Genes are not the only elements of inheritance but broadly defined seem to be the single most important information-carrying system. The genome, however, is not just a digitally arranged set of beads on a string coding for amino acids determining the traits that make up an organism.
During the previous century, our conceptual approach to genetics was heavily influenced by Mendel, who provided a fundamental understanding of how genes were inherited. However, he used traits very closely tied to individual genes to show that inheritance was particulate in nature. Whatever our definition of a gene finally ends up being, this discovery led to a century of unprecedented progress in understanding the behavior of genes. However, we may have followed Mendel's conceptual world too closely, by overinterpreting the inheritance of genes to be equivalent to inheritance of traits. There is conceptual trouble as a result because this has led to thinking of a gene for or per trait and hence of traits as simple products of unique genes.
Mendelian thinking does work very well for carefully chosen traits and for those aspects of natural variation that are at the extremes of the penetrance functions. Much if not most phenotypic inheritance does not seem to be of that type. The greater complexity provides a greater challenge to understand but also probably provides greater natural stability for traits.
The modular nature of the genome is of tremendous help in explaining the origin, nature, and arrangement of genes and for reconstructing the history of duplication and rearrangement events between species. Gene families with related and partially overlapping function, and similar characteristics or regulatory elements, provide understandable ways to account for the "evolvability" and developmental nature of complex organs and systems.
But accounting for something like a wing or a peach does not really explain what it "is" because there is so much complexity in the myriad pathways between a fertilized egg cell and a wing or a peach. We can use the machine analogy to identify parts and connections; at least up to a significant point, we are already learning tremendous amounts about the inner workings. Overall, the most important generalization may be the combinatorial use of related pathways and genetic "parts" that are also used in other structures as will be discussed in subsequent chapters.
The power of complementary base pairing in DNA and RNA leads to an essentially open-ended diversity of possible function. Floating all around a cell are thousands of DNA or RNA sequences, providing many possibilities of complementary hybridization or protein-DNA/RNA binding; this means that opportunistic evolution can in a sense "create" new function if some sequence turns out to be recognized in one of these ways (which can affect transcription or translation). The complex mix of molecules looking for partners raises an additional issue—how to avoid uncontrolled binding and/or inhibition of these many elements. This is a largely unsolved problem for science (but not for organisms, who have figured it out).
Modularity is so fundamental a principle of life that new manifestations are likely to be found, and these may be entirely different from sequence-specific modularity. Such modularity may involve the conformation of DNA near expressed genes, the shape of chromosomes as a key or code for particular differentiation, or any number of other characteristics and conformations of genes. A whole different set of simple processes can explain the nature and evolution of segmented traits with variable numbers of repeated similar structures, like petals, vertebrae, or toes. We will see many examples.
Modularity, gene and gene family evolution, and the like provide a beautiful satisfaction—these few general characteristics of genomes and their "strategies" for producing complex traits apply widely across both the animal and plant worlds, providing elements of a unified view of the way life uses the information stored in genes.
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