Evidence from Nuclear DNA & Y Chromosome Evidence

Evidence from Nuclear DNA & Y Chromosome Evidence

If, as supporters of the African Eve hypothesis claim, there was a population movement of anatomically modern humans out of their place of origin in Africa resulting in total replacement of the previous hominid populations in Europe and Asia, this should be supported not only by mitochondrial DNA evidence but also by DNA evidence from the cell's nucleus. However, in his analysis of the early African Eve reports, Templeton (1993, p. 65) said, ". . . there is no single set of assumptions that allows the mtDNA and nuclear data to

be compatible with an out-of-Africa replacement hypothesis."

One group of researchers (Breguet et al. 1990) looked at variation in the B locus of the gene for the human apoprotein. According to Templeton (1993, pp. 68-69), their detailed analysis led them to conclude that "Caucasoid populations (located from North Africa to India) were closest to the ancestral genetic stock and that worldwide genetic differentiation at this locus is best explained by westward and eastward gene flow from this geographical region and not by a sub-Saharan origin." For researchers like myself, who are operating from a perspective influenced by the ancient Sanskrit writings of India, which posit recurrent appearances of the human species (after planetary deluges) in the Himalayan region, this is quite interesting.

More recently, researchers have found yet another problem with the African origins theory. This problem involves the globin gene cluster in humans. A gene or part of a gene at a particular location on a chromosome may appear in several different forms called alleles. One individual will have one allele, and a second individual another allele. In analyzing globin alleles in various populations, authors of a recent textbook found that the observed degree of variation implied an age much greater than 200,000 years for modern human populations. Indeed, looking at another part of the globin gene cluster, the authors stated that "two alleles from a non-coding (and therefore neutral) region have apparently persisted for 3 million years." They concluded, "To date, it is unclear how the pattern found in the globin genes can be reconciled with a recent African origin of modern humans" (Page and Holmes 1998, p. 132). The globin evidence is consistent with Puranic accounts of extreme human antiquity.

Some researchers, considering the complexities surrounding genetic data, have suggested that fossils remain the most reliable evidence for questions about human origins and antiquity: "Unlike genetic data derived from living humans, fossils can be used to test predictions of theories about the past without relying on a long list of assumptions about the neutrality of genetic markers, mutational rates, or other requirements necessary to retrodict the past from current genetic variation . . . genetic information, at best, provides a theory of how modern human origins might have happened if the assumptions used in interpreting the genetic data are correct" (Frayer et al. 1993, p. 19). I agree that genetic evidence does not always trump archeological evidence. This means that the archeological evidence for extreme human antiquity documented in Forbidden Archeology provides a much needed check on the rampant speculations of genetic researchers.

So where do we stand? The whole question of human origins, analyzed from the perspective of genetic evidence, mitochondrial DNA evidence in particular, is confusing. For example, some scientists say that a small population of the genus Homo arose from Australopithecus about 2 million years ago in Africa. This population developed into Homo erectus, and then spread throughout Eurasia developing into Neandertals and Neandertal-like populations. About 100,000 years ago a small population of anatomically modern Homo sapiens emerged in Africa, and then spread around the world, replacing the earlier populations of Homo erectus and Neandertals, without mixing significantly with them (Vigilant et al. 1991; Stoneking et al.1986). These anatomically modern humans then developed in different regions of the world into the different races we see today. Other scientists, looking at the same genetic, archeological, and paleontological evidence, conclude that the different races of anatomically modern humans emerged simultaneously in different parts of the world, directly from the Homo erectus and Neandertal populations in those parts of the world (Templeton 1993). According to this idea, anatomically modern humans would have emerged in large populations over wide geographical areas, not in some small founder population confined to a small area. Another group asserts that there was a small initial population of anatomically modern humans, confined to a small geographical region. But this group holds that this population differentiated into the different racial groups we see today while still confined to this small geographical area. The racial groups then are supposed to have migrated out of this area and expanded their numbers in particular parts of the world (Rogers and Jorde 1995, p. 1). In short, there is considerable confusion about the genetic evidence and what it means.

