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.

[Jose]

I'm still a little unclear on this chart. The circles are black and white, representing non-african and african populations. But there are also headings on the chart showing african and non-african groups.

What do the labels and the headings mean? Are the dots representative of individual ethnicity and the headings indicative of geographical location?

Yes--an ambiguity in the presentation. I think the idea is that the colors of the dots indicate the location in which the individual lives. The broad brackets indicate the "overall group" location. So, the right-hand group is largely "non-Africans," but clearly includes some indivduals who live in Africa. This says to me that the right-hand group, related by sequence similarity, includes one lineage of Africans plus most of the rest of the world. The few non-African dots in the "African" groups could be people of those particular lineages who live elsewhere. Unfortunately, we didn't know how to do this kind of analysis before we invented sea-going sailing ships, and started moving around a lot.

BTW, what does the C on the left mean? Chimps?

In order to identify the "base" of a "tree" like this, it is necessary to have an "outgroup"--some comparison that is kinda similar to the rest of the data, but with enough differences to be clearly separated from all of them. I suppose it would be possible to use any non-human DNA for this, but since Chimp sequences are more similar to ours than any others, the investigators used that.

Given the emotional content of the fact that human and chimp DNA are so similar, I always like to point out that this diagram (and others like it) merely reports the similarities and differences. It's a bunch of facts. The question is what happened in the past to result in this pattern. "God wanted to do it that way" is one possible explanation, albeit one that does not lead to further investigation.

Thanks for reducing the diagram size so I don't have to fall off my chair reading it, Jose. You really are a gentleman and a man of your word. Since I couldn't read this thread properly originally, I started another since we never did get to agree on what we should call it even though I did give you the privilege of posting first.

You are quite welcome, sir. There is little point in posting stuff that we can't look at. Perhaps a second thread is OK--we should see what the consensus of the group is. You are right that the data are qualitatively different, so they require different discussions. At the same time, they are inextricably linked, since fossils cannot exist without having had genetic history prior to death and fossilization. We may need to cross-reference many posts, which could become cumbersome.

Has Lubenow's work included in peer-reviewed scientific literature? Would it be too much to ask that jcrawford provide a summary of his understanding of human origins rather than just a reference?

Lubenow's work has not been included in the peer-reviewed literature, and has therefore not been subjected to the critical (and often fairly nasty) evaluation of others. It is, therefore, what we might want to call "soft" information. I believe that jcrawford will, indeed, want to provide us with quotes from it if he uses that source. It will be necessary to counter-quote from the scientific literature to provide the information that we will need to assess the relative strengths of argument by Lubenow compared to the human evolution community.

[jcrawford]

3. Given that there is always genetic diversity within populations, how easily can we assign hominid fossils to different groups?[/b] 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).

Assuming that any human fossils may be categorized, classified and labeled with such terms as 'different and separate species' or "form-species," remains fundamentally problematic whenever there is no physical evidence based on physical tests for interfertility or inter-sterility between human fossils whose various morphologies may amount to being nothing more than racial variations.

[jcrawford]

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.

To be considered scientifically valid, all genetic data presented regarding the human fossil record must be shown not to have been contaminated by modern DNA, especially when the "notoriously contamination-sensitive" PCR technique was used. In addition, no interpretations or conclusions of mtDNA findings may be premised on any of several unfounded assumptions.

[Jose]

Assuming that any human fossils may be categorized, classified and labeled with such terms as 'different and separate species' or "form-species," remains fundamentally problematic whenever there is no physical evidence based on physical tests for interfertility or inter-sterility between human fossils whose various morphologies may amount to being nothing more than racial variations.

That is exactly the point of the term "form-species." We can't do the mating test to determine whether they are the same biological species. We can, however, determine that they look different. That's the criterion for "form-species"--their form is different.

To the extent that I am aware, there are no humans at present who would be categorized in a different "form-species," with the possible exception of those who are much taller/larger or much smaller/shorter than would be expected on the basis of a normal distribution. We know that overall size is quite variable, and that there are simple genetic mechanisms as well as non-genetic mechanisms that can affect it, so we'd need to be pretty careful in using size alone as a criterion. In any event, there is a lot of genetic diversity in existing human populations. We'd expect lots of diversity in any extinct populations as well.

