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Another poor response to ERV evidence for common ancestry by a creationist.

Zaius137

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Reply for Blayz…

Sorry I am back so late with this, please excuse me, Blayz needs a reality check.

“They are absolutely in disagreement with the facts. LTRs are entirely derived from virus sequence, and both termini are the same upon insertion. We can therefore use the independent evolution of the LTRs as a measure. Examining these regions for mutational changes to support common ancestry is entirely valid.”

OK…Then leave the LTRs attached instead of having to remove them when building the phony HERV-K con. OOPs they must be removed because they are in the wrong configuration… Why is that? Maybe because the lead LTR is turned around when constructed by reverse transcriptase. What do you think?


“In both cases, LTR sequences evolved in sequence independently from, and obviously more rapidly than, the proviral bodies. Reasons for apparently different evolutionary rates of LTRs and proviral bodies are currently not clear.”

“This is the only valid observation you have made so far”.

So your explanation is?


“In the case of HERV-k it is claimed that the infection happened just after the chimp human divergence and continued up until 100,000 years ago. That is on the order of about 5 million years according to the tale. You literally have an ape like hominid turn into a human but the HERV-k stays literally intact, enough so as to be put back together???”


What's the problem? The difference between chimp and human is ~5%. Since the virus is sitting in the genome, why wouldn't it be intact if it has only diverged 5% ?

Does the core virus really show ~5% variance? For argument sake lets say they do even though you can reconstruct a supposed virus from a consensus.

Now your ~5% would be expected since your figure of ~5% chimp human variance (another argument altogether because I think it is higher) but where is all the other variances from the active retrovirus infection times.

How can you trivialize the lack of mutations in the retrovirus over long periods of time with a mutation rate hundreds of times if not thousands of times that of supposed evolution? What about the outrageous time frames between those supposed infection times (Orders of millions of years) but only 10 families of HERV-Ks were identified. I really like your argument against evolution in the following..

“Because there is a limit to the amount of mutation that can be borne before the element loses functionality,”

But the HIV seems to get along fine with its high mutation rate.

Then you say…

the same reason we can identify similar genes between humans and bacteria. You don't need to tell me the virus mutates rapidly. Unlike you I have actually sequenced HIV samples. You know, done actual work rather than whinging about other people's on a public forum.

Yes but as you can see humans and bacteria are defiantly different species.

“The GaG, PoL, and EnG still look like the HERV-K. So your telling me that a ape like hominid changed into a modern human”

“As the result of a 5% change, give or take”

Is it 5%? It should be much, much higher. A different genus of virus, maybe even a speciation event…wait a minute according to creationism a virus must stay a virus (observed).

“What do you want it to turn into, an elephant? The virus mutates around a mean. I daresay you are forgetting the selection part of the equation again.”

Maybe a human mutates around a mean? No I am not forgetting selection it is real but does not cause a speciation event.

“If you can still say that ERV’s support evolution I can still say you are nuts.”

“ERVs support evolution. Your incredibly low incredulity threshold is not a yardstick by which we measure reality.”

Neither is the fairytale of evolution…
 
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Zaius137

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Blayz… You’re mean…

Mark understands the meaning of the word homology. You do not. Homology in the biological sense means quite literally "related by descent". Related by descent is the opposite argument to common design.

From creation Wiki…

“In contrast, creationists view most "homologous" structures as a reflection that they were designed by the same creator. It is held that a brilliant and well functioning design would be applied to multiple organisms, much in the same way as human designers apply concepts.”

Man I am glad I did not buy all that evolution crap in school… I guess some people did.
 
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Zaius137

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Mark…

“You are not arguing from science, you are and have always argued from presumption claiming fullfilled predictions that were never made and homology arguments that never deliver real world molecular mechanisms involved in major morphological innovations.”

I am sorry but I would not like to face your logic if it existed from the evolutionist stand point… simply brilliant.
 
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Zaius137

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LoudMouth…

What you don't seem to appreciate is that your homology argument is that you have to be ready to concede the divergence that undermines your anticipated commonality.

Zaius claims just the opposite. You guys need to get together and form a consistent argument.

Actually Mark’s argument is one I have already taken up but he is doing a better job of it. My current argument does not concern homology at all but disputes the premise of long term infections from a unobserved agent. I am focused on the HERV-K and those particular to events after the supposed divergence.
 
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mark kennedy

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Mark…

“You are not arguing from science, you are and have always argued from presumption claiming fullfilled predictions that were never made and homology arguments that never deliver real world molecular mechanisms involved in major morphological innovations.”

I am sorry but I would not like to face your logic if it existed from the evolutionist stand point… simply brilliant.

The fact of the matter is not one of them believe they have to find a molecular mechanism responsible for an adaptation. When you are talking about an adaptation on an evolutionary scale there is even less interest. Most of them have no real interest in science, the vast majority is just here to hurl insults and hide behind pithy clutch phrases.

I really don't lose a lot of arguments around here, not because I'm brilliant but because the evolutionist has no intention of making substantive points. I enjoy your posts, keep digging.

Grace and peace,
Mark
 
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Blayz

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Reply for Blayz…

Sorry I am back so late with this, please excuse me, Blayz needs a reality check.

Well I popped over the border to Malaysia for sea food, beer and fire works, and this thread has moved on beyond my interest in reading up, so I wont be back in the short term. Tomorrow back in reality and I'll be doing some evolutionary biology....you know, rather than whinging about other people's

And I'm the one that needs the reality check ^_^^_^^_^

 
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Zaius137

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Hey Blayz while you’re working with “evolutionary biology” you and your buddies should sit down have a beer and maybe come up with an molecular mechanism for adaptive evolution. What you are doing is like putting on a new suit before it is sewn together. There is a fairytale about an emperor with those kinds of new clothes. Evolution is naked and begging a mechanism.
 
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Blayz

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me said:
Homology in the biological sense means quite literally "related by descent".


Z said:
From creation Wiki...

Too funny. I give not a tinker's cuss what fantasy meaning creationists attach to words. I didn't say "homology in the creationist sense", I said "biological".

Hey Blayz while you’re working with “evolutionary biology” you and your buddies should sit down have a beer and maybe come up with an molecular mechanism for adaptive evolution.

Yeah, relying on Mark for arguments...not a great idea. We have a mechanism, it's called mutation with natural selection. Interestingly it applies to the entirety of evolution, not just the adaptive part.

Had a good day. Looks like the cross species homology studies have identified an anti cancer target.

Back to Z for more whinging about other people's work.
 
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Zaius137

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Evidently you did not understand what was said. It is a “Molecular mechanism for evolution”. The following article is to the point.

http://www.uchospitals.edu/news/1998/19981126-hsp90.html


This mechanism seems like it must have evolved over time. How can that be if it “is” the molecular mechanism for evolution? Maybe another simpler mechanism caused this mechanism? A real mechanism must be simple and natural, this system does not seem to fit either description.

Look at what they found… Fruit flies changed into another species; wait a minute that’s not right the fruit flies remained fruit flies… That is what always have been found, fruit flies with as many as 400 confirmed mutations exist (40 years has proven that no real speciation has taken place). Well I guess they need more research money. Maybe one of these days this money for such ridiculous research will dry up. Who is supporting your research?
 
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Naraoia

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Aw, you so walked into this...

I can't believe Mark is still on about PTERV-1.

Loudmouth said:
Mark understands the meaning of the word homology. You do not. Homology in the biological sense means quite literally "related by descent". Related by descent is the opposite argument to common design.
To be fair, the term wasn't originally coined in the context of common descent. Of course, that was like two centuries ago...

Common ancestry is untestable and unfalsifiable...
O RLY? Would you still say that if, say, humans and chimps used vastly different genetic codes?

Hey Blayz while you’re working with “evolutionary biology” you and your buddies should sit down have a beer and maybe come up with an molecular mechanism for adaptive evolution.
The fact that you demand "a" mechanism shows that your sense of scale is way out of kilter.

I'll tell you a secret. "Adaptive evolution" is a very general umbrella term. It includes everything from minor mutations in single genes (examples: malaria-resistant and high-altitude haemoglobin variants) to major phenotypic changes with a complex genetic basis (example: pick pretty much any major innovation in the history of life).

The only mechanism that is common to everything we call "adaptive evolution" is natural selection. But the processes that can generate or bias variation or influence the outcome of selection are quite diverse. Mutations fixed by genetic drift or genetic hitchhiking can pave the way towards adaptive changes (a digital example). Fitness-changing mutations can occur in genes, introns and UTRs, enhancers/insulators etc., and each of these will have different effects. Pleiotropy and other sorts of constraints can channel variation in particular ways. Epigenetics can influence how genetic variation is made visible to selection. Horizontal gene transfer/hybridisation can provide fresh variation that might have been unlikely to evolve in that lineage. All of these, and probably more that I forgot to mention, are potential mechanisms of adaptive evolution.

