Human Evolution

[Jose]

jcrawford and I have been having some interesting discussions in other threads, which have led to the notion that we really need a thread on human evolution. So, here it is.

The Rules
We want to work from data. Data that is discussed must be accessible in the scientific literature. Personally, I would prefer the peer-reviewed literature, because, as those of us in science know all too well, the peer reviewers are usually one's competitors. Thus, they are typically extremely critical of what we write.

Any other information that is brought to bear must also be accessible to everyone. Where requested, direct quotes from the sources will be important.

The questions for discussion

1. What is the current best understanding of human origins?

2. What "confounds" are there in the interpretation of data?

3. Given that there is always genetic diversity within populations, how easily can we assign hominid fossils to different groups? Here, the term "form-species" is probably most useful, referring to similar fossils with similar forms, but in the absence of information on the capacity for interbreeding. In many cases, different form-species are different species (fossil trees vs fossil insects), but sometimes they are not (fossil leaves vs fossil roots of the same tree).

4. Does information based on fossil data mesh with information based on genetic data? The true history must be genetically feasible. The fossils must have been left by individuals who were produced by normal genetic methods. To be valid, any explanation of origins must incorporate both fossil and genetic data.

5. What are the parts of human history that are most at odds with (some) Christian views, and what suggestions can we offer for reaching a reconciliation?

I will begin by posting the following genetic data, which is pictorial representation of the differences and similarities in mitochondrial DNA sequence of a whole bunch of people. Relative difference/similarity is proportional to the lengths of the vertical lines. Horizontal lines merely separate the vertical lines so we can see them.

How do we interpret these data?

[If appropriate, I will edit this post to ensure that the OP of this thread lists the important questions.

[micatala]

Maybe the moderator could incorporate my thread "Bones and Genes of Contention" into this one, now that we are all working with the same screen format. Do we have a consensus to do this?

FIne by me. It would make things easier as we are bound to be discussing both fossil evidence and genetic evidence.

[jcrawford]

Maybe the moderator could incorporate my thread "Bones and Genes of Contention" into this one, now that we are all working with the same screen format. Do we have a consensus to do this?

FIne by me. It would make things easier as we are bound to be discussing both fossil evidence and genetic evidence.

Let's see if Jose aquiesces. Then the titanic battle between the human fossils and the human genes may become the greatest event ever staged on one thread on the Internet.

[Chimp]

I thought we were only allowing peer-reviewed material.

Jcrawford,
Can you edit your post to include the dates and titles (even partial will help).

I don't think your citations refute, but instead dispute.

[Jose]

Maybe the moderator could incorporate my thread "Bones and Genes of Contention" into this one, now that we are all working with the same screen format. Do we have a consensus to do this?

Probably a good idea. We can then keep the discussion together. Any other votes?

How does using modern DNA sequences in chimps living today shed any light on the genetic diversity of humans today or in the past? And what is the "peer-reviewed" source of your claim that the "investigators' actually did use chimp sequences in the diagram?

The chimp DNA doesn't tell us anything other than the "root" of the tree. We could have used cauliflower DNA (except we probably couldn't, since it's probably too different). It merely tells us "start here."

Similarly, we could make a tree of everyone in my immediate family, and use jcrawford as the outgroup, or we could make a tree of jcrawford's immediate family, and use me as the outgroup. Or we could make a tree of all eukaryotes, and use E. coli as the outgroup.

The important information is derived from the pattern of similarities and differences among the humans.

I redrew the figure from Freeman and Herron's Evolutionary Analysis, 2nd edition, published by Prentice-Hall. Their rendition of it is a somewhat simplified version of the tree shown by Penny et al., Mol. Biol. Evol. 12(5):863-882. 1995, Improved Analyses of Human mtDNA Sequences Support a Recent African Origin for Homo sapiens.

according to Lubenow's scientific research and citations, Svante Paabo, in criticizing Bertorelle and Barbujani, claims that "Cro-Magnon DNA is so similar to modern human DNA that there is no way to say that what has been seen is real." - Alison Abbott, "Anthropologists cast doubt on human DNA evidence," Nature 423 (29 May 2003):468

Paabo is very good, so this is a valuable statement. What it says, in essence, is that finding the same sequence as modern humans is uninformative, because it may well be contamination. Conversely, finding a different sequence is more meaningful, because modern DNA would not produce that sequence. Thus, we can infer that the differences seen in neanderthal DNA are likely to be real, while the lack of difference in presumed Cro-Magnon DNA may not be real. Cro-Magnon could be like modern humans, or, perhaps, we just don't know because the investigators got contamination.

Your point is a good one: contamination is an issue. It is possible even using the best methods, so one must always be wary.

