Hey there reasonable.atheist, thanks for the hard questions. It's always good to have people around that'll make you look at your own beliefs. I've never studied the history of science, nor actually took the time to seriously know how science "works" and its goals (beyond what I *think* its goals and purposes are), and my understanding of buddhism is not quite there yet to begin lecturing people about my choice of religion, but I feel compelled to post here about my own beliefs of the two. So just bear with me here .
What I believe, is that the purpose of science is simply to understand our surroundings in a way that if we were to be able to reproduce the results in a controlled environment (e.g. a lab), the results will always be the same every single time. So when the results aren't consistent, we keep looking and looking until we find a way that works.
Sometimes though, what we arrive at to be true or false is simply due to the limits that we test them at. For example, Louis Pasteur's experiments with boiling water that proved that pasturization would work to kill off all microbes succeeded partly because he got lucky; now after more experiments we have found that some microbes do survive above 100c .
This is the beauty of science of course, that if something that was previously accepted to be true is now found out to be false, we willingly throw away our old beliefs and embrace the new result(s). It is interesting that some monks (Ajahn Brahm, Dalai Lama) have said that Buddhism works similarly, that what was found to be true should be embraced instead of scriptural authority.
So in that case, why haven't these monks defrocked since certain aspects of buddhism could not be proven to be true under science? I can't speak for them of course, but faith in the teachings, and the fact that the teachings of the Buddha worked for them probably has quite a lot to do with this. After all, science is always moving towards truth, and what is found to be true/untrue is only so for now, until new findings overturn or reinforce them.
For me personally, there are certain parts of Buddhism that I do not totally accept yet, and I will not elaborate here for fear of bad karma (heh heh!). However, I am not particularly smart, nor perceptive. Those aspects of buddhism that I'm skeptical about, I just treat as I'm unable to understand them for now. I'm confident that if I strive hard enough, I'll get to the point that I can see for myself whether they true... or not. Not sure if this has been posted, nor if it's relevant to you, but do have a read about the parable of the poison arrow: http://en.wikipedia.org/wiki/Parable_of_the_arrow .
In fact for science, I have the absolute confidence that given enough time everything can be found out to be true or false for sure. Who knows, the scientific formula for karma could be discovered 10,000 years from now, and you'll need to plug in 84,000 variables for it to work perfectly. But I am naive like that.
At the end of the day, whoever approaches religion should do so with healthy amounts of faith and the willingness to continually test the teachings. I believe that after a while at it, if you ask yourself if you're a happier, better person and the answer is positive, then there's no problem at all. Unhappy (religionists of your choice)/atheist/deists/humanists exist, so if whatever you believe in doesn't work after rigorous testing, move on and find something else that does.