1. There are a few ERVs with unusually high LTR divergent ratios. A: Given the complexity of biological systems this is not unexpected. We don't know all yet and rarely in biology are results perfect. However, a few deviations do not negate an overwhelming pattern that emerges from this data.
2. The insertion of integrase is not entirely random. A: Studies have shown that target site preference by proviral insertion is not purely random. True in one sense, however it is not locus specific. There may be some preferred integration events, but studies show little apparent sequence or site specificity. See also Smith's rebuttal to the argument that insertion sites are not random: Link.
3. Some ERVs have functions. A: True, but there are no wholly functional ERVs. All have parts that have been deleted or mutated into nonfunctioning DNA. Most ERVs are not even located on a part of the chromosome that allows it to be transcribed. In addition, the actual genes of the ERVs are not active - only their LTRs due to their promoter rich sections. Thus, the ERVs are nonfunctional, but an ERV component can be functional, and this makes up a very small percentage of the total. Lastly, any functionality ocurred AFTER the retroviral DNA was integrated into the host DNA (some have been co-opted by the host for other functions) and was not placed there as part of an 'original design'.
4. Humans don't share some ERVs that other ape species have. In small populations, alleles can be lost or are not inherited just due to chance inheritance. Link
5. ERV's are not old retroviruses. Peter Borger is a main proponent of this view. As a YEC who must fit everything into a young earth and universe, he completely flips the current interpretation of genomics around. "Darwinists are wrong in promoting ERVs as remnants of invasions of RNA viruses, it is the other way around". Link He proposes that variation was front-loaded into species' DNA and thus variation was put there by God. ERVs are really special transposons placed by God to make "kinds" able to quickly speciate from creation or after The Flood. They later degraded and became viruses. He calls these early genomes "baranomes", with built-in variable redundancy and speciation occurring as a result of "limited common descent through adaptive radiation from pluripotent and undifferentiated baranomes". He redefines LINEs, SINEs, ERVs and other non-coding DNA as "VIGEs", or Variation Inducing Genetic Elements. Natural selection becomes the "Law of natural preservation". His discussions are complex and technical, detailed in four basic parts Link. He has also written about GULO from a YEC perspective Link. In 2006 he was involved in an online discussion of mutations (Link) but it is probably too technical for anyone outside the field to follow, this author included. Some of the topics he is arguing include the sources of variation and if natural selection can account for speciation when examined at the molecular level. However, the evidence for evolution and common descent in a old universe comes from divergent and integrated scientific fields including geology, paleontology, cosmology, plate tectonics, genomics, radiometric dating, biogeography, etc. In the end, he is married to his YEC worldview and would have to explain away all the other lines of evidence. In his four part series on genetic variation and evolution, any discussion of atavisms is absent.
ERVs are shared across species and higher taxonomic phyla. Within the ERVs, mutations have occurred and also within inserted LTRs. Some of these mutations are also shared and only a common ancestor can adequately explain the concordance due to the patterns of the inheritance and mutational differences and similarities. There is no way the same virus could insert the same viral DNA at the same locus in different species or individuals often with subsequent similar random mutations accumulating in them, especially across vast geological time. The accumulation of mutations allows for dating and grouping into subsets of evolutionary lineages that match previous fossil evidence of evolutionary relationships and ancestry over millions of years.
From: Evolutionary Model.
Also see: Index to Common Creationist Claims about ERVs Link. (SA Smith)
She has recently moved her blog to Scienceblogs.com Link
Standup4Realscience - short video. Link
Human ERVs - may outnumber our genes and comprise over 200 groups. Link.
Ancient retroviruses involved in evolution. Link.
Retroviral Insertion is not Random. Common Desecent is an Illusion. Link
Inside the Human Genome: A Case for Non-Intelligent Design. Link
John Avise and what our genome is telling us with a comment about theodicy
Endogenous Retroviruses: Life-cycle and Ancestral Implications. Link
ERVs and the Nested Hierarchy Link
Evolution of ERV sequences (ERV functions) Link
ERV Nomenclature Link
More Syncytia Sweetness (ERV) Link
NAIP gene and LTR promoters Link
Endogenous Retroviruses (Wikipedia) Link
Facts of Evolution: Retroviruses and Pseudogenes (YouTube) Link
Mammals Made by Viruses Link
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