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</html> NOTEBOOK INTRODUCTION

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.

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:

http://hackteria.org/wiki/images/thumb/d/df/Mindmap1i.JPG/600px-Mindmap1i.JPG

http://hackteria.org/wiki/images/thumb/7/74/Mindmap1.JPG/600px-Mindmap1.JPG

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?

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

http://www.ias.ac.in/womeninscience/images/Lila-Daug/photo-final-1-50/p166.jpg

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.

2 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 Types

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

[[Image:]]

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? [[Image:]]

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

Nano COMPUTING

"DNA is one of the most promising candidates for molecular computing." -Richard Jones

Dennis Bray pointed out that the fundamental purpose of many proteins in cells seems to be more to process information than to effect chemical transformations or make materials.

http://www.pdn.cam.ac.uk/groups/comp-cell/Papers/Bray95a.pdf

Mechanisms such as allostery permit individual protein molecules to behave as individual logic gates; one or more regulatory molecules bind to the protein, and thereby turn on or off its ability to catalyse a reaction. If the product of that reaction itself regulates the activity of another protein, one can think of the result as an operation which converts an input signal conveyed by one molecule into an output conveyed by another, and by linking together many such reactions into a network one builds a chemical “circuit” which in effect can carry out computational tasks of more or less complexity.

http://www.softmachines.org/wordpress/?p=947

Logic gates are an interesting concept that may also be a foreign one for most people. They are extremely small structures that operate by changing data flowing through a computer into a sequence of signals that the computer utilises to complete a multitude of operations. Logic gates in our current world of technology involve the processing of electronic alerts from substances such as silicon, which take two signals that are inputted and then translate these into a single output to allow for complicated operations. Previously, logic gates used in computers were comprised of electronic structures that picked up signals from transistors. Logic gates made of DNA, however, are an entirely different concept. DNA logic gates are extremely small and they pick up various fragments of a genome as input before creating a single output from the fragments. Try to imagine a gate joining two DNA inputs to allow their end bits to lock. To fill in any gaps, an enzyme called DNA ligase creates an effective seal, which then results in a new strand. When electrophoresis is used, a scientist can measure the length of this new strand, thus giving an answer to the input strands. http://www.exploredna.co.uk/challenges-dna-computing.html

Computing with DNA - the manipulation of DNA to solve mathematical problems is redefining what is meant by "computation". http://www.cs.virginia.edu/~robins/Computing_with_DNA.pdf

Surpassing silicon? http://computer.howstuffworks.com/dna-computer1.htm

'WHAT DNA WANTS?

DNA molecules comprise a backbone of repeated sugar–phosphate units, with one of the four bases — adenine (A), cytosine (C), guanine (G) or thymine (T) — attached to each sugar. The twisting ladder of the double helix is formed by combining (or hybridizing) two antiparallel DNA strands, which are held together by hydrogen bonds between the complementary bases: adenine to thymine (A–T) and cytosine to guanine (C–G). By exploiting these exquisite base-pairing rules, which provide DNA with its ability to pass genetic information from generation to generation, self-assembled structures can be built simply by programming sequences of DNA — jigsaw pieces for one-, two- or three-dimensional puzzles. This process, combined with the current ability to synthesize almost any sequence in an automated fashion, means that it is possible to make new structures and devices that are not found in nature.

The Golden Ratio

http://hackteria.org/wiki/images/d/d2/Fibonacci-nature-3.jpg

If the DNA nano structures were allowed to 'stick' to each other naturally, without enforcing a fixed structure on them, what form would they take? Would they fall into the Golden Ratio?

In mathematics and the arts, two quantities are in the golden ratio if the ratio of the sum of the quantities to the larger quantity is equal to the ratio of the larger quantity to the smaller one. The golden ratio is an irrational mathematical constant, approximately 1.61803398874989...Adolf Zeising, whose main interests were mathematics and philosophy, found the golden ratio expressed in the arrangement of branches along the stems of plants and of veins in leaves. He extended his research to the skeletons of animals and the branchings of their veins and nerves, to the proportions of chemical compounds and the geometry of crystals, even to the use of proportion in artistic endeavors.

In contrast, "You won't find Fibonacci numbers everywhere in the natural world -- many plants and animals express different number sequences. And just because a series of numbers can be applied to an object, that doesn't necessarily imply there's any correlation between figures and reality. As with numerological superstitions such as famous people dying in sets of three, sometimes a coincidence is just a coincidence. "

http://science.howstuffworks.com/environmental/life/evolution/fibonacci-nature1.htm

File:Fibonacci-nature-3.jpg

"The golden ratio is expressed in spiraling shells. In the above illustration, areas of the shell's growth are mapped out in squares. If the two smallest squares have a width and height of 1, then the box to their left has measurements of 2. The other boxes measure 3, 5, 8 and 13."

TIME CAPSULE

The 1989 Oxford English Dictionary defines a time capsule as "a container used to store for posterity a selection of objects thought to be representative of life at a particular time." http://www.museumonmainstreet.org/exhibs_yesterdays/yesterdays_resources.htm

History of time capsule http://listverse.com/2009/04/27/top-10-incredible-time-capsules/ http://www.queenstribune.com/archives/anniversaryarchive/anniversary98/tb_an_capsules.html http://www.lomography.com/magazine/lifestyle/2011/03/18/a-brief-history-of-time-capsules

Look up fossils The modern use of the word 'fossil' refers to the physical evidence of former life from a period of time prior to recorded human history. This prehistoric evidence includes the fossilised remains of living organisms, impressions and moulds of their physical form, and marks/traces created in the sediment by their activities. There is no universally agreed age at which the evidence can be termed fossilised, however it's broadly understood to encompass anything more than a few thousand years. http://www.discoveringfossils.co.uk/whatisafossil.htm

Potential uses of the time capsule

Chhavi-if we make the capsule in a way, that its supposed to break after a certain number of years, and according to the predictions of the future, embed in it atoms of something that is predicted to not exist anturally later. very basic example- if it is predicted that you wont be able to find methane in its pure state. We can embed 'One molecule of methane-Green house gas" that can be replicated later on.

So it releases itself in the atmosphere. "The return of life" :p

Readings

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...

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?

revisiting Ted Nelson:
- Computer Lib / YOU NEED TO UNDERSTAND COMPUTERS NOW! (Do we/ Did we?) http://en.wikipedia.org/wiki/Computer_Lib_/_Dream_Machines

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

Paul Rothemond TED Talk Notes

http://hackteria.org/wiki/images/thumb/d/d1/P_z_ted_1.png/600px-P_z_ted_1.png

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?

http://hackteria.org/wiki/images/thumb/4/40/P_z_ted_3.png/600px-P_z_ted_3.png

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?

http://hackteria.org/wiki/images/thumb/8/8f/P_z_ted_2.png/600px-P_z_ted_2.png

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.

Nanotechnology in Fiction

-from wikipedia-[2]

-Nano times

http://hackteria.org/wiki/images/thumb/0/04/IMG_0752.JPG/300px-IMG_0752.JPG

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

MITS ALTAIR-To start with!

VINTAGE COMPUTERS : http://www.vintagecomputer.net/altair-poptronics.cfm http://hackteria.org/wiki/images/thumb/2/27/MITS_Altair.jpg/200px-MITS_Altair.jpg http://hackteria.org/wiki/images/f/f7/Mitsaltair.jpg http://hackteria.org/wiki/images/thumb/e/e9/Page272.jpg/600px-Page272.jpg

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 '''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….
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 ''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 -
+• 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 -
+• Escaping the Overcode
 • Not Control but Surprise/Variation
 • DNA Crystals - Self assembling
 • How will you know/ would one recognize complex behavior.
 === HCI of Nanotechnology ===