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Dennis Venema’s Vacuous Arguments Against ID

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Those of you who follow the Biologos site may have noticed a recent series of articles by Dennis Venema. In this series of articles Dr. Venema purports to recount his journey from being an ardent ID supporter to being an ID critic. The latest installment, Part 4, can be found here.

In Part 4, Venema explains how reading Michael Behe’s second book, The Edge of Evolution, caused him to do a complete about-face. As a graduate student in biology, he had greatly admired Behe’s first book, Darwin’s Black Box, but now, as a new junior faculty member, he decided that Behe’s arguments in The Edge of Evolution were all wrong, and as a result, he decided that he must reject Behe and ID.

A number of questions are raised by Venema’s account. First of all, the argument in Behe’s first book, Darwin’s Black Box, is logically independent of the argument in the second book. Darwin’s Black Box centers on the theoretical difficulties for Darwinian mechanisms raised by irreducible complexity, whereas the second book is a wholly empirical argument about what Darwinian mechanisms have in fact accomplished in the case of microorganisms. So even if Behe’s empirical arguments in his second book could be proved completely invalid, it would not follow that his arguments in the first book were invalid. Venema does not explain why he threw out the first book on the basis of alleged flaws in the second.

A number of other questions are raised by Venema’s account of the alleged flaws in Behe’s second book. Here is his argument in full:

“To this day I wish I could have recorded myself reading those opening chapters of EoE. It was not long before the first suggestion of a frown would appear. Not many pages hence the frown would deepen into a furrow. I could hardly believe what I was reading: where was the Behe of Darwin’s Black Box that had so captivated me years ago? Though it is not polite to recount it (and I want to be clear that I hold no animosity towards Dr. Behe, but merely want to share my initial reaction) I clearly recall putting EoE down on my desk thinking, “What is this?” I was shocked: I had fully expected to once again be amazed and amused watching Behe take evolution down a peg or two. Yet here I was, knowing virtually nothing of evolution, and already I was seeing nothing but holes in Behe’s argument. Later on, when Behe began to discuss a topic I was familiar with (population genetics) I confirmed what I suspected: Behe was out of his area of specialty and out of his depth. Later work would convince me that this pattern applied to the whole of the book and the core of Behe’s arguments. My note pad was filling up, but not with what I had expected.

“Before I had finished Edge of Evolution, I was done with ID. I would lose my faith in ID not by comparing it to the science of evolution, but by reading one of its leading proponents and evaluating his work on its own merits. ID, I decided, was an argument from analogy, ignorance and incredulity. I was looking for an argument from evidence. Due to an interesting set of circumstances, I was able to read Behe both as a credulous lay reader and as a skeptical trained scientist. Behe, I realized, hadn’t changed: I had changed, and what a difference it had made.”

A number of points should be noted. First, if Venema, by his own confession, at the time knew “virtually nothing of evolution,” what made him qualified to criticize Behe’s work, to see the alleged “holes” in his argument?

Second, even Behe was “out of his area of specialty” when discussing population genetics, that by itself does not invalidate the argument he was making. A scientist from a different field might make some slips or errors in commenting on another field, but what needs to be shown is that the specific slips or errors are such as to be fatal to the argument the scientist is making. It is so typical of Biologos columnists to say things like: “On Page 259 Meyer misnames this chemical, and therefore he is scientifically incompetent, therefore ID is false.” But in fact what has to be shown is that the misnaming of the chemical, or the error in population genetics jargon, is such as to invalidate the argument of an entire book, or chapter, or paragraph. Never has any Biologos columnist ever done this, and Venema has again failed to do it here. He simply makes vague unspecified charges about Behe’s incompetence, without showing how the argument is invalidated by said incompetence. This is the lazy man’s way of arguing, not the scientist’s way of arguing, and Dr. Venema should not be proud of it.

