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Author Topic:   ERV's: Evidence of Common Ancestory
pcver
Junior Member (Idle past 5101 days)
Posts: 22
From: Sydney, Australia
Joined: 03-30-2009


Message 76 of 166 (504657)
04-01-2009 7:51 AM
Reply to: Message 71 by Taq
03-31-2009 10:37 AM


Re: Poking fun at Goliath
DrAdequate said: "..."Omphalos" argument --- God might have made everything to look like the Earth was old, species evolved..."
I have no reason to believe such explanations. I do not believe God deliberately tricks his creations.
DrAdequate said: "it would hardly explain why there are any ERVs in any eukaryote genome in the first place"
I believe that is part and parcel of lifeforms at such a microscopic level. There are useful ERVs and 'useless' ERVs are unavoidable.
WoundedKing said: "I'm not sure I understand exactly what you mean by 'the mean period between two ERVs in the same apes',....I don't think there is any way to judge that period."
Earlier, Shalamabobbi answered my question by saying: "So 30,000 divided by 6,000 years = 5 ERVs per year entering the human genome for creationists!"
I agree with your sentiment and I shall not bother seeking an answer for now.
So it seems you agree with Taq that all human/apes do not have the same ERVs among the same species.
Taq said: "There are hundreds of thousands of ERV's in the human genome. Only a handful are not fixed in the population.
I notice you repeated "hundreds of thousands". Earlier Shalamabobbi claimed there are approx 30,000 different retroviruses in the human genome. That's a lot less than "hundreds of thousands".
Only a handful of ERVs accounts for differences between all human? How about assuming just 3 ERVs, (and calling them 'a,b,c')? Assuming equal probability, theoretically it is possible to divide world population into 8 distinct ERVs grouping. Everyone within the same group have exactly the same ERVs, like so:
Group 1: lack of 'a,b,c' ERVs
Group 2: a
Group 3: a b
Group 4: a b c
Group 5: a c
Group 6: b
Group 7: b c
Group 8: c
Would apes population be similar? (Bluescat48 would think so, won't he?)
This would no doubt complicate apes/human descendency, won't it? Which ERVs-group of apes might have descended into human?
Please don't be mistaken. I am not being facetious. Thank you for your answer but I would like to find out if this is the current undisputed scientific finding. Anyone agrees/disagrees with what are presented so far?
Also....
DrAdequate, I disagree with that 'proof' word. Evidence does not equate proof.
Taq said: "Theories are never proven"
Errr...I kind of disagree. DrAdequate for one claims evolution as 'proven', (but I disagree with him).
How about I say - Nothing that evolutionary biologists put forward has ever been proven, or will ever be proven
Taq said:"As for ERV's, the theory of evolution predicts three things..."
I'd like to re-visit your points later.

This message is a reply to:
 Message 71 by Taq, posted 03-31-2009 10:37 AM Taq has replied

Replies to this message:
 Message 77 by RAZD, posted 04-01-2009 8:14 AM pcver has not replied
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 Message 79 by shalamabobbi, posted 04-01-2009 11:15 AM pcver has not replied
 Message 80 by Taq, posted 04-01-2009 12:26 PM pcver has replied
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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 77 of 166 (504661)
04-01-2009 8:14 AM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Re: Poking fun at Goliath
Welcome to the fray, pcver,
DrAdequate said: "..."Omphalos" argument --- God might have made everything to look like the Earth was old, species evolved..."
There's this cute little dBCode you can use:
type [qs]quotes are easy[/qs] and it becomes:
quotes are easy
type [qs=RAZD]quotes are easy[/qs] and it becomes:
RAZD writes:
quotes are easy
or type [quote]quotes are easy[/quote] and it becomes:
quote:
quotes are easy
Everyone within the same group have exactly the same ERVs, like so:
Group 1: lack of 'a,b,c' ERVs
Group 2: a
Group 3: a b
Group 4: a b c
Group 5: a c
Group 6: b
Group 7: b c
Group 8: c
Would apes population be similar?
I believe the point is not ERV's since chimp\human split, but the ERV's that are common to all humans and all chimps.
How do you explain these common ERV's when they serve no purpose to either group?
So it seems you agree with Taq that all human/apes do not have the same ERVs among the same species.
Each group has picked up new ERV's since they split from the common ancestor population/s, but they all still carry common ERV's that they inherited from the common ancestor population/s.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 76 by pcver, posted 04-01-2009 7:51 AM pcver has not replied

