Evaluation of creationist/'intelligent design' writers: Batten Behe Bracht Dembski Gitt Meyer Strachan Joseph Truman Williams

Events: Dover trial

• 2001 June 6. William Dembski claims that the ev program does not demonstrate an information increase. These statements were critically reviewed and rebutted. He also claimed that the problem was caused by my SPECIAL RULE for handling ties in the number of mismatches between organisms. This claim was tested and shown to be false.

• 2001 September 23. "I Was Wrong" is an article in the October 2001 Scientific American (page 30) by Michael Shermer. It points out that "Those three words often separate the scientific pros from the posers". Here is what scientists in this lab do.

• 2001 November 10. The Problem of Information for the Theory of Evolution Has Tom Schneider Really Solved It? was posted by Royal Truman. I leave it to readers to identify the numerous errors and confusions. An Analysis of Truman's Criticism of the Ev Model.

• 2001 November 26. Don Batten posted a document Genetic algorithms-do they show that evolution works? An Analysis of Batten's Criticism of the Ev Model.

• 2001 November 30. A discussion started by Charles Creager Jr is posted at the Yahoo Origins Talk. Briefly, Dr. Creager apparently does not understand the term 'selection' as used in biology (it is not 'blind') and apparently he has not carefully read Shannon's works. For example, Shannon's R = H(x) - H_y(x) [Shannon1948 (Section 12)] corresponds to my R = H_before - H_after [Schneider1986]. Also, Shannon clearly stated at the beginning of his 1948 paper that meaning (and also by implication and perhaps elsewhere, knowledge and value) are not part of his measure. As for whether the Shannon's measure is a reasonable one, it has been highly respected and widely used for the past 53 years. This communication over the internet, clear phone conversations around the world and CD's are all possible because of it. As for whether or not the measure is a good one for biology, I invite Dr. Creager to read everything on my web site. In particular, the two back-to-back papers published on 2001 November 28th in Nucleic Acids Research, for which we got the cover illustration demonstrate that the method is excellent for making biological discoveries.

• 2002 January 21. The book No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence by William A. Dembski is now available from Amazon.com and other book stores. (December 2001, Rowman & Littlefield; ISBN: 0742512975). According to an email I have received, on pages 212-218 Dembski cites the Ev program as an example, but did not respond to the rebuttal and test, which completely refuted his claim.

• 2002 January 24-25. I have now read part of No Free Lunch by Dembski and added detailed comments on it in the rebuttal. Surprisingly, although he read the rebuttal page (since he quoted from it) Dembski ignored the test, which completely refuted his claim. He avoided stating that he made an error. The article "I Was Wrong" (Scientific American, October 2001, page 30, by Michael Shermer) says that "Those three words often separate the scientific pros from the posers". According to this definition, we must conclude that Dembski is a poser.

  • Like Dembski, creationist Duane Gish made specific claims about protein evolution, but when asked to provide evidence he stonewalled.

• 2002 October 18.

  American Association for the Advancement of Science (AAAS) Board Resolution on Intelligent Design Theory "Whereas, to date, the ID movement has failed to offer credible scientific evidence to support their claim that ID undermines the current scientifically accepted theory of evolution; Whereas, the ID movement has not proposed a scientific means of testing its claims; Therefore Be It Resolved, that the lack of scientific warrant for so-called "intelligent design theory" makes it improper to include as a part of science education;"

  entry 2004 Sep 19

• 2002 November 8.

  NPR Talk of the Nation, Teaching Evolution / Teaching Creationism

  This work was briefly mentioned in the program. After 12 minutes and 50 seconds, Lawrence Krauss said:

  "A recent article by a biologist named professor¹ Schneider² who is writing in nucleic acid journal.³ He discusses Behe's argument, very clearly, and he says you know, Behe has some very good points here, he calls his objections to standard models valid. And then what he purports to do is to set out to answer Behe's objections. Now suppose you've got a bright kid cruising the web maybe he's a staunch Darwinist, maybe he's an intelligent design zealot. Either way. He gets ahold of this paper and brings it into his classroom and he says: "Look here's an interesting scientific paper responding to Michael Behe, can we talk about that?"

  Notes:
  • ¹ I'm not a professor, I'm a research biologist at NIH.
  • ² The correct pronunciation is "Schneider", not "Snyder".
  • ³ The journal was Nucleic Acids Reseach.
  • ⁴ In the Discussion the validity point was directed to Spetner and Truman, and only indirectly to Behe.
  entry 2004 Sep 19

• 2003 Jan 19. Rebuttal to John Bracht's "Inventions, Algorithms, and Biological Design"

• 2003 Feb 15. Rebuttal to Richard P. Joseph's "EVOLUTION: A new perspective"

• 2003 Feb 20. In Still Spinning Just Fine: A Response to Ken Miller William A. Dembski says:

  Humans can mimic undirected selection and they can now do it very fast on the computer, thereby compressing deep time into ordinary time. And nevertheless, it remains the case that no genetic algorithm or evolutionary computation has designed a complex, multipart, functionally integrated, irreducibly complex system without stacking the deck by incorporating the very solution that was supposed to be attained from scratch (Dawkins 1986 and Schneider 2000 are among the worst offenders here).

  Let's dissect this statement.
  • undirected selection: The term `undirected selection' is an oxymoron since selection is always directed either by a person or by the environment of an organism.
  • compressing deep time into ordinary time: Of course there is no real time machine here. The simulations just run fast.
  • complex: I don't know what Dembski means by `complex' (and based on his book No Free Lunch", he doesn't seem to either) but he seemed pretty worried about the ev program, and rightly so since it can generate patterns containing arbitrarily large numbers of bits of information. In the case of the example given in the paper, there were 16 sites of 4 bits each for a total of 64 bits. It could be much more, so Ev results can be `complex'.
  • multipart: There are many parts in the Ev simulation: a set of binding sites and a recognition gene.
  • functionally integrated: After evolution by Ev the binding sites were interdependent with the recognizer gene. It was integrated and the relationship was functional. It was demonstrably functional because if an organism had a mutation that wrecked this integration, it would lose function and instantly die.
  • irreducibly complex system: As discussed in the paper, the Ev genomes are irreducibly complex systems exactly according to Behe's definition.
  • stacking the deck: Dembski is ignoring the fact that his only proposal for stacking the deck was clearly demonstrated to be incorrect. If Dembski understood the Ev paper, he would see that the program was not stacked.
  Ignoring results counter to one's claims is not proper science.

• 2003 July 7. An Evaluation of "Ev" (June 30, 2003 at ISCID, International Society for Complexity, Information, and Design) by I. G. D. Strachan critiques the Ev program.

  • discussion at ISCID (alternative address)
  I will evaluate it in detail when I get a chance. (A partial evaluation is now available.) In the meantime, Pim van Meurs wanted to know: Are the logos for different runs different?

• 2004 Feb 3: Royal Truman attacks again with a defense by Pim van Meurs (thanks!).

  Royal Member Member # 1060
  
  posted 29. January 2004 13:12
  
  About Dr. Tom Schneider: I have read most, perhaps all, his papers, with much interest. In particular the demonstration that the quantitative information content (in Claude Shannon's sense) permits binding sites to be placed in the right number on the genome and to be identified unambigiously.

  This is an incorrect summary of the Ev simulation. The information content of binding sites is a measurement of the sites. It does not permit the sites to be placed on the genome, nor is it related to their locations.

  He believes novel binding sites evolved from random sequences.

  More than that - the program demonstrates it! No belief is required. Run the program if you think it's not true.

  I am convinced most were designed.

  Based only on this statement ... which proves nothing.

  In fact, I propose they were originally created with more information content than needed, to provide fault tolerance towards mutations.

  This is inconsistent with his statement above about unambiguous identification. If Rsequence is close to Rfrequency, there is little, if any, such fault tolerance. This is consistent with evolution being blind to the future possibilities.

  I suspect the Design also included the notion of how long proteins should bind to specific sites, as part of the regulatory strategy.

  Perhaps, but this is a question independent of how the sites came to be.

  Dr. Schneider apparently approved of at least some of the things I suggested on an on-line essay (http://www.trueorigin.org/dawkinfo.asp) in which Dr. Richard Dawkins was on the receiving end, but was not quite so pleased when his own ideas received some of my friendly criticism: http://www.trueorigin.org/schneider.asp

  To make the record clear, I disagree with most of Royal Truman's ideas. See Pim's response.

  I admit I got a little carried away in the last essay. But the central challenge remains unanswered: without the necessary sensitivity analysis he is not justified in making any claims as to biological relevance. He has the software and it would require very little effort for him to plunk in the parameter settings I suggested and to then report how his critters `evolve'. The proposed simulation settings are biologically-speaking very generous on my part, and are actually unrealistic, but would permit a crude extrapolation.

  Truman can do it himself, the Ev source code is freely available.

• 2004 Mar 11: The Twin cities Creation Science Association has a page about Richard Dawkins And The 11 Second Pause leading to a discussion in which Ross S. Olson is still complaining that Dawkins did not answer the question of how information gain occurs. I invited Olson to read the ev paper, which should resolve the issue.

• 2004 Sep 3: Analysis of Meyer, S.C. "The origin of biological information and the higher.
  Intelligent design study appears: Publication of paper in peer-reviewed journal sparks controversy by Trevor Stokes.

  • Meyer, S.C. "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, 117[2]:213-239, August 4, 2004. Republished online August 28, 2004 at http://www.discovery.org/scripts/viewDB/index.php?command=view& id=2177
  • Meyer's Hopeless Monster a detailed critique by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry at The Panda's Thumb. 2004 August 24. An amusing quote:

    There are worms with guts, and worms with muscles, worms with segments, worms with appendages, and even worms with a stiff tube in them (this last would be us).

  • Meyer did not to cite the proper literature. Meyer's paper was supposed to be a review of the topic:

    "This review ... will treat the problem of the origination of the higher taxonomic groups as a manifestation of a deeper problem, namely, the problem of the origin of the information (whether genetic or epigenetic) that, as it will be argued, is necessary to generate morphological novelty."

    When discussing information theory, Meyer correctly cited Claude Shannon but did not cite recent papers directly applicable to his topic, which include the paper described on the page you are reading, Evolution of Biological Information. Another paper that should have been cited is J Theor Biol. 2003 Jun 21;222(4):477-83. Selective pressures on genomes in molecular evolution. Ofria C, Adami C, Collier TC..
  • The paper fails by the AND-multiplication pitfall. He repeatedly stated that various structures, such as proteins, have low probability. But his calculations are hopelessly flawed because they all assume that the parts of a protein came into being independently. This is clearly not the case (as the Ev program described on this page abundantly shows). As anyone with a high school mathematics background knows, it is inappropriate to multiply probabilities unless the two probabilities are independent. So it was incorrect for Meyer to multiply the probabilities of obtaining individual amino acids. Therefore his arguments fail.
  • Information coevolves with function. Meyer states that

    "... natural selection cannot contribute to the process of information generation until after the information necessary to build the requisite system of proteins has arisen."

    The Ev program, described in "Evolution of Biological Information", demonstrates that Meyer's statement is false. The information in the protein coevolves with its function.
  • Punctuated equilibrium correlates directly with information gain. Meyer states that

    "Further, punctuated equilibrium has not addressed the more specific and fundamental problem of explaining the origin of the new biological information (whether genetic or epigenetic) necessary to produce novel biological form."

    This is incorrect since the Ev program demonstrates clearly the gain of biological information as a punctuated equilibrium. See Figure 2b, which shows a rapid increase in the information in binding sites up to the predicted amount of information ("punctuation") followed by noisy stability ("equilibrium").

  If I had reviewed the paper, I would have recommend rejection, based on the points give above. The board of the Proceedings of the Biological Society of Washington has "deemed this paper inappropriate for the pages of the Proceedings."

  Stephen C. Meyer: Discovery Institute; Palm Beach Atlantic University (PBA Guiding Principles); web page.

  Richard Von Sternberg: editor, (NIH; Smithsonian Department of Systematic Biology, Invertebrate Zoology; Baraminology Study Group Editorial Board, "committed to constructive scientific research in creation biology". Baraminology? Google: baraminology: the study of created Biblical kinds), has signed a manifesto, that states that he is "skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life".

  Sternberg was to give a talk at a pseudo-scientific meeting, Evolution, Intelligent Design, and the Future of Biology on 2004 Nov 23 (cancelled as of September 21). The abstract stated: "The talk will emphasize that genes themselves are irreducibly complex structures, and pitfalls in common neoDarwinian models of gene evolution." The Ev paper demonstrates that Behe's concept of "irreducible complexity" is untenable. Sternberg's position is untenable.

• 2004 Sep 21 Q: How many things can a creationist get wrong in a single article? A: All of them. by Paul Z. Myers.
• 2004 Sep 22 Readers respond: Story on intelligent design study highlights debate on creationism and evolution. David L. Bump (Flushing, Michigan, david.bump@att.net home page, previous letter) claims:

  It's also clear that after almost 150 years of efforts, we've found no forces or processes of inanimate nature that produce complex organization ...

  David Bump was invited to study the Ev program and other genetic algorithms.
• 2004 Oct 4: The cancelled talk has been moved. google: Evolution site:http://www.studium.helsinki.fi reveals http://www.studium.helsinki.fi/ajankohtaiset/ announcing "Evolution, Intelligent Design, and the Future of Biology -eminaari 22. - 23.10.2004 peruutettu" and a link to Lecture series on Biology - Tackling Ultimate Complexity

  Helsinki University of Technology
  Main building, Mellin-auditorium, Otaniemi
  22.10. 14:15-19:15
  Nothing in modern scientific discussion raises controversy and emotions like the question of design in biology. This is understandable since the ruling paradigm of natural history is Darwinian evolution: random genetic changes guided by natural selection have created all the biological complexity. A small but growing number of scientists challenge the neo-Darwinian view (doc) and claim that biology is better understood as a product of intelligent design. Evolutionary biologist Dr Richard Sternberg and philosopher of science Dr Paul Nelson explain the reasons in this lecture series.

  Lectures are by Paul Nelson and Richard Sternberg. Paul Nelson has a lecture "How Do We Detect Intelligent Causes?" If you've followed the argument here, then you know that that the answer is we can detect living causes but not necessarily intelligent causes.

  ---

• 2004 Sep 19: As mentioned in an NPR talk of the Nation program (after 36 minutes, 40 seconds), the creationist organization Science Excellence for All Ohioans has put forth a definition of intellignt design:

  Intelligent Design: A theory about the origin of life that holds that intelligent causes best explain the origin of many features of living systems. The theory is based on the testable assumption that structures that exhibit high information content are more likely to be the result of intelligent design than of undirected natural causes. ... Intelligent design theorists examining evidence for the origin of life draw a design inference when they observe high information content and high specified complexity in biologically active molecules, for example DNA, RNA, and proteins.

  The Ev program clearly and unequivocally demonstrates that no intelligence is required for information (Rsequence) to appear in biological systems, so this definition collapses.

