Eisen Lab Blog

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.