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No evidence that there is enough time for evolution

No evidence that there is enough time for evolution[*]

Lee M Spetner

Redoxia Israel, Ltd. 27 Hakablan St., Jerusalem, Israel

Abstract: A recent attempt was made to resolve the heretofore unaddressed issue of the estimated time for evolution, concluding that there was plenty of time. This would have been a very significant result had it been correct. It turns out, however, that the assumptions made in formulating the model of evolution were faulty and the conclusion of that attempt is therefore unsubstantiated.

[This post will remain at the top of the page until 00 hours Tuesday May 31. For reader convenience, other coverage continues below. - UD News]

 

The standard neo-Darwinian theory accounts for evolution as the result of long sequences of random mutations each filtered by natural selection. The random nature of this basic mechanism makes evolutionary events random. The theory must therefore be tested by estimating the probabilities of those events. This probability calculation has, however, not yet been adequately addressed.

Wilf & Ewens [2010] (W&E) recently attempted to address this issue, but their attempt was unsuccessful. Their model of the evolutionary process omitted important features of evolution invalidating their conclusions. They considered a genome consisting of L loci (genes), and an evolutionary process in which each allele at these loci would eventually mutate so that the final genome would be of a more “superior” or “advanced” type. They let K-1 be the fraction of potential alleles at each gene locus that would contribute to the “superior” genome. They modeled the evolutionary process as a random guessing of the letters of a word. The word has L letters in an alphabet of K letters. In each round of guessing, each letter can be changed and could be converted to a “superior” letter with probability K-1.

At the outset they stated the two goals of their study, neither of which they achieved. Their first goal was to “to indicate why an evolutionary model often used to ‘discredit’ Darwin, leading to the ‘not enough time’ claim, is inappropriate.” Their second goal was “to find the mathematical properties of a more appropriate model.”  They described what they called the “inappropriate model” as follows:

“The paradigm used in the incorrect argument is often formalized as follows:  Suppose that we are trying to find a specific unknown word of L letters, each of the letters having been chosen from an alphabet of K letters. We want to find the word by means of a sequence of rounds of guessing letters.  A single round consists in guessing all of the letters of the word by choosing, for each letter, a randomly chosen letter from the alphabet.  If the correct word is not found, a new sequence is guessed, and the procedure is continued until the correct sequence is found.  Under this paradigm the mean number of rounds of guessing until the correct sequence is found is indeed KL.”

They gave no reference for such a model and, to my knowledge, no responsible person has ever proposed such a model for the evolutionary process to “discredit” Darwin. Such a model had indeed been suggested by many, not for the evolutionary process, but for abiogenesis (e.g., [Hoyle & Wickramasinghe 1981]) where it is indeed appropriate. Their first goal was not achieved.

They then described their own model, which they called “a more appropriate model.” On the basis of their model, they concluded that the mean time for evolution increases as K log L, in contrast to KL of the “inappropriate” model. They called the first model “serial” and said that their “more correct” model of evolution was “parallel”.  Their characterization of “serial” and “parallel” for the above two models is mistaken. Evolution is a serial process, not a parallel one, and their model of the first, or “inappropriate”, process is better characterized as “simultaneous” than “serial” because the choosing of the sequence (either nucleotides or amino acids) is simultaneous. What they called their “more appropriate” model is the following:

“After guessing each of the letters, we are told which (if any) of the guessed letters are correct, and then those letters are retained. The second round of guessing is applied only for the incorrect letters that remain after this first round, and so forth. This procedure mimics the ‘in parallel’ evolutionary process.”

W&E were mistaken in thinking the evolutionary process to be an in-parallel one — it is an in-series one. A rare adaptive mutation may occur in one locus of the genome of a gamete of some individual, will become manifest in the genome of a single individual of the next generation, and will be heritable to future generations. If this mutation grants the individual an advantage leading to it having more progeny than its nonmutated contemporaries, the new genome’s representation in the population will tend to increase exponentially and eventually it may take over the population.

Let p be the probability that in a particular generation, (1) an adaptive mutation will occur in some individual in the population, and (2) the mutated genome will eventually take over the population. If both these should happen, then we could say that one evolutionary step has occurred. The mean number of generations (waiting time) for the appearance of such a mutation and its subsequent population takeover is 1/p. (I am ignoring the generations needed for a successful adaptive mutation to take over the population. These generations must be added to the waiting time for a successful adaptive mutation to occur.)  After the successful adaptive mutation has taken over the population, the appearance of another adaptive mutation can start another step.

In L steps of this kind, L new alleles will be incorporated into the mean genome of the population. These steps occur in series and the mean waiting time for L such steps is just L times the waiting time for one of them, or L/p. Thus the number of generations needed to modify L alleles is linear in L and not logarithmic as concluded from the flawed analysis of W&E.

The flaws in the analysis of W&E lie in the faulty assumptions on which their model is based. The “word” that is the target of the guessing game is meant to play the role of the set of genes in the genome and the “letters” are meant to play the role of the genes. A round of guessing represents a generation. Guessing a correct letter represents the occurrence of a potentially adaptive mutation in a particular gene in some individual in the population. There are K letters in their alphabet, so that the probability of guessing the correct letter is K-1. They wrote that

1– (1 – 1/K)r

is the probability that the first letter of the word will be correctly guessed in no more than r rounds of guessing. It is also, of course, the probability that any other specific letter would be guessed. Then they wrote that

[1– (1 – 1/K)r]L

is the probability that all L letters will be guessed in no more than r rounds. The event whose probability is the first of the above two expressions is the occurrence in r rounds of at least one correct guess of a letter. This corresponds to the appearance of an adaptive mutation in some individual in the population. That of the second expression is the occurrence of L of them. From these probability expressions we see that according to W&E each round of guessing yields as many correct letters as are lucky enough to be guessed. The correct guesses in a round remain thereafter unchanged, and guessing proceeds in successive rounds only on the remaining letters.

Their model does not mimic natural selection at all. In one generation, according to the model, some number of potentially adaptive mutations may occur, each most likely in a different individual. W&E postulate that these mutations remain in the population and are not changed. Contrary to their intention, this event is not yet evolution, because the mutations have occurred only in single individuals and have not become characteristic of the population. Moreover, W&E have ignored the important fact that a single mutation, even if it has a large selection coefficient, has a high probability of disappearing through random effects [Fisher 1958]. They allow further mutations only in those loci that have not mutated into the “superior” form. It is not clear if they intended that mutations be forbidden in those mutated loci only in those individuals that have the mutation or in other individuals as well. They have ignored the fact that evolution does not occur until an adaptive mutation has taken over the population and thereby becomes a characteristic of the population. Their letter-guessing game is more a parody of the evolutionary process than a model of it. They have not achieved their second goal either.

Thus their conclusion that “there’s plenty of time for evolution” is unsubstantiated. The probability calculation to justify evolutionary theory remains unaddressed.

References

Fisher, R. A. (1958). The Genetical Theory of Natural Selection, Oxford. Second revised edition, New York: Dover. [First published in 1929]

Hoyle, F. and N. C. Wickramasinghe, (1981). Evolution from Space, London: Dent.

Wilf, H. S. & Ewens, W. J.  (2010) There’s plenty of time for evolution. Proc Natl Acad Sci USA 107 (52): 22454-22456.


[*] This paper is a critique of a paper that appeared recently in the Proceedings National Academy of Sciences USA and rightfully should have been published there. It was submitted there and was rejected without review and the reason given was that the Board did not find it “to be of sufficient interest for publication.” When I noted how unreasonable this reply was, the editor replied that the paper “makes some obvious and elementary points of no relevance to the paper, and in my opinion does not warrant publication.” The Board then refused to comment further on the matter. It was clear that the Board’s rejection was not on the merit of the substance of the paper but for some other, undisclosed reason.

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137 Responses to No evidence that there is enough time for evolution

  1. Dr. Spetner,,, Now this is a very pleasant surprise!!! :) Welcome!

  2. Let p be the probability that in a particular generation, (1) an adaptive mutation will occur in some individual in the population, and (2) the mutated genome will eventually take over the population. If both these should happen, then we could say that one evolutionary step has occurred.
    Under this definition, p varies with the number of correct letters, so you can’t use it as a constant.

    What happen if you re-do your calculations properly, allowing p to change?

  3. Dr. Spetner as to this;

    ‘This paper is a critique of a paper that appeared recently in the Proceedings National Academy of Sciences USA and rightfully should have been published there. It was submitted there and was rejected without review and the reason given was that the Board did not find it “to be of sufficient interest for publication.”’

    Well I find it of ‘sufficient interest’ and I truly appreciate you taking your time to address this important issue. Especially since math is not a strong suit of mine and I would not have been able to answer it.

  4. I disagree with your analysis. Your computation would be correct if it were assumed that evolution is directed toward attaining a particular outcome. But that is not an assumption of evolutionary theory or of neo-Darwinist theory.

  5. Neil – to be fair, it was Wilf & Ewens who introduced the model, not Spetner. So your criticism (which I agree with) should be aimed at them.

  6. Neil,

    I agree.

    Sorry to be blunt Lee but if I were reviewing this paper (even as an editor screening papers prior to sending them for peer-review) I would also reject it as well.

    If I get some spare time I’ll try and write up a response (from the perspective of a peer-reviewer) so you can see why – unfortunately I’ve got some hideous work deadlines approaching so it may take a few days :(

  7. But DrBOT, don’t you also think that avida, ev, and weasel, are proof of evolution???

  8. 8
    Elizabeth Liddle

    I doubt it, bornagain77 – scientists don’t actually deal in “proof”.

    Nothing is “proven” in science, only “supported” or “rejected”.

    We don’t even, strictly speaking, falsify, although rejection of a model that is overwhelmingly at odds with the data effectively amounts to falsification.

  9. Elizabeth, ironically, I can think of a few falsification criteria that have been set for ID right off the top of my head, while I cannot think of anything that neo-Darwinists have dared set forth that would serve as a falsification criteria of their theory.

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www.scitopics.com/The_L.....iency.html

    For a broad outline of the ‘Fitness test’, required to be passed to show a violation of the principle of Genetic Entropy, please see the following video and article:

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    ======================

    And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
    http://www.metacafe.com/watch/3994630

    Bacterial Flagellum: Visualizing the Complete Machine In Situ
    Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus.
    http://www.sciencedirect.com/s.....tImgPref=F

    Michael Behe Hasn’t Been Refuted on the Flagellum – March 2011
    http://www.evolutionnews.org/2.....44801.html

    Bacterial Flagella: A Paradigm for Design – Scott Minnich – Video
    http://www.vimeo.com/9032112

    =====================

    But luckily for you Elizabeth, at least neo-Darwinists have these wonderful evolutionary algorithms, which were designed by brilliant computer programmers, to prove that purely material, neo-Darwinian, processes are plausible. (Just don’t pay attention to the man behind the curtain!

    Pay no attention to that man behind the curtain. – video
    http://www.youtube.com/watch?v=YWyCCJ6B2WE

    etc.. etc…

  10. @bornagain77,

    I agree.

    Sorry to be blunt DrBot, but if I were reviewing your comment about the article, I would also reject it as well.

    If I get some spare time I’ll try to explain so you can see why – unfortunately I’ve got to make some oatmeal for breakfast and have no time. :P

    ….
    Just trying to egg you on for that substantive response. ;-)

  11. “you” => DrBot

  12. It seems noteworthy that the reason for not publishing was not one associated with any error or misrepresentation of the paper under critique, but rather the reviewer reportedly communicated that Lee’s paper, “makes some obvious and elementary points of no relevance to the paper, and in my opinion does not warrant publication”

    The term “obvious” seems to contradict the idea of any kind of misrepresentations.

  13. Actually, disregard my last comment. I overlooked that they argued it was of no relevance to the paper… which might imply they are saying he misrepresented the paper.

  14. 14
    Elizabeth Liddle

    Well, bornagain77, there’s always that pre-Cambrian rabbit!

    But you raise an interesting point with your citation of Behe and the null hypothesis.

    Yes, indeed, we do in science attempt to “falsify the null” (although we only do so probabilistically). However falsifying an actually proposed explanation is not the same as falsifying the null.

    Statistically, it is very difficult to falsify what is sometimes called H1 – the study hypothesis – the best we can do is “retain the null” (H0).

