Unicorns in my Ontology

A realist ontology only represents portions of reality; that is, classes of things that really really have instacnes out there in this one world in which we live. I’m told that if I’m not a realist, then I’m prepared to have unicorns in my ontology; that is, just fil the ontology up with nonsense. I’m not a realist and I’ve been criticised for therefore being willing to have unicorns in my ontologies. whilst I try and describe entities in biology, I have to deal with things that seem problematic from the realist perspective (I was involved with Phil Lord in writing a paper about some of these points). colour models, numbers, mathematics, all appear to create more heat than light from a realist perspective. I also remain to be convinced that I need a true account of numbers, units etc. just to be able to describe biological phenomena. the critical thing is a common way of doing it and this is not the same as saying the only way to achieve that common approach is to capture the “reality” of numbers and units and so on.

Here are several unicorns that I’m happy to have in one of my ontologies that apparently make my ontologies poora :

  1. Newtonian mechanics works well enough for virtually everything I need to model. However, modern physics tells us that Newtonian mechanics and the separation of time and space is not correct. We should model with only space-time. This makes life too hard for no apparent benefit, except at the very big and very small and most of the time it doesn’t matter. So, I’m happy to have the unicorn of separate classes for time and space in my ontology. It is worth noting that BFO takes this approach as well; so, BFO has unicorns and is thus “a bit realist”.
  2. My second unicorn is the cannonical anatomy. Typically, anatomies describe a cannonical organism; some idealised version of the organism. Of course, the ideal, for example, human being does not exist. So, cannonical anatomies describe an entity that doesn’t exist — another unicorn. Like space and time, the realist ontologies of OBO also model this non-existent entity. I’m happy to have the unicorn of the cannonical anatomy.
  3. My third unicorn are qualities of processes or occurants. BFO tells us that processes do not have qualities. This means, for instance, that a reaction cannot have a rate or velocity. The examples of this in biology and beyond are too numerous to even begin to properly enumerate. Again, we’re told that, according to BFO, that occurants cannot have qualities, so anything described like this doesn’t exist….; another unicorn.
  4. The Higgs boson and the graviton are conjectured to exist. I’m happy to place a class of Higgs boson into my ontology underneath sub-atomic particle, if that is the prevailing view of physicists. We have no evidence, other than the theoretical conjecture, for the particle, but it fits into the current models of sub-atomic physics. One should annotate the class with information about its status, but it is a useful class — I will wish to describe experiments from the large hadron Collider as to what they are about or for what they are looking — the Higgs Boson. I don’t need the overhead of putting Higgs boson under some hypothesis in some information ontology, though I might be willing to have a hypothesis about my Higgs boson that is a kind of sub-atomic particle. I do need to ask questions such as “describe the experiments that are about sub-atomic particles”; I don’t think I need the overheads of an ontological account of the reality of the Higgs Boson being a hypothesised class; I can just label the class as being hypothesised or putative or unproven.

Our amino acid ontology is full of simplifying assumptions that make it non-realist. It is full of arbitary defined classes combining the attributes of charge, polarity, aliphatic/aromatic side chain, size (a simple value partition that wil not be “real”), hydrophobicity, and so on. For instance, how we talk about charge is a simplifying assumption. Aimino acids have different charges in diffeerent conditions, but it is convenient to talk, for instance, of lysine having a positive charge; it helps biochemists explain its role in proteins.

As has been observed by others, a realist approach to modelling a domain is fraut with issues. Even ontologies that claim a realist stance cannot really claim to be properly realist with non-existent anatomies and useful, but untrue, simplifying assumptions about physics. Any non-real entity makes an ontology not a realist ontology, just as one cannot be a bit pregnant.

Such useful untruths may be practical, but the need to compromise on reality so we can have practicality is all too telling for a reality only approach; practicality will make an ontology non-realist. We need practicality in capturing what we need to say to accomplish what we need to do in describing our data. We don’t describe real entities very much, we describe data bout real entities; collections of those entities; approximations and smears of probability about entities. Precise simple rules are all very good, but when a complex world has to be changed in order to fit the simplistic model, things have gone wrong.

