Atoms, Genes, Ideas
I propose to ruminate briefly on the analogies between the three topics of my title. What do they have in common? The most obvious point is that they are each discrete isolable units that combine to form complexes with like units. Atoms combine with other atoms to produce molecules, which can then combine to form more complex physical structures. Genes combine with other genes to produce a genome, which produces an animal body. Ideas combine with other ideas to produce thoughts, which can combine to form theories and systems of thought. The units don’t blend, like paints on a palette; they retain their identity as discrete units while combining to form complex wholes. When the units are combined we don’t get something intermediate between the two, like a shade of color intermediate between two other shades, but a complex consisting of the original units in their original form. The units are devices of assembly, aggregation: this is why they tend to come in large packages, not individual units—chunks of matter, genomes, or minds. They exist in populations not in isolation.
Second, these entities form the basic subject matter of their proprietary science. Physics is about atoms, individually or in the form of macroscopic bodies; biology is about genes, as such or as they configure the body and behavior of animals; psychology is about ideas (concepts, mental representations), especially as they feature in mental processes. In each science we have a distinction between the basic entities and their “expression”: the properties of atoms are expressed in the behavior of matter; the properties of genes are expressed in animal bodies and behavior; the properties of ideas are expressed in thoughts, cognitive processes, and behavior. The underlying entities themselves are invisible, but they are expressed in observable phenomena. We thus have upward causation: the basic entities cause the higher-level phenomena, from which they are inferable.
Third, these entities were substantial discoveries, not given at the outset. They have the character of hypotheses, however well established, not a priori certainties. Even in the case of the mind, it was not obvious from the start that the mind is made up of discrete units—the atoms of thought. Consciousness seems like a fluid stream-like thing, but upon analysis it turns out to have a granular structure—as language also does. There are simple ideas and complex ideas, ideas of different logical types, combinations and re-combinations of ideas. Concepts are point-like elements in a web, but a web that is constantly updated; they are made to interact and join together. This was not evident to casual inspection, either introspective or perceptual. Nor were atoms and genes self-evident constituents of reality; on the contrary, they were major discoveries, revolutions in thought. Revealing the fine structure of atoms and genes took serious work (we have yet to do this for ideas).
Fourth, despite the theoretical centrality of atoms, genes, and ideas, the question of the origin of these entities is highly non-trivial, indeed deeply problematic. This is obvious for ideas, since we have little understanding of how the mind arose during the course of evolution—ideas no doubt emerged, but how? In the case of genes the problem is how self-replicating entities arose from mere chemistry—how did DNA come to exist? Genes are a cosmic novelty, not prefigured in the prior state of the material world; hence the origin of life is a mystery. Even in the case of atoms their origin is obscure: evidently they came to exist during the first few seconds following the big bang, preceded by a much hotter undifferentiated plasma in which the particles had not yet formed. Aside from the issue of the process by which this happened, there is the problem of how the superhot plasma came to exist—the cradle of particulate matter as we know it. Were there atoms before the big bang or did atoms originate with it? Whence the plasma itself? The very beginnings of the physical universe are shrouded in mystery. So in each case we know what the entities are that we are dealing with, at least superficially, but we are baffled as to how they came to exist: we don’t know what caused atoms, genes, and ideas. These are all difficult origin problems. Our best science thus invokes entities whose birth is mysterious.
There seems to be a pattern here at a very abstract level—a formal structure with three different instances. The instances belong at quite different levels, from the basic physical level to the biological level to the psychological level. It does not appear that reality must be this way: it could have been more continuous, more a matter of blending, less punctate. But nature as we find it seems to prefer the discrete and aggregated.  Its mathematics is digital not analogue. Matter could have been continuous, heredity could have worked by blending, and the mind could have been an amorphous field: but in fact all three consist of discontinuous units rigged up into conglomerations. Nature is arranged like individuals and societies, people and populations. It is not arranged like the color spectrum or musical tones. We might call this “the law of discrete organization” and postulate that the universe has a tendency to produce discrete organizations—as it has a tendency to entropy. It likes to make well-defined units that coexist and join with other well-defined units, not formless clouds or fuzzy borders. Everything is an island, linked to other islands, not a massive commingling and bleeding in. This holds at the level of physics, biology, and psychology.