Extinct retroviruses

All ERVs in humans are extinct retroviruses.

Are there any fossilized retrovruses or other strong evidence that support this claim? In case you're thinking about citing the ERVs found in modern genetic sequences, I'd call that begging the question.

That's a good one. Let's also look for fossilised raindrops to test the proposition that it used to rain in the past. No, those raindrop impact craters in the clay don't count, I want the actual raindrops!

nail in the coffin

John M. Coffin was Constructing primate phylogenies from ancient retrovirus sequences by orthologous comparison of evolving, proviral, nucleotide sequence.
He has not only analyzed the integration site but also the mutations that accumulated in the LTRs.
How will a creationist explain that you obtain the well known phylogenic tree from random damage in the LTRs?

Why, kereng, don't you know that it would be arrogant and presumptuous of us to think that an omnipotent designer couldn't have put those mutations there for their own inscrutable purposes?

:)

HIV is a lentivirus-- there are very, very few endogenous lentiviruses (found one in bunbuns, another in lemurs). HTLV is a deltaretrovirus-- I am not aware of any endogenous deltaretroviruses.

Is it possible that we could find lentivirus and/or deltaretrovirus ERVs in the human genome? Like really old ones that appeared in our common ancestors with the animals you mentioned that have lentivirus ERVs?

Kemanorel-- I dont think so, at this point. The bunny and lemur ones got in long after they diverged from humans. And people are sequencing humans left and right now, and no one has found a lenti or delta yet.

I would believe that 'XMRV' is a variant ERV in humans, though.

:-O

I dont think so, at this point.

Damn. I figured that was probably the case. I thought I might have been able to turn it into an interesting project for class even if I were to come up with nothing.

Oh well. :-)

Does that mean that the evolution of the human immune system completely dominated those viruses; that if one were reconstructed as an exogenous retrovirus that it wouldn't be able to infect anything? Otherwise, why would all of those viruses have gone extinct?

Does that mean that the evolution of the human immune system completely dominated those viruses; that if one were reconstructed as an exogenous retrovirus that it wouldn't be able to infect anything? Otherwise, why would all of those viruses have gone extinct?

That might be accurate for some viruses, but more likely is they simply evolved and became new species of virus. Similar to how old-world monkies are extinct, yet we (and the other great apes), the old-world monkies' progeny, are here now.

From the retrovirus phylogeny on wikipedia (http://en.wikipedia.org/wiki/File:Phylogeny_of_Retroviruses.jpg), deltaviruses and lentiviruses diverged from the common ancestor of alpha and beta retroviruses, so anything recognizable as an alpha or beta retrovirus wouldn't be the ancestor of a delta or lentivirus.

That's a good one. Let's also look for fossilised raindrops to test the proposition that it used to rain in the past. No, those raindrop impact craters in the clay don't count, I want the actual raindrops!--Stephen Wells

Cool story bro.

*plants a sign next to little Willy Wallace*

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Please do not let the troll side track ANOTHER thread with stupidities.

qbsmd -

Here are my informal, educated but not specifically expert thoughts about the question you asked.

If the viral phenotype associated with nucleic acid sequences still found in the human genome went extinct, as seems to be the case, then, yes, it may mean that viruses genetically close enough to those sequences to be considered members of the same species (as that concept is applied to viruses) were no longer able to successfully reproduce.

That could have been due to the human immune system, or something else, possibly including random chance. For example, they might have coinfected some kind of animal host that itself went extinct, for reasons not directly related to the virus. Losing a reservoir like that might have led to the extinction of a viral species.

I suppose it could also literally be due to the frequently high rate of variability in virus reproduction. Maybe a continuing, successfully infectious virus lineage might just accumulate so many changes with each new "generation" that over the years, descendants were no longer identifiable as being "the same" as ancestors, even if there was no selection pressure against the ancestor phenotype. This question would be quite amenable to mathematical modeling. I don't think anything like this has been observed over the hundred or so years that we have been studying viruses, but I don't think it can be ruled out.

The extinct viral lineages are likely the ancestors or relatives of modern viruses. They may very well be the ancestors of modern viruses that infect some non-human host.

"All ERVs in humans are extinct retroviruses. The viruses in your genome right now have no homologues in our population that infect modern humans."

But what about............

The Human Endogenous Retrovirus Link between Genes and Environment in Multiple Sclerosis and in Multifactorial Diseases Associating Neuroinflammation

Clinical Reviews in Allergy and Immunology

Hervé Perron and Alois Lang

Endogenous retroviruses represent about 8% of the human genome and belong to the superfamily of transposable and retrotransposable genetic elements. Altogether, these mobile genetic elements and their numerous inactivated âjunkâ sequences represent nearly one half of the human DNA. Nonetheless, a significant part of this ânon-conventionalâ genome has retained potential activity. Epigenetic control is notably involved in silencing most of these genetic elements but certain environmental factors such as viruses are known to dysregulate their expression in susceptible cells. More particularly, embryonal cells with limited gene methylation are most susceptible to uncontrolled activation of these mobile genetic elements by, e.g., viral infections. In particular, certain viruses transactivate promoters from endogenous retroviral family type W (HERV-W). HERV-W RNA was first isolated in circulating viral particles (Multiple Sclerosis-associated RetroViral element, MSRV) that have been associated with the evolution and prognosis of multiple sclerosis. HERV-W elements encode a powerful immunopathogenic envelope protein (ENV) that activates a pro-inflammatory and autoimmune cascade through interaction with Toll-like receptor 4 on immune cells. This ENV protein has repeatedly been detected in MS brain lesions and may be involved in other diseases. Epigenetic factors controlling HERV-W ENV protein expression then reveal critical. This review addresses the geneâenvironment epigenetic interface of such HERV-W elements and its potential involvement in disease.

Cynical1 -

That research is incredibly interesting on many levels.

However, it is in no way whatsoever inconsistent with this statement -

All ERVs in humans are extinct retroviruses. The viruses in your genome right now have no homologues in our population that infect modern humans

They have no homologues among known infectious viruses in the environment.

If it turns out that ancient viral genes that have literally become part of our genome can be transcribed, and possibly even translated into protein, under certain circumstances, and if this helps us to understand human disease, that will be fascinating and incredibly valuable.

But they're still ancient viral genes that have become part of our genome. The passage you quote does not imply that they have homologues among modern, fully functional viruses.

But they're still ancient viral genes that have become part of our genome.

Because....[add scientific evidence here].

Wee Willie -

That's a bizarre comment, given that this entire blog and thread are about such evidence.

You've proven over and over again that you don't have the minimum background to understand this topic, and that you aren't willing or able to obtain it. Your sole objective is to contradict the experts on a topic that you are literally completely ignorant of, because scientific reality conflicts with some kind of dogma, ideology, and/or agenda that you base your life around.

However, in the interest of third party readers, here's a really good review article that summarizes much key information on the topic. It's from 2003 but still a good read.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1187282/

But they're still ancient viral genes that have become part of our genome.

Because....[add scientific evidence here].

I'm just an interested layperson, so my knowledge is very patchy, but here's one article that looks pretty convincing to me:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665638/?tool=pmcentrez

As far as I understood, the researchers took what looked like different slightly garbled copies of the same ancient virus contained in the human genome and managed to create a fully functional virus by putting together the intact-looking pieces.

Harold,

Interesting that you think it is bizarre to ask for scientific evidence to back up a claim made under the color of science. Even more interesting is the article you cite doesn't make a case that ERVs are fossil viruses, but rather simply declares this to be the case.

Taneli's cited article, on the other hand, at least appears to both be honest, and also cites articles that supposedly (and I say this because I haven't read the citations yet) provide scientific evidence that 18 intact genes exist in the human genome. I haven't read those 3 citations, but my guess is they just note a coincidence in sequencing.

For comparison, my mobile phone number, my work phone number, my home phone number, and the first phone number I ever had all exist within the first 30e6 digits of pi, completely intact.

Now, if I thought like a biologist, this would prove that my phone numbers all evolved from Pi, and worse, that my phone numbers have a partial latent ability to determine the circumference of a circle given its diameter.

William Wallace -

Interesting that you think it is bizarre to ask for scientific evidence to back up a claim made under the color of science.

Misrepresentation. I said that the scientific evidence for what you call a claim was already clear from the contents of this blog.

The reality is that there is nothing that you would accept as scientific evidence, because of your irrational commitment to some type of dogma, ideology, or agenda.

Even more interesting is the article you cite doesn't make a case that ERVs are fossil viruses, but rather simply declares this to be the case.

I knew you'd falsely say that, because that point is brought up in the introduction. In fact, the article discusses at length what HERVs are and how we know.

To summarize for others -

Retroviruses have an RNA genome - fact. Their genetic elements - LTR, gag, pol, and env - can be recognized - fact. They use reverse transcriptase to reverse transcribe it to cDNA - fact. The cDNA is inserted into host chromosomes. - fact. The cDNA can initially be transcribed and translated into mRNA and ultimately viral proteins, as well as copies of the viral genome (in an interesting way which is discussed in the reference I gave) - fact. The cDNA sequences which are inserted onto human chromosomes can sometimes be replicated during s phase - fact. If this happens in a germ cell it will make that DNA heritable - fact.

When the human genome began to be sequenced it was found that 1% of the genome consists of endogenous, inheritable DNA sequences that are recognizable as retroviral sequences. Most of these sequences have accumulated changes, but are still clearly recognizable.

The most reasonable interpretation of this set of facts is that these endogenous retroviral sequences are exactly what they look like. A strained but logically tenable supernatural argument is that a god created them magically, using "common design" to mimic evolution.

Coincidence is not a rational argument here.

Taneli's cited article, on the other hand, at least appears to both be honest, and also cites articles that supposedly (and I say this because I haven't read the citations yet) provide scientific evidence that 18 intact genes exist in the human genome. I haven't read those 3 citations, but my guess is they just note a coincidence in sequencing.

Your guess is worthless.

For comparison, my mobile phone number, my work phone number, my home phone number, and the first phone number I ever had all exist within the first 30e6 digits of pi, completely intact. Now, if I thought like a biologist, this would prove that my phone numbers all evolved from Pi, and worse, that my phone numbers have a partial latent ability to determine the circumference of a circle given its diameter.

That's a false analogy that demonstrates that, for all your obsession with being a "genius" and all your pi phone numbers, you aren't even able to avoid gross logical errors.

In a system that reproduces by replication with limited variation, as life does (fact), similarity of sequence is evidence of descent.

Of course, when dealing with non-biological, human-designed things like phone numbers, similarities are indeed evidence of common design, or human design inspired by prior human design, or design by similar designers.

Furthermore, your own argument is even stupider than the straw man position you apply to "biologists" here. Your own argument, based on what you keep saying about ERVs, would be that the relationship between the phone numbers is a pure coincidence. That's what your on record as saying about ERV data. Not common descent, nor even "common design" by a god who magically creates ERVs to mimic evolution (the only other rational explanation), but coincidence. What kind of a moron would assume that three phone numbers, all owned by the same person, happened to be based on the first digits of pi by coincidence?

"Now, if I thought like a biologist, "

You are such an idiot. On the plus side, laughing at you has brightened my day.

What kind of a moron would assume that three phone numbers, all owned by the same person, happened to be based on the first digits of pi by coincidence?--harold

What is your explanation for the phone numbers, if not coincidence?

Oops. I misread part of Willy Wallace's comment.

Well, not being a troll, I quickly admit it when I am wrong, and correct myself.

Let's reread -

For comparison, my mobile phone number, my work phone number, my home phone number, and the first phone number I ever had all exist within the first 30e6 digits of pi, completely intact.

Oh, I see. He's just making the inane statement that his phone numbers, like anyone else's, will eventually be found among the digit string of any irrational number, if you extend it long enough. That's perfectly true.

But that just makes your entire less relevant. What if 1% of the first three billion digits of pi, 30 million of those three billion digits, were made up of exact repeats of your phone numbers? Here's an exercise - Modelling the generation of digits of pi (or some other arbitary irrational number) as being close to random digit selection, calculate the probability of a randomly chosen string composed of base-10 digits, 3 billion digits in length, including thirty million or more digits in complete local strings, randomly distributed, that are exactly the same as one of your phone numbers. This is a very doable problem. But of course, ERVs do mutate over time, and are made up of strings of only four "digits". And of course, if you extend any irrational number's digit string massively enough, eventually you would expect to find one three billion digit string with this characteristic (but the odds of any randomly sampled 3 billion digit string having it would be mighty slim) So this is just a mental exercise. But it might be a valuable one. It might clarify your understanding of "coincidence".

Now, for the sake of everyone else, in addition to recommending the references, I will repost my terse explanation.

To summarize for others -

"Retroviruses have an RNA genome - fact. Their genetic elements - LTR, gag, pol, and env - can be recognized - fact. They use reverse transcriptase to reverse transcribe it to cDNA - fact. The cDNA is inserted into host chromosomes. - fact. The cDNA can initially be transcribed and translated into mRNA and ultimately viral proteins, as well as copies of the viral genome (in an interesting way which is discussed in the reference I gave) - fact. The cDNA sequences which are inserted onto human chromosomes can sometimes be replicated during s phase - fact. If this happens in a germ cell it will make that DNA heritable - fact.

When the human genome began to be sequenced it was found that 1% of the genome consists of endogenous, inheritable DNA sequences that are recognizable as retroviral sequences. Most of these sequences have accumulated changes, but are still clearly recognizable.

The most reasonable interpretation of this set of facts is that these endogenous retroviral sequences are exactly what they look like. A strained but logically tenable supernatural argument is that a god created them magically, using "common design" to mimic evolution.

"Coincidence" is not a rational explanation here."

Oops. I misread part of Willy Wallace's comment.

Misread? How so? Which word or words did you misread?

Did you mean to say your intuition failed you, but upon second thought, you agree. (Fair enough.)

I quickly admit it when I [should add: realize I] am wrong, and correct myself.

As do I.

...Modelling the generation of digits of pi (or some other arbitary irrational number) as being close to random digit selection...

An interesting digressive point, though pertinent to the larger discussion, is: they aren't random, though I agree that modeling them as random would probably "work" for the issue of finding strings of digits embedded in larger strings of digits, even though the digits of pi are fixed for a given base.

I have, elsewhere, cited the case of quantization error validly being modeled by engineers as random, even though it is not a random process. Sometimes, modeling a process as being a stochastic process works, but one should be careful to not confuse a model--any model, not just a stochastic model--that seems to produce results consistent with reality, with reality itself.

In the case of engineers and quantization error, the error in understanding comes in taking too literally another name for quantization error, viz., the misnomer quantization noise.

To summarize, a process that can be modeled as a random process is not necessarily in fact stochastic or ergodic.

In the case of the digits of pi, quantization error, and other quantifiable areas of study, what is modeled as random is often in fact deterministic.

"Retroviruses have an RNA genome â fact."

Won't dispute.

Their genetic elements - LTR, gag, pol, and env - can be recognized - fact.

Please clarify what you mean here. Do you mean their sequences have been cataloged? Or that you can see a pattern and recognize it, absolutely, as being LTR, gag, pol, env, or one of my phone numbers converted to base 4?

They use reverse transcriptase to reverse transcribe it to cDNA - fact. The cDNA is inserted into host chromosomes. - fact. The cDNA can initially be transcribed and translated into mRNA and ultimately viral proteins, as well as copies of the viral genome (in an interesting way which is discussed in the reference I gave) - fact.

Won't dispute

The cDNA sequences which are inserted onto human chromosomes can sometimes be replicated during s phase - fact.

Won't dispute, but could you elaborate on how we know this. I assume you mean it's been observed to occur in the lab multiple times in a repeatable manner.

If this happens in a germ cell it will make that DNA heritable - fact.

Won't dispute.

However, I think at best you've made a case that the ERVs could have been from ancient viruses. I have never said they could not have been. I do think other possibilities exist, such as microevolution and mutation, latent function (designed or otherwise), coincidence, and others I haven't even considered.

How do you know, scientifically, that these other possibilities can be ruled out with certainty?

*sighs and pulls up his sign*

I know this is going to be pointless to explain it this way to little Willy Wallace, but the easiest way to explain how we know ERVs are ancient is this:

We know we find the same ERVs across multiple species. We know when these species diverged from a common ancestor, so we know a MINIMAL age because the ERV must have been inserted before speciation happened.

The same can be done in reverse to figure estimate a maximum age... if a branch of the evolutionary tree has the ERV and another branch for which they had a common ancestor doesn't, we can assume a maximum age where of about where the species diverged.

ERVs have been found among humans and other "great apes." Human diverged 150,000 - 200,000 years ago, ergo, these ERVs are AT LEAST 150,000 years old, thus making them ancient.

QED.

In the case of the digits of pi, quantization error, and other quantifiable areas of study, what is modeled as random is often in fact deterministic.

This is of course true. However, as I think was obvious, I made the point about phone numbers for a reason. The reason was to demonstrate how unlikely it would be to obtain the type of results we see with ERVs by random sampling. This is important for dealing with some of your later questions.

A particularly important point is that, in the case of ERV data, we already have a strong mechanistic explanation that explains the results, and the mechanistic explanation is 100% compatible with prior results and with underlying theory. So, rather than invoke an implausible argument that the results are due to freakishly unlikely random chance events, we draw the reasonable conclusion that they are due to what they seem to be due to.

If you have some familiarity with math, then you know that in science and math literature, adequate background is assumed, and obvious points that can be inferred by any knowledgeable reader are not excessively dwelt upon. It's the same in biomedical science.

Their genetic elements - LTR, gag, pol, and env - can be recognized - fact. Please clarify what you mean here. Do you mean their sequences have been cataloged? Or that you can see a pattern and recognize it, absolutely, as being LTR, gag, pol, env, or one of my phone numbers converted to base 4?

Of course I mean that the sequences have been determined, as well, of course, as the amino acid sequences of the proteins. To be able to recognize them without knowing the sequences would imply psychic powers.

The cDNA sequences which are inserted onto human chromosomes can sometimes be replicated during s phase - fact.
Won't dispute, but could you elaborate on how we know this. I assume you mean it's been observed to occur in the lab multiple times in a repeatable manner.

It probably has, but I don't know, and this is so obviously true that it doesn't have to be directly observed to be inferred. For it NOT to be true there would have to be something magic about ERV sequences to prevent them from being replicated. I can make a statement like "all the living feral cats in New York need a source of water to stay alive". I can't see every feral cat, and the few I do see usually aren't drinking water. Yet the statement is trivially true.

However, I think at best you've made a case that the ERVs could have been from ancient viruses. I have never said they could not have been. I do think other possibilities exist, such as microevolution and mutation, latent function (designed or otherwise), coincidence, and others I haven't even considered.

Mutation, coincidence - These are essentially saying the same thing. This all amounts to an argument that the ERV sequences are there due to a process which can be modeled as sampling random variables. This isn't reasonable. Even without a mechanistic explanation and results which are compatible with previous observations and underlying theory, we would still question the "random chance/coincidence" explanation, due the nature of the observations. With an obvious mechanistic explanation, the "random chance" results can be discarded by any reasonable person.

Latent function - They do have latent function in many cases, but that important fact is irrelevant to the direct point at hand; we are discussing how they got there, not whether or not they have latent function.

Magical Design - Of course, anything could always have been caused by the Flying Spaghetti Monster or some other deity, designing it yesterday, planting false memories of it into everybody's head, etc, etc. All we can say is that if the FSM behaves that way, She has desigined it to look exactly like evolution to the reasonable human observer. (The existence of ERVs is not, of course, an argument against religion in general; it is part of the evidence against religious stances that specifically deny evolution, but nothing more than that.)

Something you haven't thought of - You're certainly welcome to think of other testable explanations, but the mechanistic explanation we already have is very strong, so you're probably wasting your time.

Microevolution - The fact that ERVs fall along previously known phylogenetic trees with remarkable precision is of importance here. We know the expected frequencies of many types of mutations from extensive laboratory observation (please don't keep challenging these basic background points). We know the approximate time of convergence of many lineages - yes, that is approximate - from multiple lines of mutually consistent data. The ERV data is consistent with prior data from the fossil record and other unrelated molecular genetic investigations. The rational response to the fact that these completely independent observations keep converging on the same logical conclusion is to accept that conclusion.

...QED.--Kemanorel

Cool proof bro.

It probably has, but I don't know, and this is so obviously true that it doesn't have to be directly observed to be inferred.--Harold

Careful. Aristotle thought it was so obviously true that men had more teeth than women that he apparently never bothered to verify his assertion. Well, I suppose it is possible that Ancient Greek women had fewer teeth than men, and that they have since evolved additional teeth.

Latent function - They do have latent function in many cases, but that important fact is irrelevant to the direct point at hand; we are discussing how they got there, not whether or not they have latent function.

You're boxing yourself in. If an archaeologist finds a suspected artifact, he or she thinks about its latent function and how it got to where it resided. They are sometimes related. But you've ruled out a whole area for consideration a priori.

If biologists found the phrase "Ehyeh asher ehyeh" encoded into every genome, they would think that was evidence of common descent, and nothing more.

William Wallace -

Sorry, Billie Bollocks, I'm not going to let you get away with it, at least for the near future. I'm going to keep pointing out the half-baked Jedi mind tricks that you play on yourself. I know you know that you are wrong, at some level. Otherwise you wouldn't be here blabbering.

Before I shred your latest comical and probably only partially successful efforts to keep your own brainwash job from fading, I'll point out the general logical flaw in what you do.

You start from the position that common descent and evolution must be denied. (Please don't bother to engage in elementary school yard reactive projection and try to claim that "you do it too!", because I don't. I go with the objective evidence, rationally interpreted.) What this means is that your posts contain no actual information, by definition. That's just a logical fact. You're a broken clock. You start with the a priori assumption that there can be no valid evidence for common descent, so you deny even the most laughably obvious evidence.

Another one of you mental tricks - for fooling yourself, only - is to avoid learning even the basics of the field you're denying. I'd make an analogy, but I'm hard pressed to think of any scientific field I'm as ignorant of as your are of anything to do with biology. I guess having someone translate something from a language I don't understand and then standing there like the world's most ridiculous oppositional brat and denying that it said what they, but not I, could clearly see it said, is the best example I can come up with.

Careful. Aristotle thought it was so obviously true that men had more teeth than women that he apparently never bothered to verify his assertion.

False analogy/straw man. The mechanism by which human teeth develop was unknown to Aristotle. He made a bad assumption. The mechanism by which DNA replicates is well understood. Also, the fact that retroviral sequence are inherited is itself strong evidence that retroviral sequences which are part of a chromosome get copied with the rest of the DNA on that chromosome, as would be expected.

You're boxing yourself in. If an archaeologist finds a suspected artifact, he or she thinks about its latent function and how it got to where it resided. They are sometimes related. But you've ruled out a whole area for consideration a priori.

Complete crazy stupid BS - not even to the level of straw man. Just pure unwillingness/inability to understand what I said. We know exactly where the genes got their latent function - they're viral genes with essentially viral functions. Some could have been co-opted by evolution to have some benefit to human cells. Others are linked to diseases. I haven't ruled anything out - you're the one who has ruled something out a priori and can't accept or understand (or allow yourself to understand) any actual evidence. Also, of course, archaeology is the opposite of "intelligent design". It deals with the products of a known "designer", which all reasonable people agree are "designed", and which humans can reproduce.

I really want to get this point across, since it may be the last one I ever make to you. You're not being "smart", let alone a "genius". You're simply making it clear to any rational person that whatever dogma, ideology, agenda, or mental illness is driving you is dependent on a false view of basic physical reality. If your god can't live in the same universe with ERVs, your god is gone. If your superiority to some other ethnic or social group is based on ideas that aren't compatible with ERVs, your superiority was imagined.

Harold, don't be a hater just because you can't make a scientific case.

WW

I haven't read any comments in here yet, but I know Wallaids sucks at everything so I declare him the loser.

/thread

A final note here.

There is nothing hateful in my comments. Some humorous observations of the obvious in my last one.

This was an interesting exercise.

Perhaps creationists represent a newly discovered disorder - adult ODS http://en.wikipedia.org/wiki/Oppositional_defiant_disorder

Harold, don't be a hater just because you can't make a scientific case.

He did make a scientific case, as did I... and the best you can come up with in return is "don't be a hater" and "cool proof, bro."

Go study.

If we were to show Wally that a mother and her child had their fossil ERV sequences in the corresponding locations in their genomes, would he acknowledge that the child had inherited the sequences from her mother?

If so, what's his problem with "inherited feature is inherited"?

If we were to show Wally that a mother and her child had their fossil ERV sequences in the corresponding locations in their genomes, would he acknowledge that the child had inherited the sequences from her mother?

No.

Stephen Wells, sure I would. Just as soon as you show they are fossil ERV sequences.

Wiliam Wallace -

What evidence would you accept that they are "fossil ERV sequences", that is to say, sequences that result from ancient viral gene insertion into chromosomes? What test do you propose would be sufficient to convince you?

Just as soon as you show they are fossil ERV sequences.

I already gave a reasoned argument how we know the ERV sequences (at least any that are found cross-species, and those that are tracable back to the San people in Africa) are ancient.

Stephen also explained why we don't need fossil ERVs.

Just because you're too stupid/ignorant to understand or just too brainwashed to ever believe evidence that contradicts your precious religion regardless of how many times you get slapped in the face with it, doesn't mean we have to get the evidence in the way you know it can't be done.

We have the evidence. We win. Now, STFU and GTFO. You have no place among reasoned arguments.

Kemanorel, let the adults talk. Children should be seen but not heard. Now go play.

"All ERVs in humans are extinct retroviruses."

Why is that? Luck of the draw? We beat them all? Or are they just rare to begin with?

(Ignore WW's poo-flinging. You're just feeding his ego.)

William Wallace -

Can the nastiness and answer my question -

"What evidence would you accept that they are "fossil ERV sequences", that is to say, sequences that result from ancient viral gene insertion into chromosomes? What test do you propose would be sufficient to convince you?"

All ERVs in humans are extinct retroviruses (p < 0.000000001).

There you go, Willy. Can the adults get back to our conversation now?

Damn preview borked my html. Let's try it again:

All ERVs in humans are extinct retroviruses (p < 0.000000001).

There you go, Willy. Can the adults get back to our conversation now?

Thanks Harold for your response to my post (#14) and it was NOT my intention to incite (yet another) creationist debate with my post. Actually, I understand, at a cursory level what you and Abbie have been talking about and your point regarding it not being in conflict with what Abbie posted up top. I was just interested in what someone, who understands this much better than I, thinks about the claims that other viruses, particularly herpes virses, can induce HERV-W (and HERV-H) retroviral proteins in diseased tissue which then begs the question of whether there is actually competant viral particals being produced from these, otherwise, extinct HERV genetic sequences. There are groups who have claimed that they do indeed find retroviral particles in their work. Here's a link to the PDF of a review which has some of the references to the groups that make these claims. However, from what I have seen in this particular therapeutic area, these groups have not had many others follow up their findings. (Unlike the MSRV group where several groups have tried unsuccessfully to reproduce their findings. On the plus side, the HERV-W guys aren't making presentations at Autism conferences claiming the apocolyptic HERV-W is upon us.) Any opinions/comments welcome as it's a radically different mechanism for autoimmunity than many of the others that involve viral etiology.

http://www.direct-ms.org/pdf/VitDMS/Ebers%20Gio%20MS%20Cause%20Environm…

fnxtr -

I mentioned a few reasons (educated guesses) why retroviruses might become extinct -

Human immune system, but let's not flatter ourselves too much.

Loss of a non-human reservoir, say if another species went extinct, for reasons unrelated to the retrovirus.

Just so much variation between "generations" that descendants and ancestors aren't easily seen to have an obvious relationship.

Another thing I didn't think of - cellular receptors. For example, HIV cannot infect people who are homozygous at a certain allele. http://en.wikipedia.org/wiki/CCR5 An excessively virulent infectious agent can select for a phenotype that is resistant.

cynical1 -

I thought you brought up a good point.

ERV explanations disseminated here are plausible. But lots of plausible explanations ain't so.

What would it take to get me to think your explanation is the most plausible? A paper stronger than usual on math and weaker than usual on story telling--published in a peer reviewed journal; quantitatively comparing various explanations; while discussing reasonableness of various assumptions; and specifying those assumptions that affect the quantitative comparisons--would go a long way.

Telling me you can't imagine any other possibility and waving your arms dismissively at mutation, coincidence, or purpose as implausible explanations might fly with a biologist, but it won't fly with me. It might even be a useful model that best fits with common descent, but thatâs begging the question.

So far, you've argued that ERVs are very strong evidence of common descent (some imply proof), but you base your explanation of ERVs on common descent. ~'A implies B because B implies A because A implies B, and everybody knows A and B are true, except wacked out religious nuts who hate science.'

So, why do biologists hate rational discussion?

Kemanorel, it's taking you even longer to comment on my code and mathematical analysis of the Monty Hall problem than it did for you to realize you couldn't write a program to solve the toy Sudoku problem that you insisted was a 100 level problem. Why don't you post your c++ code for tic-tac-toe with 13 classes to prove your computer science prowess?

Regarding #43 and #44, are you saying the probability of that "All ERVs in humans are extinct retroviruses" is less than 0.000000001? Or did you just fail twice?

Willy, you don't get to lecture anyone about science until you learn a little more yourself. Kemanorel quoted you the level at which the result is statistically significant; overwhelmingly so.

You don't get to invoke "mutation and coincidence" without explaining what you mean; what mutations and coincidences do you think occurred? Be specific. You don't get to invoke "purpose" as an explanation because it's not an explanation. how did those nucleotides get into those genomes? "Purpose" is not an answer. What, physically, are you proposing happened?

So that leaves you with no competing explanations at all; and all you can do is mistake consistency for circularity.

To return to the question: if a mother and her child have the same ERV sequences in their genomes, do you agree that the child inherited the sequences from her mother? Yes or no?

So, why do biologists hate rational discussion?

We're fine with it. You're just not having a rational discussion in return.

it's taking you even longer to comment on my code and mathematical analysis of the Monty Hall problem than it did for you to realize you couldn't write a program to solve the toy Sudoku problem that you insisted was a 100 level problem. Why don't you post your c++ code for tic-tac-toe with 13 classes to prove your computer science prowess?

ROFL. I stopped paying attention to that thread after the best you could do with my code sample was comment on the documentation for which apparently "//reset" and "//total score" were too hard for you to follow.

Regarding #43 and #44, are you saying the probability of that "All ERVs in humans are extinct retroviruses" is less than 0.000000001? Or did you just fail twice?

No wonder the Limpster is so unconvinced by modern science. He doesn't even know what a p-value is!

What would it take to get me to think your explanation is the most plausible? A paper stronger than usual on math and weaker than usual on story telling--published in a peer reviewed journal; quantitatively comparing various explanations; while discussing reasonableness of various assumptions; and specifying those assumptions that affect the quantitative comparisons--would go a long way.

Billie Ball-less doesn't even understand the most basic quantification metric used in science. I don't hold much hope that he would understand the metrics if we held his hand and walked him through it.

Let me repeat that. Limp Willy has been bitching for years that we're ignoring possible random effects when it comes to explaining ERVs, and he doesn't even know what a p-value is!!!

Hahahahahahahhahahhehehehehhee!!!!

AHAHAHAH!

hehe

*wipes tears from eyes*

p-value

hehehehehehehehehe!

*falls out of chair*

He doesn't even know what a p-value is!--WKV

Or you're an utter failure when it comes to communicating technical information effectively. I'm going with the later.

Now, your imprecise abuse of langauge not withstanding, I argue that this amply demonstrates I understand the math involved in calculating p-values.

Please provide the equation or equations you used to come up with a p-value of 0.000000001 or less.

Show us your man tits or GTFO.

Didn't think so.

(This is almost too cruel, it's like hunting penned cattle.)

Glad to see you were shamed into learning some basic science. Please note that my usage of p-value is normal for peer-reviewed papers.

Following Limp Willy's link, I got the following:

Not Found

The requested URL /erv/2010/06/erv/2010/05/biology_and_computer_science_s.php was not found on this server.
Apache/2.2.3 (Red Hat) Server at scienceblogs.com Port 80

Yep, perfect demonstration.

However, I'm going to throw Willy a bone (since he so obviously lacks one of his own). The number I threw out there wasn't actually calculated, and was in fact an exaggeration, strictly speaking. It was merely included to show that yeah, there's some uncertainty, but it's really small (technically, I was abusing the concept). In fact, I would not be surprised if a few sequences currently identified as "possible ERV remnants" simply occurred by chance (or a simple deterministic mechanism) alone. But the point I was making was that the odds of even a significant fraction of possible ERVs resulting from the null hypothesis are incredibly low, in light of the evidence we have so far gathered and processed.

Oh and a point of consideration. Abbie's original sentence could more properly be phrased as such:

The retroviruses that endogenized in the human genome are all extinct.

Hers is more pithy.

BTW, you still haven't commented on my model on the "Facts of Evolution" thread. I'll let that model stand as proxy for my man tits.

Anatomy of a Troll -

Billie Bollocks has engaged in all of the following techniques, just on this thread alone.

1. Deliberate ignorance of the topic he is trying to discuss.

2. Failed attempts to feign expertise.

3. Failed attempts to feign expertise in other fields (he got caught trying to pass himself off as a computer scientist in another thread, too).

4. Desperate cherry-picking of snippets to argue with while ignoring the arguments that devastate his "position".

5. Straw man misrepresentation of the positions of others.

6. Attempts to intimidate with insults.

7. Projection of his own faults onto others.

8. Argumentation by false analogy.

9. Repetition of wrong arguments after they have already been corrected.

10. Attempts to create false appearance of conflict among people who agree with each other, and disagree with him.

11. Attempts to falsely imply that biomedical sciences don't make use of mathematical and statistical tools, and exist in some sort of vacuum.

12. Hiding whatever obsessive underlying agenda actually motivates him.

13. Use of terms like "purpose" to mean "magic".

14. And of course, false claims that he could be "convinced", it's just that he can't make a coherent statement of what evidence would convince him.

here, here, and here should address your concerns.

The number I threw out there wasn't actually calculated, and was in fact an exaggeration, strictly speaking. It was merely included to show that yeah, there's some uncertainty, but it's really small (technically, I was abusing the concept).

Thanks for an example of how ERV fanboys operate.

I think Wally demanding more maths and then failing to recognise a p-value is one of the funniest fails we've had for a while.

Returning to the substantial point, Wally still needs to explain what he means by "mutation and coincidence" and "purpose" before they can be considered competing explanations.

Wally, do you agree that children inherit genetic sequences from their parents? Yes or no?

Since Wlly is all about TEH MATHZ!!!!111eleventy-one!

Let's find the p-value. (Note: I am not a virologist, so much of this data is taken from my interpretation of the limited number of publications I've read (n~100). My numbers are at best rough estimates)

A recognizable ERV sequence is at least 500 bp long, with a mean of about 2,400 bp, and there area total of about 98,000 sequences. Considering various factors, such as insertion requirements and multiple viable sequences, let's require a 40% sequence match (keeping in mind that this is really a bunch of factors lumped into a single number). What is the probability that any given suspected ERV is actually the result of a random assemblage of nucleotides (assuming no base pair bias)?

Let's modify one of Willy's own equations:

P=SUM(i=200,500,COMB(500,i)*(1/4)^i*(3/4)^(500-i))

This works out to:

P=1.27527e-33

Keep in mind that that is for a 500 bp sequence. The probability decreases as the length of the sequence increases. Now what is probability that there is at least one suspected ERV that is the result of a random assemblage?

p=1-(1-P)^98,000
p=1.25013e-8

However, that number is only valid if all 98,000 sequences are 500 bp long. Since this is not the case, I find it quite reasonable to declare the p-value

p < 1e-9

as it is only a bit over an order of magnitude difference. Not bad for an off-the-top-of-my-head estimate, eh?

(For the record, I started with 70% identity, but then considered multiple sequences, so I dropped it to 40%. I didn't do any other fine-tuning)

Stephen Wells, I think it's a commentary on ERV fanboys for their failure to communicate effectively. But whatever.

As biology isn't really much of a science, they should incorporate the suffix "science" as in "biological science" to show the similarities with other so-called sciences, such as political science or social science, and to distinguish it from mathematically rigorous sciences such as physics.

Wally, do you agree that children inherit genetic sequences from their parents? Yes or no?

You've finally unloaded your question with "ERV". After I answer, please be sure to not carelessly reinsert the term.

Yes, I agree that children can inherit genetic sequences from their parents. Certainly, they inherit traits, as the Augustinian priest Gregor Mendel (that anti-science church at it again) showed in the 1800s.

Let me ask you what should be a simple calculation for people who can read tea leaves and deterimine the origins of ancienct genetic sequences so conclusively: A mother and a supposed father have brown eyes, while a paternal uncle to the children (verified full brother to supposed father) has blue eyes. Three out of three of mother and supposed father's children have blue eyes. The children were individually born on the island, starting 3 years after the adults were stranded on the island. What is the probability based on the information given that the supposed father is the actual father of all three children?

What effect, if any, will your calculation have on any future genetic testing that may be performed to more conclusively establish paternity?

It's a simple problem and is dealing with a single patent trait.

Don't have time to respond in detail, as I am going on a trip, but a post that preceeds WKV's was posted earlier today.

I am not sure you're doing the math right, on multiple counts, the most significant, intuitively, that you aren't considering the roughly 3E9 start locations. My intuition may be failing me here...I'm focused on the trip I'm taking.

But consider that 3 of my current phone numbers, and my first phone number, where found embedded *completely intact* somewhere in the first 30e6 digits of pi. This is purly coincidental.

I think such a coincidence might reflect on the actual probability that 40% of a 500 bp sequence being found embedded somewhere at roughly 3E9 start locations.

That is to say, my intuition is telling me the probability is much higher than your calculations indicate. I'm guessing it's related to you not taking into account all of the possible start and stop locations.

I could be wrong, intuition often fails in dealing with probabilities, so I will think about it while I'm traveling.

Peace. Or pile on.

How many times were your phone numbers embedded?

If you had said "my current phone number (singular) is embedded (say) 47 times in the first (for example) 100000 digits of pi", you'd have a closer analogy, wouldn't you?

I think such a coincidence might reflect on the actual probability that 40% of a 500 bp sequence being found embedded somewhere at roughly 3E9 start locations.

Fair enough, let's follow that train of thought. Instead of looking at the number of identified sequences (98,000), we're looking at the number of possible starts for the sequence, so we substitute 3e9 for 98,000 in my previous equation. In that case, we get a p-value of

p=3.83e-4

That's still two orders of magnitude more significant than most scientific papers require (any p < 0.05). Remember, that's the probability that any 500 bp sequence with 40% identity would be found anywhere in the entire genome. And this is for mere fragments of an ERV. A complete or nearly complete ERV generally runs in the 2-8 kbp range. My calculator can't even handle those probabilities because the numbers are too small.

Wally, the only reason I unloaded ERV from the question is because I wanted to check whether you actually knew that genetic material is inherited, since your tendency to babble about "mutation and coincidence" raised doubts on that point. Let me now honestly reinsert it and ask for your response: does a child inherit ERV sequences from its parents? yes or no?

Your stupid little question about eye colours is an attempt at distraction; I'll just comments that the odds of a brown-eyed couple having three blue-eyed children, if they're both heterozygous brown/blue, is about 1/8; that the odds of their producing any blue-eyed children if either of them is homozygous brown/brown is about zero; and that the odds of the kids having their claimed parentage depends on (a) the heterozygosity of the couple and (b) most importantly, whom the mother actually fucked, which is not determinable from the information given.

Also, stop babbling about phone numbers unless you (a) have a 500-digit phone number and (b) are looking for it in more than one long number.

About 1/64, sorry (1/4 cubed)

But consider that 3 of my current phone numbers, and my first phone number, where found embedded *completely intact* somewhere in the first 30e6 digits of pi. This is purly coincidental.

The odds that any given 7-digit number will appear intact in the first 30 million digits of pi at least once:

just under 5%

The odds that at least one of 4 such numbers appears:

a bit over 18%

The odds that all four appear:

roughly 6e-6, or 0.0006%

Did you actually verify your claim, Willy?

I've got a probability question for you, little Willy...

What are the odds of finding someone singing their phone number, 8675309, to someone in the year 1980?

How about in 1981? 1982?
To someone named Jenny?

@SW #62: My dad was blue-eyed, mom was brown-eyed. They had seven kids, all but one were blue-eyed. I suppose Willy will make disparaging remarks about my mom now...

Don't worry, fnxtr, the probability of that happening is roughly 5.5%. That is not an outcome of significance.

I think Willy's just killing time until he thinks of another objection to the idea that inherited genetic material is inherited.

Hmmm- 50/50 chance, seven results, six ways of getting equivalent outcome... 2 to the seventh is 128 ... 6 over 128 is about 1/20 is about 5%... yup, that makes sense.

Ignore my post 64. I managed to delete the leading "1-" when I switched from 10 digits to 7 digits. Stupid user error. Corrected answers:

95%

over 99.99%

82%

Now that's more like what I was expecting, especially given Willy's odd crowing. It is unlikely, however, that Willy was using the area code. The odds of all four 10 digit numbers being found is less than 1e-10.

Hmmm- 50/50 chance, seven results, six ways of getting equivalent outcome... 2 to the seventh is 128 ... 6 over 128 is about 1/20 is about 5%... yup, that makes sense.

seven ways, actually.

PS - I think I figured out how I managed to mangle the equation in post 64. This bloody computer has been slowing down and needs to be rebooted. The first couple of keystrokes appear to be registering before the mouse click if I type too quickly. So when I did the blockquote tag on Stephen's text, the first two characters were after the quoted text, like so:

lockquote>Hmmm- 50/50 chance, seven results, six ways of getting equivalent outcome... 2 to the seventh is 128 ... 6 over 128 is about 1/20 is about 5%... yup, that makes sense.<b

Yup, seven ways. That makes sense.

Incidentally, Kevin, I was thinking about the odds of two random 500-bp genetic sequences resembling each other at the 40% level. Using a formula of (1/4) to the power 200, times (3/4) to the power 300, times the number of unique combinations of 200 from 500, i.e. factorial 500 over (factorial 200 times factorial 300), I get an answer of around 5 times 10 to the power -14. Overestimating the odds of a resemblance in 201,202...499,500 basepairs as each being similar (clearly an overestimate at the upper end of the range!) I get an odds of resemblance at 40% or higher to be less than ten to the power -10. Do those look reasonable to you?

William @59, Stephen @ 72

I have a typo in my comment 57. The value is P=1.27527e-13, not P=1.27527e-33. The error was not made in the math itself, just in the hand-copying (possibly from the computer slowdown? - I think I remember initially typing ...e-31 and then correcting). The numbers following were all made from the correct value and are still valid.

The calculated values of the two numbers Stephen was talking about are:

P(40%)=6.45799e-14
P(&gte;40%)=1.27527e-13

Stephen clearly grossly overestimated the odds at the top end of the range. In fact, there's no significant contribution after 215 base pairs being identical. For the record, the odds of a perfect match of 500 bp is less than 1e-301

Thanks Kevin- just wanted my math sanity-checked :)