In my most recent post in this series on the science of purpose, I described how the exciting new physics of active matter could answer some otherwise enigmatic questions in cellular biology. One question was, “How are the numerous and complex molecular interactions of the cell organized within the cytoplasm?” Outside of the membrane-bound organelles, what structure exists to support those functions?
The answer I provided, based on the recent discovery of biomolecular condensates, was that there are no rigid structures outside of the organelles. Rather, there are dynamic visico-amorphous droplets generated by liquid-liquid phase separations (LLPS) described by theories of active matter. But amorphous, and dynamic as they are, the LLPS droplets support numerous crucial cellular functions, devoid of a permanent scaffolding structure. This supports my general thesis in these writings that, based on telos, function generates structure, and not the reverse. These observations refute one of the primary concepts fundamental to the materialist paradigm, in which all biological order is the result of randomly generated structure that (unintentionally) results in (necessary) function.
Here I will build on my claim by illustrating subsequent studies on active matter which continue to support the general thesis that function generates structure rather than vice versa.
The Bedrock of Scientific Materialism
The structure-function relationship (SFR) is at the bedrock of scientific materialism such that all of the concepts within that framework must adhere to that basic underlying assumption. And by having overturned one aspect of that model with the description of how function generates structures within biomolecular condensate arising out of LLPS, we can expect to find more inconsistencies in the SFR paradigm. Because the same assumptions are embodied throughout all of the tiers of that framework
And indeed that is exactly what has been found recently. Yet another fundamental structure-function canonical model is now on the verge of collapse based on this research.
At the turn of the 21st Century, fundamental changes took place in the understanding of the structure and function of proteins and intracellular space organization. A mechanistic model of the organization of living matter where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional “soft matter” lies at the heart of all living things.1
The Other Central Dogma
Throughout the 20th century we were all taught the fundamental concept that proteins exercise function based on their three-dimensional globular structure, the so-called lock-and-key model. This concept became canonical, i.e., the other “central dogma” of molecular biology.
The model of DNA structure giving rise to its apparently deterministic designation of the globular protein, and the one gene / one protein rule, also gave rise to the oxymoronic notion of “molecular machines.”
Oxymoronic indeed because organisms are not machines. The specified irreducible complexity of life remains to this day mechanistically inexplicable. Within the cytoplasm of a single cell there are an estimated 42,000,000 proteins commingled with water, lipids, polysaccharides, electrolytes, and other minerals and ions that somehow function with an orderliness that can only be described as beyond mechanism.
The preeminent molecular biologist and bio-philosopher Stuart Kauffman spent decades attempting to reduce the process of organismal self-organization to physical law. Now near the end of his career he has given up on that quest, writing as follows
No laws entail the evolution of the biosphere…Entailing laws are at the heart of mechanism and if the evolving biosphere becomes beyond entailing law, then the evolving biosphere becomes beyond mechanism.2
Intrinsically Disordered Proteins aka IDPs
Within the heterogenous milieu of the cytoplasm, rigidity is not an option. Flexibility, polyfunctionality, dynamic adaptability, and most of all, representational directedness are absolute requirements for the life of the cell. Such an array of versatility is beyond the capability of the rigid globular proteins. Accordingly, recent discoveries in the field of active matter research have identified
a number of proteins that do not have an ordered structure and nevertheless perform essential functions in the cell, i.e., they are functionally active in the absence of unique structures. Such proteins are known now as intrinsically disordered. The name emphasizes that the disorderedness of the structure as an inherent property of these proteins.3
So disruptive is this discovery to the reigning paradigm that these flexible proteins were given such a dismissive nomenclature. That was because the discovery of the IDPs fractured the “order” of the central dogma and the structure/function paradigm. But there is nothing disordered about these proteins. They are given that name because they do not function simply as a rigid three-dimensional globular structure. They are flexible. They have the ability to adapt, bind, signal chaperone, amplify, suppress, and/or organize a multitude of events as needed, in order to orchestrate many different reactions and behaviors within the cell. We know now that the majority of signaling proteins have nonrigid so-called “disordered” regions that give them those attributes necessary to respond to the nanosecond demands of the intracellular world.
Active Matter Writ Large
Not the least those, of course, is the fundamental role of IDPs in the so-called biomolecular condensates, aka the LLPS membrane-less organelles (MLOs). As previously mentioned these condensates are quite dynamic. Because they are not membrane-bound and consist essentially of droplets of liquid of varying viscosities, they can come and go as dictated by the fluctuating demands of the cell. There is quite literally no room for machines or even mechanisms as we know them within these spaces. It is in fact the so-called disorder of these non-globular proteins that allows them to coil and uncoil, bind and unbind the varying cytoplasmic constituents that allows them to manipulate viscosities so as to arrange for the droplets to come and go.
These discoveries do nothing less than bring us to the precipice of a whole new paradigm of cellular biology. Now we are in the age of active matter, and we must realize that we are faced with an entirely new metaphysical challenge. As we move into the 21st century, the science of active matter demonstrates the remarkable self-organizing capabilities of molecules. And already there is a reframing of the metaphysics of life itself. The following interpretation from the literature is illustrative:
LLPS appears capable of integrating signaling into self-organizing networks that exhibit a primitive form of information processing. These observations support a framework in which RNA, DNA, and proteins each exhibit intrinsic molecular agency — the capacity to sense, respond, and self-organize. When mediated through LLPS, these molecular agents form higher-order condensation networks that display emergent properties extending the agency of the organism and subsequently paving the way for multiscale behavior.4
The two-plus decades since the turn of the century, and millenium, have seen the collapse of the neo-Darwinian randomness-selection paradigm. But a new competing materialism might be thought possible, emanating from the science of active matter. By co-opting the science of purpose with references to molecular agency, an oversimplified interpretation of these phenomena could reinvigorate materialism itself by positing some innate natural tendency toward specified complexity. So it is incumbent upon us to be aware of this possibility in order to frame these newly described phenomena within the proper context.
For who or what is the “self” in self-organization, capable of agency? The answer is actually straightforward. Materialism must always require that material has no self; it is mindless, purposeless, and acts only at random. And yet the new science of active matter clearly describes phenomena demonstrating if not a mind within matter, as A. N. Whitehead maintained, then at least an irreducible propensity to goal-directedness, aka function.
Put into its proper perspective, the above discussion of active matter illustrates precisely what we expect to find within a Thomistic-Aristotelian ontology: all matter exists in potency to a higher-order substantial form. The self-organization of 40,000,000 protein molecules with disordered/dynamic structure in the vastly heterogeneous LLPS cytosolic matrix is clearly the realization of that potency into act, guided by representational directedness.
Why? For the empirically demonstrable fulfillment of purpose, aka telos, the most basic property of Life Itself.
Notes
- Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept, Iuliia Antifeeva, et al., Cellular and Molecular Life Sciences (2022)79:251, p 1.
- Evolution Beyond Newton, Darwin, and Entailing Law, in Beyond Mechanism, Stuart Kaufman, 2013, B. G. Henning and A. C. Scarfe, eds., p. 1.
- Iuliia A., et al., p. 2.
- Liquid-liquid phase separation as a driver of abiogenesis and evolution, Grazier, J. J. and Sylvester, P. W., Molecular Biology and Genomics, 27 Feb. 2026.