Among the BioInformaticians

Last Tuesday and Wednesday I attended the Bio-IT World Conference & Expo, at the World Trade Center in Boston. I was a booth babe for Bioinformatics.org, (“The open access institute”) and also was pimping my books. I discovered the BioInformatics organization about a decade ago while pimping my books (what else) at the O’Reilly BioInformatics conference in Tucson. They started out as basically a sourceforge for bioinformatic software, kind of a reaction to corportization of all things genomic, and have grown from there. I wrote about them a little in my famous Salon article How I Decoded the Human Genome.

Because I’m a total dummy and didn’t look at a map, it took me forever to get there from the place I was staying, one mile away, so I only caught the last twenty minutes of the talk given by Philip Bourne on the occasion of his being named 2009’s Franklin Laureate, by the Bioinformatics Organization — an award named in honor of Ben Franklin, who refused to patent his inventions. I saw virtually none of the show. I attended no sessions, and I didn’t even cruise the exhibit hall. Instead, along with Bioinformtics Organization colleagues Jeff Bizarro and Shailender Nagpal, I staffed our organization’s tiny booth and fielded whatever questions came my way– sometimes fielding them lamely, at which times I was glad to be backstopped by Jeff and Shailender.

Some impressions follow. Because my exposure to the show was so limited, they’re kind of like an image taken by a pinhole camera, so take them for whatever they’re worth. The most interesting part of the whole show, for me, was the discussion with Melina Fan, PhD, founder and executive director of the group Addgene, about which more below.

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Happy Birthday, Pete!

Sunday afternoon I went to a celebratory sing-along at the Featherstone Art Center in honor of Pete Seeger on the occasion of his 90th birthday. Pete himself was evidently in New York City at a big concert hosted by Bruce Springsteen, peace be upon him, but I am glad that I was where I was.

I’m generally not the sing-along type, but heck, this was a celebration for Pete Seeger! The man’s not only a great champion of liberty, equality, and democracy; he’s also the driving force behind Sing Out!, and who the hell am I to disrespect that? When Pete Seeger says “Sing!”, I sing. I sang as loudly and as well as I was able. Everybody sang. We sounded really good.

The United States of America skated very close to fascism in the 1950’s and 60’s. When most of country was denying or avoiding or hiding in fear from this simple, ugly truth, Pete Seeger was there singing it out to us, standing up to the House UnAmerican Activities Committee, accompanying himself on 5-string banjo and smiling like the risen Christ.

It’s not at all clear that we’ve skated away from that hideous “ism” even now. Rather than rant about that, however, (it occurred to me as I was sitting on the floor Sunday, singing like a schoolchild, laughing or crying, or both), maybe I should try to learn a thing or two from the old woodchopping folk singer.

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Books that rock

In trying to figure out how to upload to youtube one of my own book promotional videos (I know, I’m slow to the partry, give me a break), I came upon this little vid. Check out the first book. OK, in case it goes by too fast, it’s Acts of the Apostles, by me. I was pretty surprised to see that, I must say.

When the Money Gods fall silent, what will become of their priests?

Over on Reality Sandwich, Charles Eisentein has an essay called Money and the Turning of the Age. Its premise is that money is based on a consensus story and only has value so long as the people believe the story. The story of money, he argues, is based on:

— infinite expansion of stuff produced;
— theft and monetization of cultural wealth, and
— arbitrary and ever-growing differences in power between the haves and have-nots.

“Money is merely a social agreement,” Eisentein says. “A story that assigns meaning and roles.”

But what happens when people stop believing the story? What happens when they refuse to play their assigned roles?

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Hey, when I named this blog “Wetmachine” I was joking, OK?

Last fall Nicholas Carr blogged about whole brain emulation, in which one does a software simulation of every neuron & structure of a brain just like yours. Kinda like in “The Matrix” with Keanu, or one of those stupid brain in a vat science fiction novellas.

So now Science Daily tells me that “Brain Mapping Time Reduced From Years To A Few Months With New Technology”:

Mapping the billions of connections in the brain is a grand challenge in neuroscience. The current method for mapping interconnected brain cells involves the use of room-size microscopes known as transmission electron microscopes (TEMs). Until now the process of mapping even small areas of the brain using these massive machines would have required several decades.

Research teams at the University of Utah John A. Moran Eye Center and the University of Colorado at Boulder report technical advances that have reduced the time it takes to process high-speed “color” ultrastructure mapping of brain regions down to a few months.

These advances did not require the invention of new electron microscopes. The technical leap comes mostly from new powerful software that “takes over” the building, connecting and viewing of terabyte scale pictures produced by TEMs. Perhaps just as important is the fact that these researchers are now making these technologies available world-wide to scientists in multiple fields of research. ‘Our goals were to unleash a global network of electron microscopes and provide web-accessible imagery for battalions of brain network analysts,’ said Robert Marc, Ph.D. . .“

I like the parts about ”unleashing a global network“ and ”battalions“ of brain network analysts. This guy reminds me of the way-over-the-top villain Monty Meekman who keeps showing up in nanoscopically famous novels that I can’t seem to make myself stop writing.

”Wetmachine”–a water-based machine inside the cranium. An ironic conceit that becomes less ironic every day. Pretty soon this place will be completely literal, and what a drag that will be.