Biomod/2011/SRISHTI/ArtScienceBangalore/Notebook

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Notebook

INTRO:

This is a collection of some of our research and ideation that took place during the design workshop conducted by Yashas Shetty, Catherine Kramer and Zack Denfeld. During this stage of our process we tried to understand the context of nanotechnology and the historical relationship between technology, society and metaphors.

We collected exemplars of each, used mind map to assemble and categorize matters of concern, and tested out a range of design possibilities.

Readings

http://www.pnas.org/content/107/51/21996.abstract - All-DNA finite-state automata with finite memory

DNA nanomachines

JONATHAN BATH AND ANDREW J. TURBERFIELD*

We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specifi c interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specifi c signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.

All-DNA finite-state automata with finite memory

Zhen-Gang Wanga,1, Johann Elbaza,1, F. Remacleb, R. D. Levinea,c,2, and Itamar Willnera,2

Biomolecular logic devices can be applied for sensing and nano- medicine. We built three DNA tweezers that are activated by the inputs Hþ ∕OH− ; Hg2þ ∕cysteine; nucleic acid linker/complemen- tary antilinker to yield a 16-states finite-state automaton. The outputs of the automata are the configuration of the respective tweezers (opened or closed) determined by observing fluorescence from a fluorophore/quencher pair at the end of the arms of the tweezers. The system exhibits a memory because each current state and output depend not only on the source configuration but also on past states and inputs.


An autonomous molecular computer for logical control of gene expression

Yaakov Benenson1,2, Binyamin Gil2, Uri Ben-Dor1, Rivka Adar2 & Ehud Shapiro1,2

Early biomolecular computer research focused on laboratory- scale, human-operated computers for complex computational problems1–7. Recently, simple molecular-scale autonomous pro- grammable computers were demonstrated8–15 allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologi- cally active molecules as outputs, could produce a system for ‘logical’ control of biological processes. Here we describe an autonomous biomolecular computer that, at least in vitro, logi- cal l y anal yses t he level s of messenger RNA speci es, and in response produces a molecule capable of affecting levels of gene expression. The computer operates at a concentration of close to a trillion computers per microlitre and consists of three programmable modules: a computation module, that is, a stochastic molecular automaton12–17; an input module, by which specific mRNA levels or point mutations regulate software molecule concentrations, and hence automaton transition prob- abilities; and an output module, capable of controlled release of a short single-stranded DNA molecule. This approach might be applied in vivo to biochemical sensing, genetic engineering and even medical diagnosis and treatment. As a proof of principle we...


Nanotech & Metaphors

Some of the metaphors currently employed or important to nanotechnology include:

  • Casting Spells
  • Magic
  • Living Factories / Foundaries
    • Send the Acorn, Not the Tree
    • Computers that grow
    • E-Wate: We have a problem with computers that DO NOT KNOW HOW TO DIE
  • Speed of Computing (Keeping up with Moore's Law)
    • It's fast: But what is it for?!?
    • We Know What Technology DOES, But what is it for?!?
    • The World's Slowest Computer
  • Xeno's Paradox of Reality
    • Borges -> The Map is Not The Terrain
  • Jevon's Paradox of Biocomputing / Simulation?

http://hackteria.org/wiki/images/4/4b/Dream-machines-new-freedoms-minority-report.png

Paul Rothemond TED Talk Notes

http://hackteria.org/wiki/images/d/d1/P_z_ted_1.png

While watching the Paul Rothemond's TED talk these are some of the thoughts and questions that arose.

Movies to watch: Blade runner

Ted talks to watch:

http://www.ted.com/talks/lang/eng/paul_rothemund_casts_a_spell_with_dna.html

http://www.ted.com/talks/lang/eng/paul_rothemund_details_dna_folding.html

Books to read:

Shaping things Cradle to cradle

Research James King

Thoughts to write about:

What is life?

Can life be categorised by reproduction, metabolism and/or evolution?

“Life performs computation” How does that quantify or qualify life?

What are your views on metaphors, are they serious, can they be taken seriously?

Who is “Watson” in the field of nanotechnology?

When altering DNA “a sensitivity to small changes – single mutations - that result in ”meaningful” large changes”, what are the consequences, what does it take to alter DNA to produce a desires mutation?

File:P z ted 1.png

How accurate is the comparison between DNA alterations to the binary system in banking?

“Can we write molecular programs to build technology?”

File:P z ted 2.png

What is the difference?

File:P z ted 3.png

Is like about computers building computers?

Today how long do you use a cell phone?

Was it designed obsolesce? So in a way it was designed to die? What does it mean for a phone to die?

In the future if it was possible to grow a phone from a seed, when would the phone know when to stop growing and when would it know to die, and how to die?

Research “Lifecycle Analysis” How would or could this change with the introduction of molecular programming? What would the death of a product mean?

Why DNA? Because “DNA is the cheapest, easiest to understand and the easiest to program material” to create Nano scale computers. What is your opinion of this?

Look for the Moore’s Law Graph, one that validates that if it were to be true where nanotechnology would have to kick in.

What is innovation?

Can you write a nano virus?

Look up Tony Fry, What are his views on the designers of the future?


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