How Genetics Discoveries Affect Evolution Theories

Discoveries in genetics science are very important to evolution theory. For example, genetics has provided substantial confirmation of the species descendency concept. Genetic fingerprinting can not only determine if a person is related to another person but also the extent of the relationship. In the same manner, it is possible to determine that all Earth species are related, determine how closely they are related, and even approximate when two species diverged from each other. Mice and humans shared common ancestors approximately 30 million years ago.

However, at the same time, genetics discoveries have disclosed issues with the traditional evolutionary mechanics concept in several different areas. These issues have contributed to development of alternative evolutionary mechanics theories including gene-centered theories, group/kin selection theories, and evolvability theories.

To review, traditional mechanics theory says that the evolution process is entirely driven by differences in expressed phenotypic design between organisms that are then selected or rejected by natural selection. Phenotypic design includes physical properties and inherited behaviors that plausibly affect the probability that the organism will survive longer and reproduce more. Expressed means that the design property has to be operative during the life of the organism such that its existence affects survival or reproduction. Latent properties cannot affect evolution according to traditional theory. Evolution is essentially performance driven: Does the mutant design change allow the organism to survive longer and breed more?

ISSUE: Evolution of Inheritance Systems

One issue with traditional theory concerns the inheritance systems that handle transmission of genetic design information between generations of an organism. The designs of these systems nominally do not affect the phenotypic design and therefore performance (survival and reproduction) of an organism except in a negative way. An asexually reproducing organism could have the same or better phenotypic design as a sexually reproducing organism from a performance viewpoint. And yet sexually reproducing organisms developed from asexually reproducing organisms and this involved the evolution of very substantial additional complexity in their inheritance systems including paired chromosomes, meiosis, etc. Since sexual reproduction is performance neutral or disadvantageous, what drove the evolution of the inheritance system? Alternative evolutionary mechanics theories (especially evolvability) speak to this issue.

ISSUE: Digital Genetics

Genetics discoveries have determined that genetic information is digital in nature. Organism design information is carried by the sequence in which base molecules are strung together to produce a DNA molecule. Because genetic information is digital, inheritance systems share properties with and must follow the same rules as any other digital information transmission or storage system. Genetics discoveries show that this is indeed the case and that genetic data has a complex digital data structure including formats, “words”, language, codons, synchronization features, etc. Many complex genotypic design features of this system appear to have no phenotypic design consequence and therefore no traditional evolutionary motivation for their development although they do have evolutionary effects as described below. What drove evolution of the genome?

The decoding of the human genome has revealed that the genome consists of 3.3 billion genetic code letters equivalent to 825 megabytes of data. Much of this is extremely repetitive and therefore contains little information. Only about 5 percent (41 megabytes) is thought to have phenotypic (design) consequence. There are therefore finite limits to the number of design parameters that can be specified by the genetic code as well as limits on the precision with which those parameters can be specified. See Digital Genetics.

ISSUE: Evolutionary Sub-processes

The traditional concept is that the evolution process happens in two steps:

A mutation occurs in a single individual that changes the inheritable expressed phenotypic design of the organism.

Natural selection selects those changes that improve organism performance incorporating them into the species genotype.

Once a beneficial mutation occurs, the individual organisms possessing the mutant genotype immediately survive longer and perform better in propagating their mutant design. This is sometimes referred to as the “one mutation at a time concept.” Darwin suggested that any single mutational change would need to have only a minor phenotypic effect in order to propagate because a large change would almost certainly be adverse. The traditional view emphasizes the evolutionary importance of individual organisms as opposed to groups or populations and also suggests that, once a beneficial mutation occurred, propagation of that change could be rapid.

Genetics discoveries show that although mutations and natural selection are very central to the evolution process, there are many intermediate steps also involved in the evolution of complex, sexually reproducing organisms. The steps involved might look more like:

A mutational change alters the genetic data in a single individual.

Natural selection removes very adverse mutations, retains mildly adverse or neutral mutations in addition to any beneficial mutations.

Remaining mutations propagate in a population. Any two individuals may have a large number of genetic differences. The same individual could possess many genetic differences between its two genomes.

Genetic data can be occasionally copied producing a duplicate of some amount of genetic data.

Some mutations have no phenotypic effect but encourage subsequent mutations that move (transpose) data from one location in the data format (genome) to another location.

Some mutations have no phenotypic effect but can encourage subsequent copying and duplication.

Copied data can introduce redundancy and/or create a data basis for new genetic instructions. Redundancy can increase robustness or the tendency to resist alteration of the controlled function by subsequent mutation.

Recombination in miosis can produce individuals having different combinations of genetic differences and therefore different phenotypic designs even though they are descendents of the same parents. Because of cascading, phenotypic differences resulting from recombination can be much larger than differences resulting from an individual propagatable mutation.

Inheritance is affected by the relative location (locus) of mutational differences in the genetic data structure (genome) due to the genetic linkage principle(1) – encourages group inheritance of linked mutational differences. Transposing of data affects this by changing relative location.

Natural selection selects combinations of genetic differences that improve performance, increasing prevalence of the underlying alleles.

The above brief summary grossly understates the sort of evolutionary process complexity that has emerged from study of inheritance mechanisms. The sub-processes interact in very complex ways and tend to operate on long time frames even compared to evolutionary time standards. This affects the plausibility of group selection as described below. All of the steps appear to have evolvability benefits. In mammals, it is thought that less than five percent of genetic data has phenotypic effect (gene exons and promoters) while much of the remaining “junk DNA” has plausible evolutionary effects by guiding subsequent mutational changes.

Note that the complex concept is more powerful than the traditional concept because it allows for the possibility that a particular combination of mutational changes could result in a benefit even though each individual change, considered by itself, was mildly adverse.

ISSUE: Genes

Genes specify organism phenotypic design and are a specific data structure within the overall genomic data structure mentioned above. The evolution of progressively more complex organisms has required the evolution of progressively more genes. The evolution of a new gene having a different function is, for many reasons, a particularly difficult step in the evolution process. Indeed, genetics discoveries show that similar related organisms (e.g. mammals) have virtually the same genes. Their phenotypic differences are the result of relatively minor differences within the genes. Therefore: “Genes live longer than species” and represent a long-term process even relative to species life times. This is the basis of the gene-oriented alternative evolutionary mechanics theories.

ISSUE: Universality of Evolution Process

Darwin and traditional evolutionary mechanics theory assumed that the evolution process is the same for all species. All species presumably were subject to mutational change and also to natural selection. However, genetics discoveries disclosed gross differences in inheritance mechanisms that clearly affect propagation of mutational changes. Simple organisms (e.g. bacteria) only possess one (haploid) set of genetic data while most complex organisms possess two (diploid) sets of genetic data. In the latter case, phenotypic design is determined by the combined effect of both sets of genetic data. Further, early genetics discoveries revealed that in many cases one state (allele) of a mutational difference dominated the design such that the opposite allele would have essentially no phenotypic effect unless both sets of genetic data contained the same recessive allele. Propagation of mutational changes is therefore very different in diploid organisms because an adverse mutational change that was recessive could propagate more readily than in the haploid case while a beneficial but recessive mutational change would propagate less well than in the haploid case. Further analysis disclosed many other differences that plausibly affect propagation (e.g. X or Y linking, mitochondrial DNA, etc.) Obvious questions result:

If the evolution process is different in different organisms potentially enormous complexity results. Data acquired from study of bacteria is not necessarily applicable to complex organisms, etc. Perhaps mammals evolve in a different manner than plants? Are there many factors that influence the evolution process? Which species possess them? To what extent?

From a traditional mechanics standpoint, the diploid inheritance mechanism appears to be a step backward. Propagation of beneficial changes is inhibited while propagation of adverse changes is encouraged. Why would a backward step evolve and be retained?

Everybody agrees that diploid genomes and sexual reproduction are evolved designs. Is it possible that therefore organisms can evolve differences in their evolutionary processes? Can they evolve improvements in their evolutionary processes?

