Saturday, May 15, 2010

On biomechanics: simplicity vs complexity

I've been preparing this humongous post on this but decided in the end to postpone it and just put up a short and easy one instead.

I wanted to for some time to voice my opinion regarding biomechanical modelling. And in particular the subject of complexity versus simplicity. Biological systems are frequently very complex, the details of which are often poorly understood. The musculoskeletal system is no exception. I shan't linger on how complex the musculoskeletal system is, but I will comment on the approaches in which we try and model this complexity, or approximate it.

With the advent of affordable computers, it has become expected for biomechanicists to perform high-complexity analyses with many parameters. I'm all for development of sophisticated models and analyses. It helps identify elements of the musculoskeletal system that are otherwise difficult if not impossible to determine. But herein lies the problem; a lot of the complexity, be it the actual values of the parameters or the interactions between them, are at the moment shrouded in uncertainties. This is because various properties of muscle or bone are very difficult to determine and quantify in vivo. The best we can do is to use some kind of approximation, but it is quite difficult to say if our approximations are appropriate either. So what we are left with is a complex model where we don't really know if the input parameters are realistic.

My approach has been to focus on a specific aspect of biomechanical performance, using a specifically defined biomechanical metric, like mechanical advantage. The benefit of this approach is that the functional trait is defined and is based on first principles mechanics. So it really doesn't need to be validated in vivo. The added benefit of using specific metrics is that we can accumulate a sample size large enough for statistical testing due to its simplicity. This is exactly what classical functional morphologists and biomechanicists have been doing for a very long time, and more recently functional morphologists using phylogenetic comparative methods (like Mark Westneat for example). I think that this old-school approach is still very important and we shouldn't criticise it as being overly simplistic. My opinion is that it is still better than increasing uncertainty.

*Please note that I am not 'attacking' anyone doing 3D stuff, I really think it's exciting research. I just get a lot of crap thrown at me for sticking with the old-school stuff and just need to make my position clear.

Saturday, May 8, 2010

On Republic Commandos: the books not the game

I'm going to comment on Star Wars again, this time on a series of books I recently read; Republic Commando and Imperial Commando by Karen Traviss. This series is supposed to be an official tie-in to the game Republic Commando, which I really liked (although I thought it could be longer; only three stages?!). I was hesitant to read this because I was scared that I would be disappointed by the novels (which I tend to more and more these days) so I had put off reading until Order 66 had just come out. Now being a fan of stormtroopers and clone troopers, I had to read Order 66; that was a requirement for me. But because it was the newest book in a series, I had to first read the other three books, Hard Contact, Triple Zero and True Colours. So I decided to buy these books and started reading.

Hard Contact I found was kind of interesting, not bad at all. Although I found it a bit boring and not at all like the game I was so used to - you know, working as a unit and blasting through enemy defences (and destroying hundreds of droids along the way, woohoo!). In all fairness, it did kind of have the "four republic commandos against impossible odds" scenario, but for the majority of the book there isn't much coordinated squad activity. But it was all right and satisfactory enough for me to keep reading on.

Now, the next book, Triple Zero, I thought was a bit odd. It's supposed to be another Republic Commando novel, and we meet the same characters introduced in Hard Contact, but now, it's set on Coruscant, the capital planet of the Galactic Republic, rather than behind enemy lines. OK, so a bit more of a digression from the game concept than in Hard Contact. Apparently, this is because there is a terrorist threat at the capital and special forces are necessary to track them and neutralise them. ...Right... Somehow, I find that hard to follow. I'm sure Coruscant has its own version of CIA or MI6, or any of those domestic security agencies like FBI or NSA, and sure enough there is something called Coruscant Security Force (CSF) but they are portrayed as kind of useless. According to the plot line of the book, a small band of special forces clone troopers led by an old Mandalorian mercenary named Kal Skirata is the perfect if not the only group of people that can expose a terrorist network on Coruscant. But you'd think clone troopers on Coruscant would be a bit conspicuous for intel work. Don't worry, Kal Skirata arranged for a whole legion of clone troopers, the Forty-first elites, to be on leave on Coruscant. I guess the best place to hide a leaf is not in a forest, but you just dump a whole load of leaves on top of it...

Aside from a few of these strange plot devices, I kept having a strange uneasiness about the whole book that I couldn't really place where it came from. One obvious detachment I felt was the rather awkward need to place a "terrorist plot" into the Star Wars franchise; quite clearly a bad juxtaposition of current topical events. I felt that a story of a terrorist plot on Coruscant does not need to be told as a Republic Commando story. It feels like an unnecessary attempt at a topical commentary or whatever the author's intentions were - or maybe it was supposed to be the 24 of Star Wars, who knows.