(I might add by way of parentheses that it is very odd for Dr. Venema, a leading player on Biologos, to complain about ID people writing outside of their specialties, when on the Biologos site, many columnists — Karl Giberson, Darrel Falk, Oliver Barclay, Ard Louis, and others, frequently write columns about, or make comments about, theology and the history of ideas — fields in which they are completely incompetent — and say embarrassingly ignorant things. Perhaps Dr. Venema can take his complaint about non-specialists to the Biologos management and get something done about the theological and historical dilettantism of the scientists there. But I digress.)

Third, how does it follow that if Behe is wrong, all ID theorists are wrong? Did Venema take the time to read the careful argument in No Free Lunch by William Dembski? Did he read The Design of Life by Dembski and Wells, with its careful critique of Darwinian mechanisms? Did he read the many essays by Paul Nelson, Stephen Meyer, Richard Sternberg, David Berlinski, etc. which have either argued for ID or criticized Darwinism, and show the flaws in those? How can he know that ID is entirely wrong when he has found flaws in the argument of only one book by one ID proponent? The lack of logic in Venema’s conclusion is staggering, and makes the case that biologists need to add a good strong liberal arts component to their education, so that they can learn to reason competently.

(Of course, we know how Venema has dealt with Stephen Meyer’s book, Signature in the Cell. A few months back, he wrote a series of columns on that book which purported to be a refutation of it. Interestingly enough, almost of all of Venema’s comments in those columns concerned Darwinian evolution, which was not the topic of Meyer’s book. The topic of Meyer’s book was the origin of the first life. Venema did not provide one shred of evidence that Meyer had made any errors in his research and critique of chemical evolutionary theories of the origin of life. Nor is this surprising, as Venema knows next to nothing about origin-of-life theories; his field is fruit-fly population genetics, and he has published nothing at all in the origin-of-life field. So it’s understandable why he might stay away from criticizing Meyer in the area where Meyer did his Ph.D. work.  But the staggering thing is that Venema was not able to grasp, even when it was pointed out to him by several commenters, that his critique of Meyer was off-topic.  Again, one wonders what kind of general intellectual training a scientific education these days provides, when a Ph.D. in Biology cannot keep his focus on the argument that is on the table.)

Finally, if Behe was so wrong, why did Venema not publish, in a peer-reviewed scientific journal, or in a major newspaper or general-interest magazine, a review of The Edge of Evolution, pointing out its many faults? What was stopping him? Dawkins, Carroll, Coyne, Ruse and many others did so. Why didn’t Venema, if he was so sure that he was right? Venema makes sweeping generalities about Behe’s incompetence, but when it comes time to trot out the evidence, he is missing in action.

And that’s not the only place Dr. Venema has been missing in action. He says he was an ardent supporter of ID. Really? Then how come no one in the ID movement has any memory whatsoever of his support? What conferences did he organize to bring in pro-ID speakers? What positive book reviews of ID books did he write on Amazon, or in his local newspaper, or in any other venue? On what internet debating sites did he sign his name to defenses of ID against its critics? Where on Panda’s Thumb or Pharyngula or TalkOrigins will we find his sterling defense of ID?  On what platform did he debate Eugenie Scott or P. Z. Myers?

Overall, Dr. Venema’s series on why he abandoned ID is much like his series of articles on Signature in the Cell — an intellectual washout. It contributes nothing to the serious discussion of ID notions and ID arguments. If this is the best argument that Biologos can marshal against ID, its days are numbered.

Comments
Starbuck: Thanks for fixing the URL. It is now plain that this technical criticism was aimed at Meyer, not Behe. So my criticism still remains valid: in the article in question, Venema declares that Behe is incompetent and his conclusions invalid, without indicating any of the reasons for that judgment. I find this to be the unprofessional treatment of one scientist by another, especially given that we are talking about a junior scientist speaking to a senior one.Thomas Cudworth
August 19, 2011
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And as for TC, thanks for a nice thread. I'm glad you contribute here.Upright BiPed
August 19, 2011
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J/kUpright BiPed
August 19, 2011
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...other than that, pull up your pants. and don't wear those shoes with that shirt.Upright BiPed
August 19, 2011
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The figure- 5.7 on page 128 shows 5' - 3' not 5' - 5' as DV states.Joseph
August 19, 2011
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Nick, It is obvious that you do not understand the information argument. It is also obvious that you do not undertsand that ID is not anti-evolution. Also the way to refute Behe and Meyer are with actual evidence, which is something you still sorely lack.Joseph
August 19, 2011
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Nick Matzke @8: Venema does not link to Matheson's criticism of Edge of Evolution *in the article we are discussing*. He therefore provides no documentation for his criticism of Behe *in the article we are discussing*. In any case, for him to lean on Matheson's arguments would be spineless. A scientist should argue for himself. He indicates clearly that he had *his own* objections to Behe's book, independent of anything that Matheson might have said. It's his academic obligation to provide those objections, not simply to dismiss a senior scientist (Behe, who has published far more than Venema) as incompetent with a sweep of the hand, as he does in the article we are discussing. You have a lot to learn about professional ethics, Nick. Behe has discussed probability theory in relation to biology with Bill Dembski, who has two Ph.D.s in the subject and knows more about it than you and Steve Matheson and Dennis Venema combined. So it is unlikely that your charge against Behe has any substance, but if it does, you should publish it in a peer-reviewed journal, showing exactly what he gets wrong about probability theory. (It would be amusing to see a biologist try to do some math; when I was in natural science, biology was the haven of all the science undergrads who were afraid of math. The good math students all went into physics, chemistry and engineering.) As for Matheson, his point that someone made the trivial slip of calling something a virus in one place and a bacterium in another is worthless *unless he can show that that slip results in an invalid conclusion to an argument.* Errors of that trivial kind occur in scientific books all the time, and Darwinists *never* point them them out when they are in pro-evolution books, only when they are in ID books. The double standard is painfully obvious. Your defense of Venema's articles on Signature in the Cell is the same as Venema's, and equally inadequate. Even if you are right that only *half* of Venema's review of Signature in the Cell is about Darwinian evolution, that still means that half of it is off-topic. That's still a pretty solid indictment of Venema's inability to stay focused. The point is that the core argument of Meyer's book is about the origin of life, not about Darwinian evolution. Venema seizes upon some remarks about Darwinian evolution which are in the *Appendix* of the book, not part of its main argument, and spends an inordinate amount of time arguing about those. Venema says *nothing at all* which would explain how life could have arisen by chemical evolutionary means and he has no refutation at all of Meyer's detailed criticism of the various chemical origin-of-life scenarios. Which is not surprising, as Venema is a fruit fly geneticist, not an origin of life researcher. (Nor, by the way, does Matheson have any special competence to discuss origin of life issues; his field of publication is developmental biology. Maybe if he wouldn't spend hundreds of hours blogging against ID people, he could pick up another scientific specialty, like origin of life. Until then, since Meyer did his Ph.D. in the subject of origin-of-life theories, and his book is chock-full of references to recent technical literature on the subject, I'll take Meyer's word over Matheson's any day.) By the way, I notice that you vanished on my previous thread, after I showed in excruciating detail the dishonesty of your treatment of Behe and other ID proponents. Are you incapable, Nick, of ever admitting error or exaggeration of any kind? It is precisely that dogmatic, intransigent aspect of your personality that marks you off as a culture warrior rather than a genuine seeker after truth. Why don't you just admit that in the past you have willfully distorted and misrepresented the position of Behe and other ID proponents, and say that it was unprofessional and academically dishonest to do so, and that you are sorry, and that in the future you will never do so again? Then I might have an ounce of respect for you.Thomas Cudworth
