Genomic Control Process: Development and Evolution

Abstract

In our time, the sheer volume of published experimental measurements, their scope and technical sophistication, compounded with a proliferation of diverse approaches, objectives, and model systems, has made it particularly difficult to see the conceptual forest for the trees. Yet all of the elegant and sophisticated though disparate and unconnected data sets with which we are confronted represent biological output of the same fundamental operating principles. Each experimental system provides a different window which offers a pathway to these principles. In this book we provide a conceptual framework that we hope will make accessible the principles by which the genomic control system operates developmental and evolutionary process. This framework grows from the realization that the most fundamental causal principles in biology, which distinguish biology from all other sciences, emerge from the existence and function of genomic information. From the genomic sequence are to be recovered the determinants of body plan development in animals. Of course, the processes of biology are subject to the same laws of physics and chemistry as are those of the inanimate world, but it is the genome that mandates biological organization. This is not a metaphor, it is a description of mechanisms that we can now begin to perceive as an unbroken chain of causal connections, leading from the A's, C's, G's and T's of the genomic DNA to the developmental formulation of the elements of the organism. The new field that is coalescing around the concepts of genomic information processing partakes of principles and evidence from systems biology, developmental molecular biology, various aspects of body plan evolution and phylogenetics, as well as biological engineering and computational modeling. We found it useful to select and incorporate insights from all of these fields, where these illuminate the genomic control of development, without operating wholly within the paradigms of any one of them. In this book we focus on the main characteristics of the genomic control system, which include its hierarchy, its logic processing functions and its structural organization in the form of gene regulatory networks. Such networks encompass at a system level the recognition interactions between transcription factors and DNA sequence that lie at the heart of the whole regulatory process. The general operational properties of genomic regulatory systems are shared across the Bilateria, while diversity in animal forms directly reflects diversity in genomic developmental programs. Focus on the genomic programs controlling development provides a single conceptual lens through which the most disparate phenomena of development and evolution can be viewed, causally understood and interpreted.

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