Evolutionary psychology: The scam getting nailed at last?

Khan, To take the "barking dog" point 1,

1) Yes, Behe and Snoke were effectively rebutted, because their methods were not appropriate to their question and their assumptions were faulty. yes (as you and others point out), most interactions require more than two binding sites, but that is irrelevant to the content of the paper itself. to prove I’m even-handed, here’s a link to a non-ID paper that I think got nailed as well:

The supposed evenhandedness (which isn't really that evenhanded as the non-ID paper is not anti-ID) rings hollow unless the original "nailing" of the ID paper was justified. Let's briefly review how we got into this discussion. Notedscholar (#3) claimed that "ID has been repeatedly nailed by all kinds of similar publications" referring to the original post's noting of a debunking of evolutionary psychology in Scientific American. Then jerry (#21 and #22) challenged notedscholar to "summarize the articles that have nailed ID". Then you (#23) mentioned Lynch's attempted refutation of the paper by Behe and Snoke. I then (#26) critiqued Lynch's paper. Most of my critiques have not been answered by you, or anyone else here. Lynch did not give any experimental support to the assertion that "the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions." ID is not a mysterious "external force, unknown to today’s scientists", as you have acknowledged (#45). It is not "difficult to pinpoint the source of the difference between" Lynch's results and those of Behe and Snoke; the different models would naturally give different results. Lynch has grossly overestimated the average population of primates during their existence on earth. And the claim that "conventional population-genetic principles embedded within a Darwinian framework of descent with modification are fully adequate to explain the origin of complex protein functions" is clearly not demonstrated by Lynch's paper. If anybody got "nailed", Lynch did. Your major complaint seems to be that Behe and Snoke did not use "Darwinian processes, which you define (25) as "selection on slightly beneficial mutations accumulating over time", in their model. You repeat essentially the same point in #29, #31, #52, and #55. That is not the only definition of Darwinian processes. Darwinian processes can be defined as random mutations (or more broadly heritable variatios) and natural selection. These processes are both unguided almost by definition; certainly they are thought of in that way. What you call Darwinian processes would then be thought of as Darwinian pathways, where each small step has positive survival and/or reproductive value. And if you had read the original article by Behe and Snoke, http://www.proteinscience.org/cgi/reprint/ps.04802904v1 you would have found that Behe and Snoke in fact defined Darwinian processes in precisely this way. For the only occurences of the phrase "Darwinian processes" in the article (and in fact the only occurrences of the word "Darwinian") occur in one paragraph:

Although many scientists assume that Darwinian processes account for the evolution of complex biochemical systems, we are skeptical. Thus, rather than simply assuming the general efficacy of random mutation and selection, we want to examine, to the extent possible, which changes are reasonable to expect from a Darwinian process and which are not. We think the most tractable place to begin is with questions of protein structure. Our approach is to examine pathways that are currently considered to be likely routes of evolutionary development and see what types of changes Darwinian processes may be expected to promote along a particular pathway. [emphasis added]

Thus, your criticism that they did not use Darwinian processes in their model depends on a definition that they did not share, nor apparently did their reviewers. You may wish to criticize their semantics, but that is not the same as showing their concepts are wrong, and it certainly is not the same thing as "nailing" ID, which was what the discussion was about in the first place. Now, you claim that "Behe and Snoke were effectively rebutted, because their methods were not appropriate to their question and their assumptions were faulty." WHat was their question, what were the methods and why were they not appropriate to their question? And what assumptions were faulty and why? You might want to read the original article carefully before you respond. Lynch's paper may not be a completely reliable guide. Paul Giem

Khan (#45) I have limited time today, so I will limit my comments to your #2 for now.

2) Yes, humans can intelligently design things, even new genes. As you know, Darwin used this process as evidence of the power of variation and selection. Allen’s list is restricted to natural causation, though, and thus anthropogenic causation is excluded. However, if you want to add it to your list and if you argue that this has been a major force in the development of living organisms, the only logical conclusion is that we designed ourselves.

Thank you for the straightforward answer. You have convinced me that you are not one of those "no concessions" debaters that occasionally visit here, and it makes a worthwhile discussion, rather than just a set-piece debate, possible. You say that "Allen’s list is restricted to natural causation, though, and thus anthropogenic causation is excluded. " Consider what you just said: Anthropogenic causation is not natural. Why not? I can think of two reasons. First, people could not be part of nature. There has been a debate about this on UD. But in order to use the non-natural character of anthropogenic causation as a way to legitimately exclude it from a list of "natural" causation, it seems that one must exclude people from nature. Again, the question is why. People definitely live in nature. So it cannot be that nature doesn't interact with people. The only reason is that people are somehow not subject to nature. This would imply that some aspect of people (perhaps intelligence? perhaps the "soul"?) is not really natural. Certainly the human body seems to obey the usual laws of nature and not to be outside of nature as the term is being used here. It seems that to follow this line of reasoning is to concede that materialism is incomplete. But the only other rational way to exclude people from the list is to say that we know that they didn't exist before 10,000, or perhaps 1 million, years ago. But this is to exclude humanlike intelligence (space aliens, humans or humanoids from other solar systems, God, or some other superhuman intelligence) because we don't like where the evidence might lead, not because there is no evidence compatible with humanlike intelligence as a causation. One thing to keep in mind is that human intelligence acting alone is not the cause of the "human-caused" genetic variation we see. Humans called upon the information-processing capacity of computers. It is debatable how much computers added, and it is reasonably certain that computers (at least modern ones) without humans could not have done the job, but it is also true that humans without computers would have taken a much longer time to do the job, if it could have been done at all within the lifetime of our universe. So it is arguable that humans plus computers constitute a humanlike intelligence rather than a human intelligence. Let's come back to Stonehenge. Was Stonehenge designed? Do we argue this on the basis of knowing the designer, or on characteristics which reasonably match design and which do not reasonably match the results of natural causes? The admission that Stonehenge is designed puts us on the horns of a trilemma. Were humans technologically advanced enough to have created it? Did giant humans or space aliens exist at that time? Did God create it, or charge angels to create it? None of those alternatives fits well with our usual picture of prehistoric Britain. But the difficulty with these possibilities does not (usually, except in debates like this) allow us to deny that Stonehenge was designed. So, unless we are prepared to admit that humans are not really natural, and that materialism fails when it comes to us, then we must include humanlike intelligence as a possible natural cause for genetic code. Your question on lateral gene transfer is appropriate. If we use modern humans as an example, one characteristic of guided lateral gene transfer is that it often results in proteins being produced which give no particular competitive advantage to the organism itself, but benefit another organism. Thus when we find in nature symbiotic relationships, one might suspect that lateral gene transfer is more likely to be guided. This actually fits the character of a God Who, before the plan was spoiled, wanted the different organisms to mutually support each other, most clearly in altruism and love. In any case, organisms that support another organism with an apparently laterally transferred gene would be hard to explain by Darwinian processes, and guided lateral gene transfer should be considered if such genes are found. I will ignore your last sentence, as you have admitted that it was made "tongue in cheek" (#53). Paul Giem

I'll humor you. You call it a "mistake" even though they were very clear on what they were doing in the original article, which Lynch misunderstood even though they were very clear about the limited scope of their paper. The funny part is that I've seen people claim that "Darwinian processes" is "creationist terminology". That's certainly not correct, but I'm also doubtful that there is a standard definition. It's like how the word "evolution" can be used in reference to multiple concepts. In any case, your primary objection is that you do not like their choice of words. Instead of replying to others in this thread with substance you focus on defining variables to fit your purposes. This is a prime example of the zero-concession policy. This paper by Behe and Snoke has been hyped and bashed way beyond its limited scope. This type of behavior has been noticed before:

I think you’ve hit the nail on the head in noting that Darwinists redefine “lie” to mean anything that does not promote the party line. I wrote about this a few years back in my contribution to the Phil Johnson Festschrift when describing why the Darwinists can never seem to agree that our side gets even one thing right. It’s as though every aspect of everything we say and do must be discredited. --Dembski

As for Carroll's book, you are probably referring to his comparison of two opsin proteins where a change in function can be achieved by three amino acid changes. He starts by assuming an eye equipped with visual pigments and then describes how a few changes in pigment proteins alter their properties and help organisms adapt to different light environments. In reference to comment #49, I'm apparently cynical for a good reason. But is there anything specific you wanted to discuss from either Carroll's book or that other article? Also, if you're going to yank examples from Carroll you could have at least picked a better one like the trypsinogen gene in Antarctic notothenioid fish which consisted of 4 to 55 repeats of three amino acids. Patrick

