Saturday, September 15, 2012

Please don't use the word "epigenetic"

A pet peeve, and a review of E. O. Wilson's "Social Conquest of Earth".

Of all current authors, I am probably most sympatico with E. O. Wilson, biologist and proselytist for the preservation of biological diversity. Wilson has many axes to grind, and sharpens several of them in his most recent book, on the social conquest of Earth. One is his atheism. As do many thinking people, he sees religion as a vestige- a culturally rich, but philosophically impoverished expression of our group nature in complex psychological projection. So it is slightly ironic that another of his targets is the pope of atheism, Richard Dawkins, foremost exponent of the "selfish gene" model that dismisses any possibility of group selection operating in evolution.

Rhetorically, it is no contest. Dawkins is the better writer. But substantively I go with Wilson, whose main point seems to be to gloat that he was right during his sociobiology crusade of the 70's to say that our social instincts are patterned by evolution- a point that is, frankly, old hat by now. Secondarily, he argues that, that human nature, the conflicted expression of those various instincts, is better explained by group selection than by kin selection. Indeed, towards the end of his life, fellow Harvard theorist Stephen J. Gould was reluctantly also groping in the direction of group selection, in even more inarticulate ways and despite his vitriolic personal battle against Wilson over sociobiology.

As Wilson makes clear, while the nucleotide may be the unit of inheritance, it is not the target of selection. Targets of selection are any unit of life that experiences failure or success in the grand race of life. If my heart fails, there may be any number of genes at fault, but my entire organism, with all my genes including the defective ones, go with it down the drain. Likewise, if the group I live in is cohesive enough to share ideas, learn new technologies, and exterminate other groups, then all our genes, including any and all that led to this success, also succeed. Indeed, groups can gain far more than the cost of cooperation, (i.e. it is not a zero sum game), regardless of who is related to whom within the group, suggesting that group selection can be quite strong.

In the long run, as recombination and sexual reassortment happen, the genes contributing most significantly to targeted traits are specifically affected in their frequency, which is also put down to natural selection, in reductionist shorthand. But it is always the phenotype that the the world sees and reacts to that is the direct target of natural selection, and this phenotype can be complex and expressed at the group level.

Specifically, Wilson dismisses the kin selection model that he had long followed, and that Dawkins popularized and sets so much store by. In brief, kin selection posits that our altruism, as generated by evolution, extends only so far as our genetic relationships, such that parents care for their children 50% as much as for themselves, and for their nephews only 25%, for their cousins 12.5%, and so forth. One can understand its seductiveness to those trying to find systematic formulas underlying the messy process of evolution.

One problem is that genetic relationship is actually far more difficult to measure than such a pat genealogical method would have it. We are 99% identical to chimpanzees, after all. So our true relatedness to other humans is really a graded and complex function, dependent on tribal history and much else. We seek marriage with tribe-external partners after all, which doesn't fit the kinship model at all.

For example, if one has ten children, one can hardly (rationally) run 50% chances of sacrificing one's life for each one. And indeed, if all were lost in some catastrophe, one might have the opportunity of having yet more children, so the theoretical math of kin-based sacrifice makes very little sense on its numerical face, even before one gets to the putative dedication of uncles, aunts, and more distant relations.

Unfortunately, Wilson can hardly tear himself away from his ants, termites, and other insects, in making these points, and somewhat weak comparisons to human societies. And this is a shame, because- as much as I also love them, and as much as they serve as a technical model for social evolution- in the large sweep of life on Earth, the social insects are not the revolutionary force Wilson makes them out to be, and focusing on them misses a much more important story. It is a problem Wilson shares with Ernst Mayr, another stable-mate at Harvard and fellow don of 20th century evolutionary theory- a resolute focus on macroscopic life.

To me, the prime transitions in the history of life are five: First, the origin of life itself, second, the origin of photosynthesis, third, the origin of the eukaryotic cell, which is the platform for all advanced life, fourth, the generation of multicellular organisms from eukaryotic cells, and fifth, the origin of humans, who have so dramatically surpassed all that went before and are terraforming the biosphere to god-knows what condition, before dreaming of doing the same to other ill-starred planets.

Now, the first two of these transitions were biochemical innovations. But the others were social in nature, which is why Wilson's book misses out so dramatically on a more interesting story when drawing comparisons to humanity. The eukaryotic cell is the fusion of at least two very different bacterial cell types into a shocking new entity. Whether voluntary or coerced, it was a matter of intense cooperation between what is now the mitochondrion that supplies oxidative energy, and what is now the nuclear genome and its complex organellar apparatus, which supplies the command and control, and which ballooned up to enormous proportions compared to any bacterial cell. Eukaryotic cells took the path of sloppy complexity rather than typical bacterial streamlining, and this made all the difference in the long run. Later, chloroplasts were added to the mix to come up with the plant cell, which has clothed the earth in green, and helped fill the atmosphere with oxygen.

The advent of multicellular organisms is even more clearly a case of social cooperation and group selection overcoming individualism to create a phenomenally powerful new kind of life. We are collections are cells that each have a full genome, yet think nothing of killing themselves for the good of the whole. Our cells are far more dedicated to the collective than the most robotic ant, and have formed structures that surpass any ant colony in complexity.. i.e. the brain, or come to think of it, an ant colony. [Late addition- Melvyn Bragg reviews the cell.]

Wilson's distaste for the molecular is also apparent in his breezy genetics, which brings me to the word "epigenetic".  This word has two different meanings, each of which are covered by other and better words. It is so extensively butchered in the lay press that I think the best we can do for it is to retire it completely.

