Craig Venter is making history

…or at least trying to.

Venter’s J. Craig Venter Institute, the successor of TIGR and TCAG, has been working on what they characterize as the first man-made organism: Mycoplasma laboratorium. The ongoing project centers on “Synthia”, a slimmed-down synthetic chromosome that they are calling (and patenting as) a “minimal bacterial genome”. It consists of 381 of the ca. 470 genes of the tiny parasitic bacterium Mycoplasma genitalium. (The name “Synthia” comes not from Venter, et. al., but from the critical ETC Group; it seems to have stuck.) Add Synthia to an empty cell, and viola! Life!

The project builds on earlier work in which Venter’s team (led by restriction enzyme pioneer and Nobel laureate Hamilton O. Smith, Clyde A. Hutchinson, III and Cynthia Pfannkoch) recreated the genome of the bacteriophage phi X-174 from scratch and stuck it into an empty coat to create a viable phage; they generated the 5,386 base pair sequence in 14 days. In the 2003 PNAS report, they described a plan to use similarly-sized chunks of synthetic DNA to assemble whole genomes. Since the phi X-174 project, they have been developing and improving DNA cloning methods that can deal with ever larger target sequences without high levels of error–a boon for DNA sequencing as well as chromosome synthesis. (Synthetic phi X-174 could be selected for infectivity to week out high-error sequences, but that’s not an option with arbitrary 5,000 bp “gene cassettes”.)

Since 2003, they’ve gotten to the point of putting together a whole genome (if a very small one). They quietly started filing patents for “Synthia” in 2006, and in June 2007 announced that man-made life in the form of M. laboratorium was right around the corner. Proving that the synthetic genome is viable by sticking it into a genome-less cell and making it live will be a powerful proof-of-concept for new and more drastic kinds of genetic engineering.

“Man-made life” makes a great headline, but it’s worth picking apart. At the fundamental level, even Venter’s team is quick to note that M. laboratorium won’t be a wholesale synthetic organism, as it will rely on the molecular machinery and cellular environment taken from natural cells. (At least, as natural as a laboratory organism with its genome carefully removed can be.) The conflation of genes with life has been the constant complaint of all the biologists except the molecular ones since the rise of molecular biology. It was one of the chief complaints of those who thought the Human Genome Project was (all funding levels being equal) a bad idea. In a recent article in I forget which history of science journal, (atheist) Emile Zuckerkandl accuses HGP leader (Christian-turned-atheist-turned-Christian) Francis Collins of exploiting the genes=life fallacy in his best-selling quasi-intelligent design book The Language of God. (The language of God, of course, is the genome.) The all-powerful gene is a potent political and rhetorical force (and has been a great basis for securing grants, at least since the 1940s), even if biological reality is considerably more complex.

But even looking past the conflation of a genome with life itself, M. laboratorium has a dubious claim as synthetic life. As the ETC Group points out, “Synthia” only distinguishes itself from a natural chromosome by what is missing (i.e., a fifth of its genes). This organism would have a shakier claim at being man-made life even than the 1972 oil-eating bacterium of Diamond v. Chakrabarty (the landmark patent case that established the legitimacy of patenting genetically-engineering lifeforms); at least Chakrabarty’s bug had a combination of characteristics that no natural organism had. Does putting together most of the DNA of an organism (which happens to be synthesized artificially) together with everything but the DNA of that organism mean scientists have created artificial life? It’s hard not to invoke Frankenstein.

Venter has been very successful at framing his science in ways that grab headlines, generate public interest, and seem self-evidently of central historical importance (whatever the later historical verdict). I haven’t decided whether that’s a good thing or a bad thing. He’s certainly earning his place in history, one headline and Discovery channel documentary at a time.


(cross-posted to Revise and Dissent)

The other day, I was chatting with a scientist about the history of science and related matters. When I told him I had taken a class on “Biology and Society”, focused on eugenics and genetics, he replied something to the effect of “that’s not really history of science, is it?” Actually, it was more of a statement than a question.

This scientist, quite eminent in his field, had a positive reaction to my current project (on the history of molecular evolution), but was rather cool on the field in general. He sees little of value, he confided, in “anthropological studies of science” (which I took to refer specifically to the work of Karin Knorr-Cetina, though I can’t be sure).

The main constituency of the history of science, aside from fellow historians of science, has traditionally been scientists and philosophers of science. The field has been growing for decades, but (in general, at least) moving away from the kinds of work that interest scientists or philosophers.

