Remarks on the Foundations of Biology

1. INTRODUCTION To say Biology is in "crisis" is, paradoxically, a complement. It is to state that the discipline has progressed to the point where contradictions between its putative founding principles, actual practices, and results are apparent enough to suggest salutary root-and-branch reform. This paper will issue such categorical prescription in the area of Genomics. Much of the rest of what follows is simply reflecting best practice in various subfields of biology. Yet that is a non-trivial task, particularly as biology becomes invaded by researchers from other disciplines like statistics or, as in the case of the present writer, computer science. A first stumbling-block is the nature of causal explanation in biology. We refugees from the informational sciences tend to think only in terms of Aristotle's "efficient cause". Wiser heads have pointed out that the final, teleological cause was necessary as an explanatory gambit for explaining the role of the heart in the circulation of the blood; similarly, the role of whole-properties associated with entities like the cell, echoing Aristotle, has given rise for about a half-century to the notion that organization might itself be a cause in the matter. Keller (1995) famously explicated some of the metaphors underlying genomics, at a time when the HG P was quickening its pace. While the intellectual fireworks surrounding the argument about gene-as-Cartesian-homunculus were indeed spectacular, their glare perhaps blinded us to the apparently more prosaic speculations about the nature of the gene-as-computer-program. This is particularly the case as "computation" has undergone a deconstruction at least as significant as that of "cause", particularly in the work of Brian Smith (1996); see also O Nuallain (2007a). Echoing again the Aristotelian distinctions, what underlies genomics is the notion of efficient computability; the purely syntactic operations it assumes cannot yield phenotypes while maintaining their formal purity as context-independent operations. O Nuallain (2004, p. 174) summarises the situation as an essential tension between the formal requirements of syntax and the realworld exigencies of intentionality, reference in the real world, be that world a perceptual one, as cognitivism would be concerned with, or the biological phenotype. Yet, as we shall see below, that is just the beginning. Elsewhere (O Nuallain,2007d), this author specified the lacunae in current biology. The failure of the cognitive, neural and social sciences to explain cognition and consciousness; intelligent design/creationism versus "Darwinism"; the HG P and its problems, wherein biochemistry examples can be given to show the critical importance of metabolism (Strohman, 2003). On a more fundamental level, we have the observer paradox in biology, whereby reductionism results in losing life itself in a mass of physicochemical detail. The "Where is the program?" theme addresses itself to the massively complex interactions of hox (to be described below), epigenetic factors, types of rnas called sirna and microrna, both of which modulate gene expression, and so on. All these have consequences for the university-industrial complex, and how to rectify matters there in terms of faculty hires and other strategies. With respect to health and ageing there is ongoing work by Bortz (2005), Veech and others (2003) on metabolism (particularly as it interacts with diabetes 2, a new epidemic based on insulin resistance) and health. In both his academic and more popular work, Bortz (forthcoming) argues that the attempt to find a "silver bullet" drug for diabetes 2 by targeting the biochemical networks involved in getting glucose into the cell is misguided; insulin itself is unnecessary if the organisms's metabolism is, aided by exercise, functioning as it should. Of course, there now is evidence that exercise prompts neurogenesis, thus alleviating depression. …