Do Chimps and Humans Share a Common Ancestor? Primer for a formal debate

[JBJoe]

Now we can talk about the particulars if you want to read the paper.

Why don't you just start with the particulars. You've laid out at least one unsupported claim, let's see you support it.

 

[mark kennedy]

Hey, that's my gif! Get your own!

While I'm once-overing, why not start up a line of discussion?

Sorry, I just thought it would be fun to steal it but you caught me. At any rate, pay attention to the actual differences, particularly:

Single base pairs- 35 Mb
Indels- 5 million evens/90 Mb
Chromosomal rearrangements/8 inversions 20Mb.

All this is, is a direct comparison of the nucleotide sequences, based on the genome of one chimpanzee. There is a brief discussion of the ERVs and they mention natural selection in the gene evolution section. I'll just let you browse the paper and I'll be back to see what your thoughts are on the subject.

If your interested in an exposition of the text let me know, I'll be happy to post or PM one.I also have a link to some of the papers cited if you are interested.

Grace and peace,
Mark

 

[USincognito]

The only worse thing in dealing with Mark's debate style than his misunderstandings (note where he referred to ERVs as mutations earlier) is his myopia when it comes to looking at the evidence. To wit...

So the chimpanzee ancestors are in natural history musuems marked Homo XXX.

And the fact that they're more humanlike than chimp-like means nothing? I see.

Not when you look at the cranial capacity.

Cranial capacity isn't the only factor in determining how fossils are classified. As was noted earlier (sorry, I forget who pointed this out) Hominids are bipedal and and the telling characteristic for bipedalism is the location of the Foramen Magnum. All hominid fossils where we have the Foramen Magnum present (even partially) it's location is consistent with bipedalism and thus the fossils cannot be Pan.

It gets even worse for the Creationist claim that some of these fossils are chimps because even Australipithecene fossils like Taung Child have, you guessed it, a Foramen Magnum consistent with bipedalism. The question of which came first big brain or bipedalism was what allowed the Piltdown hoax to be successful. Taung put the nail in the coffin of brain first in the 1920s and every discovery since has been consistent with bipedalism first, then enlarged cranial capacity, then more human (H. sapiens) in appearance over time.

One of Mark's finest examples of myopia when it comes to the fossils though is Turkana boy. Here he trots out his cranial capacity mantra and claims that a 910cc brain is well withing "normal human limits" (it's not) and completely ignores the other facts to assert he was a normal modern human. The other facts are that he was about 12 years old, about 5 1/2 ft. tall, had cranial capacity of 880 cc, which is that of a 3 year old, and had a jaw 3 times more massive than modern humans.

Somehow though his projected adult cranial capacity makes him, in Mark's mind, a "normal" modern human.

 

[Split Rock]

It's based on my epistemology and genetics refutes Darwinism every single time.

Really, Mark? Then why don't you explain to all of us why dirty, souless chimpanzees share 95-96% of their DNA with us? Did your God blow on some dust to create them as well? Is that why their DNA is so similar to Adam's?

 

[sbvera13]

Here is a chart of cranial capacity in fossil hominids over time, from 3.5 mya to present.

http://www.pandasthumb.org/archives/2006/09/fun_with_homini.html

 

[mark kennedy]

Here is a chart of cranial capacity in fossil hominids over time, from 3.5 mya to present.

http://www.pandasthumb.org/archives/2006/09/fun_with_homini.html

Oh yea, those ridiculas scattergrams. This is what the exponential growth of the hominid family tree would have looked like:

So, 2 million years ago the cranial capacity was under 400cc-500cc. About 1.9 mya it's going to jump up to 1000cc-1200cc, no apparent reason or molecular mechanism. It stays static for about a million years. Then about 350,000 years ago it's 1600cc and drops about 10% to the modern range about 30,000 years ago.

We have no idea how our chimpanzee cousins are doing during this time. We do know that they are getting inundated with ERV germline mutations but that's about it.

By the way, does anyone know what the only known effect of a mutations in a gene involved in neural systems is? The answer should not surprise you but I doubt anyone will admit the difficulties it raises for this common ancestry myth.

 

[USincognito]

The only worse thing in dealing with Mark's debate style than his misunderstandings (note where he referred to ERVs as mutations earlier) is his myopia when it comes to looking at the evidence. To wit...

We have no idea how our chimpanzee cousins are doing during this time. We do know that they are getting inundated with ERV germline mutations but that's about it.

Hold your applause folks. The show isn't nearly over yet.

