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Author Topic:   Comparisons of Neandertal mtDNA with modern humans and modern chimpanzees
Sylas
Member (Idle past 5260 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 1 of 80 (104558)
05-01-2004 1:48 PM


Several threads have been discussing research from the late nineties, which involved the comparison of mitochondrial DNA extracted from Neanderthal remains with mtDNA in humans, and in chimpanzees, as a side issue from the main thread topic. This thread is intended to allow focussed discussion of the mtDNA comparisons.
Two papers have been cited in this regard, and both are on-line.
  1. Neandertal DNA Sequences and the Origin of Modern Humans
    by M. Krings, A Stone, R. W. Schmitz, H. Krainitzki, M. Stoneking, S. Pbo
    in Cell, Vol. 90, pp 19—30, July 11, 1997.
  2. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen
    by M. Krings, H. Geisert, R. W. Schmitz, H. Krainitzki, S. Pbo
    in PNAS Vol. 96, Issue 10, pp 5581-5585, May 11, 1999
Some commentary on the first paper in particular has erroneously described the results as saying that Neandertal mtDNA is about halfway between ours and that of a chimpanzee. However, none of the scientists involved in the research say anything of the kind, and the empirical data flatly contradicts that assertion.
It is, on the other hand, a natural error to make by a novice reading the first paper[1], since the raw data was not shown, and the following diagram does seem to suggest some kind of halfway aspect to the data.
Distributions of Pairwise Sequence Differences among Humans, the Neandertal, and Chimpanzees (Figure 6 from Krings et. al. (1997); click for full size)
To better show what is going on, I have produced another parallel diagram for comparison, based on the second paper. The diagram above omits the Neandertal-chimp differences, and the paper does not report those comparisons, although I understand that they were done. The second paper refers to a second independent experiment, involving a slightly longer sequence of mtDNA and more details on the comparison data. In this case the data set involved 663 human mtDNA sequences, 1 Neandertal sequence, 7 common chimpanzee sequences, and 2 pygmy chimpanzee sequences (bonobos), and every sequences was compared with every other sequence.
The pairwise differences can be plotted as follows (click on image for full size in a new window):
This is not a direct plot of the data set, since I do not have that available. Instead, I plotted normal curves based on the quoted mean and standard deviation for each class of comparison. Because there are two species of chimpanzee, the Chimp-Chimp comparison has a wide spread of values. Because there is only one Neandertal sequence, there is no Neandertal-Neandertal comparison.
The critical point to note here is that Neandertals and Humans are almost exactly the same distance from Chimpanzees. This is exactly what we should expect from an evolutionary perspective, since biologically speaking, Neandertals and humans are both equally evolved from chimpanzees. This result is a contrast to the common misunderstanding of evolution as a kind of ladder of progress, with some species being less evolved than others, or with one existing species between "between" another two existing species.
Cheers -- Sylas
(Added in edit. The plot has been altered since posting the article. If you don't see a curve for the differences between common chimpanzee and bonobos, then refresh your browser. Images reduced, linked. Caution... some links open in your current window.)
[This message has been edited AdminSylas, 05-03-2004]

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AdminAsgara
Administrator (Idle past 2303 days)
Posts: 2073
From: The Universe
Joined: 10-11-2003


Message 2 of 80 (104652)
05-01-2004 10:13 PM


Thread moved here from the Proposed New Topics forum.

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 3 of 80 (104739)
05-02-2004 3:28 PM
Reply to: Message 1 by Sylas
05-01-2004 1:48 PM


This is not a direct plot of the data set, since I do not have that available. Instead, I plotted normal curves based on the quoted mean and standard deviation for each class of comparison. Because there are two species of chimpanzee, the Chimp-Chimp comparison has a wide spread of values.
Very nice plot. The chimp-chimp comparison is a little misleading, however. Since they lumped two species into a single value (an odd thing to have done), the chimp-chimp comparisons won't produce anything like a single normal curve; the distrbution should have two peaks, one around 75 (for chimp-bonobo comparisons) and the other a broad peak centered around 20 or so (for within-species comparisons).
(Note that the human-Neandertal difference is smaller than the differences between chimp subspecies, so it's not obvious just from the genetic distances that humans and Neandertals were different species.)
Steve

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Steven Coles
Inactive Member


Message 4 of 80 (104743)
05-02-2004 3:57 PM


Just for clarity we could hypothesize pan as just as evolved as we are. While we have direct DNA measurement of similarities between relatively modern species, we have only mathematical models for the degree of similarity to our most recent common ancestor. Admittedly, Carole Jahme’s sketch of Lucy and a bonobo, with the exception of the pelvis, makes them look like litter mates. But we have little direct evidence beyond bone structure. (The sketch is inside the front cover of the advanced reading copy of Beauty and the Beasts. And no I’m not on any privileged reading list. The book had labels from two used book stores when I obtained it.)
Regards,
Steven

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 5 of 80 (104766)
05-02-2004 7:34 PM
Reply to: Message 1 by Sylas
05-01-2004 1:48 PM


more neander DNA
deleted
[This message has been edited RAZD, 05-02-2004]

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

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Sylas
Member (Idle past 5260 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 6 of 80 (104792)
05-02-2004 9:36 PM
Reply to: Message 3 by sfs
05-02-2004 3:28 PM


comparison with chimpazee diversity
sfs writes:
Very nice plot. The chimp-chimp comparison is a little misleading, however. Since they lumped two species into a single value (an odd thing to have done), the chimp-chimp comparisons won't produce anything like a single normal curve; the distrbution should have two peaks, one around 75 (for chimp-bonobo comparisons) and the other a broad peak centered around 20 or so (for within-species comparisons).
(Note that the human-Neandertal difference is smaller than the differences between chimp subspecies, so it's not obvious just from the genetic distances that humans and Neandertals were different species.)
That is true, on both counts. Note that the method I used to produce the plot was to enter mean and standard deviations quoted from Table 1 of Krings et. Al. (1999) into Excel, and then produce normal distributions to let them be more easily visualised. The diagram cautions that it is not a direct plot, but a crude representation of the mean and spread of pairwise differences in the given class.
That paper does also give some information which allows us to put the Human-Neandertal spread of differences into perspective, by comparison with the subspecies of common chimpanzee.
From Neandertal DNA Sequences and the Origin of Modern Humans
by M. Krings, A Stone, R. W. Schmitz, H. Krainitzki, M. Stoneking, S. Pbo
in Cell, Vol. 90, pp 19—30, July 11, 1997.
Relative Divergence Between Neandertals and Humans. In western Europe, Neandertals and modern humans coexisted from approximately 40,000 years ago to less than 30,000 years ago (34). The implications of that coexistence in terms of culture and genetic relationships are a matter of debate. The results presented here indicate that the mtDNA gene pools of these two hominid forms had diverged for a substantial time before they came into contact. To put the extent of genetic differentiation that had resulted into perspective, a useful comparison may be the differentiation found today among chimpanzees and bonobos. The number of differences between the Neandertal and modern humans is 35.5 2.3, about half that between chimpanzees and bonobos (75.7 4.6). Unfortunately, HVRII sequences are not available for different subspecies of chimpanzees. However, if the analysis is confined to 312 bp of HVRI, the average difference between modern humans and the Neandertal is 25.6 2.2, whereas that among 19 bonobos is 17.7 8.5, among 10 central chimpanzees (Pan troglodytes troglodytes) is 14.6 8.1, among 25 western chimpanzees (P. troglodytes verus) is 21.8 9.7, and among 108 eastern chimpanzees (P. troglodytes schweinfurthii) is 7.9 3.0. The observed differences between the subspecies varies from 19.7 2.9 between central and eastern chimpanzees and 36.2 6.1 and 33.0 4.5 between western and central, and western and eastern chimpanzees, respectively. Thus, the average observed difference between the Neandertal mtDNA and the mtDNA of modern humans exceeds that occurring within chimpanzee subspecies and within bonobos, but is less than what is found between two of three pairwise comparisons between currently recognized subspecies of chimpanzees.
We can illustrate this paragraph by the same method as I used for the previous plot. I enter the mean and standard deviations quoted into excel, and then produce a plot of normal distributions with those parameters. This gives a crude visual representation of the relative differences. (Click on the image to see it full size in a new window.)
There is no plot of the diversity within humans, which is unfortunate. I expect it would be less than the diversity within any chimpanzee subspecies. We can't compare directly with the numbers for the HVRII.
There is no indication of the difference between bonobos and any subspecies of common chimpanzee, but this would certainly be greater than the other differences plotted.
Unfortunately, I don't have the raw data. I would love to get a complete list of pairwise differences, or the raw sequence data. I think I will be able to do so, but if anyone can beat me to it and make the data available easily, I'll be grateful. Sequence data is available, but it is a lot of work to track down the various queries and put it all together.
The data suggests that Neandertals ought to be regarded as a subspecies, not a completely distinct species. The degree of difference is sufficient to make them a clearly identifiable distinct group, in contrast to any existing human races, where differences between races are much closer in magnitude to individual differences within races. The conclusion that Neandertals and modern humans had a long and distinct history with little if any gene flow between the populations is strongly supported. The conclusion that they were completely distinct species is weak. They would certainly have been interfertile with each other, but the extent of actual cross breeding was, as far as we can tell, minimal and had little if any contribution to the present human gene pool.
The sequence data entered into Genbank by Krings et al (accession number AF011222) identifies the source organism by a subspecies designation: Homo sapiens neandertalensis. Some authorities prefer a species designation Homo neandertalensis. For extinct groupings, this distinction takes on a rather subjective character.
Cheers -- Sylas
(Edited to reduce image size)
[This message has been edited Sylas, 05-03-2004]

