Belmont Club

Doctors Frank and Stein

I still remember the tingly feeling the first time I cloned a piece of DNA. From the moment the tiny drop of ligase fell in the tube to the moment I isolated DNA from a white colony in a sea of blue bacteria, looked at the gel, and knew for certain that I’d constructed a new plasmid, I was hooked. This probably sounds incredibly geeky, but I even bought my own copies of Old and Primrose’s Principles of Gene Manipulation and Maniatis’s Molecular Cloning, and read them, cover to cover, after work on warm summer nights. Hearing that enthusiastic amateurs are trying to build bacterial sensors in their kitchens rekindled that sense of excitement. I had to know more.

In the early 21st century Small Science, which had been eclipsed by government funded or industrial Big Science staged a partial resurgence after a long decline from the middle of the 20th century. The quotation above is an excerpt from article on DIY or do-it-yourself biology. Extending the open-source philosophy of the software industry, genetic engineering efforts are moving into amateur labs, linked together by shared databases and process flows. The influence of computer science in other areas is evident as well. The author of the quote above, Sandra Porter, wrote:

Talking with Jonathan Cline, DIYbio project manager and real-life electrical engineer in San Francisco, gave me some insights into the DIYbio philosophy. I learned that the group, as a whole, is very into the notion of building things cheaply and reducing costs, sharing information and tools, and finding ways for hobbyists to run experiments and contribute data back to a public database. Cline’s dream scenario would be to have standardized biological parts with predictable behaviors so that the parts could be combined and the cell would behave as programmed in an expected way. He described an example of putting computational logic into a cell with a memory circuit. The circuit would have multiple promoters, two genes for different shades of green fluorescent protein, and an amplifier that would create a feedback loop. Bacteria would turn green in response to a stimulus and after some period of time they would switch to producing the other color of GFP and become red.

The amateurs have their own Wiki, called OpenNetWare. And they are taking on aging. The SENS Foundation is using the new techniques to “solve parts of the aging question”. Although there is probably a lot of hype and projection in this burgeoning field, there is also a sense of possibility. HPlusmagazine describes the intellectual core of the effort — and it’s dependence on open source philosophy.

DIYbio software has been around for a long time. [email protected], which came out of Professor vinjay Pande‘s group at Stanford Chemistry Department in 2000, is designed to perform computationally intensive simulations of protein folding and other molecular dynamics. FAH, as it‘s known, is now considered the most powerful distributed computing cluster in the world. Open source software for bioinformatics, computational neuroscience, and computational biology is plentiful and continues to grow. On their own time, students, professors, entrepreneurs, and curious amateurs contribute to open source work that captures their interests. BioPerl and BioPython have hundreds of contributors and tens of thousands of users. Programs like GENESIS and NEURON have been downloaded by computational neuroscientists for over twenty years.

The software part is easy. The FOSS/OSS machine is well established, and has been successful for a long time. As the shift to open source software continues, computational biology will become even more accessible, and even more powerful. (Red Hat has recently asked the US Supreme Court to bar all software patents, submitting an amicus brief to the Supreme Court in the “Bilski case.” See Resources.) …

One unpleasant way to discover the power of new technologies is to have a malevolent organization beat civil society to the punch. The next big terrorist threat may come in the form of a biological attack. Recently, a government bipartisan commission “chaired by former Senators Bob Graham, a Democrat from Florida, and Jim Talent, a Missouri Republican, [gave] the new administration the grade of “F” for failing to take key steps the commission outlined just over a year ago in its initial report.”

Specifically, the commission concludes that the Obama administration, like the three administrations before it, has failed to pay consistent and urgent attention to increasing the nation’s ability to respond quickly and effectively to a germ attack that would inflict massive casualties on the nation.

The commission repeated its warning that unless nations acted decisively and urgently, it was more likely than not that a WMD will be used in a terrorist attack somewhere in the world by the end of 2013, and that the terrorists’ weapon of choice would be biological, rather than nuclear.

The Next 9/11 may not involve airplanes at all. Perhaps the thing to watch isn’t flight schools but courses in biology. Of course it is unlikely that such a threat would be developed with DIY bio methods which relies on open information exchanges. But the potential for Small Science has returned and with it the prospect of a substantial menace from a network of basement labs. And you can never tell whether the authorities will see a threat coming even if it is out in the open. One common failing of the giant intelligence apparatus is that it often fails to connect the dots even when the dots exist in abundance.

Maybe we are moving away from the gigantism which characterized the postwar years. Recent intellectual effort has partially moved away from the huge institutions. Big media, the academy and to some extent even Big Science are being challenged at least in some areas by the new productive paradigm of networked collaborators. Without wishing to overstate its advantages, perhaps the most enduring lesson of the last ten years is that Western societies have too many people locked up in giant, sterile bureaucracies and too self-motivated but networked entrepreneurs. At a time when many “advanced” welfare societies are investing in ever larger and eyeless monoliths, other societies, unhampered by this legacy are gaining ground simply by refusing these constraints.

Economic crises often contain a “message” about the current state of a civilization. After World War 2, the conventional wisdom was that things had to be made bigger and regulated ever more. Perhaps that era is over. When the last UAW dinosaur and SEIU shop closes down it may be a sad moment for its members. But it may also mark the day when millions of people are thrown into the real workforce, which with some luck will have the liberty and capital to absorb them, and they can get a productive job.


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