And given that

- there are 10-20k genes in your typical animal genome
- these encode a huge variety (in terms of sequence, structure and function) of proteins and RNAs
- many if not most of the proteins exist in several different splice isoforms
- AND are often subject to post-translational modifications
- AND there is shiploads of regulatory DNA that can have big effects on what genes do

... and all these buggers interact...

Why exactly should there be "a" molecular mechanism for adaptive evolution? It is far more likely that different systems, different pathways, different types of gene regulatory networks will adapt in different ways. We can talk about some generalities (e.g. the cis-regulatory vs. coding sequence debate in evo-devo), and we can analyse specific cases of adaptive evolution, but asking for "a" mechanism of adaptive evolution is a little... naive, shall we say.
 
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Naraoia

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Evidently you did not understand what was said. It is a “Molecular mechanism for evolution”. The following article is to the point.

http://www.uchospitals.edu/news/1998/19981126-hsp90.html


This mechanism seems like it must have evolved over time. How can that be if it “is” the molecular mechanism for evolution? Maybe another simpler mechanism caused this mechanism? A real mechanism must be simple and natural, this system does not seem to fit either description.

Look at what they found… Fruit flies changed into another species; wait a minute that’s not right the fruit flies remained fruit flies… That is what always have been found, fruit flies with as many as 400 confirmed mutations exist (40 years has proven that no real speciation has taken place). Well I guess they need more research money. Maybe one of these days this money for such ridiculous research will dry up. Who is supporting your research?
Newsflash: speciation and adaptive evolution are different things. You can have (allopatric) speciation by neutral drift, and you can have plenty of adaptation without speciation.

Oh, and "fruit fly" is a lot of species...

You need to work on your basics before you can start making demands, is all I'm saying.
 
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Naraoia

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Also, Zaius, let's get a reality check on the time scales involved. According to this handy manual, the generation time of Drosophila melanogaster ranges from 7 to 19 days depending on temperature. Since we're talking lab flies, we might assume around 10 days at a comfortable, balmy twenty-few degrees C.

That is less than 40 generations a year.

40 years translate to approximately 1500 generations.

Converted into human generations, that takes us back to, oh wait, around the time modern humans reached Europe and got busy screwing Neandertals in more than one sense of the word.

That's not that long, is it?
 
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Zaius137

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Naraoia…


“ Newsflash: speciation and adaptive evolution are different things. You can have (allopatric) speciation by neutral drift, and you can have plenty of adaptation without speciation.”

Mark must correct me if I am off base here. Aren’t we talking about the “molecular mechanisms”, the adaptive evolution must have a mechanical molecular basis for changing the organism. If you look at my citation this may help.

“Oh, and "fruit fly" is a lot of species...”

Yes, but none have ever been seen to change from one species to another by mutation.


“You need to work on your basics before you can start making demands, is all I'm saying.”

I demand nothing here… just that it stay intellectually honest. I do tend toward sarcasm occasionally but try and not make it personal.


“That is less than 40 generations a year.”

40 years translate to approximately 1500 generations.

Converted into human generations, that takes us back to, oh wait, around the time modern humans reached
Europe
and got busy screwing Neandertals in more than one sense of the word.”

That's not that long, is it?

If you are comparing the plight of fruit flies to that of humans; I don’t think you can say our species has been deliberately subjected to ionizing radiation, chemical mutagens or selective cross breeding in the same way. Unless you live in Los Angeles California.
 
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Loudmouth

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OK…Then leave the LTRs attached instead of having to remove them when building the phony HERV-K con. OOPs they must be removed because they are in the wrong configuration… Why is that? Maybe because the lead LTR is turned around when constructed by reverse transcriptase. What do you think?


Then didn't leave them out. They replaced the HERV-K LTR's with the LTR's from a different virus because of cell line specific expression problems.

Additionally, because the HERV-K LTR promoter is extremely weak in 293T cells (unpublished data), we replaced U3 sequences 5′ to the TATA box with corresponding sequences from the promoter/enhancer of CMV.
PLoS Pathogens: Reconstitution of an Infectious Human Endogenous Retrovirus

Now your ~5% would be expected since your figure of ~5% chimp human variance (another argument altogether because I think it is higher) but where is all the other variances from the active retrovirus infection times.


Perhaps you could cite these figures instead of claiming that there is no change?

How can you trivialize the lack of mutations in the retrovirus over long periods of time with a mutation rate hundreds of times if not thousands of times that of supposed evolution?

