Endogenous Retroviruses (ERVs) and Common Ancestry

[Techne]

Endogenous Retroviruses (ERVs) are probably one of the most compelling arguments for common ancestry. ERVs are exogenous retroviral elements that are incorporated or integrated into the genome of an organism. These retrovial elements are then sometimes passed on to future offspring.

If you and I have a common ancestor and in this common ancestor there was some kind of retroviral infection that caused the elements to be integrated into the genome of our common ancestor and passed on to it offspring, then one would expect both you and I to have the same retroviral elements in our genome.

About 8% of the human genome mass consists of sequences of retroviral origin and it is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species. Some of the proviruses are thought to have been fixed (through germ-line integration) in the population and were inherited as stable genomic components named ERVs.

According to theory and based on comparative analyses of orthologous genomic sequence and sequence divergence of flanking long terminal repeat (LTR) elements between chimpanzees and humans, the last major genomic infection of the human lineage is estimated to have occurred before the divergence of the Old World and New World monkey lineages (25-35 million years ago=mya) [1]. Flockerzi et al. (2005) are of the opinion that the +-139 proviruses present in the human genome were formed before the evolutionary split of New World and Old World primates, +-55 million years ago [2].

The phylogenetic tree based on ERVs paints the following pictures:

The Old world monkeys split from the New world monkeys +-35mya. The Human-Chimp-Gorilla-Orangutan lineage split from that of the rhesus macaque lineage after the last major genomic infection (+-25mya). Then the Human-Chimp-Gorilla lineage split from the Orangutan lineage (+-12mya), and then the Human-Chimp lineage split from the Gorilla lineage (+-7mya), and finally Humans and Chimps diverged +-6mya [3].


References
[1] Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P et al. Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 2005 Apr;3(4):e110.
[2] Flockerzi A, Burkhardt S, Schempp W, Meese E, Mayer J. Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences. J Virol. 2005 Mar;79(5):2941-9.
[3] Polavarapu N, Bowen NJ, McDonald JF. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol. 2006;7(6):R51.Nov;81(22):12210-7.

Here are a few links to help you understand the concepts surrounding ERVs:
1) Three Layers of Endogenous Retroviral Evidence for the Evolutionary Model
2) Powerpoint slides

 

[cyghost]

Your best thread ever by far.

 

[Techne]

In reply to our conversation here:

That is the definition today. Now there appears to be some rewriting of history by people like Larry Moran who criticises Wells for his definition of junk DNA. True the original definition of junk DNA was by Susumu Ohno. His paper used the term to refer to genes that could not have a function because it would cause gene "overload." Larry leaves this out however and even denies it and instead make it sound like it's always been defined as DNA with unknown function.

That is only the recent history though. After genes were discovered it was found that large regions exhibited no apparent function. It was assumed that over time genes would mutate to have no function and so be relegated to the junkyard of fossil DNA. That doesn't mean it was useless as later mutations could give it function again making it a source for evolution. After Ohno's paper in 1972 ideas started forming that it may have an unknown function. Ohno's term of junk DNA was adopted. Larry is right about the original application but leaves out that it was applied to a changed idea. The original idea was that some DNA doesn't just have an unknown function but has no current function except for a few active genes scattered about.

Larry Moran is just another one of those scientists that mix empirical science with philosophy/metaphysics and fail to see the difference between the two. When he talks about Junk DNA (as per your links for example) and evolution (e.g. here) this becomes quite evident. Just ask them to stick to the empirical data and separate their metaphysics from the science when they make any claims about reality.

It's actually hilarious to watch the circus. Darwin thought that the fossils were just undiscovered and had all the confidence they would be found. As time went by it became apparent that the fossils were not there at all and it actually came to embarrassingly confirm the creation account. So lines of descent were changed by DNA and the fossil evidence deemed unreliable and discarded. It will be really ironic when the next thing comes along, epigenetics perhaps, and Darwinists discard DNA and ERV's on the same basis as we do.

I don't why you think the fossils confirm "the creation account". YEC? ID creation? I don't think creationism is an empirical issue, so looking at the fossils as a confirmation appears to be largely missing the point really.

That's speculation. I don't see how P.E. can be accepted and not creation unless there's a bias involved.

Punctuated equilibrium does nothing to deny or confirm creation. It is simply irrelevant.

Except that it's not so simple as that. I support and believe in creationism but I don't defend it. Unless something changes both creationism and evolution is ultimately unverifiable. It seems to me you are saying that I can believe in theistic evolution and that will solve both problems. True but that is more a compromise than logic. It requires the assumption of either evolution A or evolution B. That is a logical fallacy as there could also be option 2 with A or B or a combination of option 1 & 2 with A or B.