    Unless Theory of Evolution is cast as the null, then it is difficult to set up an experiment that will falsify it.

    Instead, what scientists normally do is to compare models for fit. An authenticated pre-Cambrian rabbit would cause the ToE to fit extremely badly. It wouldn’t strictly falsify it, however.

    But it would certainly lay the field wide open for explanatory theories that might fit better.

    And yes, evolution does “have these wonderful evolutionary algorithms” :)

    From which we learn that Darwinian processes do work extremely well, and result in complex, often very ingenious, solutions to problems that we want to solve.

    From the point of view of the GA critters however, the problem they are solving is not ours, but the intrinsic problem of “persistence” within the environment in which they find themselves. That’s also the “problem” faced by populations of living things. So the two scenarios are directly comparable, and we know that the system does, in fact, work.

  15. Well Elizabeth, frankly what you said is a bunch of rationalization. And how you can possibly buy all that gobbledygook besides demanding rigorous verification for your beloved ‘scientific’ theory is beyond me. But then again, there is a reason why you do this;

    Religion drives science and it matters;
    Cornelius Hunter

  16. 16
    Elizabeth Liddle

    Well, obviously, bornagain77, I disagree :)

    I think what I said is “rational”, and it was composed in good faith, so obviously I don’t accept that it’s “gobbledygook”. It’s certainly basic statistical methodology.

    But I must insist that you are simply wrong when you think I have an ulterior reason for producing what you regard as “gobbledygook” – I’m simply posting what I think is true. Obviously you must feel free to disagree, and, of course, it’s possible that I am quite wrong. I frequently am.

    But I don’t deliberately deceive anyone, and I certainly do not regard science as “religion”. That’s precisely what all that “gobbledygook” is about – it’s part of the methodology by which science seeks to gain greater understanding of the world, not by faith, but by rigorous testing of alternative models.

    Anyway, as I said earlier, I wish you well, but we will have to agree to disagree on some of this. I do appreciate your attempts to reform me :)

    Seriously.

    Cheers

    Lizzie

  17. Elizabeth, you state;

    ‘I’m simply posting what I think is true.’

    I have no doubt that you REALLY believe your atheistic/materialistic religion to be true! But none-the-less, regardless of how much faith you put into believing materialism, specifically neo-Darwinian materialism, to be true, materialism is found to be a false view of reality, and of molecular biology in particular.

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of materialism, to explain reality:

    The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And Yet Elizabeth, quantum entanglement, which rigorously falsified local realism (materialism) as the true description of reality, is now found in molecular biology!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    Untangling the Quantum Entanglement Behind Photosynthesis – May 11 2010
    Excerpt: “This is the first study to show that entanglement, perhaps the most distinctive property of quantum mechanical systems, is present across an entire light harvesting complex,” says Mohan Sarovar, a post-doctoral researcher under UC Berkeley chemistry professor Birgitta Whaley at the Berkeley Center for Quantum Information and Computation. “While there have been prior investigations of entanglement in toy systems that were motivated by biology, this is the first instance in which entanglement has been examined and quantified in a real biological system.”
    http://www.sciencedaily.com/re.....151356.htm

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!

    ,,, as well I remind that appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology, or anything else for that matter, destroys the very possibility of doing science rationally;

    Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    =================

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

  18. BA77: I’m happy and interested in having a dialogue with you but I wish you would resist flooding the discussion with links and imprecations that people who disagree with you are wrong. We KNOW you disagree with us! We are trying to gain a better understanding of each others’ point of view NOT win an argument.

    It’s okay for reasonable, intelligent, informed people to disagree surely.

    And, to be honest, I don’t understand what you’re saying in this:

    “Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!”

    As I’ve said before, QM does not imply any non-mechanistic processes. We don’t understand the causes, just like we don’t understand what causes gravity, but we don’t ascribe supernatural causes to things that can be defined with simple statistics.

  19. 19
    Elizabeth Liddle

    bornagain77 – I think you are making some rather unwarranted assumptions as to what I believe :)

    I don’t know what “neo-Darwinian materialism” even is, and I certainly have no problem in accepting the findings of quantum physics (though I’m no physicist), which I find fascinating.

    I don’t have an “atheistic/materialistic religion”. I don’t actually have a religion at all, in the sense people usually use the word, although until fairly recently I was a firm theist (a catholic, in fact). I still have what I call a “God-model” although increasingly I call it something else (I find the God-label comes with an awful lot of baggage).

    Practically, though, I still believe what I’ve always believed: that the most important human imperative is: “Love one another”.

    And guess who I got it from :)

  20. ellazimm, but alas this is science, I have shown you guys ‘scientifically’ that you are wrong. It is not me saying you are wrong it is the science!!! Nothing personal at all, to refute the falsification of neo-Darwinism just show local realism to be sufficient to explain quantum non-locality we find within molecular biology!

  21. BA77: Assuming quantum non-locality refutes neo-Darwinism then what is the explanation for the vestigal hind limbs of whales? Or the varied sizes of genomes? Or the common insertion points of endogenous retroviruses in primate species but not others?

    I’m not making a theological argument, I’m asking a question. And I”m not saying neo-Darwinism is complete and finished. But to throw it down means finding something which has greater explanatory power. As one would want. Such is the pursuit of science.

  22. ellazimm,

    ‘But to throw it down means finding something which has greater explanatory power.’

    You mean like ID, with Genetic Entropy as overriding mechanism explaining all biological adaptations from initial point of Design implementation??? What a wonderful idea ellazimm, glad you thought of it!

    The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Michael Behe talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

  23. @Elizabeth Iddle

    “Instead, what scientists normally do is to compare models for fit. An authenticated pre-Cambrian rabbit would cause the ToE to fit extremely badly. It wouldn’t strictly falsify it, however.”

    Wouldn’t falsify it?
    ….hmmmm…
    Appears that Walter Remine is right. The theory of evolution would ‘survive’ any scenario for falsification by a ‘Smorgasbord’ of explanations. :D

  24. ellazimm you keep tickling me with this every time you mention it;

    ‘what is the explanation for the vestigal hind limbs of whales?’

    ,,,guess it is time to let you in on a secret on what the ‘vestigial whale legs’ actually do:

    An Email Exchange Regarding “Vestigial” Pelvic Bones in Whales
    by Jim Pamplin
    excerpt: The pelvic bones of whales serve as attachments for the musculature associated with the penis in males and its homologue, the clitoris, in females. The muscle involved is known as the ischiocavernosus and is quite a powerful muscle in males. It serves as a retractor muscle for the penis in copulation and probably provides the base for lateral movements of the penis. The mechanisms of penile motion are not well understood in whales. The penis seems to be capable of a lot of independent motion, much like the trunk of an elephant. How much of this is mediated by the ischiocavernosus is not known.

    In females the anatomical parts are smaller and more diffuse. I would imagine that there is something homologous to the perineal muscles in man and tetrapods, which affect the entire pelvic area – the clitoris, vagina and anus.

    The pelvic rudiments also serve as origins for the ischiocaudalis muscle, which is a ventral muscle that inserts on the tips of the chevron bones of the spinal column and acts to flex the tail in normal locomotion.

    James G. Mead, Ph.D.
    Curator of Marine Mammals, MRC 108
    National Museum of Natural History
    Smithsonian Institution
    http://www.darwinisdead.com/an.....arding.htm

    further notes:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical (i.e. that is that it is paradoxical to the reductive materialism of neo-Darwinism, but not so paradoxical from a Design perspective);
    http://en.wikipedia.org/wiki/C-value_enigma

    More Points on ERVs – JonathanM – May 2011
    Excerpt: ‘In the absence of a feasible naturalistic mechanism to account for how evolution from a common ancestor could have occurred, how can we be so sure that it did occur? In such a case, one ought to reasonably expect there to be some quite spectacular evidence for common ancestry. Unfortunately for Darwinists, however, the evidence for common ancestry is paper thin on the ground.’
    http://www.evolutionnews.org/2.....46761.html

    ,,,, ellazimm, it is interesting that you would bring up all these irrelevant points, which, as you can now see, do you no good anyway. What exactly does all that periphery stuff have to do with the fact that the ‘local realism’ of neo-Darwinism is falsified by the finding of quantum non-locality in molecular biology???

    ,,, In fact, being a Christian, I am very concerned that you get this ‘non-local quantum information’ stuff right, for I firmly believe that this quantum non-local information found, on a massive scale, in molecular biology is, among other things, a very strong indication that man has a eternal soul!

    Quantum no-hiding theorem experimentally confirmed for first time – March 2011
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.
    http://www.physorg.com/news/20.....tally.html

    Francis Chan – The Recent Discussion On Hell: We can’t afford to get it wrong – video
    http://www.godtube.com/watch/?v=FJ9JMMNU

  25. Well,…there’s always that pre-Cambrian rabbit!

    Elizabeth, as one writer (Vox Day) once put it, if you think that scientists will just rent their lab jackets, put on sack cloth, and cover themselves in ashes while then rejecting macroevolution due to a rabbit find in pre-Cambrian rock strata, then you don’t know them very well.

    The first reaction from the scientific community would be Those arent rabbit bones.

    And then once it has been conclusively shown that they are, in fact, rabbit bones, then they will change gears and go with That isn’t actually pre-Cambrian rock strata that they were found in.

    And once it is proven that it is in fact pre-Cambrian rock strata, they’ll probably come up with The theory of evolution has been around for over 100 years and numerous scientists subscribe to it and work on it. It’ll take alot more than this instance of rabbit bones to disprove the theory.

  26. Time is only one variable in the equation. All that matters is probabilistic resources, and the likelihood that they can overcome the inherent improbabilities. This is a simple mathematical concept that seems to elude Darwinists. Perhaps they all missed seventh-grade math in junior high school, or perhaps they’ve lost their ability to think rationally because of a commitment to Darwinian ideology.

  27. BA77: Thank you for the link regarding the whale rear legs. I will peruse it!

  28. 28
    Elizabeth Liddle

    JD Curtis: yes indeed, which is why I keep saying that science doesn’t, in fact, proceed by falsification (except in the negative sense of falsifying the null) but by fitting models to data and selecting the model with the best fit.

    So yes, if a rabbit fossil was found in the pre-Cambrian, the first response would have to be: is it real?

    And even if it could be shown to be a mammal-like organism with a genuine pre-Cambrian date, it wouldn’t actually falsify the ToE, not because the ToE is unfalsifiable in a Popperian sense, but because the ToE is, if you like, a general model that is fitted by means of specific parameters.

    But it would require such a radical tweak of parameters that it might indeed call the ToE into question.

    However, what it would most definitely do is to give rise to specific hypotheses, within the ToE: either we have got the entire mammalian phylogeny wrong, in which case we would immediately start to look for precursors and descendents of the pre-Cambrian organism that would support an alternate mammalian phylogeny, or it would be an example of convergent evolution, in which case we would also look for precursors and descendents that would support a parallel phylogeny.

    If none of these could be found, then, yes, perhaps a completely different model to the ToE would become a better fit to the data than the ToE.

    Just as, for example, eventually the “luminiferous ether” had to be abandoned, and Einstein’s relativity adopted in its place.

    However, the fact is that there is no pre-Cambrian rabbit fossil! So right now, the ToE serves us pretty well, although the parameters are still subject to tweaking and retweaking as more data is acquired, and indeed the elegant simplicity of Darwin’s original model has been supplemented with all kinds of other factors and mechanisms, including drift and horizontal gene transfer.

    So, if you like, what would really supplant the ToE isn’t so much a pre-Cambrian rabbit, as another theory with even greater explanatory power. And that is happening all the time (e.g. epigenetics).

  29. 29
    Elizabeth Liddle

    @GilDodgen

    All that matters is probabilistic resources, and the likelihood that they can overcome the inherent improbabilities. This is a simple mathematical concept that seems to elude Darwinists. Perhaps they all missed seventh-grade math in junior high school, or perhaps they’ve lost their ability to think rationally because of a commitment to Darwinian ideology.

    No, we didn’t all miss seventh-grad math, and a lot of us are quite good at rational thinking :)

    But probability estimates depend crucially on your priors, and I suggest it is our priors that differ.

    But good honest people can differ on their priors :)

  30. H’mm: There’s a Pre Cambrian, digital code controlled robot in the cell though, and its self-replicating facility is ADDITIONAL cause for wonder.

