All life began with prions.* Life emerged as nonspecific chemical interactions in clays gave way to more specific kinds of self-association; self-assembly is at the very root of life. Out at the branch-tip of life, maybe its apical meristem, are proteins with specific, non-toxic (broadly speaking) functionality and structure. Back at the root of life is chemical interaction. Everything interacts with something. There are limited sets of categories of interactions. There are limited sets of categories of chemical potentials.** They help define each other, as partners interact; they define the way atoms interact. Association, then, is the mutual satisfaction of interaction potential. With limited complexity comes more universal interaction possibilities. Therefore, simple molecules interact with other simple molecules. We see this, even back out at the level of the apical meristem of life. All proteins may have the ability to form amyloids: non-specific, potentially toxic aggregates. All proteins seem to have the ability to associate with each other nonspecifically and catastrophically. But why don’t they? Complexity… selection for complexity, selection for specificity, is the answer.
At the invisible root of life, we have a lack of complexity, and a lack of specificity, and an abundance of heterogeneous interaction possibilities. Nucleic acids – DNA, RNA – have a limited set of interaction potentials. Four, to be precise. Well, several more, if you’re willing to look at non-Watson-Crick base pair interactions… and who isn’t willing, really? So there are approximately four. And even though there are four, they represent the same interaction. Fundamentally the same… a couple of hydrogen bonds holding hands, linking two stacks of greasy pancakes.
The result of that fundamental identicality, similarity, unity of interaction is, predictably, a very standard set of structural outcomes. We know that DNA has the same structure, regardless of sequence.*** Asterisks notwithstanding, caveats not withstanding, DNA in water self-assembles into the B-form double helix everyone recognizes. I argue that this is a glimpse into history. When we talk about an “RNA World”, what we’re talking about is an intermediate level of interaction complexity that persists in the current “DNA” world, just as potential prions live – crypto prions hiding – in all proteins. So DNA is a kind of prion. No, it’s not a proteinacious infectious particle, no more than clay particles are. Nevertheless, DNA infects other DNA molecules, altering the structural requirements imposed upon each by their mutual potential, forcing and limiting the available set of possible chemical interactions.
If we step back further, considering that nucleic acids are intermediates, we see that self-replication also happens at the level of crystals. Mineral crystals, water crystals, all self-assembling frozen chemistry. All of these force the environment to bend to their structuro-chemical demands. Life, then, the evolution of life – or at the very least at the level of self-assembling noncomplex, heterogeneous interactors – shows that the impetus to self-organization is universal to the chemical elements and their molecular composites.
There’re many other ways this truth is expressed aside from prions. Seeing the same sets of molecules assembled from the same sets of atoms, of chemical elements, all over the universe, reveals a deep and broad uniformity of potential interactabilty. And that’s even a farther step backwards from the bud, to the root, to the nut. So I guess, in a way this insight is the same kind of insight that makes Aang the Avatar, the recognition that it’s all one. The oneness is the ability to form, define, respond to, the chemical potential of possible partners, of all available partners. And remembering that, out here at the meristem, we see mostly a limited set of acceptable and specific interactions, save only when the interloping prion, expressing the most fundamental of potentials, shatters the existing matrix.
This is not a unique observation, I think. This is merely the Gillespie articulation of the observation.
Now, words express ideas. Words are built from a limited, universal, set of components: letters and sounds. Words construct the meanings of ideas. Ideas, through words, interact with eachother. All words, and so all ideas, may interact with each other. This happens complexly (apical meristem), at the level of metaphor. It happens simply (root), at the level of the way that words are organized, of syntax. They are all self-referential insofar as they are all built from the same components, just as molecules are built from the same set of chemical interactors. Ideas, through words, through their linguistic expression, are prions. They associate, they propagate, they may move the rest of the idea matrix of possibilities in one direction or another. Ideas are contagious. Words and ideas are prions built from their fundamental characteristic of associability.
We have a complex matrix of ideas in the world today. They do not all associate, they do not all interact productively with each other. As with proteins, and DNA, the potential is there for them all to interact. That they do not reflects the growth of complexity, the growth of specificity, from the large, broader, matrix of potentials. And yet… ideas propagate. The matrix through which ideas move today is different than it was originally, than it used to be, than it might have been. Nevertheless, there is a pathway of potential interactions through the matrix of all possible interactions, all expressable interactions.
What does this mean, what does the metaphor tell us about the word-driven expression of ideas? What makes an idea more likely to propagate? Using the metaphor of the prion, what makes them more infectious, more dangerous? What feeds the idea’s potential to move through the matrix?
It’s hard to overcome the urge to identify “good” ideas… human rights, mutual respect, mutual benefit might be “good” ideas; facism, genocide… “bad” ideas. But both seem equally powerful as propagators. As a structural biologist, the defining characteristics of prions are interesting to me, the chemical traits that allow them to turn the organizing forces of molecular structure into a poison that disrupts complexity.
*I’m co-opting the term here, to mean self-assembling, self-replicating molecules. All life did not begin with proteinacious infectious particles. Prion means something specific; prions are proteins, not primordial life-stuff. I could make a up name that captured the functional aspect of chemical complementarity of the primordial life-stuff, but no one would know what I was talking about. So it’s a metaphor, ok? Maybe writer-reader types just accept that, while people like me get stuck on terminology.
**chemical potential has a specific definition in chemistry… here I’m playing fast and loose, and just mean their set of possible types of interaction.
***DNA is a structural acrobat, really. So many amazing configurations, but mostly they’re all riffs on helices held together with hydrogen bonds.