I was entertained to see the recent publication of a new paper on the definition of function (10.1186/2041-1480-5-27). I met one of the authors at a meeting a few years back in Durham, and had a very nice discussion about my own contribution to this definition which I published previously (1309.5984).

I do not want to discuss the paper in full, which is a nice paper and worth a read. I do however want to comment more specifically about the parts that explicitly and implicitly address my own paper.

At the start of the paper, the authors discuss the criteria for their definition which includes this:

Avoidance of epiphenomenalism: Functions should be determined by current performance of its bearer, not mainly by causally inert historical facts like its (evolutionary or cultural) history or a mere ascription by its producers, users, or observers

I found this a fairly strange criteria; it’s not clear to me why historical facts are inert; especially in biology the evolutionary history of an organism is surely one of the most important features. Originally, this criteria comes from another paper by Artiga who says:

We want to find out what is the lung’s function, we would probably look at what lungs actually do in our body. We would see that they enable respiration, so we would conclude that this is their function. Why they came to be here seems completely irrelevant for function attribution.

Obviously, this means “most peoples” bodies rather than just one, given that lungs do (somewhat) different things in different people. But, I do not think that why they came to be here is irrelevant, at least not if we wish to distinguish with a role. My fingers are currently engaged in typing, but few people would describe this as a function (although most would say that precise and controlled manipulation of the world is). Or to make a more extreme position, after Robert Hoehndorf, the heart actually does produce loud thumping noises. Surely not a function?

I am also slightly disappointed that what I think is one of the key points of my own function paper has been missed from their list of criteria. In it, I say:

I consider whether these definitions are applicable; for a given set of entities how do we decide whether we have a function (of either subclass) or a role.

Given a definition, I should be able to produce at least one practical test that I can use to determine whether that definition holds; I think that this notion of applicability needs to be more widely considered.

Now, my actual definition of biological function was:

A biological function is a realizable entity that inheres in a continuant which is realized in an activity, and where the homologous structure(s) of individuals of closely related and the same species bear this same biological function.

The language has been chosen to mirror BFO since it was in this context that the paper was addressed; I think it could be simplified and made more readable, but I was constrained by the language of BFO. Now, the first criticism on my definition is on technical grounds namely:

Lord claims that his definition is recursive rather than circular, despite the occurrence of the word “function” in the definiens.

My use of this form of definition was, of course, deliberate and partly provocative; perhaps, it is something that I should not have done, since it has muddied the water somewhat as this comment shows. In fact, it is very easy to work around this criticism by simply removing the recursion:

A biological function is a …. same species bear this same realizable entity.

The technical criticism has now gone. But I do not like the definition as much because “the same realizable entity” would in fact be a biological function. I think we avoid recursive definitions because they can be circular, but this is like avoiding recursive function calls because they may not terminate. And that is a shame, because, as with recursive function calls, I think this form of definition can be quite succinct. Consider:

A spouse is a person who is married to their spouse.

or:

A brother is a man with the same parents as their brother.

If we unwind the recursion, then we get

A brother is a man with the same parents as another man.

Again, we are hiding that reality that both men in this definition are brothers.

Of course, some recursive definitions might actually be circular, and that is less good. But if the applicability of a function is also considered then this issue goes away. I can determine if some one is a spouse or a brother given these definitions, so I see no problem.

A second criticism comes from my statment that:

Hence he concludes that among the instances of realizables that are realizables for the same type of process can be both roles and functions depending on the species the realizable’s bearer belongs to. This presents a problem for the distinction between functions and roles.

I do not think that this is a problem at all, because I say quite clearly that we can distinguish between roles and functions, but that we do this for the individual role or function not at a class level:

My definition distinguishes between the two based on the nature of the relationship to the independent continuant in which they inhere. I suggest that it is very hard to make the distinction at the class level[…]. For an individual continuant bearing a realizable entity, this distinction appears to be much more straightforward.

In otherwords, “for walking on” is either a role or a function. But in human hands it is a role, while for chimps it is a function. I see no reason why the distinction at the level of the individual should be considered to be less relavant than at the class, nor why this should be problematic. Actually, it reduces the need for duplication between the role and function hierarchies; while tools like Tawny-OWL (1303.0213) may ease the maintainence of duplication, avoiding altogether still seems sensible.

The final criticism is, I think, the least worrisome. The authors say:

Had evolution stopped after the first species, according to Lord’s definition, there would not have been any biological function at all.

The slightly flippant but none the less entirely valid argument to this is, “but it didn’t”. We could equally argue against a definition of human as having two hands on the basis that they might have evolved a third.

More importantly, though, in most definitions of life the ability to adapt or evolve is part of the definition. Without this, we have a chemical process. So, without evolution, we have no life. Given this, we can rewrite the last statement as:

Had life stopped after the first species, there would not have been any biological function at all.

Which is an entirely true statement; that it drops so nicely out of my definition for biological function is a strength of my definition and not a weakness.

I feel that my definition is still a good one. Rereading my function paper now the argument still seems coherent, and the examples clear. Although I put an entire section on applicability into the function, I do rather regret that I did not introduce it as a general criteria for all ontology definitions explicitly; that this criteria has been missed is surely my fault and not the readers. Perhaps I should have spent more time on that, than on my recursive definition which was not critical to the paper.

At the same time, the fact that discussions on definitions are still going on, for a term that biologists have been using for many years again leads me back to the conclusion that the definitions of such generic terms are not nearly as important as some make out. So long as they are useful, biologists will carry on describing things as functions if it fits their ad-hoc, informal definitions that have been developed over time within a community. I cannot help but think that this is a good thing.

Bibliography

3 Comments

  1. Chris Mungall says:

    Perhaps equally flippant but also equally valid response to the odd “what if life stopped after the first species” argument:

    “Nothing in biology makes sense except in the light of evolution” — Theodosius Dobzhansky

  2. Phillip Lord says:

    Couldn’t agree more. This is also why I think dismissing evolutionary history as “causal inert” is silly.

  3. Chris Mungall says:

    An interesting experiment would to apply both definitions to the question “what percentage of the human (or the onion, fugu, …) genome is functional?

    (this is currently the topic of a big brouhaha between ENCODE and detractors)

Leave a Reply