Philly and Ann Arbor

A long weekend (last weekend), a couple of days in Philadelphia with Ian and Mandy, followed by a couple in Ann Arbor with Sarah.

It is such a delight to see our kids doing so well, and so excited about their lives. Ian's a good man -- doing well at a job that he'd prefer not to do, to provide support for the two of them. He was always a reliable, hard worker once he committed to a job. He's thinking hard about what he wants to do next, and where he'd like to go in the long run. He's gotten inspired about the possibility of historical restoration, which would combine his love of history with an artistic profession (architecture). Mandy's working her tail off at University of the Arts, loving every exhausting minute. Well, almost every one. And Sarah's thriving at the University of Michigan.

We arrived in Philly on the day that the student show went up -- Mandy's first exhibition at UA. She was done with the printing, but not with all the stitching that goes into her piece. It's a sweet graphic tale, and very nicely done to these non-expert eyes. But she got pretty badly beaten up at the critique the next day. She had to leave the room and go to her studio space for a good cry, and when Marie, Ian and I got to their apartment after our day at Penn's Landing, she was sound asleep, making up for the very long days she'd been working. It was really good that Marie could be there to provide her with some perspective on the process.

Even I tried to contribute something. I told her how we beat our graduate students up at their written and oral exams, particularly when they're defending their thesis proposals. It's painful, but an essential part of developing both a sharp set of self-critical skills, and a thick skin. Any creative person -- artist or scientist -- is putting himself out there in a very vulnerable place, and it can be pretty painful sometimes. You're so invested in what you've done -- your vision -- and your ego is on the line, too, in terms of the technical skills you have brought to the task of executing the work that shows your vision.

One big ego issue is intelligence. Although the intelligences of the artist and the scientist have different forms, we're all bright, or we wouldn't be in the art game or the science game. And many of us have had a lifetime of strokes from parents, teachers and peers, telling us how bright we are. So it's really painful when we fall short in others' eyes.

Sometimes rejection comes from people we know but don't really have a lot of respect for. That still hurts, because we know that there are others who do respect their opinions.  Sometimes rejection comes from people we don't know very well. That hurts even more, because we don't know enough about them to easily dismiss their criticisms. But what really hurts is when we get rejected by someone whose opinion we do value. After such occasions, how many times have I asked myself "Why do I do this to myself???"

Ian and Marie and I had a day of tourism together while Mandy was preparing for, and then enduring, the critique of her work. We started our morning with the Seaport Museum, which was pretty cool. But the best parts were lunch, and visiting two warships after lunch.

Lunch was at the City Tavern, a reproduction of the Inn where the founding fathers often ate and drank. Waiters in knee britches, etc. I expected it to be tacky and touristy, but since it was a slow day, it was actually really nice. I'd commented on the bus headed toward the waterfront that I hoped for sauerkraut and sausages for lunch. By coincidence, the chef at the City Tavern is German, and there were some great sausages and great sauerkraut. With a pint of I-forget-which of the colonial brews, I was one happy camper!

Then to the ships...

I really like museums that feature art, or history, or anything military, or stuff related to engineering/industrial prowess. So I'm a real sucker for warships that you can walk through, because they give three out of four. We visited two of those at Penn's Landing: the Olympia, Admiral Dewey's flagship in the Philippines and later one of TR's White Fleet, and the Becuna, a WWII sub. (The latter even included some cartoons and other graphic memoribilia from the men who served on her, so it was a four for four experience...

Fortunately, Ian gets off on this stuff, too. Marie tends to be put off by the ultimate purpose of these beasts, but she humored us and enjoyed the elegantly paneled officers' mess on board the Olympia, at least after her fashion, while Ian and I wandered around the rest of this rather sweet old lady of the sea. Marie did stay topside while Ian and I prowled through the Becuna, however. Between her abhorrence of war and a tendency to claustrophobia, this boat had no appeal for her.

