January 26, 2019 | David F. Coppedge

Epigenetics in the News

Epigenetics has gone mainstream. Processes “above” genetics are showing to have more control over life than previously thought.

The science of epigenetics burst the dam of the Central Dogma of Molecular Biology, the view that DNA is a “master molecule” over genetics. This 1960’s-era dogma claimed that information flows down from DNA to protein, not the other way around. Epigenetics (“above genetics”) is now acknowledged as a contradiction to the Central Dogma. Evolutionary explanations that fail to take this into account risk being badly skewed, if not incorrect. There’s no longer just a genetic code in DNA; there are epigenetic codes, membrane codes, molecular machine codes, histone codes, splicing codes and numerous other sources of information flowing in all directions. The information in these codes is often heritable. A cell is now seen as a system of codes and regulators that operate on the DNA library. Here are some news articles about epigenetics.

Functions and mechanisms of epigenetic inheritance in animals (Nature Reviews Molecular Biology). Knowledge of epigenetic processes has been percolating up the scale of organismal complexity. It is showing up in more and more higher organisms.

The idea that epigenetic determinants such as DNA methylation, histone modifications or RNA can be passed to the next generation through meiotic products (gametes) is long standing. Such meiotic epigenetic inheritance (MEI) is fairly common in yeast, plants and nematodes, but its extent in mammals has been much debated. Advances in genomics techniques are now driving the profiling of germline and zygotic epigenomes, thereby improving our understanding of MEI in diverse species. Whereas the role of DNA methylation in MEI remains unclear, insights from genome-wide studies suggest that a previously underappreciated fraction of mammalian genomes bypass epigenetic reprogramming during development. Notably, intergenerational inheritance of histone modifications, tRNA fragments and microRNAs can affect gene regulation in the offspring.

Introns are mediators of cell response to starvation (Nature). The reasons for those mysterious introns—non-coding stretches within genes that need to be cut out by spliceosomes before messenger RNAs (mRNA) can be send out of the nucleus to the ribosome for protein assembly—have been slowly coming into focus. No longer part of “junk DNA” from our evolutionary past, introns are being seen as functional. In at least one case, they appear to regulate the level of protein production during stress. The authors explain:

A systematic deletion set of all known introns in budding yeast genes indicates that, in most cases, cells with an intron deletion are impaired when nutrients are depleted. This effect of introns on growth is not linked to the expression of the host gene, and was reproduced even when translation of the host mRNA was blocked. Transcriptomic and genetic analyses indicate that introns promote resistance to starvation by enhancing the repression of ribosomal protein genes that are downstream of the nutrient-sensing TORC1 and PKA pathways. Our results reveal functions of introns that may help to explain their evolutionary preservation in genes, and uncover regulatory mechanisms of cell adaptations to starvation.

The intelligent design community is viewing this as confirmation of a prediction that introns are functional and beneficial (Evolution News & Science Today). Notice that “their evolutionary preservation in genes” commits circular reasoning in thinking that they evolved in the first place.

Epigenetics: what impact does it have on our psychology? (The Conversation) Here’s where epigenetics gets down and close to us individually. Kevin Mitchell, Associate Professor of Genetics and Neuroscience at Trinity College Dublin, begins:

In the battle of nature versus nurture, nurture has a new recruit: epigenetics – brought in from molecular biology to give scientific heft to the argument that genes are not destiny. The overwhelming evidence for genetic effects on our psychological traits conjures up a fatalistic vision for many people, one in which we are slaves to our biology, not in control of our own psyche and our own behaviour. Epigenetics, a mechanism for regulating gene expression, seems to offer an escape from genetic determinism, a means to transcend our innate predispositions and change who we are.

Research reveals gene regulation can be digital and stochastic (Science Daily). This article likens the genome to hardware, and the epigenome to software. It also likens the epigenome to a thermostat. The digital part is the program that switches a gene on under specified conditions. The stochastic (random) part is the probability that a switch will throw when the condition is reached; the stronger the condition, the higher the likelihood of response. Researchers at the National Institutes of Health take epigenetics seriously. Their discussion sounds much more like intelligent design than evolution:

Every cell in our body has the same set of genes, or genome, and can potentially become any type of cell. During development, the epigenome mediates the process that leads a cell to become a skin cell or a neuron, for instance. If the genome is like computer hardware, then the epigenome is the software that turns certain genes on and others off to give rise to a skin cell, and turns other genes on or off to set the cell on a path toward becoming a neuron.

Epigenetics and Darwinism

Interestingly, none of these papers or articles have much to say about evolution, or about how epigenomics will effect views on Darwinian processes. The second article in Nature about introns merely suggests that their ability to regulate metabolism during stress might be advantageous, without specifying how, when, or why:

We argue from these data that, in nature, being able to control cell metabolism as a function of nutrient availability represents a major evolutionary advantage that may well compensate for the losses in growth rate in nutrient-rich environments.

Why must it be an “evolutionary advantage” instead of a designed advantage? A good designer would allow for possible fluctuations in resources. Power circuits, for instance, have built-in switching networks to prevent damage during spikes, surges and brown-outs. Inherent in the quote is an assumption that anything that exists and survives must have been a consequence of the Stuff Happens Law (natural selection) acting on chance mutations. They give all the credit to chance! CEH is like the spliceosome taking the word evolutionary out of secular jargon so as to create useful, clear explanations.

As for nature vs nurture, that is a false dichotomy. Both are stochastic and deterministic, leaving us at the mercy of either heredity or environment. Mitchell says, “We can still control our behaviour. We can work to overrule and reshape our habits. We can to some degree transcend our own subconscious inclinations.” Who is speaking? When he says that, he imports something beyond nature and nurture into his equation: Free will. Choice. Responsibility. Those indeed transcend the stale worldview of the physicalist. To think otherwise undermines his own words. Did he choose to write about epigenetics and psychology? Did he transcend his own nature and nurture to do so? Surely nature and nurture influenced his words, but they did not determine them. He chose his thoughts. Then he used his nature (fingers) and nurture (education) to state them in his own unique way. We do that, too. We cannot claim to be victims of our genetics or environment. We are responsible for our thoughts and actions.

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