Nano Design Workshop

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Nanotech & Metaphors

  • Casting Spells
  • Magic
  • Living Factories / Foundaries
  • Speed of Computing (Keeping up with Moore's Law)
  • Xeno's Paradox of Reality (Borges -> The Map is Not The Terrain)
  • Jevon's Paradox of Biocomputing / Simulation?
  • It's fast: But what is it for?!?
  • The World's Slowest Computer
  • revisiting Ted Nelson: Computer Lib / YOU NEED TO UNDERSTAND COMPUTERS NOW! (Do we/ Did we?)


  • Send the Acorn, Not the Tree

Readings - All-DNA finite-state automata with finite memory

DNA nanomachines


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...

Cellularity by James King

How do we measure life.png

Please watch this video and think about the construction of metaphors regarding "life", who and how gets constituted as life and non-living, and how your BioMod machines work in this equaction


Paul Rothemond TED Talk Notes

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:

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?

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?”

P z ted 2.png

What is the difference?

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?

Actor Network Mapping Exercise

Some basic mindmapping on Nanotech and Biomod:

Mindmap1.JPG Mindmap1i.JPG

Networking mindmaps on success: BIOMOD-nanotechnology (Click on each of the four sections to have a better look at the pointers)


An overview:

Success mindmap.JPG

Few links over researching :

Can art make nanotechnology easier to understand?

Six challenges for molecular nanotechnology:

Feasibility arguments for molecular nanotech :

Dna origami ? : &

Nano Art Competition! :

Technological and mechanical metaphors for the Human Body:

Comparisons of the body to machine are sometimes seen in a negative light; endemic of a mechanistic worldview which is overly-reductive approach to something as complex and beautiful as the human body.


Ok, a "yawn" is over-trivialising the anti-mechanist critique, but I want to argue that kid's body books employing robot metaphors are a bit more complicated than that (personally, I think you can say the same of Blake's Newton, but that's another story). My central point is that mechanical analogies provide a diverse set of cultural referents. Machines comes in a range of sizes, shapes and styles, and people use and think about them in a range of ways. Further, both machines and the way cultures have understood them has changed over time.

From Brain, mind and medicine: essays in eighteenth-century neuroscience By Harry A. Whitaker, Christopher Upham Murray Smith, Stanley Finger TpucAY60rAf61o3UBQ&sa=X&oi=book_result&ct=result&resnum=9&ved=0CFwQ6AEwCA#v=onepage&q=technological%20metaphors%20for%20body&f=false

The language of genetic technology: Metaphor and media representation

Patents and the Metaphors We Own By

"The nature and commercial uses of biologically pure cultures of microorganisms are much more akin to inanimate chemical compositions such as reactants, reagents, and catalysts ... than they are to horses and honeybees, or to raspberries and roses." Judge Giles Rich, 1977

THIS theme reads oddly, perhaps. But the title is inspired by a fascinating book by George Lakoff and Mark Johnson called Metaphors We Live By, published in 1980 by Chicago University Press. In 1957 Vance Packard wrote The Hidden Persuaders, which showed how far our minds may, without our being aware, be influenced by advertisers. Three centuries earlier, Robert Hooke identified miniature walled compartments in the tree bark he was observing through his microscope. Reminded of the enclosed spaces inhabited by monks, he called them cells. In the present century, biologist Steven Rose comments in his book Lifelines on “the power of technological metaphor in biology”, one consequence of which is that “living systems become analogized to machines”.

Intellectual property has its hidden persuaders too. It also has its questionable metaphors and analogies. Business models in the biological sciences are heavily dependent on the patent system for protecting subject matters deemed to be inventions and for the mass filing and aggressive assertion of patents. This is as true for pharmaceuticals as it is for seeds and the various commercial sectors based on biotechnology. International, regional, bilateral and national patent rulemaking has been co-opted, and is supporting these business models, irrespective of whether or not they benefit any stakeholders other than the companies concerned. In my view, this is a matter warranting serious concern.

