ERV homology argument and comparative genomics

[USincognito]

What if there was an organ that had neither the time nor the means to have evolved?

This is Mark's tired "but the human brain is unpossible" argument he's been tossing out for 5 years.

Human accellerated regions have been explained to you.
The switch to a more meat based diet requiring less jaw muscle anchored on the skull allowing it to expand had been explained to you.
The range of cranial capacity over time and through various species has been explained to you.
The fact that terrestrial artiodactyls evolved into cetaceans in ~10-15 million years, so it's no big deal that an extant structure like a brain increased in CCs threefold in 6 million years has been explained to you.

And the fact that the ERVs you myopically focus on and feign incredulousness with are not orthologous - as opposed to the ERVs that are orthologous and demonstrate a nested hierarchy indicative of common ancestry has been explained to you as well.

What's next, are you going to claim - again - that Au. species are bipedal ancestors of chimpanzees as you have in the past?

 

[Loudmouth]

I even had a chance to have a rather brief exchange with LMs source but the discussion quickly dissipated after he started repeating his argument, rather then defending it. Since some time in the 60s evolutionists have made the arguments that 'I can't find any differences' when comparing DNA sequences of Chimpanzees and Humans. The same argument is being made with regards to ERVs except that now, we know that there are hundreds of millions of differences in the respective genomes known as indels (insertions and deletions) which are really just huge sequences that are different.

The theory of evolution is a theory that explains how biological species CHANGE over time. How someone can point to differences and claim that this is evidence against evolution is beyond me since that is exactly what the theory sets out to explain.

Added in edit: In our previous discussion I used languages as an analogy, and it still works here. No one argues that French, Italian, and Spanish can not share a common ancestral language because of the differences in each language. Rather, it is the number of commonalities that evidences a common ancestor for these languages. It is expected that differences will accumulate in these populations over time which can result in the languages diverging to the point that the populations can no longer understand each other when they meet each other once again.

By far, the biggest and most significant difference regarding Human vs. Chimpanzee ERVs are the ERV class I. These PTERVs (Pan Troglodyte ERVs) is the single largest and most abundant class of ERVs in the Chimpanzee genome. There is one problem with it, there are virtually none in the human genome.

A lot of smoke and mirrors in this claim. There are about 200,000 ERV's in the human genome as shown in table 11 of the human genome paper:

Initial sequencing and analysis of the human genome : Article : Nature

When they sequenced the chimp genome they compared the ERV's in each genome and came up with this table:

(Initial Sequence of the Chimpanzee Genome, Nature 2005)​

This means that out of the 200,000 ERV's found in humans, only 5+77 for 82 insertions were not found in chimps. Of the ERV's found in chimps, only 234+45 for 277 ERV's were not found in humans. This means that the human and chimps genomes differ by less than 1% in ERV content. We share nearly 200,000 ERV's while only differing in a relative handful.

Even more, we can use the theory of evolution to make predictions about the genomic distribution of PTERV1/CERV1 insertions in the chimp and gorilla genomes. However, I don't want to spoil the fun so I will ask Mr. Kennedy (or other creationists) to tell us what predictions creationism makes. What should a comparison of PTERV1 insertions between chimps and gorillas show, and why?

The best way to win an argument with an evolutionist is to learn the actual facts. Evolutionists did a major victory dance when the ERV evidence first started being explored and they did the same thing when comparative genomics was on the rise. The commonality has been grossly overstated and when confronted with these facts evolutionists become indignant and repeat the same tired homology arguments.

The commonality is over 99%. Those are the facts. There are around 200,000 ERV's in the human genome, and only a few hundred differ between humans and chimps.

There is no null hypothesis for Darwinism, it never allows for or even considers, the inverse logic.

The null hypothesis is a lack of a phylogenetic signal for both orthologous and non-orthologous ERV's. That has always been the null hypothesis. Once again, creationists forget that it is the nested hierarchy that evidences evolution, and a nested hierarchy does incorporate lineage specific derived features.

More to the point, if things in common are valid arguments for common descent then are differences valid arguments for special, independent creation?

Violations of a nested hierarchy beyond that expected from incomplete lineage sorting would be an argument against evolution.

 

[Loudmouth]

What pattern, the largest and most abundant family of ERVs in the Chimpanzee genome being absent in the Human genome?

Why do you put so much importance on 200 or so PTERV1 insertions while ignoring the other 200,000? Why are 200 PTERV1 insertions occuring in the chimp genome since our lineages split a problem for the theory of evolution and common descent? Did we argue that retroviral insertions must stop after a speciation event? No. Why would they stop? Why would different lineages necessarily be infected by the same strains of retroviruses?

Your null hypothesis just doesn't make sense since it requires evolution to not occur. It also ignores the nested hierarchy.

If differences are a valid evidence of common decent are differences valid evidence for creation?

Differences are valid for lineages that are evolving from a common ancestor. Moreover, those differences should be lineage specific as predicted by the theory of evolution. Want to put that to the test? If the theory passes this test, will you accept evolution from a common ancestor as an accurate theory?

 

[Loudmouth]

Yea, we've discussed it all before, LM couldn't get his facts straight and not one of you knew enough to help him out. Yea, it's going to happen again and your going to throw out the first fallacious attack just to get the ball rolling. That's nice....

Then let's start with the facts. In Table 11 of the human genome paper, how many ERV's did they find in the human genome?

Initial sequencing and analysis of the human genome : Article : Nature

 

[Loudmouth]

Then explain this, 'PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon'

PtERV1 elements infected these species over the last few million years after the split between humans and chimps.

What did I tell you? I'm not arguing against evolutionary theory, just common descent. That's a key point you missed.

Then you should realize that lineage specific differences will accumulate in each lineage after they split from a common ancestor. This includes lineage specific ERV's. Do you know how they differentiate between ERV's inherited from the common ancestor and ERV's that are lineage specific?

What if the Gorilla has more in common genetically with the Chimpanzee then Humans? How does that fit into your theory.

Incomplete lineage sorting is expected, and in fact it is predicted. There will be some sections of DNA that are more similar between humans and gorillas, and this is due to the observed process of imcomplete lineage sorting. However, the overall phylogenetic signal still has chimps as our closest relative.

So you are aware of it and BTW, evolution isn't a theory, it's a phenomenon.

That phenomenon produces lineage specific differences, so why would you use these differences as evidence against two species evolving from a common ancestor?

At least the way you just defined it. Common descent isn't a theory either since there is no null hypothesis.

Lack of a phylogenetic signal is the null hypothesis.

ERVs being added to the germline is observable, that doesn't represent undeniable proof that 8% of the human genome is the result of them.

That is like arguing that fingerprints found at a crime scene were planted by Leprechauns to make it look like the defendant is guilty.

The facts are that the distribution of ERV's among primates is exactly what we would expect from a process of common ancestry followed by evolutionary divergence.

Actually Darwin proposed a null hypothesis for natural selection, remember what it was?

Yes. He stated that a species will not evolve an adaptation that is solely for the benefit of another species.

No, I'm just waiting on LM to make his comments. He is the one who asked me to post this here. We have discussed this previously but he can't post to the Origins Theology forum.

Many thanks to Mr. Kennedy for bringing the argument over here. I fully respect the rights of CF to keep a safe area for christians who do not want to argue with atheists. I asked Mr. Kennedy to move the discussion over here in a PM, and I wouldn't have hounded him if he had said no. So again, props to MK for being a good sport.

So common descent must be assumed and the inverse logic is never allowed. Got it.

Common descent is concluded from the observation of a nested hierarchy.

 

[NailsII]

After an estimated 6 million years of genetic seperation there are going to be differences - the entire structure of our Chromosome 2 is witness to that fact (which is a fact that I have never lnown a creationist to have an answer for).
Based on this one observtion, are you suggesting that the thousands of other ERVs found in the Pans & Homo genome are irrelevant?

How do you know it was 6 million years ago? Where are the chimpanzee ancestors in the fossil record since the split? I have never seen an evolutionist even try a substantive answer for that one.

You have answered a question with a question, so if you answer mine....

Nonsense.

But I think you are.
There are around 200,000 ERVs in the human and Pans genome, how can your conclusion ignore these?
Any sound conclusion must account for all the evidence, otherwise it is doomed to fail.

I understood fine, I think your the one who is misunderstanding.

I'm not so sure on that one, but we shall see.
I thought I was wrong once before, turns out I was just mistaken.

Of course you mean common descent.

Common descent is a consequence of evolution, which is an observable fact.
I don't think it is stretching our friendship too far to interchange these terms, as there is no evidence for evolution without common descent and common descent couldn't exist without evolution.

So we expect what we have in common with Chimpanzees, but the differences we explain away.

If there were no differences, we'd be the same species.
Can you see how this works?

The commonality of the DNA is 96% at best and that does not take into account chromosomal rearrangements.

So why is it not 99%?

Then explain this, 'PtERV1-like elements are present in the rhesus monkey, olive baboon and African great apes but not in human, orang-utan or gibbon'

Only if you can explain why a supernatural creator would design so many retroviruses in the first place.

What did I tell you? I'm not arguing against evolutionary theory, just common descent. That's a key point you missed.

But if evolution happens, you must have a common ancestor.
Your position is at best confused, at worst illogical.

What if the Gorilla has more in common genetically with the Chimpanzee then Humans? How does that fit into your theory.

If a whale is more closely related to a hippo than a hippo is to an elephant, does this fit into evolutionary theory?

I would be delighted to learn more about biochemistry. What kind of online reading would you recommend?

I actually said I would have to read up more, it wasn't an invitation to join me.
Sorry.

Thank you, notice how that is different from common ancestry?

So how can you have evolution with no common ancestors?

So you are aware of it and BTW, evolution isn't a theory, it's a phenomenon. At least the way you just defined it. Common descent isn't a theory either since there is no null hypothesis. It's really just a model the data is organized within.

Evolution by natural selection is a scientific theory, evolution is an observable fact.
Common descent is also a theory, and it does have a null hypothesis. If the data didn't fit into a neat little tree of life, common descent would fall on its ass.

They differ only with regard to scope. Universal common descent is transcendent, common descent is species, genus...etc,

Are you suggesting that common descent is possible, but only goes so far?
As this thread has been about evidence, I'm sure you can back this claim up with some.

Not a sin, an error. There's a big moral difference.

Only if sins really are immoral - but that is a discussion for another time and place.

Sure, it makes a lot of since to use ERVs are markers.

Exactly, and they vary more between less closely related individuals. Can you see where this leads to?

ERVs being added to the germline is observable, that doesn't represent undeniable proof that 8% of the human genome is the result of them.

So how do you think that they are classified as ERVs?
Do you think they just guess?

The same phenomenon repeated throughout human history. If you mean the biochemistry then I would expect the mutation rate to be within a safe parameter to explain the differences.

So how does this actually work with regards to ERVs?

Actually Darwin proposed a null hypothesis for natural selection, remember what it was?

He proposed several if memory serves, the most famous (and often incompletely quoted) describes how if a complex organ, like the eye, cannot be shown to have evolved by simple stages then the whole theory falls.
He also proposed a parallel for natural selection, do you know what he called it?

I have and I do.

So how can you falsify creationism?

I could come up with any number of hypothesis, the formal way scientists do inductive science seems to suggest them. There's one problem with that though:
"The number of rational hypotheses that can explain any given phenomenon is infinite."...The law is completely nihilistic. It is a catastrophic logical disproof of the general validity of all scientific method!. About this Einstein had said, "Evolution has shown that at any given moment out of all conceivable constructions a single one has always proved itself absolutely superior to the rest," ... to Phædrus... To state that would annihilate the most basic presumption of all science! Through...theories and hypotheses, it is science itself that is leading mankind from single absolute truths to multiple, indeterminate, relative ones...Scientifically produced antiscience...chaos.

(Zen and the Art of Motorcycle Maintanance)

So how do we tell them apart then?
for a theory to be useful, it must have some predictive power and fit the evidence.

Obviously I consider rejecting God's supernatural activities in creation a priori a mistake as well.

So you must have some evidence for them then?

No, I'm just waiting on LM to make his comments. He is the one who asked me to post this here. We have discussed this previously but he can't post to the Origins Theology forum.

No, I meant that by adding an unseen supernatural force you are adding something to the equation that doesn't need to be there (ie it works without it)

So common descent must be assumed and the inverse logic is never allowed. Got it.

Common descent is not assumed, it is evidenced.
The inverse logic is not supernatural by default, this is not a competition between two sides which could both be right, and even if yu could prove common descent to be on shaky ground, this is still not evidence for creationism or supernaturalism.

 

[Loudmouth]

You don't seem to appreciate the inverse logic of your argument.

I don't think you do either. ERV's found at orthologous positions are due to a single insertion that occurred in a common ancestor. ERV's found at non-orthologous positions are due to two insertions that occurred independently in each lineage. Therefore, if common ancestry did not occur then orthologous ERV's should be extremely rare (independent insertions occuring at the same spot can occur, but they are very, very rare). If common ancestry did occur and occurred in the recent past (say 5-10 million years ago), then we should find that most of the ERV's should be found at orthologous positions with only a few lineage specific insertions.

Guess what we find? We find that humans and chimps share about 200,000 ERV's at orthologous positions while only a few hundred are found at non-orthologous positions. Common ancestry is verified.

 

[Split Rock]

Against this background, it was surprising to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2) that are unlike any older elements in either genome; these must have been introduced by infection of the chimpanzee germ line. The smaller family (PtERV2) has only a few dozen copies, which nonetheless represent multiple (approx5–8) invasions, because the sequence differences among reconstructed subfamilies are too great (approx8%) to have arisen by mutation since divergence from human. (Initial Sequence of the Chimpanzee Genome, Nature 2005)​

So, Mark.. can you provide us with any reason to believe that these PtERV1 and PtERV2 elements were not introduced by infection after the split between humans and chimps?

One very important question needs to be addressed or the thread will become yet another personal attack, doomed to be buried in the stacks. Is the inverse logic to an homology argument intuitively obvious? More to the point, if things in common are valid arguments for common descent then are differences valid arguments for special, independent creation?

Differences are evidence for divergence or speciation. Not independent creation. Unless you are claiming that independent creation requires differences? I don't think you can, considering the argument I see so often from creationists here is that similarities are do to a common designer. The problem remains that Special Creation makes no predictions at all. Differences are do to Special Creation just as similarities are do to Special Creation.

 

[Loudmouth]

The funny part about creationists who cite the PtERV1/CERV1 paper is that they fail to understand how it evidences common ancestry and evolution. These insertions are actually very devastating to the creationist argument.

When it was found that there were several hundred CERV1 insertions in chimps and gorillas but not orangs and humans we can stop and make some very strong predictions right away using the theory of evolution and common ancestry. If these insertions occurred in the common ancestor of chimps and gorillas then we should find them in humans as well. We don't. Therefore, these insertions had to occur AFTER the human and chimp lineages split. This allows us to predict that these insertions will NOT be found at orthologous positions since independent insertions do not produce orthologous insertions. Only insertions inherited from a common ancestor produce orthologous ERV's, and the species distribution of CERV1 allows us to rule this out.

So what do we find? CERV1 insertions are NOT found at orthologous positions in chimps and gorillas JUST AS THE THEORY PREDICTS. Not only can the theory predict which ERV's should be found at orthologous positions, it can also be used to predict which insertions should not be found at orthologous positions.

Mark fails to understand that evolutionary theory predicts a nested hierarchy, and that pattern predicts a pattern for both non-orthologous and orthologous ERV's. Mark also fails to show how creationism can be used to explain this pattern of shared and unshared features. No creationist I have ever seen is able to explain why we find certain ERV's at the same location in multiple genomes while not finding others at orthologous positions. Evolution does explain this pattern, and it does so in a testable manner in accordance with the scientific method.

So creationists . . . please keep citing these CERV1 insertions. It allows us to once again show how evolution is the superior explanation.

 

[Loudmouth]

Going back to some specific claims made by MK.

By far, the biggest and most significant difference regarding Human vs. Chimpanzee ERVs are the ERV class I. These PTERVs (Pan Troglodyte ERVs) is the single largest and most abundant class of ERVs in the Chimpanzee genome.

MK is using the following paper for this claim:

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

So let's take a closer look. MK claims that PtERVs make up the largest family for all ERV's in the chimp genome. Is that what the paper says? NO!!!

The paper in question only looked at 425 full length ERV's. There are around 200,000 ERV's in the chimp genome. From the paper:

"Using the procedure described above, we identified a total of 425 full-length chimpanzee endogenous retroviruses. This is certainly an underestimate of the number of endogenous retroviruses in the chimpanzee genome because we consciously excluded any sequences that could not be unambiguously identified as an endogenous retrovirus."

All of the statements in the paper refer to this set of 425 ERV's, not to all ERV's in the genome. Those 425 full length ERV's did fall into 42 different families, and the PtERV's under question were the most abundant within this very, very limited data set.

At around 200 insertions, PtERV's only make up 0.1% of the total number of ERV insertions. Just 0.1%. MK is actually claiming that a difference of 0.1% somehow falsifies common ancestry, as if species are not allowed to acquire ERV's after a speciation event. As anyone can see, this is ridiculous.

 

[florida2]

Cue Mark ignoring this thread and pasting the OP into yet another thread in a few days.

If he actually comes back and responds to all these posts (and accepts their arguments) I'll be impressed.

 

[Loudmouth]

MK is not the only one misrepresenting the facts when it comes to ERV's. Other creationist sites do this as well. A great example is this site:

Do Shared ERVs Support Common Ancestry? - Evolution News & Views

First, they try to argue that orthologous insertions can be explained by insertion site preferences. What they fail to do is show that target site preferences can produce just a few hundred non-orthologous insertions out of 200,000 total insertions. All of the references they site only show very slight preferences that would produce independently inserted orthologous ERV's once in every few thousand insertions. More to the point, Wang et al. mapped around 40,000 HIV insertions and only found about 40 that inserted into the same spot more than once. So at best, we would expect 0.1% of orthologous ERV's to be produced by independent insertions. We would not expect 99.9% to insert into the same position.

The creationist website then takes a turn for the worse. They outright misrepresent the facts.

"Out of tens of thousands of ERV elements in the human genome, roughly how many are known to occupy the same sites in humans and chimpanzees? According to this Talk-Origins article, at least seven. Let's call it less than a dozen. Given the sheer number of these retroviruses in our genome (literally tens of thousands), and accounting for the evidence of integration preferences and site biases which I have documented above, what are the odds of finding a handful of ERV elements which have independently inserted themselves into the same locus?"
​

It doesn't get more dishonest than that. This article was published in 2011, 6 years after the chimp genome paper was published. There is simply no excuse for this complete failure of scholarship. There are hundreds of thousands of ERV's in the chimp and human genome, and only 0.1% of them are not found at the same position in each genome. There are hundreds of thousands of ortholgous ERV's, not less than a dozen. Sadly, this is the type of dishonesty that we have come to expect from creationist sites.

And then it gets worse . . . from the website:

We are (incorrectly) told that "There is only one, solitary known deviation of the distributional nested hierarchy; a relatively recently endogenized/fixed ERV called HERV-K-GC1."
This claim, however, is false.
In addition to the case mentioned, Yohn et al. (2005) report:

​

What follows is perhaps the best example of a dishonest creationist quote mine that I have ever seen. It is on par with the Darwin eye evolution quote mine. They use this quote mine to argue that there are orthologous PtERV1 insertions between various primates. Is that the case? First, let's take a look at the results found in the Yohn et al. paper. Their initial method was to break up the genome into big chunks and select for the big chunks that have PtERV1 insertions. These chunks are 100,000 to 200,000 base pairs, so they are pretty big. What did they find?

Within the limits of this BAC-based end-sequencing mapping approach, 24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous (Table S3). We classified these as “ambiguous” overlap loci (Figure 3). If all 24 locations corresponded to insertions that were orthologous for each pair, this would correspond to a maximum of 12 orthologous loci. The number of non-orthologous loci was calculated as 275/287 (275 + 12) or 95.8%.
​

With a really fuzzy resolution of about 100,000 base pairs only 5% were even close to being orthologous. What did they do next? They took advantage of the published genome sequencing for macaques and chimps. Here is a rather large quote from the paper with bolding on the important bits:

For the three intervals putatively shared between macaque and chimpanzee, we attempted to refine the precise position of the insertions by taking advantage of the available whole-genome shotgun sequences for these two genomes. For each of the three loci, we mapped the precise insertion site in the chimpanzee and then examined the corresponding site in macaque (http://www.ncbi.nlm.nih.gov). In one case, we were unable to refine the map interval owing to the presence of repetitive rich sequences within the interval. In two cases, we were able to refine the map location to single basepair resolution (Figures S4 and S5). Based on this analysis, we determined that the sites were not orthologous between chimpanzee and macaque. It is interesting to note that this level of refined mapping in chimpanzee revealed 4- to 5-bp AT-rich target site duplications in both cases. These findings are consistent with an exogenous retrovirus source since proviral integrations typically target AT-rich DNA ranging from 4 to 6 bp in length [24]. Although the status of the remaining overlapping sites is unknown, these data resolve four additional sites as independent insertion events and suggest that the remainder may similarly be non-orthologous. This apparent independent clustering of retroviral insertions at similar locations may be a consequence of preferential integration bias or the effect of selection pressure against gene regions, limiting the number of effective sites that are tolerated for fixation.
​

Nowhere in the paper did they find a single PtERV1 insertion that was unambiguously orthologous between any primate species, and yet this creationist site claims just the opposite, and uses quote mines to do it.

Creationists like to claim that they are working from the same evidence, but clearly they aren't. They distort and lie about the evidence. This creationist website is a perfect example of just that.

 

[Karl - Liberal Backslider]

Has it really been six years since I was last around here?

And so little has changed. Some of the faces are different, but the arguments are the same.

Loudmouth - excellent pwnage. It'll be interesting to see if Mark comes back with the same tired arguments again, because he's clearly too intelligent to not understand how he's been torn a new one here, so only dishonesty could underlie a restatement of his discredited argument. Time will, as always, tell.

 

[Split Rock]

Has it really been six years since I was last around here?

And so little has changed. Some of the faces are different, but the arguments are the same.

Loudmouth - excellent pwnage. It'll be interesting to see if Mark comes back with the same tired arguments again, because he's clearly too intelligent to not understand how he's been torn a new one here, so only dishonesty could underlie a restatement of his discredited argument. Time will, as always, tell.

Mark doesn't post as much here as he used to, but his posts haven't changed much. Still goes on about human brain size, too.

Welcome back, btw!

