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An Evolutionary Approach to "Junk DNA"

Last week scientists claimed a new project debunked the notion that some of our DNA is expendible. Evolutionary biologists say that's not necessarily so. We may yet have junk in the trunk.

An Evolutionary Approach to "Junk DNA"

Here's my column for the week of September 9. It will also appear in the health and science section of the Philadelphia Inquirer:

Last week, in response to a media blitz promoting a $288 million DNA project called ENCODE, headlines announced that most of our DNA formerly known as “junk” was actually useful.
A number of scientists both inside the study and out took issue with this claim — which centered on the 98 percent of our DNA that isn’t officially part of any gene.


Sorting the workers from the freeloaders in our DNA is crucial to understanding how our DNA works, and how it drives human evolution and influences our traits and health.
Some biologists dislike the term “junk DNA” because they already knew at least part of it is doing something essential — like regulating how the instructions in the genes are carried out.

The genes hold recipes for making proteins — the working parts and scaffolding of the body. Some of the rest of the DNA tells the genes how much of a given protein to make at any given time.

The goal of the ENCODE (Encylopedia of DNA Elements) project was to figure out which parts have those important regulatory jobs.

According to some scientists involved, they succeeded in pinning down where many of those regulators lurked and identified variants in that DNA that other studies have connected to a variety of diseases. Those findings could lead to new targets for drug research and new avenues for predictive genetic testing.

But long before this project was conceived, scientists had begun to explore our jungle of mystery DNA. The question of non-gene DNA came up in 1975, when researchers discovered that humans and chimpanzees were some 98 percent genetically identical. That meant we and chimps were more closely related than mice were to rats, or chimps were to gorillas.


The researchers who did the comparison pointed out that some of our differences might stem not from the genes, but from our other DNA that is regulating the genes.
That regulatory role is crucial when animals are developing in the womb. Some stretch of non-gene DNA could, for example, signal the human brain to keep growing long after chimp brain development would have shut off.

In recent years, various studies have not only pinpointed important regions of non-gene DNA but connected some with specific traits.

Last year, Penn State biologist Philip Reno and colleagues identified some of those regulatory regions through a comparison across different mammals, from mice and monkeys to chimps and humans. The pieces of DNA most likely to be important are those that look the same across many different organisms. Natural selection tends to hang onto more crucial parts of the genetic code. The parts that don’t influence traits can undergo all kinds of mutations and still get passed on.

Reno’s group identified 500 chunks of DNA that were “conserved” across a number of different animals but lost in us. Nearly all of these chunks were not part of genes, including one piece whose loss resulted in a crucial difference between us and our fellow mammals.

That bit of DNA endows mice, cats, and other mammals with whiskers. It’s also responsible for the little-known fact that most non-human male mammals have whiskery appendages on their penises — a feature sometimes called penis spines. Much discussion has centered on the evolutionary pros and cons of this feature.


Last week’s results from ENCODE offered nothing quite so sexy — but it did help map out where other useful parts of the non-gene material might lie.
What remains in dispute is how much of our DNA is still truly unnecessary and can fairly be called junk. At one extreme, some project leaders said more than 80 percent is “functional” but they waffled a bit on what they meant by that word. 

Other ENCODE members still think we are loaded with junk.
MIT’s Manolis Kellis and colleagues compared a variety of different mammal species and found about 4 percent of the non-gene DNA was shared.
They also looked at stretches of this non-gene DNA that were spelled the same way across humans and found another 4 percent that people share in common.
One common DNA chunk influenced genes for color vision, and another regulates genes for growth of neurons.

These results, if verified, would bring the non-junk total up to about 10 percent, which leaves open the question of what the rest is doing and how it got there.
Another ENCODE scientist, University of Washington’s Josh Akey, said the junk isn’t really there for a reason — it’s just stuff that accumulates by accident, much like the stuff in his garage. We can pick up junk when bits of DNA replicate themselves extra times or copy themselves backward, or when sequences of foreign DNA get inserted by viruses and then copy themselves in new places.

Evolution can slowly clean up genetic material, but it happens more efficiently in some organisms than others. Humans have particularly large, sloppy genomes, he said, thanks to our relatively long generations and, until relatively recently, small total population.

Akey said he’s expanding on the ENCODE results to focus on differences that distinguish us from other apes. He’s also excited about the possibility of comparing the regulatory non-gene DNA from that of the Neanderthals and another extinct human lineage known as Denisovans. Both left behind bones with enough DNA to compare.


Some creationists have tried to assert that a lack of junk proves that an “intelligent designer” did something. Harvard biologist Shamil Sunyaev points out that it doesn’t matter what percentage of our DNA turns out to be employed in some job — it still looks exactly like what you’d expect from natural selection acting on random changes, with no help from a designer.
When you see how cumbersome the system is, he said, “It’s amazing that it all works.”
Contact Faye Flam at 215-854-4977 215-854-4977 or fflam@phillynews.com, or follow on Twitter @fayeflam. Read her blog at philly.com/evolution.

references: http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html

http://www.sciencemag.org/content/337/6099/1159.summary

About this blog
Faye Flam - writer
In pursuit of her stories, writer Faye Flam has weathered storms in Greenland, gotten frost nip at the South Pole, and floated weightless aboard NASA’s zero-g plane. She has a degree in geophysics from the California Institute of Technology and started her writing career with the Economist. She later took on the particle physics and cosmology beat at Science Magazine before coming to the Inquirer in 1995. Her previous science column, “Carnal Knowledge,” ran from 2005 to 2008. Her new column and blog, Planet of the Apes, explores the topic of evolution and runs here and in the Inquirer’s health section each Monday. Email Faye at fflam@phillynews.com. Reach Planet of the at fflam@phillynews.com.

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