Chimpanzee Genome

[Tomk80]

With one exception - chimps and bonobos are more closely related to one another (sharing 99.6% of their DNA) than chimps are to humans (link). After all, bonobos are estimated to have split from chimps around 2.5 million years ago, long after humans and chimps started going their separate ways around 5-7 million years ago.

Interestingly, bonobos share about the same amount of DNA with humans as chimps do (around 98.7% according to the link above). I wonder why? You'd think we would share less DNA with them than we do with chimpanzees, considering we diverged from chimps earlier than they did.

Because the time since they split from us is still equal. Neither the chimps nor the bonobos stopped evolving after they split of from each other. The tempo of evolution remained the same for both of them (that is also one of the central features of a nested hierarchy).

Suppose that up to the split between bonobos and chimps, humans had accumulated 10 mutations and the common ancestor to bonobos and chimps had acquired 10 mutation. At this point in time, humans the common ancestor to bonobos and chimps differ in 20 mutations. Now the bonobo and chimp lineages split. In the time from the split up to now, mutation rates stay equal and chimps, humans and bonobos all acquite an extra 5 mutations. So since the common ancestor of humans, chimps and bonobos, all now have acquired 15 mutations, bonobos 15 and chimps 15. Humans now differ from chimps and from bonobos in 30 mutations, and chimp and bonobos from each other in 10.

I hope that is somewhat clear. It helps if you draw it out on paper.

 

[Loudmouth]

With one exception - chimps and bonobos are more closely related to one another (sharing 99.6% of their DNA) than chimps are to humans (link). After all, bonobos are estimated to have split from chimps around 2.5 million years ago, long after humans and chimps started going their separate ways around 5-7 million years ago.

I always forget about the bonobos for some reason. Good point.

Interestingly, bonobos share about the same amount of DNA with humans as chimps do (around 98.7% according to the link above). I wonder why? You'd think we would share less DNA with them than we do with chimpanzees, considering we diverged from chimps earlier than they did.

It is called genetic equidistance. We share the same common ancestor with chimps as we do with bonobos. Both chimps and bonobos are equally distant from that common ancestor, so they are equally distant from us. In the same way, the differences between the chimp and orangutan genome should in the same ball park as the differences between the gorilla and orangutan genome.

 

[sfs]

That's pretty abundant don't you think?

I don't think it is. If you think it is, tell us why.

I think your capable of it but you keep getting this tunnel vision that it's some kind of a smoking gun for common ancestry, it's not. For us to share a lot of DNA with Chimpanzees really prove very little, makes a nice homology argument but that's about it.

No one has offered that argument. Why are you dismissing an argument no one has made?

What you need is a molecular basis for adaptive evolution. You seem to forget, we have a brain three times bigger then a chimp.

What you need to do is support your claim that you were going to refute ERVs as an argument for common descent.

 

[sfs]

I started to write a detailed response to Mark and accidentally deleted it. It doesn't really matter, though, since there's nothing really there that says much of anything. The only substantive claim in this post was that ERVs insert preferentially in hotspots. That claim needs to be a great deal more specific before it can affect the argument. What is the experimental basis (i.e. cite the studies)? What fraction of the genome is an ERV likely to insert into? How likely are they to insert into the rest of the genome? What is the probability that 200,000 ERVs would insert into exactly the same spots in a 3-billion base pair genome in two different species? Why does the pattern of which ERV insertions are present match the phylogeny of, say, primates based on other characteristics? Why do more widely shared ERVs have more mutations in them?

In other words, try addressing the real argument for common descent.

I
Oh and BTW, how you liking Harvard? Do you miss MIT?

I haven't gone anywhere, really. The place I work was originally part of MIT (and the Whitehead Institute), and then split off to become an independent research institution (the Broad Institute) that is still affiliated with both MIT and Harvard. I've had a visiting appointment with the Harvard School of Public Health for several years, and I've recently become more closely associated with a lab at Harvard -- but I still have the same office.

