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The Edge of Peer Review

Robert Pennock’s Nature article with Richard Lenski on the evolutionary program AVIDA does not mention Michael Behe, irreducible complexity, or intelligent design (for a critique of that article, go here). And yet, when Pennock criticizes ID, the first thing he does is point to that article as a refutation of ID and, in particular, Michael Behe’s claim that irreducible complexity poses an obstacle to conventional evolutionary mechanisms. So, peer-reviewed articles that do not cite ID or its literature nonetheless constitute refutations of it, and yet peer-reviewed articles by ID proponents that do not explicitly mention ID (to avoid censorship) may not count as confirmations of it. The double-standard here is palpable. In this vein consider the following email I received:

Just writing to you to let you know that your work IS being used in peer review. Read the following link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1208958. It is a paper by Jack Trevors and David Abel about the three subsets of complexity in realtion to biology. . . . The sad thing is that Trevors and Abel have been continually publishing critical commentaries on the origin of information in peer-review without reference to any IDists, though most of their work looks like it came straight from A. E. Wilder-Smith. Don’t believe me? Go here http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15889338&query_hl=3
and then here http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15563395&query_hl=3. So, no one can say that your ideas on the origin of information are not in peer review.

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19 Responses to The Edge of Peer Review

  1. I anxiously ***await the day when Avida comes up with a step by step evolutionary path for a novel cell type, tissue type, organ, or body plan and that result can be confirmed by repeating each step in a laboratory using real matter instead of imaginary matter.

    ***I won’t be holding my breath while waiting… ;-)

  2. The interesting things about Avida are that (a) the steps must be explicitly dictated by the environment. This indicates that if the results of Avida were accurate (they actually aren’t) then it would have basically proven theistic evolution — the environment is set up in the exact way as to allow evolution to happen correctly.

    However, since the environment is nowhere near what Avida requires to produce “complex information”, this explanation is falsified.

    For proof that Avida is sneaking design in the back door, if you set the mutation by cosmic radiation to 50%, you still get functional things at the end. That’s like reproducing after being microwaved.

    I’ve got some commentary on Avida and links to even better commentary here:

    http://crevobits.blogspot.com/.....ithms.html

  3. P.S. Off topic

    Bush just nominated 3rd Circuit Court of Appeals Judge Alito for Supreme Court Justice. Alito is nicknamed by the liberal left “Scalito” because he’s like a clone of Justice Antonin Scalia.

    Scalia wrote the dissenting opinion in Aguilar part of which said that teaching pseudo-science is a shame but it isn’t unconstitutional. Alito’s confirmation by the US Senate will be a full three ring circus with the probability of a filibuster and thence the so-called “nuclear option” whereby senate procedural rules are changed to disallow filibuster in judicial advise and consent.

    This cements ID’s eventual victory over 1st amendment complainants. Public schools will be able to teach ID if their duly elected governing bodies so choose.

    Happy days are here again!

  4. A question about the Avida programing / model….

    now if the ” environment ” where Avida runs is set to a pre-convinced notion that would best give the result that the evolutionist are looking for, isn’t the answer or outcome of the product; a product of selective engineering ?.

    Should not the environment be set or be subjected to some kind of random process that would of existed millions or billions of years ago with to be accurate [ Rsc , Osc , Fsc ]?.

    Without having to be given “doggy biscuit treats” ? to jump or sit or move about ?.
    Did these so called “treats” exist in real life scenarios ?. What role did these “treats” play out in the natural scheme of Evolution that happened billions of years ago ?. Let me guess, doggy biscuits = Natural selection ?.Why run the test when you already know the answer or its outcome ?.

    Seems like this “experiment ” is more like the famous Miller-ray project ?

    Charlie

  5. Darwinists state that the “treats” are energy sources in the environment (i.e. food), and that mutations that happen to exploit otherwise unused energy sources are selected, and that many of these happen to be of greater functional complexity. It all sounds quite reasonable, which is probably why so many have fallen for it. The problem is that it’s never been tested in the real world, and virtual implementations of it don’t seem to work. In artificial life experiments (where cheating, such as excessive rewards and no 2nd law of themodynamics, is possible), actual unguided natural selection (not automated artificial selection as in the Avida research of Pennock, Lenski, and cohorts) has been observed to simplify things, not increase complexity. As any engineer can tell you, there are alot of ideas for processes and mechanisms that sound good, and even look good on paper, but contain fatal flaws that only show up when prototypes are made and tested. Everything seen to date reveals RM+NS as one such process/mechanism. There’s no substitute for testing in the real world.

