Endogenous Retroviruses in Your Genome Show Common Ancestry with Primates


Retroviruses are a well-known class of viruses. Retroviruses work by inserting their genetic material into the DNA of a cell. The inserted DNA takes over the cell’s machinery and forces it to make more copies of the virus.

This inserted genetic material is very distinctive. It includes DNA that codes for the proteins that form the structure of the virus, and DNA that codes for the enzyme which accomplishes the genetic insertions; long terminal repeat (LTR) sections are inserted on both sides of the coding DNA.

Sometimes a retrovirus inserts its genetic payload into the DNA of a “germ line” cell, i.e. an egg or sperm or a cell that makes egg or sperm. That means that every descendant, generation after generation, will have that particular retrovirus genetic material in that particular location in their genome. A retrovirus which is passed along like this from the genome of the parents will appear in the DNA of every cell of the body, and is called an “endogenous retrovirus”, or ERV.

At least 275 full-length ERV’s can be observed in the human genome. These have all the pieces of genetic material described above (viral coding DNA, LTRs, etc.), so it is clear that these are actual insertions by retroviruses at some point in the ancestry of Homo sapiens. In addition, there are over 100,000 other sequences in the genome that are portions of replicated ERVs. Each of these ERVs is at a particular location in the genome.

Chimpanzees likewise have over 100,000 ERVs (full and partial), again as the result of retroviral insertions at some time in the ancestry of that species. Of these 100,000+ ERVs, more than 99.9% are in the same location in the chimp genome as in the human genome. This demonstrates that humans and chimps are descended from a common ancestral species, which had those ERVs in those locations in its genome.

Introduction to Endogenous Retroviruses

Advances in biochemical technology since 2000 have allowed us to determine the full DNA sequences for humans and other animals. This new information has illuminated our evolutionary history. A number of patterns in our DNA are consistent with a common ancestry of humans and other primates.

One such genetic feature is the distribution of endogenous retroviruses (ERVs) in our genomes. As most readers know, viruses work by introducing their RNA or DNA into a host cell, and hijacking the host cell’s genetic machinery to start making more copies of the virus. Some viruses, called “retroviruses”, do this by having their RNA transcribed into DNA, which then gets inserted into the cell’s DNA genome. (This is considered “retro”, because normally in a cell DNA is transcribed into RNA, not the other way around). The HIV virus that causes AIDS is an example of a retrovirus. Once the virus’s DNA has been integrated into the host’s DNA, the viral genome is known as a prototype retrovirus, or provirus.

A virus may end up killing its host, or it may cause little damage. Various types of cells in an animal’s body can become infected with viruses. Most of us have experienced the common cold, where the virus thrives in the cells lining the respiratory tract. In some cases, a virus can infect a cell in the “germ line”. Germ line cells include the egg and sperm, as well as cells that produce the egg and sperm. If a retrovirus inserts its genetic load into a germ line cell of an animal, this viral DNA will then be passed down to all descendants of that animal, appearing as an “endogenous” retrovirus (ERV) in their genomes.

If that animal happened to be a common ancestor to two or more future species, all of these species would show this ERV at the same place in their genome, i.e. in orthologous (homologous) locations. Genomes mutate over time, and sometimes whole chunks of DNA get moved around, but there is generally enough genetic context to determine whether a location is homologous among the various primates. The ERVs themselves accumulate mutations that make them non-infectious and further degrade their sequences with time. Nevertheless, thousands of ERVs retain enough genetic identity to be clearly identified in the human genome.

The genetic signature of a retrovirus in the genome is very distinctive. ERVs have common features such as the genes that code for the viral coat protein and for the reverse transcriptase that copies the viral RNA genome into DNA. The ERV DNA codes for three groups of proteins, known as “gag” (matrix, capsid, nucleoproteins), “pol“ (protease, reverse transcriptase, RNaseH, dUTPase, integrase) and “env” (subunit and transmembrane). This genetic core is flanked by long terminal repeats (LTR) sections. Finally, when the retrovirus tears open the host genome for insertion, some of the torn original host DNA is recopied on either side of the viral insert.

Here is what all this looks like for the insertion of a particular retrovirus from the CERV 30 family into the chimpanzee genome:

Insertion of a member of the CERV 30 (HERVK10) family in chimps. The insertion occurred in the LINE element present in chromosome 10 of the chimpanzee genome. The orthologous LINE element is present in chromosome 12 in humans. In chimpanzees target site duplications (ATTAT) are identified. A single copy of TSD (ATTAT, the pre-integration site) is found inside the LINE element in humans. The LTRs of the element are 99.4% identical. Source: Nalini Polavarapu, Nathan J Bowen, and John F McDonald, Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses, Genome Biol. 2006; 7(6): R51 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779541/

Insertion of a member of the CERV 30 (HERVK10) family in chimps. The insertion occurred in the LINE element present in chromosome 10 of the chimpanzee genome. The orthologous LINE element is present in chromosome 12 in humans. In chimpanzees target site duplications (ATTAT) are identified. A single copy of TSD (ATTAT, the pre-integration site) is found inside the LINE element in humans. The LTRs of the element are 99.4% identical.
Source: Nalini Polavarapu, Nathan J Bowen, and John F McDonald, Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses, Genome Biol. 2006; 7(6): R51 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779541/

This happens to be an ERV that is in chimps, not in the human genome at that location. In the corresponding spot in the human genome, there is a sequence of DNA bases of: A T T A T. In the chimp genome, this sequence at the point of insertion has become duplicated on either side of the ERV, as discussed above. The ERV shows the usual features of the gag, pol, and env genes, with the LTRs on the ends.  More details about retroviral insertion are found here .

These distinctive features make it relatively straightforward to search through the human genome sequence and identify ERVs. At least 275 full-length ERV’s can be observed. These ERVs are relatively recent (e.g. last ten million years) arrivals to the primate genomes. Older ERVs tend to get chopped up by the usual shuffling of genomes over time. About 200,000 entities in human DNA, constituting a full 8% of the genome, have been identified as being ERVs or chunks of ERV’s. Most of these elements are replicated copies of ERVs which initially inserted in the genome many generations earlier. Most of these chunks are solitary LTRs [cf. Lander, et al. (2001)  and Seifarth, et al.  (2005) ], rather than full-length ERVs.

All human ERV’s except for one are found in all humans, indicating that they entered the ancestral human genome before Homo sapiens became a distinct species. The exception is in the HERV-K(HML2) family. By examining the DNA from a diverse set of people, Belshaw, et al. identified 113 elements of the HERV-K(HML2) family in the human genome. Most of these elements occur in all people. However, at least 8, and perhaps 11, of these elements are insertionally polymorphic – – some human individuals have the insertion while other individuals have the empty, preinsertion site. This shows that this virus family has been transcriptionally active within the age span of the human race.

Where in the Genome Do Retroviruses Insert?

The human genome contains some three billion base pairs, but not every one of these sites is equally likely to be the place where a retrovirus inserts. For instance, Mitchell, et al. (2004) identified insertion sites in the human genome for three different retroviruses: human immunodeficiency virus (HIV), avian sarcoma-leukosis virus (ASLV), and murine leukemia virus (MLV). They looked at a total of analysis of 3,127 integration sites. Some preferred types of locations were observed.   HIV tended to insert in gene-rich regions, MLV favored integration near transcription starts, while ASLV showed only a weak preference for active genes.

