Chapter 3 - DNA

    In addition to figuring out "Who Done It" on TV crime shows, DNA is also useful in figuring out "Who Begot Whom." It works like this. All humans have 23 pairs of chromosomes, making the total number of chromosomes equal to 46. One set of 23 chromosomes came from the mother and the other set of 23 chromosomes came from the father. Each of the father's 23 chromosomes is paired up with the corresponding chromosome from the mother. Each chromosome consists of a long string of DNA entwined with proteins called "histones." Histones unwind to permit the DNA to be read; the histones are inherited along with the chromosomes. (Segal, 2006).
    DNA is a chain of chemical units called "nucleotides." It is like a computer code (...011000101...), but instead of using only zeroes and ones, each nucleotide uses one of four different chemical bases, which are known by their first letters, A, C, G, and T (...ATTGCATCCA...). A "gene" is a string of DNA that "codes for" a polypeptide, which is just a string of chemically linked amino acids. The order of those A, C, G, and T bases in the coding portion ("exon") of the DNA sequence of a gene determines which polypeptide is made, and stringing different polypeptides together produces different proteins. 1 (See Appendix). Proteins and other substances are assembled to give various traits, the "phenotype." Less than 2% of our genome is required to make all the proteins we need to live.
    All humans have the same genes, 2 but not the same form of those genes. To clarify, we all have the EYC3 gene for eye color, but one A-C-G-T sequence of that gene makes eyes blue and another A-C-G-T sequence of that gene makes eyes brown. Each different A-C-G-T sequence of a gene is called an "allele." In some populations, a gene may come in only a single allele, so everyone in that population has the same A-C-G-T sequence for that gene and has the same trait, i.e., the allele is "fixed"; genes in other populations come in many alleles, some of which only very few people have. Some alleles are very beneficial and give an individual a highly desirable trait, such as greater intelligence, athletic ability, or good looks, and other alleles may be lethal or debilitating. There is an average of 14 different alleles for each gene.
    In addition, regulators (the "epigenome") determine whether or not a string of DNA is read. 3 The epigenome also differs between people and is inherited with the chromosomes. Putting all this together, it is obvious that unless two people are identical twins, it is extremely unlikely that they will be genetically identical, and even "identical" twins, i.e., twins with the same DNA sequences, may differ slightly due to differences in their epigenomes. 4
    And, hang on, it gets even more complicated. If two alleles have different A-C-G-T sequences they can nevertheless still code for the same polypeptide (i.e., the two alleles are "synonymous"), or they can code for different polypeptides ("non-synonymous"). 5 Each A-C-G-T difference, e.g., a "T" instead of an "A," is called a "single nucleotide polymorphism" (SNP). The difference between an "A" and a "T" may be only in how difficult it is for a cell to obtain and assemble an "A" instead of a "T," or the difference may be advantageous, disadvantageous, or even deadly.

   Very occasionally, there is a throwback ("atavism"), a person whose gene regulators have turned on genes that were turned off a long time ago in the rest of us. (LePage, 2007).
    Figure 3-1 is a picture of Azzo Bassou. Bassou was living in the Valley of Dades, near the town of Skoura in Morocco in 1936, where the original white population has mixed with blacks. If he is a throwback, he should express some primitive white and/or African traits, along with his mulatto traits. Some experts believe that Bassou was a microcephalic (e.g., had a genetic defect that left him with a small brain), but he was not a drwarf, as many microcephalics are. (The villagers would not permit an examination of his body when he died.) His behavior, aside from its primitiveness, was also not that of most microcephalics.
    "With arms so long his fingers hang below his knees when he stands upright; with massive, bony ridges above his eyes and a sharply receding forehead; with jaws, teeth, chin, and cheekbones all showing pronounced ape-like characteristics. He sleeps in the trees there and subsists on dates, berries, and insects. He wears no clothes (although he was persuaded to don a burlap sack for the photograph which appears here), uses no tools, and speaks only in grunts." (National Vanguard, Issue No. 44, 1976).

Figure 3-1
    New alleles can arise within a population by mutation or they can be acquired by interbreeding with another population that already has them. If a new allele increases reproductive success it will spread throughout the population and, if it is reduces reproductive success, it will disappear along with those who had it. 6 Almost all new alleles are detrimental because, after millions of years, almost all the alleles that are possible have already entered the population's gene pool at one time or another. Since beneficial alleles usually remain in the gene pool once they arise, there are very few new beneficial alleles that could arise and enter the gene pool. But detrimental alleles are eliminated from the gene pool, so they can arise and re-enter it over and over again. (And alleles that are detrimental in one environment may be beneficial years later when a population faces a different environment or has evolved in other ways.)
    Expanding populations acquire alleles (because there are more people in whom mutations can occur) and contracting populations lose them (because people who have unique alleles, even if they are not detrimental alleles, die without progeny) -- an example is the loss of alleles that occurred in Eurasians after vast numbers died during ice ages. Barring such disasters, an allele that increases reproductive success is unlikely to be lost. Indeed, if an allele is widely expressed in a population, one can safely conclude that the allele has increased the reproductive success of that population in its present environment. However, an allele that, for some period of time, has been only sparsely expressed either does not increase reproductive success or increases it only when it is sparsely expressed and is detrimental when it becomes widespread.
    Because populations can gain and lose alleles, and alleles that are advantageous in one environment can be detrimental in a different environment, determining descent by studying the alleles of different populations can be tricky. Suppose population A has a large number of alleles, such as an average of 20 alleles per gene, while population B has only a few alleles per gene, perhaps an average of only 5, and those 5 are also in population A. Does that mean that population A is older? Not necessarily, because population A may have acquired many of those alleles by interbreeding with other populations, not by mutations occurring over a longer period of time. Also, population B may be older, but may have suffered a catastrophic drop in its numbers, wiping out most of the alleles it had accumulated.
    Similarly, if population A has old alleles that population B lacks, it is not possible to conclude that population B descended from population A and lost the old alleles. Population A may have old alleles simply because it has stayed in the same, fairly constant, environment and has not evolved as much as population B, which has moved to a very different environment. Also, the old alleles may have entered population A because members of population A interbred with population C, which had the old alleles.
    All DNA in every plant and every animal has the same basic structure. (See Appendix). In all animals with a nucleus ("eukaryotes," e.g., every living thing other than bacteria, blue-green algae, and viruses), there are two kinds of DNA in its cells -- the DNA in the nucleus ("nuclear DNA") and the DNA in mitochondria ("mitochondrial DNA" or "mtDNA"). 7 Mitochondria, remnants of bacteria that were captured by cells over three billion years ago, provide energy for the cell. The captured bacteria helped the cells survive and that is why their DNA is still there. Later, some of that mtDNA moved into the nucleus and became nuclear DNA. 8
    There are some dramatic differences between nuclear DNA and mtDNA. Nuclear DNA is in the form of a double helix, a twisted ladder whose rungs are an A base on one side weakly bound to a T base on the other side, or a C base weakly bound to a G base. One strand is the "sense" strand that is read to make a polypeptide and the other strand is the "anti-sense" strand that is a complementary backup copy. Nuclear DNA is a two-strand string with two ends; mtDNA is a one-strand (usually) ring (a "plasmid") with no ends, except that when it is being read the ring opens. In each cell, there are only two copies of each strand of nuclear DNA, one from the mother and one from the father; 9 there are usually thousands of copies of mtDNA in each cell, almost always only from the mother. 10 There are over 3 billion base pairs (i.e., A, C, G, or T) 11 in 20,488 genes in nuclear DNA, but only 16,569 base pairs in 37 genes in mtDNA. Nuclear DNA is located in 23 pairs of chromosomes; mtDNA has no chromosomes. Nuclear DNA has a number of DNA repair molecules 12 that move along it and correct errors; mtDNA has no way to correct errors, so errors accumulate at about 20 times the rate for nuclear DNA. (Sykes, 2001, p. 55). Nuclear DNA mutates at the rate of once per billion cell divisions; mtDNA mutates about 10 times as fast as nuclear DNA. (Patterson, 1999, p. 152). Nuclear DNA comes in two types -- exons, DNA that codes for polypeptides ("genes"), and introns ("junk DNA") -- DNA that does not code for polypeptides; 13 mtDNA has no introns and it codes for RNA as well as for proteins. (RNA is the same as DNA but "U"s replace the "T"s and ribose replaces deoxyribose -- see Appendix.) Almost all racial traits are coded for in nuclear DNA; mtDNA only rarely has an effect on racial traits, e.g., respiration at high altitudes and during long distance running and metabolic advantages in the Arctic.
    A major difference for the purpose of deciphering human origins, however, is that mtDNA is in the sperm's tail and nuclear DNA is in its head. What does that have to do with human origins, you ask? Well, during fertilization, only the head of the sperm normally enters the egg (Schwartz, 2005, p. 194) and any sperm mtDNA that slips in is tagged and destroyed; therefore, the father's mtDNA does not normally contribute to the genome of the fertilized egg. 14 (Occasionally, some of the father's mtDNA slips by (Schwartz, 2002), thereby giving the fertilized egg both the mother's mtDNA and the father's mtDNA, confusing the geneticists. 15) This means that a person's mtDNA, whether that person is male or female, is (almost always) inherited only from the mother. Your mtDNA, even if you are male, came from your mother, hers from her mother, and so on.
    But there is some DNA that comes only from the father. Normally, the father and the mother each contribute half of their child's chromosomes. Females have a pair of X chromosomes (XX), so the mother can contribute only an X to her child. Males have an X chromosome and a Y chromosome (XY). If the father contributes an X, the child will have two X chromosomes and will be female (XX). If he contributes a Y, the child will have an X and a Y chromosome and will be male (XY). Thus, (almost always 16) Y chromosomes are inherited only from fathers and are inherited only by sons. This means that the DNA in the Y chromosome of a male alive today came from his father, who got it from his father, and so on all the way back.
    This information is useful in forensics, since a person's mtDNA will be the same as his mother's and her other children, and a man will have the same Y chromosomal DNA as his father and his father's other sons, but it is also useful in paleoanthropology, as we shall see.

