On my latest blog, ThinkCreeps posted a comment quoting my statement that "we do not know why natural genetic engineering systems are as successful as they have been in generating useful evolutionary novelties in the history of life." Then he goes on to answer, "Yes we do - the good ones spread quickly through the population."
If only things were that simple! Good novelties just appear, as if by magic, and then spread due to their selective advantages. ThinkCreeps apparently shares a common illusion in evolutionary thinking that natural selection is all we need in the way of basic principles to understand the evolutionary process.
All scientific views of evolution by descent with modification envision two separate and essential steps in the establishment of living organisms with novel features:
In the absence of detailed information about the mechanisms of variation, heritable differences were widely assumed to arise randomly and accidentally. After Mendelism was rediscovered at the start of the 20th century, Mendelian segregations were added as variation modes in the neo-Darwinian "Modern Synthesis." Nonetheless, the sources of new segregating alleles (genetic differences) were still assumed to be stochastic accidents.
It was even claimed by some neo-Darwinians that evolution could be ascribed to changes in allele frequencies in populations due to natural selection acting on their fitness contributions. Many thinkers did not notice that this argument neglected the large number of cases where evolutionary differences were accompanied by other kinds of heritable change, such as alterations in chromosome structure or number.
With the advent of molecular genetics and DNA sequencing in the second half of the 20th century, it became possible to study the mechanisms of genome change in detail. It is commonly assumed that genome alterations account for the vast majority of heritable variation in living organisms. Other kinds of heritable changes are known and may also play an important role in evolution. Non-DNA changes include inheritance of self-templated cell structures and protein conformations, such as prions.
The results of the molecular studies are clear. Heritable changes can occur at the genetic level, through alterations in DNA sequences and in the structures of cell DNA molecules, and at the epigenetic level, through alterations in the way DNA is modified chemically and complexed with RNA and proteins in stable chromatin configurations.
Genetic and epigenetic changes result from the actions of cell biochemical activities, not from accidents. This is a critical fundamental discovery of molecular genetics.
There are many different activities that work directly on DNA and bring about genetic changes, ranging from single nucleotide substitutions to major restructuring of chromosomes. DNA modules can move from one place to another in the genome, RNA molecules can be reverse transcribed into DNA and inserted into the genome, and broken DNA molecules can be rejoined in novel combinations. The genome sequence record provides a rapidly growing mountain of evidence showing how important such non-random events have been in evolutionary history.
There are also many distinct activities that modify DNA and chromatin structures leading to heritable epigenetic changes. Our knowledge of these chromatin remodeling processes is younger than our acquaintance with DNA changes, and they do not leave the same kind of trace in the genome sequence record. But we do know that epigenetic changes have a profound influence on genome restructuring activities, and the same ecological challenges and stresses lead to high levels of both epigenetic and genetic variability.
Important take-home lessons from the molecular studies are:
To ignore all the above and look only at selection seems to me a gross omission. How could natural selection operate so that "the good ones spread in the population" if there were no positive variants in the first place? Where would they come from? That is why I am so confounded by Jerry Coyne's comment that he can explain natural genetic engineering by "garden variety natural selection." He's confusing baking the cake with eating it.
The outstanding issue, in my opinion, is: Where does functional creativity come into play to generate useful novelties? Darwin applied his uniformitarian, gradualist ideas to suggest that it was natural selection alone: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case" (Origin of Species, Chapter 6). However, we should note that Darwin modified his position in later editions to acknowledge "variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection" (Origin of Species, 6th edition, Chapter 15, p. 395, emphasis mine).
Now that we know how "spontaneous" variations arise, it is time to recognize that we cannot have selection without variation by natural genetic engineering and epigenetic modifications. To make further progress in our understanding, we need to investigate the respective roles of natural genetic engineering and natural selection in evolutionary innovation. Where, in fact, do "the good ones" really come from?