Walky Talky

Coincidence?

So. As will have been obvious to more or less no-one, yesterday's post is directly related to one from a couple of years back, with further references in who knows how many more before that. I happened across that first post yesterday and was reminded that I intended to do some more eventually. So I did.

My memory of much of this is still surprisingly clear, given that I last heard any of it in something like 1982. Cal it a consequence of having listened to my off-the-air tapes countless times back then: this stuff is engraved on my brain in a way that I just can't seem to manage now with any number of much more useful things. Despite that, I turned out to be slightly vague on the details of dessert -- I thought the ice cream flavour was vanilla, for example -- and so it seemed worth a google.

Make no mistake, I've done that before -- at the time of those earlier posts, for sure, and at other times as well. I don't remember when the last attempt was, but at that time Hordes of the Things was still effctively unknown to the internet, and thus could only tentatively be said to have existed at all. Given the inexhaustible depths of trivia long since available online, I was beginning to wonder whether I'd imagined the whole thing. Perhaps it was some kind of ludicrous adolescent fantasy that just didn't hold up to adult inspection.

Well, no. My ancient recollections have been unexpectedly vindicated.

That there might now be a Wikipedia entry for this long-forgotten series is not the world's biggest surprise, given that it is increasingly difficult to find any fucking thing for which there is not a Wikipedia entry. What is surprising, though -- almost alarming, in fact -- is that said entry reveals said show to have started repeats on BBC7 just the other day. Indeed, at least for those in the UK, the first episode -- from which most, if not all, of the examples so far cited on WT derive -- is available on iPlayer for the rest of this week.

I mean, really. What are the chances? Is the entire world enslaved to my whims? And if so, does that make me responsible for all the fucking awful, dismally depressing shit going down?

Man, I hope not.

Anyway, this "coincidence" allowed me to correct the ice cream flavour to strawberry. And when I once again have net access I will attempt to record the relevant sequence with Audio Hijack or some equivalent, so if you can't access the legit version I may be able to help.

The reason I can't do the recording right now is that I'm writing underground, in the arches of the Shunt Lounge, a members-ish art bar buried under London Bridge station in a space previously used for such performances as Tropicana and Amato Saltone. Some areas have changed significantly since then, others not. Either way, it's an amazing venue, the sort of place that makes me feel privileged to live here in London in these interesting times. Even despite so much in the world being desperate, agonising shit, local existence is still a fucking miracle. There are doubtless luckier people than me right now, but not many.

Of course, there is a downside, which in this case is that I most likely will not be able to see the performance for which I've come all this way. Apparently all the, rather limited, seats for Dancing On Your Grave have been preallocated -- no doubt to miscellaneous friends and family of the company -- and we mere plebs will have to take our chances. Normally this would piss me off no fucking end, but on account of the great pleasure she's given me over the years I'm prepared to cut Lea quite a lot of slack. In addition to which, the whole Shunt Lounge experience is really quite entertaining. As a nearby milk float puts it:

Do not adjust your mind,
there is a fault in reality!!

Isn't there always? And isn't that how things should be?

Eigenvectors

As it turned out, the first day of Understanding ion channels in terms of mechanisms was unexpectedly undemanding. The bulk was spent on matrix algebra, with which I am reasonably familiar, and also the rudiments of MathCad, which turns out to be quirky and irritating in a very similar way to Mathematica, while being apparently less powerful; it's certainly not a patch on Matlab.

Admittedly, such distinctions are roughly in the same league as arguments about angels on the head of pin, and I'm happy to respect the preferences of anyone who actually gives a flying fuck one way or the other. Still, at least for someone with a more traditional programming background, there seems to be a measurable loss of marginal utility that comes with all attempts to make programs that do maths look in some way similar to how maths looks when done by human mathematicians on paper -- especially when this involves combining free-form positioning on the virtual page with clunky procedural rules about how the logic flows topographically. I'm not clear whether MathCad provides any of the sensible programming constructs that would make it properly useful -- probably it does -- but I'm damn sure I don't care enough to find out.

In any case, the major intellectual engagement of the day revolved around the spectral expansion of singular matrices. Wait, where are you going? Hello?

A central component of the course, and of ion channel analysis in general, is the so-called Q matrix, which -- in my currently rather vague understanding -- seems to be a transition matrix encoding the probabilities that an ion channel -- or, really, any system following a Markov process -- will shift from one of its possible states to another. Since the system has to be in some possible state, the matrix columns cannot be linearly independent. Therefore, the matrix must be singular, and thus have at least one zero eigenvalue.

Okay, I appreciate that this is probably coming across as total gibberish even to the more sciencey among you. At some level there may be no getting around that, but at least let me try to explain.

A matrix is just a table or array of numbers. That much is pretty easy to understand. Why such things are useful -- and, even more so, the strange interactions between them -- is a bit more problematic. The simplest way I can come up with of describing these benefits is in terms of graphics -- by which I mean the sort of stuff you're looking at on your computer monitor right now, though it would apply even more if you were playing a game on a Wii or PS3.

Everything you look at on a screen occupies a visual space that can be quantified in some number of dimensions. Some of these dimensions -- left or right, up or down, in or out -- are explicitly positional. Others -- say, brightness and colour -- are not. There are perspectives from which such a distinction is artificial, but for now we can just dismiss them. Let's think simply in terms of position.

Thanks ostensibly to Descartes, we know that we can define positions using a small number of orthogonal coordinates. In almost all cases, our basic positional concern for screen viewing is two-dimensional, usually in a plane roughly perpendicular to our viewing direction. Indeed, even when this isn't the case, our brains are pretty good at pretending it is, which is why it's not the end of the world when you go to the movies on a busy night and have to sit right over on the side.

Position, then, is commonly a two-dimensional quantity.

But we know that the two-dimensional context in which we view things is subject to changes in its -- and our -- viewpoint. For example, if we are watching a TV and someone comes along and turns the set upside down, we will see the pictures on the screen as being the wrong way up. The same will be true if the set remains untouched but we decide to stand on our head.

When this sort of thing happens, some kind of transformation occurs, changing our view. At the same time, we normally accept that the change is a matter of perspective rather than anything more fundamental: the TV is still showing the same programme within its own frame of reference. It is our relationship to it that has changed.

That frame of reference change is what is of interest to us right now. It amounts to a transformation of our viewpoint -- and that transformation can often be represented as a matrix. The trick that underlies this is matrix multiplication, which is at first sight a rather abstruse and incomprehensible operation. But all that it really means is that a value in any arbitrary dimension -- say, how far to the left or right an object appears to one's eyes -- depends on some combination of the values it has in all its dimensions -- say, where it actually is in space. This is hardly radical or surprising.

A matrix then, is a way of representing how things in one frame of reference get transformed into another.

This is all fine and dandy until we start to consider frames of reference that have different ranks -- that is, different numbers of dimensions. To pick the most obvious example, there's the three dimensional world on the one hand, and its appearance in a two dimensional image on the other. Under such a transformation, several different things -- a person's shoulder, a tree in the middle distance, a jagged peak on the horizon many miles away -- can all wind up at pretty much the same 2D location -- the same point in the picture. A whole bunch of information about the full three dimensional structure of the scene is necessarily lost when it's converted into a photo in this way.

At some level, this kind of transformation is fundamentally different from one that preserves all its dimensions. The latter is, at least theoretically, invertible -- all of the original scene information can potentially be recovered -- whereas the former is not. Somewhere along the line information is thrown away, such that we can never get it back.

Matrices representing such operations -- where information is not merely transformed but destroyed -- are termed singular. A characteristic of such matrices is that one or more of their eigenvalues is zero.

Eigen-wha-whosits? Well may you ask.

A matrix represents a transformation that can be applied to any vector data of a suitable rank -- eg, a 3x3 matrix can transform positions in any 3d space -- producing a transformed space of rank no greater -- but quite possibly lower -- than the original. In general, the transformation depends not only on the matrix but also on the data. For example, consider the matrix:

( 1 0 0 )
( 0 0 0 )
( 0 0 1 )

This preserves the x and z dimensions of any data to which it is applied, but any y is brutally truncated to 0. Indubitably, information is tossed away.

Even so, any point -- or vector -- with no y component will slip through entirely undulterated. Only data in the y direction are lost. Clearly, some information is more liable to be destroyed than other kinds; plenty of information may not be destroyed at all, just perhaps stretched along the way.

We can determine the directions from which data will not deviate under the transform; these are the eigenvectors of the matrix. There are as many of these as the matrix -- which must be square -- has rows or columns. And -- by definition -- every one must be non-zero. Each such vector is associated with an eigenvalue, which is the amount the transformation stretches or shrinks data along that direction. This value can be zero, which was at the root of my confusion today.

A matrix may have one or even more zero eigenvalues, in which case it will be singular. It may not have any zero eigenvectors: even zero eigenvalues must be associated with non-zero eigenvectors.

