Saturday, January 8, 2011

RTB and the chimp genome Part 6

Just when I thought I was done writing this series, Fuz Rana posted a fourth response to Venema's critique of RTB. In previous posts in this series (one, two, three, four, and five), my responses to Rana's posts can be placed in three categories. First, I've found that Rana misrepresents or misunderstands published data or arguments (both the informal blog post of Venema and peer-reviewed, scientific papers). Second, I've tested Rana's hypothesis about the similarity of the chimp and human genomes, and I found that it failed. Third, I disputed Rana's interpretation of the data, especially his assertion that the similarity of the human and chimp genome is meaningless.

In his fourth post, Rana doesn't present any new arguments. Instead, he just reiterates his previous claims. Or so it seems. Here's where he begins, in a paragraph that is copied verbatim in parts two and three of Rana's response to Venema:
Most people are familiar with the claim that humans and chimps share a 99 percent DNA similarity. Our assertion, however, is that the genetic commonality between these two primates is closer to 90 percent.
I have to confess that when I first read that statement in parts two and three, it didn't really register. Now, however, I'm very curious why he chose the term genetic "commonality." I know what percent identity is, and I know what percent similarity is. In scientific literature, "genetic commonality" refers to genotype/phenotype relationships, specifically in the context of two different phenotypes of a single organism that have a common underlying genotype. Those two phenotypes share "genetic commonality." That's obviously not what Rana is talking about here, so what does he mean by "genetic commonality?"

Interestingly enough, RTB used this idea of "genetic commonality" in a blog post by Sandra Dimas from August, 2010. The post is discussing a study of sponge genes. Here's the passage where we read about "commonality:"
RTB biochemist Fuz Rana responded to this study in the August 10th podcast of Science News Flash. He explained that sponges have around 30,000 genes (similar to the number humans and most complex animals possess). And about 19,000 of those genes are known to correspond with genes in other animals, including human beings. Evolutionary biologists see the common gene set as evidence for common ancestry. Fuz argues, however, that this commonality can be understood from a Christian perspective as evidence for common design (where God takes the same genetic framework and alters it in a purposeful and supernatural way). [emphasis mine]
Now that's really interesting. At RTB, "genetic commonality" appears to refer to the amount of genes (or DNA?) that two organisms have in common, without respect to the percent identity or similarity.

What's the big deal about genetic commonality? Recall that part of Venema's critique is that Rana is mixing percent similarity statistics with statistics that express the percentage of genes two organisms have in common (i.e. "commonality" in RTB parlance). Here's that passage:
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%.

In his respones to Venema, Rana is doing the very same thing again: mixing similarity with "commonality". Let's look one more time at what Rana wrote:
Most people are familiar with the claim that humans and chimps share a 99 percent DNA similarity. Our assertion, however, is that the genetic commonality between these two primates is closer to 90 percent. [emphasis mine]
Now do you see the subtle but crucially important shift? I almost missed it myself, but there it is for all to see. Rana is comparing two completely different measurements, and by the phrasing it's obvious that he wants us to see them as essentially the same thing. What he's written there would be like saying, "Some people think I'm six feet tall, but in reality I'm 180 pounds." The sentence structure clearly contrasts one measurement with the other, even though they're not measuring the same thing and therefore cannot be compared that way! Sequences could share both 90% genetic commonality and 99% sequence similarity. They're not mutually exclusive, even though Rana presents them as though they were.

Now it's true that in other passages of Rana's posts, he uses "similarity" when he means "commonality," so maybe Rana doesn't really recognize the difference between the two? For example, in the second post of his series (the same one where he introduces "genetic commonality"), Rana wrote, "...including indels reduces the genetic similarity between humans and chimps." Since indels involve the addition or removal of DNA, he obviously means "genetic commonality" not similarity. So maybe I shouldn't make a fuss about this "genetic commonality" term?

But maybe I should make a fuss. Thanks to Amazon's "look inside" feature, I searched all of Rana's books for the term "commonality," but I didn't find it. I also searched Hugh Ross's books Creation as Science and More Than a Theory, which were at the center of Venema's critique. No "commonality" there either. I checked the three posts on "human-chimp genetic differences" that Rana linked to from his fourth post. No "commonality."

So what we have here is the sudden appearance of the term "genetic commonality" where only "similarity" had been previously used. In RTB parlance, "genetic commonality" seems to refer to genes or DNA shared in two species. Likewise, the simple dictionary definition of commonality is "the state of sharing features or attributes," not how similar those shared features are. As far as I can tell, Rana has never used "genetic commonality" in his previous discussions of chimp/human genomic similarity, but here it is in his response to Venema's criticism that genetic similarity and genetic commonality aren't the same thing. Rana must have had a reason for choosing that word "commonality." He used it deliberately.

I don't know. Maybe I'm making a mountain out of a molehill. I just find it perplexing that he suddenly used this "genetic commonality" phrase out of nowhere, right after Venema called him on it.  But his sentence structure clearly indicates that he wants to make it an equivalent concept to genetic similarity.

Tomorrow, I'm going to end this series, one way or another.

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