Like most guys who walk through these things, I try to imagine what it must have been like. Forty or more men sharing a single toilet, one minute showers once per week, plus the constant stink of diesel fuel, oil and fumes. Days, weeks, perhaps months of sheer boredom, punctuated by hours of fear and tension, and sometimes of sheer terror. Although I never wanted to serve on a sub (although it did sound really cool!), I was, like most boys of my generation, seduced by the prospect of serving topside. Since I was raised in a time when the draft was still in full force, I always thought I'd have to serve. I was a patriot, even David looked good in dress whites, and the sea beckoned...  I thought that I would become a man the first time I landed a jet plane on the deck of an aircraft carrier. My last semester at Berkeley I took the exams for Navy OCS and passed everything that I needed for flight school. Except my sitting height, which would have precluded my flying one or two of the fighters.

Thank God I changed my mind at the last possible minute and didn't show up for induction in San Francisco in January 1963. I'd made every commitment except actually signing. When the Viet Nam war ended and the prisoners got off the transport planes at Subic Bay, the Navy pilots all looked just like me -- tall, skinny, crew cuts. Hell, I wanted to sail around the Mediterranean and flirt with Italian girls, not drop bombs on people with whom I had no quarrel.

I was a little embarrassed the first time I boarded the Alabama in Mobile, in my late thirties. The first thing I thought was, "Damn! There sure are a lot of guns!!" Then, when we went onto the armor deck, the one beneath 16 inches of steel, I couldn't help wondering what it must have been like down there when hit by a bomb, even one small enough that it didn't penetrate the armor. I say I was embarrassed, because it was as if I'd never really thought about the meaning of the damned ship.

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Our time with Sarah was very full - we walked all over campus (well, you can't really walk over all the Michigan campus, perhaps in this lifetime), and through much of Ann Arbor. Sarah's dorm, where we met her roommate and some friends, the arboretum (twice), the Union 

(I love Big Ten Unions from the 20's and 30's), the Natural Science Museum, an a capella concert by Amazing Blue, a compelling movie (The Class, based on the true story of the difficulties of an idealistic young teacher in a multiracial / multicultural school in a tough Parisian neighborhood, starring the actual teacher and his students), a great Japanese meal, an OK meal at Black Pearl ("seafood and martinis" should have been a warning)...  She's loving UM and doing really well, but like lots of students today, she is really stressed a lot of the time.

Billy, Part 2

Suspicious that there might be a second cat under the house, I reset the trap Sunday morning.

Last night, I climbed into bed beside a sleeping Marie and closed my eyes. I was quickly headed down and out. But I got brought back up by a thump that I thought came from the furnace duct. I sat up and waited.

A moment later I heard a faint meowing, and I knew there was a second cat. I got up, put on pants, shoes and a sweater, grabbed a flashlight and headed for the basement.

When I opened the door from the basement into the crawl space, I found the trap empty, except for the undisturbed cat food bait; the entrance gate was still open. "Shit," I thought, "a smart one." I figured he'd avoided the trap, either because he'd seen the other cat in it, or because he was kept away by the still strong scent of cat piss.

But when I shone the flashlight into the deeper recesses of the crawl space, there he was -- Billy -- looking right at me. I took the light out of his eyes and called to him, and he came right out. He stopped to rub against my legs and chat with me and, once I'd closed the door to the crawl space, he did the "Billy stand": rising up on his back legs to invite my hand to his head, then standing as high as he can to intensify his pleasure. And mine.

I let him out of the basement, but he hung around, waiting for a handout. So I gave him a small bowl of kitty chow. That was probably a bad idea, because he's a well-known mooch throughout this part of the neighborhood, but I was so damned glad to see him clean and sleek and healthy and happy.

Welcome back, Billy!

Qualifying Exams

Minmin and Yingying have just retreated to their respective exam rooms, to begin working on their comprehensive written exams.

We struggle, as a faculty, to come up with the best way of evaluating second-year graduate students as they make the transition into full-fledged researchers. They have to do two things: First, they must demonstrate a sufficiently broad and deep knowledge of the material they need to know to do research on their chosen problem. Second, they have to write and defend an intelligent research proposal, showing that they are familiar with the state of knowledge in their field, that they can identify an important problem, and that they can choose a logical approach to solving that problem; there must also be sufficient preliminary data to convince us that they can carry out the proposed research.