[Jose]

The unfounded assumptions upon which mtDNA interpretations and conclusions are premised are:

1. That mtDNA is passed on only by the mother. - refuted by John Maynard Smith, Richard Hudson and Henry Harpending. (Lubenow)

2. That mtDNA mutations are regular and serve as a molecular "clock." - refuted by Neil Howard. (Lubenow)

3. That mtDNA can be used to dertermine human and primate relationships. - refuted by G.A. Clark and Jonathon Marks. (Lubenow)

4. That mtDNA can determine species distance and distinguish between species. - refuted by Maryellen Ruvolo and Simon Easteal. (Lubenow)

1. That mtDNA is passed on only by the mother. - refuted by John Maynard Smith, Richard Hudson and Henry Harpending.Usually, the mitochondria are stripped from the sperm tail on fertilization, so the paternal mitochondria don't enter the egg. Perhaps it doesn't work this way once in a while, but it only matters if one insists on claiming that the mitochondrial data are only the maternal lineage. In this case, I don't think it matters at all. We're asking who our ancestors were, and we really don't care whether we find the ancestral Mom or Dad.

Besides, the Y chromosome data give the same pattern. See Cavalli-Sforza & Feldman, Nature Genetics March 2003, Volume 33 No 3s The application of molecular genetic approaches to the study of human evolution pp266 - 275.

2. That mtDNA mutations are regular and serve as a molecular "clock." - refuted by Neil Howard.This is known not to be a valid assumption, because we know mutation rates are not regular. Hence the variation in the heights of the bars in the diagram. This would be an issue if we wanted to say that the data tell us that the ancestor lived 193,000 years ago, but we can't make that claim. The "temporal calibration" of these kinds of trees depends on archeological and paleontological data. Again, however, this consideration is not an issue when interpreting the pattern of the data.

3. That mtDNA can be used to dertermine human and primate relationships. - refuted by G.A. Clark and Jonathon Marks.This, too, is a non-issue. Mitochondrial DNA was chosen for this study because it has a fairly high mutation rate, and is thus able to reveal evolutionary changes over relatively short times. By the time we get to species divergences, the time-frames are long enough that there would be too much change to build reliable trees. But that's not what's being done here. The comparison is within one species.

4. That mtDNA can determine species distance and distinguish between species. - refuted by Maryellen Ruvolo and Simon Easteal.This is, essentially, the same issue as #3, but expressed more broadly. The same reasoning holds.

are there any other assumptions that are of concern? It looks like these are valid issues, but they do not play a role (or "confound") our analysis of this particular data set.

[jcrawford]

I thought we were only allowing peer-reviewed material.

We are. Do you have any?

Jcrawford, Can you edit your post to include the dates and titles (even partial will help).

Which post are you referring to and which "partial" citations specifically? If you had Lubenow's book, I could refer you to a few page numbers. Without it, you are demanding that I type up multiple "peer-reviewed" scientific citations without reciprocating in kind to validate your own following contention.

I don't think your citations refute, but instead dispute.

Since you haven't even read the scientific citations which Lubenow scientifically documents in his "peer-reviewed" footnotes, how could you possibly know whether they refute or merely dispute the general claims and hypotheses of neo-Darwinist geneticists? Besides, you posted no "peer-reviewed" scientific citation to back up this naked 'assumption' of yours.

Give me a stenographic break, will you, (since you're not interested in investing in, and doing your own scientific research) only ask me for one "peer-reviewed" scientific citation at a time? I'm not on your payroll, you know.

[Jose]

OK, I have merged Bones and Genes of Contention into this thread. Thus, there is a post of jcrawford's that we should go back and read. He posts some links to fossil data.

I thought we were only allowing peer-reviewed material.

We are. Do you have any?

Jcrawford, Can you edit your post to include the dates and titles (even partial will help).

Which post are you referring to and which "partial" citations specifically? If you had Lubenow's book, I could refer you to a few page numbers. Without it, you are demanding that I type up multiple "peer-reviewed" scientific citations without reciprocating in kind to validate your own following contention.

Come, come. None of this kind of bickering. Let's leave that for the other threads. Jcrawford provided some assumptions that may be involved in mtDNA analysis, with a clear link to Lubenow's book (not peer reviewed) and indications of the papers that Lubenow cited (but not the journals and page numbers). These count as partial citations. I suggest that we adhere to the principle already esablished in this thread, of presenting the citations so we can all look up what we need. Frankly, I prefer to check the references that Lubenow gives, just to be sure that he's got his story straight. Maybe he does. Certainly, with the citations that jcrawford has given, I have been able to look them up and conclude that jcrawford's summation of them was right on the mark. So, let's keep up the practice of supplying such citations, especially when asked. Otherwise we look like the white house (choose your favorite administration) refusing to hand over relevant documents, thereby looking like there's something to hide.

[jcrawford]

Maybe the moderator could incorporate my thread "Bones and Genes of Contention" into this one, now that we are all working with the same screen format. Do we have a consensus to do this?

Probably a good idea. We can then keep the discussion together. Any other votes?

Jose, we hardly need ask any of the other posters whether they will permit us to merge the two threads, since you and I alone are the authors thereof and are the sole determiners of their fate, (other than the host's intervention) especially in view of the fact that you and the other posters have suddenly developed a genetic aversion to discussing the human fossil record on my thread, and micatala has recommended that we do combine the threads in order to avoid further unresolveable difficulties and encumbrances.

How does using modern DNA sequences in chimps living today shed any light on the genetic diversity of humans today or in the past? And what is the "peer-reviewed" source of your claim that the "investigators' actually did use chimp sequences in the diagram?

The chimp DNA doesn't tell us anything other than the "root" of the tree. We could have used cauliflower DNA (except we probably couldn't, since it's probably too different). It merely tells us "start here."

Why start with modern chimp, cauliflower, or even modern mouse DNA in comparitive studies of human DNA? Can you post any evidence of scientifically "peer-reviewed" justification for the natural selection of chimps over cauliflower or mice? Why is the Mouse Genome excluded from the chart?

[Jose]

Jose, we hardly need ask any of the other posters whether they will permit us to merge the two threads...

Hee hee hee...you're right, of course. I have already done so.

Why start with modern chimp, cauliflower, or even modern mouse DNA in comparitive studies of human DNA? Can you post any evidence of scientifically "peer-reviewed" justification for the natural selection of chimps over cauliflower or mice? Why is the Mouse Genome excluded from the chart?

For the purposes of "placing the root" of the tree, an outgroup is necessary. I doubt that I can post a simple reference, since there are hundreds of papers on this topic. Do you really want me to find a review of it for you? It's purely mathematical, and provides no insight into the biology we are trying to resolve. We could have shown the same figure without the little line connected to "C" and we'd still have the same information available.

And, it's not "natural selection" of chimps over any others. It's "intelligent selection" by the people who did the analysis. I think I've said why they chose chimps, but I'll reiterate for clarity. They chose chimp sequence because it's more similar to human sequence, so the math was easier. mtDNA mutates too rapidly to provide a good comparison with mice, so mouse DNA wasn't used. However, with a nuclear gene, mouse DNA might be fine. Even so, it makes no difference to the analysis of the data. The question is not who are humans related to, but how are humans related to each other?

[jcrawford]

OK, I have merged Bones and Genes of Contention into this thread. Thus, there is a post of jcrawford's that we should go back and read. He posts some links to fossil data.

Jose, you are more than a gentleman. You are a true scholar. Thanks for adding the following in post # 7.

Exhibit A: The Mauer Mandible. Homo heidlebergensis

This is the representative fossil type for a wide range of anatomically modern human fossils which predate Cro-Magnon and Neanderthal Man in Europe by .5My.

http://www.mnh.si.edu/anthro/humanorigins/ha/heid.htm

As several other webites on H. heidlebergensis indicate, this representative fossil speciman of anatomically modern humans found throughout Europe as recently as 30Kya, is a prime candidate for European and Middle Eastern common ancestry today.

http://en.wikipedia.org/wiki/Homo_heidelbergensis

http://www.geocities.com/palaeoanthropo ... ensis.html

Do you have any comments on Homo heidlebergensis as a candidate for modern European and Middle Eastern ancestry?

I thought we were only allowing peer-reviewed material.

We are. Do you have any?

Jcrawford, Can you edit your post to include the dates and titles (even partial will help).

Which post are you referring to and which "partial" citations specifically? If you had Lubenow's book, I could refer you to a few page numbers. Without it, you are demanding that I type up multiple "peer-reviewed" scientific citations without reciprocating in kind to validate your own following contention.

Come, come. None of this kind of bickering. Let's leave that for the other threads. Jcrawford provided some assumptions that may be involved in mtDNA analysis, with a clear link to Lubenow's book (not peer reviewed) and indications of the papers that Lubenow cited (but not the journals and page numbers). These count as partial citations. I suggest that we adhere to the principle already esablished in this thread, of presenting the citations so we can all look up what we need. Frankly, I prefer to check the references that Lubenow gives, just to be sure that he's got his story straight. Maybe he does. Certainly, with the citations that jcrawford has given, I have been able to look them up and conclude that jcrawford's summation of them was right on the mark. So, let's keep up the practice of supplying such citations, especially when asked. Otherwise we look like the white house (choose your favorite administration) refusing to hand over relevant documents, thereby looking like there's something to hide.

This is an admirable observation and statement on your part, Jose. BTW, I just noticed that you are both a moderator and administrator on the forum. I was wondering how you managed to incorporate part of my thread into yours. Power to you.

As far as providing "peer-reviewed" scientific citations provided by Lubenow, I guess I'll just have to spend the rest of my life typing up over 1000 scientific booknotes provided by Lubenow in his devastating critique of neo-Darwinst race theories as published by BakerBooks in 2004.

Oh, well, here go I but for the grace of God.

tbc: