Biomod/2011/SRISHTI/ArtScienceBangalore/Notebook

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NOTEBOOK INTRODUCTION

This is a collection of some of our research and ideation that took place during the design workshop conducted by Yashas Shetty, Cathrine 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.


Contents

Actor Network Mapping Exercise

After discussing a range of ideas from Science & Technology Studies and the Anthropology of Science we did a workshop about Actor Networks. Here were some of the basic mindmapping on Nanotech and Biomod:

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We then went on to do a second mind map on how success is defined in this space. Success for who? How is it defined and assessed?

MITS ALTAIR-To start with!

VINTAGE COMPUTERS : http://www.vintagecomputer.net/altair-poptronics.cfm

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Mitsaltair.jpg

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Visiting Lecture by Yamuna Krishnan

On Wed. Sept. 14th 2011 Krishnan from NCBS visited the Srishti BioMod team.

Her talk was First Blueprint, Now Bricks: DNA is Construction Material on the Nanoscale


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Here are some of the notes:

SCALE & THE FRACTAL DIMENSION

• We can Create Architecture using DNA

• HOW SMALL IS SMALL? Seemingly every Nanotech talk starts with zooming in and talking about Order of Magnitude

• What are the metaphors that are constructed in showing the scale shift: Power, Delicate, Fragile

• As a comparison from Art/Cultural History: Buckminster Fuller Breathes on a Golf Ball and says something like "the dew from my breath is all of the freshwater on the planet. So take care….

• Is there a Fractal Dimension in nanotechnology. i.e. we have been talking about the cell as a city or a computer, but we also talk about the planet/Gaia as a city or a computer, how do these scales relate to each other?

• Where does EMERGENCE happen - If the cell is an upward metaphor of the world (LIke body metaphor for the world) there is no emergence at the nano scale

• Architecture is the human extension of Geology "Make Architectures Out of Something" see Delanda on Arch. As Geology - Moving Rocks / Inorganic Material Around (Perhaps in Permaculture Architecture IS a Tree not a rock)


COMPLEXITY & CONTROL

• Do Chemists like Emergence & Complexity. Control?

• Self Assembly in an expected way, but what about in an unexpected way?

• How many interacting nano-switches would you need in order to have EMERGENT/COMPLEX BEHAVIOR?

• Escaping the Overcode

• Not Control but Surprise/Variation

• DNA Crystals - Self assembling

• How will you know/ would one recognize complex behavior.


HCI OF NANOTECHNOLOGY

• Which leads to the question: Who is Nanocomputing for?

What are the HCI implications for Nanocomputing?

• How does it include / exclude non-human actors and matters of concern?


TECHNOLOGY IS MAGIC

• " We don't need a reason to do Science & Art - We Do it b/c We are Human "

• Technology: So Much a Part of Life you don't notice it. Any sufficiently sophisticated technology can not be distinguished magic.

• As long as you are noticing technology it hasn't quite integrated itself.


TWO WAYS OF LOOKING AT TECHNOLOGIES

• Architecture: Make constructions that reflect your way of seeing the world

• Technology: A mode of communication

• Switching Devices: What kinds would you use?


APPROPRIATE NANOTECHNOLOGY?

• Tool-Making: recreating all of the functionalities of MacroTech on the NanoScale.

• But what if the current technology doesn't do what we want it too?


HOW DO YOU USE DNA NANORODS ON THE NANOSCALE?

• Persistence Length = 50 nm

• Nature has given us a bunch of rigid rods

• DNA - Sugar Phosphate backbone

• Glue - Sticky end

• Has a code attached to it in the order of the bases (cryptography)


ARCHITECTURE STYLES

• Rigid Scaffolds or Dynamic Objects (Undergo transitions and is reversible)

• Scienctists have to be showing that they are doing useful things

• RIGID // Basket - Rigid but has utility

• DYNAMIC // Scissors


History of NanoTech

• DNA can be cut, pasted & copied

• Molecular Biologists knew about this 40 & 50 years ago

• 2 Ways in which you can do SCIENCE

• Mode of DISCOVERY (ASking a Question - Biology)

• Mode of INVENTION (Create new things for the joy of creating new things - Chemist)

• Taking things of lower value and joining them together and making things of more value

• Who is the patron? Who allows / prevents the creation of new things


Tools Available

• You need to be able to manipulate this material to make new things

• DNA-cutting enzymes

• DNA-pasting enzymes

• DNA-copying enzymes (amplify)

• You can do with DNA with what you could do with Microsoft Word


Why This Took Off (in Chemistry)

• You are not restricted to the DNA that nature provided you

• Ability to make DNA artificially in a chemistry lab

• MH Caruthers, SCience, 1985, 230 , 281-285

• Frustrated Chemistry - cathch A + B and make them react

• ZJ Gardener, Nature 2004, 431


DNA scaffolds in 1D

• You can spatially arrange things so they won't see each other

• POsition things not he same or opposite sides of pillars

DNA ORAGAMI - SHOULD BE CALLED DNA KNITTING!

