“I have the stripes, but where is the zebra?”

Hi Everyone.  Sorry I haven’t posted anything in the long time.  My apology is a post that even longer and more meandering than usual.

I’m at Indiana University for the Biocomplexity X workshop on Quantitative Tissue Biology and Virtual Tissues.  It’s been great — perhaps because there are many physicists converted to biology.  There have been several talks that touched on non-linear elasticity, though most people’s background is in foams and not granular matter.   Rene Doursat gave an especially good talk today on agent-based models of morphogenesis in which he mentioned another alleged quotation, attributed to Alan Turing, who made either the titular comment or said “The stripes are easy, it’s the horse part that troubles me!” in reference to the ability of certain systems of equations to create seemingly biologically-relevant patterns without necessarily providing biological insight.  Brad has

Student Contract Jobs at EPA RTP

If you know students with science backgrounds and computer skills looking for additional funding in the Research Triangle Park area, then there are several twelve month contracts available for work at the National Center for Computational Toxicology. The contracts can potentially be extended up to a total of two and a half years and pay a bit over $21 an hour.

Apocryphal or not…

Last week I attended both the first ever workshop on Virtual Tissues conveniently (for me) held at the EPA’s RTP campus (though it was a EC-US Task for on Biotechnology event) and a partial reunion of the Lunchtime! crew. Dr. Tighe and Tina were in town and we managed to make it to the Ale House, though with no Martha and Dr. Bunton busy dealing with fires in Conway, some of the old magic was missing.

Efforts to create virtual tissues are certainly ambitious. The idea is to create a sufficiently accurate simulation of biology that the effects of perturbations (such as a toxic substance) are emergent;, rather than hard-coded. There are numerous challenges ahead and it may or may not even be possible, but as I mentioned tot he Ale House attendee’s someone presented an extremely pithy pair of quotes. They may or may not be apocryphal (a word whose own meaning is apparently somewhat dubious), since I cannot find either quote outside of this pairing, but it’s certainly an entertaining idea relevant to ;any technology on the cusp of feasibility:

On October 9, 1903 two interesting things happened.

The New York Times wrote “Hence, if it requires, say, a thousand years to fit for easy flight a bird which started with rudimentary wings… the flying machine that will really fly might be evolved by the combined and continuous efforts of mathematicians and mechanicians in from one million to ten million years…”

On that same day in North Carolina, Orville Wright wrote in his diary.

“We unpacked rest of goods for new machine. We started assembly today.”

PS: I found a reference to the NYT quote!

Is grad school a cult?

I recently stumbled across an interesting article from the Chronicle of Higher Education, in which “Thomas Benton” (a pen name) makes the case that graduate school is something like a cult. He’s driven to this conclusion largely by his sense that most graduate students, especially in the humanities, would be better served outside academia. He quotes the following rules of thumb for identifying a cult, taken from the anti-cult Freedom of Mind Center webpage:

• Behavior control: “major time commitment required for indoctrination sessions and group rituals”; “need to ask permission for major decisions”; “need to report thoughts, feelings, and activities to superiors.”
• Information control: “access to non-cult sources of information minimized or discouraged (keep members so busy they don’t have time to think)” and “extensive use of cult-generated information (newsletters, magazines, journals, audio tapes, videotapes, etc.).”
• Thought control: “need to internalize the group’s doctrine as ‘Truth’ (black and white thinking; good vs. evil; us vs. them, inside vs. outside)” and “no critical questions about leader, doctrine, or policy seen as legitimate.”
• Emotional control: “excessive use of guilt (identity guilt: not living up to your potential; social guilt; historical guilt)”; “phobia indoctrination (irrational fears of ever leaving the group or even questioning the leader’s authority; cannot visualize a positive, fulfilled future without being in the group; shunning of leave takers; never a legitimate reason to leave”; and “from the group’s perspective, people who leave are ‘weak,’ ‘undisciplined.’”

