BarryA Responds to His Critics at Panda’s Thumb

Charlie, I forgot about this thread completely, as I was participating in a very similar conversation in a different thread: https://uncommondesc.wpengine.com/index.php/archives/1447 If you're still interested in continuing this converstation, please make a post in either thread stating so. I'll check in later and see what's up. One note, you wrote: "Aside - how is a scientific model testable if it does not include the necessary parameters, variables, calculations, etc.?" If a model makes a prediction, it doesn't need to include all the parameters, variables, and calculations to be testable and therefore scientific. It's important to note that to qualify as a prediction, the prediction must be made BEFORE the evidence is discovered. For example, in the transposon model, the prediction was made that the RAG genes once contained transposase activity. This prediction was made several years before transposase activity was discovered in the existing RAG genes. So here we have a model that made a prediction (that the RAG genes once had transposase activity), and the verification of that prediction (by discovering transposase activity in the existing RAG genes). I keep forgetting one important part of the scientific method, observation. Usually, most hypotheses are generated by first making an observation of the natural world. The hypothesis is an attempt to explain that observation (or a series of observations). A scientific hypothesis will make testable predictions, and by validating those predictions, the hypothesis is supported. So in the transposon model, first it was observed that the recombination signal sequences (RSSs) had similarity to sequences of transposons. Based on a few other observations about the mechanism of recombination, the hypothesis that the recombination system evolved from a transposon was made. This led to multiple predictions, one of which was that the RAG genes were once transposases. Compare this to ID. IDists observed that many biological systems are extremely complex. They also observe that intelligent agents are capable of producing systems of great complexity. So they form the hypothesis that biological systems are a result of intelligent agents. So how do they test this hypothesis? What predictions flow logically from this hypothesis? minlay

Minlay: That if it wasn’t POSSIBLE for IC systems to evolve, then they must have originated by ID. That is still false. IC is NOT anti-evolution- IC is anti- blind watchmaker. Until you grasp that simple concept you will never grasp the debate. Minlay: How can ID be a better alternative is there’s no empirical evidence for the creation of the immune system by ID? And again if EVERY time we observe functioning systems which exhibit..."the ordering of separate components to achieve an identifiable function that depends sharply on the components" (DBB) and we know the cause it is ALWAYS via intelligent agency. Always. 100%. Therefore to claim any system which exhibit "...the ordering of separate components to achieve an identifiable function that depends sharply on the components", arose via some blind watchmaker-type process is indeed an extra-ordinary claim. Joseph

Not that I make any pretense that anyone would be waiting with bated breath for my grand pronouncements but I will be out of town for a week starting late this morning. Just so you know I am not hiding from any forthcoming challenges. Charlie

I believe that Darwinism is a congenital conditon closely linked to if not identical with political liberalism. There is no question that the vast majority of university professors are left-leaning ethical and moral relativists. Good point, John. There are a lot of things that the academy accepts or embrances with little or no evidence, yet it persecutes those who express skepticism -- even mild skeptism -- of evolution. tribune7

Matt, I'm told I am duplicating my comment, so it must be caught by the spam-filter. I'll try again tomorrow if it doesn't show up. Charlie

Matt, I was not in any chatrooms/boards/blogs before Uncommon Descent. I don't know what people discussed then but from reading Behe I know he has been badly misunderstood and misrepresented. We have seen it continuing in these threads, ten years after the publication of Black Box. Was Behe in any of these rooms focusing on the logical impasse to the exclusion of the empirical argument? You said:

However, all of this is besides the point

It's central to my point. Perhaps my only real point - Rothschild pulled a literature bluff, as these threads have contended, and did so knowing that it was a bluff that did not address Behe's project, either today, last year, or ten years ago.

Unfortunately, Charlie, I still disagree. In DBB, he still talks about “detailed” and “testable”, but doesn’t specify what he means. By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system, which the transposon model is.

I think if you look again you will find all of the criteria covered the first time out, even in the few quotes I mustered scanning my copy of DBB. Here's the DBB info again (I think I've put the bolds where I had them before)::

But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 (edit - I think I meant 176) No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion…. No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185

Here are the parts I bolded, extracted:

#1address in molecular detail the question of how immune systems originated #2detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book #3 - detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion #4detailed routes by which complex biochemical structures might have developed #5There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations

Matt said:

By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system

Behe's intial requirements included both #1 - the origin of immune system, as well as the #2 - building of the system. Explained in # 2 - scientific fashion: implying the scientific method - discovery, demonstration, observation, testing, hypothesizing, calculating, etc. Aside - how is a scientific model testable if it does not include the necessary parameters, variables, calculations, etc.? Matt said:

In DBB, Behe did not request a “mutation-by-mutation” account.

But he did. He asked for the production in a #3 - gradual, step-by-step (mutation-by-mutation) #3 - Darwinian fashion (RM and NS). Behe responded to Andrea:

What part of “numerous, successive, slight” is so hard to understand?

He asked as well for #4 - detailed routes (Not a beginning, an end, and a stop-over here or there, but the route). #5 - supported by pertinent experiments and calculations. We are talking a Darwinian process here. Everyone knows what that entails: gradual, step-by-step change by natural, heritable variation (mutations) acted upon by natural selection. How does a Darwinian model (Behe's continued criterion) not include descriptions of these? If Darwinian processes rely upon natural selection a model must show how the stops are selectable. If a Darwinian process requires that a change become fixed in a population a model must show how that could happen. He asked for the calculations from the start. What would be calculable but tinescales and population sizes? Nope. Behe never moved his goal posts and the literature presented to him did not address his question. (Here's hoping my formatting is accurate .... submit comment...) Charlie

Unfortunately, Charlie, I still disagree. In DBB, he still talks about "detailed" and "testable", but doesn't specify what he means. By the standards which you boldfaced in his early work, I interpretted that to mean that all that would be required was a detailed and testable model for the origin of the V(D)J recombination system, which the transposon model is. However, when that information was presented to Behe in Andrea's Panda's Thumb post last year, Behe's response was: "Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways...” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin's Black Box (page 176)I implied that many small details would be necessary for a real Darwinian explanation)nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand? "And not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more. Alternatively, Darwinists could present a series of experiments showing that RM/NS is capable of building a system of the complexity of the adaptive immune system." In DBB, Behe did not request a "mutation-by-mutation" account. This is not what is implied when you hear the words "detailed" and "testable". I'm not sure if you were in chatrooms in the late 90's or early 2000's, but the discussions were all focused on the logical argument of IC. Whether or not it was even possible for IC systems to evolve. The empirical argument came along later. However, all of this is besides the point. What significance is it that Behe demands a mutation-by-mutation account? What does it mean that biologists cannot meet that demand? Would you agree that the research has progressed significantly in the past few years? In DBB, Behe tried to use the logical argument of IC to support his claim that ID was a better option. That if it wasn't POSSIBLE for IC systems to evolve, then they must have originated by ID. However, you can't make that leap logically if your argument against the evolvability of IC systems is not that it's impossible, but just that it hasn't been proven yet. How can ID be a better alternative is there's no empirical evidence for the creation of the immune system by ID? minlay

I believe that Darwinism is a congenital conditon closely linked to if not identical with political liberalism. There is no question that the vast majority of university professors are left-leaning ethical and moral relativists. They do not believe in absolute truths of any sort. They are incapable of taking a firm stand and prefer to remain noncommital at any cost. They are also great joiners and tend to spontaneously aggregate in enclaves or "groupthinks." Thomas Henry Huxley and his grandson Julian Huxley are perfect examples of this condition. They, like all of us, are victims of their fate and, as near as I am able to ascertain, there is absolutely nothing that can be done for them. By way of contrast it is difficult to imagine more scholars more independent than Leo Berg or Richard B. Goldschmnidt or Robert Broom or Pierre Grasse or Otto Schindewolf or the greatest skeptic of them all, William Bateson. They stood firm and paved the way for the inevitable demise of the Darwinian myth. I am delighted to identify with them. "A dwarf standing on the shoulders of a giant may see farther than a giant himself." Robert Burton I am that dwarf. "No sadder proof can be given by a man of his own littleness than disbelief in great men." Thomas Carlyle "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison

NickM: Lampreys have a partial system and it functions. Lampreys have a complete system. True if compared with a human immune system the lamprey system would appear to be partial. If you are using the lamprey system to get a human system you have quite a bit of explaining to do- first start with lampreys and demonstrate how they arose via some blind watchmaker-type process. NickM: Therefore Behe was wrong to say that the system had to arise all at once. How did the lamprey immune system arise? And also in the ID scenario IC systems do NOT have to arise all at once. The selection process is different. NickM: It’s very simple. And you are simply wrong. MInlay: I don’t believe that’s correct. Behe claims that for an IC system to evolve, all the core parts must come together in one step. THat is "to evolve via some blind watchmaker-type process"- please keep that in mind. Minlay: The entire point of IC is that each system is [b]irreducible[/b]. If each system can be broken down into smaller subsystems, then they’re reducible and evolvable. It all depends on the function(s) of the subsystems: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions: Joseph

Excellent points, Charlie. What we have learned in this discussion children is that Behe does depend on Scientific American and the New York Times to keep up with things and has been consistent in his thinking since DBB in 1996. tribune7

*knew* By the way, I don't know how I drew that guy with the glasses up there, I was trying to cite chapter 8 of Darwin's Black Box. I need some typing skills. Charlie

So, once again, the papers offered in Dover did not address Behe's project. Reject his standards as you will, but note they have been the same for 10 years now, and Rothschild new what they were when he offered his irrelevant literature. Charlie

Matt Inlay, At this point I can only say I think we fundamentally disagree. Nevertheless, I thank you for taking the time to read what we've written and to visit and offer your expertise and comments for the benefit and enlightenment of our readers. regards, Salvador scordova

Matt, I said Behe didn't move the goalposts, and you repeat that he did. Well, an element of conflict in any discussion's a very good thing. It means everybody is taking part and nobody's left out. http://en.wikiquote.org/wiki/Harvey The goalposts in 1996 (as referenced above):

But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion…. No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185

The goalposts in 1999: Science And Evidence For Design In The Universe: The Proceedings Of The Wethersfield Institute 2000 Essay: Design At The Foundation Of LIfe 1999

For our purposes, however, the important point to keep in mind is that comparing sequences does not allow one to conclude how complex molecular machines, such as the cilium or flagellum, could have arisen step by Darwinian step. (My emphasis. Dadrwinian steps = random mutation and natural selection, numerous, successive, slight) In order to do that you have to build models, do experiments and so forth. It turns out that virtually none of the papers in the Journal of Molecular Evolution over the past decade has done such experimental work or model building.(ref. DBB, chapter 8)... Again, I hasten to say that sequence analysis is interesting and can tell us many things, but sequnce analysis alone cannot say how complex molecular machines could have been produced in a Darwinian fashion. ... page 125 The few that do consider the problems of Darwinian evolution are invariably too broad to test rigorously. page 126 The goalposts in 2000:

In the context of my book it is easy to realize that I meant there has been little work on the details of the evolution of irreducibly complex biochemical systems by Darwinian means. I had clearly noted that of course a large amount of work in many books and journals was done under the general topic of "molecular evolution," but that, overwhelmingly, it was either limited to comparing sequences (which, again, does not concern the mechanism of evolution) or did not propose sufficiently detailed routes to justify a Darwinian conclusion. Such books simply don't address the problems I raise. Molecular Evolution by Wen-Hsiung Li (Li 1997) is a fine textbook which does an admirable job of explicating current knowledge of how genes change with time. That knowledge, however, does not include how specific, irreducibly-complex biochemical systems were built. As I explained in Darwin's Black Box , comparing sequences is interesting but cannot explain how molecular machines arose. Li's book also contains chapters on the mechanisms (such as gene duplication, domain shuffling, and concerted evolution of multigene families) that are thought to be involved in evolution at the molecular level. Again, however, no specific system is justified in Darwinian terms.

http://www.arn.org/docs/behe/mb_evolutionaryliterature.htm In 2005:

In order to show that Darwin’s mechanism of RM/NS is responsible for either a new structure or a new function for an old structure, one has to show, as Darwin insisted, that there is a pathway leading to the structure by “numerous, successive, slight modifications”, each of which is an improvement for the organism. That is a much, much more difficult task than simply showing similarities between features. ... Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways...” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin's Black Box (page 176)I implied that many small details would be necessary for a real Darwinian explanation)nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand?

http://www.idthefuture.com/2005/05/calvin_and_hobbes_are_alive_and_well_in_.html The goalposts in Dover:

Well, those books do seem to have the titles that you said, and I’m sure they have then chapters in them that you mention as well, but again I am quite skeptical, although I haven’t read them, that in fact they present detailed rigorous models for the evolution of the immune system by random mutation and natural selection

(Darwinian, well, neo-Darwinaina, terms). Charlie

By Salvador, "A very good example of this is in the evolutionary pathways of Eukaryotes and Prokaryotes. What seemed an immutable hypothesis before, upon further careful scrutiny begins to fall appart. Behe’s standards have scientific value because, what if, upon further scrutiny the transposon hypothesis collapses. It does no service to the cause of science to be leaving stones unturned which may legitimately sink a hypothesis." Unfortnately, Behe's standards are meaningless because they can never be fulfilled for any biological system. Behe hasn't presented evidence against the transposon model per se, if he could do that it would be valuable. All Behe has done is say the evidence for the transposon model isn't good enough. That isn't very useful to the scientific community. minlay

Hi Charlie, The problem is that Behe's statements were more vague in DBB than they have been recently. In DBB, the implication was that "detailed" and "testable" meant what other scientists thought they meant, that is, providing details and can be tested. After all, DBB was written for a general audience, and so there was a lot of interpretation required in his writing. That requirement has been met in spades. However, once this data was presented to Behe, he then changed his requirements, adding in the stricter requirements. Maybe you disagree with the interpretation, but since Behe has still never written a formal definition of IC, this entire debate has had to rely on intepretations. Try to remember, irreducible complexity was presented as a logical argument in DBB. Now it has shifted entirely to an empirical one. "You admit that the articles and books heaped upon him did not answer what he asked, so you admit it was a literature bluff." Absolutely not. The literature provides what the scientific community considers to be the best answer to the origin of the immune system. It was not intended to convince Behe that the immune system evolved, because he moved the goalposts so far away that NO data could ever solve the issue to his satisfaction. The presentation of the 58 articles was meant to demonstrate to the judge and the audience just how far out of touch with reality Behe's statements are. And as evidenced by the judge's decision, it succeeded. Judge Jones, like the rest of the scientific community, sees that Behe has placed an unreasonable burden of proof on evolution. If you don't think it's unreasonable, then try applying those same standards to ID. minlay

Matt, Thanks for your patient and polite responses (and admissions). But in your last comment you said that Behe has moved the goalposts. When did he do this? In Darwin's Black Box I find the goalposts right where he showed them to be in Dover.

