Retroviruses and evolution
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“Turning coffee into theorems”

Since: Dec 06

Trapped inside a Klein Bottle

#1 Jan 10, 2008
I have been reading the last couple of weeks about endogenous retroviruses (ERVs) and what they tell us about evolution. What I have read is perhaps the most compelling evidence of common descent that I have seen.

Retroviruses (RVs) are viruses which insert their genetic material into our own chromosomes. They have a mechanism which allows their RNA to imprint a strand of DNA and insert it. This DNA then creates copies of the RNA, making new viruses. These strands of DNA are sometimes known as "proviruses".

Most RVs infect non-reproductive cells and have no effect on the species genome. However, a few, known as EVRs, do infect reproductive cells and on rare occasions that DNA is passed on to future generations. The ERVs' DNA then becomes part of the hosts' genome.

Roughly 8% of the human genome is made up of ERV DNA, the result of thousands of viral infections over millions of years.

Now comes the impressive evidence of common descent. DNA from the same ERV can appear in DNA of many species. An example of this is the PTERV1 virus. It appears in the genomes of African apes and Old world monkeys, but not in the genomes of humans, Asian apes or New World monkeys. It is important to note that the location of the PTERV1 DNA is different between species, which is going to an important fact later in this discussion. This infection appears to be a fairly recent one, effecting some, but not all, primates.

Now, if we look at other ERV sites in our genome, we find that there are thousands...in fact almost all...that we have in common with chimpanzees. And not just the same infections, but the DNA is located in the same locations within the genome. As shown by PTERV1, there is some variability in where ERVs locate their DNA. The fact that humans and chimpanzees (as well as all primates) share thousands of ERVs located in the same locations is all but conclusive evidence of common descent.

“Rattling for Chemistry”

Since: Dec 06

Deep Swamps of Georgia

#2 Jan 10, 2008
DS, Yes it is very exciting! I'd just recently read Chris Harrison's paper from the University of Texas that finding the same ERV in two different primate species reveals that we share 7 ERVs with the common chimp. This is irrefutable evidence of common ancestry of humans and chimpanzees.

http://interrogatingnature.blogspot.com/2007/...

Her own words are: The shared ERVs between humans and chimpanzees (as well as other primates) represent one of the most convincing and intriguing arguments for the descent of man. Fossils and comparative anatomy can take us far, but retroviral evidence chronicles the evolutionary history of our species in unprecedented detail.

“Rattling for Chemistry”

Since: Dec 06

Deep Swamps of Georgia

#3 Jan 10, 2008
oops, I meant his.
Ossuary

United States

#4 Jan 11, 2008
I've been hearing little fragments of this tale for quite some time (months, anyway) but couldn't put my finger on the source - not being a biologist, and long-since retired, I didn't know what terms might help me find it. So, it's really good to get back to that source - many thanks!

Level 1

Since: Dec 06

Saint Petersburg, FL

#5 Jan 11, 2008
Darwins Stepchild wrote:
I have been reading the last couple of weeks about endogenous retroviruses (ERVs) and what they tell us about evolution. What I have read is perhaps the most compelling evidence of common descent that I have seen.
Retroviruses (RVs) are viruses which insert their genetic material into our own chromosomes. They have a mechanism which allows their RNA to imprint a strand of DNA and insert it. This DNA then creates copies of the RNA, making new viruses. These strands of DNA are sometimes known as "proviruses".
Most RVs infect non-reproductive cells and have no effect on the species genome. However, a few, known as EVRs, do infect reproductive cells and on rare occasions that DNA is passed on to future generations. The ERVs' DNA then becomes part of the hosts' genome.
Roughly 8% of the human genome is made up of ERV DNA, the result of thousands of viral infections over millions of years.
Now comes the impressive evidence of common descent. DNA from the same ERV can appear in DNA of many species. An example of this is the PTERV1 virus. It appears in the genomes of African apes and Old world monkeys, but not in the genomes of humans, Asian apes or New World monkeys. It is important to note that the location of the PTERV1 DNA is different between species, which is going to an important fact later in this discussion. This infection appears to be a fairly recent one, effecting some, but not all, primates.
Now, if we look at other ERV sites in our genome, we find that there are thousands...in fact almost all...that we have in common with chimpanzees. And not just the same infections, but the DNA is located in the same locations within the genome. As shown by PTERV1, there is some variability in where ERVs locate their DNA. The fact that humans and chimpanzees (as well as all primates) share thousands of ERVs located in the same locations is all but conclusive evidence of common descent.
Yes, when I read about this I thought the same thing. Creationist/ID proponents would have to come up with a doozy of an explanation to account for the shared ERVs in primates.
Fossil Bob

Urbana, IL

#6 Jan 11, 2008
Dennis2 wrote:
<quoted text>
Yes, when I read about this I thought the same thing. Creationist/ID proponents would have to come up with a doozy of an explanation to account for the shared ERVs in primates.
Oh...it was just designed that way:)

(and that's probably what they WILL say...if they ever comment at all:)

“Quantum Junctn: Use Both Lanes”

Level 2

Since: Dec 06

Tulsa, Oklahoma USofA

#7 Jan 11, 2008
Dennis2 wrote:
<quoted text>
Yes, when I read about this I thought the same thing. Creationist/ID proponents would have to come up with a doozy of an explanation to account for the shared ERVs in primates.
Fossil Bob wrote:
<quoted text>
Oh...it was just designed that way:)
(and that's probably what they WILL say...if they ever comment at all:)
I'm betting that they will invoke their favorite scape-goat, "satan".