It should be noted that these preferences for types of regions does not mean that a specific virus favors insertion into any one particular spot in the genome. For each virus, there are many thousands of sites at which it could insert. The figure below shows where these three viruses inserted on the first three out of 23 human chromosomes. The blue “lollipops” are the HIV, the purple are MLV, and the green are ASLV. These insertions are spread broadly across the chromosomes (including the other 20 chromosomes), rather than being focused in just one spot or a few regions.

Relationship between Integration Sites and Transcriptional Intensity in the Human Genome For Three Retroviruses on Three chromosomes. The three human chromosomes are shown numbered 1, 2, and 3. HIV integration sites from all datasets in Table 1 are shown as blue “lollipops”; MLV integration sites are shown in lavender; and ASLV integration sites are shown in green. Transcriptional activity is shown by the red shading on each of the chromosomes ...Centromeres, which are mostly unsequenced, are shown as grey rectangles. Source: Adapted from Mitchell RS, Beitzel BF, Schroder ARW, Shinn P, Chen H, Berry CC, et al. (2004) Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences. PLoS Biol 2(8): e234. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020234

Relationship between Integration Sites and Transcriptional Intensity in the Human Genome For Three Retroviruses on Three chromosomes.
The three human chromosomes are shown numbered 1, 2, and 3. HIV integration sites from all datasets in Table 1 are shown as blue “lollipops”; MLV integration sites are shown in lavender; and ASLV integration sites are shown in green. Transcriptional activity is shown by the red shading on each of the chromosomes …Centromeres, which are mostly unsequenced, are shown as grey rectangles.
Source: Adapted from Mitchell RS, Beitzel BF, Schroder ARW, Shinn P, Chen H, Berry CC, et al. (2004) Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences. PLoS Biol 2(8): e234. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020234

These are not the only possible insertion sites for these virus, but just the spots that showed up in this limited study. A more detailed study by Wang, et al.  mapped 40,569 unique sites of HIV integration in the human genome. Thus, while the insertions of ERVs are not equally likely across all three billion sites of the genome, they may be characterized as quasi-random, since a given retrovirus will insert essentially randomly in one of many thousands of potential integration locations.

Effects of Retroviral DNA Insertions on Human Genetic Function

The DNA associated with retroviruses started out as functional genetic material, including the protein-coding gag, pol, and env genes, and the LTRs, which are rich in promoters, transcription factor-binding sites and non-coding RNAs. As these chunks of DNA get inserted at various spots in the human genome, they can have various effects on the human metabolism [1]. Some of these effects are bad, and some are good.

The human genome is moderately tolerant towards mutations. At each generation, we inherit about 50 new mutations compared to our parents’ DNA, distinct from the usual allele rearrangement. If a generation is about 30 years, compared to people 3000 years ago each one of us has about 5000 mutations in our DNA. Often, these mutations are fatal. About 40% of fertilized eggs end up being spontaneously aborted as miscarriages, due in part to genetic defects. Of the babies who survive through birth, about 3% have genetic disorders such as congenital heart disease. However, the rest of us get along fairly well, and all the genetic shuffling occasionally produces a genius like Einstein, or a modified gene which gives resistance to cardiovascular disease.

If the insertion of a retrovirus in a particular spot in some human’s genome gave a very bad effect, that human would die without reproducing, and that particular genome would not be promulgated. However, sometimes the effects of the ERV are just moderately bad, producing disorders which are not immediately fatal. For instance, ERVs in humans have been tied to a number of cancers, including Hodgkin’s lymphoma, melanoma, and bladder and breast cancer. ERVs are also implicated in a number of autoimmune disorders, such as rheumatoid arthritis and lupus. (For more information see Katoh and Kurata, “Association of Endogenous Retroviruses and Long Terminal Repeats with Human Disorders“, 2013 ).

On the good side, the proteins expressed from the env genes of several retroviruses embedded in the human genome help with the development of the placenta. Barry Desborough discusses  how the function of these genes in the human genome are similar to the function of these genes in the native retrovirus.

Also, many LTRs have retained regulatory activity, and have landed close to genes where they can influence the expression of proteins from those genes. Over 100 LTRs have been demonstrated to help control transcription of human genes, and several thousand other LTRs could potentially have that function as well. ERVs and other transposable elements are known to play roles in the three-dimensional organization of the genome by functioning as ‘anchors’ that serve to isolate regions of active transcription and by modifying the structure of chromatin. [2]

The original viral replication functions of the ERVs found in humans have been disabled by mutations. The functionalities which now observed for human ERVs are in general what would be expected for some 200,000 quasi-random insertions of chunks of DNA into the genome over tens of millions of years: most ERVs have no known effort, some cause genetic disorders, and some have useful interactions with the rest of the genome.

Young Earth (YE) creationists point to these instances of functionality as evidence that ERVs were purposefully placed in the genome by God when He created the first humans a few thousand years ago. However, ERVs bear all the marks of having come from functioning viruses. For many ERVs, we can recognize all or nearly all of the components of a retrovirus (viral gag, pol, and env genes, LTR sections, etc.), which would have the capacity to integrate into the genome if they had not been disabled by additional mutations. Even the plain LTRs are distinctive.

Another sign that ERVs were actual insertions is the duplication of some original DNA on either side of the ERV, as discussed above:

The hallmark of an insertion is a displacement of chromosomal DNA, and the hallmark of insertion by integrase is the presence of target site duplication, due to the way it attacks the 5′ and 3′ phosphodiester bonds with an offset of a few base pairs. Since full-length ERVs are accompanied by target site duplications and DNA displacement, they are necessarily endogenized/fixed proviral insertions. So any functional components are necessarily post-insertion exaptations, and the fact that they are necessarily insertion means that they cannot be part of any ‘original design.’ The issue of functionality is simply a red herring.

Moreover, if endogenous retroviruses were divinely-created portions of Adam’s DNA, all humans would possess the same set of ERVs. But HERV-K shows that this is not the case: for several instances of this ERV family, some people have them in their genomes, and some have the empty pre-insertion site. This shows that retroviruses are in fact inserted into human genomes to form ERVs.

Comparison of Human and Chimp ERV Locations

The first drafts of the complete human genome were published in 2001. This achievement was followed by sequencing the DNA of other animals, including chimpanzees. Humans and chimpanzees are thought to have diverged from a common ancestor around 6 million years ago.

As discussed in Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model, there are two broad approaches to comparing the genomes of two different species. One is to examine variations in insertions and deletions (“indels”), while the other is to analyze the whole genome. The “Three Layers” article describes these analyses in moderate detail. The conclusions from both approaches is the same: “Less than 100 ERVs are human-specific and less than 300 ERVs are chimpanzee-specific.” Thus, out of some 200,000 ERVs in the human genome, “The percentage of ERVs in identical loci is greater than 99.9%.” In other words, nearly all of the many thousands of ERVs in the human genome occur in the same locations in the chimpanzee genome.

To assess the implications of this, let’s start by considering a very simple case, where only one ERV insertion was found in both humans and chimpanzees. Suppose further that this particular retrovirus which we will call retrovirus A could randomly insert in any one of 10,000 locations in the human genome, and also in the same 10,000 locations in the matching chromosomes of chimpanzees. If retrovirus A integrated into  the genome of an ancestral chimp, and in a separate infection event also endogenized into the DNA of an ancestral human, there would be only a 0.01% ( 1 /10,000) chance that the resulting ERV A would be found in the same location in both species.

