Human Evolution: Endogenous Retroviruses prove that humans and chimps share a common ancestor.

Gene ^ | 2000 Apr 18 | Lebedev, Y. B. et. al.

[EnderWiggins]

Endogenous retroviruses are the remnant DNA of a past viral infection. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a copy of their own viral DNA and insert it into their host's DNA. This is how they take over the cellular machinery of a cell and use it to manufacture new copies of the virus.

Sometimes, the cell that get’s infected by such a virus is an immature egg cell in the ovary of a female animal. Such cells can be stored in a state of suspended animation or dormancy for as much as 50 years before they complete meiosis and become mature egg cells ready to be fertilized. Because they are dormant gene expression is suppressed and the infection cannot take over the cell and kill it. If that egg later matures and is fertilized, the newborn organism will have that endogenous retrovirus in every one of its cells, and so will all of its descendants.

Every viral infection is unique. The complete genome of an animal is so huge, and the insertion point of a virus’s DNA is so random that it is statistically impossible for any two individuals to have the same exact endogenous retrovirus in the same exact spot on the genome unless they both inherited it from a common ancestor who had the original infection. And the infection of a germ cell is so rare that ERVs make up only somewhere between 1% and 8% of the entire human genome.

If two humans have the same identical ERV, it is proof that they are descended from a common ancestor. And if two different species have the identical ERV, it is proof that they too are descended from a common ancestor. In humans, there are about 30,000 different ERVS embedded in each person's DNA. Except for those later duplicated by a duplication mutation, all of them record unique infections of a single ancestral individual. Now here is where it gets really interesting.

There are at least seven different known instances of shared ERVs between chimps and humans... i.e. ERVs which are the identical viral DNA inserted into the identical spot of the genome. 100% of all chimps and 100% of all humans have these same ERVs. This is only possible if 100% of all chimps and all humans are descended from the single individual that had these original infections.

They are proof that humans and chimps share a common ancestor.

In a 2000 paper published in the journal Gene researchers identified ERVS shared by different primates and used them to assemble a family tree of monkeys apes and humans. Yes... we share ERVs with these lower primates as well. Here is what it looked like:





Figure 4.4.1. Human endogenous retrovirus K (HERV-K) insertions
in identical chromosomal locations in various primates
(Reprinted from Lebedev et al. 2000)


The arrows show the relative insertion times of the viral DNA into the host genome (determined using the “genetic clock” of accumulated later point mutations). All branches to the right carry that ERV - a reflection of the fact that once a retrovirus has inserted into the germ-line DNA of a given organism, it will be inherited by all descendants of that organism.

Reference: Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

[EnderWiggins]

I’ve never seen you do those thing either.

I guess that means that Buzz Aldrin and Erno Rubik were created by God separately from the rest of humanity?

[Paperpusher]

They seem to be looking for differences in HERV-K LTR insertions in orthologous loci only in humans and primates.
How about looking for them in, say Ursus spelaeus, the extinct cave bear, or woolly mammoths. They have sequences for both. If even a few HERV-K LTR insertions are the same in such divergent species, then the original study would be moot. I.e. look for - proof as well as + proof.

[EnderWiggins]

First and most importantly, what you point out here is that the science here is falsifiable. In other words, were the conclusions false, they would be demonstrated false by exactly the sort of finding you noted; an identical HERV-K LTR insertion in an orthologous locus that did not fit the pattern of descent with modification. it would seem a excellent area of exploration by “ID Scientists” if there actually were such a thing. But there really is no such thing as “ID science” so no such research has been performed.

It would, in fact, only take one such discovery to dismember the argument. And further, it would not even require a look that far afield taxonomically. The same primates examined in the originally paper could have served that had a single one of the HERV-K LTR insertions violated the pattern. And yet, none did.

Yes... the “- proof as well as + proof” that you ask for was pursued by the authors of the original paper. They found only the +.

The ERVs provided two independent but mutually supporting sources of information. Their relative age was determined by the accumulated point mutations. Their pattern of distribution among the primate species was independently identified by actual sequencing. Had they not been genealogically inherited, then there would have been no reason for them to have also correlated perfectly in both time and distribution with the branching sequence of the phylogenetic tree.

Certainly, if another explanation was in the offing, some of the insertions should have been shared by (say) orangutans and humans, but not gorillas. That would have been just as powerful a falsification as finding a recent insertion shared by humans and cave bears. Such insertions were actively looked for.

Yet none were found.

I can assure you that in the decade since this study was published, no contradictory evidence of the sort you describe has been found or published, and thousands of species have been sequenced in the interim.

[divine_moment_of_facts]

I wonder how their search for that ‘missing link’ is coming along.. It must be frustrating trying so hard to prove we’re just descended from apes. :)

[mountainlion]

I don't follow the heard. The nice thing about human reasoning and creativity is that we can all do some thing and not all run over a cliff like some herd mentality. How come after millions of years whales do the same things with little change? Monkeys have hands that could make most of the things we do but they don't

[paterfamilias]

I agree that it is a great article. The whole ERV story is quite fascinating to me, and serves as an example of how we are likely to find that “junk DNA” may sometimes be the remnants of ancient viral infections that affected our hominid ancestors.

Similar techniques involving regression analysis of clade variations in HIV strains have allowed scientists to estimate when HIV made the jump from simians to humans.

This concept of remnant DNA being passed along was being discussed in the early 1970’s, when I was an undergraduate biology major. In fact, my Microbiology prof. once facetiously referred to this passed-along DNA as “original sin” (it was a Catholic college, after all).

[EnderWiggins]

"How come after millions of years whales do the same things with little change? Monkeys have hands that could make most of the things we do but they don't"

The answer to those questions is actually pretty simple... and it starts by considering a different question:

Why do whales live in the ocean and monkeys live in trees rather than the other way around?

It seems a silly question, but it's not since the answer to leads us to the answers you were looking for. There are many different ways for an organism to make a living. We call them "ecological niches." And different organisms are adapted to different ecological niches, to different ways of making a living.

Whales do the same things they did millions of years ago because the whale niche (actually there are several of them) has not changed. The organisms that live in that niche have changed continuously across time, but the niche persists. So there will almost always be an organism that has evolved to take advantage of it.

Consider for example the niche occupied by Sperm Whales. They are deep divers who subsist primarily on large cephalopods like squid. Millions of years before mammals occupied that niche, it was held by huge seagoing monitor lizards called mosasaurs.

Were sperm whales to become extinct, the niche would be vacant, and some other organism would eventually evolve to occupy it... maybe a gigantic species of penguin. Who knows?

Monkeys don't do what we do because they occupy a different niche (again more than one) than we do.. a small to medium arboreal fruit eating niche. In Madagascar where there no monkeys, lemurs take that role. In Australasia it is occupied by a group of marsupials called Cuscus. In each case they are far better at being monkeys that we ever could be.

So... not only does this answer your question, it also corrects a misconception contained in it; the idea that "little change" is involved.

In point of fact, there has been vast change between the whales and monkeys of today and the whales and monkeys of millions of years ago. They occupy the same niches and so have similar adaptations... but they are certainly not the same whales and monkeys.

[EnderWiggins]

"I wonder how their search for that ‘missing link’ is coming along."

What missing link?

"It must be frustrating trying so hard to prove we’re just descended from apes."

Lol... silly Divine. We're not "descended from apes."

We are apes.

[raygunfan]

but im talking design in general, as far as retroviruses go, again, you not being a believer, dont get the idea of the fall, and the degeneration that resulted in these sorts of viruses, etc.

[divine_moment_of_facts]

We are apes.

Speak for yourself! :)

[wolf78]

I wonder how their search for that ‘missing link’ is coming along.. It must be frustrating trying so hard to prove we’re just descended from apes. :)

Well, a biologist would argue that a.) all animals on the greater scale are transitional forms and b.) that "we" (i.e. humans) are not descended from apes (i.e. Hominoidea). We ARE apes.

[Southack]

"If two humans have the same identical ERV, it is proof that they are descended from a common ancestor. And if two different species have the identical ERV, it is proof that they too are descended from a common ancestor."

Nope. The above is poor logic akin to saying:
"If two software programs have the same identical ERV, it is proof that they are descended from a common program. And if two different Operating Systems have the identical ERV, it is proof that they too are descended from a common program."

Which is to say, the author is dismissing code re-use.

DNA is programming code. To dismiss code re-use is to ignore the entire structure of genes (software sub-routines).

Or to put the above in terms that the simpletonian Darwinists might be able to reach up and grasp: an ERV can be inserted in the lab into the same desired place in an animal's DNA; into multiple species in the same place, in fact...none of which has anything to do with Evolution, but everything to do with routine Intelligent lab work.

[divine_moment_of_facts]

Since when do apes have a conscience?

[aruanan]

Since when do apes have a conscience?

Does that mean that liberals are an evolutionary throw-back?

[divine_moment_of_facts]

Since when do apes have a conscience?

Does that mean that liberals are an evolutionary throw-back?

Exactly right! ;)

[Mr. Lucky]

Perhaps you puke too easily.

[aruanan]

I agree; I also believe that God created a rich evolutionary tapestry to test out intellects (one of His gifts to us) and to challenge our Free Will

No, he created John Calvin, Mohammed, and B.F. Skinner to challenge your free will.

[EnderWiggins]

”Which is to say, the author is dismissing code re-use.”

Oh, not even close.

First and foremost, only functional code merits reuse. A good software engineer does not reuse broken or non-functioning code, he removes it. The ERVs in question here do not express at all... they are not genes. This is clear not just because we know the virus that is responsible for the insertion, but also that natural selection is not conserving this DNA.

In actual genes (i.e. genes that express) a significant number of the random point mutations that occur are selected out of the population because they are deleterious. Not all of course, because a certain number are silent, and in any changing environment point mutations have a 50-50 chance of being beneficial. But the deleterious genes are selected out, and as a result the “genetic clock” of expressive genes runs about 30% slower than “junk DNA” where all point mutations accumulate.

These ERVs all have accumulated point mutations at the top rate of non-expressive DNA... so not only are they not “reused code,” they are not code at all.

This is (by the way) the exact same thing we see with human "fossilized genes" for things like smell. Humans possess 100% of the same genes that dogs possess for smell. But most of ours are broken. They still exist, but are no longer functional... having accumulated so many point mutations that they no longer work at all.

Natural selection stopped conserving these genes at the exact same moment we developed the capacity for tricolor vision. Once we were able to see in full color, our sense of smell became unnecessary for finding food, and so it no longer was an advantage to have an acute olfactory sense. Once the deleterious genes stopped being filtered out, these genes decayed at the full rate of the genetic clock. They were no longer "useful code."

Second, the analogy with code reuse is actually an awful one. After all... the only intelligent designers we have to analogize here are human programmers, and the way human programmers use and reuse code bears almost no resemblance to what we see reflected in the genome.

While human programmers absolutely do reuse code, they do not do it in a pattern that could possibly be interpreted as genealogical descent. A useful subroutine may show up in any number of different programs with no regard whatsoever to the larger purpose of the program. If DNA were like a human designed program, we would expect to see one ERV in both capuchin monkeys and humans, while skipping bonobos.

Human technology is contagious, leaping from clade to clade regardless of any overall similarity in technological purpose. It can do this specifically because it is not inherited... it is designed.

There is no reason (if the analogy you are promoting were true) why any ERVs at all should appear and then distribute themselves in a pattern consistent with genealogical descent. Just once or twice would be improbable enough. But 100% of the ERVs we have identified follow that pattern. This raises the explanation of inheritance form a common ancestor unassailable.

This has always been one of the biggest flaws with trying to explain the pattern of homology as “reuse by a common designer.” The only intelligent designer we have to compare the pattern to absolutely does not design that way... in any technology let alone computer programming.

I need to go back on one point... there is another possible explanation that conforms with intelligent design... but it requires a designer who is also being deliberately deceptive. I for one do not believe that God is liar.

[Southack]

"First and foremost, only functional code merits reuse. A good software engineer does not reuse broken or non-functioning code, he removes it." - EnderWiggins

Nonsense. A good programmer might re-use vast amounts of old code rather than waste development Dollars chasing down what unused code in a sub-routine is no longer needed.

This is why vastly profitable companies like MicroSoft have old DOS code remnants still in Windows 7, for example.

[EnderWiggins]

"Since when do apes have a conscience?"

As far back as we've been able to study them, the great apes (to include at least the gorillas, chimps, bonobos and orangutans) have demonstrated conscience. They also demonstrate inter-species altruism and empathy, symbolic communication, awareness of themselves as unique individuals and the ability to plan, reason, anticipate and deceive. They also possess cultures and technology.

Again I must point out that the difference between humans and other animals is exclusively quantitative. We posses no qualitative uniqueness whatsoever.