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Author Topic:   Why are there no human apes alive today?
Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 956 of 1075 (625664)
07-24-2011 10:57 PM
Reply to: Message 953 by Portillo
07-24-2011 8:23 PM


I think one of the points Mazzy is trying to make is that if neanderthal or homo erectus are fully human. Not half human, not caveman, not apeman, not transitional fossil, then why are they proclaimed as links between humans and apes.
Mazzy has never defined what features a transitional fossil SHOULD have. Without this definition she can not claim that any fossil is transitional or not.

This message is a reply to:
 Message 953 by Portillo, posted 07-24-2011 8:23 PM Portillo has not replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 957 of 1075 (625665)
07-24-2011 11:01 PM
Reply to: Message 940 by Mazzy
07-23-2011 3:29 PM


Larni .. the latest is that Neanderthal are human beings and no different to you or I as far a s humanity goes. They are 99.5% similar which is the same differences cited within the human population today.
Nice double standard you have there. That 99.5% similarity was a result of single base pair comparisons, not the 30 base pair comparisons that you use to say that chimps and humans are 30% different.

This message is a reply to:
 Message 940 by Mazzy, posted 07-23-2011 3:29 PM Mazzy has replied

Replies to this message:
 Message 968 by Mazzy, posted 07-26-2011 6:59 PM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(2)
Message 969 of 1075 (626018)
07-26-2011 7:12 PM
Reply to: Message 961 by Mazzy
07-26-2011 1:34 PM


Re: Moderator Advisory
Your post had too many points to address any compehensively at 3am. Now if you wish you can focus on one or two related points. This will aid in my giving full refutes to your points.
Sounds good with me. All I ask is that the admin's be patient as we move through each topic. I have every intention of combining our separate discussions into a whole picture which directly relates to the relatedness of humans and other apes.
First, I want to focus on retroviral integration itself. It seems that you have been pulling a lot of "facts" out of thin air, such as this one:
Mazzy: Certain viruses prefer certain places in the genome and certain chromosomes. An example would be HIV, it infects humans and chimps in the exact same location of the chromosome.
Since you have already cited PTERV-1 as solid evidence, then I will be referencing that as well.
There just so happens to be a paper that looked at the insertion of multiple HIV infections into the human genome, along with ASLV and MLV. You can read the whole paper here.
I would like to direct your attention to Fig. 1 which is pictured below:
See those light blue lollipop looking things? Guess what those are? Places in the genome where HIV inserted. HIV inserted into the entire length of every chromosome. Not one place in one chromosome. In multiple places in multiple chromosomes. IOW, you are completely wrong. Furthermore, the paper found that HIV does have preferential insertion sites, but it really doesn't help you much. From the paper:
quote:
For HIV the frequency of integration in transcription units ranged from 75% to 80%, while the frequency for MLV was 61% and for ASLV was 57%. For comparison, about 45% of the human genome is composed of transcription units (using the Acembly gene definition).
So 80% of the time, HIV inserted into features that make up nearly half of the human genome which is calculates out to 1.5 billion bases. That's a big number, a lot larger than the single base that you are claiming. On top of that, MLV and ASLV show weak to non-existent preferences for transcriptional units.
So HIV is a big swing-and-a-miss for you. Let's see how PTERV-1 works out. I will be pulling information from this paper.
First, some background on the techniques that they used. In order to determine where in the genome that PTERV-1 ERV's were found they digested the genomes of 4 different species into large chunks, about 160,000 base pairs on average. They then used probes to determine which of these big chunks of genomic DNA contained a PTERV-1 ERV. Once this was determined they sequenced the ends of the chunks to see where it fit into the larger genome. So what did they find?
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).
So they found 299 PTERV-1 ERV's and only 22 of them were within 160,000 base pairs of each other. Due to some overlap, they concluded that 24 out of the 299 could be within 160,000 base pairs of each other. Not looking so good for you. It get's worse. Next, they sequenced out from the ERV insertion itself so that they could determine the exact locus for the PTERV-1 that were within 160,000 base pairs of each other. 24 separate ERV's would be 12 orthologous pairs. So were they able to find a single unambiguous example of an orthologous PTERV-1 insertion? Nope. Not a single one.
So even your poster child PTERV-1 insertions are not found at the same position in each genome. HIV does not insert into the same position each time it inserts. Your argument is a complete failure at this point.
If you can not find a single example of a virus that inserts into the same position each and every time it inserts then the evidence above stands. You can not claim that the orthologous insertions can best be explained by independent insertions.
I would ask that your response to this post should focus on retroviral insertion alone, and not anything else. In this way we can move in a straighter path towards the topic and keep the admins happy.

