Can You Say “WEASEL”?

_{William Dembski

November 1, 2010

Darwinism, Evolution, Intelligent Design}

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Check out the following paper at arXiv. It gives yet another incarnation of Dawkins’ WEASEL. Let me suggest that Darwinists next try a horror version of it: “The WEASEL That Wouldn’t Die.” Perhaps Michael Moore can help make it.

There’s plenty of time for evolution

Herbert S. Wilf
Department of Mathematics, University of Pennsylvania
Philadelphia, PA 19104-6395
wilf@math.upenn.edu>

Warren J. Ewens
Department of Biology, University of Pennsylvania
Philadelphia, PA 19104-6018
wewens@sas.upenn.edu>

October 28, 2010

Abstract: Objections to Darwinian evolution are often based on the time required to carry out the necessary mutations. Seemingly, exponential numbers of mutations are needed. We show that such estimates ignore the effects of natural selection, and that the numbers of necessary mutations are thereby reduced to about K log L, rather than K^L, where L is the length of the genomic “word,” and K is the number of possible “letters” that can occupy any position in the word. The required theory makes contact with the theory of radix-exchange sorting in theoretical computer science, and the asymptotic analysis of certain sums that occur there.

Comments

bornagain77,
Mathgrrl, I also noticed you made this unsubstantiated assumption: Modern bacteria have evolved for just as long as every other modern organism. Yet the best evidence we have says that no evolution has occurred in bacteria:
I've got a heavy load this semester, so I'm limiting my participation in this thread to discussion of GAs that meet gpuccio's criteria. However, if you want to learn about the evolution of modern bacteria, you should read some actual textbooks and peer-reviewed papers. Your claim is completely at odds with a significant amount of empirical evidence.MathGrrl_{November 3, 2010
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BA, it appears the water got cold all of a sudden. What happened? Don't tell me you brought another bucket of ice with you!? This isn't the first time, you know! Darn it all, BA. You KNOW drive-bys like their tea hot! Better brush up on your manners. :)Oramus_{November 3, 2010
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Mathgrrl, I also noticed you made this unsubstantiated assumption:
Modern bacteria have evolved for just as long as every other modern organism.
Yet the best evidence we have says that no evolution has occurred in bacteria: The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 The oldest bacterium fossils, found on earth demonstrate an extreme conservation of morphology which, very contrary to evolutionary thought, simply means they have not changed and look very similar to bacteria of today. AMBER: THE LOOKING GLASS INTO THE PAST: Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms. http://bcb705.blogspot.com/2007/03/amber-looking-glass-into-past_23.html Bacteria: Fossil Record - Ancient Compared to Modern - Picture http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html Was our oldest ancestor a proton-powered rock? - Oct. 2009 Excerpt: “There is no doubt that the progenitor of all life on Earth, the common ancestor, possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.” http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html as well, we now have concrete evidence for photosynthetic life suddenly appearing on earth, as soon as water appeared on the earth, in the oldest sedimentary rocks ever found on earth. The Sudden Appearance Of Photosynthetic Life On Earth - video http://www.metacafe.com/watch/4262918 The oldest sedimentary rocks on earth, known to science, originated underwater (and thus in relatively cool environs) 3.86 billion years ago. Those sediments, which are exposed at Isua in southwestern Greenland, also contain the earliest chemical evidence (fingerprint) of 'photosynthetic' life [Nov. 7, 1996, Nature]. This evidence had been fought by materialists since it is totally contrary to their evolutionary theory. Yet, Danish scientists were able to bring forth another line of geological evidence to substantiate the primary line of geological evidence for photo-synthetic life in the earth’s earliest sedimentary rocks. U-rich Archaean sea-floor sediments from Greenland - indications of +3700 Ma oxygenic photosynthesis (2003) http://adsabs.harvard.edu/abs/2004E&PSL.217..237R Electron transport and ATP synthesis during photosynthesis - Illustration http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cooper.figgrp.1672 Evolution vs ATP Synthase - Molecular Machine - video http://www.metacafe.com/watch/4012706 Moreover the first DNA code in life had to be at least as complex as the current DNA code found universally in life: “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible” Donald E. Johnson – Bioinformatics: The Information in Life Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell's Design - 2008 - page 177) DNA - The Genetic Code - Optimal Error Minimization & Parallel Codes - Dr. Fazale Rana - video http://www.metacafe.com/watch/4491422 Mathgrrl I have a question for you, will you continue to claim bacteria have 'always been evolving' even though you have no evidence to substantiate your claim?bornagain77_{November 2, 2010
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Mathgrrl, pardon my intrusion, but perhaps you may be interested in this paper: LIFE’S CONSERVATION LAW - William Dembski - Robert Marks - Pg. 13 Excerpt: Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case. http://evoinfo.org/publications/lifes-conservation-law/bornagain77_{November 2, 2010
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PaV, All of your questions can be answered from the Tierra overview on its website. Google "Tom Ray Tierra" for lots of links.MathGrrl_{November 2, 2010
