Denis Alexander’s Strawman Just as Silly

Petrushka: Yes. When necessary. What's odd with that? gpuccio

I think I must say that I really appreciate your comments: they are very pertinent, simple and clear.

Thanks, that's very kind. I too have enjoyed a civil and informed debate here.

As I have argue recently with Petrushka, I don’t believe that many basic new isolated biochemical functions that are naturally selectable are available in any definite biological context.

Forgive me, I haven't read your particular comments on the topic in the past. If you could link to anything pertinent I'd happily do so. In any case, I agree with you. It's interesting how we can both observe the same thing and interpret it so differently! I guess that's the heart of our paradigm differences, right there. What we see in biology is the repeated re-use of the same genomic components. Although this isn't an argument against design, per se, it is what we'd expect from natural processes when reaching entirely new function by searching sequence space is difficult. When new genes arise, they mostly arise through duplication, with neofunctionalisation coming through subsequent modification. What this seems to indicate is that neofunctionalisation doesn't require the wholesale, bottom up construction of amino acid chains but alteration of a few bases within. This does not mean that moving between different functions is 'easy' but it does make it less of a problem than is sometimes perceived. One thing that we can't do is reconstruct an ancestral sequence and then count the number of steps in between, assume each was necessary, and then calculate the probability of the protein having arisen via evolution. Gauger and Axe did something similar - although even less realistic - in their recent paper. This is post-specifying that a particular protein-coding sequence *had to* make a particular transition to a particular function via a particular series of steps. Exactly, as Petrushka has said, this is painting a target where an arrow has struck and is - of course - not how evolution is predicted to proceed. When parentless genes arise - and you gave a nice example from the Li et al. paper - the exons appear to largely be the result of insertions from other ORFs like transposable elements. Again, the interpretation that appears most simple to me is a naturalistic one. I don't see this pointing to a designer. Of course a theoretical designer could do whatever he/she/it wants, but the lack of creativity from such extensive re-use does not match up with what we'd expect based on our own designs, where innovation, new materials, new ways of doing things are always sought. This has at least some bearing on a design inference, because it is human design that is used as a standard to detect the design of an unknown designer.

And please, consider that the whole known proteome (at present), the result of 4 billion years of evolution, consists of about 2000 protein superfamilies.

Potentially pointing to the limits of evolution rather than the number of potential proteins left 'undiscovered'.

I would like to say that exons often correspond to functional units, and therefore exon shuffling, or domain shuffling, or alternative splicing, often correspon “simply” to a different assemblage of functional units, that is a very basic modality of modular design.

Yes, fair enough. But this also points to the fashion in which evolution is postulated to work. The endless recycling of past chunks of things - ancient things often. Such things are expected to be rare to the point of only occasionally arising, which is what we see. As an opinion, I'd have thought a designer with good knowledge of function in sequence would perhaps generate lots of novel things without this long history to them, but we don't really see that happening. I hope these brief comments can help give an indication of where my thoughts lie on the matter - briefly jotted down in between other work :) paulmc

And please, consider that the whole known proteome (at present), the result of 4 billion years of evolution, consists of about 2000 protein superfamilies.

I find that argument rather odd. You are basically saying the Designer drops by every two million years or so and deposits a new protein domain. Sometimes more often, sometimes less, but interspersed throughout the history of life. Petrushka

paulmc: I think I must say that I really appreciate your comments: they are very pertinent, simple and clear. That said, a couple of comments on your last post: Do you really think we can calculate this? Within an undirected evolutionary paradigm any novel, unexpected, function could be beneficial. Obviously, it’s a small ratio whatever the number may be, but I doubt we could ever accurately characterise it. Yes, I think so. I believe that the Durston method is a simple and effective way to approximate the target space for a protein family. If you have read other posts of mine, you may know that my main argument is about the emergence of basic protein domains. Let's say the 2000 protein superfamilies in SCOP. The argument that "any novel, unexpected, function could be beneficial" is IMO weak and not convincing. As I have argue recently with Petrushka, I don't believe that many basic new isolated biochemical functions that are naturally selectable are available in any definite biological context. The main limiting factor is the existing complexity of the system, that would allow only complex and integrated subsystems to work and be useful to the point that they give a reproductive advantage. The second limiting factor is that most useful subsystem would be irreducible complex. The third point is that, even if some finite and not too big number of single new protein families were potentially selectable in a specific situation, thir probabilities should be only added one to the other. So, if there were 1000 potential new protein superfamilies naturally selectable in a prokaryote, that would increase the target space only of three orders of magnitude (about 10 bits). In a scenario where the value of complexity are of the order of hundreds of bits, that would scrcely make any difference. And please, consider that the whole known proteome (at present), the result of 4 billion years of evolution, consists of about 2000 protein superfamilies. For all these reasons, I think it is extremely reasonable to accept the point of view of ID about protein domain probabilities. Yet, if the numbers were as dire as IDists suggest, what would the odds be that such a crude mechanism as exon skipping or another method of alternative splicing could produce a novel, functional protein? First of all, we should also consider the probabilistic resources and functional space and search space of those other nechanisms of variation. I have never tried, and I believe that at the present state of knowledge it is better to stick to the emergence of basic protein domains, which is the simplest ID scenario. But only a detailed analysis of those mechanisms could tell if they are really random and crude, or guided by design. You must remember that the only real method to distinguish between true random events and designed events a posteriori is the ID theory. Darwinists have renounced to try to do that, but that is not an acceptable scientific position, and is indeed very convenient for a theory that is based on imagined results of randomness, never verified or quantitavely assessed in a correct statistical context. Even so, I would like to say that exons often correspond to functional units, and therefore exon shuffling, or domain shuffling, or alternative splicing, often correspon "simply" to a different assemblage of functional units, that is a very basic modality of modular design. Also, the degree of interspecies variation in homologous proteins suggests a lower degree of specificity than is sometimes acknowledged. When the function is preserved, and so is the structure, sequence variation can be reasonably explained as the result of neutral or quasi neutral mutations. See the theory of the big bang of protein space. The Durston method takes that into account. gpuccio

