Life performs computation much more than you’ve ever thought

23 November 2012 by Rayna Stamboliyska, posted in Weird science

“The level of intelligence has been tremendously increased, because people are thinking and communicating in terms of screens, and not in lettered books. Much of the real action is taking place in what is called cyberspace. People have learned how to boot up, activate, and transmit their brains.

Essentially, there’s a universe inside your brain. The number of connections possible inside your brain is limitless. And as people have learned to have more managerial and direct creative access to their brains, they have also developed matrices or networks of people that communicate electronically. There are direct brain/computer link-ups. You can just jack yourself in and pilot your brain around in cyberspace-electronic space.” ― Timothy Leary, Chaos & Cyber Culture

This quote brings up thoroughly discussed concepts of “wired human interactions” and “globalized self,” all describing our relationship to the internet. The quote also highlights another perspective: the ultimate connection as showcased in cyberpunk culture through the “console cowboy” Case in the Neuromancer or the “game pods”, these outlets plugged through bio-ports in Cronenberg’s movie, Existenz. But if this sounded as daring science fiction 10 years ago, achieving this ‘ultimate connection’ now looks feasible in the near future. Research unveiling the hidden potential of DNA in terms of molecular computation has been ongoing for years, and its outcomes are more promising and mind-blowing than one might have imagined. I kindly invite you to join me in a dive into the exciting waters of DNA-based computers.

The DNA talespinners

Let’s say it actually started with DNA origami. ‘Origami’ as in the original Japanese art of paper folding, and ‘DNA’ as in the molecule encoding all the information an organism needs for its structure and development. Paul Rothemund, continuing Ned Seeman’s legacy, came up with a method which allows a single-stranded DNA molecule from a virus to be folded into a shape of choice. Rothemund introduced small DNA chunks -- “staples” -- that bind at given places of the single-stranded DNA bringing these distant parts together. This endeavour initially produced 2D structures, although recently Hao Yan and his team successfully came up with a beautiful 3D vase.

Such achievements make the geek in each and everyone of us giggle like a happy kid. Beyond geekery, however, these studies are important for a number of potential human health applications. Scientists from different teams have thought of a “DNA FedEx”: a DNA parcel containing a drug, delivered to the right cells in the human body. This type of approach would ensure, for instance, the drug is dispatched without interactions with neighbouring cells which are often responsible for the infamous side effects many medicines have. Recently, researchers from MIT demonstrated a good side of Trojan horses by successfully engineering a DNA-RNA origami that carried RNA interference molecules to be directly delivered to a tumour in a mouse model. Since the origami is not recognized as a threat by the body, it could navigate unhindered to its final destination.

Molecular computation reloaded

Writing a computer language for DNA doesn’t end with DNA origami. Building a computer requires a wide range of components, and circuits are one of them. As DNA is able to accurately position on a steady surface and to bond with metal ions, IBM researches in collaboration with Paul Ruthemond have successfully built tiny circuit boards. Moreover, creating a biological computer able to read images stored into DNA has recently been done, too.

Speaking of storage, this is another component one needs. And it isn’t all that hard: after all, carrying information is DNA’s fundamental function. Salmon sandwich was a good try: scientists thought of embedding salmon DNA between silver nanoparticles connected to two electrodes. This output a 'write-once-read-many' device. Shortly afterwards, researchers from Harvard used 1 gram of DNA to store 700 terabytes, which is in fact one of the researchers’ newest book, Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. The problem of data storage might just have found a solution, as “about four grams of DNA theoretically could store the digital data humankind creates in one year.”

Short ago, Monica Ortiz and Drew Endy from Stanford succeeded in creating the ‘Bi-Fi’: the biological internet. They took the bacteriophage M13 which can be seen as a packager of information as it uses the host machinery to replicate its genetic information and package it prior to destroying the cell and invading the surrounding. Baring some violence in this interaction, this pretty much resembles a TCP/IP protocol where the source sends packets to the destination.

The researchers have thus engineered the ‘M13 system’ which is a communication channel through which cells send and receive information. Noticeably, the ‘M13 system’ even presents a fundamental feature of the internet: it is neutral, that is it transmits the message without knowing or caring what the message is. The ‘M13 system’ thus broadcasts any DNA molecule from one cell to another, extending the basic cellular communication by e.g. chemicals. Amazingly, the DNA molecule can reach 40,000 base pairs of length, and the message was shown to be transmitted at distances as astounding as 7 cm. If for us, this is more or less the size of our little finger, cellularly speaking this is really huge.

To sum it up: DNA origami aim at programming self-assembly and are a means to writing computer language for DNA. We can also build molecular computers, and store huge amounts of data in DNA. Lastly, the ‘M13 system’ is a proof-of-concept that we can send DNA molecules of various sizes through long distances and resembles an in-house LAN network. With the appropriate further engineering, it can be extended to WLAN, i.e. the internet at large, and would allow huge amounts of data to be sent around the world.

“Cyberspace. A consensual hallucination experienced daily by billions of legitimate operators, in every nation, by children being taught mathematical concepts... A graphic representation of data abstracted from banks of every computer in the human system. Unthinkable complexity. Lines of light ranged in the nonspace of the mind, clusters and constellations of data. Like city lights, receding...” ― William Gibson, Neuromancer

Seems within reach, in fact.


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