Evaluation of creationist/'intelligent design' writers: Batten Behe Bracht Dembski Gitt Meyer Strachan Joseph Truman Williams
Events: Dover trial
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) - Hy(x) [Shannon1948 (Section 12)] corresponds to my R = Hbefore - Hafter [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.
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; |
2002 November 8.
NPR Talk of the Nation,
Teaching Evolution / Teaching Creationism
|
"A recent article by a biologist named professor Schneider who is writing in nucleic acid journal. 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:
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.
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.
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 # 1060This 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.
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.
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.aspTo 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.
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).
"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..
"... 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.
"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.
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.
Helsinki University of TechnologyLectures 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.
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.
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.
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
'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.
"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."--- Richard Dawkins The atheist, www.salon.com, April 28, 2005.
"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."
"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."
"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.
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.lecb.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?
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.
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?
Fred Williams is stirring up quite a discussion.
*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:
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.
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 quotesOf 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 selectionThese 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":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."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).
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":Dr. Jones did not read the rebuttal to Dembski. (Thanks Paul, for pointing this out)
...
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.
6) Schneider's simulation is of "a genome size of 256 bases" which has "a set of 16 binding sites":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.
...
but he does not reference any actual *biological* genome that has "16 binding sites in a genome size of 256 bases".
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":There is no basis for this claim. The biological literature is full of examples of mutations and mutational mechanisms.
...
But this raises the issue that *real* "biological" genomes don't reshuffle their bases into order, like Schneider's simulation does.
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 worldSee 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":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.
"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.
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.
15) [... irelevant compaint ...] Schneider claims that his "ev model" "fits Behe's (34) definition of `irreducible complexity' exactly":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.
...
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)!
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":See above. Dr. Jones needs to read the literature more.
...
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.
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?
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
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!!!
"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."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.
Our goals are to Teach the Controversies, all of them, each and every one. ...
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
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.lecb.ncifcrf.gov/~toms/paper/ev/
T. D. Schneider, Evolution of Biological Information, Nucleic Acids Res, 28(14): 2794-2799, 2000 http://www.lecb.ncifcrf.gov/~toms/paper/ev/
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.lecb.ncifcrf.gov/~toms/paper/ev/
T. D. Schneider, Evolution of Biological Information, Nucleic Acids Res, 28(14): 2794-2799, 2000 http://www.lecb.ncifcrf.gov/~toms/paper/ev/
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.
"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 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.
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:
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 solveAnswer: Ev.
No stepwise, non-destructive process from "Easy Personal Protection Training" to "Fast Personal Protection Training"Wrong. Probability is 1/(26*26) = 1/676.
Random Mutation = NOISEWrong. Noise in biology allows evolution! SOME mutations are beneficial, as shown by the Ev program.
Noise is always bad
Claude Shannon: Noise = EntropyWrong. noise is measured in units of power. Entropy is measured as J/K.
Impossible to get information from noiseThis is wrong, as demonstrated by the Ev program.
Natural selection cannot increase informationThis is wrong, as demonstrated by the Ev program.
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.
"Thus we have an airtight inductive proof that DNA originated from a superintelligence:"
- "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.- "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.- "Therefore DNA came from a mind."
The conclusion does not follow because the first premise is false.
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.
"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?"
"What we're seeing is evolution in action"
-- Dr. Stuart B. Levy,
2005 Oct 23.
Dover Trial
"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
"... 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."Behe's weak non-quantitative statement is destroyed by examples from the Ev program.
--Michael Behe, Morning Session, October 17, 2005, page 91
Q. Is intelligent design falsifyable?Indeed! Behe's thesis is falsified by the Ev program! See the Discussion in the paper.
A. Yes, it is.
--Michael Behe, Morning Session, October 17, 2005, page 114
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?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).
A That sounds like -- sounds fine as well.
--Michael Behe, Afternoon session, October 17, 2005, page 13
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?Behe makes the same error again of confusing the origin of life with natural selection.
A Yeah, and that sounds clear.
--Michael Behe, Afternoon session, October 17, 2005, page 16
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?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.
A That sounds reasonable.
--Michael Behe, Afternoon session, October 17, 2005, page 16-17
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?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.
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
I think that in fact Darwinian theory is very difficult to falsify, but that intelligent design is easily falsify -- or easy to falsify.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.
--Michael Behe, Afternoon session, October 17, 2005, page 50
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.He conveniently ignores the Ev paper!
--Michael Behe, Afternoon session, October 17, 2005, page 59
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 113-114He 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.
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.So Behe is apparently unaware of or ignoring the Ev paper. But he asks for more:
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?
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.
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.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!
Q. By an intelligent designer?
A. Well, intelligently designed, yes, it implies a designer, yes.
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.
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.
Q. And, therefore, there would be no successive generation because that flagellum would not move on to the next generation?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.
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.
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?How can something be falsifiable if it can't be ruled out!!?????
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.
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 |
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:
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:
[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.Students need more science classes, not fewer Timesunion, 2006 Jan 14
-- Karen Kowalski
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!
Likewise, at this rate, roughly an entire human genome of ~4x109 bits (assuming an average of 1 bit/base, which is clearly an over�estimate) 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:
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.
Here's the actual text on page 7 of the document as of August 26: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).
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
This talk discusses the Dover trial and gives some really nice examples of evolution!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.
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.
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 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:
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.
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.
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/pS = 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: 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.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/ 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.
2008 Aug 13. Optimism in Evolution, Olivia Judson, NY Times, August 13, 2008
Schneider Lab
origin: 2004 Sep 29 from ev.html
updated: 2008 Aug 13
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