Matzke on Meyer: the blind leading the blind

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.

The Three Acts of the Mind

How does mind move matter? To me, the question appears rather uninteresting. A simple collision is all that’s required to move matter.

How does the mind act at all, and what are the acts of the mind?

1. Simple apprehension
2. Judging
3. Reasoning

Alan Fox asserts that knowledge consists of apprehension.

Elizabeth Liddle claims that she agrees with Alan, but fails to incorporate her belief in the construction of mental models with Alan’s reductionist denial of the incorporation of mental models.

Does knowledge consist only of what can be sensed, as Alan Fox claims?

Or does knowledge consist of only what can be sensed and modeled, as Elizabeth claims?

Can science resolve the question of what can be considered knowledge, as Alan Fox claims?

How does mind move matter

One big problem, as I mentioned here, and elsewhere, with ID as a hypothesis is that it is predicated on the idea that mind is “immaterial” (or at least “non-materialistic”) yet can have an effect on matter.  That’s the basis of Beauregard and O’Leary’s book “The Spiritual Brain”, as well as of a number of theories of consciousness and/or free will.  And, if true, it makes some kind of sense of ID – if by “intelligence” we mean a “mind” (as opposed to, say, an algorithm, and we have many that can produce output from input that is far beyond anything human beings can manage unaided, and can in some sense be said to be “intelligence”), we are also implicitly talking about something that intends an outcome.  Which is why I’ve always thought that ID would make more sense if the I stood for “Intentional” rather than “Intelligence”, but for some reason Dembski thinks that “intention”, together with ethics, aesthetics and the identity of the designer, “are not questions of science”.

I would argue that intention is most definitely a “question of science”, but that’s not my primary point here.

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Meyer’s Money Shot

DD18.7There is plenty wrong with Meyer’s book, Darwin’s Doubt.  I have outlined some of the logical inconsistencies and false assumptions myself, and professional palaeontologists have pointed to more far-reaching inadequacies.

But even granting his flawed logic and false premise, there is a major problem with his conclusion.

He puts it succinctly in Chapter 18 thus:



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Plantinga’s EAAN: Criticism and Discussion

Alvin Plantinga’s Evolutionary Argument Against Naturalism has attracted a great deal of serious critical discussion (e.g. Naturalism Defeated?) and has had a substantial impact on ‘popular’ appraisals of naturalism.  (For example, William Lane Craig frequently uses it, and it also appears in the dismissal of naturalism in The Experience of God.)  Many philosophers have pointed out various problems with the EAAN, and in my judgment the EAAN is not only flawed but fatally flawed.  Nevertheless, it’s a really interesting argument and it could be worth exploring a bit.  I’ll present the argument here and then we can get into it in comments if you’d like — though I won’t be offended if you’d rather spend your time doing other things!

The EAAN has gone through various iterations, but here’s the latest version, from Where the Conflict Really Lies: Science, Religion, and Naturalism (2011).  Intuitively, we regard our cognitive capacities — sense-perception, introspection, memory, reasoning — as reliable, where “reliable” means “capable of giving us true beliefs most of the time” (subject to the usual caveats).  Call this claim R (for ‘reliable’).   But how probable is R?

Suppose that one accepts evolution (E) but also affirms naturalism, defined here as the belief that there is no God or anything like God (N).  What is the probability of R, given N & E?    One might think it’s quite high.  But Plantinga thinks that, however high the probability of R, nevertheless the probability of R given N&E is low or inscrutable.  Why’s that?

Now, here’s the key move (and in my estimation, the fatal flaw): beliefs are invisible to selection.  Why?  Because selection only works on behavior.  If an unreliable cognitive capacity is causally linked to adaptive behavior, then the unreliable capacity will be selected for (i.e. not selected against).  Even a radically unreliable capacity — that one never or almost never yields true beliefs — can be selected for.  Selection only “cares” about adaptive behaviors, not about true beliefs.  (More precisely, we have no reason to believe that the semantic content is not epiphenomenal.)

So, Plantinga thinks, given N&E, the probability of R is very low. But, if the probability of R is low, given N&E, then that should ‘infect’ the likelihood of all of the beliefs produced by those capacities — including N&E themselves.  So, given N&E, we should it think it extremely unlikely that N&E is true.  And so the initial assumption of N&E defeats itself.  (Here I’m being much too quick with the argument, but we can get into the details in the comments if you’d like.)

Anyway, it’s a really cool little argument, and it’s not immediately clear what’s wrong with it — and I thought it might be worth discussing, given how influential it is.



The Idea of “Pseudo-Science”

When I was poking my nose around philosophy of science in the 1990s, I was told that Larry Laudan’s critique of “the demarcation criterion” had pretty much scuppered the very idea of “pseudo-science.”    Since I don’t work in philosophy of science, but take a keen (and amateurish) interest in the debates about creationism and intelligent design, I found this unfortunate.

Imagine my surprise, then, when I found that some philosophers of science still take the idea of “pseudo-science” seriously and are intent on rescuing it from Laudan’s criticism.  First, I bring to your attention a recent NY Times article, “The Dangers of Pseudo-Science” (part of the usually excellent NY Time series The Stone, which brings philosophy out of the rarefied atmosphere of academia into the very slightly less rarefied atmosphere of the NY Times readership).   The authors, Massimo Pigliucci and Maarten Boudry, are also the editors of Philosophy of Pseudoscience: Reconsidering the Demarcation Problem — which, guessing from the table of contents and reviews, will be an excellent collection.

Something Completely Different

I’ve argued for some time that design is impossible unless the designer is omniscient (because the emergent properties of organic molecules cannot be anticipated).

I have no proof of this, of course, but it seems reasonable to ask design advocates to demonstrate proof of concept. Tell us how design is done without cut and try.

This led me to think a bit about what omniscience means.

ID rage when the multiverse is mentioned — the notion that many universes having differing physical constants might exist simultaneously, making the fine tuning argument moot.

So I thought I might ask if anyone can point out a conceptual difference between an existence in which all possible universes exist, and the mind of an omniscient god, in which all possible universes exist.

I don’t know if this is a serious question, but I thought it might be fun.

Lewontin and “the A Priori”

At Thoughts in a Haystack, Pieret notes that Citizens For Objective Public Education, Inc. (COPE) has brought a lawsuit in Kansas to block the implementation of Next Generation Science Standards. (The whole complaint is here (PDF).)   The complaint alleges that teaching evolutionary theory amounts to state endorsement of atheism, and hence is unconstitutional.

In making their case, COPE quotes this well-known passage from Lewontin’s review of Sagan’s A Demon-Haunted World:

“Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.”


Firstly, this passage is taken out of context; read in context, it is fairly clear that Lewontin is attributing this dogmatism to Sagan, and not endorsing it himself.

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Junk DNA

Well, I just got banned again at UD, over my response to this post of Barry’s:

In a prior post I took Dr. Liddle (sorry for the misspelled name) to task for this statement:

“Darwinian hypotheses make testable predictions and ID hypotheses (so far) don’t.”

I responded that this was not true and noted that:

For years Darwinists touted “junk DNA” as not just any evidence but powerful, practically irrefutable evidence for the Darwinian hypothesis. ID proponents disagreed and argued that the evidence would ultimately demonstrate function.

Not only did both hypotheses make testable predictions, the Darwinist prediction turned out to be false and the ID prediction turned out to be confirmed

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