Recently I published an ebook (http://www.amazon.com/dp/B004XMQH7Q) that looks at theory in the physical sciences, and in this blog I would like to expand on some of those thoughts. One of the assertions I made was that in general, most scientists have no formal training in the forming and analysis of theories. There will be some who have done a course in philosophy, but even most doctors of philosophy have never done any formal courses in philosophy. Maybe I am wrong; if so, let me know. Another point that I made is that since the announcement of the Woodward Hoffmann rules, there has been no significant development in theory in chemistry, despite the fact that more chemists have worked after that time than before it. By significant, I also mean that it has made a major influence on chemistry at large. I expect to hear some disagreement on that point, however while there may be exceptions, I believe it stands as essentially valid. I also made a speculative explanation, through the observation that the chemical theory we use is essentially BP, i.e. before polywater. After that debacle, I believe we have gone "theory-shy". (We have refined computational procedures, but that is not the same thing.)
 
In my opinion, the methodology for forming and analyzing theories were laid down by Aristotle, but when Galileo proved Aristotle's cosmology was just plain wrong, with the bath water, out went the baby. What I find fascinating about this is that most of the criticism comes from people who have not actually read what Aristotle wrote. Aristotle's cosmology was wrong, but ironically it came from his ignoring his own advice (possibly because Physica was probably one of the first books he wrote, and he had not finalized his logic). Aristotle was probably the first to emphasize that any theory must be fully in accord with observation, and given that, and assuming that Aristotle made one key error by failing to apply his own methodology (and then this caused all the rest) the reader might wish to contemplate what that error was. (My answer in due course.)
 
Why is this important? Consider a current issue: global warming. From the following references:
Vernol, A. de, Hillaire-Marcel, C. 2008. Science 320: 1622-25.
Kopp, R. E. et al. 2009. Nature 462: 863-867.
Tripati, A.K. et al. 2009.  Science 326: 1394-1397.
The Aristotelian would state:
(a)  In each of the last four interglacials, the sea levels rose approximately 7 meters higher than now.
(b) At each maximum, the carbon dioxide levels were approximately 280
ppm.
He would also note:
(c)  Carbon dioxide levels are now about 380 ppm.
 
Now, either carbon dioxide levels are relevant to the sea level or they are not. If they are not, then it is pointless defending against sea level rises by trying to hold carbon dioxide levels to 450 ppm, the current IPCC target. If they are, then sea levels will rise eventually if the levels are 280 ppm, so again it is pointless to attempt to hold the levels to 450 ppm.  This leads to a clear conclusion: attempting to hold carbon dioxide levels to 450 ppm, or even 350 ppm as advocated by James Hansen, will not by itself prevent sea level rising, unless it was never going to rise anyway this cycle.

Thus looking at the problem in a slightly different way leads to an entirely different conclusion from that obtained from modeling, where the answer is somewhat critically dependent on the assumptions. That does not make the conclusion correct, but it does give guidance on what to do next.