On the Assembly of Things

ARC Collaboratory: Ramifying Synthetic Biology and Nanotechnology

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Standards, TSCA, and Nano

August 2nd, 2008 by ckelty
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Here’s another standards-related issue following on the issue of “functional composibility” we’ve already raised. For years now, I’ve been hearing the nano-concerned discuss the issue of whether nanomaterials like nanotubes, which are made of pure carbon, are the same thing as something like graphite, also made of pure carbon. Obviously, the answer is no, since graphite is good for pencils and nanotubes can apparently Do Anything(tm). However, the US Environmental Protection Agency’s Toxic Substances control Act, in its current form, would treat them as identical. Here, then, is a good place to focus on not only issues of substance (what is it?) but issues of mode: what is it for, what is it expected to do. TSCA is written only to deal with the former, and this may, or may not, reflect a scientific consensus as to how to treat objects, or it may reflect political expediency.

In any case, this blog post from Richard Denison at Environmental Defense finally raises an issue that I have informally raised with colleagues over and over again: why focus on only nano and its difference, when all chemicals on the list should probably be treated with respect to mode as well as to substance. Perhaps this is what is nagging me about SynBio objects as well, in that the attempt to define a standard is focused on the substance of the thing and not its mode. (Substance and mode might not be the right terms here… been reading Spinoza).

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News items

July 23rd, 2008 by rabinow
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1. There is an article in Wired on George Church and the personal genome project. Pictures at a Walden Pond equivalent. Or as Marc (my son) puts it-one of those dreary leafless places in the East.

2. two articles in nature biotechnology: Drew Endy on standardization and Adam Arkin as well.

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NYT article on InnoCentive

July 23rd, 2008 by ckelty
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An NYT article profiles the online research-contest start up Innocentive. The Article is a spin on “open source science” that confuses a lot of the issues but also raises interesting questions about both the nature of organization in contemporary science (both corporations and academic labs are too cloistered, according to this view) and is related the issues of “modularity”– namely the question of how to “decompose” a problem into doable chunks so that an open source-ish approach is worthwhile. As Karim Lakhani puts it:

The company, with offices in Waltham, Mass., has a staff of scientists who work with seekers and solvers, reviewing challenges to make sure they are clear and detailed, and guiding would-be solvers who may have a solution.

That specificity is crucial to InnoCentive’s operation, people who have studied the company say. “If you say, ‘find me a cure for cancer’ it may not work,” Dr. Lakhani said. But if problems can be “decomposed” into what he called modular questions, like “find me a biomarker for this condition, these questions may be more tractable.”

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Functional Composibility

July 21st, 2008 by gaymon
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Functional composibility (i.e. can modularized “parts” be assembled” is a central challenge in synthetic biology, on which much of the overall enterprise depends. It is a challenge that bears on questions of design and composibility, e.g. to what extent are living systems suceptible to the classic goals of engineering such as standardization and modularization. It is also a challenge that bears on questions of ontology: what is being made in synthetic biology.

A question we have is: how does functional composibility play out in nanotechnology?

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Eppendorf and Bio-rad finally target their market

July 20th, 2008 by ckelty
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Just a little weekend fun…

Apparently laboratory supply companies have cottoned on to whose actually using their equipment day and mostly night. It’s not Nature-loving eminences grises and their Science-magazine reading betes noires… it’s The Youth:

Eppendorf’s advertisement for it’s epMotion automatic pipetting system is a boy-band inspired goof.

And Bio-Rad, maker of PCR machines, goofs on “We are the World”

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Bulletin of the Atomic Scientists

July 9th, 2008 by rabinow
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We might all take a look at the Bulletin of the Atomic Scientists. It has short pieces on security in synbio and nano.
Nothing truly startling but a part of the discussion that is taking place out there.

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Problems

July 4th, 2008 by rabinow
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“The Chinese are very adept at reducing big problems to small problems, then reducing small problems to nothing at all, as the saying goes. It’s a survival skill they’ve developed over millennia.”
Beiing Come, Ma Jien,
Reviewed by Michiko Kakutani, \NY Times, July 4, 2008

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Rabinow on Contemporary Equipment

April 2nd, 2008 by gaymon
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In February 2008 Rabinow was interviewed by ADRD (Architecture and Design Research and Development) in Paris on the concept of contemporary equipment and its relevance to the relation of the human sciences and the life sciences. Here is the link to that interview: http://www.adrd.net/adrd_wip/

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Synthetic Bugs and BioTerrorism

March 3rd, 2008 by mstalcup
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“Crying wolf over bioterrorism”
in the Los Angeles Times

The threat posed by synthetic bugs is microscopic. So why are U.S. officials making such a big deal?

By Wendy Orent
March 2, 2008

‘Mother Nature is the most dangerous terrorist,” says Michael Kurilla, the nation’s unofficial biodefense czar. “The microbial world is almost unlimited in its [terrorist] potential.”

But despite the emergence of such new diseases as SARS and the H5N1 avian flu, it isn’t Mother Nature only that worries Kurilla, the director of the Office of Biodefense Research Affairs of the National Institute of Allergy and Infectious Diseases. He’s also concerned about the threat from synthetic biology — the possibility that rogue scientists and bioterrorists could make diseases in the laboratory to be used for terrorism. As he puts it, “The threat and the reality of synthetic biology is becoming greater and greater every day.”

A recent report in Science magazine seems to add another arrow to the quiver of those who worry that synthetic biology could become a source of terrorist weapons. A group of scientists, among them J. Craig Venter, whose team decoded the human genome in 2000, has succeeded in synthesizing a bacterial genome entirely from scratch.

