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

Coming back from a trip to Oak Ridge Tennessee to see the neutron facilities. (which are decidedly impressive).

Then Tennessee highway patrol had signs up that said 23% of all traffic fatalities involved speeding.   Therefore 77% did not.  So you’re three times safer speeding than not.

Similarly 27% involved drunk driving. Again you’re almost 3 times safer driving drunk than sober.

Combining them, assuming independence, gets (1-0.23)*(1-0.27) = 0.56 or 56%.  So you are even slightly better off speeding and/or driving drunk than being sober and following the speed limit.

(please don’t drive drunk and fast).

One of the harder things to do in computational chemistry is to model phase changes. Theoretically it is almost impossible as one needs very large scale (infinite) calculations to account for putative large-scale fluctuations. None the less it is a fun problem.

I took 1000 waters, using molecular dynamics constant volume and temperature in the AMMP program, and the tuna potential set (”tuna” refers to the name of the program used to adjust parameters to fit independent data, the potential is similar to the SPC water potential and reproduces radial distributions etc quite well). The goal is to look at pair correlation times as a function of temperature. The pair correlation time (how long two different molecules are close together) should be very long for ice and rather shorter for water.

As a start, though, I looked at the energy of the system. There were no surprises with the total energy which increased more or less linearly with temperature. However, the standard deviations were different, Since Cv, the constant volume heat capacity, is related to the standard deviation of the energy (Cv = c (sigma/T)^2 ) I rescaled the data by the absolute temperature squared and plotted that.

There is a dip around 250-275K! which is just the right place.
Estimated Cv

More detailed, with more time and more temperature values, simulations around the putative phase change are shown below.
Cv calcualted on a longer run and with more temperatures

Cv calcualted on a longer run and with more temperatures

So it looks like it might work.

I generally don’t discuss my scientific work in detail on this blog because

1. The proper place for it is the reviewed literature
2. I don’t want to scoop myself or my collaborators

That said, it is worth giving a link so you can see what we do here.

Pubmed makes this easy. Hitting this link should show most of my more than 200 publications on areas ranging from bioinformatics to molecular design and HIV. My apologies to the occasional other Harrison, RW (actually several – I have a common name) that it grabs.

It’s raining hard in Atlanta, and finally cold enough to get out the raingear.  It smells of pine/arborvitae smoke from this summer in Canada.  I miss it.

I had a chance to find more trilobite fossils this weekend, and unlike before they were not just impressions, but the whole critter.

The picture below shows a very small fossil that was already loose from wave action.

Looking at the local rocks and their layering suggests an explanation for the spotty distribution of fossils. When the mudstone was laid down in the Cambrian the area was a wide tidal mud flat. Much like the area around Tybee Island
(but not as sandy and NO trees) or the mudflats near the Severn river or the Gower pennisula.

Mud flats are not really flat, but tend to have little pockets where biological detritus collects.
These pockets become hotspots for fossil collection when covered with silt by tidal floods. There are occasional quasi-stable areas and these can also support a colony of animals that is subject to being covered in a local flood event and we have found a few dense patches of Crinoid stems – including one with a trilobite in it that I don’t have a picture of (yet). Shallow water above mud flats is a great location for small crustaceans and various small mollusc’s which is just what we find in the fossil evidence. Some of them were just unlucky (or lucky – it depends on your viewpoint) to get caught in a small pool at low tide and have their remains preserved for us.

One of the stronger pieces of evidence that this was an estuarine environment comes from about 100-1000 layers above the fossil rich layer(if each major layer in the mudstone reflects a season – then maybe only about 1000 years later) the river shifted and deposited a layer of gravel on top of the mudstone. There is a continuous shift in the color of the sediment from a dark gray – where the fossils are found to a lighter gray or tan and we don’t see visual evidence of a discontinuity event. It looks just like a gravel bank deposited on the side of a river. In some ways it is a pity that it is so old -because it would be a great place to look for land animal fossils – just that there aren’t any from the Cambrian.

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.

Just a short post. I’m helping (or at least trying to not get in the way of) one of the scouts from my younger son’s troop plan the next backpacking trip. He’d used the wonderful georgiahikes web site to find a few trails, and we went trough them. We initially settled on the Blood Mountain Cove trail, and as a diligent adult leader I called the district forest ranger to see if there was anything we needed to be aware of.

There was. Deer season starts October 19th in Georgia and this is a popular hunting area. It is managed with open areas for deer food – so I’m not surprised.

But we’d picked a plan b (near the Vallhala fish hatchery) and so we’ll just use that.

Last weekend I was with my younger son’s crew getting trained for Northern Tier at the Allatoona scout base.  Northern Tier is a canoeing expedition covering a mixture of lakes and portages at the boundary between the US and Canada.  His crew is on the young side – which may make things a bit “interesting” as some of the youth are not much heavier than the canoes (at least aluminum Grumman canoes ~85 lbs).  In addition to making sure that we actually bond as a crew, there is a lot of stuff (besides making sure everyone knows their J-stroke, ruddering and sweeps) that we have to learn.

The scouts need to learn  self-management and the closely related concepts of leadership.  (by the way this is often what takes graduate students a couple of years to learn – if they ever do – maybe I should take them hiking?).  Their troop hasn’t historically been that good at being “boy-led”, and for them this trip was the first time the adults simply sat back and said “we’re on vacation”.  Nonetheless, they managed to get things done (albeit slowly).

Canoe tripping is decidedly different than backpacking, although some of the ideas for lightweight and ultralight techniques will carry over.  (at least you don’t have to worry about dry camps ).  You have to pack in a more or less waterproof manner.  Because you have a vehicle, the weight of the components is less critical – we used a plastic packer for food and another for equipment.  These fit inside of a large canvas (nylon?) bag that had a hip-belt and shoulder straps and thus could be lugged across portages.

Since the portages are shorter than a typical backpacking day the weight is considered “less critical”.  I’m not convinced this is true. We won’t carry as much (if any) lightweight food and my “bette noire” of tunafish in bear country is still on the menu.    While this means the diet is more homelike and we won’t have quite as much miscellaneous packed and dried meat like food product, it’s likely that the weight for ten days of food will be very heavy.

We will have the option of larger tents – and heavier tents.  We’ll have to weigh the relative weight of one 3-4 person tent vs. two smaller tents.   Since the mosquitoes are fierce and people try to stay in the tents from sunset to about 1am the bigger size may be an advantage.

I realized that I haven’t put one of these in, and could, in principle, be up the proverbial estuary without a means of propulsion.

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so there.