These questions lead to development of the evolvability alternative evolutionary mechanics theories. The potentially enormous increase in complexity exposed by rapidly advancing genetics science affects our scientific confidence regarding evolutionary mechanics. Perhaps nobody really understands the details of evolutionary mechanics!

ISSUE: Mutational Change vs. Selectable Property

Traditional “one mutation at a time” evolutionary mechanics theory assumes that each mutational change is individually selected or rejected by the evolution process. A mutational change is the selectable property. However we now know that the digital nature of genetic data means that a genome either possesses or does not possess a given mutational difference (generally a single nucleotide polymorphism or SNP), a binary situation. Any organism property that is more or less continuously variable in a population (think bell-shaped curve) must result from combining many genetic differences that simultaneously exist in that population and affect the given parameter. Further, virtually all potentially complex selectable properties (e.g. strength, intelligence, speed, etc.) in complex organisms result from combining many mutational differences in a particular manner. The human population at large is now thought to currently contain millions of individual genetic differences, each presumably resulting from a different mutation in a different individual.

Therefore, in complex organisms, a selectable property is not the same as a mutational difference. This sort of logic tends to deemphasize the importance of individuals and individual possession of mutational changes relative to the importance of particular combinations of mutational changes where the underlying mutations are relatively widely dispersed in a population. This in turn favors alternative evolution mechanics theories.

ISSUE: Evolutionary Rapidity and Individual vs. Group Selection

Everybody agrees that the design of anything is a compromise. Theorists agree that a group benefit could be a compromise with individual disadvantage. Functionally there is no difference between individual survival and group survival. Either way, dead is dead, extinct is extinct. Therefore those who disagree with the group selection concept do so because of a timing issue. Wouldn’t an individual disadvantage tend to act more rapidly than a group advantage? How would an individually disadvantageous design survive long enough to populate a group? Wouldn’t a group benefiting design need to be possessed by most members of a group to be effective? Traditional theorists point to selective breeding in suggesting that a design feature representing an individual disadvantage would select out prior to the point in time at which a group benefit could be effective. Selective breeding can indeed cause enormous phenotypic change in a very brief time.

However, selective breeding (or rapid natural selection) can only affect (select among) the relatively tiny portion (estimated at 0.1 percent in humans) of genetic data that varies between members of a population, essentially only the last step of the complex evolution process described above. As a result, selective breeding for any one design parameter introduces changes (nominally adverse) to other parameters. In most cases the breeder does not care about the unintended changes but evolutionary advantage depends on the combined net effect of all of the organism’s characteristics so evolution is affected by the introduction of adverse changes. Change resulting from selective breeding is not the same as evolutionary change. Evolution, by means of new mutations and utilizing all the sub-processes can achieve much more comprehensive optimization of all of the organism’s characteristics. Because the comprehensive process is much longer, the apparent timing difference between group and individual selection is dramatically reduced increasing the feasibility of group selection. This issue is probably the single most important issue in the continuing controversy between traditional and alternative evolutionary mechanics theories.

ISSUE: Unnatural Variation

Darwin and subsequent theorists agreed that variation in inheritable organism design characteristics in a species population was essential to the evolution process. Without variation, there would be nothing for natural selection to select. Darwin and traditional theory assume that variation is caused by mutations, that all species are susceptible to mutations, and that therefore natural variation is a fundamental property of life.

However, we now understand that “natural” variation in complex organisms is actually largely the result of evolved design characteristics including meiosis, recombination, and many others. Trivial example: An inheritable behavior that caused an animal to prefer mating with non-relatives would increase variation in its population. Without the evolved, variation enhancing characteristics, variation in complex organisms would be much less, possibly negligible.

The idea that a property that is essential to the evolution process is itself the result of evolved characteristics leads directly to the evolvability alternative mechanics theory.

(1) Genetic linkage: Because of the meiosis genetic crossover mechanism, the probability of inheriting specific mutational alleles as a group from the same ancestor depends on the genomic (data) distance between them. Distant alleles on the same chromosome or on different chromosomes will be more randomly selected from the organism's two parents. Alleles close together on the same chromosome will tend to be inherited as a group.