Thursday, December 22, 2005
Several Notes on Human/Primate Baraminology
When I tell people that creationists believe that, in general, creationists believe that the "created kind" are usually at family level of taxonomy, they are truly surprised. After they get over their initial shock, they usually then ask, "are chimps and other primates considered one created kind?" The simple answer is no. This is one of several cases where traditional taxonomy does not help us out. The Bible clearly records the non-common-ancestry of humans, stating that we were formed from the dust of the ground.
So, is there any evidence of this position? What about other hominid fossils --- are they human?
David DeWitt gives us two pieces of evidence. In The Neandertal's Role in Human History [Virginia Journal of Science 51(2):83, 2000; DeWitt, D. and Skinner, W.], he explains that the differences between Neandertal and human mtDNA occur at genetic "hotspots", while the hotspots differ between human and other primates. Note that this is mtDNA, not a whole-genome comparison, but it is interesting nonetheless. Marvin Lubenow contributes other interesting facts to the discussion of Neanderthal being fully human.
Historically, chimp/human genome comparisons have been done only on some genes, because we have not had the genome of the chimp sequenced. However, now it has. Just this year the Chimpanzee Sequence and Analysis Consortium published their results in Nature: Initial sequence of the chimpanzee genome and comparison with the human genome. David DeWitt analyzes some of their data in his TJ article "Chimp genome sequence very different from man" [TJ 19(3) 4-5, 2005].
I haven't had the chance to view the Nature article myself (our library is a bit slow on these things) but I will share DeWitt's analysis.
Retroviral elements:
73 human-specific
45 chimp-specific
Proteins-coding sequences:
29% of proteins are identical
5% of proteins have in-frame indels (insertion or deletion of three nucleotides, i.e. the code for a single amino acid)
Proteins with the most differences: transcription factors
In order for chimps and humans to share a common ancestor, there would have had to be 40 million mutation events, a chromosome fusion event, a modification to the length of the Y chromosome, all becoming fixed in the population in 300,000 generations.
However, what I would really like to know is how different the transposons are between chimps and humans, as that is how Todd Wood hypothesized the major differences between baramins would be shown.
Another interesting article in TJ is a short one called Was Lucy Bipedal? [TJ 19(3):13, 2005] by Marvin Lubenow. He points out that the major indications that Lucy was bipedal come from (1) the Laetoli footprints (which appear to be human) and (2) the reconstruction of Lucy. Now, the interesting thing about the reconstruction of A. afarensis (Lucy) is that the foot is based on a mixture of fossils, including those of Homo habilis! So, by mixing multiple species, you can find an intermediate fossil! Unfortunately, I do not know what the status is of Homo habilis, and whether he is considered a human by baraminologists or not.
Of course, in studying human ancestry, everyone has an axe to grind -- both creationists and evolutionists. The difference being that it is obvious that creationists have a stake in the outcome, but not so obvious the other way around. Marvin Lubenow developed an interesting study to do with his students to help them realize this.
I have not read this one yet, but I found it while searching for other references in this note: Homo erectus 'to' modern man: evolution or human variability?
Sorry this article was so thrown together. I have had it on the back burner for a while, and just wanted to get it done and out the door. In addition, I was hoping to find information on the transposon differences between humans and chimps, but was unable to do so. If anyone can help me here, please email johnnyb@eskimo.com.
So, is there any evidence of this position? What about other hominid fossils --- are they human?
David DeWitt gives us two pieces of evidence. In The Neandertal's Role in Human History [Virginia Journal of Science 51(2):83, 2000; DeWitt, D. and Skinner, W.], he explains that the differences between Neandertal and human mtDNA occur at genetic "hotspots", while the hotspots differ between human and other primates. Note that this is mtDNA, not a whole-genome comparison, but it is interesting nonetheless. Marvin Lubenow contributes other interesting facts to the discussion of Neanderthal being fully human.
Historically, chimp/human genome comparisons have been done only on some genes, because we have not had the genome of the chimp sequenced. However, now it has. Just this year the Chimpanzee Sequence and Analysis Consortium published their results in Nature: Initial sequence of the chimpanzee genome and comparison with the human genome. David DeWitt analyzes some of their data in his TJ article "Chimp genome sequence very different from man" [TJ 19(3) 4-5, 2005].
I haven't had the chance to view the Nature article myself (our library is a bit slow on these things) but I will share DeWitt's analysis.