  6. Avida is utter bullshit. I hope no tax dollars are being wasted on this foolishness.

  7. It would be interesting to know exactly what role Pennock performed for this Avida study.
    Did he do any of the lab work? Did he excute and analyze the program data? Did he write any of the report? The fact that he is on the team makes me believe the entire study was aimed at falsifying what is supposed to be, by definition unfalsifiable: namely Behe’s hypothesis of IC. So much for the worse for the criticism that ID and/or its related hypotheses aren’t testable or falsifiable. Avida proves conclusively that they are. Unfortunately for them, the Avida study, having no relationship to biological reality, leaves IC as a feature of biological systems both unscathed and unexplained via any Darwinian pathway. Make that one failed attempt to falsify IC.

  8. Good point Donald

  9. “yet peer-reviewed articles by ID proponents that do not explicitly mention ID (to avoid censorship) may not count as confirmations of it. ”

    Notice the usual clap-trap about censorship. Good ol’ conspiracy theory is much better than explicitly admitting the papers have nothing to do with ID.

    Look at Punctuated Equilibrium, that was a challenging theory at the time but has gained recognition.

    If IDist had any proof they could and would be published.

    They dont, so they use books and politics to forward their religious agenda.

    Dont Christians have some ethics about this sort of thing?

  10. “Darwinists”

    Darwin never left behind a book of doctrines. He does not have followers.

    You are mixing up theism for science.

  11. “The fact that he is on the team makes me believe the entire study was aimed at falsifying what is supposed to be, by definition unfalsifiable: ”

    The error is in your understanding. Behes’ claims that Irreducibly Complex systems could not evolve is a specific hypothesis that can be tested. It has been tested and it has been falsified. Avida is just one example of the falsafication.

    But that doesnt falsify claims that an intelligent designer could have been involved. How could it? Just because ‘A’ could arise naturally does not mean that it did. So, with ID you get a regular ‘zoooiiiing!’ sound as the goal posts leap around. An island could have gained it animal population via the usual means clining to wood, flying in, etc), but that doesnt mean that some/most of the fauna wasnt specifically put there. Just because people could have built the pyramids doesnt mean that aliens didnt.

    With IC, once we get past biology (which is easy to do, and already done) you get people arguing that the ‘fine tuning’ of the universe for our sort of life is proof of a designer, you get others arguing that waters unique abilities are evidence of intelligent design.

    Thus, while specific hypothesis may be falsified, the nameless designer can just hope around to a new area and the ID proponents can point and go ‘there, there, there…that’s proof!’

  12. “Unfortunately for them, the Avida study, having no relationship to biological reality”

    Except for implementing mutation and selection in a fitness landscape, which is the essense of evolutionary theory.

    It seems a lot of people here dont know what a simulation is. And I find it funny they focus on Avida? Why not focus on computer models of epidemeology, or aurodynamics?

    Chorus: Because those dont contradict their religious beliefs!

  13. “actual unguided natural selection has been observed to simplify things, not increase complexity.”

    You are mixing up ‘simple’ for ‘short’

    In my Avida runs I have seen several when a single species has taken over the field, but the genomes were not simpler, they were shorter, and thus more efficient (faster) at reproduction. Internally, larger organisms with 50 or so NOPs are simpler than an organism with 15 instructions with each being unique (except for a nop-a IIRC). It just reproduces slower.

    “Everything seen to date reveals RM+NS as one such process/mechanism. There’s no substitute for testing in the real world. ”

    This is the exact opposite of the truth.

  14. 2perfection: “Except for implementing mutation and selection in a fitness landscape, which is the essense of evolutionary theory.”

    The fitness landscape is provided by the programmers. If you say that this does reflect biological reality, then you are actually supporting a form of intelligent design.

    2perfection: “Why not focus on computer models of epidemeology, or aurodynamics? Chorus: Because those dont contradict their religious beliefs!”

