Science at work (redux)

A couple of months ago Renyi Liu and Howard Ochman described a series of gene duplication and divergence events that could have been responsible for evolution of the core proteins in the bacterial flagellum (source). I pointed out at the time that Nick Matzke thought there were serious flaws in the paper (source). Nick now points out that Liu and Ochman have published a correction to the paper. They conlude that the errors “do not affect the conclusions of the article”.

As I said in my earlier post, this debate is well outside my field of expertise, so I'm not going to try to evaluate the arguments. I am disturbed that the correction leads the authors to find 70 flagellar core proteins with matches instead of 24. I've never used Bl2seq (the program Liu and Ochman used to find sequence matches), but a nearly three-fold change in the number of hits makes me uneasy about the whole analysis.

But the uncertainty about these results doesn't disturb me. Uncertainty is the bread and butter of scientific research. As Natalie Angier puts it in “The Canon” (a great book, by the way):

Science is uncertain because scientists really can't prove anything, irrerrfutably and beyond a neutrino of doubt, and they don't even try. Instead, they try to rule out competing hypotheses, until the hypothesis they're entertaining is the likeliest explanation, within a very, very small margin of error – the tinier, the better.¹

Let me repeat what I said last time:

Matzke's critique illustrates what makes evolutionary biology a science. Liu and Ochman present data and analyses in favor of their hypothesis – that “core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene” &ndash, and Matzke disputes their hypothesis by bringing different data and different interpretations to the table. Ultimately, the dispute will be settled by further analyses and new data. This dispute illustrates the process of successive refinement through which scientific knowledge accumulates.

As P.Z. Myers points out, this is quite different from how creation “scientists” behave, whether they be young-earth creationists, old-earth creationists, or new-fangled intelligent design creationists. They never do any of their own research. They never produce any of their own data. Their ideas never spawn new investigations. They merely misunderstand (or misrepresent) the data that scientists produce.

¹Angier, N. 2007. The Canon: A Whirligig Tour of the Beautiful Basics of Science Houghton Miflin Company, New York, NY.

If you don't understand why “scientists really can't prove anything”, take a look at the Wikipedia entry on inductive reasoning.