Also, the degree of interspecies variation in homologous proteins suggests a lower degree of specificity than is sometimes acknowledged.

The simple fact is that ID advocates have no theory at all that would shed light on the probability of sequences evolving. No way of evaluation sequences that would tell you how close they are to being functional, or even what function they might have. Even if you could determine whether a sequence codes for a protein, there is no theory that would help determine whether the sequence has utility for an organism (or whether it might induce disease). And of course, the existence of regulatory networks just compounds the problem. Petrushka

a) The ratio of the target space to the search space

Do you really think we can calculate this? Within an undirected evolutionary paradigm any novel, unexpected, function could be beneficial. Obviously, it's a small ratio whatever the number may be, but I doubt we could ever accurately characterise it. Yet, if the numbers were as dire as IDists suggest, what would the odds be that such a crude mechanism as exon skipping or another method of alternative splicing could produce a novel, functional protein? Also, the degree of interspecies variation in homologous proteins suggests a lower degree of specificity than is sometimes acknowledged.

b) The probabilistic resources (number of attempts available, usually depending on population number and reproductive rate and time available).

Yes, this is important. But we need to be careful that we are not pre-specifying something that need not have happened. paulmc

Drift leading to adaptation was observed in the Lenski experiment. A functional, near neutral intermediate sequence was confirmed by Thornton. Since it took Lenski about 20 years of painstaking research to confirm a three step adaptation, it is not realistic to expect something as complex as a flagellum to evolve in a laboratory experiment. But it is more likely than a designer sighting. Petrushka

paulmc: Just to be clear, I am not denying that drift is a form of variation. But it is a form of random variation. It adds nothing to the more general concept of RV, which obviously is not limited to single point mutations. RV includes a vast range of variation mechanisms, including drift. But all of them are random. When we are evaluating the probabilty of finding a functional target in the search space by a random walk from an unrelated state, only two things count: a) The ratio of the target space to the search space b) The probabilistic resources (number of attempts available, usually depending on population number and reproductive rate and time available). Given those variables, what kind of RV we are considering does not change anything. Each new state attempted by variation is anyway a random state in a random walk. On the contrary, positive natural selection, if and when it occurs, determines an expansion of a specific form of variation, and a multiplication of the probabilistic resources for that trait. If the selectable trait is also an intermediate step to some more complex function, then the search for that function is no more a purely random walk, and must be reevaluated. That's why RV + NS, if and when applicable, is a powerful algorithm, while RV alone, whatever its form, is just a random walk. gpuccio

paulmc (4.1.1.3.8): I think we are getting confused by terminology. You are using “modern synthesis” to mean “the assemblage of different evolutionary mechanisms that most modern evolutionary theorists employ”, whereas when most ID people speak of “modern synthesis”, they mean “The Modern Synthesis”, i.e., the “neo-Darwinism” of Mayr, Dobzhansky, and Gaylord Simpson, which was the ruling view in evolutionary theory for decades. Its formula was random mutation plus natural selection. You are right, however, to say that ID people also criticize some other proposed evolutionary mechanisms which postdate The Modern Synthesis. The reason for that is that none of those mechanisms, e.g., “drift”, seem capable of actually building any new biological form. For that matter, not even all critics of neo-Darwinism have anything much better to offer. Lynn Margulis’s mechanism of combining genomes has some application at the level of microorganisms, but beyond that level it seems a chancy and erratic mechanism to generate macroevolutionary change. What is needed is something that transcends freak mutations, freak genome combinations, and the endless shufflings of population genetics. What is needed is something that can explain apparent evolutionary tendencies toward useful form. In various ways, Conway Morris, Denton, Shapiro, Sternberg and others are all working towards an explanation of novel form that does not depend, ultimately, on blind searches. But of course the old guard, whom you apparently represent — whether neo-Darwinian or not — are going to defend the fortress on which their careers were built, until they leave the scene. Thus, no new ideas are going to come from Dawkins, Coyne, Lewontin, Eugenie Scott, Ken Miller, Francis Collins, etc. The future of evolutionary theory will not be dominated by population genetics, as it was in most of the 20th century. It will be increasingly shaped by input from fields traditionally distinct from biology: physics, engineering, computer science, information theory, pure mathematics. It is understandable that the population geneticists are a bit irritated that “evolution” will no longer be their private playground, where they don’t have to answer to anyone. They probably think that all these new “immigrants” to biology will lower the property values. But for ID people the future of biology is looking brighter than it has looked at any time since 1859, provided that the younger voices are not strangled in the crib by their jealous elders. T. Timaeus

