New Criticals

Some Philosophical Remarks on Biological Organization


I want to begin the project of trying to describe why the same physical principles which made some kind of chemical organization necessary on the early earth also ensured that this organization would evolve and differentiate with the passage of time. But first I wanna talk a little philosophy.

I don’t have any dogmatic faith in the notion of the big bang, but from what I’ve heard it seems like its doing a pretty good job of explaining most of the observations astronomers make, so let’s assume for the sake of argument that the universe began approximately 14 billion years ago. One thing that immediately follows, if this statement is true, is that the universe is a process. It’s something that is happening, and continues to happen...right now even. I’m inclined to the view that every structure we observe which comes into and out of existence should be rightfully considered a process, although its convenient and practical to consider very stable, long-lived, or particularly inert structures as being “merely things.” Really though, all things are processes on some time-scale, as is the entirety of the universe itself. So there’s a general, ontological claim which you may have heard before in a very different context: Being is being-in-time.

Life, of course, takes the processual aspect of existence through many tiers of structural hierarchy. Jeffrey Wicken said: “Living systems are processes rather than things, and their existences are contingent on steady throughputs of matter and energy.” Living, after all, is something one does. In this sense, the question “What is life?” is grammatically misguided, or it requires that one not forget that the word “Life” denotes an activity, not a thing. The carbon atoms in your body are not in any way different than the carbon atoms in a lump of coal, here on earth or anywhere else in the universe. The pattern of activity which the atoms composing your body engage in do not “make your body alive,”  this pattern of activity is life.

The same reasoning extends straightforwardly to selfhood. A self is a process performed by an organism. “Organism” denotes a specific kind of relational closure of a set of material elements which Wicken called an "autocatalytic organization". Many other similar terms may be found in the philosophy of biology literature which endorses the organismal view of life as opposed to the “bundle of selfish genes” hypothesis. Nearly all of them are formulated in direct response to the Kantian challenge of demonstrating, from physical mechanisms, how an organization in which every part is jointly ends and means for its own production could spring into existence on its own. "Biology will never have its Newton, capable of explaining the existence of a single blade of grass," the old curmudgeon claimed. LOL rite? Cuz physics, duh. 

So one pleasing consequence of the thermodynamic view of life is that it provides a physical basis for the concept of selfhood as the unified energy-processing activity of the organism. Organisms are unified selves because they were subsets of the more general and necessary network of prebiotic chemical cycles that were “selected,” in a purely physico-chemical search for stable, persistent patterns of entropy production capable of *draining* the input energy from whatever source (solar or geothermal) was driving the system into a non-equilibrium organization. As the reaction matrix spontaneously evolved into more heterogenous mixtures under the probabilistic drive to increase molecular diversity, and additionally as the density of organic matter increased to values capable of driving the formation of large scale structures which would randomly confine components with different chemical capacities, it gradually became more and more likely that a subset of the prebiotic matrix gained this property of causal closure.

As I tried to argue in my last post, life did not begin with a set of chemical relationships attempting to solve the problem of how to persist--this endows molecules with a foresight that has no physical basis. Rather, life was a solution to the opposite problem, the same problem the sun has: It can’t give itself away fast enough. Only once an autocatalytic organization emerged in the prebiotic chemical reaction matrix did the problem of survival, and thus the restricted economy aspect of Darwinian evolution, emerge. Before that, the problem was not “How am I going to survive and reproduce?” but rather, for each entrapped molecule stuck in an energy processing cycle with other molecules, “How can I get back to my ground state as fast as possible?” It is the necessary short-sightedness of inert molecules that creates the possibility of their activity being collectively frustrated: each molecule’s attempt to minimize it’s own free energy merely passes the excitation onto another in such a way that the ensemble never reaches equilibrium, and consequently further structuring through energy flows leads to networks of chemical-energy flows that become more and more removed from equilibrium and thus more and more organized.

So when we talk about the organization, or the “information content” of a cell, what we really mean is every aspect of the distribution of matter and energy inside that cell that is displaced from its equilibrium value. At the present state of the art, we can't calculate a cell's overall displacement from equilibrium. As a first approximation, it would require knowing the chemical affinity of every molecule in the cell for every other molecule in the cell, and in addition the energy involved in concentrating, confining, and adsorbing molecules onto membrane surfaces. We're getting closer to being able to do traditional physics on these problems, however, and in the future I hope to discuss some of the current approaches.

But if you know anything about cell biology, you realize this definition precludes the possibility that the information in a cell be reducible to the organism’s genome. The idea that it would be is a consequence of the mistaken view that DNA contains all of the information necessary to reproduce itself. Nowhere in nature do we see either DNA or RNA reproducing “itself” without the aid of proteins, lipids, and other components of the intracellular matrix. Cells reproduce, nothing less complex than a cell performs this autocatalytic activity. A cell is the first structure that we may legitimately call “a self.” Thus, nothing less complex than a cell is alive. Though this does not necessarily imply that single-celled organisms which we observe today are the simplest possible organisms, it does, however, mean that reproduction is not a property of any individual molecule.

Based on this, I strongly feel that the “RNA-world” is an arbitrary, unphysical assumption advanced because of the view that reproduction is the only necessary criteria for living organization and that it is something which molecules do "in their own interest." Molecules have no such thing, and a chemical cycle which copies RNA sequences for no other purpose than to make more RNA sequences will never produce enough entropy to command any significant energy flux in a prebiotic chemical environment. An even simpler critique involves asking on what basis it would be possible to segregate “RNA” from the amino acids, lipids, and sugars which would also have been spontaneously produced in the prebiotic soup. Nature, after all, doesn’t know anything about our organic molecule classification scheme. Given the fact that proteins and nucleic acids *do* spontaneously stick together, as in the transcription complexes necessary to copy a DNA sequence, I see no reason to assume they weren’t stuck together from the beginning, along with the lipids which would have spontaneously assembled into membranes the moment they were sufficiently concentrated, or “as the soup thickened.” Most importantly, as a theorist attempting to explain the spontaneous formation of a complex phenomenon, why arbitrarily restrict oneself to a limited subset of organic possibilities? Why not give oneself access to the full range of chemical possibilities of which we know nature to be capable?

At any rate, organisms are closed cycles of material transformations that require energy flow to operate. They are constitutionally circular, based on a logic in which DNA sequences are used to build proteins which in turn copy and modify the DNA sequences. Intelligent design proponents often use this fact to argue that life is too complex not to have been designed. The truth, which we see everywhere in nature, is that cycles emerge and grow spontaneously, are selected for persistent existence through the amount of energy they pull into themselves, and they "process this energy" (produce entropy) in the service of the randomizing directive of the second law of thermodynamics. Understanding this rationale for the existence of organisms begins to lay the basis for unerstanding the thermodynamic and informational driving forces which form the physical basis of evolution.