Preferential Integration of Endogenous Retroviruses

Abigail Smith has moved to http://scienceblogs.com/erv

Argument #1 Retroviral Insertion is not Random. Common Descent is an Illusion:
http://endogenousretrovirus.blogspot.com/2007/07/retroviral-insertion-is-not-...

(This video is the first in a series.)

Index of claims against ERVs:
http://endogenousretrovirus.blogspot.com/2007/07/index-to-common-creationist-...

ERV connect-the-dots:
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=ShowDetailView&...



Two sources cited by creationists:

Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences:
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.137...

An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion:
http://www.genetics.org/cgi/content/full/158/2/769



Diagram of HIV insertion points (Figure 1):
http://biology.plosjournals.org/archive/1545-7885/2/8/figure/10.1371_journal....

Category:

Science & Technology

Tags:

• endogenous
• retrovirus
• preferential
• targeted
• integration
• insertion
• random
• evolution
• HIV
• genetics
• common
• descent
• ancestry

[playd76]

What flood? lol

[scienceminded]

No but objects (chemicals) can reproduce themselves without input of information, if it can produce changes to itself when replicating it can evolve. We don't know the details but I find it much more satisfying than 'god did it' as it leaves mystery that I CANT fantasize to fit my ideals, I can't make conjectures without evidence, whatever we will find will be much grander than the small God of unimaginative redundancy and necessity, that is knowledge.

[Adventfred]

good post uploader

[phicomingatya]

Help me understand here.

Where did you get the numbers 353 and 388 of ERVs being in orthologous loci?

[SecularAstronomer]

It doesn't sound like you read the paper. The ERVs are in orthologous loci. An orthologous locus is defined as the same genomic location in two or more species.

Read the "Endogenous retroviral positional variation between chimpanzees and humans" section on pages R51.9 to R51.11.

Look at Figure 6 on page R51.11.

Read the paper.

[phicomingatya]

orthologous means in we got them in common with chimps. It does not necessarily mean we have them at the exact same spot.

[SecularAstronomer]

That puts the total number of CERVs with HERVs in orthologous loci at 388.

Polavarapu, N; Bowen, NJ; McDonald, JF. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006;7:R51.

tinyurl(DOT)com/qqdco3

[SecularAstronomer]

"Of the 41 instances where an endogenous retroviral sequence is present in chimpanzees but lacking in humans, 29 were due to novel insertions in chimpanzees while 12 were deletions in humans (Tables 3 and 4; Figure 6a). Of the 31 instances where an endogenous retrovirus is present in humans but absent in chimpanzees, we found that 8 were due to novel insertions in humans while 23 were deletions in chimpanzees (Table 4; Figure 6b) (R51.9)."

[SecularAstronomer]

Of the 425 CERVs, 353 were found to be present in orthologous loci in humans (Ex. CERV 16/HERV17 at 7p14), with several instances displayed in figure 6 (R51.11).

[SecularAstronomer]

"...how many ERVs do we share exactly with chimps at the exact same integration site? (How many have we found so far?)"

That is a good question. It would be best to ask a researcher in this field of study, but as far as I know, 425 full-length chimpanzee endogenous retroviruses have been definitively identified (Polavarapu, Bowen, and McDonald, 2006, p. R51.2) - far more would consist of solo LTRs and fragments (R51.9).

[phicomingatya]

Yea, I will. Because the facts are what they are and the same no matter what anybody claims.

But I can ser you have no faith in my claim. But perhaps you can help me doule check a few things. Like how many ERVs do we share exactly with chimps at the exact same integration site? (How many have we found so far?)

I hope you'd be kind enough to tell me what you know. Thanks.

[SecularAstronomer]

No, I expect those that find a video helpful to actually understand what they just saw and heard. But if you wish to use a video to support a claim that video doesn't support, that is your choice.