Case studies, rich in social significance but representing only a small slice of the scientific past, have become the norm. Even so, like most history today, the majority of it is only intelligible or interesting to other humanist scholars.

Though the field has grown rapidly since the mid-twentieth century, the scope of the scientific enterprise has grown much faster. A grad student can hardly write a seminar paper on post-WWII science without stumbling upon a handful of possible dissertation topics in virgin historical territory. Synthesis and grand narrative seem beyond reach, and moving further every day.

It’s enough to put one into a panic, if the state of historiography of any field were something to panic about. (Part of my own ham-fisted response was to try to piece together a comprehensive “History of Biology” article on Wikipedia.)

When I shared with the scientist my concern about the history of science accumulating faster than historians of science could handle, he said, “Give it time.” But if it’s not important, if it can wait, what’s the point in doing it at all?

My answer that question has a lot to do with why I contribute to Wikipedia.

Prospectus writing in a post-Wikipedia world

For a few weeks now (or is it months?) I’ve been struggling to get a hold of a coherent dissertation topic. I actually have a pretty good idea of the general subject I’m going to do my research on: the disciplinary splits and diversification in biology since the 1950s, especially the “Molecular Wars” between organismal and molecular biology and the history of molecular evolution, which straddled the divide. I’ve been getting to know the existing secondary material (which is very thin) and the individuals and archives that might be at the center of an extended history of molecular evolution (which are numerous).

As I collect and organize all this information, searching for a sufficiently limited yet compelling research approach, I’m increasingly drawn to the potential of prosopography (the historical study of groups of people and the connections among them). My advisor, Dan Kevles, was one of the pioneers of prosopography in the history of science with his dissertation-project-turned-first-book The Physicists: The History of a Scientific Community in Modern America. But wikis offer the potential for a new kind of prosopography, which surprisingly has seen very little development outside Wikipedia itself. (One major online non-wiki prosopography effort is Prosopography of Anglo-Saxon England, which has an amazing amount of information but has an all-but-useless interface.) As an experiment, I took my recent acquisition of the Evolving Genes and Proteins book (the proceedings from a 1964 conference on molecular evolution that produced a number of very influential papers) and created List of participants in the Evolving Genes and Proteins symposium. About 40 of the ca. 250 participants already have Wikipedia entries, including 22 of the 56 who contributed to the proceedings (and probably the majority of the rest will have entries as some point). If similar wiki-databases were created for other important conferences, contributors to important journals, scientists in specific fields who had been associated with specific instititution, etc. (either on Wikipedia, or elsewhere to facilitate original research), it could be the groundwork for the kind of quantitative history that social historians have been pining for but have never really pulled off. It could make prosopography (and maybe even collaborative history) worth doing.

A day in the wiki life

I went to bed last night with the express intention of focusing all of today’s energy on the Johannes Kepler Wikipedia article. The article, which I re-wrote almost entirely from scratch and replaced the old version with in mid-December, and have been gradually improving with the help of others in the meantime, was nominated for Featured Article status by a passerby about a week ago. This slipped under my radar until just recently (as I was still recovering from qualifiers and working on my Wii Tennis skills to avoid mental exertion), but it garnered a lot of positive feedback… despite not being finished. I had planned to spend spring break working on it casually, for a final push toward featured quality (and completeness), but the Great Wikipedia Spirit had other plans.

Anyhow, I spend some time working out the language kinks after waking up in the mid-afternoon. Then I took a break and stopped by one of those interesting but rarely-visited (by me, at least) areas of Wikipedia, the Humanities Reference Desk. I gave my two cents on what a self-motivated student interested in art history should be reading, and the proverbial three hours of fascinated clicking later, I had found my way to an interesting topic that, horror of horrors, didn’t have a Wikipedia article! So now there is a short, unsourced article about the Hockney-Falco thesis, but still no discussion of the historiographical and philosophical legacy of Kepler. (Although, the Hockney-Falco thesis is only two degrees of Wikipedia from Kepler: the Hockney-Falco thesis is about optical aids to drawing like the (click-1) camera lucida, which was first described by (click-2) Johannes Kepler in Dioptrice… a fact I did not know before this evening, despite writing the Kepler article. Wiki works in mysterious ways.)

In other Wikipedia fun (as opposed to the Wikipedia work I ought to be doing to finish the Kepler article), I recently started a trend at Featured pictures candidates (where I learned, and am learning, everything I know about photography). Now a number of editors are demanding adequate extended captions for featured image candidates, and new nominations are starting to appear that take this into account. Hooray for context!

