On The Evolution of A Theory
Almost everybody thinks they know what evolution is. Even those that deny it, have some basic understanding of what it suggests. Evolutionary theory, as proposed by Darwin, explains a great deal about how every living organism that exists today came into being. Yet, it fails to explain an equivalent (if not larger), number of changes, developments and trends witnessed in the processes that govern speciation.
The longstanding Darwinian theory of evolution suggests that evolution occurred by “random” genetic mutations over time while natural selection allowed a few of those chance mutations to persist based on whether they were useful to the organism or not. The theory extends to claim that the “fittest” would survive based on advantageous mutations and their final ability to reproduce.
For all the technology and tools available to Darwin at the time, he did a commendable job in developing reasonably strong arguments for his theory. Still, he conceded that his findings could not explain everything. Now that we know more, we should start to address the gaps in his understanding to solidify our own.
Fooled by randomness?
There is increasing evidence to suggest that “randomness” cannot be the primary basis of the beneficial mutations that allow a species to thrive. Given the time in which all life on earth has evolved, randomness alone fails to explain the emergence of specialised proteins and unique, complex structures, which begs the question – how random is random?
New research indicates a substantial amount of direction and replicability of mutation types. Researchers studying organisms like E.coli, sunflowers and sharks have found multiple instances where evolution progresses down a similar path even when genetically similar individuals (or groups) are separated in space and time [2,5]. That is to say, several evolved traits are reproducible even while some of the minor genetic mutations leading to them may be diverse.
Mutability is also enhanced in some organisms by exacerbating glitches in repair mechanisms in times of stress.  This could indicate the “awareness” that more mutations will lead to better chances of survival. Meanwhile, there also seems to be a higher tendency for mutations to occur at certain genetic “hotspots”. A number of experiments have shown some evidence of “memory” where a historical mutation site or specific mutation is “built on” to confer new functionality.
Most of these findings allude to the existence of some sort of primary logic that is being followed through evolution.
Environment, Epigenetics and Molecular Memory
Much of what Darwin didn’t and couldn’t know lies in the interplay of the environment and the genes – an area of knowledge we now call epigenetics. Epigenetics has begun to fill in several gaps in our understanding of the genome. For one, we now know that a genetic “memory” is largely passed down through the epigenetic machinery via patterns of chemical modifications made onto the genes. Evidence of epigenetic memory has been seen in studies of various populations up to 3 generations after a major environmental impact event like drought or famine.
Furthermore, a clear trend seen in many of the new experiments is that when presented with similar environmental triggers or stressors, the evolutionary response tends to “find similar solutions”[2,5]. This indicates that the environmental factors contributing to evolution have a large impact in determining the eventuality of adaptations. As mentioned earlier, replicability of evolutionary changes has been demonstrated by replication of environments at separate times and in separate geographies.
More proof lies in the evolutionary fossil record and study of conserved genes. As per the current theory, a large proportion of genes have been conserved throughout the evolutionary process. Similar genes have adapted into varied functionalities over time. Despite genetic similarities, it is now understood that significant differences seen within phenotypes, are determined by epigenetic modifications that govern what is expressed and when. In fact, most evolutionarily significant mutations have been found to accumulate in genetic repeat regions and/or “molecular switch” regions i.e. epigenetic regions that determine the expression of the genes that they flank [1,9].
For instance, while human beings share 96% of their genetic code with chimpanzees. One of the major genetic differences was seen in the area that determines the expression of the jaw muscle. A glitch in the epigenetic switch caused the protein of this muscle to be under-expressed leading to space for a larger brain to evolve.
Thus, we now know that a large proportion of what we witness as the outcomes of evolution are being orchestrated by complex epigenetic mechanisms that we are just beginning to understand.
Another underrated influencer of evolution in Darwin’s time (and now) is viral activity. Although vast areas of our genome still contain “junk DNA”, largely attributed to gene insertions by viruses, we continue to undermine the role that these parasites may have had in our evolution.
Viruses are known to infect almost all forms of life on earth, all of which have, over time developed complex immune mechanisms to fight these infections. This means, that if nothing else, viruses have definitely had an influence on the evolution of immunity across the kingdoms of life.
Further, large insertions into host genomes by retroviruses, especially into germ cells, would essentially alter the genome of that species from that point onwards (assuming subsequent generations from the altered individual). Certain experiments also indicated the potential role of viruses in promoting monogamy in Prairie Voles and placenta formation in Sheep. 
While the theory of evolution still holds true, it is important to note that some of the mechanisms by which it occurs and the nuanced nature of nature may not be fully explained yet. New research and evidence will help us to unravel more mysteries of the rationale of biomolecules and the functions that arise from them. Above all, we should remain open to accepting that logic, memory and intelligence are features not reserved for the human mind alone.
References and Further Reading
- Daxinger, L. and Whitelaw, E. 2010. Transgenerational epigenetic inheritance: More questions than answers. Genome Research. 20, 12 (2010), 1623–1628.
- Willbanks, A. et al. 2016. The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences. Genetics & Epigenetics. 8, (2016), 25–36
- Herron, M. and Doebeli, M. 2013. Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. PLoS Biology. 11, 2 (2013), e1001490.