Programming Genetic Circuits Is Fundamentally

¶ … Programming genetic circuits is fundamentally the same as programming electronic circuits, so we can just adapt an existing programming language to the problem of programming live cells to carry out specialized tasks.

Computing techniques have been used to understand biology for a long time. Technology has now advanced to the point where we may also use programming techniques to build biological systems from scratch. This is the basic idea of the field of synthetic biology. Generally, this means the design and construction of simple genetic circuits encoded in DNA, akin to building logic gates in computer hardware.

Building more complex devices requires construction of suitable programming languages which can describe the complex interactions of many simple circuits in order to carry out some complex task. This program can then be compiled into DNA and executed in a cell. It is possible to envision many linguistic approaches to this problem. For example, we already have programming languages for electronic chip design: are these suitable for genetic circuits? It may be that the object-oriented approach may be universal and we can just devise a biologically-oriented version of Java for the task. Lastly, perhaps the component-based nature of biology makes a scripting approach more appropriate.

Summary

Silicon chips have been the material that has been used to program computers until now, but the race for computer prowess seems to be coming to an end. There is only a limit that can be reached to making it faster, more memorable, more aesthetic, and it seems that soon the competition between the computer chip manufacturers to make the next super-faster microprocessor will hit an impasee.

Imaginative scientists, however, have arrived at an alternate solution. Our DNA molecules, they say, have an inherent power to perform calculations billions of times faster than the computer chips can. and, therefore, they may be used instead. In the wildest of science fiction stories, computer scientists speculate of inserting DNA into computer chips (they will be called 'biochips') and of DNA -- not silicon chips -- programming the computer. The result will be nano-computers replacing silicon-computers and DNA computers storing billions of times more data than the personal computer.

Traditional computers use the binary code (of 1 and 0) that produces an electrical surge of input, processing, and output. DNA computers, on the other hand, use the four-syllable genetic code (a [adenine], G [guanine], C [cytosine], and T [thymine]). They can do this because DNA molecules of any sort of sequence may be cut and arranged to order and this can be achieved by laboratory operations which chop and sort them out to arbitrary desired length.

History

In 1994, Leonard Adleman, a computer scientist at the University of Southern California, realized that DNA is similar to a hard drive in how it stores information about the genes and he introduced the idea of using DNA to solve complex mathematical problems. In a 1994 issue of Science, Adleman outlined how to use DNA to solve the notorious Hamilton Path mathematical problem (otherwise called the "traveling salesman" problem.). The goal of the problem was to find the shortest route between cities going through each city only once and as more cities are added, the problem becomes increasingly challenging. Using DNA as computer experiment, Adelman chose 7 cities and produced the following:

1. Strands of DNA represent the seven cities. In genes, genetic coding is represented by the letters a, T, C and G. Some sequence of these four letters represented each city and possible flight path.

2. These molecules are then mixed in a test tube, with some of these DNA strands sticking together. A chain of these strands represents a possible answer.

3. Within a few seconds, all of the possible combinations of DNA strands, which represent answers, are created in the test tube.

4. Adelman eliminates the wrong molecules through chemical reactions, which leaves behind only the flight paths that connect all seven cities. (http://computer.howstuffworks.com/dna-computer1.htm)

What Adelman demonstrated was that DNA could be successfully used to compute challenging mathematical / computer problems. DNA, therefore, could be used to calculate complex mathematical problems.

The problems with Adelman's experiment, however, were that whilst DNA rapidly produced the different answers, its implementation generated so many answers that it took days for scientists to sort through these answers in order to arrive at the accurate ones. Secondly, Adelman's implementation of DNA needed human assistance. The ideal, however, is to incorporate DNA independent of human involvement.

In 1994, researchers at the University of Rochester developed logic gates made of DNA. Logic gates interpret input signals from silicon transistors into output signals that allow the computer to perform its complex tasks. The logic gates that the University of Rochester researchers used, however, were composed of DNA script instead of electrical signals. The DNA gates were comprised of locking and interlocking DNA microchips. Currently: DNA logic gates and biochips still have a long way to go before they can ever become a fully functional computer. But if such a computer is ever built, scientists believe that it will be more compact, accurate and efficient than the silicon computers we use nowadays.

In 2002, researchers from the Weizmann Institute of Science in Rehovot, Israel, introduced a perfect prograqmmable computing machine that was composed of enzymes and DNA molecules instead of silicon microchips (Lovgren, Stefan (2003-02-24).). On April 28, 2004, Shapiro, and colleagues at the Weizmann Institute revealed in Nature that they had constructed a DNA computer that could diagnoze cell cancer, and prompt an anti-cancer drug in response.

