Francisco Ayala: Evolution is "not just a theory"

Francisco Ayala, biologist at the University of California at Irvine, recipient of the National Medal of Science, and recent winner of the Templeton Prize, has an article in Standpoint Magazine in which he confuses the relationship between science and religion (not too surprising, since the Templeton Prize is awarded for "Outstanding contributions in affirming life's spiritual dimension, whether through insight, discovery, or practical works").  PZ Myers at Pharyngula has done a nice job of dealing with this aspect of the article: I want to focus on something else for a moment. In the article, Ayala writes:

That evolution has occurred is, in ordinary language, a fact, not just a theory.

 He's right about the fact part, of course; evolution is a fact in the same sense that the Earth revolves around the Sun is a fact. But it's sad to see him contrast fact with theory, as is regularly done in popular usage where theory means an idea for which there is no good evidence, an unsupported guess.  As I wrote on this blog some time back:

For scientists, a theory is a set of interconnected hypotheses that describe and/or explain some aspect of the world. The hypotheses must be logical, falsifiable, and above all constructed from the analysis of data collected by way of systematic, objective investigation of the empirical world

It does the scientific literacy of the public no good to place theory and fact in opposition to one another in this way, and it's especially disappointing to see this done by someone with Ayala's prestige. People are confused enough as it is.