Now, let’s extend this thought experiment to having two shared ERVs. If both species were independently infected with retrovirus B as well as with retrovirus A, the probability is only 1/100,000,000 that virus B, as well as virus A, would happen to end up in matching sites in humans and in chimps. This would constitute very strong evidence that these two ERVs did not arrive at their locations through random, independent infection events in humans and in chimps. A more reasonable explanation is that humans and chimps both descend from a common ancestor, whose genome suffered the insertion of these two viruses in these two locations.

ERVs Fig Human Chimp

Moving now to the actual situation, instead of just one or two ERV’s,  there are at least 100,000 ERV insertions found in the same locations in humans and in chimps. A schematic of the pattern of such insertions (viruses A, B, C, D, etc. etc. etc.) is shown above. There is essentially no chance that all these identical insertion points could have occurred by independent insertion events in the two lineages. Again, this shows that these insertions occurred in ancestors which are common to both humans and chimpanzees.

There are a few exceptions to this co-location of human and chimp ERVs, i.e. there are a few ERV families that appear in one species but not the other. For instance, out of 42 families of ERVs in chimps, 40 appear in the orthologous positions in the human genome and 2 do not. [Polavarapu, et al., 2006].  This is to be expected, since human and chimp lineages diverged some 6 million years ago. That is plenty of time for a few new ERV families to be introduced independently to humans and to chimps, or for some previously-shared ERVs to be lost from humans or from chimps due to well-known genetic processes such as genetic drift and incomplete lineage sorting. Anyone interested in understanding  cases such as CERV 1/PTERV1  can google the subject to find valid scientific explanations of these issues.

Young earth creationists, of course, try to mount objections to the science described here. This article has answered some of the most common objections. Barry Desborough has answered additional questions.

Nested hierarchies of ERVs: More evidence for common ancestry

If all of today’s mammals evolved via a branching family tree from some common ancestral population, we would expect to find that species that are more closely related would share more genetic features of all kinds. This requirement of nested hierarchies is a mathematically rigorous test for evolution. I won’t go into it here, but these patterns show up with ERV’s, as discussed at Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model, and also at VWXYNot .

Theological Implications of Endogenous Retroviruses

The distribution of ERVs in human and chimpanzee genomes is powerful evidence of common ancestry and macroevolution. As described in The Pope Speaks on Creation and Evolution,  the Roman Catholic Church has largely made its peace with evolution, as have liberal Protestants. The more conservative evangelical Protestants hold a high view of the Bible as trustworthy, divinely-inspired revelation. I happen to share that view of Scripture. However, it is one thing to affirm the Bible as infallible, and it is a quite different thing to claim that any particular interpretation of that Bible is infallible.

A little reflection will show that even within the world of Bible-believing Protestants, there are many points of doctrine which are the subject of intense disagreement. As one example, Pentecostal Christians affirm that spiritual gifts like prophecy and praying in “tongues” are meant to continue in the church today, while cessationalists like John MacArthur denounce these practices as blaspheming the Holy Spirit. Both sides claim that Scripture is on their side. These disagreements show that it is possible for devout believers with the highest possible regard for the Bible to have fundamental disagreements in their interpretations of that Bible.

Unfortunately, many evangelicals in North America confuse their interpretation of God’s revelation with the revelation itself. Such is the case with Young Earth (YE) creationism. These folks hold that the only viable treatment of the Genesis creation narrative is a wooden literalism. Thus, the world was created in six 24-hour days about six thousand years ago, and Adam and Eve were specially created, not evolved from other primates. This view is promulgated by organizations such as Answers in Genesis.

Two Key Errors in Young Earth Creationism

YE creationism errs in several ways. First, it fails to take into account the pervasive use of figurative revelation throughout the Bible. In the Old Testament and in the book of Revelation, divine communication was often given in some indirect form, some picture or narrative which both concealed and revealed the underlying truth. The prophet in I Kings 20 confronting King Ahab and the prophet Nathan confronting King David both started off by telling a story which didn’t literally occur as though it were true. If one took a literalistic approach to interpretation like today’s YE creationists so, both of these prophets should have been reprimanded for speaking “error”. But to do so would be to completely miss the point of those narratives.

Likewise, telling stories that were not literally true was the primary teaching device of Jesus Christ: “He did not say anything to them without using a parable.” For most of Jesus’ parables, the hearer is expected to figure out that the story is not really about some son who ran away and fed pigs or about some unfortunate traveler who got mugged on the way to Jericho. The hearer needs to enter into the story and see that he or she is represented by one or more of the characters in it; that was the point of the parable, not whether the story itself ever actually happened. But all this is lost on YE creationists, who hold doggedly to simple literalism in Genesis as being somehow intrinsically more pious.

A second major theological error in YE creationism is its refusal to take seriously the evidence in God’s creation. Modern YE creationism stems from the publication of The Genesis Flood by Whitcomb and Morris in 1961. In the preface to the sixth printing, Whitcomb and Morris candidly reveal the basis of their thinking:

We believe that the Bible, as the verbally inspired and completely inerrant Word of God, gives us a true framework of historical and scientific interpretation, as well as of so-called religious truth. This framework is one of special creation of all things, complete and perfect in the beginning, followed by the introduction of a universal principle of decay and death into the world after man’s sin, culminating in a worldwide cataclysmic destruction of the “world that then was” by the Genesis Flood. We take this revealed framework of history as our basic datum, and then try to see how all the pertinent data can be understood in this context…the real issue is not the correctness of the interpretation of various details of the geological data, but simply what God has revealed in His Word concerning these matters.

On this telling, the authors KNOW that the earth was recently created, that decay and death only entered the world following Adam’s apple, and all terrestrial life was drowned apart from the humans and animals on Noah’s ark. Knowing this to be the case, they feel justified in distorting or ignoring whatever physical evidence points to an old earth – they know that old-earth evidence MUST be invalid, so they try to squash it into their young-earth model, and when that fails, simply ignore it: “We take this revealed framework of history as our basic datum, and then try to see how all the pertinent data can be understood in this context.”

As discussed in Exposing the Roots of Young Earth Creationism, this sort of solipsism runs counter to historic Protestant thought, which acknowledged the value of God’s revelation in His works as well as His word. Francis Bacon, who defined the modern scientific method, described this two-books approach: “There are two books laid before us to study, to prevent our falling into error; first, the volume of the Scriptures, which reveal the will of God; then the volume of the Creatures, which express His power.” In The Advancement of Learning (1605) Bacon wrote:

Let no man … think or maintain that a man can search too far, or be too well studied in the book of God’s word, or the book of God’s works, divinity or philosophy; but rather let men endeavor an endless progress or proficience in both; only let men beware that they apply both to charity, and not to swelling; to use, and not to ostentation; and again, that they do not unwisely mingle or confound these learnings together.

The Christian thinkers of the early 1800s followed Bacon’s advice to “not unwisely mingle or confound these learnings together”. Thus, when the physical evidence of the age of the earth contradicted their literal interpretation of Scripture, they did not try to suppress or distort those findings. Rather, they realized that their interpretation of Genesis was likely incorrect. As Davis Young notes, “Because the Christian naturalists of the era were unafraid of God-given evidence, they recognized that extrabiblical information provided a splendid opportunity for closer investigation of the biblical text in order to clear up earlier mistakes in interpretation.”