A search of the immunological literature shows ongoing work in comparative immunology (the study of immune systems from various species). But that work, valuable though it is, does not address in molecular detail the question of how immune systems originated. page 136 No one has ever explained in detailed, scientific fashion how mutation and natural selection could build the complex, intricate structures discussed in this book. In fact, none of the papers published in JME over the entire course of its life as a journal has ever proposed a detailed model by which a complex biochemical system might have been produced in a gradual. step-by-step Darwinian fashion.... To take up the questions raised in this book, one would need to find papers with titles such as "Twelve Intermediate Steps Leading to the Bacterial Photosynthetic Reaction Center", "A Proto-Cilium Could Generate a Power Stroke Sufficient to Turn a Cell by Ten Degrees", "Intermediates in Adenosine Biosynthesis Effectively Mimic Adenosine Itself in RNA Function", and "A Primitive Clot Made of Randomly Aligned Fibers Would Block Circulation in Veins Smaller tha. 0.3 Millimeters". But the papers are missing. Nothing remotely like this has been published. page 176 No scientific journal will publish patently incoherent papers, so no studies asking detailed questions of molecular evolution are to be found. page 177 No papers were published in PNAS that proposed detailed routes by which complex biochemical structures might have developed. Surveys of other biochemical journals shows the same result: sequences upon sequences, but no explanations. page 178 There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occured. There are assertions that such evolution occured, but absolutely none are supported by pertinent experiments or calculations. page 185

So, you might want to say that Behe is asking the impossible, but he has always asked the same thing. The goalposts in Dover are where they have always been, and Behe's opponents should have known where they were. You admit that the articles and books heaped upon him did not answer what he asked, so you admit it was a literature bluff. Charlie

Matt Inlay: I agree with the first part, but not the second.

I appreciate your very direct response, Matt. Futhermore thank you for visiting. However, I must protest, that if one is pretending Behe's claim was refuted, one must fairly represent what his claim was. Whether the standards of proof are disagreeable with you and the rest of Behe's critics is a separate matter. However, in the debates of this variety, I would expect that a person's ideas are represented accurately, and I'm afraid, you, Andrea, and Nick have not been doing that. Regarding detailed models, granted we may not have or ever have historical facts, but I don't think it's too much to ask to give parameters for the amounts of population resources needed and the kinds of selection pressures which must exist, the mutation rates involved, and the limits to collateral damage to other parts of the organism given those parameters. The question again was not just phylogeny or availability of parts but the pathway to their integration. One very substantial problem is the viability of the organism in transition from innate immunity to combinatorial immunity. The problem that the enitire population is dead before this transition occurs is substantial. We know what happens to immunity deficient individuals. These details have been glossed over, and it is in the study of these details that a hypothesis that once seemed immutable is overturned. A very good example of this is in the evolutionary pathways of Eukaryotes and Prokaryotes. What seemed an immutable hypothesis before, upon further careful scrutiny begins to fall appart. Behe's standards have scientific value because, what if, upon further scrutiny the transposon hypothesis collapses. It does no service to the cause of science to be leaving stones unturned which may legitimately sink a hypothesis. Granted, I'm very biased, but I can tell you of one immuno-pharmacologist who jumped ship because all that was offered were speculations such as those offered in those papers. She was recently featured here: Caroline Crocker. She was very friendly to the Darwinian story all of her life, but at somepoint, the explanations become horribly wanting, and, as she has suggest, isn't "we don't know" a better representation of the state of affairs than bold proclamations misleading the public that these miniscule predictions come even close really solving the most glaring issues? Any way, thank you for visiting. Salvador scordova

By Charlie: "So the question is, is the lamprey immune system a subset of, say, man’s, or is it a different system. Nobody ever said there couldn’t be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap." This type of reducibility I'm not discussing here. The kind of reducibility I'm discussing would be a mousetrap missing a part that performs a function other than trapping mice. I'm talking about a subset of an IC system that is functional. Since an IC system, by definition, cannot be simplified and retain it's existing function, the functions change as the number of parts are reduced. As for the lamprey immune system, the adaptive part is very different from the jawed vertebrate adaptive immune system. They don't possess any of the components of the V(D)J recombination system, at least to my knowledge. It's not a good example of the ABCD vs. ABC systems I was thinking of. minlay

By Salvador: "I’ll pose the same question to you that I did to, Nick. Do you recognize that Behe’s conception of “detatailed and testable” is not the same as your conception of “detailed and testable”, hence your suggestions of Behe being refuted are Equivocations not refutations." I agree with the first part, but not the second. Behe has arbitrarily created definitions of detailed and testable that no other scientist would use. The 58 articles provide an immense number of details on the how the system evolved, and each article tests the transposon model. So for Behe to claim that the articles are not detailed and testable, when they are certainly detailed and testable by mainstream science's standards, is IMO ridiculous. I think that it's Behe that's equivocating by using commonly used terms and redefining them. minlay

Hi Charlie, You wrote: "It is a logically possible route, empirical evidence of its plausibility is required." I'm not sure I understand your use of the word "required". Required for what? I would suggest that the 58 articles do address the plausibility of the transposon model, but not to the degree demanded by Behe. "He that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible(not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge." We don't yet have a step-by-step model for the entire V(D)J recombination system (it's much, much more complex than what Behe originally presented). However, we have a lot of evidence that support what we think are the first few steps, namely, the integration of a transposon into an antigen receptor gene through a transposition reaction. There is a ton of empirical evidence that supports the mechanism of mutation (transposition), and that the RAG genes were transposases (after all, they still possess the transposase activity), and that an ancestral antigen receptor gene existed to serve as the target of the transposition reaction. In terms of the selectability of such a system, I would argue that it's fairly non-controversial to propose that any mechanism that introduces diversity into an antigen receptor gene would be immediately beneficial to that organism. However, I realize that that may not satisfy the skeptics here, but there are strains of bacteria that have evolved a similar trick quite recently. "Even though you are satisified with the robustness of evolutionary theory are you admitting that the 58 titles did not do this?" It depends on how much detail you "require". Behe moved the goalposts so far back that no evidence will ever be able to satisfy those demands. Of course, that's what Behe had in mind when he moved them. The point we're all trying to make is that Behe's demands are entirely unreasonable. It is not how science proceeds. If you go by Behe's made-up standards, then I'd have to say no, the articles don't meet them. However, would you be willing to agree that the 58 articles increase the plausibility of the transposon model? minlay

Sorry for the bad edits: comment 111 should say "in response to Charlie:" comment 112, after second blockquote should be: "Behe has cut off the logical route of direct Darwinian evolution of IC. He says that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible (not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge. Charlie

Matt Inlay, I'll pose the same question to you that I did to, Nick. Do you recognize that Behe's conception of "detatailed and testable" is not the same as your conception of "detailed and testable", hence your suggestions of Behe being refuted are Equivocations not refutations. Salvador scordova

Matt,

Hi Charlie, the problem here is that Behe cannot logically claim that an IC system is irreducible if he concedes that co-option is a plausible route to evolution.

You've expanded this. It is a logically possible route, empirical evidence of its plausibility is required.

Furthermore, an empirical demonstration of the evolution of an IC system isn’t necessary to demonstrate the robustness of evolution as a theory of origins.

Behe has cut of the logical route of direct Darwinian evolution of IC. He that failing an empirical demonstration of the indirect route at least a step by step accounting of the plausible(not necessarily the historically accurate) mutations, effects and selectability would do to answer his challenge. Even though you are satisified with the robustness of evolutionary theory are you admitting that the 58 titles did not do this? Charlie

Matt,

Furthermore, if functional subsets of IC systems are discovered, then we have clear, empirical evidence that those IC systems are reducible.

in response Charlie:

So the question is, is the lamprey immune system a subset of, say, man’s, or is it a different system. Nobody ever said there couldn’t be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap.

Charlie

By Charlie, "Yes, Behe presents IC as a logical problem for such an evolution. However, he never, not from Black Box on, has denied the possibility of co-option, or indirect pathways. What he does say is that there is no empirical demonstration of such an evolution at the molecular level. Thus, it is not logically impossible, only more and more unlikely as the complexity increases, and something that is not demonstrated." Hi Charlie, the problem here is that Behe cannot logically claim that an IC system is irreducible if he concedes that co-option is a plausible route to evolution. Furthermore, if functional subsets of IC systems are discovered, then we have clear, empirical evidence that those IC systems are reducible. Furthermore, an empirical demonstration of the evolution of an IC system isn't necessary to demonstrate the robustness of evolution as a theory of origins. As I described in comment 34 of another thread: https://uncommondesc.wpengine.com/index.php/archives/1447 science progresses by forming models and testing them. Immunologists have been testing the transposon model for over 25 years now and have found a ton of evidence supporting it. Their consensus is that the transposon model is the current, best explanation for the origin of the V(D)J recombination system. If you think there's a better model out there, like ID, please present it. minlay

I am at the mercy of the moderator regarding this post, but I think dialog between adherents of not only diametrically opposed faiths but world views won't change anyone's opinion, but even worst, I don't think the Darwinians would ever consider evidence, no matter its integrity. I agree with John, and would go further: this is a waste of time. On another thread I posted on plasma cosmology. Perhaps the electrical universe point of view is considered too "out there", perhaps the more conventional plasma cosmology is more "credible" but in truth it is equally opposed. Yet despite the evidence, despite the fact of observations of what is clearly explained as the behavior of plasma, main stream scientists cling to unobservable concepts such as "dark matter", "dark energy" and twist and contort language. Sound familiar? That is all relevant to ID because despite the issue that Casey Luskin raised of testability, it won't mean a damn to your "opponents". But the leaders have an agenda. The followers obey the leaders. They will interpret black as white and white as black. And they will ostracize anyone who proposes an alternative to their cherished "Humanistic religion", as James P. Hogan calls it. They find comfort in believing there is nothing greater than the human mind, and that nothing exists outside of matter and energy, although I'm sure they have no clue what matter and energy are. Superstrings and multiverses and the observer (man) creates the universe. Does anyone else find those concepts humorous. Of course, the proponents are laughing all the way to the bank. And as Eric Lerner wrote, and he has made great progress in nuclear fusion on a shoe string budget, science has suffered and stagnated. Look at this essay about the "lawn sprinkler"; NASA personnel got indignant and defend the lawn sprinkler, despite all the contrary evidence. http://www.thunderbolts.info/tpod/2006/arch06/060210hhtornado.htm Excerpt: The explanation begins with these words: “Stellar jets are analogous to giant lawn sprinklers. Whether a sprinkler whirls, pulses or oscillates, it offers insights into how its tiny mechanism works. Likewise stellar jets, billions or trillions of miles long offer some clues to what's happening close into the star at scales of only millions of miles, which are below even Hubble's ability to resolve detail”. Those who know what a plasma discharge is might say, “if you think a lawn sprinkler offers a good analogy for the picture above, put a sprinkler in space and try it”. Any attempt to understand stellar jets across light years of space in terms of a nozzle on one end should be a career-ending embarrassment. ################################## To the contrary, anything that opposes the High Priesthood is career ending. And I think the Darwinians don't embarass easily! And so with the Darwinians. No matter how embarassing their concepts, they won't give them up, even if experiments do verify ID or anything contradicting their "faith". Here's Casey's link: http://www.evolutionnews.org/2006/01/intelligent_design_is_empirica.html So, I suggest the molecular biologists who support I.D. still do the work, keep their heads down until tenure, but have no delusions that whatever they discover and verify will ever be acceptable to the "opposition". Let judge Jones rule an end to "Global Warming" -- for his next trick. P. Phillips

Michael Behe is a fine biochemist and a decent man. To see him treated like this makes me sick to my stomach. Got that! Write that down. He once explained to me that he does not choose to engage in the ephemeral world of cyberspace. He has got better sense than I have! I do it mostly for recreation myself and for Darwinian "steer" goring. Darwinians are intellectual geldings don't you know. It is hard to believe isn't it? I love it so! "A past evolution is undeniable, a present evolution undemonstrable." John A. Davison John A. Davison

Nick Matzke, Does the lamprey have a partial version of the immune system present in 'higher' vertebrates. ie: jawed ones? Or does it have its own, simpler, yet functioning immune system? Do you think that that the system the lamprey uses evolved into the more complex one, say that of man, or do you think that the two are examples of convergent evolution? In insisting that this conversation go off-topic have you conceded the points of the OP and the related posts? Minlay, You are representing a slightly twisted version of IC. Behe does not claim that all the parts must come together at once in order for it to evolve. You are talking only about a direct Darwinian pathway. Yes, Behe presents IC as a logical problem for such an evolution. However, he never, not from Black Box on, has denied the possibility of co-option, or indirect pathways. What he does say is that there is no empirical demonstration of such an evolution at the molecular level. Thus, it is not logically impossible, only more and more unlikely as the complexity increases, and something that is not demonstrated. Is the immune system present in the lamprey ABC of the system ABCD in higher vertebrates? Or is it, perhaps, AGM, arrived at independantly of ABCD? So the question is, is the lamprey immune system a subset of, say, man's, or is it a different system. Nobody ever said there couldn't be simpler versions of a given IC system. It is certainly true that you can whack a mouse with a hammer, but that does not make the mouse trap any less IC, nor indicate that a hammer evolved into the mousetrap. Charlie

[quote]In the lamprey scenario you would have to demonstrate how that immune system arose via some blind watchmaker-type process BEFORE using that as a stool to climb to higher verts. Then to get to the higher verts you have to demontrate that blind watchmaker-type processes allowed those to “evolve” again BEFORE getting to their immune system.[/quote] I don't believe that's correct. Behe claims that for an IC system to evolve, all the core parts must come together in one step. If an IC system has a core of 4 parts (parts A, B, C, and D), all four parts would have to assemble at once, and we should not expect to find a system containing 3 of those parts. However, if we find a subsystem with parts A, B, and C, and we also find in this organism part D (either alone or as a component of another subsystem), then the evolution of the 4 part IC system is entirely feasible. It's irrelevant whether or not the subsystem composed of parts A, B, and C is IC because it still demonstrates how a 4-part IC system can evolve from a 3-part IC system. From there it's not a giant leap to envision how the 3-part could have evolved from a 2-part, and so on and so on. The entire point of IC is that each system is [b]irreducible[/b]. If each system can be broken down into smaller subsystems, then they're reducible and evolvable. minlay

Lampreys have a partial system and it functions. Therefore Behe was wrong to say that the system had to arise all at once. It's very simple. Nickm

NickM: Would someone explain to me how this squares with Behe’s claim that IC systems have to arise all at once, “because any precursor missing a part would be by definition nonfunctional”? Geez NickM, do you even understand the debate? In order for NS to act on some structure/ feature that structure/ feature has to be fully present and functioning. In the lamprey scenario you would have to demonstrate how that immune system arose via some blind watchmaker-type process BEFORE using that as a stool to climb to higher verts. Then to get to the higher verts you have to demontrate that blind watchmaker-type processes allowed those to "evolve" again BEFORE getting to their immune system. Is the lamprey immune system IC? Can we take the lamprey immune system, replace a human's immune system with it and have the human survive infections? If not then any point using that system is moot. IOW a lamprey immune system although containing less components than a human immune system does nothing to help your argument. You see NickM YOU don't get it. Without the detail Behe talks about- the SAME detail that anti-IDists require of ID- NO ONE should be able to censor ID from science classroom discussions- that is IF science is about discovering the reality to our existence. Seeing that NickM appears to be fond of transposons- Dr. Spetner discussing transposons:

The motion of these genetic elements to produce the above mutations has been found to a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of the variation for evolution were point mutations, we could say the variation is random. But if the source of the variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events.