Y Chromosome Evidence

In the foregoing discussion about mitochondrial DNA, I briefly mentioned nuclear DNA, the DNA found in the nucleus of human cells and gave a few examples. Let us now look carefully at another example of such evidence-the Y chromosome.

Human beings have 23 pairs of chromosomes in the nucleus of each cell. One of these pairs of chromosomes determines the sex of the individual. The pair of sex chromosomes in females is made up of two X chromosomes (XX). The pair of sex chromosomes in males is made up of one X chromosome and one Y chromosome (XY).

So, how is the sex of a particular individual determined? The reproductive cells (sperm and eggs) are different than the other cells in the body. Nonreproductive cells have the full complement of 23 pairs of chromosomes, for a total of 46 chromosomes. But a sperm cell or egg cell gets only half that number, just one set of 23 chromosomes instead of 23 pairs of chromosomes. When the sperm and the egg combine, the full number of chromosomes (46, or 23 pairs) is restored. When an egg is produced in a female, it will always have an X chromosome, because in the female, the pair of sex chromosomes is always XX. So when the chromosome pair XX splits to form eggs, each egg will get one X chromosome. But in the male, the pair of sex chromosomes is XY. So when the pair splits to form sperm, some of the sperm will have an X chromosome, and others will have a Y chromosome. If a sperm carrying an X chromosome combines with an egg, the fertilized egg will have an XX pair of sex chromosomes, and the egg will develop into a female child. If a sperm carrying a Y chromosome combines with an egg, the fertilized egg will have an XY pair of sex chromosomes, and the egg will develop into a male child. The Y chromosome is passed down only from father to son. Females do not carry the Y chromosome.

Certain parts of a chromosome are subject to a process called recombination, whereby parts of one chromosome are exchanged with parts of another chromosome. But a large section of the Y chromosome is not subject to such recombination. Theoretically, the only changes that accumulate in this nonrecombining part of the Y chromosome would be random mutations. The Y chromosome is the male counterpart of the mitochondrial DNA, which is passed down only from the mother and is also supposedly not subject to variation other than random mutations. The Y chromosome can therefore be used in human origins research in just about the same way as mitochondrial DNA-as a molecular clock and geographical locator. Some researchers propose that just as there was an African Eve, there was also an African Adam, or, as some call him, a "Y-guy." As we shall see, however, the conclusions that can be drawn from Y chromosome studies are not very perfect, and therefore some researchers view "Y-guy" as "a statistical apparition generated by dubious evolutionary assumptions" (Bower 2000a).

In the May 26, 1995 issue of Science, Robert L. Dorit of Yale University and his coauthors published a study of the variation in the ZFY gene on the Y chromosomes of 38 humans from various parts of the world. They compared this variation with that found in chimpanzees. In converting the difference in the degree of variation into years, Dorit relied on the assumption that the human line separated from the chimp line about 5 million years ago. This led him to the conclusion that all the humans in his sample had a common ancestor who existed about 270,000 years ago. This differs from the usual age estimate of 200,000 years that comes from mitochondrial DNA studies (Adler 1995). However, a report in Science News (Adler 1995) pointed out that "Dorit and his coauthors acknowledge that factors other than a recent common ancestor could explain their findings" and that their conclusions relied on a lot of "background assumptions."

In the November 23, 1995 issue of Nature, Michael Hammer, of the University of Arizona at Tucson, published a study of Y chromosome variation in eight Africans, two Australians, three Japanese, and two Europeans. He concluded that they all had a common ancestor who lived 188,000 years ago. The geographical location of the common ancestor was not clearly defined. Hammer's study also suggested that a reanalysis of Dorit's data would give an age of 160,000 to 180,000 years for the most recent common ancestor of the individuals in the study (Ritter 1995).

In 1998, Hammer and several coauthors published a more comprehensive study of human Y chromosome variation. The time to coalescence for the observed variation was 150,000 years, and the root of the statistical tree was in the African populations. The researchers, using nested cladistic analysis methods, proposed that the Y chromosome evidence showed two migrations. One out of Africa into the Old World, and a movement back into Africa from Asia. "Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements," said the researchers (Hammer et al. 1998, p. 427). Hammer and another set of coworkers reached similar conclusions in a 1997 study of the YAP region of the Y chromosome (Hammer et al. 1997). The movement of Asian populations into Africa is interesting, in light of accounts from ancient Indian historical writings, which tell of the avatar Parasurama driving renegade members of the ancient Indian royal families out of India to other parts of the world, where according to some sources, they mixed with the native populations.

In the November 2000 issue of Nature Genetics, Peter Underhill and his coauthors said Y chromosome data suggested that the most recent common male ancestor of living humans lived in East Africa and left there for Asia between 39,000 and 89,000 years ago. By way of contrast, mitochondrial DNA evidence suggested that our common female ancestor left Africa about 143,000 years ago. Underhill simply suggested that the Y chromosome and mitochondrial DNA rates of change are different (Bower 2000a). Henry Harpending of the University of Utah in Salt Lake City thinks the Y chromosome's mutation rate is slower than Underhill and his coworkers reported. According to Harpending, this would bring Y Guy's age close to that of Mitochondrial Eve (Bower 2000a). But just as the mitochondrial DNA rate of change is really not known with certainty, the Y chromosome rate of change is also not known with certainty. In an article in Science News, Bower (2000a) says, "The Y chromosome segments in the new analysis exhibit much less variability than DNA regions that have been studied in other chromosomes. Low genetic variability may reflect natural selection, in this case, the spread of advantageous Y chromosome mutations after people initially migrated out of Africa, the researchers suggest. That scenario would interfere with the molecular clock, making it impossible to retrieve a reliable mutation rate from the Y chromosome, they acknowledge." And geneticist Rosalind M. Harding, of John Radcliffe Hospital in Oxford, England, says, "We don't know what selection and population structure are doing to the Y chromosome. I wouldn't make any evolutionary conclusions from [Underhill's] data" (Bower 2000a). For example, Underhill thought that Africa was the home of the most recent common ancestor of modern humans, because the African populations in his studies showed the most diversity in their Y chromosomes. But Harding points out that this diversity could have arisen not because African was the home of the original human population, but because Africa was more heavily populated than other parts of the world. Also, the diversity in populations outside of Africa could have been reduced by the spreading of particularly favorable genes throughout those populations. Bower says (2000a), "If the critics are right, Y guy could be history, not prehistory." In other words, humans could be millions and millions of years old, and the genetic diversity we see today could simply reflect some recent genetic events in that long history. The earlier results could simply have been erased with the passage of time.

The most recent Y chromosome studies demonstrate that firm conclusions about human origins based on this kind of evidence are still out of reach. A group of Chinese and American researchers (Ke et al. 2001) sampled 12,127 males from 163 populations from East Asia, checking the Y chromosomes for three markers (called YAP, M89, and M130). According to the researchers, three mutations of these markers (YAP+, M89T, and M130T), arose in Africa, and they can all three be traced to another African mutation, the M168T mutation, which arose in Africa between 35,000 and 89,000 years ago. The researchers found that all the East Asian males they tested had one of the three African mutations that came from the African M168T mutation. They took this to mean that populations that migrated from Africa completely replaced the original hominid populations in East Asia. Otherwise, some Y chromosomes without the three African markers should have been found.

As Ke and his coauthors (2001, p. 1152) said, "It has been shown that all the Y chromosome haplotypes found outside Africa are younger than 39,000 to 89,000 years and derived from Africa." However, they noted that "this estimation is crude and depends on several assumptions." The assumptions were not directly mentioned in their report. The authors also admitted the possibility of "selection sweep that could erase archaic Y chromosomes of modern humans in East Asia." Furthermore, they admitted that Y chromosome data is "subject to stochastic processes, e.g., genetic drift, which could also lead to the extinction of archaic lineages."

Ke and his coauthors (2001, p. 1152) acknowledged another problem, which they said "creates confusion." They observed that age estimates for a most recent common ancestor arrived at by analysis of variation in mitochondrial DNA and the Y chromosome DNA differ greatly from age estimates derived from analysis of variation in the DNA of the X chromosome and autosomes (chromosomes other than the sex-determining X and Y chromosomes). They said, "The age estimated with the use of autosome/X chromosome genes ranges from 535,000 to 1,860,000 years, much older than the mtDNA and Y chromosome" (Ke et al. 2001, p. 1152). The authors speculate that in the course of population "bottlenecks" during a supposed migration out of Africa, there may have been three or four times as many men as women, leading to the greater diversity in the autosome/X chromosome DNA.

