Programming genetic circuits with biological programming languages

¶ … 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 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.

Endy, meanwhile, suggests that we could one day have: " living bridges or buildings constructed by the self-directed growth of their natural materials, controlled by internal biological circuits, or even tiny medical "submarines" with on-board DNA computers navigating the insides of our bodies." (Heaven 02 April 2013).

Its limitations?

DNA computers are excellent in working with mathematical problems but there are still limitations that have to be worked around. Aran Nayebi, for instance, was able to implement Strassen's matrix multiplication algorithm on a DNA computer, although he faced problems with scaling. Caltech researchers, too, were able to create a circuit made from 130 different DNA strands, which calculated the square root of digits up to 15 (Strain, 2011 )). DNA computing, however, does not contribute anything new to computability theory where problems are computationally solvable using different models of computation. But these limitations pale in contrast to the revolutionary mass of contributions that DNA computer can theoretically bring to human and general development.

Amos in the Encyclopedia Britannica, for instance, opines that:

By harnessing the power of molecules, new forms of information-processing technology are possible that are evolvable, self-replicating, self-repairing, and responsive. The possible applications of this emerging technology will have an impact on many areas, including intelligent medical diagnostics and drug delivery, tissue engineering, energy, and the environment. (DNA computing http://www.britannica.com/EBchecked/topic/941575/DNA-computing)

DNA computerization will herald a new age. There is no end to the uses that DNA biochips can be expended for.

Let's hope that it will be used ethically and wisely.

Sources

Brumfiel, G (March 29, 2013) Tiny DNA Switches Aim to Revolutionize 'Cellular' Computing. NPR. http://www.npr.org/2013/03/29/175604770/tiny-dna-switches-aim-to-revolutionize-cellular-computing

Lovgren, Stefan (2003-02-24). Computer Made from DNA and Enzymes. National Geographic. http://news.nationalgeographic.com/news/2003/02/0224_030224_DNAcomputer.html

Heaven D (02 April 2013) DNA transistors pave way for living computers Newscientishttp://www.newscientist.com/article/dn23337-dna-transistors-pave-way-for-living-computers.html

Strain D (June 2, 2011 ) Flexible DNA computer finds square roots Science News http://www.sciencenews.org/view/generic/id/330621/description/Flexible_DNA_computer_finds_square_roots_

Ehrenburg, R (January 23, 2013 ) DNA stores poems, a photo and a speech . Science News http://www.sciencenews.org/view/generic/id/347702/description/DNA_stores_poems_a_photo_and_a_speech

Bonsor, K (nd) How DNA Computers Will Work. How stuff works.com http://computer.howstuffworks.com/dna-computer3.htm

Olympus Optical Co., Ltd. (2002) Development of World's First DNA Computer for Gene Analysis

http://www.olympus-global.com/en/news/2002a/nr020128dnacome.jsp