Joseph

Tada! “presumably”, “inferred rapid appearance”, “suggested sudden”, bada bigga banga bing, just love that astronomy comparison. Voila - Immunity Big Bang! This is just one of the speculative points in the paper. This is foolish. The transposon model is exactly the model that explains the sudden emergence of the recombination system of adaptive immunity. As for the PNAS paper mentioned by MichaelJ, the key figure in the paper shows that lampreys have only 12 of the 16 components found in vertebrate immune systems -- and yet lampreys have functioning immune systems anyone. Would someone explain to me how this squares with Behe's claim that IC systems have to arise all at once, "because any precursor missing a part would be by definition nonfunctional"? PS: My chronology post still needs to be freed from the spam buffer, for whoever has the power to do that. Nickm

Hmm...

So Behe was not overwhelmed with the titles of 58 titles because he’s seen the bluffs before. A little as well on data-base searches:

Was not supposed to be in quotes above. Charlie

Behe is no stranger to literature bluffs and web searches: http://www.arn.org/docs/behe/mb_evolutionaryliterature.htm

Michael J. Behe Discovery Institute July 31, 2000 I. Summary Although several persons have cited numerous references from the scientific literature purporting to show that the problem of irreducible complexity I pointed out in Darwin's Black Box is being seriously addressed, the references show no such thing. Invariably the cited papers or books either deal with non-irreducibly complex biochemical systems, or do not deal with them in enough detail for critical evaluation. I strongly emphasize, however, that I do not prefer it that way. I would sincerely welcome much more serious, sustained research in the area of irreducible complexity. I fully expect such research would heighten awareness of the difficulties of Darwinian evolution.... A prominent claim I made in Darwin's Black Box is that, not only are irreducibly complex biochemical systems unexplained, there have been very few published attempts even to try to explain them. This contention has been vigorously disputed not so much by scientists in the relevant fields as by Darwinian enthusiasts on the Internet. Several web-savvy fans of natural selection have set up extensive, sophisticated sites that appear to receive a significant amount of notice. They influence college students, reporters, and, sometimes, academic reviewers of my book ... The Empty Box site is, I think, actually a valuable resource, containing links to many reviews, comments and other material, both critical and favorable, related to my book. One subsection of the site is entitled "Alive and Published," and contains citations to a large number of papers and books which Catalano believes belie my claim that "There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems." (Behe 1996) (p. 179) The citations were solicited on the web from anyone who had a suggestion, and then compiled by Catalano. Something, however, seems to be amiss. The assertion here that very many papers have been published clashes with statements of the reviews I quoted earlier which say, for example, that "The problems have indeed been sorely neglected." (Cavalier-Smith 1997) Would reviewers such as Jerry Coyne and Tom Cavalier-Smith--both antagonistic to my proposal of intelligent design--be unaware of the "hundreds, possibly thousands, of scientific papers that deal with this very subject"? Both claims--that the problems have been neglected and that the problems are being actively investigated--cannot be correct. Either one set of reviewers is wrong, or there is some confusion about which publications to count. Which is it? In the context of my book it is easy to realize that I meant there has been little work on the details of the evolution of irreducibly complex biochemical systems by Darwinian means. I had clearly noted that of course a large amount of work in many books and journals was done under the general topic of "molecular evolution," but that, overwhelmingly, it was either limited to comparing sequences (which, again, does not concern the mechanism of evolution) or did not propose sufficiently detailed routes to justify a Darwinian conclusion.... Such books simply don't address the problems I raise. (For instance,) Molecular Evolution by Wen-Hsiung Li (Li 1997) is a fine textbook .... (but) Since those investigators who do work in that area have not yet published a detailed Darwinian pathway in the primary literature (1), we can conclude that the answer will not be found in a more general text. ... Catalano's site lists other books that I specifically discussed in Darwin's Black Box, where I noted that, while they present mathematical models or brief general descriptions, they do not present detailed biochemical studies of specific irreducibly complex systems. (Gillespie 1991; Selander et al. 1991) There is no explanation on Catalano's web site of why he thinks they address the questions I raised. The site also points to papers with intriguing titles, but which are studies in sequence analysis, such as "Molecular evolution of the vertebrate immune system" (Hughes and Yeager 1997) and "Evolution of chordate actin genes: evidence from genomic organization and amino acid sequences." (Kusakabe et al. 1997) As I explained in Darwin's Black Box, sequence studies by themselves can't answer the question of what the mechanism of evolution is. ...

So Behe was not overwhelmed with the titles of 58 titles because he's seen the bluffs before. A little as well on data-base searches:

Another website that has drawn attention (as evidenced from the inquiries I receive soliciting my reaction to it) is authored by David Ussery (Ussery 1999), ... For example, in a section on intracellular vesicular transport he notes that I stated in Darwin's Black Box that a search of a computer database "to see what titles have both evolution and vesicle in them comes up completely empty." (Behe 1996) (p. 114) My search criterion, of having both words in the title, was meant to be a rough way to show that nothing much has been published on the subject. Ussery, however, writes that, on the contrary, a search of the PubMed database using the words evolution and vesicle identifies well over a hundred papers. Confident of his position, he urges his audience, "But, please, don't just take my word for it--have a look for yourself!" (Ussery 1999) The problem is that, as I stated in the book, I had restricted my search to the titles of papers, where occurrence of both words would probably mean they concerned the same subject. Ussery's search used the default PubMed setting, which also looks in abstracts. ... Since the word evolution has many meanings, and since the word vesicle can mean just a container (like the word "box"), Ussery picked up equivocal meanings. The paper cited above shows Ussery's misstep in an obvious way. However, there are other papers resulting from an Ussery-style search where, although they do not address the question I raised, the unrelatedness is not so obvious to someone outside the field...

But I bet I'm not showing the critics here anything new with reference to these websites claiming to have refuted Behe. Charlie

To all commenters: Thank you for a great discussion. BarryA BarryA

Tribune 7 - funny how many questions are cleared up when one actually reads what was said at Dover. As I mentioned a few days ago, the Thumbsmen are building a legend around this supposed failure on Behe's part in the trial, and those of us who read the transcripts see it as an unjust fabrication. Andrea -

As for Behe’s keyword searching, well, I wish it was that easy to learn about the content of science papers.

Is it a sound strategy when Darwinists do it to show how often "evolution" shows up in the literature as opposed to "ID" or "design theory"? Especially when IDers can't even publish without removing such terms, and then can't even tell the judge why they can't. Andrea-

To the later posts that mention that Behe was aware of the latest literature regarding the transposition hypothesis, of course we knew he did, since that was the object of my initial PT essay, to which Behe directly responded months before.

So when the developments arise in the literature Behe is made aware of them, and responds. Your essay was in the New York Times, was it? Charlie

I sent a post with a bunch of links in it summarizing the chronology. Probably those links made it get stuck in the spam buffer. Nickm

The chronology is getting people confused here. Basically, we have: 1996 -- Darwin's Black Box, Behe's "no answers" claim 1996-2004 -- various research findings support the transposon hypothesis (reviewed in the Nature Immunology essay). The transposon hypothesis finds its way into immunology textbooks, popular science articles, and the review literature, as well as the peer-reviewed research 2002 -- Matt Inlay's TalkDesign.org essay "Evolving Immunity" makes the ID critic community generally aware of just how bad Behe's immune system chapter is, compared to the peer-reviewed literature. http://www.talkdesign.org/faqs/Evolving_Immunity.html May 17, 2005 -- Behe deposition, Behe admits not being familiar with 3 important papers on evolutionary immunology, makes his statements about expecting to be informed about papers by email, Scientific American, New York Times, etc. http://www2.ncseweb.org/kvd/index.php?path=depo/ May 30, 2005 -- Andrea Bottaro posts on PT "The Revenge of Calvin and Hobbes", which cites the Kapitonov and Jurka article (just published in the June 2005 PLoS Biology) http://www.pandasthumb.org/archives/2005/05/the_revenge_of.html May 31, 2005 -- Behe responds on ID the Future, emphasizes his requirement for near-infinite detail http://www.idthefuture.com/2005/05/calvin_and_hobbes_are_alive_and_well_in_.html June 2, 2005 -- Bottaro replies in "Behe's meaningless complexity" http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html September 26, 2005 -- Kenneth Miller cites 8 immune system evo articles against Behe in his direct testimony http://www.talkorigins.org/faqs/dover/day1pm.html#day1pm93 October 18, 2005 -- Behe's direct testimony. Behe rebuts Ken Miller by arguing that: (1) Behe ran a computer search on the articles for the terms "random mutation" and "natural selection" and didn't find them, and (2) the articles weren't detailed enough http://www.talkorigins.org/faqs/dover/day11am.html#day11am221 October 19, 2005 -- On cross-examination Rothschild (1) gets Behe to admit that transposition is a form of mutation, and is mentioned throughout the papers, and that the selective advantage of the immune system is pretty obvious, and (2) performs the long-prepared stack-up-the-literature cross, getting Behe make the absurd claim that it wasn't enough detail http://www.talkorigins.org/faqs/dover/day12pm.html November 7, 2005 -- Behe claims his testimony went swimmingly (reply to a reporter who thought the opposite). Brushes off the immune system episode. Testifying in Dover Trial Was No "Ordeal" http://www.idthefuture.com/2005/11/testifying_in_dover_trial_was.html December 20, 2005 -- Judge Jones issues opinion, cites Behe immune system example http://www.talkorigins.org/faqs/dover/day12pm.html January 2006 -- Behe replies to the decision and says again the immune system stuff wasn't detailed enough, again showing he doesn't get it http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=697 May 2006 -- Bottaro et al. Nature Immunology article and Supplemental Material. http://www.nature.com/ni/journal/v7/n5/abs/ni0506-433.html I have seen no reply to the NI article from anyone yet, despite it being all over the evolution blogs. Nickm

Hurrah for Tribune7. As you are probably already aware, I decided his information fit better as a separate post instead of as comment 92 to this post. BarryA

To the later posts that mention that Behe was aware of the latest literature regarding the transposition hypothesis, of course we knew he did, since that was the object of my initial PT essay, to which Behe directly responded months before. It would have been truly bizarre if he later said he was not aware of those papers. He was not aware however of most of the literature in the field (and of a few later papers specifcally on trnasposition, if I am not mistaken), which was the point that was made above. As for Behe's keyword searching, well, I wish it was that easy to learn about the content of science papers. (At cross, Behe IIRC agreed that transposition is in fact a form of mutation, and that the fact that increased antigen receptor diversity is selectively beneficial is pretty much uncontroversial.) Andrea

Did anyone read my rebuttal to Andrea's claim of evidence in the recent paper on Rag1 and Rag2 re: immunology? Here's the paper Andrea claimed for evolution of immunology... http://www.pnas.org/cgi/content/full/103/10/3728. I highlighted portions of it in the comments section here: https://uncommondesc.wpengine.com/index.php/archives/1421#comments It is very telling what Andrea considers as evidence agaisnt Behe and pro-evo. It also explains why Behe, nor ID need not worry and in fact can march forward. If this is what Andrea calls evidence for evolutionary pathways, then it is not science, but historic speculation. It is scifi history. And if this paper is representative of the other 58 papers and books, then the evidence is slim at best. A bunch of guessing, highly paid, highly educated - guessing. Call it a hypothesis - but it aint testable yet - again. This is why Reverse Engineering wins and thus Design will win out. Because, by the time we figure out(that's reverse engineer for the PhDs in da house) all those "infinite details" we'll be designing with them. Maybe Andrea should reread the suggested paper posted here as evidence. Since the scientist themselves state about immunology the following mix mash of assumptive logic: The evolutionary shift that presumably accompanied this event correlates with the phylogenetically inferred rapid appearance of the entire complex of Ig/TCR/MHC-mediated adaptive immunity (3, 8, 9). The suggested sudden emergence of this system has been referred to as an immunological “big bang” (10). Tada! "presumably", "inferred rapid appearance", "suggested sudden", bada bigga banga bing, just love that astronomy comparison. Voila - Immunity Big Bang! This is just one of the speculative points in the paper. Please see the above link for the rest of my highlighting or read the PNAS paper for more speculative "scenario" posing. You can shred "as evidence" the paper's attempt of 'evolutionary hypothesis' without being an immunologist or biologist. The fortunate thing about all this is I can read english. It is speculation thru out. Please point to us Andrea in this one paper alone the detailed pathways that are known which conclusively provide evidence of unguided RM/NS. Then point to the lab test which makes it undeniable that RM/NS did it. Then we might have something at which to look upon and thus the NYT would indeed have it listed as frontpage news. Some real observable data. But until then, its great fiction. Seriously, if this is McEvo's best evidence, no wonder Behe does not need to dabble in such non-sensical diatribes. And again, he is correct - with such a breakthru, you would think the news would be as Big as... well, as Big as the BIG BANG. Barry made a good point about the law, the Judge was wrong. And the 58 papers if measured by this one that Andrea thinks is evidence highlights the false dogma pushed upon our educational systems and on the public. It also shows why one must be vigilent in what they accept as "evidence". Reading thru that paper for "evidence of historical evolution" which leads to testable hypothesis shows to the contrary, there is no such evidence and that Andrea's claims are overstated. This would lead one to believe that the ACLU lawyers were overstating their case as well - whats new. On the other hand, the more important aspect of learning how the immunological system performs, comparative analysis is useful, worth funding, and can increase our knowledge base for future medical breakthrus and better living. But just because scientist push 'evolution' into speculative "scenarios" in a paper - does not make it so. Michaels7

