IBM is publicizing a novel gene sequencing technology they are developing as the “DNA Transistor”. With this system a single strand of DNA can be sequenced by being pushed through a tiny hole on a microprocessor that will read the small changes in the electrical field depending on whether the letter passing through the pore is an A, T, C, or G. I have recently become fascinated with the “computer language” that people use to describe biological systems and novel biotechnologies. Often the metaphor between electronic and biological systems is instructive in some way, but in the case of the “DNA Transistor” I think the metaphor to electrical components is inappropriate and confusing. My background is in biology, so it’s possible that my grasp of the basics of electronics is not as good as it should be, but I’m pretty sure microchip sequencing technology doesn’t really have much to do with a transistor. Even as a reference to the transistor as a basic unit of electronics the association with high-tech sequencing technology eludes me. Am I missing something?
via Singularity Hub
Wanted - Home Computers to Join in Research on Artificial Life - NYTimes.com
The ambiguity in the term “synthetic biology” is fascinating. Evelyn Fox Keller points it out as “the conspicuous difference between the production of artificial life and the artificial production of life.” The kind of synthetic biology that I do is closer to the latter definition, changing existing biology in order to do something “useful” (making fuels in my case), and to hopefully learn more about how biology works in general. In my lab we use computer models of cellular processes such as metabolism in order to help inform some of our “design” decisions, something alluded to in the article:
Software simulations that can model evolution could be used by human designers, Mr. Damer argued. “We can’t build cars and airplanes or even toys these days without computer modeling and simulation,” he said. “So why not biochemistry?”
but what do computer models of life mean on their own, without testing the predictions in a real cell, without data from biochemical experiments (no matter how distant from “real” life those may be, but that’s another story)? How does our concept of what life is depend on our unique point of view and how does this affect what we program into our computer models? How is the search for extraterrestrial life tied to the search for the origin of life?
The GenoCAD point-and-click user interface guides the user through the process of designing new sequences. By successively clicking on icons representing structural features or functional blocks, complex DNA sequences composed of dozens of functional blocks can be designed in a matter of minutes. Upon completion of the design process, the sequence can be downloaded for synthesis or further analysis.
The idea of computer aided design in synthetic biology is fascinating, intellectually interesting and important, and infuriating at the same time. As a biologist who works full time trying to build synthetic gene networks, the idea of being able to computationally design a system of genes in minutes that actually works is a beautiful dream. The problem is that right now it’s not coming up with ideas or designs that is the hard part, it’s actually getting the designed systems to work the way we think that they will in the cellular context. I wish this money was going into trying to understand some of the underlying biology—What constitutes a “part”? How do genes from different organisms work in your “chassis” strain? How can you regulate gene dynamics and cellular noise in a way that allows genetic networks to function predictably? I do hope that the community building aspect of the project does take off so that people can more easily share this kind of information with each other, because only through an enormous and concerted effort to collect this kind of data will we be able to understand genetic networks and be able to build new ones. At that point, software will only be icing on the cake.
Scientists love analogies; they make it easier to discuss and understand complicated systems in terms of things that are familiar to many people. Synthetic biology is still trying to define itself, but the analogy that prevails thus far is synthetic biology:biology/life::electrical engineering:physics. With the data from decades of biological research, we can put together novel biological pathways and maybe even whole genomes, creating new living “circuitry”.
Since the industrial revolution, Nature has been seen as both a source of resources to be used and shaped into human invention, but also as somewhat of a machine itself, something that has parts that can be systematically understood and then used as a tool [1]. As technology has developed to embrace the digital machine, our analogies for Nature and specifically biology have changed with it. In synthetic biology we have DNA as “software”, genes as “parts”, biochemistry as “logic gates”, all the way up to cells as computers and networks [2].
With this kind of analogy in place, synthetic biology can make “devices” that behave like toggle switches, logic gates, diodes, or oscillators, and even develop real computer software to help build living circuits like you would electronic circuits. This intertwining of biology and electrical engineering has almost moved beyond simple analogy, that biological molecules are electrical components (I too am guilty of this) and that progress in synthetic biology will mirror progress in computer engineering in the 20th century.
This analogy is useful, and certainly interesting, but is it limiting? Biology does a lot of amazing things that computers can’t (yet?), and vice-versa. There are some people working on cyborg interfaces between computers and cells as a way to take advantage of both (see the Harvard 2008 iGEM project, for example) but in a lot of ways cells and computers are not alike in what they are, what they do, and how we interact with them (and that’s ok). I think most importantly, this kind of analogy doesn’t really take into account the basic science implications of synthetic biology as a tool.
I’m not sure if we need an analogy at all, but the one that I like the best is synthetic biology:biology::synthetic chemistry:chemistry from Brian Yeh and Wendell Lim’s 2007 Commentary “Synthetic biology: lessons from the history of synthetic organic chemistry” [3].
Chemical synthesis of organic compounds in the mid 1800’s shattered the notion that there is something magical about the chemicals that make up living systems. Most importantly, synthesis led to enormous insights into the physical structure of molecules. Despite the very limited knowledge of chemistry that existed at the time of the first synthetic projects, attempts at creating molecules opened up new avenues for learning about chemistry, with obvious implications for how we make drugs, dyes, plastics, food etc.
We may be at such a turning point now. There is a lot that we don’t know about how cells work, but attempts at synthesizing rudimentary biological pathways will possibly allow synthetic biologists to better understand how cells work, and will very likely develop many useful technologies and research tools along the way. In the end synthetic biology may redefine biological engineering and the study of biology into something uniquely different.
I’m fascinated by the ways that people discuss biological engineering, the language that they use to talk about what cells, proteins, and DNA do. Often, these words come from computer engineering: DNA is the code, proteins are machines, cells can interact to form networks, etc.
A recent article in the UK version of Wired points out that even though we like to talk about biology as machines, the reality is that while “the 1s and 0s of software live in shiny metals shielded by colourful plastics; biological data lurks in dampness, in pipettes and test tubes.” How does the grossness associated with bacteria affect how synthetic biology and biotechnology are received?
I love the idea that if the domestication of biotechnology is going to dominate our life for the next 50 years, as Freeman Dyson predicts, the aesthetics and perceptions surrounding biology are going to change dramatically. Will germophobes be the new luddites? Will bacteria be beautiful? How about lab supplies?
