Yes, really.

This post is written largely as a response to Phil Lord’s thoughtful response to my previous post on realism and to a marathon pair of threads on the OBO-discuss e-mail list realism and ontology building (taster here). I thought the initial discussion in those threads was useful and pointed the way towards some progress and compromise. Unfortunately, and perhaps inevitably, by the end people’s positions appeared more polarized than ever. I’m not sure this is justified.

Anyway, back to my response to Phil. I’ll try to deal first with the philosophy (or my probably naive take on it), and only after that with how that might relate to practical issues of ontology building.

Phil wrote:

“Most scientists believe in reality so, when faced with realism vs conceptualism, their gut feeling is that the former will be right. They believe in a mind-independent reality so, therefore, conceptualism must be wrong.”

Not only do I believe in mind-independent reality, I believe that science makes claims about mind independent reality that it is reasonable to believe are true. In my experience, most scientists (certainly most biologists) believe this too. In making claims about mind independent reality, science makes claims about the regularity of the universe. When a chemist states some conclusion about a reaction involving benzene molecules, she is referring to a class of things with shared properties (something like: 6 carbon atoms arranged in a hexagon around which, electrons are delocalized from the carbon atoms, resulting in even length and strength C-C bonds… (I’m no chemist)) many instances of which exist. I have no problem with someone calling such classes universals as a way of distinguishing them from arbitrary or contingent collections of objects. I, perhaps naively, believe this to be a form of realist position. And it’s a position I hold irrespective of its application to ontology building (of which more later). My views on this largely come from two years I spent arguing with postmodernists who taught a masters degree in Science Communication I took at Imperial College.

It strikes me that what Phil calls realism seems to be much more specific than this – he at least sometimes gives the impression that a realist position involves accepting the BFO + whatever Barry Smith proposes. My knowledge of philosophy is quite limited, but I’ve read enough to know that this is unwarranted – it seems to stem largely from ongoing arguments about nature of the OBO-Foundry .

I’m also not convinced by Phil’s arguments about mathematical abstraction. Mathematical abstraction is clearly a critical part of science (or at least much of it), and I’m convinced that the current OBO foundry / BFO approach is fundamentally flawed in its obvious inability to cope with it. But I also think one should be careful about reducing scientific claims to mathematical abstractions alone. Phil quotes Feynman:

The next question was – what makes planets go around the sun? At the time of Kepler some people answered this problem by saying that there were angels behind them beating their wings and pushing the planets around an orbit. As you will see, the answer is not very far from the truth. The only difference is that the angels sit in a different direction and their wings push inward.

Character of Physical Law
— Richard Feynman

And goes on to say “The statement that g∝1/r2 is the same as Fwingsofangels∝1/r2. So long as we agree that the angels behave in a precise, predictable way, there is no deep reason to distinguish between the two, except for simple pragmatism: “gravity” is shorter and easier to say than “the wings of angels”.”

The obvious response is: even if Kepler had got the maths right, is it really irrelevant to our acceptance or rejection of his theory whether he believed that force was exerted on the planets by creatures with wings sprouting from their backs? Even in the most mathematically abstracted areas of science, we can’t completely purge ontological claims.

Why should this be of any relevance to ontology building?

Well, first of all, this position is a useful counterbalance to those (depressingly common) who confuse ontology building with building dictionaries or thesauri. If I tried to take into account every usage of a particular word by biologists, I don’t believe I could build a logically consistent structure, or one that is at all useful for reasoning. It is also a counterbalance to those (once depressingly common, now less so) who think that the job of ontology building involves simply asserting is_a and part_of heirarchies of undefined terms without worrying much about logic. I’ll concede that a conceptualist approach may also provide a counterbalance to these approaches.

Secondly, and more importantly, I care about whether it is reasonable to believe, on the basis of the scientific evidence we have, that instances of the classes I define exist. I care about this because

(a) One major aim of my work is to provide a reference for wild-type anatomy. If I mix in classes of structure that have no instances, my ontology ceases to be a reliable reference.
(b) I see no reason to expect logical consistency if classes lacking instances are allowed.
– I hold the assumption that the real world that our scientific theories make statements about does not contradict itself

I should qualify this by saying that, realistically, only making terms for classes that have we have good reason to believe have (or have had) instances is an aspiration. I’m sure I fall short all the time, but I still think it a worthwhile aim. I also have no objection to people building ontologies that include classes we have good reason to believe to do not have instances, as long as we have some clear label them so that those of us who don’t want to work with these can filter them out.

Now, talk of instances means, as far as I can tell, that reality (or claims about it) are at least sometimes of importance to conceptualists. I have to admit, I’m still puzzled by how one can claim to be a conceptualist and talk of the exist>ance or not of instances, but that they do points to potential compromises:

Can we find ways to mark classes to make this disinction clear? Something along the lines of:

– Class we have good reason to believe has no instances [REFS?]
– Class believed on theoretical grounds alone to have instances [REFS]
– Class for which there is experimental evidence for the existance of instances – evidence summary [REFS]

With these distinctions made, I can choose to only import terms of the third class into the ontologies I build (even then I may set criteria for accepting terms based on the quality of the evidence).

Finally, I see talk of universals as useful only in *guiding* what I do – making me wary of classes that appear arbitrary, contingent, cobbled together for convenience. I don’t see the need to get hung up on drawing a clean line between universals and other classes – in my experience, this is neither practical nor useful.

None of this means I reject engineering considerations in ontology building. In fact, they’re essential to what I do. I lose sleep over whether the ontologies I build are maintainable and scaleable – in part because I know the pain of untangling a poorly constructed ontology that has been used for massive numbers of annotations, but also because I’d like to think I’m building a structure others could build on in the future. It is also essential that the ontologies I build can be used with a reasoner to answer particular types of query, and to do so as rapidly as possible. Such queries are running live on our test site. Again, engineering considerations are essential to this.

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2 responses to “Yes, really.

  1. Pingback: Ontological realism, methodologies, and mud slinging: a few notes on the AO trilogy « Keet blog

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