And still waiting for you to explain why all hominid fossils have the foramen magnum of a biped, but we don't have any bipedal chimpanzees walking around? We need to worry about the simple stuff before rehashing old news you've been corrected on many times previously.

 

[sfs]

If your interested in an exposition of the text let me know, I'll be happy to post or PM one.

If you want to understand the paper, however, you would be well advised to skip Mark's exposition. (If there really is a question about the chimpanzee genome paper, ask me instead -- I'm one of the authors.)

 

[Skaloop]

If you want to understand the paper, however, you would be well advised to skip Mark's exposition. (If there really is a question about the chimpanzee genome paper, ask me instead -- I'm one of the authors.)

For the win!

 

[lemmings]

By the way, does anyone know what the only known effect of a mutations in a gene involved in neural systems is? The answer should not surprise you but I doubt anyone will admit the difficulties it raises for this common ancestry myth.

What do you mean only one outcome? Changes in the genes can result in dramatically different outcomes influencing both the size and operation of the brain.

Harvard University managed to increase the size of a rodent’s brain by 50% by changing only one gene.
http://www.hno.harvard.edu/gazette/2002/10.10/01-genes.html

 

[Mumbo]

If you want to understand the paper, however, you would be well advised to skip Mark's exposition. (If there really is a question about the chimpanzee genome paper, ask me instead -- I'm one of the authors.)

I have a question. Is Mark's take on your paper entirely based upon misconceptions? If so, I think I'll take my leave from the thread.

Edit: In either case, I'd like to hear your version of things. Given that you presumably don't share Mark's belief that chimps and humans are unrelated, and that you seem to have glimpsed Mark's arguments before, why are his perceived differences between the two species insufficient in casting doubt upon current theory?

 

[Tomk80]

Um? What? I'm not sure what you're saying here. There are thousands of HERVs in the human genome. HERV-K is a family of ERVs that is present in both human and chimpanzee.

One of the paper's Mark likes so much stated that ERVs are all but extinct in the human lineage. I'm at work right now so don't have the exact paper, but what it meant was that HERVs are all but extinct now and for some time in the past. Mark apparantly thinks this means there aren't any HERVs in the human genome.

Individual ERVs are not introduced by mutation slowly over time. They are knocked out reverse-transcribed viral RNA that infected a germ cell. This happens in a single generation.

 

[Tomk80]

I'm guessing they used different criteria for each figure, but go on.
Great! Now just show that the 95% figure is correct while the 98% one is not, and you've got a case.

Both are correct. They just measured different things. The 98% figure measured the difference when purely looking at base changes, but did not take into account indels. The 95% figure is including indels.

 

[Chalnoth]

Mark, here's the basic problem with your entire argument.

We're saying that the evidence shows that we share a common ancestor with chimpanzees.

You are saying that we don't know exactly how all of the mutations between now and the common ancestor occurred, therefore it didn't.

In other words, your claims simply do not mean what you claim them to mean. Your claims, at best, would force us to rethink how we believe humans evolved, were your claims correct. Your claims cannot falsify common descent by their very nature.

The way to falsify common descent, instead, is to look for violations of a nested hierarchy. There are none that are not easily explainable, while there are a heck of a lot of opportunities for the nested hierarchy to be violated, morphologically and genetically. So the case is solid: humans and chimpanzees share a common ancestor. Your quibbling over how it occurred is completely and utterly meaningless to that conclusion.

 

[mark kennedy]

The only worse thing in dealing with Mark's debate style than his misunderstandings (note where he referred to ERVs as mutations earlier) is his myopia when it comes to looking at the evidence. To wit...

So the chimpanzee ancestors are in natural history museums marked Homo XXX.

Notice the ERVs are mentioned but the point I made concerning them is not addressed. The Chimpanzee genome has 235 lineage specific ERV Class 1 insertions > 1 Mb while the human genome has 5 that are 8 kb.

Cranial capacity isn't the only factor in determining how fossils are classified. As was noted earlier (sorry, I forget who pointed this out) Hominids are bipedal and and the telling characteristic for bipedalism is the location of the Foramen Magnum. All hominid fossils where we have the Foramen Magnum present (even partially) it's location is consistent with bipedalism and thus the fossils cannot be Pan.

That does not mean that the Austropithecenes cannot be Pan ancestors.

Taung Child,Astralopithecus africanus cranial capacity of about 440 cc.Chimpanzee ancestors being semi-bipedal creates no difficulties for Creationism that I am aware of.

It gets even worse for the Creationist claim that some of these fossils are chimps because even Australipithecene fossils like Taung Child have, you guessed it, a Foramen Magnum consistent with bipedalism. The question of which came first big brain or bipedalism was what allowed the Piltdown hoax to be successful. Taung put the nail in the coffin of brain first in the 1920s and every discovery since has been consistent with bipedalism first, then enlarged cranial capacity, then more human (H. sapiens) in appearance over time.

Every African and Asian ape fossil is automatically considered a human ancestor. Taung is not a nail in the coffin it's an ape with gracial features.

One of Mark's finest examples of myopia when it comes to the fossils though is Turkana boy. Here he trots out his cranial capacity mantra and claims that a 910cc brain is well withing "normal human limits" (it's not) and completely ignores the other facts to assert he was a normal modern human. The other facts are that he was about 12 years old, about 5 1/2 ft. tall, had cranial capacity of 880 cc, which is that of a 3 year old, and had a jaw 3 times more massive than modern humans.

The cranial capacity is well within human limits and except for a cranial capacity well below the mean average Turkana Boy is human.

III.1. VOLUMETRIC SURVEYS UPON BRAIN SIZE
12. Jay Giedd and colleagues of the National Institute of Mental Health, Child Psychiatry Branch received 624 responses to a newspaper advertisement for a MRI brain scanning study of 4-18 year-olds (1996). This group was carefully screened with psychometric tests and a psychiatric interview. Those with a learning disorder (or family members with one) were excluded. Of the 624 responses, only 112 met their stringent criteria for "normality." After MRI scans, volumes for various brain areas were measured. Striking variance was found. Of the 104 individuals who successfully completed their scans, volume for the cerebral hemispheres ranged from 735 cc (a 10-year-old male) to 1470 cc (a 14-year-old male) (taken from scatter diagram, Fig. 4). Unfortunately, Giedd did not report total brain volumes, but these can be inferred. The cerebral cortex makes up only 86.4% of brain volume when measured by MRI (Filipek, Richelme, Kennedy & Caviness, 1994), so the total brain volume of the 10-year-old would be larger at 850.7 cc. Brains at 10 years are about 4.4% smaller than adult size (Dekaban & Sadowsky, 1978), suggesting that that brain would grow to an adult size of 888 cc. Even using the lower figure of 80% cerebrum to brain ratio derived from anatomical studies suggests a figure of only 960 cc.(HUMAN EVOLUTION EXPANDED BRAINS TO INCREASE EXPERTISE CAPACITY, NOT IQ Target Article on Brain-Expertise, PSYCOLOQUY, Dr. John R. Skoyles skoyles@globalnet.co.uk )​

Well within the range and consistent with modern variance:

III.2.2 DANIEL LYON
20. One report of normal intelligence exists for a brain smaller than Homo erectus. According to Wilder (1911), Daniel Lyon was a nonretarded white watchman who worked for 20 years at the end of the nineteenth century in New York at the Pennsylvania Railway Terminal. He could read, write, and according to legal representatives of the company that employed him "there was nothing defective or peculiar about him, either mentally or physically." He was of average weight 65.8 kg, though of a below average height of 1.55 m. After he died at age 46 in 1907 from bronchitis, his brain was removed and subject to a professional autopsy with "accurate scales." It weighed just 680 grams (624 cc assuming a specific gravity of 1.09 for fresh brain).
21. Upon examination, Wilder could not attribute the small size of Lyon's brain to either pathology or atrophy. Indeed, the only unusual feature he noted was that the cerebellum was near normal size. This suggests that the volume of Lyon's cerebral hemispheres might have been small even for his already small brain. Indeed, the total size of his cerebral hemispheres, 371 cc is 128 cc less than the 499 cc (80%) which would be expected of a normally proportioned brain of 624 cc.
III.2.2 ANATOLE FRANCE
22. All these cases have been average or only slightly above average in intelligence. Perhaps small brains prevent extremely high levels of intelligence. But distinguished modern people have had brains within the size range of Homo erectus. For example, the brain of the Noble Prize winning novelist Anatole France (1844-1924) weighed 1017 grams (933 cc) post mortem (Gould, 1981, p. 92). One qualification to this figure is that brains shrink slightly with age and Alzheimer's disease. Although 80 years old, he was nondemented (he had married one Mademoiselle Emma Laprevotte only a few months before he died). Estimates for brain shrinkage over the 20 to 80 year age range for men vary in six studies between 3.9% and 8.6% (Dekaben & Sadowsky, 1978), suggesting France's brain when young could have been as big as 1013 cc, yet still well within the SD range of Homo erectus, 930 cc - 130 cc. (PSYCOLOQUY, Skoyles)​

Somehow though his projected adult cranial capacity makes him, in Mark's mind, a "normal" modern human.

