Genetic Clocks

A human’s genes provide a blueprint for making that human — and they can also tell time. Using genetic clocks and fossils to figure out what certain genes do…

The human genome — or blueprint for life — is made up of thousands of genes . . . And each gene does something different. Steven Benner is a biochemist at the University of Florida. He says even if you know the genetic code stored in a gene, you still don’t know the most important thing.

Steven Benner: What does this gene do? We have all these sequences from the human genome . . . but it’s been very difficult to decide what the gene actually does in human physiology.

Benner and his team use a two-step process to guess what a certain gene does. First, they estimate how old the gene is by comparing the same gene from two kinds of animals with a common ancestor. The more differences, the longer it’s been since the original gene first appeared.

Next, they turn to the fossil record, which provides a history — for example, when mammals began to sprout hair. If a certain trait — such as hair — appeared around the time a certain gene appeared, then the gene may be responsible for that trait. Last December, Benner announced that his team used this techniqe to identify genes that let cows digest grass and yeast make beer.

He plans to apply the technique to other genes with unknown functions.

Question: Why hasn’t this technique of comparing genes to fossil history been used before?

Coming up with a way to date genes has been a long and complicated process. Even now, dating techniques are still being fine-tuned. But as time passes, dating becomes easier and easier because more and more animal genomes have been sequenced.

Having a lot of available genomes is important, because dating a gene involves comparing the genes in different organisms. The more organisms you have, the easier it is to pinpoint when the gene first emerged.

Steven Benner says, “This is the age of the genome, we have many, many genomes emerging, so you have mouse and man, you have a sizable fraction of rat that is sequenced, and you have the fish, and if you don’t like the fish you have the fruit fly. Using these, you can start going back in time and reconstructing many many histories, for many many proteins. ”

Why is the age hidden in the silent sites of the DNA, not the part of the gene that the makes proteins? Scientists can’t use mutations in the gene itself to date the gene. Mutations in silent sites, or junk-DNA, accumulate more or less steadily over time, But mutations in the gene itself will occur in fits and starts. Here’s why: Imagine there was a gene that was necessary for every single cell on this planet to survive. If this gene mutates, the protein it makes would malfunction and the cells would die. This probably means every living thing will have preserved this gene and its protein pretty much in its original form — it will look pretty much the same in every single animal. But this won’t be true of the junk DNA hidden in the gene. The junk DNA inside the gene is taken out before the gene provides the recipe for the protein. So if mutations occur in the junk DNA, this won’t affect the protein recipe or kill off the organism. So the junk DNA can accumulate mutations. The scientists can then count the mutations and compare them with other species to figure out an approximate age of the gene and the protein it makes. Here’s another reason why tracking mutations in the proper part of the gene won’t give you much of a sense of how old it is.

If you track a cluster of genes through time, you see that changes happen in flurries — the gene doesn’t change slowly and regularly, it changes very quickly over relatively short periods of time.

This happens because some genes can help organisms survive in a certain environment. If the environment changes, any gene that was fine-tuned to the earlier environment will have to adjust. This can lead to a series of rapid changes in a gene, and the protein that it produces. But Benner suggests if you can date the flurry of changes — flurries themselves can give valuable clues, since they suggest the environment is changing. That’s one way to pick genes to date — look for genes that underwent a flurry of changes at some point in history. It’s likely that there will be clues in the fossil record that would give hints about what was going on.

At the American Geophysical Meeting last December, Benner described how his team used this techniqe to find genes that allow cows to digest grass and yeast to make beer.

What you have in your mind?