  31. ER:

    Nothing is “proven” in science, only “supported” or “rejected”.

    And there isn’t any evdence to support the claim that geneti accidents cn accumulaten such a way as to construct useful, functional multi-par sysems ad living organisms are full of them.

  32. Neil Rickert:

    Your computation would be correct if it were assumed that evolution is directed toward attaining a particular outcome.

    That isn’t in the paper, so why would you say that?

    The papehe was addresig used a goal-oriented process, perhaps that is what has you confused.

  33. ellazimm:

    And I”m not saying neo-Darwinism is complete and finished. But to throw it down means finding something which has greater explanatory power.

    Nope- no need to wait for something else before getting rid of what you have that is junk.

  34. Elizabeth you state;

    ‘But good honest people can differ on their priors’

    No Elizabeth, proper priors, or presuppositions, can only be formed by Theism. Thus malformed ‘priors’, or presuppositions, formed by anti-theism eventually, and always, lead to erroneous conclusions in the end;

    i.e.

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    Nuclear Strength Apologetics – Presuppositional Apologetics – video
    http://www.answersingenesis.or.....pologetics

    John Lennox – Science Is Impossible Without God – Quotes – video remix
    http://www.metacafe.com/watch/6287271/

    Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    Can atheists trust their own minds? – William Lane Craig – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines
    http://creationsafaris.com/cre.....#20110227a

    as well, as I recently pointed out to you, it is a malformed ‘prior’ anti-theology, that was the basis of Darwin’s book:

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    http://www.evolutionnews.org/2.....46391.html

    ,, Thus Elizabeth your assertion that ‘good honest people can differ on their priors’ completely misses the fact that malformed priors must be addressed and ‘rooted out’ so that the weeds that spring from erroneous presuppositions ‘priors’ never spring forth again!

  35. 35
    CannuckianYankee

    Elizabeth,

    “But probability estimates depend crucially on your priors, and I suggest it is our priors that differ.”

    What do you find faulty in the probability argument from Dembski’s “No Free Lunch?”

    What do you think are Dembski’s priors that are different than your own?

    What do you think Gil’s priors are when he states?:

    “All that matters is probabilistic resources, and the likelihood that they can overcome the inherent improbabilities.”

    More importantly, what do you think a person who accepts Darwinian evolution’s priors are when he/she accepts speculation into the existence of multiverses in order to increase probability resources?

    What would be a reason to seek an increase in probability resources if it isn’t doubtful that Darwinian evolution already has sufficient resources?

    If in fact the multiverse hypothesis is an attempt to increase the probability resources, what do you think is overlooked (if anything) in such a hypothesis? Does this matter to you?

    You say you’re not a materialist (or at least that such a label doesn’t mean anything to you). As such, what evidences are important to you in determining that there is sufficient time provided by the probabilistic resources in the observable universe for a naturalistic abiogenesis?

    If the NFL argument is sound, what priors do you hold that would reject it?

    What priors do you think a person who accepts it as sound would adhere to?

    A lot of questions, I know, but I’ve been thinking about these issues for some time, and I think it doesn’t come down to priors, but thinking logically about all the evidential parameters involved. It is my view that those who accept some form of naturalistic abiogenesis are not considering all the parameters, and that is their prior – not the evidence. The probability estimates depend on the evidence, not the priors.

  36. 36
    CannuckianYankee

    Me: “…..sufficient time provided by the probabilistic resources in the observable universe for a naturalistic abiogenesis?”

    Ok, that doesn’t quite make sense, because time is one of the resources.

  37. 37
    CannuckianYankee

    Elizabeth,

    This may all sound kind of silly, but when Richard Dawkins was interviewed for the film “Expelled,” he admitted that he could accept scientifically, a panspermia explanation for the origin of life on our planet, but not a supernatural one scientifically. He then stated that whoever those hypothetical aliens are, they too must have begun from a naturalistic abiogenesis (or so to speak). Personally, I can’t see what the difference would be on a scientific level other than Dawkins’ prior commitment to only naturalistic explanations. Do you see a difference? Why?

    In short, Dawkins has a limited imagination. He can’t imagine how the universe could have been created by an intelligent designer. He accepts that life on Earth could have been started by one, but not the universe, because that could lend some doubt to his own views on abiogenesis.

    There’s two issues here. One is, I doubt if Dawkins actually believes in panspermia, and neither do I. Panspermia introduces a problem of infinite regresses of panspermia on planet after planet, unless as Dawkins states, there was abiogenesis on the planet of the hypothetical aliens, and who would know or care? This doesn’t solve anything, so Dawkins is likely to reject that, and stick to naturalistic abiogenesis.

    The second issue that isn’t resolved by Dawkins’ position is just what we’ve been talking about; the probabilistic resources for abiogenesis right here on Earth where it could be observed if true.

    If it’s silly, I haven’t got us very far. It it isn’t silly, I’ve just introduced some thinking, which gets us beyond any priors we may have. Thinking about intelligent designers (no matter who they are) does not take us outside of science, as Dawkins reluctantly demonstrated. Furthermore, a designer who is something greater than an agent of panspermia can make a lot more sense than naturalistic abiogenesis – given a limit in probabilistic resources. This is so because a designer of the order we’re talking about is not limited by probability constraints, since a designer does what he does intentionally, not by chance and necessity. Agreed?

    With that in mind, I should go back and ask my original question once more: “what are your priors, which cause you to reject NFL?” If you say that you as Dawkins can accept only a naturalistic abiogenesis, then your argument about priors may apply to you; but do you honestly infer by this that they necessarily apply to everyone? In short, do you (unlike Dawkins) have an imagination outside of naturalism, which would allow for a design inference outside of it? If not, what on earth are you doing here? (I ask this honestly, not to judge you in any way).

    If you really desire to understand the argument from design, you must understand it outside naturalistic constraints and assumptions. If those are your priors, they are not ours, and this makes a huge difference in how we view life and the universe.

    Thanks for your thoughts, though. I find them interesting and informative.

  38. 38
    Elizabeth Liddle

    Actually, all I meant by “priors” are the probabilities you give the various factors in your probability estimate.

    For example, if you are computing the probability of some chemical reaction, that probability will depend on a number of factors (the likelihood of the co-presence of the reacting compounds; the likelihood of a give temperature; the likelihood of a promoting catalyst) etc.)

    And each of those will come with a prior probability estimate, which itself is subject to adjustment in the light of new data.

    I wasn’t actually talking about anything fancier than that!

    But it’s an important point, nonetheless. For example, Fred Hoyle, Crick, and others, proposed “panspermia” because they thought the probability of abiogenesis was so low, it needed a longer time to have a decent chance of happening.

    Since then, a number of discoveries have led to an adjustment of those priors. These are of course subject to controversy and argument, but the the take-home message, it seems to me, is that you can’t just sit down with a paper and pencil and a good head for permutation and figure out the probability of life.

    The answer will depend on, among other things, data. It’s an empirical question as well as a mathematical one.

  39. 39
    Elizabeth Liddle

    @ CannuckianYankee (I guess I was a CannuckianBrit for a while….hi!)

    Elizabeth,

    This may all sound kind of silly, but when Richard Dawkins was interviewed for the film “Expelled,” he admitted that he could accept scientifically, a panspermia explanation for the origin of life on our planet, but not a supernatural one scientifically. He then stated that whoever those hypothetical aliens are, they too must have begun from a naturalistic abiogenesis (or so to speak). Personally, I can’t see what the difference would be on a scientific level other than Dawkins’ prior commitment to only naturalistic explanations. Do you see a difference? Why?

    Well, exactly what you said – Dawkins is committed only to naturalistic explanations.

    However, I think that is entirely valid, and has nothing to do with whether or not you are an atheist or not. “Supernatural”, essentially, means “unexplained”. It may well mean more than that too, but something cannot be, as I see it (and I think in the sense Dawkins is saying it) both “supernatural” and “an explanation”.

    Now, it may well be that some events do not have an explanation – they are “miracles” or “supernatural events”. But by definition, then, we cannot go further with the explanatory process. We just have to say: “well, clearly a supernatural event happened here, so we aren’t ever going to know how it happened”. In other words, science, which is, by definition, about explanations cannot go further once “supernatural” is reached.

    However, the problem is the only way we can know that the “supernatural” has been reached is when we run out of explanations.

    So it does seem entirely reasonable, to me, to keep pursing naturalistic explanations, even when you suspect there isn’t one. So if I were to be convinced by you guys (and I’m not :)) that life could only have been intelligently designed, then as a scientist, the next question has to be “by whom” and “how”. Of course I could just stop, and say “well, God, obviously”. But the only thing that would allow me to infer “God” would be lack of a natural explanation. And simply not bothering to look isn’t a good enough reason for concluding “God”.

    Science can investigate natural intelligent agents. It is simply not equipped, by definition, to investigate God. Not because scientists are evil atheists but because by definition, what is amenable to science is what is “natural”, and what is “supernatural” cannot be (or it wouldn’t be supernatural!)

    For example,if someone figures out what psi is all about, then that won’t be evidence for the supernatural, it will simply be evidence for yet another natural force.

    At least that’s how I see it, and I guess Dawkins does too.

    In short, Dawkins has a limited imagination. He can’t imagine how the universe could have been created by an intelligent designer. He accepts that life on Earth could have been started by one, but not the universe, because that could lend some doubt to his own views on abiogenesis.

    Actually, I think the opposite. Dawkins has a scientific imagination that doesn’t stop at the “explanations stop here”. He, like most scientists will keep going, keep looking for explanations.

    There’s two issues here. One is, I doubt if Dawkins actually believes in panspermia, and neither do I. Panspermia introduces a problem of infinite regresses of panspermia on planet after planet, unless as Dawkins states, there was abiogenesis on the planet of the hypothetical aliens, and who would know or care? This doesn’t solve anything, so Dawkins is likely to reject that, and stick to naturalistic abiogenesis.

    Well, there’s some evidence that amino acids are fairly common in the universe, so to that extent we already have evidence for “panspermia”. But I think the reason most scientists don’t go the whole hog and postulates that “protobionts” or even cells first appeared on non-terrestrial bodies is that there are a fair few good hypotheses around now about how it might have happened here.

    But, as I say, I don’t myself think it has a lot to do with atheism or theism. It just has to do with fitting models to data :)

    The second issue that isn’t resolved by Dawkins’ position is just what we’ve been talking about; the probabilistic resources for abiogenesis right here on Earth where it could be observed if true.

    If it’s silly, I haven’t got us very far. It it isn’t silly, I’ve just introduced some thinking, which gets us beyond any priors we may have. Thinking about intelligent designers (no matter who they are) does not take us outside of science, as Dawkins reluctantly demonstrated. Furthermore, a designer who is something greater than an agent of panspermia can make a lot more sense than naturalistic abiogenesis – given a limit in probabilistic resources. This is so because a designer of the order we’re talking about is not limited by probability constraints, since a designer does what he does intentionally, not by chance and necessity. Agreed?

    Yes indeed. Well, we may want to discuss what we mean by “intentionally”, but yes.

    I certainly have always regarded the argument that “intelligence” or “intention” is not amenable to scientific investigation simply wrong. After all, what do people think psychologists do? (Dembski himself has made this error in one of his papers).

    With that in mind, I should go back and ask my original question once more: “what are your priors, which cause you to reject NFL?” If you say that you as Dawkins can accept only a naturalistic abiogenesis, then your argument about priors may apply to you; but do you honestly infer by this that they necessarily apply to everyone? In short, do you (unlike Dawkins) have an imagination outside of naturalism, which would allow for a design inference outside of it? If not, what on earth are you doing here? (I ask this honestly, not to judge you in any way).

    If you really desire to understand the argument from design, you must understand it outside naturalistic constraints and assumptions. If those are your priors, they are not ours, and this makes a huge difference in how we view life and the universe.

    Well, I hope my post above this one has cleared up at least some misunderstanding about what I meant by “priors”.

    But no, I don’t think the supernatural is amenable to scientific investgation, as I said, by definition. But in principle it might be possible to make a confident scientific inference that life was designed by an intelligent agent. I don’t myself, make that inference, because I don’t think it is supported by the data.

    Also, what do you mean by “reject NFL”?

    Thanks for your thoughts, though. I find them interesting and informative.

    Thanks! And nice to talk to you too.