gpuccio, just to be clear I am not denying a place for positive selection. But removing genetic drift from the equation only leads us to the unfortunate strawman of classical darwinism, rather than the more complex, but also more realistic, contemporary version of evolutionary theory. If I understand you, you are arguing that drift is essentially unhelpful because it is difficult to see how it would assist in producing complex, specified information. In fact, drift is rather effective at maintaining the variation that may later play important evolutionary roles. paulmc

paulmc: I would just like to mention that genetic drift and neutral evolution, as I have argued many times, are of no help in overcoming the probability barriers outlined by ID theory. That's why ID concentrates most on the mechanism of RV + NS: at least, that is a mechanism that could potentially work, if its false assumptions were true. gpuccio

ID proponents don’t refer to all evolutionary biologists as Darwinists, at least, the more careful ID proponents don’t.

From the glossary here at UD: Darwinism: When ID proponents on this site use the term “Darwinism,” they are referring to Neo-Darwinism, also called the modern evolutionary synthesis or Neo-Darwinian evolution (“NDE”). So, the policy of this website is to refer to the bulk of mainstream evolutionary biologists as "Darwinists" regardless of how poor a description that actually is. The modern synthesis of course encompasses neutral evolution - to subscribe to the modern synthesis is not by any means to claim that every step in an evolutionary process is the result of +ve selection. paulmc

So, they didn't mention it at all, did they? Paul, do you think representation-protocol-effect is an irreducibly complex system to transfer mutable genetic information? Upright BiPed

paulmc: ID proponents don't refer to all evolutionary biologists as Darwinists, at least, the more careful ID proponents don't. Indeed, this site, long before other sites (atheist or TE), tried to get the world interested in non-Darwinian formulations of evolution. I first heard about the work of Shapiro and the Altenberg group here. And many on this site have promoted the work of Michael Denton, another non-Darwinian evolutionist, and Sternberg, who is still another. ID is not opposed to "evolution" or "evolutionary biology" as such. It is opposed only to such forms of evolutionary theory (Darwinian or otherwise) which rely entirely upon unguided mechanisms to produce novel biological form. By the way, there are still plenty of ultra-Darwinists around, including Dawkins, Ken Miller, and Eugenie Scott. You appear to agree with me that the classical Darwinian account must be abandoned. You would perhaps also agree with me (against Petrushka) that Denton has abandoned it. Where we disagree is that you merely supplement the Darwinian mechanisms by other chancey mechanisms, whereas I, with other ID people, deny that the sum total of all the mechanisms propounded by Mayr, Kimura, etc. can produce radical biological novelty. T. Timaeus

paulmc and Petrushka- when has genetic drift ever been observed or hypothesized to construct new, useful multi-part systems? BTW Darwin used natural selection as a designer replacement/ designer mimic, not for all change. That is Darwin used it to explain the things that drift cannot. To explain complex proteiin machinery by referencing drift you may as well use sheer dumb luck. Joe

He was arguing for the implausibility of naturalistic evolutionary mechanisms to account for some complex features of biology. In this context, genetic drift is fairly important. paulmc

Timbo, If by sounding like a YEC you mean someone who goes by what the evidence says by applying our knowledge of cause and effect relationships, then yup, you got me. Joe

He wasn't arguing against evolution either. How many times did Jerry Coyne mention representations and protocols in Why Evolution is True? How many times did Ken Miller mention semiosis when he wrote Only a Theory? How many times did Richard Dawkins mention the observable dynamics of symbol systems in The Blind Watchmaker? How many time did any of them mention anything at all about the immaterial relationships required for recorded information to even exist and be transferred? Upright BiPed

In Darwin's Black Box Behe includes genetic drift once in a list of evolutionary mechanisms, without any discussion of its consequences. In The Edge of Evolution he mentions genetic drift not at all. paulmc

You'd think that somewhere in a four hundred page book Behe would have mentioned neutral drift. Oh well, at least we can be certain that he mentioned ERVs in the list of evidence supporting common descent. Petrushka

Oh, I agree, it's fun mostly. I was just struck by the hubris of post 4.1.1. Timbo

[Petrushka's] grasp of history of evolutionary theory, and of the crucial assumptions of the theory, appears to be poor. If the individual steps are not selectable, the classical Darwinian approach must be abandoned.

The classical Darwinian approach where all change must be the result of positive selection was in vogue in the 1930s based on Fisher's (1930) mathematical arguments, but even then was not universally accepted (Sewall Wright, for instance argued for the importance of drift concurrently). Since the 1960s, this type of classical ultradarwinism has been abandoned at the molecular level (e.g. Kimura 1968). This is one of the reasons why it frustrating that IDists insist on referring to evolutionary biologists as Darwinists, a ridiculous and misleading title. At the morphological level, there is certainly evidence of positive selection for traits in some instances, but there is little reason to exclude large amounts of nearly neutral change by genetic drift resulting from comparable change at the molecular level. There simply are no robust, modern predictions in evolutionary biology that every change must be the result of positive selection, nor theory to form the basis of such predictions. paulmc

Oh, that’s right, the whole mainstream scientific community are brainwashed/engaging in an intellectual conspiracy. Exactly. Well, at least you can “prevail” here… Well, at least I can say what I think here. And you too. And whoever prevails, prevails. It's not bad. gpuccio

You sound like a YEC Timbo

Carry out research as opposed to your position's propensity of throwing unresearchable eons of time around to solve all problems? Who needs research when you have the "Father Time" trump card? All that is left is "cleanup on aisle 7".... Joe

If the individual steps are not selectable, the classical Darwinian approach must be abandoned.

