Digital Genetics and the Theory of Evolution

Theodore C. Goldsmith 12/2004

As most people know, Darwin's theory of evolution is, in general, almost universally accepted by the scientific community. Darwin's main conclusion, that species are descended from other species, has been confirmed by an overwhelming and growing body of evidence. 

Many are also aware that some practitioners of religion-based "science" totally reject Darwin's theory and instead believe that present-day species were individually created by God or under the direction of some other intelligence.

However, many people are not aware that there have always been discrepancies between the details of Darwin's theory and some scientific observations concerning our natural world. These discrepancies have resulted in the development of various "sub-theories" that are proposed as modifications or adjustments to "orthodox" Darwinism.

Much more extensive and comprehensive treatment of this subject can be seen in the free online book The Evolution of Aging available at

Here is a very brief summary of Darwin's evolution theory as a base for this discussion:

  1. Main Conclusion: Species are descended from other species.
  2. Living organisms can adapt to their environments by means of natural selection.
  3. Species and individual organisms are in competition for available resources.
  4. Evolved characteristics (adaptations) of organisms are determined by natural selection (survival of the fittest).
  5. Evolution is a slow, incremental, process.
  6. Natural variation between individual members of a species is essential to the evolutionary process.

One of the largest discrepancies concerns aging or other features of organisms that act to restrict life span. Darwin's theory is largely based on "survival of the fittest". If an individual organism has a trait that allows it to survive longer and therefore breed more, its traits are more likely to be represented in descendents. If an individual has traits that limit its survival relative to other individuals, those traits tend to "select out" and be removed from the gene pool. It is therefore impossible, according to orthodox Darwinism, for an organism to evolve a trait that restricts or regulates survival without any compensating individually beneficial effect such as an increase in reproductive capacity. Nevertheless, most organisms display either aging or other less subtle mechanisms that act to regulate life span in a species specific and individually non-beneficial manner. This issue was raised by Darwin's contemporaries shortly after initial publication of The Origin of Species and remains an area of legitimate scientific disagreement 145 years later.

Another discrepancy is concerned with the behaviors of various animals. According to Darwin, competition should be fiercest between animals that are most similar in their needs for food and habitat. The fiercest competition should therefore be between members of the same species. However many animals are observed to cooperate, even if increasing the risk to their own survival. Some appear to have "societal" behaviors that benefit groups at the expense of individuals. Evolution of these characteristics appears to be incompatible with orthodox Darwinism.

More recently, our increasing understanding of the exact mechanisms of biological inheritance has exposed other discrepancies. We now know that inheritance takes place by means of digital data communicated between parent and descendent via an organism's genetic code. The actual inherited data or genome of various organisms has been determined. The "format" or organizational structure of the genetic digital data has also been largely determined. These discoveries disclose that the genetic digital data scheme shares limitations and benefits that are common to any digital communications system and that therefore "communications analysis" and "information theory" apply to the genetic system.

One "digital discrepancy" has to do with variation. A detail of Darwin's theory says that "natural variation" between individuals is essential to the process of natural selection. Darwin thought that such natural variation was a fundamental property of nature and therefore applied equally to all organisms, a reasonable assumption in 1859. However, variation is not a fundamental property of digital communications. It is now apparent that observed "natural variation" is the product of a large number of complicated and obviously evolved mechanisms such as meiosis, gene crossover, and even sexual reproduction that vary between species. This introduces a discrepancy because natural variation is individually adverse and therefore it should have been impossible, according to orthodox Darwinism, for the variation producing characteristics to evolve. 

Why is variation adverse? Let's consider the fittest animal in a large herd. If this animal's descendents were identical clones of their parent, they also would be the most fit. However, natural variation results in a situation in which most or all of its descendents will be less fit than their parent, a disadvantage. Natural variation results from evolved characteristics and causes an individual disadvantage, a violation of orthodox Darwinism.

Another digital discrepancy is concerned with the organizational structure of the functional digital data in an organism's genome (including the order in which genes are found, as well as the grouping of genes on particular chromosomes). Current genetics theory says that the genome organizational structure (with some exceptions such as sex chromosomes) does not affect the functional (i.e. fitness) aspects of the organism. If we put the genes in a different order or even on different chromosomes they should still produce the same result. The functional differences are determined by the digital data content of the genes, not their order.  

However, it is known that the grouping of genes drastically affects inheritance. When meiosis merges the data in two parent genomes to produce a single sperm or egg cell genome, the probability that a gene from a given parent will be transmitted along with another gene from that parent is inversely proportional to the "data" distance (i.e. number of bases) between the two genes on their chromosome. Since the effects of thousands of genes obviously interact, this "grouping" property of the meiosis mechanism clearly allows a situation in which certain groupings are more beneficial than others in regard to the future properties of descendents. A species could "evolve" a particular grouping that provides an evolutionary benefit. At the same time the different groupings do not affect fitness of current animals. This situation does not appear to be handled by orthodox Darwinism.