The FPC process on English Wikipedia is an interesting beast. As with Featured Articles, the standards for Featured Pictures have risen enormously over the last two years or so. And the way editors at FPC analyze pictures, and what they expect out of a good picture, is quite different than what a random viewer values in an image. The most dramatic example of this is the Picture of the Year on Wikimedia Commons. Commons has a separate featured picture process (which unlike on Wikipedia, does not take encyclopedicity into account), and it recently held a well-publicized vote for the best picture of the 321 that achieved featured status in 2006. The winner (below) was not yet an FP on Wikipedia, and its subsequent nomination only stood a chance of passing FPC (which it did not) in deference to its Picture of the Year status; it was widely criticized on both technical and aesthetic grounds.


History of science manifesto

Here is my

As someone with aspirations to change the world, I figured it was high time I wrote a manifesto. I’ve never written one before, so I found the style hard to master… writing skills don’t completely transfer from genre to genre, and blog posts, encyclopedia articles and archive-based research papers all require practice individually. So I’m not completely satisified with it, but I’ll try to improve it in the future. One nice thing about writing in Wikipedia (as I did with the manifesto) is that you can use links to avoid having to choose between a) over-explaining things for the readers that share your background and b) confusing the uninitiated with jargon and obscure allusions.

I was inspired somewhat to write this after reading an article on “Good and Bad Procrastination,” which quotes from this essay the following:

ask yourself three questions:

  1. What are the most important problems in your field?
  2. Are you working on one of them?
  3. Why not?

I’d say the most important problem in my field is popularization, without a doubt. Historical study of the ways scientific ideas move and transform between the elite and popular realms is just one part of that. Even more crucial is the popularization of history of science itself; translating between esoteric scholarship and mass culture, making history of science an essential component of cultural literacy. Think history of science dramas replacing medical dramas, crime dramas, and lawyer dramas as the top TV shows; that’s the level of popularization to aim for. So my Wikipedia adventures are the first step in this regard.

After popularization, pedagogy is the next most important problem. Again, both the relationship between training and scientific development, and the effective teaching of history of science itself (with the latter taking precedence again). The ultimate goal with history of science pedagogy is take over every other academic field; the sciences, literature, garden-variety history, art, all specializations with history of science.

I’ll have to think some more about what other problems are important. Meanwhile, back to reading about the social construction of nuclear missile guidance.

Ballad of Gresham College

Something wonderful was brought to my attention by one of the participants in the History of Science WikiProject: the Ballad of Gresham College. The ballad is a 1663 ode to the Royal Society, recounting the noble exploits of the Fellows. It was first (and probably only) published in 1932 (ISIS, vol. 18, no.1, pp. 103-117), along with Dorothy Stimson’s speculation on authorship and sparse notes about the individuals and RS publications to which it alludes.

Topics include:

These be the things with many more
Which miraculous appere to men
The Colledge intended: The like before
Were never donne, nor wilbe agen.

For anyone with a casual interest in the early Royal Society (or fans of The Baroque Cycle), you should definitely check it out. It’s now on Wikisource for the enrichment of the masses lacking JSTOR access.

“This is, for historians of science, the equivalent of finding one of the original gospels.”

So says ‘manuscript expert’ Felix Pryor.

Huge history of science news breaking today: A 520-page manuscript of Robert Hooke‘s Royal Society meeting minutes from 1661-1691, found in the bottom of a cabinet. Hopefully the Royal Society will drum up enough cash to win the auction or find a “white knight” buyer, so it doesn’t end up locked in the private library of some collector.

This reminds me, I need to quit getting distracted with all these “required” readings and get back to Quicksilver.

The Military-Industrial-Academic Complex, then and now

This week in Peter Westwick’s Science, Arms and the State, I got a chance to reread Paul Forman’s seminal “Behind quantum electronics: National security as basis for physical research in the United States, 1940-1960”. (Gender-sensitive young scholar that I am, I don’t use that adjective lightly; in addition to originality, the essay is remarkable for its macho-ness: dense graphs, dense footnotes, and a dense argument; sparse examples and lots of data… it’s enough to fill out a 400 page book, distilled into 60 pages.) My HSHM compatriot Brendan and I were both much more impressed with it than when we first encountered the “second Forman thesis” last year (I think we both remain skeptical of the first). The connection between scientific culture and military funding seems like a rich historical vein that hasn’t been explored enough yet. How much was the turn in physics from a positivistic, universalizing philosophy to more instrumentalist, application-oriented approach the result of the forces of money, and how much was just the manifestation of American pragmatism as the U.S. came to dominate the field (or whatever other cultural/philosophical/sociological/scientific-intellectual reasons might apply)?

