Chimpanzee Genome

[Loudmouth]

Wiggle out?

Yep. That is exaclty what you do in the rest of your post.

What the table says is that the ERV class 1 sequences are 79 million base pairs total, comprising under 3% of the entire sequence with 72 families. Ok, this is what we know about the Chimpanzee Genome:

According to this table the Chimpanzee Genome has 234 ERV class 1 elements greater the 1 million base pairs (MPS). Do you see a problem here yet?

That is not what that chart says. That chart lists the ERV's that are specific to that lineage. Those are the ERV's that are not shared with humans. The other 200,000 are shared with humans which is why they are not listed in the chart for lineage specific transposable element activity. The ERV's listed for humans in that chart are the ERV's that have inserted into the human genome since the two lineages split. The ERV's listed for chimps are the ERV's that have inserted into the chimp genome since the two lineages split. That is why the chart lists separate lineages.

Want to guess how they determined which ERV's are lineage specific?

Just so we are on the same page, do you agree that there are ~200,000 ERV's in the human genome and that it is substantiated by Table 11 from the human genome paper.

 

[Loudmouth]

Only one actual scientist posted in this thread, Steve and he wasn't interested in the discussion. I am neither offended nor threatened by your theatrics, I'm informed by them. Why would a scientist need you?

Why does it matter? There are tons of scientific authors for the human genome paper and yet you ignore their reported results which includes 200,000 ERV's for the human genome. You also ignore the scientists who authored the chimp genome paper who reported that just 100 of those 200,000 human ERV's are human specific, that the rest of them are shared with chimps.

Ok, so where are the Chimpanzee ancestors in the fossil record then?

Sitting in the ground.

Everything I have said is either inescapably true or a matter of opinion.

The number of ERV's in the human genome and the number of human specific ERV's is not a matter of opinion. They are a matter of record. It is time that you dealt with that record.

 

[StormanNorman]

Why does it matter? There are tons of scientific authors for the human genome paper and yet you ignore their reported results which includes 200,000 ERV's for the human genome. You also ignore the scientists who authored the chimp genome paper who reported that just 100 of those 200,000 human ERV's are human specific, that the rest of them are shared with chimps.



Sitting in the ground.



The number of ERV's in the human genome and the number of human specific ERV's is not a matter of opinion. They are a matter of record. It is time that you dealt with that record.

I'm not a genetics expert, but just to see if I have this straight. Mark's "analysis" is based on those elements of the human and chimp genomes that differ from one another, e.g., the lineage specific transposable element activity portions. And, low and behold, we see lots and lots of differences. However, these lineage specific transposable element activity portions only make up very small percentages of the human and chimp total genomes. In other words, he is ignoring the remaining vast majority of the genomes that are similar in terms of ERV locations, etc.

Does that sum it up??

 

[USincognito]

To me it looks like a rehash of every misunderstanding of genetics you've ever posted here. Not exactly an exciting menu.

I was thinking, haven't we been there and done that, re: trying to correct mark's misuderstanding of what is being measured before in at least 4 or 5 previous threads he's started.

eta -

Almost the same OP:
http://www.christianforums.com/t7728562/
http://www.christianforums.com/t7682737/
http://www.christianforums.com/t7682738/
http://www.christianforums.com/t7545375/


also here:
http://www.christianforums.com/t7528893/
http://www.christianforums.com/t7528899/

 

[mark kennedy]

Yep. That is exaclty what you do in the rest of your post.

No it's not, getting you focused on the actual facts is a constant uphill climb.

That is not what that chart says. That chart lists the ERV's that are specific to that lineage.

Specifically, this table says that the Chimpanzee Genome has 234 ERV class 1 elements greater then 1 million base pairs (MPS). Class I ERV family PTERV1 has 100 members and is one of the most abundant families of ERVs in the Chimpanzee genome.

Those are the ERV's that are not shared with humans. The other 200,000 are shared with humans which is why they are not listed in the chart for lineage specific transposable element activity.