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 7 of 80 (104799)
05-02-2004 10:31 PM
Reply to: Message 6 by Sylas
05-02-2004 9:36 PM


Re: comparison with chimpazee diversity
There is no indication of the difference between bonobos and any subspecies of common chimpanzee, but this would certainly be greater than the other differences plotted.
They do give the difference between bonobos and all chimps (75.7).
There is no plot of the diversity within humans, which is unfortunate. I expect it would be less than the diversity within any chimpanzee subspecies.
Probably so -- human mtDNA diversity has been measured to be quite low compared to chimp. For nuclear diversity, humans are lower than central chimps (~factor of 2), higher than western chimps.
They would certainly have been interfertile with each other
Not necessarily. A handful of key mutations may make hybridization difficult or impossible. Raw genetic distance can't tell you whether they've occurred or not. (Of course, small distance does make it less likely, but not certain.)

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Sylas
Member (Idle past 5260 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 8 of 80 (104804)
05-02-2004 11:03 PM
Reply to: Message 7 by sfs
05-02-2004 10:31 PM


Re: comparison with chimpazee diversity
sfs writes:
Sylas writes:
There is no indication of the difference between bonobos and any subspecies of common chimpanzee, but this would certainly be greater than the other differences plotted.
They do give the difference between bonobos and all chimps (75.7).
No; that was the HVRII. There was no difference given for the HVRI, which was the subject of my second plot. We could add the 75.7 difference to the first plot, which was based on HVRII; but I omitted it first time round as I was working from data in table 1. I will add it in for comparison to the first plot, by modifying the deep linked diagram in Message 1. I'll indicate when it is complete by a comment in the post; after which readers may need to refresh the browser to get the new image.
There is no plot of the diversity within humans, which is unfortunate. I expect it would be less than the diversity within any chimpanzee subspecies.
Probably so -- human mtDNA diversity has been measured to be quite low compared to chimp. For nuclear diversity, humans are lower than central chimps (~factor of 2), higher than western chimps.
I'm collecting a set of references for this. Can you give a cite where I could track down more on these, please? Does mtDNA diversity give any different result to nuclear DNA diversity?
One reference I have is A view of Neandertal genetic diversity by Krings et. al. in Nature Genetics (brief communications) pp 145-146, vol 26, Oct 2000, but it lumps chimpanzees as one grouping, with consequent high diversity.
They would certainly have been interfertile with each other
Not necessarily. A handful of key mutations may make hybridization difficult or impossible. Raw genetic distance can't tell you whether they've occurred or not. (Of course, small distance does make it less likely, but not certain.)
Yes, I should not have said "certainly". However, there is no actual evidential basis for inferring lack of interfertility, and the close similarity on morphological and genetic grounds makes it very implausible. I'm not saying that there was any great amount of gene flow; available evidence suggests this was minimal to non-existent. But that is a different matter to lack of interfertility.
Cheers -- Sylas

