"Anonymity is your name"

When I started this blog over a year ago, I intended to keep it purely anonymous. As it has developed, however, the notion of anonymity has diminished in my mind as something to care about. This is partly motivated by a large portion of my reader base actually knowing me in real life (as well as a few very obvious failures on my part at maintaining anonymity, such as accidentally responding to emails using my name rather than my online label), but it is also partly because I have gotten to the point where I figure if people are doing Google searches for my name anyway, they might as well find this instead of cross country statistics from my junior high days. Plus, for those readers who don't actually know me in person, the following story from this past weekend would not make any sense.

You see, this weekend I took a trip to the German town of Calden. It is not much of a town, with a population of not quite eight thousand, and it was also rather difficult to get there as it is one of the seemingly few places in German not to be situated on a rail line. The reason I wanted to go there, though, is because my name is Calden Wloka. It is an unusual name, chosen by my parents based on the inability of my two year old (at the time of my birth) sister who was unable to say their original choice of Calvin. In my entirely non-objective stance, though, I am rather a fan of my name and prefer it to Calvin (also, being a precocious blonde child named Calden already netted a significant number of references to Calvin and Hobbes... I can only imagine how much more common that would have been had I actually been named Calvin). It is an unusual but not exceedingly difficult name. However, as a child and adolescent, there were times when I lamented it. One thing I always wanted as a little kid was one of those souvenier objects (keychains and the like) that had my name on it. Of course I never actually found one, and that always seemed rather sad for me. When I went through the awkward adolescent experience of moving to a rural town in a foreign country, having not only a Polish last name that had the temerity to follow a 'W' with an 'l' without an intervening vowel, but also an unusual first name meant there was always an awfully unwelcome pause at my name when teachers took attendance. For people with names that they do not have to repeat a few times when they meet someone new (and subsequently just settle for whatever pronunciation seems to suit your new aquaintance best), my giddiness about going to an entire town with my name (replete with signs and business names testifying to that fact) might not make sense. You will just have to take my word, then, that this was an exciting trip for me. Of course, I made the mistake of taking the trip on a Sunday, when everything in Germany seems to be closed, but I still managed to make it there, get plenty of pictures, and then make it back without too much hassle and lack of food (the only thing I found open was an icecream parlour, which wasn't much of a lunch). There were a few awkward moments when I had to explain to people why I was taking pictures of random signs and company names, but on the whole I got through it without too much embarrassment.

Even better than visiting a town with your name, though, is the experience of discovering that your name has an associated coat of arms displayed in stone. Behold, the Calden Coat of Arms:
For a geek, that is an awfully exciting discovery.

Timothy Williamson and the Philosophy of Philosophy

A couple weeks ago, I went to a lecture at the Paulinerkirche given by Professor Timothy Williamson, a philosopher from Oxford, entitled Armchair Knowledge and the Philosophy of Philosophy. The talk was for a general audience, so I am sure Professor Williamson simplified his arguments and glossed over some of the supporting ideas that have helped spur his own, but I still felt somewhat dissatisfied with overall presentation and thrust of his argument.

Professor Williamson started with a description of the general practice of philosophy as an exercise of cogitation one performs from the comfort of an armchair. He then gave a humorous anecdote about an Irish chemist being surprised that English universities regularly also had philosophy departments (the chemist had assumed that Dublin's Trinity College philosophy department continued to exist as a matter of tradition rather than for any sort of pragmatic utility). Thus, Williamson set up the central conflict on which his talk centered as the question of whether or not the criticism of philosophy as antiquated and made obsolete by experimental science was apt, and what that meant for the motivations and practice of philosophy (the philosophy or philosophy, if you will).