Interesting that you accuse me of not grasping the history of evolutionary history. Petrushka

Well, perhaps it is time to venture out of the confines of an ID friendly blog, carry out some research, and present your findings to the scientific community. Maybe write a paper or two for publication. Oh, that's right, the whole mainstream scientific community are brainwashed/engaging in an intellectual conspiracy. Well, at least you can "prevail" here... Timbo

Good work, Eric and gpuccio. Petrushka may or may not have some understanding of some of the technical aspects of biology or information theory, but his grasp of history of evolutionary theory, and of the crucial assumptions of the theory, appears to be poor. If the individual steps are not selectable, the classical Darwinian approach must be abandoned. This is what Behe and Denton have stressed. But Petrushka does not take the time to read Behe and Denton. He contents himself with rumor and hearsay about what they think. He also appears to have little knowledge of the actual writings of Darwin, Goldschmidt, Gaylord Simpson, Shapiro, etc. But of course we are all used to this here. Our Darwinian combatants, with the exception of Allen MacNeill, aren't very scholarly. They prefer to argue from blogs and Wikipedia and other snippets they've read about evolutionary theory on the internet. We, on the other hand, take time to read entire books on the history of evolutionary theory, and entire books on the most recent developments in evolutionary theory. This is why we know their position much better than they know ours, and why we will always prevail. One can't argue about what one hasn't studied. T. Timaeus

To say that a species 'needs an adaptation' implies a target. To describe their extinction as a "failure to achieve" it emphasizes it. Just to clarify - are we to understand that certain spiders were on their way to extinction but avoided it by adapting (in countless unspecified genetic, phenotypic, and behavioral changes) to weave, monitor, inhabit, and feed from orbital webs? That just doesn't seem like a reasonable explanation when other creatures supposedly "adapted" just be getting bigger, faster, and stronger. Isn't that a much simpler change, since it doesn't require evolution to plan as many complex, coordinated changes which require foresight and purpose it didn't possess? That's absurd. And, when you maintain that it must have happened without any idea how and despite good reason to think it couldn't have, it's clear that you're leading with the conclusion rather than following the evidence to it. If a ground-dwelling spider's best chance at avoiding extinction was to develop the numerous changes to become an orbital web-weaving spider (even with several transitional states invented as required to fit the evidence to the conclusion) then why wouldn't it just become extinct? If, on the other hand, they could accomplish something so spectacular and complex to avoid extinction, how does anything ever go extinct? The features of living things are real. Extinction is real. The story of needing and achieving or not achieving adaptations is a "narrative gloss" with no substance. ScottAndrews2

The most common result of a species needing an adaptation is failure to achieve the adaptation, and eventual extinction. The simpler the organism and the more prolific, the less likely to become extinct. the more specialized the organism, the more likely to go extinct. Bacteria and viruses are the dominant life forms because their population size and reproductive rate favors finding adaptations. Petrushka

Eric: Very well said. I think that perfectly corresponds to my argument, many times repeated here, that: "Complex functions cannot be deconstructed into simple, functional, naturally selectable steps". Well, it feels good to be narcissistic, sometimes! :) gpuccio

dmullenix: What if there are no goog tickets? What if the probability of printing a good ticket is simply too law if compared to the actual number of tickets printed? There will be only bad tickets in circulation, and you will win exactly nothing. That's exactly the situation for biological information. gpuccio

Any evidence for the accuracy of your claim? Joe

A more accurate statement would be that mutations constantly rain free lottery tickets down upon a species. Bad tickets are thrown away and good ones are kept. It's easy to win ten thousand hundred-dollar lotteries that way. dmullenix

Hi Barry, I told Larry Moran that I would correct your explanation of the evolvability of IC systems. As Behe says on p.39 of his book, IC systems cannot, by definition,evolve directly, i.e., cannot evolve from simpler systems that have the exact same function. However, as Behe points out on p. 40, IC systems might be able to evolve indirectly, i.e., from simpler systems that have other functions. Behe goes on to say that the more complex the IC system, the less likely that this would happen. However, for the sake of clarity we should make it clear exactly what the issue is: improbability, not impossibility. Bilbo I