  • (Not Manly Enough?)
  • A long piece of string wrapped on itself
  • Flowers on a string - wrap in the shape as a pixel
  • Scared to see Millions of Smiley Faces


DNA Architecture with 2D Scaffolds

  • Gold NanoParticles at intersection for measuring

Assembly in 3D: DNA polyhedra

  • Turberfield Science 2005
  • Geometry -
  • Abstraction vs. Naturalism -
  • Greenberg Abstraction vs. Geometric Abstraction


What does the material want to do?

  • Polyhedra
  • Copying the Western Cannon?
  • Could you make Japanese prints or other spatial relationships?


Can we do something useful with these structures

  • Icosohedron
  • Compression~! - Only 3 parts / / /
  • 2 jelly fish with sticky ends
  • Platinum Shadows - 3D space to a 2D Problem
  • Some guys will trap, some guys will be free
  • Naturalism vs. Abstractionism *
  • POWERFUL BUILDING BLOCK
  • Flexibility & Position Things


  • ' "There is a value to minimalism"
  • "Forget about saving the world - we just want to know how things function"
  • One possible functional use: targeting in-vivo
  • Encapsulated polymer doesn't reduce functionality
  • PH sensing


Dynamic Architectures

  • DNA Nanomachines
  • Seeman nature, 1999, 397
  • Yurke Nature 2000, 406
  • 1 Hour Switch - Design affordance / Constraint


Unusual Structures of DNA and Their Uses

  • A pH biosensor from an I-motif based DNA nanoswitch
  • Wear & tear over time - Organic - Enzyme so it doesn't decrease over time
  • For the extent that you are using it the wear & tear is negligible
  • END OF LIFE ISSUES?
  • What is NanoComputing's E-Waste
  • Is there E-waste of Nano-Computing?
  • Ratiometric pH sensing
  • IF WE ARE GOING TO DRAW A SHAPE, LET'S AT LEAST BE SURPRISED
  • Control & Efficiency (compression)
  • Complexity & Redundancy
  • A Cell is A City
  • Food from the village - shipped in by truck - feeds itself from the outside
  • Surprise - that something that was artificially engineered could perform qualitatively and quantitatively
  • Engineering fallacy - Efficiency as a fitness function

Increasing infrastructure //


STABILITY OF DOMAINS

  • Give it a choice What does DNA want to do?
  • If you give DNA a choice….working along with the flexibility of the DNA
  • The angle of your joint can not be controlled
  • Let's provide an environment where DNA can decide the curvature
  • Enough incentive for the DNA would stick - Maximum satisfaction
  • The angle is enduced by the environment
  • Allow it different possibilities for being satisfied for maximum base pairing
  • Giving a system a choice

Icosohydron - made Polymerize into many shapes Flat sheets


WHAT DOES DNA WANT - AGENCY

  • Create Conditions that Work with the Material rather than against it
  • Melting Temperature
  • allowable angles -

Articles in reference- http://pubs.rsc.org/en/Content/ArticleLanding/2010/DT/c0dt00238k


WHAT HAPPENS TO THE NANOBOTS?

  • FREQUENCY SPECTRUM OF NANOTECHNOLOGY
  • Ends break apart if you shine light at a frequency
  • Photocleavable levers - at a wavelength of light!!! (frequency spectrum)
  • Nanotechnology Frequency Spectrum (communication)

THREE FINAL IDEAS

Based on our initial research, mind mapping, readings and visiting lectures we came up with three ideas that we took forward:

· NANOCOMPUTING

· WHAT DNA WANTS?

· TIME CAPSULE

Readings

DNA nanomachines

JONATHAN BATH AND ANDREW J. TURBERFIELD*

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

An autonomous molecular computer for logical control of gene expression

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

All-DNA finite-state automata with finite memory

http://www.pnas.org/content/107/51/21996.abstract

Can art make nanotechnology easier to understand?

http://news.nationalgeographic.com/news/2003/12/1223_031223_nanotechnology.html

Six challenges for molecular nanotechnology

http://www.softmachines.org/wordpress/?p=175

Feasibility arguments for molecular nanotech

http://www.acceleratingfuture.com/michael/blog/2008/03/feasibility-arguments-for-molecular-nanotechnology/

Dna origami ?

http://www.nature.com/nindia/2011/110622/full/nindia.2011.86.html & http://www.nature.com/ncomms/journal/v2/n8/full/ncomms1452.html

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?

