Empty Criticisms

Don't worry, this one has nothing to do with mtDNA.

There's been a bit of a hubbub recently in the ScienceBlogs community about science journalism. Sometimes we're a bit too hard on the journalists. In this week's issue of Nature, Robert Barton takes the journal to task for their coverage of the Pollard et al paper describing a rapidly evolving non RNA gene. Barton makes a good point at the beginning of his letter:

You state in your News story on genetic differences between humans and other species . . . that research is beginning to pin down genes that "evolved rapidly during the transition from chimps to people". No such transition occurred, of course, because chimpanzees are not human ancestors; they have been evolving for exactly the same amount of time.

Amen to that. The same thinking that causes people to believe humans evolved from chimps, leads them to claim that there is some sort of evolutionary hierarchy from bacteria to eukaryotes to animals. It would be fine if Barton stopped there, but what he says next makes me think that he only read the news story and not the actual research paper:

A mutation is, in principle, just as likely to have occurred in the chimpanzee lineage as in the human lineage, during the time since their common ancestor lived. There is no way to discover from any comparison of the two species which is the case.

To determine the evolutionary history of a trait and its genetic basis, it is necessary to make phylogenetic reconstructions based on comparisons among many species. Chimp-human differences make good headlines, but tell us little about how human uniqueness evolved.

I agree wholeheartedly. Simple comparisons between two species reveal little. That's why Pollard et al used outgroup taxa to infer upon which lineage (human or chimp) the mutations occurred. You don't even need to read that far into the paper to learn this; it comes in the introduction:

Here we scan these ancestrally conserved genomic regions to find those that show a significantly accelerated rate of substitution in the human lineage since divergence from our common ancestor with the chimpanzee.

The authors use sequences from mouse, rat, and chicken, in addition to human and chimp, when inferring substitutions along the human lineage. This is the phylogenetic reconstruction that Barton demands. But other research papers were also reviewed in the Nature news story. One used the macaque, mouse, and rat genomes to identify the copy number expansion of a neuronally expressed gene along the human lineage since the divergence of humans and chimps. The other cited papers were on different topics, so they can't reasonably be targets of this criticism.

It's hard to tell whether Barton is going after Nature's coverage of the research or the research itself. If his criticisms are of the research, he sorely is misguided. Nature's reporting was less than stellar (as Barton explicitly points out), but they do get one thing right:

A draft of the chimpanzee genome was released last year and a draft sequence of the macaque genome is also publicly available. The data are enabling scientists to compare chimp, human and monkey DNA to search out signals that seem unique to people.

So Barton is unhappy that Nature made it seem like human-chimp comparisons tell us what happened along the human lineage, which they didn't. And he doesn't like that the researchers failed to do the proper comparisons, which they did do. At least he got the stuff about humans not evolving from chimps right.