Junk DNA: A Journey Through the Dark Matter of the Genome by Nessa Carey

An Introduction to Genomic Dark Matter
    Imagine a written script for a play, or film, or television programme. It is perfectly possible for someone to read a script just as they would a book. But the script becomes so much more powerful when it is used to produce something. It becomes more than just a string of words on a page when it is spoken aloud, or better yet, acted.
    DNA is rather similar. It is the most extraordinary script. Using a tiny alphabet of just four letters it carries the code for organisms from bacteria to elephants, and from brewer’s yeast to blue whales. But DNA in a test tube is pretty boring. It does nothing. DNA becomes far more exciting when a cell or an organism uses it to stage a production. The DNA is used as the code for creating proteins and these proteins are vital for breathing, feeding, getting rid of waste, reproducing and all the other activities that characterise living organisms.
    Proteins are so important that in the twentieth century scientists used them to define what they meant by a gene. A gene was described as a sequence of DNA that codes for a protein.
    Let’s think about the most famous scriptwriter in history, William Shakespeare. It can take a while for us to tune in to Shakespeare’s writings because of the way the English language has changed in the centuries since his death. But even so, we are always confident that the bard only wrote the words he needed his actors to speak.
    Shakespeare did not, for example, write the following:
vjeqriugfrhbvruewhqoerahcxnqowhvgbutyunyhewqicxhjafvurytnpemxoqp[etjhnuvrwwwebcxewmoipzowqmroseuiednrcvtycuxmqpzjmoimxdcnibyrwvytebanyhcuxqimokzqoxkmdcifwrvjhentbubygdecftywerftxunihzxqwemiuqwjiqpodqeotherpowhdymrxnamehnfeicvbrgytrchguthhhhhhhgcwouldupaizmjdpqsmellmjzufernnvgbyunasechuxhrtgcnionytuiongdjsioniodefnionihyhoniosdreniokikiniourvjcxoiqweopapqsweetwxmocviknoitrbiobeierrrrrrruorytnihgfiwoswakxdcjdrfuhrqplwjkdhvmogmrfbvhncdjiwemxsklowe
    Instead, he just wrote the words which are underlined:
vjeqriugfrhbvruewhqoerahcxnqowhvgbutyunyhewqicxhjafvurytnpemxoqp[etjhnuvrwwwebcxewmoipzowqmroseuiednrcvtycuxmqpzjmoimxdcnibyrwvytebanyhcuxqimokzqoxkmdcifwrvjhentbubygdecftywerftxunihzxqwemiuqwjiqpodqeotherpowhdymrxnamehnfeicvbrgytrchguthhhhhhhgcwouldupaizmjdpqsmellmjzufernnvgbyunasechuxhrtgcnionytuiongdjsioniodefnionihyhoniosdreniokikiniourvjcxoiqweopapqsweetwxmocviknoitrbiobeierrrrrrruorytnihgfiwoswakxdcjdrfuhrqplwjkdhvmogmrfbvhncdjiwemxsklowe
    That is, ‘A rose by any other name would smell as sweet’.
    But if we look at our DNA script it is not sensible and compact, like Shakespeare’s line. Instead, each protein-coding region is like a single word adrift in a sea of gibberish.
    For years, scientists had no explanation for why so much of our DNA doesn’t code for proteins. These non-coding parts were dismissed with the term ‘junk DNA’. But gradually this position has begun to look less tenable, for a whole host of reasons.
    Perhaps the most fundamental reason for the shift in emphasis is the sheer volume of junk DNA that our cells contain. One of the biggest shocks when the human genome sequence was completed in 2001 was the discovery that over 98 per cent of the DNA in a human cell is junk. It doesn’t code for any proteins. The Shakespeare analogy used above is in fact a simplification. In genome terms, the ratio of gibberish to text is about four times as high as shown. There are over 50 letters of junk for every one letter of sense.
    There are other ways of envisaging this. Let’s imagine we visit a car factory, perhaps for something high-end like a Ferrari. We would be pretty surprised if for every two people who were building a shiny red sports car, there were another 98 who were sitting around doing nothing. This would be ridiculous, so why would it be reasonable in our genomes? While it’s a very fair point that it’s the imperfections in organisms that are often the strongest evidence for descent from common ancestors – we