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.

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.

Meta comments – and some rude ones

It’s difficult to find time to write with some reasonable estimation of quality on a variety of topics in which I’m interested. I’ve meant to write about the Tour de France, the confirmation process of Sonia Sotomayor, and a variety of scientific topics. One difficulty I’ve found is not being able to discuss my work in a meaningful manner on an informal website such as this. I prefer to let my formal talks and (hopefully soon) published papers to communicate interesting results or explored ideas, and I think that peer reviewed science is still the best model, despite something so seductively democratic as the arXiv model of publication, which would be a nightmare to sort through. So there’s an apparent lack of science-related stuff on here, simply for these reasons.

One thing I think I can write about, briefly, is the publication process that I’m currently learning about for the first time in my scientific career. I recently submitted a manuscript with two collaborators to a journal that specializes in computational science, and it was out for peer review about a month ago. We recently received comments back from just the first of two external reviewers, who are not affiliated with the journal directly but presumably experts in the area of research that we are in.

For this first reviewer, the respectfulness of the written comments and questions was greatly appreciated, and I proceeded to incorporate changes and answer questions from that reviewer. The second reviewer apparently did not submit comments to the authors (us), but upon inquiring about this, it turns out that the second reviewer simply did not fill out the review form correctly and the comments to the editors were allowed to be forwarded. The tone of the comments was more caustic, almost accusatory, though there were several valuable points that were made. The reviewer made a few comments that were not at all constructive, simply providing an opinion without any possible suggestions for meeting his or her otherwise arbitrary criteria. I refrain from giving examples here due to confidentiality. Finally, the reviewer was simply wrong about the guidelines of the journal itself in at least one comment that was made, which makes satisfactory revision on this point impossible. Given the tone of this reviewer’s argument, I expect a difficult task in appeasing him or her for the revised submission.

Cocktail party concerto

Zeroth order thought.

Someone recently was listening to a Brahms’ Violin Concerto and asked the question of whether or not the soloist could be picked out amid the background of the much louder orchestra, when playing tutti. I recently had seen some evidence presented by a speaker that might apply here, and I thought it would be fun to consider the two things together.

Essentially, the problem is the following. You have a very large contingent of instruments playing, with a single instrument playing something different. We would like to hear the soloist, either in harmony with the other parts or distinctly, above the din. Now, there is clearly an absolute volume at which the soloist would be drowned out — we believe this from experience. However, assuming we’re not at that level yet, there’s sort of an interesting problem of differentiating a very loud section of instruments that is often of equal timbre but of higher amplitude.

The cocktail party problem refers to the observation that, when in a crowded room in which people are speaking, by looking at a single speaker, one can often hear what she is saying, despite the distracting, surrounding noise. So the concerto problem is similar in this regard.

Dream job post

I was looking at job offerings and came across a post for a neurobiophysicist. Because it contained both the roots “neuro” and “biophysics,” my interest was piqued, since I’ve never heard of anyone referred to by this compounded title. It turns out that I’m apparently training to be a neurobiophysicist, and despite the location of the position (San Antonio, Texas), I am very intrigued by the job post. My hope is that other academic places are looking for someone who fits this description (emphasis added):

We seek to recruit a vigorous academic with an established track-record of research in the broad area of the physics of neurobiological processes. This might be anyone from a “patch clamper” to a computational biophysicist to someone studying signal transduction mechanisms but not necessarily limited to these examples. Trinity University has secured funds to endow the position and provide continuing funding for the position after our HHMI award expires. This professorship will be at the level of full professor. The position comes with a dedicated half-time support staff position, discretionary funds, and a reduced teaching load (6 rather than 9 contact hours per semester).

This position will be an appointment in the Department of Physics, providing some support to introductory physics courses, a course in biophysics (suitable for both physics and neuroscience majors), and a course in the faculty member’s specific area of expertise (specifically supporting neuroscience majors) in the teaching repertoire. In addition, the person hired in the position will maintain a vigorous research program that will engage undergraduate student researchers. The neuroscience major requires independent research as a culminating experience for the degree. Further details about the position are available in the position announcement.

The position will also work with faculty from biology, chemistry, and psychology in supporting the neuroscience major. This interdisciplinary major was established in 2005 with funding from our 2004 HHMI award. Through a combination and retirement and this HHMI-funded neurobiophysicist position, the neuroscience program will be expanded and redefined. In addition to this position, we will be hiring a cognitive scientist in Psychology and an animal behaviorist in Biology to support the neuroscience program.

It’s so accurately describes what I am interested in (and doing) because of aspects of combining computational approaches with electrophysiological techniques. Additionally, the appointment is in a physics department (my undergraduate degree is in physics), with teaching duties in both neuroscience and physics. I’m pretty far from doing a job search, but here’s to hoping positions like this become more common by the time I graduate!

Gattaca arrives (in part)

I’ve always maintained that Gattaca is an important film because my generation would be encountering several of the raised issues within its lifetime. Here’s yet another manifestation of that, with the first steps toward designer babies. While I admit that on its face I’m uneasy with the idea, I am sure I’m not aware of the full range of the possible implications. It most certainly won’t eradicate all disease or make perfect humans. But the eerie line from Gattaca rings in my head:

“We want to give your child the best possible start. Believe me, we have enough imperfection built in already. Your child doesn’t need any more additional burdens. Keep in mind, this child is still you. Simply, the best, of you. You could conceive naturally a thousand times and never get such a result.

The career plan (revised)

When I began my graduate educational journey, which started with a dead end job working in IT for a small business, I didn’t really have a good concept of how things might unfold. I did all of my applications with the not-so-professional guidance of close friends who had as much experience as I did in successfully applying to neuroscience graduate schools (none). When I was fortunate enough to have a choice between graduate programs, I had the luxury of choosing a research direction, between the genetically minded approach of one school to the computationally minded approach of the other.

I ultimately chose the computational direction because while clearly genetics is relevant now and will be forever relevant, I think that the coming of age of computational neuroscience is now. Genetics presents an ethical minefield that threatens to ultimately slow the scope of its reach (for better or worse), and I think this will delay the onset of the true age of genetic “understanding” with respect to nervous systems.

Additionally, another branch point came during rotations in my first years in graduate school, when I had some experimental opportunities to weigh against learning computational techniques. In the end I chose the mathematics, though, because I feel like these are techniques that are far more difficult to learn on one’s own. The anecdotal evidence for this has been realized time and again by experimentalists who are struggling to learn modeling techniques in a meaningful way. In contrast, I’ve seen a number of computational folks who have made the transition to experimental techniques seamlessly.

My plan thus far was to continue developing my computational techniques throughout grad school and then transition into a postdoctoral position and learn some electrophysiology. However, a phenomenal opportunity arose in which I might be able to do in vivo electrophysiology now, as part of my dissertation. I jumped at it, almost without proper or deliberate consideration. It sounds reasonable enough to me, though it obviously is accompanied by a bit of trepidation, considering the magnitude of this change.

I already have experience in biophysical modeling, and I’m working on some data analysis techniques which will serve me well. If I do electrophysiology now, then I can devote my postdoctoral appointment to different computational techniques, or perhaps a more mathematical project. Since the landscape of computational neuro is in a sense just as large as experimental neuro, there are far more techniques I have no experience with but am interested in learning. Once again, at this stage it’s unclear which approach will be more fruitful, but here’s to the uncertainty of the journey!

Project Euler

Project Euler is a small database of computational/mathematical problems that one can solve using any method he/she knows. I think it’s going to be a fascinating way to learn different numerical programming techniques.

I only solved the first few problems^* so far, and while I think in MATLAB/GNU Octave for the time being, I am certain I can learn enough Perl or C to do (at least some of) these problems as well.

^*I am sure someone’s pointed this out in the 8 years since its introduction, but I might as well mention it here. The original problem 1 statement reads:

“If we list all the natural numbers below 10 that are multiples of 3 or 5, we get 3, 5, 6 and 9. The sum of these multiples is 23.

Find the sum of all the multiples of 3 or 5 below 1000.”

If we expand the boundary from 10 to 20, we see that the numbers divisible by 3 include 3, 6, 9, 12, 15, and 18. The numbers in the set divisible by 5 include 5, 10, and 15.

We are told to look for the sum of all the multiples of 3 OR 5 below 1000. In this toy example, I do not think the solution should include 15, which is divisible by 3 AND 5. In any case, they meant and/or (and go so far to say so in their PDF solution), so my qnd solution was correct. Feel free to contact me for at least one MATLAB solution to this problem.

Observations on making music

My Mom and Dad valued music, and while my brother somehow managed to escape from our childhood without learning an instrument, I learned the violin. I wasn’t always eager about it and sometimes outright did not enjoy it, which was probably just a product of hard work and sacrifice to get better at it.

It’s been quite a long time since I have taken lessons, and my music teacher has since passed away, but I’m thankful that I can, at any time, pick up a violin and have a repertoire of songs that I can play. The delay since the last time I played almost doesn’t seem to matter. I don’t often need the sheet music in order to play difficult pieces I haven’t played in years. I find that when I don’t think about the piece and just let my motor memory perform, I get much better results than if I think consciously about the piece.

In fact, often I’ll be playing a piece I knew well once, and the moment I try to think of what note or shift might come next, I have to stop completely. I don’t understand the neural mechanism behind this.

Now my music theory is pretty poor, as I always avoided it as a kid, and I regret that now. And while I don’t have perfect pitch, I have pretty good relative pitch, which means that I can’t name a note randomly, but as soon as I have a known reference point, I can half-step and whole-step my way around just fine. I am sure that there are memory systems associated with the semantic ability to name notes that requires a highly functioning auditory ability to discern notes. It’s something like being able to name colors, irrespective of the subtleties of the shade. These are subtleties of sound.

On a side but possibly related note, I love my music and my jazz music, and I have a really hard time naming tunes with no words, even for songs that I can sing from memory completely. I wonder if this semantic naming system is associated with perfect pitch abilities. Additionally, this kind of evidence suggests to me that the recall for the actual tune (even for tunes I haven’t played but only heard) is very much separate from a lot of the metadata knowledge associated with it, such as the name. The performer might fit into this category, except it’s hard for me to dissociate since I can usually, based on style, make a good guess at the composer, even when I can’t name the exact tune.

I also learned a few other things today. While at a friend’s house this weekend, the subject of Christmas music came up, and I got out the old violin and started to pluck out a few tunes on it. I found myself doing something very strange. I can sing or hum tunes and avoid inciting thrown tomatoes. However, I find that when I’m searching on my violin for that first note, I often end up with a note that falls somewhere in the middle of the song, instead of the one I’m searching for!

That single note in the context of the song I’m thinking about is generally enough for me to play at least a few bars if not the entire rest of the simple song. I can even backtrack and find the first note and start from there, incorporating my new song phrases into a complete song.

I’ve always been fascinated by this apparent ability of mine to identify a song by as few a couple of notes. It really only takes one or two notes, in some kind of rhythmic and timbre (such as the instrument) context, to elicit a memory of the entire song. I can usually name songs I hear from one or two notes, in loud restaurants or on the radio, etc. It can be a pretty random recall of songs I don’t think I know well or haven’t heard in years. It’s annoying when it’s songs that are bad. I’m not sure how that works, either, though it’s not too far fetched to imagine a synfire chain-like string of activity that elicits a memory from a particular stimulus (the sound).

It took me only a few minutes to work out each one of the Christmas songs I was thinking about today. I am classically trained, which for me means that my improvisational skills are pretty poor, though I’m trying to work on them through exercises like transcription and fooling around with variations on a melody.

But I was searching for some sheet music and found a nice resource for Christmas carols, and it had easy transcriptions of a lot of songs, including several I hadn’t thought of. For the ones I had already worked out, the keys were sometimes different. Perhaps because of my reliance on relative rather than absolute pitch, the differences to me are more a matter of taste than of correctness.

For the songs that I was familiar with but didn’t think to work out earlier, playing just a few bars was more than enough to elicit the entire song’s playback in my head, and I was often able to play the rest of the song, without relying on the sheet music, at tempo! Granted, we’re not talking about anything at all complex, but it was pleasing to play the entire melody only to scroll down the sheet and find it was identically transcribed.

