Do Endogenous Retroviruses (ERVs) Support Common Ancestry?

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The strength of Darwin’s argument was common ancestry.1 Darwin agreed that if we evolved from monkeys, then we shouldn’t see monkeys today. Thus, rather than suggest we came from monkeys, he insisted that we shared a common ancestor with them. According to Darwin, we share certain features with other organisms because of common ancestry rather than common design. Even though the science of genetics revolutionized Darwinian evolution, some “old” ideas persisted within neo-Darwinism with a twist. Instead of looking for visible features that organisms share in common, secular scientists are looking for DNA sequences that organisms share in common. One of these evidences that evolutionists commonly cite is called Endogenous Retroviruses (ERVs).

What Is an Endogenous Retrovirus (ERV)?

Endogenous Retroviruses can easily turn into one of those terms evolutionists hide behind to try to “prove” they are right. While the word can be a mouthful and the letters sound like alphabet soup, ERVs can be understood by separating the various parts into understandable chunks.

The easiest part to understand about ERVs is that they are viruses. In this fallen world, we understand viruses to be obligate intracellular parasites. That’s a fancy way to say that viruses are extremely small parasites that feed off our cells. Viruses are efficient machines that carry only what they need to infect the next cell. Among the variation of viruses that exist is a subset of viruses known as retroviruses.

Perhaps the most famous retrovirus is the Human Immunodeficiency Virus (HIV). The claim to fame for all retroviruses is that they modified what is known as the Central Dogma of Molecular Biology. The Central Dogma of Molecular Biology says that DNA is converted to RNA, which is converted to protein. Retroviruses modified the Central Dogma by demonstrating a method of converting RNA into DNA using the enzyme reverse transcriptase. Reverse transcriptase is the hallmark characteristic of all retroviruses.

One of the unique features of retroviruses . . . is their ability to integrate into the host genome and remain there for long periods of time.

Typically, we think of retroviruses existing outside of us and spreading from one person to another (exogenously). While this is how retroviruses often work, there is a significant proportion of retroviruses that remain inside of cells. Retroviruses that remain inside cells are referred to as endogenous retroviruses. One of the unique features of retroviruses (and one of the mechanisms that makes HIV such a deadly disease) is their ability to integrate into the host genome and remain there for long periods of time (possibly even permanently).

So an Endogenous Retrovirus (ERV) is a piece of DNA found inside an organism’s genome that looks like a retrovirus. ERVs have particular DNA sequences that molecular biologists can use to identify them.

To limit the disruption these viruses can cause, mammals produce proteins that can keep most of them locked down. Eventually, most endogenous retroviruses mutate so much they are reduced to genetic baggage, unable to do anything at all. Yet they still bear all the hallmarks of viruses, and are thus recognizable to scientists who sequence genomes.2

ERVs normally stay in one location in the genome, but they are also known to jump around the genome and insert into different places.3 For that reason, ERVs are often called “jumping genes.”4 ERVs are one potential way to generate diversity within a species from generation to generation, depending on where the insertion occurs.

How Do Evolutionists Claim the ERVs Support Common Ancestry?

A powerful source of evidence that modern species diverged from ancestral species via descent with modification is that of endogenous retroviruses (ERVs).5

One important aspect of ERVs that garners a lot of attention is that ERVs can be found in the exact same location in the genome across a variety of species. Evolutionists combine this fact with their preconceived ideas of common ancestry and come up with the idea that ERVs demonstrate evolution. For example,

ERVs are usually species-specific, inserted almost randomly in the host genome, and the error or mutation that inactivated the gene is random. If two organisms share the same ERV in the same location with the same inactivation mutations, then they almost certainly share them due to common inheritance and not two separate infections. Researchers analyze shared ERV insertions across species to construct phylogenetic trees. For example, the common ERVs in simians indicates they share a common genome. When phylogenetic trees are constructed based on the pattern of ERVs, they indicate humans share more ERVs with chimps than either share with gorillas. Other examples are known. This is strong evidence for common descent.6

Evolutionists argue that ERVs should be found in evolutionarily related species because of common ancestry. Therefore, they claim ERVs to be proof of evolution since we find certain ERVs in the exact same location across the genome of “evolutionarily related” species. As a result, ERVs have become an often cited evidence “proving” that evolution is true.

However, we know that evidence doesn’t speak for itself. Part of the scientific method demands interpretation. Since every scientist has to interpret the evidence, their interpretation bias affects what they say about origins. So ERVs, in and of themselves, do not prove evolution any more than they prove creation. Since we know the Word of God is true, we know that ERVs cannot be proof of evolution. There are several arguments opposing the evolutionary fairy tale that ERVs prove common ancestry.

Where Did ERVs Come From?

Evolutionists will say that shared ERVs prove evolution to be true because of common ancestry and that common ancestry assumes that there will be shared ERVs. Making such a claim is silly because this kind of circular reasoning is unsupported by any outside information. In fact, there are several characteristics of ERVs that strongly support a biblical worldview.

1. ERVs Are Not Junk

The fact that any ERVs . . . exist among primates at all strongly argues against common ancestry by itself.

Assuming the Darwinian hypothesis is correct, ERVs would have inserted into the genome and remained there for millions of years. This is why evolutionists say they see shared ERVs in many organisms today that shared a common ancestor millions of years ago. Josh Dubnau at Cold Spring Harbor Labs said, “We’ve had these things in our genomes for millions of years. Anything that can be used by evolution will be used by evolution.”7 Dubnau’s statement can easily be turned into the following assertion: evolution eliminates what will be eliminated by evolution. It is important to realize that evolution works based on a “use it or lose it” basis. The fact that any ERVs (which are “leftover, useless” pieces of DNA) exist among primates at all strongly argues against common ancestry by itself.

But why should so-called junk DNA be conserved for millions (even billions) of years of evolution when it supposedly has no purpose? The argument of junk DNA simply perpetuates the problems with the vestigial organs argument, but at the molecular level. If the genome has no purpose for such elements by evolutionists’ reasoning, then it should have been eliminated millions of years ago. You can’t have your cake and eat it, too.

2. Saying “ERV” Does Not Prove Evolution

Another problem with the idea that ERVs support common ancestry is the logical fallacy known as the “argument from ignorance.” Simply finding ERVs in a genome is not sufficient proof common ancestry occurred. ERVs do not come with a birth or death certificate. Therefore, there is no way to know beyond a shadow of a doubt (as many evolutionists claim) that this somehow proves evolution. Moreover, evolutionists are not willing to imbibe arguments suggesting alternative explanations for why we find ERVs where we do. Surely some evolutionists could retort saying that we are holding to a “God of the gaps” to rescue our position, but that simply is not the case. For one, evolutionists have their own version of a “God of the gaps.” It’s called “Evolution of the Gaps.”

Further, scientists are finding actual functions for a number of ERVs, which declassifies them as junk and demotes the argument that they are evolutionary proof for common ancestry to just wishful thinking. “Absence of proof is not proof of absence”—attributed to William Cowper.

I would really like an evolutionist to tell me why the only reason an ERV exists in the genome is to prove common ancestry. Pigeonholing ERVs as solely proof of common ancestry leads to myriad problems in doing good science. When you assume the outcomes of your experiments before conducting them and fit the data to your own interpretation, you leave the realm of science and enter the realm of self-fulfilling prophecy.

3. ERVs Are Strong Support for Design, Not Evolution

Perhaps the strongest argument against ERVs proving common ancestry is the idea of “plagiarized mistakes” presented by Dr. David DeWitt. In his book Unraveling the Origins Controversy (2015), he states,

When a teacher has two tests submitted that are the same, it suggests that the two students cheated. However, if the students both got 100%, the fact that they are the same does not mean that they cheated. However, if the students both got 60% and had identical incorrect (original emphasis) responses, then this would be convincing evidence that the students did in fact cheat. . . . Plagiarized mistakes lead one to believe that they are both derived from a common source. In the same way, evolutionists argue that there are plagiarized mistakes that are common in different types of organisms. . . . However, in order to have a “plagiarized mistake” two conditions must be met. Both sources [of information] must be the same and there must be an error (or in this case a mutation without a function.) While there are examples of these mistakes in common, there are plenty of ones that are not. (234–236)

When comparing any given stretch of DNA sequence, the best anyone can say in favor of common descent is that it appears related. However, this idea is limited because it ignores the fact that ERVs could exist in similar places in different genomes with the exact same sequence in order to perform an essential function. The number of ERVs coding for important proteins continues to grow and the concept that they have no function is disappearing with each genome sequenced.8 One example is an essential ERV required for mammalian development.9

When sequences are identical, claiming common ancestry is a moot point because they could be part of what is considered essential for life as designed by God, and we simply don’t know what they do yet. When the sequences are similar, claiming common ancestry is disputable because they aren’t identical. If there were a common ancestor identified because of ERV similarities, then the ERV mistakes would have to be in exactly the same places consistently through shared common ancestry; however, while there are some similarities, the kinds of the differences and their magnitudes are inconsistently shared through supposed common ancestral lineages. Therefore, an ERV similarity cannot be the basis for determining whether two organisms share common ancestry (no matter what kind of convergent evolutionary rescuing device is used). It is a vicious catch-22 that they cannot reason their way out of. At the end of the day, it is reminiscent of the question, which came first—the chicken or the egg? No one can even say which came first when ERVs are quickly becoming or already were an essential feature of the genome.

