Endogenous retroviruses

[Mekkala]

I have to ask a favor!
Could some people summarize what the "endigenous retroviruse" is?
I didn't really understand the article or win-ace's post.
So I would really appreciate someone explaining it to me in simpler terms!

You're the expert who knows all about how wrong we are, right? Fortunately you're not saddled with any inconvenient actual knowledge

 

[Mekkala]

LOL Either you posted just as I was posting Loudmouth, ot I didn't see it.

-- Okay, so it's established that it is a virus because of conducted tests.
-- All races of humans have same identical imprint.
-- The exact same imprint as apes.
-- Concluding a common ancestor.

1: is this imprint in an identical position in ALL humans and ALL apes ?

That would depend on where in the history of the line it was inserted. If the viral DNA appeared in the genome after gorillas split off from the line that later produced chimps and humans, we would find the insertion in humans and chimps, but not in gorillas.

EDIT: If we were to find an insertion in humans and gorillas, but not chimps, and there were no indication of a deletion mutation at the position in the genome, this would serve as a fairly effective falsification of the nested heirarchy of species as we understand it. Since we never do, we can conclude that this evidence pretty solidly supports common ancestry.

 

[Loudmouth]

EDIT: If we were to find an insertion in humans and gorillas, but not chimps, and there were no indication of a deletion mutation at the position in the genome, this would serve as a fairly effective falsification of the nested heirarchy of species as we understand it. Since we never do, we can conclude that this evidence pretty solidly supports common ancestry.

Indeed. This is another method of falsifying common ancestory. I don't see how creationists, with a straight face nonetheless, claim that evolution and common ancestory can not be falsified. This, and many other tests, could have falsified evolution. It is strange that each new discovery, both in the fossil record and in genetics, keep supporting the Theory of Evolution. If creationism were true, or we were misinterpreting the data, it should have been blazingly obvious by now.

 

[Drotar]

From Evowiki:

ERVs are identifiable due to the presense of sequences that code (or once coded) for viral proteins, including gag (structural proteins), pol (viral enzymes), and env (surface proteins), as well as tell-tale LTRs (long terminal repeats).

If we honestly think that that answer is going to suffice, we deceive ourselves.

First, if it's an ancient virus, how do we know what it's sequence was?

If it's around today, how do we know it wasn't independently inserted in "hotspots"?


How do we know that it codes for a viral protein? Don't different sequences encode for different things at different loci? Which fossils were they discovered in? And most importantly, is there any citation of evidence of such every possibly being discovered, or may we safely file this under theoretical biology?

I know that these questions seem critical, and they are, but before I use them I want to make sure that they are, for all practical purposes, irrefutable.

ERV's have my special interest in evidences for evolution, but I cannot use this unless I know that it has actually happened. TTYL Jesus loves you!

 

[Loudmouth]

First, if it's an ancient virus, how do we know what it's sequence was?

It is assumed that viruses in distant history had similar sequences to what we find today. Of course, the sequences will be slightly different due to eons of mutation and selection. Also, viral sequences are flanked by tandem repeats, sections of repeating sequence such as AGGCAGGCAGGCAGGC, for example.

If it's around today, how do we know it wasn't independently inserted in "hotspots"?

It would have to have been very lucky and very accurate to become part of the entire human populations genome. Remember, it has to integrate into a germ line cell in order to become part of the genome. If viruses were actively inserting themselves into germ line cells the human genome would be littered with these sequences. If our genomes were 50% primary viral sequence then we could conclude that viral insertions are very common. However, this is not the case. There are, however, remanants of viral code that has been transposed and moved around in the genome. This also helps in tracking phylogenies by comparing the movement of the manipulated viral code as it moves through the genome.

How do we know that it codes for a viral protein? Don't different sequences encode for different things at different loci?

Talked about above. By comparing the sequence of the genes to extant viruses.

Which fossils were they discovered in?

None that I know of. ERV research is done on extant species. They construct cladograms, or trees, that correspond to the viral insertions. These trees match what we find in the fossil record.

And most importantly, is there any citation of evidence of such every possibly being discovered, or may we safely file this under theoretical biology?

We might be able to find ERV in recently extinct species, such as neanderthals or wooly mammoths. This would require extremely well preserved specimens, but could be possible. As an example, they have been able to sequence neanderthal mitochondrial DNA, showing that they are distinctly different from humans in this respect.

 

[Drotar]

Thank you. Though questions remain, that answer will do nicely.

 

[Phred]

bump

 

[ifriit]

Bumpity!

 

[lucaspa]

Science generally doesn't deal with Omphalos hypotheses for good reason, because there is no reasonable way to verify or falsify them; they throw explanatory and predictive power, much less parsimony, entirely out the window.

Excellent essay on ERV's.

However, the killer argument against Oomphalos' arguments doesn't come from science. As you pointed out, science can't falsify them. The killer argument comes from Christianity. No Christian can tolerate the Oomphalos' argument for the simple reason that it makes God into a liar. That is, God put the ERV's into the genome that give evidence for evolution when, supposedly, evolution did not happen! God deceived us.

As I said, for a Christian, God as deceiver is not acceptable. It might rescue God creating by the desires of creationists, but the cost is a God that can't be trusted, one that can't save people, and one that can't be worshipped. The cost, therefore, is a complete destruction of the Christian God. That's way too high a price to pay to preserve Biblical literalism and creationism.

