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Saturday, May 31, 2008

Some Links

I've added a Places of Interest sidebar (with links in no particular order). I'll give a brief description of each of the places:

Science News: The Science magazine homepage. Plenty of links to articles on general science news. Homepage of a great scientist doing his bit for the furthering of secular thought. It is mostly news involving religion and atheism, but there are also some occasionally interesting tidbits on science.

The Jolly Bloger: A fellow from BC's blog. He has an enjoyable smack of wit and sarcasm and a healthy enjoyment of playing with language. He doesn't post particularly often (though more frequently than I do), but is an enjoyable addition to an RSS feed.

The Evilutionary Biologist: A recent addition to my RSS feed, so I don't yet have much to say about this blog. Perhaps you will just have to go and have a look yourself.

Pharyngula: PZ Myers' quite popular science blog, Dr. Myers posts links with uncanny frequency. I don't know how he has time for it, but it is an enjoyable source of wit and (ir)religious news.

The Wild Side: Olivia Judson's blog, she writes a small number of voluminous and quite interesting posts about evolutionary biology.

Good Math, Bad Math: Another science blog, this is primarily a foray into applied mathematics. The writing is clear and engaging, so even when I am familiar with the concept being discussed I still find it an enjoyable review.

Developing Intelligence: This is a science blog by a neuroscientist graduate student who basically takes what I started my blog to be and does it better. It makes me a little sad, but hopefully in a few years when I'm doing my own graduate work I will have a similar blog. While many of the posts are technical enough that I'm not sure they would be interesting to those without at least some background in neuroscience, if you are interested in the brain I think it is worth having a look.

Conspiracy Factory: While it hasn't been updated much recently, this is an enjoyable blog primarily concerned with the public education of science (and the unfortunate ubiquity of pseudoscience).

So, there you have a brief description of the links. Really, though, it would probably make more sense just to go and have a look yourself.

Oh No! It's Saturday!

Oh dear, it is Saturday and there was no post yesterday. That means I missed my weekly attempt to further the appreciation of a group of highly intelligent people that is sadly given far less respect than I believe said group deserves. In other words, I missed making a Scientist Appreciation post. I suppose I should briefly explain myself.

These days I am busy busy busy. I am working two jobs (one full time, the other part time and from home, but it's still a job with a certain number of hours required) as well as taking a course (which I believe I mentioned in some earlier posts - a political theory course to satisfy my social science credit requirement). The full time job is working in one of my physiology professor's laboratory. His research over the past few years has primarily focused on taking and analysing EEG readings from subjects performing various motor tasks. So far most of my time in the lab has been spent trying to figure out how to port the raw EEG data (taken by the LabView program) into MatLab where I will then develop some non-linear dynamical system analysis to augment the more traditional forms of analysis he has used in the past (mainly power spectrum analysis). Unfortunately, my drastic lack of skill in dealing with LabView has thrown a snag in things as the data does not seem to be making the transition to MatLab in any sort of accurate manner. It is a bit of a mystery, and it seems to be taking far many more hours than it should in figuring it out. Once it actually gets going, though, I plan to make a few posts describing the EEG and the various forms of analysis I am performing in more detail.

The second job I have is as a software development consultant for a start-up company called Cumulus One. My job is essentially to make the software run in the Windows environment (it was developed in Linux), and it will likely involve a GUI development as well. To be perfectly honest, I have only a vague idea of what I am doing, so it has been a lot of learning as I go. It is an interesting project, however, and the original developer of the software is a friend of mine. He is a very talented programmer, so I enjoy working with him.

Anyway, I would expound upon my impressions of Plato and Thucydides from my course, but my break for lunch is now over and I really should be getting back to work. Figuring out how to get different compilers and operating systems to talk to each other can be a rather confusing and arduous task.

Tuesday, May 27, 2008

Subject for this Sunday: Crazy Debunking Crazy

I just wanted to mention that the Church of Christ, Scientist is going to be presenting a sermon this Sunday with one of my favourite of their titles: Ancient and Modern Necromancy, alias Mesmerism and Hypnotism, Debunked. I believe that is the accurate and full title, but I might be mistaken since they haven't updated their website and I am having to try and remember this from glancing at the sign on my way to work this morning. I think it just begs the question, however, of whether it really counts as debunking something when you do so with ideas that are equally as ludicrous?

EDIT: The proper title is "Ancient and Modern Necromancy, alias Mesmerism and Hypnotism, Denounced".

