Ontologies in Physics and Chemistry

My colleague Nico Adams has just posted on ontologies (Ontologies are overrated?!?)

Here’s a video by the indefatigable Michael Wesch and done in his inimitable style, arguing that maybe ontologies are not needed anymore and that the shelf is obsolete in the area of digital information. In the blurb next to the video it says:

“This video explores the changes in the way we find, store, create, critique, and share information. This video was created as a conversation starter, and works especially well when brainstorming with people about the near future and the skills needed in order to harness, evaluate, and create information effectively.”

 

[NA] It ties in with arguments made by Weinberger and even gels nicely with a short “after-dinner” talk I gave recently. Are you committing ontological apostasy now, I hear you ask? And you have only just blogged about ontology development methods.Will I incur Aristotle’s wrath? No, I don’t think so….ontologies are still useful if they are used to provide a general frame of reference that describes both likeness and limits of likeness. As long as we appreciate that there may be more than one top node…..
PMR: I’ll know more when the video appears, but also to say that Nico did, indeed, give a nice after-lunch talk with cleverly aggregated visual material.
PMR: I also bumped into the problems of ontologies when talking with Michael Kohlhase last week on PhysML. a language to support physics, developed by Michael and Ebs Hilf and in close conjunction with the OpenName (OM) community. We are working together to make PhysML, MathML and CML interoperate. Some of this is technical, some is ontological.
It may be that physicist think in terms of perdurants and chemists in terms of endurants. Here’s Wikipedia:

Common Terms in Formal Ontologies

The Difference in terminology used between separate Formal upper level ontologies can be quite substantial, but the one and foremost Dichotomy most Formal upper level ontologies apply is that between ‘Endurants’ and ‘Perdurants’.

Endurant

Also known as continuant, or in some cases ‘substance’. Endurants are those entities that can be observed-perceived as a complete concept, at no matter which given Snapshot of time. Were we to freeze time we would still be able to perceive/conceive the entire endurant. Examples are material objects, such as an apple or a human, and abstract ‘fiat’ objects, such as an organisation or the border of a country.

Perdurant

Also known as occurrent, accident or happening. Perdurants are those entities for which only a part exists if we look at them at any given snapshot in time. When we freeze time we can only see a part of the perdurant. Perdurants are often what we know as processes, for example ‘running’. If we freeze time then we only see a part of the running, without any previous knowledge one might not even be able to determine the actual process as being a process of running. Other examples include an activation, a kiss, or a Procedure.

PMR: Ebs and Michael had reviewed CML and questioned why the key concepts were atoms, molecules, electron, substances, whereas they suggested it would have been better to start from reactions. I think that’s a very clear difference in orientation between endurants and perdurants. Although chemists publish reactions, most of the emphasis is on (new) substances and their properties. CML is designed to map directly onto the way chemists seem to think – at least in their public communication – e.g. through documents. Of course we can also do reactions in CML, but even there the emphasis is often on the components. For my part it has been a useful change of vision to see how the physicists think. Michael will correct me but there are three basic components:

  • create a theory (this can be quite a general term)
  • devise an experiment to test it
  • collect observations (observable) and give the allowable error limits

There is no set list of material endurants (I think) – such as apparatus or material. These are described by dictionaries as and when required.
In our discussions we explored the difference in thought between the formal representation of a chemical equation with a formula for the rate (constant). For a mathematician it must be formally correct. For a chemist it must be useful and work. Both are desirable, but the real world probably requires a compromise.

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