04-08-2013, 08:53 AM
Nanotechnology has excited the public’s eye ever since Eric Drexler detailed its possibilities in his 1986 book “Engines of Creation”. Much research had been done in the past 20 years regarding this topic, and many a million was invested in the development of the first nano-scale machines. However, molecular nanotechnology is a very tricky field and, although the past 20 years have yielded much insight and useful experiments, manipulation of matter on the atomic and molecular scale remains far from having widespread industrial use. However, new research regarding synthetic biology may present us with the opportunity to control living matter at the molecular scale, a possibility of building, inserting and using cell and molecule sized computing machines regarding not only our own bodies, but any living system. Synthetic biology is a new, promising area of biological research that evolved in past few years. It deals with the building blocks of life, DNA and proteins, and manipulating them to create, control and use mechanisms within living systems. Recently, a new, interesting boom has arisen from research in synthetic biology. Dubbed “biological computing”, this new strain of thought may provide scientist with the means of creating biologically based computers, utilizing living cells and their mechanisms as the computer parts.
March this year, a paper was published, unveiling the discovery of biological transistors, the basic building blocks of logical circuitry by Stanford University’s bioengineering laboratory. This same laboratory, last year, has published another paper regarding biological computing, proving that DNA can be used as a rewritable mass data storage medium. These two papers combined give the basic building blocks of electronic circuitry, and the ability to program living systems for a variety of uses.
“We can write and erase DNA in a living cell, now we can bring logic and computation inside a cell itself.” – Says Jerome Bonett, a scientist at Stanford’s bioengineering department.
In their paper from April 2012, they first presented their results from experiments with DNA. The researchers at Stanford choose to use DNA as a memory medium, as it already is, as they say “the stuff of memory”. They used enzymes called recombinases to flip segments of DNA on or off. The enzymes came from bacteriophages, viruses that use it to flip bacterial DNA and insert their own instead. In their experiment, they used the enzyme to flip a certain segment of DNA, so it reads backwards. With another signal, they were able to flip it back again, thus representing the basic computing language of 1s and 0s. They then “programmed” DNA of an Escherichia Coli bacterium to glow a certain color depending on the way the segment of DNA is oriented, green for one direction, red for the other. They could then observe as the bacterium changed color red to green, and back again, every time the segment of DNA was flipped over. This represents only one bit of memory, but is the first, most important step. In the next few years, the researchers are confident to be able to scale up to several bytes, and speed up the process. However, the most important thing these experiments have yielded is the ability to preserve the flips, or bytes of memory, through 100 generations of bacteria.
A year later, March 2013, the same laboratory published another paper, this time about biological transistors, dubbed “transcriptors”. This time, the laboratory was able to manipulate strands of DNA, and DNA snipping enzymes to create a basic building block of logical circuitry, a “yes/no” switch. Different from electronic chips, which direct the flow of electrons to flip switches on and off, this “biological chips” manipulate the flow of a protein along a strand of DNA (or RNA), sending information along its way, telling the cell to synthesize or not synthesize a specific molecule. The same “flipping technology” was used as with the DNA memory storage experiments, only this time the orientation of the strand, coupled with the protein traveling along it, sent out certain information to the cell itself. Although now only at a level of several different responses, or logical switches, this technology can be very useful for some basic cellular computing. For example, a cell can be programmed to release a certain cue in case it detects a cancer marker, coloring your stool or urine green or blue, as an early warning mechanism. Bacteria can also be altered to glow a certain color in case it detects a contaminant in water or the ground, thus warning us of pollution or contamination.
Although this technology is not very likely to replace electrical computing, it nonetheless provides great possibilities and opens many interesting doors for further research and experimentation.
Resources:
J. Bonnet et al. Amplifying genetic logic gates. Science. Published online March 28, 2013. doi: 10.1126/science.1232758.
J. Bonnet, P. Subsoontorn, and D. Endy. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proceedings of the National Academy of Sciences. Published online May 21, 2012. doi:10.1073/pnas.1202344109.
March this year, a paper was published, unveiling the discovery of biological transistors, the basic building blocks of logical circuitry by Stanford University’s bioengineering laboratory. This same laboratory, last year, has published another paper regarding biological computing, proving that DNA can be used as a rewritable mass data storage medium. These two papers combined give the basic building blocks of electronic circuitry, and the ability to program living systems for a variety of uses.
“We can write and erase DNA in a living cell, now we can bring logic and computation inside a cell itself.” – Says Jerome Bonett, a scientist at Stanford’s bioengineering department.
In their paper from April 2012, they first presented their results from experiments with DNA. The researchers at Stanford choose to use DNA as a memory medium, as it already is, as they say “the stuff of memory”. They used enzymes called recombinases to flip segments of DNA on or off. The enzymes came from bacteriophages, viruses that use it to flip bacterial DNA and insert their own instead. In their experiment, they used the enzyme to flip a certain segment of DNA, so it reads backwards. With another signal, they were able to flip it back again, thus representing the basic computing language of 1s and 0s. They then “programmed” DNA of an Escherichia Coli bacterium to glow a certain color depending on the way the segment of DNA is oriented, green for one direction, red for the other. They could then observe as the bacterium changed color red to green, and back again, every time the segment of DNA was flipped over. This represents only one bit of memory, but is the first, most important step. In the next few years, the researchers are confident to be able to scale up to several bytes, and speed up the process. However, the most important thing these experiments have yielded is the ability to preserve the flips, or bytes of memory, through 100 generations of bacteria.
A year later, March 2013, the same laboratory published another paper, this time about biological transistors, dubbed “transcriptors”. This time, the laboratory was able to manipulate strands of DNA, and DNA snipping enzymes to create a basic building block of logical circuitry, a “yes/no” switch. Different from electronic chips, which direct the flow of electrons to flip switches on and off, this “biological chips” manipulate the flow of a protein along a strand of DNA (or RNA), sending information along its way, telling the cell to synthesize or not synthesize a specific molecule. The same “flipping technology” was used as with the DNA memory storage experiments, only this time the orientation of the strand, coupled with the protein traveling along it, sent out certain information to the cell itself. Although now only at a level of several different responses, or logical switches, this technology can be very useful for some basic cellular computing. For example, a cell can be programmed to release a certain cue in case it detects a cancer marker, coloring your stool or urine green or blue, as an early warning mechanism. Bacteria can also be altered to glow a certain color in case it detects a contaminant in water or the ground, thus warning us of pollution or contamination.
Although this technology is not very likely to replace electrical computing, it nonetheless provides great possibilities and opens many interesting doors for further research and experimentation.
Resources:
J. Bonnet et al. Amplifying genetic logic gates. Science. Published online March 28, 2013. doi: 10.1126/science.1232758.
J. Bonnet, P. Subsoontorn, and D. Endy. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proceedings of the National Academy of Sciences. Published online May 21, 2012. doi:10.1073/pnas.1202344109.
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