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What everybody knows but nobody says
can hurt interdisciplinary research
John V. Carlis
University of Minnesota
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“What we have here is a lack of communication”
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Messages What everybody knows, nobody says Missed (not mis-) communication:
painful surprises Plan for success
exponential growth in data beyond human scale
Yeah! good work to do invent together
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Inter-Disciplinary Research
IT-ist [CS/Eng. … /Math/Stat] Tool Builder [content neutral]
Biologist [soils/neuro/microbio/dent/biochem/ecol/vet] Content Seeker/Maker [tool user]
Surprises & Do
Inter-Alien Research
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Can an IT-ist become a Biologist or vice versa?
Well, life’s too short specialization of labor bioinformatics grad minor
CBCB in our future?
Ante-Disciplinary?
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Business Surprise User: NO! IT: but I built what you told me to build User: I gave you a typical example, but of
course there are exceptions IT: you didn’t tell me User: you didn’t ask,
and, besides, everybody knows that
worse in science – but why?
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Science for IT is harder Business – human decides complexity Science -- reality >> models Exponential growth in data Competing models Lots of vocabulary Specific vs Abstract Vocabulary sloshes
Surprises
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Surprise (1/5): Context Ph is not Ph
need to remember instrument used Annotation
Beyond genome is harder What
plus When & Where [microarray; mass spec]
harder to share/re-use data
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Surprise (2/5): Casual Vocabulary
chimp chimp + baby chimp + offspring chimp + offspring
+ close personal friend
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Surprise (3/5): Success Brings Pain Prosite’s curated protein patterns + descriptions: ~2 mb of free (con)text
human browses toooo little success tooooooo many
Genbank Obsolete fields “misc”
Parsing free text is hard & error prone
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Surprise (4/5): Vocabulary missing/overloaded/off
Text readable only by those who already know Nouns – pretty good Verbs -- Janeway’s “Immunology”:
mediate, … “Pathway” BAD diagrams
248
e.g., “metadata”
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Surprise (5/5): Idiosyncratic brain viewing Different machines,conditions &
warping parameters Fuss ‘til it looks right
a day’s work! requires scarce expertise Doesn’t scale to comparisons among images
processing plan is data too
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Can IT-ist ignore performance?
IT-ist expects specifications Short run efficiency for given specs
get it working but cycles/space cheap/available
Change? Plan for unplanned changes
not trained/rewarded attitudelack vision
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Togetherness
Communication
Anchored/Enabled/Rewarded
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Vocabulary Mantra:what do we mean by one of this type?
Data Model What to remember, not how Fine distinctions [singular/plural]
disease vs affliction host vs pathogen Multi, not single function,
so not partition cluster
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Hit Limits DBMS Extensions
“manual” brain image manipulations new content-neutral operators
“this” is a special case of what more general task
constant vector multi-hull
not “the” query;parachute in then explore territory
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Interdisciplinary Impedance Mismatch
Mundane vs interesting Messy problem (seeking insights)
vs optimal solution (irrelevant but hopeful)
Good clusters/fast algorithm/DB not directly a Bio goal
Some professional danger but big potential reward
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Good Work Expect to struggle to communicate
invent vocabulary define verbs
Seek visionary colleagues
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