Hello World in Synthetic Biology

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

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"

1. Assign 1 of the 21 amino acids to each letter of Hello World
2. 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

1. order cell and sequence from Blue Heron
2. send activator protein
3. see if petri dish flouresces
4. send terminator protein

Hello World DNA Retina Based

1. 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