Ontologies of biology

Start: 
Fri, 2015/09/04
Location: 
Heriot-Watt University, Edinburgh, UK

An ontology is well suited for a hierarchical system such as a living organism, going from atoms and small molecules, through polymers, cells, tissues, organs, organisms, etc.  Depending on the fineness of separation of the hierarchies, up to 20 levels can be recognised in a rainforest. However, the heritability which occurs from class to sub-class to sub-sub-class, etc, has to be carefully managed.

The philosophical rigour which people like Barry Smith try to impose is not recognised by biology, and can result in the inability to define a state for a species since the biological system of inheritance means that offspring are always different from their parents. Some of these difficulties will be illustrated in an ontology of biomimetics, which compares biology and technology. Can it ever work?

Time: 4th of September - 11:15am - Earl Mounbatten Building EM2.43

Details of the invited speaker:
Julian Vincent is a biologist who got taken up by materials science, biomimetics, engineering, and sustainability, the one leading inexorably into the next.  He regards his 40 years in academia (first as a zoologist in Reading, then as a mechanical engineer in Bath) as his apprenticeship. He is currently trying to bring all these strands together into a model of biomimetics based on the concept that the evolution of organisms is an unbroken trail of pragmatic solutions to the problems of existence. This is expressed in an ontology that uses the Russian system TRIZ as a function-based guide to the identification of the Hegelian dialectic: thesis---antithesis---synthesis. Out of this will come - he hopes - a design guide that can direct technology into greater responsiveness to its immediate environment. Which is, of course, what genes do.

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salustri's picture

The thing about

The thing about ontologies...

...is they don't actually exist in nature.  They're mental/logical constructs that we use to organize knowledge for the sake of managing it, abstracting it, and, ultimately, using it better.

And since nature tends to pay little attention to what is cognitively convenient for humans, it's not surprising that it's very hard to generate an ontology suitable for biological entities/systems.

There is no question ontologies are a great way to capture knowledge formally. The question is, IMHO, how to do it for biosystems while preserving the advantages that ontologies are supposed to provide.

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