Biology {Cookbook}

Recipes - Tools - Community and Events - References - Inspiration - To do

Recipes

• Cell : a universal distributed 3D printer, not just an extremely impressive bulding block
  • A cell gets code in, puts structure out, the organism own growth is the result of a set of "tiny synchronized printers" that print it over and over again
    • Wikipedia:Ontogeny, Wikipedia:Asymmetric cell division, see also MyAphorisms#PerpetualSelfRebuilding
  • Cells have the blueprint code as DNA and make a complex network in 3D through which other type of information go through including chemical messaging (over synapses, immunitary network), electrical messaging (over nerves), etc.
    • DNA is a binary chemical code and blueprint because this code describe what proteins the cell should assemble
    • Wikipedia:Autopoiesis Wikipedia:Cell potency Wikipedia:Nerve fiber
  • consequently I think it can be the ideal architectural model for Seedea:Oimp/VirtualAtelier and Cookbook#BuildAction
    • which could also benefit from LayeredModel
    • the idea of the universal printer seems to also be developped in Gregory Chaitin's work on metabiology
• ColorChangingFlower plants to have different flowers cycliquely
• DIY Health#PersonalGenomics

Metabiology

Some papers have been read after initially discovered WithoutNotesOctober10#MathematicsBiologyAndMetabiology and should be linked here.

• Chaitin: Mathematics, Biology and Metabiology
  • random walk model was inspired by the stimulating critique of Darwinian evolution in The Devil's Delusion by D. Berlinski, Crown Forum 2008
• several papers at G J Chaitin Home Page, University of Maine
  • Metabiology: life as evolving software (162p) 21/09/2010
    • a field parallel to biology, dealing with the random evolution of artificial software (computer programs) rather than natural software (DNA), and simple enough that it is possible to prove rigorous theorems or formulate heuristic arguments at the same high level of precision that is common in theoretical physics.
  • On Turing, Creativity and Metabiology (8p) 21/09/2010
    • Remarks on Alan Turing's oeuvre for the book Alan Turing, His Work and Impact edited by S. Barry Cooper and Jan van Leeuwen.
  • To a mathematical theory of evolution and biological creativity (22p) 29/09/2010
    • We present an information-theoretic analysis of Darwin's theory of evolution, modeled as a hill-climbing algorithm on a fitness landscape.
  • To a mathematical theory of evolution and biological creativity (23p) 30/09/2010
    • We present an information-theoretic analysis of Darwin's theory of evolution, modeled as a hill-climbing algorithm on a fitness landscape.
  • Metaphysics, Metamathematics and Metabiology (10p) 30/09/2010
    • In this essay we present an information-theoretic perspective on epistemology using software models.
• probably going back as early as 1970 with AIT and Life
• see also Programming, WithoutMiracles, ProgrammingTheUniverse, MyBeliefs, ScanningNotes, ScanningNotes#ScienceFromFisherInformation

Tools

• BiOS A framework to collaboratively solve our shared challenges.
• OpenPCR DNA printing for everyone
• partsregistry.org the Registry of Standard Biological Parts
• BioBrick Studio integrated development environment (IDE) that facilitates review, annotation, design, and implementation of standard biological parts from non-standard DNA, RNA, and protein sequences
• OpenWetWare an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.
• DNA2.0 Gene Synthesis and Synthetic Gene Applications - Fastest Gene Synthesis Service

Community and Events

• Free Fermentology Foundation in Paris
• Ginkgo BioWorks
• Institut Pasteur in France
• arkfab appropriate biotech collective located in Atlanta
• Synthetic Biology 4.0 Conference, October 2008
• DIYbio aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety.
• BiO Community Cluster (BioCC)
• Livly non-profit company that aims to create true, sustainable cures for the major diseases plaguing humankind.
• Biocurious weblog about biology. Quantified.
• Futurefarmers people who know how to sew, cooks and bus drivers with a common interest in creating work that challenges current social, political and economic systems.
• WWOOF World Wide Opportunities on Organic Farms
• Reclaim the fields
  • Bulletin RtF nº1

References

• Synthetic Biology Engineering Research Center (SynBERC) develop the foundational understanding and technologies that will allow us to routinely build large numbers of useful biological systems from standard interchangeable parts.
• Do-It-Yourself Biology by Natalie Kuldell and Reshma Shetty, MIT World 2009
• my notes on Intelligent Bioinformatics : The Application of Artificial Intelligence Techniques to Bioinformatics
• my links on Biobazaar and related topics in the research bibliography
• Protocells Bridging Nonliving and Living Matter, MIT Press 2008

Inspiration

• previous discussion in #hplusroadmap on freenode about bioengineering
• Synthetic Biology Extended Interview with Drew Endy of Stanford University and Decoding Synthetic Biology

To do

1. integrate Chemistry
2. add links to other mad scientists pages like http://www.madsci.org/
3. check
   1. Agrarian Studies - Synthetic Work at the Cutting Edge by James C. Scott and Nina Bhatt, Yale University Press 2001
4. The Epigenome at a Glance, The University of Utah 2009
   1. more generally http://learn.genetics.utah.edu/

• Interactorium, Skyrails Blog 2009
• Eduardo Kac's Bio Art Transgenic works and other living pieces
• Algorithmic Botany website of the Biological Modeling and Visualization research group in the Department of Computer Science at the University of Calgary
• Next Generation Genomics: World Map of High-throughput Sequencers
  • discovered through http://www.top500.org and later on CollegeDeFranceColloqueDeRentree2010#JeanLouisMandel

1. favorite protein Wikipedia:Protein kinase M zeta

• check The Biocomplexity Institute at Indiana University
• OpenPCR

Categories

• Biology