Tuesday, September 11, 2012

Junk DNA

An article in New Scientist (subscription required) describes what researchers are discovering about the human genome and how it works. It's turning out that our cellular machinery is far more complex than anyone imagined just a couple of decades ago.

It's also turning out that one of the widely-accepted assumptions - the assumption that vast amounts of DNA were little more than vestigial junk (an assumption that intelligent design people have been predicting for fifteen years would turn out to be false) - is turning out to be false. Researchers are finding that as much as 80% of our genetic material has a function in the cell and that number appears to be a lower limit.

All of which is to say that however the cellular machinery came about it's becoming increasingly unlikely with every passing year that it came about by purely purposeless, mechanistic processes.

Here's an excerpt from the New Scientist article:
After the genome was sequenced, another major project was launched to try to understand which bits of the genome do what. The results, released this week, reveal that our genome is far more complex and mysterious than biologists imagined just a decade ago.

Back in the 1960s, a beautifully simple picture emerged. Our DNA consisted of recipes for proteins. The double helix could be unzipped to allow RNA copies of these recipes to be made and sent to the protein-making factories in cells. But by the 1970s, it had become clear that only a tiny proportion of our DNA codes for proteins - just 1.2 per cent, we now know. What about all the rest? Some assumed it must do something, others suggested it was mostly junk. "At least 90 of our genomic DNA is 'junk' or 'garbage' of various sorts," the geneticist Susumu Ohno wrote in 1972.

Ohno knew, though, that some of the DNA that didn't code for proteins still played a vital role. For instance, the process of making RNA copies of genes - transcription - involves clusters of proteins binding to specific sequences near the genes. These proteins - called transcription factors - control the activity of genes by either boosting or blocking transcription, so the sequences to which they bind are known as regulatory DNA or switches.

So how much DNA acts a switch, or has some other function? To provide an overall picture of which parts of the genome do what, the Encyclopedia of DNA Elements (ENCODE) project was set up in 2003. It involves many teams around the world using a variety of techniques. The results of a pilot study looking at just 1 per cent of the genome were released in 2007. This week, the results of its study of the entire genome were released, with the publication of more than 30 papers in Nature and other journals.

Among other things, ENCODE looked for switches that control gene activity. The researchers did this by taking known transcription factors and seeing which bits of DNA these proteins bound to. So far, they have found 4 million sites, covering 8.5 per cent of the genome - far more than anyone expected.

Even this is likely to be a gross underestimate of the true number, because ENCODE hasn't yet looked at every cell type, or every known transcription factor. "When we extrapolate up, it's more like 18 or 19 per cent," says Ewan Birney of the European Bioinformatics Institute in Cambridge, UK, who is coordinating the data analysis for ENCODE. "We see way more switches than we were expecting, and nearly every part of the genome is close to a switch."
You can read the entire article at the link for free for the next four days.

It used to be that anyone who believed that living things were the product of intentional, intelligent engineering were thought to be benighted, hopelessly superstitious, credulous simpletons. It seems that that description is currently shifting toward those who insist that this breathtaking complexity could just happen by mindless accident.

Why He's Still Ahead

John Hinderaker at Powerline wonders why it is, given the state of the economy and the failure of the President to articulate any plan for getting us out of the morass we're in, that Mr. Obama is still leading in the polls:
On paper, given Obama’s record, this election should be a cakewalk for the Republicans. Why isn’t it? I am afraid the answer may be that the country is closer to the point of no return than most of us believed. With over 100 million Americans receiving federal welfare benefits, millions more going on Social Security disability, and many millions on top of that living on entitlement programs–not to mention enormous numbers of public employees–we may have gotten to the point where the government economy is more important, in the short term, than the real economy. My father, the least cynical of men, used to quote a political philosopher to the effect that democracy will work until people figure out they can vote themselves money. I fear that time may have come.
If Mr. Obama wins in November it will be another historical milestone to add to his achievement as the first black president. It'll be the first time a president was ever reelected with unemployment this high. Hinderaker is surely correct that when so many people are dependent upon government, attempts to reduce its size and power fall on deaf ears, but I think there's also another dynamic at play.

I can't prove it, but I suspect that another part of the reason Mr. Obama is still afloat is that there are a lot of people who would vote for him no matter how bad the economy is simply because he's black, he's pro-choice, and he's "cool."

The people hardest hit by unemployment are African Americans, but, unlike years past when the choice was between two white candidates, a large number of African Americans will vote for Mr. Obama whether they have a job or not. The same is true of many women who care more than anything else about keeping abortion legal. Mr. Obama could be found to be giving state secrets to the Russians and many people will still vote for him for these two reasons alone.

Nor should we underestimate the "cool" factor. There are perhaps millions of people who will vote in November who have no grasp whatsoever of the issues that are being debated, but they know whether a candidate is cool or not, and they'll vote for cool over competence every time. They voted for JFK over Nixon largely on that basis, they voted for Bill Clinton over George H. W. Bush largely for the same reason and reelected him over Bob Dole again because he was cool and Dole was not. George W. Bush ran against Al Gore and John Kerry, elections in which the coolness factor was a wash, but in 2008 it reemerged with unfortunate consequences for the hapless and decidedly uncool Senator McCain. And in 2012 cool is once again pretty much on the side of President Obama.

The notion that the state of the economy will make a difference is, in my opinion, simply mistaken. It only matters if the candidates are both the same race and of approximately equal "coolness."

I know this is not a very flattering picture of those who would vote for someone largely on the basis of superficialities, and I repeat that I can't prove it, but there you have it. I'd bet that many if not most people who'll vote in November couldn't even name five Supreme Court Justices or their own U.S. Senators. They don't know much about the national debt and deficits, and they don't much care. What they do care about is that Mr. Obama is black, he's pro-choice, and he's cool.