 

[Drotar]

If everyone is still interested, I would like a reference to the actual loci where ERV's were detected, simply for clarification purposes. I know this argument is a potential gold mine,and so I would prefer to be able to quote the exact chromosome when using this argument. Is it theoretical, or have these actually been detected, and in which species of hominids and primates have they been detected?

 

[caravelair]

If everyone is still interested, I would like a reference to the actual loci where ERV's were detected, simply for clarification purposes. I know this argument is a potential gold mine,and so I would prefer to be able to quote the exact chromosome when using this argument. Is it theoretical, or have these actually been detected, and in which species of hominids and primates have they been detected?

i think the references here might be a good place to start.

 

[Jimmy The Hand]

Seems like a good time for a bump.

Although since the OP is LONG and has BIG words, the people that should read it probably won't.

 

[ProbePhage]

Seems like a good time for a bump.

Although since the OP is LONG and has BIG words, the people that should read it probably won't.

Indeed. It's a shame.

 

[JohnR7]

bump

 

[pureone]

bump

huh? john why are you bumping this? I'm as confused as a kitten in a dairy barn...

 

[JohnR7]

huh? john why are you bumping this? I'm as confused as a kitten in a dairy barn...

To make it easier to find. I was having a discussion with someone about retroviruses and I can not find that thread, but I found this one. I wanted to do a little bit more research on it.

 

[pureone]

To make it easier to find. I was having a discussion with someone about retroviruses and I can not find that thread, but I found this one. I wanted to do a little bit more research on it.

What do you want to know about retroviruses? I would be glad to help you.

 

[Dexx]

It's pretty simple. Here's the Cliffs' Notes version.

• Egg or sperm cell.
• That cell gets attacked by a virus.
• Virus injects genetic fingerprint, but botches the hijacking.
• Cell survives.
• Cell now contains easily identifiable and unique viral fingerprint in DNA.
• Cell is fertilized and becomes a new creature.
• That creature contains easily identifiable and unique viral fingerprint in all of its individual cells.
• All descendants of said creature are the same.
• Thus, finding two creatures with identical viral fingerprint in their DNA indicates they're related.
• Humans and chimps have identical viral fingerprints in all of their cells.

• 
  This isnt an attempted refute - rather a question: Its rare for an egg or sperm which is attacked by a virus to survive viable. You then need the resultant organism to survive to adulthood and reproduce. Lets go back in time 2 million years to the common ancestor of chimps and humans. Out of the entire population (say 100,000) the one who chanced to survive a viral attack as a sperm/egg is the one to father all chimps and humans? That sounds exceedingly unlikely.
  
  How common are incidents of egg/sperm surviving and exhibiting an erv? If 1% of the population suffer a virus which leaves them with an erv, then any one of them would make a valid progenor. I suppose thats how natural selection works anyway - the specific genetic code of a breeding pair is carried on through their ancestors. Its just difficult to grasp that an entire species would originate from one pair of creatures.

 

[Jet Black]

This isnt an attempted refute - rather a question: Its rare for an egg or sperm which is attacked by a virus to survive viable. You then need the resultant organism to survive to adulthood and reproduce. Lets go back in time 2 million years to the common ancestor of chimps and humans. Out of the entire population (say 100,000) the one who chanced to survive a viral attack as a sperm/egg is the one to father all chimps and humans? That sounds exceedingly unlikely.

well it is not so much father to all chimps and humans, but an ancestor to them all. remember within a breeding population of finite size, eventually you will end up breeding with a relative. this results in a stochastic effect known as "genetic drift" where particular alleles or DNA segments can become more or less prevalent in the population. in this case the DNA segments containing the ERV spread throughout the population. Here is a little challenge for you just to show how easy this is. assume a constant sized breeding population breeding population of 1000, ignore all relations at this point. assume there is no differential reproductive success and each member of the population leaves one replacement in the next generation. how many generations would it take before an individual has to breed with a relative, no matter how distant.

here is an article that might be useful to you:

http://en.wikipedia.org/wiki/Genetic_drift

How common are incidents of egg/sperm surviving and exhibiting an erv? If 1% of the population suffer a virus which leaves them with an erv, then any one of them would make a valid progenor. I suppose thats how natural selection works anyway - the specific genetic code of a breeding pair is carried on through their ancestors. Its just difficult to grasp that an entire species would originate from one pair of creatures.

the point though is that there are some six billion locations that an ERV could be placed - literally anywhere within the genome. ok, we can ignore in the middle of genes since that would be crippling, but it doesn't save you much. and then there are a umber of different ways in which the retrovirus could be crippled. the odds of an ERV being inserted in exactly the same place and croppled in exactly the same way in two different gametes that go on to be fertilised and have lots of offsprint is well, quite small.

again, the question of the entire species having a common ancestor is one of genetic drift. it's pretty easy to see once you work through it. if you have any more questions check through that article and feel free to ask.

 

[joelazcr]

While retroviral integration can take place at many locations in the genome, individual virus show distinct target site preferences.

This recent article shows these preferences, while searching for a safe gene therapy vector.

"Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences"

www.plosbiology.org

"Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection."

"Thus it appears that each retrovirus studied to date has a unique pattern of integration site selection within the human genome, suggesting that there may be local recognition of chromosomal features unique to each virus."

This shows that common ancestry is not required to explain similar
retroviral insertions between species.