Wednesday, June 3, 2009

Reply to Jonathan Wells, Part 2

This is a continuation of my response to Jonathan Wells’ review of The Language of God by Francis Collins. His words will be in italics. In this post we’ll look at his attempts to poke holes in evolutionary theory through inconsistent family trees (showing relationships of living things to one another):

Not only can phylogenies constructed with DNA conflict with each other, but they can also conflict with phylogenies based on morphology. Take whales, for example – fossils of which Collins asserts are “consistent with the concept of a tree of life of related organisms.” On morphological grounds, evolutionary biologist Leigh Van Valen proposed in the 1960s that modern whales are descended from an extinct group of hyena-like animals.13

I’ve read Wells’ citation, and it seems that this paper proposes that whales are descended from Mesonychians, a group of carnivores. Note that Mesonychians are artiodactyls, so the discrepancy in this hypothesis and more recent findings is not quite as dramatic as one might think (artiodactyls are still the group which whales belong to).

Then, in the 1990s, molecular comparisons suggested that whales are more closely related to hippopotamuses 14. In 2001, however, evolutionary biologist Kenneth D. Rose reported that “substantial discrepancies remain” between the morphological and molecular evidence 15.

This is true. However, it seems to me that Wells is sensationalizing this a bit. As Ken Rose’s paper demonstrates, there are three major hypotheses to take into consideration: That whales evolved from mesonychians, or that they evolved from artiodactyls (there are two hypotheses here, one being that hippopotami are more closely related to whales and the other being that hippopotami are more closely related to other artiodactyls). This debate seems to me to be a simple argument not over which groups are related, but precisely how closely they are related. It’s simply not worthy of the sensationalism Wells gives it.

Furthermore, he overplays controversies while failing to recognize the overwhelming consistency of phylogenies. For instance, molecular biologists had long been saying that hippopotami were closely related to whales (making whales artiodactyls and not mesonychians) and fossil evidence later confirmed this view, as Rose’s paper shows.
Even more intriguing is that one of the papers he cites says the following:

“‘Every gene I've ever sequenced says the same thing. The molecular data is all fairly consistent,’ says John Gatesy of the University of Wyoming in Laramie, one of the first who reported the whale-hippo connection. Some researchers have taken to calling this the whippo hypothesis.”**

And in 2007, J. G. M. Thewissen and his colleagues pointed out that since whales appear in the fossil record 35 million years before hippopotamuses “it is unlikely that the two groups are closely related.” Thewissen and his colleagues concluded from morphological comparisons that whales are descended from a raccoon-like animal instead. 16

I emailed Dr. Thewissen about this paragraph, and here is how he responded:

“Not a very honest citation of my 2007 work. My paper found that the closest relative to whales is among the even-toed ungulates, and says so explicitly. We did comment on the large gap in the fossil record, but only to make the point that there must be closer, extinct relatives to whales than hippos are. Our analysis shows that that gap is filled by a small even-toed ungulate from India. However, our analysis did not discuss the modern even-toed ungulates very exhaustively (which we state explicitly in that paper). After our paper, that has been done by Theodor and Geisler (in 2009 also in Nature), and they did confirm our results that the Indian fossil even-toed ungulate is the closest relative to whales and further found that hippos, in spite of the absence of very old fossils for them, are the closest living relative, to whales, thus confirming what the molecular scientists had found. As often happens in science, when new evidence is discovered and evaluated, scientists have the opportunity to test hypotheses they had. In this case, new evidence brought the morphological and molecular evidence in line and the discrepancy that existed before is resolved.
“The gap in the hippo fossil record remains. Scientists use the phrase ‘ghost-lineage’ to describe this. There must be a substantial period when hippos were around, but there is no fossil evidence for them, or they cannot be recognized in the fossil record (because the fossil material is very incomplete). In that period, hippos were a ghost lineage.”

One more thing I’d like to address: What about the minor discrepancies seen in phylogenetic trees? Well, as Talk.Origins put it,

“A few inconsistencies are to be expected, because biology is messy. Genes need not always evolve at the same rate in different lineages. Some molecules may converge as a result of selection or chance. Horizontal gene transfer occasionally occurs. Such exceptions will be rare, but there will be a few of them among the vast body of consistent results. Most inconsistencies can be resolved by basing an analysis on multiple genes (Rokas et al. 2003).
“Other inconsistencies will occur as a result of methodological and interpretive mistakes (Sanderson and Shaffer 2002). Phylogenetic analysis is a very complex subject; people who do not understand it well cannot be expected to get it right all the time.”

I would like to thank Dr. Hans Thewissen for his helpful comments on this writing.

** Dr. Thewissen suggested that this had little bearing on my argument, since it concerned only molecular data. However, since Wells seems to be trying to play up the inconsistencies in phylogenetic trees, I think that pointing out consistencies in molecular data is pertinent because it contradicts his overall thesis.

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