SHAPEThe final frontier?

Janna Hastings1 Oliver Kutz2, Mehul Bhatt2, Stefano Borgo3

1 European Bioinformatics Institute, University of Geneva2 University of Bremen, Germany

3 Laboratory for Applied Ontology, ISTC-CNR

Image credit: Jonathan J. Dickau

SHAPE is outline or form

closely related to functionacross different domains

It is a property of the whole object that may disappear in its parts

What is shape?How does shape relate to function

in natural and artificial systems?What is the relationship of the shapes of

wholes to that of their parts?How do humans and computers

perceive shape? How do humans and computers

reason about shapes?What are the puzzles of shape, and how do we

teach machines to solve them?

Parts and wholes, shapes and holesin living beings

Janna Hastings, EBI, UK; Geneva, CHColin Batchelor, RSC, UK

Stefan Schulz, MUG, Graz, Austria

Is the human hand bucket-shaped?

Bucket Human hand

Rigid structure Flexible structure -- some rigid parts, some soft parts

Similar properties at all points of structure

Different properties at different points

Only one function: to carry liquid (e.g. water)

Many functions, including to carry water

Biological reality is dynamic and multifaceted

Ontology backgroundCONTINUANT

OCCURRENTtime

participates

Image credit (cat): Panther

digestion sleeping

colour

Inde

pend

ent

Dep

ende

nt

inhe

res

weight

ability – and desire – to catch mice

Biological molecules have shapes,some are flexible

WHAT IS THE SHAPE OF CYCLOHEXANE?

BENZENE?

ATP? RIGID

FLEXIBLE

The perplexing ontology of holes(Typology according to Casati &Varzi)

TUNNEL HOLLOWCAVITYlocated in a wall part of the cheese

contained in the eggHOLE = nothing? HOLE = absence?HOLE = hole lining? HOLE = SHAPE?

SHAPE OF HOLE = shape of ideal filler“inverse” to SHAPE OF HOST

Binding sites in proteins behave like holes

Glycogen phosphorylase caffeine

another ligand(jointly inhibitory)

The minimal lining for a hole in a protein must be subatomic

Casati and Varzi : hole linings defined in terms of the surface of the host object -- the minimal part of the host object that is in contact with the external world -- the outermost part of the object … that we can “see and touch”

Hole lining = thinnest outer layer of atoms?

Hole lining = area whereelectron density of atomsis sufficiently low

Holes are granularity-dependent

CAVITY MANY TUNNELS

Cavity of stomach: Organ cavity which is bound by the internal surface of the wall of stomach

Anatomical cavities serve a protective function

CHANGE GRANULARITY

SELECTIVEFILTERING

Conclusions

Flexibility is a shape-related disposition – the disposition of an entity to change shape

(without breaking)

Explicitly taking granularity into account requires redefinition of the notion of hole lining as the disposition to resist intrusion by other objects

(at the same level of granularity)

Thank you!

Questions?

For more information:

http://cindy.informatik.uni-bremen.de/cosy/events/shapes/