Thursday, June 14, 2007

Stone washed genes












Do not get rid of the junk in the attic. It's evolution--
Life just turns out to be more complicated every day and don’t look for genetics to figure it out just yet. The common concept is that genes are strung like beads on a string (pearls for some of us) and that the individual, discrete genes are what makes us. Not so.

Rick Weiss in the Washington Post went through a whole bunch of papers published in the Encyclopedia of DNA Elements (Encode), which among other things suggested that the $3 billion Human Genome Project produced a cartoon of the human genome. Weiss’ survey indicates that there is growing awareness that the individual genes is not just a biological code; they are elements in a complex operating system. It is what happens between and among the genes that counts. Many genes overlap and share stretches of code. The system would be totally chaotic but a switching system has evolved to make sense and order out of the instructions contained in the genes. Diseases like cancer are probably not errors in genes but errors in the DNA between them, which should disturb those in molecular medicine who have been aiming their attention on the genes, especially in their attempts at producing targeting medicines.

Another new concept concerns the so-called junk genes, the 95% of genes that did not appear to do much. When you think about it, that notion is silly. Evolution doesn’t waste 95% of anything. Now it appears that those junk genes are anything but. In fact some researchers have found that many creatures share their junk genes, meaning they are probably crucial for life and even the billion of years of evolution has failed to alter them.

“Oh my gosh,” one scientists told Weiss. “This is really complicated.” Yup. That’s us.

Encode, incidentally, is an interesting project. The goal is to find out whether it is worth the time to go deeply into each section of the human genome. For 3-1/2 years, scientists explored 1% of the genome as deeply as they could to see if this idea would be fruitful. The answer is a resounding yes, if for no other reason than to discover the misconceptions in the common wisdom. Of particular interest are those genes that do not appear to produce proteins. What are they doing hanging around?

Speaking of DNA, we reported earlier that James Watson, he of the Double Helix, had chickened out to having his DNA sequenced. He changed his mind, apparently. He donated some of his illustrious DNA to Baylor in 2003 but then decided he did not want it published because of privacy concerns and because his children might find out things about their own genetics they might not want to know. Now he agreed to have it published, or at least almost all of it. One spot shows a predisposition to cancer and Watson has survived skin cancer. He is not going to find out about Alzheimer's’ however, or have it published. He had a grandmother with the disease and that gives him a one in four chance, he says, and he simply doesn’t want to know. On the other hand, he’s 79 and probably would know by now.

1 comment:

Monte said...

Good highlighting of a good article. It's going to take a while to disabuse ourselves of the assumptions built into the phrase "genetic engineering": that knowing the genome, or even the proteome, automatically gives us the same capabilities we would get from having, say, source code or a wiring diagram.

Not so: genetic information is what a programmer would consider extremely gnarly, re-entrant "spaghetti code," with the same module (protein) doing six different things in different tissues. Clean points of control, where activating or inactivating one gene has one desired therapeutic effect and no other, are the exception rather than the rule.

If we insist on the comparison to IT, we should at least realize that we're going to spend a long time drawing flow charts before we can get much past "hello world."