Continuing where I left off. This is still Part 1: The mystery of the
missing fossils.
5: The genes tell the story? Meyer starts by attacking the molecular
clock, which is admittedly an easy target. Estimates of the age of the
bilaterian common ancestor vary widely depending on data and methods. To
Mayr this means that all such estimates are meaningless, but that isn't
necessarily true. We might, in fact be learning more about how to do it
right. But I will agree that error bars should generally be wide. Meyer
does however compound the problem by failing to clearly distinguish at
least three separate nodes: Metazoa, Bilateria + diploblasts, and
Bilateria. These all presumably have different ages, so randomly listing
dates as if they all estimate the same thing is a problem. We now also
believe there are multiple clades of both sponges and diploblasts, so
lumping them conceals further nodes.
This, however, is perhaps the weirdest claim, which bears quoting:
"Histones exhibit little variation from one species to the next. They
are never used as molecular clocks. Why? Because the sequence
differences between histones, assuming a mutation rate comparable to
that of other proteins, would generate a divergence time at significant
variance with those in studies of many other proteins. Specifically, the
small differences between histones yield an extremely recent divergence,
contrary to other studies. Evolutionary biologists typically exclude
histones from consideration, because the times do not confirm
preconceived ideas about what the Preambrian tree of life ought to look
like." In other words, he's accusing biologists of cherry-picking data
to fit (the irony of which escapes him). No that isn't why. It's because
histones have an evolutionary rate (not, incidentally, equivalent to
mutation rate) much slower than that of other proteins, and this can
easily be shown by comparing divergences much more recent than the
Cambrian. Though it may be that Meyer doesn't believe in different
evolutionary rates, because he doesn't seem to believe in those recent
divergences either, or in evolution of pretty much any sort.
In another part of the chapter, Meyer begins to doubt that there is such
a thing as homology or phylogenetic relationships. While it's true that
tree-building methods assume that there is a tree to build, there are
also ways of testing whether the tree built is a better fit to the data
than some other tree, or in fact than no tree at all (e.g. Theobald
2010). But to Meyer, phylogenetic analyses do not count as evidence of
common ancestry. Conveniently.
And finally there is an attempt at Catch-22. A bilaterian ancestor must
lack the special characters of descendant groups, so those characters
must arise later. And he thinks that there can't be time for such
characters to arise (because, as he tells us later, no amount of time,
including the entire history of the earth, would be sufficient for even
one of those characters to evolve).
The question of whether there was a bilaterian ancestor is of course
separate from the question of its age. We end with a shameless
quote-mine from Simon Conway Morris that doesn't at all say what Meyer
wants to make it say, much less mean what he wants it to mean. "A deep
history extending to an origination in excess of 1000 Myr is very
unlikely", which Meyer takes to mean that Conway Morris thinks metazoan
evolution must begin very close to the Atdabanian. How 1000 became close
to 520 is unclear.
6: The animal tree of life. Although Meyer doubted common ancestry in
the previous chapter, it's necessary here to drive a stake through its
heart by showing that phylogenetic analyses are invalid. And we do that
the same way we dealt with the molecular clock: different analyses
disagree! For this he goes as far back as the 1940s, never acknowledging
that significant consensus has emerged more recently. Meyer falsely
claims, though I'm not sure he realizes what he's saying, that
phylogenetic analyses assume a molecular clock.
By the way, either the quote-mining is thicker in this chapter than in
previous ones, or I've just read more of the papers. He cites a paper
about conflicts among gene trees due to lineage sorting to claim that
phylogenetic analyses are spurious. Of course it means nothing of the
sort, only that the histories of genes may differ slightly from the
histories of the species in which they are embedded. And he uses studies
that claim extensive horizontal transfer to make the same point.
Finally, he uses other studies that point to the possibility of very
short branches that would be hard to resolve. In other words, if history
is more complicated than a simple, single, obvious tree, it therefore
doesn't exist. Oddly enough, though Meyer rejects the tree, he accepts
affirmations based on it that the Cambrian radiation was quick.
Next he attacks the agreement between molecular and morphological
phylogenies by pointing out that there are disagreements. Should have
actually read Theobald's "29+ Evidences" instead of merely quote-mining it.
After that, we discover that morphological characters are not always in
agreement with each other, and that some are quite labile. Therefore, of
course, there is no real phylogeny.
We finish with repetition of an earlier point, that phylogenetic
algorithms assume a tree; again, no mention of statistical tests. And
anyway, convergent evolution (or, to Meyer, a hypothesis of convergent
evolution, since he never accepts that evolution really happens) makes
phylogenies invalid. Because hey, if there's any homoplasy at all, we
can't trust anything, right?
7: Punk eek! The existence of this chapter is inexplicable, since PE was
never intended, by Eldredge, Gould, or anyone else, to account for the
Cambrian explosion. Nevertheless, Meyer triumphantly and at length
proves what everyone knew from the start. Meyer indulges in two main
confusions (neither limited to creationists). First, confusion of time
scales. The difference between PE and "gradualism" isn't about the
mechanism of evolution -- natural selection in each case -- but about
whether change has a constant rate over geological time or is episodic;
but while PE episodes are rapid in geological time, they are gradual on
the human scale. Second, confusion of magnitude. The lack of transitions
PE is intended to explain are those between closely related, similar
species, not those between higher groups. Nothing at all to do with the
Cambrian explosion. Meyer, despite a long explanation of its genesis,
doesn't seem to know that PE was originally intended as an exploration
of the consequences of Ernst Mayr's ideas of speciation for the fossil
record.
Here's another fine quote mine, again just one I happened to notice
because I've read the relevant paper. Meyer says "As Foote explained
(writing with Gould in fact), the adequacy of punctuated equilibrium as
an account of the fossil record depends on the existence of a mechanism
'of unusual speed and flexibility'". But in fact Foote & Gould weren't
writing about PE at all, or even about a mechanism. Here's the actual
sentence in which that fragmentary quote is embedded: "Moreover, even if
their conclusion were correct, it would support the idea of unusual
speed and flexibility in Cambrian evolution followed by constraint upon
fundamental anatomical change." In that sentence, "They" are Briggs et
al., who attempted to show that arthropod disparity in the Cambrian was
about the same as that of present-day arthropods, and the Foote & Gould
letter is a methodological critique. The underlying issue is whether
rates of evolution were unusually fast in the Cambrian explosion because
of increasing developmental canalization toward the present. Again,
exactly nothing to do with PE or any evolutionary mechanisms.
OK, that's all the paleontology. The rest of the book is just about why
evolution to any significant degree is impossible. So all the argument
about how long the Cambrian explosion lasted, or just how much happened,
is irrelevant, since no matter how much time is available, it isn't
enough, and all of the other radiations in the history of life are
impossible too.
Still left to consider:
Part 2: How to build an animal
8: The Cambrian information explosion
9: Combinatorial inflation
10: The origin of genes and proteins
11: Assume a gene
12: Complex adaptations and the neo-Darwinian math
13: The origin of body plans
14: The epigenetic revolution
Part 3: After Darwin, What?
15: The post-Darwinian world and self-organization
16: The other post-neo-Darwinian models
17: The possibility of intelligent design
18: Signs of design in the Cambrian explosion
19: The rules of science
20: What's at stake
Foote, M.