Power is of course central to any explanation of why particular economic actors get more of what they want than rival ones, and why public policy institutions such as patent systems get “captured”, or at least disproportionately influenced, by certain interest groups. Academics have an important role to play in challenging and speaking truth to power, at least in our areas of competence. Reversing massive power disparities takes a lot more than a provocative article, book chapter – or webpage! But exposing and scrutinising the metaphors, analogies and registers disguising the apparent objectivity of the language deployed by the powerful to get what they want is something that social scientists ought to be well placed to do. Since both patent law and biology, arguably an immature and inexact science, are highly dependent on shared language to function at all, they are also susceptible to strategic promotion of persuasive yet questionable metaphors, analogies and styles of communication which become universally adopted.

Businesses’ deployment of language has been extremely successful, and for a very long time. This is not of course to say that metaphors, analogies and styles of communication are inherently dubious. Far from it: metaphor is integral to language and therefore to verbal and written communication. Reasoning without the use of analogy will not take us far at all. The point is that they should not be taken for granted and that just as they can helpfully explain and illuminate the complex and obscure, they can also mislead and deceive. They are not objective, and they have a shelf-life. Hooke’s usage of the word “cell” is of course completely outdated: no-one any more thinks that cells look like cells. But despite the metaphor’s obsolescence, we seem to be stuck with it for the time being. As we will see below, there are others that would do a far better job.

Cells: Rooms, Factories, Business Park ... or Ikeas?

In his book, The Origins of Life, Paul Davies describes beautifully the mysterious, wonderfully complex and chaotic yet orderly hustle and bustle of life at the cellular level

As a simple-minded physicist, when I think about life at the molecular level, the question I keep asking is How do all these mindless atoms know what to do? The complexity of the living cell is immense, resembling a city in the degree of its elaborate activity. Each molecule has a specified function and a designated place in the overall scheme so that the correct objects get manufactured. There is so much commuting going on. Molecules have to travel across the cell to meet others at the right place and the right time in order to carry out their jobs properly. This all happens without a boss to order the molecules around and steer them to their appropriate locations. No overseer supervises their activities. Molecules simply do what molecules have to do: bang around blindly, knock into each other, rebound, embrace. At the level of individual atoms life is anarchy – blundering, purposeless chaos. Yet somehow, collectively, these unthinking atoms get it together, and perform the dance of life with exquisite precision.

Let us suppose that Robert Hooke came back to life in an alternative today’s world different from the actual one only in the absence of any curiosity about microbiology, and decided to be first to look at something living through an electron microscope. Would he really name them after the little places monks go to pray alone? This is unlikely in the extreme. He is far more likely to call them IKEAs. As most people are aware, IKEA is a massive windowless Swedish furniture superstore, packed on Saturdays with millions of biological compositions of matter milling around apparently aimlessly, and constantly getting in each other’s way, yet almost magically ending up at a place called the exit wielding bulky flatpacks almost but not quite falling off inadequately-sized trolleys. There are two kinds of biological composition (if you’ll forgive for a moment some rather crass gender stereotyping - I don't really mean any of it. Honest). There are the males, who are quite versatile. Their task is to pull the flatpacks off the racks, drag them onto the trolley, push it along without knocking into things, find the exit, join a long queue, and then pay. They are also supposed to turn the flatpack into a piece of furniture when they get home, but let’s not overcomplicate matters. The others are females. These could be called “smart compositions”. Their role seems quite simple: to choose what to put in the trolley. But usually this task turns out to be very complicated involving peculiar convoluted and sudden abrupt movements. And yet they know exactly what they are doing. Admittedly, describing the painful choreography of masses of IKEA visitors, many of whom wish to God they’d gone to the football that day, searching interminably for the bloody exit as a “dance of life” sounds a bit far-fetched. None of this may of course matter. Perhaps what’s good for GlaxoSmithKline or Syngenta is good for the rest of us: give them what they want and they will give us what we need. However, as I will argue, the ‘fit’ between the patent system and biology is highly questionable, much more so than business and governments supporting these business models would have us believe. Unfortunately, the strategic use and acceptance of misleading and deceptive metaphor, analogy and register makes it seem as if biological patenting is completely unproblematic. This impedes a proper debate on how biological innovation should best be promoted. With the age of synthetic biology about to start, this is a debate that we urgently need to have.

