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Scientists have developed a “biological computer” capable of deciphering images encrypted on DNA chips. As a proof of concept, the scientists encrypted the Scripps Research and Technion logos on a single DNA chip and, using software, decrypted the separate fluorescent images. Image courtesy: Keinan lab.
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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.
The study was published in Angewandte Chemie.
Instead of using traditional computer hardware, a group led by Professor
Ehud Keinan of Scripps Research and the Technion created a computing system
using biomolecules. 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 DNA
molecules 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.
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