The central thrust of Williamson's argument started with the idea that no one is a pure empiricist, as basing all of one's beliefs on direct empirical evidence is impossible. In this, Williamson is certainly correct. Earning one's education is in many ways an exercise in academic trust, although, as was astutely pointed out in the How To Think About Science series, one of the inherent strengths of science rests not so much with its skeptical roots as with its ability to determine who and what to trust. One of the problems I continually run into in subjects outside of the realm of science (and even within some discourse that claims it is scientific - namely certain branches of psychology) is that the established basis for some discourse is not clearly defined or, in some cases, is clearly defined but erroneous (either in light of later discoveries, in which case it may be excusable, or simply because it was assumed true without empirical evidence, in which case it is less excusable). For example, as those who remember my reviews of a selection of historical treatises on political theory may recall, I was thoroughly disappointed with both Plato and Aristotle. I thought Hobbes did a much better job by specifically and carefully defining his terms and assumptions (some might claim that this was a little overly pedantic on his part, making his text more difficult to digest than one which skips over such dry discourse as careful definitions, but it is important nonetheless). Of course, I think Hobbes' analysis still ends up flawed, but it is much easier to follow his reasoning and in that way determine where I disagree thanks to his methodological approach. I seem to be getting away from myself, however. Getting back to Williamson's talk, I grant that calling for a purely empirical framework for knowledge and belief is not feasible. We do choose to trust knowledge disseminated by other sources, but I think the important point here rests on our determination of the trustworthiness of sources. Basing trust on human charisma, while often the most common method, is unfortunately a highly flawed method as it easily leaves one open to being taken advantage of. The system created around unbiased and rigorous verification of knowledge rooted entirely within the natural world that is modern science is the best that I think we can currently hope for in the department of trust.

Continuing from the fact that everyone accepts knowledge not personally empirically derived, Williamson also brings up the fact that even empirical scientists further process empirical results with a set of mental reasoning tools which Williamson classified as akin to imagination. We are mentally capable of trying out ideas and following avenues of thought which have not explicitly been borne out in the real world. At this point, Williamson went on a slightly odd detour by ruminating on the origins of the human capacity for reasoning given our evolutionary past. He justified its survival advantage by giving an example of a person running from a tiger - the person would be able to gage the appropriate response by running through possible future scenarios in their mind (such as hiding behind a rock, climbing a tree, and so on). Of course, it was a simplistic example, so I won't spend too long quibbling with it, but I do want to point out that any person who stopped to think so carefully while being chased by a tiger was going to be caught and eaten. Our capacity for rational thought serves more to modulate what sorts of behaviours we practice to increase our future survival capacity rather than serving us in speedy split-second survival decisions. Ignoring that nuance for the sake of the argument, however (and it does not particularly change the logic to go from reasoning about what sorts of behaviours are best to practice for future enactment and what sorts of behaviours one should execute in the current moment), it is true that we continually process empirical information (often in ways we are not even immediately aware of - see my series on top-down processing in vision).

Essentially, those two points are what led Williamson to his justification for philosophy. Philosophy is therefore, according to my understanding of Williamson, simply engaging our capacity of hypothetical rational thought as a valid exercise in knowledge derivation. I would contend, however, that Williamson's version of philosophy is continuous with and enveloped by the combined fields of mathematics and science, and the areas of philosophy that remain outside of those fields still have no valid justification as sources of worldly knowledge. As I see it, there are two possible ways in which one can engage the rational faculties that Williamson established to exist. One can ruminate on the purely abstract, such as the field of logic. Philosophy of that sort, however, becomes indistinguishable from the field of mathematics. It can be a valuable avenue of thought, but it does not tell us directly about the world. When philosophy moves beyond the abstract and begins to make statements about reality, then I think it should be held to the same empirical accountability as any theoretical science. Philosophers may not be the ones gathering the empirical data, but that does not excuse them from being aware of the implications of that data. Far too often people entirely ignorant of neurophysiology and even behavioural psychology embark on developing vast treatises of the philosophy of the mind. Of course, philosophers often focus on different questions and aspects of a field, and in that I think they make their most valuable contributions (for example, fields like the philosophy of physics or the philosophy of mathematics, which often draw upon the larger philosophical field of epistemology, are exceedingly important for any scientific field and, in the same way that I think philosophers should make an effort to be aware of at least general trends of empirical results, so too should more scientists be aware of the philosophical underpinnings of their fields). Fundamentally, though, all knowledge of our world is rooted in empirical data, and thus I think the philosophy of philosophy leads us to the same place as the philosophy of science and mathematics.

Idle Thoughts Can Have Consequences

I'm sure most of my readers, even if they have been reading this blog since October of last year, have likely forgotten about this post on my rather trivial enjoyment of a couple of names. I certainly had forgotten I had posted it... until I got a comment and an email from Cosimo Commisso himself! Thankfully, Cosimo Commisso seems to have a good sense of humour and rather enjoyed the post. Still, it is a reminder for minor bloggers like myself - you might be used to prattling on about whatever happens to pop into your head, but you never know who might actually decide to have a look at what you have written (even months after the fact). So, Dr. Commisso, thank you for having a sense of humour.