Even with all its metaphysical assumptions Ruse still argues that there is such a thing as pure scientific evolution but concedes that that is NOT what we have. Instead it's a movement of new age atheism that is using science as a tool for its own ends.

Evolution is just change. Change happens. Change/evolution are ontologically two different processes.
There are a few criteria that have to be met in order for something to undergo a process of change. These include:
I) A starting state when the change begins.
II) An end state when the change is done.
III) A transition state between the beginning and the end.
IV) Something that persists through the change.

Creation and annihilation on the other are different. When something lapses into nothingness then it is annihilation. When something begins to exist from nothingness then it is an example of creation. Empirical science deals with the observations of contingent things interacting with each other i.e. undergoing change. Empirical science cannot observe “nothingess”, in fact “nothingness” cannot be directly observed since it is derived or defined negatively or as the absence of being, hence, creation cannot be directly observed. In a nutshell, creation is a logical and philosophical issue and not an empirical issue. There are ontological views of reality that is consistent with the reality of change as well as simultaneously compatible with creation (theistic creation, not deistic creation). The point being, empirical science cannot be used to support creation, neither can it be used to argue against or deny creation. Natural philosophy is needed. So it is largely futile to argue against or for the findings of empirical science (whatever it may be) to try and support or deny creation.

 

[Swa]

The fact that many ERVs have crucial regulatory functions is explained by co-option.

Re the statement above site-specific insertions. This does not explain why the shared ERVs fit into a nested hierarchy, see the figures in the thread about ERVs. I would be glad if we could continue discussions about it in that thread.

Please explain what you mean by ERV's and co-option.

As I said about the hierarchies they were not predicted by evolution or the fossil record. Lines of descent were altered by genetics and from the article I provided you with it also seems like the authors are arguing they should be changed based on ERV's as well. Some lines of descent may already have been altered this way. It's circular to claim that the evidence supports the model when it was used to construct the model.

So let's look at the two options:
1. ERV's are misunderstood functional DNA. Of course they would fit into hierarchies because they were used to construct them.
2. They are ERV's in which case I refer back to the article. If ERV's can easily be lost the authors would have jumped on that. As it turns out humans have an intact preintegration site so the chances are much less that it could have been lost. That being the case it leaves two options:
2.1. Line of descent is wrong. In this case it contradicts genetic evidence for descent which in turn also contradicts the fossil evidence. That's a double contradiction.
2.2. Separate infections. In which case they are a lot more target specific.

See here for more of these: http://www.evolutionnews.org/2011/05/do_shared_ervs_support_common_046751.html

Larry Moran is just another one of those scientists that mix empirical science with philosophy/metaphysics and fail to see the difference between the two. When he talks about Junk DNA (as per your links for example) and evolution (e.g. here) this becomes quite evident. Just ask them to stick to the empirical data and separate their metaphysics from the science when they make any claims about reality.

Yeah that I knew. Seems to be a common phenomenon. But what about the junk DNA? Before it was named junk DNA it was thought most of it served no current function. True or not?

I don't why you think the fossils confirm "the creation account". YEC? ID creation? I don't think creationism is an empirical issue, so looking at the fossils as a confirmation appears to be largely missing the point really.


Punctuated equilibrium does nothing to deny or confirm creation. It is simply irrelevant.


Evolution is just change. Change happens. Change/evolution are ontologically two different processes.
There are a few criteria that have to be met in order for something to undergo a process of change. These include:
I) A starting state when the change begins.
II) An end state when the change is done.
III) A transition state between the beginning and the end.
IV) Something that persists through the change.

Creation and annihilation on the other are different. When something lapses into nothingness then it is annihilation. When something begins to exist from nothingness then it is an example of creation. Empirical science deals with the observations of contingent things interacting with each other i.e. undergoing change. Empirical science cannot observe “nothingess”, in fact “nothingness” cannot be directly observed since it is derived or defined negatively or as the absence of being, hence, creation cannot be directly observed. In a nutshell, creation is a logical and philosophical issue and not an empirical issue. There are ontological views of reality that is consistent with the reality of change as well as simultaneously compatible with creation (theistic creation, not deistic creation). The point being, empirical science cannot be used to support creation, neither can it be used to argue against or deny creation. Natural philosophy is needed. So it is largely futile to argue against or for the findings of empirical science (whatever it may be) to try and support or deny creation.

And now things are starting to make sense. You are using definitions in an overly narrow or broad way.

Seen strictly creation only happened in one instant assuming there was nothing before. So if used in this way the word should never be used but it has a classic and popular meaning as well. To make something from other material(s) e.g. a chair from wood. Not to make something from nothing.

Broadly defined evolution is just change but there are different kinds. Nucleosynthesis - the formation of elements. Stellar - how stars form and change over time. Abiogenesis - transition from non living elements to living systems. Organic or biological - change in inherited traits of organisms from one generation to the next. Then there's a bunch of abstracts as well. Popularly it means biological and more specifically genetic change.

Another problem is you think of creation and evolution as single issues. There's in fact the philosophical of who and why. That counts for evolution as well and is not an issue for the natural sciences. Then there's the how. That could be through evolution or creation. Creation here being from matter of from other genetic material. Both are issues for science. As I already said creation has nothing to do with whodunnit. It's simply the study of the past.

 

[rwenzori]

There's in fact the philosophical of who and why.

There has to be a who? And a why?

Do tell us who and why. Was it Pikkiwoki so he could dish out coconuts?

 

[rwenzori]

Seen strictly creation only happened in one instant assuming there was nothing before.

Pikkiwoki did it in 5 days - on the 6th and 7th he rested and ate coconuts.

 

[Techne]

Please explain what you mean by ERV's and co-option.

Take the HIV-1 virus. It is a retrovirus and may incorporate itself into your genome if you become infected. Once it is there is may start to contribute towards crucial functions or disrupt others. This is co-option or exaptation.

As I said about the hierarchies they were not predicted by evolution or the fossil record. Lines of descent were altered by genetics and from the article I provided you with it also seems like the authors are arguing they should be changed based on ERV's as well. Some lines of descent may already have been altered this way. It's circular to claim that the evidence supports the model when it was used to construct the model.

Well, if you look at the ERV patterns (in the figure in the OP) they fit in quite well with the split between the old world and new world monkeys and prosimians.

So let's look at the two options:
1. ERV's are misunderstood functional DNA. Of course they would fit into hierarchies because they were used to construct them.
2. They are ERV's in which case I refer back to the article. If ERV's can easily be lost the authors would have jumped on that. As it turns out humans have an intact preintegration site so the chances are much less that it could have been lost. That being the case it leaves two options:
2.1. Line of descent is wrong. In this case it contradicts genetic evidence for descent which in turn also contradicts the fossil evidence. That's a double contradiction.
2.2. Separate infections. In which case they are a lot more target specific.

See here for more of these: http://www.evolutionnews.org/2011/05/do_shared_ervs_support_common_046751.html

There is an option 2.3 as explained by biological susceptibility.
It was also found that the R332Q mutation in human TRIM5alpha improved the ability of human TRIM5alpha to restrict the HIV-1 virus. The authors suggested that the R332 TRIM5alpha was present in the common ancestor of humans and chimpanzees and that the R332Q mutation was fixed in our common ancestor, or that the human and chimp lineages independently fixed R332 after the species diverged at different intervals, both likely. So the CERV1 may have been restricted or even removed due to differences in biological susceptibility.

Yeah that I knew. Seems to be a common phenomenon. But what about the junk DNA? Before it was named junk DNA it was thought most of it served no current function. True or not?

I am under the impression that the original idea of junk DNA was that it merely applies to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified

And now things are starting to make sense. You are using definitions in an overly narrow or broad way.

Seen strictly creation only happened in one instant assuming there was nothing before.

This would be true if deism is true. But theistic creationism (as accepted by many Christians) accepts that you, me and every other thing that begins to exist was created out of nothing and sustained in existence (or prevents from lapsing into nothingness) whenever you continue to exist.

So if used in this way the word should never be used but it has a classic and popular meaning as well. To make something from other material(s) e.g. a chair from wood. Not to make something from nothing.

The way I see it, those are just be examples of design by contingent beings or the intentional arrangement and rearrangement of stuff, not creation in the sense that is relevant to theism.

Broadly defined evolution is just change but there are different kinds. Nucleosynthesis - the formation of elements. Stellar - how stars form and change over time. Abiogenesis - transition from non living elements to living systems. Organic or biological - change in inherited traits of organisms from one generation to the next. Then there's a bunch of abstracts as well. Popularly it means biological and more specifically genetic change.

Fair enough.

Another problem is you think of creation and evolution as single issues. There's in fact the philosophical of who and why. That counts for evolution as well and is not an issue for the natural sciences. Then there's the how. That could be through evolution or creation. Creation here being from matter of from other genetic material. Both are issues for science. As I already said creation has nothing to do with whodunnit. It's simply the study of the past.

I disagree, or I don't see it that way. The study of the past is simply historical science and the concept of "creation from something to something else" does not make sense to me. That is just change/evolution, be it intentional (in which case it is designed) or not.

 

[Swa]

There has to be a who? And a why?

Do tell us who and why. Was it Pikkiwoki so he could dish out coconuts?

Stop trolling...

 

[rwenzori]

Stop trolling...

Give us an answer, kid. You were the one who brought it up - what is your opinion?

 

[Techne]

Give us an answer, kid. You were the one who brought it up - what is your opinion?

Troll somewhere else.

 

[Techne]

Stop trolling...

Ignore him please, it's not worth it.

 

[rwenzori]

Troll somewhere else.

You're the prime troll, so I'll ignore your insult. After all, who is the one repeatedly banned for trolling?

 

[Techne]

You're the prime troll, so I'll ignore your insult. After all, who is the one repeatedly banned for trolling?

Yawn, take your personal issues somewhere else. Cheers.

 

[rwenzori]

Another problem is you think of creation and evolution as single issues. There's in fact the philosophical of who and why. That counts for evolution as well and is not an issue for the natural sciences.

Let us try again - what is your view on the who and the why?

 

[Swa]

Well, if you look at the ERV patterns (in the figure in the OP) they fit in quite well with the split between the old world and new world monkeys and prosimians.

Well they would if they were functional DNA and not ERV's. The hierarchy is established through DNA similarity so no surprise then they would fit into it. There's also the fact that ERV's are not species specific but are also selective. So they are likely to infect DNA within a given range of similarity.

There is an option 2.3 as explained by biological susceptibility.
It was also found that the R332Q mutation in human TRIM5alpha improved the ability of human TRIM5alpha to restrict the HIV-1 virus. The authors suggested that the R332 TRIM5alpha was present in the common ancestor of humans and chimpanzees and that the R332Q mutation was fixed in our common ancestor, or that the human and chimp lineages independently fixed R332 after the species diverged at different intervals, both likely. So the CERV1 may have been restricted or even removed due to differences in biological susceptibility.

First we are talking of HERV-K and I can't find what CERV1 is. It still does not address the problem though. For HERV-K to be present in chimpanzees, bonobos and gorillas it had to have been fixed in their common ancestor which is also supposed to be a human ancestor. So the only option if that is true is it had to have been removed. But that is a big problem because there's an INTACT preintegration site in humans suggesting a high probability it was never present. That's why the authors suggest a different line of descent.

I am under the impression that the original idea of junk DNA was that it merely applies to DNA that is a provisionally labeled for sequences of DNA for which no function has been identified

When it was named junk DNA yes. Everything I can find on this is rather sketchy but seems to say it was originally thought of by most as DNA with no current function. The only problem was they weren't sure which was the junk part and which were the few functional genes scattered about.

This would be true if deism is true. But theistic creationism (as accepted by many Christians) accepts that you, me and every other thing that begins to exist was created out of nothing and sustained in existence (or prevents from lapsing into nothingness) whenever you continue to exist.



The way I see it, those are just be examples of design by contingent beings or the intentional arrangement and rearrangement of stuff, not creation in the sense that is relevant to theism.

That is not true. It can be either out of nothing or formed from something. Even the bible doesn't say it was from nothing but formed out of the ground or dust. It uses the words 'made' and 'bring forth'. That is the majority view I've heard of.

I disagree, or I don't see it that way. The study of the past is simply historical science and the concept of "creation from something to something else" does not make sense to me. That is just change/evolution, be it intentional (in which case it is designed) or not.

That's because you're using an overly narrow view of creation. You can view it as change/evolution but that's an overly broad view of evolution. It does not seem consistent to me.

 

[Techne]

Well they would if they were functional DNA and not ERV's. The hierarchy is established through DNA similarity so no surprise then they would fit into it. There's also the fact that ERV's are not species specific but are also selective. So they are likely to infect DNA within a given range of similarity.

The won't necessarily fall in such a hierarchy even if they are fully or merely potentially functional now.

First we are talking of HERV-K and I can't find what CERV1 is. It still does not address the problem though. For HERV-K to be present in chimpanzees, bonobos and gorillas it had to have been fixed in their common ancestor which is also supposed to be a human ancestor. So the only option if that is true is it had to have been removed. But that is a big problem because there's an INTACT preintegration site in humans suggesting a high probability it was never present. That's why the authors suggest a different line of descent.