  Intelligent design theorists look for: Complex arrangements or patterns that are unlikely to occur by chance, from which design can be inferred based on comparisons with other things that exhibit similar complexity and are known to be designed.

  In this statement SEAO makes The AND-Multiplication Error and therefore their logic and their definition are invalid.

• 2004 Sep 19: As mentioned in a 2002 NPR talk of the Nation program (after 40 minutes, 40 seconds), Stephen Meyer stated "We are saying you can detect intelligence scientifically." This is incomplete and therefore wrong. The correct statement is: You can detect life scientifically - from the information patterns. Intelligence is a subset of all living things. The "Intelligent Design" movement has made a fatal misunderstanding, to attribute patterns that living things evolve to intelligence.

• 2004 Nov 1: The creationist meeting in Finland went ahead in a different location on 2004 October 22: Lecture series on Biology - Tackling Ultimate Complexity.
  • Dr. Paul Nelson spoke about "How Do We Detect Intelligent Causes?" Briefly, the fatal flaw in his presentation is the one mentioned above 2004 September 19. He neglected a major viable and extremely well documented alternative hypothesis: living systems evolve new patterns.
  • Dr. Richard Sternberg spoke on "Genomes as Complex Systems". The examples Sternberg begins with are well known (except for vague and undefined references such as 'inexplicable effects'). They all can be understood in terms of molecular evolution. Sternberg set up a straw man: an incomplete, non-modern view of molecular evolution. It has no relation to modern understanding. The presentation on the web ended before coming to a conclusion. The second part pointed out that genetic systems are complex and modular, which has been known since the 1960's. Again, the presentation on the web ended before coming to a conclusion.

• 2004 Nov 2: Home Page of Dr. Richard M. v. Sternberg. Here he explains his positions. The critiques above were not addressed.

• 2004 Nov 6: Wisconsin district to teach more than evolution. CNN. The Grantsburg Wisconsin school board is making an error to teach creationism as science. This is the typical creationist tactic - a call for "equal time" even though the ideas have been repeatedly discredited.

• 2004 Dec 13: Response to "Dissecting Dembski's 'Complex Specified Information'" by Walter Rothe. I'll just respond to his response step by step:
  • He says that I claim "that specified complexity can be produced though evolutionary mechanisms." and `This allows Schneider to make the claim that evolution can create "specified complexity" that isn't smuggled in by a designer.' These statements are incorrect since I never use the unscientific and ill-defined terminology "specified complexity" in the scientific literature.
  • "the reproducibility by chance figure Schneider achieved by computer evolution was so intriguingly small (5x10-20), that I couldn't believe it was real." If Rothe would follow the argument in the paper closely he would see that it is a straight forward computation based on the results of the Ev run. (The relevant text is in the Discussion.)
  • "Schneider's standard program simulates a genome that evolves 16 regulatory binding sites and a single regulatory gene that makes a protein that binds to the sites." This is technically incorrect, the number of sites is supplied to the program in a parameter file. It would be more correct to say that this was an example run.
  • "Nature does not produce reproductive fitness functions that without stress are perfectly determinative in a single generation over all individuals like Schneider's fitness function is." Fair enough. Modify the program to make it more probabilistic. It is easy to see that the same results will be obtained, but the computer run time and the wait for results will be longer. Note also, that there is some degree of probability of death of a particular organism, depending on how many mistakes it makes. This function changes with time because the population changes with time. So I find the concept of 'fitness' to be misleading and generally useless since 'fitness' is modified by the evolving organisms when they change their environment.
  • "A real regulatory protein is tuned to the shape of the binding site, where changes to one base partially affect the binding of neighboring bases instead of the binding of bases being individually tunable." It turns out that the assumption of positional independence is reasonably good for binding sites, and there is a literature on this subject (a paper by Gary Stormo in particular). Even if positions were not independent, the program could be made to account for such effects.
  • "Furthermore, development of complex structure seems to involve a cascade of genes synchronized with other cascades in different parts of the body, through signaling interactions." Irrelevant to the problem at hand.
  • "I think it's reasonable to assume that many gene cascades have a negative selection coefficient until they are in their final form - a sort of irreducible complexity." That is not a reasonable assumption. See the discussion in the Ev paper itself (!) for why the idea of "irreducible complexity" is untennable.
  • Rothe had an 'epiphany' when he realized the mutation rate was high in the simulation. What he is missing is that under good conditions bacteria can reproduce in about 20 minutes and they have had as long as 2 billion years to evolve, even with error rates that are held down by error correction systems. Also, there are plenty ways to try variations since there is a huge planetary sized population. Bacteria and their viruses are the main living things on the planet.
  • "However, we know that this level of fine tuning [obtaining the results found with Ev] is extremely difficult to achieve for single individual traits". We do not "know" this. Rothe has apparently not read Schneider1986, which is the basis of the Ev simulation and which shows that the results found by Ev are what one (approximately) observes in nature. Trying to understand that the 'fine tuning' of binding sites in which Rsequence is close to Rfrequency is, of course, why I wrote Ev in the first place.

• 2005 Mar 22: Q&A: MRSA 'superbugs'. BBC News gives a nice explanation of "Why does MRSA exist?" in evolutionary terms.

• 2005 Apr 2: http://tccsa.tc/debate.html gives Dawkin's response to the question "Professor Dawkins can you give an example of an evolutionary process which can be seen to increase the information in the genome?" They then cite "Dr. Thomas D. Schneider's Challenge". Apparently they have not studied Ev enough to understand that it is the simplest possible model that shows how information is gained in living things. They point to Strachen, who, of course, ran the program and got information increases ... They have the answer in their hands (i.e., how information increases occur) and ignore it! See: Richard Dawkins And The 11 Second Pause.
• 2005 Apr 12:

  The world is a mirror representing the divine life... Intelligent design readily embraces the sacramental nature of physical reality. Indeed, intelligent design is just the Logos theology of John's Gospel restated in the idiom of information theory.
  --- William Dembski, Touchstone Magazine, Signs of Intelligence, July/August, 1999

  • google: "The world is a mirror representing the divine life"
  • The Religious Basis of Intelligent Design. The creationists themselves admit that ID is not science.
  • Touchstone (not availble online)
• 2005 Apr 21: Evolution Fairytale Forum -> Tom Schnieder's [sic] 'the And-multiplication Error' Article Refuted http://www.evolutionfairytale.com/forum/index.php?showtopic=165. Gosh they pile up the errors quickly ... One or two notes:
  • Not responding to all objections does not mean that reasonable answers do not exist! It means I have more important things to do than to respond to everything. Learn the basic information theory before making comments.
  • The ev program does not evolve a genetic code in the sense of codons and amino acids. Read the paper: it evolves a weight matrix directly.
  • If you don't like the form of selection, make it different (e.g. probabalistic). Try it out yourself!
  • The goal of ev was to see if Rsequence evolved to Rfrequency. The answer was yes. How about dealing with that? Does Ev show information increase based entirely on replication, mutation and selection? Of course! Look at the data!
• 2005 May 1: In the Evolution Fairytale Forum http://www.evolutionfairytale.com/forum/index.php?showtopic=165 at Apr 29 2005, 04:35 PM, Fred Williams complains that the "program is not real-world, not even close. New information was not created naturalistically." It is not clear what he means by 'real-world' or 'naturalistically'. If you read the Ev paper carefully you will note that the model parallels the natural situation. There are places on the genome where having a binding site would be advantageous whether or not there is a site there. Genomes are of a certain size. These two factors determine Rfrequency in natural genomes and the situation is the same in the ev simulation. So Fred Williams needs to be explicit about what his problems are. I suggest that he do some honest work and write his own program. I think he will find when he does this that the Ev program is about the minimum coding that one can do that still matches the natural world. Sure, you could do molecular modelling in three dimensions of molecules diffusing through space and binding. Unfortunately you won't have enough computer power to do this simulation. So replace the molecular modelling with a model of a sequence recognizer - a weight matrix. These are well recognized in the molecular biology literature, if you read even a few papers! The sequence does not need to be three dimensional, it can be a string in the computer. That does not alter the computation of the Shannon information at all, so it is still a good model.
• 2005 May 1: In the Evolution Fairytale Forum http://www.evolutionfairytale.com/forum/index.php?showtopic=165 at Apr 28 2005, 09:07 AM Fred Williams complains that codes do not evolve. I suggest reading: Shannon1949 and ccmm. All specific molecular interactions in biology are part of codes. See the glossary definition: code.
• 2005 May 4: Evolution on trial in Kansas, CNN. The Kansas Board of Education is holding another debate on evolution. Why hold a debate about evolution at this point unless you don't know the facts? John Calvert (Intelligent Design Network) said: "We're not against evolution. But there is a lot of evidence that suggests that life is the product of intelligence. I think it is inappropriate for the state to prejudge the question whether we are the product of design or just an occurrence."
  • Question: If he is not 'against' evolution, then why hold a debate? Answer: We have to conclude that he is actually 'against' evolution. That is, he denies that evolution does occur. Direct evidence that this is the case is that that is the purpose of his institute. He is ignoring or neglecting the huge body of facts about evolution and that the observations of evolution are well explained entirely by Darwin's hypothesis: replication, mutation and selection.
  • What is the evidence? Did you see a martian tinkering with genomes? Show me photographs please. The evidence that evolution did occur are found in miles of thick rock layers, in thousands of taxonomic observations, in relationships between a huge variety of DNA, RNA and protein molecular sequences, etc. The evidence is recorded in literally thousands of scientific papers and new papers are published daily. With the web there is no excuse anymore!
    • I googled for 'evolution and quickly found this open journal. Read! Evolution
    • I googled for molecular evolution Lots of nice references, one of which is:
    • Journal of Molecular Evolution Unfortunately you would need a subscription to read this one.
    • I went to Pubmed Central and searched for 'evolution'. I found 19250 papers all of which you can read!
      So you have no excuse! The OVERWHELMING evidence for evolution in the scientific literature is just a mouse click away!
  • Presumably, the so-called evidence is that there are PATTERNS in living things. The ev program shows that PATTERNS appear by evolutionary processes. See the ev movies - there is no need to hypothesize anything beyond replication, mutation and selection.
  • Saying that it is a 'design' introduces unnecessary, unexplained, mysterious factors. If it is an intelligence, how can you distinguish that from the patterns that living things themselves evolve? Where is this so-called intelligence? How does this so-called intelligence affect the thermal noise that affects DNA polymerases?
  • Saying that evolution is 'just an occurrence' is a complete misrepresentation of what happens during evolution, which is composed of replication, mutation and selection. This is a typical creationist misrepresentation.
  John Calvert is putting out a religious viewpoint and this has no place in a science education.
• 2005 May 4: Intelligent Design Network claims:

  'Positive evidence of design in living systems consists of the semantic, meaningful or functional nature of biological information, the lack of any known law that can explain the sequence of symbols that carry the "messages," and statistical and experimental evidence that tends to rule out chance as a plausible explanation. Other evidence challenges the adequacy of natural or material causes to explain both the origin and diversity of life.'

  Let's break this statement down:

  'Positive evidence of design in living systems consists of the semantic, meaningful or functional nature of biological information,'

  First, a gain of information occurs when the Ev program runs, see figure 2B. Since there is no 'design' going on by an external agent during an ev run, information gain is not evidence of 'design'. To the contrary, the information gain is fully explained by reproduction, mutation and selection because Rsequence evolves up to Rfrequency. That is, the amount of observed information gain, Rsequence, exactly fits the amount predicted by the theory, Rfrequency. So this claim is false.

  'the lack of any known law that can explain the sequence of symbols that carry the "messages,"'

  This is wrong: the explanation is widely known (evolution). The laws are: reproduction, selection and mutation. Read the Ev paper for the discussion on the thermodynamic increase of entropy in the genome (by mutation) being countered by the selection.

  'and statistical and experimental evidence that tends to rule out chance as a plausible explanation.'

  This is a misleading statement. Evolution by natural selection is not 'chance' since it is driven by selection. This misunderstanding is repeated frequently by creationists, but it is wrong every time. See: The AND-Multiplication Error for a discussion of the error they are probably making here. Finally, what is the experimental evidence they are talking about? That living things are complex? The ev program produces a complex result without any design, read the paper!

  'Other evidence challenges the adequacy of natural or material causes to explain both the origin and diversity of life.'

  What is the evidence? There is none, this is a vague statement. The diversity of life is WELL EXPLAINED by a huge body of knowledge on mutation mechanisms, including jumping genes.
  What's left of the statement? Nothing!
• 2005 May 5:
  

  "It's often said that because evolution happened in the past, and we didn't see it happen, there is no direct evidence for it. That of course is nonsense. It's rather like a detective coming on the scene of a crime, obviously after the crime has been committed, and working out what must have happened by looking at the clues that remain. In the story of evolution, the clues are a billion-fold."
  
  "There are clues from the distribution of DNA codes throughout the animal and plant kingdoms, of protein sequences, of morphological characters that have been analyzed in great detail. Everything fits with the idea that we have here a simple branching tree. The distribution of species on islands and continents throughout the world is exactly what you'd expect if evolution was a fact. The distribution of fossils in space and in time are exactly what you would expect if evolution were a fact. There are millions of facts all pointing in the same direction and no facts pointing in the wrong direction."
  

  --- Richard Dawkins The atheist, www.salon.com, April 28, 2005.
  (We might note that horizontal transfer has been found, but it is clearly the exception not the rule and we understand its mechanism: jumping genes.)
• 2005 May 5:
  DNA: The Tiny Code That's Toppling Evolution by Mario Seiglie (The Good News) is full of errors and incorrect conclusions. Here's why.

  "In addition, this type of high-level information has been found to originate only from an intelligent source."

  This statement is disproven by the Ev program. That simple computer program generated information by Darwinian evolution - no intelligence was required.

  "For instance, the precision of this genetic language is such that the average mistake that is not caught turns out to be one error per 10 billion letters. If a mistake occurs in one of the most significant parts of the code, which is in the genes, it can cause a disease such as sickle-cell anemia. Yet even the best and most intelligent typist in the world couldn't come close to making only one mistake per 10 billion letters-far from it."

  • The error rate is indeed that low.
  • Sickle-cell anemia and many other genetic diseases do indeed occur.
  • The error rate of a typist is irrelevant! The DNA polymerase makes low errors and in addition there are correction systems. Each information system has its own error rate.

  "So to believe that the genetic code gradually evolved in Darwinian style would break all the known rules of how matter, energy and the laws of nature work."

  The argument is a straw man because Shannon's channel capacity theorem allows for an error rate as low as necessary for survival.

  "In fact, there has not been found in nature any example of one information system inside the cell gradually evolving into another functional information program."

  This is wrong, there are thousands of examples. The ev program shows how. CONCLUSION: The page is full of errors.

  "We therefore have in the genetic code an immensely complex instruction manual that has been majestically designed by a more intelligent source than human beings."

  Because of the errors above, this is not a valid conclusion.