The reformer John Calvin wrote that in the Genesis creation narrative God accommodated the story to the limited understanding of common people, rather than giving a scientifically precise account. “He who would learn astronomy, and other recondite arts, let him go elsewhere” – – meaning, the Bible was not written for the purpose of telling us about the physical universe. In Calvin’s view, the way to understand the stars and the planets in a God-honoring manner was to go scientifically study them, not to rely on inferences from Biblical statements.

In their mistaken commitment to literalism, YE creationists overlook and minimize what the Bible does claim for itself. The clearest teaching of the Bible on the Bible is found in II Timothy 3:15-17:

from infancy you have known the Holy Scriptures, which are able to make you wise for salvation through faith in Christ Jesus. All Scripture is God-breathed and is useful for teaching, rebuking, correcting and training in righteousness, so that the servant of God may be thoroughly equipped for every good work. (NIV)

The wording here is instructive: “wise for salvation”, “faith in Jesus Christ”, “for teaching, rebuking, correcting and training in righteousness.” This is all about doctrine and morals; nothing about geology or biology. Those who try to extend the range of the Bible’s authority to geology and biology think they are being faithful, but in fact are merely imposing their own fallible opinions on the infallible Word.

Various examples can be adduced which demonstrate that Scriptural statements about the physical world, which were appropriate and meaningful for the original audience, can be incorrect according to modern knowledge. To take a simple example, Jesus taught:

“What shall we say the kingdom of God is like, or what parable shall we use to describe it? It is like a mustard seed, which is the smallest of all seeds on earth. Yet when planted, it grows and becomes the largest of all garden plants, with such big branches that the birds can perch in its shade.” [Mark 4:30-32 NIV].

The literal statement here is that the mustard seed is the “smallest of all seeds on earth”. Jesus was speaking here proverbially, and the mustard seed is used elsewhere (e.g. Matt. 17:20) as an example of smallness. The context is sowing and growing. The mustard seed was the smallest seed that first-century Jewish farmers would sow in the earth, so this was an appropriate word picture for that audience to illustrate the growth of the kingdom from tiny beginnings. However, even in ancient Galilee folks were likely familiar with seeds from non-agricultural plants which were smaller than mustard seeds, and modern naturalists have found other seeds which are smaller yet.

If a Bible literalist were truly consistent, he should respond, “I don’t care what those godless scientists say, Jesus said that the mustard seed was the smallest seed, and that’s that. This is the infallible Word of God, so every statement regarding the natural world must be correct.” This would be to make the same mistake, of course, that Bible literalists make with Genesis 1. Most Christians understand that this parable was not really intended to teach horticultural facts; to obsess over whether Jesus taught “error” here would be to entirely miss the point of the passage.

The plain, literal meanings of a number of verses depict an unmoving earth and a moving sun (e.g. “He set the earth on its foundations; it can never be moved” Ps. 104:5; “…The world is firmly established; it cannot be moved” I Chron. 16:30; cf. Isa. 66:1, Eccl.1:5, and Josh. 10:13). In the 1500s and 1600s, the literal interpretation of these passages was seen as an essential element of Christian belief. Catholic theologians held that the only faithful way to interpret these verses was that the earth was in fact stationary. According to Cardinal Roberto Bellarmine (1615), “…to affirm that the sun is really fixed in the center of the heavens and the earth revolves swiftly around the sun is a dangerous thing, not only irritating the theologians and philosophers, but injuring our holy faith and making the sacred scripture false.”

Here is what John Calvin in his sermon on 1 Corinthians 10-11 had to say about those monstrous, malicious, devil-possessed people who claim that the earth “shifts and turns”:

We will see some who are so deranged, not only in religion but who in all things reveal their monstrous nature, that they will say that the sun does not move, and that it is the earth which shifts and turns. When we see such minds we must indeed confess that the devil possesses them, and that God sets them before us as mirrors, in order to keep us in his fear. So it is with all who argue out of pure malice, and who happily make a show of their imprudence.

This is the sort of accusation that today’s YE creationists make against those who teach that evolution is compatible with biblical Christianity.

Astronomical observations eventually led Christians to conclude that the verses that speak of a stationary earth and a moving sun were not intended to be teaching astronomical facts.  Nowadays nearly all believers find ways to justify a non-literal interpretation of these verse. But note well, it was the modern scientific understanding of planetary motion that forced this reinterpretation. Just looking at the Biblical text itself, there is no clear pointer that all these verses were not meant to be taken as literal statements about the physical world.

These examples where the plain, literal meaning of Bible passages must be set aside due to modern science demonstrate that Whitcomb and Morris are utterly mistaken in their assertion that the Bible gives us a “true framework of … scientific interpretation.” The Bible does not do that, never claimed to do that, and could not possibly do that if it were to be an effective means of communication to an ancient people with a pre-scientific world view.

YE creationists hold to this failed mind-set, and thus are forced to ignore, deny, or misrepresent the physical facts. I have documented some of these maneuvers in Evidences for a Young Earth.

When it comes to ERVs, a look at the discussions of this topic on the internet shows a ongoing effort by YE creationists to deny the obvious. They claim that ERVs are not really viral insertions, or that each ERV could only insert in one site in the genome, and so on. It is tedious to pick through all the misrepresentations, so I won’t do that here.

It seems impossible to get a YE creationist to really engage with the evidence, as long as he fears that acknowledging common ancestry entails abandoning all that he holds dear. The most fruitful way forward is for him to re-examine his assumptions on Bible interpretation. I have sketched out my reconciliation of evolution with Scripture in Evolution and Faith: My Story, Part 2 .   The Biologos article, “Why should Christians consider evolutionary creation?” includes a number of good links to further testimonies and articles on this subject.

Made in God’s Image

A key concern about common ancestry is that it might threaten our status as being created by God and being bearers of God’s image. This calls for careful thought, not defensive pronouncements. Traditionalists are offended at the thought that we came from monkeys, but the reality is even more humiliating. We come not from monkeys, but from single-celled eggs. Every human alive today came into existence as a fertilized egg, like a fertilized chimpanzee egg but with slight differences in the sequences of nucleotides along the strands of DNA. This raises a host of questions:

Is the unfertilized egg (a single, microscopic cell with only the mother’s DNA) the image of God? Does it become the image of God the instant that a sperm cell delivers the other half of the DNA to this single cell? After the fertilized cell has divided a number of times to form a hollow sphere? When the heart first beats, but there is no real consciousness? At birth? How is Adam’s nature passed down? Which genes in our DNA were mutated to make us into sinners? If an egg from a donor mother is fertilized in vitro and implanted in a second woman, is original sin transmitted through the donor mother or the birth mother? It cannot be the case that God simply assigns a soul to an egg as soon as it is fertilized: identical twins result from the division of an egg after it is fertilized, yet presumably they each have their own soul.

Until the answers to these questions are clarified, there is no place for dogmatic pronouncements on evolution being incompatible with a Biblical view of man. We, today, are all made from chemicals (starting from the complexly organized egg and sperm), under the superintending providence of God. This is true of all humans now living, and their parents and grandparents. Therefore, exactly how God made the first humans (from dust or from other primates) is completely irrelevant to the status of us today – – our humanity or value or image of God.