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redwolf
Member (Idle past 5791 days)
Posts: 185
From: alexandria va usa
Joined: 04-13-2004


Message 9 of 80 (104806)
05-02-2004 11:09 PM
Reply to: Message 1 by Sylas
05-01-2004 1:48 PM


For anybody who hasn't really followed the argument, the question as to whether the neanderthal dna findings would justify a claim that the neanderthal was "about halfway between us and chimpanzees" is not crucial to the case I would try to make. That's just a figure of speech. What the findings DID indicate is that neanderthals made no detectable contribution to the genetic pool of modern man, and were so far removed from modern man as to preclude interbreeding.
This in fact answered the huge question of how modern humans and neanderthals had managed to live in close proximity to eachother for protracted periods of time without any evidence of interbreeding.
Of course, in order to be descended from something, at some point, you have to be able to interbreed with the something. The findings clearly rule out the neanderthal as an ancestor for modern humans.
Now, the point I would make from all of this, is that evolutionists are studiously ignoring an obvious deduction. The problem is, that the neanderthal was the most advanced (or the most like us) of all the hominids. If we couldn't be descended from the neanderthal, it seems clear enough there's nothing else we COULD have been descended from.
I would argue that this rules out the idea of modern man having evolved and leaves three possibilities:
  • Modern man was created here from scratch, recently.
  • Modern man was brought here from somewhere else.
  • Modern man was genetically re-engineered from the neanderthal.
Obviously without a time machine, I don't have a perfect way of choosing one of the three. If I HAD to bet it, my money would be on the third choice.
Now, the one argument anybody could try to make against all of that would involve what is known as the "archaic homo sapiens", and what that amounts to seems to depend on who is telling it.

{Image linked to source}
Some of the skulls classified as archaic homo sapiens do not appear much different from neanderthal skulls; you wouldn't figure it would be any easier for modern man to be descended from something like that than from the neanderthal.

{Image linked to source}
The skull at the left above is said to be the most complete skull of an "archaic homo sapiens" ever found and, to compound the problem, virtually everybody with anything to say about 'archaic homo sapiens" is claiming that it evolved from homo erectus, which is much further from us than the neanderthal. The DNA findings would appear to preclude that.
The only real remaining question in my mind is what exactly the following two pictures amount to:
Archaic Homo sapiens skull Neanderthal skull {Click images for full size; [source]}
One is said here to be a neanderthal and the other an archaic homo sapiens.
The archaic hs skull may be an artists rendition (if the skull noted early is the most complete ahs skull as claimed); nonetheless it remains highly unlikely (to me at least) that you could evolve from a real (more typical) neanderthal like this:
Neanderthaler from Amul {Click image for full size; [source]}
to one of the images above with the more compact jaws.
That seems like a species difference, which you're not going to bridge and, again, there's no believable way to picture evolving from homo errectus to something like that.
Again the basic problem: Scientists now claim that the gap between the neanderthal and modern man cannot be bridged (by evolution) due to the extent of the DNA difference. Which, if any, of the other gaps involved in the supposed rise of modern man from hominids then remains bridgable?
{{AdminSylas has reduced large images, but added links for full size. Nice pics!}}
[This message has been edited AdminSylas, 05-03-2004]

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 10 of 80 (104807)
05-02-2004 11:13 PM
Reply to: Message 9 by redwolf
05-02-2004 11:09 PM


If we couldn't be descended from the neanderthal, it seems clear enough there's nothing else we COULD have been descended from.
Woah, pal. There's an enormous assumption there - that we're aware of all homind species that have ever existed.
What on Earth would lead you to believe that a) all hominid species left fossils and b) there are no hominid fossils we haven't discovered yet?
Did you think we weren't going to catch that, or what?

