Equally unimaginable at mid-20th century was the idea that transposable elements are essential to understanding chromosome structure and evolution, much less organismal evolution. The efforts of Bateson and other geneticists had firmly established Mendelian “laws” as the central paradigm of genetics and the identification and mapping of genetic “loci” through the study of mutant alleles was proceeding apace. Because genetic mapping is predicated on the invariance of recombination frequencies, there was plentiful evidence that genes have fixed chromosomal locations. Written at this time, Stebbins' book in general and in particular his third chapter, titled “The Basis of Individual Variation, ” clearly acknowledges the existence of many chromosomal differences among organisms in a population, including duplications, inversions, translocations, and deletions. At the same time, the book reflects the prevailing view that these “. . . are not the materials that selection uses to fashion the diverse kinds of organisms which are the products of evolution” (Stebbins, Jr., 1950). Instead, Stebbins concludes that the majority of evolutionarily important changes in physiology and morphology are attributable to classical genetic “point” mutations.
Another half century has elapsed and the geneticist's “black box,” sprung open, spills nucleotide sequences at an ever accelerating pace. Our computers sift through genomes in search of genes, knee-deep in transposons. How could we not have seen them before? The answer is as straightforward as it is mysterious and worthy of consideration: they are invisible to the geneticist. Well, almost invisible. And of course it depends on the geneticist.
The study of unstable mutations that cause variegation dates back to De Vries, who formulated the concept of “ever-sporting varieties ” and eventually came to the conclusion that these types of mutations do not obey Mendel's rules (de Vries, 1905). The first person to make substantial sense of their inheritance was the maize geneticist Emerson, who analyzed a variegating allele of the maize P locus during the first decades of this century (Emerson, 1914, 1917, 1929). His first paper on the subject opens with the statement that variegation “. . . is distinguished from other color patterns by its incorrigible irregularity” (Emerson, 1914). What follows is a brilliant analysis of “freak ears” containing large sectors in which the unstable P allele has either further mutated or reverted. Emerson was able to capture the behavior of unstable mutations in the Mendelian paradigm by postulating that variegation commenced with the temporary association of some type of inhibitor with a