4. ERV Identities and Similarities Are Not One and the Same

An idea related to “plagiarized mistakes” is the basis on which it is built: percent similarities. Evolutionists often hide behind the idea of percent similarity at the DNA level on a number of issues (ERVs are no exception). However, biologists often use the word similarity in a very different way than the general public perceives it. Biologists have three working definitions for the word similar: similar-similar, similar-dissimilar, and dissimilar-dissimilar. Similar-similar means identical and is like comparing an orange to an orange. Similar-dissimilar means that there are slight differences, but it is mostly identical, like comparing an orange to a lemon (i.e., they’re both citrus). Dissimilar-dissimilar means that there are no identical regions and that it is completely different, like comparing an orange to an apple. The analogy of different fruits works in a common understanding of percent similarity, but it breaks down horribly at the DNA level because these different kinds of “similarities” abound everywhere. The only reason that some ERVs are used as evidence for common descent at all is because they are similar-similar. Others are brought into the conversation to bring additional weight to the argument because they are similar-dissimilar. But what about the ERVs that are dissimilar-dissimilar? Should they even be considered? With all three categories of similarity, it is confusing to really get at what is meant by “similar” when a biologist uses the term. For ERVs, one cannot help but wonder where to draw the line between the relevant and the irrelevant. God only knows, and He hasn’t revealed these details to us in His Word.

5. Evolutionists Have No Origin of Any ERVs

Without a clear naturalistic selective mechanism for how ERVs are selected for in a particular place, or the function they serve, we cannot see the big picture.

One last problem associated with citing ERVs as proof of evolution is that no one can provide a naturalistic selective mechanism for how they “jump” in DNA from generation to generation. The movements are said to be random, and how can anyone describe a random event? While we know the parts to the molecular puzzle, we are missing the big picture (natural selection acting on DNA) of why each piece fits where it does (or moves where it does from generation to generation). Without a clear naturalistic selective mechanism for how ERVs are selected for in a particular place, or the function they serve, we cannot see the big picture. It is highly probable that ERVs “jumping” is a result of the Fall of Adam. Sin entered the world and what was once perfect, and properly functioning, changed into something that it was never meant to be. The picture painted by evolutionists is that they are the only ones who can provide a naturalistic mechanism for why certain ERVs are selected for and conserved in disparate genomes. Even more, they insist that they, therefore, should be the only trusted ones. People claiming to be the sole source of information for the general public ought to be heavily scrutinized, and the burden of proof remains with them if they cannot prove otherwise. Without having a clear selective advantage, they don’t have a leg to stand on.

A Biblical View of ERVs

It is relatively easy to see that ERVs are poor evidence for common ancestry. With arguments such as these presented here, one can easily shoot down critics and silence the opposition. But the real question remains: is there any model available to describe what is actually happening? Several biblical creationist ideas exist.

In a recent study performed by Dr. Alfred Roca and his team at the University of Illinois, Dr. Roca found that there are retroviruses that have integrated into the genome of the koala and seem to be “protecting the host”; however, this is only after the host has accepted the ERVs.10 Dr. Roca stated,

It seems likely that for thousands of years since this virus integrated, the koala host has suffered fitness effects. It is possible that across species, when a host lineage has been invaded by ERVs, it had to go through this process of adaptation between host and virus, which is a very sad finding.

A number of ideas have been suggested as to why the retrovirus is inserting into the Koala genome, but the Koala clearly isn’t dying from this event and seems to be thriving to the contrary. Dr. Roca says,

[Once] retroviruses become part of the host, they begin to help the host . . . Which is the lesser of two evils? . . . Do you try to conserve genetic diversity, which is present in the northern populations along with the retrovirus or do you conserve southern populations that don’t have the retrovirus but are horribly inbred?

Thriving because of an ERV is worth giving serious consideration, because it provides genetic diversity. Why does the retrovirus have to become part of the host to begin helping as opposed to already having been there and helping from the beginning? It could be that this ERV existed elsewhere in the original genome and has inserted elsewhere over the past millennia, leading us to where we are observing them moving across the genome in a novel way. You can only imagine that these retroviruses inserting into the Koala genome were originally part of the Koala genome and that it has deteriorated over time (thus leading to the inbreeding). Dr. Roca goes on to say,

In order to end up with 100 ERVs in an organism, the species may have to start with 10,000 ERVs in its ancestors.

Unknowingly, Roca is affirming the biblical concept of genomic entropy in arguing that the original genome was more gene rich and is losing information over time. It is not unreasonable to presume that all ERVs for a given organism were probably part of its original genome (in this particular case, the Koala genome) before they began to “jump” to other locations within the genome and into a retroviral form.

The ERVs’ ability to exit a genome and invade another organism’s genome probably began at the Fall and is happening still today. In fact, ERVs probably provide the best model to describe the origin of viruses and how they operate in a fallen world. An additional example of an organism that changed post-Fall was presented in Dr. Alan Gillen’s paper on malaria, The Genesis of Malaria. In his article, Dr. Gillen discussed how the parasite Plasmodium was possibly once a form of algae that, after the Fall, became a parasite. Much like ERVs, Plasmodium is a wonderful example of something that was not originally harmful, but ceased to function the way they were supposed to and became so detrimental at the molecular level.

Upon closer examination, ERVs strongly support a biblical worldview of an originally perfect world marred by the effects of sin.

All viruses are molecular machines, which means they are designed. But God didn’t design His creation to be killing machines. Therefore, these machines must have been part of His original very good creation and began to deteriorate ever since. It should be no surprise to biblical creationists that many ERVs are degenerate machines that are unable to perform their original functions. In this fallen world, genetic entropy is ever at work, causing good DNA sequences to quit working efficiently. Less efficient DNA sequences are subsequently selected against and disappear eventually. In the case of ERVs, degenerate DNA sequences are now malfunctioning and infecting other genomes. In the example of the koala, the ERVs are now beneficial to the koala; however, as Dr. Roca stated, this may not always have been the case. At first the ERVs may not have helped the host. Rather than asking how ERVs support common ancestry, perhaps the better question to ask is this: why do so many ERVs exist in the first place? Upon closer examination, ERVs strongly support a biblical worldview of an originally perfect world marred by the effects of sin.

Footnotes

  1. I wish to thank my student Lauren Janiec for her assistance in editing this article.
  2. Carl Zimmer, “We Are Viral from the Beginning,” The Loom (blog), Discover, June 14, 2012, http://blogs.discovermagazine.com/loom/2012/06/14/we-are-viral-from-the-beginning/.
  3. Jonathan P. Stoye, “Koala Retrovirus: A Genome Invasion in Real Time,” Genome Biology 7, no. 11 (2006): 241, doi:10.1186/gb-2006-7-11-241.
  4. Leslie A. Pray, “Transposons: The Jumping Genes,” Nature Education 1, no. 1 (2008): 204, http://www.nature.com/scitable/topicpage/transposons-the-jumping-genes-518; Sandeep Ravindran, “Barbara McClintock and the Discovery of Jumping Genes,” PNAS 109, no. 50 (2012): 20198–20199, doi:10.1073/pnas.1219372109; and Virginia Hughes, “The Jumping Gene: Friend or Foe?,” Only Human (blog), National Geographic, April 25, 2013, http://phenomena.nationalgeographic.com/2013/04/25/the-jumping-gene-friend-or-foe/.
  5. “Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model,” Evidence for the Evolutionary Model, November 2009, http://www.evolutionarymodel.com/ervs.htm.
  6. RationalWiki, s.v. “common descent,” last updated June 2, 2015, http://rationalwiki.org/wiki/Common_descent.
  7. Hughes, “The Jumping Gene . . . ”
  8. Yasuko Ishida et al., “Proliferation of Endogenous Retroviruses in the Early Stages of a Host Germ Line Invasion,” Molecular Biology and Evolution 32, no. 1 (2014): 109–120, doi:10.1093/molbev/msu275.
  9. Hughes, “The Jumping Gene . . . ”; Zimmer, “We Are Viral . . . ”
  10. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, “Koala Study Reveals Clues About Origins of the Human Genome,” Science Daily, November 6, 2014, http://www.sciencedaily.com/releases/2014/11/141106132315.htm.

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