August 19, 2011
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Nick, you know you could forever silence ID by creating life in the lab, or by passing the bacterial fitness test by 500 bits!!! This should be a piece of cake for someone as certain as you are that you are the product of purely material processes!~!!bornagain77
August 19, 2011
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Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe - Oct. 2009 Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact. http://www.evolutionnews.org/2009/10/richard_dawkins_the_greatest_s.htmlbornagain77
August 19, 2011
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The Fact-Free "Science" of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence Jonathan Wells June 8, 2010 Excerpt: One might think that professors Matheson, Hunt and Moran would address the conceptual issue calmly, rationally, and collegially. But they don't; instead, they stoop to misrepresentation and ridicule. And one might think that they would address the empirical issue by citing published scientific evidence. But they don't; instead, they simply proclaim themselves the only authorities on the subject. Who you gonna believe, them or your own eyes? http://www.evolutionnews.org/2010/06/the_factfree_science_of_mathes035521.htmlbornagain77
August 19, 2011
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"In light of this, I formulated a conservation law of my own as a working hypothesis to distill my experience and what I had discovered about origin-of-life research. Since I was not principally concerned with whether biological evolution could generate specified information, I decided to formulate a “conservative” conservation law—one that applied only to a nonbiological context (and thus not to an information-rich initial state). My statement of the law does not say anything about whether undirected natural processes could produce an increase in specified information starting from preexisting forms of life. But it does encapsulate what repeated experience had demonstrated about the flow of information starting from chemistry and physics alone." "Here’s my version of the law of conservation of information: “In a nonbiological context, the amount of specified information initially present in a system, Si, will generally equal or exceed the specified information content of the final system, Sf.” This rule admits only two exceptions. First, the information content of the final state may exceed that of the initial state, Si, if intelligent agents have elected to actualize certain potential states while excluding others, thus increasing the specified information content of the system. Second, the information content of the final system may exceed that of the initial system if random processes have, by chance, increased the specified information content of the system. In this latter case, the potential increase in the information content of the system is limited by the “probabilistic resources” available to the system. As noted in Chapter 10, the probabilistic resources of the entire universe equal 10^139 trials, which, in turn, corresponds to an informational measure of less than 500 bits. This represents the maximum information increase that could be reasonably expected to occur by chance from the big-bang singularity to the present—without assistance from an intelligent agent." Meyer, Stephen C. (2009-06-06). Signature in the Cell (pp. 293-294). HarperCollins e-books. Kindle Edition.material.infantacy
August 19, 2011
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I've read through Venema's critique in SITC, and it becomes glaringly obvious (by his repetition that 'Meyer's won't deal with RM+NS' that the poor man just doesn't understand the distinction between evolution and origins.Upright BiPed
August 19, 2011
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Venema's review of Meyer's Signature in the Cell in PCSF contains a link to Steve Matheson's detailed review of Behe's mistakes in Edge of Evolution, see footnote 34:
