31-05-2012, 12:48 PM
biological computers
BIOLOGICAL COMPUTING.docx (Size: 97.56 KB / Downloads: 30)
1.INTRODUCTION:
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.
2.THE WORLD’S SMALLEST COMPUTER:
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.
3.DOCTOR IN A CELL:
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.
In one series of test-tube experiments, the team programmed the computer to identify RNA molecules that indicate the presence of prostate cancer and, following a correct diagnosis, to release the short DNA strands designed to kill cancer cells. Similarly, they were able to identify, in the test tube, the signs of one form of lung cancer. One day in the future, they hope to create a “doctor in a cell”, which will be able to operate inside a living body, spot disease and apply the necessary treatment before external symptoms even appear.
The neuron is a functional unit of the body's nervous system that transmits electro-chemical impulses through the system. These electrochemical impulses are the way information is exchanged in our bodies. Think of the neurons as phone or network lines that make up the Internet and the electrochemical impulses as e-mail, and you get idea. Just as e-mail is used to send messages between people, electrochemical impulses are used to send message between different body parts
4.The Biological Bits and Bytes of DNA Computing :
Computers use 1 or 0 and DNA uses 1 ,2 ,3 and four. Or in the geneticists jargon A C T G. We are built of proteins , each protein is assembled from twenty different building blocks called amino acids. The order in which these amino acids are assembled is obtained from the sequence contained in DNA. I am told this leads to 64 different combinations.
DNA computers take advantage of DNA's physical properties to store information and perform calculations. In a traditional computer, data are represented by and stored as strings of zeros and ones. With a DNA computer, a sequence of its four basic nucleotides — adenine, cytosine, guanine, and thymine — is used to represent and store data on a strand of DNA. Calculations in a traditional computer are performed by moving data into a processing unit where binary operations are performed. Essentially, the operations turn miniaturized circuits off or on corresponding to the zeros and ones that represent the string of data. In contrast, a DNA computer uses the recombinative properties of DNA to perform operations.
4.1 Guinness Book of World Records :
The computer is listed in the 2004 Guinness Book of World Records as the world's smallest biological computing device. Prof Shapiro's device is a development of a biological computer that he first built in 2001. DNA is the software of life: it carries huge quantities of information, programs the operating system of every cell, controls the growth of the whole organism and even supervises the making of the next generation. The first biological computers were used to make mathematical calculations. They may not outperform silicon-based technology in the world of banking, aviation and databases, but the Weizmann team realised that they might be agents of medical treatment.
They could be provided with specific `search and destroy' programmes, administered as drugs, and delivered by the bloodstream to autonomously detect disease in cells. They could even be used in late-stage cancer, to detect and prevent secondary growths That is the dream. However, the biology in the latest experiments was hugely simplified: the little machine identified cancer molecules in a sterile saline solution in a laboratory under ideal conditions.
To actually track down and disable cancer cells in a human body, it would have to survive the hurly-burly of proteins, lipids, polysaccharides and nucleic acids, any of which could block or disable it. "There could be many reactions with many other molecules that may be detrimental to either the computer or the cell in which it operates,'' said Prof Shapiro.
5. COMPUTERS & BIOLOGICAL COMPLEXITY:
The mathematics of DNA has a complexity of 2^64 and before you say no, try to say 18446744073709551616 and mean it. The point of this is, the makers of the chip that is at the heart of the common or garden PC are casting the dies for the next generation of CPUs namely a 64 bit data bus. There are two ways of looking at computer architecture. The simplest way to understand this , is to imagine a road and imagine how many cars you could get to travel along it in an hour. To increase the traffic on the road you either widen it or make the cars go faster or make smaller cars. The next generation of personal computers will have a complexity matching our own. I say this because of genetic algorithms. The fact that most of today's computers are linked up via the internet makes it more likely that once change starts to happen, it will happen fast .
There is an awful similarity between DNA and machine code. The complexity of our machine code gets to the complexity of our DNA. 64 bit processors have twice the exponental complexity 32 bit processors have.
