The Fat Man Cometh

The Fat Alberts Man, that is. Just came back from hearing Bruce Alberts speak. He talked in general terms about his early career, his work on Molecular Biology of the Cell, his time as president of the National Academy of Sciences, and most recently about his work as editor of Science magazine. He had some interesting things to say, although nothing really ground-breaking. He generated a lot of good will by talking about his early graduate work and about how it was a complete failure, and how he literally failed his thesis defense and was required to go back and do another six months of research. One of the things I found most interesting, though, was his repeated insistence that young scientists need to come up with new, novel ways of doing things, and not just repeating the type of work that others have done before them, and about how he personally wanted to use the journal Science to encourage that sort of thinking. But this seemed to me to be highly ironic. Journals like Science and Nature, have a system of pre-peer-review editorial review, where they reject a large fraction of papers for not being interesting enough, or sexy enough, or relevant enough, irrespective of the quality of the science. This is actually the complete antithesis of what he seems to be striving for, and I think it's well accepted (at least among people that I know) that major journals play a pretty active role in discouraging experimentation on innovative systems with innovative techniques, because the journal editors just won't understand why it's interesting or important if it strays too far from the known corpus.

Compare this with the talk I heard at the Science Commons salon recently, by Peter Binfield, the managing editor of PLoS ONE. PLoS ONE operates in exactly the opposite fashion: they will publish anything, as long as the science is sound. They then rely on the community to rate the work based on relevance, importance, or whatever else they deem interesting, sort of like Digg or Reddit. The question, of course, is whether the Intarwebs-at-large is a better judge of what's interesting, useful, and innovative than the editors of Science. I'm not really sure. I'm not even sure that "interesting" is a useful metric. But, "interesting" is what interests people, so it will always have some relevance.

Pair Sciencing?

I attended the Science Commons Salon last night and spent some time talking to intargoogles celebrity Joi Ito. He was very interested by my comments about the lack of a "Journal of Failed Experiments" and the question about why such a journal doesn't exist (even though most people agree it would be useful) and what cultural, institutional, and scientific barriers prevent it. The topic also touched on some questions about what Science(tm) could learn from Silicon Valley. Joi seemed to believe, as an article of faith, that making science more responsive to outside interests (money, medicine, engineering, et cetera) would be a good thing, and I was not entirely convinced of that, being a bit of a purist. I often like to point out that J.J. Thomson did not have cell phones and computers in mind when he discovered the electron. But I actually didn't broach this topic with Joi, preferring to try to glean from him what I could, rather than argue about Science(tm) versus "science".

One interesting idea I came away with was the thought that, if you look at most of the fast growing high tech firms, they gave up long ago on having extended 9AM meetings in which people put up PowerPoint slides and discuss their latest progress. This management model would be considered downright ossified in places that practice methods like "agile programming", and "extreme programming". (In the latter, for instance, 15 minute "stand up" meetings (nobody is allowed to sit) are the norm, to keep the meetings on track and short, and to keep people on the important stuff.) But, strangely, our project management style is exactly this, interminable 9AM meetings filled with PowerPoint slides and people falling asleep (literally, in some cases.) I started to think about some alternative ways to structure research, at a very basic level, and was thinking about an extension of the "pair programming" methodology, of which Joi seemed to be a big fan.

Imagine, if you will, the following: a research group is divided into two groups, 1 and 2. Alice, Barbara, and Cathy are in group 1, and Arthur, Bob, and Carl are in group 2. Each person is the lead on one project, so Alice has her own project, Bob has his own, et cetera. During the first week, one person from team 1 and one person from team 2 get together to work on the team 1 projects. So, for instance, Alice and Arthur work on Alice's project, Barbara and Bob work on Barbara's, et cetera. During week two, they switch, and work on the team 2 project with the same partner. In week three, now, they rotate partners, but go back to the team one project. So, now Alice works with Bob, Barbara works with Carl, and Cathy works with Arthur. Week three is for team 1 projects, and week 4 for team 2 projects. And so on, and so forth.

What would be the practical consequences of this arrangement? Well, for one thing, everybody is invested in everybody else's project, and everybody gets their name on every paper. One of the impediments to collaboration in the lab is the question of lead authorship: if I give over too much control to somebody else, I might lose my slot as lead author! But this system preserves lead authorship, which, although artificial, is extremely important for job searching and funding. The principle on each project is still the lead author. It gives everybody in the lab a broad range of experience working on a lot of projects, and it allows people with fresh eyes to contribute to projects, by bringing new perspectives, which is often what's needed. And, by maintaining the rotation, people stay up to speed on their peers' projects, and don't need to be retrained too often (hopefully.) I'm curious if this would be a workable lab environment. I can see pitfalls (what if Alice and Bob hate each other?). And, also, this organization isn't idea, because Alice never gets to work with Barbara. But, there's probably some simple permutation that could get us around that problem. In any case, I think it would be a bold experiment. If I ever have my own lab, it would be something I genuinely think I'd like to try.

You have mistaken me for someone who cares

From: "Lynda T. Carlson, Director, Division of Science Resources Statistics"


Dear Matthew Paul Gordon,

Help! The survey is closing soon, and your perspective is important to us.

The National Science Foundation (NSF), Division of Science Resources Statistics (SRS) really needs your input on the survey of early career researchers with doctorates or equivalent degrees, including postdoctoral researchers (postdocs).

Dear NSF:
I asked you for some money a bunch of years ago, and you said "Go shove it, kid." So, allow me to return the favor. You can take your survey and stick it where the sun don't shine.
Sincerely,
Dr. Matthew P. Gordon, Ph.D.