This message is a reply to:
 Message 961 by Mazzy, posted 07-26-2011 1:34 PM Mazzy has replied

Replies to this message:
 Message 976 by Mazzy, posted 07-27-2011 3:21 AM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 970 of 1075 (626019)
07-26-2011 7:17 PM
Reply to: Message 968 by Mazzy
07-26-2011 6:59 PM


Again I ask, what is this all about?
Your double standard when comparing DNA homologies. When you compare human and chimp genomes you use 30 base pair segments. When you compare human and neanderthal genomes you use single base pair comparisons.
Let's say that there is a 30 base pair segment that differs by one base between humans and chimps. Using a 30 base pair comparison there is 0% homology between the species. Using a single base pair comparison there is 97% homology. For the chimp-human comparison you are using the 30 base pair comparison. For human-neanderthal comparisons you are using the single base pair comparisons. All I am asking for is some consistency.

This message is a reply to:
 Message 968 by Mazzy, posted 07-26-2011 6:59 PM Mazzy has not replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 971 of 1075 (626020)
07-26-2011 7:19 PM
Reply to: Message 968 by Mazzy
07-26-2011 6:59 PM


Did not comport with established primate history means to me that you may pick and choose what you use as evidence and disregard anything that is uncomfortable, and propose more theories to explain the unpredicted and contradictory.
It does comport. In fact, it comports quite nicely. None of the PTERV-1 insertions are orthologous as one would expect if the consensus phylogenies are accurate. That you fail to understand this only highlights your ignorance.

This message is a reply to:
 Message 968 by Mazzy, posted 07-26-2011 6:59 PM Mazzy has replied

Replies to this message:
 Message 980 by Mazzy, posted 07-27-2011 1:13 PM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 974 of 1075 (626048)
07-26-2011 8:37 PM
Reply to: Message 973 by Admin
07-26-2011 8:31 PM


Re: Repeating the Topic
The recent discussion has been a great improvement, but I think it would be helpful if someone could make it clear how the genetic side of the discussion fits into the constrained version of the topic I've defined, which I'm further clarifying now to exclude extinct species.
I am only replying to clarify my own posts and how it relates to the topic. I plan to show that ERV's do group humans with the rest of the apes. To do this, we first have to establish a working knowledge of how ERV's insert into genomes. Mazzy has made claims about retroviral insertion that are just plain wrong. If I am to show that ERV's do group humans with other apes I have to clear up the misinformation concerning ERV insertion. If that part of the discussion does drag on I will be happy to move the discussion to a different thread.

This message is a reply to:
 Message 973 by Admin, posted 07-26-2011 8:31 PM Admin has seen this message but not replied

Replies to this message:
 Message 984 by Mazzy, posted 07-27-2011 3:36 PM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 979 of 1075 (626133)
07-27-2011 11:27 AM
Reply to: Message 976 by Mazzy
07-27-2011 3:21 AM


Re: Moderator Advisory
Before we can move on I need Taq, and Nuggin to make up their minds. I am replying to your post this time Taq. What is the proof that ERV's are proof of common ancestry..is it that the ghosts of ERV's are found in the exact same position in the genome such that it would defy chance or is that they are scattered everywhere willy nilly and this proves common descent?
Before I can explain why ERV's can be used to evidence common ancestry you need to agree that retroviruses insert randomly amongst billions of insertion sites. Until we have an agreement on how retroviruses insert into the genome we can not proceed.
Now to highlight more of your mistakes.
Here is a reseach paper that suggests 95.5% of ERV's are in non-orthologous regions.
False. It says that 95.5% of PTERV-1 insertions are not within 160,000 base pairs of each other, the resolution of the BAC clone technique that the authors are using. It does not say that 95.5% of ALL ERV's are non-orthologous. They are looking at PTERV-1 insertions specifically which are a subset of all ERV's.
So when an ERV is placed in a similar spot in two species this proves common descent. When it doesn't this means it just got there some other way. It seems ERV's are unfalsifiable.
False. An orthologous ERV indicates that the insertion happened once in a common ancestor. A non-orthlolous ERV indicates the opposite, that the insertion occurred independently in both lineages.
The way to falsify the ERV data is to show that:
1. Orthologous ERV's do not produce a single nested hierarchy.
2. LTR divergence greatly differs from the tree created through orthologous loci.
3. Overall ERV divergence differs from the two trees above.
So Taq, would you like to repost or shall I try to reply seriously to this post of yours.
You do realize that there are more than PTERV-1 insertions in these genomes? You do know that PTERV-1 and HERV-K are different, don't you?
Edited by Taq, : No reason given.