Yes, we know of that response by Behe, So when you said "he learns of breakthroughs in the field from the pages of the New York Times and such” you were, um, what? tribune7

Oh, good, looks like we are getting back to the evidence and its interpretation, finally. Thanks. Now, let's get to it: Nick: I find Behe’s response to your above claim to be of interest: [snip] Yes, we know of that response by Behe, and I linked and responded to it myself in the second link I provided above: http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html As I have discussed above, Behe's is a particularly weak objection to the findings supporting the evolution of the VDJ recombination system, first because the standards he raises are obviously empirically unattainable, and second because by setting them he completely deflates the importance of his own brain-child, IC. But rather than quoting Behe, I'd like to know what you guys think of the issue yourselves. Andrea

Nick and Andrea, You two took some real cheap shots:

Q. May I approach, Your Honor? THE COURT: You may. Q. I'm just going to quickly identify what these articles are. Exhibit P-256, "Transposition of HAT elements, links transposable elements, and VDJ recombination," that's an article in Nature by Zau, et al. P-279, an article in Science, "Similarities between initiation of VDJ recombination and retroviral integration," Gent, et al. "VDJ recombination and RAG mediated transposition in yeast," P-280, that's in Molecular Cell by Platworthy, et al. P-281 in the EMBO Journal, "En vivo transposition mediated VDJ recombinates in human T lymphocytes," Messier, et al, spelled like the hockey player. P-283, it says PLOS Biology, do you recognize that journal title? A. Yes. It stands for Public Library of Science. Q. And that's an article by Kapitnov and Gerka, RAG 1-4 and VDJ recombination, signal sequences were derived from transposons." P-747, an article in Nature, "Implications of transposition mediated by VDJ recombination proteins, RAG 1 and RAG 2, for origins of antigen specific immunities," Eglewall, et al. P-748 in The Proceedings of the National Academy of Science, "Molecular evolution of vertebrate immune system," Bartle, et al., and now finally Exhibit P-755 in Blood , "VDJ recombinates mediated transposition with the BCL 2 gene to the IGH locus and follicular lymphoma." Those were the articles in peer reviewed scientific journals that were discussed by Mr. Miller which you listened in on, correct? A. I recognize most of them. Some of them I don't recall, but that's fine. Q. They discuss the transposing hypothesis? A. Yes, they do.

tribune7

Nick and Andrea have been implying Behe was ignorant of the challenges that arose to IC, specifically regarding the development of adaptive immune system. I went back and checked the transcripts and lo and behold Behe was specifically addressed on that issue. Note the papers he cites and the conferences he attends. A bit more than Scientific American and the New York Times. Here is how it goes:

Q. I just want to make a point clear. You said there were two examples where those who claim that irreducible complexity does not work or is not a valid explanation, they use experimental evidence, and that was the blood clotting system and the lac operon. How does the immunity system, is that experimental evidence or is that a theoretical claim? A. No, this is mostly a theoretical claim. There is no experimental evidence to show that natural selection could have produced the immune system. And I think that's a good example of the different views that people with different theoretical frameworks bring to the table. If we could show the next slide. Professor Miller shows this slide from a reference that he cited by Kapitonov and Jurka, and he has titled Summary, Between 1996 and 2005, each element of the transposon hypothesis has been confirmed. He has this over this diagram. But again, as I mentioned previously, whenever you see diagrams like this, we're talking about sequence data, comparison of protein, sequences, or gene sequences between organisms. And such data simply can't speak to the question of whether random mutation and natural selection produced the complex systems that we're talking about. So Professor Miller -- so, in my view, this data does not even touch on the question. And yet Professor Miller offers as compelling evidence. And one more time, I view this as the difference between two people with two different expectations, two different theoretical frameworks, how they view the same data. And I'd like to take a little bit of time to explain why such studies do not impress me. And I'll do so by looking at one of the papers that Professor Doolittle -- I'm sorry, Professor Miller, that's his name, cited in his presentation, Kapitonov and Jurka, that was published this year. I just want to go through, and just kind of as a quick way to show why I am not persuaded by these types of studies. I want to excerpt some sentences from this study to show what I consider to be the speculative nature of such studies. For example, in this excerpt, the authors say, something indicates that they may be important. This may indicate. It may be encoded. It might have been added. If so, it might have been derived. Alternatively, it might have been derived from a separate unknown transposon. It was probably lost. And we have a lot more of those, one more slide at least. It says, we cannot exclude the possibility. In any case, the origin appears to be a culmination of earlier evolutionary processes. If so, this might have been altered. Again, without going into the detail of the article, I just wanted to emphasize those phrases to point out what I consider to be the very speculative nature of such papers. Here's what I view to be the problem. The sequence of the proteins are there. The sequence of the genes are experimentally determined. And the question is, what do we make of that information? People like Professor Miller and the authors of this paper working from a Darwinian framework simply fit that data into their framework. But to me, that data does not support their framework. It does not offer experimental evidence for that framework. They're simply assuming a background of Darwinian random mutation and natural selection and explaining it -- or fitting it into that framework, but they're not offering support for it. Q. Dr. Behe, is there another paper that scientists point to for the support that the immune system can be explained by this Darwinian process? A. Yes, there is. There is one more that I have to discuss. Here is a recent paper, again the year 2005, by Klein and Nikolaidis entitled The Descent of the Antibody-Based Immune System by Gradual Evolution. And on the next slide is an excerpt from the initial part of their discussion where they say, quote, According to a currently popular view, the Big Bang hypothesis, the adaptive immune system arose suddenly, within a relatively short time interval, in association with the postulated two rounds of genome-wide duplications. So these people, Klein and Nikolaidis, are going to argue against what is the currently popular view among immunologists and people who study the immune system on how that system arose. Q. And what is the Big Bang hypothesis that's referred to here? A. Well, that's kind of a label that they put on to kind of indicate the fact that the immune system appears in one branch of animals, the vertebrates, and any obvious pre-cursors or functional parts of such a system do not appear to be obvious in other branches of animals. So it seems like the immune system arose almost complete in conjunction with the branching of vertebrates from invertebrate. Q. Do scientists acknowledge that or treat that as a problem for Darwin's theory? A. Well, in my experience, no, nobody treats such a thing as a problem for Darwin's theory. Q. Do you consider it a problem? A. I certainly consider it a problem. But other scientists who think that Darwinian evolution simply is true don't consider much of anything to be a problem for their theory. Q. Why do you consider it a problem? A. Because the -- as Darwin insisted, he insisted that adaptations had to arise by numerous successive slight modifications in a very gradual fashion. And this seems to go against the very gradual nature of his view. Q. Now has this paper been held up by scientists as refuting claims against intelligent design? A. Yes, it has. As a matter of fact, Professor Miller cited it in his expert report, although he didn't refer to it in his testimony. Additionally, I attended a meeting on evolution at Penn State in the summer of 2004 where one of the authors, Juan Kline, spoke on his work, and he interpreted it in those terms. Q. Now we have some quotes, I believe, from this paper that you want to highlight? A. Yes. Again, I want to pull out some excerpts from that paper just to show you why I regard this as speculative and unpersuasive. For example, they start with, by saying, quote, Here, we sketch out some of the changes and speculate how they may have come about. We argue that the origin only appears to be sudden. They talk about something as probably genuine. It probably evolved. Probably would require a few substitutions. It might have the potential of signaling. It seems to possess. The motifs presumably needed. One can imagine that a limited number. It might have been relatively minor. Quote, The kind of experimental molecular evolution should nevertheless shed light on events that would otherwise remain hopelessly in the realm of mere speculation. They're talking about experiments that have yet to be done. Next slide, I have even more such quotations. These factors are probably genuine. Nonetheless. They might have postdated. Nevertheless. Albeit. It seems. This might have been. These might represent. They might have been needed. This might have functioned. This might have. And this might have contributed. So again, this is just a shorthand way of trying to convey that, when I read papers like this, I do not see any support for Darwin's theory. I read them as speculative and -- but nonetheless, people who already do believe in Darwin's theory fit them into their own framework. Q. Now Dr. Miller cited numerous papers in his testimony to support his claims on irreducible complexity, the type III secretory system, and so forth. Have you done a review of those papers and have some comments on them that you prepared slides for? A. Yes, I did. I went through many of the papers that Professor Miller cited, as many as I could, and simply, as a shorthand way of trying to indicate or trying to convey why I don't regard any of them as persuasive, I simply did a search for the phrases, random mutation, which is abbreviated here in this column, RM, and the phrase, natural selection. Random mutation, of course, and natural selection are the two elements of the Darwinian mechanism. That is what is at issue here. And so this is, you know, this is, of course, a crude and perhaps shorthand way, but nonetheless, I think this illustrates why I do not find any of these papers persuasive. When I go through the papers that Professor Miller cited on the blood clotting cascade, Semba, et al, Robinson, et al, Jiang and Doolittle, there are no references to those phrases, random mutation and natural selection. Q. Some of your indications on this slide, you have 0 with asterisks and some without. Is there a reason for that? A. Yes. The papers that have asterisks, I scanned by eye. I read through them visually. Ones that do not have an asterisk, I was able to do a computer search for those phrases because they are on the web or in computer readable form. I have a number of other such tables. On the next one are references that Professor Miller cited on the immune system. And again, none of these references contain either those phrases, random mutation and natural selection. There were a couple more references on the immune system that Professor Miller cited, and they didn't contain those phrases either. In references for the bacterial flagellum and the type III secretory system, there was one paper by Hauch, a review in 1998 that did use the phrase natural selection. However, that phrase did not occur in the body of the paper. It was in the title of one of the references that Hauck listed. And on the next slide, I think there are papers cited by Professor Miller on common descent of hemoglobin. And again, those phrases are not there. I think there's another slide or two, if I'm not mistaken. This is the one on what he described as molecular trees, Fitch and Margoliash, from 1967. And I didn't find the phrase there either. So again, this is a shorthand way of showing why I actually considered these off-the-point and unpersuasive. Q. So all these papers that are being used to provide evidence for Darwin's theory of evolution, in particular, the mechanism evolution of natural selection, yet they don't mention random mutation or natural selection in the body of the works? A. That's correct. Q. Could you summarize the point then, Dr. Behe, that you are making with, referring to these studies and the comments you made about the speculative nature of some of these studies? A. Yes. Again, much of these studies, in my view, are speculative. They assume a Darwinian framework. They do not demonstrate it. And certainly, you know, certainly scientists should be free to speculate whatever they want. You know, science usually starts with speculation, but it can't end with speculation. And a person or, and especially a student, should be able to recognize and differentiate between speculation and actual data that actually supports a theory.

And here's some more. Guess MB does keep up with things -- at least according the Dover transcript. LOL

Q. Is this -- so you've done work in this area with the histone H4 and the molecular clock? A. Yes, uh-huh. I've written this commentary in 1990 in a journal called Trends in Biochemical Sciences, commenting on the work of somebody else who experimentally took an organism called yeast into the lab and altered its histone H4 and actually chopped off a couple amino acids at the beginning portion of that protein. And when he looked, it seems that it didn't make any difference to the organism. The organism grew just as well without those mutations, which is surprising, which is not what you would expect if all of those residues were critical for the function of that protein, histone H4. Later on, in the year 1996, I and a student of mine, Sema Agarwal, we were interested in this problem of histone H4 and molecular clock, and so we experimentally altered some amino acid residues into protein and changed them into different amino acids, with the expectation that these might destroy the function of the protein. But it turned out not to. These positions, these amino acids could be substituted just fine, which is unexpected, and which kind of complicates our interpretation of the molecular clock hypothesis. So there are two complications; complications upon complications. One, we would expect the number of mutations to accumulate with generation time, but it seems to accumulate, for some unknown reason, with absolute time. And the second is that, proteins accumulate mutations at different rates. We would expect that it would have to do with how vulnerable they are to mutations, and mutations might destroy the function of one protein that evolved slowly, but that is not experimentally supported. Q. Now has this problem been discussed in the scientific literature? A. Yes, this has been continuously discussed ever since the idea of the molecular clock hypothesis was first proposed in the early 1960's by two men named Emile Zuckerkandl and Linus Pauling. And here are a couple of papers which deal with the difficulties of the molecular clock hypothesis. Here's a recent one, Gillooly, et al, published in the Proceedings in the National Academy of Sciences, entitled The Rate of DNA Evolution, Effects of Body Size and Temperature on the Molecular Clock. In this publication, they say that, in fact, the size of an organism and temperature can affect how fast or how slow this clock might tick. Francisco Ayala has written on this frequently. Here's one from 1997. And I should say, Francisco Ayala is a very prominent evolutionary biologist. He wrote an article in 1997 entitled Vagaries of the Molecular Clock. And I think the title gets across the idea that there are questions with this hypothesis. And in 1993, a researcher named Tomoka Ohta published an article in the Proceedings of the National Academy of Sciences entitled An Examination of the Generation-time Effect on Molecular Evolution in which she considers exactly that complication that the textbook Voet and Voet pointed out, this generation-time effect. You know, why shouldn't organisms that reproduce more quickly accumulate more mutations. I have another slide just from one more recent paper. This paper by Drummond, et al, is entitled Why Highly Expressed Proteins Evolve Slowly. And it's referring to the sequence evolution that I've been discussing. It was published in the Proceedings of the National Academy of Sciences, and this was from an online version. This is so recent that I don't think it has yet appeared in print. The point I want to make with this is that, these people treat this question as a currently live question. They start off by saying, a central problem in molecular evolution is why proteins evolve at different rates. So that question I was trying to illustrate with histone H4, why does one protein tick faster and another one tick more slowly, that's still -- that is still unknown. And I think I will skip the rest of this slide and go to the next slide and just point out a couple words here. Drummond, et al, say, Surprisingly, the best indicator of a protein's relative evolutionary rate is the expression level of the encoding gene. The only point I want to make with this is that, they are reporting what is a surprise, what was not expected, which was not known, you know, 40 years ago, which has only been seen relatively recently. And they say, quote, We introduce a previously unexplored hypothesis, close quote. And the point I want to emphasize is that, here in this paper published, you know, weeks ago, that they are exploring new hypotheses to try to understand why proteins have the sequences that they do.