Anyway, I am off on a day trip to a nearby town tomorrow, but be sure to check back early next week. I am putting the finishing touches on a review of a talk I went to a couple of weeks ago by the philosopher Timothy Williamson, so that should be up Monday or Tuesday.

Puzzle Number 6: Star Media Quotations

This is a light-hearted weekend puzzle based on a game my research partner and I played last summer while performing the tedious task of mixing electrode paste for our EEG cap. The game my friend and I played was to take turns saying a line from one of the original Star Wars movies (I limited it to those because I had only seen the new ones once each), and then the other person had to try and name who said it, to whom, and what the context was. For this puzzle, I have extended it to include television shows with star in the name. This should increase the difficulty somewhat, although I have tried to pick at least somewhat memorable lines. So, to be clear, the task for each quotation is to name the movie or television show it is from, who is saying it, to whom it is being said, and the general context of the scene. Occasionally, there is more than one context or listener, but those should hopefully be fairly obvious. Also, I came up with most of these by memory, so if I've made any errors, please be sure to let me know. Also, as usual, partial solutions are also welcome.

1.) "I'll make it up to him next year; I promise."

2.) "There are four lights!"

3.) "He is as clumsy as he is stupid. General, prepare your troops for a ground assault."

4.) "Welcome home, Mr. President."

5.) "Yub yub."

6.) "your basic hedonistic predilection for rhythmic stroking of your fur, to demonstrate affection."

7.) "I've lost the fellatus to speak properly."

8.) "sometimes a cake is just a cake."

9.) "Hey, look! I'm an engineer! I can do math!"

10.) "I can arrange that. You could use a good kiss!"

Surly in the Morning

Some of my readers may notice that my previous post was uncharacteristically petulant and childishly indignant, but I am feeling cantankerous this morning. Part of that is the fact that I have spent long hours over the last two days continuing my duel with Mathematica, while nary a peep has been heard from their staff since last week (despite assurances of a response this week - even if just to say that nothing had yet been done). Of course, they may respond this afternoon, at which point I will have to offer another apology, but my expectations are currently low. Anyway, rest assured that I do not intend to turn this blog into a tirade of self-righteous whining, but sometimes I am irked and it is relaxing to vent.

Chris Mooney and SIWOTI

I am annoyed with Chris Mooney, not, as some might guess, because every time I hear his name a little voice in my head annoyingly pipes up, "...Wormtail, Padfoot, and Prongs", but rather because I think he is wrong (and, as I have shown in the past, I am rather susceptible to SIWOTI syndrome). Of course, I have not had a chance to read his book, so I will concentrate my criticism on his blog. The situation would seem to go like this: Chris Mooney and his compatriot Sheril Kirshenbaum wrote a book called Unscientific America that had a section highly critical of PZ Myers. PZ Myers read the book, pointed out that he was admittedly biased but would nevertheless give an attempt at a proper review, and then proceeded to write a post of substantial criticism for the book, followed by another one. Chris Mooney responded first by pointing out a small collection of people who liked the book, and then dismissing PZ Myers' review because he was criticized and therefore not objective. Promising more on PZ Myers response soon, he then cherry-picked a (admittedly awful) comment off of Pharyngula and used that to once again dismiss PZ Myers' response.

Although I doubt Chris Mooney will ever read this blog, in the off chance that he does, here is my response:
It is not a valid objection to an argument to say, "I criticized this person, therefore he is not objective, and therefore his criticism of my work is not valid." If I wrote an essay (baseless or not) all about some sort of horrible aspect of your character or work, and you responded to it with a series of both general and specific criticisms of my essay, would you expect me to respond to your list or dismiss it out of hand because you are "not objective"? Remember that you sent your book to PZ Myers for review, and he has offered (granted, publically) a review. To then thumb your nose at his review as not worth responding to in substance because he was criticized in your book (something you presumably were aware of when sending the book to him with an oddly redundant little note asking him to try to suspend judgement until after reading the book) brings up the suspicion that you only sent the book to him so that he would publically criticize it, thereby drumming up potential readers based on the old pearl of wisdom that there is no such thing as bad publicity. If that is the case, then you are, frankly, being an ass. If somehow you actually do ever end up reading this, take offense to my assessment of your motives, and respond, I assure you that I at least will endeavour to respond to your specific points detailing how you are not an ass, rather than dismiss any response as not objective and thus not worthy of my notice.