Retroviral elements:
73 human-specific
45 chimp-specific
Proteins-coding sequences:
29% of proteins are identical
5% of proteins have in-frame indels (insertion or deletion of three nucleotides, i.e. the code for a single amino acid)
Proteins with the most differences: transcription factors
In order for chimps and humans to share a common ancestor, there would have had to be 40 million mutation events, a chromosome fusion event, a modification to the length of the Y chromosome, all becoming fixed in the population in 300,000 generations.
However, what I would really like to know is how different the transposons are between chimps and humans, as that is how Todd Wood hypothesized the major differences between baramins would be shown.
Another interesting article in TJ is a short one called Was Lucy Bipedal? [TJ 19(3):13, 2005] by Marvin Lubenow. He points out that the major indications that Lucy was bipedal come from (1) the Laetoli footprints (which appear to be human) and (2) the reconstruction of Lucy. Now, the interesting thing about the reconstruction of A. afarensis (Lucy) is that the foot is based on a mixture of fossils, including those of Homo habilis! So, by mixing multiple species, you can find an intermediate fossil! Unfortunately, I do not know what the status is of Homo habilis, and whether he is considered a human by baraminologists or not.
Of course, in studying human ancestry, everyone has an axe to grind -- both creationists and evolutionists. The difference being that it is obvious that creationists have a stake in the outcome, but not so obvious the other way around. Marvin Lubenow developed an interesting study to do with his students to help them realize this.
I have not read this one yet, but I found it while searching for other references in this note: Homo erectus 'to' modern man: evolution or human variability?
Sorry this article was so thrown together. I have had it on the back burner for a while, and just wanted to get it done and out the door. In addition, I was hoping to find information on the transposon differences between humans and chimps, but was unable to do so. If anyone can help me here, please email johnnyb@eskimo.com.
Permanent Link posted by crevo @ 6:05 AM 
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I have some nice reconstructions from actual fossils of Neandertal here. You may want to check them out.
Also, a nice review of the taxonomical evaluation of hominidae and human placement within.
So, over at the other comment, are you implying that god put gene sequences inside human beings at the beginning of creation? Or do you admit that these came from what were exogenous viruses (considering the genes that produce real viral coat proteins, etc) that got embedded in our genome through infection and were not excised due to mutation?
Let's start there first.
Also, a nice review of the taxonomical evaluation of hominidae and human placement within.
So, over at the other comment, are you implying that god put gene sequences inside human beings at the beginning of creation? Or do you admit that these came from what were exogenous viruses (considering the genes that produce real viral coat proteins, etc) that got embedded in our genome through infection and were not excised due to mutation?
Let's start there first.
Fabulous stuff, Dan. Thanks for contributing! If you have reconstructions for other primates and hominids, or good links to them, I'll post them on the front page. I'd love to allow my readers to be able to visualize these things.
As to your question, I really don't know for sure. Here's why:
If you view the genome as a software program, and for viruses to essentially be able to add "plugins" to your genome, the question is, would God have originally designed humans plugin-free? When developing software, often times you develop a core package that may even be useless without plugins, and then provide a base set of plugins to use with it. Similarly, these could just as well be pre-included plugins -- it's a valid (and actually often-practiced) design strategy. In addition, if the genome can identify the characteristics of plugin-added material, it is possible that there could be a mechanism to identify destructive or useless plugins and excise them if necessary. So, not only might it be a design possibility but also a functional enhancement.
However, I would not have any problem viewing them as coming in later. The high homology between human and primate retrovirus positions could be just as well served from the existing high homology of the chromosome structure. Retroviruses were previously thought to integrate more-or-less ad-hoc throughout the genome, but recent research indicates that they actually have varying degrees of site-specificity.
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As to your question, I really don't know for sure. Here's why:
If you view the genome as a software program, and for viruses to essentially be able to add "plugins" to your genome, the question is, would God have originally designed humans plugin-free? When developing software, often times you develop a core package that may even be useless without plugins, and then provide a base set of plugins to use with it. Similarly, these could just as well be pre-included plugins -- it's a valid (and actually often-practiced) design strategy. In addition, if the genome can identify the characteristics of plugin-added material, it is possible that there could be a mechanism to identify destructive or useless plugins and excise them if necessary. So, not only might it be a design possibility but also a functional enhancement.
However, I would not have any problem viewing them as coming in later. The high homology between human and primate retrovirus positions could be just as well served from the existing high homology of the chromosome structure. Retroviruses were previously thought to integrate more-or-less ad-hoc throughout the genome, but recent research indicates that they actually have varying degrees of site-specificity.
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