The real problem is the first part -- what, exactly, is "a sufficiently broad and deep knowledge of the material they need to know"? My students need to have strong backgrounds in biology and/or chemistry and/or physics and/or biochemistry and/or biophysics and/or computer programming and/or mathematics and/or ...  Hell, they need to know everything I know, and everything I should know but don't!

The really hard part is testing the ability to think. The written qualifier isn't supposed to be a regurgitation, although it almost always contains huge doses of that. It's supposed to demonstrate the student's ability to apply what he/she knows to new problems. But it's really hard to design questions that test that.

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I remember my own written comprehensive exam. It ranged from overly simple to delightfully tough.

The overly simple part was a mechanics question that shouldn't have bothered an undergraduate: a bowling ball is launched with velocity v0 and without rolling, so it slides along the floor; after a while it is rolling without sliding. If there were no loss of kinetic energy due to friction, what would the final velocity be?

The delightful question was: Suppose the electron had spin 3/2. Discuss. (b) Suppose the electron had spin 1. Discuss.  I loved this, because I could tackle anything from the structure of stars to the periodic table. I chose the latter and did pretty well, at least on part a. I blew the second part, because I forgot the difference between fermions and bosons. Shouldn't I have failed, just for that?

I had lunch with the usual crowd the day after the exam. John Merrill, a young assistant professor was always part of the group. When I commented that I loved the question, John admitted that he'd written it. I asked him what the answer was, and he said, "I have no idea. I'm looking forward to reading your answer and then trying to figure it out myself."

The exam took two days, if I remember correctly. When I got home after the second day and was relaxing and celebrating that it was over, Eric Jakobsson called me. "Congratulations!!" he said. When I protested that I'd barely finished the exam and didn't yet know the outcome, he said, "Regardless of whether you pass or fail, I'm congratulating you, because right now you know more physics than you ever have or ever will again!"

Billy

Awful experience first thing this morning.

I'd closed up a hole in the foundation. Some animal (I suspected a cat) had dug through so it could get into the basement. It had to be fairly recent, as we only finished the renovation of our back porch 3-4 months ago, and George, Tom and I had all checked out every square inch of the outside of the house several times. (They'd done a number of small repairs.)

I worried that I might have trapped some animal under there -- probably Billy, because I knew he doesn't sleep in Tommy's house at night -- particularly after I heard a caterwaul only a few hours after placing the trap. I was sure it was coming from under the house, and Sweetpea ran to one of the furnace ducts...

So I borrowed a trap from Atlanta Pet Rescue (from which we'd gotten Wally and Lumpy), baited it and put it into the crawl space. There was still no sign of activity when I checked after dinner last night.

But this morning, when I opened the door between the basement and the crawl space, I was met by a jumping cage and violent spitting. I thought for a moment it was a raccoon, but it was Billy.

We'd gotten acquainted with Billy very slowly over the years. He's one of the nine (I think) cats that Tom (and Diane, before she died) kept. 

Skid lived on our porch, convinced it was his. He was old and filthy, but sweet.  Though Sebastian tried to befriend him, Skid would back away when Sebastian came out. One morning, Tom found Skid's body on the walkway I'd put in between our sidewalk and the driveway.

Felton wanted to live on our porch, but Skid wouldn't let him. But he would stroll along the path to our water faucet, haughty, wary of me. He'd then wander back home, or on to Carolyn's house, often stopping to spray our steps or one of our bushes before he moved on. I put a bowl under the faucet and kept it filled for him – I've never known a cat who drank so much water. For over a year he wouldn't let me touch him, even though I would rinse out and re-fill the bowl each time we met; he'd wait until I moved away, then stroll over and take a deep draught. Gradually we became friends, on his terms. After many months, when I'd come out, he would deign to roll around happily on the sidewalk, just out of reach, but move away if I got too close. Finally I got to touch him, but I would have to work my way slowly over to where he was lolling. After Skid died, he began sleeping on the wicker couch on our porch and, to demonstrate his approval of our relationship, he stopped spraying the plants and the steps; now he sprays the porch right in front of the door. For the past year or two, he has been meeting me on the steps, and he's become downright affectionate. 