Friday, May 23, 2008

Scientist Appreciation: Sven Dickinson

The scientist for this week is actually one of my professors, Dr. Sven Dickinson. He taught the Image Understanding course I took this past spring, which is a specific area of machine vision involved in the most unconstrained vision problems (many objects with many different orientations and articulations). The reason I feel he should be should be appreciated is because he is very much the sort of professor I would like to be. He is extremely engaging while at the same time is very approachable without an overbearing aura of intimidation. In his lectures he incorporates a wide range of subject matter to help give an impression of how the field fits into scientific endeavours as a whole, as well as helping students realise that multidisciplinary knowledge, even just superficial knowledge, can provide insights that otherwise would have been missed. In addition to his impressive abilities for delivering lectures, he also gives the strong impression that he genuinely cares about the students in his course, both in terms of their understanding of his course as well as their overall well-being and future goals. He takes time to offer advice on a wide variety of subjects, and fairly adjusts schedules and course work in the light of unforeseen difficulties.

He is an impressive scientist not just in his role as a teacher of science, however. He has a broad view of his field that allows him to see the trends that come and go without getting swept up in the short-sighted the frenzy of adoration that can sometimes captivate large groups of researchers over the newest method or algorithm that shows any promise. It is professors and researchers like Dr. Dickinson who should be sought out and listened to if we are to effectively support and guide future scientific research.

Saturday, May 17, 2008

Vision is Hard

Vision is a remarkably difficult problem. One of my favourite "trick" images that demonstrates some of the challenging aspects of vision is the one displayed above. In the image, there are two squares labelled A and B. Those squares are identical in colour. It takes a bit of effort for most people to accept that, however. If you don't believe me, try loading the image into an image editing program and either get colour information from each square, or copy and paste regions of each next to each other.

Once satisfied that the two squares are actually identical in colour, it is worth stopping for a moment and thinking about why they look so remarkably different. In my experience, most peoples' initial reactions to this image are "how could our eyes screw up so badly?" However, if you think about it, it could equally be viewed a mistake to see the two squares as being identical in colour. It all comes down to the job one wishes to do. In most complex vision tasks, however, grasping the overall pattern of the scene is quite important, which makes viewing the two squares as different shades the more desirable perception to have. However, attaining the perception that a human effortlessly has (in fact, it takes a fair bit of effort to overcome the apparent difference in magnitude of grey) is actually quite difficult for a computer.

Say, for example, that you wish to take an image of a checkerboard like the one in the above image, find all the exposed squares, and label each square as either a dark or a light square. Since we are allowing the possibility of occlusion, variable illumination, and shadows, clearly there can be no simple global threshold used to label each pixel as either a dark or light pixel and then simply group like pixels with each other. If one attempted to do that, A and B would be labeled in the same manner and, therefore, one would be incorrect. So, perhaps you decide to be a little more complex and a little cleverer than that. You decide to locate the top left corner of your checkerboard (assuming that it is never occluded, which can sometimes be a hefty assumption, but we'll allow it) and then find its boundaries using either a blob tool (group all nearby pixels within a certain range of the starting pixel's value) or edge finder. Then, once all the boundaries have been located, compare neighbouring square average pixel values to determine which ones are the light and which ones the dark squares. Unfortunately, there are several problems with this approach. The first is the possibility of falsely splitting a square because of a shadow lying across only part of it. The second is that the thresholds used to find the boundaries of each square will not work at all illumination levels. Algorithms do exist for trying to dynamically find appropriate thresholds, but they are beyond the scope of this brief discussion and are not completely reliable.

Thus, you might decide to try one last method of being to clever to fix the downfalls of your previous method. You model the size of the squares with predetermined values, so once you find one you will be able to know where the others are even if the edge or blob detector fails to find a boundary or finds an extra boundary. However, this will only work if the orientation and apparent size of the board are completely fixed, which is not a reasonable assumption for any but the most constrained environments.

This is not an impossible task. It is not even a particularly difficult vision task if one were able to constrain the position and illumination of the checkerboard. Constraining at least one would still make it much simpler. However, I hope this simple discussion has made it clear just how much more complicated even a simple task like this might be, especially once the light levels and orientation are allowed to vary. When the task is scaled up to allow a wide assortment of objects, it becomes virtually intractable. I say virtually intractable because it clearly must not be, since it is a task that nearly every person on the planet manages to accomplish every day. Figuring out just how that is done, though, is a very fun problem to cogitate.

