Genome complexity; epigenetics: Lamarck is back (Introduction)

by David Turell , Thursday, August 17, 2017, 15:32 (2436 days ago) @ David Turell

Another essay on how important epigenetics is:

https://aeon.co/essays/on-epigenetics-we-need-both-darwin-s-and-lamarck-s-theories?utm_...

"One of the most common such processes is ‘DNA methylation’, in which molecular components called methyl groups (made of methane) attach to DNA, turning genes on or off, and regulating the level of gene expression. Environmental factors such as temperature or emotional stress have been shown to alter DNA methylation, and these changes can be permanently programmed and inherited over generations – a process known as epigenetic transgenerational inheritance.

"Another major epigenetic process discovered in recent years is ‘histone modification’.
Histones are proteins that attach to and alter the structure of DNA, which in turn wraps around the histones like beads on a string. The combination of DNA and histone together has been called ‘chromatin structures’ – and the coils, loops and twists in chromatin structures in response to environmental stress can permanently alter gene expression as well.

"More recently, researchers have documented ‘RNA methylation’ in which methyl groups attach to the genetic helper molecules, in the process altering gene expression and subsequent protein production for generations down the line. Likewise, the action of so-called ‘non-coding RNA’, small RNA molecules that bind to DNA, RNA and proteins, also alter the expression of genes, independent of DNA sequence.

"All of these epigenetic mechanisms are critical and have unique roles in the molecular regulation of how DNA functions. The regulation of biology, it follows, will never involve a ‘genetic-only process’, nor an ‘epigenetic-only process’. Instead, the processes of epigenetics and genetics are completely integrated. One does not work without the other.

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"In another recent study, we examined evolution on the macro-evolutionary scale – speciation. One of the classic examples of speciation involves Darwin’s finches in the Galapagos Islands. A group of finches radiated out from a single species to become 16 different species of varying size and with different traits such as altered beak structure. Our team and collaborators set out to examine the DNA from five of those distinct species. We observed DNA sequence mutations from one species to the next, but the epigenetic changes in DNA methylation (epimutations) were higher in number and more correlated with the phylogenetic (family tree) distance between the species. Although the field of evolution is currently focused on neo-Darwinian genetic concepts, our findings suggest that epigenetics also has a role in the speciation and evolution of Darwin’s finches.

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"Nearly all types of genetic mutations are known to have a precursor epigenetic change that increases the susceptibility to develop that mutation. We observed that direct environmental exposure in the first generation had epigenetic changes and no genetic mutations but, transgenerationally, an increase in genetic mutations was identified. Since environmental epigenetics can promote both trait variation and mutations, it accelerates the engine of evolution in a way that Darwinian mechanisms alone cannot.

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"I’m convinced that we have reached the point where a paradigm shift is due. Accepting that epigenetics plays a role in evolution does not topple the science of genetics; embracing neo-Lamarckian ideas does nothing to challenge classic neo-Darwinian theory. The accepted sciences are essential and accurate, but part of a bigger, more nuanced story that expands our understanding and integrates all our observations into a cohesive whole. The unified theory explains how the environment can both act to directly influence phenotypic variation and directly facilitate natural selection,

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"A unified theory of evolution should combine both neo-Lamarckian and neo-Darwinian aspects to expand our understanding of how environment impacts evolution. The contributions of Lamarck more than 200 years ago should not be discounted because of Darwin, but instead integrated to generate a more impactful and insightful theory. Likewise, genetics and epigenetics must not be seen as conflicting areas, but instead, integrated to provide a broader repertoire of molecular factors to explain how life is controlled."

Comment: Lamarck lives. The author is an active research scientist in the field of epigenetics.