Jan 12 2010

Endogenous Viruses and “Junk” DNA

A recent report in Nature discusses the finding of a new type of viral inclusion in animal DNA, including humans. About 8% of the human genome is actually comprised of viral DNA – bits of viral genetic code that have been inserted at sometime in the past through a process called endogenization.

Up until now the only source of these viral endogenous elements was retroviruses – virsues that can take their RNA and make it into DNA that can be inserted into the DNA of the host organism it is infecting. Retroviruses then exploit the replicating machinery of the host to crank out more copies of themselves.

So it makes sense that these retroviruses can have their DNA occasionally wind up in the genomes of the animals they infect – which can happen when the viral DNA is inserted into a germline cell (sperm or egg) and then can be passed onto the next generation. Usually cells that are so infected die, but it can happen that a mutation occurs in the viral DNA after it is inserted rendering it non-functional. It is therefore stuck there and gets pass on as “junk” in the DNA.

Now researchers report the first evidence of non-retroviral endogenous regions from many animal species, including humans – from the bornavirus, or borna disease virus (BDV). BDV is not a retrovirus and does not have reverse transcriptase – the enzyme necessary to turn RNA into DNA – but its life cycle takes place in the nucleus of host cells. Apparently it spends so much time replicating in the nucleus that bits of its RNA can get converted to DNA and stuck in the host genome. This is a less common event than with retroviruses, but it happens. BDV DNA has been found in infected cells.

They also found two instances in humans of endogenous BDV sequences that had open reading frames – which means they were functional enough to actually code for proteins. These proteins are actually being made inside cells, but they have no apparent function.

This is not the first instance of this phenomenon. Essentially, viral bits get stuck in genomes where they mutate and degenerate and become useless bits of junk. But occasionally mutations may render these bits viable – able to make proteins. These proteins probably start out as useless, and may mutate back into uselessness. But they also may be co-opted by the host (through chance mutations) to serve some useful purpose.

Implications for Evolution

Creationists don’t like the notion of junk DNA, any more than they like the concept of vestigial organs – the two concepts are closely related. Both imply an evolutionary past. Both also are partly founded upon an argument of exclusion, which they try to present as an argument from ignorance (but there is a subtle difference). An argument from exclusion basically says that we do not know of any function for junk DNA therefore it probably has none. Such arguments are only as good as the extent to which we have searched for a function. After about a century of genetics, and half a century of studying DNA, we have a reasonable level of confidence that much of junk DNA is indeed junk. You cannot prove once and forever a negative claim, but you can get to high levels of confidence.

An argument from ignorance takes the form – we do not know what the function of junk DNA is, therefore it has this specific function (for which there is no positive evidence).

It is also true that over the years we have discovered functions for some of what was previously considered junk DNA, but only a small fraction. This was to be expected. Initially scientists identified the coding regions of DNA – those bits for the parts of genes that directly code for proteins. Near these coding genes were also identified regulatory regions – these determine when and how the gene is expressed. But between these coding and regulatory regions are vast sections of DNA with no apparent function, despite extensive efforts to find one. This is the so-called junk DNA.

But it is not surprising that over the years, as we learn more and more about the complexity of DNA, its function and regulation, we would discover that some parts of that junk DNA do play a role in DNA function (for example, in regulating gene expression). What creationists do is immediately extrapolate from such discoveries to the unwarranted conclusion that all of junk DNA has some hidden function. This is a position they can maintain forever, as it does not require any evidence on their part.

But there is also more to our knowledge of junk DNA than just that we cannot find a function for it – such as the identification of viral endogenes and pseudogenes. These are stretches of DNA that not only have no known function but also correspond to known segments of viral RNA. Why would there be a stretch of DNA in the human genome that looks like a bit of a viral gene, but incomplete and apparently non-functioning? This is more than an argument of exclusion. Also – why would it be that the only viral segments we have discovered are from retroviruses and now BVDs?. If you make the argument that the creator is recycling some viral code, why only from those that either place their RNA in animal genomes as part of their lifecycle, or at least replicate in the nucleus and occasionally make some DNA?

But it also gets better, because these viral endogenous DNA segments are not sprinkled at random throughout the animal kingdom – they occur in a pattern consistent with our picture of common descent. In other words, we find the same endogenous viruses in the same locations in related species – in an evolutionary pattern.

There is a coherence to the evolutionary explanation of endogenous viruses, with multiple lines of evidence converging on evolution as the answer.


We are likely to find more functions, or at least effects, of some of what is now called junk DNA, but not all of it. Nature is resourceful and makes use of what is there, but it is also messy and clutter does not go away unless it provides a significant enough disadvantage to survival. So our DNA is a bit cluttered.

But there is useful information in that junk DNA – it is partly a record of our evolutionary past, and it provides powerful evidence for common descent. In fact, common descent is the only viable explanation for the pattern of endogenous viruses we have discovered in various species. Creationists don’t have a viable alternative scientific hypothesis (just their go-to default untestable explanati0n – goddidit) – they can only take pot shots at the science in order to generate confusion and doubt. That is because creationism is not a science, it is denialism, and confusion and doubt is all they have.

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