Bad Bob! No biscuit!

I like Bob Park's "What's New" newsletter, but he can be pretty shrill at times. And the times that I've written him to point out errors, I've gotten a cursory reply. If he's going to play the "I'm a physicist so I'm smarter than you" card, he should at least be, you know, correct. To wit, in regard to cell phones not causing cancer, we are told today, "[A]ll known cancer agent act by breaking chemical bonds, producing mutant strands of DNA." Uh, Bob, have you ever heard of HPV?

Arbitrary Friday: Happy New Year

I'm spending today cleaning up and RNAse purifying a PCR, so it's a lot of waiting and not a lot else to do until I get back on the optical trap. In the meantime, thoughts turn to Rosh Hashana, the beginning of the Jewish new year on the lunar calendar, which starts this evening. The high holidays tend to make me lonely, and a bit homesick. I don't know a lot of Jews in the bay area, my immediate family all lives in Chicago, and my extended family lives on the east coast, so I usually spend my high holiday time in a contemplative mode (read: alone.) I go to the campus Hillel, I follow along with the prayers, and I think about my relationship to the ineffable, and how that relationship can help me be a better person.

I say "the ineffable" because my relationship to God qua God, which is to say, God as a disembodied entity, has changed radically over the last twenty years or so. In my youth (said the sage, as he shook his gray locks) I was a devout adherent to the Reform Jewish movement. I went to Jewish summer camp, I had my Bar Mitzvah, and I had a strong and personal relationship with God. When I prayed, it was fervently, and with intention.

But, as much as it sounds like a cliche, 10 years in the relentless, ruthless pursuit of empiricism at all costs has had its toll on me. I now think of myself as somewhere between deism and agnosticism. The more I learn about the natural world, and the more time I spend with my brain in a mode of empirical observation, the less room there seems to be for a God in the universe. At the same time, it's obvious that "God", as an idea, serves a purpose to people, giving them hope and meaning, so there's an incentive to believe in such a thing, an incentive that has nothing to do with what can be deduced about the world. Occam's razor thus cuts God to pieces*.

So, then why not atheism? Why settle for agnosticism? A few reasons. First: Gödel's Incompleteness Theorem puts limits on what we can deduce from purely mechanistic logic. No matter how ruthless our logic is, there are still statements that can be notionally outside of our ability to prove them. It's obvious that the Occam's-razor-appoach to God (i.e., why believe in God if we don't need one?) is not a proof, and one can readily construct ideas about God (such as deism) that are beyond our capacity to prove or disprove, at least within a logical framework. Does this mean that I believe in God? No. But it means that I accept that I cannot prove that there is none. And given the very idea of God as an interloper and creator of human affairs, it is not unreasonable to suppose that such a being might hide himself behind layers of obscurity.

On the other hand, logic itself is a system of belief, and it also has its dogmas, such as induction. We base most of our "logical" conclusions on induction, but induction is really only a rule of thumb, and one that we can't even prove: try proving the validity of inductive reasoning without using induction. (Go ahead, I'll wait here.) So, our instinct that logic is the only reasonable mode of interpretation of the universe is itself suspect. It tends to produce useful results, so I'm willing to stick with it for most things. But, once again, I'm not willing to rule out the possibility that there are other modes of understanding our experience and our universe that might not also be valid. As an example, we have an entire emotional life that is not governed by logic. We believe things that we have no reason to believe, we frequently know with great certainty things that are provably false, and we make errors in judgment all the time because of our feelings. We can, at a fundamental level, understand this by logic, by understanding the evolutionary processes that got us to this point, and by understanding the neurological processes that underlie these feelings. But that doesn't make the feelings any less real or urgent: you can explain lust as a biochemical reaction, but it doesn't make me want what I want any less. And I'm here, inside this meatbag, trying to make sense of a world distorted by these chemical reactions, and logic sometimes doesn't help with that. A different paradigm is sometimes needed.

So, all that said, what do I do on the high holidays? What do I do when I'm sitting there, being urged to repent my sins, and trying not to fall asleep? Why subject myself? The answer is kind of the same as the above: I'm still inside this meatbag, and I still crave meaning. I still need direction. And whether that direction comes from a book purportedly written by an entity, or from a feeling that I owe certain things to my fellow man because of some comsic duty, or because Dogar and Kazon command it of me, I have to find it somewhere. To do otherwise is to give in to nihilism, which may be logical, but isn't very satisfying. And, deep down inside, when the cantor intones the age old melodies of Kol Nidre, asking God to forgive me for the vows that I cannot keep, I can feel the stirrings of that truth, that urgent feeling I had at age 13, that there's something outside of myself that talks to me from without, but also from within, and that asks me to think of my life as part of a giant Rube Goldberg contraption with a singular end, to improve the world. And I am invited to examine those pieces, and see which of them are helping, and which are hurting. And to make a choice. And for who do I make that choice? אהיה אשר אהיה‎...I am that I am...



*Perhaps this is what was meant by Hattori Hanzo in Kill Bill Part 1, when he says, "If on your journey you encounter God, God will be cut" by the superb craftmanship of the sword he produced. The relentless pursuit of perfection in engineering leaves no room for chance, or God, if every factor can be accounted for and controlled. The perfect sword will indeed cut God.

The Elements

I know I posted another video from this new They Might Be Giants science album, but this one is just too awesome to not post (via BoingBoing):


Not to be confused, of course, with:

Science is Real, Yo