You have not shown a lack of retroviral evolution, and you have also ignored the effect of selection on the mutation rate. We are talking about a very small genome. The smaller the genome the more stringent the selection.

What about the outrageous time frames between those supposed infection times (Orders of millions of years) but only 10 families of HERV-Ks were identified. I really like your argument against evolution in the following..

Please cite any data showing that there should be more than 10 families.

But the HIV seems to get along fine with its high mutation rate.

Why don't you cite the sequence diversity for HIV and compare it to HERV-K?

No I am not forgetting selection it is real but does not cause a speciation event.

Evidence please.


Neither is the fairytale of evolution…

Ignoring the evidence is not helping your argument.
 
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Loudmouth

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Evidently you did not understand what was said. It is a “Molecular mechanism for evolution”. The following article is to the point.

http://www.uchospitals.edu/news/1998/19981126-hsp90.html

Let's see what the article says:

"The mechanism works by allowing multiple small genetic variations to accumulate and then expose themselves when that organism is under environmental stress."

So mutations build up and then are expressed, and the beneficial genetic variants are selected for. Hmmm, sounds like mutation and selection to me, the very mechanism that has been put forward for 70 or so years now.

A real mechanism must be simple and natural, this system does not seem to fit either description.

There is nothing requiring simplicity.

Look at what they found… Fruit flies changed into another species; wait a minute that’s not right the fruit flies remained fruit flies…

Look at what you are complaining about . . . Apes changed into another species; wait a minute that's not right the apes remained apes . . .

Humans are apes. Chimps are apes. Their common ancestor was an ape. So where is the problem?

That is what always have been found, fruit flies with as many as 400 confirmed mutations exist (40 years has proven that no real speciation has taken place). Well I guess they need more research money. Maybe one of these days this money for such ridiculous research will dry up. Who is supporting your research?[/quote]
 
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Loudmouth

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“In contrast, creationists view most "homologous" structures as a reflection that they were designed by the same creator. It is held that a brilliant and well functioning design would be applied to multiple organisms, much in the same way as human designers apply concepts.”

Man I am glad I did not buy all that evolution crap in school… I guess some people did.

This doesn't explain why homologous structures, be it DNA sequence or phenotypes, should fall into a nested hierarchy. If three middle ear bones are such a wonderful design for bats then why don't we see them in birds? If feathers are such a wonderful design for birds then why don't bats have them? Why do adaptations fall into a nested hierarchy, something that no designer is limited to?

Common design fails to explain the pattern of homology between species. Period.

Also, Linnaeus used homology to organize life into the taxonomy that many of us are familiar with. He did this without assuming common ancestry. Homology and common ancestry are two different conclusions. Like I have said in other threads, if birds had a middle ear homologous to that in bats then this would disprove common ancestry. It is the pattern of homology that evidences evolution, not just the presence of homology.
 
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Loudmouth

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The fact of the matter is not one of them believe they have to find a molecular mechanism responsible for an adaptation.

Compare the human and chimp genomes. The parts of the sequence that are identical were inherited from a common ancestor. The parts that are different are lineage specific mutations that have lead to adaptations in each lineage (ignoring the neutral changes). That is the mechanism.

When you are talking about an adaptation on an evolutionary scale there is even less interest. Most of them have no real interest in science, the vast majority is just here to hurl insults and hide behind pithy clutch phrases.

I have a lot of interest in it. The problem is that you ignore it.

I really don't lose a lot of arguments around here, not because I'm brilliant but because the evolutionist has no intention of making substantive points.

Plenty of substantative info in my previous posts that you have yet to reply to, such as PTERV-1 insertions. I see that you have suddenly avoided this discussion when it became apparent that no only are PTERV-1 insertions not a problem for the argument, but are actually confirmation of the argument.
 
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Naraoia

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Naraoia…


“ Newsflash: speciation and adaptive evolution are different things. You can have (allopatric) speciation by neutral drift, and you can have plenty of adaptation without speciation.”

Mark must correct me if I am off base here. Aren’t we talking about the “molecular mechanisms”, the adaptive evolution must have a mechanical molecular basis for changing the organism. If you look at my citation this may help.
Define "changing the organism". Full-fledged bithorax flies are quite obviously changed from their wild type ancestors, and this can be traced back to a few mutations affecting their Hox genes. They are still Drosophila melanogaster. (Bithorax type mutations are not exactly adaptive, but the change they reverse - converting the hind wings into halteres - was a pretty nifty trick at the origin of the Diptera)

And as I said, going from DNA to phenotype is a long and complex journey. A lot of the molecular mechanism of adaptation is bound to be specific to each individual adaptation.


“Oh, and "fruit fly" is a lot of species...”

Yes, but none have ever been seen to change from one species to another by mutation.
You started by asking for a molecular mechanism for adaptive evolution. Now it's "changing one species to another". I told you the two are not the same. Are you interested in adaptive evolution or speciation? Decide, please.

(FWIW, I'm 100% that several breeding/evolution experiments achieved some degree of reproductive isolation between fruit fly populations. Since that's practically the definition of speciation, "another species" is probably not what you're really interested in. In the unlikely event that I'm mistaken, there is a pretty extensive list of observed speciation events on TalkOrigins...)

I demand nothing here… just that it stay intellectually honest. I do tend toward sarcasm occasionally but try and not make it personal.
I don't see a problem with Loudmouth's intellectual honesty.

If you are comparing the plight of fruit flies to that of humans; I don’t think you can say our species has been deliberately subjected to ionizing radiation, chemical mutagens or selective cross breeding in the same way. Unless you live in Los Angeles California.
What experiment subjected flies to any of these for 40 years? Not the Hsp90 study that you linked, based on the information presented in that article. (For that matter, you certainly didn't get the 40 year figure from that article, so where does it come from?)

A final note on the Hsp issue: Hsp90 is a very ancient protein. It was there before anything resembling animals, let alone fruit flies. And proteins have been misfolding and denaturing for as long as they existed. So hsp-dependent unmasking of cryptic variation didn't specifically have to evolve. It's a by-product of an ancient survival mechanism.
 
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Blayz

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Aw, you so walked into this...

I can't believe Mark is still on about PTERV-1.

Really? I'd have trouble believing he was on about anything else. Anyway, since PtERV is not in the human lineage, it hardly counts.

As for the rest of your post: Nice explanantion, but it is a bit pearls before swinish.
 
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Zaius137

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LoudMouth…


“In both cases, LTR sequences evolved in sequence independently from, and obviously more rapidly than, the proviral bodies. Reasons for apparently different evolutionary rates of LTRs and proviral bodies are currently not clear.”

From Blayz…
“This is the only valid observation you have made so far”.

Still no responses on this… want to toss in your two cents. There should be no reason for the lower mutation rates in proviral bodies except maybe they hold more importance than just being fossil infections.


Now your ~5% would be expected since your figure of ~5% chimp human variance (another argument altogether because I think it is higher) but where is all the other variances from the active retrovirus infection times.


Perhaps you could cite these figures instead of claiming that there is no change?


I did not claim ~5% Blayz did. There should be massive changes in the retrovirus which is not observed in the proposed infections of HERV-K because as I noted earlier the mutation/ evolution rate is enormous…

“Thus, oncogenes seem to exemplify a general feature of genome evolution: the rate of evolution of RNA genomes can be more than a million times greater than that of DNA genomes because of a high mutation rate in the RNA genome.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC397963/


How can you trivialize the lack of mutations in the retrovirus over long periods of time with a mutation rate hundreds of times if not thousands of times that of supposed evolution?


“You have not shown a lack of retroviral evolution,” and you have also ignored the effect of selection on the mutation rate. The lack of evolution is?


“Reasons for apparently different evolutionary rates (faster) of LTRs and proviral bodies are currently not clear.”

I guess not clear…

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479102/?tool=pubmed




What about the outrageous time frames between those supposed infection times (Orders of millions of years) but only 10 families of HERV-Ks were identified. I really like your argument against evolution in the following..


Please cite any data showing that there should be more than 10 families.


“ Phylogenetic analysis of HERV reverse transcriptase sequences have identified 10 HERV-K families in the human genome which were termed human MMTV-like (HML-1 to HML-10) because of homologies to the betaretrovirus mouse mammary tumor virus (MMTV) (1, 32). Repbase Update also lists 10 HERV-K families.”

That is what has been found… You can explain why there should not be more than 10 families… And a retrovirus can have an evolution rate 1 million times faster than DNA.

Chimp human divergence time ~5 million years so retrovirus evolution time would be 5 million times 1 million ~ 5x10^12 years or about a thousand times the age of the universe according to the Big Bang. Again:

“Thus, oncogenes seem to exemplify a general feature of genome evolution: the rate of evolution of RNA genomes can be more than a million times greater than that of DNA genomes because of a high mutation rate in the RNA genome.”

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC397963/





Neither is the fairytale of evolution…
Ignoring the evidence is not helping your argument.

That’s right ignoring the evidence is a trait of evolutionists.

 
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