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Tuesday, October 21, 2014

The RNA Virus Paradox

Posted by jlwile on May 18, 2010

A diagram of HIV, which is a retrovirus (image in the public domain)

Dr. Peter Borger has an incredible series of articles on genetics and the design of life over at Creation Ministries International’s website. The ones to which I refer begin with “Evidence for the design of life…” While I plan to write about many of the major concepts discussed in these articles, I want to start with sort of a “sidelight” that appears in part 3 of his series.

Not too long ago, I wrote about the fact that evolution (in the ‘goo to you’ sense) is, at best, an unconfirmed hypothesis. A commenter, Grant C, tried to convince me that it is something more by offering several lines of evidence for evolution. Of course, I attempted to educate Grant on what the evidence really meant, but after only a few exchanges, he stopped responding.

One of his major lines of evidence for evolution was endogenous retroviral insertions (ERVs) in the genomes of primates. If you don’t know what ERVs are, you need to first learn what a retrovirus is.

Many viruses, such as the chickenpox virus, are DNA viruses. They either get into a cell or inject their DNA into a cell, and the cell’s reproductive machinery is “hijacked” by this DNA to produce more viruses. Eventually, so many viruses are produced that the cell is killed, and the new viruses are released to infect and kill more cells.

Other viruses, like the influenza virus, are RNA viruses. Rather than having DNA as their genetic material, they have RNA. Nevertheless, the mechanism of infection is often similar to that of the DNA virus. In this case, however, the RNA “hijacks” the cell’s reproductive machinery to produce new viruses, which eventually kill the cell and leave it to infect other cells. Compared to DNA, RNA is much more prone to mutation, so RNA viruses mutate rather rapidly. As a result, RNA viruses are often harder to combat with vaccination than are DNA viruses. This is why the chickenpox vaccine produces long-term immunity to chickenpox (caused by a DNA virus), but the flu vaccine must be given every year. The influenza virus (an RNA virus) mutates frequently, so the vaccine must be changed to deal with the new versions of the virus that mutation produces.

Retroviruses (like HIV, the virus that causes AIDS) are a special type of RNA virus. They don’t infect cells in the same way that DNA viruses or the other types of RNA viruses do. Instead, when they infect cells, their RNA is converted into DNA, and that DNA is then inserted in the cell’s genome. That way, the retrovirus is replicated as a part of the cell’s DNA. Usually, a retrovirus doesn’t kill the cell it infects, because if the cell stays alive, it can produce more retroviruses.

The main point for this discussion, then, is that retroviruses actually end up inserting DNA into a host’s cell. This has been studied long enough that we know what these insertions look like, and if we look at a genome, we can recognize segments of DNA that look like the things a retrovirus would insert. In the human genome, for example, there are more than 300,000 such segments, which make up about 8 percent of the total human genome.

Evolutionists think that these sequences, which they call ERVs, are the remnants of retroviral infections that occurred long ago. In fact, they think that they can find ERVs that humans share with other primates, and by tracking the similarities between human ERVs and the ERVs in other primates, they can demonstrate evolutionary relationships. This, however, leads to a paradox.

When evolutionists actually compare the gene sequences of RNA viruses that exist today and make their typical assumptions about mutation rates and evolutionary dynamics, they come to the conclusion that the RNA viruses we see today originated, at most, 50,000 years ago. Why is this a paradox? Well, remember that retroviruses are RNA viruses, and they are supposed to have been infecting primates long before humans evolved. Thus, in evolutionary terms, they need to be much older than 50,000 years old.

The paper I linked above has a good discussion of this paradox, and it proposes three explanations for the fact that the RNA viruses we see today seem to be of far-too-recent origin. The first two explanations revolve around the assumptions used to produce the conclusion that these viruses originated only 50,000 years ago. According to the paper, it is possible that the mutation rate assumptions are wrong, which would mean the figure of 50,000 years is wrong. It is also possible that the concluded evolutionary relationships are wrong, which would also mean the figure of 50,000 years is wrong.

The third explanation is that the 50,000-year figure is correct, and that the previous RNA viruses that gave rise to the current viruses are all extinct now. In other words, RNA viruses have been around for a long, long time, but the ancient lines have all gone extinct, and only the most recent lines are around right now.

Dr. Borger proposes a fourth explanation. He doesn’t think the assumptions about mutation rates are correct, but he does think that the relative order of origin is. In other words, he thinks that people came first, and retroviruses came later. In fact, he thinks that retroviruses have formed as a result of the design of different creatures’ genomes.

In his articles, he argues that God created the original kinds of creatures with genomes that were designed to produce variation. These original genomes, which he calls baranomes, had several elements that were designed to produce genetic variation. He calls these elements variation-inducing genetic elements (VIGEs), and he thinks their function is to encourage genetic variation that leads to adaptation. He identifies specific types of VIGEs in the genomes of the major forms of life, and ERVs are one kind of VIGE in mammals.

So where do retroviruses come from? According to Dr. Borger

Now that we have redefined ERVs as a specific class of VIGEs, which were present in the genomes from the day they were created, it is not difficult to see how RNA viruses came into being. RNA viruses have emerged from VIGEs…all RNA viruses have their origin in the genomes of living cells through recombination of host’s DNA elements (genes, promoters, enhancers). Every now and then such an ‘unfortunate’ recombination produces a molecular replicator: it is the birth of a new virus. Once the virus escapes the genome and acquires a way to re-enter cells, it has become a fully formed infectious agent.

So in Borger’s mind, ERVs are not the remnants of retroviral infections. Instead, retroviruses are the products of ERVs. Obviously, such an explanation will require a lot more work and a significant amount of evidence, but I see two things that currently point in its favor. First, the RNA virus paradox is no longer a paradox. Retroviruses did, indeed, come after mammals and people. Second, the fact that ERVs have been demonstrated to have function in the human genome makes a lot more sense if they were are part of the created genome and not something that was the result of an infectious agent.

Thus, while this question is far from settled, I think Dr. Borger is on a productive track. I am glad that excellent, original scientists like Dr. Borger are in the young-earth creationist camp!

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