Yet another digital genetics problem is concerned with non-functional "junk" DNA. According to various estimates, as much as 95 percent of the human genome consists of non-functional DNA such as introns, various repeat patterns, and pseudogenes, thought to have no fitness effect. However, here again, non-fitness changes in junk DNA can affect the future adaptability of an organism. Instances have been described in which the presence or absence of a particular pattern in junk DNA affected, by means of "digital pattern sensitivity",  the probability of subsequent mutations such as the duplication of part of a genome or the transposition of part of a genome to another position in the genome. Differences in junk DNA patterns could therefore affect the sorts of future mutations possible even though they have no effect on current fitness. We could envision some animals acquiring a mutation that would essentially "poison" future adaptation in a part of the genome. Others could acquire a mutation that would facilitate future adaptation. Both mutations could freely propagate because they had no effect on current fitness. Advantages or disadvantages of this sort are not handled by Darwin's theory because they are not expressed as differences in fitness.

Comparative genome analysis does in fact disclose that similar species can have very different genome organizations and very different junk DNA content and distribution even though they have similar genes. This "evolution of the genome" is not handled by orthodox Darwinism.

The issues described above have encouraged development of a number of proposed adjustments to orthodox Darwinism. All of these adjustments consider that Darwin's primary conclusion was correct: Species are descended from other species. The details of Darwin's theory are also mainly correct: Survival has a major effect in determining whether a trait is retained in the genome. Variation is important to the process of natural selection. Evolution proceeds in tiny increments. However, they all deemphasize the importance of "individual" survival and question whether survival of the fittest is the only factor that determines if a characteristic will be evolved and retained.

The group selection theory holds that benefit to a group such as a herd or even a whole species could override an individual disadvantage in the selection of a trait. Group selection has been mainly proposed as an explanation for non-Darwinian behaviors and has more recently been proposed as an explanation for aging and other life span regulating characteristics.

The selfish gene theory proposes that individual organisms are vehicles for the propagation of their genes and is an alternative to group selection in the explanation of non-Darwinian behaviors.  Because all the animals in a species share essentially the same genes, cooperation between members of the same species makes sense from a "gene's eye view" even though individually adverse in Darwin's view. 

The evolvability theory proposes that in addition to maintaining the ability to survive, species need to maintain the capacity for further adaptation. This evolutionary capacity or evolvability requires characteristics that can vary between organisms and can also be detrimental to fitness such that there can be a tradeoff between fitness and evolvability. For example: more variation benefits evolvability but is adverse to fitness.  Less variation would benefit fitness but is adverse to evolvability. Evolvability theory works as an explanation for aging and the digital discrepancies and also explains some troubling behaviors.

There does not appear to be any fundamental conflict between these "sub" theories. They could all be valid. All of the proposed adjustments suggest that evolution is probably a more complex and "longer-term" process than contemplated by Darwin, a finding that certainly appears to be justified by the enormous complexity emerging in the inheritance process. Another reasonable inference is that survival or non-survival of species (relative to individuals) might be much more important to the process of evolution than suggested by Darwin. Speciation, by "genetically isolating" individuals, drastically affects inheritance and therefore the process of evolution.

Although these minor adjustments to the theory of evolution might seem to be very "academic", one practical area, anti-aging research, has been and continues to be greatly affected by these scientific disagreements. Feasibility of and directions of anti-aging research are greatly affected if aging is determined to be an evolved characteristic (group selection and evolvability theories) or not an evolved characteristic (orthodox Darwinism).

Analysis of genetic data is in its infancy. At this point we know that a human genome contains about 825 megabytes of data which is 99.9 percent identical between normal individuals. (Approximately one in every thousand DNA letters is different.) "Natural variation" and the effects of natural selection are therefore currently confined to this .1 percent of the genetic code. We think that there are approximately 25,000 - 35,000 human genes. Work has just begun on determining which specific variable characteristics are associated with particular parts of the data, which characteristics are therefore grouped together, and which groupings are common between related species. Answers to these questions will provide great insight toward confirming adjustments to evolution theory.

A recent (November 2004)  National Geographic cover story title asks "Was Darwin Wrong?". The scientific answer is "No, Darwin was not wrong". Newton wasn't wrong either. However, it is now universally recognized that Newton's theories were not totally comprehensive and that discrepancies existed. "Relativistic physics" is now accepted as a necessary adjustment to "Newtonian physics".  Eventually it will be similarly recognized that Darwinian evolution theory needs similar adjustments.

Copyright 2004 Theodore C. Goldsmith