This message is a reply to:
 Message 976 by Mazzy, posted 07-27-2011 3:21 AM Mazzy has replied

Replies to this message:
 Message 982 by Mazzy, posted 07-27-2011 1:48 PM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 981 of 1075 (626154)
07-27-2011 1:25 PM
Reply to: Message 980 by Mazzy
07-27-2011 1:13 PM


The article plainly states 'DOES NOT COMPORT', If you disageee you should call the researchers up and tell 'em what's what, according to Taq.
You are ignoring the context. The PTERV-1 insertions would not comport IF THEY WERE FOUND AT ORTHOLOGOUS POSITIONS. That is why the authors went to so much trouble to find the genomic locus for all of the PTERV-1 insertions. What did they find? PTERV-1 ERV's are NOT FOUND AT ORTHOLOGOUS POSITIONS, therefore they do comport with the consensus phylogeny. Notice the title of the paper? See that part that says "Lineage Specific"?
Getting back on track, do we have agreement that retroviruses insert randomly amongst millions to billions of insertion sites? As soon as we agree on this well evidenced point we can move to the next part of my explanation of why ERV's can be used to evidence common ancestry.

This message is a reply to:
 Message 980 by Mazzy, posted 07-27-2011 1:13 PM Mazzy has not replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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Message 983 of 1075 (626171)
07-27-2011 2:49 PM
Reply to: Message 982 by Mazzy
07-27-2011 1:48 PM


Re: Moderator Advisory
Ok ..I'll go along. Let's say ERv's insert randomly. What's next?
We then calculate the probability of two retroviruses inserting into the same position in two genomes. Given that there are millions to billions of bases where these retroviruses can insert into the chances of this happening multiple times in multiple species is in the range of winning the Powerball lottery several times in a row. Do you agree with this?
Added by edit: Just thought I would do the math for you. Let's say that a virus has 1 million possible insertion sites (which is a VERY low numer, so I am erring in your favor). This means that, on average, there will be one orthologous insertion out of every 1 million independent infections. Just one. So how many ERV's do we need in order to see 10 orthologous ERV's? That would be 1 in 1 million to the 10th power or 1 to 1E60 (thats a one with 60 zeros after it), and that is just for 10 orthologous ERV's.
Are we agreed on these figures?
Now to clean up your understanding of the PTERV-1 paper which will become important later on.
It also says
"We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species."
Again, context is everything. Retroviral integration sites of which virus? What probe did they use for BAC clone selection?
The answer is that they used a PTERV-1 specific probe to select for the large chunks of genomic DNA that contained PTERV-1 insertions, and PTERV-1 insertions only. Their methodology would not have picked up HERV-K or HERV-W insertions, to use two examples. That 95.5% figure is for PTERV-1 ERV's (within the resolution of 160 kb BAC clones), not for all ERV's as you suggested before.
"Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3—4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes."
What led them to this conclusion? The fact that PTERV-1 insertions were found at non-orthologous locations, along with sequence divergence data.
I'd say some virus have a preference bias for particula genomic sites. Hence they end up in the same region due to preference and not ancestry.
It only took you 4 paragraphs to go back on your word. Go figure.
This discussion can not go forward if you are going to go back on your word. Either agree that retroviral insertions are random or that they are directed to specific locations. Pick one, and we will discuss further.
I have stated all along that ERV's could be the result of something like a mossie bite, not common descent.
You have around 200,000 ERV's in your genome. Are you telling me that all of those ERV's are due to infections that you acquired during your lifetime? At the same time, your parents and sibilings have these very same ERV's in their genomes. Did your parents and siblings also suffer these same infections, and did those same infections result in identical insertions at identical positions in their genomes?
Edited by Taq, : No reason given.

