Tuesday, January 4, 2011

RTB and the chimp genome Part 2

In my previous post, I began examining a recent blog exchange between Dennis Venema and Fuz Rana. In Venema's post, he documented that RTB's position on the chimp/human genome comparisons as published in three RTB books appeared to ignore the sequenced chimp genome published in 2005. Here are Venema's conclusions:
Taken together, these findings demonstrate the following: (a) RTB carefully followed the primary literature on human / chimpanzee comparative genomics up until and including a major paper published in 2004, even if it represented such studies selectively to their constituents; (b) RTB was aware of the key 2005 whole-genome study and correctly understood its implications at the time the first 2006 edition of Connections was drafted in late 2005; (c) RTB has made no mention of this paper (nor any paper in this field published since 2004) in two major works published after this paper was available; (d) RTB continues to claim, five years after this paper was published, that the most recent and most extensive evidence supports their preferred value of 85-90% homology (and that higher values can only be supported with small, biased samples), despite the fact that this conclusion is starkly at odds with the best and most extensive study available, and is itself derived from a comparatively small, biased sample; and (e) RTB has shifted from acknowledging (in 2006) that whole-genome comparisons have been done to denying (in 2009) that they ever have.

In his first response, Rana tried to summarize Venema's conclusions as follows:
1. We [i.e., RTB] intentionally ignored a key scientific paper about genetic comparisons between humans and chimpanzees that went against our model.
2. We erroneously claim that the genetic similarity between humans and chimpanzees is around 90 percent, not 95 percent (or about 99 percent) as the above-mentioned paper reports.
3. We claim that the genetic comparisons between humans and chimpanzees that describe the differences (or similarities) in terms of percentages are meaningless, which according to Venema misrepresents and is contrary to scientific opinion.
Notice how different these two summaries are.

Rana's first point is actually an exaggeration. Venema's post does give the impression that Venema is accusing RTB of wrongdoing, but Venema's conclusions (quoted above) are strictly factual and can be documented directly from RTB (and other) publications. Venema never ascribes motives or tries to discern why RTB continues to make the claims that they do. While misconduct is one way of interpreting these facts, there are other possible explanations, and Venema is careful not to make accusations.

I have to take issue with Rana's second point as well. Venema's main point was not that RTB erred by claiming that the chimp and human genomes are 85%-90% similar but that RTB contradicted (and therefore misrepresented) the best research on the subject without explanation. That might seem like I'm splitting hairs, but it's an important distinction. I think Venema is far more concerned with how RTB represents the scientific literature than whether or not RTB is right in its scientific claims.

Rana's third point seemed like it came out of nowhere.  So I went back and read Venema's post again. Sure enough, he did mention something about the "meaning" of the similarity of the chimp and human genomes. Here it is:
The argument he makes is an attempt to cast doubt on the relevance of the human / chimpanzee comparison: if humans and chimps are 90% similar and humans and frogs are 80% similar, Rana claims these "are not meaningful comparisons in a biological sense." Rana’s argument, however, is deeply flawed in that he is comparing two very different measures of similarity and claiming they are equivalent. The human / chimpanzee value, as we have seen, is 95% genome-wide identity (including indels) for the completed genomes of both species compared across approximately three billion DNA base pairs (Table 1). The 80% value Rana touts for the human / frog comparison, however, is merely a measure of the percentage of genes in the frog genome that have a similar gene in humans implicated in a human disease. It is not even a measure of the genetic similarity of those genes, but merely a fraction of the genes identified in frog that might be useful for studying human diseases. Rana, however, presents these two values as equivalent measures in an attempt to disparage human / chimpanzee genomic similarity. In reality, the genome-wide homology between Xenopus tropicalis and humans is slightly over 30%.
Notice that Venema is not directly addressing the claim that gross measures of genomic similarity are or are not "meaningful." Venema's point is that in making this claim, Rana has misunderstood the similarity of human and Xenopus genes.

Despite these misunderstandings, Rana assures us that "The grounds for these complaints, however, are baseless." Why? Rana gives us two reasons in his first post. (1) On the September 20, 2005 webcast of Creation Update, RTB addressed the publication of the chimp genome. (2) "The intent of these two works [CAS and MTT] was to summarize the RTB creation model and to present a sampling of scientific studies that support our model. Neither work was meant to be an exhaustive treatment. There was nothing underhanded about the omission (as Venema asserts)."

Neither of these issues have anything to do with Venema's points. First of all, Venema already reported that RTB had addressed the chimp genome paper (see his conclusion B above). As I see it, the primary point that Venema made is that MTT claims that a whole genome comparison of chimp and human genomes "had not been done" when it very clearly had been done and published in 2005, and RTB knew that it had been done before MTT was written.

Regarding the second point, the "intent" of CAS and MTT is irrelevant to the primary question at hand, which is this: The complete genome sequence of the chimpanzee and a comparison of that sequence to the human genome sequence were published in 2005. In 2009, RTB's book More Than a Theory denied that this analysis had ever been done. I could accept Rana's explanation of this if the passage was carried over unaltered from CAS to MTT, but that is not the case. In CAS, they claimed the study in question had "only recently begun" (true), but in MTT, they said the study had "yet to be done" (false). For some reason, someone altered that text from a correct statement to a false statement. This wasn't just lazy editing or a cut-n-paste error. There must have been a reason for the change. "We weren't trying to be exhaustive" does not explain the change.

Finally, it's also false to claim that "Venema asserts" that there was something "underhanded about the omission." Venema merely reported the facts. He leaves his readers to draw their own conclusions. In fact, Venema stressed this very point in a comment left on his original post (#39607):
RTB is an overtly Christian organization, and this pattern, whatever the cause behind it, hinders my Christian witness to my colleagues in the biological sciences. From their viewpoint, they see it as deliberate deception in order to support a religious view. I have been careful here not to accuse RTB of wrongdoing, but merely lay out the data and explain how it appears to outsiders.
Besides misconduct, I can think of several explanations for RTB's treatment of the chimp and human genomes, and I'll discuss what I think happened in a future post in this series.

Feedback? Email me at toddcharleswood [at] gmail [dot] com.