biological computer

Biological computer that ‘lives’ inside the body comes one step closer as scientists make transistor out of DNA and RNA.

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Molecular computer graphic of DNA double helixMolecular computer graphic of DNA double helixMolecular computer graphic of DNA double helixmolecular_computer3Finding could lead to new biodegradable devices based on living cells that are capable of detecting changes in the environment

Scientists believe they are close to building the first truly biological computer made from the organic molecules of life and capable of working within the living cells of organisms ranging from microbes to man.

The researchers said that they have made a transistor – the critical switch at the heart of all computers – from DNA and RNA, the two biological molecules that store the information necessary for living things to replicate and grow.

Silicon transistors control the direction of flow of electrical impulses within computer chips, but the biological transistor controls the movement of an enzyme called RNA polymerase along a strand of the DNA molecule, the scientists said.

Ultimately, the aim is to use the biological transistors – called transcriptors – to make simple but extremely small biological computers that could be programmed to monitor and perhaps affect the functioning of the living cells in which they operate, researchers said.

It could lead to new biodegradable devices based on living cells that are capable of detecting changes in the environment, or intelligent microscopic vehicles for delivering drugs within the body, or a biological monitor for counting number of times a human cell divides so that the device could destroy the cell if it became cancerous, the scientists said.

“Biological computers can be used to study and reprogram living systems, monitor environments and improve cellular therapeutics,” said Drew Endy, assistant professor of bioengineering at Stanford University in California, who led the study published in the journal Science.

Last year, Professor Endy announced new ways of using biological molecules to store information and to transmit data from one cell to another. The latest study adds the third critical component of computing – a biological transistor that acts as a “logic gate” to determine whether a biochemical question is true or false.

Logic gates are critical for a computer to function properly. In a biological setting the use of logical data processing is almost as limitless as its use in conventional electronic computing, said Jerome Bonnet, a bioengineer within the Endy laboratory, and the lead author of the study.

“You could test whether a given cell had been exposed to any number of external stimuli – the presence of glucose and caffeine for instance. [Logic] gates would allow you to make the determination and store that information so you could easily identify those which had been exposed and which had not,” Dr Bonnet said.

Biological computers have been the dream of electronic engineers for decades because they open the possibility of a new generation of ultra-small, ultra-fast devices that could be incorporated into the machinery of living organisms.

“For example, suppose we could partner with microbes and plants to record events, natural or otherwise, and convert this information into easily observed signals. That would greatly expand our ability to monitor the environment,” Professor Endy said.

“So the future of computing need not only be a question of putting people and things together with ubiquitous silicon computers. The future will be much richer if we can imagine new modes of computing in new places and with new materials – and then find ways to bring those new modes to life,” he said.

Source: http://www.independent.co.uk

Scientists develop biological computer to encrypt and decipher images.

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Scientists at The Scripps Research Institute in California and the Technion–Israel Institute of Technology have developed a “biological computer” made entirely from biomolecules that is capable of deciphering images encrypted on DNA chips. Although DNA has been used for encryption in the past, this is the first experimental demonstration of a molecular cryptosystem of images based on DNA computing.

Instead of using traditional computer hardware, a group led by Professor Ehud Keinan of Scripps Research and the Technion created a computing system using bio-molecules. When suitable software was applied to the biological computer, it could decrypt, separately, fluorescent images of The Scripps Research Institute and Technion logos.

A Union Between Biology and Computer Science.

In explaining the work’s union of the often-disparate fields of biology and computer science, Keinan notes that a computer is, by definition, a machine made of four components—hardware, software, input, and output. Traditional computers have always been electronic, machines in which both input and output are electronic signals. The hardware is a complex composition of metallic and plastic components, wires, and transistors, and the software is a sequence of instructions given to the machine in the form of electronic signals.

“In contrast to electronic computers, there are computing machines in which all four components are nothing but molecules,” Keinan said. “For example, all biological systems and even entire living organisms are such computers. Every one of us is a biomolecular computer, a machine in which all four components are molecules that ‘talk’ to one another logically.”

The hardware and software in these devices, Keinan notes, are complex biological molecules that activate one another to carry out some predetermined chemical work. The input is a molecule that undergoes specific, predetermined changes, following a specific set of rules (software), and the output of this chemical computation process is another well-defined molecule.

“Building” a Biological Computer.

When asked what a biological computer looks like, Keinan laughs.

“Well,” he said, “it’s not exactly photogenic.” This computer is “built” by combining chemical components into a solution in a tube. Various small DNAmolecules are mixed in solution with selected DNA enzymes and ATP. The latter is used as the energy source of the device.

“It’s a clear solution—you don’t really see anything,” Keinan said. “The molecules start interacting upon one another, and we step back and watch what happens.” And by tinkering with the type of DNA and enzymes in the mix, scientists can fine-tune the process to a desired result.

“Our biological computing device is based on the 75-year-old design by the English mathematician, cryptanalyst, and computer scientist Alan Turing,” Keinan said. “He was highly influential in the development of computer science, providing a formalization of the concepts of algorithm and computation, and he played a significant role in the creation of the modern computer. Turing showed convincingly that using this model you can do all the calculations in the world. The input of the Turing machine is a long tape containing a series of symbols and letters, which is reminiscent of a DNA string. A reading head runs from one letter to another, and on each station it does four actions: 1) reading the letter; 2) replacing that letter with another letter; 3) changing its internal state; and 4) moving to next position. A table of instructions, known as the transitional rules, or software, dictates these actions. Our device is based on the model of a finite state automaton, which is a simplified version of the Turing machine. ”

Unique Biological Properties.

Now that he has shown the viability of a biological computer, does Keinan hope that this model will compete with its electronic counterpart?

“The ever-increasing interest in biomolecular computing devices has not arisen from the hope that such machines could ever compete with electronic computers, which offer greater speed, fidelity, and power in traditional computing tasks,” Keinan said. “The main advantages of biomolecular computing devices over electronic computers have to do with other properties.”

As shown in this work, he continues, a wealth of information can be stored and encrypted in DNA molecules. Although each computing step is slower than the flow of electrons in an electronic computer, the fact that trillions of such chemical steps are done in parallel makes the entire computing process fast. “Considering the fact that current microarray technology allows for printing millions of pixels on a single chip, the numbers of possible images that can be encrypted on such chips is astronomically large,” he said.

“Also, as shown in our previous work and other projects carried out in our lab, these devices can interact directly with biological systems and even with living organisms,” Keinan explained. “No interface is required since all components of molecular computers, including hardware, software, input, and output, are molecules that interact in solution along a cascade of programmable chemical events.” He adds that because of DNA’s ability to store information, major computer companies have been extremely interested in the development of DNA-based computing systems.

Source: The Scripps Research Institute