"Bob Loblaw"

As I have been mentioned a few times over the last couple of days, I gave a talk yesterday morning. I mentioned it so often because I was fairly nervous about it, and I was fairly nervous about it not because it was a talk of any great importance, but because I don't have a lot of experience giving technical talks to highly academic people. The talk was titled Phase Response as a Function of Graph Structure, and was essentially an overview of what I have spent my last month doing. The first half of the talk was a mathematical and intuitive development of the concept of phase response, and then the second half was how that related to dynamical networks (primarily of identical weakly coupled oscillators). Robert left a comment to my post about being nervous, pointing out no one was likely to remember my talk in ten years. As this was an intra-departmental talk to an audience of about ten people, I would be surprised if memories lasted even half that long. What was nice, though, was that I received several compliments on the talk, including from the head of the research group. What was less nice was the Ph.D. student I've been working with and I discovered a handful of minor mistakes on the slides the morning of the talk during my last practice run-through, and my audience managed to spot all but one of them (at least it means they were paying attention). I guess that is what happens when you give a talk to an audience primarily composed of mathematicians and physicists... they actually pay attention to the equations you have on your slides!

I will now try to give a brief overview of what the subject Phase Response as a Function of Graph Structure actually means. If you take an arbitrary dynamical system (which is essentially a fancy word for saying a system that evolves through time) that has a stable periodic limit cycle (which means the system has a state that repeats after a period of time T, and small perturbations to that system will disappear over time and it will settle back to the periodic motion), then you can define something called the phase of the system as how far along in the period the system is. Phase is usually parameterized to be between either 0 and 1 or 0 and 2π by convention. I find the 0 and 1 parameterization more intuitive (it essentially translates to what percentage of the period has already passed, with 0.5 being 50% of the way through from whatever point is defined as the period beginning). The idea of phase can then be generalized to the basin of attraction around the limit cycle (which is essentially the region of your dynamical system's feature space which eventually settles onto your limit cycle), such that a point on the limit cycle and point within the basin of attraction are considered to have the same phase if they evolve through time to the same point on the limit cycle. A rough picture of this idea is shown in Figure 1. This leads to the idea of an isochron (the dotted lines in Figure 1), which is the collection of points in your feature space that all share the same phase.

Figure 1: A point on the limit cycle and off that have the same phase. The mustard yellow curve represents the time evolution of a point off the limit cycle as the moves back to the cycle, while the green curve represents the evolution of a point that starts on the limit cycle. When the mustard yellow curve rejoins the limit cycle, it does so at the same point that the green curve reaches in an equivalent length of time. The two starting points are therefore said to have the same phase.

With phase now defined both on and off the limit cycle, one is able to develop the idea of phase response. If a perturbation (essentially, some sort of externally applied influence that drives the system away from its normal time evolution) is applied to a dynamical system with a stable limit cycle, the phase of the unperturbed system and the perturbed system are both defined (assuming the perturbation is small enough that your system remains within the basin of attraction of the limit cycle), and the change in phase resulting from the perturbation is the phase response of the system (see Figure 2).

Figure 2: The phase response (Δφ, where φ is the phase of the system) to a perturbation ε.

Until now, I have left the discussion fairly open-ended about the properties of the dynamical system under analysis. The idea of phase response is usually applied to the analysis of single oscillators. An example of such a system would be the Hodgkin-Huxley model of a neuron exposed to a constant ambient current such that it is tonically firing at a set period. The feature space of the system is then the voltage across the membrane, the applied current, and the ionic concentrations (both intracellularly and extracellularly) of several key ions (such as potassium and sodium). What we have been investigating is the phase response of networks of oscillators coupled together, at which point the coupling relationship between oscillators becomes part of your feature space. A perturbation applied to one element of the network might ellicit a different phase response than a perturbation applied to another element.

On the surface, one might wonder what the point of all of this is. The thing is, coupled dynamical systems are found in all sorts of areas. Networks of neurons are an obvious example, but gene expression is another area of biological research where there are large systems of interacting biochemical pathways. There are examples outside of biology as well, but I am having a hard time thinking of one off the top of my head since my group tends to focus on the biological tie-in of our research. Therefore, having a better understanding of the phase response of networks will lead to a better understanding of these exceedingly complex systems.

Note: Figure 2 was pulled from Christoph Kirst's diploma thesis, Dynamics of Pulse-Coupled Neuronal Oscillators with Partial Reset. Figure 1 was a (rather shoddy) edit of Figure 2 that I made over the weekend using GIMP.