Natural Kinds, Complexity, and the Particular: Part 2 (regarding causality, natural laws, and unversals)

In Part 1, we saw that DeLanda's universals were based on probability manifolds which shape the tendencies of complex systems by causing a tendency for them to take on particular states.  Thus, emergent properties of complex systems are a consequence of the mathematical properties described by fields including chaos theory and dynamics, and the emergence of these properties are described by the nature of the universals that mathematically describe the shape, statistically, of that system's points of stability.

Is description causation?  No, but what if the description fits a rule of how something behaves? Is that rule a cause? Are natural laws descriptive or causal, or both?  Hard to say.  We will assume they are causative in some sense in what follows.

Examples can be offered in physics, biology, and behavior. In physics, we can consider the orbital of an electron, say that of a ground state (point of stability) electron as part of the typical hydrogen atom (a proton-electron pairing). The orbital of the electron is described by a probability manifold, with higher probabilities that the electron will be located in any given time interval in the space near but not immediately adjacent to the proton nucleus of the atom:

The parameters (natural laws and their consequences, if you like) governing the orbital's probability space are a kind of abstract universal, which interacts with a physical object (the hydrogen atom) to cause an emergent phenomenon (the hydrogen atoms's physical and chemical properties).  This is causal interaction (formal causation) by the probability manifold on the physical object (the electron).

In biology, we can consider the computer model of the Mycoplasma cell constructed by Karr et al and published in 2012 in the journal Cell. In that model, protein, RNA, and DNA replication could be predicted and analyzed as an emergent phenomenon given the cell's genome.  The parameters and causal direction given to the simulation are analagous to the ways in which the cell functions to keep its metabolic characteristics stable enough to maintain its life and reproductive capability:

Karr, Jonathan R.; Sanghvi, Jayodita C.; Macklin, Derek N.; Gutschow, Miriam V.; Jacobs, Jared M.; Bolival, Benjamin; Assad-Garcia, Nacyra; Glass, John I.; Covert, Markus W.  A Whole-Cell Computational Model Predicts Phenotype from Genotype.  Cell doi:10.1016/j.cell.2012.05.044 (volume 150 issue 2 pp.389 - 401) .

It's important here to note that the causal role of the probability manifold is not a kinetic one (the probability manifold does not directly push the cell or the orbital into its shape) but a probabalistic one (the manifold determines the probability of a given parameter or vector to be close to what we actually measure). Formal causation thus works via probabilities, and natural laws are thus subject to exceptions, though by the laws of large numbers we can suggest that some exceptions are never going to be seen in the history of the universe. Furthermore, in the case of the Mycoplasma cell model, the model is not in closed equilibrium, so the probability manifold does not violate any conservation laws (which by definition apply only to closed, not open systems) by maintaining the system outside of its maximum entropy state.

In behavior, consider the tendency for a rat to swim across a small pool in order to obtain food. The rat has a reason (obtaining food) to do the swim, and a different reason (avoiding cold water) to not do the swim. The rat's reasons shape its behavior as measured by whether it swims the pool, yet they do not violate physical conservation laws:  the choice of behavior is done by an open system (the rat) which is not subject to conservation of energy or mass requirements, since the system is not closed:

Whishaw IQ, Pasztor TJ. Rats alternate on a dry-land but not swimming-pool (Morris task) place task: implications for spatial processing. Behav Neurosci. 2000 Apr;114(2):442-6. PubMed PMID: 10832805.

It's important to make the above point about reasons for behavior and the conservation laws, since in philosophy of mind it is sometimes claimed that causal closure of the physical means that mental reasons for choices cannot determine our actions unless they are themselves physical (i.e unless a reason is somehow identical to a particular brain configuration).  That stricture is based on a flawed, kinetic model of causation.  In an open system, mental properties (as opposed to physical properties) of the organism may affect the probability of a behavior without violating any conservation laws.  Causal closure need only apply to systems as measured under the constraints of the mass/energy/momentum conservation laws. Thus, behavioral choices need not be epiphenomenal or forbidden due to any causal closure concerns.