The SHAPES workshop, and Holes in living beings
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Transcript of The SHAPES workshop, and Holes in living beings
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/