The Ontology of Potent Proteins

It is a basic disposition of the human mind to assume that entities are form or structure through and through. On this assumption, only what is definite enough to be measured and stable enough to retain that measure is a proper entity. Accordingly, modern science proceeds by measurement and regards what can’t be quantified either as unreal or—if in a  modest mood—as beyond its scope. Though quantum physics is slowly challenging it, the conventional view remains that everything that exists is made of elements which themselves also have definite structure. It’s structure all the way down.

And rightly so, you may say, for what on earth are we talking about if it’s not definite enough to be measured?

Aristotle has an answer to that question. Generally speaking, he called what we’re talking about in this case “matter” (Greek is hule) or “potency” (dunamis). In contrast to their analogues of “form” and “act”, matter and potency are ways of being characterized by a lack of definite structure: they can’t be quantified and they can’t be known directly in the manner that form is. Nonetheless, Aristotle argued that these are not only real ways of being but the very ones that underlie all change and motion.  What exists in the world, said Aristotle, possesses not just determinate form but also relatively indeterminate matter.

With all this in mind, Aristotle would have been charmed, but hardly surprised, to read the news that “proteins without a definite shape can still take on important jobs.” This is the subtitle of a fascinating article in our cherished Science News (the best available digest of current science, in my opinion).

What jobs do these indefinite proteins do? Research indicates that their role is to facilitate change: they “act like switches, triggering or stopping an action.” (Aristotle would say that researchers are discovering how the matter-form relation is at work in proteins.)  The article begins thus

Richard Kriwacki refused to give up on his protein. He had tried again and again to determine its three-dimensional shape, but in every experiment, the protein looked no more structured than a piece of cooked spaghetti. Normally, this lack of form would be a sign that the protein had been destroyed, yet Kriwacki knew for a fact it could still do its job in controlling cell division. While discussing the conundrum with his adviser in the atrium of their La Jolla, Calif., lab, insight dawned: Maybe the floppy protein didn’t take shape until it attached to another protein. . . . Once joined, a seemingly ruined mess gave way to a neatly folded structure. The finding defied a foundational dogma of biology, that structure determines function.

some parts of this protein take on a definite structure (gray model) while other regions remain flexible and disordered (other colors).

some parts of this protein take on a definite structure (gray model) while other regions remain flexible and disordered (other colors).

Having long assumed that entities are structured through and through, the conventional thinking had been that the “disordered” or “chaotic” nature of proteins like the one Kriwacki was observing made them anomalous outliers.  Whereas the fascinating truth is that they’re not outliers at all, but common and vital players in the functioning of proteins. “We are finding that these proteins were not only unstructured, but had to be.”

I’m not persuaded that calling these proteins IDPs (short for “intrinsically disordered proteins”) or “chaotic” best describes what scientists are observing.  These terms reflect the old prejudice that if entities don’t have proper form, they lack form altogether, whereas the truth looks more nuanced. As a friend to whom I showed the article said, those proteins aren’t chaotic or disordered, they’re “just not as determinately structured as you used to think.”

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