|Biological Computer Cracks the Code
|Sivan Shoshani recently completed her breakthrough PhD research in the Keinan lab. She is a graduate of the interdisciplinary program in biotechnology within the Jacobs Graduate School
A code-breaking interdisciplinary team created a computing system using biomolecules that, with appropriate software, was able to decipher two overlapping fluorescent images that were encrypted on a single DNA 5476-pixel chip. The group was led by Prof. Ehud Keinan of Technion’s Schulich Faculty of Chemistry and adjunct professor at The Scripps Research Institute, California.
Published online in the journal Angewandte Chemie in February 2012, this is the first experimental demonstration of a molecular cryptosystem of images based on DNA computing. Since multiple images can be encrypted on the same chip, this method can be used for a higher level of encryption in which each individual image is meaningless but their linear combination represents the complete picture.
Biomolecular Computing (BMC) is a rapidly evolving independent field at the intersection of computer science, chemistry, and biology. The main advantage of autonomous BMC devices over electronic computers arises from their ability to interact directly with biological systems.
Keinan explains that a computer is, by definition, a machine comprising four components: hardware, software, input, and output. Traditional computers are electronic, namely, machines in which both input and output are electronic signals, the hardware is a complex composition of metal and plastic components, and the software is a sequence of instructions given to the machine in the form of electronic signals.
Cracking the encryption: Scientists developed a biological computer capable of deciphering images encrypted on DNA chips. As a proof of concept, they encrypted the Scripps Research and Technion logos on a single DNA chip and, using software, decrypted the separate fluorescent images. (Image courtesy of the Keinan lab)
“In contrast to electronic computers, there are computing machines in which all four components are nothing but molecules,” he says. “All biological systems, and even entire living organisms, are such computers. Every one of us is a biomolecular computer.”
Jacobs Graduate School PhD student Sivan Shoshani explains further that when the macromolecules representing these four essential computer components are mixed together in a solution, they are “capable of performing a computational task by a cascade of chemical events based on a programmed pathway,” she says.
The research team “built” the biological computer by combining chemical components in the lab. DNA molecules were mixed in solution with selected DNA enzymes and ATP - the substance that provides energy for our own cells. “It’s a clear solution - you don’t really see anything,” Keinan said. “The molecules start interacting with one another, and we step back and watch what happens.”
Prof. Ehud Keinan is the incumbent of the Benno Gitter and Ilana Ben Ami Chair in Biotechnology at Technion; he is also Adjunct Professor, Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California.
Technion and The Scripps Research Institute logos were both encrypted on a single DNA chip. To decipher either of these images a mixture of input molecules was processed, which led to image visualization by fluorescent output molecules. This is the first demonstration of a cryptosystem based on BMC.
“Our BMC 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.”
While electronic computers offer greater speed, fidelity, and power in traditional computing tasks, the scientific community has shown much interest, over the past decade, in BMC due to their ability to carry out a vast number of operations in parallel - speeding up the overall computing process. As shown in this study, a wealth of information can be stored and encrypted in DNA molecules with high fidelity, having potential applications in medicine, agriculture and more.
Keinan and Shoshani’s paper was coauthored with Dr Yoav Arava of the Faculty of Biology, and Dr Ron Piran, Technion alumnus and postdoctoral fellow at Scripps Research.