Patrick, It might seem like a word game but it is critical to the discussion. No one has ever suggested that genetic drift (random fixation of neutral and, rarely, deleterious alleles) is a leading cause of the formation of complex or even simple structures. But this is what B+S were actually testing, while claiming they were testing Darwinian processes. I'm not saying they did so with an intent to deceive, but they made a mistake and were corrected on it. their paper basically shows what everyone already knows- that it's hard to make new features w genetic drift alone. this is another example of why having good definitions is so critical. Well the best reference on color vision is Sean Carrol's book "Making of the Fittest" but here's an open-access referecne that seems interesting: http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0001054 Khan

Ugh, so basically your objection comes down to a word game. If it makes you happy then, yes, by that definition Behe and Snoke's model did not include "Darwinian processes". But you should know that when most people on here (UD) say "Darwinism" or "Darwinian" they're referring to modern evolutionary theory and all related non-foresighted, unguided mechanisms or processes. We're examining all potential pathways, not just ones we know should work. Sure, it may be imprecise language but this is not just something we do, as referenced on this page here in relation to Margulis. And, quite frankly, I don't appreciate people making an argument on such a basis since it wastes people's time, including your own. You could have cleared up the point you were trying to make much earlier. Oh, and you don't need to write anything on color vision. Just link to what you're referencing and then we can all discuss it. I'll even create a new thread for it (if the paper is quite lengthy please quote the parts you feel relevant so I can quote them in the thread page). Patrick

Patrick,

Their research was narrow in scope, “restricted to point mutations and assum[ing] intermediate states to be deleterious”. These ARE Darwinian processes

You (and B+S) are mistaken about what constitutes Darwinian processes. Darwinian processes are gradual accumulations of slightly beneficial mutations that produce slightly more fit intermediates (King, J.L. and Jukes, T.H. 1969. Non-Darwinian evolution. Science 164:788–798). The assumption that intermediates are deleterious makes the model non-Darwinian. B+S are actually talking about genetic drift, which is something that Darwin could not have envisioned. THe model is Kimura-ian, rather than Darwinian.

What if you were to study what constitutes intelligence in general?

hm, it would be a tough sell to a science panel (unless you were trying to design AI), but maybe a philosophy panel would bite. but they don't give you much money :) speaking of science, I'll write a bit about color vision evolution soon. Khan

However, this approach fails bc they do not use Darwinian processes in their model. THus, they can not test what Darwinian processes can or can not do.

At this point all I can do is repeat myself: "As already discussed they were examining a limited scenario which they know would not apply uniformly." Their research was narrow in scope, "restricted to point mutations and assum[ing] intermediate states to be deleterious". These ARE Darwinian processes but they did not "look to more complicated pathways, perhaps involving insertion, deletion, recombination, selection of intermediate states, or other mechanisms, to account for most MR protein features." Their study only provides data on what Darwinian processes can achieve in a worst case scenario where all available stepwise pathways are deleterious. So obviously this is not intended as a wholesale refutation of Darwinism since there ARE some gradual stepwise pathways that can produce functionality. As for their model's relevance to real life I would think the biggest application would be to OOL studies and the original simple life that did not have a variety of islands of functional information to build upon.

were I to submit a grant application to study a non-human, unspecified intelligent agent it would get laughed at and tossed into the trash bin.

What if you were to study what constitutes intelligence in general? Patrick

and I think my reasoning is better than my blockquoting :) here we go:

if you want to add it to your list and if you argue that this has been a major force in the development of living organisms, the only logical conclusion is that we designed ourselves. Seriously, can you not spot the silliness of that reply? Obviously, we would want to add “intelligence and associated mechanisms in general”, not human intelligence specifically.

Yes, it was meant to be tongue in cheek (and actually was ripped off from another commenter), but the basic truth holds. We have seen humans and humans alone design things, so at this point we should limit "design" to "human design." I'm sure you won't agree, but I have no desire to have a drawn-out conversation about it. I can tell you this, though: were I to submit a grant application to study a non-human, unspecified intelligent agent it would get laughed at and tossed into the trash bin. Khan

Patrick, I'll respond to one thing at a time. [QUOTE]You already said, “they do not use…selection on slightly beneficial mutations accumulating over time…in the model” but that’s precisely the point! They’re examining what Darwinian processes are capable of achieving in a worst-case scenario where there does not exist an “easy” pathway.[/QUOTE] Your ellipses omitted a major point. What I wrote was: [QUOTE]they do not use Darwinian processes (selection on slightly beneficial mutations accumulating over time) in the model.[/QUOTE] They state in the intro to their paper [QUOTE]Our approach is to examine pathways that are currently considered to be likely routes of evolutionary development and see what types of changes Darwinian processes may be expected to promote along a particular pathway. [/QUOTE] However, this approach fails bc they do not use Darwinian processes in their model. THus, they can not test what Darwinian processes can or can not do. That is my reasoning. Khan

Behe and Snoke were effectively rebutted, because their methods were not appropriate to their question

Explain your reasoning. As already discussed they were examining a limited scenario which they know would not apply uniformly.

and their assumptions were faulty.

You already said, "they do not use...selection on slightly beneficial mutations accumulating over time...in the model" but that's precisely the point! They're examining what Darwinian processes are capable of achieving in a worst-case scenario where there does not exist an "easy" pathway. But all you can do is assert that such a scenario is not applicable at all. Essentially we're arguing over the supposed features of Mount Improbable. You assert that climbable slopes exist for everything and we claim the opposite (although with the caveat that some cliffs should be climbable via intelligent mechanisms) saying that these climbable slopes are limited in number.

if you want to add it to your list and if you argue that this has been a major force in the development of living organisms, the only logical conclusion is that we designed ourselves.

Seriously, can you not spot the silliness of that reply? Obviously, we would want to add "intelligence and associated mechanisms in general", not human intelligence specifically. On lysozyme, I believe I've read that paper before. Personally I'd have to spend more time analyzing the proposed pathway but even the first time I read up on this subject it "appeared" reasonable. We know that with slight alterations SOME gene products can acquire very different functions. Lactalbumin and the lactose synthetase enzyme are encoded by genes that differ only slightly in sequence from the gene for lysozyme. The difference is only a couple amino acid residues. Although it just occurred to me that their scenario was "attributed to selective pressures in the stomach". They briefly mention that lysozymes are in tears, and in fact it is a very important component that the eye secretes since without it eye infections cause most victims to go blind. Lysozymes are also used in other various ways as part of the immune system. I'm just curious when the lysozyme family is supposed to have originated considering its importance to many systems throughout the bodies of higher animals.

I would also be happy to hear any examples of structures where the possible pathways of evolution have been elucidated and have been shown to have too many deleterious intermediates to be viable.

Perhaps you can even produce ANY pathway in order to continue this topic: https://uncommondesc.wpengine.com/irreducible-complexity/computers-vs-darwinism-a-computer-teacher-comments/comment-page-1/#comment-299856 https://uncommondesc.wpengine.com/intelligent-design/chance-law-agency-or-other/#comment-289741 The end of this conversation puts the problem in perspective: https://uncommondesc.wpengine.com/intelligent-design/chance-law-agency-or-other/#comment-290187 Other major points: https://uncommondesc.wpengine.com/evolution/behes-multiple-mutations-needed-for-e-coli/#comment-290408 https://uncommondesc.wpengine.com/intelligent-design/chance-law-agency-or-other/#comment-289702 https://uncommondesc.wpengine.com/philosophy/id-and-catholic-theology/#comment-212175 Patrick

Patrick --So if someone were to say, “Hey, we can produce a color-based system with only a couple switches” I’d roll my eyes. Exactly and, if some said I can take this color system and turn it into a grayscale one in just a few steps, we'd have no trouble accepting it :-) tribune7

So, do you want to hear about the evolution of color vision, or do you already know about it and consider it a trivial case?

