care and feeding of graduate students (life as a professor)

Being almost the new year, it is a good time to reflect. Personally, this has been a tough year with aging parents running into serious health issues. One of the things that happens when you have the final visit is the chance to see some of the old photographs, and one of the ones my father kept and scanned is from when I was a scout. It made me think about the differences between when I was a scout and the experience my sons are having as scouts today.

The photo is from a scouting exposition that Chester County Council had in 1975. My troop elected to do a pioneering and a cooking demonstration. As SPL I delegated the cooking to my ASPL, and organized the pioneering project. We knew that the pioneering demonstration had to be stable on a parking lot without guy lines or stakes. We wanted it to be spectacular. The picture shows the results. In the background is an ugly tower – but clearly scout designed and scout-built. It was also taller than the competition, and stable enough for visitors to climb. The foreground shows the competition (our rival troop – but a more or less friendly rivalry – both troops are still in existance in that district so I won’t give the numbers). They had built a spectacular, adult-engineered, set of projects. However, their projects couldn’t handle traffic. You may notice that they are looking across the parking lot at our tower in disbelief – we actually won! They are also looking at their ScoutMaster – (well really adult acting as SPL) – who ran the troop very efficiently.

We really had a scout-run troop – much more so than either of my son’s. (although in fairness I think both troops are trying to move in that direction, and one has made great strides). So what is the difference? Why did we pull it off?

• One possibility is that parents, schools and teachers were far less protective. I could carry my scout knife in my pocket to elementary, middle and high school and no one cared. Heck, in high school I brought a machete in as a prop for a class play (for Laeretes to fence with Hamlet). I think the extra freedom allowed us to develop a sense of responsibility – mom or dad wasn’t there to fix it all the time.
• Another possibility was our meeting time. We met Saturday morning. This let us have a stronger outdoor program than we usually do today. We pretty much were guarantied two outdoor events a month -a hike and a campout. I think this may have been important as the troops that met on a weekday evening were much less scout run than ours.
• Kids were less scheduled. Sure there was little league, but that was only in spring and early summer. Basically you got home from school and entertained yourself until dinner time.
• The patrols camped as patrols. The patrols cooked as patrols. If there wasn’t a troop campfire then we had patrol fires
• Patrols met separately from the troop meeting and planned for their events without adult supervision. If you messed up – well you messed up. (one of the reasons that I didn’t do the food at that exposition was that I messed up badly the first time I was a patrol leader on food planning for a campout).
• Scouts were involved in planning the year at all levels. The current standard approach is that the scoutmaster and the patrol leaders council meet and then the scoutmaster presents the plans to the troop committee. We just met together and bounced ideas off each other.
• Older scouts were allowed and encouraged to plan their own “high adventure” trips. Sort of like venturers today.

Some things were the same and cannot be the root cause of problems. Adults were around. When we went on an outing the drivers and assistant scoutmasters were there. Like today, they camped as an “adult patrol” off on the side, but they kept an eye on us. In fact, the times we had trouble were when the adult supervision failed. It wasn’t uncommon for one of the adults to meander through the patrol area and check that everything was OK. I don’t think boys were fundamentally any different than then.

Finally I’ve managed to find a trilobite fossil. It’s been something for which I’ve been searching for many years. Northeast Alabama has rocks of the appropriate ages and it is just a matter of finding the right layer and the right location (as the fossils are somewhat sporadic). I can usually find the rocks, but it is my eagle-eyed wife who usually finds the interesting fossils (she found one last year).

Anyway, in the Lake Weiss area (and especially the spring creek area) there are two layers of sedimentary mudstone. The upper layer, which is light tan in color and contains a fair amount of alluvial gravel is generally barren. The lower layer, which is grayish, has a fair number of interesting fossils in it. We’ve found soft corals, something that looks like a sponge or squashed sea-urchin, a small number of shells, some mysterious tracks, and (finally!) trilobites. This lower layer is right below the full pool limit – so if you want to look – now is the time.

so here’s my best fossil which has 5 small casts. I’m not sure what the dark brown thing in the middle is (it looks like an ammonite, but could be something else).

There is another species of trilobite as well, and this fossil – which my son found – is a good example.

postscript: These are probably Cambrian fossils. If you look closely at the right hand edge of the second picture you can see a fringe of scales. S. M. Gon III’s page has a good set of information.

From a recent speech by our president-elect:

Whether it’s the science to slow global warming; the technology to protect our troops and confront bioterror and weapons of mass destruction; the research to find life-saving cures; or the innovations to remake our industries and create twenty-first century jobs – today, more than ever before, science holds the key to our survival as a planet and our security and prosperity as a nation.  It’s time we once again put science at the top of our agenda and worked to restore America’s place as the world leader in science and technology.

Right now, in labs, classrooms and companies across America, our leading minds are hard at work chasing the next big idea, on the cusp of breakthroughs that could revolutionize our lives.  But history tells us that they can’t do it alone.  From landing on the moon, to sequencing the human genome, to inventing the Internet, America has been the first to cross that new frontier because we had leaders who paved the way: leaders like President Kennedy, who inspired us to push the boundaries of the known world and achieve the impossible; leaders who not only invested in our scientists, but who respected the integrity of the scientific process.

Because the truth is that promoting science isn’t just about providing resources – it’s about protecting free and open inquiry.  It’s about ensuring that facts and evidence are never twisted or obscured by politics or ideology.  It’s about listening to what our scientists have to say, even when it’s inconvenient – especially when it’s inconvenient. Because the highest purpose of science is the search for knowledge, truth and a greater understanding of the world around us.

I heard part of this speech this morning, and the parts I’ve emphasized are why we scientists do it. It is very rare that I am moved by what any politician says, but these statements so clearly express the ideals of science that is is hard not to be moved. This is the ethos that I try to instill in my students.  It is a succinct and clear statement of the hypothesis that underlies the entire scientific revolution – from the 1600’s to the 2000’s – namely that by understanding the world we can make life better for those who inhabit it.

Part of the reason for my recent hiatus at writing entries is a combination of attending meetings and finishing up with semester business.  Anyway, I have some interesting results from casp-8.

1. We did pretty well on the targets where there was one good template and we found it.  (by some measures we were #1 and #2 on a couple of targets).  This is good because high-quality molecular mechanics is a major research focus for my group.  Our potential probably slightly enlarges protein models and one of the “tricks of casp” is to compress your model.
2. Our server was not designed to handle many simultaneous hits and one of the neat features of profile-profile methods is the number of homologs that they can fish out.  Usually if it finds one, it finds 20.  The problem is which combination of these 20 is the best model.
3. It is critical to keep the profiles up to date.  Psi-blast has its problems and one of them is non-stationarity.  If you run on different databases then you get radically different profiles – and with updates over time the profiles sort of “rot”.   (Its other problems include some rather poor software engineering and a context dependence).  It doesn’t run in my hands with the non-redundant database (nr) but does work much better with the refseq_protein database.  This caused a number of problems where we missed the best profiles.  ARRGH!
4. It is probably a good idea to move from a single geometric measure (gdt and related variations) to explaining the data.  For NMR this means can your model reproduce the NOE’s and backbone restraints used to produce the “structure”.  For crystallography, it is probably good to ask what is the height of the cross-rotation function.  I’m debating building a server for this.  There are more than one group that does very well by having trained their method to generate models with poor geometry (useless models) that generate good scores on the geometric measures.  Forcing evaluation against data would fix this issue as well as be statistically and mathematically the best measure.  – you can argue about measures but you can’t argue against data.