As a historian of science and ex-scientist, I always find it astounding every time I see the breakdown of R&D budgets (even though by now, I’ve seen the statistics many, many times). All I’ve seen is university research, and all the professors I worked for were funded by the NSF, so it’s hard to wrap my mind around the fact that the scale military research simply dwarfs so-called basic science. Science had always been nationalistic since there were nations, and was always shaped by patronage, but Big Science—which in the context of the military also means classified science—was and is a whole different beast.

Obviously military funding of applied science has produced major dividends in terms of technology that can be used for basic research (and consumer technologies), and to some extent scientists are able to utilize grants for their own ends that only tangentially contribute to the goals of military planners. But I can’t help thinking that for the physical sciences, probably 75% of the money (and researchers’ time) since the rise of the military-industrial-academic complex has essentially produced nothing of lasting value (I’m trying to be conservative here; Forman argues that only about 1% of federal funding went to what can reasonably be called “basic” research). Maybe historically that’s an unfair deprecation of national security concerns (coming from someone approaching history from a post-Cold War perspective), but at least since the first Gulf War (when our military showed the world that it was overwhelmingly superior—thanks to all those nice toys the researchers built—to any other convential forces), I can’t see any reason to continue pouring money into military research at the current levels.

Coincidently, I heard two segments on NPR relevant to Science, Arms and the State. The first was about Bush’s FY 2007 budget: former Secretary of Labor Robert Reich (who sounds a lot like the annoying yet charismatic host of NOVA, Robert Krulwich) cuts into Bush, oddly enough, for not being enough of a capitalist. Reich is outraged that Bush is spending $6 billion on the NSF for basic physical science research, which he characterizes as corporate welfare, and it doesn’t even give us a leg up on foreign competition, since the whole world has access to the results. And funding alternate fuel technologies (nuclear power and ethanol) undercuts the economy as well; apparently, the profit motive should be sufficient to solve the nation’s energy problems…despite that unaided capitalism really has no way to deal with the consequences of peak oil until the crunch actually sets in.

I’m much more concerned about the fact that while NSF gets $6 billion, up slightly from last year (with some more grants coming from DOE) , education funding is being cut almost 20%, from $90 bn to $74 bn. Meanwhile, defense spending is going strong at $504 bn (actually down $8 bn, but up very significantly over pre-Bush levels, with the $43 bn for Homeland Security as an added bonus). And nearly half the the DOE’s $23 bn is for the National Nuclear Security Administration, i.e., for upkeep on our nuclear stockpile, which serves no purpose after the end of the Cold War anyway. To repeat, NSF: $6 bn, nuke warehouses: $9 bn.

The second NPR segment was a interview/political analysis with Joseph Cirincione, looking at the problems with trying to stop Iran’s nuclear program. In a nutshell, if we bomb the easy targets, it will only push the program underground and cement Iranian support for the nuclear program (plus the likely proxy war in Iraq and possibly even outright war with us or our allies). If we impose sanctions and actually managed to get other major players in the global economy to go along with them (namely, India and China), there would be a global oil crunch; Cirincione suggested $5/gallon gasoline. Thus, statements like McCain’s “the only thing worse than a military action is a nuclear armed Iran” are basically just talk (though perhaps talk that serves a purpose).

Getting the word out

I figured it was time to move the History of Science WikiProject to the next level, so I sent an email about it to h-sci-med-tech. While no one has responded directly on the listserv so far, a surprising number of readers from the list have blogged about my message:

Medical Museion Weblog – The blog of Thomas Söderqvist
Paradigms Lost – A new History of Science and Medicine blog from Saint Joseph’s College of Maine
LIS 569 – A library science course blog at U. Wisconsin (Madison)
Rational rants – The technology and media blog of Mitch Ratcliffe (a journalist who apparently lurks on h-sci-med-tech)

The response by each is quite positive. Then again, the people who are blogging at all are probably more disposed to see Wikipedia in a positive light than the average historian.

Update: – The blog of Thad Parsons, a graduate student at the Museum of the History of Science at Oxford.