  
Jazzns
Member (Idle past 3911 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 78 of 166 (504672)
04-01-2009 11:12 AM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Re: Poking fun at Goliath
Assuming equal probability, theoretically it is possible to divide world population into 8 distinct ERVs grouping. Everyone within the same group have exactly the same ERVs, like so:
Group 1: lack of 'a,b,c' ERVs
Group 2: a
Group 3: a b
Group 4: a b c
Group 5: a c
Group 6: b
Group 7: b c
Group 8: c
Would apes population be similar? (Bluescat48 would think so,
won't he?)
You have the situation completely wrong. What provides the proof of common ancestry are the ERVs that are in fact fixed in the populations.
Try this analogy instead for ERVs a, b, c, for a very linear simplification of evolution.
Monkeys: a, ...(other monkey only ERVs)
Gorillas: a, b, ...(other gorilla only ERVs)
Chimps: a, b, c, ...(other chimp only ERVs)
Humans: a, b, c, ... (other human only ERVs)
The result of comparing the similarities would create a nested heirarchy which is not something that you would expect unless the ERVs were the result of heredity.
Change a, b, and c from representing a single ERV to an entire class of ERVs that those species share and suddenly the evidence is overwhelming in favor of common ancestry.

If a nation expects to be ignorant and free, in a state of civilization, it expects what never was and never will be. --Thomas Jefferson

This message is a reply to:
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shalamabobbi
Member (Idle past 2849 days)
Posts: 397
Joined: 01-10-2009


Message 79 of 166 (504673)
04-01-2009 11:15 AM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Re: Poking fun at Goliath
pcver writes:
How about I say - Nothing that evolutionary biologists put forward has ever been proven, or will ever be proven
Here are some video summeries of logical fallacies. I believe yours is found in the 2nd, if memory serves. Lack of absolute proof does not mean that something for which the evidence is say 99%, proves the opposite since it isn't 100%. That one is called false dichotomy. It's in the videos as well.
https://www.youtube.com/watch?v=zW8uO2P-YNE
https://www.youtube.com/watch?v=NWNILsqpNqk&feature=related
https://www.youtube.com/watch?v=trZBXuP3kIs&feature=related

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 80 of 166 (504676)
04-01-2009 12:26 PM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Re: Poking fun at Goliath
Taq said: "There are hundreds of thousands of ERV's in the human genome. Only a handful are not fixed in the population.
I notice you repeated "hundreds of thousands". Earlier Shalamabobbi claimed there are approx 30,000 different retroviruses in the human genome. That's a lot less than "hundreds of thousands".
I get this from the chimp and human genome papers (these are large .pdf's so be warned if you are on dial up).
The human genome paper:
http://www.nature.com/...journal/v409/n6822/pdf/409860a0.pdf
The chimp genome paper:
http://www.nature.com/...rnal/v437/n7055/pdf/nature04072.pdf
In Table 11 on pg. 880 of the human genome paper it states that there are 112,000 ERV-class I insetions, 8,000 ERV(K)-class II insertions, and 83,000 ERV(L)-class III insertions for a total of 203,000 ERV's in the human genome.
In Table 2 on page 75 of the chimp genome paper it lists the species specific ERV's, those ERV's that are not shared between humans and chimps. Chimps have 279 ERV's that are not found in humans and humans have 82 ERV's not found in chimps. This would mean that the bulk of ERV's found in humans (203,000) are also found in chimps.
As for ERV's that are not found in all humans, these are a tiny, tiny minority. I am only aware of a handful of such ERV's, such as this one:
quote:
Neurosci Lett. 2006 Nov 20;408(3):226-9. Epub 2006 Sep 26.
Insertional polymorphism of endogenous retrovirus HERV-K115 in schizophrenia.
Otowa T, Tochigi M, Rogers M, Umekage T, Kato N, Sasaki T.
Department of Neuropsychiatry, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo 113-8655, Japan.
Retroviruses are implicated in the pathogenesis of schizophrenia. Human endogenous retrovirus type K115 (HERV-K115) is a full-length, potentially transcriptional retrovirus and is also polymorphic. We investigated the frequency of HERV-K115 in Japanese schizophrenia patients and healthy controls. No difference was found in the frequency between patients and controls (8.4% versus 9.4%, respectively). However, a marginal difference was observed in age at onset between the HERV-K positive and negative patients (p=0.057). The HERV-K115 insertion appeared to be more frequent in patients with younger onset than those with later onset. These results preliminarily suggest that HERV-K115 may not be associated with schizophrenia in general, but that it could play a partial role in early precipitation of the disease.
It is also interesting to note that these polymorphic ERV's are HERV-K's, the retrovirus that has been active since our split from the chimpanzee lineage.

This message is a reply to:
 Message 76 by pcver, posted 04-01-2009 7:51 AM pcver has replied

Replies to this message:
 Message 83 by pcver, posted 04-02-2009 10:10 AM Taq has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 81 of 166 (504679)
04-01-2009 1:07 PM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Omphalos
I believe that is part and parcel of lifeforms at such a microscopic level.
Why do you believe that?
There are useful ERVs and 'useless' ERVs are unavoidable.
But why should it be "unavoidable" for an all-wise and all-knowing creator to supply his creations with genetic material which is of no use ... that is, no use except as evidence for evolution? Why should it be "unavoidable" for him to write on our genomes one vast and superfluous lie? Is there really no other way to make a man?
If you cannot demonstrate that the evolutionary pattern of ERVs is also a prediction of the creationist hypothesis, then you are just using God as an ad hoc argument, as in the following exchange:
Evolutionist : John Smith's fingerprints are on this gun, proving that he handled it.
Creationist : It proves no such thing. God might have put them there.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
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shalamabobbi
Member (Idle past 2849 days)
Posts: 397
Joined: 01-10-2009


Message 82 of 166 (504684)
04-01-2009 2:18 PM
Reply to: Message 76 by pcver
04-01-2009 7:51 AM


Re: Poking fun at Goliath
pcver writes:
I notice you repeated "hundreds of thousands". Earlier Shalamabobbi claimed there are approx 30,000 different retroviruses in the human genome. That's a lot less than "hundreds of thousands".
Also, showing that two sources of information disagree about the amount of data, because one source is more up to date than the other or one is in error, does not disprove the argument supported by that data.
Now that the number of ERVs is greater than my source claimed, my argument is even stronger - that 6,000 years is insufficient for ERVs to be explained by YECs.
And if you are an OEC it does nothing to explain why or how the same ERVs got into the same locations in two distinct genomes.
Edit:
So is it true? You can lead a creationist to data, but you can't make him think.
Edited by shalamabobbi, : No reason given.

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pcver
Junior Member (Idle past 5101 days)
Posts: 22
From: Sydney, Australia
Joined: 03-30-2009


Message 83 of 166 (504728)
04-02-2009 10:10 AM
Reply to: Message 80 by Taq
04-01-2009 12:26 PM


Re: Poking fun at Goliath
RAZD, Thank you for the tips.
RAZD writes:
I believe the point is not ERV's since chimp\human split, but the ERV's that are common to all humans and all chimps.
How do you explain these common ERV's when they serve no purpose to either group?
ERVs that are common to humans/chimps tell important stories. I hope to find out whether non-common ERVs provide clues that are more useful.
There seems to be an assumption that if God created something it must be useful. Let's say hypothetically God created some useful retroviruses. At such a microscopic level, by their viral nature, some retroviruses are bound to eventually mutate and invade animals where they would serve no useful purpose.
DrAdequate writes:
But why should it be "unavoidable" for an all-wise and all-knowing creator to supply his creations with genetic material which is of no use ... that is, no use except as evidence for evolution? Why should it be "unavoidable"...?
At an atomic level, particles are wave-like. That's the way things are, governed by law of Physics. Perhaps viruses are physic's equivalent of atoms in micro-biology. There is always unavoidable elements of unpredictability and randomness associated with organisms of that magnitude. (Just my unorganised thought).
Jazzns writes:
You have the situation completely wrong. What provides the proof of common ancestry are the ERVs that are in fact fixed in the populations.
Actually I was interested in the non-fixed ERVs for a different reason, as this post will show.
Shalamabobbi writes:
Here are some video summeries of logical fallacies. I believe yours is found in the 2nd, if memory serves. Lack of absolute proof does not mean that something for which the evidence is say 99%, proves the opposite since it isn't 100%. That one is called false dichotomy. It's in the videos as well.
I merely said that evidence does not equate to proof. That is not a logical fallacy.
shalamabobbi writes:
So is it true? You can lead a creationist to data, but you can't make him think
A thinking brain is far more important than data. Data without correct thinking is useless. But accurate data are vital if a thinking brain is to arrive at a correct conclusion.
Taq writes:
As for ERV's that are not found in all humans, these are a tiny, tiny minority. I am only aware of a handful of such ERV's...
It is also interesting to note that these polymorphic ERV's are HERV-K's, the retrovirus that has been active since our split from the chimpanzee lineage.
Thanks for presenting solid information in easy-to-understand manner. It is so difficult to analyse the vast amount of information on related subjects. One may be totally confused and not see the wood for the trees. So I cannot do any worse by guessing, partly using information made available to me.
I'm sure Shalamabobbi scoffs at suggestion that human history is only 6,000 years old. I notice numerous articles suggesting human history is 6.3 million years old. So to compromise, let me propose for argument sake that human history is only 10,000 years old.
Why 10,000 years? Partly because I believe in creationism. But mainly because I believe humans cannot possibly take much longer than that to evolve a modern society. (Got to love the word 'evolve'). To me this is common-sense logic
Put it this way - if human existence is 6.3 million years, then I would expect 6,290,000 years ago humans were already using Internet and driving cars to get around. For it's totally inconceivable to me that intelligent human could possibly be 'apes-like' for 6.2 million years and then... Bingo! ... Some mysterious awakening caused them to start doing more with their brains.
Therefore unless/until proven wrong, my thinking is -- An old earth but very recent human existence.
Now let me see if I can beat a square to fit a circle...
According to Taq:
1. Total human genome = 203,000 ERVs
2. Chimps have 279 ERVs not found in humans
3. Humans have 82 ERVs not found in chimps
4. Only a handful non-fixed ERVs in humans
The data suggest to me chimps did not descend to humans because I cannot reconcile why chimps have 279 more ERVs when humans only have 82 more, since the time they split, (assuming new ERVs were infused at the same rate). Perhaps an explanation is that chimps get viral insertion at a much higher rate than humans. But I suspect lifespan of chimps, being half that of human might lower the success rate of new ERVs in chimps. I also assume viral infusion might increase the death rate of animals.
Another explanation is of course chimps never descended to human but merely share a common ancestor. Which leads me to a puzzle - If chimps were picking up ERVs along geological time scale then it is nearly impossible for all chimps to have exactly the same 279 'new' ERVs today. Imagine periodically spreading a new ERV among the entire chimp population, how much time will that take? It is far more likely the distribution of ERVs in chimps would follow the likes of a bell curve -- A small chimps minority only has a couple of 'new' ERVs whereas another minority possesses all 279 'new' ERVs; yet at the same time majority of chimps would have approximately 150 'new' ERVs. Granted that most are probably fixed ERVs, it is reasonable to assume that over a long time chimps population may mutually 'contaminate' through breeding and one day all chimps end up possessing the same number of ERVs, (until yet another new ERV comes along).
What if all chimps have all those 279 ERVs right at the dawn of their existence? The above puzzle would not be an issue. Which is why today we can assert that all chimps have 279 ERVs not found in all humans. This is of course suggesting that ERVs were not viral insertion, but integral part of creation process. But of course we also need to account for real viral insertion. Perhaps only a handful of ERVs since existance of mankind - mostly those unfixed ERVs that Taq mentioned earlier, that accounts for very minor differences among all humans. Is the rate of 5 (ie. a handful of) new ERVs over 10,000 years of human existence a reasonable one? This works out to be 2,000 years per viral infusion.
If you refer to the diagram posted by Loudmouth in Message 1, you'd notice 16 ERVs over 70 million years for the primates!! Not that I believe 70 million years is correct. That works out to be approx 4 million years per ERVs!! At that rate, for chimps to acquire 279 new ERVs through viral infusion would take (4 x 279) million years! Now that's incredible! ( 2,000 years per viral infusion is more sensible )
I think I'm getting into trouble with this post (Hopefully Goliath is not taking notice).

I think I'm safe because Goliath is only seeking out David...

