The Genomic Theory of Self: The Rise of the Microbiome

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Who am I? Ask your bacteria.

The question “Who am I?” has been a mainstay of philosophy for centuries, at least, if we discount “me” as a complete response. It might even be the mother of philosophy, as “who am I?” was probably asked before the more difficult, “why am I?”. Of course, “what do you want to do now?” was probably asked even earlier, but that only led to the birth of the shopping mall.

Thomas Aquinas gave us an answer (cribbed from Aristotle, and then filtered through a theological perspective). He said that we are defined by our body plus our intellect, a soul, and together these two describe who each of us is. These two aspects of ourselves are not distinct entities; the soul, he said, was the form, or principal, that allows our bodies to live. Our soul, he further defined, had an intellectual aspect that was unique to humans. It also has a sentient activity, that is, it could sense and perceive our environment. This part of our soul is shared with animals, and arises from the activity of the body and soul acting as one. The intellectual aspect is unique to humans, he thought. Together, all these defined who we were. Separate they have little meaning.

Attributing our thinking processes to regions of the brain based on a comparison to the brain of more simple animals is in part due to Thomas Aquinas. And the fact that some people really do have a ‘reptile brain’ (they’re called lawyers).

This description of what a human being is has stayed with us, and is still largely in line with Catholic church doctrine. It is in many ways a largely materialist perspective; the soul is dependent on the body, and if the body goes, so does anything that we would think of as being “ourselves”. Divine intervention, he believe, could preserve our sense of self, but the naturalistic aspects of his description matches our modern notions. Even our description of our brain has been shaped by his depiction of a human being. Certain regions of the brain have, until recently, been described as being largely devoted to sensory management and managing the basic works of keeping a body functioning, while the intellect was largely confined to the neocortex. Part of the brain has even been termed the ‘reptile brain’, which supposedly governs the most basic functions of living. Recent advances in mapping brain function are changing this conceptualization of how the brain works, and we know now that our thinking and other neural functions are distributed in complex manners. However the historical compartmentalizing of brain functions based on how our brain compares to that of more simple animals is in part due to Aquinas’s definition of a human.

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All the World In an NIH Grant Application Form

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The intersect of applying for grants, the writings of St. Augustine, and William Blake

William Blake said that we can see the world in a grain of sand. Probably he was speaking metaphorically. If not, considering that sand is very small and the Earth is very large (comparatively), you’d have to be standing pretty far from our planet in order to be able to do this. Just how far from the Earth would we have to stand to see it reflected within the surface of a crystal of sand? We can solve this equation:

 2*arctan(diameter of earth/(2*distance grain of sand is from earth))= 2*arctan(diameter of grain of sand/(2*distance sand is from eye))

Assuming the grain of sand is a millimeter across and we’re holding it about 10 cm from our eyes, the answer is about 1,275,000 kilometers, or about three times the distance from the earth to the moon. So Blake probably meant this figuratively; the wonder of creation is found just as profoundly in the small as it is in the big…. or possibly he thought interplanetary space travel was possible in the year 1803. Reading some of his later prophetic poems will lead one to conclude that this latter intent is a distinct possibility.

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How many genes in our genome?

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The metaphysics of genomics

“None shall pass,” declaimed the Black Knight when confronting King Arthur (and Patsy with his coconuts) in Monty Python’s ‘The Holy Grail’. Facing Arthur- King of the Britons- in single combat, the Black Knight was careful to sidestep the debate over whether “none” is singular or plural. His statement, “None shall pass” is safely ambiguous in this regard. However if he had been able to defeat Arthur (he didn’t), back at the castle that night would he have clarified his “none” with the singular, “No one was able to pass me!”, or the plural, “Not any were able to pass me.”? Being completely dismasted in the battle, it’s a moot point for him, but the question still stands.

Back in the early heady days of the genome project, a similar question that often got booted about was, “How many genes are there in our genome?” No lopping off of limbs was involved, but much argument was had, and heavy betting was on a number around twenty-five to thirty thousand, though some factions advocated for a much higher number, nearer to one hundred thousand. I was in the camp of the latter group. The resolution of the disagreement depended on agreeing upon what, exactly, is a gene, for which there can be many possible definitions, and whether “gene” is singular or plural. The 30K faction’s “gene” was not the same as the 100+K faction’s “gene”. Reporters learned to ask other, easier, questions, or just to leave geneticist alone entirely.

This isn’t just a problem in genetics, but a basic one of philosophy. That is, “How do we know what anything is?” This dog may look different than that dog, but we can agree this dog is a dog. Why, or how?

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