Anthropology.net

MSNBC, NPR, and BBC News have run articles about a publication in Science run nearly two weeks ago about one of the genes that control skin pigmentation in humans. The source article is titled, “SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans” and is led by a team of pathologists, molecular biologists, geneticists, and biochemists primarily from the Penn State College of Medicine.

Actually, finding SLC24A5 was an accident. The group of researchers were seeking cancer genes and stumbled upon pigment cells in zebrafish that resembled human pigment cells. The researchers were using zebrafish as the model organism for cancer genes, primarily because of their fast developmental cycle and the similarities in vertebrate genome.

SLC24A5 was first identified by the Penn State team and was not identified initially as a pigmentation gene, since they were on the prowl for cancer genes. As a gene, SLC24A5 is an acronym for solute carrier family 24, member 5, which lies in on the long (q) arm of chromosome 15 on postion 21.1, from base pair 46,200,461 to base pair 46,221,881 (Source), Entrez Gene has more on the specifics of the gene, however it should be noted that the gene is conserved throughout the lineage of Eukaryota to Metazoa, Vertebrata, Mammalia, Primates, Catarrhini, Hominidae, and onto Homo. Remarkably, the human and fish versions of the gene share nearly 70 percent of the same protein sequence!

It was not until the the scientists drew tangents between the similarities in zebrafish and human pigment cells, which both contain granules called melanosomes. In specific strain of zebrafish, named golden for its ligher appearance, there are less melanosomes. Similarly, in lighter skin toned humans there are less melansomes which is due to a slightly different variation of the gene — one that codes the amino acid threonine. The reverse is for the dark, or wild-type, strain of zebrafish and humans with darker skin tones, which codes for the amino acid alanine — there are more melanosomes and a higher expression level of SLC24A5, as high as 38% in people of African origin. Whereas there is a 25% expression level of SLC24A5 in people of European origin. The image to your right, displays the wild-type zebrafish above has darker stripes than the golden zebrafish below. The insets show that the golden zebrafish has fewer, smaller and less dense pigment-filled compartments called melanosomes than the wild-type zebrafish.

The researchers then looked at two different human populations in which people with European and African ancestors had mixed relatively recently — African-Americans and African-Caribbeans. They found that, on average, people with two copies of the European version of the gene had the lightest skin. People with two copies of the non-European version of the gene had darker skin, and people with one copy of each version of the gene had skin color somewhere in between.

Ultimately this gene has deep roots into the debate over the validity of race. Personally, I was taught during my undergraduate career, that race is completely a social construct. And this is true for most anthropologists, who live by the mantra that there are more ‘differences’ amongst described races than between the races… meaning there is more prey area and things are not simply black and white. This opinion can be traced back to a 1972 paper by Richard Lewontin.

But this gene changes the foundation of that mantra, in my opinion. I wonder does a 7% difference in expression levels between SLC24A5 genes of peoples of African and European decent indicate somewhat a molecular indication different races? Especially when the difference is between 1 amino acid. Though, I must state that my curiousity will not go as far to follow conservative voice of Vincent Sarich and Frank Miele, in Race: The Reality of Human Differences, who say,

“racial differences in humans exceed the differences that separate subspecies or even species in such other primates as gorillas and chimpanzees” and that “race is a biologically real phenomenon with important consequences”

I still wonder the how this finding shakes the validity of race debate?

I also wonder how the identification of this gene also relates to the theory of human skin color varies with the amount of exposure to the sun’s ultraviolet (UV) radiation, or rather the more sunlight you receive the darker your skin will become. I was once taught in my Human Adaptability and Variation class, that

genotype + environment = phenotype

and won’t argue that if you are genetically predispositioned to be black that environment can or will change your phenotype, but I ask what role does environment have in the expression of this gene? Does skin not react to amount of sunlight to produce more melanin and therefor more melanosomes? Won’t people around the equator, and exposed to more sun, have darker skin tones than those farther from the equator and/or exposed to less sun regardless of how much this gene is expressed or regulated? How does acclimatization affect SLC24A5?

I guess this all boils down to what is race? Simply put is race solely a social construct, or is it biologically driven, or both? And why? Maybe it is another one of my rhetorical questions that can never be answered, but I’d like to know what y’all think about race, especially after reading about this gene.

Sudhir Kumar, from the Center for Evolutionary Functional Genomics in the Biodesign Institute at Arizona State, has led a paper published in yesterday’s Proceedings of the National Academy on Sciences redefining the time human lineage diverged from chimpanzee lineage. Previously, there was a wide time range between the divergence… roughly 3 million to 13 million years ago. With new research methods, using comparisons of 167 nuclear protein-coding genes, Kumar et. al. has generated a genomic view of the human-chimpanzee divergence adding another line of evidence in the pursuit of understanding the mechanisms evolution. Furthermore, Kumar says,

“This divergence time also has considerable importance because it is used to establish how fast genes mutate in humans and to date the historical spread of our species around the globe.”

However, this study suggests that bipedalism and large brains and all these other traits that we associate with humans evolved in a short period of time and not over a long period of time. Also this study does not use any fossil evidence because the paleoanthropologists who have discovered the earliest fossils don’t always agree among themselves about whether certain fossils belong to the human branch or the chimpanzee branch or are ancestral fossils…ahem the controversies with Tim White’s fossils. Anyways this is a substantial finding because it was the largest study of its kind ever done — from people and their closest biological relatives, chimpanzees. Macaques, a type of monkey, and mice and it incorporated genetic evidence to recalibrate the molecular clock. Here is the abstract for the article.

Placing confidence limits on the molecular age of the human-chimpanzee divergence
Sudhir Kumar, Alan Filipski, Vinod Swarna, Alan Walker, and S. Blair Hedges
Molecular clocks have been used to date the divergence of humans and chimpanzees for nearly four decades. Nonetheless, this date and its confidence interval remain to be firmly established. In an effort to generate a genomic view of the human-chimpanzee divergence, we have analyzed 167 nuclear protein-coding genes and built a reliable confidence interval around the calculated time by applying a multifactor bootstrap-resampling approach. Bayesian and maximum likelihood analyses of neutral DNA substitutions show that the human-chimpanzee divergence is close to 20% of the ape-Old World monkey (OWM) divergence. Therefore, the generally accepted range of 23.8-35 millions of years ago for the ape-OWM divergence yields a range of 4.98-7.02 millions of years ago for human-chimpanzee divergence. Thus, the older time estimates for the human-chimpanzee divergence, from molecular and paleontological studies, are unlikely to be correct. For a given the ape-OWM divergence time, the 95% confidence interval of the human-chimpanzee divergence ranges from -12% to 19% of the estimated time. Computer simulations suggest that the 95% confidence intervals obtained by using a multifactor bootstrap- resampling approach contain the true value with >95% probability, whether deviations from the molecular clock are random or correlated among lineages. Analyses revealed that the use of amino acid sequence differences is not optimal for dating human-chimpanzee divergence and that the inclusion of additional genes is unlikely to narrow the confidence interval significantly. We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations.

From Savage Minds, I have upsetting news of an archaeologist who has been kidnapped in Iraq,

“Susanne Osthoff, a German archaeologist who has worked since the invasion to document looted and damaged sites in Iraq, and to deliver humanitarian aid for a German relief agency, has been kidnapped, along with her driver. Saving Antiquities For Everyone (SAFE), with whom Osthoff was working, has a petition/show of support that you can sign onto (in left-hand column).”

Also, Francis Deblauwe adds, “There is also another online petition by BAJR. For continuous updates on the situation, see The Iraq War Archaeology site.”

I hope for her safe return.