Biological Computers
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07-11-2009, 04:09 PM


Biological computers have emerged as an interdisciplinary field that draws together molecular biology, chemistry, computer science and mathematics. The highly predictable hybridization chemistry of DNA, the ability to completely control the length and content of oligonucleotides, and the wealth of enzymes available for modification of the DNA, make the use of nucleic acids an attractive candidate for all of these nanoscale applications

A 'DNA computer' has been used for the first time to find the only correct answer from over a million possible solutions to a computational problem. Leonard Adleman of the University of Southern California in the US and colleagues used different strands of DNA to represent the 20 variables in their problem, which could be the most complex task ever solved without a conventional computer. The researchers believe that the complexity of the structure of biological molecules could allow DNA computers to outperform their electronic counterparts in future.

Scientists have previously used DNA computers to crack computational problems with up to nine variables, which involves selecting the correct answer from 512 possible solutions. But now Adleman's team has shown that a similar technique can solve a problem with 20 variables, which has 220 - or 1 048 576 - possible solutions.

Adleman and colleagues chose an 'exponential time' problem, in which each extra variable doubles the amount of computation needed. This is known as an NP-complete problem, and is notoriously difficult to solve for a large number of variables. Other NP-complete problems include the 'travelling salesman' problem - in which a salesman has to find the shortest route between a number of cities - and the calculation of interactions between many atoms or molecules.
Adleman and co-workers expressed their problem as a string of 24 'clauses', each of which specified a certain combination of 'true' and 'false' for three of the 20 variables. The team then assigned two short strands of specially encoded DNA to all 20 variables, representing 'true' and 'false' for each one.

In the experiment, each of the 24 clauses is represented by a gel-filled glass cell. The strands of DNA corresponding to the variables - and their 'true' or 'false' state - in each clause were then placed in the cells.

Each of the possible 1,048,576 solutions were then represented by much longer strands of specially encoded DNA, which Adleman's team added to the first cell. If a long strand had a 'subsequence' that complemented all three short strands, it bound to them. But otherwise it passed through the cell.

To move on to the second clause of the formula, a fresh set of long strands was sent into the second cell, which trapped any long strand with a 'subsequence' complementary to all three of its short strands. This process was repeated until a complete set of long strands had been added to all 24 cells, corresponding to the 24 clauses. The long strands captured in the cells were collected at the end of the experiment, and these represented the solution to the problem.


The world's smallest computer (around a trillion can fit in a drop of water) might one day go on record again as the tiniest medical kit. Made entirely of biological molecules, this computer was successfully programmed to identify - in a test tube - changes in the balance of molecules in the body that indicate the presence of certain cancers, to diagnose the type of cancer, and to react by producing a drug molecule to fight the cancer cells.


In previous biological computers produced input, output and "software" are all composed of DNA, the material of genes, while DNA-manipulating enzymes are used as "hardware." The newest version's input apparatus is designed to assess concentrations of specific RNA molecules, which may be overproduced or under produced, depending on the type of cancer. Using pre-programmed medical knowledge, the computer then makes its diagnosis based on the detected RNA levels. In response to a cancer diagnosis, the output unit of the computer can initiate the controlled release of a single-stranded DNA molecule that is known to interfere with the cancer cell's activities, causing it to self-destruct
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Biological Computer

.docx   Biological Computer[.docx (Size: 523.9 KB / Downloads: 36)

The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored to discuss the possibilities of a new computing paradigm. We assume the reader to possess a basic knowledge of Biology and Computer Science. Biological computers are special types of microcomputers that are specifically designed to be used for medical applications. The biological computer is an implantable device that is mainly used for tasks like monitoring the body's activities or inducing therapeutic effects, all at the molecular or cellular level. The biological computer is made up of RNA (Ribonucleic Acid - an important part in the synthesis of protein from amino acids), DNA (Deoxyribonucleic Acid - nucleic acid molecule that contains the important genetic information that is used by the body for the construction of cells; it's the blue print for all living organisms), and proteins.


It is easy to miss nature’s influence and subsequent impact on living forms. This applies to our day to day activities as well. Humans use a variety of gadgets and gizmos without realizing that the gadget could be working on a pattern already patented and perfected by Mother Nature. Computers and software are no exception. The last few decades have ushered in the age of computers. Electronics have invaded all walks of life and we depend on electronics to accomplish most of our day to day activities. As predicted by Dr. Gordon E. Moore, modern day electronics has progressed with miniaturization of electronic components. According to Dr. Moore, the miniaturization of integrated electronics will continue to be bettered once every 12 – 18 months with a reduction in cost (Moore, 1965).

The New Biology

Biocomputing research is one of those new disciplines that cuts across well-established fields—in this case computer science and biology—but doesn’t fit comfortably into either culture.“Biologists are trained for discoveries,” says Collins. “I don’t push any of my students towards discovery of a new component in a biological system.” Rockefeller University postdoctoral fellow Michael Elowitz explains this difference in engineering terms: “Typically in biology, one tries to reverse-engineer circuits that have already been designed and built by evolution.” What Collins, Elowitz and others want to do instead is forward-engineer biological circuits, or build novel ones from scratch. But while biocomputing researchers’ goals are quite different from those of cellular and molecular biologists, many of the tools they rely on are the same. And working at a bench in a biologically oriented “wet lab” doesn’t come easy for computer scientists and engineers—many of whom are used to machines that faithfully execute the commands that they type. But in the wet lab, as the saying goes, “the organism will do whatever it damn well pleases.”

Amorphous Computing

Two-gene switches aren’t exactly new to biology, says Roger Brent, associate director of research at the Molecular Sciences Institute in Berkeley, Calif., a nonprofit research firm. Brent—who evaluated biocomputing research for the Defense Advanced Research Projects Agency—says that genetic engineers “have made and used such switches of increasing sophistication since the 1970s. We biologists have tons and tons of cells that exist in two states” and change depending on external inputs. For Brent, what’s most intriguing about the B.U. researchers’ genetic switch is that it could be just the beginning. “We have two-state cells. What about four-state cells? Is there some good there?” he asks. “Let’s say that you could get a cell that existed in a large number of independent states and there were things happening inside the cell...which caused the cell to go from one state to another in response to different influences,”


This paper talks about how two diverse systems, biology and computers are brought together to take mankind into the future. A basic understanding of the lowest unit (Deoxyribonucleic acid - DNA) of life will help. People should not imagine that DNA will replace the CPU in biological computing. In our opinion such a scenario is at least two decades or more away from reality. As like other inventions one can safely anticipate or expect baby steps in this direction before conceiving bigger pictures. Although not exceeding a few microns in size, the DNA molecule has a number of tricks that will be useful for biological computing. One of them is the ability to generate proteins. Once programmed, by altering the cell by chemical or changing the environment the reprogrammed cell does its job to near perfection as per the changed environment Another trick that may be useful is the ability of DNA to make exact copies of itself. Imagine the advantage of having such molecules programmed for different purposes and its impact on applied sciences like medicine, agriculture, and various industries, in fact such molecules act like micro computers.

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