Kudos to New Scientist’s "24 myths and misconceptions" about evolution

New Scientist has a pretty good article on myths and misconceptions about evolution (see Evolution: 24 myths and misconceptions).

They really hit on many of my pet peeves on evolution. Among my favorites:

Many of these fit in well with my Adaptationomics Award which I will start giving out again soon ….

Adaptationomics Award #2 – Washington Post and David Brown

This is a bit late, but I am now giving out my second “Adaptationomics Award” to David Brown, for his article in the Washington Post on “How science is rewriting the book of genes.” This award is for somehow misusing genomics to push forward ideas that are excessively adaptationist (i.e., somehow claiming that something must be adaptive simply because it is observed to exist). I have given out one before (see here).

The article by Brown itself reports on some moderately recent changes in human genetics. Among the items discussed are “junk DNA”, alternative splicing, and “inefficiencies” in genetic machinery. Some of the discussion in the article in interesting. But it is the last topic, the “inefficiencies” that really gets to me.

It starts off

“It used to be a rule — actually, more of an assumption — that the genetic machinery of living organisms was never intentionally wasteful or inaccurate. It turns out this isn’t always true, either.”

First of all, there is no “intention” in genetic machinery (or by implication, in evolution). I note that this is one of the hallmarks of adaptationism (and adaptationomics) – the anthropomorphizing of DNA.

Then Brown describes some recent papers suggesting that for some protein coding genes, there are (get ready for this) phenotypic differences in alleles that have only synonymous differences. That is, these alleles code for the same protein but use different codons for certain amino acids. Now, never mind that it has been known for 20+ years that codon usage is under selection in some cases (e.g., see papers by Hiroshi Akashi such as this one).

What gets me here is that the discussion that centers on the notion that some synonymous differences are either “inefficient” or “wasteful” and that there MUST be an explanation as to why a cell would do this.

He asks

” Why would evolution favor this built-in inefficiency?”

No – nowhere in the discussion has there been any evidence presented that evolution “favors” this kind of thing (by favor, I assume he means something akin to positive selection, but emotions make evolution so much closer no?). So it would be better to ask “Is this under positive selection” or, in emotional terms “Does evolution favor this?”

And the next discussion is even more adaptationistic. Here he discusses “nonsense mediated decay” whereby translation is terminated in the middle of making a protein. Brown then asserts that this wastefulness must have some adaptive explanation. And he does this by a painful analogy:

Think of a cell as containing a factory that makes both tractors and tanks. In peacetime, few tanks are made, but the knowledge and capacity is never lost. Most tanks are built halfway and then broken down, with the parts sent back up the assembly line for reuse.

But then comes great stress; say the cell is experiencing too much heat or not enough oxygen or food. That’s where nonsense-mediated decay (NMD) comes into play. It’s suddenly wartime, but instead of refitting the factory to make tanks, all the cell has to do is give the order to take the half-made tanks to completion.

Umm — I do not even know where to begin with this. Is he implying that the ribosome needs to keep its wheels greased in order to know how to make the protein when it is needed? I am not clean. But regardless, the implication is clear — there MUST be an adaptive explanation for all examples of NMD. Just in case oyu did not see the push for adaptationism — the end sentence reminds us:

Just the right amount of wrong instructions and wasteful habits — that’s what evolution has built into all of us.

Ick. And thus my Adaptationomics award #2.

Adaptationomics Award #1 – Wolbachia DNA sneaking into host genomes

Well, I have decided to start a new award. For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick – it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word – Adaptationomics. And I am giving out my first award in this to Jack Warren Werren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. This is interesting because it is the first report of strong evidence for such “stable” transfers from bacteria into multicellular species. Of course, one could say that this finding is not that surprising given that Wolbachia infect germ cells and given that DNA transfer from organellar genomes to nuclear genomes is quite common. But Wolbachia are not organelles and since it appears that their DNA can readily move into genomes of multicellular species, this opens up a new window into our understanding of gene transfer.

This of course does not mean that the DNA is anything but “junk” in terms of functions in the host genome. And this is where the adaptationomics comes in. One of the press releases associated with the paper has a bit of an outrageous adaptationomics claim that I would like to counter. In response to their finding of a nearly complete Wolbachia genome in the nuclear genome of a fly Warren Werren says

The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host.

And Dunning Hotopp in a Nature article says:

The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. “You’re talking about a significant portion of its DNA that is now from Wolbachia,” says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. “There has to be some sort of selection to carry around that much extra DNA.”

This notion that the DNA MUST have an beneficial function is pure adaptationomics. Consider the movement of DNA from organellar genomes into the nucleus. Such movement occurs at an incredibly high rate and the DNA seems to be maintained in the host genomes for millions of years. For example, when we were sequencing the Arabidospsis genome, we found at least one if not more whole copies of the mitochondrial genome embedded in the nuclear genome and we concluded this was likely a non adaptive event. That is, the mt DNA was not conferring some advantage on Arabidopsis plants. There is extensive work on what are called “numts” (nuclear mitochondrial DNA) in humans and other species that makes similar conclusions – the mtDNA in the nucleus is basically junk but it is maintained for long periods of time. Sure, occasionally, the DNA confers some selective advantage. But this is a very rare event and one cannot infer that some DNA is advantageous simply because it is present. This is especially the case for eukaryotes which are generally more able than bacteria to maintain DNA that confers little selective benefit.

So I would argue that WarrenWerren and colleagues appears to have fallen for the adaptationomics trap – they want to believe these Wolbachia DNA inserts confer some selective advantage. But there is no need to assume this simply because the DNA is there.

Anyway – as is the case more and more. Read the paper. Ignore the interviews and the press releases.