Another awkwardness I felt from Triple Zero (and this was further confirmed beyond doubt when I read True Colours) is the "buddy-buddy", "warmy-touchy" kind of attitudes that all the characters seems to feel towards Kal Skirata, and this includes not only most of the clone troopers mentioned by name but also the CSF officers and the two Jedi, Etain Tur-Mukan and Bardan Jusik, the latter even going as far as wearing Mandalorian armour and acting like a Mandalorian instead of a Jedi. So considering how weird the plot was, I just couldn't help but think that this whole book was just an excuse to introduce Kal Skirata, his Null-Arc troopers, and the whole Mandalorian family business. If I remember correctly, the book even had a glossary of Mando'a or the supposed language of the Mandalorians. This last bit got me a bit unnerved (and perhaps may be a future post) - why would you want to learn an incomplete fictional language when there are hundreds of real living languages out there that are much much more interesting, even only for the simple fact that there is a real live culture associated with it (in other words it's not totally made up)?

I can't even remember now what the plot of the third book True Colours was aside from a lot of Mandalorian culture (lots of dinner table scenes) and lots of Jedi bashing. That's all I got from this third book. Mandalorians = kind and loving, while Jedi = evil hypocrites. Now before I read these books, I also thought Jedi are hypocritical characters to a certain extent so I didn't have much of a problem initially (though I did feel a bit uneasy reading all the Jedi bashing). Up to that point, I've never bothered to read any of the prequel tie-in books so I didn't know much about Jedi philosophy aside from what was depicted in the six films. After I read Traviss's books, I went ahead and read the novelisation of Revenge of the Sith that I had bought a long time ago and never bothered to read (I got the hard back edition even before the paper back came out so imagine how long it's been sitting on my bookshelf). To my surprise I found a completely opposite depiction of Jedi through the narrative of both Obi-wan Kenobi and Anakin Skywalker (even Anakin!). Obi-wan is a very compassionate character and very humble as well. There is a scene in Revenge of the Sith where a Jedi council member says something along the lines of "we must send our best" clearly meaning Obi-wan who is present in the room but Obi-wan is thinking "oh, who must that be?". He has no idea how his peers (and even seniors) view him. I liked reading the novelisation of Revenge of the Sith because I got a better sense of the character's thoughts and emotions than I got from watching the film (...sadly...).

I suppose you can argue that these books are written from the point of view of Mandalorians and clone troopers trained by Mandalorians so maybe it's an alternative view of Jedi, a public opinion if you will. I suppose that would be fine and I'm sure lots of Star Wars citizens would have animosity towards Jedi in one way or another. However, I find it strange that all of Karen Traviss's Jedi characters are sympathetic towards Mandalorians (even the bureaucratic Master Arligan Zey). Jusik and Etain even leave the Jedi Order to become Mandalorians. There are no other Jedi in the series that have a narrative (that we read through their point of view) and behave like a normal Jedi. In fact, I don't think there are any normal Jedi depicted at all. So there is clearly a Mandalorian bias.

The other two books I read, Order 66 and Imperial Commando 501st were equally unmemorable in terms of plot except that lots of Jedi get killed - some young padawans were even slaughtered by the protagonists because one of them unintentionally kills Etain. However, there are a lot of Mandalorian culture, especially lots of dinner table and kitchen scenes. I really don't know why. I guess there is much to know about a culture from their food (I must admit that one of my favourite parts about travelling is the local food) but I kind of think that excessive depiction of family dinners (with lots of uncles and aunts) is really at odds with a Republic Commando setting (at least in the sense of the original game). I got so sick of it I started skipping these scenes all together.

Any part of the story that was vaguely memorable was driven mostly by Kal Skirata or his Null-ARC clones, so again, there really was no "Republic Commando" in the sense of the game. The excitement I got from the game play just wasn't recreated in these books. Instead I got a lot of Kal Skirata and his Nulls following trails in a kind of spy or detective mystery story, not really a coordinated special forces feel you get from the game.

Having said that, I was a bit overwhelmed by the military slang that was prevalent in the whole series. I know Karen Traviss was specifically brought in as a military Sci-Fi author, and Star Wars has always had some military feel to it, but having a strong military overtone just doesn't sit with me too much. The reason for it is that even if Star Wars has a certain military look, the dialogues don't show any hint of modern military culture. For instance, any commanding officer (even Moff Jerjerrod!) of any unit no matter the size (e.g. a legion, a squad, or a Death Star!) is referred to as "Commander" repeatedly throughout the films. Very rarely do we really get to hear actual military rank, like Private or Lieutenant. This suggests to me that we're not supposed to take the military organisation or structure too seriously. The whole usage of "Legion" in Star Wars to refer to a military unit, to me indicates that we are supposed to think of the Republic or Imperial armies much in the same way as the ancient Roman legions, not modern military. The "Grand Army of the Republic" says it all. Everything is grandiose and operatic in Star Wars, so modern military slang just doesn't fit in comfortably. But of course, this is just how I felt; I'm no expert on ancient or modern military topics so I may be wrong in this interpretation.

