Science It’s Alive™!
posted by on December 18 at 14:05 PM
The Washington Post featured a muddled-but-interesting article on artificial organisms.
I see a cell as a chassis and power supply for the artificial systems we are putting together,” said Tom Knight of MIT, who likes to compare the state of cell biology today to that of mechanical engineering in 1864. That is when the United States began to adopt standardized thread sizes for nuts and bolts, an advance that allowed the construction of complex devices from simple, interchangeable parts. If biology is to morph into an engineering discipline, it is going to need similarly standardized parts, Knight said. So he and colleagues have started a collection of hundreds of interchangeable genetic components they call BioBricks, which students and others are already popping into cells like Lego pieces.
BioBricks has the potential to be simply amazing—the life sciences equivalent of the GNU or BSD tools underling the internet, linux and even the Windows networking stack.
This is biology as it should be done, open and freely available. How? If you want to accept federal funds for your research, you’re required to publish and provide what you learn for free to other researchers. Check out the NCBI: Your tax dollars at work.
The workhorse of modern molecular biology is the E. coli bacteria—available for free from your colon. If you want a strain better suited to lab work, stick DH5-alpha. Most of the troublesome bacterial genes are removed, the bacteria ready and willing to pump out your synthetic DNA. Cheap and free, after the initial purchase.
The NIH model works brilliantly, keeping the scariest research under the glare of public oversight, the most interesting and useful results well distributed between scientists worldwide. Free, carefully regulated, and effective—can’t be left alone in Bush’s America. The NIH budget, in real dollar terms, steadily shrinks each year.
With public funding increasingly scarce, companies are moving in. By definition, it’s difficult to patent existing living things; the e. coli are doing most of the work, right? So, in comes synthetic organisms!
Some experts are worried that a few maverick companies are already gaining monopoly control over the core “operating system” for artificial life and are poised to become the Microsofts of synthetic biology. That could stifle competition, they say, and place enormous power in a few people’s hands.
Who?
In the past year, the U.S. Patent and Trademark Office has been flooded with aggressive synthetic-biology claims. Some of Venter’s applications, in particular, “are breathtaking in their scope,” said Knight. And with Venter’s company openly hoping to develop “an operating system for biologically-based software,” some fear it is seeking synthetic hegemony. “We’ve asked our patent lawyers to be reasonable and not to be overreaching,” Venter said. But competitors such as DuPont, he said, “have just blanketed the field with patent applications.”
Poor him. The publicly funded human genome project ruined his profit model last time. Perhaps he’ll be luckier this time.
Wow, I don't know if anyone out there in Radioland has any connections to the UW, but this subject would make for a great lecture at the Burke Museum (NW tip of griddible campus)!
In fact, when I attended the earthy sponsored talk/slide demo at Town Hall earlier in the month, I was given a get out of jail...er, two admit for one coupon. See, the Burke was involved because the event was about y2y.org? It hinged on the Yukon to Yellowstone photo exhibit. The artist was a very good speaker (English not 1st language), funny, and really emphasized the encroaching, money-grub-giving developer du jour imperial-IZMS who are destroying species from plant to critters, one by onje, how lovely.
Sounds like a good and snarky trip for the Public IOntern. He could take Jen Graves and they could have a serious discussion to be edited over cocktails later that night at the Funny Art closing at Francine Cedars. Two for One! Not to be missed!
If you do stop by say hi to the guy who curates the canoe and NW art holdings. His office, Bill Holm?, was next to our classroom for drawing eagle's wings and the like.
Paranoia in the Streets! Notify the Officials!
truly, i completely fail to see how stories like these bear any relation to the fact that The Hobbit will hit theaters in 2010. come on guys, get it together.
An article on artificial orgasms? I'm afraid to click the link . . .
Well, we have to say something in the two years before we get trailers, SF.
On the slog, inserting a gratituitious attack on George Bush and the evil coporations is usually enough to innoculate yourself against all critique. But this article is just too egregiously incorrect even for that proven technique.
The NIH budget, in real dollar terms, steadily shrinks each year.
Wrong. The NIH budget (see http://www.nih.gov/about/almanac/appropriations/part2.htm) has grown in real terms in every year of the Bush administration. Using the most common inflation adjustment (see http://www.measuringworth.com/uscompare/) it grew 22% in real terms from 2001 to 2006.