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gpuccio,
I don’t agree with you. Resources are limited everywhere, in a general purpose computer environment like in any other setting. Competition arises everywhere.
That's a good point. It should, in theory, be possible to create a version of Tierra that runs on a standard OS. It would look a lot like a very nasty software virus. Security issues aside, there is no logical difference between a simple simulation environment and Windows or Linux in this context, although the environments like Tierra's do allow much easier monitoring. That's quite important when doing research.
Could you explain for example why bacteria would have evolved to eukaryotes and then to multicellular beings, when they still are the most successful reproductors on our planet?
Well, that's kind of off-topic, and also a bit inaccurate. Modern bacteria have evolved for just as long as every other modern organism. The general issue of the rise of multicellularity is an interesting topic, but definitely outside the scope of this discussion.
What environment favoured the more complex structures?
The real world. It;s must more complex than even our best computer simulations.
I believe that everybpody emphasizes too much the concept of “selection pressure”.
My point was that, unless it provides some survival benefit to the program, there is no reason to expect a sorting algorithm to evolve.
Maybe because the only real model of darwinism is antibiotic resistance?
You should know that is a grossly inaccurate statement.
And then, isn’t RV the real originator of the new functions? RV knows nothing of selection pressure. If a new function arises by RV, it will be a new useful function also in a general purpose computer environment, I believe.
It can only be "useful" in a particular context. If the only context is efficient utilization of RAM and clock cycles, a sorting algorithm is useless.
Or shoud we believe that each new protein superfamily arose because of a new specific selection pressure in the environment? That would be an interesting concept.
It would be more accurate to say that the alleles that result in those proteins arose over time via evolutionary mechanisms, providing benefit (or at least no significant disadvantages) at each iteration in the environment in which that iteration existed. This is evolutionary biology 101 -- it should be understood by anyone participating in a discussion such as this.MathGrrl_{November 2, 2010
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MathGirl: Here's the other foot in the water! You said:
ierra is about the simplest environment possible, given that RAM and time are the only two resources available. Programs live or die based on how well they use those resources.
This type of programming seems harmless enough. But the devil is in the details. Viz., when you say that the programs "live or die based on how well they use those resources," just what, exactly, determines "how well" they're doing. Why kind of a comparison is involved? And who decided that this comparison is a good one to make?PaV_{November 2, 2010
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PaV, Hop right in, the water's fine!
Isn’t this exactly the problem? How does one “create” an environment that ‘rewards’ certain configurations without inputting some selection functions?
While there are some GAs that use explicit fitness functions, in those like Tierra fitness is implicit in how well a program performs in the environment.
But this then means that human intelligence has to come up with a ‘reasonable’ selection function that will then operate under ‘reasonable’ conditions. This is information, located in an intelligent agent. How do you surmount this problem?
By not creating a fitness function! Tierra is about the simplest environment possible, given that RAM and time are the only two resources available. Programs live or die based on how well they use those resources. Interestingly, even in such a simple environment we see parasites evolve, and resistance to parasites, and "hyper parasites" that prey on the new programs.MathGrrl_{November 2, 2010
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MathGrrl: I don't agree with you. Resources are limited everywhere, in a general purpose computer environment like in any other setting. Competition arises everywhere. Could you explain for example why bacteria would have evolved to eukaryotes and then to multicellular beings, when they still are the most successful reproductors on our planet? What environment favoured the more complex structures? I believe that everybpody emphasizes too much the concept of "selection pressure". Maybe because the only real model of darwinism is antibiotic resistance? But you know, that is an extreme scenario. And then, isn't RV the real originator of the new functions? RV knows nothing of selection pressure. If a new function arises by RV, it will be a new useful function also in a general purpose computer environment, I believe. Or shoud we believe that each new protein superfamily arose because of a new specific selection pressure in the environment? That would be an interesting concept. And the DNA code? Selection pressure that too?gpuccio_{November 2, 2010
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Math Girl: Please excuse me for jumping into this conversation---I haven't really looked at all the earlier posts, but I can't help but note this:
While it should be possible to create an environment in which sorting algorithms evolve, there is no reason to expect it to happen in a general purpose OS where there is no benefit to doing so.