You really need to get your facts straight, I'm getting really tired of chasing you around this mulberry bush. When you look at, 'Table 11 Number of copies and fraction of genome for classes of interspersed repeat'. It shows that the ERVs make up ~127 Mbps which comes to ~4% of the human genome. This one is telling me the ERVs make up ~8% of the human genome

Would you kindly tell me which is correct because we are talking about a difference of over 100 Mbps. It is impossible to have a technical discussion with someone who on the one hand wants to condescend to me about scientific facts and then stubbornly refuses to present accurate facts.

Which is it?

The first line of this paper, Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes, specifically states:

The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence.​

Do you think it's possible that the specifics have been revised substantially over the last decade? Why don't you do the reading, get your facts updated and maybe we can talk about this substantively.

The ERV's listed for humans in that chart are the ERV's that have inserted into the human genome since the two lineages split. The ERV's listed for chimps are the ERV's that have inserted into the chimp genome since the two lineages split. That is why the chart lists separate lineages.

Yea....so....

Want to guess how they determined which ERV's are lineage specific?

Guess? I've told you so many times I'm turning into a spamer.

Just so we are on the same page, do you agree that there are ~200,000 ERV's in the human genome and that it is substantiated by Table 11 from the human genome paper.

I'm not entirely sure, is this the source of your statement. If it is we should correct that number slightly, if it's not I am going to need a direct reference. I mean, just so we are on the same page:

Have a nice day
Mark

 

[mark kennedy]

I'm not a genetics expert, but just to see if I have this straight. Mark's "analysis" is based on those elements of the human and chimp genomes that differ from one another, e.g., the lineage specific transposable element activity portions. And, low and behold, we see lots and lots of differences. However, these lineage specific transposable element activity portions only make up very small percentages of the human and chimp total genomes. In other words, he is ignoring the remaining vast majority of the genomes that are similar in terms of ERV locations, etc.

Does that sum it up??

Hardly, I have never really thought ERVs had anything to prove with regards to lineage. What I was deciphering when I finally gave up on this forum a few years back was the overall divergence. My principle interest was the basis for the most dramatic differences between Chimpanzees and humans. That has always been my interest in evolutionary biology, not these lame homology arguments, but how the Polar Bear evolved from the common ancestor it shared with the Grizzly for instance.

That's really all that has kept my interest. Over time I discovered a remarkable thing, these apologists for Darwinism can't get their facts straight. USincognito want's to post links to whatever mistakes and misunderstandings he thinks I made, guess he keeps a database or something. But when LM makes an obvious, fundamental error, again and again, he doesn't help the poor guy out.

I debated USincognito as well:

Forma Debate - Piltdown Man Should Not Be Cited By Creationists, it was a hoot.

Have a nice day
Mark

 

[46AND2]

Darn, was really hoping Mark had some new arguments for this topic. Instead, it's the same thing Loudmouth destroyed him on months ago; like he thought it would mature with age, or something.

Mark, why do you keep ignoring the fact that your 100 PtERV1 ERVs are a minuscule percentage of the total ERVs in the human and chimp genomes?

So what if they are the most popular family? 100 out of 200,000+ is next to nothing. All 100 of them were fixed in the chimp genome since the lineages split.

Furthermore, those 100 are the most popular out of the 425 that they tested, which were full length ERVs. The REST OF THE 200,000 were excluded from the study, because they were older and incomplete/damaged by mutation.

AND THIS MAKES PERFECT SENSE. Of course the PtERV1 viruses would be the most popular of these full length ERVs, because they were fixed in the genome of the chimps, since the split from humans. In other words, they are RECENT ERVs, giving them less time to be mutated, and more likely to be intact, full length ERVs, which was the focus of the study.

 

[USincognito]

I debated USincognito as well:

Forma Debate - Piltdown Man Should Not Be Cited By Creationists, it was a hoot.

Yeah, it would have been awesome if you could actually have stuck to the topic.

 

[mark kennedy]

Yeah, it would have been awesome if you could actually have stuck to the topic.

I did, I pointed out that it was not only a hoax but not a very good one at that. The Smithsonian article even said that, 'affirmed many scientists' hypotheses, they were reluctant to put it under scientific scrutiny'. That was pretty much your premise.