Billy was a cute and very rambunctious nearly-full-grown cat when we first met him. He'd hide in the bushes and play with a stick or leaves, just out of reach. Tommy told us that he'd use the cat door to get food, but he spent more and more time outdoors, apparently intimidated or abused by the other cats. I coaxed and coaxed, and I was finally able to get him to come and rub against my legs as I sat on the steps. At first he wouldn't let me touch him -- I'd get a swipe and a slash if I tried. Later he let me pet him some, but he remained skitterish, prone to a wild-eyed look and a swipe. His preferred mode was to drop down on a stair or the sidewalk beyond my reach, roll around passionately for a while, then come and rub against my legs, maybe get a few strokes, then retreat to a lower step or the sidewalk, just out of reach, and resume his rolling. Two or three iterations of this, and he'd take flight.

This morning's Billy was a completely different animal, violent, aggressive, and clearly terrified. He scared the hell out of me. I'd never seen any creature acting like that. The cage contained only fragments of the styrofoam bowl into which I'd put the bait, along with pieces of the plastic sheet that used to line the cellar floor below the cage, which he'd shredded. There was the awful stench of cat piss over everything.

After putting on a glove for protection (even though the mesh of the cage was fine enough to prevent him reaching out), I carried the cage out on to the back stoop. He was hissing and thrashing about the whole time. When I opened the trap door, he took off across the yard and disappeared.

Poor Billy. I'd not seen him since the last warm days of fall, and I'm sure this experience has rendered him completely feral. I'm sure he'll never come calling again...

Spring Break!

Today I finished the twentieth class (out of thirty) in my Molecular Modeling course – but who's counting? It's going well, but I'm tired, and I'm ready for Spring Break, which is next week. (It actually starts for me tomorrow, because I've set aside the full day to stay home and work on The Book.) When I was a student, it never occurred to me that the only person in the class who was more ready for breaks than me was probably the professor...

This point in the course marks a sharp boundary. We've finished the stuff that was reasonably well prepared coming into this year (because much of it has been there since the first time I taught the course in 2004, and it's been growing and evolving ever since). We've finished six tutorials with Oscar, the nice little program that Geoff Rollins wrote for me last year. Lying ahead is the last third of the course, the part through which I've sort of stumbled and faked things in the past, or which I've hoped to cover but never actually gotten to... Over the break the kids will carry out their first NAMD simulations, on two models of myoglobin (with four xenon molecules), an in vacuo case, and a solvated case. I've got Burak working hard to develop two or three more NAMD tutorials – the kids will have to do about one per week – and we'll finish with the structure prediction problem and the free energy perturbation simulation that Geoff developed last year. But I still have ten lectures ahead, none of which is really solid... Some of the material covers things I know little about. In particular, there are substantial gaps in my knowledge of recent literature. I need to identify appropriate material – then actually sit down and digest it. So I've still got my work cut out for me.

I love the material, and I like many of the students. And of course I like standing up in front of any group and talking... I think one of my strengths as a teacher is that I care how the kids respond and how I come across. I always try to get things to an appropriate level for them. My biggest weakness is that I strongly prefer the best students – I love it when some kid pulls some insight that I hadn't thought of out of thin air, but I get frustrated pretty quickly when the slower ones don't grasp the most basic things. Since I wear my heart on my sleeve in everything I do, I suspect that I'm not very good at disguising my prejudices in this area. And I've long believed that the best teachers are those that bring the slower students up to their potential, whatever it may be – anybody can "teach" the bright ones who figure things out on their own. So I think I'm a decent teacher, but not a really good one.

Teaching is hard work. Satisfying, but hard. It's amazing how much time I have to spend preparing for two 2-hour classes each week, even though I've taught much of the material in the past five years. Part of the problem is that I procrastinate, so the day of the class (and often the night before), I'm racing to get something done for class, often finishing at the last minute. And part of the stress comes from the fact that I'm too much of a perfectionist when it comes to details of figures – I rework and rework my PowerPoint presentations and handouts far more than I should.

And one special part of the difficulty this year is that I really want my syllabus (and figures) to crystallize into the form this material will take in The Book...