  "It is good to remember that, in spite of all the efforts of all the scientific laboratories around the world working over many decades, they have not been able to produce so much as a single human hair. How much more difficult is it to produce an entire body consisting of some 100 trillion cells!"

  Our technology is not sufficient yet. This does not have anything to do with the validity of the evolutionary explanation, so it is an irrelevant argument. However, when our technology reaches that point they will undoubtedly argue inappropriately that it was done using human intelligence, even if we use genetic algorithms to develope the sequences! Such genetic algorithms are already in use, an example is Nanev. (NANEV: a program employing evolutionary methods for the design of nucleic acid nanostructures. Russell P. Goodman, BioTechniques Vol. 38, No. 4: pp 548-550, Apr 2005)

  "Up to now, Darwinian evolutionists could try to counter their detractors with some possible explanations for the complexity of life. But now they have to face the information dilemma: How can meaningful, precise information be created by accident--by mutation and natural selection? None of these contain the mechanism of intelligence, a requirement for creating complex information such as that found in the genetic code."

  The ev program disproves the above statement! Note also the flawed logic: information is created by a combination of accident (mutation) AND replication AND selection! There is no requirement for 'intelligence'.

  "So how could the genetic information of bacteria gradually evolve into information for another type of being, when only one or a few minor mistakes in the millions of letters in that bacterium's DNA can kill it? Again, evolutionists are uncharacteristically silent on the subject. They don't even have a working hypothesis about it."

  This is blatently wrong for several reasons at once. First, some changes will indeed kill but many will not. See, for one example out of potentially thousands, our RFS paper. So the question implies the author does not understand basic biology. Second, biologists are far from silent on the subject! Quite to the contrary there is a huge and rapidly growing literature written on this subject every year, so this author is just depending on the ignorance of the reader. The only people who would make and believe the above statement have not done their homework! Finally, it is quite wrong that there are no hypotheses. The main working hypothesis is (obviously) Darwinian evolution! (I find it amazing that the creationists can pack so many blatant errors into a single statement.)

  "No hypothesis has come close to explaining how information got into biological matter by naturalistic means" (Strobel, p. 282)."

  The ev program proves that Lee Strobel's statement is incorrect.

  "Werner Gitt, professor of information systems, puts it succinctly: "The basic flaw of all evolutionary views is the origin of the information in living beings. It has never been shown that a coding system and semantic information could originate by itself [through matter] . . . The information theorems predict that this will never be possible. A purely material origin of life is thus [ruled out]" (Gitt, p. 124)."

  Gitt will have to withdraw his statment in light of the success of the ev program. See Errors in Werner Gitt's work with Information Theory for an evaluation of Gitt's work.
  (Permission has been granted to reproduce the quotes above. "Cause and Effect: An Often-Overlooked Principle," The Good News, November/December 1998, Volume 3, Number 6, page 10, ©2003 United Church of God, an International Association. The United Church of God is on the Internet at www.ucg.org and www.gnmagazine.org.)
• 2005 May 9: Scientists snub Kansas evolution hearings. Education hearings rigged, say science organizations CNN. The Kansas State Board of Education would do well to read some of the literature before calling a `debate'.
  • The Fact of Evolution: Implications for Science Education James R. Hofmann and Bruce H. Weber, Science & Education 12: 729 760, 2003.

• 2005 May 13. After listening to some creationists speak without rebuttal from scientists, Kansas State Board of Education member Kathy Martin concluded 'that evolution is "an unproven, often disproven" theory.' (CentreDaily 2005 May 12). She seems not to know that the evolutionary theory has never been disproven and that the intelligent design theory failed a critical test.

  From toms Fri May 13 00:38:53 2005
  To: JWaugh1052@aol.com, MSGamble@swbell.net, bill.wagnon@washburn.edu,
  carolrupe@hotmail.com, conniemorris2010@yahoo.com, contact@ksde.org,
  jwmsbacon@aol.com, krw@ourtownusa.net, martinkathy@yahoo.com,
  sabrams@hit.net, vanmeter@terraworld.net
  Subject: disproving creationism
  
  Dear Ms. Martin:
  
  http://www.centredaily.com/mld/centredaily/news/nation/11632864.htm CentreDaily (2005 May 12) quotes you as saying that evolution is "an unproven, often disproven" theory. As a working scientist, I gather evidence directly by doing experiments in the lab or indirectly by reading the peer reviewed literature. The evolutionary theory has never been disproven in the peer reviewed literature. On the other hand, the creationists proposals have been repeatedly debunked. For example, I wrote a paper about the evolution of what they call 'complexity' and published it in a top scientific journal (T. D. Schneider, "Evolution of Biological Information", Nucleic Acids Res., 28(14): 2794-2799, 2000, see http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/ for an online copy.) My paper debunks three creationists by showing how information (`complexity') appears in DNA by natural selection. A creationist, William Dembski thought this was incorrect. His prediction was sufficiently precise that I could test it. When I did so, the intelligent design theory failed the test.
  
  Please review this paper carefully as it will reveal to you that the creationists arguments are full of holes.
  
  You may also find the accompanying program to be an excellent teaching tool for your students.
  
  Sincerely yours,
  Dr. Thomas D. Schneider
  PS: May I have permission to post your responses on the internet?

• 2005 May 14.

  From martinkathy@yahoo.com Sat May 14 00:14:38 2005
  Date: Fri, 13 May 2005 21:14:19 -0700 (PDT)
  From: Kathy Martin
  Subject: Re: disproving creationism
  To: Tom Schneider
  
  Dear Dr. Schneider, Thank you for the information. As a working scientist I would imagine evolution could be used extensively. Did the CentreDaily include the part where I said it is unproven in many of it's claims for explaining origins of life? I'm sure both you and Dr. Dembski could dwarf any scientific knowledge I have. We did hear from many learned individuals and I found it very interesting and informative. This could be a great source for students as they research and critically analyze the scientific data in search of answers for themselves.
  Sincerely, Kathy Martin
  
  Subject: Re: disproving creationism
  To: martinkathy@yahoo.com (Kathy Martin)
  Date: Sat, 14 May 2005 11:17:53 -0400 (EDT)
  Cc: JWaugh1052@aol.com, MSGamble@swbell.net, bill.wagnon@washburn.edu,
  carolrupe@hotmail.com, conniemorris2010@yahoo.com, contact@ksde.org,
  jwmsbacon@aol.com, krw@ourtownusa.net, martinkathy@yahoo.com,
  sabrams@hit.net, vanmeter@terraworld.net
  
  Dear Ms. Martin:
  As you can read in the article, the CentreDaily did indeed quote you:

  The witnesses led board member Kathy Martin, who had expressed doubts about the theory before the hearings began, to conclude that evolution is "an unproven, often disproven" theory.

  I disagree with this view and ask that you point out the specific 'unproven' and 'disproven' problems in the scientific literature that you are referring to. The creationists do not have any literature that stands up to careful scrutiny. For example, they claim that living things are too 'complex' to be explained by evolution. The first problem with this claim is that 'complex' is ill defined. The solution to this is to use Claude Shannon's precise definition of information. When one uses Shannon's measure for understanding biology, one comes to the clear conclusion that the evolutionary mechanism proposed by Darwin is completely sufficient to explain the information ('complexity') of living organisms. Re-read my paper on Evolution of Biological Information. There is your proof.
  Dr. Thomas D. Schneider
  PS: Again, may I have permission to post your responses on the internet? Since you did not indicate what to do in your initial reply, I am posting your responses.

• 2005 May 14.

  From toms Sat May 14 11:48:57 2005
  To: JWaugh1052@aol.com, MSGamble@swbell.net, bill.wagnon@washburn.edu,
  carolrupe@hotmail.com, conniemorris2010@yahoo.com, contact@ksde.org,
  jwmsbacon@aol.com, krw@ourtownusa.net, martinkathy@yahoo.com,
  sabrams@hit.net, vanmeter@terraworld.net
  Subject: Evidence for evolution
  
  Dear Ms. Connie Morris:
  
  The CentreDaily reported:

  "I can only conclude that they don't have evidence (for evolution)," board member Connie Morris said.

  Please take a look at this link:
  http://www.pubmedcentral.nih.gov/
  
  It is the PubMed Central repository of open scientific papers. This is only a fraction of the available scientific papers, since only open papers are included and most papers before 1995 are not online.
  
  Enter the word 'evolution' in the search box.
  
  You will find that there are thousands of papers on evolution, about 19000 as of today.
  
  Even if you read 1 percent of the literature immediately available to you, that's 190 papers.
  
  Clearly, when you ask biologists to give a 2 minute summary of the evidence in favor of evolution, they are overwhelmed by the evidence, since presenting a single paper may take typically take an hour. The evidence in favor of evolution cannot be given justice in a few days of combative debate since there is too much of it.
  
  Please read some books and papers on evolution and molecular biology (20 or 30 will do for starters) and then please re-evaluate your conclusion publically.
  
  Sincerely yours,
  Dr. Thomas D. Schneider
  PS: May I have permission to post your responses on the internet?

• 2005 May 14.

  Fred Williams is stirring up quite a discussion.

  • He claims: "I believe Schneider's Ev program has been overwhelmingly proven to be bad science and I think it would serve him best to abandon it and remain focused on his sequence logo work." Dr. Williams does not specifically point out the "overwhelming" problems, and the known issues have been resolved. Such non-specific attacks are meaningless because there is nothing to respond to.
  • However, it is important to note that the program confirmed a scientific hypothesis. I did not know before I ran Ev whether it would confirm the hypothesis or not. Whether or not the Ev model confirmed the hypothesis, it was a clear test and was therefore good science. Further, Ev is a direct extension of the 'sequence logo work'. It is not appropriate for Dr. Williams to attempt to direct the work of a publishing scientist. If he feels that there are significant errors, I suggest that he demonstrate these errors clearly and publish his papers in the peer reviewed literature. I do not respond to every illogical argument dreamed up because I am publishing more papers. See you in the scientific literature Dr. Williams!
  • Dr. Williams complains about my not responding to a particular ephimeral web based news group. I do not have time to respond to every blatently poor argument the creationists dream up. If a creationist such as Truman has been repeatedly shown to have multiple flaws in his argumentation AND he has not corrected any of them (the current state of affairs) then it does no good to rebut the repeated errors. Any smart person will review the literature and find that Dr. Truman's and Dr. William's logic is flawed from the initial pages.
  • Dr. Williams claimed that the use of truncation selection makes the Ev program invalid. I have put a response on another page about truncation selection. Bottom line: his complaint does not apply to Ev!
  • In another inappropriate attack, Williams claims "I think there is a good reason Tom told you this personally and did not mention it in his paper. smile.gif Even through a biased evolutionary journal, this claim would have been tough for any reviewer to swallow because it is blatantly incorrect." Perhaps Dr. Williams has not published any papers? The Ev paper is focused on a very specific issue. The question of whether a binding site is a code had already been resolved 8 years earlier with the publication of the ccmm paper. I mentioned this above. It was not necessary to bring up the point that Ev generates a code in the Ev paper.
  • For those who are confused, the "genetic code" is a code. It maps between RNA and protein. From the viewpoint of a single tRNA, there is one (or a few) codon(s) that correspond to the amino acid carried by that tRNA. The tRNA is a recognizer within the reading frame imposed by the translation system. In the same way, a genetic recognizer such as a repressor or activator recognizes a particular pattern. From this you can easily see that every genetic recognizer is using a code to distinguish sites from nonsites.
  • Williams claims that the mutation rate is too high. Solution: run with a lower rate. Is he claiming that with a lower rate the Rs will not approach Rf? Try it yourself or think about it for a minute. Clearly Rs will still approach Rf but at a lower rate!
  • Williams agrees with Truman that "Error catastrophe would be inevitable." Try it. If you set the error rate too high in Ev, it doesn't evolve. So what? "negative effects of accumulating genetic load" ... the organisms that accumulate too many errors get wiped out. It's called selection ... Without specific predictions Dr. William's arguments hold no water. With specific predictions, Dr. Williams could be running the program and showing that the information gain does not occur!
  • 50% is hardly a high rate of selection. Look at the dandilion seeds. Look at any species. Calculate how long any specific species would take to overwhelm the entire planet. How many sperm are carried by a man? Millions!! How many babies come from those sperms? At most, and then only rarely, tens! So for humans the selection factor is on the order of 100,000 to 1. 50% looks lenient ...
  • Williams claims: "There is another way to look at this. Consider the fact that Schneider's program, at least on my inspection of it, appears to be set up to work every time. It's odds of success are unity!" The program was not written to 'work every time', it was written to test a hypothesis. It runs without crashing (works every time) because it has reasonably good code. The fact that Rs approaches Rf is a result. It was not put into the program. Dr. Williams may write his own programs to test other hypotheses instead of complaining! Note: In the above, Dr. Williams is implicitly admitting that information gain occurs by mutation, selection and replication!
  • Williams claims: Whenever a program has a guaranteed outcome, we know the information is already present from the beginning. Dr. Williams has yet to explain why Rs approaches Rf. This is not in the program, go take a look at the code. Determining whether Rs approaches Rf is what the program was originally intended to test. These days it is merely used to be, as one person pointed out "a thorn in the sides of creationists".
  • Williams claims "Dawkins was one of the reviewers of his paper." Now how does he know that? That is inside information at Nucleic Acids Research. Generally, only the reviewers and the editor know this, it is not made public. So the statement is probably false. Dr. Williams can demonstrate otherwise by documenting his sources. (Note: Dawkins did read an early version of the Ev paper and comment on it, this is not 'review'.)
  • Williams claims "the information is there from the start, this is simply indisputable". This is blatently wrong. Rs = 0 at the start. To demonstrate it concretely, run with selection off. You should find no increase in the Rs over time.
  • Dr Williams does a lot of complaining but no programming. He could write the code he is dreaming of and run it to test his ideas. Everything else is just words.
  • Dr Williams says `As I said a few posts ago (Post #37), "Schneider's program already has the information Rsequence ~= Rfrequency."' Clearly Dr. Williams doesn't know what he is talking about since Rsequence = 0 at the start of the program and Rfrequency is generally a positive integer such as 4 bits!
  • Dr. Williams says "I submit that since his program guarantees Rsequence ~= Rfrequency every time, that no new information is created since Rsequence ~= Rfrequency is encoded in the program before you run it." But if Dr. Williams would look at the code he will find that this is not true unless you believe that evolution by natural selection is guaranteed to create the situation. Of course then Dr. Williams would have conceeded that Ev does demonstrate that evolution by natural selection leads to an information increase.

• 2005 May 16: I found a humerous, but typical, discussion with creationists.
• 2005 May 18: Response to discussion at Kansas Citizens for Science:

  *Salvador T. Cordova, IDEA GMU* You wrote: *quote:* * Dembski's work has not been refuted, and there is a good chance his displacement theorem will pass peer review! *

  Dembski's work has been completely refuted. Read these pages, which represent only a fraction of all the rebuttals:
  • Dissecting Dembski's "Complex Specified Information"
  • Rebuttal to "No Free Lunch"
  • Rebuttal to William A. Dembski's Posting and to His Book "No Free Lunch"
  But my absolute favorite is: Effect of Ties on the Evolution of Information by the Ev program which demonstrates clearly that his hypothesis about how information gain occurs in Ev was wrong. Notice that Dembski *accepted* that information gain occured. He claimed that I had cheated in writing the Ev program, but when his prediction was tested, it failed.

