tedpwkr/talks/TED2007.pdfSo computer programs are spells, and verbal or written directions to humans...

TED

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TED

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http://www.arwen-undomiel.com/images/saruman.php http://img.timeinc.net/ew/img/review/011214/lord_l.jpg

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http://www.arwen-undomiel.com/images/saruman.php http://ljk.imag.fr/membres/Jocelyn.Etienne/avalanches.html

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We love the idea that words pronounced, little more than pure information, can evoke actions in the physical world.

Great (but lazy) hackers

And of course, given programmablecomputers and robots, they can.

Sorcerer's ApprenticeLinus Torvalds

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I only have "execute" permissions for such spell-programson your brain-computers for the duration of my talk.

http://www.bbc.co.uk/herefordandworcester/content/image_galleries/hereford_morecambe_fans_gallery.shtml

Leader/Politicians are much better. They are good at gettingarbitrary programs run almost all of the time:"Build a pyramid" or "Go to war!"

or, sometimes, "Drop the price of AIDS drugs."

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1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...

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1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...

"pronounced"with a computer

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Hello TED!

1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...


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Hello TED!Hello TED!

1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...


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Hello TED!


1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...


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Hello TED!


#include <stdio.h>#include <stdlib.h>

int main(void){ int i; for (i = 1; i < 4; i++) { printf("Hello TED!\n"); }}

1110110110001001100011010010011000001010011011110100111110000100110100011110000011101010111011100110010010010000110100001000100010000010100000011110000010111011011011110100011111000...


compiled from a high level language

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So computer programs are spells, and verbal or written directions to humans are spells,but this is unsatisfying.

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The wonderful fact is that there are spells that workwithout a computer (or human robot).

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The wonderful fact is that there are spells that workwithout a computer (or human robot).

The fact is, that at the molecular level, when spells are pronounced as molecules,physics can directly interpret information and run programs.

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PLPVYKPAASRMQIEKAVEMLIQAERPVIVAGGGVINADAAALLQQFAELTSIPVIPTLMGWGCIPDDHELMAGMVGLQTAHRYGNATLLASDMVFGIGNRF...

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Strings of sequence informationpronounced as amino acid chains fold into 3D protein nanomachines.

(Roughly, different combinationsof letters stick to other combinations of letters in complex, context-dependent ways.)

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A green and purple enzymethat attacks a poor little DNA,and cuts it.


Strings of sequence informationpronounced as amino acid chains fold into 3D protein nanomachines.

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ANRHTGSVEKYTEGRKIVHIDIEPTQIGRVLCPDLGIVSDAKAALTLLVEVAQEMQKAGRLPCRKEWVADCQQRK...

Changing the sequence...

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Changing the sequence...changes the spell and the 3D folding.

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The resulting nanomachineis now a ligase that connectstwo DNA strands together likea DNA stapler.

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In the end the total action of all of these molecule programs and the nano-machines they create is to build a person like you, with its buggy and insecure neural computer.



The resulting nanomachineis now a ligase that connectstwo DNA strands together likea DNA stapler.

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Erik Winfree Bernie Yurke

Len Adleman Ned Seeman

DNA nanotechnologists cast molecular spells with DNA.

Father of DNA nanotech.First DNA computer

Algorithmic self-assembly

DNA tweezers and motors

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DNA is cheaper, easier to handle,and easier to understandthan proteins.

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DNA is cheaper, easier to handle,and easier to understandthan proteins.

We want to build stuff.

Smaller faster computers.

Black boxes in cells.

DNA analogs of protein motors.

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We want to build stuff.

Smaller faster computers.

Black boxes in cells.

DNA analogs of protein motors.

DNA may be handicapped;perhaps less functional thanprotein.But we have a head start.And we have a hope ofwriting compilers...

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How can one make any arbitrary shape or patternout of DNA strands?

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How can one make any arbitrary shape or patternout of DNA strands?

Perform a type of "DNA origami":Fold a single long strand of DNA (the paper)into the desired shape.

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100 nanometers

Given a shape:

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100 nanometers

Given a shape:

1. s10t15f, A1, AAAGACAAGCAAGGCCGGAA ACGT 2. s10t17f, B1, AGAGAGAACCACAAGA ATTGAGTTCCAGCGCC 3. s11t14e, C1, AGCACCATTACCATTAAAGGGCGA ...250. s11t16e, D1, CATTCAACA TATCAGAGAGA TAACTAAC ATAA

A computer program designsa set of 250 short DNA sequences,on average each is about 32 letters:

Their job will be to fold the long strand.

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100 nanometers

Given a shape:



Sequences are "pronounced" using a DNA synthesizer

(The "opposite" of a sequencer.)


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100 nanometers

Given a shape:



Sequences are "pronounced" using a DNA synthesizer

Each letter is replaced by a 30-atomcluster, a different one for eachDNA base A, C, G, or T.