Years ago I've read it about such hypotheses but honestly my memory is hazy and I don't recall reading a recent genetic analysis. It really depends on the underlying machinery and the corresponding code, does it not? I may be cynical but what I expect to see from Darwinists is the claim that a full color system can be produced in total with only a handful of mutational events. If that's the claim excuse my skepticism. The totality of the system must be considered. There will be much overlap between a grayscale-based system and a color system. I even imagine that there is a degree of dynamic functionality when it comes to the neural network of the brain interpreting the incoming signal. The key is that components specific to only color must be recognized. This informational difference may be relatively small, and there may be many functional intermediates between grayscale and full color spectrum (detecting any additional wavelengths may give selective advantage), but from a functional perspective I would happily consider this macro-evolution if it's within the reach of non-foresighted Darwinian processes. And the reason I say I'm cynical is because with such a complex system it probably is possible to reduce the functionality down to grayscale only with a couple informational changes, rendering the components specific to color useless. In general it's much easier to break than to build. Or to restore lost functionality. So if someone were to say, "Hey, we can produce a color-based system with only a couple switches" I'd roll my eyes. What is the information difference in total? What pathway can produce this system in total, and what functional intermediates are there? EDIT: Speaking of restoring functionality, on a related topic.

“Contrary to previous belief, blind cave fish have the genes to build eyes but turn them off during development. When a body part is no longer needed, scientists usually assume that mutations accumulate in the genes controlling the structure, eventually preventing it from working or being made. “That was the dogma," says Stephen Ekker of the University of Minnesota, Twin Cities. But because the cave fish eyes are actively killed, natural selection is probably doing its thing, says Jeffery. And that, he adds, might come as a surprise even to Darwin, who thought the cave fishes' loss of sight might be an exception to the rules of natural selection.”

So it's not simply an issue of "use it or lose it," the article also states: “new research suggests that for some cave-dwelling fishes, blindness results from the careful coordination of gene expression, not simply from lack of use.” There was an article in January this year where 2 populations of blind cave fish were hybridized resulting in sight regained 2-3 generations later. In short, the blindness is temporary (genetics wise) and I think ID proponents should look for a system (foresighted mechanisms) reacting to dynamic environments. Patrick

Clive: Great link at no 2 -- I am enjoying the breath of fresh air and sparkling light of sharp insight from one certain G K Chesterton! (Just as I have long learned to love C S Lewis; for pretty much the same reason -- and BTW, first on the recommendation of my University's then resident leading atheist student . . . Thanks, FL.) GEM of TKI kairosfocus

Paul: Re 43 supra: Thanks. GEM of TKI kairosfocus

Khan said, "I would like to know if you consider color vision to be a “trivial” trait." I don't know. That is not being evasive. I do not know what is needed for a species to have color vision or not, nor how many species have colored vision. It is not a topic that has come up before. We would certainly be willing to listen to any description of what color vision is about and how it might have grown from a non color vision and whether this can be classified as novel complex functionality. It would probably be interesting. I can completely understand how color vision could lead to differential survival for many species but would be interested in the array of species that possess it. From what I understand all eyes were developed during or before the Cambrian explosion so is color vision a more recent innovation? If the differences between color and non color vision are small changes in the DNA then we would consider it trivial. If it involved complex changes to the DNA of species then it would be an interesting example. You assert that "The point is that I'm assuming that for every existing functional object that there exists an indirect genetic pathway that can be traversed by Darwinian mechanisms within realistic conditions (population size, time, etc.). In short, I'm asserting that Darwinism is a “cure all” or a panacea of information.” That is an interesting claim that I have not seen any evolutionary textbook or any book on evolution ever make or that it is backed by empirical data or examples. One of ID's contentions is that there are few if any examples so we would be all ears to hear what you have to say. We do present evidence but it of the kind that you may not like. It is evidence for a negative. Namely, that there does not exist (m)any examples of Darwinian evolution that leads to the formation of novel complex capabilities that is not speculation. We use the empirical data that evolutionary biology has unearthed and presents in defense of its case that all evolution is due to naturalistic causes. We do not deny that there are many trivial examples of Darwinian processes leading to species change but we have yet to see any clear examples where these processes lead to the development of the necessary information for novel complex capabilities. There are those in ID who are very interested in finding a statistical technique that would classify certain things as designed of not. I personally think that this process if accurate is not currently accessible to anyone except those well versed in certain mathematical techniques. However, there is a subset of this process that is easy to understand and is at the heart of ID, namely the development of functionally complex specified information. or FCSI. Every example of such has always been attributed to human intelligence except one, the DNA and RNA in living beings. There are no examples of FCSI existing in nature except for DNA and RNA nor any coherent speculation as to how DNA/RNA could arise You are an empirical biologist so you should be starting to understand the type of evidence that is necessary to support the claims of evolutionary biology or refute the claims of ID. If you are able to do so then you will have done what no textbook has done nor any book on evolutionary biology has done nor any biologist including evolutionary biologists have done on this site or anywhere we have found. It will be an interesting discussion and one that should lead the presenter to a Nobel prize if he/she can explain it with empirical data to back it up. We are interested here in empirical data and what can be reasonably concluded from it. If you thought otherwise or you thought we were ill informed then you have been mis informed. You have an advantage over me in that you are a trained biologist. But I have an advantageous over you in that I have seen hundreds of prior exchanges on this very topic so using inductive reasoning I have concluded that the next exchange will not be any different. But maybe you will be the black swan. jerry

Paul, lysozyme paper here: http://mbe.oxfordjournals.org/cgi/reprint/11/6/921?ck=nck In response to your barking dogs that question my manhood: 1) Yes, Behe and Snoke were effectively rebutted, because their methods were not appropriate to their question and their assumptions were faulty. yes (as you and others point out), most interactions require more than two binding sites, but that is irrelevant to the content of the paper itself. to prove I'm even-handed, here's a link to a non-ID paper that I think got nailed as well: http://www.nature.com/nature/journal/v422/n6934/full/422833a.html 2) Yes, humans can intelligently design things, even new genes. As you know, Darwin used this process as evidence of the power of variation and selection. Allen's list is restricted to natural causation, though, and thus anthropogenic causation is excluded. However, if you want to add it to your list and if you argue that this has been a major force in the development of living organisms, the only logical conclusion is that we designed ourselves. Khan

"The point is that you’re assuming that for EVERY functional object that there exists ANY indirect stepwise genetic pathway that can be traversed by Darwinian mechanisms within realistic conditions (population size, time, etc.). In short, you’re asserting that Darwinism is a “cure all” or a panacea of information." add "existing" after "every" and replace "any" with "an" and delete "stepwise"and I would agree that this is a hypothesis that is supported by a lot of evidence, that I would be more than happy to discuss with you. I would also be happy to hear any examples of structures where the possible pathways of evolution have been elucidated and have been shown to have too many deleterious intermediates to be viable. I am an empirical biologist and I like to see empirical evidence. of course there are lots of limits to evolution (including the simple truth that natural selection does not preserve deleterious mutations); everyone has acknowledged this since Darwin. otherwise 99% of species that have ever existed wouldn't be extinct. It is in these extinct species that we find the "Edge of Evolution", not the living ones. Khan

Khan, I've got to admire your faith. You state (#38),

Herein lies (one of) the problems w your logic. evolution does not work like a ladder- there is no specified endpoint and rather than being a single path there are millions of different paths. if one path gets cut off bc intermediates are selected against, then it goes another way. as evidenced by lysozyme, organisms can arrive at the same endpoint through different paths.

The ladder fails becasuse there are millions of different pathways, and at least one must be viable. We know this because strongly similar lysizymes in widely divergent species exists. That is, there must be an unguided pathway to us because here we are. And you expect us to be evangelized on that basis, even though we keep pointing out that from our POV there is no reason to demand unguided pathways because we consider that guided pathways may also exist (or exist instead). Furthermore, you have not demostrated that there are such unguided pathways to lysozyme. You have not even cited a paper which claims to have found such pathways. In fact, you seem to consider a request for such pathways somehow odd (#37):

Jerry and Paul, you both seem to want mutation-by-mutation accounts of protein evolution. This is also Behe’s chief demand, which I assume comes from his background as a biochemist where pathways are everything.

