GENETICS TUTORIAL ‑ PART I

"...organisms die but their genes pass on ‑ often mutated and redistributed, it is true, but genes nevertheless; and it is difficult, therefore, to escape the conclusion that the design of the organism is merely to provide for gene multiplication and survival..."  Carl Sagan, "Radiation and the Origin of the Gene," Evolution, January, 1957.

People once believed that the universe was created for Mankind and all other life was placed here for our use. This was gradually replaced by the harsher belief that our species competed with other species, and that Human Nature was designed to do what was good for the species. Anyone who acted selfishly was aberrant, and would be punished in a later life. Darwin believed that individuals competed with each other, and the victors of individual conflict shaped human nature. But now, the level at which competition occurs has descended one more level: sociobiologists argue that gene alleles compete with each other for positions on chromosomes (W. D. Hamilton, 1964a,b; G. C. Williams, 1964; E.O. Wilson, 1975; R. Dawkins, 1976). 

If the combatants are the genes, then what are we individuals? We are the "lumbering machines" carrying the genes that assembled us for the genetic competition (Dawkins, 1976). An individual is like a puppet, whose behavior is directed by strings that are pulled, ultimately, by tiny genes (please excuse the poetic license and anthropomorphism of this phrasing). The demotions our egos suffered during the past couple centuries continues into the 21^st, as people must now deal with the thought that we are created by our genes for gene battles, and the genes do not care about the individual's welfare.

If the genes are this important then we should know their story, from the beginnings of life to the present. I shall present a recapitulation of the evolution of life on earth, with a proper emphasis on the role of genes. Some of these descriptions are speculative, yet illustrate ways that I believe the subject should be approached. The essence of every speculation is, of course, mechanistic reductionism!

A Brief History of Life 

When earthly life started, 3.5 billion years ago, tiny replicating molecules resembling DNA (or maybe RNA) must have competed with each other for incorporating their molecular building blocks into copies of the replicating molecules. In time those molecules that accidentally created a protective "coating" survived longer. This crucial event might have been hastened by the existence of water droplets that would naturally form surface layers of like‑charged molecules with hygrophobic ends (Donaldson et al, 2004). A droplet with such a covering is a rudimentary cell, as the cell "wall" may have protective properties.

Approximately 2 billion years ago, a well‑functioning one‑celled form appeared which housed cell‑creating DNA floating inside (prokaryote). Later, a variant of the prokaryotic one‑celled life form had the several DNA molecules confined to a cell nucleus (eukaryote). This represented one more structural level of protection of the DNA. Whereas it must have helped the DNA survive it also required that a solution be found for the slightly more complicated replication process. 

A trend is evident, and it has continued throughout the long story of life on Earth. To compete better, DNA molecules have had to wrap themselves in an ever‑more complex structure, devise ever‑more complex methods for replication, and retain control of their protective structures for competition with other life forms.

Multi‑celled creatures did not appear until about 1 billion years ago. Each cell contained a nucleus with an identical set of genes inside. It is possible that initially all cells in a multi‑celled life form were identical. A grouping of cells has a smaller "surface area per mass" exposed to the watery environment than one‑celled forms, and this added protection may have rewarded the forms that tended to stick together. 

Specialization of some cells in a many‑celled creature may have been the next step in the evolution of life. With a reliable association of cells having the same DNA, there existed a reward for any gene mutation that helped the outermost layer of cells specialize in protective matters. Since all cells had the same nucleus, it could still be argued that the sacrifice of a few cells to become mere "protective skin" while forsaking reproduction themselves nevertheless enhanced the reproductive prospects of the identical genes inside the cells that were being protected. This concept is a kernel for "inclusive fitness," described below.

In this way, skin might have been the first "organ" to evolve. Once a method had evolved for guiding a cell's properties to be responsive to its surroundings, the path lay open for the evolution of any number of organs. Organisms competed with differently constructed organisms in seeking food - and perhaps in consuming each other. Although the organisms competed with each other for food, and perhaps attempted to destroy or devour each other, since the fate of this competition was determined by the properties produced by the genes within it, is more insightful to view the competition as occurring between the various gene groups than between individuals.  

Gene Competition Within and Between Species

Specifically, only the genes that differed were in competition. Identical genes in competing organisms might appear to be in competition, but only because they were part of an organism that had different genes. Since the fate of identical genes in different organisms was not in question, they were not competing with each other. If organisms had chromosomes that differed at only one gene location, and only two gene forms (alleles) existed at this location throughout a population of organisms, then it would be the two genes (gene alleles) that were in "competition." 

The casual observer who thought that two kinds of organisms existed that were competing with each other (for food, let's say) would be misunderstanding the situation. A deeper understanding shows that two genes were competing with each other.

The word "competing" is a human‑invented concept. It is important to remember that the entire process of genes competing, with one gene mutation slowly yielding to another, is purely mechanistic. Obviously, the genes are unaware that they are "competing." Only a human observer would remark "these two genes are in competition." 

Individuals within a species may "compete" with each other, and so may individuals belonging to different species. The underlying dynamic is the same:  every gene acts as if it wants to proliferate and last forever. Again, a gene does not "want" to proliferate. Rather, those that in fact proliferate are the ones that express themselves as individual characteristics that the human mind will identify as "wanting" to proliferate. Thanks to our primitive right brain (that evolved for dealing with social settings) it is helpful to use social metaphors for explaining mechanical processes.

It is theoretically possible that two species could exist in competition with each other while having no genes in dispute within each species. In other words, all individuals of one species would be genetically identical, and the same for the other species. Yet, since we are supposing that they are competing for the same resources in their environment, for example, the two species are in competition with each other. We should further specify that the two species hold some of the same genes (this is very likely, since they have common ancestors). For this hypothetical situation, two large chunks of genes are in competition with each other and the "winner will take all" after one species is exterminated (which is common for species that occupy identical niches). 

This is one extreme of a continuum of situations. At the other end is a situation in which there is no between‑species competition, but there is competition between genes within the single species. In other words, some gene loci on the chromosomes have two or more alleles, and these alleles are in competition with each other. The simplest case would be one gene locus with two alleles, and the two alleles are competing with each other for exclusive presence at one locus on the chromosome.

This simple situation is likely to end with a complete win by one of the alleles.  However, there are special cases where there will be a steady‑state percentage representation of both gene alleles (i.e., an evolutionarily stable strategy, or ESS, as described originally by J. M. Smith and later by Dawkins, 1976). 

In the real world there will be some within‑species competition of counterpart gene alleles and some between‑species competition between all the genes that are different between the two species. For the between‑species competition, large chunks of genes are involved; but only some of these will be under the influence of selection pressures.

Thus, for the typical situation, some gene alleles will be changing their representation frequency within the species gene pool due to "other species" selection forces, while other gene alleles will be changing their representation frequency within the species gene pool due to "within species" selection forces. 

Appendix B presents examples of the ruthless nature of gene competition using human virus examples. 

Inclusive Fitness 

The individual organisms called humans should be forgiven for seeing everything in terms of what they're good for to the individual organism. Dawkins (1982) describes an aberrant period in biology when the paradigm shifted from a "selfish organism" perspective (starting with Darwin) to "adaptation for the benefit of the species" paradigm (during the mid‑20th Century). Given that many (unsophisticated) people believe that people do things that benefit the species, the level at which people perceive evolutionary competition to occur should shift in the other direction, leading eventually to the "selfish gene" paradigm.

In other words, if we seek insight into how evolution works we should not ask "what good are genes to individuals?" but "what good are individuals to genes?" 

An example will serve to show how ridiculous an imperfect paradigm can be. A graduate student, who must still retain remnants of the belief that adaptation is for the good of the individual, studied the Australian redback spider. She describes how the male positions himself during copulation so that the female can eat his body during a leisurely insemination process, thus satisfying her into not seeking another male. This assures that the sacrificing male's sperm will not be competing with the sperm of another male. To sum up the article, the magazine author presents the following astounding quote attributed to the student: "Sexual cannibalism has always been thought of as a conflict between males and females, in which males are just being overpowered. It's important to realize that it can be advantageous for the male."

Only someone handicapped by the "good of the organism" paradigm could say such a ridiculous thing! The benefactor, clearly, is the gene that causes the male to behave in this bizarre manner, not the individual male. He is a victim, more than the female. What's missing in this summarizing statement is an acknowledgement that genes produce behaviors which can manipulate and victimize individuals with behaviors that benefit only the genes that create the behavior? 

Inclusive fitness states that genes tend to produce individual behavior which maximizes the presence of the behavior‑producing gene in succeeding generations (Hamilton, 1964a,b). Since biological relatives are likely to be carriers of the same genes as the behaving individual, the fate of the genes in relatives matters as much as the genes in self. For social animals that live among relatives the merit of an action must take into account the consequences upon those "genetically related" carriers of the genes.

The mathematical treatment of inclusive fitness is straightforwardly presented in many places. I shall simply give a feeling for it by repeating a traditional example. A gene will reward a self‑sacrificial act if it saves at least two cousins, or at least four second cousins, etc., as in each case the same number of identical genes is preserved (on average). 

Inclusive fitness provides an explanation for "altruism" by the argument that an altruistic act promotes the proliferation of genes generating the act. Sometimes these altruistic acts are at the expense of the individual; but that's OK from a gene's perspective, for the individual is merely a tool created by the genes for gene proliferation!

The inclusive fitness paradigm is useful in many other situations, some of which will be dealt with in the following chapters.

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