All living systems are exceedingly complex transport-reaction networks, and all three of the physical transport processes, along with reaction kinetics, can be involved. The problems we face in dealing with them are normally poorly posed in a mathematical sense, and they are too complex to permit obtaining compete solutions. We shall define such complex problems as mysteries. Description of even relatively simple such systems necessarily requires heuristic approximations, and for those that we encounter here the insoluble mysteries are replaced by approximations taking the form of tractable transport descriptions. We shall refer to these deterministic models as puzzles.

Much of the difficulty in replacing mysteries by puzzles is the almost inconceivably large parameter space in which biological processes take place. However, it is increasingly recognized that the parameter space actually needed to provide useful descriptions can be surprisingly small. This is even true for such complex processes as species evolution and organism development (evo devo).

This short discussion will be limited largely to physiological modeling while at the same time trying to obtain some insight into transport/reaction aspects of evo devo. Fundamental to both efforts is the necessity of reducing the enormous apparent parameter space to the much smaller regions actually needed for the problem of interest. In both we will concentrate on transport related aspects of the overall problem: even tens of thousands of genes are not sufficient by themselves to produce an organism or to facilitate evolution of new species. The importance of non-genetic factors was already recognized by Jacques Monod, but we are just beginning to understand their significance.

Discussion will begin with an overview of universality, pre-disposition, plausibility and self organization, and it will conclude with specific examples. The entire discussion emphasizes the most important characteristic of all evolving systems, whether biological or resulting from human creativity: the phenomenon of emergence. This term is used here to describe the appearance of unexpected results from combining familiar components.

As pointed out by Kirschner and Gerhart (K&G) “understanding of life and life processes is not, however, an immediate goal; it is a long-term evolutionary effort involving many disciplines”. Transport phenomena are among these, and the modeling of physiological transport-reaction systems is itself an evolutionary process.