Why, in the future, all sciences will be computer sciences Barry Smith

Pythagoreanism Analogue vs. digital Analogue vs. digital Quantum physics: The world is a digital object Quantum physics: The world is a digital object The science of digital objects as Master Science The science of digital objects as Master Science

All science is computer science ~ All science is laboratory science ~ All science is laboratory science All intellectual disciplines are computer science All intellectual disciplines are computer science

Classics Thesaurus Linguae Graecae Thesaurus Linguae Graecae digitised versions of all extant Greek texts from Homer to 600 AD Computer as (indisensable tool) Computer as (indisensable tool)

Archeology Registry of all extant pre-historical artefacts Registry of all extant pre-historical artefacts

History Cavalli-Sforza (languages, dialects, mapped to DNA) Cavalli-Sforza (languages, dialects, mapped to DNA)

History How far can we document every single human being in the entire history of the planet? How far can we document every single human being in the entire history of the planet? The Sykes’ shared Y chromosome The Sykes’ shared Y chromosome Scientific geneaology: The promise of Mormonism Scientific geneaology: The promise of Mormonism How far can we document every single historical event in the entire history of the planet? How far can we document every single historical event in the entire history of the planet?

Increasingly, both linguistics and history overlap with biology Medicine, too, increasingly overlaps with biology (becomes biomedicine) Medicine, too, increasingly overlaps with biology (becomes biomedicine) and with chemistry (the legacy of the Human Genome Project) and with chemistry (the legacy of the Human Genome Project) (knowledge intensive vs. theory intensive disciplines) (knowledge intensive vs. theory intensive disciplines) increasingly, all these disciplines become like astronomy increasingly, all these disciplines become like astronomy

Part I: The Human Genome Project Completed in 2003 Completed in 2003 Goals: Goals: identify all the approximately 20,000-25,000 genes in human DNA, 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, determine the sequences of the 3 billion chemical base pairs that make up human DNA, store this information in databases, store this information in databases, improve tools for compuational data analysis improve tools for compuational data analysis

Complexity About 25,000 genes in a human About 25,000 genes in a human ,000 proteins ,000 proteins Individual variation in most genes Individual variation in most genes 100s of cell types 100s of cell types 100,000s of disease types 100,000s of disease types

From Gene to Disease

Biochemical Disease Pathways Alzheimer Pathway

Electronic Health Records

Personalized medicine gene therapy / manipulation gene therapy / manipulation the addition of new genes to existing humans the addition of new genes to existing humans the creation of new types of humans the creation of new types of humans drugs tailored to your genetic make-up drugs tailored to your genetic make-up improved efficacy improved efficacy reduced side-effects reduced side-effects based on home genetic testing (the $1000 genome) based on home genetic testing (the $1000 genome)

genomics genomics proteomics proteomics reactomics reactomics metabonomics metabonomics phenomics phenomics behavioromics behavioromics connectomics connectomics toxicopharmacogenomics toxicopharmacogenomics Terabytes of data

-omics data -omics data biochemical disease pathway data biochemical disease pathway data biomedical image data biomedical image data electronic health record data electronic health record data hospital management data hospital management data hospital insurance data hospital insurance data public health data public health data Chinese chicken data Chinese chicken data Terabytes of data

The ideal of seamless communication Electronic Health Record (EHR) Data Hospital Process Ontology (+billing services) SNOMED GALEN GO

a vast new problem of communication medical researchers, clinical practitioners, first responders, customs agencies, pharmaceutical companies, disease control centers need to communicate in ways which involve huge amounts of data 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 Stanford University Medical Informatics Stanford University Medical Informatics Mayo Clinic Mayo Clinic Berkeley Fly Genome Project Berkeley Fly Genome Project Cambridge University Department of Genetics Cambridge University Department of Genetics University at Buffalo Department of Philosophy University at Buffalo Department of Philosophy