You brought up some good one, the Taung child is described in this way in the Wikipedia article about it:

3' 6" (105 cm) and weighing about 20–24 pounds (9–11 kg). It had a cranial capacity of 400-500 cc. and lived mainly in a savanna habitat. Examinations of the Taung Child fossil compared to that of an equivalent 9-year-old child suggest that A. africanus had a growth rate to adolescence more similar to that of modern apes like chimpanzees (genus Pan) than to that of modern Homo sapiens. (Taung_Child)​

This is priceless, the Taung Child was regarded as a Chimpanzee until right around the time the Piltdown hoax was uncovered. I don't think that's a coincidence, nor do I think it's a coincidence that Louise Leaky got the expression 'Homo habilis' (Handy Man) from Raymond Dart. It has a chimpanzee skull, it lived in the savannas and had a growth rate more like Chimpanzees then humans. Conclusion, it must be one of our ancestors.

Probably the best debates I have had on here was the one with you and the one with Arikay. To this day, I would have to say Arikay is by far the most civil poster I've ever seen on any board discussing the subject matter. Still, you got into the actual fossils which is strangely hard to get people to do, Creationist or otherwise.

I guess I do have a tendency to ramble a bit, but in my defense, there are an awful lot of hominid fossils out there. I have always thought it a bit odd that there were no chimpanzee ancestors in the fossil record. I think the Taung Child could tell us why. Every time one is found it's automatically one of our ancestors, even if it is more like a Chimpanzee.

Have a nice day
Mark

 

[mark kennedy]

Darn, was really hoping Mark had some new arguments for this topic. Instead, it's the same thing Loudmouth destroyed him on months ago; like he thought it would mature with age, or something.

LM and I had our debate back in 2007. Then, like now, he had real problems getting current facts and figures. Not much has changed so the arguments are going to be about the same.

Mark, why do you keep ignoring the fact that your 100 PtERV1 ERVs are a minuscule percentage of the total ERVs in the human and chimp genomes?

They are one of the most abundant families of ERVs and they are absent in the Human Genome. They account for 7% of the divergence due to indels, which accounts for 3-4% of the divergence overall. This isn't much of an argument, as a matter of fact, I think it's a pretty strong argument against common ancestry.

So what if they are the most popular family? 100 out of 200,000+ is next to nothing. All 100 of them were fixed in the chimp genome since the lineages split.

There are 200,000 copies in the human genome according to the Human Genome paper. The table I think LM got his statistics concerning ERVs in the Human Genome reports just over 100 families and just over 200 subfamilies. You are mixing up families with copies.

How am I suppose to take these arguments seriously when I'm constantly dealing with bogus statistics?

Furthermore, those 100 are the most popular out of the 425 that they tested, which were full length ERVs. The REST OF THE 200,000 were excluded from the study, because they were older and incomplete/damaged by mutation.

Going to need to know where your getting your information.

AND THIS MAKES PERFECT SENSE. Of course the PtERV1 viruses would be the most popular of these full length ERVs, because they were fixed in the genome of the chimps, since the split from humans. In other words, they are RECENT ERVs, giving them less time to be mutated, and more likely to be intact, full length ERVs, which was the focus of the study.

If it makes perfect sense then why was it surprising to the Chimp Genome researchers, 'to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2)'?

It also says the 'the sequence differences among reconstructed subfamilies are too great (~8%) to have arisen by mutation since divergence from human'.

Perfect sense? I really don't follow the logic at all.

 

[USincognito]

As I've been explaining for nearly 7 years now, the topic was "Should Creationists cite Piltdown". It was not "A General Hominid Fossil Discussion" nor "Mark's Pet Theory That All Non-Homo Hominid Fossils Are Chimp Ancestors". I would have gladly discussed that in a proper context and we can do so here (you are the OP after all and a little drift within context won't hurt), but any discussion of fossils outside of the context of the Piltdown hoax was off topic for that debate.

As far as Taung, I explained why Piltdown was accepted by the British and the context of Dart's find was to show that the question of "big brain first" (Piltdown) or "bipedalism first" (Taung and all subsequent finds) was answered as soon as he removed it from it's matrix. Remember the importance of the location of the foramen magnum.