I never said normal but there is every indication that he very easily could have been.

 

[JBJoe]

Notice the ERVs are mentioned but the point I made concerning them is not addressed. The Chimpanzee genome has 235 lineage specific ERV Class 1 insertions > 1 Mb while the human genome has 5 that are 8 kb.

Well, yeah. That's because the chimpanzee still has a number of active ERVs in its genome and humans do not. I do not see the problem here unless what Tomk80 says is true: you do not know what an extinct HERV actually is.

 

[sfs]

I have a question. Is Mark's take on your paper entirely based upon misconceptions? If so, I think I'll take my leave from the thread.

Edit: In either case, I'd like to hear your version of things. Given that you presumably don't share Mark's belief that chimps and humans are unrelated, and that you seem to have glimpsed Mark's arguments before, why are his perceived differences between the two species insufficient in casting doubt upon current theory?

I often have difficulty understanding what Mark's intended point is, so there is no guarantee that I'm responding to the right thing -- but I'll try anyway. The basic facts that Mark reports are correct: human and chimpanzee genomes differ by a little more than 1% if you count only single-base differences, but by about 5% if you include insertions and deletions (i.e. genetic material that is present in one species but not in the other. There's also a substantial amount of sequence that is inverted between the two species (i.e. it's the same DNA, more or less, but it has been flipped around in one species relative to the other). Mark's point seems to be that these differences are much too large for them to be the result of accumulated random mutations since the two species separated.

Why exactly Mark thinks that is the case I've never been able to tell. For single-base differences we have a pretty good estimate of the mutation rate based just on new mutations in humans, and it matches the observed single-base differences between humans and chimps very well (see here for details). So single-base differences are as expected.

The insertion/deletion differences were larger than expected, but the expectation didn't actually have a good basis: there was no good estimate of the insertion/deletion mutation rate prior to the first large-scale chimpanzee sequencing, and no one really knew what to expect. In the last several years (starting in ~2004), it has in fact become clear that large insertions and deletions are much more common in the human population than previously believed. So work within the human population and comparisons of humans with chimpanzees both indicate that insertion/deletion variation is common and sometimes involves large amounts of sequence, meaning there is good qualitative agreement between the two approaches. Detailed quantitative comparisons are not yet possible, since human insertion/deletion variation is still too poorly understood for that.

Inversions are also turning out to be common in the human population, although again they have not been nailed down well enough to compare to the human/chimp differences.

 

[Split Rock]

Mark's point seems to be that these differences are much too large for them to be the result of accumulated random mutations since the two species separated.

Why exactly Mark thinks that is the case I've never been able to tell.

Your problem is that you are looking at this from the wrong end. What Mark has done is to work backward from the conclusion that Humans and Chimps have no common ancestor. Therefore, how ever many differences there are between human and chimp DNA sequences are, by default, too many. I once asked him how many base-pair differences were too many for us to have a common ancestor with chimps, and he answered it was the number that we differ in. If the number were 10 or 100 fold less, it would still have been the answer.

 

[mark kennedy]

I'll get into the ERVs later, this one is entirely too easy to pass up.

Why exactly Mark thinks that is the case I've never been able to tell. For single-base differences we have a pretty good estimate of the mutation rate based just on new mutations in humans, and it matches the observed single-base differences between humans and chimps very well (see here for details). So single-base differences are as expected.

The insertion/deletion differences were larger than expected, but the expectation didn't actually have a good basis: there was no good estimate of the insertion/deletion mutation rate prior to the first large-scale chimpanzee sequencing, and no one really knew what to expect. In the last several years (starting in ~2004), it has in fact become clear that large insertions and deletions are much more common in the human population than previously believed. So work within the human population and comparisons of humans with chimpanzees both indicate that insertion/deletion variation is common and sometimes involves large amounts of sequence, meaning there is good qualitative agreement between the two approaches. Detailed quantitative comparisons are not yet possible, since human insertion/deletion variation is still too poorly understood for that.

No one predicted the indels and the link you provided does not calculate the mutation rate. Lets do this again since you have so much trouble following my main point. There are five million indels in 5 million years in addition to the single base substitutions you describe in the link. These indels add up to something like 90 Mb.

That is one indel per year for 5 million years. Sounds pretty consistent with known mutation rates does it not?

That means all of us have 20 indels, with a mean average of 280 base pairs involved.

Sound about right Steve?

 

[mark kennedy]

I once asked him how many base-pair differences were too many for us to have