 

[Karl - Liberal Backslider]

Don't know how much you'll see me. I started looking over a few weeks ago and could hardly believe how the creationist contributions appear to have got even more hatstand than they used to be. Or maybe staying away from it for a while I'd forgotten just how completely potty it could get.

My main thrust these days is pointing out the dishonesty of the creationist machine - not the deluded followers we mostly see on here - but the people generating the crap they regurgitate, because I find it very hard to believe they don't know they're telling a bunch of porkies - professional LCWs (Lying Creationist Weasels) indeed. You'll never win by arguing the science because honest scientists have to stick to actual reality, whereas the LCWs can just pull whatever rubbish out of the smelly end of their alimentary canals suits their purpose. *Cough* human sunflower Cytochrome C *Cough* Duane Gish *Cough*

It's fun to be back for a while though. Don't know how long it'll last; sooner or later I point out to a LCW that he's a LCW and get banned for flaming

 

[Loudmouth]

whereas the LCWs can just pull whatever rubbish out of the smelly end of their alimentary canals suits their purpose. *Cough* human sunflower Cytochrome C *Cough* Duane Gish *Cough*

BULLFROG!!!!

 

[Karl - Liberal Backslider]

He does rather resemble one, so perhaps it's true of his proteins.

 

[Elendur]

BULLFROG!!!!

Thanks for the read. It makes me a bit sad though...

 

[Loudmouth]

Thanks for the read. It makes me a bit sad though...

It is a bit frustrating as well. It is one thing to come to different opinions based on the same facts. It is an entirely different thing to disagree on the facts. All too often, professional creationists like Gish lie about the facts. Perhaps at first they misspeak, or are just honestly mistaken. It happens to all of us. However, when they are shown their mistake in no uncertain terms and they still continue with same argument then they are lying. There is no way around it.

I hope that MK has the honesty and temerity to admit that he got the facts wrong. A good place to start would be the statements about the null hypothesis. ERV's are evidence for common ancestry because the fall into a nested hierarchy. This includes both orthologous and non-orthologous ERV's. It is the phylogenetic signal that evidences common ancestry. The null hypothesis is a lack of a nested hierarchy and phylogenetic signal. The null hypothesis is not nonorthologous ERV's. If MK could fix this one glaring error of fact in his argument then we could move forward to the other errors of fact.

 

[Loudmouth]

More info is never a bad thing . . .

People may also ask how we know that ERV's are from retroviruses. The most obvious answer is that the DNA sequence of ERV's match modern retroviruses. In full length ERV's we can find all of the hallmarks of a retrovirus, from the long terminal repeats to reverse polymerase. Everything a retrovirus needs is found in ERV's.

There is also some other very interesting evidence that ERV's are from retroviruses. Scientists have aligned several HERV-K insertions in order to produce a consensus sequence which is a sequence based on the "majority vote" at each base. For example, if 20 of 30 insertions have an T at a specific base then you put a T in the consensus sequence. This process will remove a lot of the mutations that have built up in the ERV's since insertion and also give us a sequence that will best resemble the ancestor of those sequences. When they constructed this concensus sequence guess what they got? A functional retrovirus.

This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny.
Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements
​

I have also seen some creationists argue that ERV's are producing retroviruses. They claim that mutations build up in ERV's which then make them into retroviruses. IOW, they claim the opposite of what biologists are claiming. Phoenix refutes this argument. If you don't understand how genetics works this may be difficult to understand, but I will try to explain why this is.

The creationist idea is that new mutations cause ERV's to become retroviruses. Therefore, the most divergent sequences (those with the most mutations) should be the closest to becoming retroviruses while the least divergent sequence should be inert. What do we see with Phoenix? Just the opposite. The consensus sequence produces an infectious retrovirus. The consensus sequence removes divergence and mutations. If the creationist idea was correct then the consensus sequence should have the least chance of producing a retrovirus, and yet it does. The idea that ERV's are the product of retroviral insertion is strongly supported by the work done with Phoenix.