http://www.asa3.org/ASA/PSCF/2010/PSCF12-10Venema.pdf Odds and Ends Although other flaws are less serious in and of themselves, they are still indicative of the level of argumentation in the book, as well as of the quality of its peer review. For example, it was in chapter three that I first arrived at what I now call a “Behe moment” when reading antievolutionary literature. In Michael Behe’s book Edge of Evolution, he makes a few obvious “rookie errors” when discussing how probabilities work in population genetics.34 This, for me, was the clear signal that the book was written by an amateur in the field and not adequately peer reviewed. In Signature, this moment arrived when Meyer calls Pnemonococci a bacterium and a virus in the same paragraph.35 This impression was confirmed anew when Meyer describes, over the course of several pages, his epiphany that DNA bases do not have bonds between them and thus cannot selforganize into specified sequences. This “epiphany” is something that biology majors learn (or at least, should learn) in their introductory courses. This theme continued apace in the figure describing translation. 36 Signature shows tRNAs aligning to the mRNA in a 5' to 5' orientation, tRNAs with codon instead of anticodon sequences, and several inappropriate nucleotide pairings: all very basic mistakes. In short, Signature clearly was not written or peer reviewed by individuals with a working knowledge of molecular biology. Now, these issues in and of themselves would not be a serious problem for Signature, if not for the fact that the strength of Meyer’s argument rests entirely on his assertion that he has made a thorough search through all proposed mechanisms for generating biological information through natural means and found them lacking. Meyer is asking his audience to trust him that his analysis is thorough and sound. However, that Meyer’s understanding of molecular biology appears to be at or below a first-year college level should give even the most pro-ID reader pause here. It means that Meyer, well intentioned though he may be, is simply not equipped to grapple with these issues beyond an introductory textbook level. Nor has Meyer sought the advice of those who are able to do so. And as we have seen, Meyer has made neither a thorough search for the origin of biological information by natural mechanisms, nor a fair assessment of current origin-of-life research. [...] 34 See http://sfmatheson.blogspot.com/2010/04/behe-andprobability- one-more-try.html (last accessed September 28, 2010).
This presumably tells us the specific problems that Venema sees with Behe's argument as well -- e.g., Behe completely misunderstands basic probability, which is rather a problem, when Behe draws such grand conclusions based on probability. Even more problems with Behe's argument, specifically empirical ones, are here: http://www.pandasthumb.org/archives/2007/10/full-text-of-th.html ...which Behe mostly didn't even try to address in his reply: http://pandasthumb.org/archives/2007/11/behe-replies-to.html As for Venema's criticism of Meyer, it's pretty tenditious to claim the following:
(Of course, we know how Venema has dealt with Stephen Meyer’s book, Signature in the Cell. A few months back, he wrote a series of columns on that book which purported to be a refutation of it. Interestingly enough, almost of all of Venema’s comments in those columns concerned Darwinian evolution, which was not the topic of Meyer’s book.
First, this isn't really true -- the review is about half-and-half (I'm looking at the PDF right now). Second, Meyer himself makes the core of his argument the claim that only intelligent processes can produce new information. If evolution can produce new genes with new functions, new binding sites, new specificity, etc., then Meyer's own argument, as he himself phrased it, is shot down. If natural processes can create new information, then intelligence isn't the only explanation of new information. Meyer's claim that information is uniquely a product of intelligent processes, which he relies on throughout the book, is sunk.
Third, how does it follow that if Behe is wrong, all ID theorists are wrong?
Behe is the most famous and most credible ID proponent. If he's badly wrong, it's a huge problem. It's also a problem if other ID advocates don't notice and correct his errors -- which they don't. It indicates a lack of intellectual seriousness.NickMatzke_UD
August 19, 2011
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That's interesting. Can you expand on what you mean by "accidents"? (I would agree that they may not be entirely "random".)Elizabeth Liddle
August 19, 2011
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Starbuck @4: It's perfectly fair to attack the piece. Venema makes audacious claims in it that he does not substantiate. He says that Behe is incompetent in population genetics and evolutionary theory. He implies that this incompetence invalidates Behe's argument. This is demeaning to Behe and his work, and is dishonorable scientific behavior unless it is accompanied by argument to establish the claims being made. It is no excuse to say that Venema has made technical arguments against ID elsewhere. If he made specific arguments *against Behe's Edge of Evolution* elsewhere, and linked to them, that would be acceptable, but he did not provide any such link. In any case, much better biologists than Venema -- Coyne, Carroll -- have offered detailed critiques of Behe's book, and Behe has refuted them in detail. I wouldn't expect to hear from Venema anything but the same set of arguments repeated. But he can surprise me, and show his mettle, by making the effort of actually writing a detailed refutation of EOE and putting it out for scientific scrutiny. Until he does so, his claims are all bluster, like most of columns (and comments) published on Biologos. By the way, your link breaks. It takes one to Biologos but not to the Venema article you are directing people to. The note says that the article is not found there. It would help if you would give a title. I do not recall any article dedicated specifically to criticism of EOE by Venema on the Biologos site.Thomas Cudworth
August 19, 2011
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Grunty @3: You should check your chronology before making statements. The Dover Trial was in 2005; Behe's book The Edge of Evolution came out in 2007. The lawyer could hardly have "taken down" an argument which Behe had not yet formulated. And no lawyer would capable of "taking down" Behe anyway; the legal team was simply parroting talking points fed to them by the "expert" witnesses -- Miller, Pennock, etc. (And even those arguments were lousy, and have been refuted dozens of times since the trial.)Thomas Cudworth
August 19, 2011
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While I agree with the broad critique of Venema's argument, is there technically anything wrong with making an argument from analogy? Granted, that isn't all that ID has to offer, but an analogical argument can be quite compelling, and it can conform to all available evidence. In "The Cell's Design" Fazale Rana's argument is pretty much unapologetically analogical. He basically attempts to resuscitate Paley's watchmaker argument by noting that the analogy between products of human design and certain biological machines and motors is actually valid (contra Hume), given the wealth of new knowledge on their specific characteristics. FWIW, Venema had an extensive dialogue with Rana on this, and this may be where he's getting the idea that ALL of ID is an argument from analogy. But what's wrong with a strong analogical argument anyway?illegit
August 19, 2011
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Starbuck, me thinks you are much too easily impressed. Until Darwinists can actually generate novel functional genes and/or proteins by what are perceived to be purely evolutionary processes (or even significantly modify existing genes and/or proteins by what are perceived to be purely evolutionary processes), everything you claim as evidence is in fact merely speculation. Whereas to refute Doug Axe's work experimental verification is exactly the burden that Darwinism must bear to be considered scientifically legitimate.,,, Imagination is a wonderful thing for forming a hypothesis but it has absolutely no place in the testing phase of the scientific method that determines whether that hypothesis is actually feasible or bunk!!! i.e. Darwinists have completely failed to concretely demonstrate, by empirical science, the feasibility of their claims!!! notes; Proteins Did Not Evolve Even According to the Evolutionist’s Own Calculations but so What, Evolution is a Fact - Cornelius Hunter - July 2011 Excerpt: For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude. http://darwins-god.blogspot.com/2011/07/response-to-comments-proteins-did-not.html Fancy footwork in the sequence space shuffle - 2006 "Estimates for the density of functional proteins in sequence space range anywhere from 1 in 10^12 to 1 in 10^77. No matter how you slice it, proteins are rare. Useful ones are even more rare." http://www.nature.com/nbt/journal/v24/n3/full/nbt0306-328.html It is interesting to note the 'low end' 1 in 10^12 (trillion) estimate for functional proteins (Szostak), is still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario, How Proteins Evolved - Cornelius Hunter - December 2010 Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function. http://darwins-god.blogspot.com/2010/12/how-proteins-evolved.html ============= The Case Against a Darwinian Origin of Protein Folds - Douglas Axe - 2010 Excerpt Pg. 11: "Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin." http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1 The Case Against a Darwinian Origin of Protein Folds - Douglas Axe, Jay Richards - audio http://intelligentdesign.podomatic.com/player/web/2010-05-03T11_09_03-07_00 When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/bornagain77
August 19, 2011
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If you accept evolution via an accumulation of genetic accidents lading to the diversity of living organisms from some unknown population(s) of single-celled organisms, that is the materialistic philosphy. That said Intelligent Design is not anti-evolution. Rather ID claims that not all mutations are genetic accidents.Joseph
August 19, 2011
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posted to quickly, these are meant to be quotes:
vpu is found only in HIV-1 and simian immunodeficiency viruses isolated from chimpanzees (SIVcpz), and three species of old world monkeys within the genus Cercopithecus.
has been limited to a small number of subtype B and more recently subtype C
Starbuck
August 19, 2011
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If it interacts with other ion channels than there are more protein interactions going on right? But at any rate, that gp120 binds CD4 is similar to the way MHCII binds to CD4, is quite impressive to me. In fact, gp120 covers much more area on CD4 than MHCII does. That is the reason gp120 can compete MHCII in binding to CD4, resulting in viral infection. As far as the creation.com article, I'm not completely caught up with the studies in this area, but afaik the vpu gene has been found only in HIV-1 and simian immunodeficiency viruses isolated from chimpanzees (SIVcpz), and three species of old world monkeys within the genus Cercopithecus (SIVsyk). These proteins are quite diverse in sequence and predicted secondary structure. Most of the functional characterization of Vpu, including viroporin capabilities, has been limited to a small number of subtype B and more recently subtype C Vpu proteins from HIV1. Recent genetic characterization of a new SIVsyk showed that SIVden which carries the vpu gene (bearing no resemblance to any known vpu) is phylogenetically related to other Syk members which do not encode vpu. As for Venema's article, there are people that guess the WGD at the origin of vertebrates may have increased neofunctionalization, but others argue that it did not, because there is no strong evidence to prove that claim. Actually the evidence might well have been largely erased by 450 million years. However, his discussion of the one family, shows strong positive selection on sequence evolution after the genome duplications, and this provides some direct evidence for the claim. Not enough for you perhaps, how about all the studies that show, from a protein "foldability" and stability standpoint, you can get from here to there in a plausible step-wise manner ("here" being extant protein and "there" meaning simple peptide motif) involving gene duplication & fusion processes. Or the fact that the evolution of different proteins towards creation of binding ligands against a target molecule may go different ways. When you have the same target, fibrinogen, and very different libraries of the major coat protein, we received competing ligands having absolutely different binding peptides. Also I am a Christian and do not have a "materialist philosophy", the equation of acceptance of evolution with materialism is a folly that you share with the new atheists.Starbuck
August 19, 2011
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Starbuck; As to VPU's: Behe responded here; Response to Ian Musgrave’s “Open Letter to Dr. Michael Behe,” Part 4 Excerpt: One should, however, also make some distinctions with this example. First, although there apparently are five or so copies of Vpu in the viroporin complex, that does not mean that five binding sites developed. Only one new binding site need develop for one area of a protein which binds to a different area of the same protein, to form a homogeneous complex with, say, C5 symmetry. That is all that is required for a circularly symmetric structure to form. Second, the viroporin is not some new molecular machine. There is no evidence that it exerts its effect in, say, an ATP- or energy-dependent manner. Rather, similar to other viroporins, the protein simply forms a passive leaky pore or weak channel. (4,5) This situation is probably best viewed as a foreign protein degrading the integrity of a membrane, rather than performing some positive function. And third, I explicitly pointed out in Chapter 8 of The Edge of Evolution that HIV had undergone enough mutating in past decades to form all possible viral-viral binding sites, but commented that apparently none of them had been helpful (now I know that one of them helped). This I discussed as the “principle of restricted choice”: A third reason for doubt is the overlooked problem of restricted choice. That is, not only do new protein interactions have to develop, there has to be some protein available that would actually do some good. Malaria makes about 5,300 kinds of proteins. Of those only a very few help in its fight against antibiotics, and just two are effective against chloroquine. If those two proteins weren’t available or weren’t helpful, then, much to the joy of humanity, the malarial parasite might have no effective evolutionary response to chloroquine. Similarly, in its frantic mutating, HIV has almost certainly altered its proteins at one point or another in the past few decades enough to cover all of shape space. So new surfaces on HIV proteins would have been made that could bind to any other viral protein in every orientation. [Emphasis added here.] Yet of all the many molecules its mutated proteins must have bound, none seem to have helped it; no new protein-protein interactions have been reported. Apparently the choice of proteins to bind is restricted only to unhelpful ones. (pp. 157-158) 'So Dr. Musgrave’s “core argument” turns out to be a decidedly double-edged sword. Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane. However, in the past fifty years many, many more potential viral protein-viral protein interactions must have also developed but not been selected because they did the virus little good. That, dear readers, is “restricted choice,” a very large contributor to the edge of evolution.' http://behe.uncommondescent.com/2007/11/response-to-ian-musgraves-open-letter-to-dr-michael-behe-part-4/ and,, Response to Ian Musgrave's "Open Letter to Dr. Michael Behe," Part 4 "Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane --- not something to crow about after 10^20 replications and a greatly enhanced mutation rate." - Behe ---------------- further notes: In fact, I followed this 'VPU' debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were 'crowing' about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a 'leaky cell membrane' in binding site complexity. Thus the 'evolution' of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined for millions of years, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive. An information-gaining mutation in HIV? NO! http://creation.com/an-information-gaining-mutation-in-hiv ------------- As well Starbuck; as to your linked article, I noticed they mentioned Doug Axe's quote from this video: Nothing In Molecular Biology Is Gradual - Doug Axe PhD. http://www.metacafe.com/watch/5347797/ "Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way. - Doug Axe PhD. Starbuck I also noticed that they did not refute Axe by actually 'physically demonstrating' the origination of any new gene or protein, but merely trotted out 'just so stories' of how it could have happened. Does this truly constitute a rebuttal for you??? If so you have left the bounds of empirical science and have let your materialistic philosophy cloud your judgment! further notes: Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe: Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. http://www.ncbi.nlm.nih.gov/pubmed/15321723 Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe http://biologicinstitute.org/2011/05/04/correcting-four-misconceptions-about-my-2004-article-in-jmb/ ID Scientist Douglas Axe Responds to His Critics - June 2011 - Audio Podcast http://intelligentdesign.podomatic.com/entry/2011-06-01T15_59_43-07_00 Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 ================== etc.. etc.. etc..bornagain77
August 19, 2011
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Well, once again my comment wound up in the wrong thread. This should be in the Carnivorous Plants thread.dmullenix
August 19, 2011
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Here's Granville Sewell's take: "But certain carnivorous plants pose these problems in such a spectacular way that they are a focal point of the Darwinism debate, ever since Alfred Wallace warned Darwin about the problems posed by Utricularia, saying “I feel sure they will be seized on as inexplicable by Natural Selection” and implored him to address these difficulties in a future edition of his book “On the Origin of Species.”" Granville, couldn't you have at least Googled 'darwin carnivorous plants' before writing that? That would have taken you to "Carnivorous Plant" at wikipedia which mentions Darwin's book, "Insectivorous Plants" where he answered Mr. Wallace's questions and then some. With the name of Darwin's book, it's not hard to find it online at http://darwin-online.org.uk/content/frameset?itemID=F1217&viewtype=text&pageseq=1 if you want to read it. And NEWS, what is so difficult about a pitcher plant? They have leaves which collect water, insects fall into the water and drown. They rot and the plant absorbs some nuturients from them. I don't see where evolution is even necessary there.dmullenix
August 19, 2011
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fixing the url http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-5Starbuck
August 19, 2011
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I don't think it's fair to attack this piece, since it is a generalized recounting of Venema's thought life regarding this topic. Venema has written more technical criticisms, for example here. Frankly I had already been convinced with the finding of a channel forming protein with preference for cations (VPU), new findings also suggest that there is protein-protein interaction with other ion channels.Starbuck
August 19, 2011
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Hey Grunty...could you perhaps give an example or two of the so called "taking down" of the DBB and EOE. Personally, I've never read a rebuttal to Behe's claims that is satisfactory.ForJah
August 18, 2011
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The strange part is there isn't any chemical named on page 259...Joseph
August 18, 2011
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It- the crossexamination- is an interesting read but it exposes both Rothchilds' agenda and ignorance. Is that what you were shooting for?Joseph
August 18, 2011
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An interesting account, but I think Eric Rothschilds crossexamination of Behe is a much better read and takes down both DBB and EOE.Grunty
August 18, 2011
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