TWENTY-FIVE years ago, when I was a graduate student, there were departments of natural science that no longer exist today. Departments of anatomy, histology, biochemistry and physiology have disappeared, replaced by innovative departments of stem-cell biology, systems biology, neurobiology and molecular biophysics. Taking a page from Darwin, the natural sciences are evolving with the times. The perfection of cloning techniques gave rise to stem-cell biology; advances in computer science contributed to systems biology. Whole new fields of inquiry, as well as university departments and majors, owe their existence to fresh discoveries and novel tools.
My fiancée, and one of her bridesmaids, will be very surprised to learn there are no longer departments of biochemistry, as they each recently earned a PhD in that subject, and from schools one would rather expect to be on the leading edge of such things.
More pertinently, the problem is that the allocation of departmental resources is sticky, even in the natural sciences, even when faculty members receive most of their funding from outside grants. Labs that are not housed within traditional departments often have a lot of trouble, as do their students (in my small but not tiny observed sample, these labs are disproportionately likely to switch universities). The reasons for this are banal enough that even a social scientist could explain them: institutions--like departments in subjects you've heard of--reduce transaction costs and make coordination simpler. (I would also, in social scientist mode, hazard the guess that the change in departmental structure was not driven by anything so pure as scientific inquiry, but by the sorts of inquiries for which one could receive grant money. Scientists are purely motivated truth-seekers, after all.)