Junk DNA and selfish DNA

Selfish DNA is a term that became popular with the publication of a series of papers in Nature in 1980. The authors were referring to viruses and transposons that insert themselves into a genome where they exist solely for the purposes of propagating themselves. These selfish DNA sequences are often thought, incorrectly, to be the same as the Selfish Genes of Richard Dawkins¹ [Selfish genes and transposons]. In fact, "selfish genes" refers to the idea that some DNAs enhance fitness and the frequency of these genes will increase in a population through their effect on the vehicle that carries them. It's an adaptationist view of evolution. The selfish DNA of transposons and viruses is quite different. These sequences only propagate themselves—the fitness of the organism is largely irrelevant. These elements do not contribute directly to the adaptive evolution of the species.

Transposons and integrated viruses are subjected to mutation just like the rest of the genome. Deleterious mutations cannot be purged by natural selection because inactivating a transposon has no effect on the fitness of the organism.² As a result, large genomes are littered with defective transposons and bits and pieces of dead transposons. This is not selfish DNA by any definition. It is junk DNA [What's in Your Genome?].

It's important to remember that real selfish DNA makes up only a tiny percentage of the human genome. This is a fact that was not widely known in 1980 although some of the discussion back then alluded to the possibility.

This brings me to a recent article by Itai Yanai and Martin Lercher [Life doesn’t make trash]. They are the authors of The Society of Genes. I wrote a short review of this book where I said that my main beef was their over-emphasis on The Selfish Gene and their adaptationist approach to evolution [Human genome books].

The article in Eon continues the emphasis on selfish genes and adaptation. Read it yourself to see if Yanai and Lercher are adaptationists or not.

Most of the article is about junk DNA. You have to read very carefully to see that the authors have gotten the basic facts correct. They conclude that about 10% of our genome is functional based on the criterion that it is conserved—although I'm not sure that point comes across very clearly. They say,

There is good evidence for this 10 per cent. If we compare our genome to that of other mammals, we find that 90 per cent of the genome was free to change through random mutations. Those DNA letters apparently did not contribute to the efficiency of the survival machine, us. By contrast, mutations in the remaining 10 per cent were weeded out by natural selection because they would have compromised the DNA sequences’ ability to spread – either by damaging the survival machine’s functioning, or by reducing the sequences’ freeloading capacity. This is the definition of function that has traditionally been used by evolutionary biologists as well as by philosophers of science: if something is conserved by natural selection, then it is functional. Function, then, is identified as the feature that ensures the spread or maintenance of a particular DNA sequence.

So far, so good. I disagree with their description of the rest of the genome. They imply that most of it is selfish DNA composed of transposons like Alu's and LINE-1 sequences. I wish they had put more emphasis on the fact that much of our genome consists of defective transposons and viruses that are junk, plain and simple. They aren't acting like selfish DNA today, although they did in the past.

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1. The confusion stems from the fact that Dawkins briefly mentioned these selfish DNAs in his book The Selfish Gene.

2. Strictly speaking, this isn't true. There may be some fitness advantage to eliminating transposons. In species with large populations, this small fitness advantage can lead to small genomes. That explains why most bacteria are not littered with defective transposons.