BIOLOGICAL COMPUTING.docx (Size: 97.56 KB / Downloads: 30)
1.INTRODUCTION:
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.
2.THE WORLD’S SMALLEST COMPUTER:
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.
3.DOCTOR IN A CELL:
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.
In one series of test-tube experiments, the team programmed the computer to identify RNA molecules that indicate the presence of prostate cancer and, following a correct diagnosis, to release the short DNA strands designed to kill cancer cells. Similarly, they were able to identify, in the test tube, the signs of one form of lung cancer. One day in the future, they hope to create a “doctor in a cell”, which will be able to operate inside a living body, spot disease and apply the necessary treatment before external symptoms even appear.
The neuron is a functional unit of the body's nervous system that transmits electro-chemical impulses through the system. These electrochemical impulses are the way information is exchanged in our bodies. Think of the neurons as phone or network lines that make up the Internet and the electrochemical impulses as e-mail, and you get idea. Just as e-mail is used to send messages between people, electrochemical impulses are used to send message between different body parts
4.The Biological Bits and Bytes of DNA Computing :
Computers use 1 or 0 and DNA uses 1 ,2 ,3 and four. Or in the geneticists jargon A C T G. We are built of proteins , each protein is assembled from twenty different building blocks called amino acids. The order in which these amino acids are assembled is obtained from the sequence contained in DNA. I am told this leads to 64 different combinations.
DNA computers take advantage of DNA's physical properties to store information and perform calculations. In a traditional computer, data are represented by and stored as strings of zeros and ones. With a DNA computer, a sequence of its four basic nucleotides — adenine, cytosine, guanine, and thymine — is used to represent and store data on a strand of DNA. Calculations in a traditional computer are performed by moving data into a processing unit where binary operations are performed. Essentially, the operations turn miniaturized circuits off or on corresponding to the zeros and ones that represent the string of data. In contrast, a DNA computer uses the recombinative properties of DNA to perform operations.
4.1 Guinness Book of World Records :
The computer is listed in the 2004 Guinness Book of World Records as the world's smallest biological computing device. Prof Shapiro's device is a development of a biological computer that he first built in 2001. DNA is the software of life: it carries huge quantities of information, programs the operating system of every cell, controls the growth of the whole organism and even supervises the making of the next generation. The first biological computers were used to make mathematical calculations. They may not outperform silicon-based technology in the world of banking, aviation and databases, but the Weizmann team realised that they might be agents of medical treatment.
They could be provided with specific `search and destroy' programmes, administered as drugs, and delivered by the bloodstream to autonomously detect disease in cells. They could even be used in late-stage cancer, to detect and prevent secondary growths That is the dream. However, the biology in the latest experiments was hugely simplified: the little machine identified cancer molecules in a sterile saline solution in a laboratory under ideal conditions.
To actually track down and disable cancer cells in a human body, it would have to survive the hurly-burly of proteins, lipids, polysaccharides and nucleic acids, any of which could block or disable it. "There could be many reactions with many other molecules that may be detrimental to either the computer or the cell in which it operates,'' said Prof Shapiro.
5. COMPUTERS & BIOLOGICAL COMPLEXITY:
The mathematics of DNA has a complexity of 2^64 and before you say no, try to say 18446744073709551616 and mean it. The point of this is, the makers of the chip that is at the heart of the common or garden PC are casting the dies for the next generation of CPUs namely a 64 bit data bus. There are two ways of looking at computer architecture. The simplest way to understand this , is to imagine a road and imagine how many cars you could get to travel along it in an hour. To increase the traffic on the road you either widen it or make the cars go faster or make smaller cars. The next generation of personal computers will have a complexity matching our own. I say this because of genetic algorithms. The fact that most of today's computers are linked up via the internet makes it more likely that once change starts to happen, it will happen fast .
There is an awful similarity between DNA and machine code. The complexity of our machine code gets to the complexity of our DNA. 64 bit processors have twice the exponental complexity 32 bit processors have.