The publicly funded human genome project ruined his profit model last time.
Wrong. Venter started his map after the HGP had already begun, so it would have been rather strange for him to have a "profit model" that assumed the HGP didn't exist. Oh, and even though it started later, Venter's map finished earlier and at tiny fraction of the cost of the HGP map. Venter's profit model what that his superior mapping technology would be adopted by all workers in the field, and it pretty much worked out that way. Venter now spends his time sailing the word on his mega-yacht, doing hobbiest genomics of sea life.
DW, you're wrong. Just our supplies go up around 8 to 10 percent each year.
Maybe you should get a clue stick. Or live in the real world instead of Bush fantasyland.
In the real world, Middle Class America has gas prices and other costs going thru the roof. And biotech has to deal with massive inflation in materials costs.
Will: Let me get this straight. I point you to the actual NIH buget records, but I'm still wrong because your lab supplies have got expensive lately?
Thanks for that clear and convincing rebuttal. Just remember, saying that your opponent lives in a "Bush Fantasyland" always makes you right.
Yeah, and I'm trying to tell you that the actual cost of doing the research - the literal raw materials - went up far more than the CPI during those years.
In case you haven't been paying attention, the CPI doesn't include gas either. It's an artificial economic measurement representing a household basket of goods designed back when housewives didn't work and assumes a number of things that are no longer relevant.
Now, do you want to discuss how our borrowing money from China and importing goods from there causes oil prices to go up even higher, or did you have a point other than that you don't understand true economic costs and can't even read the inside pages of the Wall Street Journal if your tutor stands over you?
Wow, Will, you sure sound like an angry person. What exactly is wrong with DW's analysis? He did point you to NIH numbers, and all that.
Also, perhaps you can clarify how a biotech company's materials cost increase is related to the NIH public grant system of funding academic research.
It sounds like you'd rather rail against Bush, and if so, fine, but it detracts from the inaccuracies that DW pointed out.
Using the CPI to adjust for inflation on something like the NIH budget is not correct. The website dw referenced states in an example about what the cost to put a man on the moon today: “If we used the CPI, it would be $136 billion, but this would not be a very good measure since the CPI does not reflect the cost of rockets and launch pads.”
The NIH budget for between 2001 and 2007 in billions:
2001: 20.5
2002: 23.3
2003: 27
2004: 27.9
2005: 28.5
2006: 28.5
2007: 28.6
Projected in 2008: 29.2
Even using the CPI it has shrunk every year after 2004.
There you go, Jonathan is correct, the NIH budget does shrink each year in real dollar terms.
Since 2003--after the democrats lost control of the congress, the Bush budget priorities were finally enforced and the start of the occupation of Iraq--the NIH budget has been at best flat in real dollar terms.
Using the table to which you linked, the budget decreased from 2005 to 2006 in nominal (let alone real) dollars. It did so again in 2007, and will as well in 2008--thanks to the Democrats cave on the budget over the weekend. So, what I said is accurate: the NIH's budget is decreasing, even putting aside Will's (correct) point that inflation in research is higher than general inflation.
The other more subtle stats are even more disturbing. Since you're not accepting what I write, look up the R01 acceptance rate. I refuse to believe that the quality of proposals has declined by 30-40%. Good science is being blocked or denied by the current budget, regardless of the dollar terms. This short-sighted absurdity is forcing good science to be done with private dollars--with the accompanying loss of openness and access to results.
As far as Venter--he is very busy, primarily tying up intellectual property around biofuels. You sympathize with "The Genome War." I find "The Common Thread: A Story of Science, Politics, Ethics and the Human Genome" more compelling. Perhaps we can agree Venter's human genome project would have failed without genbank--why he couldn't start it until the HGP was at least partially completed--and shotgun sequencing is here to stay.
He *was* shamed into sharing his data, after an initial attempt to hoard and sell it. Venter is a bright guy and is more deserving of obscene wealth than most. Still, his initial moves with the celera assembly were shady at best. I'm not ready to give him the benefit of the doubt on the new patents. Read the link; I'm not the only one concerned.
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