The kilomile

A lot of runners chase the 1,000 miles per year distinction. It’s kind of a nice, round number, so it’s a fun goal to aspire to. I’ve been logging miles on RunningAhead since mid-June of 2008. Today, on a run with RH, I completed my 1,000th mile (i.e. the kilomile), which ended precisely (plus/minus) at GYT’s house, complete with finishing line tape, applause from a live studio audience (or a recording thereof), and donuts. More specifically, I had a Boston Creme filled donut and a curious red one that may have been a Red Sox themed donut. I stayed for the Boston Creme donut and had to take the red one to go but finished it on the run home. I go on these long stretches of donut cravings, which have recently been supplanted by a muffin craving. The inter-event intervals of muffin consumption (which is not some horrible muffin-related disease as the name may suggest) is far too long, since I feel like it must take a special occasion (like KRMS birthday surprise) to go to Wakefield MA and get muffins. Anyway, I feel strongly that there is a class of pastry related cravings that this runner has that actually can be satisfied by any member of the genus Pâtisserie, though sometimes the craving is specific, most often for Pâtisserie frittericus.

Oh, to anyone with whom I’ve run over the past kilomile, many thanks. I’ve run with dozens of people in that time for just a few miles and just once. I’ve run with a few people very long distances just a few times. And I’ve run with several people, short and long distances, many times. Here’s to a thousand more miles with you all. Let’s share a donut.

Some stats:
Apr 19 – Dec 6: 1000.8 miles (logged)
Total time: 168+ hours
Longest month: September, 235.3 miles
Shortest month: October, 50.6 miles (guess who overdid it in Sept?)
Longest single run: 63 miles

FIFA World Cup 2010 Group Predictions

Today the FIFA World Cup 2010 South Africa groups were drawn. I don’t have my finger on the pulse of football as much these days, so most of this will be more established wisdom than anything particularly groundbreaking, but here goes some early predictions. Of course, anything can change from now and next summer, so it’s all tentative.

Group A:
I don’t think the hosts have ever missed the Round of 16, and yet in this draw there are so many situations in which that scenario seems likely, on paper. But with the whole continent behind them, and hopefully with a little more disorganization and all eyes on the hands of French strikers (ahem), I think that South Africa do have a chance at moving forward. Of course, any good American understands that our friendly rivalry with our southern neighbors means that we do not wish them well, and actually, it’s not hard to imagine Mexico getting ousted in the opening round. Uruguay are back into the Finals after a long hiatus, and they are certainly not the dominant footballing nation that they once were, long ago. Nevertheless, where my head might be inclined to think that French Coach Raymond Domenech and his squad might get their act together in seven months, my heart is really hoping that the hosts and Uruguay move into the next round: one for the home team and one for old time’s sake.

Group B:
Speaking of hearts, it’s difficult to see the outcome of Group B objectively. While Argentina might be an obvious choice to advance at the top of the table, their seemingly ill-placed faith in Diego Maradona at the helm could lead to their early exit — the shame of a nation. Of course there’s always a chance that El Diego takes them to their former glory à la 1986, but that’s a very long shot that I’m not putting money on. And I do have the next several months of trash talking with my Nigerian friends to look forward to, but in reality they are a strong squad who could do interesting things in South Africa, especially with their effective home field advantage. But my heart is true; there’s no way I can discount the speed and tenacity of a fiery South Korean squad who are pretty stable and no doubt motivated in part by the North Korean presence in the tournament. I guess for the sake of some peace over the next few months with the Nigerians, I’ll say Nigeria and South Korea advance, while Argentina make the first round exit due to their skipper. Oh, how I hate to bet against Argentina, though, my adopted nation. It will be Argentina and South Korea. Nigeria, you are going down in 2010! Bring it!! Also, see you in 2014, Greece. It’s not personal.

Group C:
I think it’s clear that the favorites are England and the United States. One/two ranking is important for the Round of 16, and I will give the upper hand to England, especially with the critical loss of Charlie Davies recently to a non-fatal but horrific car accident (here’s hoping for his full recovery). It could however come down to a goal differential if England and the USA tie, since England are traditionally poor performers in the World Cup (that isn’t hosted in their backyard, ahem).

Group D:
While Germany and Australia are the favorites here, there is a lot of young Ghanian talent, and I would not be surprised if Ghana were able to best either Australia or, dare I say, Germany. Germany will likely advance, but Australia despite their scrappy play may just turn up slightly short, which is a minor tragedy since they’re a talented squad.

Group E:
With a group of the always-powerful Dutch, I expect them to come out on top. They got a friendlier draw this year, compared with their Group of Death draw in 2006. The real fight will come for that second spot, and I hope that Cameroon enjoys home field-like advantages that propel it to the top of that stack. Having such an incredible striker as in Eto’o cannot hurt that cause.

Group F:
Italy in theory should have no trouble moving forward, and I expect to see a lot of Italian defense after they score once or twice early in each game. I suppose Paraguay are the logical next pick, but honestly, so long as Italy advance, it doesn’t matter a whole lot to me.

Group G:
This group contains North Korea, who are making their first World Cup Finals appearance since 1966, when they famously beat the Italian powerhouses 1-0 and managed to give up a 3-0 advantage to Portugal. Expect Brasil and Portugal to easily take this group, though I suspect that Cote d’Ivoire will not go silently into the night, and I also will make the not-so-bold prediction that Cote d’Ivoire will come close to beating Brasil, a team who show up in big games but seem to only manage to barely arrive in early round play. This is in contrast to Portugal, who start strong in tournaments but traditionally fade late. I expect Portugal/Brasil to go 1/2 in that order.

Group H:
In the group containing Spain, Switzerland, the Honduras, and Chile, I suspect most are thinking Spain and Switzerland. But really in my mind, that second place berth into the Round of 16 is probably a crapshoot at this point. I think the Honduras have the ability to surprise at the world’s biggest stage; they could be an interesting dark horse team in 2010.

I honestly don’t see a crystal clear Group of Death in 2010. There are a lot of quality sides however vying for Round of 16 spots in some form or fashion, and this may be either one of the most entertaining finals ever … or one of the dullest.

Numerical ODE Solvers

In MATLAB, the suite of numerical solvers for systems of ordinary differential equations are functions that accept variables, including other functions. Since I learned to program MATLAB for my numerical solutions, I am accustomed to this system of passing a function of equations and variables to the ODE solver function. While there is something gratifying in my mind about the distinct separation and, in theory, plug-and-play ease of this system, I cannot help but think that it’s computationally more efficient to have the ODE solver integrated into the numerical application. When people say that they write their own ODE solvers, I always assumed that they meant an ODE solver that accepted a function file of equations and iterated over them, in much the same way as MATLAB. However, it’s finally becoming clear to me that this is not the case, and by ODE solvers, most mean that they are simply hard-coding a numerical algorithm or scheme for iterating their equations. The difference is subtle and may boil down to a difference in computational versus mathematical approaches. In my current project, I am interested in interacting rhythms in biophysical models of neural systems, which requires me to solve large systems of ODEs numerically.

While I make the transition from MATLAB to GNU Octave/R, I’m learning about what implementations are reasonable to translate and what new things I need to learn. Of course, I am interested in maximizing efficiency in the shift, but I have to be careful not to do so at the expense of lost computational efficiency, which happened in my first attempt at using ‘lsode’ as a drop-in solver replacement for a complicated system of ODEs. Since I have decided to ditch graphics in MATLAB in lieu of another system that has fewer four letter words associated with it, the ODE solver was my last true obstacle in the translation from MATLAB to Octave. Now that I am going to solve that problem by “writing my own” scheme, I am that much closer to being completely free and open source in my science.

Saving figures in MATLAB and string concatenation

An economics graduate student and friend of mine recently asked Google out of frustration, “How the hell do I save a plot in MATLAB?” Google, being the unfeeling robot that it is, did not empathize with his question, but many of us certainly can. The useful commands here are ‘print’ and ’saveas’. Here is a qnd guide to them in the ways I use them, with lots of examples.

I always save the raw .fig figures so that I can edit plots in MATLAB without having to regenerate them. To do so, we will use the ’saveas’ command in the following way:

saveas(gcf, '~/Desktop/fig1.fig', 'fig');


The ’saveas’ command in this functional form is taking 3 arguments. The first argument in this example is ‘gcf’, which tells saveas to “get current figure” handle. This is the active or topmost figure window. This can be replaced with a figure handle reference. If you don’t know what that means, then look it up! Figure handles are very useful! The second argument is simply the full path name of our file. Finally, the third argument tells MATLAB to save in the file format .fig. Note the quotes. Respect the quotes. Abide by the quotes.