And whether Piltdown was accepted for 40 years or Taung was rejected (it seems like other finds by the 30s we're already supporting the latter) - Dart was ultimately vindicated and he was right all along.
Raymond Dart and our African origins
I hope this Google Books link works so you can see that the Taung skull is not a chimpanzee skull.

 

[mark kennedy]

They look pretty close to me and I'm not the only one who thinks so:

In Study of Brain Evolution, Zeal and Bitter Debate

Current estimates
Taung’s cranial capacity (uncorrected for age) is 382 cc
402–407 cm3 (4–6) are in fairly close agreement,
especially compared with Dart’s earlier estimate of 520 cm3

(Falk et al, PNAS)

As I've been explaining for nearly 7 years now, the topic was "Should Creationists cite Piltdown". It was not "A General Hominid Fossil Discussion" nor "Mark's Pet Theory That All Non-Homo Hominid Fossils Are Chimp Ancestors". I would have gladly discussed that in a proper context and we can do so here (you are the OP after all and a little drift within context won't hurt), but any discussion of fossils outside of the context of the Piltdown hoax was off topic for that debate.

Your premise was that it couldn't happen again, I don't think so. I suppose an obvious fabrication where a human skull is taken from a Black Plague burial site and an jawbone of an ape with the teeth filed down and painted couldn't. But taking a Chimpanzee skull and passing it off as a human ancestor seems perfectly permissible.

As far as Taung, I explained why Piltdown was accepted by the British and the context of Dart's find was to show that the question of "big brain first" (Piltdown) or "bipedalism first" (Taung and all subsequent finds) was answered as soon as he removed it from it's matrix. Remember the importance of the location of the foramen magnum.

Or perhaps the Chimpanzee ancestors were bipedal. You are forgetting, perhaps ignoring that a three-fold expansion of the brain is in order. Bipedalism is almost trivial compared to the evolution of the requisite genes in this evolutionary giant leap. Getting a bigger case for you computer isn't an upgrade, I think a Chimpanzee skull being passed off as a human ancestor is related to the Piltdown Hoax.

But why didn't anyone recognize this forgery? One reason is that beacause Piltdown affirmed many scientists' hypotheses, they were reluctant to put it under scientific scrutiny that might have proved it wrong. (Smithsonian)​

Why indeed did they not recognize the forgery, even in the United States? It's because it fit their hypothesis just like the Taung Child fits the current Darwinian thinking.

And whether Piltdown was accepted for 40 years or Taung was rejected (it seems like other finds by the 30s we're already supporting the latter) - Dart was ultimately vindicated and he was right all along.

Taung is and was a Chimpanzee ancestor, I think that would at least be a possibility if it were permissible to suggest that in the Darwinian theater of the mind.

 

[Tomk80]

Mark apparently did not read the article he himself cited. From the article:

"Among the features Dr. Dart identified was the lunate sulcus, a crescent-shaped furrow near the back of the brain that divides its occipital lobe, where visual information is processed, from the rest. The Taung child’s lunate sulcus, Dr. Dart reported, had been “thrust backwards” as it is in humans, rather than forward as in chimpanzees and other apes. The resulting size reduction of the occipital lobe, he concluded, had been accompanied by an enlargement of parts of the brain associated with higher cognitive functions.

Dr. Holloway created endocasts of the Taung child and other australopithecine skulls. Although Dr. Dart’s conclusions had been controversial, Dr. Holloway confirmed the bulk of them, including the posterior location of the lunate sulcus."

 

[NoPostDocFrock]

They look pretty close to me and I'm not the only one who thinks so:

And there we have it. Science-dilettantes like Mark think that scientists take a casual look at various brain specimens and decide which "look pretty close to me."

When one has zero familiarity with the evidence for evolution and common descent, that makes it a whole easier to dismiss the science. (Ignorance it not only bliss. It simplifies decision-making immensely!)

It also makes it easier to strut about declaring oneself the victor and to look down on all of those deluded scientists and their meaningless Ph.D. degrees!

