Evolution 101

Saturday, March 04, 2006

What is Junk DNA?

Chris Morris asks “What are currently the best explanations for the origin and function (if any) for so called ‘junk DNA’?”

What does it mean to talk about “junk” DNA? Well, first of all, it’s not a scientific concept, and so it’s extremely vulnerable to confusion, especially by laypeople. Briefly, “junk” DNA refers to the content of a genome that does not contain functional genes. A more accurate term to use is “noncoding” DNA, because “junk” is a pretty subjective adjective. One man’s junk can be another man’s treasure, as anyone who’s ever shopped at a yard sale knows well. The same thing could be said, more or less, about “junk” DNA.

An organism’s genome is comprised of the sum total of all the genetic information it contains. In most organisms, this is divided up into distinct units called chromosomes. Each chromosome, in turn, is a long chain of nucleotide bases, millions and millions of bases long. The analogy is often used of a genome being compared to a library of books, with each separate bookshelf compared to a separate chromosome. Each book represents a section of the chromosome, and contains different stories, which represent individual genes.

The problem with this analogy is that in the books, the stories are separated by pages and pages of garbled text, that aren’t meaningful as stories at all. In addition, the stories themselves are cut up into many different parts, each separated by pages or sections of pages of nonsense text. I’ve never seen a book like this, but I have seen plenty of magazines. To understand this better, it helps to think of noncoding DNA as advertisements in a magazine, and the genes as individual articles. Usually there are pages and pages of advertisements that separate each article from each other, and the articles themselves are often split up. A three-page article might start on page 50, be interrupted by ads on page 51, resume on page 52, be interrupted again on page 53, and then finish on page 54. Although the article itself only took up three pages in the magazine, it was a full five pages from start to finish, if you include the advertisements.

Genes are split up like this in the genome. If you examine the genomic sequence that results in the expression of a particular protein, you’ll find that there are segments of the sequence that don’t actually translate into protein sequence, but which separate regions of the sequence that do. In molecular biology, the regions of the genomic sequence that are translated into protein are called exons, and the regions that are not are called introns. So, exons are analogous to the article itself in a magazine, and the introns are analogous to the ads.

Now, the obvious question is, why have introns? Just like you could go through a magazine, cut out the advertisements, and lose none of the article, it’s also possible to cut out the introns from a genomic sequence and get normal expression of a gene. (This is called cDNA- briefly, it’s made by reverse-transcribing mRNA) It’s this question that gets most creationists fidgety- having introns just seems more than a tad inefficient, since each cell has to expend some energy in cutting them out during gene expression. The criticism has been made that a perfectly efficient Creator wouldn’t design a gene expression mechanism and then clutter it up like ads clutter up the average magazine. Well, it turns out that having gene expression work this way actually makes great evolutionary sense. You see, if an organism is able to radically modify an existing gene, then it might be able to use it for a different purpose. A good comparison for this is something like a cordless electric screwdriver. It would cost too much to buy a dozen different screwdrivers, each with different bits, and so they all come with interchangeable bits that all interlock with the motorized axle. This lets you use the same basic function for different applications. Many genes are like this also. It turns out that the existence of introns allows for the gene expression machinery to decide which exons to include in the final gene product. This process is called “alternative splicing,” and it effectively increases the amount of variability in the genome without being dependent on individual mutations. Instead, any given gene can produce alternatively spliced versions of itself that may be advantageous in different situations.

So, even though intronic sequences are noncoding, it’s pretty clear that they’re certainly not useless.

Well, okay, that’s all well and good for the noncoding DNA that exists within a gene itself, but what about the long stretches of noncoding DNA that separates each gene from the other?

Well, that’s not completely worthless either. There exist in an uncertain boundary around each gene in the genome, a region of noncoding DNA that still plays an important role in DNA expression. These are called regulatory sequences. Imagine that the DNA expression machinery is a road crew truck filled with safety barrels. The road crew only wants to put the barrels down where there’s going to be work done, and so it looks for a sign along the road to guide it. Let’s say, the work is going to be done between mile marker 13 and 14 on a particular highway. Well, the road crew is going to watch for the mile marker 13 sign on the side of the road, and then they’re going to start putting barrels down. Regulatory sequences work in a similar way. The DNA machinery is looking for a gene sequence in the genome, so it can start making protein. But in order to start transcribing the DNA, it needs to know where to start. The regulatory sequence is a physical marker for this, in that it physically interacts with the DNA machinery. Once the DNA machinery binds to the regulatory sequence, it can start transcribing the sequence downstream, even though the regulatory sequence itself doesn’t get transcribed. Because this sequence promotes the transcription of the gene it’s next to, it’s called a promoter sequence, and it’s very important.

So, here are two clear-cut examples of how noncoding DNA is actually very essential to the proper expression of genes in the genome, despite the fact that it doesn’t get transcribed itself, and never becomes a protein. It’s at this point that creationists often crow about the “supposed junk DNA” that isn’t really junk at all. Clearly, there’s an important purpose to this junk DNA, so it can’t be used as a criticism against special creationism, right?

Well, not exactly. You’ll notice that most of the concepts I discuss here are not clearly black or white, and this is no exception. While it is true that there are some sequences of noncoding DNA that are important, there is far more noncoding DNA that has no recognizable purpose. For example, there are short repeating segments of DNA called microsatellite regions. These differ wildly between different individuals, and are most commonly used to screen for genetic parentage. There are regions of DNA that do nothing but shuffle around inside the genome itself, called transposons and retrotransposons, depending on their mechanism of mobility. One variant of these, called Alu sequences, make up close to 10% of the human genome. There are genes which have become broken and do not work anymore, called pseudogenes, that still inhabit the genome despite being completely nonfunctional.

Now, despite the fact that most of the noncoding genome could be considered truly junk, creationists often raise the objection that there could be some unknown purpose for the rest of the noncoding genome that science has not yet discovered. This may be true, but it is not a good argument. We should no more assume that all noncoding DNA isn’t junk because we haven’t yet found a use for it than we would assume that all rocks are gems just because we haven’t yet found anyone who wants to wear a limestone necklace.

So, just to review, the majority of a genome (at least, the human genome) is noncoding sequence. Some of this noncoding sequence is truly junk, as in the case with transposons, pseudogenes, etc., and some of it is important for proper genetic expression. It’s not all junk, but it’s not all gold, either.

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