Good ways to handle scientific disagreements.

One of the things I think scientists like about doing science (besides the cool lab coats and safety glasses, of course) is that, in cases of disagreement, there's good reason to think you'll be able to work it out in the end. The reason this is so is that scientists share a commitment to testing their hypotheses and theories, whether by comparing them to the available empirical evidence, or by assessing its logical consistency, or evaluating it based on other agreed-upon standards of goodness.

Even when the going gets tough -- when the standards of theoretical goodness are not so agreed upon, or when one laboratory is having a hard time reproducing another laboratories experimental results -- scientists are looking to data that ought to be obtainable by anyone (once the equipment is working and the scientist has mastered the technique), trying to make their cases with reasons that are laid out for public scrutiny. Winning the argument only matters if you win because your reasoning and/or your experimental result is better. Better to lose the argument if it helps the community as a whole get closer to the truth.

In other words, scientists try hard to avoid disagreements that degenerate to the "Jane, you ignorant slut" level of discourse.

A nice example of a scientific disagreement in the literature is discussed by Ricardo Azevedo. The scientific dispute centers on whether evolutionary mechanisms like mutation are sufficient to explain the complex adaptive features of proteins. One set of authors presented a model to demonstrate that they were not. Another set of authors offered a detailed critique of the biological assumptions, modeling techniques, and logic upon which this model was based. Indeed, they looked to empirical evidence (about the frequencies of neutral versus deleterious mutations, in a number of experimental systems, in studies conducted by several different research groups) to undermine certain of the crucial assumptions in the earlier article.

Sadly, the response to this response seems not to really engage. Rather than taking seriously the empirical grounds for worrying about the central assumptions of the model, the advocates of that model seem to say the critics have misinterpreted what the experiments are really saying. There's no satisfying, side-by-side duel of competing models given a set of empirical results both sides can agree on. In the end, the attempt at engagement is followed by an attempt at disengagement. So dissatisfying.

Does it matter that one of the authors of the original article is a staunch advocate of ID, and that this model was supposed to demonstrate that ID is all that makes sense once evolutionary mechanism prove inadequate to the explanatory task?

I don't think it would matter so much, at least from the point of view of how dissatisfying it feels to not get the real scientist-on-scientist engagement one hopes to encounter in the literature. It might, however, give us clues to why that kind of serious scientific dialogue didn't end up happening here.

At least in the romantic ideal, the scientist cares only for the truth. Serious engagement with others is how to get there. You don't want to run from such engagement: you want to seek it out, to see if your theory is really as good as you think it is.

If the goodness of your theory can't be demonstrated with public reasons and public data, you're supposed to suck it up and be ready to cut that theory loose. You may get to keep tinkering with it to rehabilitate it, but you will at least understand why other scientists are skeptical. If you go for the underdog theory, you live for the day you can convince the doubters in a fair fight. And, you accept the possibility that it is you who will be convinced to change your point of view.

Good, clean scientific engagement yields a scientific community where everyone comes out smarter. Purposely dodging such engagement, on the other hand, leaves one feeling dirty.