[ 1 ]     Chuong et al. explain how the inherent features of ERVs and other transposable elements (TE) would be expected to yield various types of functional activity when they (quasi-randomly) insert in the genome (no supernatural intervention required):

“Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs. Many recent studies reinvigorate the idea that these elements are pervasively co-opted for the regulation of host genes. We argue that the inherent genetic properties of TEs and the conflicting relationships with their hosts facilitate their recruitment for regulatory functions in diverse genomes… In this Review, we consider emerging evidence revealing TEs as a genome-wide source of regulatory elements. We also discuss recent advances in our ability to experimentally capture the regulatory activities of TEs, with a primary focus on their contribution as cis-regulatory DNA elements. We argue that most of these regulatory activities can be interpreted as relics of strategies used by TEs to spread within genomes and host populations… Autonomous TEs encode genes that promote their replication independently of that of host chromosomes. However, as genomic parasites, TEs rely on host cell machinery to express their genes. Thus replication-competent TEs have evolved cis-regulatory sequences that function to mimic host promoters… all ERVs originate from infectious retroviruses that must have infected germ cells (or their progenitors) but possibly also somatic cells from diverse tissues. The past viral lifestyle of ERVs may thus explain why their LTRs harbour complex regulatory elements that are capable of driving transcription in a variety of tissues and cell types… Evidence is mounting that TEs provide a profusion of other types of cis-regulatory elements including enhancers, insulators, and repressive elements. In mammals, chromatin immunoprecipitation followed by sequencing (ChIP-seq) studies have revealed that for any given transcription factor (TF) and cell type examined, TEs contribute a substantial fraction of binding sites across the genome (5-40%, average ∼20%). LTR elements tend to contribute more than other TE types, probably because LTRs are more likely to possess and retain their ancestral cis-regulatory activities… TEs have also been documented to function as insulator and/or boundary elements. Such sequences serve to partition the genome into domains of active or inactive transcription ranging in size from 100 kb to 1 Mb, often by preventing the spread of heterochromatin. Several studies showed that many TEs, in particular SINEs, harbour binding sites for factors such as CTCF or TFIIIC that confer insulator activity and organize nuclear architecture. A subset of these TEs appear to play roles in the three-dimensional organization of the genome by functioning as ‘anchors’ that serve to isolate regions of active transcription…”

Chuong EB, Elde NC, Feschotte C , Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet. 2017 Feb;18(2):71-86.       https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498291/

[ 2 ]  Yanxiao Zhang, et al., “Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells”. Nature Genetics, volume 51, pages1380–1388(2019)       https://www.nature.com/articles/s41588-019-0479-7

About Scott Buchanan

Ph D chemical engineer, interested in intersection of science with my evangelical Christian faith. This intersection includes creation(ism) and miracles. I also write on random topics of interest, such as economics, theology, folding scooters, and composting toilets, at www.letterstocreationistists.wordpress.com . Background: B.A. in Near Eastern Studies, a year at seminary and a year working as a plumber and a lab technician. Then a B.S.E. and a Ph.D. in chemical engineering. Since then, conducted research in an industrial laboratory. Published a number of papers on heterogeneous catalysis, and an inventor on over 100 U.S. patents in diverse technical areas. Now retired and repurposed as a grandparent.
This entry was posted in Evolution, Genome and tagged , , , , . Bookmark the permalink.

40 Responses to Endogenous Retroviruses in Your Genome Show Common Ancestry with Primates

  1. JimV says:

    Since I coincidentally just read a post elsewhere which contradicts it, this caught my eye:

    “The mustard seed was indeed the smallest seed that ancient Galilean farmers were familiar with …”

    According to, for example, https://diogenesii.wordpress.com/2007/06/22/what-is-the-smallest-seed-in-the-world/ :
    “Well then, was the mustard seed the smallest seed known in Palestine? No, not even in Jesus’ time. There would be numerous plants familiar to his audience with smaller seeds, of which the best example would be the seed of the black orchid. And just for the record, the mustard seed doesn’t grow to be the greatest of all the shrubs on Earth, either.”

    The source above goes on to agree that there is no point in taking such statements literally, for a number of reasons. However, for the sake of accuracy I think your statement either needs a good reference source or an amendment, as otherwise you may be falling into the same trap (taking the Bible as gospel – pun intended) as you warn against.

    • Jim, I don’t think the ancient Jews would have been familiar with the black orchid, which is found in rain-forests, not in arid regions. But you make a good point that folks back then were likely familiar with small seeds from non-agricultural plants, so I revised the wording to reflect that. Thanks for upgrading the accuracy.

  2. Reblogged this on Primate's Progress and commented:
    The argument from endogenous retroviruses to evolution in general, and to specific family trees, is to my mind one of the most immediately convincing (compare http://www.talkorigins.org/pdf/comdesc.pdf, 29+ Evidences for Macroevolution, Sec. 4.5).

    As the article points out, the odds against any ERV occurring in the sae place in humans and chimps is about 1 in 10^4; humans and chimps share 100,000 ERVs in the same locations, and the odds against this would then be 1 in 10^400,000. By my arithmetic, allowing for the 0.1% where there is no match changes this to 1 in 10^399,800, still a ridiculously vast number.

    I would also have welcomed numbers showing where gorillas, for instance, fit into the picture, and numbers of ERVs specific to each species.

    The final section of this post is addressed to those who, like the author, regard the Bible as divinely inspired but not as literally true. The argument goes back to Maimonides, if not Augustine, and here forms part of the ongoing civil war within the Abrahamic religions between Fundamentalists and Modernists. Not my battle.

  3. TomS says:

    One thing that was brought up which I do not see very often mentioned, is the origin of the individual.
    So often, rather, I see someone complaining about evolution as if the scientific study of the origin of the species devalues the individual. If people want to claim that science stands in the way of a one-on-on relationship between the creature and the creator, they should be talking about the science of reproduction or some such “local” science, not about what happened to a group in the distant past. For example, if they don’t like the role of chance, what about the chance element in genetics?
    To confuse reproduction with evolution involves the fallacies of composition and division, saying what is true of the individual what is properly said of the group (or vice versa). In terms of Christian theology, it is something like the minority opinion (“heresy”) of Universalism.



  5. Pingback: “Big Daddy” Chick Tract: The Most Widely-Distributed Anti-Evolution Publication | Letters to Creationists

  6. Nice piece. You might find my FAQ for creationists interesting. It addresses the “objections” creationists try to come up with regarding orthologous ERVs. http://barryhisblog.blogspot.fr/p/endogenous-retroviruses-frequently.html

    • Barry, that is an excellent resource. I have put a link to it in the text of my post. Thanks, and keep up the good fight.

    • Jim Thinnsen says:

      “Is it not strange that a Christian will accept Darwinism as a substitute for the Bible when the Bible not only does not support Darwin’s hypothesis but directly and expressly contradicts it?” William Jennings Bryan


    • Onward with quotes taking a stand against watering down literal interpretations of the Bible:

      “To affirm that the sun is really fixed in the center of the heavens and the earth revolves swiftly around the sun is a dangerous thing, not only irritating the theologians and philosophers, but injuring our holy faith and making the sacred scripture false.”
      Cardinal Roberto Bellarmine

      ”The Earth is not rotating…nor is it going around the sun. Today’s cosmology fulfills an anti-Bible religious plan disguised as ‘science’. The whole scheme from Copernicanism to Big Bangism is a factless lie. “
      Marshall Hall, fixedearth.com

  7. D Helland MD says:

    I was wo

  8. D Helland MD says:

    Sorry. This is a little bit off topic.

    I was wondering what the author thinks of the research on soft tissues found in dinosaur bones and other fossils.

    • Hi Dr. Helland, I have reviewed that topic in some detail. If this link does not work, you can click on “Dinosaur Soft Tissue” near the very top/right of the window for this blog.


      • D Helland MD says:

        Thank you for your reply.