 

[Loudmouth]

I started to write a detailed response to Mark and accidentally deleted it. It doesn't really matter, though, since there's nothing really there that says much of anything. The only substantive claim in this post was that ERVs insert preferentially in hotspots. That claim needs to be a great deal more specific before it can affect the argument. What is the experimental basis (i.e. cite the studies)? What fraction of the genome is an ERV likely to insert into? How likely are they to insert into the rest of the genome? What is the probability that 200,000 ERVs would insert into exactly the same spots in a 3-billion base pair genome in two different species? Why does the pattern of which ERV insertions are present match the phylogeny of, say, primates based on other characteristics? Why do more widely shared ERVs have more mutations in them?

In other words, try addressing the real argument for common descent.

The creationist "refutations" are a moving target where this is concerned. I have seen creationists who start out arguing for orthologous insertions occuring through independent insertions using hotspots as basis for their argument. When it becomes clear that there are millions of hotspots they quickly change arguments and use the "common creator" argument, as if a creator would include viral insertions as part of a design, and make sure to keep LTR divergence, insertion site, and overall ERV divergence in line with a nested hierarchy that evolution would produce.

 

[sfs]

The creationist "refutations" are a moving target where this is concerned. I have seen creationists who start out arguing for orthologous insertions occuring through independent insertions using hotspots as basis for their argument. When it becomes clear that there are millions of hotspots they quickly change arguments and use the "common creator" argument, as if a creator would include viral insertions as part of a design, and make sure to keep LTR divergence, insertion site, and overall ERV divergence in line with a nested hierarchy that evolution would produce.

It's a modular system: any argument can be plugged in, as long as the conclusion remains the same.

 

[USincognito]

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

"Pretty close" =/= "is" or "the same as". And seriously, did you take a long hard look at the comparison of the brain and the endocast? A cursory glance would tell almost anyone that the Taung endocast is not the same as the chimp brain. And "look{ing} pretty close" isn't good enough - which relates back to your problem understanding why your objections to ERV evidence doesn't withstand scrutiny. An Ichthysaur and a dolphin "look pretty close", but they couldn't be more different.

Your premise was that it couldn't happen again, I don't think so.

You're welcome to have that opinion, but it won't change the facts I cited in the debate:
- In 1912 the only widely known hominid fossil examples were the Java erectus fossils and Neanderthals. Many other hominid fossils have been discovered since then and not a single one of them has been proven to be a hoax.
- In 1912 the cutting edge of communications technology was the newspaper and the candlestick telephone. Over the last ~100 years various recording and reporting media have been developed so that any sort of claim is quickly disseminated and dissected by people who are in the know. Look at "Archaeoraptor". The article promoting it appeared in the November 1999 issue of National Geographic. By February 3rd they were putting out a press release admitting they'd been duped. And to add a layer of irony to your opinion, it turns out that the fossils used to create "Archaeoraptor" were legitimate dino-bird transitionals that have increased the knowledge of that transition despite the hoax.

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.

Except Taung, nor any other Au. afarensis or Au. africanus skulls aren't those of Chimpanzees. The cranial volumes don't match. The measurements don't match.

Or perhaps the Chimpanzee ancestors were bipedal.

This is a possibility and one lineage remained bipedal (Au. and Homo) while the other returned to a basal state (Pan), but the more likely explanation - especially given all of the fossil, genetic and molecular evidence is that the basal ancestor to Pan and the Au./Homo lineage was quadrapedal like gorillas and the basal Homininae species that gave rise to all three lines.

You are forgetting, perhaps ignoring that a three-fold expansion of the brain is in order.