  40. BA77 @5:

    But DrBOT, don’t you also think that avida, ev, and weasel, are proof of evolution???

    Elizabeth Liddle @6:

    I doubt it, bornagain77 – scientists don’t actually deal in “proof”.

    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

    here

    OOPS.

    Does this mean Dr. Schneider isn’t a scientist?

  41. CY: You should look into the controversy surrounding Dr Dawkins’ selfish gene notion. I’ve personally had discussions with a PhD level biologist who thinks Dr Dawkins reductionist approach is rubbish. He’s had to defend and argue his position over the decades. And, like a good scientist, he’s given way on some aspects of his idea. And his support of the meme concept has also taken some heat.

    In short, the man is used to pushing and arguing over the boundaries of science. Did you know he and Stephen Jay Gould used to have quite public feuds about punctuated equilibrium? Read Dawkins’ The Blind Watchmaker to get his version of the conflict.

  42. BA77: I’m happy and interested in having a dialogue with you but I wish you would resist flooding the discussion with links and imprecations that people who disagree with you are wrong.

    I second the motion.

  43. Didn’t take long to stray far afield of the OP. I don’t imagine we’ll see Dr. Spectre back to discuss it.

    “The paradigm used in the incorrect argument is often formalized as follows: Suppose that we are trying to find a specific unknown word of L letters, each of the letters having been chosen from an alphabet of K letters. We want to find the word by means of a sequence of rounds of guessing letters. A single round consists in guessing all of the letters of the word by choosing, for each letter, a randomly chosen letter from the alphabet. If the correct word is not found, a new sequence is guessed, and the procedure is continued until the correct sequence is found. Under this paradigm the mean number of rounds of guessing until the correct sequence is found is indeed K^L.”

    What are the authors talking about?

    Anything recognizable to anyone here?

    I mean, I don’t think even Dawkins Weasel program works like this.

    Isn’t this just a random search?

    Talk about setting up a straw-man. I mean, how difficult could it be to come up with a better model than that?

    IS there anyone here who would argue that the above program did not have a target?

    What if we increased the number of possible words to 16.

    What if for each round we introduced a chance that each of the 16 words would itself be changed.

    Does our new program now have no target?

    Let’s name our new program rev, for Random EV.

    Now what are some things we could do to make our search more efficient?

    Well, one think we could do, is sort of model our search using techniques we think are found in nature.

    In steps the Evolutionary Algorithm (EA).

    But those pesky targets are still there.

  44. “After guessing each of the letters, we are told which (if any) of the guessed letters are correct, and then those letters are retained. The second round of guessing is applied only for the incorrect letters that remain after this first round, and so forth. This procedure mimics the ‘in parallel’ evolutionary process.”

    Again I agree with Spetner. To this point his analysis has been spot-on.

    This is still a serial process. It now sounds very much like the Weasel program, but it still isn’t even to that point yet.

    So how do we introduce parallelism?

    Through having not one string trying to find the target, but rather through multiple strings trying to find the target. By introducing the concept of a “population.”

    The term “replicational resources” comes to mind.

    This is an even better model, not necessarily because it more closely models evolution, but because it allows the program to search a larger space.

    But it’s still a search, and it still has targets. We’re just increasing the efficiency.

    I forget how many strings the Weasel program started with. I think ev started with a population of 64, iirc.

    Anyone not still with me so far?

    The first model has a search space the size of which is determined by the word length and the number of letters in the alphabet.

    The target string is at a “fixed location” within that search space.

    Every new attempt tests a completely different location in the space, unless by pure chance the same letters are chosen more than once.

    In the “rev” program we increased the number of targets, and we introduced a chance that they might perhaps move a bit from their original “location” in the search space.

    But it’s still a search space, the search space is still bounded, or still the same size, but by introducing more targets we’ve actually improved our chances of finding one of them (success).

    That’s basically what ev does, and therefore it still has targets. So what if there are more than one and they can move a bit in the search space.

  45. mung,

    ‘I second the motion’

    Sorry mung, could you please give me your e-mail so I can run my posts by you for your approval before I post them??? :)

  46. http://arxiv.org/abs/1010.5178

    New mathematics research proves there’s plenty of time for evolution

    We need more models like this…

    Notice that this is not a concrete estimate of the time it would take for something to evolve! It’s a grossly simplified version of the story: the example overstates the power of selection (amino acids won’t be locked in, but will only be less likely to change), and overstates the required accuracy of matching to a target (there would be more tolerance for variation), and the whole idea of meeting a specific target is not necessarily a good model. As a guide to short-circuiting the invalid assumptions of creationists, though, it’s handy to have a simple mathematical formula to remove that naive combinatorial model from the table.
    P.Z. Myers

  47. Sorry mung, could you please give me your e-mail so I can run my posts by you for your approval before I post them??

    We’re supposed to be self-moderating.

  48. Well dang it mung, how can I please you if I don’t let you see them first???

  49. There are D amino acids and L amino acids. (I’m not exactly sure why we use the latin name for D and the english name for L). I’m pretty sure this difference only matters for origin of life scenarios because the genome only codes for L amino acids. Is that true? Can L amino acids and D amino acids bind together?

  50. Occasionally someone, often a mathematician, will announce that there has not been time since the origin of the earth for natural selection to produce the astonishing diversity and complexity of life we see … The only way I know to give a quantitative answer is to point out that if one estimates, however roughly, the quantity of information in the genome, and the quantity that could have been programmed by selection in 5000 MY, there has been plenty of time. If, remembering that for most of the time our ancestors were microbes, we allow an average of 20 generations a year, there has been time for selection to program the genome ten times over.
    – John Maynard Smith

  51. Mung: Well, after that John Maynard Smith quote I can sleep quite easily! ;-)

    Night all! I really AM going to bed now.

  52. 52
    CannuckianYankee

    Elizabeth,

    Thanks for your answers. I realize I was asking a lot, and perhaps a little off topic.

    “However, I think that is entirely valid, and has nothing to do with whether or not you are an atheist or not. “Supernatural”, essentially, means “unexplained”. It may well mean more than that too, but something cannot be, as I see it (and I think in the sense Dawkins is saying it) both “supernatural” and “an explanation”

    I’m not sure I would agree. It seems that if one is already committed to naturalistic explanations, then anything outside of them is inexplicable. Too me this sounds a lot like begging the question.

  53. mung, that JM Smith quote proves nothing. Smith offers no reasons why he thinks 5 billion years is enough time.

  54. @ noam-ghish
    Don’t forget about to use your “Imagination.” With your imagination 5 billions years is plenty of time.

  55. 55
    CannuckianYankee

    Mung,

    John Maynard Smith’s statement sounds a lot like begging the question too. You have to assume first of all that “if one estimates, however roughly, the quantity of information in the genome” is something that developed out of the naturalistic processes you’re attempting to show there’s enough time for. Therefore, “and the quantity that could have been programmed by selection in 5000 MY, there has been plenty of time,” doesn’t follow.

    Why? You have to rule out that the quantity of the information in the genome did not arise by an intelligence placing it there without the constraints of probabilistic resources.

    I hope Elizabeth is reading this.

    And then we have old faithful PZ stating that it’s wrong but useful against the alternative – creationists. As if that isn’t laughable.

  56. 56
    CannuckianYankee

    El,

    “CY: You should look into the controversy surrounding Dr Dawkins’ selfish gene notion. I’ve personally had discussions with a PhD level biologist who thinks Dr Dawkins reductionist approach is rubbish. He’s had to defend and argue his position over the decades. And, like a good scientist, he’s given way on some aspects of his idea. And his support of the meme concept has also taken some heat.”

    This is what I really like about you. Sometimes you’re with us and sometimes you’re not. And the times you’re not really with us, you’re still pleasant. It takes guts to pull that off consistently.

    That bit about Dawkins and Gould I’m quite aware of. I think Dawkins ultimately disagreed with Glould because of his rather arbitrary non-overlapping magisterium rule. For Dawkins, the only magisterium is “science” according to his definition. Any other magisterium is irrelevant and/or non-existent. No sense in placating to those who are wrong about the existence of gods.

    I personally don’t believe Dawkins’ selfish gene hypothesis is that significant, and I don’t find many people actually pushing it, save those on the fringes of science. It really is pop science, or pseudo science, but Dawkins would rather me not go there. :)

    Isn’t it interesting how we can sort of agree with Dawkins but really not? We can agree with him in his consistency with his materialistic position, and that this is how Gould should have behaved, but we can disagree ultimately with his materialistic presuppositions.

  57. smidlee, there is not enough time not even on earth but on every planet in the whole universe for the time needed for evolution to work. there are only 10^150 events that have happened in our universe’s history. that’s 10^80 particles, 10^26 seconds and 10^43 divisions of a second, put that all together and you get 10^150 events. well, just to form one protein 200 aa long, that’s 10^260 possible sequences.

  58. CY, I just thought the Simpson quote fit in well with the overall subject of the thread. I’m hoping someone can show me the maths, lol.

    Because I think it’s garbage.

    1. What does it take to program a genome even once, much less ten times over?

    2. For most of those 5000MY life was, as he says, microbes (as far as we know). So don’t we need to take that into account rather than counting on it to give us the figures we want?

    Don’t we need to take into account what it takes to program a human genome, and don’t we need to take into account generation times other than those of microbes?

    He’s just tossing figures out with no basis in fact for believing that they are even relevant. Pretty much what he appears to be accusing those mathematicians of doing.

    Pot. Kettle. Black.

  59. Again I agree with Spetner. To this point his analysis has been spot-on.

    Really? See my comment at 2 – it only recently appeared thanks to the joys of being moderated over a holiday weekend.

  60. Heinrich,

    To this point his analysis has been spot-on.

    I said to this point.

    The paragraph I was quoting appears two paragraphs above the one you quote.

    So yes, really.

  61. It’s a shame that very little of the discussion so far has anything to do with Dr. Spetner’s post.

    First, I remember seeing this paper and looking briefly at its math. It looked straightforward enough. I didn’t see any glaring error.

    But, of course, their conclusion had to be wrong since, otherwise, the force of their conclusion would have been already noticed in

    the lab.

    That is, it’s too rosy a scenario for evolution.

    But I didn’t want to take the time to think it through, thinking that eventually someone with a population genetic background would

    address its errors.

    So, thank you Dr. Spetner for pointing out some of their errors; viz., that assuming that change is only “beneficial” and never

    “harmful”—i.e., when the correct letter is chosen, nothing more happens—does not realistically reflect what happens to biological

    populations.

    However, now forced to think a little bit more about their reasoning, I believe there is another, perhaps more fatal, error present.

    W&E’s scenario, per Spetner’s quote above, let’s us know that: “[a]fter guessing each of the letters, we are told which (if any) of

    the guessed letters are correct, and then those letters are retained. The second round of guessing is applied only for the incorrect

    letters that remain after this first round, and so forth. This procedure mimics the ‘in parallel’ evolutionary process.

    As Dr. Spetner points out above, their ‘first case’ is not “serial”, but “simultaneous”. And, it turns out, so is their second case.

    W&E assume that all L loci are involved ‘simultaneously’ in each “round” of “guessing”. But, how is that possible?

    Here’s what I mean:

    We can assume that W&E are thinking here of a ‘genome’ that is made up of L loci=genes. No problem there. And we can think of

    each “gene” as being composed of a large number of different configurations; K, in fact. We can assume that ‘mutations,’ in the

    form of nucleotide substitutions, allows ‘evolution’ to produce these K alleles at each of the L loci/genes.

    Now here’s the problem: how can all L (=20,000) loci provide a “new letter” after each “round”?

    W&E write: “The second round of guessing is applied only for the incorrect letters that remain after this first round, and so forth.”

    Per W&E, their K = 40 is arrived at in this fashion:

    (1) 5 “letters”/L = 5 “letters”/20,000 loci/ individual x 10^6 individuals = 250 “letters”/loci/population
    (2) Only 1 in 10,000 “letters” (mutations) are beneficial
    So, (3) 10,000 “letters”/ ‘correct letter’ x “rounds” (generation)/250 “letters” per population = 40 “rounds”/’correct letter’-population.

    So, L=20,000 and K = 40.

