Transcript AllScience_is_Comput.. - Buffalo Ontology Site

Why, in the future, all sciences
will be computer sciences
Barry Smith
Pythagoreanism
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Analogue vs. digital
Quantum physics: The world is a digital object
The science of digital objects as Master Science
All science is computer science
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~ All science is laboratory science
All intellectual disciplines are computer science
Classics
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Thesaurus Linguae Graecae
digitised versions of all extant Greek texts from
Homer to 600 AD
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Computer as (indisensable tool)
Archeology
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Registry of all extant pre-historical artefacts
History
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Cavalli-Sforza (languages, dialects, mapped to
DNA)
History
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How far can we document every single human
being in the entire history of the planet?
The Sykes’ shared Y chromosome
Scientific geneaology: The promise of
Mormonism
How far can we document every single historical
event in the entire history of the planet?
Increasingly, both linguistics and
history overlap with biology
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Medicine, too, increasingly overlaps with biology
(becomes biomedicine)
and with chemistry (the legacy of the Human
Genome Project)
(knowledge intensive vs. theory intensive
disciplines)
increasingly, all these disciplines become like
astronomy
Part I: The Human Genome Project
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Completed in 2003
Goals:
identify all the approximately 20,000-25,000 genes in
human DNA,
 determine the sequences of the 3 billion chemical
base pairs that make up human DNA,
 store this information in databases,
 improve tools for compuational data analysis
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Complexity
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About 25,000 genes in a human
100-200,000 proteins
Individual variation in most genes
100s of cell types
100,000s of disease types
From Gene to Disease
Alzheimer Pathway
Biochemical Disease Pathways
Electronic Health Records
Personalized medicine
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gene therapy / manipulation
the addition of new genes to existing humans
 the creation of new types of humans
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drugs tailored to your genetic make-up
improved efficacy
 reduced side-effects
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based on home genetic testing (the $1000
genome)
Terabytes of data
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genomics
proteomics
reactomics
metabonomics
phenomics
behavioromics
connectomics
toxicopharmacogenomics
Terabytes of data
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-omics data
biochemical disease pathway data
biomedical image data
electronic health record data
hospital management data
hospital insurance data
public health data
Chinese chicken data
The ideal of seamless communication
GALEN
GO
SNOMED
Hospital Process
Ontology
(+billing services)
Electronic
Health Record
(EHR) Data
a vast new
problem of
communication
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medical researchers, clinical practitioners,
first responders, customs agencies,
pharmaceutical companies, disease control
centers need to communicate in ways which
involve huge amounts of data
... have created a vast new
problem of communication
What happens when medical researchers, or
pharmaceutical companies, or government
healthcare agencies, work primarily with
data inside computers?
How can we overcome the incompatibilities
which arise when data from distinct sources
need to be combined, if each information
system uses its own classification ?
Answer from Tim Berners-Lee:
The Semantic Web
National Center for Biomedical
Ontology
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Stanford University Medical Informatics
Mayo Clinic
Berkeley Fly Genome Project
Cambridge University Department of Genetics
University at Buffalo Department of Philosophy