Saturday, September 6, 2014

"Junk" DNA? Not really, or how "selfish gene" metaphor has gotten out of control

ENCODE systematically scouted the genome as a whole for specific functions. One function could be coding for proteins; another function could be acting as a ‘molecular switch’ that regulates the operation of other genes. In one experiment, for example, ENCODE surveyed the entire genome for DNA that is bound by ‘transcription factors’ - proteins known for calling other genes into action. In this way, ENCODE compiled a comprehensive and very useful catalogue that provided a functional clue for 80 per cent of the 3 billion nucleotides that comprise all the genes of the human genome. The ENCODE results seemed to confirm that our genome is indeed a tidy blueprint; that almost every bit of the human genome is there for a reason, and that our genetic heritage is not a small heap of information buried under a pile of junk.
And then:
Yet viewing our genome as an elegant and tidy blueprint for building humans misses a crucial fact: our genome does not exist to serve us humans at all. Instead, we exist to serve our genome, a collection of genes that have been surviving from time immemorial, skipping down the generations. These genes have evolved to build human ‘survival machines’, programmed as tools to make additional copies of the genes (by producing more humans who carry them in their genomes). From the cold-hearted view of biological reality, we exist only to ensure the survival of these travellers in our genomes.
Hmmm…Selfish gene lecture coming up. I understand the selfish gene argument, I really do. But I also think this is a category mistake: "we exist to serve our genome." Why not scrap all this sloppy teleological language across the board. We simply exist.

Here's comes the anthropomorphic parade, in spades:
At the most fundamental level, then, our genome is not a blueprint for making humans at all. Instead, it is a set of genes that seek to replicate themselves, making and using humans as their agents. Our genome does of course contain a human blueprint – but building us is just one of the things our genome does, just one of the strategies used by the genes to stay alive. In their selfish desire to leave offspring, our genes have evolved to form a society where they work together efficiently, dividing the labour to ensure that each makes it into the next generation. Like Adam Smith’s invisible hand, the genes in this society co-operate with one another not from a sense of fairness or design, but simply to maximise their own survival. From the myriad interactions of genes in this complex society emerge the striking biological adaptations we see in the living world.
At this point Dawkin's metaphor, selfishness, has taken over and is running the show. The core metaphor CAN be cashed out in terms of technical explanation of how genes function in the world, but when you run the metaphor like it's running in that paragraph you've left the world of technical microbiology and genetics far behind.

Somewhat later:
Junk is not trash and, as the Nobel laureate and genetics pioneer Sydney Brenner has pointed out, it might come in handy at some point, even if that is not its function. Any stretch of DNA can by accident turn into something that then contributes to the spread and survival of the genome.
Survival of the genome? Where'd that come from? That wasn't Dawkins' argument. He was arguing about individual genes. From his point of view, just as the whole human exists to serve this that and yet that other gene, so does the whole freakin' genome. No difference. The same logic applies.

Oh snap! Would you guys just stop it:
A misunderstanding persists in the wrong-headed notion that our genome encodes the blueprint of human life. It does not. The blueprint analogy does not apply to the majority of our genome, nor is the non-blueprint component useless junk. Someone or something benefits from much of this genetic code, but value is in the eye of the beholder. For the majority of functional repeats such as Alu and LINE-1, the only beneficiaries are they themselves; attributing human benefit to junk imagines harmony and purpose where none exist.
The blueprint notion is questionable in the first place. But if you're going to use it, then sure, "our genome encodes the blueprint of human life." If not our genome, then where? To use another, somewhat crude analogy, saying that "our genome encodes the blueprint of human life" is a bit like saying "Peoria exists in the United States." The latter DOES NOT at all imply that Peoria is the only thing that exists in the US. Well, the "blueprint" for human life isn't the only thing that exists in the human genome either. So?

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