The evidence from retroviruses provides powerful evidence for different kinds of creatures having had common ancestors.

The following is a critique of an article by a Dr. Yingguang Liu, Were Retroviruses Created Good? (link) at a site called Answers in Genesis (AiG), plagiarized here (link) and brought up in various_blogs and discussion fora (link). The article does not so much argue against common ancestry, as ignores it and instead attempts to argue for a role for a designer-creator.
The article uses technical terms that mean little to the reader who has not already studied the subject. However, the facts behind these technical terms are very easy to understand. Dr. Liu provides a brief glossary, but in my opinion, it is inadequate for the general reader. To familiarize yourself with the subject of retroviruses, please click on this introductory course (link) which will open in a new window or tab. For further assistance, I have attempted to explain and clarify Liu's writing at the same time as critiquing it. I will also be adding links throughout this page, both in my quotes of the AiG article, and in my own notes. All such links will be my own.
We begin by examining Dr. Liu's abstract.
[quote]Abstract: Retroviruses that are not normally present in healthy hosts are called exogenous viruses, …[/quote]
More precisely, they are called 'exogenous retroviruses', but usually, they are simply called 'retroviruses', the exogenous bit being implicitly understood. 'Exogenous' means 'originating from outside the body'. Retroviruses, (the human immunodeficiency virus HIV is an example of a retrovirus) reproduce by invading the cells of their hosts and inserting their genetic material into the host cells' DNA. This causes the host cells to create new virus particles.
[quote]... while DNA sequences in cellular genomes that are homologous to retroviruses are called endogenous retroviruses (ERVs).
Here, 'homologous to' means 'having the same structure as'. The structure of a retroviral insertion is detailed and distinctive. It is specific to the task of causing the cell to produce new virus particles that can go on to infect new cells. Sequences of DNA with the same detailed structure as retroviral insertions are to be found in the DNA of the cells of all creatures. Each sequence appears in exactly the same position in the DNA of every cell of the body. There are typically hundreds of thousands of these sequences in each and every cell. These are known as 'Endogenous RetroViruses' or ERVs, 'endogenous' meaning 'arising from within the body'.

An essential point to grasp, and which Liu fails to stress sufficiently, is that ERVs are inherited. You and I each began with a single cell, which divided and divided as we developed. Our cells also continue to divide in order to maintain our bodies. At each and every division, our DNA is duplicated, including our host of ERVs. We originally inherited our ERVs from our parents, and they from theirs. This is the distinction between endogenous retroviruses (inherited retroviruses) and exogenous retroviruses (retroviruses acquired by infection).
[quote]While the belief that all ERVs are remnants of germline infection seems logical,...[/quote]
It is a conclusion based on evidence, not a 'belief', that ERVs are originally created by exogenous retroviruses infecting germline cells, (egg or sperm cells). We will be looking at the evidence and the reasoning behind this conclusion as we proceed.
[quote]... there are also facts against the endogenization theory, such as xenotropic ERVs ...[/quote]
A xenotropic ERV is an ERV that is unable to infect the cells of the species it is inhabiting. We will go into this 'problem' for the endogenization theory (the theory that ERVs are remnants of infections of germ cells) in more detail later. The problem amounts to the same sort of problem one might have if one fails to understand how a horse can come to be in a stable, because the stable door is shut. (The solution involves recognizing that the stable door was not necessarily always shut.)
[quote]... and essentiality of some ERVs in host physiology. Syncytins, products of the envgene of HERV-W and HERV-FRD, contribute to human placenta development. Similar genes are also found in mouse and sheep. Indeed, the sheep ERV genes have been shown essential for sheep reproduction. Furthermore, regulation of the human syncytin-1 gene involves a complex regulation network including both viral and host factors.[/quote]
Again, we will go into this in more detail later, but it is worth noting here that

  1. The env (envelope) proteins of retroviruses have the job of binding the retrovirus to the target cell. This makes them ideal candidates for being coopted by the host as syncytin proteins, which bind cells of the placenta with those of the uterus.
  2. No rational designer would embed this gene, unnecessarily, in an ERV structure.
  3. It is often claimed that a common design speaks of a common designer. Here we have uncommon 'designs' in humans, mice and sheep, all involving different env genes, unnecessarily embedded in different ERV structures. If someone wanted to claim that some feature was the product of design, they would not point to syncytia.
[quote]Conclusion: While intact ERVs with positional polymorphism are likely germline copies of exogenous viruses, ERVs with fixed locations and conserved beneficial genes may have been incorporated into the host genome at the time of creation. Exogenous retroviruses may have been created to help the ERVs and to transfer useful genes between hosts.[quote]
'Positional polymorphism' just means 'found in different locations'. The koala retrovirus, KoRV, for example, has been inserted into germ cells in different DNA locations in different groups of koalas. Each example, however, is heritable, and appears in the same location in every cell of the offspring that inherit it. Liu tries to contrast these with "ERVs with fixed locations and conserved beneficial genes", neglecting to mention their non-conserved nonfunctional genes and neglecting to mention ERVs and ERV remnants with fixed locations and no conserved beneficial genes at all - only around 200,000 of them in our genomes. As has already been noted, ERVs with beneficial genes are hardly star witnesses for design anyway.

And it appears that Liu is not, after all, arguing for a designer as much as trying to argue against the natural explanation, that all ERVs are remnants of germline infection. Even if the viral explanation could be shown to be inadequate, it would not mean that the 'design explanation' 'wins'. Neither would it mean that common ERVs do not mean common inheritance for different kinds of creatures - common inheritance is the obvious explanation even if there was a designer. Any proffered explanation requires positive evidence in its favor. We will see, as we go on, whether Liu provides it or not. So far, we have two supposed arguments against the viral explanation, xenotropic ERVs, and a subset of ERVs with components that perform useful or even essential functions. In favor of the design explanation, we have three 'maybes'. Maybe some ERVs just got created, somehow or other (other than via infection) in our genomes. Maybe they got created somehow in order that a few of them could have a component that could do a useful job. Maybe retroviruses were created to transfer useful genes, even though now they transfer any old stuff (in addition to retroviral genomes).

The elephant in the room that Liu is desperate to ignore and have us ignore, is that if you and I share hundreds of thousands of ERVs and ERV remnants, each one in a particular location in all of our cells. Whether the parts of some of them that have any function have been scavenged and recycled by evolution, or are there by design, the simple explanation for the fact that we share them is that we inherited them from ancestors we share in common. Similarly, if you and I and Charlie the chimp share hundreds of thousands of ERVs, each one in a corresponding particular location in all of our cells, then the simple explanation is that we have inherited them from ancestors we all share in common. Either that, or the designer had been desperately trying to fool us into falsely concluding common ancestry by designing in a huge mass of unnecessary and misleading features and details pointing to common inheritance.

To be continued.