    This brings up a good point. The reason that a lot of attention has been paid to Avida probably is because of the critics’ religious beliefs. But this doesn’t change the fact that in order to get it to do anything creative, the programmers have had to tell it what to do (i.e. it actually models evolution by random mutation and automated artificial selection, not natural selection). Other types of computer models used for research and development (e.g. computational fluid dynamics) actually bear out the scientific theories they are based on without the boundary conditions being falsified.

    2perfection: “You are mixing up ’simple’ for ’short’ ”

    As long as the fitness landscape is provided by the programmer(s), your answer is not relevant to Darwinian theory.

  15. “The fitness landscape is provided by the programmers.”

    Yes, because they are computer simulations.

    “If you say that this does reflect biological reality, then you are actually supporting a form of intelligent design.”

    Not at all. Simulations are simulations and reality is reality. The fact we can model reality on a computer does not mean that reality is designed, simply that it can be copied.

  16. The error is in your understanding. Behes’ claims that Irreducibly Complex systems could not evolve is a specific hypothesis that can be tested. It has been tested and it has been falsified. Avida is just one example of the falsafication.

    You missed the point. The anti-ID crowd has said endlessly that ID isn’t testable or falsifiable, and therefore notscientific. Now AVIDA comes along and supposedly falsifies what was previously claimed to be unfalsifiable. Something is amiss.

    Now, whether or not AVIDA succeeded in falsifying IC is different matter. I think you are incorrect because the study assumes the very thing it supposed to be demonstrating.
    If this study mapped to biological reality, then all the researches would have to do is point to the biological examples that demonstrate what it is that evolution requires to build up an IC system from scratch. No such biological examples exist. To claim that their study built in exactly what evolution requires is begging the question. Thus, AVIDA is a failed attempt at falsifying ID or IC.

    Behe – 1
    AVIDA – 0

  17. Notice the usual clap-trap about censorship. Good ol’ conspiracy theory is much better than explicitly admitting the papers have nothing to do with ID.
    ———–

    does 2perfection not live in the real world? did he miss all the news on sternberg? did he mention the recent post where the blog run by the professor refused to accept an entry from an ID proponent, and he didnt even bother to consider the argument? no one can claim with a straight face that peer review is dependent on the peers themselves and what they allow in…and we have scores of examples of ID proponents being refused even a hearing…and many of them hacve actually been attacked and campaigns to get them removed from their positions have been started. if darwinists (yes, they are darwinists if they follow his concepts) are out on a witch hunt to destroy anyone who dissents, then of course IDers have little chance of getting peer reviewed papers published or getting their ideas out on various blog sites, newspapers, the media, etc.

    these arent conspiracy theories- theyre clear fact. ask sternberg. ask Guillermo Gonzalez, who is being attacked for his views and many are trying to stifle is right to speak on the issue…ask those who participated in the smithsonian viewing of the priveleged planet when the smithsonian suddenly attacked them and demanded they pay for the showing and cancelled other things related to it.

  18. also- 2 perfection claims that IC has been falsified via avida. hello! avida does not represent reality! not in any way shape or form! so, he claims that a non-realistic computer program has falsified IC. but, you also notice that he claims: “They dont, so they use books and politics to forward their religious agenda.”– so, he claims ID is a religious ID, and thus it isnt science. then he claims that avida (a program that doesnt represent the real world we live in) has falsified IC.

    im tired of seeing these absurd contradictory claims. ID is religion not science. oh, and it doesnt matter because weve falsified IC which is a big part of ID! its either science or it isnt. plus, these scientists have to explain away the existence of IDers who dont think the designer is God- they must simply pretend they dont really exist…that these agnostics are actually figments of the imagination that can be ignored because theyre not real people with real bodies.

    the nonsense has to stop. darwinistic dogma might be the worst thing that has ever happened to science. they complain ID would be the downfall of science…but look at their easily refuted attacks of religion, look at their constant contradictions- THEY are the ones damaging science with their narrow view of what constitutes truth, their amazing just-so narratives that have no basis in reality, and so forth…

  19. 2perfection: How can you say that you had Avida runs where smaller genomes took over, by virtue of being smaller and thus more efficient at reproduction? In Avida, the merit of a genome grows at it gets larger, in order to avoid this very problem (otherwise, there would be selection pressure for small organisms, and not enough room to gather up mutations to create new organisms).

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