-arrestins in GPCR Desensitization How Lisp Will Save the World - - PowerPoint PPT Presentation

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-arrestins in GPCR Desensitization How Lisp Will Save the World - - PowerPoint PPT Presentation

Sep 14, 2023 362 likes •995 views

-arrestins in GPCR Desensitization How Lisp Will Save the World 15,596 abstracts 15 abstracts 15,596,125 abstracts Cyanobacteria http://www.anselm.edu/homepage/jpitocch/genbios/27-11x1-Cyanobacteria.jpg Prochlorococcus

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ß-arrestins in GPCR Desensitization

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How Lisp Will Save the World

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15 abstracts 15,596 abstracts 15,596,125 abstracts

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Cyanobacteria

http://www.anselm.edu/homepage/jpitocch/genbios/27-11x1-Cyanobacteria.jpg

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Prochlorococcus

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Tools for Thought

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Qualitative Quantitative Not enough data

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Qualitative Quantitative Not enough data Can’t do “operating logics”

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ß-arrestins in GPCR Desensitization

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Qualitative Quantitative Not enough data Can’t do “operating logics” Not expressive enough

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Parts Processes Dynamics Operating Logic

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RNA polymerase is a huge factory with many moving parts. The one shown here, from PDB entry 1i6h, is from yeast cells. It is composed of a dozen different proteins. Together, they form a machine that surrounds DNA strands, unwinds them, and builds an RNA strand based on the information held inside the DNA. Once the enzyme gets started, RNA polymerase marches confidently along the DNA copying RNA strands thousands of nucleotides long.

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ß-arrestins in GPCR Desensitization

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www.biocarta.com

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Eukaryotic protein translation www.biocarta.com

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Action of PPARa, PPARb(d) and PPARg and effects on gene expression www.biocarta.com

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Granzyme A mediated Apoptosis Pathway www.biocarta.com

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Multi-step Regulation of Transcription by Pitx2 www.biocarta.com

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Cell Cycle: G2/M Checkpoint www.biocarta.com

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p53 Signaling Pathway www.biocarta.com

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Double Stranded RNA Induced Gene Expression www.biocarta.com

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Photosynthesis (light reactions)

PhotoSynthesis PhotoSynthesis (light reactions) (light reactions)

http:// http://www.bio.ic.ac.uk/research/barber/photosystemII.html www.bio.ic.ac.uk/research/barber/photosystemII.html

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How Lisp Will Save the World

Biological models are complex webs of parts, processes, dynamics, and operating logics.

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How Lisp Will Save the World

Biological models are complex webs of parts, processes, dynamics, and operating logics. The expressions in these models range over both qualitative and quantitative value spaces.

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Prochlorococcus

Only 1700 Genes!

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ß-arrestins in GPCR Desensitization

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Qualitative Quantitative

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Causal/Regulatory Model Causal/Regulatory Model

DFR DFR NBLA NBLA NBLR NBLR RR RR Photosynthetic Photosynthetic activity activity PBS PBS Health Health

  • +

+ + + + +

  • psbA1

psbA1 psbA2 psbA2 cpcB cpcB + + + +

  • Light

Light + +

Shrager, et al. (2002) Shrager, et al. (2002)

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“little b”, aneil mallavarapu

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http://qr05.tugraz.at/files/p18.pdf

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ß-arrestins in GPCR Desensitization

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How Lisp Will Save the World

Biological models are complex webs of parts, processes, dynamics, and operating logics. The expressions in these models range over both qualitative and quantitative value spaces.

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Prochlorococcus

Only 1700 Genes!

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Biologists base their theories about what something does upon what

  • ther biologists think some other

things that look similar do.

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Homology of hexokinase across species:

www.bio.davidson.edu/Biology

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High-Resolution Solution of a Potassium Channel www.pdb.org

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High-Resolution Solution of a Potassium Channel www.pdb.org

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Biologists base their theories about what something does upon what

  • ther biologists think some other

things that look similar do.

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Cyanobacteria

http://www.anselm.edu/homepage/jpitocch/genbios/27-11x1-Cyanobacteria.jpg

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?

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The Fiction of Function

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Gene Ontology Gene Ontology

From GenNav, the NIH Gene Ontology Browser

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View Application

Transport Ions pH Gradient Phosphorylation pH gradient driven ion Transport phosphorylation

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How Lisp Will Save the World

Biological models are complex webs of parts, processes, dynamics, and operating logics. The expressions in these models range over both qualitative and quantitative value spaces. Creating such models requires being able to compare and combine submodels.

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How Lisp Will Save the World

Biological models are complex webs of parts, processes, dynamics, and operating logics. The expressions in these models range over both qualitative and quantitative value spaces. Creating such models requires being able to compare and combine submodels.

Each of these Demands Symbolic Computing

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Prochlorococcus

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Photosynthesis: The Photosynthesis: The “ “Turing Test Turing Test” ” of

  • f

biological knowledge representation biological knowledge representation

PhotoSynthesis PhotoSynthesis (light reactions) (light reactions)

http:// http://www.bio.ic.ac.uk/research/barber/photosystemII.html www.bio.ic.ac.uk/research/barber/photosystemII.html

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Where Prochlorococcus Go; The BioSphere Follows!

Chlorophyll loading (NASA)