Well, yea. The whole point of Behe and Snoke's article (which IMO neither Lynch nor you have refuted) is that if one needs two steps in an evolutionary pathway, and the first step is selected against, then the pathway is essentially out of reach (without assistance) for large mammals (which would include cows developing lysozyme). That means that Behe would be within his rights to demand a mutation-by-mutation account of how cow lysozyme originated, with each step at least neutral. Biochemists understand that they are dealing with science, which demands testable hypotheses that can survive the tests, in contrast to much biological thinking, where just-so stories are accepted as evidence (I say this as an applied human biologist with an undergraduate chemistry degree). You have to remember that Behe was theologically comfortable with unguided evolution; he simply came to realize that the hard evidence wasn't there; indeed, it pointed in another direction. Now, as Patrick (#39) mentioned, I perfectly understand that the ladder analogy is not completely accurate. The ladder essentially operates in one dimension, and there are actually multiple dimensions. It is more like having multiple branching ladders that intertwine. But the point remains. Given Behe and Snoke's paper, for evolution to work on cows there must be at least one such pathway with no obstacles for every new protein if unguided evolution is true, and demanding one such pathway is perfectly reasonable. Your statement that

i can’t address all your questions about lysozyme evolution bc that would involve explaining large parts of evolutionary logic to you (and i try to have a life).

is therefore not helpful. We (at least some of us) already know evolutionary logic. The first paragraph quoted above gave us that. What we want is biochemical pathways, and you don't appear to be able to give us any. You mentioned color vision. Whether it is significant depends on the length and contour of the biochemical pathways involved. If you can demonstrate a mutation-by-mutation pathway, I am happy to concede (although the concession would include color vision, not the absence of ID altogether; for that you would have to explain at a minimum the origin of life). If not, you would be wasting time unless you wish to concede, which does not appear likely given your faith and your previous behavior. You seem at least theoretically open to proof; if we test all possible pathways from the (now non-existent) DNA of all ancestors to the hoatzin to hoatzin lysozyme and find them all blocked, you will consider it compelling evidence. Thanks. But in the meantime we should work incognito, without even mentioning ID, but rather spin our research "as a test of some fundamental evolutionary process". I'm afraid that won't work for me; all they have to do is google my name and my funding would dry up faster than that of Robert Marks. Your comments on the ladder remind me of a controversy going on at another thread at UD, where the complaint is raised that someone has posted too long a comment. I have chosen to be more brief, but the attempt to dodge the force of the argument by complaining about the analogy used makes the length of the comment on the other thread a little more understandable. If you don't want text walls, try to be more understanding and less nitpicking. Finally, I am interested in two "barking dogs". First, there was no comment about whether Lynch really refuted Behe and Snoke on this round of comments. Do you still really believe that? Or are you hoping to remain silent so that you can stop defending an indefensible position without ever actually conceding? Second, you made no response to my statement that intelligent design was a demonstrated cause of genetic variation. Again, do you wish to retire without conceding, or do you really wish to maintain that intelligent design has not been demonstrated to be able to change genetic makeup? Or are you man enough (or woman enough) to admit it and change your mind when you are wrong on some specific issue? Paul Giem

Jerry, I am not sure what you are responding to in your reply. I was offering to walk you through an example of nucleotide-by-nucleotide evolution of a system. Is that not what you wanted? So, do you want to hear about the evolution of color vision, or do you already know about it and consider it a trivial case? you always ask for the debate to be about evidence, yet you have presented absolutely no evidence thus far. Khan

Jerry states: "The modern synthesis, Darwinian paradigm or whatever is the current version of evolutionary thought" you can bet "the current version of evolutionary thought" will always be something other than the proposed mechanism you refute in a debate with a Darwinists. bornagain77

Khan, The modern synthesis, Darwinian paradigm or whatever is the current version of evolutionary thought proposes that variation takes place somehow, mainly by some form of gradualism but not necessarily. When variation has taken place, natural selection processes or other processes operate to bring some of this variation to a high frequency in the population. Gradualism is still clung to dearly by modern evolutionary biology thinking though it is not the only play in the book (American football metaphor) that is accepted. So however evolution happened, an evolutionary biologist must propose a mechanism for the changes and the one mechanism that has failed miserably is gradualism. Now if you want to propose another mechanism besides gradualism, go ahead but be ready to defend it not just assume it is true. And by the way gradualism does not have to depend upon a nucleotide by nucleotide change. We are very much aware of other engines of variation. It can happen in lots of other ways but each would leave a forensic trail of which no one has ever been able to demonstrate. So don't appeal to our lack of knowledge to support your position when it is you who seem to lack an understanding of the issues. We ask for acknowledgment that we have a point not a constant shifting by you to somehow bolster your faith in something that is not based on any empirical data but is as much like a faith in Christianity for those who are in a church on Christmas. Your faith is to an unknown unseen process and you seem to cling to it without acknowledging that others which do not agree with you may have some points. By the way I can make the Darwinist's points with the best of them since I have read many pro Darwinist books. So I understand the strong points but this process of reading the pro Darwin books had pointed out the consistent weaknesses in every book which they fail to acknowledge. But I acknowledge their strong points. You should do the same if you want a dialog, not a constant battle to get a gotcha. jerry

Herein lies (one of) the problems w your logic. evolution does not work like a ladder- there is no specified endpoint and rather than being a single path there are millions of different paths. if one path gets cut off bc intermediates are selected against, then it goes another way. as evidenced by lysozyme, organisms can arrive at the same endpoint through different paths.

I think Paul understands this completely, and your disliking his ladder analogy does nothing to counter his main points. The point is that you're assuming that for EVERY functional object that there exists ANY indirect stepwise genetic pathway that can be traversed by Darwinian mechanisms within realistic conditions (population size, time, etc.). In short, you're asserting that Darwinism is a "cure all" or a panacea of information. Now given the prior existence of a complex system(s) there should be many such pathways. And as an ID proponent I believe we'll find more and more examples. I even believe we'll eventually find very limited cases that can produce anyone's definition of macro-evolution, perhaps even CSI, and that ID theory will need to be adjusted to account for such limited cases (presuming they're limited and not uniformly active). I'm even open to the "designed to evolve via non-foresighted mechanisms" hypothesis, although so far that seems unlikely. Having worked with evolutionary searches we know via simulations that there exists limitations to such mechanisms, but all people can do is assert that the biological system is different "somehow". In essence, all Behe and Snoke were doing was analyzing a hypothetical scenario where an evolutionary search is limited to difficult pathways when trying to achieve certain states. But they did it with real biology. Obviously this scenario would not apply to a good percentage of cases where there are varied pathways in abundance. And, yes, for the purpose of the experiment they are presuming that such scenarios exist in reality and it could be argued that they need to be proven to exist in great abundance in return. But I don't see that as too difficult since I've seen examples where even imagination fails to provide tenable scenarios (although great leaps of imagination/belief are often the bridges). Patrick

Paul, " If one thinks of Darwinian theory as a ladder.." Herein lies (one of) the problems w your logic. evolution does not work like a ladder- there is no specified endpoint and rather than being a single path there are millions of different paths. if one path gets cut off bc intermediates are selected against, then it goes another way. as evidenced by lysozyme, organisms can arrive at the same endpoint through different paths. i can't address all your questions about lysozyme evolution bc that would involve explaining large parts of evolutionary logic to you (and i try to have a life). but i am curious how would one distinguish between guided and unguided lateral gene transfer? "I’d be interested to know if you would really concede that easily if ID researchers were to find an absence of viable paths between hoatzin lysozyme and, say, hoatzin ovalbumin" first, I would question why (and how) they would look for evolutionary pathways between proteins in the same species. this would defy all evolutionary logic. second, (assuming they looked for pathways to hoatzin lysozyme from ancestral species), if they could show that every possible path from that ancestral sequence to the lysozyme sequence involved multiple deleterious mutations, I would certainly consider it compelling and worthy of further study. that would involve a lot of work and money, but would certainly be fundable and could be spun as a test of some fundamental evolutionary processes without mentioning ID. Khan

Jerry and Paul, you both seem to want mutation-by-mutation accounts of protein evolution. This is also Behe's chief demand, which I assume comes from his background as a biochemist where pathways are everything. I am sure you realize that gathering these types of data is an extremely methodologically difficult, expensive and time-consuming endeavour. With that in mind, I have a v nice example I can walk you through. but to avoid wasting time, I would like to know if you consider color vision to be a "trivial" trait. Khan

StephenB @ 23

I don’t think that the conclusion follows from the premise. Chesterton was simply saying that there is a limit to how much we can know about the past. He didn’t say we can know nothing. If anyone was extravagant it was Doyle in his capacity to believe in almost anything except God.