  Those links appealed to Tom Schneider,

  How does he know what appealed to me?

  and that's an absolute joke.

  I wonder what he thinks the joke is ...

  He worked on the Avida project, and, of all things, I (an IDists) can claim even a small part of their source code in version 1.6 was improved on account of me.

  ... because I didn't work on Avidia! He didn't get his basic facts right!

  Schneider, like the rest of Dembski's detractors raise strawman representations of Dembski's work.

  Take a look at the links above. Dembski's predictions about Ev were wrong.

  Royal Truman and I absolutely demolished the claims of Avida at ISCID, and to add insult to injury, I can claim Avida has a fix in version 1.6 on acocunt of me.

  Spelling? Note that contributing a bug fix to a program is nice work, but that does not prove that the model is wrong. For example, Strachan found a bug in Ev. Good for him and thanks! That's HONEST work! But at the same time, Strachan ended up proving that Ev does have a consistent information gain (measured rigorously by Shannon information) ... which completely demolishes his, and every other creationist's, position. Intelligent Design has no substantiated facts or theoretical constructions.

  We invite schneider and elsberry and shallit to discuss this stuff with us. Maybe they best avoid us, just the rest did when they wimped out in the Kangaroo Kourt.

  How about we square off in the scientific literature? My first move was finished 5 years ago. Your turn.
• 2005 May 18. I was reading from William Dembski's page and found this gem: The Truth about How I Got into ID wherein he admits "My plan quickly fell into place: I would concoct a specious mathematical theory of design detection that critics of evolution could use as a weapon against Darwinism." It seems to be what he did ... is this some kind of joke? ;-)
• 2005 May 21. Stephen E. Jones writes on "Re: My critique of Thomas D. Schneider's Ev program paper" CreationEvolutionDesign.

  1) "Schneider's paper is misleadingly titled: "Evolution of biological information". But it is just a *computer* simulation. No actual *biological* materials (e.g. genomes of nucleic acids, proteins, etc) were used, nor does Schneider propose that his simulation be tested with *real* genomes or proteins.

  Actual biological materials were used to determine the original hypothesis. Read the literature: Schneider1986.

  He even uses the word "protein" in quotes

  Of course. I didn't want real biologists to think I meant actual proteins, but I did want people to know that it was analogous.

  it would not be *biological* information. *Computer* electrons and photons are not *biological* DNA and proteins. The substrates are *very* different. Nor is *computer* random mutation and natural selection *biological* random mutation and natural selection

  These are not relevant to the problem. The Ev program is a model of a natural process. If you wish to do an equivalent experiment on bacteria and have the guts and resources to do it, then do it.

  (it is significant that only once in the entire paper - see below - does Schneider use the words "natural selection" of his model, everywhere else he uses the single word "selection", indicating that he knows it is not *real* biological "natural selection).

  That's wrong in several ways. First, you are pretending to know what I know and you don't. If you are able to know what I know, then what did I do last night? Second, I didn't distinguish much between 'natural selection' and 'selection' in the paper because the latter is shorter. The ev program is not doing breeding selection as Darwin talked about, but it is indeed selection. The Ev program is a model of nature, so it is probably appropriate to use just 'selection'. Picky about words, you are! Miss the big picture, you do.

  It only becomes *real* biological information and random mutation and natural selection, when the simulation is tested in the *real* world, using *real* DNA, proteins, with *real* mutations and a *real* environment does the selecting. It is significant that Schneider does not propose this, presumably because he knows it wouldn't work..

  You are very bad at reading my mind, I have considered doing this experiment. Given the right conditions, it WILL WORK. Do you have th gumption to do the experiment yourself? That's the way real science works! FURTHERMORE, if you read the literature, you will recognize that related experiments have been repeatedly done for 20 years. Look up SELEX.

  2) By "from scratch" Schneider means "with zero information" (pp.2794, 2795). But he contradicts himself by admitting that he "needed [to] code the recognizer into the genome": But coding recognition into a genome is hardly "begin[ning] with zero information" in that genome (this comes up again later)!

  You read the paper and didn't understand that the relevant measure of information is Rsequence. It is indeed zero if you look at the graph. Read and study the paper until you understand this. ALSO, the recognizer gene has random numbers in it at the start!

  which is *false*, unless he build an *exact* replica of an entire ecosystem, containing "a population of organisms" subject to "random mutations and selection".

  No, Ev is a model and it does not need a replica of an ecosystem to demonstrate what it was aimed at demonstrating, namely whether or not Rs evolves to Rf. However, instead of complaing, you are welcome to pull together several thousand supercomptuers and do the simulation that you are thinking of. Good luck. I'll be very interested to read your paper in the scientific literature. My bet is that after about 1000 years of computation you will discover that ... Rs evolves to Rf. But please don't trust me on this. Think it through or do the experiment. Complaining gets you nowhere in science.

  Remember what Darlington said that the reason computer weather models get it wrong is because they do not *faithfully* simulate the weather and evolution is *far* more complex than the weather.

  That's a bad analogy. Weather is a complex chaotic [in the scientific sense] system. If modelling in one system does not work, it tells us absolutely nothing about modelling in another system! Clearly, since Ev works, the evolution of binding sites is far simpler than weather. Weather involves a whole planet/star system and perhaps things like interplanetary dust ... binding sites are tiny and much simpler. Again, note that the function of Ev is to explain and model an observation about natural systems, Schneider1986.

  The ... minimum information content of the protobiont must be in the range of hundreds of thousands to several million bits. [quote from Yockey]

  This was before the discoveries about self splicing RNA and the RNA world hypothesis. My bet is that a self replicating RNA might be quite small. But the exact number of bits needed is still a wild guess by everyone. But let's make a wild guess. Suppose it took 2 billion years to trigger life on earth. Suppose that the planet is essentially one huge RNA chain generating factory, putting out merely a mole of RNA chains every year. That's 10^23 * 10^9 = 10^32 molecules. One succeeded, and they became us. So the information is about log2(10^32) = 32 log2(10) = 100 bits, or about 50 basepairs. That's a decently complex structure. Intriguingly, Szostak's group has been evolving structures with about 70 bits in the lab, J Am Chem Soc. 2004 Apr 28;126(16):5130-7. Informational complexity and functional activity of RNA structures. Carothers JM, Oestreich SC, Davis JH, Szostak JW.

  So either Schneider's simulation smuggles in an "information content of [its] protobiont ... in the range of hundreds of thousands to several million bits" or it is not even a simulation of a minimum self-replicating system.

  Dr. Jones has confused the simulation of binding site evolution with simulating an entire replicating organism.

  4) Schneider even admits that his simulation" may not be representative of all biological systems":

  "Because half of the population always survives each selection round in the evolutionary simulation presented here, the population cannot die out and there is no lethal level of incompetence. While this may not be representative of all biological systems, since extinction and threshold effects do occur, it is representative of the situation in which a functional species can survive without a particular genetic control system but which would do better to gain control ab initio." (p.2794).

  Dr. Jones has missed the point. It is well understood that gene duplication leads to new functions. The genome projects have driven this concept forward strongly - there are (for example) lots of membrane pumps all variations of a single theme. So duplication and divergence is quite natural. Furthermore the fact that strong pressure was put on the Ev population is not relevant to the question (does Rs approach Rf?) and if Dr. Jones would like to modify the program he can verify this.

  5) Schneider gives no actual details of his Ev program's source code, so it can be checked against what Schneider claims for it.

  Dr. Jones did not read the paper carefully, and did not look at the web site carefully. The source code has been online for 5 years. Amazingly, after the above complaint, he then immediately contradicted himself by pointing to this web site, which has a page documenting the source code in explicit detail and which contains the entire functional source code!

  Dembski has delved into Schneider's code and gives an example of "Schneider ... fine-tuning his evolutionary algorithm to obtain the results he wants":
  ...
  This alone invalidates Schneider's entire Ev program as a faithful simulation of the "Evolution of *Biological* Information". By artificially constraining the program by a "SPECIAL RULE" (and I expect that this is not the only one), Schneider has smuggled in his own human *intelligent design* information into his program.

  Dr. Jones did not read the rebuttal to Dembski. (Thanks Paul, for pointing this out)

  6) Schneider's simulation is of "a genome size of 256 bases" which has "a set of 16 binding sites":
  ...
  but he does not reference any actual *biological* genome that has "16 binding sites in a genome size of 256 bases".

  Small sizes were used to get results in reasonable computational times. Dr. Jones is invited to run the program with other parameters on his own computer system.

  On p.2796 this "gene" is only "125" bases long. There are AFAIK *no* biological genes 125 bases long, nor are their organisms that have "a genome size of 256 bases" with a gene of 125 bases. So again, this is *not* a "simulation" of a *real* "biological" organism.

  tRNA genes are typically 76 bases long. Lots of small RNAs have been discovered in the the last few years. This is a huge topic in modern biology. But that doesn't really matter because this is a model. Again, Dr. Jones can run the program with sizes that he would prefer. A clear prediction is that the program will give similar results for larger geneomes and gene sizes.

  Within this crucial paragraph, the crucial sentence is: "The number of mistakes made by each organism in the population is determined." Who or what determines the number of mistakes?

  The environment of course. Think about it. If you don't have the binding site to turn on hemoglobin in your blood, you will turn pale like a vampire and die. If you have binding sites in the wrong places, your eyes would turn red like a devil and you would not see. Those would be 'mistakes' and you would probably not reproduce. [Note: vampires and devils are mythological/fictional characters.]

  This is also misleading (indeed *ridiculous*) for Schneider to claim that this has anything to do with what Gould and Eldredge, who are mentioned at references "(18,19)" meant by "punctuated equilibrium", which was at the *species* (or higher) level, not at the gene level.

  No, it is exactly what they mean since the punctuation is in reference to phenotypes of organisms and these are controlled at the genetic level. There is no control at 'higher' levels since the structure of an organism is well known to be determined by its genes!

  10) Schneider say his "ev model" "starts with a completely random genome", yet it has "transcription and translation [that] are part of the housekeeping functions of all cells":
  ...
  But this raises the issue that *real* "biological" genomes don't reshuffle their bases into order, like Schneider's simulation does.

  There is no basis for this claim. The biological literature is full of examples of mutations and mutational mechanisms.

  Also, "transcription and translation ... functions" are hardly "from scratch", "start[ing] with a completely random genome" "with zero information" (pp.2794, 2795) , but even in the simplest bacteria are at least 50 molecular machines with *immense* CSI.

  CSI ('complex specified information') is a bogous term from Dembski. It is meaningless. Furthermore, this is not relevant to the function of Ev.

  If Schneider's Ev program carries out these "transcription and translation ... housekeeping functions" then it is imparting that CSI into its output. So far from "The exact mechanisms of translation and locating binding sites are irrelevant", if Schneider's simulation does not faithfully represent them, then it is his simulation that is "irrelevant"!

  Dr. Jones has not read the paper carefully. The information increase being observed is in the binding sites. The rest is housekeeping functions outside the scope of the model.

  In the rest of the paper he uses the single word "selection". I take this as a tacit admission that his model is not a simulation of *real* biological natural selection.

  No. A rose is a rose by any other name. Selection is selection whether it be natural (generally meaning the environment of earth), breeding (by humans usually, though perhaps some ants select their fungi), SELEX or in a computer simulation. Of COURSE it is a simulation of natural selection! The paper would not be relevant to biology and would not have been published in a major scientific journal if it were not!

  12) Even if Schneider did eventually test his computer simulation against the real world

  See above. First, Dr. Jones neglected to read the scientific literature and so didn't understand why the program was written. Second, there are already natural data that Ev is designed to simulate. Third, instead of complaining Dr. Jones can do his own simulations.

  However, as Gould pointed out (and it is his "punctuated equilibrium" that Schneider claims his model represents), macroevolution (e.g. " the most profound structural transitions in the history of life") is not just "microevolution (flies in bottles) extended":
  
  "Orthodox neo-Darwinians extrapolate these even and continuous changes to the most profound structural transitions in the history of life: by a long series of insensibly graded intermediate steps, birds are linked to reptiles, fish with jaws to their jawless ancestors. Macroevolution (major structural transition) is nothing more than microevolution (flies in bottles) extended.

  Dr. Jones didn't even manage to misquote Gould correctly! (Note: Creationists typically quote scientists out of context thereby making it look like the scientist said something they didn't mean. In this case Dr. Jones simply said that Gould didn't say something and then quoted Gould saying it!) Note that what Gould was saying is that the so-called microevolution occurs and then halts (punctuated equilibrium). A series of such steps is macro evolution.

  I should again point out here that I would not personally be bothered if it is eventually shown that RM&NS can increase biological information. That would still just be microevolution. And as evolutionists from Goldschmidt (and before) have pointed out, there are *plenty* (if not *all*) major transitions that have yet to be explained by the "accumulation and selection of small mutants", e.g.:

  Microevolution, with an understanding of punctuated equilibrium, is macroevolution.

  I have in the past used the example of a newspaper "The Sunday Times" misprinting its front page "The Sundry Times". I had previously thought that "not even the most ardent Darwinist would seriously propose that this tiny increase in information, extrapolated over millions of years, could ever write even a newspaper, let alone something different like a book" (indeed a "30 volume ... *Encyclopaedia*") but after reading Schneider's paper I am now not so sure that there are not some "ardent Darwinist[s] [who] would seriously propose it!":

  What's missing from this picture? The change in the newspaper was a 'mutation' and it was rapidly 'killed'. How about reading some Shakespeare? Within a few centuries the language DID CHANGE! It is quite interesting to go back further to Chaucer and see how it is even more different in the more distant past. So, contrary to Dr. Jones' claim above, the language does change just the way living organisms do.

  13) Schneider lets slip that there is another unrealistic element in his (and indeed all) computer simulations in that it (they) "does not correlate with time":

  So? Run the program slower if you want. Make one generation per 20 minutes to match rapid bacterial growth. THIS WILL NOT CHANGE THE FINIAL RESULT!

  Well, when Schneider's simulation is actually tested with *real* "life" (e.g. a bacterium), and under *real* mutation and natural selection it gains information, then, and only then, would "creationists" be favourably impressed. But if they are like me, they would already be impressed (but unfavourably) that Schneider does not mention in his paper that his simulation should now be so tested in the *real* "biological" world.

  1. The simulation was of phenomena in the "real" world.
  2. Dr. Jones is invited yet again to do an experiment.

  15) [... irelevant compaint ...] Schneider claims that his "ev model" "fits Behe's (34) definition of `irreducible complexity' exactly":
  ...
  But a "recognizer gene" of "125" bases, is hardly what Behe had in mind by `irreducible complexity' (interestingly Schneider puts it in single quotes, as though even he realises that it isn't), given Behe's examples of IC being "a single system composed of several well-matched, interacting parts", such as the bacterial flagellum and the blood-clotting cascade, etc)!

  Now Dr. Jones is mind-reading Dr. Behe! Dr. Behe's definition did not specify an amount in his "irreducible complexity" concept. See his definition. He only required that loss of one part of several interdependent parts would cause destruction of the whole system. This is true of the organisms in Ev after evolution.

  It is also interesting (and significant) how many evolutionists ignore Behe's proposed examples of IC and invent their own as straw men to more easily knock down.

  Plenty of other folks are gnawing away and have destroyed Behe's examples. However, for a concept to be useful in science, it has to apply broadly. Behe's concept clearly applies to the situation in Ev, yet the organisms evolve the 'irreducible complexity' within a few hundred generations. So 'irreducible complexity' is no barrier to the model of evolution by natural selection. This entirely demolishes Behe's position, even without discussing any of Behe's examples!

  16) The unrealism of Schneider's model is shown by "the mutation rate of" a *virus* "HIV is ... 10 times slower"

  So what's the problem? Revise the program to make mutations 10 times slower. You should find (a prediction!) that the results are the same, but it takes 10 times longer to get them! Isn't this obvious?

  17) Schneider's extrapolation above from a *computer simulation* of "256 bases" (so-called), to "at this rate, roughly an entire human genome of ~4 x 10^9 bits ... could evolve in a billion years" is just absurd.

  Yup, evolution is absurd and there are tons of evidence that it happened! Actually, we probably started from a little 50 base RNA (see above) generated randomly.

  As though humans are just a "HIV" virus writ large!

  And so we are. What's your problem with that? Electricity is ridiculous too! Don't you 'believe' in electricity? Magnitism is even weirder!

  And remember in Schneider's simulation, for it to work, "half of the population always survives each selection round ..., the population cannot die out and there is no lethal level of incompetence." However, this was evidently too much for even Schneider (or one of his reviewers) and as an afterthought he concedes that "this rate is unlikely to be maintained for eukaryotes"! (p.2799).

  No, this rate need not be maintained. It now begins to look like small changes in the control genes are enough to switch FOX2P to give us speech. Second guessing what happened in writing a paper is very dangerous. I put that phrase in myself, the reviewers had nothing to do with it.

  18) Finally, Schneider concludes, "contrary to ...Spetner ... the ev program also clearly demonstrates that biological information .. can rapidly appear in genetic control systems subjected to replication, mutation and selection":
  ...
  Well, Spetner in his works cited by Schneider, gave examples of a lot of *real* "biological information", i.e. actual *organisms* complete with species names. When Schneider tests his *computer* model against *real* organisms and it produces *real* "biological information" of the amount predicted, then I am sure that Spetner (like me) would be impressed, but not before.

  See above. Dr. Jones needs to read the literature more.

  Indeed, I don't know about Spetner, but as for me, there are so many *obvious* fallacies in this paper, that I have no confidence in Schneider's judgment. He strikes me as someone who has not learned Feynman's "first principle ... that you must not fool yourself-and you are the easiest person to fool":

  Speak for yourself. Dr. Jones has not pointed out even one single fallicy, but had made numerous errors in his posting.

  and so Schneider's Ev program is just another example of what Feynman called "Cargo Cult Science"!

  Ad homium attacks reflect the author. Dr. Jones ends with a quote from Dembski. Dembski's work has been completely debunked on this web site and yet Dembski has not admitted his errors. Conclusion: Dr. Jones is putting out a lot of complaints, none of which are substantial and many of which indicate fundamental misunderstanding about biology and the original purpose of the Ev program which was to model and explain observed natural phenomena. There are a number of serious errors in his posting. However, I encourage Dr. Jones to do some real biological experiments himself. How about a SELEX for starters?
• 2005 May 26:

  ID is not science for the simple reason that it doesn't produce testable hypotheses that could be used in an empirically-based research program. ... I once debated ID proponent William Dembski at the NY Academy of Science, and pointedly asked him what he would do if he got a grant from the National Science Foundation. He couldn't come up with anything..."
  --- Massimo Pigliucci, Evolutionary biologist speaks rationally on "ID", Humanist Network News, May 25, 2005

• 2005 May 28: Smithsonian to Screen a Movie That Makes a Case Against Evolution!
  by John Schwartz, New York Times, May 28, 2005.
  • Kansas Citizens for Science discussion board. Sandpiper reports: "The article also says that Randall Kremer is the museum spokesperson on this issue. Here is the link to the museum's email addresses. I hope persons will take time to send Mr. Kremer a letter. http://www.mnh.si.edu/email.html". Office of Public Affairs at the Smithsonian Randall Kremer, Director of Public Affairs.
  • The "Discovery" Institute announcement is at June 23, 2005 Smithsonian Institution Premiere of The Privileged Planet
  • The Privileged Planet web site for the book by Guillermo Gonzalez and Jay W. Richards.
    • Synopsis:

          For centuries scientists and philosophers have marveled at an eerie
          coincidence. Mathematics, a creation of human reason, can predict the
          nature of the universe, a fact physicist Eugene Wigner referred to as
          the "unreasonable effectiveness of mathematics in the physical
          sciences."
          

      GEEPERS!! This is a quote out of context!!!
    • See: The Unreasonable Effectiveness of Mathematics R. W. Hamming and the link at the bottom of that page to Eugene Wigner's paper: The Unreasonable Effectiveness of Mathematics in the Natural Sciences (at Dartmouth)
    • The point of these lovely papers is that Mathematics was selected by humans! It's not some mysterious design of the universe, it's us! This is an example of the logical fallacy Appeal to Authority. Their book is based on an inappropriate quote of the title of Wigner's paper without fully explaining to the reader what is going on.
    • The synopsis goes on with "For some reason our Earthly location is extraordinarily well suited to allow us to peer into the heavens and discover its secrets." The logic is backwards. WE were selected to live by the environment, so we fit the environment and (now, mostly) thrive here.
    • "Elsewhere, you might learn that Earth and its local environment provide a delicate, and probably exceedingly rare, cradle for complex life." This is silly. First, we don't know how rare planets with life are. Second, earth has been stable for several billion years, so what's delicate about that? Third and most importantly, we have adapted to this environment so we fit it quite well.
  • post-darwinist.blogspot.com incorrectly assumes that the objections are by people who don't think.
  • www.pandasthumb.org reports too.
• 2005 Jun 1: The reDiscovery Institute

  "Our primary focus is to extend and promote Design Theories, which have been so successful in Biology, to the fields of Chemistry, Astronomy, Geology, Atmospheric Science, Oceanography, Material Science, Acoustics, Condensed Matter Physics, Fluid Dynamics, Nuclear Physics, Anthropology, Physiology, Algebra, Geometry, Statistics and Calculus."
  Our goals are to Teach the Controversies, all of them, each and every one. ...

  The New Periodic Table is an important contribution, demonstrating that in the last few centuries chemists have had many fights about where to place elements.
• 2005 Jun 2: Smithsonian Distances Itself From Controversial Film
  by Tommy Nguyen, Page C01. The Smithsonian statement:

  On the Private, Invitation-only Screening of the "The Privileged Planet"
  
  The Smithsonian's National Museum of Natural History recently approved a request by the Discovery Institute to hold a private, invitation-only screening and reception at the Museum on June 23 for the film "The Privileged Planet." Upon further review we have determined that the content of the film is not consistent with the mission of the Smithsonian Institution's scientific research. Neither the Smithsonian Institution nor the National Museum of Natural History supports or endorses the views of the Discovery Institute or the film "The Privileged Planet." Given that the Discovery Institute has already issued invitations, we will honor the commitment made to provide space for the event, but will not participate or accept a donation for it.
  01-June-2005

• 2005 Jun 6: How could information, such as in DNA, assemble itself? at EvoWiki:org. I added the following statement:

  The Ev program, by Thomas Schneider, shows exactly how information gain occurs in genetic control systems through the selective process. Information is measured using Shannon's measure. The paper and the program are available at http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/
  T. D. Schneider, Evolution of Biological Information, Nucleic Acids Res, 28(14): 2794-2799, 2000 http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/

• 2005 Jun 6: Cybernetic simulations show Darwinian processes don't produce order at EvoWiki:org. I added the following statement:

  1970 is hardly 'recent'. The Ev program, by Thomas Schneider, shows exactly how a 'cybernetic simulation of genetic control systems produces 'order' as measured using Shannon information theory. The paper and the program are available at http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/
  T. D. Schneider, Evolution of Biological Information, Nucleic Acids Res, 28(14): 2794-2799, 2000 http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/

• 2005 Jun 16. Dembski tried to defend Behe's thesis and failed.

• 2005 Jun 16. Things Creationists Hate by R. J. Riggins, has a lovely collection of evolutionary examples hard to explain other than by evolution.

  Creationists: why are there no wild poodles?
  And think about this: if all breeds of modern dogs were actually wild animals, would we ever consider Great Danes and Yorkies to be the same species? The two could not possibly interbreed without human intervention. If they were wild animals, they would clearly be different (but related) species. In other words, WE have created numerous "species" of domestic dogs. We technically consider them all to be Canis familiaris only because we know that they all came from the same stock starting a short few thousand years ago---that is, we know their evolutionary history. New species CAN arise, and we can cause it ourselves.

• 2005 Jun 22. Flying Spahetti Monsterism is a second Intelligent Design theory challenging both the conventional one(s) and evolutionary theory. See also Flying Spaghetti Monsterism at Wikipedia.
• 2005 Jun 23. The Design Revolution: Answering the Toughest Questions About Intelligent Design by William A. Dembski, Charles W. Colson (InterVarsity Press, January 1, 2004). I decided to see if he cites this guy Schneider, so I did a search using the Amazon search function. The name appears in three places: The index, the front matter, as an acknowledgment(!) and on page 258:

  "Evolutionary biologists regularly claim to obtain specified complexity for free or from scratch. (Richard Dawkins and Thomas Schneider are some of the worst offenders in this regard.)"

  The problems with this statment are:
  • The term 'specified complexity' is poorly defined. Shannon information is a published and precise substitute.
  • Allowing for this substitution in the Ev program (to which Dembski refers) the information gain observed is not obtained for free (there are thousands of deaths of organisms to pay for it).
  • It is never claimed that the information gain was for free.
  • It was claimed that the information gain occured from scratch: Rsequence is clearly zero when the program starts. This is obvious from the figures in the paper. Dembski seems to be attacking something that is obvious.
• 2005 July 19. Do You Believe in Evolution? I don't. Read the link for why. If that link is broken, you can use this copy:
  Do You Believe in Evolution?
• 2005 Aug 2. God and Darwin Editorial in the Washington Post, 2005 Jan 24.
• 2005 Aug 10. Kansas moves to stem role of evolution in teaching, Reuters.
• 2005 Aug 15. Harvard to explore origins of life, CNN. "Origins of Life in the Universe Initiative" by David R. Liu
• 2005 Aug 20. A Debate Over Darwin: Politicized Scholars Put Evolution on the Defensive, New York Times by Jodi Wilgoren. The article gives details of where the Discovery Institute gets its funding.
• 2005 Aug 20. David Berlinski writes in an article dated March 9, 2005 All Those Darwinian Doubts:

  The suggestion that Darwin's theory of evolution is like theories in the serious sciences - quantum electrodynamics, say - is grotesque. Quantum electrodynamics is accurate to thirteen unyielding decimal places. Darwin's theory makes no tight quantitative predictions at all.

  This is demonstrated to be incorrect by the evolution of Rsequence towards Rfrequency.

  Where attempts to replicate Darwinian evolution on the computer have been successful, they have not used classical Darwinian principles, and where they have used such principles, they have not been successful.

  The ev program disproves this statement since it uses classical Darwinian principles and was successful.
• 2005 Aug 25. KANSAS Science Education Standards (PDF), July 12, 2005, page 76 states:

  STANDARD 3: LIFE SCIENCE Grades 8-12. The student will develop an understanding of the cell, molecular basis of heredity, biological evolution, interdependence of organisms, matter, energy, and organization in living systems, and the behavior of organisms.

  This is fine. However they go on to say:

  c. The sequence of the nucleotide bases within genes is not dictated by any known chemical or physical law.

  This is incorrect on two counts:
  • First, Rsequence evolves towards Rfrequency (Schneider1986, Schneider2000). The binding of proteins to DNA is a physical and chemical reaction. The selective process is caused by physical interactions. Thus the nucleotide base sequences are determined by physics and chemistry.
  • Secondly, the information is bounded by the energetics of the interaction by the Second Law of Thermodynamics (Schneider1991).
• 2005 Aug 28. www.cosmicfingerprints.com by Perry Marshall claims that information does not occur by natural processes. The Ev program demonstrates that this is incorrect. Untangling his errors will take a web page. Here are a few notes on his errors in www.cosmicfingerprints.com/ifyoucanreadthis.htm.
  • chaos theory - misdefined!
  • fractals - misdefined!
  • "All information is based on language". Incorrect.
  • "All information requires a thought process." Incorrect. In 1976 he was 7 or so - born in 1969. Currently 36 years old.
  • "Information cannot be created without intent." There are no examples Incorrect. The Rsequence information in appears by selection and mutation.
  • slide 26:

    The Atheist's Riddle "Show me a language that does not come from a mind." So simple, any child can understand So complex, no atheist can solve

    Answer: Ev.
  • slide 48:

    No stepwise, non-destructive process from "Easy Personal Protection Training" to "Fast Personal Protection Training"

    Wrong. Probability is 1/(26*26) = 1/676.
  • slide 49:

    Random Mutation = NOISE
    Noise is always bad

    Wrong. Noise in biology allows evolution! SOME mutations are beneficial, as shown by the Ev program.

  • Claude Shannon: Noise = Entropy

    Wrong. noise is measured in units of power. Entropy is measured as J/K.

  • Impossible to get information from noise

    This is wrong, as demonstrated by the Ev program.
  • slide 53:

    Natural selection cannot increase information

    This is wrong, as demonstrated by the Ev program.
  • Discussion at the end:

    DNA is a language. Where did it come from? Where did the code come from?

    The analogy to a languge is weak at best. The answer to the question is clear: natural selection, and this is demonstrated by the Ev program.
  • In the discussion at the end he makes the The AND-Multiplication Error.
• 2005 Aug 30. Here is Perry Marshall's main statement from Information Theory and the Origin of DNA: Frequently Asked Questions, followed by an analysis:

  "Thus we have an airtight inductive proof that DNA originated from a superintelligence:"

  1. "All languages, codes, protocols and encoding / decoding mechanisms come from a mind - there are no known exceptions"
     The premise is false. A counter example is the Ev program results in which the sequence logo represents the code. It has appeared by the mechanism of natural selection. All the factors in the Ev program exist in nature and presumably carve the shapes of the natural sequence logos. Note that there are other factors besides those in the Ev program such as which side of the DNA a protein binds to and special structures such as base flipping, but these do not alter the fact that the patterns and codes evolve by themselves.
  2. "DNA is a language, a code, a protocol, and an encoding / decoding mechanism"
     This is very vaguely stated. He gives no examples of what the code looks like, what the protocols are or how things are encoded and decoded. Although this can be done - see the rest of this web site! - it is not so easy as he makes it out to be because the relationship between Shannon's work and molecular biology must be built. See, in particular, Theory of Molecular Machines. I. Channel Capacity of Molecular Machines.
  3. "Therefore DNA came from a mind."
     The conclusion does not follow because the first premise is false.