One final observation about music and memory. One major misconception about rhythm is that it’s completely dissociated from pitch. This is more often than not incorrect in real life, as different percussion instruments generally associated with strong rhythms (like drums) all have unique pitch qualities that probably are often overlooked (this is part of why sometimes cymbals are used instead of snares; they each have a harmonic quality). While rhythm technically does exist in the time domain, I find that I cannot dissociate certain rhythms (William Tell Overture, as an example) from their melodic content. If I tap out, with my fingers on a desk, that famous rhythm, I cannot hear just fingers tapping on a desk, since I was very young. Not even consciously. I always hear the melody riding on that rhythmic structure. This leads to the curious phenomenon of random songs entering my head when I hear clapping or doors shutting, etc.

The latter of these observations reminds me of those visual tests with the old and young woman, in which you naturally see one or the other. Once you are aware of the presence of the other, you cannot help but see it.

All of these curious observations just make me wonder about how our brains are capable of such breadth (numbers of songs) and depth (detailed knowledge about each). How is this memory stored, and where? How many listens does it take to learn a song and under what conditions is it most salient? We have hints at the answers to many of these questions, but many more remain. It’s a fascinating time to be in the field of neuroscience.

While I’m thinking about it, this all reminds me that I just recently started reading Oliver Sack’s book Musicophilia. It’s essentially a collection of case studies involving patients with peculiar relationships with music. From what I’ve read so far, I highly recommend it.

Yet another argument on creation(ism)

All of this was prompted by an article in the Guardian on creation that I found particularly well written in a sea of poor discourse on the subject.

I am convinced that nearly everything meaningful to be said about the argument of creationism, intelligent design (ID), and evolution has been said. My position from a scientist and Christian’s point of view is straightforward. Obviously, there is a lot of evidence that exists regarding evolution. With respect to origins of the universe, there is also a surprisingly consistent amount of evidence for the big bang theory. So, my current belief, based on the evidence available, is that the big bang happened, and separately science currently paints a reasonable picture of the origin of life.

Now there’s something very intuitive about the idea that something had to precede the big bang, and that’s fundamentally what I’ll call God. (Call it what you like.) So, the event of creation, in my mind, occurred, but it’s not God placing tiny Lego humans, in their modern forms (whatever that is), on a pre-formed Earth. Creation was the release of energy from an infinitesimally small point into the expanding universe.

So that explains my theism. I am particularly Christian because I believe the fundamental story of Christ, based on all available evidence (Biblical and extra-Biblical accounts). My understanding of the canonization of the New Testament makes me believe that the Bible is more of a human document than it is handed down from God. While I’m much more inclined to take the Hebrew Bible on faith, it remains a question of faith and not science, though I’m pleased to see scientific and archaeological inquiries into the subject. Yet many of these fundamental beliefs I take on faith, and many of these questions cannot be addressed by science directly. It’s perhaps in my nature, however, to attempt to reconcile these two logical worlds in order to ensure that some sort of weird singularity doesn’t implode my head.

The theory of evolution, on the other hand, asks questions that are within the realm of science and testable science. We as scientists would be remiss if we did not admit that explicit statements about the past may well not be testable, but our observations are still meaningful, like a forensic puzzle, and we have the unique opportunity of having systems we can closely monitor in labs and in real environments to check consistency with current ideas.

For one broad example, biological conservation is striking. The preservation of even single, complex ion channels is maintained throughout species whose brains are vastly different. Just one of many, many examples of this is the human 6 transmembrane domain K⁺ channel herg, which is 70% similar in genetic sequence to a channel in the worm C. elegans and also similar to channels in the Drosophila fly and elk.

Modern evolutionary theory accounts for this. At least one alternative explanation to evolution that one might hear from the ID folks is that God could have placed these sequences in each species when God created them. This is not a testable hypothesis, and it is not scientific by definition. As far as science is concerned, until this is reconciled, end of discussion with respect to science!

With respect to education policy, and I probably have more to say at a later time on this issue, all of this sums up to the following. Evolution is a theory (like ALL other theories in science). It is not proven (like all other ideas in science). Evolution and big bang theories should be presented as a theory in science curricula. ID and creationism, on the other hand, have zero place, whatsoever, in a science curriculum. What could be explained is why this is, since it is such a curiously heated topic. As far as this scientist and Christian is concerned, it’s pretty binary.