Biological Computing

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This article was published by ComputorEdge, issue #2420, 2006-05-19, as a feature article, in both their print edition (on pages 18 and 20) and their website.

When science fiction writers and other visionaries first began dreaming of artificial creatures that were internally powered, self-guiding, and capable of making their own decisions — or at least following rudimentary instructions — the entities depicted were fully mechanical, in the sense of containing no living tissue or other biological components. This was largely the result of the mechanistic view that swept the Western world during the Industrial Revolution, combined with limited understanding of cellular biology.

Since those basic yet essential beginnings, researchers have extended their knowledge and creations to much lower levels of detail, in both the fields of biology and computation. At the same time that microprocessor designers and manufacturers were shrinking the sizes of chips, memory modules, and other hardware components, microbiologists and genetic researchers were greatly expanding their knowledge of how cells and genetic materials perform their astounding functions.

As a consequence of these separate — but in some ways similar — fields growing and eventually overlapping one another, the imaginative artists and scientists of today are dreaming up new ways in which biology and technological applications can be combined. From the killer cybernetic organisms portrayed in movies, to the real-life medical advances such as artificial ears and eyes, the current developments in this new field — often termed "synthetic biology" — have the potential to revolutionize the way humans live.

Der Blinkenlights

The overarching idea of melding biology with computing, allows for a tremendous amount of leeway, including at what level of size the research is done. Some scientists focus on genetic modifications to attempt to cause genetic material to behave in a deterministic, and thus computational, manner. But the real progress is currently being made in the areas of bacterial and enzymatic computing, in which the elements are caused to structure themselves into complex and computationally meaningful shapes.

One example of this is an intriguing advancement accomplished in early 2005, at Princeton University, by a team led by Ron Weiss, an assistant professor of electrical engineering and molecular biology. Weiss and his colleagues biologically programmed strains of E. coli bacteria to emit red or green fluorescent light in response to signals emitted from another set of E. coli.

Superficially, this might appear to the uninitiated to be simply a clever but technologically valueless feat. After all, flashing lights of various colors are typically not an essential part of computers. They are usually little more than nerd "eye candy" tacked on to a customized PC case, or at best an LED indicator to communicate, for example, that a hard disk is being accessed at the moment.

A Byte of Bacteria

But that is actually the key purpose of the bacteria's fluorescent lighting: communication. It is the communication among the E. coli bacteria, via light, that commands them to form structures determined by the researchers. According to Weiss and his team, by enabling these bacteria to communicate among themselves, for the first time, it makes it possible for the bacteria to group themselves into predictable patterns, even when there are millions or even billions of them.

Experiments utilizing huge numbers of E. coli bacteria are likely being conducted now and will be extended in the future. Yet using only a fraction of the number of bacteria, the Princeton scientists were able to coax the bacteria into forming several different patterns, including a bull's-eye, a simple flower, and — for the romantic side of every molecular biologist — a heart.

But for those of us living outside of a laboratory, of what use are light-chatting bacteria auditioning for Valentine's Day? One potential use, which admittedly is several years off, is to employ such bacteria for detecting chemicals intended to be used for bioterrorism. Another potential application is the programmed growth of new human tissue, such as that found in a patient's damaged spinal cord or an injured inner ear.

Enzymes Instead of Electronics?

More recently, in February of 2006, a team of molecular researchers at the Hebrew University in Jerusalem, headed by Itamar Willner, announced that they had created a molecular computer made of enzymes — specifically, glucose dehydrogenase (GDH) and horseradish peroxidase (HRP), which were used for generating two interconnected chemical reactions.

The most necessary part of any digital computation is the ability to represent binary digits, 0 and 1. In the case of the enzyme computer, two additional chemicals, hydrogen peroxide and glucose, were utilized for representing values input to the computing device. Binary 0 was represented by the absence of both chemicals, and binary 1 was represented by the presence of each chemical.

Using just those few elements, the researchers were able to have the enzyme computer perform two simple but essential logic computations on two values: logical AND (when both values are equal to 1) and logical XOR (when both values are not equal to one another). By adding two more enzymes — glucose oxidase and catalase — into the mix, the scientists were able to add together binary numbers, using the aforesaid logic functions. The results of these computations were detected optically.

As with the bacterial computer, the value of this new development lies not so much in its contribution to basic research, but instead to its potential for future applications. Enzymes are already being employed for making calculations, in the form of specially encoded DNA, largely because it is believed that they will eventually have the ability to far exceed the speed and computational power of conventional, non-biological processors. This is achieved by performing multiple calculations in parallel, as well as packing large numbers of components into miniscule spaces.

In contrast, Willner's enzyme computer is far slower than any conventional counterparts. His device can require many minutes just to perform a single calculation. Instead, the enzyme computer could be integrated into a patient's body, and serve as part of some sensing equipment, such as monitoring and even reacting to the patient's response to various dosages of a drug. Willner notes that such devices could calculate an entire metabolic pathway in the human body.

The research breakthroughs and devices discussed above, are but some of the more newsworthy examples of synthetic biology. However, they do illustrate how far we have advanced in the field, as well as some of the potential uses of the technology.

Whether utilized for detecting biochemical threats, or delivering drugs intelligently, biological computers are clearly going to play role in our future — where science fiction becomes science fact.

Copyright © 2006 Michael J. Ross. All rights reserved.

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