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 always done a good job of drawing the distinction between analog systems and applied systems (in his case, the B-Z reaction and cardiac electrophysiology) and though his work is getting close to being one and the same as the biology, either version of Turing’s comment seems useful.

I have been traveling since last Thursday, when Ann accompanied me up to Michigan for the Gargoyle’s 100th anniversary and her first (of hopefully many) Michigan football game.  The reunion was great but the weather and the beat-down by Penn State were less than ideal, though still fun.  We did have fourth row seats around the 13-yard-line so we were really in the game.  Ann handled the weather like a champ and now has much better standing to complain about future weather.

Michigan’s loss came despite Duke winning it’s second ACC game in a row for the first time since 1994 (over oh-so-lowly Maryland, how sweet, and did I mention Maryland was lowly?) and Georgia Tech beating Virginia to improve to 7-1.  However — even though it did not occur this weekend, this is finally the season!  Since I enrolled at Duke in 2001 there had never been a weekend where Duke, Michigan, and Georgia Tech all won.

On September 12, 2009 the trifecta was nearly achieved!  Georgia Tech beat Clemson (sorry Brian) in a Thursday night game, and then Duke beat Army (sorry armed forces), and Michigan beat some school from Indiana.  Indiana State maybe?  I think it was the one with the fat guy and leprechauns.    So, after eight long years of at least one of the three teams finding a way to lose I wasn’t going to be picky.  One win on a Thursday and two on a Saturday was enough for me.

But, believe it or not, after eight pathetic seasons of anti-synchronized misery, the trifecta was achieved in full on September 26.  Mostly this is due to Duke improving (and NC Central sucking) but I am thrilled.  It was beginning to seem unreal.

Which brings me to pig lickers.  Though sadly Brian-less and Dawesless, Ann and I met up at the State Fair with a sun-kissed Mary just back from Hawaii and Jonathan, who checked into the fair early to minimize the Village of Yesteryear time for the rest of us.  This year’s atrocity was not deep-fried, but made up for a lack of batter with sheer audacity.  Fried bacon, threaded with a stick, and dipped into dark chocolate similar to what you might find at a banana stand.  It was not bad.  The bacon tasted fine.  The chocolate was good.  But there was no synergy.  No third heat.  Still, I kept it, and a country ham biscuit, and most of a chicken on a stick, and some kettle corn, and some hushpuppies, and some fried pickles, down.

Well, that’s it for me now.  I hope the rest of you are doing relatively well.

Those of you who aren’t current in your APS subscriptions might miss this “Quick Study” article by Bob in this month’s Physics Today.

Every so often I make up a mix CD of my favorite songs at the moment; mostly new songs, but with some old songs sprinkled in for flavor. I thought it’d be a neat feature of this new blog to go through, song-by-song, and explain a little about why it appeals to me.

I first encountered Iron & Wine on the soundtrack to Garden State (thanks, Brian). I didn’t realize that “Such Great Heights” was a reinterpretation of a Postal Service tune, and hearing it first I actually prefer it. In any case, I was taken with the singer’s unique voice, but I wasn’t moved to act on it.

Soon after I moved back to South Carolina, I discovered the KEXP Song of the Day podcast. Every weekday, a free mp3 selected by the staff at one of the arguably few “real” radio stations anymore, KEXP out of Seattle. One of the first songs I downloaded was “Boy with a Coin” (video) by Iron & Wine, from his album The Shepherd’s Dog. It’s addictive and glorious. Two years later, it’s still the most-played song in my iTunes. I still haven’t found a single thing he’s sung that I haven’t enjoyed, but for some reason I haven’t purchased any of his albums.

Next time: perhaps the most over-played song in recent memory

Mathematicians at Carlton University (which a Canadian friend of mine has described as the country’s “last chance” school) have studied the way a zombie outbreak would occur, and what human strategies would work in stemming the tide. Unfortunately, it doesn’t look good for us. The entire paper is amusing, but I especially enjoy the introduction that establishes the difference between zombie folklore and “Hollywood” zombies.