    These numbers are true only if we are considering the entire population. IOW, somewhere in this million-fold population, there are

    “rounds” taking place at EACH of the 20,000 loci. But, for any individual in the population, only 5 of the 20,000 loci are having

    “letters” changed. Considering that only 1 in 10,000 “letters” is the correct one, it would take 2,000 rounds, = generations, for any

    one individual to find the correct “letter” (10,000/5 ‘letter’s per generation) ASSUMING that the 5 ‘letters’ were always occurring in

    the same 5 loci. If they were to happen anywhere among the 20,000 loci as each individual replicated, then it would

    require (20,000 loci x 10,000 letters/ correct letter)/ 5 letters/ generation = 4 x 10^7 generations, on average, for just ONE of the loci

    to get the right “letter” (=allele=gene). Obviously this is a whole lot more than W&E’s value of 390 “rounds”=generations.

    So, what is going wrong here? Well, the model that W&E use is looking at all of the million-fold individuals in the population

    simultaneously. And, apparently, implicit in their model, they’ve simply assumed that once a “correct” letter is obtained,

    ANYWHERE in the population, that it is “instantaneously” ‘fixed’. And, further, that because there is “instantaneous

    fixing” taking place, they in effect are also assuming that none of the already accumulated mutations are lost to the population via

    this fixing event.

    As Dr. Spetner points out, this is not how “natural selection” operates. He points out that when the “correct” letter is found, there is

    no reason to believe that in the next “round’ it won’t be lost by substitution. We can further point out, that the assumption implicit in

    their calculations are valid ONLY for the entire population, and that to assume that nothing is lost to the population and that

    everything is just instantaneously fixed, are not realistic assumptions.

    Let me put in another way: the model their assuming is comparable to Dawkin’s model of the monkeys banging away at typewriters

    hoping to type out the phrase: “Methinks it is like a weasel”. In that model, as soon as the correct “letter” is typed, it, too, is

    instantaneously saved, and, thereafter, only the “wrong letters” are to be newly typed.

    If this is true, then the equation that W&E give us should also apply to Dawkins’ model.

    As I’m typing this, I am opening up Dawkin’s Blind Watchmaker” to see what Dawkins came up with. In his model, K=27 and

    L=28. W&E’s equation is: log 28/log(27/26) = 88 generations. Dawkin starts with three different strings of letters and his generation

    times are: 43, 64 and 41 using a computer that mimics W&E’s model.

    These are very similar results. In fact, on close inspection, his starting string for the 41 generation case contained two correct letters.

    Hence, for that case, L=26. Then, W&E’s equation would give us: log 26/log(27/26) = 86. The discrepancies are probably due to

    stochastic effects that are present when L is so small, and thus, “r” being so small. Also, each of the 20,000 loci (=genes) in W&E’s

    model are different, whereas in Dawkin’s model the “letters” can be the same (this should have the effect of changing the probability

    distribution towards a smaller running time).

    Averaging the times, we have 49.3 generations versus a calculated value of 87 (average). Obviously, we’re very much in the same

    ballpark as far as models go.

    And what does Dawkins say about his computer model?

    “Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative

    selection, it is mesleading in important ways. One of these is that, in each generation of selective ‘breeding’, the mutant ‘progeny’

    phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A

    WEASEL.” (p. 50 paperback)

    In the case of W&E, they’re assuming the instanteous fixation of the “correct” letter. This just isn’t how natural selection works out in

    nature.

    It would be nice to see other population geneticists criticize this work. The rejection of Dr. Spetner’s paper gives the impression that

    those who would criticize it will not receive a very friendly reception. Too bad.

  62. Sorry for all the disconnections: when I pasted it from Notepad, I didn’t bother reading it through since I had already done that on Notepad.

  63. Noting that there are only 13 kinds of characters actually used in Dawkins’ example of METHINKS IT IS LIKE A WEASEL (including the ‘space’), and understanding this ‘alphabet’ to be equivalent to the number of different ‘alleles’ for each loci (i.e., K=40 for each loci), adjusting the formula and using the value of 13 (actual letters used=alleles) for K gives the following number of generations: 41

  64. 64
    Elizabeth Liddle

    It is trivially easy to write a “weasel” program in which the “correct” letters are not fixed once they appear, and the sentence still evolves.

    There are many on the web, and I believe at least one is authored by Dawkins. I’ve certainly made one myself. I’ve also made one in which I did not specify the sentence in advance, rather I biased reproduction (which is what natural selection is) in favour of pronouncable syllables, real words, and grammatical combinations.

    Eventually recognisably English sentences, of a sort, evolved. As you’d expect,including some “irreducibly complex” words – text strings that were not selected until several letters were in place.

    I don’t think it’s a terribly relevant model for DNA, for many reasons, so I think that arguing about WEASEL programs is a bit pointless, but there is simply no doubt that grammatical English sentence can evolve by random mutation and natural selection, without fixing “correct” placements. as long as you have a fitness function that selects for features of English text.

  65. Sorry for all the

    disconnections:

    when I pasted it

    from Notepad,

    I didn’t bother reading it

    through

    since I had already done that

    on Notepad.

    And here I thought you were just waxing poetic and finding an interesting way to emphasize certain points.

    lol

  66. Mung:

    I’m here to entertain!!!

  67. Elizabeth:

    EL: “Eventually recognisably English sentences, of a sort, evolved.”

    ” . . . of a sort . . .”

    Humm.

    EL: “As you’d expect,including some “irreducibly complex” words – text strings that were not selected until several letters were in place.”

    ” . . . several letters were in place . . .”

    Humm.

    None of this sounds very impressive. I would fully expect that using a computer you could (by a “biased reproduction”) develop a “sort of” sentence. What I would not expect is that you could develop a paragraph using your program—which could only happen, I would suspect, if you were using a target paragraph.

    It’s the difference between micro and macro evolution.

    EL: “I don’t think it’s a terribly relevant model for DNA, for many reasons, so I think that arguing about WEASEL programs is a bit pointless, but there is simply no doubt that grammatical English sentence can evolve by random mutation and natural selection, without fixing “correct” placements. as long as you have a fitness function that selects for features of English text.”

    I’ve already commented on the sentence-part of your comment.

    However, you seem to have missed my point entirely.

    The logic is quite simple.

    (1) Patently—on the face of it—Wilf and Ewens model can’t be right: it makes evolution too easily had—something no one has seen, and something that would easily be seen. So we know they’re wrong.

    (2) They make a serious error. The equations they develop can only work for “simultaneous” evolution; and “simultaneous” evolution cannot take place at the individual level. It can only happen if the whole population (a million-fold) is involved. But, then W&E have to make clear how newly arrived “correct letters” can sweep through the population: which, of course, is exactly what they hope their equations would obviate.

    (3) Wilf & Ewens’ model sounds like, and WORKS like, Dawkins’ “Methinks it is like a weasel” program in BW. But Dawkins clearly states that his program does not realistically represent how natural selection operates. Thus W&E’s model is not what they think it is.

    Have you noticed that W&E’s equations don’t include a ‘selection factor’?

    How can you present a model of “natural selection” that contains no selection factor whatsoever? It doesn’t make sense.

  68. 68
    Elizabeth Liddle

    No, I don’t think it is “very impressive”, PaV, which was part of my point!

    It’s a fairly trivial achievement.

    With enough time and effort I might even make a paragraph, but of course it wouldn’t be worth reading, even if I achieved it.

    My more serious point was that English is very “brittle” and highly redundant – only a tiny set of possibly combinations actually make pronounceable syllables, let alone recognisable words or phrases.

    Whereas digits are quite different – any combination of digits represents a number.

    Between those two extremes, I suggest, lies DNA – not all combos produce anything at all, but the ones that produce nothing don’t actually get in the way, and the ones that produce something can do it in a number of ways (witness the large number of polymorphisms that still result in a functional gene).

    As for the rest of your post, I need to read it more closely (it’s 3 in the morning here, and I’ve been working on a studentship proposal!) but if I read your last sentence aright, I most emphatically agree!

    You can’t model natural selection without, um, selection. Sometime tomorrow I’ll try to figure out who isn’t doing it ….

  69. My more serious point was that English is very “brittle” and highly redundant

    To me, that statement sounds self-contradictory.

    Redundancy is just the sort of thing one would want to cure brittleness.

    Information Theory 101.

  70. EL:

    Between those two extremes, I suggest, lies DNA – not all combos produce anything at all, but the ones that produce nothing don’t actually get in the way, and the ones that produce something can do it in a number of ways (witness the large number of polymorphisms that still result in a functional gene).

    You say “not all combos produce anything”. But the reality is that all but an infinitely few produce anything. And this is so even when we include polymorphisms.

  71. 71
    Elizabeth Liddle

    You say “not all combos produce anything”. But the reality is that all but an infinitely few produce anything. And this is so even when we include polymorphisms.

    Well, not “infinitely few”, and of those “few” (a large number, in fact), many variants are perfectly viable, which is not true of English text.

    When a genotype is replicated, or shuffled with another genotype, as in sexual reproduction for example, many of the resulting variants do what they always did, but slightly differently (are expressed slightly more readily; produce a slightly different protein; are expressed under slightly different chemical conditions) and all these variations my result in selectable phenotypes.

    Importantly of course, stretches can be duplicated and either do what one did twice as much, or become redundant, if the stretch in question is “switched off” by a certain concentration of product. At that point, potentially, the copies are “free” as it were, to “explore” a new search space.

    In other words, the probability space is nested, as it were (i.e. is Bayesian in structure); the probability of a single “original” gene might be small (but we are going back to abiogenesis arguments now) but once you have a gene that does something that allows its possessor to replicate more efficiently, then the probability of variants that are also viable is much greater than the probability of finding that original, and, indeed, the probability of finding variants of, for example, the word “elephant” that are also viable.

    And if, of those viable variants, some confer greater reproductive success than others, you have the beginnings of evolution; and if you also have a system that means that duplication is one of the variants, then you have the potential for finding not just a variant, but a variant that performs some additional pro-reproductive function to the one you started from.

    But I assume you know this argument :)

    So I look forward to the rebuttal.

    Cheers

    Lizzie

  72. EL:

    In other words, the probability space is nested, as it were (i.e. is Bayesian in structure); the probability of a single “original” gene might be small (but we are going back to abiogenesis arguments now) but once you have a gene that does something that allows its possessor to replicate more efficiently, then the probability of variants that are also viable is much greater than the probability of finding that original, and, indeed, the probability of finding variants of, for example, the word “elephant” that are also viable.

    You’re assuming here a breezy type style. And all seems so quite forward. But let’s take a closer look.

    Here is the critical claim: ” . . . the probability of a single “original” gene might be small (but we are going back to abiogenesis arguments now) . . . ”

    Can we simply assume that the problem of gene origin is relegated only to time of abiogenesis? I think not.

    Here’s what I mean. To assume that all genes were fabricated all at once would be the case of complete “front-loading” of the genome. Yet, this would mean that all the needed genes throughout the evolution of various life forms were already present from the beginning. How, then, can this be accounted for other than by a Creator?

    If, then, we abandon the complete “front-loading” hypothesis, then we’re left to conjecture that during the unfolding of various life forms inevitably new genes will have had to arisen. Now we have the problem of how full-length gene sequences could develop when the odds of such a thing happening are so staggeringly low.

    I, too, look forward to you rebuttal.

    Cheers.

  73. 73
    Elizabeth Liddle

    I think that’s a fair point. I don’t have an answer, because I don’t think there is one (yet). We don’t yet know what the minimum viable genome might be.

    But I think it’s premature to assume that whatever it is, it is too complex to have arisen from a series of simpler self-replicating stages, themselves subject to natural selection.

    Nonetheless, I agree that the problem of how the simplest DNA genome formed has not been solved (although not with the idea that it isn’t in principle, solvable).

    Where I probably do disagree with you is over just how simple that first genome had to be. It’s possible that was contained within a simple lipid membrane and it had one gene, with one codon, and that codon resulted in the production of an amino acid that, for example, made the membrane slightly more (or less) elastic, and that this enhanced the probability that it would divide successfully.

    This is, of course speculation, but at the heart of the Darwinian argument is the idea that once you have something that self-replicates with variance, and where the variants differ in the efficiency with which they self-replicate, then you have the “recipe” if you like for increasing complexity (if complexity is beneficial), and no more “frontloading” is required than those key initial conditions.