Dream-machines-new-freedoms-minority-report.png

Paul Rothemond TED Talk Notes

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

  • What is life?
    • Can life be categorised by reproduction, metabolism and/or evolution?
    • “Life performs computation” How does that quantify or qualify life?
  • How accurate is the comparison between DNA alterations to the binary system in banking?
  • “Can we write molecular programs to build technology?”
  • 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 NOT 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?

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  • Nanotechnology & “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?

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PROTOCOL FOR BUILDING A DNA COMPUTER

from [1]

Methods Synthetic DNA Double-stranded synthetic DNA molecules were prepared by annealing 2,000 pmol of commercially obtained deoxyoligonucleotides (Sigma-Genosys) in a ®nal volume of 10ml of 10mM Tris-HCl buffer, pH8.0, containing 1mM EDTA and 50mM NaCl. The annealing was performed by heating the solution to 94 VC followed by slow cooling. The formation of a duplex was con®rmed by native PAGE (20%). The oligomers were 5W-phosphorylated and PAGE-puri®ed by the supplier and used without further puri®cation. Input molecules These were constructed stepwise by ligating one or more synthetic DNA segments of thedesired sequence to a 1,457-bp fragment obtained by digestion of the pBluescript II SK+ plasmid (Stratagene) with FokI, followed by polymerase chain reaction (PCR) ampli®- cation of the coding segment and a 300- or 325-bp tail region. The sequences of the resulting input molecules were con®rmed by sequencing.


Output-detecting molecules The output-detecting molecule for the S0 output (S0-D) was formed by ligating a synthetic adapter of 30 bp containing a FokI recognition site to a 181-bp fragment obtained by digesting the pBluescript II SK+ plasmid with FokI, PCR ampli®cation and additional FokI digestion to form the 160-bp fragment bearing the desired sticky end. The output-detecting molecule for the S1 output (S1-D) was obtained by PCR ampli®cation of a 285-bp fragment corresponding to positions 1,762±2,047 of the pBluescript II SK+ plasmid followed by FokI digestion of the PCR product to form a 250-bp fragment.


Computation reactions Reactions were set by mixing 2.5 pmol of the input molecule, 1.5 pmol of each output- detection molecule and 15 pmol of each transition molecule with 12 units of FokI and 120 units of T4 DNA Ligase (both from New England Biolabs) in 120 ml of NEB4 buffer supplemented with 1 mM ATP and incubating at 18 VC for 70 min. In case of multiple inputs in the same reaction, equal amounts were used, summing up to 2.5 pmol. The mixtures were puri®ed by the Qiagen PCR puri®cation kit and eluted using 30 ml EB buffer (Qiagen). Aliquots (10 ml) were assayed by gel electrophoresis using 3% MetaPhor agarose (FMC Bioproducts) unless indicated otherwise. The lengths of the DNA species were veri®ed using a commercial 50-bp DNA step ladder (Promega). To further con®rm that output reporting molecules were formed as expected, we ampli®ed by PCR and sequenced the output-detection molecule/output molecule junction region in both output-reporting molecules S0-R and S1-R and found the expected sequences (not shown).

Laboratory techniques with potential use for computation

-- Synthesizing a desired polynomial--length strand, used in all models. In standard solid-phase DNA synthesis, a desired DNA molecule is built up nucleotide by nucleotide on a support particle in sequential coupling steps. For example, the first nucleotide (monomer), say A, is bound to a glass support. A solution containing C is poured in, and the A reacts with the C to form a two-nucleotide (2-mer) chain AC. After washing the excess C solution away, one could have the C from the chain AC coupled with T to form a 3-mer chain (still attached to the surface) and so on.

-- Mixing: pour the contents of two test tubes into a third one to achieve union. Mixing can be performed by rehydrating the tube contents (if not already in solution) and then combining the fluids together into a new tube, by pouring and pumping for example.

-- Annealing : bond together two single-stranded complementary DNA sequences by cooling the solution. Annealing in vitro is also known as hybridization.

-- Melting : break apart a double-stranded DNA into its single-stranded complementary components by heating the solution. Melting in vitro is also known under the name of denaturation.

