Open Source GE

Here's a quick video on Fora.tv (sort of like Ted) where Michael Pollan makes a good point against genetically engineered crops. It's not about health or even the environment, it's about intellectual property being used to own the crops on which we all depend. He calls for open source genetic engineering. I don't know if the open source concept really works well for biotech. It's cheap for an individual to sit down and make some code for an open source project and therefore these things can be accomplished as a hobby. Biotech is expensive, and the only way labs are going to work on a genetically engineered crop is if there is a patent on the horizon. Here are some arguements that the comparison of open source software and biotech is valid.

Rent-A-Bay?

Was looking at this article on the booming market for renting virtual office space for small business.

"I wanted to launch my company, but the cost of having a professional location was simply too high," says Mr. Gerochi. "This gave me the push to do it. I pay $300 a month and I can appear big-time to major clients.

"I use their reception staff -- they take all my calls -- office space, mailing service. The building address is advantageous. It's more professional than a home address and filters out unwanted solicitation. I can rent a cubicle for $15 an hour or a window office on the 57th floor at First Canadian Place in Toronto for $25 an hour instead of sitting in the food court with my laptop." He also uses the boardroom ($70/hour) to network with industry leaders."

Great way for entrepreneurs to overcome crippling infrastructure and basic staffing costs. It occurs to me that even higher infrastructure and start-up equipment costs pose a similar huge obstacle to the would-be biotech entrepreneur. Research space is like office space, except way more high-tech and costly. Rental lab space sounds like a great solution. Does your institute have any empty lab bays or equipment sitting unused? Let's see that shit up on Craigslist. Starving PhDs with great ideas are ready to put it to good use. You could even sell off those unused technical support staff people-hours. Like lunch.

Oh, cool. Apprently you can already do something like this. Like here. Not to be confused with here.

Bayblab Bio-Patent Watch

In this feature, I review newly-filed biotech patent applications published by the US Patent and Trademark Office. Comments are welcome. What do you think of the inventions? Are they useful? Commcerically viable? Should the patents be granted? Are they novel? Overly broad and restrictive of future research or individual rights? Will society reap rewards if the patent is granted and the technology is exploited?

This month we have:

"METHODS TO IDENTIFY POLYNUCLEOTIDE AND POLYPEPTIDE SEQUENCES WHICH MAY BE ASSOCIATED WITH PHYSIOLOGICAL AND MEDICAL CONDITIONS"
Application number: 11/781,818
Filing date: Sep 12, 2007
Inventor: Walter Messier
Assignee: EVOLUTIONARY GENOMICS LLC

This invention describes a method for finding gene sequences responsible for the resistance of non-human primates, such as chimps, to diseases that afflict humans, such as HIV/AIDS, cancer and neurodegeneration. The method basically involves comparing genetic sequences from human and non-human primate species to determine which human disease genes have undergone evolution in primates since our lineages diverged. Information about these genes would then be used to design novel therapeutics. As an example, the inventors propose to determine how the gene encoding 17-beta-hydroxysteroid dehydrogenase has evolved in chimps to mediate cancer resistance.

CE7-SPECIFIC REDIRECTED IMMUNE CELLS
Application number: 11/849,643
Filing date: Sep 4, 2007
Inventor: Michael JENSEN
Assignee: CITY OF HOPE
This application describes how to engineer cytotoxic (cell-killing) immune cells that target a protein antigen specifically expressed on the surface of neuroblastoma tumor cells. An antibody against the neuroblastoma antigen is fused to the zeta chain of the T-cell receptor. This chimeric receptor can then be introduced into T cells, natural killer cells, neutrophils and macrophages so that they express it on their surface and thereby recognize and kill neuroblastoma cells.

"PORTABLE NMR DEVICE AND METHOD FOR MAKING AND USING THE SAME"
Application number: 11/851,291
Filing date: Sep 6, 2007
Inventors: Chang-Min Park, Shriram Ramanathan, Patrick Morrow, Kenneth Cadien
Assignee: INTEL CORPORATION

This one's pretty self-explanatory. NMR (nuclear magnetic resonance) technology is used in medicine for MRI imaging scans, as well as certain types of chemical analysis. This invention is describes a hand-held device that analyzes clinical DNA samples to perform disease diagnosis.

"TETRAPLOID WATERMELONS PRODUCING SMALL FRUITS"
Application number: 11/854,362
Filing date: Sep 12, 2007
Inventor: Xingping Zhang
Tetraploid watermelons are used to breed the triploid, seedless variety that we all love so much. This invention describes a way to make smaller, tastier tetraploid watermelon with a higher ratio of flesh-skin.