Isn't this exactly the problem? How does one "create" an environment that 'rewards' certain configurations without inputting some selection functions? But this then means that human intelligence has to come up with a 'reasonable' selection function that will then operate under 'reasonable' conditions. This is information, located in an intelligent agent. How do you surmount this problem?PaV_{November 2, 2010
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gpuccio, As the old joke goes, "I think I see the problem." From your post above:
If a replicator can reproduce and survive in Windows, and if it is allowed random variation, why shouldn’t it in time develop complex new functions? If the darwinian model is correct, I mean! But it won’t. A simple software program will never develop something like an ordering algorithm of 200 bits (or any similar complex function), which was not present in the original replicator, only as a result of random variation and true “natural selection”. Not in Windows, not in Linux. Never.
Why would you expect a new function to evolve in the absence of any selection pressure? This is exactly why any simulation of evolutionary mechanisms must run in a simulated environment rather than a general purpose operating system. Tierra, for example, provides an environment where the limited resources are RAM and clock cycles. The programs that evolve in that environment, via random mutation and recombination, demonstrate increasing efficiency in using those resources. While it should be possible to create an environment in which sorting algorithms evolve, there is no reason to expect it to happen in a general purpose OS where there is no benefit to doing so.MathGrrl_{November 2, 2010
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This paper is "proof by equivocation". The phrase "natural selection" in the paper is not the same as natural selection in the wild.
I should mention the remarkable feats being reported concerning the use of selection in computation to design shapes, robots and products using the likes of 'genetic algorithms'. The claim here is that, given a complex shape coded for by several to many "genes", a selection process can be instituted to improve any function imposed upon that shape. The resulting shape changes are not predictable (not built into the program to begin with), nor is the trajectory taken during the improvement. In other words, this models a multigene selection process. However, it does not escape Haldane's dilemma, because there is only one function being selected at a time -- one selection pressure. Perhaps two functions could be optimized simultaneously, given a large enough population of robots. This is not like selection among organisms, where only fitness is maximized, not any particular function. Another disanalogy can be seen when we note that much, if not most, genetic information in organisms is pleiotropic. This means that not just any old change that will improve some function can be selected in organisms without consequence for other functions. The selection model seems to work better in genetic algorithms than it could in organisms! Stanley Salthe
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es58: The interesting paper you link is a very good example of diversification in a single protein superfamily. That is completely in line with what I have argued many times, that continuity can be found only inside a functional island (a basic protein domain, or a superfamily). That is what is meant by the "big bang theory of proteins". Fundamental protein superfamily appear independently, and then undergo limited variation in time inside the functional island. That's why I always focus on the origin of protein superfamilies as the main point in the present ID debate. The following variation can be interpreted in two different ways: 1) Neutral mutations can explore the functional island without significantly altering the function, while negative mutations are removed by negative selection. In this case, the function and folding remain the same. 2) A diversification of specific subfunctions can be obtained through minor variations, usually at the level of the active site, while the main function and basic folding are retained. I think that the paper in question deals with this second aspect. In essence, these events are microevolutionary, and don't require great variation of the molecule. We may ask: are these tweakings of function simple darwinian micrevolutionary events, or are they designed too? I don't think we can answer that, at present. I confess that, for function diversifications like those described in the paper, which deal with complex regulatory systems, they are probably designed. The point is, the variation in the single molecule is probably not so great that it must necessarily fall into the design category (IOWs, it is not of the order of dFSCI). So, I don't believe we can infer design on the basis of the events in the single molecule. But, if we could analyze the variation at system level, things would probably change, and design could be probably inferred. Anyway, as you probably know, I don't even try to analyze complexity at system level. It is too big a challenge. I prefer at present to consider only the single molecule level. And so, back to our protein superfamilies...gpuccio_{November 2, 2010
