Noisebridge - User contributions [en]

Hello World in Synthetic Biology

2009-05-12T21:43:24Z

Xp prg: /* Hello World DNA Cell Based */

'''Hello World in Synthetic Biology'''

== Overview ==

Computation is occurring in biology that is extremely similar to silicon based computation if not exactly the same but using different symbols, instructions, etc...

== Silicon Based Computation to Biology Based Computation Comparison ==

{|width="80%" border="1" cellpadding="2" cellspacing="0"
|-
!Concept
!Silicon
!Biology
!Notes
!Exceptions
!Examples
|-

|CPU
|CPU
|Cell, Retina
|It is possible to use nerves for computation but these are also cells
|None
|E-coli, Yeast

|-

|Machine Language
|0/1
|21 amino acids
|DNA only uses 4 amino acids CGAT but proteins use all of the amino acids
|None
|GFP (fluorescing protein)

|-

|Fetch, Execute, Write CPU Cycle
|CPU toggles address bus with ram address, latches bits into cpu registers (fetch), opcode is analyzed and processed through arithmetic logic unit (execute), CPU toggles bus with ram address and bits to write to ram (write)
|Protein binds to cell surface receptor and enter cell via endocytosis then goes into nucleus of cell (fetch), protein binds to gene promotion area causing protein to be transcribed (execute), transcribed protein exits cells via exocytosis (write)
|Look at biology central dogma
|A virus could alter dna, not all proteins exit the cell, some rattle around causing other genes to express doing further computation until the final protein exits the cell. You could grow a cpu using nerve cells to do the exact same circuits a cpu has as well.
|Often proteins are tagged with a fluorescing protein so that if the protein is expressed it will fluoresce. There are now infrared proteins so you can see what is happening inside a cell through flesh in realtime!

|-

|Graphic Processor/Numerical Processor
|Nvidia graphic processor
|Retina
|Rods and cones turn light into electrical signals which go through massive signal processing before sent to optical nerve
|None
|Human retina

|-

|Manufacturing
|substrates, channels, silicon, etching
|Embryo, Egg
|Starts with only one cell that is fertilized
|Craig Ventor is very close to actually creating a cell. He can make everything but the cell surface/envelope which is a bi-lipid layer. A scientist at Santa Rosa Community College discovered a radioactive particle in a meteorite that causes water molecules to form an envelope around it which may be how this cell envelope was first formed.
|The ostridge egg is the largest cell in the world

|-

|GPS
|radio waves/signals from 3 separate satellites, the intersection is your position in space
|protein gradient cascades in an embryo occurring at certain times intersecting certain cells in 3d space with binding receptors allowing them to know where they are in 3d space
|The salamander knows how to grow an arm back based on chemical concentration etc..., still lots of research going on, but doesn't appear to be a protein gradient cascade but could be.
|None
|Xenopus and fish eggs are transparent and you can see what is happening in realtime! With gfp and infared proteins perhaps we can prove this is really occurring now!

|-

|Efficiency
|Instructions per second
|Base pairs per second
|Cells transcribe proteins very slowly :( that is why I recommend using nerves for computation, that is what nature has chosen for intense/fast computation
|If you use nerves you have instructions per second again. The ability to analyze and generate proteins in bps is now exceeding computation innovation in cpus
|GFP transcribing for bps, retina for ips

|-

|Libraries
|bios, <io.h> etc...
|dna genes etc..., BioBricks
|Microsoft Word has over 3 billion bytes, human DNA consists of 3 billion base pairs
|Not all human DNA are genes, less than 1% is considered "useful", 20,000 genes in the human genome, these genes are shared in other species, flies, bacteria etc..., some genes act differently in other species as well. Obviously there must be complex signal processing libraries with nerves as the retina is using these.
|Insulin created with e-coli via the insulin gene

|-

|Programming/Software
|Keyboard typing, compilation, linking, execution, flashing eproms
|Specify dna sequence and have it manufactured from a 3rd party like blue heron, deliver dna into cell via virus, gene gun, zinc fingers, micropipette en vitro, injection
|BioBricks can be used to create dna to put into cells to "program" them easily and are designed to be linked together
|Reprogramming of cells into stem cells is done via particular solutions applied to the cell for a particular time and different solutions etc..., not strictly DNA programming but is a kind of programming. Cells have been proven to sense their environment physically, such as grooves or smooth and will program themselves differently as a result
|Turning a human skin cell to a stem cell, then into a nerve cell, Glofish. Some DNA may be historical and could be tapped into for novel purposes, for ex: bird egg altered to become a dinosaur by injecting proteins to activate and silence other genes.

|-

|Hardware
|cpu, ram, latches, clock, transistors, capacitors, resistors, conductors
|cells: organelles: cell receptors, cytoplasm, mitichondria, flasks, test tubes, agar, solutions, microfluidic chips, antibiotics, fluorescing proteins, autoclaving equipment, knockout proteins, thermocycler, incubator, model organisms (e-coli, yeast)
|Hardware is a point of view, some is used in the cell, some outside of the cell to help the cell grow etc...
|None
|None

|-

|Power
|photo voltaics, lead acid battery, capacitor
|photosynthesis, lipids, glycogen, atp, mitochondria
|fat is turned into glycogen which is then converted to atp which power the cell, mitochondria is integral in this conversion
|None
|Mitochondria has its own dna inherited from the mother

|-

|Communication
|voltage differentials, radio waves
|chemicals via proteins, sound and radio waves, voltage over nerves
|bacteria establishes quorums via chemical signals that are only that bacteria's language, all bacteria's do share chemical signals however! Bats and whales communicate via radio waves, humans use voice waves etc...
|None
|bat signals, etc...

|}

== Hello World DNA Cell Based ==

print "Hello World"

# Assign 1 of the 21 amino acids to each letter of Hello World
# create gene that will code Hello World in a polypeptide sequence with the following:
* A GFP flourescing tag
* the proper promotor and terminator gene regions
# order cell and sequence from Blue Heron
# send activator protein
# see if petri dish flouresces
# send terminator protein

== Hello World DNA Retina Based ==

# Create a sequence of dna that will be injected into the xenopus cell that will grow:
* a cpu like structure to process signals like a retina
* an antenna like structure to communicate via wifi radio signals
* bind to wifi port and send start via xml
* antenna gets signals, puts them into the cpu like strucure, returns Hello World

Hello World in Synthetic Biology

2009-05-12T21:39:48Z

Xp prg: /* Hello World DNA Cell Based */

Hello World in Synthetic Biology

2009-05-12T21:38:17Z

Xp prg: /* Hello World DNA Cell Based */

'''Hello World in Synthetic Biology'''

== Overview ==

Computation is occurring in biology that is extremely similar to silicon based computation if not exactly the same but using different symbols, instructions, etc...

== Silicon Based Computation to Biology Based Computation Comparison ==

{|width="80%" border="1" cellpadding="2" cellspacing="0"
|-
!Concept
!Silicon
!Biology
!Notes
!Exceptions
!Examples
|-

|CPU
|CPU
|Cell, Retina
|It is possible to use nerves for computation but these are also cells
|None
|E-coli, Yeast

|-

|Machine Language
|0/1
|21 amino acids
|DNA only uses 4 amino acids CGAT but proteins use all of the amino acids
|None
|GFP (fluorescing protein)

|-

|Fetch, Execute, Write CPU Cycle
|CPU toggles address bus with ram address, latches bits into cpu registers (fetch), opcode is analyzed and processed through arithmetic logic unit (execute), CPU toggles bus with ram address and bits to write to ram (write)
|Protein binds to cell surface receptor and enter cell via endocytosis then goes into nucleus of cell (fetch), protein binds to gene promotion area causing protein to be transcribed (execute), transcribed protein exits cells via exocytosis (write)
|Look at biology central dogma
|A virus could alter dna, not all proteins exit the cell, some rattle around causing other genes to express doing further computation until the final protein exits the cell. You could grow a cpu using nerve cells to do the exact same circuits a cpu has as well.
|Often proteins are tagged with a fluorescing protein so that if the protein is expressed it will fluoresce. There are now infrared proteins so you can see what is happening inside a cell through flesh in realtime!