        I did look at your article on dinosaur soft tissues.
        You have some dates for the Hell Creek formation from radioactive dating in that article. Do you have a reference for those dates?

        I live here in eastern Montana and this area is about a 100 miles from here.

        I am a Christian who has done a lot of reading on different issues like ERVs etc. I try to keep an open mind and listen to all sides.

        Just a couple more questions.

        Do you believe in miracles? For example did Christ literally raise Lazarus from the dead?

        Do you believe in theistic evolution? Or do you subscribe to strict methodologic naturalism? Or something else?

        Best regards


      • Don,
        The sentence ” Here are some radioactive datings of these tektites and of the ash layers (using sanidine and zircon minerals) at the Z-coal bed ” has a link (“radioactive datings”) to a 2000 article by Brent Dalrymple with those dates. That article in turn references a 1993 U S Geological Survey article which you could probably chase down. Dalrymple has been professionally involved with radioactive dating for many years.

        If you are interested in Montana geology, you might want to skim this article: https://letterstocreationists.wordpress.com/2015/07/09/exposing-the-roots-of-young-earth-creationism/ . It is mainly about the genesis of The Genesis Flood, a seminal YE creationist book of 1961. A key area of controversy is the Lewis Overthrust in Glacial National Park, so there are several diagrams of that geology.

        As to my beliefs, I try to take the Bible as literally as I can. I affirm all the New Testament miracles, including the various resurrections. And also the Old Testament except where the physical evidence says it cannot possibly have happened. I am not happy about having to pull back from a literal six-day creation and special creation of humans, but there came a point when I could not affirm those with any integrity. My personal journey on all this is here: https://letterstocreationists.wordpress.com/2013/11/09/evolution-and-faith-my-story-part-1/ . And there is a part 2 there. I would be classified as a theistic evolutionist, though “evolutionary creationist” better expresses it.

        I affirm both biblical miracles and the possibility of present-day miracles. For instance, see here for healings of vision and hearing impaired persons, as written up in a medical journal: https://letterstocreationists.wordpress.com/2010/10/11/study-healing-miracles-in-mozambique/ . And here for a video of a hearing-impaired boy gaining essentially normal hearing: https://letterstocreationists.wordpress.com/2012/08/14/healing-of-nearly-deaf-boy-on-youtube/ . Of course, we need to be cautious about claiming anything like as absolutely positively miraculous, but these people who could see and hear much better after prayer sure appreciated it.

      • D Helland MD says:


        Thank you for your reply. I also appreciate your rather civil tone. It seems like most online discussions have a lot of rancor involved, which I don’t think is particularly helpful.

        I just recently came across your website “Letters to Creationists”. I am very impressed. You certainly have put a lot of good work into it.

        When studying Genesis, origins, etc., I always have Isaiah 55:8-9 in the back of my mind: “For my thoughts are not you thoughts, neither are your ways my ways, saith the Lord. For as the heavens are higher than the earth, so are my ways higher than your ways, and my thoughts higher than your thoughts.”

        There is one particular thing that I have thought a lot about over the years. If one believes in God, and believes in miracles, then one believes in a “supernatural realm” which is not constrained or confined by the natural laws that we know. The question that I have in my own mind is: How exactly does this “supernatural realm” interact with the natural laws and “reality” that we humans are familiar with? (I hope this is making sense.)

        This has always made me very cautious when studying Genesis, the origin of life, the origin of the Universe, the age of the earth, etc., etc. I feel cautious because I have no idea how God’s actions actually interact with the natural laws and reality that we know. What are your thoughts on this?


      • D Helland MD says:

        One other comment regarding “intelligent design”. To me the intelligent design of the human body is a given. The heart with its conduction system, the kidneys, the brain and nervous system, etc., etc.

        Anatomy and physiology to me just scream out “This was designed.” No one in heaven or earth will ever convince me differently. (I believed in “intellegent design” long before there was an ID movement.)

        (I am a 60 yo board certified radiologist. My BS was in civil engineering.)

      • Don,
        Well, you certainly know how to get right to the meat of things: ” How exactly does this “supernatural realm” interact with the natural laws and “reality” that we humans are familiar with? ” I don’t have a satisfactory, overarching answer.
        (I just went and asked my wife how she would answer this question, and she said I should recommend to you an authoritative book on this topic, but neither one of us could think of such a book….)

        On one level, this may be straightforward, if we think of God willing and in some deep sense causing every event, and if it happens to please Him to have nearly all such events that occur in our universe to do so with the rigorous regularities we call “natural laws”.
        (Philosophers like Hume have noted that there is no metaphysical necessity for things to happen with this regularity; we just observe that they have always happened in that way in the past, and assume [hope? faith?] that these regularities will continue in the future).

        Christian thinkers have offered various thoughts on why God might want to normally have things happen in a regular fashion. For instance, He may wish to stay hidden in this manner so people could choose to love Him with some measure of freedom. Also, only an orderly world would enable humans to demonstrate and grow in responsibility and wisdom — if events were mainly random, with no cause and effect, there would be no point in doing anything.
        That said, if God should wish for a few events to occur that don’t fit the usual pattern, He could easily do so, if He is the underlying causer of all things. (The extent to which God directly causes things, vs. merely allows them is a knotty question. It bears on theodicy, free will , and other mysteries. I don’t know…).

        C. S. Lewis has written a whole book on Miracles, which you might enjoy. It probably does not answer all your questions, but has a number of nuggets. As I recall, Lewis noted that the miracles of Jesus were not like random magic tricks. Rather, they focused and accelerated the workings of God already displayed in ordinary nature. For instance, the body has God-given healing capabilities, that often suffice to fix what is wrong (injury, disease). When Jesus healed people, he was doing (supernaturally) quickly and thoroughly something much what God does slowly and more weakly through the immune system and healing mechanisms. When he turned water into wine, he was in some sense mimicking what God has already provided when water is drawn into a vine and turned into grape juice.

        Since I am at a loss for a theoretical perspective, I’ll switch to some personal experience. On more than one occasion I have been in the room when someone received prayer for healing, and within a few minutes reported relief of long-standing, troubling symptoms (pain, disability, etc.). Often the person reported feeling heat in the affected region. If, for the sake of discussion, we assume that some of these were actual miracles as opposed to just reversal of psychosomatic conditions, what does this mean? I don’t know. It just is.

        I will add an observation, that these sorts of things seem to happen more in the presence of certain Christians who apparently have a gift of healing, as mentioned in I Corinthians 12. If you ever have a chance to get to a meeting featuring Bill Johnson of the Bethel church in Redding, CA, or Randy Clark of Global Awakening in Harrisburg, PA, I recommend you go for it.
        Also, in my observation as well as in the gospels, Jesus seems to respond more to heartfelt faith than to desperate need, when it comes to miracles. Someone has put it, “Faith is the currency of the kingdom”. I don’t know why this would be the case, but as an engineer I am used to working with reality as it is, even if I don’t fully understand it.

        I have given links to some articles on this blog on healings. Here is one more: https://letterstocreationists.wordpress.com/2012/12/11/engineers-wife-healed-of-multiple-sclerosis/
        This concerns a woman who has healed of M.S. Note the usual feeling of heat when the healing came. The woman’s husband is, like you and I, an engineer by training, and offers some left-brained analysis of this matter, including answers to questions like : .“Why doesn’t God seem to heal people as much in this country as He does in other lands, as reported back by missionaries?”
        Well, I don’t know if I have scratched your itch here. I’d be interested to hear your thoughts on this matter.


  9. I have created my own FAQ on ERVs, written with creationists in mind. http://barryhisblog.blogspot.fr/p/endogenous-retroviruses-frequently.html

  10. Don Helland MD says:

    I have come across quite a few interesting articles in the scientific literature the last couple years about ERVs.

    For example “The Decline of Human Endogenous Retroviruses: Extinction and Survival”. Magiorkinis et al, 2015, BioMed Central.

    Please see Table 1, column 2, labeled “Number of old loci (6.6-31.6 my), in the above article. The authors state “The difference in Table 1 among hominoids can probably be attributed to differing methods and quality of genome sequencing and assembly, e.g. the number of loci in the human, chimpanzee, bonobo, and gorilla genomes that are older than 8 my should by definition be identical – as until this time they share the same genome – but in our analyses they differ, with the gorilla being particularly low”.

    This is one of the things about evolutionary theory that bothers me a great deal. If the data doesn’t fit the theory, there is ALWAYS some explanation to justify continued belief in the theory. In this particular case the explanation is “…differing methods and quality of genome sequencing and assembly…”

    In other cases where the data doesn’t quite fit, the explanations include ILS (incomplete lineage sorting), recombination, etc. (In the case of birds ILS seems to be taken to the extreme.)

    The case for ERVs proving common descent isn’t quite as “tight” as some put it forth to be. At least not in my mind.

  11. Don Helland MD says:

    Another interesting article on retroviral integration: “Retroviral Integration: Site matters”, Demeulemeester, et al, Bioessays 2015.

    Page 1202: “Retroviral integration is not a random process….” (Please see the article for details.)

    This is one of the best reviews of retroviral site selection that I have come across.

    • That is an informative article — it has lots of details on retroviral site selection processes. It reinforces what is in my article above: (a) Certain types of retroviruses preferentially bind to certain types of regions on the genome, and (b) This does not mean that a specific retrovirus will be directed to a specific site. Rather, there are many thousands of suitable sites for a given retrovirus (“…have ample binding sites across the genome. “)

      • Don Helland MD says:

        “This does not mean that a specific retrovirus will be directed to a specific site…”

        I think the jury is still out on this.

        For example, mobile group II introns are bacterial retrotransposons that perform a site specific integration reaction (retrohoming). “Group IIA and IIB introns have a high DNA target specificity and integrate ONLY RARELY into ectopic sites…” They have been used as “targetrons”. They are thought to be evolutionary ancestors of spliceosomal introns, the spliceosome, retrotransposons, and RETROVIRUSES. (“Biotechnological applications of mobile group II introns….” Enyeart et al, Mobile DNA, 2014.)

        In addition, research has shown some spliceosomal intron gain to demonstrate integration homoplasy. “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes,” Lynch said. “This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.” (“Introns–nonsense DNA–may be more important to evolution of genomes than thought.” Science Daily, Demember 14, 2009)

        Finally, “Although mobility mechanisms may vary, most forms of transposition involve simple nucleoprotein assemblies that orchestrate complicated enzymatic reactions, often with HIGH TARGET SPECIFICITY.” (“The pathway for DNA recognition and RNA integration by a Group II Intron Retrotransposon.” Aizawa et al, Molecular Cell, 2003.)

        Most of these ERV integrations took place in the distant past. How do we know what the site specificity of retroviral integrases was in the distant past? There are just a lot of questions in my mind about the “insertion site specificity” of retroviral integrases.

        (Another interesting article is “Retroviral intasomes search for a target DNA by 1D diffusion which rarely results in integration.” Jones et al, Nature Communications, 2016.)

  12. Don Helland MD says:

    Quite an interesting article by James Tour:

    “Animadversions of a Synthetic Chemist”, Inference, International Review of Science, 2016.

    • Interesting – – impressive synthetic chemistry.

      • Don Helland MD says:

        What do you think about his comments on abiogenesis and the origin of life?
        Best regards.

      • Don,
        I tend to agree that abiogenesis has not been explained. Once the first complete cells, with all their DNA self-repair machinery, are going , I can see (you may disagree) a path forward for ongoing changes. But I have seen no convincing explanation of how the first cells arose from the soup. But it was all so long ago, and so unlikely that any intermediate forms could have been preserved, that I am not sure we can even know what happened.

        We seem to have the religious folks happy to find such a large gap in understanding for which to invoke God, and the secular folks simply asserting that such-and-such (e.g. RNA replication) can easily explain matters. I prefer to humbly refrain from making assertions where we simply do not have enough information.

  13. Pingback: A Creationist Speaker Comes to Town | Letters to Creationists

  14. Pingback: Whatever Happened to Intelligent Design Theorist William Dembski? | Letters to Creationists

  15. Pingback: Listing of Articles on Science, Faith and Other | Letters to Creationists

  16. Pingback: Evolution Before Our Eyes: Complex Mutations in Microbes Giving New Functions | Letters to Creationists

  17. Pingback: Evolution and Faith: My Story, Part 2 | Letters to Creationists

  18. Don Helland says:

    16 August 2018

    “Retroviruses integrate into a shared non-palindromic DNA motif”, Nature Microbiology,14 November 2016.

    Seems as if insertion is not random, even down to the base pair resolution level.

    “Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates”, Biophysical Letter, May 22, 2018.

    Also an interesting article about Alu integration. “Evidence of a strong association between NIEB borders and the polyA tails of ALU sequences in human. These results suggest that NIEBs provide adequate chromatin patterns favorable to the integration of ALU retrotransposons and, more generally to various transposable elements in the genomes of primates and other vertebrates”.

    Seems like integration of ERVs and ALUs is less random than previously thought.

    • Don,
      Just getting around to look at this. These two references confirm what is stated in my article here.

      The article makes it clear that ERV integration is not uniform (random) across the WHOLE genome. There are certain preferred TYPES of sites. But within those preferred regions, there are typically many thousands of individual sites where a retrovirus can insert (whether by initial integration or later duplication). I showed, for instance, part of a graphic mapping some 3,127 separate locations for three retroviruses. These were indeed clustered in preferred regions, but there was not a single preferred site for each retrovirus. I also noted a more complete study which identified 40,569 different locations in the human genome for the HIV retrovirus to insert.

      Having a single, unique, integration site for each unique full ERV, and a few other single specified sites for each particular type of ERV fragment is the only way to evade the common ancestry implications of human and chimp genomes sharing over 100,000 ERVs in the same locations in the two genomes. But the examples I showed in the article demonstrate that having a unique integration site is not the case, and the two articles you cited likewise demonstrate that is not the case.

      The 2016 article discusses certain preferred types of retrovirus insertion sites, but again does not demonstrate any single unique sites. Their data set included thousands of sites for each virus (e.g. 4,521 locations for HTLV-1 and 13,442 locations for HIV-1). And, as the references in that article demonstrate, this all has been known for over a decade. The situation is even worse for the anti-evolution case with the 2018 article you cited – – that article identified a class of over 1.6 million preferred sites for ALU integration.

      Your remark that “Seems as if insertion is not random…” is ill-informed. It has been known and published since at least 2005 that ERVs occur in preferred classes of sites, not randomly across all 3 billion sites in the human genome.
      Your statement ”… less random than previously thought” is likewise ill-informed. Nobody in the past decade “thought” that integration of ERVs and ALUs is uniformly distributed across the whole genome.

      • Don E Helland says:


        The examples you cite were integrations in somatic cells I believe.
        The integrations used to “prove” common ancestry had to be integrations into germ cells in the distant past. How do we know that integration in germ cells is not more site specific than in somatic cells? How do we know that the ERV integrase wasn’t even more site specific in the past?

        You seem to agree that integration of ERVs and other mobile elements is not random. But just how “not random” in germ cells remains an open question. See for example: “Functional Characteristics of a Highly Specific Integrase Encoded by an LTR-Retrotransposon”. PLoS One September 2008.

        I don’t know. I just feel like we are missing something here.
        You seem to believe you have a “water tight” case for common anscestry. But I remain skeptical. Especially in light of the recent findings that many ERVs have function in the early embryo, etc.

        Also there is much evidence that ALUs have function.

        The “junk” hypothesis for mobile elements, and then the supposed GAINING OF FUNCTION AFTER INTEGRATION, etc, seems too contrived to me.

        And then there is the question: Where did these mobile elements like ERVs come from in the first place?

        Lastly, since many mobile elements do indeed have function, how do we know that they were not placed there by God himself? I believe that the genome (genes and intergenic regions) was created by God. I do not believe that it is the sole product of random evolution. So how do we know FOR SURE that God was not involved in the integration of ERVs? Seriously, how do we know? I believe that you are a “theistic evolutionist”? God supposedly directed evolution. If so, how do you know that God wasn’t involved with ERV integration?

        Best regards


      • Don,
        Once again you cite a literature reference, hoping to cast doubt on evolution. And once again I will shoot it down. This is getting tedious.

        The 2008 PLoS article that you cite in your comment deals with the “ZAM” (endogenized) retroelement found in the genome of Drosophila melanogaster (fruit fly). This retroelement appears to insert only at sites where the specific ordered sequence of five bases, CGCGC, is present. About half the time, a sixth base, G, appears at the end of this sequence, so the article includes a lower case “g” to describe the targeted sequence of ~ 5 ½ bases: CGCGCg.

        Is this evidence that a retrovirus can insert in one and only one site in the host genome? No, not in the slightest. First, we note that this example is for an insect, not a mammal, and second, the article acknowledges that this ZAM is the only known example of this sort of sequence specificity – every other known retrovirus are observed to NOT have this specificity. So the ZAM example appears to be an outlier, not representative of typical mammalian retroviruses.

        But even for this ZAM, it does not insert into one and only one site, which would be the requirement to challenge the ERV evidence for evolution. First, let’s do some numbers. Let us assume that for some retrovirus, it can insert only in locations where a particular sequence of six bases is present, such as CGCGCG. Some rough arithmetic shows that there should be well over 100,000 (the exact number is unimportant) occurrences of such a six-base sequence in a human genome of 3 billion base pairs. Thus, there would be over 100,000 potential insertion spots for this retrovirus. End of story.

        Second, we find empirically that the ZAM retroelement does not appear in only one spot in the Drosophila genome. The 2008 paper that you cite harkens back to a 1999 article [J. Virol, Vol. 73, 1999, p. 7061–7064] by some of the same authors. Using the lab technology back then, they identified at least 16 unique sites where ZAM appears in the Drosophila genome. This is not 16 sites where it could insert (there are many thousands of such potential insertion sites), but rather 16 sites (not just 1 site) where it actually did get inserted over the course of the contingent evolutionary history of Drosophila. This ZAM case, of course, involved germline insertion.

        You now seem to be making objections just for the sake of making objections. First, you keep bringing up issues that were answered already in my article here. You did this in your previous (August 16) comment regarding the randomness of ERV insertions, and you do it again here regarding the fact that some ERV fragments have function in the human genome. That functionality issue was clearly dealt with in my article, including the reference/link to Barry Desborough’s description of how the function of some of these genes in mammalian genomes are similar to the function of these genes in the native retrovirus. That shows that the gaining of their function in the human genome is not at all “contrived”.

        Second, you are now coming up with some pretty desperate attempts to deny the evidence for evolution:

        ( a ) re: “How do we know that integration in germ cells is not more site specific than in somatic cells?“
        Answer: The basic biochemistry for germline cells is the same as for somatic cells, so there is no fundamental reason to believe that retroviral insertion in germline cells is vastly different than in somatic cells. And so, the same gene editing techniques (some of which involve using retroviruses to insert DNA payloads into the genome) work on both somatic and germline cells. But surely you already know this. Also, as noted, for the article you cited there were multiple (16) separate insertions identified for germline insertion of ZAM over the over the past evolutionary history of Drosophila. So, no special site specificity here.

        ( b ) re: “How do we know that they were not placed there by God himself?”
        Answer: Well, if we want to get that wacky, fine, we don’t really *know* much of anything. You don’t *know* that the external world exists at all – – maybe your brain is sitting in a vat, and is being manipulated by The Matrix to think you have eyeballs and are reading on the internet. Maybe God did insert the same retroviruses or pieces of retroviruses in the same spots in human and chimp genomes, to fool us into thinking evolution is true; and while He was at it, He also created rock layers with the appearance of age, which contain intermediate fossils between fish and amphibians and between reptiles and mammals, to further deceive us into thinking evolution is true.

        But then again, maybe He created the whole world at midnight last night, looking apparently old, including your marked-up Bible and you with your fictitious memories of many decades of living. We can’t *know* one way or the other. There is no end of such desperate speculation. But that is not the real world that we actually live in.

        Anyway, your comments indicate that (whether you admit it or not) you are so wedded to your religious interpretation that no amount of evidence can convince you to accept the reality of evolution. So I don’t think further dialog here will be fruitful.

        Re: “So how do we know FOR SURE that God was not involved in the integration of ERVs?”
        Answer: I never said God was “not involved” in the integration of ERVs. You seem to think that unless there is some miraculous intervention, that God is “not involved”. But (Eph 1:11) God “works out everything in conformity with the purpose of his will”, whether by natural or supernatural means. This includes all events, natural and supernatural. Even events that are completely random as far as we can tell are ultimately determined by God: “The lot is cast into the lap, but its every decision is from the LORD” (Proverbs 16:33). The mechanism of how He achieves His will within the regularities of natural laws is often mysterious to us – – theologians talk of primary and secondary causation, etc. I don’t claim any special understanding here.

        As an example, you have roughly 50 mutations in your genome compared to your parents’ genomes (not counting the usual shuffling of alleles from sexual reproduction). Presumably those mutations occurred via normal biochemical mechanisms. Yet I would say that this does not mean they occurred outside of God’s providential plan for you. I trust you would agree. But this little snip of your recent evolutionary history illustrates the way that ALL of evolutionary history has occurred, with seemingly random and/or mechanistic natural events occurring all under God’s sovereign plan.

        Either (A) these events are as they appear, i.e. millions of plain natural events occurring just as the natural laws of evolution would predict (under God’s providential oversight), or (B) God miraculously inserted millions of details in the observable order to deceptively make it LOOK like it all evolved naturally. If you want to opt for (B), so be it.
        I wish you well.

  19. Pingback: Science and Faith at the American Scientific Affiliation 2018 Meeting | Letters to Creationists

  20. Pingback: Adam, the Fall, and Evolution: Christianity Today and WORLD Push the Panic Button | Letters to Creationists

  21. Pingback: Saint Augustine on Interpreting Genesis | Letters to Creationists

  22. Pingback: John Sanford Disputes Evolution [2020 NCCA Apologetics Confc, 5] | Letters to Creationists

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s