 

[sfs]

Wiggle out? Dude, you doing what you always do, painting yourself into a corner. What the table says is that the ERV class 1 sequences are 79 million base pairs total, comprising under 3% of the entire sequence with 72 families. Ok, this is what we know about the Chimpanzee Genome:

According to this table the Chimpanzee Genome has 234 ERV class 1 elements greater the 1 million base pairs (MPS). Do you see a problem here yet?

I don't know about anyone else, but I don't see a problem here. According to this table, the chimp genome has 234 ERV class 1 elements not found in the human genome, and they total more than 1 million base pairs of sequence. If all 234 were full length, and they run about 7 kb per repeat, that would be 1.6 million base pairs. That's 2% of the total contribution of ERV class 1 elements to the human or chimp genome. (234 is a much smaller fraction of the total number of ERVs in the genome, but that's not surprising: the recent, lineage-specific insertions are much more likely to still be full length, and therefore much longer than the typical ERV fossil, which just consists of the terminal repeat portion.)

So what was the problem again? And what does this have to do with the evidence that ERV insertion points were inherited?

 

[Tomk80]

I don't know about anyone else, but I don't see a problem here. According to this table, the chimp genome has 234 ERV class 1 elements not found in the human genome, and they total more than 1 million base pairs of sequence. If all 234 were full length, and they run about 7 kb per repeat, that would be 1.6 million base pairs. That's 2% of the total contribution of ERV class 1 elements to the human or chimp genome. (234 is a much smaller fraction of the total number of ERVs in the genome, but that's not surprising: the recent, lineage-specific insertions are much more likely to still be full length, and therefore much longer than the typical ERV fossil, which just consists of the terminal repeat portion.)

So what was the problem again? And what does this have to do with the evidence that ERV insertion points were inherited?

Also, if it concerns 234 insertion sites, that basically means 234 ERV insertions in 7 million years, ie approximately one every 206,000 years. Not exactly a high number.

 

[Loudmouth]

LM and I had our debate back in 2007. Then, like now, he had real problems getting current facts and figures. Not much has changed so the arguments are going to be about the same.

Yes, you are still ignoring the facts.

They are one of the most abundant families of ERVs . . .

Of the 425 ERV's that those authors looked at. You keep ignoring this fact. There are 200,000 ERV's in the chimp genome.

They account for 7% of the divergence due to indels, which accounts for 3-4% of the divergence overall.

Why is this a problem?

This isn't much of an argument, as a matter of fact, I think it's a pretty strong argument against common ancestry.

Why is divergence after speciation an argument against common ancestry?

There are 200,000 copies in the human genome according to the Human Genome paper. The table I think LM got his statistics concerning ERVs in the Human Genome reports just over 100 families and just over 200 subfamilies. You are mixing up families with copies.

No, I am not. There are 200,000 insertions. Those 200,000 insertions fall into 100 families.

Going to need to know where your getting your information.

Table 2 from the chimp genome paper only lists lineage specific insertions which are the non-orthologous insertions. Of the 200,000 human ERV's only about 100 are not found in chimps at the same location in the chimp genome. That is where I am getting my information. Do you know what "lineage specific" means?

If it makes perfect sense then why was it surprising to the Chimp Genome researchers, 'to find that the chimpanzee genome has two active retroviral elements (PtERV1 and PtERV2)'?

Please explain how PtERV insertions are a problem for common ancestry. I would really like to know why you keep bringing them up. Do you really think that evolution is falsified by pointing to mutations that produce divergence?

It also says the 'the sequence differences among reconstructed subfamilies are too great (~8%) to have arisen by mutation since divergence from human'.

Right, so the mutation was not occuring in apes, but in the virus which has a higher mutation rate.

 

[Loudmouth]

No it's not, getting you focused on the actual facts is a constant uphill climb.

So says the person who doesn't understand the difference between shared and lineage specific insertions.

Specifically, this table says that the Chimpanzee Genome has 234 ERV class 1 elements greater then 1 million base pairs (MPS). Class I ERV family PTERV1 has 100 members and is one of the most abundant families of ERVs in the Chimpanzee genome.

False. That is NOT what either paper says. First, the 234 ERV class I insertions are not all of the insertions in the chimp genome. Those are the lineage specific insertions found in chimps. You keep leaving this fact out. Also, the "PtERV1 is one of the most abundant families" is based on a survey of just 0.2% of the total ERV's in the chimp genome. You keep ignoring this fact as well.