Venter’s feat, however, doesn’t mean that terrorists will be making new germs to kill us. And it shouldn’t mean that the government should spend billions of dollars trying to counter a chimerical threat by developing an equally chimerical antidote.

Synthesizing a bacterium from an existing genome changes nothing fundamental in our understanding of synthetic biology. Virologist Eckhard Wimmer synthesized poliovirus in 2002, and Venter’s team made a bacteria-eating virus in 2003. But Venter’s latest experiment was the first to synthesize so large a piece of DNA. He hasn’t gotten his germ to “boot up” yet — it still has to be put into a living cell and show that it can grow and multiply. Even so, scientists skeptical about the significance of his achievement think Venter will get his synthetic germ up and running in a matter of months.

Venter’s work makes the creation of murderous new life forms seem more believable. Indeed, the fear of dangerous synthetic germs has prompted the enormous, cumbersome apparatus that is the U.S. biodefense program to lurch in a new direction. If we don’t know what pathogens are coming, the reasoning goes, we had better develop new ways of countering them — not one at a time but all of them.

After the anthrax letter attacks of 2001, which began a week after 9/11 and killed five people, the biodefense establishment’s immediate response was to focus on the greatest and likeliest of bioterror threats — the unholy trinity of anthrax, smallpox and plague. In 2004, billions of dollars were set aside for Project Bioshield, which was jointly run by the departments of Homeland Security and Health and Human Services. The program aimed to produce new, safer vaccines and treatments for anthrax and smallpox, in particular.

Almost four years later, Project Bioshield has little to show for all the billions of dollars showered on it. The old “one-bug-one-drug” strategy — designed to develop vaccines and therapies for anthrax, smallpox and plague separately — has been abandoned in favor of “broad spectrum technology” — drugs and methods that will, at least in theory, kill many types of germs.

Rutgers microbiologist Richard Ebright believes that the broader approach is better. As the effectiveness of the antibiotics we already have wanes, it makes sense to search for new classes of these drugs, he believes. The same goes for antivirals. Very few effective ones exist, and viral strains can develop resistance to them too, as some influenza strains have already done with Tamiflu, the newest licensed drug for treating the flu.

But new antibiotics and antivirals represent only a small part of the National Institute of Allergy and Infectious Diseases’ current biodefense program, according to Ebright. The institute is assigning higher priority to radical new approaches. Chief among them is the modulation, or enhancement, of “innate immunity.”

Simply put, there are two components to human immunity: innate, or general, immunity and acquired, or specific, immunity. Innate immunity involves killer cells and chemicals the body launches to fight invading germs. While the germs are held at bay, so to speak, the body develops specific antibodies to mop up the infection. In theory, enhancing innate immunity means creating ways to intensify or strengthen these immune responses so the body can fend off all infections, whether newly evolved or artificial, as soon as they appear.

This sounds good. If you could treat any new disease before the germ is even identified, then artificial bioweapons, or such naturally emerging germs as SARS, would cease to be terrorist specters.

But things are never that simple. Innate immunity is an exquisitely fine-tuned system, honed by millions of years of natural selection.

“It’s not like a stereo system where you can just turn the volume up or down,” says evolutionary biologist Paul W. Ewald of the University of Louisville. He points out that ratcheting up innate immunity might turn the body against itself, producing such autoimmune diseases as lupus or multiple sclerosis. Besides, if innate immunity could really wipe out all infections, why hasn’t it already done so? Why did we evolve the second system of acquired, or specific, immunity at all if innate immunity could completely protect us from disease?

There’s lots of research into innate-immunity enhancement but precious little data supporting it. The scientist most prominently associated with the idea is Ken Alibek, a bioweapons designer who defected from the Soviet Union in 1992 and for years peddled an immunity-boosting nostrum on his commercial website. Harry Whelan, professor of neurology and pediatrics at the Medical College of Wisconsin and lead author of a 2005 article backing this approach in the Journal of Allergy and Clinical Immunology, cites Alibek as one of the “experts” consulted for the article. But though Whelan and his coauthors reviewed a host of research projects testing how various chemical compounds boosted innate immune activity, they reported no data on how well these compounds worked in preventing disease and death.

Charles Hackett of the National Institute of Allergy and Infectious Diseases offers some evidence that limited stimulation of innate immunity can provide some advantages. He points to various vaccine adjuvants, or boosters, that prompt innate immunity to turn on acquired immunity more quickly. But that, Hackett acknowledges, isn’t the same thing as enhancing general innate immunity. “Innate immunity is an area that’s evolved over millenniums and is very clever,” he told me. “If you want to [enhance] it, you really have to understand it better than we understand it now.”

Artificial germs remain an illusion. Venter, like scientists before him, has not made a new germ. He used a genome map to re-create an old one. Similarly, despite all the interest in enhanced innate immunity, no one has been able to show that the approach works. The wreckage of Project Bioshield shows that the one-bug-one-drug approach is a failure. But by banking on the possibility of boosting innate immunity, the U.S. biodefense leviathan could well be, once again, staggering in the wrong direction.

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Patent Booty in NanoBio

June 3rd, 2007 by ckelty
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Nano-Terra is receiving over 50 patents from Harvard University– according to the article, the largest transfer in Harvard history– from the lab of George Whitesides, chemist and nano-bio pioneer. It’s not clear what the transfer means, since NanoTerra was “founded in 2005 with the goal of creating a home for the Whitesides patents.” Is it news or just business as usual?

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