In January 2013, researchers stored a JPEG photograph, Shakespearean sonnets, and Martin Luther King's speech I Have a Dream on digital storage that was made from DNA (Ehrenburg, 2013 )).

Silicon vs. DNA Microprocessors

Moore's Law states that the number of electronic devices put on a microprocessor will have doubled every 18 months, and this is indeed what has occurred with microchips becoming smaller, more crammed, and doubling in complexity every two years. Soon, however, the number of microchips that can be crammed onto a computer will have to come to an end and scientists are predicting that Moore's Law will soon reach its end, because of the physical speed and miniaturization limitations of silicon microprocessors.

This is where DNA computers come into the equation.

DNA computers are superior to silicon-computers in the following ways:

There will always be a supply of DNA.

The large supply of DNA makes it a cheap resource.

Traditional computers are made of toxic material; DNA chips, on the other hand, are clean

DNA computers are hugely smaller than today's computers.

DNA computers will not only be smaller than any of the computers that we are used to dealing with today, but they will also be able to hold a billion more bytes of giga-data than these we currently work with:

One pound of DNA has the capacity to store more information than all the electronic computers ever built; and the computing power of a teardrop-sized DNA computer, using the DNA logic gates, will be more powerful than the world's most powerful supercomputer. More than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time. By adding more DNA, more calculations could be performed. (Bonsor, nd)

Conventional computers calculate linearly, taking on tasks one at a time. DNA computers, however, calculate tasks in a parallel fashion parallel to other calculations. So, for instance, it may take silicon computer years to perform a certain complex calculation, whilst it will take DNA computers only a few hours to do so.

The Many Capabilities of the DNA computer

In a 2002 news release intended only for Japanese readers, Japan's Olympus Optical Co., Ltd. introduced the world's first operational DNA computer for gene analysis. The machine can accomplish the following:

High-precision, high-speed, low-cost gene expression profiling.

Versatile artificial DNA fragments for reactions designed using special software.

In other words, the computer can modify DNA strands for its own ends

The researchers also have integrated specific computer programs to make the DNA more accurate and reliable in their task.

The computer (as seen below) consists of two sections (molecular and electronic), both of which perform computational calculations.

The integration of both sections into one helps the rapidity of the whole.

Research occurring since then in other countries shows that DNA computers can also be used to other ends with the computer end being applied to the DNA end in order to transform the DNA capabilities.

In March 2013, for instance, Drew Endy, a synthetic biologist at Stanford University aimed to get into the cell's genetic machinery and engineer it to do human computing. He tried to do this by creating logic cells, or transistors, in the human cells themselves. In other words, instead of transferring DNA to computer, Endy transferred the idea of computer to DNA and used computer concepts to engineer the human cell. To elaborate, he used his 'transistor' to build logic circuits that program each cell's behavior. For instance, he was able to tell a cell to change color in the presence of both a specified two enzymes. Remarked Kleem (online): "Endy envisions plant-based environmental monitors, programmed tissues and even medical devices that "make Fantastic Voyage come true," (Kleem, 04.02.13).

In the first (grainy) image below, Endy's DNA "buffer gates" flash different colors according to their situation. In the image below that, we have a string of DNA -- we see the code of the a's, C's, T's and G's -- that has been programmed by synthetic biologist Eric Winfree of the California Institute of Technology --.

(Excerpted from Keim, B Computers Made Out of DNA, Slime and Other Strange Stuff

Wired. http://www.wired.com/wiredscience/2013/04/strange-computers/?pid=6598&viewall=true)

Timothy Lu, a researcher at the Massachusetts Institute of Technology, is taking this idea further by building cellular computers that can, for instance, program cells to automatically investigate bowels for cancer. Here DNA is transplanted to computer to help the computer achieve medical miracles (Brumfiel, 2013)

The idea of DNA in conjunction with computer can, therefore, be used in two ways: DNA can be used to revolutionize computer and computer ideas can be integrated into the DNA circuitry of the human -- or animal -- cell.

The Future of DNA Computers

The first DNA computers are likely to be used by governments for cracking secret codes, or by airlines wanting to work out better air- routes. They may also be used by neuroscientists for analyzing the brain and by scientists for unraveling medical or other mysteries. According to Lovgren (2003), in fact, there is no end to the possibilities to which the new technology could be used: bacterial cells, for example, are excellent at 'sniffing out' pathogens or chemicals, such as heavy metals. They could for used for elements such as this and by redesigning the circuitry of bacteria, we can produce cheap biosensors that may even monitor quality of water as well as of other things.