Matzke on Meyer: the blind leading the blind

http://pandasthumb.org/archives/2013/10/meyer-on-medved.html

Major criticisms of Darwin’s Doubt by informed critics:

1. Meyer’s book, which is supposed to be about the Cambrian Explosion, gets the Cambrian Explosion fossil record wrong.

2. Meyer says that transitional fossils for the Cambrian groups don’t exist, but fossils with morphology transitional between the crown phyla do exist, oodles of them.

3. Meyer claims that phylogenetic methods are worthless, but doesn’t know that phylogenetic hypotheses are statistical statements and are statistically testable through standard methods – methods which themselves are testable and well-tested.

4. Meyer claims that the evolution of new genetic information is virtually impossible, a claim he is able to sustain mostly because he doesn’t understand the phylogenetic methods (see above) that are necessary for inferring the history of the origin of genes.

5. Meyer’s claim that “massive amounts” of new genetic information was required for the Cambrian Explosion is belied by the fact that gene number, and most of the key developmental patterning genes are shared broadly across the phyla, and even outside of bilaterians, rather than looking like they originated in the midst of the divergence of the phyla.

6. Meyer claims that the “junk DNA” hypothesis has been refuted, and that therefore the 90+ percent of large animal genomes that doesn’t code for genes or gene regulation is actually a massive additional amount of new information, but Meyer doesn’t rebut or even acknowledge the massive, basic, evidential problems with this idea.

6a. Simple calculations show that if most of the DNA in large-genomed organisms like humans was essential, given known mutation rates, we would die from fatal mutations each generation. This was Ohno’s original argument for junk DNA, and it has not been rebutted by ENCODE, the creationists, or anyone else.

6b. Genome sizes in complex animals and plants vary by orders of magnitude within many specific groups (tetrapods, onions, ferns, salamanders, arthropods, whatever), but despite this, within each group they all have about the same number of genes, and approximately the same organs and developmental complexity.

6c. When you actually look at the sequences in the variable fraction of the genome, most of it looks like the product of mutational processes with no selective filtering – transposon remnants, fossil viruses, duplications and other mutational errors, etc. Furthermore, unlike genes and important regulatory regions, which are well-conserved between closely related species, the apparent junk DNA looks like it has no constraint.the same organs and developmental complexity.

Edited to fix 6c.

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31 thoughts on “Matzke on Meyer: the blind leading the blind

  1. Oh, and then there’s no actual design explanation for anything. No evidence for anything that would have the desire and ability to make organisms for no apparent purpose, and none of the rational leaps beyond what evolution can do that one would reasonably expect from intelligence.

    The long ignored complaint against ID that bears repeating precisely because it is ignored as the ID-science-killer that it in fact is.

    Glen Davidson

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  2. C’mon petrushka, you know that citing the criticisms provided by professional paleontologists and recognized experts in the Cambrian biota over Meyer’s ignorant bumbling and deliberate misrepresentations isn’t allowed!.

    Everyone has to read Meyer’s latest recycled garbage for themselves in order to form a valid opinion on Meyer’s ideas. Just like every IDiot Creationist always reads On The Origin Of Species before their rabid attacks on Darwin’s Theory of Evolution.

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  3. At least everyone must respond to his book. He seized initiative.
    The reason the word explosion has always been made by all who study the cambrian explosion is because of the sudden appearance of life forms in great complexity relative to the fossil record’s record of before that time.
    A great assemblage is apparent and claims of a few intermediates is irrelevent.
    If evolutionists want to discredit such a important book then officially banish the term CAMBRIAN EXPLOSION. Words mean things.
    If there was no explosion then commit to it. Repent of previous explosion acceptance.
    I read the CE claim decades ago and by evolutionists.
    Anyways its all a humbug.
    its attempting to draw biological conclusions from geological settings containing biological data points.
    Its not biological science at play here and so its not science investigating evolution here by all tribes.

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  4. Robert Byers,

    Repent of previous explosion acceptance.

    Repent? Wrong room, Robert. Down the corridor, third on the left. Grab yourself a scourge on the way in.

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  5. thorton,

    A figure emerges from the shadows, clutching for your lapels. In a voice hoarse from overuse, it croaks “Have you read …. [cough] … the book!”.

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  6. 1. Pendantry. what? we’re gonna watch dueling citations, argumentation over the length of the cambrian explosion which doesn’t alter one iota the fact that replication acting on random heritable variation can only handle its day job as a maintenance junkie.

    2. Argument from assertion, argument from authority, argument from ignorance. A trifecta. If we only compare similarities, we could come up with an appearance of transition. If we compare both similarities and dissimilarities we come up with a composite result. So logically replication acting on random heritable variation is not the most satisactory blanket explanation. Rather front-loaded programming, where the original mother cell gives birth to the first forms then fades away is the better blanket explanation. In fact when Behe proposed such a scenario, he was laughed off. Yet, if I remember correctly such a scenario is being taken seriously now.

    Mind organized and kick started the symphony then went off for a smoke, impressed with the skill and artistry of the musicians. Mind never left, mind’ you, the sheet music is still there…what you can’t see it? but the smoke trails are gone, I’ll give you that.

    3. Phylogenetics creates an explanation for the relatedness of organisms. It provides absolutely no evidence to support the claim that replication acting on random heritable variation is the cause of that relatedness; Meyers point that Matzke et al of course wont touch that with a 1MY pole.

    4. No, see above. Meyer’s claim is that evolutionists are erroneously using phylogenetics as supporting evidence for replication acting on random heritable variation being the cause of the Cambrian explostion. Evolution is a maintenance junkie, not a building contractor.

    5. STFW!!! explain the presense of these genes and how they were responsible for the explosion. What was that ??? Replication acting on heritable variation is the engine you say??? Cooked and ate that turkey ages ago. Lets try the ham, shall we?

    6. Bold assertion. Dueling citations, again??? Plenty of new information coming out that non-coding DNA is responsible for plenty of stuff. Matzke is guilty of evolution-of-the-gaps. We haven’t pinned down what ALL of the non-coding DNA is doing, therefore it’s not doing anything. Patience man, patience. A trickle, then a flood.

    6a. Who said anything about ALL of it needing to be essential. Are two eyes, two arms, two legs, two cranial hemispheres essential? No. Again, argument from ignorance. Knock-out experiments do not provide supporting evidence for non-function, but rather for non-essential function. Phew, its smokey in here!

    6b. STFW!!! Argument from ignorance. Give science an opportunity to flesh out what types of functions are present. Then we’ll here the refrain ” So that’s what it does. Well I’ll be damned!” Then, they’ll here the reply “We told you so!!? Then the counter-reply “Shut up, will you? You get on my nerves”. Then the counter-counter reply ” You need a drink!” and finally the surrender, “OK, whatever you want; I’ll be Catholic, Jewish, Turkish, whatever, but please, please kill the ‘1,000 mile journey starts with a single step” virus!

    6c. Alas, more argument from ignorance. IDist say if it quacks like a duck….evolutionists reply it only looks like a duck, but its not really a duck. Evolutionists say if it quacks like a duck……IDists say you haven’t bothered to look. Oh, and by the way weren’t you just arguing that ducks are not always ducks. Whatsupwiththat?.

    The truth is probably somewhere in between; an element of junk due to degradation from environmental wear and tear with the majority still functioning. For now anyways.

    So, enough of the ignorant arguments, Matzke. Meyers is kickin’ your intellectual arses……not a pretty sight.

    How does the saying go? “The one that screams the loudest is guilty”.

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  7. which doesn’t alter one iota the fact that replication acting on random heritable variation can only handle its day job as a maintenance junkie.

    You contradict Behe, but then you are obviously more qualified than Behe.

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  8. Steve:
    So logically replication acting on random heritable variation is not the most satisactory blanket explanation. Rather front-loaded programming, where the original mother cell gives birth to the first forms then fades away is the better blanket explanation.

    The front loading hypothesis has already been disproven by the Lenski Long Term E coli Experiment. Twelve identical colonies were all started from the same cloned individual organism. All twelve were subjected to identical environments and selection pressures. All twelve evolved noticeably different genomic changes, including the famous lineage that evolved the ability to digest citrates. If front loading was present you’d expect to see all twelve lineages evolve the same changes, but they didn’t. Also, samples from each generation were saved which allowed the experimenters to try and “turn back the clock” and restart from a know position. When this was done the new lineages also followed different evolutionary paths than the originals.

    Claiming cells were ‘front loaded’ with all the genetic variations we see today is as dumb and as unsupported as claiming the dice in Las Vegas were all “front loaded” with numbers that let the house win all that money over the years.

    In fact when Behe proposed such a scenario, he was laughed off.

    As well he should be.

    Yet, if I remember correctly such a scenario is being taken seriously now.

    Like most Creationists you remember wrong.

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  9. Front loading. Heh. So the ur-genome was an elephantosalmonelloaktulipostrichosnailo[…]sparrowhawkodon?

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  10. Lizzie: It may be a saying, but it is clearly untrue.

    Must be Biblical, like the mother who screamed to Solomon to save her child. The quiet one was clearly innocent.

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  11. Steve: Phylogenetics creates an explanation for the relatedness of organisms. It provides absolutely no evidence to support the claim that replication acting on random heritable variation is the cause of that relatedness; Meyers point that Matzke et al of course wont touch that with a 1MY pole.

    It’s Meyer that won’t touch it. He won’t even touch the phylogenetic evidence for relatedness. In fact, he implies (but won’t quite say) that phyla just appeared ex nihilo somewhere during the Cambrian period.

    Even though the phylogenetic evidence says quite otherwise.

    You are correct of course that relatedness doesn’t tell us how diversification occurred, merely that it did.

    But given that phylogenetics tells us that it did, Darwin’s proposal works pretty well as an explanation (but throw in drift as well).

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  12. Darwin’s proposal works pretty well as an explanation (but throw in drift as well).

    aka descent with modification.

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  13. Lizzy,

    t’s Meyer that won’t touch it. He won’t even touch the phylogenetic evidence for relatedness. In fact, he implies (but won’t quite say) that phyla just appeared ex nihilo somewhere during the Cambrian period.

    The argument for evolution is multidimensional, and it is stupid and dishonest to focus on one dimension, such as fossil evidence and claim it isn’t biological or doesn’t “prove” descent.

    Of course fossil evidence doesn’t prove descent. It is one facet of the argument. Other pieces include the observation of variation and selection by plant and animal breeders, the detailed experiments of Lensky and Thorton and others, genomics, and more.

    Let one of the evolution critics participate as juror and come back here and discuss how evidence is evaluated.

    It’s interesting that many ID supporters are lawyers, but none seem to have a clue about jury instructions. None of them have the guts even to bring it up.

    ETA:

    People are routinely convicted or exonerated on less evidence than we have for common descent. If fact it is often exactly the same kind of evidence as used for common descent, except the courts accept an abbreviated version of DNA matching, compared to that used by biologists.

    So Barry Arrington et al presumably support a legal system that makes life and death decisions on evidence that would be considered skimpy by biologists.

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  14. Steve,

    we’re gonna watch dueling citations, argumentation over the length of the cambrian explosion

    There is no duel over citations regarding the duration of the Cambrian. Whatever gives you the idea that there is any controversy among authorities?

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  15. sure there are. what to include and what not to include. isn’t that what Matzke is complaining about. Myers purposefully narrowing the length of CE to bolster his claims and Matzke insisting that such and such must be included, thus in turn bolstering his own claim that replication acting on random heritable variation (say RARHV for short) is not only a plausible mechanism but the only game in town.

    Yet, Myer specifically addresses his characterization of the length of the CE based on recent authority speaking to this issue.

    So if we must, if we must tread softly and speak with a deferential, polite voice then lets go with ~ there are rather noticable ‘differences of opinion’ on the matter, which both sides can bend to their iron wills.

    Yet, the EiTR is STFW.

    petrushka:
    Steve,

    There is no duel over citations regarding the duration of the Cambrian. Whatever gives you the idea that there is any controversy among authorities?

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  16. Steve,

    Phylogenetics creates an explanation for the relatedness of organisms. It provides absolutely no evidence to support the claim that replication acting on random heritable variation is the cause of that relatedness;

    That’s incorrect. See this post.

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  17. thorton,

    First off, pleasantly surprised at your ‘rhetorical’ restraint. I won’t ask whatsupwiththat? but just hope its a trend reversal signal I can bank on.

    As you to assertion regarding Lenski, it could not be evidence against front-loading unless the programming was piss-poor. Rather, all you need to do is consider your first sales call to some scraggly corner of the city bordering the boondocks. You lean on your trusty iphone, with google maps and all.

    Then, then, you notice the area is in a grid pattern. There are myriad ways to get there. I can turn right, then left, then right, straight, then left and left again. Or I can go straight, then right, then right, then left and left again, on and on. I get there within approximately the same time.

    Now, i find out this is a good customer and start making routine visits. But its not always me who goes on the calls. sometimes my colleagues will fill in when I am backlogged with calls. I tell them how to get there. They report back that they found a bit shorter route. Another colleague reports back that they had to take another route due to construction work, but didnt loose much time.

    Point being, bacteria arriving at different solutions to the problem of digesting citrate speaks to variable, flexible, dynamic programming. It does not speak to random, goal-less biological activity.