In CERV and HERV, the H and C stands for Human and Chimpanzee respectively.

Ok, so phylogenetic analyses suggest that most of HERVs (including HERV-K) integrated after the separation of Old and New World monkeys and before the separation of hominids and OWM at 30 to 45 million years ago. HERV-K families are ERVs that once employed lysine tRNA to prime reverse transcription. It is believed that the human ERV-K (HERV-K) family includes some of the most active retroviral elements in human genome. In total, there may be about 550 HERV-K proviruses and about 6400 solitary LTRs in the human genome. All HERV families have ceased proliferating and have effectively become extinct with one possible exception, HERV-K(HML2). The HERV-K(HML2) family, presumably must have initially invaded the ancestor of the human genome before the divergence of humans from Old World monkeys, +-30 mya.

Seeing that HERV-Ks integrated into primate genome after the separation of Old and New World monkeys and before the separation of hominids and Old world (+-30-45mya) it should be reasonable to expect to find not only homologous, but also orthologous ERV-K sequences between homonids and OWM.. For some we don't such as the one in the paper you cite.

However, Romano et al (2007) screened the genomes of Pan troglodytes (build 2 v.1) and the Macaca mulatta draft assembly (v.1) by BLAT search for ERV-K genomes. They found 19 complete RhERV-K proviruses, and 12 new elements in Pan troglodytes (CERV-K). 55 previously reported human HERV-K and 20 previously reported CERV-K were also included in the analysis. Romano et al (2007) found that no RhERV-K orthologue was closely related to those in either the chimpanzee or human genomes and concluded that all RhERV-K proviruses appear to have arisen by active transposition rather than chromosomal duplication and the lack of orthologous sequences may be the result of host driven excision and purging.

So in essence, the explanation again would be difference in biological susceptibility. Some HERV-K may have been purged in the human linage while other may have arisen due to active transposition.

References:
Greenwood AD, Stengel A, Erfle V, Seifarth W, Leib-Mösch C. The distribution of pol containing human endogenous retroviruses in non-human primates. Virology. 2005 Apr 10;334(2):203-13.
Lebedev YB, Belonovitch OS, Zybrova NV, Khil PP, Kurdyukov SG, et al. Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene. 2000 Apr 18;247(1-2):265-77.
Medstrand P, Mager DL. Human-specific integrations of the HERV-K endogenous retrovirus family. J Virol. 1998 Dec;72(12):9782-7.
Mayer J, Meese E. Human endogenous retroviruses in the primate lineage and their influence on host genomes. Cytogenet Genome Res. 2005;110(1-4):448-56.
Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, et al. Rate of recombinational deletion among human endogenous retroviruses. J Virol. 2007 Sep;81(17):9437-42.
Romano CM, de Melo FL, Corsini MA, Holmes EC, de A Zanotto PM. Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys. PLoS ONE. 2007 Oct 10;2(10):e1026.

When it was named junk DNA yes. Everything I can find on this is rather sketchy but seems to say it was originally thought of by most as DNA with no current function. The only problem was they weren't sure which was the junk part and which were the few functional genes scattered about.

Well, the way I see it, the original definition (that of "DNA that is a provisionally labeled for sequences of DNA for which no function has been identified") may have later been transmogrified to "actually non-functional". And it is this subtle change that may confuse people to draw weird conclusions.

That is not true. It can be either out of nothing or formed from something. Even the bible doesn't say it was from nothing but formed out of the ground or dust. It uses the words 'made' and 'bring forth'. That is the majority view I've heard of.

That's because you're using an overly narrow view of creation. You can view it as change/evolution but that's an overly broad view of evolution. It does not seem consistent to me

The Bible doesn't explicitly say either way. While the Bible says humans were created in the image of God, it also says God formed humans from dust.

I don't see this as literal or univocal, rather as analogous. And it compatible with the view that change and creation are separate processes and both of them being true.

For example, given a Scholastic view of change and creation, one may reasonably provide an account as follows.
Humans (like any other material substance) are composites of prime matter and substantial form. Dust may represent matter, more specifically prime matter. Change is described as prime matter changing form. For humans to be formed, prime matter is conjoined with substantial form, more specifically, substantial form here just means "form of a human being". Hence humans formed from dust. But, the substantial form of a human being (as with the substantial form of every material substance) is created out of nothing and simultaneously conjoined with matter to form a human being. And in the image of God just refers to our limited intellects which is analogous to that of God's unlimited intellect.