Petrushka (6.1): Regarding your first objection above, I made a statement, implied by a quotation *you* had selected, that Denton did not believe that there were functional morphological intermediates for all evolutionary changes. Your response about fossils is not relevant to this claim. Even if the fossil record is as you say it is, my claim was about what Denton believed, not that Denton's belief was borne out by the fossil record. And the fact that Denton believes what I said he believes shows that your *interpretation of Denton* is wrong. And that is what we have been arguing about, *your interpretation of Denton*. We have not been arguing over whether Denton's view of evolution is correct or incorrect, but over what Denton's view of evolution is. It happens that I understand Denton's view of evolution and that you do not. That is why I jumped in, so that the readers here would not be misled by your lack of understanding into adopting a false understanding of Denton's position. As for your quotation from Darwin, it has nothing to do with the point I was making. No one has denied that the rate of evolution can vary. And nothing in that passage changes the fact that Darwin believed there were selectable morphological intermediates all the way up. Behe and Denton both deny that. I've already explained this. If you really think that this passage from Darwin refutes what I have said, then your reading comprehension is so poor that you have no business debating evolution and ID. And if you know that this passage doesn't refute my point, but are just pulling it up to try to throw smoke and dust in everyone's eyes, you are being intellectually dishonest. If you are really interested in learning what Denton thinks, you will invest 20 to 30 hours reading what he wrote. If you are not willing to do that, you are not entitled to an opinion. It's as simple as that. And now I will truly exit. T. Timaeus

Petrushka (5.1.1.1.2): Assuming that you were indeed referring to Denton's first book rather than Behe's first book, then you wasted somewhat less of my time, but still a considerable amount, as guessing what you meant and writing it up in my last post still took quite a chunk. More important is the point that if you were referring to Denton's first book, we are back to my original answer, i.e., you are flat-out wrong to say that Denton's second book reached a conclusion that was the "opposite" of his first book. I already explained why, and won't again. Your words: "As for “Nature’s Destiny” I have to *assume* that despite your protests, it is as I described ..." indicate clearly what I had inferred, i.e., that you have not read the book. It is intellectually and socially irresponsible to vigorously defend an opinion on a book you haven't read. Put less politely, what you are doing is called bullsh***ing. I repeat, not for you, since you have made up your mind and are not interested in the facts, but for the benefit of other readers here, that Denton does *not* regard mainstream evolutionary theory, i.e., Darwinian theory, as correct. And his position on that -- that Darwinian theory has been largely wrong -- did *not* change between his two books. The difference between his two books lies elsewhere. Of course, to know that, one would have to have read and carefully compared the two books, and you have done neither of those things. T. Timaeus

Denton clearly implies that sometimes there are no functional morphological intermediate stages, which is dead against Darwin’s account

I hope you are aware that as the fossil record stands today, there are many sequences where the "gaps" are smaller than the differences between dog breeds. Anyway, Darwin was well aware of different rates of change. From Origin of Species, fourth edition:

Species of different genera and classes have not changed at the same rate, or in the same degree. ... [p377] I believe in no fixed law of development, causing all the inhabitants of a country to change abruptly, or simultaneously, or to an equal degree. The process of modification must be extremely slow. The variability of each species is quite independent of that of all others. Whether such variability be taken advantage of by natural selection, and whether the variations be accumulated to a greater or lesser amount, thus causing a greater or lesser amount, thus causing a greater or lesser amount of modification in the varying species, depends on many complex contingencies,—on the variability being of a beneficial nature, on the power of intercrossing and on the rate of breeding, on the slowly changing physical conditions of the country, and more especially on the nature of the other inhabitants with which the varying species comes into competition. Hence it is by no means surprising that one species should retain the same identical form much longer than others; or, if changing, that it should change less. [p378] Groups of species, that is, genera and families, follow the same general rules in their appearance and disappearance as do single species, changing more or less quickly, and in a greater or lesser degree. [p380]

Petrushka

You’ve just wasted about two hours of my time, and chunks of several other people’s time, because you have been too careless to even determine who wrote the books you have been reading! Every thing I wrote was in reverence to Michael Denton and his two books. The quote I responded mentioned Denton by name, and I specifically said I was talking about Denton's two books.

Consider Denton. He re-examined the evidence used in his book and wrote a follow-up book that reached the opposite conclusion. I was saying that Denton re-examined the evidence used in Denton's first book. The unfortunate reference to "Black Box" comes several posts down, long after I established that I was talking about Denton. It was not intentional, and I apologize for the error. At no point was I comparing Behe and Denton. As for "Nature's Destiny" I have to assume that despite your protests, it is as I described, a theory of design that requires only one intervention -- at creation -- and which accepts mainstream science and mainstream biology as essentially correct. Whether Behe accepts this theory, I don't know.

Petrushka

Petrushka (5.1.1.1): You've just wasted about two hours of my time, and chunks of several other people's time, because you have been too careless to even determine who wrote the books you have been reading! *Darwin's Black Box* is by Michael *Behe*, not Michael *Denton*! Michael Denton's first book was *Evolution: A Theory in Crisis*! You think you have been contrasting two different books by the same author, when in fact you have been contrasting two books by two different authors! No wonder you couldn't follow my explanations, or anyone else's! If there is such a thing as the "Anti-ID Dork of the Year Award," you've just won it. But even if Michael Behe's *Darwin's Black Box* really *were* Denton's first book, you *still* would have things wrong, because the two books are not in contradiction. As I already explained, Denton agrees with Behe that some morphological boundaries cannot be crossed by small genetic changes which are reflected in small, stepwise, morphological changes. That is, Denton agrees with Behe about the inadequacy of the Darwinian mechanism. What Denton suggests in his second book is not a refutation of Behe, but an explanation for how evolution might work in a non-Darwinian way. (Which is fine with Behe, since he is himself an evolutionist, just not a Darwinian.) If morphological change could occur in leaps, one could go from one irreducibly complex system to another without passing through non-functional and generally lethal intermediate forms. So if there were some way of "storing" small genetic changes until they "added up" to a big morphological change, one could have evolution of radically new forms without having to pass through unselectable intermediaries. That is what Denton is talking about in *Nature's Destiny*, how there might be incrementalism in genomic change but large leaps in morphological change. Of course, if you had even elementary common sense, you would wonder why Behe would have written a strong endorsement for *Nature's Destiny* when (on your interpretation) it contradicted the basic premise of Behe's own *Darwin's Black Box*. But then, of course, since you thought *Darwin's Black Box* was written by Denton -- oh, forget it. I give up even trying to figure out the sources of your incredible confusion. Petrushka, give it up. You have nothing to contribute to these discussions, when you not only can't get straight the ideas in the books you are reading, but can't even figure out who wrote them. T. Timaeus