Because of the way it is formulated, the Q matrix will always have at least one zero eigenvalue. And yet one of the important things we need to do with it -- calculate its exponential -- depends on being able to invert a matrix of its eigenvectors, which in turn requires that that matrix be non-singular. If any eigenvector were zero that would be impossible.

My initial impression was that this would have to be the case, because the Q matrix is singular. No-one present could quite explain why this wasn't so, but fortunately it isn't. Eigenvectors are, by definition, non-zero. When the associated eigenvalues are zero, that just means that there are non-zero vectors that the matrix transforms to zero, and these can be found.

Thus, all remains right with the world. As if you care.

Filler 56

Despite the continuing feebleness of our summer, a nice weekend was had. As already documented, yesterday took us to the Farnborough International Air Show to watch a bunch of aeronautical hardware being put through its paces in the company of vast numbers of other interested parties. This is inevitably a slightly uneasy experience, since so much of the hardware exists for the purpose of unleashing death and destruction, and the event itself is primariy a trade show. But it's also amazing stuff from a technological standpoint and damnably exciting in the air.

Today was the day of the annual Italian parade and festival in Clerkenwell, of which I've posted photographic evidence in the past. No need to do so again, as it never changes much, but I couldn't in any case as we were absent for the parade itself. Instead, we took young master Oliver, who as you may or may not recall is Ian's godson, to see Wall-E, which I loved to bits. I can't imagine that any of the few people reading this blog need my urging to see it, but if you do, consider yourself urged. It's a marvel.

After that, all that remained was to head back for a glass of prosecco amid the Warner Street throng, an early dinner, and a little preparatory reading for DC's ion channels course, which starts tomorrow and will probably provide some blogging material in the coming days.

Also to come this week, hopefully, are the latest Cholmondeleys and Featherstonehaughs piece at the Shunt Lounge -- period memberships are all sold out, so I'm reduced to queueing on the day -- and, of course, The Dark Knight. That's sold out too for the IMAX (well, there are perfs at 2.30 and 5.30 in the morning, but I'm not that desperate), so I guess it'll have to be boring old Leicester Square...

Show of Skill

Show of Force

Quis Custodiet

Another day, another video, this time courtesy of Robin. I'm embedding a YouTube version out of habit, but since this is all about the visuals you'd be better off skipping to the official version. This one may vanish anyway.

It certainly looks like Watchmen -- too much so, frankly: the slavish recreation of Dave Gibbons's artwork borders on the unhealthy. And, in its relentlessly trailery way, it does a trailer's job, which is to hint that there might be a halfway decent movie on the other side. That seems rather unlikely in this case, though.

You do have to admire the chutzpah: they actually have the nerve to describe Zack Snyder as a "visionary director". Augh.

In any case, I guess I can no longer remain in denial about this. The movie really is happening. It is almost impossible to imagine how it can not suck -- but of course I'll be right there on opening day just to see how bad...

Tourism

I usually shy away from other people called Matt, but this one, courtesy of the lovely Stairs, is just too charming to miss:

I especially love the transcendent moment where he dances someone else's steps. The whole thing is just a beautiful trip. Read his site if you want to like him even more.

In other news, it was Ian's piano diploma exam today. Obviously these things are never perfect, but it seems to have gone fairly well, so we're happy about that :)

Geekery

Only about six months after buying it, I've finally started playing around with my Arduino, and it's a cute little fella:

In a sense, programming for a microcontroller is no different from doing so for an all-singing, all-dancing modern computer -- apart from the target being so much less sophisticated. But there's something charmingly tactile about being able to interface so directly -- and clunkily -- to the outside world, with only a few lines of code and some bodged-together components. It has the feel of something much more physical than the coddled environments I'm more used to.

Of course, all I've done so far is blink a few lights and read from the crudest sensors, but it's only been an hour or two. Hopefully I'll be able to come up with some fun things to do with it. Suggestions on a postcard, please...

Drowning

This is Ian's ringtone. Try to imagine how annoying that can be. Go on, try.

Of course, I have nobody to blame but myself, seeing as I provided him with it, but it was under duress. Or at least it is coming to seem so in retrospect...

Gripping Stuff

Inevitably, this everyday posting business is becoming a chore. My life just isn't that interesting, its days spent bumbling along in blah-de-blah activities that don't necessarily merit reportage. And even when the activities are entirely fascinating, they still might not be when converted into prose and/or pictures; or I may not be willing to expend the effort to make them so.