(The "opposite" of a sequencer.) Fedex!


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All 250 different DNA strands are mixed together.

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Mg2+

Add a little magnesium salt.

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M13mp18 viral genome 7249 bases

Mg2+

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100 nanometers

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100 nanometers

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100 nanometers

Atomic force micrograph(AFM) image.

Gray is DNA, black is themineral mica on which it sits.

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100 nm

Change the sequence of staples and one can make a shape with precise holes.

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100 nm

Change the sequences of staples and one can make a shape with precise holes. Who likes to stick to friends.

72% are well-formed

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100 nm

The technique is not limited to raster-filled shapes. Rigid domains can be combined at defined angles.

88% are well-formed

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With still different staple sequences, arbitrary patternsof dots (DNA bumps) can be made on top of rectangles---200 pixels with a resolution of 6 nanometers.

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A small change to thesequences does the trick.Better, higher yieldways must be found (2%)

How can we combine pattern covered shapes into larger objects?

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An atomic forcemicroscope "feels" the heightof DNA structures with a microscopic finger.Thus these false color3D topographic images are appropriate.

Many scientistsare working toturn this DNAartwork intofunctioning devices and circuits.

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Eventually we want to learn how to self-assemble anything...

A desalination plant

Solar farm

Bizarro Erik

Why attempt to make self-assembly an exercise in programming?

(I don't really pretend to know what the real applicationswill be; what will we want to make?)

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Erik Winfree

Inventor of algorithmic self-assembly This is the very coolest approach,

is truly programming DNA, (in the computer science sense)but I don't have time to talk about it!!!

I work in this guy's lab.

Paul [email protected]/~pwkr

Real soon now (as soon as I get a job)I will release my crappy MATLABcode for DNA origami.6-12 months from now, a company willrelease 3D WSIWYG free, open sourcepython for DNA origami. Yay!Send me email to join the release list.

A 2nd year grad student in China has reproduced thiswork and made China--Lulu Qian.

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10000111111110101110100100001000101000100111101001101000100101010010010100101110101001101010100101001010101000101010100110101001001010110010101110010010010100011101011110101000101000010101111001101110100101001000011010111001111010111000011101101101010001000111100111011001111101101000110001110101001010011011011101010110111110011010010110011101010111100101111100100010100101001001011111101000010001111110011110010101011111110101001001010110100011110111101010001101011111010101110111100010010100000100110111101010110101111001011111011000010001010001010101000010100111110101110001011111100110111001...

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GACTTTGGTGGCAAGAGGAGCTGGCGGAGCCCAGCCAGTGGGCGGGGCCAGGGGAGGGGCGGGCAGGTAGGTGCAGCCACTCCTGGGAGGACCCTGCGTGGCCAGACGGTGCTGGTGACTCGTCCACACTGCTCGCTTCGGATACTCCAGGCGTCTCCCGTTGCGGCCGCTCCCTGCCTTAGAGGCCAGCCTTGGACACTTGCTGCCCCTTTCCAGCCCGGATTCTGGGATCCTTCCCTCTGAGCCAACATCTGGGTCCTGCCTTCGACACCACCCCAAGGCTTCCTACCTTGCGTGC...

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Wri tten using ~30 atomsper A, C, T or G base.

The writing is "molecular".

http://www.web-books.com/Mobio/Free/Ch3B.htm

2 nm

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"pronounced" in a fertilized egg cell,through the processes of RNA transcription,protein translation, and biological development

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"pronounced" through biological development ?

evolved code, we don't know biology'shigh level language very well.

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"pronounced" through biological development ?

Clearly, molecular information can direct the spontaneousself-organization of amazingartifacts.

How can we write such programs?

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Homo Sapiens

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AACCGCTGCCGGTCTACAAACCTGCTGCCAGCCGTATGCAGATCGAAAAAGCTGTAGAAATGTTAATCCAGGCCGAACGTCCGGTGATTGTTGCCGGAGGCGGGGTAATCAATGCTGACGCAGCTGCACTGTTACAACAGTTTGCTGAACTGACCAGCATTCCGGTGATCCCAACGCTGATGGGCTGGGGCTGTATCCCGGACGATCATGAACTGATGGCCGGGATGGTGGGCCTGCAAACCGCGCATCGTTACGGTAATGCAACGTTGCTGGCGTCCGACATGGTGTTTGGTATCGGTAACCGTTTTGCTAACCGTCATACCGGTTCGGTAGAGAAATACACTGAAGGGCGCAAAATCGTTCATATCGAT...

2 microns

E. ColiHomo Sapiens

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AATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATG...

2 microns

0.2 microns

E. ColiHomo Sapiens

M13 bacteriophage

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tedpwkr/talks/TED2007.pdfSo computer programs are spells, and verbal or written directions to humans...

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