tribune7

BarryA: "Nick, I clicked on your first link and got only the list of authors and the first paragraph. Is this the right link?" On the right side, click on "Download pdf" to get the file. ofro

Nick: I find Behe's response to your above claim to be of interest:

Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways...” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin's Black Box (page 176)I implied that many small details would be necessary for a real Darwinian explanation)nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand? And not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more. Alternatively, Darwinists could present a series of experiments showing that RM/NS is capable of building a system of the complexity of the adaptive immune system. Professors Orr and Bottaro seem to think that because Darwinists’ fantastic claims are very difficult to support in a convincing fashion, then they should just be given a pass, and that everyone should agree with them without the required evidence. Fuggedaboudit. As Russell Doolittle helpfully showed, Darwinists find it easy to imagine that evolution could proceed along pathways which nature would never allow. Like Calvin and Hobbes, in their imaginations they hop into a box and fly over treacherous evolutionary terrain that nature would have to try to cross on foot. There is no reason for skeptics to trust Darwinists’ imaginations.

Scott

Nick, I clicked on your first link and got only the list of authors and the first paragraph. Is this the right link? BarryA

Say, does anyone want to bother to read what Andrea and I wrote about this back in May? We said what we had to say back then, and despite Andrea's repeated linking, the questions etc. here indicate that no one has read it (or at least no one has bothered to mention it, which is very very odd, given the topic): Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). "Immunology in the spotlight at the Dover 'Intelligent Design' trial." Nature Immunology. 7(5), 433-435. May 2005. The article is freely online here: http://www.nature.com/ni/journal/v7/n5/abs/ni0506-433.html Supplementary Material: http://www2.ncseweb.org/kvd/exhibits/immune/index.html Nickm

That the “evolution” of a system occured is not the issue. It is the mechanism which drives the change which is the issue: was it purely undirected external natural forces in conjunction with fortuitous mutations, or preprogrammed information [which may or may not be taking cues from the environment]? The molecular mechanism of transposition is well studied. Transposons are excising and inserting themselves all the time in various genomes. It is a standard natural process. Experiments show that the immune system RAG genes act basically like standard transposons. This is one of several confirmations of the model. This constitutes an answer to how adaptive immunity evolved, therefore Behe's statement that there are "no answers" was wrong. Behe tries to escape this embarrassing conclusion by moving the goalposts to where evolutionists have to provide every single mutation over a half-billion years, and also they evidently have to prove that every single mutation was not due to sneaky intervention by God. This new standard is ludicrous and would destroy science if consistently applied. The judge was perfectly well aware that the articles didn't meet Behe's new standard of near-infinite detail. He noted it explicitly in his decision: We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution. Showing the ludicrous nature of Behe's demand for near-infinite detail was the actual main point of the immune system episode at the trial. The fact that you guys don't get it is actually pretty funny, because it just means you will keep making the same mistakes that led to Behe's cross-examination collapse in the first place. Nickm

NickM --So, you think scientists have to ignore massive amounts of evidence for the evolution of a system, . . . I'd think you'd at least should have "the ultimate logic" of it before making such an assumption. Why assume? Why not get those all those small details and observe it occurring in a controlled setting? tribune7

Jason, “I guess maybe we can blame extreme biases Barry?” Precisely. And the remedy is to call it “utter nonsense,” as you did. There is usually no need to attack the person’s integrity. Just a guess here, but I suspect you are a young guy. I know exactly how you feel. Many years ago in my first run for the legislature I was the classic angry young man, and my campaign speeches reflected it. I will never forget the day one of my campaign staffers (an ex-marine) said to me, “Barry, you’ve got to stop [vulgar term for urinating] napalm.” He was right. I lost that election. Two years later in the next campaign I moderated my language and demeanor, and I won that race. If you review my posts and comments you will see that I hit hard, especially with the use of sarcasm. But I hope that I am attacking only stupid arguments, not the people who make them. This is what charity requires. BarryA

What did Behe say at deposition? That he had not read the papers shown to him, because he “would be waiting for larger news stories to point to these things”. THAT’S NOT WHAT BEHE SAID! Bizarre. --- Q: So in your efforts to keep abreast of the literature on the evolution of the immune system, neither of these articles is something that you have stumbled upon? A: I have not read these, and I would be waiting for larger news stories to point to these things — to point to significant developments in understanding these systems. ---- i.e., Behe had not read the papers shown to him, but he would have if they had been in "larger news stories". "Their conclusion is- Behe gets all his scientific info. from the NY Times “and such.” That is utter nonsense. From Behe’s quote alone, it’s obvious that’s not at all what he was saying." (emphasis added) Of course it's nonsense, but it's not what I said either. I said, instead, that "he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such." See the difference? Who's putting words in other people's mouth? And again, everyone seems to be getting very excited about this, but has anyone bothered reading the links I provided here at UD days ago, and would like to discuss them? Andrea

Nick. This is NOT difficult to understand. Behe made it clear that the INFORMATION IN THE PAPERS is available in other areas. The information itself, the breaktrhoughs, the work, the pathways discussed are within other papers, reviews, etc. He made that quite clear when he said the stuff about information being shared among many papers. I have a feeling you'll do anything, distort any quote to claim that Behe is some fool sitting on the sidelines, refusing to do any scientific work. That's surely how you're coming off in this thread. JasonTheGreek

That's also not what he said Nick. He said that he hasn't seen any detailed step by step pathways in any of the literature. He says that he has to put in less effort, not in that he's sitting on his butt, but that others started sending him all the info. so he didn't have to do as much leg work to search for all the information. You and Andrea both are misconstruing what Behe has said on the subject. You didn't show above that he missed the information in the 2 articles- you merely showed that he doesn't think the work meets the challenge put with in DBB! You've no idea if he has or hasn't read the information and work from those papers. He made it perfectly clear that most papers cite others and info. within others, thus you need not read EVERY paper on earth, but that most of what you do read has the info. from the other papers and work in them. JasonTheGreek

His point was that he HAS read the literature but he doesn’t see the evidence that the system has come about via NS and RM, or that there’s a truly detailed step by step pathway found. If Behe "HAS" read the literature, why then did Behe admit he had never read the three key peer-reviewed articles we showed him at the deposition? Nickm

Matzke said:

So, you think scientists have to ignore massive amounts of evidence for the evolution of a system, until such time as they completely understand every last detail about it?

That the "evolution" of a system occured is not the issue. It is the mechanism which drives the change which is the issue: was it purely undirected external natural forces in conjunction with fortuitous mutations, or preprogrammed information [which may or may not be taking cues from the environment]? And 3 or 4 papers which speculate about the relationship to preceeding sub-systems does not constitute massive amounts of evidence that it was indeed the unguided process of NS + RM which was responsible for the change. Scott

Regarding "sitting on his butt", let's look at the Behe deposition, p. 231: Q. Since the publication of Darwin's Black Box, have you continued to survey the scientific literature in the way you did to write Darwin's Black Box for answers to the questions of the evolution of the immune system? A. Well, since the book has been published, I have certainly kept my eye out, but I have had to make a lot less effort because people send me candidate articles, e-mail me about them. So I do try to keep abreast of that, yes. And then after that, we showed Behe several key articles that Behe had not seen, and then Behe explained his lack of knowledge by saying that he would have expected to see discussion in Annual Reviews journals, Scientific American, the New York Times, or other secondary literature. (And I showed above that he missed already-published artices in Annual Review of Immunology, Scientific American, and Science News. This is part of how we knew Behe would flop on cross-examination: Rather than actually familiarizing himself with the scientific literature, Behe comes up with excuses for not dealing with the scientific literature. This may be good for his mental health and for keeping his fans content, but it is totally unimpressive to the neutral observer who can compare the hard work of hundreds of scientists, vs. Behe's hand-waving dismissals. Nickm

I guess maybe we can blame extreme biases Barry? I just really don't see how one could conclude something like 'Behe gets all his scientific information from the Times' from Behe's quote. I'd wager if I showed this quote to 100 people, maybe 2 would come to this conclusion, and I have no idea what we could blame their mistaken conclusion on. I'd expect more from scientists in general. JasonTheGreek

Barry- I guess I'm just confused as to how college-educated men can be so confused by a simple quote, taking it so wildly out of context and ignoring 90 percent of it to come up with this conclusion that is totally unwarranted. Their conclusion is- Behe gets all his scientific info. from the NY Times "and such." That is utter nonsense. From Behe's quote alone, it's obvious that's not at all what he was saying. I just can't understand how this seems to be so confusing to some at PT. JasonTheGreek

I type too fast. Well, what the heck, since now my integrity is being attacked, let’s review all the statements: I said that Behe does not know the details about the evidence, because “by his own admission he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such.” “Your integrity”, although I would not use that phrase — I 'd say credibility on a narrow issue — is being attacked because you left yourself open. Behe did not say what you are implying that he said. tribune7

Well, what the heck, since now my integrity is being attacked, let’s review all the statements: I said that Behe does not know the details about the evidence, because “by his own admission he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such.” "Your integrity", althouh I would not use that phrase -- I said credibility on a narrow issue -- is being attacked because you left yourself open. Behe did not say what you are implying that he said. tribune7

What did Behe say at deposition? That he had not read the papers shown to him, because he “would be waiting for larger news stories to point to these things”. THAT'S NOT WHAT BEHE SAID! Oh my gosh, it's like talking to a brick wall. He also never claimed he learns of the latest breaktroughs from the NY Times. I'm sorry, but this is either willfull ignorance or dishonesty. Go back and paste Behe's ENTIRE quote. His point was that he HAS read the literature but he doesn't see the evidence that the system has come about via NS and RM, or that there's a truly detailed step by step pathway found. And that if there had been such a breakthrough it would have made front page news everywhere. He's not saying that this was the only place he would have seen it- he's saying that he hasn't read every single article on planet earth. He hasn't read every single paper tossed in his face at trial, but that the information within is familiar to him, as it's included in later papers that rehash the old data. JasonTheGreek

Jason, You ask: “My point, by the way, was that I can’t see how you can distort something without doing so in a dishonest way. To distort is to basically dishonestly portray someone or their words. If we agree that he’s distorting what Behe said and Behe’s overall scientific work ethic- isn’t that itself dishonest?” Yes, I agree that Andrea was distorting (and continues to distort, as in comment 66) what Behe said. I do not necessarily believe the distortion is the result of dishonesty. To answer your question, yes, it is entirely possible to distort without being dishonest. How is it possible? Glad you asked. Let’s take the Behe statement as an example. (see comment 61 where it is set forth in full). Our opponents focus on Behe’s reference to the New York Times. Well, Behe did mention the New York Times. It would be dishonest if they were to say Behe mentioned the New York Times if he had not. It is not necessarily dishonest to give undue emphasis to the statement. From their perspective, it probably stands out like the proverbial sore thumb. The corrective is not to call them names but to call them out on the distortion. My point is very simple. Unless we know beyond a reasonable doubt that a commenter is being dishonest (as opposed to commenting from his perspective even if the comment is wrong or distorted), charity (I use that term in its old-fashioned sense) requires us to give them the benefit of the doubt. Does this make sense? BarryA

He isn't sitting on his butt in some office waiting for someone to E-Mail him the info. He was clearly saying that if a detailed pathway that DEALT WITH ALL THE MANY PROBLEMS involved would be MAJOR news. So major that people would literally be E-Mailing him the information. He NEVER said he wasn't familiar with the scientific literature. It's clear that he said that he is familiar with it, but that he doesn't think it deals with all the problems that are involved. Pointing to a paper that claims to show the evidence of a detailed pathway of the system via RM+NS doesn't amount to much if the person in question doesn't agree with the conclusion that the paper itself has resolved the issue. I can claim that 9/11 was an inside job. Then, I can 'prove' as much by pointing to a paper from some professor who claims A, B, and C. I can then disagree with his conclusion, concluding myself that his evidence doesn't meet the challenge. Listing some papers that claim to show A, B, and C obviously doesn't meet the challenge in Behe's mind. That's quite different from him saying he hasn't read the literature or that he's unfamiliar with the recent findings. JasonTheGreek

Well, what the heck, since now my integrity is being attacked, let's review all the statements: I said that Behe does not know the details about the evidence, because "by his own admission he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such." What did Behe say at deposition? That he had not read the papers shown to him, because he "would be waiting for larger news stories to point to these things". And where would Behe find such "news stories"? "One would see reviews in scientific literature such as the annual reviews" (several of which however were presented to him and he admitted not having read), and "maybe even Scientific American or the New York Times or some such publications". So, the only revision I could perhaps make to my original statement would be: "by his own admission [Behe] has not read all of the literature, and expects to learn of breakthroughs in the field from the pages of the New York Times and such." To say that I unfairly reflected the content of Behe's deposition is very much a stretch, and at this point seems like a diversion from the original topic, which was the evidence presented to behe at Kitzmiller. Andrea

Andrea -- Objectively, he says he gets his info not from primary papers, You are mischaracterizing it but I think that stems from the fact that you misunderstand his point. He's saying that if the evolution of a molecular system was established it would be enormous news and that he couldn't help but hear about it. tribune7