This message is a reply to:
 Message 982 by Mazzy, posted 07-27-2011 1:48 PM Mazzy has replied

Replies to this message:
 Message 987 by Mazzy, posted 07-27-2011 6:23 PM Taq has replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 985 of 1075 (626183)
07-27-2011 4:07 PM
Reply to: Message 984 by Mazzy
07-27-2011 3:36 PM


Re: Repeating the Topic
It is simply a fact that one example of inconsistecy or contradiction should falsify any theory. I have produced one example and more.
In order for me to address this claim we first need to agree on the basics of retroviral insertion.
Above, I made a calculation for the probability of getting 10 orthologous insertions. Do you agree with these calculations or not?
Added by edit:
*How about we progess no further untill you explain 1. how PtERV1 is found in African great apes but not human and 2. how a guinea pig has the same ERV in the exact same region as a human but is not closely related.*
PTERV-1 was species specific and these infections occurred after the different lineages branched of of their common ancestors. The fact that retroviruses continue to infect species does not, in any way, refute the fact that orthologous ERV's are inherited from a common ancestor. If humans do not share a common ancestor with other apes then you should not find a single orthologous ERV, but instead you find tons of them.
You might as well try to refute the argument that French and Spanish share a common ancestral Latin language by pointing to the differences between the languages, forgetting that it is the commonalities that point to their common ancestral language.
Also, the pages you linked to talked about the GULO pseudogene. This is not an ERV.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 984 by Mazzy, posted 07-27-2011 3:36 PM Mazzy has replied

Replies to this message:
 Message 986 by Panda, posted 07-27-2011 6:09 PM Taq has not replied
 Message 988 by Mazzy, posted 07-27-2011 6:36 PM Taq has replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(2)
Message 990 of 1075 (626219)
07-27-2011 7:04 PM
Reply to: Message 987 by Mazzy
07-27-2011 6:23 PM


Re: Moderator Advisory
If we are talking about PTERV-1, it was not found in the right spot in humans nor orangs so these calculations do not apply to how amazing it was for PTERV-1 to reside in a particular exact spot of the human and chimp genome.
PTERV-1 insertions are NOT found at the same spot in human and chimps genomes, or any genome for that matter. That's the whole point. They are non-orthologous. Not one PTERV-1 insertion was unambiguously found at the same same base in any of the genomes. The PTERV-1 insertions in the chimp and gorilla genomes were NOT found at the same bases.
So again, what is wrong with the calculations? Those calculations are for predicting how many insertions it takes before two occur at the same position.
They can construct their models to pick up what they want, the point is they did not pick up PTERV-1 in the human and orang where it should be if it was inhereted, thereby falsifying the validity of any ancestral connection between chimps and humans.
No one is saying that PTERV-1 insertions were inherited from a common ancestor. They were inserted after each lineage branched off from the common ancestor. That is why they are NOT found at the same location in each genome.
Can you please explain how acquiring non-orthologous ERV's after splitting from the common ancestor invalidates orthologous ERV's as evidence of that common ancestor?
As for how this retroviral infection bypassed orangutans and humans, the authors offer a number of possible scenarios. Whatever conclusions that are made of this are based on predetermined assumptions of what is related to what and this becomes a part of the insertion values in any model.
No predetermined models. In order to determine which lineages were infected by PTERV-1 they looked for the lineages that had PTERV-1 inserts. That's it.
WOW!...Integration site preferences as I mentioned...Go figure!
How many sites are there? How many bases in the genome are found in these integration sites?
From the paper I quoted earlier for HIV integration site preferences:
quote:
For HIV the frequency of integration in transcription units ranged from 75% to 80%, while the frequency for MLV was 61% and for ASLV was 57%. For comparison, about 45% of the human genome is composed of transcription units (using the Acembly gene definition).
Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences | PLOS Biology
45% of the human genome is about 1.5 BILLION bases. The chances of a HIV virus inserting into the same base twice is 1 in 1.5 billion. The odds of winning the Powerball lottery are better than that, and yet you think it happens with ease. Care to explain?
What I am saying is that your ghosts and so called remnants could be saying nothing at all as far as ancestry to apes is concerned.
All this time you have been arguing that they are retroviral insertions, and now you are saying that they are not? You should really make up your mind.
The fact remains that you and your siblings (assuming you have siblings) share the same ERV's at the same location in your genomes because you inherited them from your parents which are the common ancestor of you and your siblings. It is not due to being infected by the same virus 200,000 times and having those viruses insert at the same location in each genome.
With that said, if one of your siblings acquired a new ERV through a new infection would the presence of that new ERV negate the evidence of common ancestry seen in the ERV's you do share? If your sister gets infected by a retrovirus are you no longer sisters?
1. Can explain why PTERV-1 is not found at an ancestral point in humans and orangs?
Because PTERV-1 did not infect the common ancestor of humans and orangutans. It infected a select few apes species after each lineage had split from the common ancestor of those lineages. It is the same as your sister acquiring a new ERV after you are both born. That is why the ERV is found in your sister and not in you while the orthologous ERV's you inherited from your parents are still there for everyone to see.
2. Why guinea pigs have the same ERV in the same genomic region as humans?
GULO is not an ERV, it is a pseudogene.
3. How can researchers tell if an ERV has been transmited via HGT, epigentic inheritance etc, as opposed to ancestry?
They can tell by the base they are inserted into. ERV's found at the same base (i.e. orthologous) in two or more species are due to a single insertion in a common ancestor. ERV's that infect the lineage after they have split from the common ancestor are not found at the same base (i.e. non-orthologous).
If humans and other apes do not share a common ancestor then you should only find non-orthologous ERV's. You don't. You find orthologous ERV's as well as non-orthologous ERV's.
Also, epigenetic inheritance has nothing to do with DNA sequence. Epigenetic inheritance has to do with DNA methylation and histone packaging. We are talking about sequence data, so epigenetics is not a factor.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 987 by Mazzy, posted 07-27-2011 6:23 PM Mazzy has not replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