So, there's genetic variation. If the variation within one group of fossils is within some range, and the variation within a different group of fossils is within some range, but the two groups show no overlap, then we would be justified in deciding that the two groups are, indeed, different. For convenience of discussion, we might want to give them different names.

Did they interbreed? We can't tell, but we'd predict that if they had, there would be individuals with some mix of characteristics of each of the groups. This would show up as overlap between the two groups, and would lead us to believe that they are not two biologically distinct groups.

But the issue here is not where we draw the arbitrary lines that we'd use to define the boundaries of various "form-species." The issue is how the overall lineage has changed over time. In the absence of fossils of every individual of every species who ever lived, the data set will necessarily be incomplete. Nonetheless, there are data that require interpretation.

[jcrawford]

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 suppose those differences will emerge as different POV's on the data are posted and would hope that suggestions for reconciling those differences will depend on the perceived validity of the data.

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?

1. I interpret "a whole bunch of people" as representative of various racial groups around the world.

2. Where did the State of Indiana Department of Education get this diagram from?

[Jose]

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.

To be considered scientifically valid, all genetic data presented regarding the human fossil record must be shown not to have been contaminated by modern DNA, especially when the "notoriously contamination-sensitive" PCR technique was used. In addition, no interpretations or conclusions of mtDNA findings may be premised on any of several unfounded assumptions.

Needless to say, contamination by modern DNA must be ruled out. In our building, this is done by obtaining DNA samples from everyone in the building, so that you can determine exactly whose DNA has contaminated the sample. When the presumed-fossil DNA sequence bears some relationship to the present sequences, but is moderately different from all off the available samples, it is likely that it really is from the ancient sample.

In general, the folks who do this work are so keenly aware of, and worried about, this obvious problem that they take extraordinary care to prevent contamination and to evaluate their data in the light of possible contamination. The reviewers of the manuscripts are also aware of this, and are prepared to nail the authors for it if they can find any hint that it might have occurred.

As for the assumptions upon which the interpretations are based, it might be good to evaluate them. You are particularly concerned, it sounds, about mitochondrial DNA. What are the assumptions that concern you?

[jcrawford]

Thanks for reducing the diagram size so I don't have to fall off my chair reading it, Jose. You really are a gentleman and a man of your word. Since I couldn't read this thread properly originally, I started another since we never did get to agree on what we should call it even though I did give you the privilege of posting first.

You are quite welcome, sir. There is little point in posting stuff that we can't look at. Perhaps a second thread is OK--we should see what the consensus of the group is. You are right that the data are qualitatively different, so they require different discussions. At the same time, they are inextricably linked, since fossils cannot exist without having had genetic history prior to death and fossilization. We may need to cross-reference many posts, which could become cumbersome.

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?

[jcrawford]

BTW, what does the C on the left mean? Chimps?

In order to identify the "base" of a "tree" like this, it is necessary to have an "outgroup"--some comparison that is kinda similar to the rest of the data, but with enough differences to be clearly separated from all of them. I suppose it would be possible to use any non-human DNA for this, but since Chimp sequences are more similar to ours than any others, the investigators used that.

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?

[jcrawford]

In general, the folks who do this work are so keenly aware of, and worried about, this obvious problem that they take extraordinary care to prevent contamination and to evaluate their data in the light of possible contamination. The reviewers of the manuscripts are also aware of this, and are prepared to nail the authors for it if they can find any hint that it might have occurred.

Yes, and 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

Bert and Barb said that "they were very careful to use all of the methodology guidelines that had been worked out by one of their critics (Alan Cooper of Oxford) - Barbujani and Bertorelle, "Were Cro-Magnons too like us for DNA to tell," correspondence, Nature 424 (10 July 2003):127

[jcrawford]

As for the assumptions upon which the interpretations are based, it might be good to evaluate them. You are particularly concerned, it sounds, about mitochondrial DNA. What are the assumptions that concern you?

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)