It's not a distortion. In Black Box he denied it was possible for life to be connected by small, incremental steps (common descent by small steps). In destiny he argues it was inevitable. The things most argued against on this forum are the small steps (the connectedness of functional sequence space) and the historical fact that macroevolution took place without additional interventions. In the past week I've seen two of the most respected and prolific posters here argue that evolution by incremental steps is impossible, and that the naturalistic origin of life is impossible. Denton argues "that carbon-based life is therefore inevitable on any planetary surface where conditions permit it."(p265) Denton's position on sequence space is compatible with my position. I suspect I first encountered the concept with "Destiny." Please show how I have contradicted myself. Simply asserting that I have misrepresented Denton or contradicted myself is not equivalent to demonstrating it. Petrushka

Petrushka: I did not undertake to discuss or defend the various forms of ID held by anyone else who posts here. If you have a problem with the views of anyone who posts here, you will have to argue with each such person individually. I undertook only to correct your erroneous and misleading statements about Denton. You continue to make them. And you continue to cherry-pick your quotations. You are avoiding the many places in the book where he explicitly challenges the Darwinian understanding of evolution. So I maintain my position: you have not read the book, or you have not read it in anything more than a cursory way, and what you are doing now is just flipping through the book looking for proof-texts for a preconception you have about Denton. That is neither science nor scholarship. Nevertheless, in one of your quotations, the second, you should be able to see the difference between Denton and Darwin. Denton clearly implies that sometimes there are no functional morphological intermediate stages, which is dead against Darwin's account (but in line with Behe's account of the problem of moving from one irreducibly complex system to another). That is why Denton's discussion of DNA sequence space is important -- it allows for large and sudden leaps in morphology. Of course, such large leaps are neither Darwinian nor neo-Darwinian. In fact, several decades earlier, when the idea of large morphological leaps (the "hopeful monster") was proposed by some biologists, the Darwinians overwhelmingly jumped all over it, denouncing it as a heresy against incrementalism. Again, I find your understanding of both Denton and Darwin inadequate. You are fixated on showing that Denton believes in natural causes and in common descent, which everybody here already knows. You are avoiding the fact that he believes that Darwin and the neo-Darwinians took a major wrong turn and that the future of evolutionary biology lies in a mainly non-Darwinian direction (with Darwinian mechanisms perhaps playing an ancillary role). You also seem unaware that, while Denton has long since left the Discovery Institute and separated himself off from all aspects of ID that have to do with Biblicism, he is still on good terms with many of the ID folk and speaks with respect for their project. There are videos of him on YouTube or some such site, speaking at a recent conference in Italy, where he makes this clear. On the other hand, he does not chum around with the Darwinians -- Coyne, Miller, Lewontin, or any of the Biologos folk (who are all diehard Darwinians). You clearly have misinterpreted what Denton is about. You see in him what you want to see, and you do not hear what he is trying to say. He is arguing for a new way, a way that is neither creationist (in the normal American sense of that term) nor Darwinian, and for a process that is both evolutionary and designed. I'm done with this thread. T. Timaeus

Petrushka, here is your initial statement: "Consider Denton. He re-examined the evidence used in his book and wrote a follow-up book that reached the opposite conclusion." Your own comments disprove this statement. You need to keep better track of your distortions; posting mutually inconsistent statements so close to one another only makes you look foolish. Barry Arrington

If you had a case you would no doubt be happy to present it, but you are bluffing. Denton is not far from Deism. He posits a universe designed to produce humans due to the initial conditions at creation. That is consistent with one branch of ID thought, but not with the thoughts of most of the people who post here. The majority of posters here do not accept naturalism, not even a version of naturalism in which the universe is designed to make evolution happen. Try Denton's interpretation on gpuccio or upright biped. Reading a serious book and understanding it would make it possible to pinpoint any major misinterpretation. You haven't actually said what I got wrong. And I doubt if you will try, because you know I have it right.

"One of the most surprising discoveries which has arisen from DNA sequencing has been the remarkable finding that the genomes of all organisms are clustered very close together in a tiny region of DNA sequence space forming a tree of related sequences that can all be interconverted via a series of tiny incremental natural steps" (p276): "Thus, new organs and structures that cannot be reached via a series of functional morphological intermediates can still be reached by change in DNA sequence space." (p279) "We can envisage such a contriving or tampering of the DNA space to be analogous to rearranging the structure of the English lexicon to permit the evolution of a particular word tree, ... However, by playing God and restructuring the lexicon we would be able to arrange a vast word tree within the letter space, so that all functional words were clustered together..." (p434).