Chapter 4

Table of Contents


1. Because polypeptides can be assembled different ways, humans have over 500,000 proteins but only 20,488 genes, though more genes may be found. Exons are only 1.5% of the human genome. (Carroll, S.B., "Regulating Evolution," Scientific American, May, 2008). Back

2. There may be a few exceptions. (Miller, 2006; also see gene APOE). Back

3. Epigenetics is an exciting new science with much promise of important discoveries. (Watters, 2006, p. 33; Cropley, 2006). Back

4. (Fraga, 2005). The number of copies of an allele may differ in identical twins. (Bruder, 2008). Back

5. See the Appendix for an explanation. Until recently, it was assumed that synonymous alleles produced exactly the same biological product. Although they do produce the same string of polypeptides, it has been found that they can cause the resulting protein to have different shapes. (Soares, C. "Codon Spell Check," Scientific American, May, 2007). Back

6. Because reproductive success is a sine qua non for all life, with large numbers of individuals over long time periods, reproductive success determines even the finest details of a species' traits. (Miller, 2007). Back

7. DNA is also found in the chloroplasts of plants. Inherited RNA is found in centrosomes, which oversee cell division. (Alliegro, 2006; Wikipedia, Extranuclear Inheritance). Back

8. Some other parts of cells (e.g., cilia, flagella, and centrioles) are also believed to be the remnants of captured microbes. (Patterson, 1999, pp. 133-134). In addition to the incorporation of microbe DNA into our own DNA, we have 10 times as many microbial cells in our body as our own cells. Back

9. One parent may contribute more copies of a gene than the other, resulting in greater genetic differences between people, including racial differences. (Redon, 2006). Back

10. The last two sentences explain why it is much easier to find mtDNA than nuclear DNA in fossils. Bones and teeth are made of a hard, calcium-based mineral, hydroxyapatite, that helps preserve DNA by keeping out bacteria and fungi. Although strongly acidic soil can kill the microbes, acid also attacks both the calcium and DNA; heat and temperature fluctuations also destroy DNA. (Sykes, 2001, pp. 171-172). Back

11. That may seem like a huge number, but the single-celled amoeba, Amoeba dubia, has over 670 billion base pairs. (Wikipedia, "Gene"). Back

12. An example is the UDG ("uracil DNA glycosylase") enzyme, which latches on to DNA blocks that are the wrong size. (Parker, 2007). (Wikipedia "DNA Repair"). Back

13. Genes account for only 1.2% of our genome's three billion base pairs. (Birney, 2007). Junk DNA can regulate the expression of a gene, e.g., how exons are spliced and folded to make them active. Humans have more junk DNA than other vertebrates. Back

14. Also, the human egg has about 250,000 mitochondria, while the sperm has only a few, just enough to create the energy needed to swim the last few millimeters to the egg. (Sykes, 2001, p. 54). Back

15. Even more confusing, it has just been found that, at least in mice, RNA in the sperm can also enter the egg and affect traits. (Rassoulzadegan, 2006). A similar phenomenon may occur with crosses between wild Mallards and White Pekin ducks, where the color of the duckling is determined by which species lays the egg. Back

16. A female may occasionally have an XY (androgen insensitivity syndrome, "AIS") or three sex chromosomes, an XXY. Thus, if the female gives her male child a Y chromosome and the normal (XY) father gives the male child an X chromosome, then the assumption that the Y came from the father will be false. (A male could also have three sex chromosomes, an YYX, or extremely rarely, even an XX, but that is not important here.) Back