Again. <rolls eyes>

“Turning coffee into theorems”

Since: Dec 06

Trapped inside a Klein Bottle

#8 Jan 11, 2008
Dennis2 wrote:
<quoted text>
Yes, when I read about this I thought the same thing. Creationist/ID proponents would have to come up with a doozy of an explanation to account for the shared ERVs in primates.
From what little response I have seen from creationists is that ERVs always put their DNA in the same place, even in different species.

However, PTERV1 shows that is NOT what happens.

Level 1

Since: Dec 06

Saint Petersburg, FL

#9 Jan 11, 2008
Darwins Stepchild wrote:
<quoted text>
From what little response I have seen from creationists is that ERVs always put their DNA in the same place, even in different species.
However, PTERV1 shows that is NOT what happens.
Even if it were true, it still wouldn't do much to undermine the evidence. The fact that the similarities in ERVs match the expected relationships between the primate groups (all have some shared similarities, major branches then have other shared similarities with each other but not with the other branch, and so on down the line until what we say is the most closely related species happen to have the most similarities in ERVs). It would be one hell of a coincidence that it just happened that way!

Level 1

Since: Dec 06

Saint Petersburg, FL

#10 Jan 11, 2008
Fossil Bob wrote:
<quoted text>
Oh...it was just designed that way:)
(and that's probably what they WILL say...if they ever comment at all:)
Hi Bob. I posted an interesting article on using computer modeling to simulate plant evolution to increase photosynthetic efficiency. The study was done by a researcher at U of I, Urbana-Champagne. Is that the school at which you teach? It's a fascinating concept.

http://www.topix.com/forum/news/evolution/T4E...
Fossil Bob

Urbana, IL

#11 Jan 11, 2008
Dennis2 wrote:
<quoted text>
Hi Bob. I posted an interesting article on using computer modeling to simulate plant evolution to increase photosynthetic efficiency. The study was done by a researcher at U of I, Urbana-Champagne. Is that the school at which you teach? It's a fascinating concept.
http://www.topix.com/forum/news/evolution/T4E...
Neat... I did just see this article locally.

I don't teach at the U of I (but I DO have a Faculty\Staff card...isn't that confusing?:)

Level 1

Since: Dec 06

Saint Petersburg, FL

#12 Jan 11, 2008
Fossil Bob wrote:
<quoted text>
Neat... I did just see this article locally.
I don't teach at the U of I (but I DO have a Faculty\Staff card...isn't that confusing?:)
Are you affiliated as a researcher with U of I but don't have a lab or classes on campus? That's not an uncommon set up at many Universities.

“Turning coffee into theorems”

Since: Dec 06

Trapped inside a Klein Bottle

#13 Jan 11, 2008
I'm very glad to see this generating some discussion.

Rock on!!!(and I realize that can be a pun in FB's case)

Since: Dec 06

Urbana, Illinois

#14 Jan 11, 2008
Darwins Stepchild wrote:
I'm very glad to see this generating some discussion.
Rock on!!!(and I realize that can be a pun in FB's case)
You can take it for granite that I will participate in a gneiss discussion...

Since: Dec 06

Urbana, Illinois

#15 Jan 11, 2008
Dennis2 wrote:
<quoted text>
Are you affiliated as a researcher with U of I but don't have a lab or classes on campus? That's not an uncommon set up at many Universities.
Yep:)

“we do sarcasm and irony here”

Since: Aug 07

San Bernardino, CA

#16 Jan 11, 2008
This is so cool.

“Turning coffee into theorems”

Since: Dec 06

Trapped inside a Klein Bottle

#17 Jan 11, 2008
FossilBob wrote:
<quoted text>
You can take it for granite that I will participate in a gneiss discussion...
Fair warning. You might get me started on bad math jokes.

Since: Dec 06

Urbana, Illinois

#18 Jan 11, 2008
Darwins Stepchild wrote:
<quoted text>
Fair warning. You might get me started on bad math jokes.
Going to start throwing pi's???

“we do sarcasm and irony here”

Since: Aug 07

San Bernardino, CA

#19 Jan 11, 2008
FossilBob wrote:
<quoted text>
Going to start throwing pi's???
The only opponents I have are exponents, naturally.

“Turning coffee into theorems”

Since: Dec 06

Trapped inside a Klein Bottle

#20 Jan 11, 2008
FossilBob wrote:
<quoted text>
Going to start throwing pi's???
<Heavy psi> No, I'll figure out something nu to do.

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