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MathGrrl: The subject is certainly interesting, and I hope I have the time to investigate it better. Anyway, I thank you for your input. The point with Windows or Linux is that those systems have certainly not been conceived by the author of the simulation. That is the important requirement. The environment must not have been designed thinking of the simulation. Otherwise, it is really difficult to judge if there is no form of hidden information about the results to be obtained in the system. I don't mean intentional. The authors of Avida were probably convinced that they were running a correct simulation, but Dembski and Marks have shown that this is not the case. Probably, even Dawkins was convinced that the Weasel was a fair example, when he wrote what he wrote. The fact is, the ideas of people, including scientists, about information, function and searches are really confused. I really find the work of Dembski very clarifying under that respect (and you may know that I don't always agre with anything which Dembski says). So, a thorough investigation of a wholly designed system like Tierra, where the environment is virtual and conceived together with the replicators, would require a careful critical analysis of the software, which is not in my power to do. My suggestion to use a pre-existing environment would give the highest assurance of equity to the simulation. It would be like working in double blind. Many biases would be avoided. You say: "Those operating systems are designed for general purpose computing. The environment for a simulation is supposed to reflect aspects of reality in which we observe evolution working.". No. First of all, no computer simulation can reflect a biological context. The purpose is not that. The purpose is to reflect the mathematical aspects of "evolution". A general purpose operating system is the best equivalent, in computer environment, of the "general purpose" environment of a planet (unless you believe that that environment was designed for life, abd are a theistic evolutionst). But I think that simulations are created to test the simple materialist model of darwinian evolution, and not theistic evolutionism. We could conceive special simulations for that :) So, the environment has to be independent from the happenings of the replicators'destinies. A "general purpose" computing environment has all those requirements. It has resources, and rules. And they are "natural" resources and rules, not the special "soup" or virtual resources specifically designed in Tierra. If a replicator can reproduce and survive in Windows, and if it is allowed random variation, why shouldn't it in time develop complex new functions? If the darwinian model is correct, I mean! But it won't. A simple software program will never develop something like an ordering algorithm of 200 bits (or any similar complex function), which was not present in the original replicator, only as a result of random variation and true "natural selection". Not in Windows, not in Linux. Never. This is not a dogma. It is a prediction. Ready to be falsified.gpuccio_{November 2, 2010
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gpuccio, Why should the simulation have to run on Windows or Linux? Those operating systems are designed for general purpose computing. The environment for a simulation is supposed to reflect aspects of reality in which we observe evolution working. What's important is not the operating system of the simulation but that, as you note above, the environment provides no other feedback than relative fitness, just as the real world does. In particular, mutation and recombination must be independent of the environment. With those restrictions in place, the simulation reflects the essential aspects of reality necessary for evolutionary mechanisms to be demonstrated. I used to have a list of a many such simulations; I'll try to dig it up over the next couple of days. In the meantime, Googling for "Santa Fe Institute", "genetic algorithms", and "artificial life" should get you a lot of examples. I believe there is a list on the Tierra website as well. I'll close with emphasizing that my only purpose in hopping in here was to point out that systems like the one you describe have been implemented, by many researchers. I'd be curious to hear your thoughts on those you choose to investigate further.MathGrrl_{November 2, 2010
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MathGrll: I checked quickly about Tierra. The main point seems to me that it is a "virtual computer". IOWs, here again the environment is set by the designer, and a very detailed analysis of the software would be needed to check how much additional information is incorporated into the system. But I leave that kind of work to Dembski and Marks. My point was very different. The designer must not design the system for his simulation. He must only design the replicators for an existing real system (I suggested Windows 7, but Linux would fit too). And obviously the mutation system, more or less adjustable. And nothing else. And the replicators should select themselves in that "natural" system, which has not been set by the designer of the experiment, and therefore is certainly "neutral". Moreover, it seems that anyway the results of Tierra, whatever it is, are not so stunning. I quote from Wikipedia: "Mark Bedau and Norman Packard developed statistical method of classifying evolutionary systems and in 1997, Bedau et al. applied these statistics to Evita, an Artificial life model similar to Tierra and Avida, but with limited organism interaction, and no parasitism, and concluded that Tierra-like systems do not exhibit the open-ended evolutionary signatures of naturally evolving systems.[3] Russell K. Standish has measured the informational complexity of Tierran 'organisms', and has similarly found limited complexity growth in Tierran evolution.[4]" But I am always open to your contributions on the subject.gpuccio_{November 2, 2010
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MathGrrl: I have considered in the past the Tierra program, and I believe you are absolutely wrong. But if you want to bring on the details to support your statement, I am willing to listen. And I am waiting for the "more sophisticated examples" too. Convince me (but please, don't compromise your studies: there are priorities in life).gpuccio_{November 2, 2010
