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Models and Illusions.

One sometimes reads about how a particular DNA sequence has a consensus sequence at such-and-such a position [Robberson et al., 1990]. Thus using consensus sequences has led these biologists into a philosophical trap: confounding the model of reality (the consensus sequence) with reality (the binding sites). Even the original title of our paper on sequence logos reflects our initial confusion on this issue [Schneider & Stephens, 1990]. Logos and walkers let us see more deeply into the genetic structure, revealing the details of sites and how mutations work. But no matter how sophisticated we are in depicting the patterns at binding sites, all we have are models. Logos and walkers are clearly better than consensus sequences (and can replace them completely), but they are still only representations of the universe `out there' [Box, 1979]. It is surprising, then, that scientists forget this and treat the consensus as reality. The effect was understood more than 30 years ago by Thomas Kuhn: once a paradigm is formed it occludes other ways of thinking and molds the way scientists perceive the world [Kuhn, 1970]. Yet a consensus can no more be `in' a DNA sequence than the meaning of these words is on the page. These words are interpretations in your mind; the page only has some disconnected black squiggles. One way to see this is to consider the perennial myth of a face on Mars that appears in American tabloid magazines. Whether or not there is a face on Mars, most of us have seen faces in clouds. Are there really faces there? Evidently not. Experiments with sheep and monkeys have identified neurons that become excited when a face is presented in the visual field[Kendrick & Baldwin, 1987]. So faces in clouds, words, and consensus sequences are all constructs in our brains. Stranger still, the words may not be there when you perceive them since neural impulses take 300 milliseconds to travel from your eye to your brain[Rager & Singer, 1998], where, after another 80 milliseconds, they are finally perceived[Eagleman & Sejnowski, 2000]. All that we see, hear, feel, smell, touch, and taste is delayed, so the entire perceived world is a model in our minds. Optical illusions remind us, and Zen masters understood, that everything is illusion [Purves et al., 2002].