Last but not least, I felt really uneasy in one of the books where Kal Skirata enlists the help of a university professor to try and find a cure for the accelerated aging engineered into the clones. What I found disturbing was the depiction of university academics as useless snobs completely detached from reality. Now, I know many people feel this way towards academics and maybe because Skirata is a mercenary we are supposed to see the world through his "practical" eyes. But I've had enough of this "ivory tower" prejudice in real life that it's not necessary in a Star Wars novel. I mean come on, I've gone through unemployment recently, and I still have to go through extreme competition to get a job in the future. How detached from reality am I? Further, throughout the books I got the message, "if you don't put your life in the line of fire then you are a coward and not worth any respect". Perhaps this is a Mandalorian view of life but judging that Mandalorians are glorified throughout all the books I get the feeling that this really is the message of the books.

Wednesday, May 5, 2010

On calipers

I'll ramble on about calipers today, just because I like calipers. In my line of business I use calipers very frequently. And not just a normal handy 150mm caliper, but a larger 300mm caliper or an even larger 600mm calliper. So I'll just list my callipers in size order.

150mm glass fibre dial calliper
I really like this one, despite the fact that I bought it at a local hardware shop - if it's good enough to refurbish your kitchen or build a bed, then it's good enough for me. So far I've trusted my life with the works of carpenters/engineers so I don't see why I can't trust my measurements using their tools. To begin with, craniometrics are not the most precisely defined measurements and taking these at the precision of 0.01 mm is absurd - rounding to the closest mm is fine, at least it's accurate to the mm or maybe 0.1mm.

Anyway, I digressed. I like this dial calliper because first of all it is very easy to read. Unlike vernier calipers dial callipers are very straight forward; you can just simply read off the dials and there is no need to get confused with the vernier scale. Of course you sacrifice the precision - vernier scales typically can let you read to the precision of 0.02mm whereas dials only allow to the level of 0.1mm - but like I rambled on above, I don't really need that level of precision. Secondly, my dial calliper is glass fibre so it pretty much doesn't leave any scratches. This is kind of important when you're working with fragile or old specimens in bad conditions - sharp metallic callipers can leave scratches on specimen surfaces if you're not careful.

300mm digital calliper
After visiting a couple of museums it soon became clear that a 150mm calliper wasn't going to be enough for some larger specimens, for instance crocodilian skulls or all the mid- to large-sized cat skulls. So I got myself a decent 300mm digital calliper from ebay (I was a self-funded student so I didn't have the luxury of charging it to a grant). This calliper is very nice in that it has the precision at 0.01mm but also it is digital so the measurement gets displayed on a LCD which reduces transcription error considerably. I remember being very excited by this large calliper and I happily measured larger specimens. Again, I rarely read the measurement to the 0.01mm scale.

600mm vernier scale caliper
Despite my delight at the size of the 300mm calliper and its capabilities in measuring larger specimens, it became apparent once again that some measurements for very large specimens could not be measured by even my 300mm calliper. So I got myself a decent 600mm vernier scale calliper (I think I found this on ebay as well). This was good to some extent but this calliper was difficult to use in several ways. First, I could never read the vernier scale correctly, despite having had training in University (I just vaguely remembered I had to line up the scales). Second, and more importantly, I found out that the jaws were too short for any easy use against objects that had considerable depth, like a lion or tiger skull. Frankly, I don't really know what kind of object would be 600mm in length but can be measured by callipers with jaws that are only about 50mm. Skulls are typically obscure in shape and can be very awkward to measure direct distances between two landmarks, and too frequently the 600mm calliper proved to be a very clumsy tool for this. For instance, if you wanted to measure the greatest length of the skull taken as the direct distance between the tip of the snout to the tip of the occipital crest, then quite frequently, the skull roof would get in the way of the calliper. It was clear that I needed something with longer jaws.

600mm tree caliper
Initially I couldn't find any callipers with jaws that were long enough. However, after many hours of searching online using a variety of key word combinations, I finally came across something close to ideal: tree callipers. Tree callipers are commonly used by forestry people to measure tree trunk diameter and are available in very large sizes, even up to 2m in length. But most importantly tree callipers have very long jaws, exactly the kind of thing I was looking for. It is worth noting here that there was an option to buy an anthropometer but the price of such an instrument was way beyond my then financial capabilities (maybe now I can charge my grant). But in any case, a tree calliper is sufficient for my purposes. Unfortunately, my tree calliper only has the precision to a mm, but given the specimen size of 350 or 400mm (and sometimes even bigger) a mm precision is good enough; e.g. 404mm and 405mm is nearly identical, let alone 404.3mm and 404.4mm. In other words, a precision of less than a mm is overkill in these cases.

I am very happy with this calliper. The jaws are sufficiently long enough to bracket large cat skulls with ease so it allows me to measure distances more or less parallel to the direct distance between two landmarks by taking the jaws roughly perpendicular to that imaginary straight line. One drawback is that the jaws are too long for easy transport so I always have to take it apart when I leave the museum; fortunately, the jaws can easily be detached by unscrewing a couple of screws.