The schools of Duke and Coastal Carolina continue to get closer together. The first overtures were made when I went from graduate school in the Triangle to a job in the Grand Strand. Since, the link has remained strong. John and Ann visited in the spring to speak to my physics seminar classes, and I’ll be venturing back up to Duke very soon to collaborate with my former advisor, both activities I hope will become standing. An extensive interstate system will simplify the route between home cities. But perhaps the most important link between the two happened just this past week: CCU just got its very first Jimmy John’s.

Subs so fast, you'll freak.

That’s right, as of Sunday, July 19, I have been able to relive my halcyon days of graduate school, when the Lunchtime crowd would head down to Ninth St. for a couple of bootlegger club sandwiches and Jimmy Chips.  Unfortunately, I don’t live nearby like our colleague Dr. Hidas once did, so probably no free food for me, but it is on my drive home. I’ve already eaten there twice, and have formulated a plan to do a full sweep through the menu on consecutive visits. I also plan to heavily proselytize the Cult of JJ among my colleagues.

Now, if we could just open up a Zaxby’s in Durham, the link would nearly be complete.

Brontosauruses have a lot of problems these days.  Foremost being that they don’t exist.  But that had never stopped the Durham Brontosaurus at the Musuem of Life and Science.  Unfortunately, some teens were too much for it and decapitated the landmark (well, a landmark in my mind, at least) last month.  Fortunately the museum has hired a sculptor to repair the behemoth.  It make actually work out for the best since the mueseum had been letting the elements have their way with the brontosaurus for quite some time (somewhat understandable given the upcoming dinosaur trail, which I expect will be awesome).

If the sculpture meant anything to you (having your wedding pictures taken there is not a prerequisite, please think of making a donation or buying a t-shirt at the Farmer’s Market this Saturday.

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.

ExpoCast
RFQ-RT-09-00199
Project Description:
The National Center for Computational Toxicology (NCCT) is responsible for developing computational tools and solutions for improving environmental risk assessments and regulatory decisions. Environmental chemicals are the subject of concern and the NCCT is developing methodologies to characterize chemicals based on both hazard and risk for exposure. NCCT is investigating the development of computer models of chemical exposure that can be extended to evaluate thousands of chemicals.
Description of Student Services:
The student shall work within a multi-disciplinary research team and shall provide technical support for research projects modeling exposure potential of environmental chemicals. Specific duties shall include assisting research staff in support for NCCT’s chemical prioritization research program, ToxCast, and in particular its extension to the exposure field, called ExpoCast. This project will involve investigating exposure models that currently exist and evaluating them for their use in a high-throughput exposure modeling effort. Some of these models are in the open literature and some have been developed at the EPA. The outcome of the initial phase of this work will be a written report summarizing the state of the field of exposure modeling, with a focus on models relevant to many chemicals. The second phase of the project will involve the design of a model that can be used for the ToxCast / ExpoCast project. The third phase will involve building tools (databases, spreadsheets, statistical models) that implement a model usable for thousands of chemicals. This final phase will be carried out in collaboration with other NCCT staff who will assist with technical details of database design and tool building.

ToxRefDB
RFQ-RT-09-00200
Project Description:
The National Center for Computational Toxicology (NCCT) is responsible for developing computational tools and solutions for improving environmental risk assessments and regulatory decisions. Environmental chemicals are the subject of concern and the NCCT is developing methodologies to characterize chemicals based on known and predicted toxic effects. As a part of this effort, the NCCT is compiling a database capturing in vivo animal toxicity study data on hundreds of environmental chemicals.
Description of Student Services:
The student shall work within a multi-disciplinary research team and shall provide technical support for research projects characterizing the toxicity of environmental chemicals. Specific duties will include assisting research staff in (1) Continued development and expansion of NCCT’s reference database of in vivo animal toxicity studies called ToxRefDB. (2) Assistance in standardized vocabulary development relevant to toxicology. (3) Assist in analysis of multi-dimensional data from multiple databases, including ToxRefDB, requiring that the candidate have a working knowledge and understanding of MySQL, SQL, MSAccess, and MSExcel.

v-Tissues
RFQ-RT-09-00201
Project Description:
The National Center for Computational Toxicology (NCCT) is responsible for developing computational tools and solutions for improving environmental risk assessments and regulatory decisions. Environmental chemicals are the subject of concern and the NCCT is developing methodologies to characterize chemicals based on known and predicted toxic effects. As a part of this effort, the NCCT is compiling a knowledgebase capturing all relevant in vivo and in vitro data on molecular and cellular physiology of the human and rodent liver.
Description of Student Services:
The student shall work within a multi-disciplinary research team and shall provide technical support for research projects on modeling the toxicity of environmental chemicals. Specific duties shall include assisting research staff in (1) Continued development and expansion of the Virtual Liver Knowledgebase (VLKB). (2) Assistance on information curation from literature and standardized vocabulary development using public domain information sources. (3) Assist in developing queries, query tools and to assist on other scientific programming tasks.

There’s a recent article up at Slate spin-off DoubleX that does a nice job explaining some practical consequences of statistics in the real world.

Seems several major retailers have recently stopped carrying women’s plus sizes. At first blush it sounds odd at best — we don’t want your business, ladies. But it’s actually an economically motivated decision, due to the fact that 1) fabric represents the greatest part of production costs and 2) the probability distribution of women’s weights has a fat tail, meaning there are many different plus sizes. The plus market is spread out over lots of sizes, each of which is expensive to make and, compared to smaller sizes, relatively unpopulated — even though the total plus market may be sizeable.

Pardon me for talking shop for a minute, but I have a question for the group.

The subject of a coming controversy in my program has to do with the curriculum. As it exists, the four “upper level” physics courses undergraduates are required to take are mathematical methods, analytical mechanics, electromagnetism, and thermodynamics and statistical mechanics. In addition, one must take four other science or math courses numbered 300 or above, the reason being that the degree is Applied Physics, whatever that means. One choice is, of course, quantum mechanics.

It would probably not shock you (based on my research) to learn that I advocate making quantum mechanics a required course. The vocal opponent to the idea is, perhaps unsurprisingly, a solid state physicist, though her argument is simply that the lack of a QM requirement is what sets the program apart from a regular physics degree.

Now, why is that important? you may ask. South Carolina has a rule (arcane, I say) that any new degree program in the state must be “needed”. Either there should more students in the state than can be serviced by the schools currently offering it, or the program should be sufficiently different from those at other schools. Our program falls into the latter category. The original members of the program, both of whom are still here and one being the vocal opponent, framed the degree as being versatile; an AP degree allows the holder to pursue a large range of career paths. It has been explicitly stated to me that we are not in the business of churning out physics grad students, although they may do so if they choose. In any case, it’s now been four years since the program was implemented, and there’s no rule stating that we must continue to justify the program.

However, I am willing to stipulate that retaining the “Applied” label (again, there is no clear definition of the term, the one given above was chosen) is in our best interest. But is stat mech more important than quantum? The opponent argues that everyone needs stat mech, but not everyone needs quantum. To her credit, she concedes that I may feel the opposite, which indeed I do.

So I throw the question to you, gentle reader: what is more important, statistical or quantum mechanics?

I suppose I can now call myself a real scientist. I have applied for funding from the NSF.

I’m listed as a co-PI on a Course, Curriculum, and Laboratory Improvement (CCLI) grant proposal. We’ve called it Improving the APplied Physics Laboratory Experience, or iAPPLE. The purpose of the grant would be to create a junior-level lab course sequence,

which hasn’t existed to date. Instead of doing the “classic” experiments, though, students would propose, design, and carry out independent projects. They would have to create mathematical models (using Mathematica, naturally) for the phenomena they’re investigating and produce some sort of physical apparatus of demonstration equipment-level quality. In turn, these would be folded back into the introductory courses, and the lab students would be responsible for assessing the quality of their work as it’s used in the intro classes. Therefore, a feedback loop is created, in which students come into the program and learn from materials more advanced students have made, then they make more materials for the next “generation”. These educational materials would accumulate in our department over time. It’s win/win/win… or so we believe.

The grant-writing process itself has been hectic, especially toward the end. I was gone on vacation for a week, though, so I missed a lot of the slog of writing and editing. I feel a bit guilty about it, but my responsibility in the actual execution of the grant is quite significant. But the last few days since I’ve gotten back have been a constant cycle of re-writes and edits and meeting to talk about grammar and re-formatting. We submitted it today, though, so the pressure’s off. We think we have a very good shot of getting funded. We’re all very excited about the project anyway, regardless of the NSF’s decision.

Now, it’s on to write another NSF grant about starting an REU program here…