Information talk privileges genes over other causal actors in biology (which is the point of the Griffiths and Gray "Parity thesis" counter-argument). But genes are only genes in the context of complex developmental systems - in a test tube, DNA sits there and slowly denatures. So by using information talk we allow causally significant parts of the system to fade into the background.
Information is not a physical cause of anything. Take my computer - it "reads" information from keystrokes, right? Well, only in an abstracted manner. What physically happens is that I complete a circuit when I hit a key, which causes electrons to be transported to processing circuitry, which converts that signal into a particular sequence of high and low voltages, which... and so on. The abstraction "information" does nothing here. The physical processes that we abstract out as information do.
in these days of particle and quantum physics, do we need the notion of form+substance any more? Certainly not for molecular biology, at any rate - let's leave those fundamental physics guys to do their thing for a century or so. Morphology no longer plays a causal role in biology except as the arrangement of particles and ensembles of particles. Want to explain why protein A cleaves to nucleotide X? Do so in terms of the shape if A and X, but do not stop there - form is the effect of the properties of the parts; the strong and weak bonds, the medium, the ambient energy level, and so on. We might be able to infer similar properties from similar forms, but the full explanation, in biology at any rate, has to include the makeup of the molecules and their degrees of freedom in folding and bonding properties.
So I think that if we are to take modern science seriously in our ontology of biology, we have to treat information as an abstraction made for our benefit, rather than as an inherent property of the objects themselves. This means of course, that my claim to treat as IPSs only those system that are isomorphic to a formal IPS resolves down to what we intend to take as satisfying those conditions. But as an instrumentalist, I am happy with that. Human brains process information. Genes don't. Somewhere in the middle is a border case in which I cannot say for sure, but my instrumentalist rule of thumb might be - can we use it as an IPS, even just theoretically? If so, it's an IPS.
This is a much more rigorous way of saying something that I feel somewhat intuitively about attempts to discuss biological processes as information processing -- that it's not so much wrong as it is not useful. Biological molecules do what they do in the way that they do it -- they work according to rigorous laws of physics and chemistry, and enough of them working in tangent can create some very non-obvious results. (Namely, us, and by us I mean life in general.)
To try to reduce this to some sort of general information-processing routine might make sense in a sort of metaphysical way, but getting away from the reality of the biology to a "higher" or "more abstract" level is also to get away from, well, the reality of the science. So everything is information? So what -- the whole universe is really just made up of solutions to Schrodinger's Equation, and in principle every problem of every discipline (up to and including sociology and economics) reduces to that simple fact. But just as it's useless to try to calculate waveforms in understanding budget deficits, it's nonsensical to try to use some computational analogy in trying to understand real biological phenomena.
The world is complex. Trying to understand hugely disparate phenomena based on narrow interpretations gleaned from pop-science books on computation (I'm looking at you, Stephen Wolfram!) is madness. If a computational approach to biology starts to produce real results, then I'll sit up and take notice, until then, stop using that silly "genes are like bits" notion that sets my teeth on edge.