This message is a reply to:
 Message 80 by Taq, posted 04-01-2009 12:26 PM Taq has replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 84 of 166 (504733)
04-02-2009 10:30 AM
Reply to: Message 83 by pcver
04-02-2009 10:10 AM


Re: Poking fun at Goliath
Nothing to do with the science, but may I say that post is 100 times clearer due to the changes in formatting, kudos for that.
TTFN,
WK

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 85 of 166 (504743)
04-02-2009 11:26 AM
Reply to: Message 83 by pcver
04-02-2009 10:10 AM


Re: Poking fun at Goliath
Hi Pcver,
You still seem to have a very tenuous grasp of any sort of evolution. For instance I suspect ...
I notice numerous articles suggesting human history is 6.3 million years old.
... is complete nonsense. What you have encountered numerous times is the conclusion from various sources of genetic and paleontological data that the human and chimp lineages diverged ~6 million years ago(MYA). That does not make 6 MYA the time when modern Homo sapiens evolved, most current estimates for that are closer to 400,000 to 250,000 years ago.
For it's totally inconceivable to me that intelligent human could possibly be 'apes-like' for 6.2 million years and then... Bingo! ... Some mysterious awakening caused them to start doing more with their brains.
When we are talking about cars and computers those are all only from the last century essentially, even with only a 6000 year history for the earth we might as well ask why Jesus didn't have an iPhone by your reasoning. Do you really believe that there was a steady linear progression in technology that has got us to our modern state? Do you find hundreds of thousands of years any more plausible than millions?
The data suggest to me chimps did not descend to humans because I cannot reconcile why chimps have 279 more ERVs when humans only have 82 more, since the time they split
Another explanation is of course chimps never descended to human but merely share a common ancestor.
Unless you assume that once the human chimp lineages split chimps never evolved any further genetically then these two things are exactly the same explanation.
But I suspect lifespan of chimps, being half that of human might lower the success rate of new ERVs in chimps.
I would suggest rather that being able to go through twice as many generations in the same time would allow them to undergo almost twice as much genetic change in terms of accumulated neutral mutations (if we consider ERVs neutral).
Your explanations of the existence of ERVs seem to be ad hoc in the extreme.
One problem is your apparent assumption that every ERV is the result of a novel retroviral insertion event. This is by no means the case, once an ERV has inserted itself into the genome it is as liable to duplication, rearrangement and mutation as any other sequence, more so in some ways since it plays no functional role and will therefore not be maintained by selection. As well as this while ERVs retain enough retroviral function they can actively copy themselves through a process called transpostition.
Which leads me to a puzzle - If chimps were picking up ERVs along geological time scale then it is nearly impossible for all chimps to have exactly the same 279 'new' ERVs today.
This is quite an assertion. Bottlenecking is a well recognised mechanism for fixing a number of loci effectively simultaneously in a population. Perhaps one or more bottlenecking events were the basis for these chimp specific fixed ERVs.
Your entire argument seems to hinge principally upon your own capability for belief in a particular explanation. This is understandable for your own subjective opinion but surely you can appreciate that it isn't a line of argument calculated to sway anybody else?
TTFN,
WK

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 86 of 166 (504750)
04-02-2009 12:39 PM
Reply to: Message 83 by pcver
04-02-2009 10:10 AM


