Monday, August 13, 2007

SciFoo Camp - The End and New Beginnings

Well, I am finally getting around to writing about the last day of SciFoo camp (see here for my other blogs on the topic).

For Day 3, I got up early, packed up my bag, and then polished up my presentation for a session on "The Human Microbiome." This was particularly difficult for me since I do not really at this time work on the human microbiome much (although I want to). But I figured, of all the things microbial I know about, this would be the one that would be most fun to talk about to scifooers and would catalyze the most interest. So I searched around for slides and figures and ideas on the web for a while and then said "WTF - I can do a chalk talk if I need to" and I headed downstairs to the lobby in the hopes of getting over to Googleplex and enjoying the last bits of scifoo.

There was quite a crowd in the lobby and I ended up talking to a few other evolutionary biologists which was good and then finally got a bus ride over to camp. At Google, I had a bit of breakfast and then went inside to sit at a table to do the last bits of preparation for my talk. If I had been at a normal conference I would have simply skipped the first two sessions to prepare for my talk at 11:30 (the last session of the meeting). But I said this would be silly and decided to go to a session at 9:30. My choices were:

Golem: Data Mining for Materials (and Non-Programmers): sketching information systems (Andrew Walkingshaw) --AND-- Searching the Edges of the WebNovel Biofuels, smart materials in energy production, the energy mix in the short term.Genome Voyeurism -- Let's poke through Jim Watson's genomeInternational polar year, an opportunity to... (Dave Carlson)
Simplifying citation linking (Dan Chudnov)Would You Upload? (Melanie Swan)

Future health care delivery and transport models: When "science" is not enough, benefit of new research vehicles (Berman and Neelagaru)Reforming Patent Systems, patent informatics and innovation5 mins on your favorite science website / tell us your dream science web tool (Richard Akerman)How to Celebrate Darwin in 2009 (Phil Campeck)Innovation is Not Pointless...But It's So 20th Century (Bingham)

And again, the choosing was brutal. Though I really wanted to go to Lincoln Steins Genome Voyeurism session, I followed my rule of going to things I did not know a lot about and went to the session on the International Polar Year. This was one of those sessions in a giant room and I expected a huge crowd. Instead, there were about seven people. But boy did the others miss something brilliant. Dave Carlson not only told us about the whole IPY project but proceeded to tell us about how their project was completely Open Science. That is, everyone involved was required to post their data on the web for anyone to use. OK - well apparently they are allowed to publish in non Open Access journals, which seems counter to their whole philosophy, but their openness about data is brilliant (Note - I just found out from a Google search that a childhood friend of mine, Thomas Nylen, is participating in the IPY project -- see this blog here for some of what Tom has been up to).

Unfortunately, I missed the next session due to my computer having issues and me freaking out about whether it would work for my presentation at 11:30. The choices for the session I skipped were:

Incorporating science into social networks (Josh Koarer and Jon Durant)
Assessing the risks of tech innovation, ethics of synthetic bio. Do we have any choice? (Caruso)Tree of Life: Fractal Data Problem (Sereno)
Provenance analytics: illuminating science trails. Future of scientific publications, dynamic and evolving papers. (Juliana Freire)Planetary Defense Against Asteroids (Pete Worden)

Science Blogging
Towards an open source science learning collaboratory (Ted Kahn Design Worlds)Opening the scientific literature: OpenLibrary, Google Scholar (Aaron Swartz)21st century medicine: electronic medical records, privacy, and data mining (Erez L. and Kevin F.)

Then it was time for the final session. And I was up -- the Human Microbiome. Here is what I was up against

Social limits of scientific knowledge - can too much information impede science? (Dalton Convoy)Culture of Fear: Scientific Communication and Young Scientists

(Alex Palazzo, Andrew Walkingshaw)

Towards DataWiki (Hugh Rienhoff, Alan Littleford)Do systems organize themselves to produce entropy at the maximum rate? (Ralph Lorenz)

Science on the Stage, "science-in-theatre" (Djerassi)Human Microbiome, microbes in and on us (Jonathan Eisen)Science fiction: what is it for? (Henry Gee)

It would have been funny if I had gone to someone elses session and skipped mine, but I am glad I did not as actually quite a few people showed up to mine. I started by saying I had a presentation but would prefer if people just asked questions along the way. And the great part was - did they ever. This included some by Freeman Dyson - kind of cool to have the guru asking me questions about microbial colonization of babies. Finally, after I had spent too much time on background - Drew Endy said something to the effect of "Lets get to the technically hard stuff" and I briefly discussed using genome sequencing to study microbes that live in and on humans. And then - we just had to stop.

I decided to linger for the wrap up session after lunch so I had lunch, made some phone calls, and then we had a wrap up which was mostly an open mike for comments and this ended up being a bit too much of "It was great" and not enough of "How could we make it better." But hey - it was great so I guess I understand. I went around saying thanks to the Google team and the Nature and O'Reilly folks and then moseyed on to the train back to Davis.

Some brief notes about the end and the new beginnings:
  • I got lots of ideas for new projects and new things to do from this meeting as with the last one.
  • Over the next few weeks I will be posting about some of the other things I saw there and discussing why/how they are interesting.
  • I think this "un-conference" style would be really good to emulate for other gatherings. Not sure how to pull it off though.
  • I know I will get in trouble from some of my Open Access colleagues, but I definitely came away from the meeting being really impressed with some of the things Nature Publishing group is doing. They really seem to be trying to move into the Web 2.0 area for science communication with Nature Preceedings, and the Nature Network and Scintilla and Connotea and Podcasts and of course Scifoo. Sure there were probably too many people from Nature at Scifoo, but hey, they were sponsoring it so why shouldn't they send them? Here's hoping that they continue to experiment with Open forums and Open material and that they change to OA for all their publications as a way to bring in more people to their Web services. And lets hope other publishers, especially truly open ones build similar resources for the community.
  • Thanks to Timo Hannay, Tim O'Reilly, and all the folks at Google, Nature, and O'Reilly for organizing this and inviting me.
Some interesting scifoo collections and follow up discussions:


  1. Where on the IPY website is the link to the Open Data?

  2. Good question - I may have spoken too soon as I have been looking around for their data. I will ask Carlson and see what he says. Maybe they are open but slow?

  3. Jonathon,

    Funny to run across you blog and your reference to the IPY project I am working on. I am just finishing up work in eastern Greenland. Hanging in the largest village, Tasiilaq, on the east side of this island, waiting for the weather to clear so we can finish our work. This island reminds me of Antarctica, though there are full time residents here and there are plants growing here. The nematode is not the top of the food chain here. I hoping to be home by the end of the week.

    When did you move to Davis? How's the family? I see the Red Sox are sliding again. Somethings never change.

    cheers...Thomas (


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