How far can the analogy for a Cell as a Machine be taken?

List of molecular machines in a cell -

Body/Cell Metaphors: Visual Research

Fritz Kahn: Man as an Industrial Palace Fritzkahn.jpg Watch the video here:


The Body and the Metaphors of the Engine

The article examines the specific language used to describe norms and models employed to explain the body, language on this subject that is reused and thus may be deemed, as with any discourse, to have an effective function ; in other words, to be a language that has practical efficacy in reality.

Natural Selection & Machines ?



The four common mechanisms of evolution :

•• Natural Selection -> Directional - Stabilizing - Disruptive

•Genetic Drift


•Gene flow

•• Artificial Selection

•• Sexual Selection

Fisherian Runaway theory

The quandary of female choice: This leads to an interesting question: how did female choice for traits like a long, colorful tail evolve? After all, if a female chooses a male with a long, awkward tail, her sons will probably have a similar tail—and that tail might hurt their chances of survival by attracting predators. How could natural selection act to produce a preference for a disadvantageous trait?




Mitochondrial DNA based chart of large human migrations (Numbers are millenia before present)

Body Politics

Body Politics.jpg Leviathan gr.jpg

Inscriptions identify parts of the human body with functions and offices of certain social classes and institutions of government. The resulting hierarchy of political and social values corresponds to the traditional evaluations of the organs of the human body in ancient and medieval anatomical and philosophical texts. For example, occupying the representational and metaphorical top of the hierarchy of the body politic is the king who is its head. As the most distinctive part of the human anatomy, in which the soul, reason, intelligence, and sensations reside, the head is the ruling principle to which all other parts of the human body and the body politic are subject. Next, associated with the vital human faculties of vision and hearing, the seneschals, bailiffs, and provosts and other judges are compared to the eyes and ears of the body politic. The counsellors and wise men are linked to the essential function of the heart. As defenders of the commonwealth, the knights are identified with the hands. Because of their constant voyages around the world, the merchants are associated with the legs. Finally, laborers, who work close to the earth and support the body, are its feet.;;doc.view=print

The belly and the members.jpg

Social Darwinism


Many people living in nineteenth century society believed in the concept of Social Darwinism. According to Social Darwinism, humans were going through an evolutionary process in which the fittest would survive, and the weakest would perish. Obviously, the wealthy and successful members of society were the fittest, and the poor were the weak or unfit. Wealthy industrialists actively supported this concept as it reinforced their belief that their success in life was a product of their superiority over the inferior masses. Government or social intervention programs on behalf of the poor were inadvisable under the Social Darwinist belief. Such programs would enable the unfit to survive and reproduce, rather than allowing them to die out, naturally, on their own.

Lipid Rafts


A Intracellular space or cytosol

B Extracellular space or vesicle/Golgi apparatus lumen

1. Non-raft membrane 2. Lipid raft 3. Lipid raft associated transmembrane protein 4. Non-raft membrane protein 5. Glycosylation modifications (on glycoproteins and glycolipids) 6. GPI-anchored protein 7. Cholesterol 8. Glycolipid

Signal transduction is initiated by complex protein–protein interactions between ligands, receptors and kinases, to name only a few. It is now becoming clear that lipid micro-environments on the cell surface — known as lipid rafts — also take part in this process. Lipid rafts containing a given set of proteins can change their size and composition in response to intra- or extracellular stimuli. This favours specific protein–protein interactions, resulting in the activation of signalling cascades.

Certain lipids and cholesterol in the cell membrane which are comparatively more rigid and can move around in the cell membrane.

Satyajit Mayor (NCBS)

On Wed. Sept. 14th 2011 Yamuna Krishnan from NCBS visited the Srishti BioMod team. Her talk was First Blueprint, Now Bricks: DNA is Construction Material on the Nanoscale

[[Image: ]]

Here are some of the notes


  • 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


  • (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? [[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 *
  • 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
  • What is NanoComputing's E-Waste
  • Is there E-waste of Nano-Computing?
  • Ratiometric pH sensing
  • 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 //


  • 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


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

Articles in reference-


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


  • "Smart" Nanostructures ->



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.

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.

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