Ontologies of biology
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Ontologies of biology
Fri, 04/09/2015 - 11:15 to 12:15
Location:
Speaker:
Prof. Julian Vincent
Affiliation:
University of Oxford
Synopsis:
The best known biological ontology must be the Gene Ontology. But this concerns only a very small, although important, area of biology. Other ontologies cover cell types, insects such as the fly, plants, ecology, taxonomy.
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.
Molecules and structures form different degrees of association at different levels of complexity. Taxonomy might be seen as easy, but there are many different types of species and forms of speciation.
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?
Biography:
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.