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Viral Genome Is Bunk - Or Is Tomkins' Article Bunk?



"Viral Genome Junk Is Bunk" from the "Institute for Creation Research" 
by Jeffrey P. Tomkins, Ph.D., critiqued by yours truly.

My comments in red.


One of the great ongoing myths of evolution is that the genomes of animals and humans are littered with vast amounts of genomic viral DNA fossils.

Not a good start, Jeff. That our genomes are littered with such material is a conclusion based on a great deal of evidence, some of which is gone into in this FAQ. Also see the FAQ home page linked to above.

These alleged ancient viral sequences are thought to have entered the genome via viral infection, initially served no purpose in the host, and then later during evolution’s long, slow changes were supposedly converted (“exapted”) to various useful purposes—like aiding in the elaborate process of human reproduction. However, like other evolutionary tales, advancing research in the field of genomics utterly contradicts this popular dogma.

Conclusions from evidence. Not "dogma". Dogma belongs to religion, but is apparently a dirty word for you! So it's not worth mentioning how this research contradicts the conclusions? By the way, it is not necessarily by "long slow changes" that viral DNA can become exapted. Reverse transcription goes on at a massive scale, and at a massive rate. It is error-prone, with no error detection or correction mechanisms. Mutated DNA may be integrated and provide some sort of advantage for the host right from the get-go.

Re. aiding reproduction, syncytin formation, if that's what you were alluding to, is a native trick of retroviruses. It's no great surprise that several environment proteins have been exaptated from various retroviruses, in various lineages. See 
ERVs are essential in reproduction (syncytin and the formation of the placenta). How can this be?

According to evolutionary theory, viruses have repeatedly integrated themselves into the DNA of germline cells (those that produce eggs and sperm) over the past 100 million years of mammalian evolution—with their viral-like DNA proliferating across creatures’ genomes.1 These are called endogenous retroviruses (ERVs), and 8% of the human genome is populated by these sequences. However, there are least three major problems with this idea.

It's not according to evolutionary theory at all, but according to virology and genetics. That it confirms evolutionary science is what drives dishonest creationist attempts at damage limitation. But the more this is talked about, the more and more people are seeing through these attempts.


First, genetic data indicate that these sequences are not millions of years old. Using the comparative tools of evolutionary genetics, secular scientists compared the gene sequences of viruses to their counterparts in animal genomes and found that, at most, the variation in these sequences indicates they can be no more than 50,000 years old. (Holmes, 2003) So, if these viral-like sequences are not millions of years old, then where did they come from?

From a Ph.D. in genetics, this is utterly inexcusable. Holmes is discussing modern exogenous retroviruses (retroviruses in the environment) and modern proviruses (DNA forms of modern retroviral genomes embedded in the DNA of somatic cells). It is completely beside the point, and grossly misleading. You have fabricated a "puzzle" about ERVs which doesn't exist. Essentially, this is a lie.


Second, the alleged process whereby these ERV sequences were supposedly stably integrated into the germlines of animals has never been documented. The process itself is an exercise in speculation. In studies where their random and uncontrolled integration has occurred in regular body cells (called somatic tissue), cancerous tumors are often the outcome.(1) In reality, most modern ERV-like viruses do not readily integrate into a host’s genome; only a few, like the AIDS virus, have been found to do this. And the ones that do perform this integration type of behavior do not target germline cells that would then enable them to be passed on to the next generation.

Oh dear, Jeff, yes it has been documented. Extensively. Are you playing dumb again, abusing your credentials to fool the flock? Have you never heard of the gammaretrovirus, KoRV? This is a rerovirus which is in the process of endogenizing in koalas, and yes, it causes cancer. It is also present, endogenized, in koalas that have successfully reproduced!

HIV, by the way, is a lentivirus. There are very few cases of the endogenization of lentiviruses, and none of them are HIV. Are you just making this crap up?


Retroviruses integrate in nuclear DNA. Mostly, they integrate in somatic cells. Relatively infrequently, they integrate into the DNA of gametes. But not HIV. "Integrate into a host's genome", in the sense that you use it, and "target germline cells" are one and the same thing! Where did you get your Ph.D.?

Third, important functions are now being attributed to ERV sequences in mammalian genomes. In fact, several studies in recent years have highlighted the importance of many ERV gene sequences in placenta development and maintenance—a process crucial to reproduction and life.(3,4) Not only are important genes contained in these sequences, but also many different regulatory elements that function as key genetic switches.5

Yes. We know. We found this out and told you.


So, where do viruses come from that essentially share the same sequences as those found in their host genomes? Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, “The most parsimonious answer is: the RNA viruses got their genes from their hosts.”(6)
In other words, mammalian viruses may not have existed at all before the Curse, but after mankind’s sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins.

See creationist Todd Wood falsifying this unevidenced speculation in a couple of sentences!

References

1. Magiorkinis, G., D. Blanco-Melo, and R. Belshaw. 2015. The decline of human endogenous retroviruses: extinction and survival. Retrovirology. 12: 8.
2. Holmes E. C. 2003. Molecular Clocks and the Puzzle of RNA Virus Origins. Journal of Virology. 77 (7): 3893–3897.
3. Lavialle, C. et al. 2013. Paleovirology of ‘syncytins’, retroviral env genes exapted for a role in placentation. Philosophical Transactions of the Royal Society. 368 (1626): 20120507.
4. Liu, Y. and C. Soper. 2009. The Natural History of Retroviruses
5. Exogenization vs. Endogenization. Answers Research Journal. 2: 97–106.
6. Chuong, E. B. et al. 2013. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nature Genetics. 45 (3): 325-329.
7. Borger, P. 2009. The design of life: part 3—an introduction to variation-inducing genetic elements. Journal of Creation. 23 (1): 99-106.

* Dr. Tomkins is Research Associate at the Institute for Creation Research and received his Ph.D. in genetics from Clemson University.


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