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CHAPTER TWOTHE MATTER OF METABOLISM
After Aristotle, several millenia of wondering about the nature of materiality finally led through the likes of Galileo in the past few centuries to the fruitful methodical investigations of science, the topic of Chapter Three. Nowadays our collective knowledge provides every child able to progress through middle school with a narrative about the material world so clearly valid that the likes of Thales must thrash with envy.
Today most educated adults of our species would agree that it makes sense to explain materiality in terms of atoms and molecules. We find it easy to say, "It's all just chemistry, and that's explained by physics!" If honest, we might also add, "But I don't understand much of it. I was bored with it in school and find it a tedious topic even now." We take for granted a knowledge of Nature's secrets for which Pythagoras might have killed to protect. We were given the goods without much need to struggle for their value. Thus Chapter One may recall the humble origin of our collective knowledge and Chapter Two needs to facilitate appreciation of our current knowledge about the basic elements of matter and energy. Harnessed by metabolism to serve the needs of the metabolizer, matter and energy are the what of the who of which we'll explore in Chapters Three and Four.
You may have noticed several geographical maps in Chapter One. The maps served to both anchor and stimulate a few related thoughts. That's my metaphysics. This narrative is all about maps, mapping, and the mapper. Those who study atoms and molecules-- physicists and chemists-- make maps, in a way, using data gained from experiment, mathematical models, and theory in their efforts to explore the terrain. Like all good mappers, they know the map is not the territory and try their best to get down to it, the stuff mapped, in order to improve their maps. While such maps may be filled with technical terms and mathematical equations-- ever so useful for deeper understanding--, our exploration requires a lighter touch with mere metaphor in combination with colorful figures and important facts boxed in-between. Now, at the risk of mixing metaphors, let's imagine the mapping of a dance.
The metabolic process is something of a waltz, a timely dance of atoms and molecules composed of atoms. It is neither simply chemistry nor readily reduced to basic physics. Nor is it a matter of reducing the complexities to simpler parts. (For a complete critique of reductionism, see Physics and the Real World by George F R Ellis.) Rather, we may come to comprehend metabolism as we grow to appreciate nuances made clear through the investigations of chemists and physicists-- the traits of particular species of atom, the idiosyncracies of atomic bonding, and the specific possibilities of molecular interactions. Then as we eventually begin to discuss the dynamic of these dancers interweaving, the larger wholes (our selves included!) which are produced by them will be more readily comprehended as works of lively art.
Time to meet the dancers. This chapter offers a brief description of the generic atom and the most biologically active atomic species in the periodic table: hydrogen, carbon, nitrogen, oxygen, phosphorous, sulfur, and a few others which manifest as ions. With these in hand, we'll examine a small sample of their bonding patterns as a prelude to a discussion of the primary molecules which are both produced by and productive of the metabolic dynamic. Once these molecules are made familiar, we will procede in Chapter Four to map out the pathways of metabolism in some detail. All this may serve as a prelude to comprehending the metabolic core of cognition, i.e., comprehension itself.
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