• 2005 Sep 1. "Show Me the Science" by Daniel C. Dennett, The New York Times, Saturday 28 August 2005. (also at www.truthout.org) briefly mentions this author ...
• 2005 Sep 4. Classroom Evolution's Grass-Roots Defender: Va. Group Sees Threat To Darwinist Teaching by Peter Slevin Washington Post, Wednesday, July 20, 2005; Page B04.
  • Irving Wainer
• 2005 Sep 15. Evangelical Scientists Refute Gravity With New 'Intelligent Falling' Theory August 17, 2005 | Issue 41-33. (Sorry, Onion links are not stable, read it while you can.)
• 2005 Sep 15. One side can be wrong by Richard Dawkins and Jerry Coyne, Thursday September 1, 2005, The Guardian.

  In all cases there is a hidden (actually they scarcely even bother to hide it) "default" assumption that if Theory A has some difficulty in explaining Phenomenon X, we must automatically prefer Theory B without even asking whether Theory B (creationism in this case) is any better at explaining it. Note how unbalanced this is, and how it gives the lie to the apparent reasonableness of "let's teach both sides". One side is required to produce evidence, every step of the way. The other side is never required to produce one iota of evidence, but is deemed to have won automatically, the moment the first side encounters a difficulty - the sort of difficulty that all sciences encounter every day, and go to work to solve, with relish.

• 2005 Sep 18. In a book review Hrundi V. Bakshi (which is apparently a fake name) asks:

  "Why can't there be a reasoned, civil debate about even the ~ possibility ~ of issues such as intelligent design or some of the deep flaws in Darwinian evolution? Why are "scientists" so afraid to investigate or challenge some of their own cracked presuppositions?"

  1. There is civil debate on intelligent design, look across the web and you will find hundreds.
  2. Intelligent design, when testable (rarely!), fails the tests of science. See these web pages.
  3. So the "possibility" of intelligent design has been tested and found wanting at every stage. It's pure pseudo scientific junk.
  4. Darwinian evolution has no deep flaws. It works perfectly well as a model of how living things came to be. See these web pages. What IS happening is there are rambunctious debates about specific mechanisms - see the excellent article by Dawkins and Coyne in the September 15th entry. If you think there are flaws, you have been misled and have a lot of reading ahead to straighten out your thinking! (Don't believe me - go do some reading and thinking!)
  5. Scientists are not afraid to challenge their own hypotheses. It is done all the time, if you read the literature! Furthermore, someone who manages to overturn the general consensus will become extremely famous, so there is plenty of carrot there! (A good example is, of course, Einstein, who over overturned Newtonian mechanics.)
• 2005 Sep 29. In a New Analyses Bolster Central Tenets of Evolution Theory: Pa. Trial Will Ask Whether 'Alternatives' Can Pass as Science, by Rick Weiss and David Brown Washington Post, Monday, September 26, 2005; Page A08.
• 2005 Oct 13. Being Stalked by Intelligent Design: Scientists must stop ignoring "Intelligent Design"---religious prejudice disguised as intellectual freedom (American Scientist 93(6): 500), by Pat Shipman gives a general overview of the Intelligent Design movement.
• 2005 Oct 21. Do antibacterial soaps work? CNN.

  "What we're seeing is evolution in action"
  -- Dr. Stuart B. Levy,

  ---

• 2005 Oct 23. Dover Trial

  • talkorigins Transcripts
  • ACLU Transcripts
  • Dover Ruling

• 2005 Oct 14. Kitzmiller et al. v. Dover Area School District.

  "In December 2004 the ACLU-PA sued the Dover Area School District on behalf of eleven parents who objected to the recent policy that required the teaching of intelligent design in biology classes as an alternative to evolution."

  Dover Trial Transcripts
• 2005 Oct 22. Michael Behe on the Witness Stand. Dover Trial Transcripts, Testimony of Michael Behe - morning session (PDF) and Testimony of Michael Behe - afternoon session (PDF)

  • "... since nothing other than an intelligent cause has been demonstrated to be able to yield such a strong appearance of design, Darwinian claims notwithstanding, the conclusion that the design seen in life is real design is rationally justified."
    --Michael Behe, Morning Session, October 17, 2005, page 91

    Behe's weak non-quantitative statement is destroyed by examples from the Ev program.

  • Q. Is intelligent design falsifyable?
    A. Yes, it is.
    --Michael Behe, Morning Session, October 17, 2005, page 114

    Indeed! Behe's thesis is falsified by the Ev program! See the Discussion in the paper.
  • Quoting from the Dover school statement:

    Q "Intelligent design is an explanation of the origin of life that differs from Darwin s view. The reference book Of Pandas and People is available for students who might be interested in gaining an understanding of what intelligent design actually involves." Do you have any problem with that paragraph?
    A That sounds like -- sounds fine as well.
    --Michael Behe, Afternoon session, October 17, 2005, page 13

    No, that's wrong. The origin of life problem is not addressed by Darwnian theory! The statement confounds two entirely separate problems and Behe doesn't realize it! Further, his affirmation of the statement is unreasonable because Intelligent Design is not on the same footing as natural selection. ID has been falsified while evolution has been affirmed (see the remainder of this web site).
  • Quoting from 'a newsletter was sent out by the [Dover] district that discussed some of the biology curriculum':

    Q And another one, "What is the theory of evolution? The word evolution has several meanings, and those supporting Darwin s theory of evolution use the confusion in definition to their advantage. Evolution can mean something as simple as change over time, which is not controversial, and is supported by most people. However, evolution in its biological sense means a process whereby life arose from non-living matter and subsequently developed by natural means, namely, natural selection acting on random variations." Is that accurate?
    A Yeah, and that sounds clear.
    --Michael Behe, Afternoon session, October 17, 2005, page 16

    Behe makes the same error again of confusing the origin of life with natural selection.
  • Quoting from 'a newsletter was sent out by the [Dover] district that discussed some of the biology curriculum':

    ID attempts to explain the complexity of the world by interpreting the scientific data now available to modern biologists. Its principal argument is that certain features of the universe are best explained by an intelligent cause rather than undirected causes such as Darwin s theory of natural selection. That s the first paragraph in the answer. Do you have any problem with that section?
    A That sounds reasonable.
    --Michael Behe, Afternoon session, October 17, 2005, page 16-17

    The statement is false because natural selection is a directed cause! Mutation is undirected. Amazingly, Behe, on the witness stand, makes this basic scientific error.
  • Quoting from 'a newsletter was sent out by the [Dover] district that discussed some of the biology curriculum':

    In fact, since the 1950s, advances in molecular biology and chemistry have shown us that living cells, the fundamental units of life processes, cannot be explained by chance." What s your reaction to that section?
    A Well, I think I would have phrased things somewhat differently, but I think for a newsletter, it s fine.
    --Michael Behe, Afternoon session, October 17, 2005, page 17

    The statement is not fine. The fundamental processes are explained well by natural selection. All arguments that I have seen about improbabilities --- as by Dembski, see above --- are demonstrably false.

  • I think that in fact Darwinian theory is very difficult to falsify, but that intelligent design is easily falsify -- or easy to falsify.
    --Michael Behe, Afternoon session, October 17, 2005, page 50

    Wrong. The ev program was a test not only of whether Rsequence evolved towards Rfrequency but also of whether one could explain the existance of binding sites by evolution. He is right on one point - the ev program demonstrates clearly that Behe's 'irreducible complexity' is also falsifiable -- and is falsified.
  • In the Afternoon session, October 17, 2005, page 57 is a reference to an interesting statement: Lehigh's Biology Department Position on Evolution and "Intelligent Design" which basically says that the rest of the department rejects Behe's ideas!

  • Well, as I tried to make clear in my testimony, findings accumulated over 140 years that support the contention that Darwinian processes could explain complex molecular systems total a number of zero.
    --Michael Behe, Afternoon session, October 17, 2005, page 59

    He conveniently ignores the Ev paper!

  • As I ve tried to make clear in my testimony, although some -- many scientists do not like it, if you look at their statements, you do not see any scientific evidence which, when examined closely, is -- when examined closely, shows that intelligent design is incorrect. --Michael Behe, Afternoon session, October 17, 2005, page 113-114

    He again conveniently ignores the Ev paper!

  The mistake that Behe and others make is to assume that design cannot occur by evolution. They assume that the systems are 'too complex', generally by hand-waving arguments. But I recently demonstrated that Dembski's "Universal Probability Bound", which lays down a probability bound on such complexity, is easily beaten in a few minutes by an evolutionary process. This cuts the legs off of ID.

• 2005 Oct 23. Behe's Testimony, day 12:

  Q. If you could turn to page 185 of that book. I'd actually like you to read -- we'll take turns here -- from the last paragraph on 185 beginning, molecular evolution, and go to the end of the chapter, which is one more paragraph.
  A. Molecular evolution is not based on scientific authority. 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 occurred.
  There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, and since there is no authority on which to base claims of knowledge, it can truly be said that, like the contention that the Eagles will win the Super Bowl this year, the assertion of Darwinian molecular evolution is merely bluster.
  Publish or perish is a proverb that academicians take seriously. If you do not publish your work for the rest of the community to evaluate, then you have no business in academia. And if you don't already have tenure, you will be banished.
  But the saying can be applied to theories as well. If a theory claims to be able to explain some phenomenon, but does not generate even an attempt at an explanation, then it should be banished. Despite comparing sequences and mathematical modeling, molecular evolution has never addressed the question of how complex structures came to be.
  In effect, the theory of Darwinian molecular evolution, has not published, and so it should perish.
  Q. That was your view in 1996?
  A. Yes, that's correct.
  Q. That is still your view today?
  A. Yes, it is. And if I may elaborate on that?

  So Behe is apparently unaware of or ignoring the Ev paper. But he asks for more:

  A. The detail is actually simply this, that by these publications, I mean detailed rigorous accounts for complex molecular machines, not just either hypothetical accounts or sequence comparisons or such things.

  Let's see. Ev applies to all genetic control systems in general because it models the approach of Rsequence towards Rfrequency. We know in rigorous molecular detail how binding works in many cases. Ev shows how the "complexity" of the binding sites and the recognizer appear during evolution by natural selection.
• 2005 Oct 23. Behe's Testimony, day 12:

  A. I think it would be good pedagogy to discuss the fact that some scientists do think that some aspects of life were intelligently designed, yes.
  Q. By an intelligent designer?
  A. Well, intelligently designed, yes, it implies a designer, yes.

  That's an incorrect conclusion. If something is designed (e.g., the binding sites and recognizer matrix in ev after evolution) then it might well not have a designer!
• 2005 Oct 23. Behe's Testimony, day 12. Ah! Behe was forced to change his definition! Let's see if it crumbles further.

  Behe's New Definition of Irreducibly Complexity

  By irreducibly complex, I mean a single system which is necessarily composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly, that is by continuously improving the initial function which continues to work the same mechanisms by slight successive modifications of a pre-cursor system, because any pre-cursor to an irreducibly complex system that is missing a part is, by definition, non-functional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually, it would have to arise as an integrated unit in one fell swoop for natural selection to have anything to act on.

  The only difference is the underlined words! (Compare to the version at Amazon So it really hasn't changed. The Ev program still produces an irreducibly complex system by his new definition.
• 2005 Oct 23. The next part of Behe's Testimony is very telling: Behe's Testimony, day 12.

  Q. And, therefore, there would be no successive generation because that flagellum would not move on to the next generation?
  A. No, that's not right. A bacterium that is missing a flagellum would certainly go on and continue to grow. It can reproduce and so on. But the flagellum doesn't work. And this is from my article, I believe, in Biology and Philosophy, where I responded to Professor Orr.
  And in that article, I specifically said that he had a misconception that irreducible complexity meant that an organism could not live without this, without the system that we were talking about. And that's not what I meant by it.

  In other words, just as in the ev program Behe allows that the organism may survive. Apparently Dr. Orr thought it must die. But a non-functional system will eventually be selected against, of course, so the genetic line disappears in either direct death or eventually.
• 2005 Oct 23. Here Behe contradicts himself: Behe's Testimony, day 12.

  Q. Okay. So my question is, how would you falsify the claim that a biological system, like the bacterial flagellum, which is clearly a purposeful arrangement of parts, is not intelligently designed?
  A. Well, since it's an inductive argument, since the purposeful arrangement of parts is an inductive argument, then in order to falsify an induction, you have to find an exception to the inductive argument.
  So if somebody said that, when you see this purposeful arrangement of parts -- and again, the -- as I stress, the argument is quantitative, when there is a certain degree of complexity and so on. If it was shown that that did not always, did not always bespeak design, then the induction would not be reliable, and we would -- so -- and the argument would be, would be defeated.
  Q. Now you, in fact, have stated that intelligent design can never be ruled out, correct?
  A. Yes, that's right.

  How can something be falsifiable if it can't be ruled out!!?????
• 2005 Oct 23. Behe's Testimony, day 12.

  I said, if it can be demonstrated that random mutation and natural selection can produce complex systems, then intelligent design would be falsified.

  So - Dembski defined 'complex systems' as those with a probability of less than 10^-150 of occuring randomly. Such a system hs been produced by random mutation and natural selection! Thus by Behe's own statements intelligent design has been falsified

• Judge rules against 'intelligent design' in science class

  by Delia Gallagher and Phil Hirschkorn, CNN.
  • Kitzmiller opinion at the US District Court in Pennsylvania.
  • Kitzmiller opinion from CNN (PDF).
  • Defending Science by Defining It By David Brown and Rick Weiss, Washington Post, Wednesday, December 21, 2005; Page A20
• 2006 Jan 4. School board rescinds 'intelligent design' policy, CNN.
  