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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 11 of 80 (104808)
05-02-2004 11:17 PM
Reply to: Message 9 by redwolf
05-02-2004 11:09 PM


Nonsense.
No one has said that Homo Sapiens was descended from Neanderthal.
In fact, every bit of evidence shows that the two were concurrent species for most of their existence.

Aslan is not a Tame Lion

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redwolf
Member (Idle past 5791 days)
Posts: 185
From: alexandria va usa
Joined: 04-13-2004


Message 12 of 80 (104827)
05-02-2004 11:38 PM
Reply to: Message 10 by crashfrog
05-02-2004 11:13 PM


Basically, somebody who wanted to go on believing that modern man had evolved would have to come up with some new hominid, closer to us (than the neanderthal) in both time and morphology, to claim as a human ancestor. Moreover, since neanderthal works and remains are all over the map and very easy to find, the works and remains of the new hominid type should by all rights also be very easy to find, in fact they should be all over the place, IF such a thing had ever existed. The fact that nothing like that has ever been found indicates that no such closer hominid ever existed.

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Sylas
Member (Idle past 5260 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 13 of 80 (104828)
05-02-2004 11:43 PM
Reply to: Message 9 by redwolf
05-02-2004 11:09 PM


redwolf writes:
For anybody who hasn't really followed the argument, the question as to whether the neanderthal dna findings would justify a claim that the neanderthal was "about halfway between us and chimpanzees" is not crucial to the case I would try to make.
Of course it isn't critical. Your case is rather different. That is one of the things I have been trying to tell you, and why it is so weird that you can't acknowledge the error in the description you have quoted from the Indian newspaper.
Rather than fix up your presentation to match the actual data, you have continued to insist on the reporter's erroneous description, and even insisted that this phrasing is repeated by the scientists involved. That's false as well, as we saw with the Google searches in the other thread.
Why is it so hard for you to fix such straightforward errors?
That's just a figure of speech. What the findings DID indicate is that neanderthals made no detectable contribution to the genetic pool of modern man, and were so far removed from modern man as to preclude interbreeding.
The first phrase is true, and the second is false. The findings do not give any indication that interbreeding was precluded. They only indicate that there was no detectable genetic contribution made. These are different claims.
The paper indicates that the difference between Humans and Neandertals is less than the difference between Western and Eastern varieties of the common chimpanzees... and they are completely interfertile, and yet also with distinct gene pools because interbreeding does not usually occur.
Now, the point I would make from all of this, is that evolutionists are studiously ignoring an obvious deduction. The problem is, that the neanderthal was the most advanced (or the most like us) of all the hominids. If we couldn't be descended from the neanderthal, it seems clear enough there's nothing else we COULD have been descended from.
There is a hilarious irony here in you speaking of ignoring deductions, given that you've had YEARS to fix the halfway error.
But in any case, the above paragraph is very silly. The reason we are not descended from Neandertals is because we already know that Homo sapiens lived at the same time as the Neandertals.
The question is not really ancestry it is whether or not there was interbreeding. The data had the potential to show Neandertal genetic contributions to the current human gene pool. Even if this had been the case, we already know that humans Homo sapiens have a fairly continuous lineage distinct from the Neandertals. What was at issue was the multi-regional hypothesis, and the question of whether, when Homo sapiens moved into those regions where the Neandertals were living, there was much gene flow between the populations.
The data suggests that there was not. All the various human "races" are pretty much equally distant from Neandertals. If there was interbreeding, we should expect to find people in Europe to be a bit closer to the Neandertals. But they aren't. The genetic distance indicates a common ancestor around several hundred thousand years ago, whereas we lived side by side with Neandertals about 40,000 years ago.
If Neandertals remains were all dated to several hundred thousand years ago, there would be no particular problem with ancestry. Ancestry is emphatically not ruled out just on difference. You need to consider timing.
Rest ignored; it's just based on the error that excessive difference alone rules out ancestry. That's incorrect.
Cheers -- Sylas
[This message has been edited Sylas, 05-02-2004]

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redwolf
Member (Idle past 5791 days)
Posts: 185
From: alexandria va usa
Joined: 04-13-2004


Message 14 of 80 (104846)
05-03-2004 1:16 AM
Reply to: Message 13 by Sylas
05-02-2004 11:43 PM



The first phrase is true, and the second is false. The findings do not give any indication that interbreeding was precluded. They only indicate that there was no detectable genetic contribution made. These are different claims.
The paper indicates that the difference between Humans and Neandertals is less than the difference between Western and Eastern varieties of the common chimpanzees... and they are completely interfertile, and yet also with distinct gene pools because interbreeding does not usually occur.
I posted this the other day and you supposedly read it. Here it is again:
http://www.findarticles.com/cf_dls/m0BFU/11_86/70362289/p2/article.jhtml?term= {Link fixed... AdminSylas}

"...Following the discovery of the Neanderthal DNA, the German scientists compared it to the DNA of humans living today. (No early modern human DNA has ever been uncovered.) A clear difference was apparent between the two types of DNA. So marked was that difference that the Germans concluded that Neanderthals were an entirely separate species of human. A species is a group of organisms that have common characteristics and cannot breed with another species.
Because of the distinct difference in DNA, any attempts at interbreeding by Neanderthals and the early modern humans would have failed to yield offspring, the scientists reasoned."
Again, James Shreeve made an overwhelming case for the impossibility of crossbreeding between neanderthals and modern man and this paper is generally acepted as definitive on the subject at this point. The dna findings basically just confirmed Shreeve's analysis.
AdminSylas: Edited to fix a 404 error in the link. Error was caused by the link construction code, not by redwolf himself.
[This message has been edited AdminSylas, 05-03-2004]

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 15 of 80 (104847)
05-03-2004 1:22 AM
Reply to: Message 9 by redwolf
05-02-2004 11:09 PM


again?
If we couldn't be descended from the neanderthal, it seems clear enough there's nothing else we COULD have been descended from
This is just an argument from incredulity, and has no factual basis. There are plenty of other hominids in the family tree to show descent of both from a common anscestor, and the current trees shown on various websites (already given when this issue was raised before) do show both neanderthal and sapiens descending from Homo heidelbergensis.
In post #13 ted\redwolf contiues this misconception with:
Basically, somebody who wanted to go on believing that modern man had evolved would have to come up with some new hominid, closer to us (than the neanderthal) in both time and morphology, to claim as a human ancestor.
Which is not true. His whole argument is like saying because you can't be descended from your sister therefore you can't be descended from your mother.
This is the pertinent section of the chart from
http://www.handprint.com/LS/ANC/evol.html
Redwolf aka ted has yet to address this issue, even though it has been raised several times ... as in virtually every time he has presented his faulty argument.
He also tries to muddy the argument with his pictures, and more faulty tree data.
The oldest Homo sapiens sapiens skulls (160,000 years) look like the skull on the left (taken from UCBerkely News Release), the middle skull is Homo heidelbergensis (from Handprint webpage), while the skull on the right is Homo ergaster (KNM ER 3733, taken from Smithsonian website):
Note that I have assembled these pictures from the sources given and sized them so that the eybrow to jaw distance is comparable (I make no claim that these are absolute similar scales) so that the trend in shape can be easily seen.
I see no problem with this lineage of ancestors.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}

This message is a reply to:
 Message 9 by redwolf, posted 05-02-2004 11:09 PM redwolf has not replied

Replies to this message:
 Message 28 by RAZD, posted 05-03-2004 5:25 PM RAZD has not replied

  
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