Re: Poking fun at Goliath
There seems to be an assumption that if God created something it must be useful. Let's say hypothetically God created some useful retroviruses. At such a microscopic level, by their viral nature, some retroviruses are bound to eventually mutate and invade animals where they would serve no useful purpose.
This doesn't explain the pattern of insertion nor the sequence comparisons that both point to common ancestry. If these insertions occurred independently then the vast majority should be non-orthologous (not at the same spot in the genome). The opposite is true. The vast majority are orthologous which is inconsistent with indepedent insertion. If these ERV's are caused by a single insertion that is then passed on through heredity then the vast majority should be orthologous, and they are. As for the sequence comparisons, your explanation does not explain why there is more LTR divergence between orthologous ERV's shared by orangutans, chimps, and humans than there is in orthologous ERV's shared by humans and chimps but not orangutaons. Common ancestry and subsequent evolution does explain these facts.
So I cannot do any worse by guessing, partly using information made available to me.
The problem is that your guesses contradict the evidence we do have. So yes, you are doing worse.
Put it this way - if human existence is 6.3 million years, then I would expect 6,290,000 years ago humans were already using Internet and driving cars to get around.
You are assuming that all of our ancestors possessed the same mental capacity and technological knowledge that we do. This is a very bad assumption.
The data suggest to me chimps did not descend to humans because I cannot reconcile why chimps have 279 more ERVs when humans only have 82 more, since the time they split, (assuming new ERVs were infused at the same rate). Perhaps an explanation is that chimps get viral insertion at a much higher rate than humans. But I suspect lifespan of chimps, being half that of human might lower the success rate of new ERVs in chimps. I also assume viral infusion might increase the death rate of animals.
First of all, let's do the math. 200 lineage specific ERV's compared to 200,000 orthologous ERV's. The lineage specific ERV's only make up 0.1% of the total. 99.9% of ERV's are orthologous, or thereabouts.
Secondly, you actually did describe the answer. There was an influx of ERV's into the genomes of Old World monkey and Old World great apes with the exception of humans and orangutans. You can read about it in this paper. It is a very interesting topic as to why all of these other primate species were infected by this virus but not humans nor orangutans. This retrovirus goes by the name PTERV1. From sequence analysis, it appears that this elevated influx of ERV's occurred over a relatively short time period.
This also allows us to test the theory of evolution once again. Scientists found a specific retrovirus in monkeys and some great apes. The theory of evolution predicts that because it is not found in orangutans or humans, but is found in chimps and other great apes, that these insertions had to of occurred after the human and chimp lineages split. IOW, these have to be independent insertions. Therefore, these insertions will be occur at non-orthologous positions in each genome. THAT IS EXACTLY WHAT IS OBSERVED. From the paper:
quote:
Based on an analysis of 1,467 large-insert clones, we mapped 299 retroviral insertion sites among the four species (Figure 3; Table S2). A total of 275 of the insertion sites mapped unambiguously to non-orthologous locations (Table 2), indicating that the vast majority of elements were lineage-specific (i.e., they emerged after the divergence of gorilla/chimpanzee and macaque/baboon from their common ancestor).
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%. This is almost certainly a lower-bound estimate owing to the limitation of our BAC-based mapping approach to refine the precise locations of the insertions. . .
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 (National Center for Biotechnology Information). 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. . . 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.
Another explanation is of course chimps never descended to human but merely share a common ancestor.
Precisely.
Which leads me to a puzzle - If chimps were picking up ERVs along geological time scale then it is nearly impossible for all chimps to have exactly the same 279 'new' ERVs today.
Why? Studies of human DNA variation leads us to interesting conclusions. For example, the most recent common ancestor of human mitochondria existed just a few hundred thousand years ago. There were certainly other mitochondrial lineages in existence at that time, and there were after that as well. However, genetic drift lops off branches in any population, and over time only one ancient branch makes it. This is how ERV's become fixed in populations. If you looked at ERV distributions a few million years ago the picture may very well be different.
What if all chimps have all those 279 ERVs right at the dawn of their existence?
Again, that does not explain the placement of these ERV's in genomes (non-orthologous vs. orthologous), nor does it explain the sequence divergence.
If you refer to the diagram posted by Loudmouth in Message 1, you'd notice 16 ERVs over 70 million years for the primates!! Not that I believe 70 million years is correct. That works out to be approx 4 million years per ERVs!! At that rate, for chimps to acquire 279 new ERVs through viral infusion would take (4 x 279) million years! Now that's incredible! ( 2,000 years per viral infusion is more sensible )
That only applied for the ERV's that were part of that study.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 87 of 166 (504759)
04-02-2009 2:24 PM


Does everyone understand what I mean by "LTR divergence" and overall sequence divergence? These are very important concepts for understanding why ERV's evidence common ancestry. However, I don't want to write a long post about stuff that people already understand.

