December 13, 2013

DNA not for genes only

Epigenetics has been in the news more and more recently, with new claims that a propensity to suffer from anxiety, even anxiety over exposure to a specific smell, can be passed on from generation to generation, at least in mice.

Then came David Dobbs' new article about gene plasticity and expression, which starts with this:
At the front of the room, a bug-obsessed neuroscientist named Steve Rogers was describing these two creatures — one elegant, modest, and well-mannered, the other a soccer hooligan.

The grasshopper, he noted, sports long legs and wings, walks low and slow, and dines discreetly in solitude. The locust scurries hurriedly and hoggishly on short, crooked legs and joins hungrily with others to form swarms that darken the sky and descend to chew the farmer’s fields bare.

Related, yes, just as grasshoppers and crickets are. But even someone as insect-ignorant as I could see that the hopper and the locust were radically different animals — different species, doubtless, possibly different genera. So I was quite amazed when Rogers told us that grasshopper and locust are in fact the same species, even the same animal, and that, as Jekyll is Hyde, one can morph into the other at alarmingly short notice.
Dobbs goes on to note that two animals with the same DNA can express it in radically different ways, and goes further, with these rhetorical questions:
This raises a question: if merely reading a genome differently can change organisms so wildly, why bother rewriting the genome to evolve? How vital, really, are actual changes in the genetic code? Do we always need DNA changes to adapt to new environments? Are there other ways to get the job done? Is the importance of the gene as the driver of evolution being overplayed?
He doesn't reject the importance of genes, but suggests, as I understand, their "centrality" should be reduced from 98 percent to, say, 78 percent, on average. But, I'm giving a brief summary of a long article.

Some old-line geneticists poo-pooh reading too much into epigenetics, or even Dobbs' article. That would be you, Jerry Coyne.

P.Z. Myers is a cautious one on epigenetics, though not as tight as Coyne. And, while admitting he's in the minority of a selective sampling of his peers, he sees nothing wrong with Dobbs' piece:
I am saying that understanding genes is fundamental, important, and productive, but it is not sufficient to explain evolution, development, or cell biology. ...

I will also rudely tell you that we don’t understand the process (of gene expression) yet. Knowing the genes is not enough.

It’s as if we’re looking at a single point on a hologram and describing it in detail, and making guesses about its contribution to the whole, but failing to signify the importance of the diffraction patterns at every point in the image to our perception of the whole. And further, we wave off any criticism that demands a more holistic perspective by saying that those other points? They’re just like the point I’m studying. Once I understand this one, we’ll know what’s going on with the others. ...

We forget that our theories are purely human constructs designed to help us simplify and make sense of a complex universe, and most seriously we fail to see how our theories shape our interpretation of the data…and they shape what data we look for! That’s my objection to the model of evolution in The Selfish Gene: it sure is useful, too useful, and there are looming barriers to our understanding of biology that are going to require another Dawkins to disseminate.

Let me try to explain with a metaphor — always a dangerous thing, but especially dangerous because I’m going to use a computer metaphor, and those things always grip people’s brains a little bit too hard.

In the early days of home computing, we had these boxes where the input to memory was direct: you’d manually step through the addresses, and then there was a set of switches on the front that you’d use to toggle the bits at that location on and off. When a program was running, you’d see the lights blinking on and off as the processor stepped through each instruction. ...

That’s where we’re at in biology right now, staring at the blinking lights of the genome. 
P.Z.'s Gnu Atheism? Totally disagree. But, he has some solid evolutionary biology insights. Also, vis-a-vis Coyne, he's not a hard-core determinist on free will, which I think is driving Coyne's thoughts on evolutionary genetics, too.

And now, the newest applecart upsetter of the "genetic dogma" of Francis Crick and James Watson is this — the idea that there may be two codes in our DNA, one for coding for proteins (i.e., genes) and another for epigenetic-like modulation:
“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Dr. James Stamatoyannopoulos, who led the UW team. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The researchers discovered that some codons, part of the 64-letter alphabet which makes up the genetic code, can have two meanings – one related to protein sequence and another related to gene control.

These duons apparently evolved together, researchers said, and the gene control instructions appear to stabilize beneficial features of proteins and how they’re made.
Maybe this will finally break the slavish devotion some people have to Richard Dawkins' The Selfish Gene. I know Myers feels at least a bit that way.

Of course, really, Stanley Prusiner's fingering of prions as causing mad cow disease long ago upset the central dogma of Crick and Watson. That's why so many biologists were so strident against Prusiner getting a Nobel. It's also why the one he got was in chemistry, and not physiology or medicine.

And, it's also why John Horgan is wrong with a book called "The End of Science." We're not even close to that.

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