METHOD FOR DIAGNOSING IMMUNOLOGIC FOOD SENSITIVITY
Application number: 11/899,670
Filing date: Sep 7, 2007
Inventor: Kenneth D. Fine

This invention describes methods for diagnosing food allergies by determining whether the patient produces antibodies against commonly ingested foods. The approach is to collect fecal samples ( ie, "poop") and analyze it for the presence of antibodies against food antigens by ELISA. I would not want to be the poor sucker who works in this diagnostic lab:
"One method of concentrating the stool specimen is to spin the stool in a centrifuge to obtain a watery supernatant...Another method of concentrating the stool specimen, which is particularly used when the specimen is watery or diarrheal, is to freeze-dry or lyophilize the specimen to solid material and reconstituting it with water at a dry matter to water ratio equal to that of non-diarrheal stool".

Michael Crichton on Gene Patent Lunacy and Global Warming Myths

In this great conversation with the mind that brought you Jurassic Park, Crichton discusses why genetic patents need to be eliminated, why the global warming "consensus" and its mouthpiece Al Gore are wrong, and why real science has nothing to do with consensus anyway. Watch the video and if you think Crichton's got it wrong, I'd be interested in knowing why.

Biotechnology is SO 19___

Recently the AC questioned the novelty of human genome sequencing (albeit from fossilized specimens), the work of one of Discover magazine's picks for last year's scientist of the year. He has inspired me to also question the novelty of their other two picks, just for old time's sake:

1. Using microorganisms to produce fossil fuel alternatives is SO 1934 (and probably even older).
William J. Hale of Dow Chemicals discussed this idea as a part of his broader plan for increasing the scope of agricultural manufacturing in his 1934 classic The Farm Chemurgic. I'm sure the notion had been floating around before, as it was well-known by this time that ethanol is a natural product of fermentation. But hey, who wants to burn it when you can get hammered and take off on a gasoline-guzzling joyride instead. Of course the synthetic biology approach in the context of this problem is still sexy - but doesn't necessarily change the economics of the approach, unless it increases efficiency or allows new types of starting materials to be converted.

2. The Man-Machine Interface is SO 1948.
Craig Taylor was one of the founders of one of the world's first biotechnology programs at UCLA, and kick-started the field of man-machine interfaces (and apparently liked to participate in his own experiments). Military and aeronautical engineers took a particular interest in the nascent field. I think this picture of him from Life magazine really shows that the technology of the day just cannot be beat (I that an egg he's frying with the power of his brain??):(Reproduced from R. Bud, The Uses of Life: A History of Biotechnology, 1993.)

As always, find these stories and more in The Uses of Life: A History of Biotechnology, .by Robert Bud (1993).

Pharming Interferon in Tobacco Plants

Those of us who work with VSV know interferon as a secreted protein that can protect cells from viral infection. The interferon response is also the basis for selective tumor cell killing by many experimental oncolytic viruses.

However interferon is also biotherapeutic of significance in its own right - it is the world's third most produced biological, second only to insulin and erythropoietin. Interferon-alpha is currently administered as first-line treatment in Hepatitis C and is also approved for Hepatitis B and some types of cancer. Another variant of interferon (beta) is approved for use in multiple sclerosis patients.

But biologicals ain't cheap. A years worth of IFN treatment for HepC costs $26, 000 USD, placing a huge burden on health care systems and making it inaccessible to the majority of infected individuals worldwide, who lack the privilege of luxurious health care. One of the major reasons for the high cost of biologicals such as IFN lies in production. Currently, IFN is produced in cultured cell lines, which require stringent growth conditions and laborious sterile handling procedures. In an effort to lower production costs, this new paper describes the production of human interferon in the chloroplasts of tobacco plants. Thus the protein is produced through standard agriculture, leaves are harvested (each makes 3mgs of IFN) and the protein is purified through a relatively straightforward and scalable process. I couldn't find a patent for this technology on Google patents, and Henry Daniell's lab, which conducted this research, seems to have a specific policy of developing biotechnology that is globally accessible. Hopefully plants like these will lead pave the way to cheap, disseminated biological production capacities to meet local demand across the world.

1010 by 2010

That's 10¹⁰ base pairs of DNA sequenced or synthesized by one person in a single day. That's a hell of a lot. More than enough to cover the whole human genome several times. And that's just one person. Imagine how much a factory full of monkey could do. If you think this sounds ridiculous, read the rationale for the prediction in this great article. As shown below, the projection is based on the current exponential growth of biotechnology, mimicking the trend known as Moore's law, where the number of transistors that can be fit on a microchip has been growing exponentially for the last 50-60 years. The article makes some interesting comparisons between the two industries and also features some of the best discussion I've read on the future of biotechnology and its place in society.