Replies to this message:
 Message 90 by shalamabobbi, posted 04-02-2009 5:49 PM Taq has replied

  
shalamabobbi
Member (Idle past 2849 days)
Posts: 397
Joined: 01-10-2009


Message 88 of 166 (504760)
04-02-2009 2:27 PM
Reply to: Message 83 by pcver
04-02-2009 10:10 AM


Re: Poking fun at Goliath
pcver writes:
This is of course suggesting that ERVs were not viral insertion, but integral part of creation process.
quoting the OP..
quote:
As to the falsification of evolution, if you were able to find a sequence shared by gorillas and humans that was not found in chimps then the theory of evolution would be in serious doubt. Additionally, find an ERV only shared by orangutans and humans and not chimps or gorillas, you would again cast serious doubt on the theory of evolution. However, these potential falsifications have never been observed.
If they are part of some design process then they are ineffective in causing design differences in most cases. Also, a designer would not be forced to make the pattern of similar ERV’s between species follow what is found in the fossil record. That is, a designer would not be forced to follow the rules set forth by common ancestry and the theory of evolution.
The insinuation by some in the creationist movement that ERV’s are the fingerprints of design is not supported, nor is it substantiated by any data. ERV’s are random mutations and viral in origin.
When dealing with Goliath you are better off avoiding him altogether or slaying him. Poking just gets him annoyed.
This reminds me of a group of kids that had a 22cal rifle and thought it'd be fun to shoot a polar bear. The bear was annoyed and ate them.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 89 of 166 (504766)
04-02-2009 4:03 PM
Reply to: Message 83 by pcver
04-02-2009 10:10 AM


Re: Poking fun at Goliath
There seems to be an assumption that if God created something it must be useful.
There is an assumption that if God created something, he must have done it with some purpose in mind other than to convince evolutionists that they're right.
At an atomic level, particles are wave-like. That's the way things are, governed by law of Physics. Perhaps viruses are physic's equivalent of atoms in micro-biology. There is always unavoidable elements of unpredictability and randomness associated with organisms of that magnitude. (Just my unorganised thought).
Well that is unorganized.
Look, let's try it again.
The evolutionary hypothesis predicts certain patterns in ERVs. We look at the world, and find that these patterns exist. This would seem to be a score for evolution.
You claim that God made these patterns, but challenged to say why, you start talking about "unpredictability and randomness", something that we do not usually associate with an omnipotent Creator.
I'm sure Shalamabobbi scoffs at suggestion that human history is only 6,000 years old. I notice numerous articles suggesting human history is 6.3 million years old. So to compromise, let me propose for argument sake that human history is only 10,000 years old.
Why 10,000 years? Partly because I believe in creationism. But mainly because I believe humans cannot possibly take much longer than that to evolve a modern society. (Got to love the word 'evolve'). To me this is common-sense logic
Put it this way - if human existence is 6.3 million years ...
Well, it isn't.
I don't know where you got that figure from, but I note that it is approximately the time it has taken our lineage to diverge from that of chimpanzees.
But that doesn't mean that all that time ago our lineage had modern brainy brains.
Another explanation is of course chimps never descended to human but merely share a common ancestor.
That's exactly what is being claimed. No-one in the entire universe claims that humans are descended from chimps.
Which leads me to a puzzle - If chimps were picking up ERVs along geological time scale then it is nearly impossible for all chimps to have exactly the same 279 'new' ERVs today. Imagine periodically spreading a new ERV among the entire chimp population, how much time will that take?
The only ERVs that are relevant to our discussion are those that have become fixed in the genome.
If you're interested in the math, I wrote an article on Genetic Drift.
---
I think you're a bit out of your depth here. You haven't quite understood what is being claimed, and then you try to pick holes in evolutionary biology based on your lack of understanding. But the things that you don't understand about biology are not a problem for biology, they're a problem for you.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
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shalamabobbi
Member (Idle past 2849 days)
Posts: 397
Joined: 01-10-2009


Message 90 of 166 (504774)
04-02-2009 5:49 PM
Reply to: Message 87 by Taq
04-02-2009 2:24 PM


LTRs
Tag writes:
Does everyone understand what I mean by "LTR divergence" and overall sequence divergence? These are very important concepts for understanding why ERV's evidence common ancestry. However, I don't want to write a long post about stuff that people already understand.
I think I get the gist of it but I am only about 2/3 through the free online MIT biology course and non of this has been covered yet, so I'm interested in more details if you are willing. It probably wouldn't hurt the lurkers either.
I think that creationists only look into data that supports their viewpoint and think something is either wrong or incomplete about data that doesn't support their viewpoint, that the actual data available is as sparse as their awareness of that data, and that it is tenuous enough to admit of more than one self consistent interpretation.
Edited by shalamabobbi, : No reason given.

This message is a reply to:
 Message 87 by Taq, posted 04-02-2009 2:24 PM Taq has replied

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