    The fact that bacterium kick in genetic algorithms to save themselves from starvation speaks extremely loudly to state-of-the- art programming. Again, from whence did genetic algorithms come? Why evolve algorithms if physic and chemistry is sufficient.

    Or are you saying that physics and chemistry do math problems in their spare time?

    The front loading hypothesis has already been disproven by the Lenski Long Term E coli Experiment. Twelve identical colonies were all started from the same cloned individual organism. All twelve were subjected to identical environments and selection pressures. All twelve evolved noticeably different genomic changes, including the famous lineage that evolved the ability to digest citrates. If front loading was present you’d expect to see all twelve lineages evolve the same changes, but they didn’t. Also, samples from each generation were saved which allowed the experimenters to try and “turn back the clock” and restart from a know position. When this was done the new lineages also followed different evolutionary paths than the originals.

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  18. Steve,

    The fact that bacterium kick in genetic algorithms to save themselves from starvation speaks extremely loudly to state-of-the- art programming.

    Only one single bacterium, out of countless trillions, kicks in this supposed ‘genetic programming’. What of the rest? The whole set of bacteria doesn’t change; the amended founder leaves descendants. It looks exactly like mutation.

    You misunderstand the experimental setup.

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  19. Steve: Point being, bacteria arriving at different solutions to the problem of digesting citrate speaks to variable, flexible, dynamic programming. It does not speak to random, goal-less biological activity.

    Perhaps you could give an example of what you would expect to see in each case?

    You know, design an experiment that would determine if what was happening was random, goal-less biological activity or variable, flexible, dynamic programming.

    And that way you’d actually have evidence for your claims. Then they’d be more then claims. But you and yours are not actually interested in that sort of thing are you? If you were, you’ve had decades to do it in already.

    So, propose an experiment that would determine if this “programming” you claim helps cells in certain circumstances really exists. The Templeton people will likely fund you! I’ll even help you write the proposal, if you can detail your proposed experiment in any level of detail!

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  20. One of the outcomes of the Lensky experiment is that a tiny population of bacteria, all descended from.one individual, can and will try every possible point mutation.

    That’s complete and total refutation of the hypothesis that mutations occur as a result of foresight or anticipated need.

    Shapiro — who is friendly to the notion that evolution is smart — also agrees that there is no foresight.

    As for the duration of the Cambrian, there is no controversy. Meyers simply misrepresents the duration with bullshit phrases designed to imply that tens of millions of years is near instantaneous.

    He also ignores or misunderstands that the genes that enable body plan divergence were already in existence in the precambrian.

    All in all he’s either ignorant or dishonest. Or both.

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  21. On of the conceptual errors of ID is exaggerating the size of the search space traversed by evolution.

    Evolution doesn’t start from scratch. It always modifies what already works, and it does so by feeling its way. If you must have a metaphor, it’s like sending out shoots or seeds, some of which arrive on fertile ground. But never far from the source.

    The scattering of seeds is an effective strategy for exploring a region of space, and mutation is an effective strategy for exploring functional space. There is no need to bias the search. And no way to know in advance what will work and what won’t

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  22. Steve:

    Point being,bacteria arriving at different solutions to the problem of digesting citrate speaks to variable, flexible, dynamic programming.It does not speak to random, goal-less biological activity.

    As expected, you don’t understand the experiment or the results.

    Bacteria didn’t arrive at different solutions to the problem of digesting citrates. One E coli bacterium in 1 of the 12 colonies did, and the mutations were so successful it took over that colony. None of the millions of other bacteria in the other colonies found any way to digest citrates, even though all the bacteria in the experiment started with the identical genetic ‘programming’.

    Where is your evidence of any species anywhere being the result of this genetic ‘front-loading’? You may as well claim magic pixies did it. You have no mechanism, no timeline, no testable hypotheses so no falsification criteria, and of course no Front-Loader.

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  23. One could safely conclude from the Lensky experiment that the program tries everything and keeps anything that works.

    It’s a pretty powerful program.

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  24. petrushka:
    One could safely conclude from the Lensky experiment that the program tries everything and keeps anything that works.

    It’s a pretty powerful program.

    When I was messing around with some toy projects I was actually quite taken aback at the quality of results that can be achieved with just a few lines of code.

    I could never perfectly solve the TSP with mathematical methods but I can, and have, written a (frankly trivial) GA that’ll generate good solutions for crazy big maps and even hit perfection for smaller maps.

    So, um, iterative testing is extremely powerful even in it’s barest, simplest form. I hope in the coming months to put some web toys up along these lines.

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