I think Chesterton was a little more pessimistic than was warranted about our ability to learn about the past. While we may never be able to achieve a precise and detailed reconstruction of all past events neither do we know what future discoveries may enable to us to do. Who knows what we may be capable of in say 10,000 years - assuming we are still around, of course.

I suspect that he was offended by Chesterton’s apt quote: “If a man will not believe in God, the danger is not that he will believe in nothing, but that he will believe in anything.” Clearly, Doyle fell into that camp, and I suspect that his comments reflected a reaction against that inconvenient truth.

I never understood the appeal of that quote. Yes, in principle, people could believe in anything but in practice they are unlikely to believe in things that harm their prospects for survival. They can believe in things that are false to fact as long as it makes little difference. Most people assumed that the Sun went around the Earth for a long time because that's what it looks like. All those people believing it didn't make it true but in practice it made no difference so it didn't matter whether it was true or not. Seversky

Thanks, gpuccio (#30). And your work is also excellent. Khan, you say (#28),

as Lynch mentions, non-Darwinian processes are considered all the time in evolutionary theory- drift, biochemical constraints, genetic linkage to adaptive traits, symbiosis, etc. are all evolutionary processes that Darwin could not have conceived of

We are quite familiar with this list. Allan MacNeill has familiarized us with it (he had some 47 members last I saw). The question that needs answering is, which member of this list explains insulin-producing yeast, or vitamin A-producing rice, or blue roses? Or, for that matter, chihuahuas? You have, along with much of the rest of the scientific community, deliberatey omitted a physically demonstrated cause of genetic change. "Ah," one might say, "but we know the causal story for insulin-producing yeast. We don't know the causal story for yeast itself." Then let's discuss two stone formations. There are lots of reasons why stone formations might happen the way they do. Look at the formations in Bryce Canyon, or in Arches National Monument. But we know, because we know the causal story, that Mt. Rushmore had an additional cause besides the usual wind, rain, freezing, and other erosion. Intelligent design can produce stone formations. How about one where we do not know the causal story? For example, Stonehenge. Is Stonehenge designed? Do we know the designer, or the mechanism? Can we detect design without either a designer or a mechanism, or, for that matter, a purpose? Or must we write off Stonehenge as the result of a freak tornado or earthquake or something? If we find an arrowhead on Mars, we may be reasonably certain that it was made by intelligence. If we find hundreds of arrowheads, we may be as certain as science will permit us to be that those arrowheads were the product of intelligent design. We may not know who (Martians? Space aliens? God? Someone sneaking them onto the Mars explorer from earth?), or how (Flaking obsidian? Pouring obsidian into a mold? Creation ex nihilo?). But we can be as certain as we can be of anything, that those arrowheads were designed, even though not knowing anything about who or how or why. You say,

but using a non-Darwinian model to show that Darwinian processes can not work is a non-starter.

That depends on what you wish to show. If you wish to show that Darwinian processes can create new structures that require two amino acid changes if the first change is neutral, the answer is yes, you can show that. If you wish to show that Darwinian processes can create anything, including new structures requiring two amino acid changes where each change individually is selected against, the answer is clearly no. To paraphrase gpuccio (#30), the proper question is not whether Darwinian theory is coherent. The proper question is, how closely does Darwinian theory correspond to reality? If one thinks of Darwinian theory as a ladder, the paper of Behe and Snoke showed that if only one rung of the ladder was spiked so as to discourage stepping on it, the organism climbing the ladder would reach to a rung two steps higher only rarely, and usually with massive population and reproduction resources, resources out of reach of higher mammals. Saying that Darwinism won't work on non-Darwinian landscapes should be trivial, but there are those that deny even this. It sounds like you assent to this trivial truth, but somehow want to blame Behe and Snoke for pointing it out. What Behe and Snoke have reasonably shown is that if any rung of the step-by-step ladder is damaging to an organism, only the most athletic organisms in terms of reproductive resources can be expected to take the step, and then only rarely. Lynch doesn't really challenge their results. This means that, in higher organisms, evolutionists have the job of showing that every single amino acid change is either beneficial, or at least neutral. For a brain protein with 16 changes in it between chimpanzees (and gorillas) and humans, we should be able to show in what order these 16 changes took place, with viable intermediates for each mutation. Otherwise Darwinian evolution fails for this protein. AFAICT, that has not been done, and I doubt it can be done. In #31 (skipping where you repeat yourself) you say,

look at the convergent evolution of lysozyme in the bird hoatzin and the cow as an example. they evolved v similar proteins with seven identical amino acids from v different ancestral states. ID researchers could test whether each of the steps in this evolution involved a neutral or beneficial intermediate step. that would be useful and interesting.

I'm not sure what you mean by "v". But note your assumption. They evolved. Presumably you mean by unguided evolution. How do you know that? How do you know that they were not guided, or that there was not lateral gene transfer and subsequent divergence in non-essential amino acids, perhaps guided lateral transfer, or perhaps even flat-out design from scratch, with two different instantiations? Who says that they had to evolve from two different ancestral states? I'd be interested to know if you would really concede that easily if ID researchers were to find an absence of viable paths between hoatzin lysozyme and, say, hoatzin ovalbumin. The standard approach would be to claim that we had not tried all possible selective environments, or that we had the wrong proteins to compare, or the wrong species, or that the original protein was not ovalbumin but some unspecified protein halfway between them; anything to blunt the force of the argument. In the meantime, the ID researchers would probably be Gonzalized (Sternberging is too kind). The problem is that this is a religion versus science argument, with the one side dogmatically insisting that science must be made safe for atheism. I hope you haven't gone that far, although the claim you make that Lynch has "nailed" ID by his non-refutation of Behe and Snoke's paper is not encouraging. Paul Giem

gpuccio @ 18

Although I have really loved Holmes and felt amazed at his deductions, I have always known that they were mostly artificial, and that if I had really tried to deduct in advance who was coming next through the door, I would have failed miserably.

Same here. I read all the stories but it's clear they were contrived to illustrate Holmes's genius. The Universe is probably not so obliging with the evidence it provides and there are few ordinary mortals with his powers of observation and deduction.

Regarding History, I certainly believe that there was a Battle of Gettysburg, and in my most optimistic moments I am also convinced that there was a great flowering of culture in classical Greece (although ancient Egypt already starts giving me real trouble…), but I don’t share the faith and assurance which most people seem to have that we really know much about those things, or that what we know is reliable.

There is a temptation to present some of these things a more settled and certain than they really are. If you read about Custer's Last Stand at the Battle of The Little Big Horn you find there are several versions of what might have happened. There were no survivors of his detachment so the only eyewitness testimony we have came from Indians and those accounts are unclear and contradictory. That said, archaeological studies of the battlefield, in particular the type and distribution of spent cartridge cases have shed some light on how the fighting moved across the field. By matching the marks left by strikers on the base of the shells they have been able to track the movement on individual weapons. Obviously, it's not a blow-by-blow, minute-by-minute account of what happened but it's more than there was before. Seversky

I am traveling for the next few days and have limited time to respond. And I am not a micro biologist in reality or in any dream I ever had so if I said I could understand all the details of the technical parts of the two papers, it would be a great mis representation. But I do understand logical thinking. A criticism of one paper is hardly nailing of ID. If the criticism is accurate it is no more than a small correction of one's peripheral point of view. But from reading between the lines of what has been discussed it would seem that Lynch's paper is illogical. Briefly, if we are trying to explain the migration of one protein to another, supposing a duplicate is the origin of the new protein to minimize problems to the organisms, one has to show how an Darwinian evolutionary path could have arisen. Note ID would not dismiss such a path because it does not really challenge ID's fundamental position. But ID has pointed out that such a pathway has never been found except for some small trivial examples. If such a Darwinian path happened in nature, there would be loads of forensic evidence that it existed. Each step on the path to the new protein or system would be viable and there would be examples of these way stations on the way to the new protein/system in the world. But there are none and that is why the Darwinian explanation has failed as an explanation for evolution. To use a Sherlock Holmes' expression: "The dog barking in the night." But there was no dog barking and that is what Holmes meant. There are no pathways and consequently there is no path that barks to us that this is how Darwinian evolution or any other form of evolution has occurred. jerry

