In my most recent posting, I've been exploring a quite classic mathematical model of an ecosystem: the Salt Marsh ecosystem model developed at Sapelo Island and described in the fascinating 1981 volume, "The Ecology of a Salt Marsh". For those of us who are devoted to grasping the "wholeness" of an ecosystem, the question arises whether matching such a system to a mathematical model helps in grasping this wholeness - or whether it may even detract. The concern would be that true unity is broken when a whole is described in terms of relationships among discrete parts: as if the "whole" were no more than a summation of parts - in Parmenides' distinction, an ‘ALL" (TO PAN), exactly the wrong approach to a true "WHOLE" (TO HOLON). An excellent guide in these matters is James Clerk Maxwell, who faced this question as he searched for equations that would characterize the electromagnetic field in its wholeness. As soon as he learned of them, he embraced Lagrange's equations of motion, and as he formulated them, his equations derive from Lagrange's equations, not from Newton's. For Lagrange, the energy of the whole system is the primary quantity, while the motions of parts derive from it by way of a set of partial differential equations. Fundamentally, it is the whole which moves, the moving entity, while the motions of the parts are quite literally, derivate.
The components of such a system may be any set of measurable variables, independent of one another and sufficient in number to characterize the state of the system as a whole. Various sets of such variables may serve to characterize the same system, and each set is thought of as representing the whole and its motions by way of a configuration space. If we have such a space with the equations of its motion, we've caught the original system in its wholeness: not as a summation of the components we happen to measure, but in that overall function in which their relationships inhere.
Now, it seems to me that a mathematical model of an ecosystem, to the extent that it is successful, is exactly such a configuration space, capturing the wholeness of the ecosystem whose states and motions it mirrors. Specifically, the authors of the Sapelo Island Marsh Model were if effect working toward just this goal, though it may not have appeared to them in just these terms. All their research on this challenging project was directed toward discovering and measuring those connections, and the integrity of the resulting mathematical system was exactly their goal.
They had chosen to construct their model in terms of carbon sinks and flows; the measures of these quantities were sufficient to characterize the state of the system and its motions, and therefore constituted a carbon-configuration space of the marsh. A different set of measures might have been chosen, and would have constituted a second configuration space for the same system: for example, they might have constructed an energy-model, which have been equivalent and represented in other terms the same wholeness of the marsh. Carbon serves in essence as a representative of the underlying energy flows through the system.
I recognize that this discussion may raise more questions than it answers, and I would be delighted to receive responses which challenged this idea. But I think it sets us on a promising track in the search for the wholeness of an ecosystem - an effort, indeed, truly compatible with the wisdom of Parmenides!