Of course, there are plenty of points to pick at — it may speak more to the “definition” given above than it does to grad school — but I think it’s an interesting observation.

A Motley Crue of Toxicologists

Motley Crue Still Exists -- Who Knew?

Three years ago this month a phalanx of Duke physics grad students, including most all Lunchtimers except “field theory” Brian descended upon Baltimore, MD for the American Physical Society’s “March Meeting.” At the time most of us were desperate to find post-doc positions or other jobs given that in January several of us had been told there was no funding left to continue our research past May.  I must have gone on a half-dozen interviews myself, including a memorable one for Wolfram’s theory group.

(Incidentally, nuclear people do get to go to an APS meeting every year, just not the “March Meeting.”  They have to settle for the “April” meeting, which this year is May 2-5.)

Little did I know that three year’s later would find me with a permanent job (inexplicably in toxicology) attending another March conference in grey and chilly Baltimore.  This time around I’m here for the Society of Toxicology’s annual meeting. 

No Big Fish Story Here

Barreleye Fish

I just got out of our virtual tissues journal club and there was disagreement on whether or not the “Barreleye” fish pictured above was real. I was trying my best to be agnostic on the issues (especially given the CGI-ishness of the image). Turns out that it is real. This deep sea fish has a translucent head so that it can look in all directions in the darkness of the deep sea and snatch food from between the stinging tentacles of other deep sea life. Be sure to check out the movie.   Too cool.

Carolyn can add this one to the list of fish that Ann and I have definitely not eaten.

Also, Duke swept Maryland.

Grand Unified Weekly

Hit-n-run: The brand new Grand Unified Weekly site/blog/podcast. (Is there a difference anymore?) Blogroll’d.

Being Trendy

So my sinus headaches have progressed into an eye infection requiring that I now get antibiotic eye-drops just like Emil (Ann’s cat).  I guess he made it look cool and I sub-consciously wanted in on the trend.

Apparently epidemiologists work may be similarly replaced by simply monitoring the frequency of search terms using Google Trends (awesomeness previously discussed). Lunchtime’s unwilling blogger Ann reports (by forwarding a New York times article) that Google Flu Trends is having remarkable success at correlating the flu incidence reported by CDC and the prevalence of flu-related search terms:

Correlation between trends in flu-related searches and incidence

I know it’s been a long time since I last posted, but I have become a massive Digg addict and if you care what random web-pages I’m looking at you can follow me there.  Last week I finally replaced my computer (purchased in 2001) that died this summer.  It has a mere four cores, so Brian’s cyber-manhood is safe for now).  The upshot is that in a few weeks I will be blogging more regularly.  In the mean time I am playing some games I have been waiting on for, oh, four or five years.  I started with Gears of War, which is a lot of fun but not as awesome as Gary Jules’ cover of Mad World for Donnie Darko.

Relative cost of the Iraq war

The idea of comparing the cost of the war in Iraq with the money spent on science research in the United States has crossed my mind a few times in recent months, so I finally looked it up. Brace yourselves. The US is spending the equivalent of the annual National Science Foundation budget every two weeks fighting the war in Iraq (about 6 billion dollars). In total, the war has cost us the equivalent of 100 years of NSF funding.

The NIH budget is substantially higher than the NSF budget. It takes two months of Iraq war to spend the annual NIH budget.

The war cost referenced here is just the upfront cost of counting the war. It does not count the backend costs of retooling the military, taking care of our wounded and killed soldiers, and the negative impact on our economy.  Sources estimate these costs double the true cost of the war.

Hard to resist…

I’ve been in a bit of a funk — my tv and computer broke last month, we don’t have cable/internet in our temporary apartment, and I’ve been swamped with work — but I simply cannot resist posting this video:

[Today's Big Thing]

One of the things I always liked about our work with force chains was how much they seemed like lightning. Even in slow motion that seems to be the case. Compare, for instance, with the distribution of force during a simulated meteor impact: