Junk DNA

Ever have that urge to go out on a dig and discover your very own fossil?  Or is that a bit too hot/cold for you?  A bit too dirty?  Then let me suggest a more sedentary alternative.

Most people know that the majority of our genome is composed of what we call “junk” DNA.  Much of it is non-functional templates left by ancient viruses, accidental copies of functional genes, or places where the mRNA is copied back into the genome.  Academically thrilling, perhaps, but a bit of a yawner for the rest of us.

But there is another kind that I think is fascinating: “fossil DNA.”

Fossil DNA is the term Sean Carroll (author and researcher in Evolutionary Developmental biology or Evo Devo) uses to describe DNA that once had a function, but has been made unnecessary by evolution.  Genes that are truly necessary for our survival are the exact targets for natural selection.  Any mutation in such a gene tends to be quickly weeded out.  In effect, the gene’s integrity is protected.

But how about genes that once were vital and have become less so?  Natural selection simply does not operate there.  Such genes are no longer protected from changes.

Take, for instance, the human sense of smell.  Once it was at least as important as sight, but we changed.  Our upright posture and the open savannas combined to make sight much more useful than smell.  And you can see this in the genome.

There are olfactory genes (i.e., genes that directly or indirectly contribute to the acuity of the sense of smell) that we share with some of our animal cousins.  But they have about twice as many functional genes than we do.  Interestingly, we can see damaged copies of some of those missing genes in our junk DNA.  In other words, we can actually see that once upon a time we used those genes, implying a lifestyle where smell was vital, but then took another path.  As smell became less important to us, damage to those genes was no longer selected against.  Mutations were tolerated to the point that the genes became non-functional.

But a lot of information can still be derived from those genes.  Since mutations occur at a fairly predictable rate, scientists can look at those non-functional genes, compare them to the functional versions in animals, count the differences, and figure out how long ago we changed to being sight-oriented.

So we can say that every organism’s DNA has some “fossils” that mark the evolutionary path it followed and many of those fossils can be dated.  We can also say that if two related organisms have comparable “fossils” sharing many DNA errors but not all, we can figure out when they split from their common ancestral branch.

For another example, let’s look at vision.  Specifically, color vision.

Color vision involves some proteins called opsins.  There are five different types: one type in the rods for night vision and four in the cones that help see at specific wavelengths (i.e., in color).  If all of those four opsins are to be protected by natural selection, all four frequency ranges (i.e., color bands) have to be necessary.  And for some animals, that’s no longer true.

The owl monkey, the only nocturnal species of the higher primates, has acquired nighttime habits that make short wavelength vision (i.e., violet) useless.  Hence, that part of his genome displays lots of errors and it no longer makes that group of opsin proteins at all.

Whales, although they used to be land mammals, have such modified DNA that they really only see in a fairly narrow blue band.  All the other opsins genes are inactive.  The fascinating part is that their functional opsins are shifted over to peak at exactly the narrow range of blue where ocean water has the best transmission.

Hard rock fossils, wonderful as they are, are static.  By looking at them we can see the result of evolutionary changes (feathers, teeth, etc.), but not the changes themselves.  By parsing DNA and comparing its genes to its cousins’, we can see the how and when of the behavioral and environmental changes that an organism went through in its evolution.

Still, if you have that urge to dig, let me suggest an alternative:

Among the many things I don’t understand, there’s this: There are people in this world who, when they are invited to a ’60s party that calls for tie-dyes, bell-bottoms, and a furry vest, simply have to dig into the back of the closet.  To put it another way, there are people whose closets are made up of stratigraphic layers.  The deeper you dig, the further back you move in time.  You get the feeling that, if you dug long enough, you’d reach the level where actual petrification was occurring.

Just think: With a little effort, you could be the discoverer of Fossil Jeans.

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