I originally wrote this as a brief comment in reply to David Osumi-Sutherlands excellent post. But, the formatting got mixed up and is unfixable there, so I posted I am posting it here.

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.

— David Sutherland

I agree. However, this has little or no bearing or relevance to whether you are a realist or not. The assumption that it does it based on an etimological fallacy — “realism” chose a good name, this is all. Conceptualists, or people like myself who just don’t care about the philosophy, but who simply find that realism is resulting in bad ontologies, do not automatically believe that the world is a fluffly place, dreamed up in someone’s head. Believing in reality does not make you a realist.

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 .

— David Sutherland

This is a criticism that others have made — Matthias Samwald pointed it out on my blog. Yes, you (both) are entirely right. In my paper, I am explicit about this, saying “In short, for this paper, when we say “realism”, we largely mean realism as practiced by BFO. We do not claim, in this paper, to address all the philosophical perspectives that through time carried the name realism.” Even this is hard — as Gary Merrill’s excellent paper describes, what “realism as defined by Barry” means changes from paper to paper.

I’m not trying to address the philosophy — as I say, I don’t care. I am trying to address the problems being caused in ontology development now.

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.

— David Sutherland

[mathjax]

Gravity and Newton are not ontological claims. They are phenomenological. We do not stick to the earth because of gravity; rather, gravity is the name we give to phenomenon. The cleverness and the understanding is that one simple piece of phenomenonology (\1/r^2\ can explain a lot of others.

There’s a nice Feynman quote on this as well, as there appears to be on anything. “Feynman, inertia” and google should provide.

The creatures with wings theory starts to break down when you realise that electrons assert a gravitation force on each other. You would have to ask, “could the angels really be bothered”, and “what are the angels made of”? But at the level of planets, I think it mostly works.

Of course, “gravity” sounds much more sciency than “wings of angels”, which means it’s better.

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.

— David Sutherland

Fine. But unless you have a clear definition of what you mean, it’s useless. Apparently, according to realism instances of “Dog” exist but no instances of “Dog or Cat” exist. According to realism, zero, by definition, doesn’t exist. I don’t know what to make of this.

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

— David Sutherland

Maybe. We won’t know till we have finished. In the meantime, contradictions occur. There is not point building a computational framework for representing our data that can’t cope with this. I think that this is no that significant an issue for reference ontologies which are, by definition, likely to be behind the times!

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

— David Sutherland

Again, very little to do with realism. Ironically, one of my main issues with realism is the introduction of lots of abstract and frankly incomprehensible concepts into ontologies. What is the evidence for the existance of instances of Generically Dependent Continuant? Or as Chris Mungall says on my blog:

Instead we have to say ‘book content’ has_concretization of some (inheres_in some book). This gives me a headache and seems to just be making busy work for no practical reason. Also I feel lost with respect to what the intermediate unnamed entity is here.

— Chris Mungall

But, yes, standards for reporting of evidence are a good thing. I think, we should also be investigating metrics for looking at the usage of ontology terms — those which are never used are also problematic. These are simple, pragmatic steps that we could take.

I think that we need to consider readability metrics for our English definitions, we need to consider metrics for complexity (“as simple as possible, but no simpler!”) for both our logical definitions and for the ontologies overall. All of these things are important steps, in determining whether the distinctions we choose to make are worthwhile. And I think that we need better tools to tie all of this together.

All of these things will come in time. But not while we waste time arguing about philosophy. Not if we push forward the idea that correctness comes from thinking hard about things, rather than testing them. And not if we give the impression that ontology building is about understanding large numbers of unsupportable, untestable and probably meaningless statements about the nature of reality. This is why I wrote my paper.

Oh dear, this was meant to be brief. I apologise to all three of my subscribers. I will stop. Honest.