P.Z. Explains It

P.Z. Myers has a very helpful post up explaining the biological details behind the Michael Behe quote mine I reported on here. Basically, Behe’s treatment of the subject was even worse than I realized. Recall that Behe was arguing that straightforward reasoning from Darwinian principles led certain mathematicians astray in resolving problems related to morphogenesis. Myers replies as follows:

But there are other problems with Behe’s claim. What he’s about to explain are not “basic features of life”, but the specifics of metazoan pattern formation. We know already that there are multiple ways you can generate patterns in an organism; the “mistake” we saw made was that developmental biologists sensibly proposed the simplest explanation first, as wise old Ockham would have instructed us, and discarded that as more complications were discovered.

Another error by Behe: these were not ideas derived from “Darwin’s theory”. Darwin’s theory was a general description of how organisms evolved. He did not know anything about genes, morphogens, reaction-diffusion models, computers, or any of the concepts used in this kind of work.

And finally, the early conclusions were not opposite biological reality. The early modeling is still useful and can be used to explain what’s going on in, for instance, vertebrates; it simply turned out that the animal model used in early investigations of the molecular basis of pattern formation, Drosophila, is highly derived and has acquired some very specific, hard-coded regulatory elements on top of a general principle.

I have occasionally commented that one of the reasons I spend so much time pondering creationist claims is that I learn lots of real science by researching their errors. P.Z.’s post is a useful reminder of that fact:

Mathematicians weren’t “fooled”. They were trying to model how, for instance, a chemical gradient could be transformed into a reiterating pattern of specific activation of other chemicals. It was good stuff; read some of Hans Meinhardt’s modeling work, for instance, which was very useful in explaining patterns of gene activation, once the genes had been identified. It was also not just free-floating speculation with a computer–Klaus Sander, as one example, was an excellent experimentalist who postulated the existence of gradients of morphogens from perturbations of embryos before the specific molecular agents were identified.

Go read the whole thing!

Comments

  1. #1 Blake Stacey, OM
    June 24, 2007

    You’ve got an “&rduqo;” in there.

  2. #2 Jason Rosenhouse
    June 24, 2007

    Thanks. I’ve fixed the error.

  3. #3 PC@
    June 25, 2007

    One thing to remember in your chemicals to life scenario, chemical pattern to the Information in dna. That is the information DNA (and RNA) is free from any underlying constrants of the laws we find in chemistry. Thus chemicals to life scenario is implausible from first principle

  4. #4 Torbjörn Larsson, OM
    June 25, 2007

    That is the information DNA (and RNA) is free from any underlying constrants of the laws we find in chemistry. Thus chemicals to life scenario is implausible from first principle.

    First, origin of life isn’t a consideration within evolutionary biology which describes how already existing life behaves.

    Second, life as we know it is chemicals. The “NASA definition” is roughly a replicator obeying evolutionary processes, i.e. a chemical or sets of chemical that pulls that off can be considered life. And that happens to describe our cells as well.

    Third, if you read up on biology (say, on the site TalkOrigin), you can see that biology is about characteristics and functions, not information. For example, when you are reading this, your eyes (a characteristic) observes (a function) the reflected or transmitted light from your screen. And how characteristics and their functions evolves is described by evolutionary biology.

    Fourth, you are correct in that a description of biological characteristics and functions are mostly very well isolated from low level constraints in chemistry. (Though some cases such as energy constraints are not.) That is a factor that was favorable, perhaps necessary, for life to evolve.

  5. #5 PC2
    June 25, 2007

    Torbjörn Larsson states:
    First, origin of life isn’t a consideration within evolutionary biology which describes how already existing life behaves.

    Then you should be able to demonstrate clear change in bacteria that violates the principle of genetic entropy instead of just minor variations to the left and right that only degrade preexisting molecular function.

  6. #6 Torbjörn Larsson, OM
    June 25, 2007

    Torbjörn Larsson states

    Well, claims are more like it.

    A biologist writes:

    One should also note that the theory of evolution doesn’t depend on how the first life began. The truth or falsity of any theory of abiogenesis wouldn’t affect evolution in the least. ( http://www.talkorigins.org/faqs/faq-misconceptions.html#observe )

    And a summary description of evolutionary mechanisms shows why that is – nowhere is abiogenesis required in them.

    the principle of genetic entropy

    You forgot that “biology is about characteristics and functions, not information”. There is nothing called ‘genetic entropy’ within biology.

    Really, read a primer. For example http://www.talkorigins.org/faqs/faq-intro-to-biology.html .

  7. #7 PC2
    June 25, 2007

    Torbjörn Larsson,

    I would really like to see any example you have of a beneficial mutation to the genome that has caused evolution without degrading preexisting molecular function. Indeed there are quite a few scientists that would like to see this conclusive proof for evolution.
    If you can cot produce empirical evidence for evolution then you have not proved your case!

  8. #8 Tyler DiPietro
    June 25, 2007

    “Then you should be able to demonstrate clear change in bacteria that violates the principle of genetic entropy instead of just minor variations to the left and right that only degrade preexisting molecular function.”

    When you can actually define an entropy function for genetics, and rigorously lay it out so that it’s efficacy in measuring it’s object can be tested, get back to us. As it is this is just the typical creationist shell game of setting up motorized, all-terrain goalposts that can move on demand.

  9. #9 Science Avenger
    June 25, 2007

    there are quite a few scientists that would like to see this conclusive proof for evolution

    More MSU. Mathematicians like proofs. Physicists and biologists like evidence. IDer/creationists like rhetoric.

  10. #10 PC2
    June 25, 2007

    Tyler:
    The entropy function is called CSI, complex specified information, which is laid out by Dr. Dembski, which rigorously quantifies the irreducible complexity of biological systems pointed out by Dr. Behe. So the efficacy in measuring it’s object can be tested rigorously by a proven method of empirical rigor rooted in unimpeachable math. If you want I will get you the latest papers which goes into the details of his proofs.

  11. #11 PC2
    June 25, 2007

    P.S. I would still like to see a empirical proof for evolution through mutation to a genome that does not in reality reduce the functionality of the organism

  12. #12 Tyler DiPietro
    June 25, 2007

    The entropy function is called CSI, complex specified information, which is laid out by Dr. Dembski, which rigorously quantifies the irreducible complexity of biological systems pointed out by Dr. Behe. So the efficacy in measuring it’s object can be tested rigorously by a proven method of empirical rigor rooted in unimpeachable math. If you want I will get you the latest papers which goes into the details of his proofs.

    You might want to take precaution before issuing such a condescending tone. I am familiar with computational complex and information theory, and like everyone else with even a perfunctory backround in the subject matter I know that Dembski’s CSI is pseudomathematical twaddle. I’ve read his “papers” and they are nothing but warmed over think pieces that demonstrate nothing, and needless to say contain no rigorous research. And furthmore, they haven’t been published in either a peer reviewed biology, mathematical or theoretical computer science journal. It’s hardly “unimpeachable”.

  13. #13 PC2
    June 25, 2007

    Well Tyler,
    I guess since you don’t accept the mathematical evidence of Dr. Dembski and even call it pseudomathematical twaddle, I will have to hope you respect empirical validity for your hypothesis of evolution. On what specific empirical evidence do you base your belief of evolution on? I truly want to know which mutation to which genome is the conclusive empirical evidence you have. I’ve looked at numerous examples and they all turn out to decrease the functionality of the information in the genome. If you could humor me in this respect I would appreciate it.

  14. #14 Science Avenger
    June 26, 2007

    PC2 said: CSI … rigorously quantifies the irreducible complexity of biological systems…

    Fine. Choose a biological system and tell me what it’s irreducible complexity is. Dembski yaps a lot about what CSI isn’t, but not too much on what it is.

    So the efficacy in measuring it’s object can be tested rigorously by a proven method of empirical rigor rooted in unimpeachable math.

    Except that the mathematicians think Dembski’s math is crap. See Mark Chu-Carroll’s fisking here.

  15. #15 Tyler DiPietro
    June 26, 2007

    “I guess since you don’t accept the mathematical evidence of Dr. Dembski and even call it pseudomathematical twaddle…”

    That isn’t simply my estimation of Demsbki’s work, it’s the estimation of just about every credentialed expert whose taken a look at it. This would, in fact, include one of the co-authors of the Optimization theorem (“No-Free Lunch”) that he took the liberty in abusing to construct creationist flapdoodle. He isn’t a renowned figure in the pertinent fields, and those practioners who know of him almost universally regard him a charlatan.

    “On what specific empirical evidence do you base your belief of evolution on?”

    On just about every piece of biological evidence uncovered since Darwin and even some prior. This article would be a good place to start.