Behe gave that answer as a reason for why he wasn't familiar with the scientific articles -- key articles in the field, actually -- that we showed him at the deposition. He also said that he expected people would email him if the literature was out there. It is ludicrous, and rather arrogant, but that is what he said. As it happens, he wasn't even familiar with the popular science and review literature. I already mentioned the Scientific American and Science News articles. He also missed this major article in Annual Review of Immunology: Litman, G. W., Anderson, M. K. and Rast, J. P. (1999). "Evolution of antigen binding receptors." Annual Review of Immunology 17: 109-147. http://dx.doi.org/10.1146/annurev.immunol.17.1.109 For the latest, see: Pancer, Z. and Cooper, M. D. (2006). "The Evolution of Adaptive Immunity." Annual Review of Immunology 24. http://dx.doi.org/10.1146/annurev.immunol.24.021605.090542 Nickm

Andrea, that's NOT what Behe said! The atty threw a bunch of papers in his face and said have you read this this and that? NOWHERE did he said or imply that he doesn't read the primary or review literature. He made the point that he HAS but that most of it includes OLDER material that he hasn't directly read. How is this so difficult? I'm not even going to try anymore. You're unwilling to discuss the issue without distorting Behe's words. If you can't get past that distortion, there's no hope period. JasonTheGreek

"I wonder what quotes we can get from you Andrea- then twist and distort them to claim nonsensical things about you and your scientific work." Why do I have the feeling this is being done already? ;-) Anyway, I guess anyone who reads the quotes above, and learns from the Kitzmiller transcripts that Behe had not read the majority of the primary and review literature on immune system evolution that was presented to him, can draw their own conclusion regarding Behe's literature searching methods. That's really not an important point. Let's discuss the evidence itself. Andrea

My point, by the way, was that I can't see how you can distort something without doing so in a dishonest way. To distort is to basically dishonestly portray someone or their words. If we agree that he's distorting what Behe said and Behe's overall scientific work ethic- isn't that itself dishonest? JasonTheGreek

Distortion itself IS dishonest. You distort something to cover up the truth of what's being said, so they go hand-in-hand. Andrea's lame attacks on Behe (that anyone who reads the entire quote can see are dishonesty attacks) need to be called out, I'd say. Else we allow him to continue these false attacks against Behe's character. I agree with Dave Scott above: "Andrea is perhaps forgetting that Behe is a working Professor of Biochemistry with a respectable list of peer reviewed publication in the field rather than the interested semi-literate layman Andrea wishes to portray him as." JasonTheGreek

"So why do you assume that evolution is responsible for it?" So, you think scientists have to ignore massive amounts of evidence for the evolution of a system, until such time as they completely understand every last detail about it? Nickm

Nickm, Why yes, we are saying Andrea mischaracterized Behe’s statement. Seriously. He took Behe’s offhand mention of the New York Times and tried to make it appear as though that was the central thrust of Behe’s statement. You can’t seriously say that is not a mischaracterization. BarryA

Reading back through the thread. I think just pasting Behe\\\'s quote that Andrea includes makes the distortion very clear. Andrea, in [snip] attack mode, bolds the part I have in bold below. Fortunately, I\\\'d guess that 99% of us can actually read the ENTIRE quote. Of course, by reading the first half of the quote, Andrea\\\'s distortion of Behe is quite clear.

A: Well, a real detailed explanation for understanding such a system would I think be large news across the scientific community. So that one would see not only an occasional article even in Nature dealing with a topic, one would see reviews in scientific literature such as the annual reviews summarizing not only some step that some people are trying to address, but the overall multiple problems that such a system would have to deal with. I would expect maybe even Scientific American or the New York Times or some such publications to have large headlines saying that finally we have an understanding of at least one molecular system.

Behe\\\'s quote was CRYSTAL CLEAR. He never makes any mention of what literature HE himself reads. His point is that if there was a detailed step by step pathway that was introduced and it also addressed the \\\"overall multiple problems that such a system would have to deal with\\\"- it would be MAJOR news. SO major that it would be mentioned in every popular publication out there. Andrea has totally distorted everything Behe he said. edited per comment 59 above BarryA JasonTheGreek

You guys can't seriously be accusing Andrea of mischaracterizing Behe, when Andrea said from memory "New York Times and such", and Behe said in his deposition "maybe even Scientific American or the New York Times or some such publications." Nickm

My Dear Mr. \"The Greek,\" Please stick to issues and ideas. No need to call people dishonest.  You wrote:  \"Stop being dishonest and twisting what Behe said.\"  It would be better if you had written:  Stop twisting what Behe said.\"  One thing I have learned after 20 years of practicing law (which is mostly just professional arguing) is that people are rarely flatly dishonest when they argue. Even when I think their argument is way over the top, usually they are just speaking from their perspective. Attack their arguments with reckless abandon and with as much hyperbole as you like. Please don\'t attack them. Remember, it is very important that our opponents feel free to post here. Otherwise this forum will degenerate into a boring \"me too\" club. Thank you. BarryA

Andrea -- In fact, our current understanding of the immune system as it is today does not fulfill this standard - we don’t have a complete knowledge of all its components, their molecular, cellular and functional inter-relationships, their pattern of engagement by different kinds of pathogens and foreign substances, etc - we don’t even know for sure what the ultimate logic is (”self/non-self discrimination”? “danger signals”?). So why do you assume that evolution is responsible for it? tribune7

I wonder what quotes we can get from you Andrea- then twist and distort them to claim nonsensical things about you and your scientific work. Shameful. JasonTheGreek

You provided no evidence to suggest that. You're purposefully distorting what Behe said. Stop being dishonest and twisting what Behe said. He clearly said, as any fool can tell, that he sees no evidence that a detailed step-by-step pathway has been introduced. His point is clear- if there was major evidence of this, it would be on the front page of major newspapers. He never said not even implied he gets his info. from the Times, or that he doesn't read the primary literature. He actually make it quite clear he DOES read the primary literatur, and pointed out that this literature nearly always includes information from older sources, which means you need not read ALL of the primary literature of the past decades. Like I said- how can anyone take anything you say seriously with this nonsense? JasonTheGreek

Read further, Jason: I just presented quotes showing that Behe barely if at all reads the primary literature, sporadically reads the relevant professional reviews, and expects to read about major breakthroughs in the lay press. And again, this is just a distraction from discussing the evidence. Come on. Andrea

Andrea said: "Now, let’s try to focus on the evidence and not on irrelevant side issues." I say: Practice what you preach. JasonTheGreek

Andrea- how can anyone take ANYTHING you say seriously when you make absurd comments like this:

since by his [Behe's] own admission he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such.

NOWHERE did Behe make this claim, nor did he even get anywhere near to giving this impression. JasonTheGreek

Hard to accuse me of quote-mining, since I didn't quote. At best, I can be accused me of mischaracterizing Behe's statement. Objectively, he says he gets his info not from primary papers, but from secondary literature (reviews) and lay publications (SA, NYT and such). However, the literature list presented to Behe at Kitzmiller contains many reviews that he admittedly had not seen. So, my point remains: Behe does not follow the primary literature, or for that matter properly follow the secondary literature, and seem to mostly rely to lay publications and, I guess, the occasional personal communication/web interaction. This doesn't mean that he is necessarily a bad scientist (I certainly don't keep abreast of all the literature on nucleic acids structure, Behe's former field before he switched to ID), and certainly not "a semi-literate layman" (which I never stated or implied) - just that immunology is not his field and he's doesn't know the literature "full well". Now, let's try to focus on the evidence and not on irrelevant side issues. Andrea

Of course, evolutionary immunology has been published in Scientific American: Beck, G. and Habicht, G. S. (1996). \"Immunity and the invertebrates.\" Scientific American 275(5): 60-63, 66. Litman, G. W. (1996). \"Sharks and the origins of vertebrate immunity.\" Scientific American 275(5): 67-71. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8875809 ...and Behe still didn\'t know about it. Here is another good article (though out of date) on the transposon hypothesis. Many of the leaders in the field are interviewed. The case was impressive even in 1998, and has gotten stronger now that they have found the transposon (which they clearly were thinking about in that 1998 article). John Travis (1998). \"The Accidental Immune System - evolution of the combinatorial immune system.\" Science News, Nov 7, 1998. http://www.findarticles.com/p/articles/mi_m1200/is_1998_Nov_7/ai_53280922 Nickm

The prior link to Behe's publications was inadvertantly just those from the past 5 years which are swamped by evolution controversy. This list is more reflective of peer reviewed publication in biochemistry. DaveScot

Behe: "large news across the scientific community" Behe: "even Scientific American" Why did Andrea clip those out and only use the partial quote "New York Times and such"? This is unadulterated quote mining out of context. Large news across the scientific community is much more (dare I say infinitely more :razz: ) than just the New York Times and such. Behe made no admission that his sources begin and end with the New York Times and such but that he would expect to be tipped off to a major discovery outside his focused interests by more than just an occasional article in Nature but rather "one would see reviews in scientific literature such as the annual reviews". Any reasonable person would read Behe's statement as saying that he expects to read about major discoveries in annual science reviews (and even Scientific American and the New York times and such) and then, if he is further interested, go to the source for details. Andrea is perhaps forgetting that Behe is a working Professor of Biochemistry with a respectable list of peer reviewed publication in the field rather than the interested semi-literate layman Andrea wishes to portray him as. DaveScot

BarryA wrote about Dover Decision:

Here is the excerpt from Jones’ opinion where he relies on the literature bluff.

“The immune system is the third system to which Professor Behe has applied the definition of irreducible complexity. Although in Darwin’s Black Box, Professor Behe wrote that not only were there no natural explanations for the immune system at the time, but that natural explanations were impossible regarding its origin. (P-647 at 139; [128]2:26-27 (Miller)). However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system. ([129]2:31 (Miller)). In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty- eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” ([130]23:19 (Behe)).”

Note that Jones ignored the distinction Behe made. Behe said there were no DETAILED ACCOUNTS of the evolution of the immune system through Neo-Darwinian mechanism. By the time it got to Jones’ opinion Behe was being quoted as saying there are no accounts of any kind of the evolution of the immune system. As is clear from the transcript above, Behe said exactly the opposite. Behe’s position is that yes, there are general accounts, just no detailed accounts.

Judge Jones wrote:

"he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.”"

The last words are in quotes, like they were Behe's words. But what Behe really said on cross-examination, was, that "it's NOT that they aren't good enough. It's simply that they are addressed to a different subject.", and the judge still wrote, that Behe had said, that "it was not "good enough."" I think, that the judge has put words in Behe's mouth. Analyysi

"Fascinating. A Darwinist can admit that the scientific community’s understanding of a system is deeply incomplete and uncertain. Then the same Darwinist can turn around and say the Neo-Darwinist paradigm gives us a fully acceptable account of the system we don’t understand. That’s some trick." No "trick". We have a sufficient, albeit clealry incomplete, understanding of the immune system to describe how it generally works, how certain of its components are organized and interact, why things can go wrong with it some times and even, in some cases, how to fix them when they do, to predict future findings and succesfully test those predictions. We also have a sufficient, albeit incomplete understanding of immune system evolution to account for the available information about it and successfully test predictions about what the next sets of findings will be. That's just how science works. "Let me ask you this. Does the Neo-Darwinist paradigm give an acceptable account of the origin of only the parts of the system that are understood? Or does it also give an acceptable account of the origin of the parts of the system about which our understanding is deeply incomplete and uncertain? If the latter, how can Neo-Darwinism explain the origin of the part of a system that is not understood?" Not sure I understand you. For instance, as I mentioned above there is some discussion among immunologists about two non-mutually exclusive models of the basic principle by which the vertebrate immune system works: one is based on the structural, molecular discrimination between "self" and "non-self", and the other sees the distinction between "self" and "non-self" as secondary, and says that what matters is the context in which certain structural determinants are detected by the system ("danger signal"). Evolutionary immunologists are contributing to this discussion by trying to understand the principles that underly the immune responses of "primitive" vertebrates and of other organisms whose immune system may be representative of the pre-vertebrate ancestral state, and clarifying along which lines it could have evolved. Basically, evolutionary biology is of course based on available independent knowledge of whatever system it is studying, while at the same time it can help address some open questions by analyzing them in a phylogenetic framework. Does that answer your question? Andrea

DS: "Andrea’s must know his case is exceedingly weak to purposely create these false statements." Quoting from Behe's expert deposition: --- Q: So in your efforts to keep abreast of the literature on the evolution of the immune system, neither of these articles is something that you have stumbled upon? A: I have not read these, and I would be waiting for larger news stories to point to these things -- to point to significant developments in understanding these systems. ... Q: You said you would expect to have been made aware of an article through other news or something to that effect. I wasn't sure what you meant by that. A: Well, a real detailed explanation for understanding such a system would I think be large news across the scientific community. So that one would see not only an occasional article even in Nature dealing with a topic, one would see reviews in scientific literature such as the annual reviews summarizing not only some step that some people are trying to address, but the overall multiple problems that such a system would have to deal with. I would expect maybe even Scientific American or the New York Times or some such publications to have large headlines saying that finally we have an understanding of at least one molecular system. ---- IOW, Behe does not routinely read the primary scientific literature (even in major journals like Nature) about the progress of the research on the evolution of the immune system or other IC systems, but expects any big news to appear in the secondary literature or in lay publications, such as the New York Times. That's why he had not read the vast majority of the papers presented to him at Kitzmiller. This was just in response to someone saying that Behe knows "full well" the evidence I was talking about - he doesn't (or better - didn't when he was asked about it, as he may know it now). Andrea

Interestingly and revealingly, the Behe quote proffered by Andrea does not contain the word "infinite". The point stands. Andrea made a straw man by asserting that Behe asked for the impossible (infinite detail) when he did no such thing. Even in light of this Andrea refuses to give up the claim. Behe very well might have asked for the impossible for it is not possible to demonstrate that a non-existent thing exists. This is not the same as asking for an infinite amount of evidence. Behe asked for a sufficient amount of evidence. DaveScot