Happy belated Christmas everyone!! I hope that there are more ID books released in 2009. In particular I like the idea of creating an ID textbook. It was mentioned on this website. http://post-darwinist.blogspot.com/2008/08/thoughts-toward-intelligent-design.html "My fantasy ID textbook would actually treat biology as a branch of engineering – i.e. God’s engineering." "The phylogenetic tree would be treated as purely a taxonomic device to show how certain bio-machines result once certain changes are made to their structure. The book would be completely neutral on origins, in terms of either when or how the various bio-machines we call species were produced. These would be matters treated separately – as it were, in another course." Platonist

gpuccio, "But the problem is not what is darwinian and what is not.The problem is what is a realistic model and what is unwarranted assumption" I hate to repeat myself, but B+S were testing whether Darwinian evolution could produce new interactions, but failed to actually use any Darwinian processes in their model. this is like testing whether a new car runs without putting any gas in it. their assumption that intermediate states were non-functional was unwarranted both for this theoretical reason and because of the vast amount of empirical data showing that intermediate states are frequently functional or neutral. and what about when they are harmful? they will be selected against and will not evolve (not an earth-shattering result). this is fine, because evolution has plenty of material to work with, as Lynch's paper nicely summarizes.there is not one and only one path to a new interaction or new protein, as you suggest. look at the convergent evolution of lysozyme in the bird hoatzin and the cow as an example. they evolved v similar proteins with seven identical amino acids from v different ancestral states. ID researchers could test whether each of the steps in this evolution involved a neutral or beneficial intermediate step. that would be useful and interesting. Khan

Khan: "using a non-Darwinian model to show that Darwinian processes can not work is a non-starter." But the problem is not what is darwinian and what is not. The problem is what is a realistic model and what is unwarranted assumption. The purpose of Behe and Snoke's paper was obviously to show that even a very small transition of two aminoacids can be a real challenge to evolution when the first mutation has negative effects on function. Lynch's answer is that things are a little better if the first mutation is neutral. I suppose that things are still better if the first mutation is favorable and is positively selected. I bow to Lynch's wisdom. And by the way, he employs a lot of complex population genetics and mathematics to show that! I can only support Paul's conclusion: "But given that most protein-protein binding sites require multiple residues to match on both sides, it seems that Behe and Snokes actually underestimate the average difficulty of creating a new protein interaction". And not only we need new protein interactions, but new significant protein interactions, and, in case we forget, new proteins! (see my post #24). In other words, Behe and Snoke's paper shows that, unless darwinian theory can show that all transitions from one protein to another one are deconstructible in simple steps where single aminoacid substitutions are at least neutral, and double aminoacid substitutions are favorable and selectable, it will face bigger difficulties than those shown in their article. Is that point relevant to darwinian model? You bet! Has darwinian model ever even tried to demonstrate that those assumptions are at least reasonable? No, it hasn't. Why? Because it is frankly impossible, as should be obvious to anybody. Well, if that is your best example of ID being "nailed", I believe we can relax a little... By the way, Paul, thank you for your wonderful review of the paper. Your work is practically perfect, as usual. gpuccio

Paul, Many of your points can be dealt with by pointing out that this paper is a specific response to Behe and Snoke's paper. thus, "It’s almost like it is a crime to suggest that some biochemical pathways might be non-Darwinian. Furthermore, we are not allowed to consider difficult cases" Since the Behe-Snoke paper claims to address Darwinian processes, they should have included Darwinian processes in their model. a non-Darwinian model can not test Darwinian hypotheses. agreed? as Lynch mentions, non-Darwinian processes are considered all the time in evolutionary theory- drift, biochemical constraints, genetic linkage to adaptive traits, symbiosis, etc. are all evolutionary processes that Darwin could not have conceived of, but are standard material in the evolutionary literature. so it is hardly a crime to consider them. but using a non-Darwinian model to show that Darwinian processes can not work is a non-starter. Khan

tragicmishap @ 17

Seversky: The reason we believe in historical events is because the people who lived in that time found a way to record them for posterity and we believe their testimony. It has nothing to do with reason by induction. We take the people who lived during that time at their word, which is exactly the argument Lewis is making in this essay.

Granted we use personal testimony as evidence of past events but are we limited to it? As I see it, there are two problems with personal testimony. The first is that we have experimental evidence that eyewitness accounts are unreliable. The second is that human beings have only been writing down their accounts for a few thousand years. That leaves an awful lot of history where we have to look for other types of data from which we can infer tentative explanations of what might have happened. That is why the Sherlock Homes quote seemed apposite. His emphasis on observation and deduction - as well as giving due consideration to the testimony of witnesses, which he does - is a model for how we should approach any investigation of the past. Seversky

I missed correcting an error: The sentence that begins with "Snoke then develops a model" should read, "Lynch accepts a basic model adopted by Behe and Snoke". Paul Giem

Khan, Since you (#22) recommended that we read Michael Lynch's article in Protein Science, "Simple evolutionary pathways to complex proteins", I decided to review it carefully. First, the claim of the abstract is that

Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

So I would expect the article to give supporting evidence for that assertion. Almost immediately one sees an egregious error. The claim is made that

Although an alternative mechanism for protein evolution was not provided, the authors are leading proponents of the idea that some sort of external force, unknown to today’s scientists, is necessary to explain the complexities of the natural world [Darwin's Black Box is referenced].

Intelligent design is unknown to today's scientists? What does this guy think was the cause of insulin-producing yeast? Or the organisms that produce t-PA, or rice with the ability to produce Vitamin A, or any number of other genetically modified organisms? This is either stupidity (that was approved by peers), or deliberate blindness. One can, if one wants, claim that no intelligence existed before or during the time that the fossil record was being laid down, but that is a different kind of claim. The paper then claims that "a fundamental flaw" in the argument of Behe and Snoke is that

Contrary to the principles espoused by Darwin, that is, that evolution generally proceeds via functional intermediate states, Behe and Snoke consider a situation in which the intermediate steps to a new protein are neutral and involve nonfunctional products.

It's almost like it is a crime to suggest that some biochemical pathways might be non-Darwinian. Furthermore, we are not allowed to consider difficult cases:

Moreover, given that the authors restricted their attention to one of the most difficult pathways to an adaptive product imaginable, it comes as no surprise that their efforts did not bear much fruit.

Instead, presumably we can only concentrate on the successes of Darwinism. What a way to stack the deck! Snoke then develops a model requiring two amino acid residue changes (one example would be a disulfide bond between two cysteines). This is assumed to be happening on a duplicated gene, so that the original gene can go on functioning. Lynch makes changes in the model considered by Behe and Snoke. One, starting with a single member of a population with a duplicate gene, should make Lynch's model less effective at creating new functions than that of Behe and Snoke. Another, assuming that the first mutation does not inactivate the old enzyme, makes Lynch's model much more effective. Lynch then goes on to say,

It is difficult to pinpoint the source of the difference between the results of Behe and Snoke and those contained herein

You use a different model, and get different results! Simply amazing! Who'd a thunk it? The real argument is whether the one model or the other fits a specific needed two-amino-acid change. There, Lynch's paper is quite weak. The best he can do is to argue that many single amino acid substitutions are neutral for the functioning of a specific protein. Sure, but all of them? Even if only 1% of the protein-protein interactions fit the Behe-Snoke model, that would still be a huge absolute number of protein-protein interactions and a huge problem for unguided evolution. Complaining that the pathway is non-Darwinian is just that, complaining. Who says that biology has to be Darwinian? Behe and Stokes may have been even more generous than necessary. As Lynch says,

An additional logical problem implicit in the Behe-Snoke model is how an organism producing 50% functional and 50% nonfunctional protein would avoid a reduction in fitness.

The point is, the Behe-Stokes model may be an overly optimistic estimate when one mutation will inactivate a protein and it will take two such mutations to allow a new function, for the reason Lynch gave. I had to chuckle upon reading this:

That is, the upper limit to N is probably higher than the 10^9 used in this study. [exponential modified]

I'd have to agree for E. coli, but for humans?, I mean really. Even for chimps and gorillas, I doubt that populations greater than 1 million have existed for most of history, and for that matter, most of prehistory. It has only been in the very recent past that the human population has crossed 1 billion. The final sentence is rich:

Thus, it is clear that conventional population-genetic principles embedded within a Darwinian framework of descent with modification are fully adequate to explain the origin of complex protein functions.