    “I’ve looked at numerous examples and they all turn out to decrease the functionality of the information in the genome.”

    If you’d even bother to define what you mean by either “functionality” or “information” or what would count as a “decrease” in either, I’d be more inclined to comply. But your use those terms indicates that you’re playing the typical creationist shell-game of leaving your motorized goalposts running so you can move them at will.

    Try googling the “Nylon bug”, a bacterium that can digest nylon (an artificial polymer that didn’t even exist 100 years ago). Does that no count as a mutation increasing the “functionality” of the genome?

  16. #16 Science Avenger
    June 26, 2007

    I guess since you don’t accept the mathematical evidence of Dr. Dembski and even call it pseudomathematical twaddle, I will have to hope you respect empirical validity for your hypothesis of evolution.

    “Mathematical evidence”? Obviously you wouldn’t understand any of the biological evidence, which I guess explains your confusion.

  17. #17 Brian
    June 26, 2007

    See, but a frameshift mutation, as in the flavobacterium hydrolase, is somehow a “decrease in information.” I can say that because I’ve never defined what a “decrease in information” is. Which is what, I think, PC2 meant. Because clearly antibiotic resistance is an increase in functionality. But evolution is still wrong because everything is a “decrease in information.”

  18. #18 Richard Simons
    June 26, 2007

    The entropy function is called CSI, complex specified information, which is laid out by Dr. Dembski, which rigorously quantifies the irreducible complexity of biological systems pointed out by Dr. Behe.

    You realize that Behe’s ‘irreducible complexity’ is the same as the ‘interlocking complexity’ that Herman Muller, in 1918, predicted could be expected as a consequence of evolution?

    If CSI rigorously quantifies the irreducible complexity of biological systems you will presumably have no trouble in giving us comparable figures for two organisms. Please show us. If you can’t manage that, at least tell us what units are used to measured it.

    If even that is beyond you, perhaps you should reconsider whether you (or Dembski) have any grasp on the subject.

  19. #19 Brian
    June 26, 2007

    And, on the subject, I think it’s time to start coming up with a CSI for God. An omnipotent being has to be far less likely than a staphylococcus. And, since everything is clearly reduceable to its probability of occurring, and you can make up those probabilities at will, then God is impossible.

  20. #20 Science Avenger
    June 26, 2007

    PC2 said: … I’ve looked at numerous examples [of mutations to genomes] and they all turn out to decrease the functionality of the information in the genome.

    This is easily disproved with simple math and the fact that genomes can change one way, and then back again (ie ATA -> ATG -> ATA). Now we assume:

    the functionality of ATA = f(ATA) = X
    f(ATG) = Y

    Thus, according to PC2′s assumption, f(ATA -> ATG) = X – Y > 0 => X > Y. But also according to PC2′s assumption, f(ATG -> ATA) = Y – X > 0 => Y > X.

    Thus his assumption is disproved by contradiction, and that’s granting the unwarranted premises that these terms are meaningfully defined in the first place. PC2 is just anothe MSU practitioner.

  21. #21 jotetamu
    June 27, 2007

    PS2

    Don’t be discouraged. If you really want to learn anything, stick with it. But please, follow the suggested links or google around a bit to get some basic information about chemistry, biology and maths, including information theory. Avoid at all costs just repeating the same old well-known creationist points: if you do, you will no longer be taken seriously; but if, after doing a bit of homework, you have sincere questions, we are here to help you.

    Jim Roberts

  22. #22 Torbj�rn Larsson, OM
    June 28, 2007

    PC2:

    Sorry for late response, trying to catch up now.

    I would really like to see any example you have of a beneficial mutation to the genome that has caused evolution without degrading preexisting molecular function.

    A mutation as such may not cause evolution if it isn’t fixed.

    So, to make your question meaningful, let’s assume a minimal model of variation and selection, disregarding drift and other mechanisms for fixation (evolution) of traits. That means we must consider a population.

    It is generally the case that strong selection constrains the remaining variation in the genome of a population. So while the population becomes more fit now, it may be less fit later.

    And indeed most species die out eventually, perhaps in some cases because they haven’t time to recover the earlier variation of alleles.

    This is however not a problem for continuing life, adaption and speciation – enough individuals survive.

    As other commenters, I hope you see that the above shift of perspective, to check out what the theory really describes and predicts, is helpful for you.

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