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gpuccio, I'm in the middle of a very tough semester, but I want to delurk to point out that what you're asking for has been implemented numerous times. One good place to start is Tom Ray's Tierra program. There are many more sophisticated examples developed since then that model many aspects of modern evolutionary theory in exactly the way you describe.MathGrrl_{November 2, 2010
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This is too funny- they write computer programs and explanations yet they don't have any evidence that genetic acidents can accumulate in such away as to give ise to functional multi-prt systems. There is lso a peer-reviewed paper abut the highly improbale act of getting two specified mutations. So what happens when 3 or more specified mutations are required? As for natural selection it is a rsult and doesn't do anything.Joseph_{November 2, 2010
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nullasalus: How does science tell the difference between ‘natural selection’ and ‘artificial selection’? And wouldn’t any computer demonstration be artificial selection regardless? In a sense, it is true that any computer model would be "artificial selection". And yet, I believe that it is possibly to build a computer model which mimics true "natural eselection". I have proposed the concept a couple of times here, but nobody seems to care. First, I will give explicit definitions of artificial selection and natural selection. a) Artificial selection is a selection of replicators arranged and structured by a designer. b) Natural selection is a form of selection entirely caused by the properties of the replicator in its natural environment. It is import to notice that, in natural selection, it is only the reproductiove advantage (in positive selection) or disadvantage (in negative selection) which selects, obviously in the context of the existing environment. Another important point is that the environment is in no way "aware" of the necessities of the replicators. It acts, s to say, "passively". It has no specific information about how the replicaors work, replicate, live or die. That is true natural selection. Now, let's go to artificial selection, like in so called evolutionary computer models. The problem with practically all of them is that they do not mimic natural selection at all. They are, invariably, forms of intelligent selection, that is of intelligent design. So, let's define intelligent selection: c) Intelligent selectio: any form of artificiaòl selection where the designer is influenced by his knowledge of the properties of the replicator in designing the environment. What happens in intelligent selection is that the environment is more or less explicitly designed to be able to select a specific property, a property which in itself would not be able to be recognized by true natural selection, IOWs a property which in itself would never confer a reproductive advantage to the replicator in an unaware environment. The simplest form of ontelligent selection is the weasel and similar: here the designer introducts explicitly the solution in the system. If you look at the saftware defining the enviornment and its "fitness function", you will find the weasel phrase somewhere. But there are cases where the designer favours a certain output more indirectly. I suppose that AVIDA is one of them. The Szvostak paper, on which I have abundantly commented here, is another example. A specific function, the ability to bind ATP, is chosen by the designer of the system, searched for, recognized and actively selected. That function, in that form, would never be recognized and selected in a true natural cellular environment. In this way, intelligent selection hugely increases the potentiality of natural selection. RV + intelligent selection can easily achieve most results. RV + NS can achieve almost nothing. So, is there a way to build a system with artificial selection which mimics NS, IOWs that is not "intelligent selection"? Yes, it is. It would go more or less this way. The designer chooses a priori a computer environment. Let's say Windows 7. Then he designs simple replicators which can replicate in the system (spomething like simple computer viruses), using the system's natural resources. The designer fixes some system in the replicator which causes completely random variation in the replicators. And then the designer does nothing more. He just waits He does not write any fitmess function. He does not program any specific environment to look for any specific property of the replicators. He waits. And occasionally, he just checks if new, more complex replicators have evolved, utilizing better the resources of the operating system thanks to the random mutations in their code. And if that happens, he can just check what those mutations are, if they are simple or complex, their complexity in bits, and if they have any tendency to become "steps" toward more complex functions. That would be a good simulation. Not natural selection, but artificial non intelligent selection. Why nobody seems interested to do simply that?gpuccio_{November 2, 2010
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William Dembski: Thank you for bringing to our attention this really remarkable paper. It's intellectual horror at its best. I am completely speechless.gpuccio_{November 2, 2010
