - or the genetic information needed to produce them - to balloon beyond comprehension. In 1983 distinguished British cosmologist Sir Fred Hoyle calculated the odds of producing the proteins necessary to service a simple one-celled organism by chance at 1 in 10^40,000. At that time scientists could have questioned his figure... Axe's experimental findings suggest that Hoyle's guesses were pretty good. If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10^164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or in in 10^41,000. This kind of number allows a great deal of quibbling about the accuracy of various estimates without altering the conclusion. [The last sentence should suffice to refute claims made on the Internet that the 1 in 10^164 estimate for the likelihood of a single functional protein arising by chance is far too pessimistic. Even if we revise the estimate by dozens of orders of magnitude, we are still left with an astronomically improbable event, for a cell which requires 250 functional proteins - VJT.] Pages 256-257 Energy flowing through an open system will readily produce order. But it does not produce much specified complexity or information. The astrophysicist Fred Hoyle had a similar way of making the same point. He famously compared the problem of getting life to arise spontaneously from its constituent parts to the problem of getting a 747 airplane to come together from a tornado swirling through a junk yard... Energy might scatter parts around randomly. Energy might sweep parts into an orderly structure such as a vortex or funnel cloud. But energy alone will not assemble a group of parts into a highly differentiated or functionally specified system such as an airplane or cell (or into the informational sequences necessary to build one). [NOTE: Here the point Meyer makes is a purely qualitative one - that energy alone cannot generate sequence specificity - VJT.] Evaluating the self-organization hypothesis for the origin of life Pages 267-268 As I examined Kauffman's model, it occurred to me that I was beginning to see a pattern. Self-organizational models for the origin of biological organization were becoming increasingly abstract and disconnected from biological reality. [T]hese models claimed to describe processes that produced phenomena with some limited similarity to the organization found in living systems. Yet upon closer inspection these allegedly analogous phenomena actually lacked important similarities to life, in particular, the presence of specified complexity, or information. But beyond that, I realized that self-organizational models either failed to solve the problem of the origin of specified information, or they "solved" the problem at the expense of introducing other, unexplained sources of information. ...In my view, these models either begged the question or invoked a logical contradiction. Proposals that merely transfer the information elsewhere necessarily fail because they assume the existence of the very entity - specified information - they are trying to explain. And new laws will never explain the origin of informatiom, because the processes that laws describe necessarily lack the complexity that informative sequences require. Page 294 As noted in Chapter 10, the probabilistic resources of the entire universe equal 10^139 trials, which, in turn, correponds to an information measure of less than 500 bits. This represents the maximum information increase that could be reasonably expected to occur by chance from the big-bang singularity to the present... Taking these caveats into account allows a more general statement of the law [of conservation of information - VJT] as follows: "In a nonbiological context and absent intelligent input, the amount of specified information of a final system, S_f, will not exceed the specified information content of the initial system, S_i, by more than the number of bits of information the system's probabilistic resources can generate, with 500 bits representing an upper bound for the entire observable universe. The RNA World Page 305 Problem 3: An RNA-based Translation and Coding SystemIs Implausible RNA-world advocates offer no plausible explanation for how primitive self-replicating RNA molecules might have evolved into modern cells that rely on a variety of proteins to process genetic information and regulate metabolism... Page 312 Problem 4: The RNA World Doesn't Explain the Origin of Genetic Information [A]s I studied the [RNA world] hypothesis more carefully, I realized that it presupposed or ignored, rather than explained, the origin of sequence specificity - information - in various RNAmolecules. Page 315 To make matters worse, as Gerald Joyce and Leslie Orgel note, for a single-stranded RNA catalyst to produce an RNA identical to itself, (i.e. to self-replicate), it must find an appropriate RNA molecule nearby to function as a template, since a single-stranded RNA cannot function as both replicase and template. Moreover, as they observe, this RNA template would have to be the precise complement of the replicase. Pages 318-319 Problem 5: Ribozyme Engineering Does Not Simulate Undirected Chemical Evolution Ribozyme engineers tend to overlook the role that their own intelligence has played in enhancing the functional capacities of their RNA catalysts. The way the engineers use their intelligence to assist the process of directed evolution would have had no parallel in a prebiotic setting, at least one in which only undirected processes drove chemical evolution forward. Yet this is the very setting that ribozyme experiments are supposed to simulate. Page 322-323 Theorists relying on necessity awaited the discovery of an oxymoron, namely "a law capable of producing information" - a regularity that could generate specified irregularity. Meanwhile, theories combining law and chance begged the question as to the origin of the information they ought to explain.... But as I examined these new approaches [to the origin of life], I found them no more convincing than those they were seeking to supplement. Even apart from their limited success, the very fact that these experiments required so much intervention seemed significant. By involving "programming" and "engineering" in simulations of the origin of life, these new approaches had introduced an elephant into the room that no-one wanted to talk about...This led me back to where I had started - to the idea of intelligent design...
Well, I hope that settles the matter, regarding the writings of Dr. Meyer.vjtorley
January 25, 2010
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It is science but it there is no domain of design detection. OK, I can see that point.tribune7
January 25, 2010
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"ID is part of that field. I’d call it every bit as much of a science as physics etc." It is science but it there is no domain of design detection. It is more like mathematics and in fact is heavily dependent on statistics/probability. Science is generally defined by the domain of phenomena it investigates. ID spans several of these domains just as mathematics and statistics does. It is definitely science but the particular inferences take place within forensics, cosmology, evolutionary biology, anthropology, etc. That is my take on it.jerry
January 25, 2010
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Zeph and Jerry --ID is not a science such as physics, thermodynamics, evolutionary biology, plate tectonics Design detection is something that can be, and has been done, using a methodology that limits itself to measurable and testable observations of nature. ID is part of that field. I'd call it every bit as much of a science as physics etc.tribune7
January 25, 2010
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The last sentence of my previous post should be "If there are no or few alternatives, then what Darwinian selection?"jerry
January 25, 2010
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"You can scour ID works until doomsday and not find any CSI (or FSCI, or FCSI) analysis that allows for a possibility of Darwinian factors. " Why should it? We are told Darwinian processes started after the first cell appeared. The components of the cell supposedly appeared before life began unless someone wants to make the case that a different form of life existed before our life arose. What was the pre ATP synthase, pre Ribosome? What were the steps along the way? Darwinian factors assume zillions of possibilities and selection led to the ones we see. In life it is easy to see the zillions of possibilities but for the basic organization of life to begin with, what are the alternatives. None have been found so how are Darwinian processes relevant? Did one of the few miracle solutions somehow get discovered by chance? That is a not a 747 in the junkyard solution but maybe a 757. We are not talking about a slightly different microbe here. We are talking about the building blocks and how essential they are. What alternatives are there to all these essential parts? If there are no or few alternatives, then was Darwinian selection.jerry
January 25, 2010
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