|-

|Graphic Processor/Numerical Processor
|Nvidia graphic processor
|Retina
|Rods and cones turn light into electrical signals which go through massive signal processing before sent to optical nerve
|None
|Human retina

|-

|Manufacturing
|substrates, channels, silicon, etching
|Embryo, Egg
|Starts with only one cell that is fertilized
|Craig Ventor is very close to actually creating a cell. He can make everything but the cell surface/envelope which is a bi-lipid layer. A scientist at Santa Rosa Community College discovered a radioactive particle in a meteorite that causes water molecules to form an envelope around it which may be how this cell envelope was first formed.
|The ostridge egg is the largest cell in the world

|-

|GPS
|radio waves/signals from 3 separate satellites, the intersection is your position in space
|protein gradient cascades in an embryo occurring at certain times intersecting certain cells in 3d space with binding receptors allowing them to know where they are in 3d space
|The salamander knows how to grow an arm back based on chemical concentration etc..., still lots of research going on, but doesn't appear to be a protein gradient cascade but could be.
|None
|Xenopus and fish eggs are transparent and you can see what is happening in realtime! With gfp and infared proteins perhaps we can prove this is really occurring now!

|-

|Efficiency
|Instructions per second
|Base pairs per second
|Cells transcribe proteins very slowly :( that is why I recommend using nerves for computation, that is what nature has chosen for intense/fast computation
|If you use nerves you have instructions per second again. The ability to analyze and generate proteins in bps is now exceeding computation innovation in cpus
|GFP transcribing for bps, retina for ips

|-

|Libraries
|bios, <io.h> etc...
|dna genes etc..., BioBricks
|Microsoft Word has over 3 billion bytes, human DNA consists of 3 billion base pairs
|Not all human DNA are genes, less than 1% is considered "useful", 20,000 genes in the human genome, these genes are shared in other species, flies, bacteria etc..., some genes act differently in other species as well. Obviously there must be complex signal processing libraries with nerves as the retina is using these.
|Insulin created with e-coli via the insulin gene

|-

|Programming/Software
|Keyboard typing, compilation, linking, execution, flashing eproms
|Specify dna sequence and have it manufactured from a 3rd party like blue heron, deliver dna into cell via virus, gene gun, zinc fingers, micropipette en vitro, injection
|BioBricks can be used to create dna to put into cells to "program" them easily and are designed to be linked together
|Reprogramming of cells into stem cells is done via particular solutions applied to the cell for a particular time and different solutions etc..., not strictly DNA programming but is a kind of programming. Cells have been proven to sense their environment physically, such as grooves or smooth and will program themselves differently as a result
|Turning a human skin cell to a stem cell, then into a nerve cell, Glofish. Some DNA may be historical and could be tapped into for novel purposes, for ex: bird egg altered to become a dinosaur by injecting proteins to activate and silence other genes.

|-

|Hardware
|cpu, ram, latches, clock, transistors, capacitors, resistors, conductors
|cells: organelles: cell receptors, cytoplasm, mitichondria, flasks, test tubes, agar, solutions, microfluidic chips, antibiotics, fluorescing proteins, autoclaving equipment, knockout proteins, thermocycler, incubator, model organisms (e-coli, yeast)
|Hardware is a point of view, some is used in the cell, some outside of the cell to help the cell grow etc...
|None
|None

|-

|Power
|photo voltaics, lead acid battery, capacitor
|photosynthesis, lipids, glycogen, atp, mitochondria
|fat is turned into glycogen which is then converted to atp which power the cell, mitochondria is integral in this conversion
|None
|Mitochondria has its own dna inherited from the mother

|-

|Communication
|voltage differentials, radio waves
|chemicals via proteins, sound and radio waves, voltage over nerves
|bacteria establishes quorums via chemical signals that are only that bacteria's language, all bacteria's do share chemical signals however! Bats and whales communicate via radio waves, humans use voice waves etc...
|None
|bat signals, etc...

|}

== Hello World DNA Cell Based ==

print "Hello World"

# Assign 1 of the 21 amino acids to each letter of Hello World
# create gene that will code Hello World in a polypeptide sequence with the following:
## A GFP flourescing tag
## the proper promotor and terminator gene regions
# order cell and sequence from Blue Heron
# send activator protein
# see if petri dish flouresces
# send terminator protein

Hello World in Synthetic Biology

2009-05-12T20:59:53Z