Message 991 of 1075 (626220)
07-27-2011 7:06 PM
Reply to: Message 988 by Mazzy
07-27-2011 6:36 PM


Re: Repeating the Topic
No we don't.
So what is wrong with the calculation? For HIV, there are about 1.5 billion bases amongst all of the insertion sites that it can insert into. Therefore, the odds of an HIV virus inserting into the same base in two different insertions is 1 in 1.5 billion, is it not?

This message is a reply to:
 Message 988 by Mazzy, posted 07-27-2011 6:36 PM Mazzy has replied

Replies to this message:
 Message 993 by Mazzy, posted 07-27-2011 7:28 PM Taq has replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 994 of 1075 (626224)
07-27-2011 7:48 PM
Reply to: Message 993 by Mazzy
07-27-2011 7:28 PM


Re: Repeating the Topic
It is not about the calculation it is about the fact that PTERV1 is NOT found at an ancestral site in the human and orang.
No, it is about your inability to understand the difference between non-orthologous and orthologous ERV's. Do you understand what the difference is, and what each one indicates? It has everything to do with the calcuations I have been showing you.
BTW, PTERV1 insertions are all non-orthologous as is consistent with the virus infecting the chimp and gorilla ancestors after they split from the ancestor we share with them.
Isn't it interesting that out of 30,000 ERVs only 7 of them are known to have inserted at the same site in humans and chimps?
That's a complete lie that your source is feeding you.
quote:
In 2005, the available sequence of the Chimpanzee genome was aligned with that of the human genome, and an extensive comparison analysis was performed. As part of this analysis, the researchers looked at every available solo LTR and full-length ERV in the chimpanzee genome, and checked to see if there was also one at each corresponding locus. Just as with the examination of indels, the results were that less than 100 ERVs are human-specific and less than 300 ERVs are chimpanzee-specific (Chimpanzee Sequencing and Analysis Consortium, 2005; R. Waterston, personal communication, April 22, 2010).
Just a moment...
So there are only 100 human specific and 300 chimp specific ERV's out of hundreds of thousands. The rest of the nearly 200,000 are orthologous. Sorry, but you have completely failed in this line of reasoning.
Evos go on and on about testable theories supported by validation and observation. ERV's as a method of demonstrating ancestry has exceptions, inconsistency and contradictions.
Non-orthologous ERV's are not inconsistent with the model. Or did you think that after a speciation event neither of the two new lineages could be infected by viruses anymore?
How are these anomolies validating this ERV theory by evidence and observation?
You haven't pointed to any anomalies yet. Species acquiring ERV's after a speciation event is not anamolous.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 993 by Mazzy, posted 07-27-2011 7:28 PM Mazzy has replied

Replies to this message:
 Message 1037 by Mazzy, posted 07-29-2011 3:36 PM Taq has replied

Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 1007 of 1075 (626293)
07-28-2011 10:17 AM
Reply to: Message 1004 by Admin
07-28-2011 6:47 AM


Re: Number of Matching ERVs Between Chimps and Humans
Taq has said something very similar about there being 200,000 matching ERVs between chimps and humans. I've been following many of the links to technical articles that have been provided and have not been able to track down a source for this claim. Could someone please supply it?
Table 11:
Initial sequencing and analysis of the human genome | Nature
From the 2001 human genome paper:
Initial sequencing and analysis of the human genome | Nature
There are 112,000 class I, 8,000 class II, and 83,000 class III ERV's for a total of 203,000.
In the 2005 chimp genome paper they only found ~300 ERV's in chimps that were not found in humans at an orthologous position, and ~100 ERV's in humans that were not found at an orthologous position in chimps. That is found in table 2:
Initial sequence of the chimpanzee genome and comparison with the human genome | Nature
Of the 2005 chimp genome paper:
Initial sequence of the chimpanzee genome and comparison with the human genome | Nature

This message is a reply to:
 Message 1004 by Admin, posted 07-28-2011 6:47 AM Admin has seen this message but not replied

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


(1)
Message 1008 of 1075 (626294)
07-28-2011 10:25 AM
Reply to: Message 997 by Mazzy
07-28-2011 12:40 AM


Re: Moderator Advisory
If guinea pigs and humans share a retrovirus then for this to show the ancestry of all mammals to humans it should be in all mammals It isn't.
Which ERV are you referring to?
"A retrovirus endogenous to guinea pig cells was earlier shown to be morphologically similar to type B and type D prototype retroviruses. Molecular hybridization techniques were used to show that guinea pig virus nucleotide sequences are endogenous to both domestic (Cavia porcellus) and indigenous (Cavia aperea) guinea pigs, but cannot be detected in the DNA of either other hystricomorph rodents or other mammals tested. "
Immunological relationships of an endogenous guinea pig retrovirus with prototype mammalian type B and type D retroviruses. - PMC
And . . ?
This is also avoiding the question. Once a horizontally transmitted ERV reaches the germ line, which they sometimes do, how do you differentiate this ERV was transmitted horizontally rather than vertically if it is dated back past 1my or more.
ERV's transmitted horizontally are non-orthologous. ERV's transmitted vertically are orthologous. I have said this multiple times now.
Once anhorizontally transmitted ERV hits the germ line it may well show its preference by ending up at the exact ame place in both species, anyway, and through vertical transmision.
No, it won't. There are billions of hotspots. The chances of two viruses inserting into the same hot spot is 1 in 1.5 billion for HIV. Remember those calculations you keep ignoring? This is where they come in.
I am saying, and have given many examples of where ERV's show inconsistent results that do not link close species together and rather link very distantly related species together.
You have yet to show how PTERV1 insertions are inconsistent with the consensus phylogeny. PTERV1 insertions are non-orthologous which is consistent with HGT.
Of tens of thousands of ERV's only about 7 have been shown to demonstrate this magic in humans
The real number is around 200,000, not 7. Only a few hundred ERV's are non-orthologous between chimps and humans. Over 200,000 are orthologous. Links can be found in my post above.
I have cited near as many examples of this all being nonsense as your reserchers have actual examples of this occuring.
You haven't cited one yet.
So the remaining question to give a simplistic answer to is "Why are ERV's used to show common descent re humans and apes when there are more examples that falsify it available then there is actual evidence for it?"
PTERV1 insertions do not falsify common descent because they are non-orthologous. I have said this time after time and you refuse to deal with it. If PTERV1 insertions were orthologous then that would falsify the ERV evidence, but they aren't.

This message is a reply to:
 Message 997 by Mazzy, posted 07-28-2011 12:40 AM Mazzy has replied

Replies to this message:
 Message 1013 by Mazzy, posted 07-28-2011 5:43 PM Taq has replied
 Message 1014 by Mazzy, posted 07-28-2011 5:53 PM Taq has replied

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