-- Amplifying (copying) : make copies of DNA strands by using the Polymerase Chain Reaction (PCR). PCR is an in vitro method that relies on DNA polymerase to quickly amplify specific DNA sequences in a solution. Indeed, the DNA polymerase enzymes perform several functions including replication of DNA. The replication reaction requires a guiding DNA single-strand called template, and a shorter oligonucleotide called a primer, that is annealed to it. Under these conditions, DNA polymerase catalyzes DNA synthesis by successively adding nucleotides to one end of the primer. The primer is thus extended in one direction until the desired strand that starts with the primer and is complementary to the template is obtained. PCR involves a repetitive series of temperature cycles, with each cycle comprising three stages: denaturation of the guiding template DNA to separate its strands, then cooling to allow annealing to the template of the primer oligonucleotides, which are specifically designed to flank the region of DNA of interest, and, finally, extension of the primers by DNA polymerase. Each cycle of the reaction doubles the number of target DNA molecules, the reaction giving thus an exponential growth of their number.

-- Separating the strands by length using a technique called gel electrophoresis that makes possible the separation of strands by length. The molecules are placed at the top of a wet gel, to which an electric field is applied, drawing them to the bottom. Larger molecules travel more slowly through the gel. After a period, the molecules spread out into distinct bands according to size.

-- Extracting those strands that contain a given pattern as a substring by using affinity purification. This process permits single strands containing a given subsequence v to be filtered out from a heterogeneous pool of other strands. After synthesizing strands complementary to v and attaching them to magnetic beads, the heterogeneous solution is passed over the beads. Those strands containing v anneal to the complementary sequence and are retained. Strands not containing v pass through without being retained.

-- Cutting DNA double-strands at specific sites by using commercially available restriction enzymes. One class of enzymes, called restriction endonucleases, will recognize a specific short sequence of DNA, known as a restriction site. Any double-stranded DNA that contains the restriction site within its sequence is cut by the enzyme at that location.

-- Ligating : paste DNA strands with compatible sticky ends by using DNA ligases. Indeed, another enzyme called DNA ligase, will bond together, or ``ligate, the end of a DNA strand to another strand.

-- Substituting : substitute, insert or delete DNA sequences by using PCR site-specific oligonucleotide mutagenesis. The process is a variation of PCR in which a change in the template can be induced by the process of primer modification. Namely, one can use a primer that is only partially complementary to a template fragment. (The modified primer should contain enough bases complementary to the template to make it anneal despite the mismatch.) After the primer is extended by the polymerase, the newly obtained strand will consist of the complement of the template in which a few oligonucleotides have been ``substituted by other, desired ones.

-- Marking single strands by hybridization: complementary sequences are attached to the strands, making them double-stranded. The reverse operation is unmarking of the double-strands by denaturing, that is, by detaching the complementary strands. The marked sequences will be double-stranded while the unmarked ones will be single-stranded.

-- Destroying the marked strands by using exonucleases, or by cutting all the marked strands with a restriction enzyme and removing all the intact strands by gel electrophoresis. (By using enzymes called exonucleases, either double-stranded or single-stranded DNA molecules may be selectively destroyed. The exonucleases chew up DNA molecules from the end inward, and exist with specificity to either single-stranded or double-stranded form.)

-- Detecting and Reading: given the contents of a tube, say ``yes if it contains at least one DNA strand, and ``no otherwise. PCR may be used to amplify the result and then a process called sequencing is used to actually read the solution. The basic idea of the most widely used sequencing method is to use PCR and gel electrophoresis. Assume we have a homogeneous solution, that is, a solution containing mainly copies of the strand we wish to sequence, and very few contaminants (other strands). For detection of the positions of A 's in the target strand, a blocking agent is used that prevents the templates from being extended beyond A 's during PCR. As a result of this modified PCR, a population of subsequences is obtained, each corresponding to a different occurrence of A in the original strand. Separating them by length using gel electrophoresis will give away the positions where A occurs in the strand. The process can then be repeated for each of C , G and T, to yield the sequence of the strand. Recent methods use four different fluorescent dyes, one for each base, which allows all four bases to be processed simultaneously. As the fluorescent molecules pass a detector near the bottom of the gel, data are output directly to an electronic computer. The bio-operations listed above, and possibly others, will then be used to write ``programs. A ``program will receive a tube containing DNA strands encoding information as input, and return as output either ``yes or ``no or a set of tubes. A bio-computation will consists of a sequence of bio-operations performed on tubes containing DNA strands.



Building our own PCR

COMING SOON!!

Some links that we were looking at:

http://pimm.wordpress.com/2009/10/31/lavaamp-cheapest-pocket-pcr-thermocycler-dreamed-for-diy-biologists/

http://makezine.com/07/fingerprinting/

http://openpcr.org/build-it/

http://www.rsc.org/chemistryworld/news/2007/may/01050701.asp

http://www.scribd.com/doc/104545/Mini-PCR-Machine

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