Professional Duties, Personal Convictions.
The stereotype is that the scientist values knowledge above all else. Despite the impression people get that research scientists are emotionally detached when it comes to their lab animals -- viewing them as a means to obtain more information, and thus of merely instrumental value -- I don't know of a scientist who does or has worked with animals in research who hasn't had to do a gut-check.
Some scientists decide that the importance of the knowledge they produce in animal experiments really outweighs the harms to the animals. This is not a decision that it's morally acceptable to harm the animals at will, nor that the animals are "things" that can't suffer. Otherwise, committed scientists wouldn't go to such pains to figure out humane ways to euthanize experimental animals. (Check out, for example, PZ Myers's discussion of how to euthanize fish.) Some end up in situations where a choice is not forced, perhaps because they end up in fields where the research doesn't involve animals. (This was my situation. As an undergraduate, I worked in research labs that did animal research, but I did physical chemistry in graduate school. Not having to use animals to answer the questions we were trying to answer, there was no pressure to work out how we felt about animal research. I must confess, though, some people in my research group messed around with plants ...)
Still other scientists make a principled decision, based on their own convictions, not to participate in animal research (or on research with certain kinds of animals, like primates or vertebrates). Thinking For Food has a very nice post about making such a personal decision about one's scientific activities.
I fully appreciate the benefits of animal research, would not seek to ban it altogether, and understand that it is a necessary evil of modern society. On the other hand, many of the techniques are cruel and a fair percentage of research using animals isn't necessary. I personally have no desire to cause pain to animals (at least, not those with with backbones... I have fewer qualms when it comes to insects and other invertebrates, although there are certain animals within these groups I would be hesitant to experiment on) and having worked in animal research once, I'm well aware of the pain that can be inflicted even under the best animal welfare regulations.
The ethical stance that I've adopted has real world consequences for me as a biologist, and these are consequences I have accepted. Much of molecular biology, including the best paying jobs, involve research with mammals (mice in particular), and by refusing to work on mice, I have willingly and knowingly cut myself out from a large part of the job market.
Among the nice features of this musing is a recognition that research on animals is not a black-and-white issue. The choice is not between getting the information we want at the animal's expense and sparing the animals but not getting the information. Rather, there may be good ways to get some of the information animal research yields without using animals. Moral qualms can thus be a useful trigger to innovative thinking about how to answer various scientific questions. And certainly, you'd think that the information gained from studies without animals would be a useful complement to the results of animal studies.
The other thing I really like about this post is a recognition that choices have consequences (in this case, a narrowing of one's prospects of employement as a molecular biologist), but that accepting these consequences is a legitimate choice for a scientist to make. In other words, it is not the case that Science Central Command hands down the marching orders to all the scientists, who then execute them without question. Rather, the community of science consists of a bunch of agents who decide what kinds of personal sacrifices they're willing to make to have more job mobility, a higher scientific profile, or stacks of good data. The fact that different scientists weigh the factors in these choices differently makes the community as a whole stronger, rather than weaker.
The contrast, of course, would be to accept a job where you knew you had to work with mice and then refusing to do so on principle. This kind of move would get attention, but would also tend to communicate that you think the other people doing work with mice haven't given it any kind of thought. (It's perfectly possible that people who have given the issue a lot of thought, and who feel the pull of arguments against animal research, still decide that the animal research they're doing is justified; two people can deliberate on the same issue and come to different conclusions without one of them being a callous jerk.) To convince other scientists to pursue alternatives to research with mice, it would be more effective to actually do successful research without mice.
And this is where the discussion shifts from the scientist to the pharmacist:
I understand codes of ethics, and I understand how they can place limitations on what a person can do, but I also understand that if you have a limiting code of ethics, you should not pursue a career where you are going to come into ethical conflict with the requirements of your job. If you cannot bring yourself to dispense certain pharmaceuticals (and it need not just be contraception... anti-depressants and vaccines can be just as controversial among certain segments of the population), you shouldn't take a job as a pharmacist.
Doing research is rather more open-ended than filling a prescription, it is true. However, if your personal convictions are at odds with an essential requirement of your profession -- one where there really is no innovative way to get to the same goal by a different path that you can reconcile with your convictions -- it is time to look for a new profession.
(There are complicated issues here about the differences between the scientist and the health care provider, which I started thinking about back in April. Perhaps I'll untangle a bit more here soon.)