Which brings us to today, which was really a pretty fine one all round, but somewhat lacking in event. What is there to say about it, really? Shall I attempt to describe another day in the lab? Or a quiet night of domesticity? No, I bloody well shan't. Perhaps it'll come to that, but here's something else entirely.

After a nice lunch with Handsome Jack, I found myself outside Evans and finally remembered to buy some new grips for my bike. The old ones have been in a bad way for awhile, quite worn through in places and generally slick to the touch:

These were the ones that came with the bike in the first place, and were of the old rubber type that attach themselves to your handlebars by virtue of their own tackiness. I've changed such grips before, and they're an incredible pain in the arse to get off and -- especially -- on. They're specifically designed to cling tightly, and so manhandling the little bastards over the bars is not merely difficult but increasingly so: the further you get them on, the more immovable they become. I actually bought a new pair in this style prior to the Isle of Wight trip, but I couldn't face fitting them and so they have remained on the shelf gathering dust.

At some point in the last few years a new kind of "locking" grip got invented, and it was a pair of these that I finally acquired today. Unlike the old kind, they attach not by their rubberiness, but via some screw-tightened clips. Consequently, they're an absolute breeze to fit, and they look rather stylish too:

I can now take to the streets without fear of my hands slipping all over the handlebars, and grind out another blog entry to boot. I can't imagine just how fascinating this must be for you. Tomorrow we can discuss laundry or cooking or -- I know! -- drying paint.

City Jitters 9

Won't you Charleston with me?

On the way home from a nice dinner at Skylon, it was rather delightful -- and almost even summery -- to chance upon an outdoor dancehall complete with live swing band in front of the National Theatre, full of people happily jiving their evening away. It made me want to lock up my bike and join in -- but, despite being with Ian, I didn't have anyone to dance with. The experience was just lovely even so...

Technophobia

As mentioned in passing before, I am now, along with the lovely Ed, loosely responsible for the CoMPLEX computer network. In particular, that means the machines and technology used by those cannon fodder systems biology lab rats, the MRes students. You remember them -- I was one myself this time last year.

On the one hand, this means I can look forward to a certain amount of income over and above my research council pocket money for these next few years, though hardly enough to live on. On the other, Gordon fucking Bennett but computer support is a pain in the arse. It is an absolute dead cert stone cold guarantee, for a tech monkey, that merely walking into the computer room will see you besieged by unsolvable requests about the imbecilities of Microsoft Office or somesuch soul-destroying awfulness, requests that will expand to fill all the time you allow.

Abandon hope, all ye who enter here.

Abandon your afternoon, at least.

That said, and notwithstanding the fantastic levels of frustration and annoyance that go with this territory like a horse with marriage, it is also quite nice to spend a few hours a week working in an area of relative competence rather than trying to nag away at the limits of a scientific discipline one grasps dimly at best. Computers may be wayward and infuriating and vexatiously non-deterministic, but all that is nothing compared to the vagaries of the scanning ion conductance microscope, or electrophysiology in general, or the whole fucking voodoo world of tissue culture. That stuff really is black magic.

Actually, the SICM/fluorescence/ephys is looking tentatively promising, although there are big question marks over the visualisation just now. Partly this is because phase contrast illumination is pretty much impossible with the paraphernalia of SICM squatting in the illumination pathway, partly it's because of the limited interoperability of high-magnification, high-NA, almost context-free, oil-immersion optical microscopy with the more straightforward, but much lower resolution, air objective version. We're still looking for a workable compromise for both these difficulties.

With all that laid out, it was entertaining, in a distressing way, when two of my supervisors spent the day experimenting with us (ie, my postdoc colleague Simon and myself) and the more senior came away disappointed because we couldn't reliably patch presynaptic boutons just yet. Excuse me? Reliably patch boutons? Hello? If we could do that, we wouldn't be keeping it some kind of secret, we'd be writing the fucking Nature papers already. This whole gruesome goatfuck of techniques is in its infancy. Maybe one day it'll be routinely magical, but give us a chance to get there, please.

In the meantime, the iPhone 2.0 software is so close you can almost smell it, and yet still -- despite leaks -- not quite practical to install. Just a few more hours, or at least so we hope...

Blast from the Past

Given this month's dusting-off vanity project, I really ought to take the opportunity to add a few more entries to this long neglected backwater of the site. Ought to is not the same as will, however, so we'll just have to wait and see what the future brings.

In the meantime, though, here's a little teaser: