In the preceding overview of the ways DNA encodes various kinds of biological information, the relationships between genotypes and phenotypes, the multiple functions in cells, and the various classes of genes that have evolved to serve these functions, we have tried to outline a general picture of the working tools with which biological traits are made. There are important broad generalizations that are seen repeatedly.

Biological processes use a limited number of genetic regulatory factors and their interactions. The diversity of mechanisms has been elaborated by gene duplication from a few ancestral starting points and by multiple uses of the same factors and pathways. This generic logic rests on overall principles of evolution and/or biochemistry, which can perhaps be attributed in a general way to the modular nature of coding, the fact that so many biological reactions involve the interaction among proteins (including ligands and their receptors), and the nature and ubiquity of cell membranes. All of this is constrained by the core of basic biochemical reactions from which so many of the constituents are derived and upon which it all depends.

A few of the "classic" kinds of genes, like single enzymes or structural proteins, are used only in one context for a direct function. Hemoglobin and tooth-enamel proteins are examples. But we need a different kind of explanation of specificity for the broader set of complex functions. Are signaling factors Fgf4 or Shh, which we know are expressed in limbs and teeth (and many other structures), genes "for" teeth or limbs? Is the distal-less homeobox TF an insect wing spot or leg or tooth gene? Is the answer simply "yes," or are there better ways to think of it? In a meaningful sense, many aspects of a biological trait are perhaps better defined not by the specific genes that bring it about but by their interactions. Many if not most of the signaling pathways have both positive and negative feedback components, which can be viewed as providing a stabilized interaction tool (Niehrs and Meinhardt 2002) that can function under a variety of circumstances.

There is degeneracy in RE sequences for a given TF. There is also similar regulatory degeneracy (sometimes referred to as promiscuity) in developmental signaling. The regulatory toolkit comprises sets of gene family members that are able to substitute for each other experimentally or evolutionarily—and this probably means that there is considerable cross-reaction among SFs and their receptors under normal conditions. For many traits, this leads to the many-to-many phenogenetic relationship described earlier.

The genes in the regulatory tool kit are also arbitrary relative to traits they control. This is reminiscent of the arbitrary coding nature of DNA. The complex nature of gene interactions is such that we can typically no longer associate a gene with a single function (Greenspan 2001). The action is in the specifics of interactions, and this also provides malleability and robustness. Just as a given type of tRNA transports the same amino acids to any protein whose message has the appropriate codon-anticodon match, a Hox or Ffg protein can regulate any gene that has the appropriate flanking RE sequences. In each case, there is binding specificity but functional arbitrariness.

Thus, the biological traits that have been the focus of evolutionary biology (limbs, flight, and the like) are the very specific end-stages of complex developmental processes, but much of how the traits get here is genetically arbitrary. This is very different from the view of evolution that has predominated since Darwin and of molecular biology since the modern synthesis and Central Dogma. Throughout the remainder of this book, we will see these principles in action.

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