This comes as close to fact-free science as one can get. There is no attempt to connect any specific function containing two amino acids to his model rather than that of Behe and Snokes. One could fault Behe and Snokes for also not specifically connecting their model to a particular protein active site (for example, a binding site). But given that most protein-protein binding sites require multiple residues to match on both sides, it seems that Behe and Snokes actually underestimate the average difficulty of creating a new protein interaction. These comments were written before looking at the critique of Behe and Snokes. Their points are also valid (and some of them match mine). You call that nailing ID? Paul Giem

gpuccio, what exactly do you mean that their response was "clear enough"? do you think their paper has any relevance to evolutionary theory? Jerry asked for any examples of ID being "nailed" in the literature. I thought that was a pretty clear example. Behe and SNoke's model has so many incorrect assumptions that it is irrelevant to evolutionary theory- for example, although they claim to be critiquing classical Darwinian models of evolution, they do not use Darwinian processes (selection on slightly beneficial mutations accumulating over time) in the model. I hope to hear a response from Jerry. does this, a clear refutation of a peer-reviewed paper by one of the leading figures in ID, count as ID being "nailed"? Khan

Khan: I think Behe's answer is clear enough. And I would remind that all that discussion is about models implying a two-residue adaptation! I have recently read in a darwinist site an unilateral critic by someone to my affirmations about uniform distribution in the search space of proteins. This unilateral critic, of whom I was naturally not aware until by chance I read his post following, for other reasons, a link from here, argued that I was wrong in assuming an uniform, or quasi uniform, distribution, because an evolutionary search does not work that way, but works with what already exists, and the sequences near an existing functional protein are extremely likely, while most other sequences have amost zero probability to occur. That argument really susprised me, because it is so true that it is almost trivial. I think we may happily agree that, if we start mutating an existing protein, it is easier to obtain another functional protein which differs only by two aminoacids (see above models) than one which is completely different. Does that make sense? It certainly makes sense, even if, as shown above, even two aminoacids can be quite a challenge. Let's remember that the same Behe, later, in his TEOE, has put at two aminoacids the apparent limit for a random evolutionary step, and that only in very fast replicating beings. But that's another story... Our story here is instead about what does not make sense at all. What does not make sense is that the proteins we observe in nature are very different one from the other. Sometimes completely different. So, according to my darwinist critic, how did they arise through evolutionary searches which "work with what is already there"? I assume a quasi uniform distribution for the search space for two important reasons: 1) It is perfectly reasonable from what we know of random genetic mutations. 2) The proteins we do know (and we know a lot of them) are really interspersed in the search space, in myriads of different and distant "islands" of functionality. You don't have to take my word for that. It's not an abstract and mathematical argument. We know protein sequences. Just look at them. Go, for example, to the SCOP site, and just look at the hyerarchical classification o protein structures: classes (7), folds (1086), superfamilies (1777), families (3464). Then, spend a little time, as I have done, taking a couple of random different proteins from two different classes, or even from the same superfamily, and go to the BLAST site and try to blast them one against the other, and see how much "similarity" you find: you will probably find none. And if you BLAST a single protein against all those known, you will probably find similarities only with proteins of the same kind, if not with the same protein in different species. Sometimes, partial similarities are due to common doamins for common functions, but even that leaves anyway enormous differences in term of aminoacid sequence. So, I appreciate the discussion about possible microevolutionary mutations of two aminoacids, but please, let's remember that we have thousands and thousands of known different functional proteins. That's what we need to explain, not just one existing protein acquiring a single disulfide bond between two cysteines. In other words, the problem is to explain the whole biological information (let's call it macroevolution, although I don't like the term very much), and not to defend a small (and very dangerous, anyway) frontier of how an existing function could in theory be slightly modeled by minimal microevolutionary changes of one or two aminoacids in fast replicating organisms. gpuccio

-----"If Chesterton’s doubts were well-founded then the forensic science of detection would be impossible and Sherlock Holmes would be just one more cocaine addict." I don't think that the conclusion follows from the premise. Chesterton was simply saying that there is a limit to how much we can know about the past. He didn't say we can know nothing. If anyone was extravagant it was Doyle in his capacity to believe in almost anything except God. I suspect that he was offended by Chesterton's apt quote: "If a man will not believe in God, the danger is not that he will believe in nothing, but that he will believe in anything." Clearly, Doyle fell into that camp, and I suspect that his comments reflected a reaction against that inconvenient truth. StephenB

Jerry, Here's one, responding to Behe's Protein Science paper: http://www.proteinscience.org/cgi/content/abstract/14/9/2217 Behe responded to it: http://www.proteinscience.org/cgi/content/full/14/9/2226 Khan

Noted Scholar, I suggest you summarize the articles that have nailed ID so we can debate the substance of them or to use a religious expression, "speak now or forever hold your peace." jerry

"whereas I doubt that you would admit that ID has been repeatedly nailed by all kinds of similar publications. So the distinction is: Something you happen not to like was “nailed.”" When has ID ever been "nailed?" All I have seen is distortions of ID and conflation of it with creationism. I have never seen an honest article about ID anywhere in the scientific press, so "nailed", I doubt it. jerry

If Chesterton’s doubts were well-founded then the forensic science of detection would be impossible and Sherlock Holmes would be just one more cocaine addict. Heaven forbid it should turn out that Holmes was just fictional character or something :-) tribune7

Seversky: Your approach is balanced enough, and I do believe that truth is someway in the middle, somewhere between Doyle and Chesterton (or, if we want, Lewis). As we cannot look for complete truth in scientific theories, so we should not hope to find it in literary authors (who are, however, much more fun than scientific theories). Although I have really loved Holmes and felt amazed at his deductions, I have always known that they were mostly artificial, and that if I had really tried to deduct in advance who was coming next through the door, I would have failed miserably. And I have spent some very good time with Father Brown, always aware that those fascinating metaphors about good and evil were sometimes a little too bold and self-conscious. Regarding History, I certainly believe that there was a Battle of Gettysburg, and in my most optimistic moments I am also convinced that there was a great flowering of culture in classical Greece (although ancient Egypt already starts giving me real trouble...), but I don't share the faith and assurance which most people seem to have that we really know much about those things, or that what we know is reliable. I often think that, as it is really so difficult to agree about what really happened last year, the only reason we feel that we understand ancient History is because, thanks probably to God's grace, we know too little about it. The same is probably true about biology, and scientific knowledge in general. Up to now, we really knew too little. But now we are starting to understand "a little bit more". And, as another author I very much love has written, a little knowledge is a very dangerous thing. gpuccio

Seversky: The reason we believe in historical events is because the people who lived in that time found a way to record them for posterity and we believe their testimony. It has nothing to do with reason by induction. We take the people who lived during that time at their word, which is exactly the argument Lewis is making in this essay. tragicmishap

(Off-topic) I started reading another essay in that book called "Modern Theology and Biblical Criticism" and ran across this tidbit: "Now let us suppose that the first hypothesis has a probability of 90 percent. Let us assume that the second hypothesis also has a probability of 90 percent. But the two together don't still have 90 per cent.[sic], for the second comes in only on the assumption of the first. You have not A plus B; you have a complex AB. And the mathematicians tell me that AB has only an 81 per cent. probability. I'm not good enough at arithmetic to work it out, but you see that if, in a complex reconstruction, you go on thus superinducing hypothesis on hypothesis, you will in the end get a complex in which, though each hypothesis by itself has in a sense a high probability, the whole has almost none." tragicmishap

That is from an essay called "The Funeral of a Great Myth" from the collection "Christian Reflections". tragicmishap

"Foolish stories about cave men won’t help. Few cave men lived to an age where late life diseases even become an issue." ROFL! Oh really? LOL! That's just...wow. Denyse I really think you should read something else for awhile and clear your head. Clive I will join you with the quoting. "It was all (on a certain level) nonsense: but a man would be a dull dog if he could not feel the thrill and charm of it. For my own part, though I believe it no longer, I shall always enjoy it as I enjoy other myths. I shall keep my Cave-Man where I keep Balder and Helen and the Argonauts: and there often re-visit him." -C.S. Lewis tragicmishap