  74. Lizzie:

    …but once you have a gene that does something that allows its possessor to replicate more efficiently, then the probability of variants that are also viable is much greater than the probability of finding that original,

    Isn’t it true, by definition, that some entity which replicates more efficiently is more viable than one that doesn’t replicate at all?

    Basically, what I think you are saying is, once you have a functional system, changing that system and having it still function is much more likely than coming up with a functional system in the first place.

    Now frankly, I’m not sure that’s even true. I’m also not clear on it’s relevance to the current discussion.

    But maybe I just don’t understand the argument you’re making.

    How does having a functional system increase the chances of finding a functional variant of that system?

  75. EL:

    I think that’s a fair point.

    It’s good that you trying to remain open-minded.

    But I think it’s premature to assume that whatever it is, it is too complex to have arisen from a series of simpler self-replicating stages, themselves subject to natural selection.

    I don’t know how old you are, but I’ve been looking for Darwinian answers for nigh thirteen years. I bet you were in grade school then. And what have I found? Nothing that gives any kind of realistic answer for how highly improbable informational events can be accounted for.

    I don’t think it’s premature.

    There have been a number of great thinkers who have concluded that Darwinian mechanisms simply can’t explain observed biological phenomena.

    So, don’t hold your breath.

    This is, of course speculation, but at the heart of the Darwinian argument is the idea that once you have something that self-replicates with variance, and where the variants differ in the efficiency with which they self-replicate, then you have the “recipe” if you like for increasing complexity (if complexity is beneficial), and no more “frontloading” is required than those key initial conditions.

    To produce a protein you need a ribosome. To divide, you need cytochrome c. What you’re envisioning is way too stripped down.

    I would recommend Stephen Meyer’s Signature in the Cell as a way of understanding just what a big problem “origin of life” is.

  76. 76
    Elizabeth Liddle

    heh. I was born in 1952, PaV. Turning 60 next year. But my mind has been pretty open from birth, and I hope will remain that way for a couple more decades still.

    How about you?

    I haven’t read Signature in the Cell, although did borrow a copy when it first came out and read some of it. I’m afraid I didn’t find what I read convincing. I guess that might seem like evidence that my mind isn’t as open as I think it is. From where I’m standing, though, it seemed like Stephen Meyer’s mind wasn’t very open. I guess my problem with arguments like the one he seemed to be making, which seemed to be, essentially, the Irreducible Complexity argument applied to the genetic code, is exactly the problem I see with Behe’s version, namely that just because a structure or function is Irreducibly Complex (will break if you take any part away) doesn’t mean that it was assembled from its constituent parts (this is leaving aside the other big problem for IC, which is that IC functions are in fact evolvable by incremental unselected, even deleterious, steps).

    A clunky structure can be pared down “decrementally” until only the essentials are in place. And there is a fair bit of reason to suppose that clunkier ancestors of self-replicating DNA containing cells could have been “pared down” to leave the DNA code that we know.

    There’s a paper here, for instance:

    http://www.springerlink.com/co.....lltext.pdf

    Now, its thesis may or may not be true, but it seems to me plausible, and a problem with making an ID inference from “there isn’t another plausible explanation” is that you only need a plausible explanation to appear, and you lose your inference.

    It doesn’t mean your inference is wrong, but it does mean that you have to check out each alternative hypothesis extremely thoroughly, because unlike most competing hypotheses, ID makes comparatively few differential predictions (at least ones that I’ve seen.

  77. heh. I was born in 1952, PaV.

    He did say 13 years, lol. I wonder if he meant 30.

    I’ve been debating evolution on the net since the early 90′s. I remember when there were no blogs or forums and the days when we used newsgroups instead.

    Ah, talk.origins. Those were the days.

  78. lol. Funny you should mention the Yarus paper. Didn’t someone else just suggest in another thread that you should read it? UprightBiped comes to mind.

    Now to be sure I agree with you about Sanford’s book, it’s confusing on a number of levels and doesn’t present a compellingly coherent argument.

    But Signature in the Cell is altogether different, as is Darwin’s Black Box.

    But again, in the same way that I think you didn’t understand the thesis of Sanford’s book, it also appears you don’t understand the thesis of SitC.

    It’s not about complexity at all. It’s about information and information systems.

    You really should read it with an open mind and try to understand the arguments. It’s one of the best ID books out there.

  79. Mung:

    According to Stephen Matheson, a developmental cell biologist at Calvin College, Dr Meyer made a basic error on page 66 of Signature in the Cell mistaking a virus for a bacteria. Is that true??

  80. 80
    Elizabeth Liddle

    Mung, at

    My more serious point was that English is very “brittle” and highly redundant

    To me, that statement sounds self-contradictory.

    Redundancy is just the sort of thing one would want to cure brittleness.

    Information Theory 101.

    Well, there must be a communication problem here, maybe over the my use of the word “redundant”.

    So let me rephrase: English is very “brittle” in that there are a great meany combinations of words and sounds that have no referent. In this sense there is a high proportion of “redundant” code – possible sequences that have no assigned referent.

    In contrast (and I would argue because there is no “assignment” process, just physical and chemical laws), in the case of DNA, there are many possible alleles of a gene that make a functional protein, or regulate the expression of a protein according to a viable time-table or level of incoming chemical input.

    In that sense it is less “redundant” – more possible combos result in viable output, and so less easy to “break” (i.e. less “brittle”)

    This is why I find the analogy often made between mutations to a gene and misprints in a text.

    A better analogy would be misprints in a bank statement, 50% of which will be advantageous to at least one of the parties :)

    But neither analogy is good, as both ignore the fact that in living things, the probability of even a rare advantageous mutation propagating through the population has a strong positive bias (by definition).

  81. 81
    Elizabeth Liddle

    Apologies, I messed up the blockquote tags above. Mung’s words end at “Information 101″ and the indented text is mine (quoted by Mung).

    The reference is to post 69

  82. 82
    Elizabeth Liddle

    I’ve read Darwin’s Black Box, BTW. Obviously, I wasn’t persuaded :)

    I’ll try to take another look at Signature in the Cell.

  83. Wha is it about the current theory of evolution that has you persuaded?

    To date there isn’t any evidece that an accumulation ofgenetic accidents can construct useful, functional multi-part systems, so what does the theory have?

  84. ellazimm:

    According to Stephen Matheson, a developmental cell biologist at Calvin College, Dr Meyer made a basic error on page 66 of Signature in the Cell mistaking a virus for a bacteria. Is that true??

    Not unless Pneumococci is a virus that Dr Avery was injecting into mice.

  85. Joseph: Well, I haven’t got the book so I can’t look it up but the claim is that Dr Meyer mistook Pneumococcus (a bacteria) for a virus somehow.

    Oh wait, I found the review and the quote from SitC:

    “If a deadly strain of the bacteria was first heated to death, the strain was harmless when injected into mice. No surprise there. The mice were also unharmed when injected with a living but nonvirulent strain of the virus.”

    Ah, I see, he starts off talking about a bacteria and then uses the term virus.

  86. ellazimm:

    I have a copy of SitC: it has bacteria in both places.

    But I have a paperback version. It’s possible the hypothetical mistake was corrected; but, of course, it’s possible it was never there.

    However, it is typical of those who are not in pursuit of the truth to want to cling to their erroneous views simply because somebody with an opposite viewpoint has made a mistake.

    It’s one thing when the mistake undermines the conclusion being made, but when it is simply the case where someone has used the wrong terminology, but without affecting the argument, then anyone interested in the truth would simply overlook such an error.

    But not Darwinists. Which tells us they’re perhaps not really interested in the truth, but in simply believing themselves to be ‘right’.

  87. PaV: I figure it was a type, lots of books have mistakes. I only brought it up initially to see what the fuss was about. Turned out to be nothing that got fixed in the paperback edition. Pffft.

    Yeah, that does happen. I’m trying to avoid snap judgements. I figure you got spend some time if you want to see the best in something and not the worst.

  88. 88

    Ella, PAV,

    Soon after SitC was published, the materialist horde went apopletic on the Amazon forums when it was discovered that early in the book Dr Meyer dscribed the ribosome as a protein complex.

    He was repeatedly accused of lying to the stupid Jesus people in order to keep them from the knowledge that an RNA had been found in the Ribosome that actually did the catalytic work. The phrase “peptidyl transferase” was used to bludgeon anyone who dared to come to Meyer’s defense. The phrase “Meyer is a LIAR” was repeated over and over and over again. Not only was Meyer a LIAR, but Skell and anyone else who positively reviewed the book were LIARS as well.

    It made no difference to them that a few pages later he specifically describes the RNA catalytic action. Nor did it matter that where Meyer refered to the ribosome as a protein he did it in a context that had no bearing whatsoever on the issues at hand.

    Materialist are a desperate bunch in many ways, and counter-intuitively, they become more desperate the more we know about matter.

  89. ellazimm, speaking of lots of books having mistakes,,, Have you noticed the recent peer-reviewed paper that found Darwin’s masterwork book, “Origin Of Species”, was actually a Theological book infused with Theological presuppositions, about how God would and wouldn’t act, as opposed to being a purely science book infused with merely a unbiased presentation of evidence???

    Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011
    http://www.evolutionnews.org/2.....46391.html

    ==============

    “Certainly, my own research with antibiotics during World War II received no guidance from insights provided by Darwinian evolution. Nor did Alexander Fleming’s discovery of bacterial inhibition by penicillin. I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No.
    Philip S. Skell – Professor at Pennsylvania State University.
    http://www.discovery.org/a/2816

    Is evolution pseudoscience?
    Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other?pseudosciences — astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
    http://creation.com/is-evolution-pseudoscience

  90. UB: I bet next time he checks his proofs (pre-publication copies sent to the author and reviewers) more carefully!!

    Mistakes do happen, obviously . . . I think some of the reviewers were surprised there were some that were so obvious but . . . it happens.

  91. 91

    Ella, he made no mistake. He was taking a lay audience through a layering of complex issues. He described it as a protein complex (which it is) and later he described it in greater detail – naming peptidyl transferase as the active constituent.

    The issue was not the book, it was the rabid response to having these issues explained to laypeople. An educated layperson is the absolute bain of the scientism cult. :)

  92. BA77: I’ve heard about it. I’m not really smart enough about that stuff to judge. And, as I’ve said, I’ve never even read the book. And, as I’ve said, my own support for the modern synthesis is based on other things.

    If all we had was Darwin’s original arguments then I think they would be worth tearing to shreds. He got some things wrong but his evidence has been built upon for 150 years. If he got the basic outline wrong he would be a sideshow now, like Lamarck.

    I feel the same way about any science: it’s the modern, updated versions that count. That’s one of the reasons I don’t refer to common descent with modification as Darwinism. It’s gone way beyond him now. When we refer to Newtonian mechanics we know we are referring to old, limited models.

  93. UB: I’ll take your word on it; not having read the book myself. I did hear several interviews with him via ID: the future and some other sources. I never even read any reviews, I only found that issue I brought up via Wikipedia this morning. I never heard any of the uproar; I don’t pay much attention to that kind of thing anyway.

  94. 94

    Ella….a wise choice.

    Of course, we on this side of the fence don’t have that luxury.

  95. UB: Well, you don’t have to read the reviews either!!

    I know what you mean though.

    Brings up an interesting point . . . given that the biological community is not going to agree with a book by Drs Meyer (or Wells or Behe or Dembski) is it worse having it vilified in the press or ignored? Partly, at least, negative reviews get the books into the public eye and some people will find them because of that.

    What did Oscar Wilde say? The only thing worse than being talked about is not being talked about. I think.

  96. 96

    “given that the biological community is not going to agree with a book by Drs Meyer (or Wells or Behe or Dembski)”

    Given?

    Ella, the value that the greatest of scientists gave to the world (Newton, Maxwell, Gallileo, Pasteur, etc etc etc) is that their scientific output was not based upon them sheparding their worldview, but upon them having a deep respect for the evidence itself.

    Is it too much to ask that such a standard remain in science forever? Or have we reached a point in knowledge and culture that such standards can be cast down and replaced with the scientific grounding that animates the likes of PZ Meyer?

  97. UB:

    “Given?”

    Well, I think so. Just an opinion.

    I agree with you about the standard. The people who decry ID are looking at the evidence as they see it. You disagree. I think . . . I know they think you’re misinterpreting the evidence.

    It’s not the standard that’s been degraded, there’s no conspiracy. You’re not viewed as seeing all the evidence.

    Please don’t shout at me. I’m only saying things you already know. Don’t shoot the messenger.

  98. ellazimm, the paper that showed Darwinism was a theological argument from the get go, resonated loudly with me, for it hit the nail on the head for the exact type of argumentation that neo-Darwinists make today, especially in regards to “junk DNA”, the ‘backwards retina’ of just recently overturned stature, and moreover the vestigial organ argument of a longer history. i.e. neo-Darwinists prey on ignorance of any biological function so as to declare, completely without solid merit, non-functionality, and thus God would have not done it that way. It is horrendous and appalling that neo-Darwinists are allowed to get away with such tripe, and moreover that you personally would cosign such shallow and despicable practices!!

  99. 99

    Hello again Ella,

    If someone thinks I (personally) am misinterpreting the evidence, that is fine. For their claim to be scientific, or even to appeal to the values of science, it must be validated in some way. That is the part that is missing.

    Recently, Mathgrrl claimed I was misinterpretiong the evidence. She said I was equivocating on the presence of an actual code in DNA. I stood here for two weeks trying to get to show me the distinction between a system that ACTS like a code as oppossed to one that IS a code. For there to even BE an equivocation, then she must know of a distinction.

    Did she ever provide that distinction?

    No.

    I asked Prof MacNeil on these very pages if DNA contains “meaningful information” and he said yes. I then asked if “meaningful information” required perception (observation, to be sensed or experienced in some manner) in order to come into existence, and he said yes. I then asked if the meaningful information in DNA fell under that requirement.

    Did he ever answer?

    No, he left the conversation and refused to return.

    - – - – - – -

    Actually engaging the evidence of ID is never on the agenda.

  100. BA77:

    “It is horrendous and appalling that neo-Darwinists are allowed to get away with such tripe, and moreover that you personally would cosign such shallow and despicable practices!!”

    Hang on. I didn’t say I agreed with the style. I have always been honest about my opinion so that shouldn’t surprise you.

    The ‘God wouldn’t have done it that way’ is an argument against ID not for common descent with modification. That’s the way I see it. And I’ve promised not to pull that argument here anymore.

    Look, I’ve come to terms with the fact that a lot of people disagree with me but I don’t think less of them as long as they’re being honest and straight. I gave you the benefit of the doubt and now I believe you are playing straight. Do you really think your ‘opponents’ are despicable?

  101. Upright BiPed,

    Recently, Mathgrrl claimed I was misinterpretiong the evidence. She said I was equivocating on the presence of an actual code in DNA. I stood here for two weeks trying to get to show me the distinction between a system that ACTS like a code as oppossed to one that IS a code. For there to even BE an equivocation, then she must know of a distinction.

    Did she ever provide that distinction?

    No.

    You apparently misremember the discussion. As I pointed out several times in that thread (comment 57), you never clearly stated your argument nor summarized the evidence you believe supports it. Based on the limited information you did provide, I noted that you seemed to be confusing the map with the territory. I told you there that I would be happy to discuss your argument further whenever you were willing to articulate it and your evidence clearly. Should you choose to do so, I am still interested.

    PS to kairosfocus and Mung: The Footnote thread has been closed to comments. I’ve replied to both of you in the closest to on-topic thread I could find.

  102. UB:

    I’m not going to defend MathGrrl. I didn’t even follow much of that thread. So I’m not going to condemn her either. I don’t read her blog or markf’s. I listen to ID: the future, read Evolution News and Reviews and I’m on the Discovery Institute’s emailing list. In the past I have exchanged emails with Casey Lusken.

    I am not responsible for anyone but myself. Maybe MathGrrl thought she had answered your questions. Maybe Dr MacNeil’s life turned hideous and he hasn’t had time to come back. I don’t know either of them. I don’t even know (or care) who MathGrrl really is.

    You’re going to have to take up your disagreements with them with them.

  103. MathGrrl: Hey!

    I’ve got a question: Can you tell me a good online resource that I can access that explains GA programming?

    Let’s open that up to everyone actually. I know a few programming languages but I have no experience with GA stuff. Where can I go for a decent primer?

  104. 104

    Mathgrrl,

    You say I never articulated my argument. Yet somehow that didn’t stop you from claiming that I was “equivocating”, did it not?

    Did you not say that I was “mistaking my map for the territory”? So are you now just going to repeat your claim that it is unreasonable for me to ask you to substantiate the objections you’ve already made?

    Did you not say that I was equivocating? Did you not repeat that claim several times? Yes you did, or no you did not? Which is it?

    So my question still stands. For you to say there is an equivocation, then you must first know of a distinction. So lay it out, Mathgrrl.

    How do you make the distinction that one thing acts as a code, while another thing is a code?

  105. 105

    Here is the final post in our previous exchange Mathgrrl, I invite you to deal with it straight up.

    - – - – -

    You see Mathgrrl, the only way your objection can make any sense at all, is if you can substantiate a distinction where one relationship is a code, while another only acts as a code.

    Without that distinction, then you cannot say there is an “equivocation”. I do not believe that you can make that distinction, therefore your claim of an equivocation is absolutely meaningless.

    Prove me wrong.

  106. Upright BiPed,

    You say I never articulated my argument. Yet somehow that didn’t stop you from claiming that I was “equivocating”, did it not?

    I explained myself in the original thread, in comment 52:

    I’ve responded to my interpretation of your statements, based on similar arguments from equivocation I’ve seen in the past. The few hints you’ve given to your thought process suggest to me that you are mired in a similar fallacy.

    You have not, however, clearly stated your argument nor summarized the evidence you believe supports it. Rather than continuing to speculate on what it is you are trying to say, I have invited you to provide more clarity.

    I extend the invitation again. Perhaps once I understand exactly what you’re talking about, I’ll be able to answer your question.

  107. ellazimm,

    David Goldberg’s Genetic Algorithms in Search, Optimization and Machine Learning is one of the classics. If you’re just interested in getting your hands dirty quickly, the comp.ai.genetic FAQ is a dated but good start. There are also libraries available for most programming languages, discoverable through Google. Finally, to tie this back to some earlier discussions, the various GA solutions to the Steiner problem are based on GA engines, most of which are open source, if I remember correctly.

    What languages are you interested in using?

  108. MathGrrl:

    Thanks!

    I’m looking to understand the underlying logic, the language is no big deal. I get the basic idea of the data structures . . . I think. And the kind of processing . .. I think. I’d just like to see how it’s really done.

    I suppose if I had a choice I’d go with Pascal or Ada or some such structured programming language. I can do C . . . if I must. Ugly stuff. I used to submit FORTRAN programs, typed on punch cards in batch mode so I really shouldn’t complain.

  109. 109

    Mathgrrl,

    You’ve been forced to back off your claim because someone had the unmitigated temerity to call you on it.

    This crap that you need me to explain myself so that you’ll know what you were talking about is patently ridiculous, so much so that words fail to describe it.

    On top of that – its demonstrably deceptive.

    Case in point:

    BiPed: You made the claim that my challenge to you was “not valid”, but just as before, you failed to actually engage the argument in order to substantiate your claim.

    Mathgrrl” That is not true. Your argument hinges on mistaking your map for the territory. You loosely model biochemical structures and reactions using the language of semiotics, then equivocate to conclude that a semiotic agent is required. Basically, as I said before, you’re trying to define your terms such that an intelligent agent is required.

    Your comment is not a demonstration of you fumbling around for what you think I might mean. You were coherent and deliberate.

    Now cut the rhetorical gamesmanship, and substantiate the distinction where one relationship is a code, while another only acts as a code.

  110. According to Stephen Matheson, a developmental cell biologist at Calvin College, Dr Meyer made a basic error on page 66 of Signature in the Cell mistaking a virus for a bacteria. Is that true??

    I think it’s perhaps both true and not true.

    IOW, I think it may say virus or bacteria when the other term is meant, but if you actually look at the context it’s clear what is being discussed.

    It was more a typo missed in editing than a mistake on Meyer’s part as if he doesn’t know the difference.

  111. Upright BiPed,

    You’ve been forced to back off your claim because someone had the unmitigated temerity to call you on it.

    That’s an . . . interesting interpretation of the situation. Not one I suspect an objective observer might endorse, though.

    As you yourself note, I explained my thought process in that previous thread:

    Your argument hinges on mistaking your map for the territory. You loosely model biochemical structures and reactions using the language of semiotics, then equivocate to conclude that a semiotic agent is required. Basically, as I said before, you’re trying to define your terms such that an intelligent agent is required.

    I then made it very, very clear that my conclusion was based on previous experience with such arguments and that you had failed to provide enough information about your particular version for me to answer further questions.

    If you disagree with what I wrote, please make your argument and explain why my interpretation is incorrect. If my supposition is incorrect, I will happily retract it.

    Continuing to demand answers to loaded questions lacking sufficient context is not a substitute for presenting a reasoned argument.

  112. …in living things, the probability of even a rare advantageous mutation propagating through the population has a strong positive bias (by definition).

    Even if we grant the case, this does not mean that the mutation will be fixed.

    In fact, by far the vast majority of even beneficial mutations are lost(according to current pop gen theory).

  113. ellazim,

    I know there are a number of GA libraries in C and C++, and I wouldn’t be surprised to find a couple in Ada. Pascal I’m not so sure about. I find dynamic languages like Python to be easier to use for the kind of exploratory coding that I usually do with GAs. Python is quite easy to pick up, especially compared to C.

  114. MathGrrl, I know your an expert on these matters, so have these wonderful GA’s developed by brilliant engineers, had there primary coding opened up to the random variation and natural selection process yet???

    If they have opened up the operating system as such, I really want to call Berlinski for saying this outright lie;

    “Computer simulations of Darwinian evolution fail when they are honest and succeed only when they are not.”
    David Berlinski

    ,,,Even doubting the sufficiency of Darwin to program computers in front of the nation in EXPELLED,,,

    Accounting for Variations – Dr. David Berlinski: – video
    http://www.youtube.com/watch?v=aW2GkDkimkE

    You can see my concern MathGrrl, and once we stop that Berlinski character, we have some more work to do,

    Refutation of Evolutionary Algorithms
    https://docs.google.com/document/pub?id=1h33EC4yg29Ve59XYJN_nJoipZLKIgupT6lBtsaVQsUs

    ,,,but with your persistence MathGrrl, in spreading the GA gospel, I am sure we can expose these frauds for who they are. I mean really MathGrrl who do these guys think they are for questioning the almighty power of evolution???

  115. ellazimm:

    I’ve got a question: Can you tell me a good online resource that I can access that explains GA programming?

    Clever Algorithms:
    Nature-Inspired Programming Recipes

    http://www2.econ.iastate.edu/t.....aintro.htm

    http://lancet.mit.edu/~mbwall/.....ntroToGAs/

    http://www.rennard.org/alife/e.....ntrgb.html

    Learn Ruby, then we can talk code to each other, lol.

  116. MathGrrl:

    Yeah, some of my website buddies like Python. I’ve used a bit of Perl and PerlScript and thought: hey, this is all looking like C and I ASSUMED that Python was like that too so I didn’t give it a try. Perhaps I shall . ..

    So basically you’re using predefined functions and procedures to do some of the processing. Which means semi-standard data structures, etc. I really should find the time. I had a play with ev the other day (Java Mac version) and thought: hmmmm . . . I’d like to see what’s going on under the hood . . .

    Anyway, thanks for the tips. Have fun with the thread!

  117. Mung: Ruby. That’s another one I’ve heard about. Ruby on Rails.

    Thanks for the links!!

  118. BA77: I don’t know exactly what Dr Berlinski what thinking or addressing but no one thinks their evolution program is modelling all of the evolutionary process. We don’t even understand it all yet so we can’t model it.

    But some people are honestly trying to model some aspects of some evolutionary processes. They don’t prove evolution happens/happened, but they do show, hopefully, that some aspects seem to fit in the proposed timeline or lead to some expected results.

    As far as I know, for the serious, published research the source code is available for anyone to look at. It’s hard to lie when the program is in the public domain.

  119. MathGrrl @107:

    David Goldberg’s Genetic Algorithms in Search, Optimization and Machine Learning is one of the classics.

    Quoting Goldberg:

    This book is about genetic algorithms (GAs) – search procedures based on the mechanics of natural selection and natural genetics.