Andrea said: “Still, this deep incompleteness and uncertainty [about our PRESENT understanding of the functioning of the immune system] doesn’t seem to prevent Behe (or anyone else) from accepting that the immune system exists and works, from describing its properties along general lines that are accepted by the scientific community, etc.” Fascinating. A Darwinist can admit that the scientific community’s understanding of a system is deeply incomplete and uncertain. Then the same Darwinist can turn around and say the Neo-Darwinist paradigm gives us a fully acceptable account of the system we don’t understand. That’s some trick. Let me ask you this. Does the Neo-Darwinist paradigm give an acceptable account of the origin of only the parts of the system that are understood? Or does it also give an acceptable account of the origin of the parts of the system about which our understanding is deeply incomplete and uncertain? If the latter, how can Neo-Darwinism explain the origin of the part of a system that is not understood? BarryA

Okay Andrea, I'll bite. Please tell me what tests were performed to determine that the detailed and testable evolutionary pathway traversed to get the antigen receptor recombination system were due to random chance mutations filtered by natural selection. Also, please provide a link to this detailed and testable evolutionary pathway and explain why, if it exists as you claim, why it wasn't read into evidence. Barry is entirely correct that a mere exhibit is insufficient in and of itself. The relevance of the exhibit must be read into evidence. DaveScot

And yet another straw man by Andrea in the assertion that Behe gets his immunology updates from "the New York Times and stuff". What Behe actually said was he need not read everything printed on a subject in the last 50 years to become familiar with the state of the art because more recent articles are inclusive of what has gone before. Andrea's must know his case is exceedingly weak to purposely create these false statements. DaveScot

DaveScot: there is no strawman. The current explanation for the evolution of the antigen receptor recombination system is detailed and testable. It is more detailed, tested and verified than, for instance, the model for the evolution of hemoglobin, which Behe thinks is perfectly OK. However, Behe is not asking for a run-of-the-mill, conventional "detailed and testable" scientific explanation but, and I quote: ... not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more." This is infinite detail (note also the "and much more"), and Behe knows it is literally impossible to obtain empirically. Seriously, even if it were possible to have this level of resolution for anything in science, we don't have it for pretty much anything. In fact, our current understanding of the immune system as it is today does not fulfill this standard - we don't have a complete knowledge of all its components, their molecular, cellular and functional inter-relationships, their pattern of engagement by different kinds of pathogens and foreign substances, etc - we don't even know for sure what the ultimate logic is ("self/non-self discrimination"? "danger signals"?). Still, this deep incompleteness and uncertainty doesn't seem to prevent Behe (or anyone else) from accepting that the immune system exists and works, from describing its properties along general lines that are accepted by the scientific community, etc. Andrea

DaveScot! Welcome back. I missed you. BarryA

Note how Andrea creates a straw man by using the nonsense term "infinite detail" in place of "detailed and testable". Behe said there was no detailed and testable explanation for the evolution of the immune system. Why does Andrea need to mangle that into Behe asking for "infinite detail"? The answer is obvious. A detailed and testable hypothesis is the first milestone on the way to a theory while infinite detail is, by definition, never attainable and thus an impossible task to fulfill. Andrea wishes to make it seem that Behe asked for the impossible instead of something reasonable. DaveScot

"I think you are forgetting that Behe is a scientist himself, and he knows full well what you have posted."Not "full well", since by his own admission he has not read all of the literature, and learns of breakthroughs in the field from the pages of the New York Times and such. But regardless, when directly confronted with some of the evidence, his response was the same I am criticizing here: "It's not enough (and - implicitly - it's never going to be)". That's not a valid scientific response (besides undermining his own argument about IC). "By the way, what there successful predictions done in regards to the immune system, that gives Darwinists the confidence that natural selection and random mutation are able to account for its origins?" The evidence I have linked to over and over here at UD, as original sources, professional reviews and, in some cases, lay "digests". Andrea

"Please note that in “intelligent design” it’s normally small changes that are made to improve the product." First note -- Incremental != small. I just finished an incremental change to one of our applications. It probably changed maybe 100 lines. However if those changes were not made in coordination, there is no path leading from one to the other. For each requied coordination, the search space increases by a full order of magnitude. So, this was a very small change, yet the jump is impossible for an atelic mechanism. The change was holistic (i.e. irreducibly complex). It made no sense as a sequence of selectable steps (no step would have been selectable), but it made complete sense as a holistic idea. And, even if someone were to figure out an extremely convoluted pathway, there is no way the change sequence could become fixed in a reasonable time frame. johnnyb

Andrea, I think you are forgetting that Behe is a scientist himself, and he knows full well what you have posted. The question everyone wants to know is: When will Darwinists openly say that they don't have any detailed account of the origin of ONE Irreducible COmplex system, instead of tossing sand to ppl's eyes, with bogus "refutations"? By the way, what there successful predictions done in regards to the immune system, that gives Darwinists the confidence that natural selection and random mutation are able to account for its origins? Mats

Well, it's a bit disappointing that no one seems to be tackling the evidence I linked to, but maybe you need more time. As for the comments that scientists should just "be honest", admit what they don't know and be done with it - well, they do. All scientists will tell your their conclusions are provisional, and no scientist will claim they have achieved 100% detail in their explanations. However, depending on the topic, scientists will tell you they can reach good, often high levels of confidence in an explanation even in the absence of absolute knowledge. For instance, they can send people to the Moon without knowing what gravity really is. Successfully testing predictions is probably the main way scientists achieve that confidence, and the number of successfully verified predictions with regard to the immune system make scientists very confident about, for instance, the evolutionary origin of the antigen receptor rearrangement components. You can't honestly ask for more from science (or, if you do, you should apply the standards consistently and reject all of science). Andrea

idnet: As you and Andrea both said: "severe reductions in function generally result from the alteration of even one component". They generally will be, just not always. You say "What I am saying is that to go from system 1 to system 2, that is vastly improved". Why vastly improved? It just has to be ever so slightly better at making into the next generation within that particular environment. And if, for example, in system ABC you get a great reduction in efficiency if you remove A, what if instead of removing A it turns out that removing B only results in a smaller decrease in efficiency. Indeed removing B then A could result in the smaller steps required. The order with which you remove components could have a huge bearing on the size of steps required. Also, the small steps don't have to be in terms of efficiency. A large step could be made in terms of efficiency if it is a small step in "genespace". Evolution proceeds in small steps in genespace, but can take huge steps in other ways. Small changes in genes can result in some bizarre changes. Here's a non-evolution (I think) example that blew my mind recently: http://scienceblogs.com/loom/2006/08/09/an_old_dog_lives_on_inside_new.php . Is this a new phyla? Is it still a dog? Further, you have lost track of what Andrea's comment was, it was particularly in relation to that complex system - not of any general system or of a simpler system from which an intermediate may have evolved. Without knowing the ancestral system we don't know whether or not it was as "fragile" as the descendant. Please note that in "intelligent design" it's normally small changes that are made to improve the product. I'm almost tempted to use Microsoft Windows as an example of "Intelligent Design", but I won't. :) We should also note that elegant solutions can and have arisen through evolutionary algorithms, and this technique is increasingly being explored in the computer industry. Did you read about the Avida "organisms" that evolved the ability to recognise when the researchers were looking? MikeFNQ

Incremental change never had anything to do with organic evolution. "A past evolution is ideniable, a present evolution undemonstrable." John A. Davison John A. Davison

MikeFNQ Sorry I am not making myself clear. What I am saying is that to go from system 1 to system 2, that is vastly improved, we must mutate system 1 in some way. Each of these mutations must be small and must have a selective advantage. This is Dawkins small steps to the top of Mt Improbable. I am arguing that Andrea said that changes to known existing systems are almost always damaging. We should expect that the present system 2, should have some beneficial mutations so it may become the new system 2.0001 then 2.002 etc like Adobe Reader. Improved systems in my experience, for example in the drug industry, come from Intelligent Design not random processes. idnet.com.au

idnet: Again, you are thinking backward. Evolution isn't taking a piece out. It's starting point is not the final system. Any reduction in the function of the system by removing a piece is irrelevant. The only question is whether that intermediary is better than what was there before, the ancestral form. You are saying System 3 is much better than System 2 therefore the it can't have gone from System 1 to System 2. That's simply wrong. System 2 can be much worse than System 3, just as long as it is better than its ancestor, System 1. And again, this is assuming that that's the only possible path. MikeFNQ

Rule 803(18) of the Federal Rules of Evidence expressly states that statements from "learned treatises" may be read into the evidence but may not be received as exhibits, and there are no exceptions given --

If admitted, the statements may be read into evidence but may not be received as exhibits. -- from http://www.law.cornell.edu/rules/fre/rules.htm#Rule803

Some Darwinists have been arguing that the above rule does not apply because allegedly the issue was just the existence of the publications and not whether the publications refuted Behe's claims. However, the final opinion assumed that the publications refuted Behe's claims, even though no statement from the publications was read into the record -- the final opinion said,

In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not "good enough." (23:19(Behe)).

The opinion said later,

We therefore find that Professor Behe's claim for irreducible complexity has been refuted in peer-reviewed research papers and has been rejected by the scientific community at large.

So the ultimate issue in the opinion was not whether the publications existed but whether their evidence for the evolution of immune systems was "good enough" to refute Behe's claims -- and Judge Jones assumed that the answer was "yes." And as Behe pointed out, the words "good enough" were not his but were the attorney's. Larry Fafarman

MikeFNQ My comments on Andrea are based on a big picture overview. We are not talking about A going to AB etc. We are talking about an essay on mathematics evolving into an essay on geography, with every change random, and small, and with each change an improvement on the original excellent essay. "Severely reduced function is still better than no function at all and hence would be selected for." This only applies looking back from excellent function. In reality, we see experimentally that almost any change to anyhting we know of, causes a severe reduction in function. This would decrease future survival and the new organism would be snuffed out, as we see in the real world. idnet.com.au

Remember that the question isn't "Is the system with a piece missing as good as the system?", it's "Is the system with a piece missing better than no system at all?" We also have to remember that a system ABC doesn't have to arise A - AB - ABC, it could be D - DA - DAB - DABC - ABC. The function of the system can also change. MikeFNQ

idnet.com.au emphasises Severe reductions in function generally result from the alteration of even one component. Of course this doesn't help his argument at all. Severely reduced function is still better than no function at all and hence would be selected for. So even if the that is the only pathway it could have followed, it is viable. It provides a working system. While idnet thinks what Andrea said is supportive of ID, the opposite is actually true. MikeFNQ

I have studied Andrea's PT posting http://www.pandasthumb.org/archives/2005/05/the_revenge_of.html When in Medical School, I was fascinated by the human immune system. The VDJ recombinant immunoglobulin system was as yet unelucidated. I spent many hours in lunch time meetings with the Department Head discussing the possible source of the impossible diversity in these proteins. The problem is essentially, that we have a complex system of compressed information. We need "an almost infinite variety" of antibodies, yet we have a very compact genome. Of course, there was an elegant system, and someone got the Nobel Prize for finding it. ID would predict that a designer would use compressed data, a system that used a small "alphabet" of genes, to construct a myriad of immunological "words". The complexity of the system defies simple explanation. It is not, as Andrea describes it, that "there is only one you" and that all the immune system has to recognise is the "very many different forms of "non-self"". No, there are actually very many "forms of self", and in the offspring, those "forms of self" are very different from the "self" of either parent. There is a complex system of exclusion of the immunological "words" that turn out to act against "self". That has to occur very early in the development of the organism. The systems here involve complexity imposed on complexity to an overwhelming degree. The reaction of IDists is not, as Andrea claims, "giving up". ID supporters are just as good at doing the here and now research as convinced materialists. Reverse engineering can be accomplished for many engineered systems, those designed by a designer, and those designed by RM and NS, if there are such systems. The most IDists should be accused of is having less fertile imaginations than materialists. idnet.com.au

From Anrdea at his uni web site http://www.urmc.rochester.edu/gebs/faculty/Andrea_Bottaro.htm "Antibodies (also called immunoglobulins, or Ig) are B lymphocyte-derived serum proteins involved in the immune response to foreign substances and micro-organisms (antigens). To become fully productive, Ig-encoding genes have to undergo multiple rearrangements of their DNA sequences through unique recombination mechanisms. Early in B lymphocyte development, VDJ recombination originates the antigen-binding region of the antibody molecule; a second type of rearrangement, class switch recombination (CSR), is activated in mature B cells during an immune response and allows the generation of different classes of antibodies with specific effector functions. These processes are crucial for normal immune system function, and their alteration can lead to severe immunodeficiency." Note the last sentence uses the word "crucial" and states that their alteration can lead to "severe immunodeficiency". IC states that intemediates are unlikely, given that from all we know about changing existing systems, what Andrea says is true. Severe reductions in function generally result from the alteration of even one component. I would cite what Andrea writes as supportive of IC. idnet.com.au

Also take heart in the fact that fewer than one in five Americans buy the blind-watchmaker argument, and that percentage appears to be shrinking with time, despite government sponsorship of indoctrination in the public schools, legal sanctions against those who dissent from Darwinian orthodoxy, and the systematic persecution of academics who dare to question. Darwinian orthodoxy is hanging on precariously by a very slender thread. If I were a Panda, I wouldn't gloat too much over Judge Jones' decision. GilDodgen

Gil, I take heart in the fact that my main point, after over 100 comments on this site and all the comments on PT, remains unrebutted. Thank you for touching this off with your post and getting me to look at this issue more closely. It just seems to me that the rules of evidence were suspended in Dover. I guess that's what you get when you elevate a member of the Liquor Control Board to the federal bench. BarryA

The entire Darwinian edifice (by that I mean the blind-watchmaker thesis) is one giant literature and storytelling bluff, and it has been since the beginning. This is what Phillip Johnson picked up on immediately and what inspired him to write Darwin On Trial. Barry, take heart. When I wrote my UD essay, "Writing Computer Programs by Random Mutation and Natural Selection," the Pandas established a special thread in an attempt to refute my arguments. When this happens you can be assured that they are in wild-eyed thrashing mode, desperate to defend the indefensible. GilDodgen

Andrea wrote: Well, I beg to differ, and so would pretty much every other immunologist out there. Not this one: Caroline Crocker, and she was on your side for most of her life, until she investigated the matter further.