The original meaning of epigenetic is any mechanism of generational inheritance that does not follow usual (Mendelian) mechanisms dependent on DNA sequence. A prime example is the little war that goes on in the embryo/fetus between the paternal and the maternal genomes. The DNA sequences of the genomes are not the problem. Rather, selected areas of DNA are marked in each gamete with additional chemical alterations that selectively cause some genes from the male genome to be expressed more or less, and vice versa in the female genome. The fight is for maternal resources, which the male genome wants to extract maximally (growing big fetuses) and the maternal genome wants to conserve for other children and the mother's health (smaller and less needy fetuses). Several genes that have roles in fetal and especially placental development are known to be competitively imprinted, with the allele from each parent either on or off in early development. This phenomenon is more precisely known as genomic imprinting.

The other meaning of epigenetic is cited by Wilson himself, in the midst of a truly atrocious piece of genetics: "If you are genetically prone to mesothelioma and you work in a building leaking asbestos dust, you are more likely that you co-workers to develop the disease. If you are genetically alcoholism-prone and socialize with heavy drinkers, you are more likely than your genetically less-prone friends to become addicted. The epigenetic rules of behavior that affect culture, and have arisen by natural selection, act the same way but have the opposite effect. They are the norm, and strong deviations from them are likely to be scrubbed out by either cultural evolution or genetic evolution, or both. Seen in this light, both genetic rules of gene-culture coevolution and disease susceptibility are consistent with the broad definition of 'epigentic' used by the U.S. National Institutes of Health as 'changes in the regulation of gene activity and expression that are not dependent on gene sequence', including both heritable changes in gene activity and expression (in the progeny of cells or individuals) and also stable, long-term alterations in the transcriptional potential of a cell taht are not necessarily heritable.'"

All I can gather is that Wilson simply means to say that the penetrance of various traits and disease susceptibilities is not 100%, due to our biological complexity. Again, Wilson is not molecularly inclined, which is unfortunate. But this second definition itself is a big mess. It is far more broad than the one given above, applying grossly to all biological development. Why do liver cells give rise to other liver cells? Epigenetics! Apparently all programs of cell differentiation that lock in a cell type and maintain that cell type in progeny cells is epigenetics. Or even changes in gene activity that are not heritable, but only "long term". No wonder people are confused. This should all simply be called biological development and differentiation.

Needless to say, the popular press doesn't know what to do with this term either. It is often presented as some fundamental challenge to Darwinian evolution, as though natural selection was now "facing a challenge" from "new findings" in epigenetics. As outlined for the first definition, genomic imprinting can indeed mess with Mendelian models of inheritance. But this is in no way a challenge to natural selection, and indeed remains completely dependent on gene sequences, just in a more indirect way than usual paradigm.

Suppose for instance, that a parent's or grandparent's experience of famine predisposes children to lower diabetes and cardiovascular disease risk. The mechanism behind this might be altered methylation of a few gametic genes, (conferred by an environmental effect on regulation of these methylase genes, combined with pre-existing target preferences among disease-affecting genes), which is carried through to one or two subsequent generations to alter gene expression and produce this phenotypic effect.

Such methylation patterns don't happen by magic, but by enzymes in turn regulated by other processes, such as an environmental effect of starvation. So the inheritance pattern might resemble the Lamarkian model in some superficial way, but ultimately, the source lies in the genes, their products, and their interaction with the environment. Whether the trait is in any way affected by natural selection over the long term, or is just a random effect in a complex system, there are genetics going on here, just not typical Mendelian genetics.

Anyhow, confusion is rampant, and partly due to the extraordinarily broad and ambiguous meanings of "epigenetic" as a word. So I would suggest that it not be used at all, and other more precise descriptions provided, without all the freight of novelty and mystery that "epigenetic" tends to bring in its wake. Incidentally, "emergence" has a similarly bad influence in the popular media, being little more than a signpost for "extremely complicated, so don't even ask".

Getting back to Wilson's book, the beginning and end seemed to me the strongest parts, where he speaks directly to his concerns and hopes for mankind. Religion falls clearly into the group selection theory, as one of our strongest psychological peculiarities and social glues. Just ask Mitt Romney and his fellow Mormons. Indeed, it has been doing a bit too good of a job, as you can see in the Middle East among many other places & times, rationalizing inhumanity in the name of the group.

When discussing religion with a believer, typically the last argument, after all the pseudo-science and reason have been left behind, is- how can you be moral without religion? This is a clear expression of the core religious value- of promoting the group values (what we commonly regard as "good" morals) over individual selfishness independence, disobedience, and skepticism. It is a serious social conundrum, but antiquated organized religions are hardly the best way to resolve it. With our increasingly planetary society and planetary problems, it is high time to tone down such groupishness and follow a different model, such as the secular Scandinavians do, to a more broadly responsible and conscious form of society.

  • Jesus carries an M16.
  • And you can call him up for whatever you might want. No, really.
  • Speaking of phone calls, why does the joint Chief genuflect to a nutbar?
  • Mitt's close relation to his group, and distant relation to his own brain: "In Salt Lake, they told me it was okay to take that [pro-choice] position in a liberal state." ... "With any bishop who excommunicates a woman, I will not question his reasoning. I will support the bishop."
  • Utter corruption in the business arbitration biz.
  • The beginnings of our current cycle of plutocratic capture of the political system, in the Nixon administration.
  • Yes, Obama is an introvert- and that is a good thing. Lincoln was too.
  • The chief rabbi, refracted though Peter Hearty, on how science is rubbish.
  • Financial right-wingery rampant in Europe too.
  • Money supply experts agree with MMT.
  • US economic growth will not get better.
  • Sister Rosetta Tharpe- smokin' blues guitarist and vocalist, 1960.

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