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Chapter 2. Are Gene Regulation Networks Evolvable?
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2 Are Gene Regulation Networks Evolvable? “Exactly how does an egg produce legs, head, eyes, intestine, and get up and start running about?” With this question, Conrad Waddington (1966, p. iv) expresses wonder at both any system that is capable of overcoming the difficulty of development and the difficulty of understanding such a system. The difficulty of a task can be understood in terms of the range of possible physical systems that can overcome that task. For example, opening a particular lock is difficult, because only a relatively small range of systems have the necessary features to be a key that can be inserted and turned to open that lock. Opening many different locks is more difficult. A smaller range of systems are skeleton keys. In contrast, the range of systems that will make an adequate paperweight is much broader. The requirements of moderate size and solidity are easily satisfied. Many of the various things lying on my desk would make an adequate paperweight, but none of them will open a lock. Some of the difficulty of development lies in the fact that, to develop, an organism must do different things at different times or in response to changes in its environment. For example, E. coli will consume lactose only if there is no glucose available (Reznikoff 1992). In addition, cells in organisms face different microenvironments within the organism and must change their activities accordingly.1 This happens most dramatically during the early development of complex organisms. Each of us humans began as a single cell. That zygote underwent about fifty cell divisions to form an infant with 10 trillion cells. Those cells differentiated from one another to form about 100 cell types. The cells differ not because they have different genes inside them (most cells share very similar DNA, and most cell differences are not explained by differences in primary DNA sequence), but differences in the expression of genes instead (i.e., which genes are 24 Chapter 2 transcribed to produce proteins). The gene regulation system must be one of the most ingenious systems in the body, because it must solve one of the most challenging difficulties of development. 2.1 Gene Regulation Networks The term “gene” has multiple definitions in evolutionary biology (Griffiths and Neumann-Held 1999). In this book, I take a gene to be a section of DNA that is directly utilized in the production of a messenger RNA transcript , which is then used to synthesize a particular protein. A gene has two sections. The transcribed region is used as a template to form messenger RNA in the transcription process. The messenger RNA is then used to produce a protein in the translation process. Whether or not the transcribed region of each gene is transcribed is determined by the interaction of transcription factors and the regulatory region of the gene. The regulatory region has binding sites that specific transcription factors may bind to and thereby either activate or repress the transcription of the gene. In eukaryotes, the regulatory region of a gene need not be adjacent to its transcribed region and may be involved in regulating multiple genes. Transcription factors are themselves proteins that are produced by transcription and translation of a subset of genes. Thus, the expression of some genes can influence the expression of others. The relationship between the expression of genes of an organism (i.e., the expression of which gene activates or represses the expression of which other gene) makes up the organism’s gene regulation network. Gene expression is crucial to many cellular activities. We can ascribe a significant aspect of the difficulty of development of the organism to the difficulty faced by the gene regulation network in expressing adaptive gene products for each microenvironment faced by each cell over the life of the organism. Though understanding this gene regulation network is not all that is required to understanding biological development, it is a crucial step (Wright 1982; Raff 1996; Wilkins 2002). Even Waddington, who was well aware of levels of organization above gene regulation, such as structures inside cells, tissues consisting of many cells, organs, and finally the body as a whole, still endorsed Thomas Hunt Morgan’s (1866–1945) view “that the fundamental agents that bring about embryonic development are the genes, and the only finally satisfactory theory of embryology must be a [35.175.232.163] Project MUSE (2024-03-29 16:57...