In answer to the quote from Chesterton, consider this from Arthur Conan Doyle: "Sherlock Holmes closed his eyes and placed his elbows upon the arms of his chair, with his finger-tips together. "The ideal reasoner," he remarked, "would, when he had once been shown a single fact in all its bearings, deduce from it not only all the chain of events which led up to it but also all the results which would follow from it. As Cuvier could correctly describe a whole animal by the contemplation of a single bone, so the observer who has thoroughly understood one link in a series of incidents should be able to accurately state all the other ones, both before and after. We have not yet grasped the results which the reason alone can attain to. Problems may be solved in the study which have baffled all those who have sought a solution by the aid of their senses. To carry the art, however, to its highest pitch, it is necessary that the reasoner should be able to utilize all the facts which have come to his knowledge; and this in itself implies, as you will readily see, a possession of all knowledge, which, even in these days of free education and encyclopaedias, is a somewhat rare accomplishment. It is not so impossible, however, that a man should possess all knowledge which is likely to be useful to him in his work, and this I have endeavored in my case to do." Sherlock Holmes, in "The Five Orange Pips" If Chesterton's doubts were well-founded then the forensic science of detection would be impossible and Sherlock Holmes would be just one more cocaine addict. More than that, whole fields of research which investigate events far distant in space and time would be so unreliable as to be worthless. But is such pessimism justified? How many here doubt that there was a First World War or a Battle of Gettysburg during the Civil War or a Battle of Yorktown during the War of Independence or Christian crusades to the Holy Land or a Roman Empire or a great flowering of culture in classical Greece or a great civilization in ancient Egypt and so on? But how many here witnessed any of those events in person? How far back in time does an event have to be before we decide it did not happen? We now know that we live on a small, rocky planet orbiting an unremarkable yellow star which is just one of a congregation of billions of such bodies that comprise our galaxy which, in turn, is one of billions of galaxies strung out through space as far as the telescope can see. Or is that all worthless speculation and are all the stars just lights embedded in a crystal sphere? While there is debate about how far pure reason can carry us toward a complete explanation of the world, is there any doubt that inference from slender and fragmentary data has shed light on events far distant in space and time? There is nothing wrong with speculation, be it about the nature of God or an intelligent designer or the origins of the Universe or how the mind evolved. The scientist's favorite philosopher, Karl Popper, urged them to be bold in their conjectures. All we need to remember is that we should not place the same confidence in unverifiable speculation or unverified hypotheses as we do in explanations that have withstood repeated and extended testing. Seversky

Merry Christmas to everyone here as well! You guys are all awesome! Domoman

Thank you bb. Merry Christmas to all, especially the lurkers, for whom this blog mainly exists. Barry Arrington

Off topic....Merry Christmas to everyone here at UD. Thanks for all you do. I daily look forward to your blog posts. bb

And will you ripple your brawny muscles at Kant as well, Noted Scholar, when he says that the study of origins lies outside the realm of science because origins cannot be observed? Would it be too much to ask you to descend from Olympus and demonstrate to us benighted souls at UD that you understand the historical conflict between theory and empirical science? Is evolutionary psychology science or theory? Does it actually demonstrate any tangible knowledge of nature—for as you know, “science” means knowledge—or is it pure speculation? You want us to call it a “soft” science. Is this because you are soft-hearted, a kindly professor with twinkling eyes, exhibiting a magisterial tolerance of all manner of academic tomfoolery, with the exception of intelligent design? Or are there darker forces at work in your magnanimity? allanius

Clive: Thank you again for the new Chesterton quote. I was just thinking, what would Chesternon have thought of OOL theories? I really would like to apply that back-yard concept to the primordial soup of the RNA world... notedscholar: I understand you are a scholar, and a noted one, but aren't you a little too unsmiling? Denyse has written many times, and with reason and passion, about the evident abuses of evolutionary psychology: why shouldn't she feel some satisfaction when it is finally partially recognized that such a discipline is mainly bogus thinking? As Clive suggested, let's say that it was nailed via scientific methods. And Denyse was very happy of that, like me and many others. Yes, we are nasty people here at UD, as recently discussed! :-) Regarding your affirmation that "ID has been repeatedly nailed by all kinds of similar publications", I was going to counter it, but I suddenly realized that, thanks probably to your accurate choice of words, it is perfectly true: ID has certainly been repeatedly nailed by all kinds of similar publications. But without any good motive, least of all "via scientific methods"... gpuccio

What if evolutionary biologists were terrible story tellers? What if their powers of imagination were totally lacking? I think the overall explanation would suffer terribly. Clive Hayden

Anyway, it’s well-known that evolutionary psychology is not well-respected by those in the natural sciences.

What's interesting to me about this statement is that in the formulation of their just so stories, evolutionary psychologists often employ the same method as evolutionary biologists (the imagination method). In fact, some of the most popular atheist biologists and scientist make fairly frequent use of their imagination to develop evolutionary psychology just so stories when they're not busy invoking their imaginations in their chosen field. I reference them as 'atheists,' because they make such a big deal out of it. TCS

It ( the article) means absolutely nothing. Natural selection is the core of Darwinism. When a “just so story” is criticized, it is not the concept of adaptational just so stories that is under attack, but only that particular story. The stories that are rejected today in Scientific American will be replaced with “better” stories tomorrow. There is no demise of evolutionary psychology, it’s only beginning. OLDMAN

Well, it was nailed, (in and of itself that point is perfectly true), and the question of motive you're implying from O'Leary for simply pointing out that fact, is irrelevant and erroneous. "Nailed" things can be "nailed" via scientific critiques. There is no need to invoke the motive game here NS. Clive Hayden

A very odd post on a blog that JUST promoted with approval Justin Barret's work on the, yes, evolutionary psychology of religion. Anyway, it's well-known that evolutionary psychology is not well-respected by those in the natural sciences. It operates mostly by conjecture within a good system. The article you cite is evidence for this. Note that many psychology classes at universities in fact begin with saying why psychology is a science. The reason they have to do this is because the field is so controversial, occupying a netherworld between "soft" and "hard" science. And in any case it doesn't get "nailed" in the articles you mention. It gets critiqued via scientific methods, as is expected and proper. Interesting that this counts as "nailed," whereas I doubt that you would admit that ID has been repeatedly nailed by all kinds of similar publications. So the distinction is: Something you happen not to like was "nailed." Nothing new here. NS notedscholar

The chapter quoted above from Chesterton is called "Professors and Prehistoric Men" from The Everlasting Man. http://www.cse.dmu.ac.uk/~mward/gkc/books/everlasting_man.html#chap-I-ii Clive Hayden

G.K. Chesterton, from The Everlasting Man: "Science is weak about these prehistoric things in a way that has hardly been noticed. The science whose modern marvels we all admire succeeds by incessantly adding to its data. In all practical inventions, in most natural discoveries, it can always increase evidence by experiment. But it cannot experiment in making men; or even in watching to see what the first men make. An inventor can advance step by step in the construction of an aeroplane, even if he is only experimenting with sticks and scraps of metal in his own back-yard. But he cannot watch the Missing Link evolving in his own back-yard. If he has made a mistake in his calculations, the aeroplane will correct it by crashing to the ground. But if he has made a mistake about the arboreal habitat of his ancestor, he cannot see his arboreal ancestor falling off the tree. He cannot keep a cave-man like a cat in the back-yard and watch him to see whether he does really practice cannibalism or carry off his mate on the principles of marriage by capture. He cannot keep a tribe of primitive men like a pack of hounds and notice how far they are influenced by the herd instinct. If he sees a particular bird behave in a particular way, he can get other birds and see if they behave in that way; but if he finds a skull, or the scrap of a skull, in the hollow of a hill, he cannot multiply it into a vision of the valley of dry bones. In dealing with a past that has almost entirely perished, he can only go by evidence and not by experiment. And there is hardly enough evidence to be even evidential. Thus while most science moves in a sort of curve, being constantly corrected by new evidence, this science flies off into space in a straight line uncorrected by anything. But the habit of forming conclusions, as they can really be formed in more fruitful fields, is so fixed in the scientific mind that it cannot resist talking like this. It talks about the idea suggested by one scrap of bone as if it were something like the aeroplane which is constructed at last out of whole scrapheaps of scraps of metal. The trouble with the professor of the prehistoric is that he cannot scrap his scrap. The marvellous and triumphant aeroplane is made out of a hundred mistakes. The student of origins can only make one mistake and stick to it." rip was right, I like quoting Chesterton and Lewis, but that doesn't make me "smarmy" or "extremely ill." On the contrary, I think it makes me quite well, it certainly puts silly things like evolutionary psychology in the correct perspective, or what might be called the "reality-based" perspective. :) Clive Hayden