Hmm, I don't think Caroline Crocker is an immunologist, and would thus probably not like to be characterized as such. HodorH

"We simply cannot get that kind of detail for anything in science, so it that’s the new standard, we may just as well close up MIT, the NIH, etc and all go home." Perhaps instead of "closing up and going home" you should instead be honest with what you know and what you don't. That's really all anyone is asking for. We're tired of baseless claims being trumpetted as if they had the rigor of testable observations. It is apparent that we have stepped on dogmatism when scientists are unable to admit when they don't know something, and think that someone disagrees with them about facts that they don't know something for sure means that they should pack up and go home. That's the behavior of schoolchildren, not adults, and I would hope not scientists. johnnyb

Andrea wrote: We simply cannot get that kind of detail for anything in science, so it that’s the new standard, we may just as well close up MIT, the NIH, etc and all go home.

Then perhaps saying "we don't know, or may never know" is better than insisting on a theory that maybe almost surely wrong. The issue for Behe is not evolutionary phylogeny, it is the adequacy of the mechanism in question. Even in physics we have uncertainty principles which limit what we can scientifically say about reality. I have less problem with "we don't know" than raising forensic speculations (like Darwiism) to the level of operational observations (like operatioal chemistry, physics, medicine, and engineering). Intelligent Design, though important to this trial, was not specifically the topic in this line of questioning. The line of questioning was the adequacy of Darwinian accounts, not merely phylogenies. In any, case, as frustrating as it may be for you to visit here Andrea, I thank you for taking the time to participate. You're certainly more articulate and knowledgeable than 95% of the anti-IDers I encounter on the net. I hope you will continue to participate. Salvador scordova

BarryA -- Exactly. The problem is that there are so many mutations that would lead to catastrophic behavior for a system. Neo-Darwinists have to show that (a) there is a route available to RM+NS that doesn't have points of system catastrophe, (b) that each of these points is in addition selectable, and (c) that there is enough time available for the routes to be generated, and (d) there is enough time available to fix the mutations in the population. Somehow the Darwinists miss the fact that Darwinism is a _mechanism_. Therefore, to say that X is due to Darwinism is to say that the Darwinian mechanism is capable. To say that science has shown the Darwinian mechanism capable is to say something very specific, that is a-d above have been solved. If the challenge has not been met, then it is disingenuous to, as Sal has pointed out, merely point out phylogeny as if that establishes the mechanism which established the phylogeny. The question that ID poses to evolutionary biology is what is the mechanism that establishes phylogeny, and pointing out the insufficiency of non-telic explanations in that mechanism. johnnyb

BarryA: Actually, I **have** linked (now repeatedly at UD) to discussions of the evidence that disproves Behe's claim in DBB that the verterbate immune system's antigen recombination machinery would doom evolutionary hypotheses to frustration. Not only it didn't, but all the crucial predictions of the very hypothesis Behe originally dismissed have been verified in a series of major papers. That's how science normally proceeds. You can read the original evidence, or the lay discussions of it, and argue its relevance or correctness. I have also linked to a response to Behe's current request for a slow-mo, mutation-by-mutation, population-by-population, selective step-by-selective step, etc-by-etc account of the evolutionary pathway, which you will not find in the literature because that's a demand that cannot be empirically fulfilled for any evolutionary pathway (including that of hemoglobin - which Behe says is plausible - or of things that even traditional Creationists are comfortable with, like antibiotic resistance). We simply cannot get that kind of detail for anything in science, so it that's the new standard, we may just as well close up MIT, the NIH, etc and all go home. I am sorry I can't help you more than that. Andrea

MikeFNQ, You say: “DETAILED, Intelligent Design definition: That amount of detail presently available, plus just that little bit more.” I would put it more like this: “DETAILED, meaning that level of detail necessary to make the account something more than, as Behe writes, an imaginary box flying over treacherous evolutionary terrain that nature would have to try to cross on foot.” BarryA

Andrea, I am skeptical of your claims. If a detailed account exists, why don’t you just point out where it is and I will go look at it. You might say I\'m calling your bluff.  In the mean time, I will refer back to a previous post on this issue by Dembski, where he quoted Behe as follows: \"Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways…” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin’s Black Box (page 176) I implied that many small details would be necessary for a real Darwinian explanation) nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand? \"And not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more. Alternatively, Darwinists could present a series of experiments showing that RM/NS is capable of building a system of the complexity of the adaptive immune system. Professors Orr and Bottaro seem to think that because Darwinists’ fantastic claims are very difficult to support in a convincing fashion, then they should just be given a pass, and that everyone should agree with them without the required evidence. Fuggedaboudit. As Russell Doolittle helpfully showed, Darwinists find it easy to imagine that evolution could proceed along pathways which nature would never allow. Like Calvin and Hobbes, in their imaginations they hop into a box and fly over treacherous evolutionary terrain that nature would have to try to cross on foot. There is no reason for skeptics to trust Darwinists’ imaginations.\\\" [Dembski again:] The following reply to this passage on Talk.origins is pure Darwhiner. The amazing thing is that this actually passes for high level argumentation in Darwhiner circles, replete with backslapping and hearty congratulations for showing up those IDiots. The level of dysfunctional group-think in these circles is staggering. But hey, enough of my commentary — enjoy: [The reply, such as it is:] \"In fact, all of this suggests to me a better way to oppose Behe’s views. Instead of discussing the validity of his arguments, I think we should challenge his identity, his very humanity if you will. After all, how do we know that Michael Behe was born of human parents? I mean, we know that humans are generally born of human parents, and Behe is demonstrably human, so reasonable inference (rather than an insistence that we explore the facts of every single individual’s development) would normally allow us to assume that the same processes were at work in Behe’s case, wouldn’t they? Behe has convinced me otherwise. I think it is only fair to suggest that until he can provide cell division by cell division documentation of his development from embryo to adult, plus a detailed account of the environmental influences upon this development along with the expected time scale for each of the changes he _claims_ occurred, we are justified in believing he is the progeny of little green men (and women?) from Mars. Absent evidence to the contrary, I believe Behe should relinquish his position at Lehigh until this mess is cleared up. Oh, and a visit to the INS is probably a good idea (for a, yes you guessed it, green card). I mean, what part of “perverse, evidential, demand” is so hard to understand?\" BarryA

Andrea wrote: Well, I beg to differ, and so would pretty much every other immunologist out there.

Not this one: Caroline Crocker, and she was on your side for most of her life, until she investigated the matter further. The "predictions" you speak of deal with confirmation of some sort of hierarchical relationships among organisms. Such information is supportive of either common design, common descent, or some combination of both. It does not imply Darwinism was the mechanism of immune system formation. Even Behe is accepting of the phylogentic relationships posed, but what is at issue is mechanism, not phylogeny. Your side argues Darwinism causes patterns that look phylogentic and that because we see patterns that look phylogentic, therefore Darwinism is true. But one could conversely say Design causes patterns that look phylogentic and because we see patterns that look phylogentic, therefore Design is true. I hope you see therefore, the weakness in the inferences being promoted by the anti-IDers. Salvador scordova

No on two grounds. First, a book or article can be authoritative in a general sense without addressing, much less refuting, Behe’s position. That is the case here. I don’t know for certain, but I feel fairly confident that the 58 books and articles were authoritative accounts of the current learning with respect to the evolution of the immune system. At the same time, none of the books or articles provided a DETAILED account of that evolution via Neo-Darwinian mechanisms — i.e. none of them refuted Behe’s point. Well, I beg to differ, and so would pretty much every other immunologist out there. As far as the evolution of the VDJ recombination system, all the critical predictions of the model have now been empirically confirmed (even beyond expectations, I should say), which pretty much settles it, unless of course contrary evidence surfaces. In DBB, Behe argued that the system would doom evolutionary explanations to frustration not because we didn't have a step-by-step account of the entire evolutionary pathway (with mutations, selection parameters, population sizes etc), but because the individual components or subsets of the system would not be functional in isolation, which is the IC claim in a nutshell. This has been proven wrong. The claim for infinite detail is just a fall-back position by Behe, and one which makes the issue of IC pretty much meaningless at this point (we don't have infinite detail for the evolution of pretty much anything, IC or not). As I mentioned in a different thread here, I have discussed both the evidence and Behe's response to it at PT: http://www.pandasthumb.org/archives/2005/05/the_revenge_of.html http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html As for the legal issues, again, I am entirely unqualified to argue with your interpretation regarding the rules, and I do not intend to. All I am saying is that, one way or another, the content of the articles would have ended up in the record, even if it would have taken a significant amount of time to read through the salient parts. Certainly the plaintiffs' team was aware of the articles' content (as Nick Matzke's annotated bibliography shows). At best, Behe could have argued that he disagreed with this or that statement, which a plaintiff's expert later on could have confirmed was in fact "authoritative". By all means, I understand that legal proceedings have specific rules to follow, but my impression is that the outcome would have been the same, and probably the last thing Behe would have wanted was to actually having to discuss in court each individual piece of evidence and conclusion supporting the evolution of the immune system, knowing full well it represented the consensus in the field. Andrea

"For instance, Behe argued in Darwin’s Black Box that the immunoglobulin gene recombination system would “doom all Darwinian explanations to frustration”, but in fact the very explanation he dismissed turned out to be very successful in predicting future evidence since then, and the then-tentative model is now overwhelmingly accepted among immunologists. That’s how science progresses." - Andrea Andrea, I'm not a scientist, so I don't know if what you've written is right or not. But I'm very skeptical after seeing how the Panda people misconstrued Behe's testimony, then refuted what he didn't say. Are you saying that immunologists have a detailed, testable model of how the immunoglobulin gene recombination system might have evolved? Or are you making a lesser claim? russ

DETAILED, Intelligent Design definition: That amount of detail presently available, plus just that little bit more. MikeFNQ

Andrea “So, the issue is not that the papers were not authoritative, but that the “official rulebook” may not have been followed in presenting them at trial.” No on two grounds. First, a book or article can be authoritative in a general sense without addressing, much less refuting, Behe’s position. That is the case here. I don’t know for certain, but I feel fairly confident that the 58 books and articles were authoritative accounts of the current learning with respect to the evolution of the immune system. At the same time, none of the books or articles provided a DETAILED account of that evolution via Neo-Darwinian mechanisms -- i.e. none of them refuted Behe’s point. Secondly, you can read rule 803(18) in my first post. You will see that it allows only the relevant portion of the text to be read into evidence. It does not allow the book as a whole to be admitted under any circumstances. BarryA

In order to comply with Rule 803(18), the plaintiffs should have asked Behe one by one if each of the 58 books and articles was authoritative. I am sure that after reviewing them one by one Behe would have said that all or most of them were. For those that Behe refused to admit were authoritative, plaintiffs could have had another expert testify they were. So, the issue is not that the papers were not authoritative, but that the "official rulebook" may not have been followed in presenting them at trial. Fair enough, though that doesn't seem to alter the substance of the matter (the papers exist and are authoritative), nor would have affected the outcome if the rules had been followed (they would have been admitted). Also, I doubt Behe would have come out looking very good challenging the authoritativeness of peer-reviewed papers written by experts in a field rather distinct from his own, some of them Nobel Prize winners. "The very fact that the Darwinist side presented a stack of *58 books and articles* on the immune system, shows that it in fact has *no* “detailed testable answers to the question of how the immune system could have arisen by random mutation and natural selection.”" That's an oversimplification. What that shows is just that understanding the evolution of something like the immune system is not something that can be addressed in a single paper, but it's a process that spans over decades of hypothesis testing and evidence collecting. With regard to specific sub-systems, however, which can be dealt with within a reasonable literature size, Behe's resistance to accept evolutionary explanations has clearly been shown to be - shall we say - premature. For instance, Behe argued in Darwin's Black Box that the immunoglobulin gene recombination system would "doom all Darwinian explanations to frustration", but in fact the very explanation he dismissed turned out to be very successful in predicting future evidence since then, and the then-tentative model is now overwhelmingly accepted among immunologists. That's how science progresses. Andrea

"I enjoy hearing strong arguments from the other side. In fact I find it much more interesting to encounter a strong argument from a critic than a weak argument from a supporter. By showing us our own blind spots they help us to build better arguments and to the degree that their criticisms are valid they can lead us to new insights." Sagebrush, I agree. I just read a bunch of (mostly) worthless reviews of Jonathan Wells' latest book at Amazon, and it was mostly "He's a crazy Moonie", "ID has no peer-reviewed papers", "Judge Jones proved that..." type of stuff. Kind of hard to sharpen your intellect rubbing up against that type of stuff, and it definitely provides no new insight. russ

I enjoy hearing strong arguments from the other side. In fact I find it much more interesting to encounter a strong argument from a critic than a weak argument from a supporter. By showing us our own blind spots they help us to build better arguments and to the degree that their criticisms are valid they can lead us to new insights. Unfortunately PT is disappointing in this regard. Among the shining intellects that champion the dominant paradigm I would hope to find many insightful and helpful criticisms. But instead I see only deliberate obtuseness, sophomoric reasoning, and frat-boy humor. Is this sort of ankle-biting the best that they have? C'mon pandas -- raise your standards. You would be doing us all a favor. sagebrush gardener

This reminds me of the story when Einstein was asked about the many scientists who had refuted his theory of relativity, and Einstein replied that there only needed to be *one*! The very fact that the Darwinist side presented a stack of *58 books and articles* on the immune system, shows that it in fact has *no* "detailed testable answers to the question of how the immune system could have arisen by random mutation and natural selection." If it did, it would only have to read out *one page* in all those 58 books and articles where it is. That they didn't, proves Behe's claim that there is *no* such "detailed testable answer... to the question of how the immune system could have arisen by random mutation and natural selection." Stephen E. Jones http://creationevolutiondesign.blogspot.com/ senojes

Barry, if you don't touch a sore point, they don't cry out. Keep it up. They cry out for rational thought. That is your gift, use it. idnet.com.au

Darwinists think that they are the world's greatest legal experts. Ed "It's My Way or the Highway" Brayton permanently kicked me off his blog "Dispatches from the Culture Wars" because he did not like my interpretation of a federal court rule. On Panda's Thumb I cited a Supreme Court ruling that actually supported the position of Lenny Flank and he responded by sneering, "when did you become a lawyer, Larry?" Larry Fafarman

Scott, Whoops, my bad. BarryA

Remember, Barry... it's The Panda's Thumb crowd. We need to speak very sllllloooooowwwwlllyyy and use small words. Scott

Barry, I think you've drawn blood. tribune7