I'm neither forgetting nor ignoring your "I can't believe it happened in ~6mil years despite the fact that I don't believe in 6mil years and also think hyperevolution that lead to much more astounding evolution occured within ~1000 or less years because of my Noah's Flood interpretation" argument from selective incredulity. You have been shown the graph demonstrating a gradual increase in brain size from Au. africanus through H. sapiens repeatedly. There is no mystery. Changes in diet and the loss of chewing muscles attached to the top of the cranium allowed for the braincase to increase gradually over time.

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.

As has been noted many times previously, none of the Hominan skulls are Chimpanzee skulls. You have failed to make that case in the past and you fail to make it now. Wasn't there some study you found particularly powerful in supporting your genetic argument a while back? HAR1 wasn't it? I provided you with an e-mail address of one of the papers authors and suggested you contact him and tell him that the findings, instead of supporting evolution, were actually the silver bullet that killed it.

You never did that, did you?

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.

Again, 1912. Nine... teen... twelve.

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.

Wait a minute. At least twice in this post you have claimed that Taung was a Chimpanzee and at the very end you change your story to suggest it was a Chimpanzee ancestor? Do you have any idea how hard such inconsistency makes it to take you seriously?

 

[StormanNorman]

"Pretty close" =/= "is" or "the same as". And seriously, did you take a long hard look at the comparison of the brain and the endocast? A cursory glance would tell almost anyone that the Taung endocast is not the same as the chimp brain. And "look{ing} pretty close" isn't good enough - which relates back to your problem understanding why your objections to ERV evidence doesn't withstand scrutiny. An Ichthysaur and a dolphin "look pretty close", but they couldn't be more different.



You're welcome to have that opinion, but it won't change the facts I cited in the debate:
- In 1912 the only widely known hominid fossil examples were the Java erectus fossils and Neanderthals. Many other hominid fossils have been discovered since then and not a single one of them has been proven to be a hoax.
- In 1912 the cutting edge of communications technology was the newspaper and the candlestick telephone. Over the last ~100 years various recording and reporting media have been developed so that any sort of claim is quickly disseminated and dissected by people who are in the know. Look at "Archaeoraptor". The article promoting it appeared in the November 1999 issue of National Geographic. By February 3rd they were putting out a press release admitting they'd been duped. And to add a layer of irony to your opinion, it turns out that the fossils used to create "Archaeoraptor" were legitimate dino-bird transitionals that have increased the knowledge of that transition despite the hoax.



Except Taung, nor any other Au. afarensis or Au. africanus skulls aren't those of Chimpanzees. The cranial volumes don't match. The measurements don't match.



This is a possibility and one lineage remained bipedal (Au. and Homo) while the other returned to a basal state (Pan), but the more likely explanation - especially given all of the fossil, genetic and molecular evidence is that the basal ancestor to Pan and the Au./Homo lineage was quadrapedal like gorillas and the basal Homininae species that gave rise to all three lines.



I'm neither forgetting nor ignoring your "I can't believe it happened in ~6mil years despite the fact that I don't believe in 6mil years and also think hyperevolution that lead to much more astounding evolution occured within ~1000 or less years because of my Noah's Flood interpretation" argument from selective incredulity. You have been shown the graph demonstrating a gradual increase in brain size from Au. africanus through H. sapiens repeatedly. There is no mystery. Changes in diet and the loss of chewing muscles attached to the top of the cranium allowed for the braincase to increase gradually over time.



As has been noted many times previously, none of the Hominan skulls are Chimpanzee skulls. You have failed to make that case in the past and you fail to make it now. Wasn't there some study you found particularly powerful in supporting your genetic argument a while back? HAR1 wasn't it? I provided you with an e-mail address of one of the papers authors and suggested you contact him and tell him that the findings, instead of supporting evolution, were actually the silver bullet that killed it.

You never did that, did you?



Again, 1912. Nine... teen... twelve.



Wait a minute. At least twice in this post you have claimed that Taung was a Chimpanzee and at the very end you change your story to suggest it was a Chimpanzee ancestor? Do you have any idea how hard such inconsistency makes it to take you seriously?

If someone doesn't want to believe something, then they are going to convince themselves that it's just not true; the evidence has been forged, the experts really aren't very expert and some Joe (or Mark) on the internet knows better than they do, etc.

Taung, Lucy, Ardi, etc. were all found in Eastern and Southern Africa in a grasslands environment and away from the dense forests and jungles where Chimpanzees typically live. And all of these fossils are 2.5 million+ years old and exhibit decidedly human characteristics. They weren't chimps.... that's just wishful thinking...

 

[Loudmouth]

To sum up this thread . . .

Mark Kennedy has argued that ERV's are not evidence of common ancestry because . . . Mark says so. He has never explained why ERV's are not evidence for common ancestry.

The only thing that Mark has tried to do is cloud the issue of how many ERV's there are, and his reasons for doing so are very transparent. He knows that we share hundreds of thousands of ERV's with chimps while only differening by a few hundred. Mark thinks that by emphasizing the differences as much as possible that we can ignore the overwhelming number of genetic markers shared by humans and chimps.

This is a very strange argument indeed. First, he is trying to use divergence to argue against evolution while forgetting that divergence is exactly what evolution predicts. Not only that, but evolution predicts a pattern of divergence which is a nested hierarchy, and that is exactly what we see with ERV's at three different levels: loci, LTR divergence, and overall sequence divergence.

Second, Mark argues that common ancestry can not be evidenced by homology. This is the strangest argument of all. We observe that siblings share homology because of shared ancestry. DNA paternity tests are based on homology. Forensic DNA fingerprinting is based on homology. Homology is EXACTLY what we would expect to see if common ancestry is true, and we would once again expect to see a nested hiearchy of shared features which we do. Perhaps Mark could help us out be describing what a comparison of ERV's should look like if humans and chimps really did share a common ancestor, in his opinion.

Mark Kennedy is the Black Knight.

http://en.wikipedia.org/wiki/Black_Knight_(Monty_Python)

 

[USincognito]

It appears that Mark has yet again abandoned a thread started with basically the same OP he has for the last 5 or 6 years. I've tagged this thread with "mark ERV" and "mark genomics" so when he starts the exact same thread again in 3-6 months, we can use them to refer back to this thread instead of wasting time providing him with the same answers he has ignored over and over again.

 

[Loudmouth]

Mark seems to be continuing the same flawed argument. He thinks that if similarity evidences common ancestry then differences falsify common ancestry. He actually thinks that evolution falsifies evolution.

 

[Wiccan_Child]

Having read the first few posts, I was enthralled, and before I knew it I've got to page ten and the thread is over. This was truly an enjoyable thread to read, and I learned a lot about ERV genetics and why it's such good evidence for evolution.

Bravo to you, Loudmouth, and everyone else, for calling Mark out on his sloppy statistics and quote mining.

 

[ThouShaltNotPoe]

Mark Kennedy's nonsense got totally shredded.

Don't bring a pea-shooter to a hand-grenade fight, Mark.

 

[super animator]

Having read the first few posts, I was enthralled, and before I knew it I've got to page ten and the thread is over. This was truly an enjoyable thread to read, and I learned a lot about ERV genetics and why it's such good evidence for evolution.

Bravo to you, Loudmouth, and everyone else, for calling Mark out on his sloppy statistics and quote mining.

Here a thing I notice with mark, he appears to being copying and pasting his arguments for years now.

 

[USincognito]

Here a thing I notice with mark, he appears to being copying and pasting his arguments for years now.

Indeed. If you check out post #44, I found at least 6 over the years with basically the same OP/MO.

 

[46AND2]

Pity that Mark is abandoning his thread...This is one of my favorite topics of discussion in the creation/evolution debate. A google search for it is what brought me to these forums in the first place.

 

[USincognito]

Unfortunately that's part of his MO. I've added the tags "mark erv" and "mark genomics" so we can refer back to this thread when he basically starts the same one in 2-3 months.