Genes and environment - ecological genetics

Environmental flux permeates tissues and cellular membranes through signal molecule cascades, altering genetic expression and volume of transcription and also influencing post-transcription modification of RNA (ARN) before it is translated into protein sub-units. After protein subunits have been made at ribosomes, further post-translation environmental regulation of the assembly and function of proteins occurs. Such environmental orchestration of genetic expression is termed 'epigenetics' (higher-than genes alone). Environmental signals also tag DNA with chemicals such as methyl and extra phosphate groups, altering its future expression, and cause transposition of genes and transcription promotors from one part of the genome to another, resulting in changed expression of genes in current and, to a lesser extent, future generations. Thereby through the feedback between pre-existing cellular components, molecules and environmental cytoplasmic signals, and information input from ancestral responses to environmental challenge, in the form of the tagging and rearranging of the molecule DNA (ADN), cells, tissues and organisms may have the opportunity to survive changes to their internal and external environments by having the capacity to produce novel proteins (new combinations of pre-existing protein sub-units), that better match the new conditions of 'environmental challange' as proposed by the nobel prise winning geneticist Barbara McClintock. This leads to a reappraisal of the role of genes and DNA from controlling an organism from the nucleus outwards, in a genetically pre-determined and utterly predicatble fashion, to one where genes, DNA and environmental signals can be co-described as a fluid molecular information system that channel protein formation possibilities, which help the cytoplasm of the living cells that make up an organism to stay alive despite environmental change. This reappraisal of the role of genes as in a fluid dynamic genetic-environment continuum has a knock-on effect on the way that we conceptualise the role of environment in evolution because it increases the extent to which the environment is thought to be responsible for the evolutionary changes that have occurred over geological time, in the diversification of species that live on our beautiful planet. This is not counter to the prevailing idea that point and frame-shift mutations take place from the distant cosmic environment via random mutation caused by background radiation (historically the only expanation for changes in the DNA code). Undoubtedly, cosmic radiation is responsible for many (mostly deleterious) random genetic mutations. Indeed, DNA has evolved a wonderful ability to withstand quite a high amount of random mutation events through the way in which several similar triplet codons of nucleic acid translate into the same amino acid, and through genetic redundancy whereby several copies of genes exist in different parts of a genome meaning that if one becomes badly mutated, there may still be existing healthy copies of the gene for the cell to make healthy proteins. However, by maintaining that cosmic and therefore random mutation events are the only driver of evolutionary diversity, the biological sciences may have perhaps missed an opportunity to appreciate a subtle but significant aspect of genetics that may have been working alongside the rate of mutation, iteratively and gradually over eons of evolutionary time (millions of years) regarding a progressive iterative epigenetic channeling of protein re-arrangement, with whatever DNA code that is available in a cell, that may enable a greater survival rate of offspring particularly during periods of environmental change. Such concepts have given rise to the fluid genome. A metaphor for this environmental induction of genetic rearrangement is mirrored in de novo antibody production - the immune responses way to deal with newly encountered pathogens (a kind of change in the environment). The way that the immune system creates antibodies to newly encountered pathogens is very different (primary response) to the way the immune system deals with previously encountered pathogens (secondary response). We think that the primary response works by taking parts of pre-existing genetic sequences, usually protein sub-units, and splicing them together in completely new ways in order to create a 3D protein shape that exactly fits the 3D shape of a newly recognised antigen (on the surface of an invading pathogen). The primary immune response mirrors that of how genomes respond to environmental change, whereas the secondary immune response mirrors the way genomes respond in constant conditions. The primary response genetic process is so complex that it is still barely understood, and it does take time (up to 14 days for a successful new antibody to be produced). It is as if we have understood genetics by first by appreciating the secondary immune response, fit for constant conditions, and only now realise how important the primary response may be with regard to how the genome responds to environmental change. This is especially the case when considering the broader theory of evolution that proponents including Darwin argued was driven by the changes in environmental conditions in which a population of organisms live. Through such a lens, it is possible to re-conceptualise that DNA (ADN) acts as an environmental information conduit; a molecule that informs cells about ancestral responses to internal and external environments that enabled past survival. This environmental information from which cells make proteins when triggered by environmental change, is then epigenetically tagged and passed from parent to offspring enabling the ancestral cell lineage (both from the recent and ancient evolutionary past) to pass environmental information into the current living cytosol;' information that increases the chances of cellular survival given the developmental changes in its surroundings over time. A great book regarding epigenetics is by Claude Kordon; The Language of The Cell published in 1993 by McGraw-Hill, Inc, London, Madrid, Paris, Tokyo and Mexico. Another good read on this topic is by Lynn and Dorion Sagan; Microcosmos - four billion years of microbial evolution, published in 1997 by University of California Press, Berkley, Los Angeles and London. Of course there is also Alan Rayner's 1997 classic: Degrees of Freedom living in dynamic boundaries, published by Imperial College Press, Singapore, River Edge (NJ - USA) and London, which deals extensively with how the highly adaptive genetic and metabolic systems within fungi, can shed new light on the rest of the Biological sciences, as well as our own species. Alan went on to describe Hyper-epigenetics as applied to the non-linearity in the way in which fungal metabolisms and genes can respond rapidly to environmental change. There is also a 2014 compendium of chapters written by different scientists called Entangled Life - organism and environment in the biological and social sciences (Volume 4 in the series History, Philosophy and Theory of the Life Sciences), edited by Gillian Barker, Eric Desjardins and Trevor Pearce, published by Springer.

Bio-ethics in the age of extinction

Regarding averting the 6th mass extinction event, which would be the first to be caused by another species, namely us, the work of Edward O. Wilson immediately comes to mind with his recent book entitled Half Earth which was published in 2016. One of the arguments put forward in the book is that if we managed to change our diet by reducing meat intake on a global scale we could potentially liberate enough land from agricultural production for ecosystem restoration to prevent the 6th mass extinction. Another argument put forward in the book is that if everyone put half of whatever land, roof-space, window box, allotment, balcony or garden into use for biodiversity conservation, there would be enough space for wildlife to continue to live alongside our species, in both rural and urban settings. In other words relevant to both sustainable diets and ecosystem services. The philosophical ideas of E.O. Wilson were first put forward in his book Biophilia which argues that all humans have an innate urge to identify with and to ultimately protect nature. He argues that therefore the door (to a sustainable society) is already half open, we only need to fully embrace this at philosophical, political, economic, and at local and international governance levels (e.g. through the education and planning systems). Another ecological philosopher you may be interested in looking up is Alan Rayner, an evolutionary mycological ecologist turned philosopher and (bio)artist. His idea of the philosophy of natural inclusion allows us to re-orientate our identities and relationships around and into symbiosis with nature. He has several books, one called Degrees of Freedom - living in Dynamic Boundaries is published by Imperial College Press. Chapter 8 of this book includes how human society, economically and politically, can learn from mycosophy so that a sustainable society might inevitably emerge. Another book of his is called Nature Scope - which develops Natural Inclusion into a formal body of philosophy and ethics around protecting nature. Another book called The Origins of Life Patterns, published by Springer develops these ideas further. A famous Canadian bio-ethicist is David Suzuki who has written many works including the book Genethics - the ethics of engineering life (relevant to the sustainable diets pathway). A further ethics for nature advocate is Joanna Macey in her many works including her book World As Lover, World as Self, published by Parallax Press, Berkeley, California. Another writer on these themes, particularly ethics regarding biodiversity conservation and agriculture is Vandana Shiva in her many works including the book Staying Alive - women, ecology and development, published by Zed books. There is also Stewart Brand's book Whole Earth Discipline - an eco-pragmatist manifesto, published by Atlantic Press, London. Of course, there is also the wonderful Lynn Margulis with her body of works on the endosymbiont theory, which embraces the symbiotic partnership of species as the main way in which evolution operates. Her works would fit well into thinking about ecosystem services, but could also link to sustainable food production regarding the design of agricultural systems that enhance the co-habitation (symbiosis) of species in benefitial partnerships such as is practiced in Permaculture (the agricultural system that uses ecological design principles to integrate biodiversity and food production). Permaculture uses 3 ethics that feed into its design principles; these being Earth Share, People Care and Fair Share. Lynn Margulis was married briefly to Carl Sagan who wrote the book Cosmos - the story of cosmic evolution, science and civilisation, published by Abacus. In the final chapter, like in the first book I mentioned above by Alan Rayner, he sets out how human society can emerge ethically to embrace a sustainable epoch. Happy reading!