So what you have in Denton is the assertion that sequence space is designed so that evolution is inevitable. If true, this makes all arguments against evolution (and Darwinism) superfluous. Darwin is right, and evolution proceeds exactly as mainstream biology proposes. Cake and eat. This is a kind of design, but it is quote different from anything I see being supported here. I find this kind of interesting, because I have a word evolving program that depends on words being connectable in sequence space. It works better in some languages than in others, which demonstrates that the structure of sequence space determines whether evolution is possible or not. And that's a question to be decided by research rather than by thinking about it. Petrushka

Petrushka (1.1.1.1.4): You "cherry-picked" by quoting one passage out of a 400-page book, a passage which did not deal with some very important aspects of the argument of the book, aspects relevant to the discussion we are having here. No, I am not going to quote at length from Denton to refute you. You are irresponsible to offer opinions about a book you have not read, and I will not do your work for you. Prove that you have read the book by showing me that you understand Denton's argument, and then I will give you a more detailed response. Right now, you haven't earned one. Your reply further shows that you have misunderstood Darwin as badly as you have misunderstood Denton. I would guess, again, that you have not read Darwin, but are relying upon hearsay and summaries from people who agree with your position. Darwin certainly did not claim to have invented the idea of common descent (though he presented it more clearly and forcefully than his predecessors). And while he was certainly trying to convince his readers of common descent, he saw his main new contribution to be precisely what you are trying to minimize in importance -- his mechanism, i.e., natural selection, working on variations which have no intentionality. Denton does not think that Darwin's mechanism (not even as revised and modified by the neo-Darwinians) is the primary driver of evolutionary change. Thus, Denton certainly did not accept "everything which Darwin considered most important." In fact, he explicitly opposes his understanding of evolution to the Darwinian -- something you would know, if you actually read Denton's book, instead of "winging it." The account of Denton that I am giving in no way departs from his opening statement. His opening statement was about naturalism versus direct creation, and he maintains that throughout the book. But that opening statement, because you have read only that, and not the rest of the book, completely misleads you as to Denton's thesis, which is an attack on neo-Darwinian evolution in the name of a front-loaded model which is radically different. Petrushka, reading a serious book, and understanding it, requires a great deal of time, and serious intellectual work. You may be of the internet generation that sees "study" as quickly looking up a quick summary on Wikipedia, and then rushing back into the argument. I'm of the generation that believed that unless you have done your homework, you shouldn't be allowed a place at the discussion table. We ID people have read, not skimmed, but read, slowly and carefully, literally thousands of pages of Darwin, Wallace, Huxley, Denton, Gould, Dawkins, Simpson, etc. If you pseudonymous critics aren't willing to put in that much time and effort, there is no reason why we should take any of your criticisms seriously. T. Timaeus

I didn't cherry pick. I quoted the entire abstract. At least two-thirds of Darwin's Origin is devoted to common descent, so Denton has accepted everything that Darwin considered most important. Darwin proposed natural selection as the main, but not the only steering factor in evolution. He also accepted Lamarkian evolution, and was possibly the first to recognize sexual selection and female choice. But he knew nothing about genetics, and the actual physical mechanism of heredity and variation remained a mystery to him. So it is not really important whether one updates and corrects his mechanism. He was more interested in the fact of common descent and the time span involved. Denton contradicts nothing about common descent as a fact, nor contradicts the small incremental nature of change parent to child. If you want to argue this, feel free to quote at length from Nature's Destiny, and show me where Denton departs from the opening statement. Petrushka

Petrushka: You clearly do not understand either of Denton's books. Instead of cherry-picking one quotation, out-of-context, from Denton's book, why don't you do what I did -- read the entire book carefully and make extensive notes on it? And then do the same for his first book? Denton never argued, even in the first book, that "intervention" was required. He argued that the results of fossil and protein studies seemed more compatible with creationism than with Darwinian evolution, but he did not from that draw the conclusion that creationism was a correct account of what had happened. He left the problem unanswered. Evolution (and what he meant by that was Darwinian evolution) was a "theory in crisis," but he did not claim that science had proved creationism to be true. (Nor is it likely that he would, since he had already ceased to be a practicing Christian by that time.) In his second book he strove to show how both evolution and naturalism could be preserved in light of the difficulties raised in his first book. He does this by jettisoning Darwinism for a design-oriented understanding of evolution. The language of design is strong all the through his book, especially in the conclusion, so if you didn't pick that up, you didn't read the book very carefully. More probably, you didn't read it at all, but just read summaries of it by people who disagree with it. Haven't I corrected you on Denton before? Why do you guys (you, Nakashima, etc.) keep coming back here with bluffs about books that you have not read, or that you have only skimmed hastily and sloppily and therefore do not understand? You are not dealing with amateurs here. You are dealing with people who have read the ID, TE and Darwinist literature inside out, and you can't put anything over on us. We know the relevant writings better than you guys do. And until that changes, you will continue to take an embarrassing drubbing every time you come here. Do your homework, or don't bother showing up -- unless it is your intention to make your own side look unprepared for debate in front of thousands of readers. (Which is fine with us.) T. Timaeus

So Denton opposes special creation, big deal. Are you suggesting that because he is opposed to special creation that he should be viewed as a true believer in evolution and that his criticisms of evolution -- which is what got Behe started thinking about the evidence -- should be ignored? Your point is? Eric Anderson

"it is important to emphasize at the outset that the argument presented here is entirely consistent with the basic naturalistic assumption of modern science - that the cosmos is a seamless unity which can be comprehended ultimately in its entirety by human reason and in which all phenomena, including life and evolution and the origin of man, are ultimately explicable in terms of natural processes. This is an assumption which is entirely opposed to that of the so-called "special creationist school". According to special creationism, living organisms are not natural forms, whose origin and design were built into the laws of nature from the beginning, but rather contingent forms analogous in essence to human artifacts, the result of a series of supernatural acts, involving the suspension of natural law. Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world - that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies." (page xvii-xviii).

I recognize that some in the ID movement are fine tuners, but I defy you to reconcile this with gpuccio's position, which requires numerous interventions by active designers. Petrushka

Eric: Indeed, I was thinking exactly of people like Miller and company. And, obviously, I was paraphrasing, in my way, Dawkins'famous statement about "us". gpuccio

Petrushka, I assume you mean Denton's Nature's Destiny. He did not come to an "opposite" conclusion in that book. Here's the irony. Did you know that and you're just lying. Or are you ignorant? Hmmmm. Barry Arrington

Consider Behe. He was going along minding his own business, believing the party line, and then one day read Denton’s book, which piqued an interest, which slowly grew into full-fledged doubt.

Consider Denton. He re-examined the evidence used in his book and wrote a follow-up book that reached the opposite conclusion. Petrushka

gpuccio:

So, another lie of the darwinists (and I use the term lie because I prefer to think that they are lying, rather than thinking that they are simply ignorant of the basics of science, and therefore stupid and arrogant).

I don't know. That is a tough call. I think there are lots of people, even those involved in the biological sciences who simply haven't thought through the numbers. Further, they've been told all through school that Darwinism "explains" everything, so, they reason, someone else must have the answer. Consider Behe. He was going along minding his own business, believing the party line, and then one day read Denton's book, which piqued an interest, which slowly grew into full-fledged doubt. There are no doubt a lot of folks like that. Now if we're talking about people like Ken Miller, Eugenie Scott, Richard Dawkins, PZ Myers, etc., it is hard to believe that they are not being purposely deceiptful. Yet is it possible that they simply don't understand -- or are incapable of understanding -- rather than intentionally lying. Closed minds coupled with confirmation bias is a powerful thing . . . Eric Anderson

It might be narcissistic to quote oneself, but this discussion reminds me of something I wrote a while back in discussing the logical tension between the concept of tiny changes and changes that are significant enough to actually confer a survivability advantage. Perhaps worth repeating:

The intellectually-consistent approach to natural selection’s logical limitations, put forth by Richard Goldschmidt, and later given a hesitant nod by Stephen Jay Gould, is to propose abrupt changes that are large enough to provide a real (as opposed to hypothetical) selective advantage – the so-called “hopeful monster.” Most modern-day evolutionists, however, shy away from the hopeful monster for one simple reason – it is not believable. It looks like reliance on fortuitous events. It looks too much like a miracle. So they posit tiny changes and long periods of time, and imagine that together these two elements will result in the significant changes that are needed for natural selection to do its magic. After all, small changes are more believable, and surely there must have been ample time, the thinking goes . . . Unfortunately, the miracle they seek to avoid in the hopeful monster’s sudden physiologically significant changes, is invoked on the other side of the equation with just enough tiny changes, in just the right sequence, at just the right time, and with just the right effect, to carry out the creative work.

Eric Anderson

Phil Johnson once quipped that instead of entailing that evolution means instantly winning a million-dollar lottery, Darwinists instead insist that it merely involves winning ten thousand successive hundred-dollar lotteries, thereby cleanly solving the problem. Matteo

Minor correction- Natural selection, not "evolution", requires step-wise selectable steps Joe

Barry: This is another good example of how darwinists do not understand probability theory, or just pretend not to understand it. The "all in one go" argument is irrelevant. Let's say that we start from a non coding gene and I am computing the probabilities that it becomes a specific protein coding gene (unrelated at sequence level) by random variation. If the final gene codes for 100 AAs, the search space is 20^100 (10^130, 432 bits). Let's say that we have an approximation of the target space by the Durston method, and that the functional complexity is about 350 bits (about 10^100). That means that the probability of finding by chance a functional state is 1:10^100. Now, there is no reason at all that we have to find that result "all in one go". That would mean that we have only one attempt. But Dembski has always explained that we have to take ninto account the "probabilistic resources" of the system. So, each event of RV (either it involves one aminoacid, like in single point mutations, or all of them, like in frameshift mutations) is just a random generation of a new state among the 10^130 of the search space. The probability of getting a functional result is 1:100. If the system can make, say, 10^30 attempts of RV, still the probability of getting a functional result remains extremely low. And 10^30 attemnpts certainly does not mean that the result must be obtained "all in one go". So, another lie of the darwinists (and I use the term lie because I prefer to think that they are lying, rather than thinking that they are simply ignorant of the basics of science, and therefore stupid and arrogant). gpuccio