Friday, May 16, 2008

Scientist Appreciation: Isaac Asimov

Most people do not remember Isaac Asimov as a scientist. There are probably a great many who do not even realise that he was a scientist. However, he did have a doctorate in biochemistry and spent a long period of his life as a professor associated with the Boston University School of Medicine. Although he was not personally responsible for any drastically sweeping scientific work that I am aware of, he is the subject of scientist appreciation for this week to honour his vast contribution to scientific literature. This contribution was mainly in the generalist category of popular science, but I think it is significant nonetheless. His writing was beautifully clear, succinct, and engaging, making it some of the easiest to read and most interesting science writing. His promotion of rationalism and love of knowledge was of great importance to my own intellectual development, and, I believe, judging by the quantity of books he published and sold it was significant to many others as well. I therefore wanted to make the point with this week's instalment of Scientist Appreciation that there are many ways a person can contribute to the furthering of science, and educating others to appreciate science is one such vital aspect.

Wednesday, May 14, 2008

Possible Summer Shift in Emphasis

Just a warning for what readers this blog actually has: there may be a slight shift in emphasis for the summer. Yesterday I started my political science course (since I need a social science credit), which means that the wheels of my brain might be travelling the roads of the arts for a while. While I will still have my research job with one of my physiology professors to keep my thoughts in the realm of science, I probably won't be able to help myself from dwelling on politics a little more than usual. There, you have been warned. I am now being bothered to give up the computer for some television watching, so perhaps I should be going.

Monday, May 12, 2008

The Crazy for this Sunday: Mortals and Immortals

The sign outside the Church of Christ, Scientist is back. It has been back for a couple weeks now, I just haven't gotten around to posting anything about it. It disappeared for a while in what appeared to most likely be an act of vandalism with someone stealing the "Subject for this Sunday" portion of the sign. Really, as acts of vandalism go, I think I can actually understand this one the most. Unlike stealing a stop sign, where you risk seriously injuring someone, this does not really run the risk of any serious ramifications, plus whoever does the stealing gets an incredibly crazy sign to put on his wall. Of course, it is still stealing, so I do frown upon it. Also, an absent sign means I miss my weekly dose of crazy.

In case you are not familiar with the Church of Christ, Scientist, it is an odd cult that manages to somehow convince its followers that modern medicine is bad, and prayer is better. I've never actually gone to one of the sermons, but I often think it might be fun. The reason for that is they often have really ridiculous titles for the week's subject. When I first moved in and started noticing them, they had a whole string of slightly normal (even science-like) sounding ones. After several weeks of seeing subjects such as "Matter", "Energy", and "The Universe" advertised, I actually briefly thought that maybe it was an educational institute masquerading as a church (you know, kind of like Intelligent Design masquerading as science, only the other way around and actually helping people by giving them a nice physics lecture every Sunday). Unfortunately, on closer inspection of their sign I noticed "Wednesdays: Testimonials of Healing". That was my first inkling that something might be a little off. Then the subjects changed, and I knew there was an institution peddling craziness located within easy walking distance. I think my favourite to date has been something about modern necromancy (I forget the full title, but it was quite long and completely full of ignorance). Of course, in order to get full enjoyment out of this sign, I need to detach myself from the knowledge that people actually go to this institution and believe what it teaches. If I can perform that little mental dance, then I can just chuckle on my way to class at what an absolutely insane subject is being advertised, and wonder just what could possibly be said about it for two hours without anyone realising the speaker was completely off. Then, the sign disappeared, and I spent several weeks wondering just what the crazy for this Sunday might be. Now, however, it is back, and I can have my weekly dose of crazy again.

Friday, May 9, 2008

Scientist Appreciation: David Lowe

Oddly enough, the scientist for this week doesn't have a Wikipedia page. While there are plenty of scientists without Wikipedia pages, this fellow was repeatedly mentioned in two of my courses this semester with several ground-breaking computer vision algorithms to his name. The ubiquity of his name in my courses while at the same time his relative anonymity online I find slightly odd (though, of course, he has his own website from UBC where he currently teaches).