Simple messages are, however, easier than complex messages; compromise is always a bit mealy mouthed. The criteria for pragmatism and the rules that govern it are woolly, but we do need to move away from “just ask the guru” or “I feel it in my bones” – something that is all too common in bio-ontology building at the moment. The pragmatics agenda will be developed.

Advertisements

10 Responses to “Unicorns in my Ontology”

  1. Mikel Egaña Says:

    I agree.

    And I’m a big LHC fan 🙂

  2. Matthew Says:

    Science is really all about coming up with and then doing the experiments that let us discover which ideas are the unicorns and which are the horses. Any representation of scientific knowledge that goes beyond simply cataloguing perceived scientific truth must take this into account. In short, if you construe ontologies by definition to rule out describing unicorns then you can’t usefully describe science. It may work for natural history, and perhaps for some people these are the same thing.

  3. An Exercise in Irrelevance » Blog Archive » The Pici Principle: What you should not say Says:

    […] has described the problems that this causes by preventing the ontologist from modelling “unicorns“, such as Newtonian mechanics, or canonical anatomies. The unicorn principle says, if it is […]

  4. Managing synonomy in OWL | Ontogenesis Says:

    […] it is unclear whether “brimstone” should be considered a synonym of sulphur, or a mythical substance of historical, rather than scientific […]

  5. An Exercise in Irrelevance » Blog Archive » Semantics-Free Ontologies Says:

    […] The problems of identifiers and their semantics are not new. I have written about these problems previously in the context of: blog permalinks (http://www.russet.org.uk/blog/2011/05/permalink-semantics/); and with conversion between OBO format and Manchester syntax (http://www.russet.org.uk/blog/2009/09/obo-format-and-manchester-syntax/). The basic issue is one of choosing your compromise. Identifiers with semantics in them (which this blog uses although I wish it did not) are considerably more human readable, but are not resiliant to change, as the semantics in the identifiers can become out of date with respect to the content they describe. But neither compromise is entirely satisfactory; we need a more pragmatic approach (https://robertdavidstevens.wordpress.com/2011/05/26/unicorns-in-my-ontology). […]

  6. Background: Standards as a shared structure for data (Thesis: 1.4) « the mind wobbles Says:

    […] Stevens. Unicorns in my Ontology, May […]

  7. Background: What are ontologies? (Thesis 1.5) « the mind wobbles Says:

    […] Stevens. Unicorns in my Ontology, May 2011. Share this:TwitterMoreFacebookEmailDiggRedditPrintStumbleUponLike this:LikeBe the […]

  8. An Exercise in Irrelevance » Blog Archive » Programming OWL Says:

    […] approach we are taking at the moment, toward the pragmatic environment that I and others (https://robertdavidstevens.wordpress.com/2011/05/26/unicorns-in-my-ontology/) feel we […]

  9. An Exercise in Irrelevance » Blog Archive » OWL Concepts as Lisp Atoms Says:

    […] language, which should enable us to build a more pragmatic ontology building methodology (https://robertdavidstevens.wordpress.com/2011/05/26/unicorns-in-my-ontology/). The first of these is a unit testing environment. Clojure already has one of these integrated. So […]

  10. Tim Clark Says:

    As Lavers points out in _The Natural History of Unicorns_ (New York: Harper, 2010), the unicorn was originally described by Ctesias in 398 BC from reports of travelers in the Middle East, and was simply an erroneously described piece of natural history conflating various animals seen imperfectly at a distance.

    The descriptive errors were corrected over time while the fantastic elements took on a life of their own.

    Robert is right to suggest that forbidding unicorns in ontology means proscribing first approximations and useful simplifications. It also makes ontologists responsible for determining scientific truth – a fantastic notion if ever there was one.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s


%d bloggers like this: