Q. I wonder what open problems there are in bioinformatics/computational
biology? Which tasks are in need of an effective computer algorithm?

A. How to get biologists to write down their experimental procedures
before they begin an experiment.  This may be too hard to be
solved this century.

 | The study of tractability, and of universal systems, received its
 | impetus from an investigation of biological fractionation
 | procedures.  It would not have arisen from physics, which expects
 | its theories to be couched in forms of tractable systems rather
 | than statements of general interaction (the heart of intractability).
 | Indeed, it might not be amiss to consider biology as the physics of
 | intractable systems.  If this is so, then far from physics swallowing
 | up biology, the situation may well be the other way around.
 | Our analysis of the reductionist hypothesis has thus shown the
 | fertility of biology in generating important new insights in
 | mathematics in the sciences --though doubtless in a way different
 | from what was orignially intended.
Robert Rosen, "On Mathematics and Biology" in _The Sprit and the
Uses of the Mathematical Sciences_, Saaty & Weyl, editors, Mcgraw-
Hill, 1969 p. 209

20 years later:
 | One of the few physicists to recognize that the profound silence of
 | contemporary physics on matters biological was something *peculiar*
 | was Walter Elsasser.  To him, this silence was itself a physical
 | fact and one that required a physical explanation.  He found one by
 | carrying to the limit the tacit physical supposition that, because
 | organisms seem *numerically* rare in the physical universe, they
 | must therefore be too special to be of interest as material systems.
 | His argument was, roughly, that anything rare disappears completely
 | when one takes averages;  since physicists are always taking
 | averages in their quest for what is generally true, organisms sink
 | completely from physical sight.  His conclusion was that, in a
 | material sense, organisms are governed by their own laws ("biotonic
 | laws"), which do not contradict physical universals but are simply
 | not derivable from them.
 | Ironically, ideas like Elsasser's have not had much currency with
 | either physicists or biologists, although one might have thought
 | they would please both.   Indeed, in the case of the former,
 | Elsasser was only carrying one step further the physicists' tacit
 | supposition that "rare" implies "nonuniversal."
 | The possibility is, however, wide open that this supposition
 | itself is mistaken.  On the face of it, there is no reason at all
 | why "rare" should imply anything at all; it needs to be nothing
 | more than an expression on how we are sampling things, connoting
 | nothing at all about the things themselves.  Even in a humble and
 | familiar areas like arithmetic,  we find inbuilt biases.  We have,
 | for instance, a predilection for rational numbers, a predilection
 | that gives them a weight out of all proportion to their actual
 | abundance.  Yet in every mathematical sense, it is the rational
 | numbers that are rare and very special indeed.   Why should it
 | not be so with physics and biology?  Why could it not be that
 | "universals" of physics are only so on a small and special (if
 | inordinately prominent) class of material systems, a class to
 | which organisms are too *general* to belong? What if physics is
 | the particular, and biology the general, inste