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es58 further notes: Many times evolutionists will mention evo-devo (Evolutionary Developmental Biology) to try to support the Darwinian claim that minor changes/mutations to DNA can drive major morphological novelty, yet, in this following comment, from a 2005 Nature review article, evolutionary geneticist Jerry Coyne expressed strong skepticism at the proposed mechanism of 'gene switches' for evo-devo: "The evidence for the adaptive divergence of gene switches is still thin. The best case involves the loss of protective armor and spines in sticklebacks, both due to changes in regulatory elements. But these elements represent the loss of traits, rather than the origin of evolutionary novelties...We now know that Hox genes and other transcription factors have many roles besides inducing body pattern, and their overall function in development - let alone in evolution - remains murky." http://www.evolutionnews.org/2010/06/scott_f_gilbert_developmental035931.html Here is a more thorough critique of evo-devo: Nature's "Gems": Microevolution Meets Microevolution - Casey Luskin - August 2010 http://www.evolutionnews.org/2010/08/nature_gems_microevolution_mee037171.html#more Here are many more lines of evidence arguing against any DNA mechanisms for body plan development, Evo-Devo included: Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html As well, recent 'cloning studies' give evidence against DNA/Genetic reductionism: "There is now considerable evidence that genes alone do not control development. For example when an egg's genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact." The Design of Life - William Dembski, Jonathan Wells Pg. 50 If that wasn't enough, the Human Genome Project really put the last nail in the coffin for "Genetic Reductionism": DNA: The Alphabet of Life - David Klinghoffer Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell's building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn't there. Instead, "It is as if the 'idea' of the fly (or any other organism) must somehow permeate the genome that gives rise to it." http://www.evolutionnews.org/2009/07/dna_the_alphabet_of_life.html This following video gives a glimpse of this 'higher level' information in action: Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713bornagain77_{November 2, 2010
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es58, from the article:
'Tinkering with an ancestral template is also a core idea research in developmental evolution, more commonly known as "evo-devo": the morphology of animals -- from jellyfish to fly to worm to fish to human -- is built using the same basic genetic toolkit, subtly reorganised and redeployed to build the wing of a fly or the limb of a human.'
The main problem with the paper is that it assumes genetic reductionism, the idea that Body-Plan morphogenesis is directly controlled by mutations to DNA, but genetic reductionism is shown to be false in the first place. notes: Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488 “Live memory” of the cell, the other hereditary memory of living systems - 2005 Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2K-4FJXNG6-1&_user=10&_coverDate=06%2F30%2F2005&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1273117547&_rerunOrigin=google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bfa74d6bb0937402472343daa6bdef8 The Gene Myth, Part II - August 2010 Excerpt: So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.,,, So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used.,,, Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show 'exceedingly rare' beneficial morphological changes from mutations to the DNA code. The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer"Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion." http://eyedesignbook.com/ch6/eyech6-append-d.html Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 This following video is a bit more clear for explaining exactly why mutations to the DNA do not control Body Plan morphogenesis, since the mutations are the found to be the ‘bottom rung of the ladder’ as far as the 'higher levels of the layered information’ of the cell are concerned: Stephen Meyer on Craig Venter, Complexity Of The Cell & Layered Information http://www.metacafe.com/watch/4798685 further notes: Hopeful monsters,' transposons, and the Metazoan radiation: Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" render these explanations untenable. Paleobiologists Douglas Erwin and James Valentine “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan)." Michael John Denton page 172 of Uncommon Dissent This lack of beneficial morphological novelty also includes the highly touted four-winged fruit fly mutations: ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_fliesbornagain77_{November 2, 2010
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The authors seem to look at the algorithm which you described as partitioned search in your paper with R. Marks Conservation of Information in Search - Measuring the Cost of Success. So, at least it isn't about Dawkins's weasel...DiEb_{November 2, 2010
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any comments on this item? http://www.guardian.co.uk/science/punctuated-equilibrium/2010/oct/06/1 not directly on this topic, but purports to explain complexityes58_{November 1, 2010
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Nice catch, Dr. Dembski. The imaginary form of evolution, where every novel feature can be built on a continuous, or near-continuous, gradient of mutations, continues to live. Unfortunately for natural evolutionists, it only exists on blogs, in journals and in imaginations. Congratulations on another proof of the validity of an imaginary form of evolutionuoflcard_{November 1, 2010
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Did anyone notify Bill Gates about this breakthrough? :)bornagain77_{November 1, 2010
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I have one simple question. How does science tell the difference between 'natural selection' and 'artificial selection'? And wouldn't any computer demonstration be artificial selection regardless?nullasalus_{November 1, 2010
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