    Now can someone tell me how to conduct a search with no target(s)?

    One must be searching for something. GA’s search for potential solutions to a given problem.

    More from Goldberg:

    Genetic algorithms are search algorithms based on the mechanics of natural selection and natural genetics. They combine survival of the fittest among string structures with a structured yet randomized information exchange to form a search algorithm with some of the innovative flair of human search. In every generation, a new set of artificial creatures (strings) is created using bits and pieces of the fittest of the old; an occasional new part is tried for good measure. While randomized, genetic algorithms are no simple random walk. They efficiently exploit historical information to speculate on new search points with expected improved performance.

    Genetic algorithms are theoretically and and empirically proven to provide robust search in complex spaces.

    Having been established as a valid approach to problems requiring efficient and effective search

    The genetic algorithm is an example of a search procedure that uses random choice as a tool to guide a highly exploitative search through a coding of a parameter space. Using random choice as a tool in a directed search process seems strange at first … The important thing to recognize at this juncture is that randomized search does not necessarily imply directionless search.

    Thus optimization seeks to improve performance toward some optimal point or points. Note that this definition has two parts: (1) we seek improvement to approach some (2) optimal point.

    Yup. It’s a good book. But it puts the lie to MathGrrl’s claims about ev. Will she now abandon her claim that ev is a GA?

  120. 120

    Mathgrrl,

    You explained your thought process?

    No you didn’t, you lodged an objection without substantiating it. You said that I was equivocating, and so I asked you “How”.

    Now you refuse to engage in an answer to that question.

  121. 121

    from the previous thread…

    - – - – - – -

    I have now asked you four times to substantiate your claim… How do you know when one thing is a code and another is not a code. You have repeatedly refused to substantiate this claim which you’ve already made.

    The reason for this is now painfully obvious; you can’t substantiate it, and you never could.

    What you can do however, is hope that I will start talking and give you something (anything) to attack in order to draw the glaring attention away from the fact that you’ve been called out to deliver (on a comment you’ve already made) and are unable to do so.

  122. Mung: Ruby. That’s another one I’ve heard about. Ruby on Rails.

    RoR is a web application development framework written in Ruby, so your website friends have probably heard of it. Ruby and Python are more alike than either is to C or Java.

    So basically you’re using predefined functions and procedures to do some of the processing. Which means semi-standard data structures, etc. I really should find the time. I had a play with ev the other day (Java Mac version) and thought: hmmmm . . . I’d like to see what’s going on under the hood . . .

    The original version of ev was written in Pascal. There’s also a C version available. The source code for all three versions can be downloaded from Tom Schneider’s site. Let me know if you want the links.

    So when MathGrrl tells me to read the papers I tell her to read the source code, lol. I’ve looked under the hood at all three versions of the source code.

  123. Mung: If an algorithm picks winners based on ‘who’ did something the best or got a higher ‘score’ then there isn’t a target per say.

    Let’s say you were trying to figure out a way to run wiring around a Boeing plane and you were using a GA to try and modify different approaches. (I’m making this up obviously.) You keep the approaches that were the cheapest and throw out ones that are more expensive. There is a task: find a wiring scheme, but there is no target. The fitter routines are the ones that are more efficient in this example.

    MathGrrl is that a decent explanation? Probably not. Tell me when to shut up.

  124. 124

    For you to stand there and suggest I need to explain myself so that you’ll know what you were objecting to is an embarrassment to reason.

    Simply admitting that you have no basis for claiming an equivocation on my part is the only dignified response to make.

    You are a materialist ideologue, hell with freeze over first.

  125. p.s. you’ll see a lot of similarities to Perl in Ruby, but it’s completely object-oriented.

  126. Continuing to demand answers to loaded questions lacking sufficient context is not a substitute for presenting a reasoned argument.

    STOP! The IRONY is killing me!

  127. ellazimm, since you believe that GAs, programmed by brilliant engineers, are fully capable of mimicking evolutionary processes, and even eventually reaching the point of ‘self-evolving’ to greater and greater heights of undreamt computational power, do you think it plausible that we are now living in some type of gigantic GA computer simulation that was programmed by some future humans???

    ,,,for example ellazimm, this following philosophical argument closely parallels what we should expect to see if evolutionary processes were truly unbounded in their information generation capacity, as neo-Darwinists hold, in computational evolutionary algorithms,,,:

    ARE YOU LIVING IN A COMPUTER SIMULATION? BY NICK BOSTROM
    Department of Philosophy, Oxford University

    VII. CONCLUSION

    A technologically mature “posthuman” civilization would have enormous computing power. Based on this empirical fact, the simulation argument shows that at least one of the following propositions is true: (1) The fraction of human-level civilizations that reach a posthuman stage is very close to zero; (2) The fraction of posthuman civilizations that are interested in running ancestor-simulations is very close to zero; (3) The fraction of all people with our kind of experiences that are living in a simulation is very close to one.

    If (1) is true, then we will almost certainly go extinct before reaching posthumanity. If (2) is true, then there must be a strong convergence among the courses of advanced civilizations so that virtually none contains any relatively wealthy individuals who desire to run ancestor-simulations and are free to do so. If (3) is true, then we almost certainly live in a simulation. In the dark forest of our current ignorance, it seems sensible to apportion one’s credence roughly evenly between (1), (2), and (3).
    Unless we are now living in a simulation, our descendants will almost certainly never run an ancestor-simulation.
    http://www.simulation-argument.com/simulation.html

    Thus ellazimm, according to your reasoning of virtually unlimited computational power in the future, either we are currently living in a computer simulation, or future humanity becomes extinct so as to run the simulation!!!,,, or, an option that was not mentioned above philosophical argument, GA’s are, in reality, extremely limited in their ability to optimize computers above what man has currently programmed them to achieve;

    My bet is on the latter,,, :)

    ========================

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    ======================

    Song by the world – Gimme Shelter – Inspirational Videos
    http://www.godtube.com/watch/?v=FJFM2FNU

  128. correction,, future humanity becomes extinct so as to NOT run the simulation!!!

  129. BA77:

    “ellazimm, since you believe that GAs, programmed by brilliant engineers, are fully capable of mimicking evolutionary processes, and even eventually reaching the point of ‘self-evolving’ to greater and greater heights of undreamt computational power, do you think it plausible that we are now living in some type of gigantic GA computer simulation that was programmed by some future humans???”

    I don’t think they ever will be capable of mimicking all evolutionary processes.

    And no I don’t think we’re living in some giant GA computer simulation. There’s no time lag. If I shoot a bullet at something there’s not enough time for the software and the wiring to respond unless there’s a severe time distortion . . . hmmmm . .. .. I still don’t believe it.

    I also don’t think evolutionary processes are unbounded in their information generating ability.

    “….GA’s are, in reality, extremely limited in their ability to optimize computers above what man has currently programmed them to achieve;”

    GAs are not optimising computers, where did that come from?? They are used to try and find better methods for processing some kind of tasks. They could be used to optimise some of the computers tasks though . .. hmmm .. . . in fact, I just read something about that . . . did it come up on one of the threads??

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010

    Interesting, I didn’t know Cantor was partially motivated by theology. Fascinating.

  130. “correction,, future humanity becomes extinct so as to NOT run the simulation!!!”

    At least I wouldn’t have to pay off the mortgage then.

  131. Well folks it’s late here in Ye Olde England so I’m off to bed.

    The God of the Mathematicians is pretty interesting, don’t let the discussion of the transfinite numbers and different sizes of infinity put you off.

    No comments about my attempt to differentiate between targets and tasks. Well, I don’t know if it’s right or not anyway. Just thought I’d try to see if I could build a bridge or two.

    GAs are separate from evolution simulations. GAs seem to be quite good at helping to find pretty good solutions to intractable problems. Evolution simulations are getting more sophisticated but they have a long, long, long way to go yet. AND they only do what we tell them too based on our understanding and some assumptions. Modelling is when you simplify the real situation to get at part of it, you know you’re missing some things, and that’s where evo simulators are now.

    Anyway, later all.

  132. Mung: If an algorithm picks winners based on ‘who’ did something the best or got a higher ‘score’ then there isn’t a target per say.

    So when Goldberg says that GA’s are a directed search, what does that mean? Directed towards what?

    If you query some oracle and it returns “warmer” or “colder” (or “higher” or “lower” if you want to think in terms of a landscape), how does the oracle determine which of the two values to return?

  133. But alas ellazimm, you actually DO hold that all the amazing diversity of life we see around us to be generated by the neo-Darwinian process, thus I find it extremely suspect that you would, all of the sudden, find such reservation for your imagination when these same evolutionary processes are projected forward as to their impact on man. ,,, Barrow and Tippler, of anthropic principle fame, had no such limit of imagination grasping the full implications that neo-Darwinism presented to the future of man, as is clearly illustrated in this video at the 6:45 minute mark;

    The Anthropic Principle – Fine Tuning Of The Universe – Michael Strauss PhD. – video
    http://www.metacafe.com/watch/4323661/

    In fact ellazimm, I think the computer sim argument is excellent for pointing out the inherent fallacy within ‘Evolutionary algorithm thinking’, of unbounded future computational power. In fact, materialism, upon which neo-Darwinism is built, always crumbles into absurdity when pushed to extremes, such as in the computer sim argument:

    Michael Behe has a profound answer to the infinite multiverse argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.
    http://www.uncommondescent.com.....ent-362912

    ==============

    Godel has another piece in that article;

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: Gödel’s personal God is under no obligation to behave in a predictable orderly fashion, and Gödel produced what may be the most damaging critique of general relativity. In a Festschrift, (a book honoring Einstein), for Einstein’s seventieth birthday in 1949, Gödel demonstrated the possibility of a special case in which, as Palle Yourgrau described the result, “the large-scale geometry of the world is so warped that there exist space-time curves that bend back on themselves so far that they close; that is, they return to their starting point.” This means that “a highly accelerated spaceship journey along such a closed path, or world line, could only be described as time travel.” In fact, “Gödel worked out the length and time for the journey, as well as the exact speed and fuel requirements.” Gödel, of course, did not actually believe in time travel, but he understood his paper to undermine the Einsteinian worldview from within.
    http://www.faqs.org/periodical.....27241.html

  134. Mung: I am just guessing you understand but . . .

    Directed in that you are trying to find a good solution to a problem? But not a particular solution. So no target.

    Of the options/choices that arise you pick the how-ever-many-warmest or highest? Isn’t the idea that you get a generation of options and you are keeping the ‘best’ and chucking the ‘worst’?

    You write code, take a look at the algorithms!! Don’t ask me!!

    BA77:

    “In fact ellazimm, I think the computer sim argument is excellent for pointing out the inherent fallacy within ‘Evolutionary algorithm thinking’, of unbounded future computational power. In fact, materialism, upon which neo-Darwinism is built, always crumbles into absurdity when pushed to extremes, such as in the computer sim argument:”

    Good think I didn’t make the computer sim argument then!! Are you sure you’re arguing with me? I don’t see how believing in common descent with modification implies some hideous Matrix-like future for humans. The laws I support and vote for are non-Darwinian so . . . Maybe I haven’t paid enough attention. I think you’re assuming I’m saying something I’m not so I have to admit my attention did wander.

  135. Mung: Sorry, that first line is subject to mis-interpretation.

    I meant I’m just guessing, you understand, but . . .

    NOT: I’m just guessing YOU understand but . . .

    Punctuation does matter. Sigh. Need more tea.

  136. No comments about my attempt to differentiate between targets and tasks. Well, I don’t know if it’s right or not anyway. Just thought I’d try to see if I could build a bridge or two.

    And it’s appreciated. I’ve been trying to get MathGrrl to participate in a discussion about what constitutes a target.

    GAs are separate from evolution simulations.

    I agree with you.

    Confusion arises when someone uses a GA in order to simulate evolution, which is what happened with ev.

  137. According to Stephen Matheson, a developmental cell biologist at Calvin College, Dr Meyer made a basic error on page 66 of Signature in the Cell mistaking a virus for a bacteria. Is that true??

    There are so many mentions of bacteria in the passage that one has to wonder how Matheson could even reasonably be confused about whether Meyer knows the difference.

    For more on Matheson’s “review,” including this particular incident, see Ch. 21:

    http://www.discoveryinstitutep.....ntroversy/

    Any thought as to why Matheson has yet to update his comments?

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