The algorithm of his that I am the most familiar with is called SIFT (scale-invariant feature transform, which does have a Wikipedia page), which is a remarkably robust image recognition algorithm for finding specific objects in images. The actual difficulty of this problem is a great deal higher than most people realise (a subject that I might write about in the near future), and the accuracy of the SIFT algorithm is quite impressive. In addition to SIFT and other recognition work, Dr. Lowe has also done work on automatically stitching together panoramic image scenes from a disjointed set of images, robot guidance, and scene manipulation.

While his list of accomplishments and influential algorithms is quite long and impressive, what is also great about David Lowe is that he is still conducting research at UBC. This means that there is actually a small iota of a chance that I might actually get to meet him one of these days and make some sort of silly, awestruck comment about how remarkably clever his work is.

Tuesday, May 6, 2008

The Cerebellum

I'm studying for my Motor Control Systems course tonight, and thought I might make a post about one of the regions of the brain that the course focuses on: the cerebellum. The cerebellum is a bit of a conundrum for me in my understanding of the brain, which makes it fascinating. The cerebellum is the "little brain" that sits at the back of a person's head and looks a bit like the head of a piece of cauliflower in anatomical drawings. While volumetrically much smaller than the rest of your brain, the vast majority of a person's neurons are in the cerebellum. Oddly enough, despite the concentration of neurons, it is actually possible to survive without a cerebellum. Quality of life will be dramatically reduced, as cerebellar damage results in a condition known as dysmetria, which basically means that movements are not properly timed. For example, if one were trying to lightly toss a ball while suffering from dysmetria, one may just as well hurl the ball with great force or even release it at a random moment during the arm swing. One of the other oddities about the cerebellum is that, despite it being virtually entirely involved in motor control and that entire post I previously made about the brain being primarily set up with contralateral control, most cerebellar functions are ipsilateral in nature.

However, what puzzles me the most about the cerebellum is that it is made up in a large proportion by constantly active neurons. Basically, the way in which it functions to deliver precise motor timing is that a set of nuclei project to several different motor areas (interestingly, the nuclei clearly follow an evolutionary pattern in which the most medial, and therefore oldest, nuclei project to the older motor areas of the brain. The most medial, the fastigial nucleus, projects to two of the spinal tracts, the next in line, the interposed nucleus, projects to the red nucleus and the ventralis intermediate nucleus of the thalamus, and finally the dentate nucleus projects to both the ventralis intermediate and the ventrooralis nuclei of the thalamus). The output from the cerebellum to these motor areas triggers activity in the corresponding motor areas (the target motor areas are where the movement patterns are actually stored, which is why a person can still survive without the cerebellum. Only the precise timing of those movements is lost with destruction of the cerebellum). However, what is strange about the architecture of the cerebellum is that the neurons of the cerebellar nuclei are tonically active, which means that they are constantly firing. The only thing that prevents their continuous activity is the set of cerebellar cells, the Purkinje cells located in the cerebellar cortex, which inhibit the cerebellar nuclei and are also tonically active. It all gets extremely confusing (to me, at least) at this point, but it basically boils down to a chain of constantly active excitation and inhibition (though to varying degrees, which is where the computational part of the cerebellum must come in), which is extremely metabolically expensive. That, to me, is where the biggest mystery of the cerebellum lies. What makes such a ridiculously expensive system of tonic activity computationally worth the metabolic cost it incurs? Perhaps someday I will know the answer to that question, but for now the cerebellum remains an intriguing oddity in my mind.

Friday, May 2, 2008

Scientist Appreciation: John Maynard Smith

Oh dear, it's Friday again already. The scientist being appreciated this week is John Maynard Smith, aeronautical engineer turned evolutionary biologist. Part of what draws me to him is that I feel a slight kinship with him in terms of the change of fields (after all, I left aerospace engineering to pursue a degree in computational neuroscience). More to the point, though, is that Dr. Maynard Smith is a perfect example of the great impact a person can have on a traditionally descriptive field simply by applying mathematical reasoning. Instrumental in bringing game theory to bear on some of the more nuanced and difficult areas of evolution (such as cooperative behaviour), his best known game theory model is the Hawk-Dove game. I was first introduced to the works of John Maynard Smith by his mention in Richard Dawkins' The Selfish Gene, where his arguments and models are used extensively in framing the thoughts of, in my admittedly not entirely informed opinion, one of the greatest evolutionary biologists of the last century. Of course, like so many of my intellectual heroes, John Maynard Smith is now unfortunately deceased, leaving me without hope of ever getting to meet him and thank him for helping me see the beautiful obviousness of evolution by simply knowing how to look.