  ---

• 2005 Oct 30. Intelligent Design 101: Short on science, long on snake oil by James Curtsinger, The Minnesota Daily, 2005 Oct 11. This is a rather funny debunking of Behe's ideas.
• 2005 Nov 8. Kansas school board redefines science: New standards question accuracy of evolutionary theory CNN. For the second time, Kansas proves that they do not understand science and have no regard for the facts. Next up: Let's make a law that says that pi is exactly 3.0. This will significantly simplify teaching mathematics!!
  • Kansas State Department of Education
  • National Science Teachers Association and the National Academy of Sciences denied materials to the board
  • Kansas Education Board First to Back 'Intelligent Design': Schools to Teach Doubts About Evolutionary Theory by Peter Slevin, Washington Post, Wednesday, November 9, 2005; Page A01
• 2005 Nov 9: 'Intelligent-design' school board ousted in Penn by Jon Hurdle, Reuters.
• 2005 Nov 22: College course seeks to debunk intelligent design. Proposed religion class labels creationism as 'mythology' CNN. The class is entitled: "Special Topics in Religion: Intelligent Design, Creationism and other Religious Mythologies." It will be taught by Professor Paul A. Mirecki.
  • 2005 Dec 11 Anti-creationism professor: Resignation was forced. CNN "On Monday, Mirecki was treated at a Lawrence hospital for head injuries after he said he was beaten by two men on a country road. He said the men referred to the creationism course."
• 2005 Nov 26: DARWIN, and exhibit at the American Museum of Natural History, November19, 2005 - May 29, 2006, New York. The Evolution of a Darwin Show by Melena Z. Ryzik, The New York Times 2005 Nov 27.
• 2005 Dec 01: The Evolution of Charles Darwin, Smithsonian Magazine, December 2005.

• 2005 Dec 05: Kurt P. Wise, creationist, writes Why do so many scientists endorse Evolution? This is incorrect because scientists don't "endorse" theories in the sense of "approve". We support a theory and, if a scientist is honest, we will abandon a theory that does not fit evidence. (Of course we may still hold on because we feel it has more explanatory power, and not fitting evidence might indicate problems with the evidence.) Though we don't endorse evolution, it is the best explanation of all the available facts. Nothing else comes close in explanatory power. So, for starters, the article carries a fundamental understanding about how science works. But that's not the main point here.

  Wise quotes George Caylor who wrote a column The Biologist. In this column he claimed to speak with a molecular biologist named "Sam" who is talking about reading genetic material:

  • G: "How did all that information happen to get there?"
  • S: "Do you mean, did it just happen? Did it evolve?"
  • G: "Bingo. Do you believe that the information evolved?"
  • S: "George, nobody I know in my profession truly believes it evolved. It was engineered by 'genius beyond genius', and such information could not have been written any other way. The paper and ink did not write the book. Knowing what we know, it is ridiculous to think otherwise.
  
  Evidently "Sam" was unfamiliar with the Ev paper. Fair enough, the article is copyright 2000 and Ev was published in 2000.

  So let's see what we can find. google: George Caylor evolution "Do you believe that the information evolved?"

  It turns out that the article appears in a number of places on the web. It is now an urban legend. It is mutating while it propagates. For example, in one case "Sam" was renamed "Jeff" and there is no green cheese.

  google: Caylor Bed and Breakfast lynchburg. The Bed and Breakfast place does indeed exist.

  There has been some discussion on this:

  • www.infidelguy.com (A "George" version)
  • groups.google.com (A "Jeff" version)

• 2005 Dec 21: The "Intelligent Design" Hoax by William J. Bennetta is a very hard hitting essay on "Intelligent Design".
• 2006 Jan 18: Robert Pennock asks everyone to join him in a toast to Judge Jones for the results of the Dover trial.
• 2006 Jan 19

  [O]ne does not "believe" in evolution ... Belief has no place in science. Instead, one either accepts or rejects the evidence for evolution based on scientific evidence.
  -- Karen Kowalski

  Students need more science classes, not fewer Timesunion, 2006 Jan 14
• 2006 Feb 07 Caroline Crocker, professor at George Mason University in Fairfax, Virginia, lectured the usual poor arguments 'against' evolution. Article in the Wasthington Post by Shankar Vedantam Sunday, February 5, 2006; Page W08
  • google Caroline Crocker evolution
  • Intelligent design: Who has designs on your students' minds? by Geoff Brumfiel, Nature 434, 1062-1065 (28 April 2005).
• 2006 May 29 "Alan Kleinman" wrote to me with the same arguments he put forth a few days ago. Ed Brayton gave a nice response and gave a quote from Marshall Berman which can be found here and there:

  Let's run a scientific experiment. Go outside and pick up a small rock. The probability of that rock being on that spot on the Earth by chance alone is roughly the area of the stone divided by the surface area of the Earth, or about one chance in 10 to the 18th power (one followed by 18 zeros). If picking up the stone took one second, the probability of such an event occurring at this precise moment over the lifetime of the universe is now even smaller by another factor 10 to the 18th power! This simple event is so incredibly unlikely (essentially zero probability) that one wonders how it could be accomplished!

• 2006 Jun 27. Alan Kleinman started a discussion at Evolution Is Dead!. He ran the Evj program with exponentially increasing genome size and proportionally increasing number of binding sites. He found that the time to evolution increases exponentially. From this he claims that although Ev is a good model for small genetic elements, it cannot be extended to large genomes. In particular, he is responding to this statement in the Ev paper:

  Likewise, at this rate, roughly an entire human genome of ~4x10⁹ bits (assuming an average of 1 bit/base, which is clearly an over­estimate) could evolve in a billion years, even without the advantages of large environmentally diverse world-wide populations, sexual recombination and interspecies genetic transfer.

  There are a number of errors in Dr. Kleinman's argument:
  1. The mutation rate was kept constant per genome. This is not what occurs in nature, where DNA polymerases make errors at a certain rate per base. I used a fixed mutation rate in Ev because that made the program simple and it was not the focus of the initial model. Paul Anagnostopoulos has modified Evj so that it can now have a constant error per base.
  2. Large genomes are known to appear by many duplication mechanisms that are not in the Ev model. There are polymerase slippage, illegitimate recombination, transposons, insertion sequences, tetraploidization, and Robertsonain translations. These can all increase genome size rapidly. The mechanisms are currently not part of the Ev/Evj model.
  3. Genes diverge after duplication. Once a genome has increased in size or a gene has duplicated, we know that genes diverge and take up similar but not identical function. An example is the vast family of ABC transporter genes.

  Kleinman objected to the idea of duplication because he could not see that there can be advantages eventually as the genes diverge. That is, he neglected the third point.

  When Paul Anagnostopoulos ran a model with 96 creatures, 16 sites, and 1 mutation per 256 bases, varying the genome size from 256 to 16,384 he got (generations to Rs >= Rf) = 3.37 (genome size)^0.97 with r=.99. This is less than exponential.

• 2006 Jun 27. Alan Kleinman stated: Some people may start questioning the validity of ev based on the marked variations of the generations for Rs->Rf simply by changing the random seed to start the calculation. Given that Evj is a stochastic process, we expect variation in the generation time. To investigate this, I ran Ev (the original Pascal program) 1000 times and got this distribution. Clearly it is not a Gaussian but it is a defined distribution. (The full analysis is available.)
• 2006 Aug 12. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines." PLOS Genetics 2006 Jun 15. Not only can we figure out evolution, but even who ate whom by the evolution of parasites! (paper at PLOS Genetics).
• 2006 Aug 26. Evolution Major Vanishes From Approved Federal List
  • Evolution Major Vanishes From Approved Federal List New York Times, Cornelia Dean, August 24, 2006.
  • Evolution Major Vanishes From Approved Federal List from Common Dreams.

  Part 26, biological and biomedical sciences, has a number of sections, each of which has one or more subsections. Subsection 13 is ecology, evolution, systematics and population biology. This subsection itself has 10 sub-subsections. One of them is 26.1303 - evolutionary biology, "the scientific study of the genetic, developmental, functional, and morphological patterns and processes, and theoretical principles; and the emergence and mutation of organisms over time."

  Though references to evolution appear in listings of other fields of biological study, the evolutionary biology sub-subsection is missing from a list of "fields of study" on the National Smart Grant list - there is an empty space between line 26.1302 (marine biology and biological oceanography) and line 26.1304 (aquatic biology/limnology).

  Here's the actual text on page 7 of the document as of August 26:

  26.13 Ecology, Evolution, Systematics and Population Biology
  26.1301 Ecology
  26.1302 Marine Biology and Biological Oceanography
          
  26.1304 Aquatic Biology/Limnology
  26.1305 Environmental Biology
  

• 2006 Sep 27.

  THE NIH DIRECTOR'S WEDNESDAY AFTERNOON LECTURE SERIES (WALS) SEPTEMBER 13, 2006 - JUNE 28, 2007

  WALS, WEDNESDAY, September 27, 2006, 3:00-4:00 PM Clinical Center, Jack Masur Auditorium, Bldg.10 OVERFLOW: The Lipsett Auditorium

  "God, Darwin, & Design: Evolution and the Battle for America's Soul" Kenneth R. Miller, Ph.D. Professor of Biology, Brown University
  Details about the talk; Podcast.

  This talk discusses the Dover trial and gives some really nice examples of evolution!
• 2006 Nov 14. When ignorance applies scientific vacuity, a posting at The Panda's Thumb
• 2007 May 03. Arguments in Intelligent design is not creationism, an article in the Telegraph by Stephen C Meyer (12:01am GMT 28/01/2006), are fatally flawed.

  Is there a better explanation? Based on our uniform experience, we know of only one type of cause that produces irreducibly complex systems: intelligence. Whenever we encounter complex systems - whether integrated circuits or internal combustion engines - and we know how they arose, invariably a designing intelligence played a role. ... So the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

  This ignores the direct experience with Ev/Evj which show clearly that the information in DNA can arise purely by Darwinian selection.
• 2007 May 4. In The Talk of the Times: Intelligent Design vs. Evolution, Stephen C Meyer says that

  The key test [for Intellegent Design] is show me a process that generates information, and large amounts of specified information, without the guidance of an intelligent agent.

  Ev does that.
• 2007 May 21. Molecular Biology and the New Creationism? by Sahotra Sarkar on January 02nd 2006 cites this work (reference 13).
• 2007 Jun 10. How Evolution Causes an Increase in Information Part II a Youtube video.
  
• 2007 Jul 04. Evolution and Natural Selection. ~ Population evolution model is a discussion that led to Ev at richarddawkins.net.

• 2007 Aug 03. An Interview with Dr. William A. Dembski by Mario Lopez. (Note: by 2008 Aug 04, the interview was "Updated" and the name "Schneider" was removed.) In this interview, Dembski complains:

  Perhaps the most striking instance of silence is that of Thomas Schneider, whose article on the evolution of biological information in Nucleic Acids Research (2000) claims to refute my colleague Michael Behe. When Robert Marks and I recently showed that his evolutionary program was equivalent to a neural network and that it works worse than pure chance (http://web.ecs.baylor.edu/faculty/marks/T/ev2.pdf), he too fell silent though in the past he would reply in a day's time on his own website to any challenge from me. I have found that Darwinists make a habit of staying quiet about problems with their theory and ignore the best criticisms of it.

  Several people told me about that paper soon after it came out in early June 2007. The paper has no date, no authors and is on a personal web site. It was presented initially as a draft of a paper. As such it is a moving target so I decided to wait for it to be properly published in a peer reviewed journal. As for not responding, I had other much more important things to work on, rebutting Dembski's obviously incorrect arguments is low priority and I will respond in time. As of August 4, 2007, the original page, with link http://web.ecs.baylor.edu/faculty/marks/eil/Publications/ev/index.html is gone. So how can Dembsky complain about me not responding? (NOTE: please do NOT send me this or any other document - I have my own copies!) On the other hand, Dembski has had 6 years to deal with these:
  • Dissecting Dembski's "Complex Specified Information"
  • Effect of Ties on the Evolution of Information by the Ev program
  but as far as I can tell, he ignored them.

  Clearly Dembski has not run the Evj program or he would have seen that it does not work "worse than pure chance". Here's what you do. Run the Evj program with 'Pause on Rseq >= Rfreq' turned on, max out the speed and let it evolve until Rs >= Rf. This standard run completes in 675 generations on any computer and takes under 8 seconds on a 3 GhZ Mac Pro. That evolutionary run is supposedly, according to Dembski, "worse than chance".

  Now, to model "chance", turn off "Perform selection" and click Run again (keeping 'Pause on Rseq >= Rfreq' turned on). Wait until Rsequence reaches Rfrequency. Obviously it's not going to happen in a long time, perhaps your lifetime! If someone does a run and finds the number of generations necessary, please tell me. That represents the chance run. So though I have not read Dembsi's paper in detail, the abstract itself contains a fatal flaw.

  So then I did the standard run, as described above to 100,000 generations which took less than 30 minutes. Rsequence is 0.15 at that moment but as soon as I started it again, it went both positive and negatively so there was no progress. Reaching 4 bits by 'chance takes more than 100,000 generations by "pure chance" but only 675 generations by Darwinian selection. Dembski's statement that "Based on query count, repeated random queries outperform the evolutionary algorithm by over 10,000%." is clearly off by 9 orders of magnitude! I ran to 200,000 generations without selection and Rsequence = -0.28. This is nowhere near the 4 bits to be evolved. We don't seem to be making progress, though Dembski would say the opposite. I finally stopped the run at 1,000,000 generations at which time Rsequence was 0.04. Clearly one won't get those 4 bits by 'random chance' BUT they evolve quite rapidly by natural selection!

  I used the original ev program to characterize this precisely. Using the standard Evj parameters and with selection off, I ran 1000 generations. The mean is (as expected) close to zero and the standard deviation is 0.26253. How many standard deviations out is 4 bits? 4/0.26253 = 15.24 standard deviations. The probability can't be computed on my machines, but 15 standard devitions can be on a 64 bit Mac, that's 5.55E-17. So the probability of getting Rs to fluctuate as high as Rf by random mutations less than 5x10^-17. By Darwinian selection the probability is close to 1 within 1000 generations.

• 2007 Aug 04. Evaluation of Unacknowledged Information Costs in Evolutionary Computing: A Case Study on the Evolution of Nucleotide Binding Sites". This paper was apparently written by Robert Marks and perhaps William Dembski (no authors or date were listed). The paper was removed by 2008 Apr 10.

  • page 2: It's not clear why the authors are concerned about the number of 'queries' required to achieve evolution in Ev. (Ev "required 45,056 queries before achieving success.") The Ev model is designed to match the natural situation and every biologist knows that evolution is "wasteful". Just look at all the seeds on a dandylion or the number of sperm produced by a male. So the authors may as well complain about the wastefullness of nature. Despite this waste, Ev achieves evolution of Rsequence to match Rfrequency rapidly.
  • page 2: claims that Ev only has potential sites outside the gene. This is incorrect.
  • page 3: "each basis therefore corresponds to 2 bits of information." That should be each 'base'.
  • page 3: "Ev uses the specic locations²
    t = [1; 10; 17; 26; 33; 43; 50; 60; 70; 76; 83; 92; 101; 109; 117; 125]: (1)
    The choice of this target, we shall see, is the key to making the search problem easy." Using Evj one may try a variety of choices, including randomly overlapped sites. Evj usually solves them quickly so this statement is incorrect. Just yesterday we watched an Evj evolution with 6 sites overlapping 3 deep and it was solved. To try this run, launch the Evj program . Click 'New', set Placement to random, overlapping. Run. The complex overlaps are around postion +150. Even this rather difficult problem is solved at generation 4623.
  • page 3: "Our purpose is not to discuss the biology motivating ev". This is a critical error since the question is whether Ev/Evj is a reasonable model of what happens in nature. It is to most biologists - thats why the paper got published. In the past 7 years no biologist has complained that the model was not reasonable and invariably biologists reacted positively.
  • page 3: "Alternately, we could repeatedly choose random values for the weights, genome sequence, and bias to see whether the binding sites are properly matched. We will show, surprisingly, that the random search outperforms the evolutionary search used by ev for the inversion of the perceptron." As discussed above, this is incorrect. If one uses selection the evolution is rapid. The random search, mutation without selection, takes more than a million generations and has a probability less than 10^-17.
  • page 3: "Endogenous information" is a misdirection. First, in nature gene duplication occurs all the time. So obtaining a spare recognizer protein is trivial and has essentially no cost: genomes are littered with duplications. This is part of the house keeping genes that run the system. They are not part of the model, which is aimed to understand how Rsequence evolves towards Rfrequency. Second, the recognizer gene is NOT the problem to be solved. The problem is to match the gene to the binding sites. Ev/Evj do this easily.
  • page 5: "An inescapable conclusion is that the perceptron structure of ev has been constructed, consciously or not, to favor solution of the binding site problem." Well, it wasn't conscious, I simply wanted to match nature. So if nature favors solving the problem by evolution then what's the problem? Notice that Dembski doesn't include mutation in his analysis, which makes it irrelevant to the natural problem.
  • page 5: The 439 queries is complete replacement of the genome. I don't believe this result given that the probability of getting all 16 binding sites was 10^-17 (above). Dembski's making an irrelevant and incorrect computation. It's clearly irrelevant because biology does not replace its entire genome every generation!
  • page 8: The Conclusions complain about the weight matrix having lots of 'information'. How is this different from the proteins that already exist ready to mutate after a duplication in biology? Dembski is complaining that biology is cheating because it is set up to evolve easily!
  • page 8:

    To maintain its integrity, the field of evolutionary computing needs to institute the following control: all computer simulations of evolutionary search must make explicit (1) a numerical measure of the inherent difficulty of the problem to be solved (i.e. the endogenous information) and (2) a numerical measure of the information contributed by the search structure toward solving the problem (i.e., the active information). This control acts as a safeguard against inflated claims for the information-generating power of evolutionary algorithms.

    Dembski is doing a misdirection in this paper. The problem to be solved is to obtain the binding sites matching the recognizer. That is, the inherent difficulty of the problem is Rfrequency, which Dembski managed not to mention at all! This is the number he is calling for in part (1) and he doesn't even mention it in his paper. Clearly since Rsequence is zero at the start, the search structure contributes no information to this required information, so part (2) is irrelevant.
  Conclusion: Dembski is doing a misdirection in this paper. Apparently he is complaining about the fact that DNA proteins can be duplicated and then evolve to match new sites. This is well documented, for example in our own work on the coevolution of T7 polymerasese and their binding sites. Given that a freshly duplicated recognizer protein exists the problem is only to determine how the binding sites and the recognizer co-evolve. This is demonstrated clearly in the Ev/Evj model. So Dembski did not deal with the essential result that binding sites in this model and in nature easily evolve to match their recognizer.

• 2007 Aug 12. In "Unacknowledged Information Costs in Evolutionary Computing: A Case Study on the Evolution of Nucleotide Binding Sites" Dembski claims that "Using repeated random sampling of the perceptron, inversion is therefore expected in 1/p_S = 439 queries." That is, according to Dembski random generation of sequences should give a solution in which there exists a creature with zero mistakes more quickly than the Ev program running with selection on. If this were true, then random generation of genomes would be more efficient than natural selection, which takes 675 generations for Rs to exceed Rf in the standard run. While anyone familiar with natural selection will immediately sense something wrong with Dembski's numbers, it is reasonable to test his 'hypothesis'. For the discussion of 2007 Aug 03 I used the running Ev program and counted each generation. This was a little unfair because there was only had one mutation per generation. This might make a tighter Rs distribution around zero bits because each generation is similar to the last one. Thus the estimate may be too high. A more fair test is to generate a completely new random genome each time. What is the distribution? For 100 independent generations, the mean was -0.02114 bits and the standard deviation was 0.26227 bits. This is essentially the same standard deviation as before! so the probability of getting 4 bits is, again, gaussian probability(Z = 4/0.26227) = 5.5x10^-17. Dembski's estimate of 439 queries is off by about 14 orders of magnitude.

  2008 Apr 10. What happened to this paper? The link to the paper "Unacknowledged Information Costs in Evolutionary Computing: A Case Study on the Evolution of Nucleotide Binding Sites" is broken. Google for "Unacknowledged Information Costs in Evolutionary" gets one link The Austringer » Marks and Dembski Acknowledge Withdrawing ... "Unacknowledged Information Costs in Evolutionary Computing: A Case Study on the Evolution of Nucleotide Binding Sites". After bragging about how their work ... austringer.net/wp/index.php/2007/11/16/marks-and-dembski-acknowledge-withdrawing-unacknowledged-costs-paper/ but that link is broken too and can't be located at the wayback machine. The paper is listed as "in review" at Robert J. Marks II PUBLICATIONS - ARCHIVAL JOURNALS. A discussion is at www.BobMarks.org.

• 2007 Aug 17. In the Discussion of the Ev paper, the link to http://www.trueorigin.org/dawkinfo.htm has been broken. ("The Problem of Information for the Theory of Evolution Has Dawkins really solved it?" by Royal Truman 1999.) Using the fabulous WayBack Machine we find it: Search for http://www.trueorigin.org/dawkinfo.htm. The page was captured by them from Jun 02, 2001 to Feb 07, 2006. A search at http://www.trueorigin.org/ gives the new location: http://www.trueorigin.org/dawkinfo.asp.

• 2007 Aug 23. Behe has published a new definition of irreducible complexity. (Google scholor: Behe MJ 2001): Michael J. Behe, Reply to My Critics: A Response to Reviews of Darwin's Black Box: The Biochemical Challenge to Evolution, Journal Biology and Philosophy 16(5) 683-707, 2001. The new definition (page 694) is:

  irreducible complexity ...: a single system which is necessarily composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.

  Original 1996: a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning

  Revised 2001: a single system which is necessarily composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.

  Essentially, the word 'necessarily' was added. The changes do not appear to alter the definition sufficiently to escape the challenge from Ev (which Behe did not respond to). As pointed out in the discussion of of the Ev paper (page 2797), the organisms in Ev match this definition exactly, but they evolved. This completely destroys Behe's thesis.

• 2007 Oct 22. Doubting Darwin by Sahotra Sarkar, page 121 cites this work (ISBN 9781405154901).

• 2008 Feb 09. Dawkins stumped? Examples of added information cites this work (02:02).

• 2008 Apr 09. Intellectual Honesty - The Truth About Genetic Mutations, apparently a clip from the movie Expelled, neglects the Ev paper, claiming incorrectly that "natural selection does not provide any new genetic information."

• 2008 Apr 13. Intellectual Honesty - Information, another clip from the movie Expelled that neglects the Ev paper.

• 2008 Apr 14. Evolution in a Nutshell, was a presentation at Science Unrestricted on 2008 Apr 2.

• 2008 Jul 07. Unacknowledged Errors in "Unacknowledged Costs" Essay, by Wesley R. Elsberry (Tue, 2007-10-09 15:16) reviews the critique of the Ev program by Dembski and Marks (see 2007 August 03 and 2007 August 04 above). The Dembski and Marks program was shown to contain errors and these explain their anomalous results. This critique of the Ev program failed. Update 2008 Aug 04: The original paper critiqued above has been removed from the web. The interview was rewritten to exclude the word 'Schneider'.

• 2008 Jul 07. Why the theory of evolution is mathematically impossible, another unsubstantiated attack by Kleinman at Richard Dawkins net.

  Note on 2009 Apr 27: Dr. Kleinman claims that the Ev program shows that evolution of large genomes is not possible but the ev model does not include a number of important natural biological processes including recombination, chromosome sorting, deletions, insertions, horizontal gene transfer, genome fusion/duplication and genetic element transposition, all of which are known to be important for evolution of large genomes.

• 2008 Aug 13. Optimism in Evolution, Olivia Judson, NY Times, August 13, 2008

• 2009 Mar 07. In the podcast Well-Informed: Dr. Robert Marks and the Evolutionary Informatics Lab, (January 30, 2009 02:34 PM PST) Marks makes vague claims against the Ev program. At Marks' website, The Evolutionary informatics Lab, under EV Ware is EV Ware: Dissection of a Digital Organism (February 14, 2009: Version 3.1 posted.) which claims that statements in the original ev paper are incorrect.

  The description of the program is completely incorrect. The supposed Hamming code has a deeper layer which represents the binding sites as found in nature. The reference to "the enormous active information" is incorrect - the amount of information is Rfrequency, a precise amount.

  Perhaps Dr. Marks doesn't appreciate the background biological science behind the Ev program. I wrote Ev to test my PhD thesis, which is that the information contained in binding sites (called Rsequence) is approximately equal to the information needed to locate the sites on the genome (called Rfrequency). I came up with this hypothesis because that's what I observed in nature. So I put the ev program together to see if I could test my thesis.

  The key concept is that the information needed to locate the sites is a function (negative logarithm) of the size of the genome and the frequency of sites in the genome. Of course the frequency of sites is the number of functional sites divided by the size of the genome. But the size of the genome is reasonably fixed over millions of years. For example, a gut bacterium like E. coli has 4.7 million base pairs and this does not change much over time because they don't have huge changes in the number of genes compared to changes in the gene control systems. The other number, the frequency of sites is also reasonably fixed because the genetic control is responding to the external environment. For example, there are about 50 genes turned on after E. coli has its DNA damaged by UV (as when it ends up on the surface of the ground after being excreted from an animal). These genes repair the DNA and there are only a certain number of them. The bottom line is that Rfrequency is reasonably fixed over long periods, but Rsequence is variable. So Rsequence must evolve towards Rfrequency. That's exactly what Ev shows. Initially Rsequence, the information in the genome is zero and it climbs as the evolution proceeds.

  Now notice that Rsequence is the information in the organism while Rfrequency represents the information in the environment of the gene system. Chris Adami was, I believe, the first person to point out that the organism is getting information from the environment. The ev program show this explicitly. But of course, that's what Darwin meant by 'natural selection', without explicitly putting numbers on the situation.

  Sound bite: The Ev program does use external information, just as happens in nature. Organisms get the information for their genomes from their environment and the mechanism for this is natural selection.

  Dr. Marks claims: "From our dissection of the ev digital organism, claims about the computer program can now be made." Let's look at his claims:

  • Ev purports to show "how life gains information." Specifically "that biological information... can rapidly appear in genetic control systems subjected to replication, mutation and selection." It is the active information introduced by the computer programmer and not the evolutionary program that reduced the difficulty of the problem to a manageable level.

    The information provided to Ev is the size of the genome and the number of sites. The Ev organisms evolve to capture this information (Rfrequency) in their binding sites (as Rsequence). Dr. Marks didn't understand the basic biology. The key point is that this is exactly what happens in nature where the size of the genome and number of sites are determined not by a person but by the environment.

  • Ev purports to show illustrate punctuated equilibrium: "The transition [i.e. convergence] is rapid, demonstrating that information gain can occur by punctuated equilibrium." The active information from the Hamming oracle and ev's number cruncher are responsible for the rapid convergence - not the evolutionary program.

    No, clearly the process of natural selection causes the rapid convergence, and this is exactly a model of punctuated equilibrium. Indeed one can SEE the punctuated equilibrium in the curve:
    While selection is being applied in the first 1000 generations the evolution happens rapidly, this is the punctuation. After 1000 generations (green curve) the situation is stabilized in an equilibrium. So the program does indeed illustrate punctuated equilibrium.

  • Ev purports to disprove "Behe's [7] definition of `irreducible complexity' ... (`a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning'. " Billions of input nucleotide sequences will produce the binding sites required by ev.

    This is not a response to the claim! Ev clearly has "irreducible complexity" according to Behe's claim and it clearly evolves the information Rsequence, which shows that Behe's thesis is incorrect.
  
  Conclusion: No problems for Ev have been raised by Dr. Marks.

• 2009 Mar 07. Only a Theory: Evolution and the Battle for America's Soul, by Kenneth R. Miller, discusses the Ev program on pages 76-79. (See also pages 227 and acknowledgment in the front matter [page not available].)

• 2009 Apr 16. Evolution in a Nutshell, was a presentation at Science Unrestricted on 2008 Mar 31.

• 2009 Dec 18. A contest gets a winner: common creationist claims refuted, Posted on: December 17, 2009 10:42 PM, by PZ Myers, says: "Can natural processes produce an increase in complexity?" and cites this paper. Further discussion (search for 'Schneider'):

  • Posted by: raven | December 19, 2009 5:40 PM #99
  • Posted by: Alexander the Good Enough | December 20, 2009 1:10 AM #133
  • Posted by: Alexander the Good Enough | December 20, 2009 9:59 AM #134

• 2009 Dec 19. CREATIONISTS-READ THIS. Post by Calilasseia Mon Nov 02, 2009 9:02 pm at RichardDawkins.net.

• 2010 May 20. A new book has come out from the Discovery institute, Signature of Controversy which claims "few---if any---of the critics really grappled with the substance of Meyer's argument." I have not read the book yet, but suspect they have not read the earlier blog entry which lays out the errors in Meyer's thesis.

• 2010 May 21. The paper by Kimura in 1961

  @article{Kimura1961,
  author = "M. Kimura",
  title = "{Natural selection as the process of accumulating genetic
  information in adaptive evolution}",
  journal = "Genetical Research",
  volume = "2",
  pages = "127--140",
  year = "1961"}
  

  would have been an appropriate reference for the Ev paper!

• 2010 Jun 14. Dr Schneider's Ev Computer Model, How mutation and selection works is a discussion started by Alan Kleinman. He claims that I "won't publish all the data from [my] model". In the first place, I have much bigger fish to catch. Second, I don't have more data. Work was done by him and Paul Anagnostopoulos and they collected data about what happens in Evj with large genomes. They found that Evj doesn't evolve well with large genomes. Kleinman's conclusion was that large organisms could not evolve. However, he is still missing the point that Ev does not account for many well known mechanisms, especially including recombination, that make genomes more fluid and able to evolve more quickly. A proper test would be to incorporate recombination, sex, chromosomal assortment etc into evj to see what the effects of these are. However, my bet is that the rather vast evolutinary literature already has hundreds of papers on these topics that probably show how these factors speed up evolution. See the blog entry of 2006 Jun 27. (Note: I agree with his point that combinatoric drug application is useful.)

• 2011 Feb 16. Dissection of "A Vivisection of the ev Computer Organism: Identifying Sources of Active Information", a paper by G. Montanez, W. Ewert, W. Dembski and R. Marks.

Schneider Lab
origin: 2004 Sep 29 from ev.html
updated: 2012 Apr 06


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