You really need to get your facts straight, I'm getting really tired of chasing you around this mulberry bush. When you look at, 'Table 11 Number of copies and fraction of genome for classes of interspersed repeat'. It shows that the ERVs make up ~127 Mbps which comes to ~4% of the human genome. This one is telling me the ERVs make up ~8% of the human genome

Yes. It is a question of how each chart incorporates MaLR's which have features of both ERV LTR's and retrotransposons. If I understand it correctly, the LTR from an ERV has hitched a ride on a transposon so the insertions themselves are not retroviral driven but transposon driven. At the same time, they do contain viral DNA in the form of LTR's. It all depends on how you want to count MaLR's. For clarity, I prefer to focus just on the insertions that are driven by retroviral insertion which would be the 3 classes listed in the Table 11 of the human genome paper.

Would you kindly tell me which is correct because we are talking about a difference of over 100 Mbps. It is impossible to have a technical discussion with someone who on the one hand wants to condescend to me about scientific facts and then stubbornly refuses to present accurate facts.

I have presented accurate facts throughout. I have referred to the same table from the very start of this thread. That table has not changed.

The first line of this paper, Divergent Patterns of Recent Retroviral Integrations in the Human and Chimpanzee Genomes, specifically states:

The human genome is littered by endogenous retrovirus sequences (HERVs), which constitute up to 8% of the total genomic sequence.
​

Do you think it's possible that the specifics have been revised substantially over the last decade? Why don't you do the reading, get your facts updated and maybe we can talk about this substantively.

Again, your reading comprehension is getting in your way. It all has to do with the MaLR's. MaLR's do have ERV sequences, but they were not created by the insertion of a retrovirus into the genome. Rather, they were produced by transposon activity. Instead of having to discuss two different mechanisms of insertion I wanted to focus on just one, the mechanism that retroviruses use to insert their genome into the host genome. For that purpose, I have focused on the 200,000 insertions spread over ERV's I-III in table 11 of the human genome paper.

Yea....so....

So it demolishes your entire argument.

Guess? I've told you so many times I'm turning into a spamer.

So how did they determine which HERV-K insertions were lineage specific and which were shared? Please, humor me.

 

[Loudmouth]

I'm not a genetics expert, but just to see if I have this straight. Mark's "analysis" is based on those elements of the human and chimp genomes that differ from one another, e.g., the lineage specific transposable element activity portions. And, low and behold, we see lots and lots of differences. However, these lineage specific transposable element activity portions only make up very small percentages of the human and chimp total genomes. In other words, he is ignoring the remaining vast majority of the genomes that are similar in terms of ERV locations, etc.

Does that sum it up??

That sums it up nicely. For whatever reason, Mark thinks that the subsequent evolution of both the human and chimp genomes after they split from a common ancestor is evidence against evolution. Strange, isn't it? I don't know where he got this idea, but he somehow thinks that once humans and chimps split that they should be incapable of incorporating any new ERV's into their genomes even though each carried hundreds of thousands of ERV's from their mammalian ancestors.

Perhaps Mark can explain why evolution should arbitrarily prevent new retroviral insertions at a specific branch in one clade.

 

[Loudmouth]

I would also like to focus on one of Mark's other misrepresentations. He claims that PtERV1 and 2 insertions are the most numerous in the chimp genome, and he cites this paper as his support:

Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses

So let's see what the paper really says. First, how many ERV's did they look at?

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

Notice the bolded part. Even the authors admit that this is a definite underestimate for the total number of ERV's in the chimp genome. They used very stringent criteria, so what they ended up with were a lot of very recent and full length insertions. Of course, this would include most of the PtERV1 and 2 insertions since they are very recent in origin and many are still full length (older insertions can recombine at the LTR's which produces a solo LTR).

So to sum up, the authors admit that they did not look at all ERV's in the chimp genome. Second, they used a method that will strongly bias their samples towards the most recent insertions.

This paper can not be used to make the claim that PtERV1 and 2 insertions are the largest family across all insertions within the chimp genome.