To save figures in png or eps format, I use the command ‘print’, somewhat non-intuitively. In MATLAB, the print command can print to either a physical device (a printer) or print to a file. We are using the latter in this case, with the example of the eps.

print(gcf, '-depsc', '~/Desktop/fig1.eps');

Again, ‘print’ in the functional form takes 3 arguments here. The first is ‘gcf’, much like in saveas. The second is a device specification. The leading ‘d’ stands for device, I think, and here it tells the print command that the device is a color eps file. Finally, the last argument is the path, much like the second argument of the saveas command. It’s important to note that, as of MATLAB 7.6, there is no native support for embedded fonts in eps files. Journals and possibly collaborators will yell at you. Send a worded letter to the fine folks at The MathWorks in Natick, MA, if you feel this should be included. Alternatively, there is a package on MATLAB Central that may be helpful in this.

As always, other features of these two commands can be found by using the MATLAB help system, either ‘help saveas’ or ‘help print’.

One quick note about path names: throughout MATLAB, strings and variables for strings can be concatenated on the fly using the square bracket notation. This comes in handy with long path names and automating file saving in a script. The notation can be used in the following way:

ext = '.fig';
path = '~/Desktop/';
file_name = 'fig1';

The saveas command now becomes:

saveas(gcf, [path, file_name, ext], 'fig');

Note that there are no single quotes around the variables; the strings in the variables automatically get substituted for the concatenation. Again, variables and strings can be combined here:

saveas(gcf, ['~/', file_name, ext], 'fig');

will save the figure now in the home directory. Just know that this option exists — it is useful for me quite often. Hopefully all of this is useful to someone out there in the world, too.

Evolved to run?

In a new book called Born to Run, author Christopher McDougall explores an interesting theory that humans have evolved to be distance runners. Woven into the story of a running tribe called the raramuri of the Copper Canyons of Mexico, McDougall explores the research from human evolutionary biologists Daniel Lieberman and Dennis Bramble. The basic theory is that humans have evolved as bipedal animals with the specific capacity for endurance running that is not shared by other primates such as chimpanzees. It’s a very seductive idea to distance runners to think that we’re just doing what we so naturally do. In fact, we have evolved to do exactly this, so we’re really doing it old school! And to top it off, the McDougall book has gotten hundreds of runners interested in barefoot running, which is put forth as a far more natural way of running than in overbuilt shoes. Biomechanically this is a seductive idea as well, one that I’ve had fair success in implementing in my own running. (I’m up to around 12 miles comfortably in nothing but foot-form fitting slippers.)

Recently the find of an Ardipithecus ramidus, or Ardi, was unveiled to the public. Ardi is 4.4 million years old (Myo), far older than Lucy (an Australopithecus afarensis), who is a mere 3.3 Myo. I wonder whether or not the features of Homo sapiens (us!) that are posited to be beneficial for endurance running are found in these precursors to Homo.

For science and running geeks interested in reading some of the work done on the evolution of humans as endurance runners, see this Nature review by Lieberman and Bramble. A few other articles by the same authors exist, accessible via PubMed, and that review points to several good places to look for other relevant work.

Running angry. On skis. For 50 miles: A VT50 race report

I hate mud. That was the mantra that carried me through my last 13 miles of the Vermont 50 race this weekend. Actually, that’s the G rated, family friendly version of the actual thing that I was chanting throughout the end of the race, which starred the Mud.

Psychosomatic health

I can’t qualify posts like this enough; they are zeroth order thoughts that are more like armchair musings than they are even close to anything scientific.

Fairly often I come across a science news article about some study that correlates behavioral/mental health with some kind of somatic manifestation. There’s a term that many bandy around, “psychosomatic,” often used superciliously to indicate that one’s pains are somehow made up in one’s mind. However, pain is a very personal, neurological experience that makes objectivity difficult to assess. A recent headline I saw posits a link between loneliness in women and a higher incidence of breast cancer. To assume without qualification, for a moment, that there is a mechanism behind this observation, I was thinking about what that might be. The intuitive reaction is often to assume that it may be through inaction that the brain/body might not fight aggressive cancer cell growth if the loneliness is associated with less than optimal brain function (as is easy to imagine). However, what happens when we think about this in the opposite way? What if the mechanism of action is similar to programmed organism death? What if, in detecting a sub-optimal neurological state, the brain actively contributes to a condition that makes it susceptible to a parasitic toxin such as cancer cells?

This is all firmly in the domain of a gedanken experiment at the moment, but I bet there is some research that investigates several of these issues and potentially how they might work together to understand this. To extend these vagaries further, understanding may lead to effective treatment that could be as simple as “being social” or “making oneself happy.” Mechanism unknown, perhaps, these kinds of simple things may have far greater ramifications for our psychosomatic health (in the non-pejorative way).

Update: the original article will be published in a journal called Cancer Prevention Research.