Milford Wolpoff, a committed multiregionalist, says that it's not surprising that the Y chromosome shows an apparent African origin. Africa had the largest populations for the longest periods of time. Therefore, the African populations were responsible for the greatest number of Y chromosome lineages, which could over time have wiped out other lineages that originally existed along with the African lineages (Gibbons 2001, p. 1052). Ann Gibbons observes that it is difficult to check the reliability of the Y chromosome and mitochondrial DNA evidence. Ideally, one would want to compare this evidence with DNA evidence from many other chromosomes in the nucleus, to see if they all support the same conclusions about the age and geographical origin of anatomically modern humans. But Gibbons (2001, p. 1052) notes: "The dating of nuclear lineages is complicated because most nuclear DNA, unlike that of the mitochondria and the Y chromosome, gets scrambled when homologous chromosomes exchange their genetic material during egg and sperm formation. That makes detection of an archaic lineage so difficult that many geneticists despair they will ever be able to prove-or disprove-that replacement was complete. Says Oxford University population geneticist Rosalind Harding: 'There's no clear genetic test. We're going to have to let the fossil people answer this one.'"

Conclusion

Biochemical and genetic evidence is not as reliable as some would have us believe. Many researchers say that the fossil evidence is ultimately more important than the genetic evidence in answering questions about human origins and antiquity. As Frayer and his coauthors (1993, p. 19) said, "Unlike genetic data derived from living humans, fossils can be used to test predictions of theories about the past without relying on a long list of assumptions about the neutrality of genetic markers, mutational rates, or other requirements necessary to retrodict the past from current genetic variation . . . genetic information, at best, provides a theory of how modern human origins might have happened if the assumptions used in interpreting the genetic data are correct." Contemplating the difficulties of using genetic evidence to establish theories of human origins and antiquity, Oxford University population geneticist Rosalind Harding said, "There's no clear genetic test. We're going to have to let the fossil people answer this one" (Gibbons 2001, p. 1052). And when we do look at the fossil evidence in its entirety, we find that anatomically modern humans go so far back in time that it becomes impossible to explain their presence on this planet by current Darwinian theories of evolution. Furthermore, when we look at human origins in terms of the larger question of the origin of life on earth, we find that modern science has not been able to tell us how the first living things, with their genetic systems, came into existence.

Also, both artificial intelligence (AI) and artificial life (Alife) researchers have failed to provide convincing models of living things. Rodney Brooks, of the Artificial Intelligence Laboratory at MIT, wrote in a perceptive article in Nature: "Neither AI or Alife has produced artefacts that could be confused with a living organism for more than an instant. AI just does not seem as present or aware as even a simple animal and Alife cannot match the complexities of the simplest forms of life" (Brooks 2001, p. 409). Brooks attributes the failure to something other than lack of computer power, incorrect parameters, or insufficiently complex models. He raises the possibility that "we are missing something fundamental and currently unimagined in our models." But what is that missing something? "One possibility," says Brooks (2001, p. 410), "is that some aspect of living systems is invisible to us right now. The current scientific view of things is that they are machines whose components are biomolecules. It is not completely impossible that we might discover new properties of biomolecules, or some new ingredient. . . . Let us call this the 'new stuff' hypothesis-the hypothesis that there might be some extra sort of 'stuff' in living systems outside our current scientific understanding." And what might this new stuff be? Brooks gives David Chalmers as an example of a philosopher who proposes that consciousness might be a currently unrecognized state of matter. But Brooks (2001, p. 411) goes on to say, "Other philosophers, both natural and religious, might hypothesize some more ineffable entity such as a soul or elan vital-the 'vital force.'" Going along with such philosophers, I would propose that both a soul (conscious self) and vital force are present in humans and other living things. This conscious self and vital force are necessary components in any explanation of living things and their origins.

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