Do Endogenous Retroviruses (ERVs) Support Common Ancestry? Yes, they do!

https://tinyurl.com/Fabich-these-are-bacteria

Yet another creationist article on ERVs. This one from Answers in Genesis. Before we even start reading it, we know, from the "Answers in Genesis Statement of Faith", that the writer is going to be anything but objective. Similar statements swearing to ignore any inconvenient facts can be found in all the for-profit commercial creationist blogs.

As usual, my comments are written in red.

A critique of an article by Dr. Andrew Fabich, who wrote the original article on December 10, 2015

The image depicts bacteria, not viruses. The fact that still no "peer review" process at Answers has picked this up is not a good sign!

The strength of Darwin’s argument was common ancestry. Darwin agreed that if we evolved from monkeys, then we shouldn’t see monkeys today. I could be wrong, but I don't think he ever suggested that we descended from monkeys. Thus, rather than suggest we came from monkeys, he insisted that we shared a common ancestor with them. No. He concluded from the evidence (evidence you have sworn to disregard) that we share common ancestors 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).

The "old" ideas never went away. It was always that heritable characteristics that favoured reproduction will tend to increase in representation in subsequent generations. This idea has been spectacularly confirmed by genetics.

But the argument from common ERVs is much, much more than mere similarity. They are specific, precisely located genetic signatures, that, as we shall see, can only have been formed by retroviral integration into the germ-line DNA of common ancestors.

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.

Far from "hiding", many 'evolutionists' (non-creationists) go to great pains to explain ERVs. Here is my FAQ on the subject.

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.

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.

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

The main thing not made clear from the above section is that ERVs are heritable. If you, or I, or Charle the chimp have ERVs in the same locations in the DNA of every one of our nuclear cells (cells containing chromosomal DNA - which is most of them) then it means that we have inherited them, and our progeny will inherit them also. This is the main difference between endogenous retroviruses and retroviral proviruses (a retroviral DNA genome integrated directly with the native DNA of somatic host cells.)

"Jumping genes" is a bit of an unfortunate term. ERVs can copy themselves and re-integrate in different loci. They can also disappear from a given location, but they do not jump around like fleas!

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.

The constant drip, drip, drip of misleading spin! 'Evolutionists' (geneticists and virologists not hampered by any statements of faith) do not 'preconceive' anything. That is projection on the part of creationists with their presuppositions. Common ancestry is concluded from the fact that retroviruses cannot target specific DNA locations, so large numbers of retroviruses in precisely corresponding locations in two species can only have got into those locations by inheritance. See here for a summary of the case for common descent from ERVs.

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.

Let us see.

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.

From Isn't this just circular reasoning, assuming evolution to 'prove' evolution?
No. No assumption of evolution is made when concluding that commonly located ERVs are due to common ancestry.

A conclusion drawn from evidence and reasoning is not an assumption or a presupposition.

The conclusion is drawn from the following items of evidence -

1. ERVs have the same detailed structure as proviruses. This fact does not require us to assume evolution.
2. Retroviral integration does not target specific loci in DNA. This fact does not require us to assume evolution.
3. Inheritance places the same genetic material in the same locations in DNA. This fact does not require us to assume evolution.

1. ERVs Are Not Junk

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.

So Fabich seems to be arguing that useful, recycled bits of retroviral DNA will remain in our genomes, and anything not of use will be eliminated. Well, deleterious material will be - um - deleted, but neutral elements will stick around, gradually becoming more and more corrupted and - slowly - lost or difficult to recognize. And this is exactly what we see!

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.

Now he seems to have become rather confused. Perhaps from reading too many creationist straw-man (dishonest) versions of the scientific evidence. Nobody says that all endogenous retroviral material is functionless! Certain elements have been recycled by evolution (exapted is the word), and this is to be expected. See ERVs do stuff. Doesn't that prove that they didn't originate from retroviruses, but were designed? 

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.

In brief: Integrase cannot target specific DNA loci. ERVs in common loci, in the huge numbers in which they are found, cannot be explained by direct infection, only by inheritance. It is only inheritance from ancestral DNA that will produce the same DNA in the same loci in descendant cells. Creationist attempts to provide "alternative explanations" cannot be made to work. See, for example, On "The Natural History of Retroviruses". As I said above, function is a red herring. The proof of common descent that ERVs provide in no way depends on the notion that all retroviral material in our genomes is junk. It is dishonest to keep repeating this. It's only purpose seems to be to try and allay the fears of the least informed of creationists followers. "Oh. They say it's all junk." (A lie.) "They are wrong, so I can dismiss ERVs as evidence for common descent."

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. One example is an essential ERV required for mammalian development.

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.

As I keep having to say, certain parts of certain ERVs have function. But what is the rest of it for? See here for a list of problems with the notion that all the retroviral material has function, and that function was designed. Take particular note that the position of a genetic unit has no significance for its functionality.

Re. "the kinds of the differences and their magnitudes are inconsistently shared through supposed common ancestral lineages", where does this come from? It appears to be a bit of rambling wishful thinking, as does the rest of the paragraph.

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.

Yet another straw-man. The argument from ERVs is not based on mere similarity, but on the fact that they exist in exactly corresponding DNA locations in different species. ERVs are undoubtedly of retroviral origin. They cannot target precise DNA locations, and yet there they are, in precisely corresponding loci in different species. 

5. Evolutionists Have No Origin of Any ERVs

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.

I don't know what on earth is going on in Fabich's mind here! Retroviral proviruses (which is what ERVs derive from) cause host cells to transcribe them from DNA back to RNA, to form the components of exogenous forms of the retrovirus. These components include reverse transcriptase and integrase. These can cause yet another cycle of reverse transcription and integration back into the DNA of the same cell. By the nature of integrase, the re-integration locus is highly variable. I can't comment on the rest of what he says here, because it is unintelligible.

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. 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 koala retrovirus KoRV is powerful evidence that ERVs are derived from retroviruses, and were not part of the original koala genome. Just go to this link to discover the truth - that Fabich's speculations, unsupported by any evidence, are factually false.

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.

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.

Speculations are ten-a-penny, but in science, we require evidence before we give ideas any serious consideration. However, we are not looking at a science piece by Fabich here. It is an exercise in firefighting. A propaganda piece designed to calm the faithful and persuade them not to study or worry about ERVs. The facts don't matter. This is where we came in.

Regarding the "scientists" who write for Answers in Genesis, acceding to their statement of faith is tantamount to abdicating your positions and responsibilities as scientists. Regardless of whether or not you have scientific qualifications and a track record of scientific achievement, to relinquish the basic skepticism inherent the scientific mindset is to relinquish science. Deciding on an outcome and seeking to promote it, whatever the evidence actually suggests, is an anathema to science. Indeed, we gain confidence in scientific ideas precisely because we seek to destroy them, rather than shield them from enquiry. The fact that they withstand testing is the way in which we gain confidence in their veracity. If creationist ideas were true, they would not need to be corralled away and protected from examination in this way. To agree to this faith statement is essentially to admit to having no confidence whatsoever in it's truth! It should be unnecessary, and it is only necessary because it is fundamentally unsupportable.

Some interesting reading on Andrew Fabich.