Weekend

Marie and I are putzing around late Sunday afternoon, cleaning up and arranging stuff in the new back room, but mostly being very lazy, when the phone rings. It's Eileen, just leaving a meeting at All Saints, and she wants to know if it's cocktail time yet.

It's a pleasure having the kind of friends who will occasionally drop in, and who are pleased if you drop in occasionally. Eileen is one of those. I didn't get the hole in the basement wall patched, so a squirrel or a cat may be coming in for another day or two, but it was delightful mixing martinis and sitting on the porch, drinking, munching, chatting, laughing.

Marie and I got gentle vengeance by scanning through some of the guys on the dating service (or whatever you call it) that Eileen has been using, and then persuading her to let us send four of them messages that she'd be interested in talking and maybe meeting. Eileen admitted later that she was pleased we'd done it, because she'd always waited for the guys to contact her first.

I have to call Eileen and tell her about the docent at the Birmingham Museum of Art that I wanted to meet back when I was single. After a noon group tour, I found someone who knew her and could give me her number, and I called her and asked her out. She seemed genuinely sorry that she was busy that weekend, and she urged me to call her again. I told her that I'd taken the first chance, and now it was her turn. When she replied that she couldn't call a guy and ask him out, I told her that there was no way then that we'd ever really hit it off, because I was only interested in women capable of an egalitarian relationship. She again told me she hoped that I would call her again, and I said that I hoped she'd make the next call.  She didn't, and the rest is history.

Boston

To Boston for Biophysical Society Meeting Feb 27 - March 3.  COLD. Things started out poorly when I told the taxi driver I was at the Westin next to the Convention Center and he took us to the new Convention Center, right near the airport. I re-directed him to the Westin Copley Square, which is near the Hynes Convention Center, where the BpS always meets -- or always had. Turns out the meeting this year was at the new one, so I was stuck with commuting, $15 and 15 minutes by cab, or 45 minutes by subway...

Phone call from Phil Nelson while I was en route -- to the office, message relayed by Bee. When I called him back he told me that David Beveridge had to cancel his appearance at the Monday discussion group on the use of computers in graduate and undergraduate education, and he asked me if I could fill in. (David had told him about the tutorials in my modeling course.)

Dinner with Jack Johnson on Friday night. As always, long, good conversation, ranging over science and life. Drinks at the bar before dinner, then two bottles of a very nice Pinot Noir with dinner. I haven't had that much to drink in forever. I knew it was time to go home when I could hear myself unable to pronounce "taxi" without a slur. How hard a word is that?

Saturday night I made the mistake of meeting Burak at the Society Mixer, hoping to meet someone I know to join us for dinner, forgetting that almost none of the old farts go to the mixer. (I'd invited Phil to join us when we talked on the phone, and he'd initially accepted; he cancelled on Saturday when he decided not to fly to Boston until Sunday.) Ended up with just Burak, Anton and me at a very good seafood restaurant. I was disappointed that I failed to introduce them to anyone at all.

A few good talks Sunday morning, though there was direct overlap between the only two sessions that interested me. Spent the afternoon getting ready for my talk on Monday.

Sunday night dinner with Summers Scholl, the editor of my text, plus two of her compadres from Garland, along with three other authors; Steve White among them, but a week later I've forgotten the other two names. Legal Seafood for the second time in three days.

Monday morning slept in. E-mail etc. at the hotel in the morning, then lunch with Jason Mears before the 1:30 Ed Committee session. It went OK. Phil Nelson, Dorothy Becket and me. Then a OneToOne session at the Boylston Apple Store, followed by an interview with Eric Downes, an MIT student who visited Tech over the weekend on a recruiting visit. He's interested in stuff at the other end of the spectrum from me and came back interested in Joe Montoya among others. I left Joe a voice mail telling him that if Eric ends up in his lab, Joe owes me a drink or three.

A delightful dinner with Rami Osman at the Neptune Oyster House before Dorothy Kerns's National Lecture. I'd heard from several people what a great speaker she is and what wonderful work she does, but she had far too many slides, all far too cluttered, and it was a rambling disappointing talk.

I've not been crazy about BpS meetings for several years, and this one reminded me why...