Looking Around

2005-02-22T21:51:00.000+10:00

I'm happy. I just worked out (finally, after a few years of occasional bursts of inspiration, followed by crushing defeat...) how the hell C++ builder works. Yay!!

Finally, I can do some programming again!!

Let my inner geek (well... more of the inner geek...) awake again!

2005-02-14T23:03:00.000+10:00

Today got off to an interesting start when I was precisely 1 day and 20 minutes early for an appointment. Hopefully I won't be late tomorrow...

Anyway --- the day continued to increase in interestingnessosity when my supervisor gave a talk on some recent work he's been involved with in Chile. (Work I was also going to be involved with, but wasn't in the end due to unfortunate prior engagements, darn it!). The talk was fascinating. I'm not going to try to reproduce any of it here, but the vague topic area was on visual attention in pigeons (though, by analogy, it should apply to a lot of different animals.... comparitive neurophysiology is really cool :) ). In particular, this Chilean group has recently obtained some results which suggest the existence of a so-called "attentional spotlight" --- a mechanism to select important information for inclusion in conscious awareness.

Aside from the subject matter of the talk (I might try to explain it at some point in the future), what really impressed me was the way he explained it, and the effect it had, at least on me. My supervisor has an amazing ability to draw people in to his way of seeing things. Over the past year, it's been something I've really noticed. He has some very idiosyncratic ideas about the brain, and the way it works --- ideas which, over the last year or so of reading and thinking, I continually convince myself are not true.

But everytime I hear him speak, at least momentarily, he convinces me otherwise. I'd love to know how he does it! :) What's more, his vision of the world is such a wonderful place --- so wonderful that it's hard for me to believe it could be that way. But I know that that's the world he lives in (at least most of the time). He exudes a sort of magic, in that he can draw the people he talks to into it as well.

I'd *really* love to know how he does it....

2005-02-10T10:02:00.000+10:00

Meaning and Stories.

"The universe is made of stories not atoms." --- Muriel Rukeyser

I wonder why it is that we tell stories? Or why it is that we have such appreciation for stories? When we meet someone new, one of the first questions we ask is "What's your story?".

The theory I have heard is that story-telling is a way of searching for meaning in our lives: that as we grow and experience life, we fit our experiences into the narrative we are constructing for ourselves. It is a narrative that we are constantly writing and rewriting; testing out new ideas on, and even completely restructuring it as we begin to understand ourselves better. When we ask "Why?", we answer with a story --- it is never a "complete" answer, I suppose because there are no complete answers to that question, but it is an answer that provides some insight.

So I wonder: I often want to write a book or story. As a kid, I remember writing all the time --- stories and words just flowed out of me. As I grew, they dried up: as with so many people, that seemed to coincide with my passage through school, and the repeated division of my work into "good" and "bad". Now I don't write all that often. The excuse I give myself is that I don't have anything to say. What does that really mean? Does it mean that I have stopped asking "Why?", or at least, that I have stopped asking "why?" in the right way? Or are my experiences too cut and dried now?

I think not. Over the past year or so, I have been struggling with a big change in my life. I have just started a phd in neuroscience, which is another way of saying that my "work" life has undergone a complete upheaval. Anyway --- the thing I have found interesting is that when people ask me what I'm doing --- "What's your story?" --- I have noticed that I always answer with something different. The things I say aren't in any way untrue, or misleading. They are simply different. So why do I do that? I think that what I am trying to do by telling these stories is come to terms with the change; to understand what meaning it has in the context of my life. It has been a time of great emotional upheaval, and real uncertainty --- a great part of that, I think, has been mirrored by my inability to "get my story straight".

To me, that shows a great deal about human nature; the telling of stories to understand ourselves and our actions. It leads to so many questions.

Anyway --- there are more things I want to write about at the moment. I'm not clear in my mind where I was going with that.

The next thing I'd like to look at are stories in science. When we ask "why" in science, we often don't answer with a story; or at the very least, at first glance it doesn't look like a story. But sometimes, when something really captures the imagination, there is an underlying story. For example, perhaps the reason the big bang has captured so much attention is because it gives a story; in fact, so much of cosmology tells a story: the life-cycle of a star or the last trip down a black hole. Biology too, provides us with stories --- "How did the birds get their wings?", "Why did the dinosaurs die out?". What role do stories play in science?

The thing I see as the most dehumanising aspect of science is its obsession with reductionism. The continual breaking-down of things into smaller and smaller parts, with no attempt to reconstruct them. With the plethora of particles in high-energy physics, or proteins and genes in molecular biology it is no wonder that we get lost when we look for the meaning in our endeavours --- we "understand" so much, yet "understand" so little. It is as though we take a story, and then entirely destroy its structure, and as a consequence, lose all its meaning, at least in human terms. I wonder if this is like "deconstruction" in philosophy? In any case, this tendancy towards reduction is probably why great theories such as natural evolution, or the central dogma of biology are so revered --- they at least provide a framework in which to construct a story from all these fragments.

It's funny; I can't remember who told me about it, but I've heard that there are very competent writers, even famous writers, who are unable to keep their plot consistent and logical, or even to understand where the inconsistencies are: to a scientist, that is an almost heinous crime. I guess that's essentially the thing that science regards as most important. But regardless, these folk still write great stories. Scientists are also well known for picking at plot holes in movies. But I wonder, are scientists as receptive to the other aspects of the story; the metaphorical or aesthetic sides? I'm not sure that we are...

2005-01-11T23:17:00.000+10:00

In the beginning, we didn't ask why.

Then we asked "why?", and were answered by the Sun and the Moon, the Earth, the Sea, the Sky.

Then we asked "why?", and we guessed that the universe would answer. We couldn't understand the answer, but we called it "God".

Then we asked "why?", and fell in despair, because the echoes of our question simply faded away.

Now I ask "why?".
I can sense an answer glowing faintly.

2004-12-17T01:36:00.000+10:00

We're flying across India. Lights spill out across it like embers kicked from a fire... or... looking at it as I notice some patterns in the spacing of the lights, maybe the mad scrawlings of a ritual --- a question or demand for the gods?

That obviously can't be it --- I think our culture today is too obsessed with function for anything so primal or spiritual... it's almost impossible to understand why anyone would ever have sketched horses with white rocks; we know there aren't any gods. At least none who'd care. In reality, the lines that emerge as you group the smaller splashes of light trace out paths running straight between the larger smears. I guess smaller towns will always tend to spring up along the major roads. My inner-physicist thinks that might be fun to model.

Some of these conduits are better defined. Tiny pinpricks, if you watch carefully, inch along them --- maybe trucks carrying produce? If India were a brain slice, we're seeing the axons highlighted by a phosphorescent dye. Occasionally a shooting star drops.

As I watch, an entire sea of black flares suddenly; perhaps some coven of witch-doctors has finally completed then next stage of their grand design, with another casual flick of fuel from the fire.

At some point we cross an almost imperceptible boundary. The glow has shifted from orange to white; sodium to neon. No longer embers spread out to sputter faintly, but sparks falling from a grindstone. Maybe this area is the property of a new tribe; do the colours mark sides in an endless war? The boundary is ambiguous --- is that section white with flecks of orange, or orange touched with white? Will the gods be angry if we can't keep our colours separate?

As the coast approaches, the pinpricks cluster closer together, to ward off the dark swathe of ocean. Can't build on that. Just over the horizon, an orange glow marks the presence of one of the huge cities of India; perhaps Mumbai? Or it could be the faint aura of the fire that gave birth to all these baby conflagrations. Maybe it's both.

2004-10-28T23:53:00.000+10:00

I'm a sleepy D. Last night held a bit too much excitement: A few weeks ago, the aiki school had a trip to Japan, and last night was the official "boring" slide night. Argh. Too much sake.

Still --- we had a good time, and I didn't get home until 5:00. I haven't done that for a while. The party also involved a good drunken philosophical debate on the existence of reality --- always a favourite (Though I don't believe we had *any* matrix quotes... I guess I'll blame that on Luke going home early). I'm sure I'd get bored of it if it happened more than once or twice a year, but every now and then, it's really fun.

Anyway --- as a result, today was exhausting. I took a trip out to the Wesley hospital to talk to a researcher there about my ideas on looking for interesting things in the EEGs (electroencephalogram: i.e. measuring the electrical signals generated by the functioning of the brain) of bipolar vs. non-bipolar folk. Very exciting :) I may end up having my first ever EEG next Monday. Oooooh... I get to see my brain working... (though apparently long hair makes for dirty data: I'm thinking mine will look like it's been hit with the ugly stick...)

It's pretty cool: the whole EEG field has been taking off again recently with the introduction of nonlinear data analysis techniques. Of course, the old-guard don't trust anything that doesn't involve a fourier transform, or at the very least, a cross-correlation plot.... but I think eventually the power of the new techniques will be hard to ignore.

Right. I'm going to bed.

2004-10-25T13:34:00.000+10:00

Righto... over the past 6 months or so, there are some ideas which keep coming back into my thoughts, and I've finally decided to write something down about them. They're certainly not fully developed, but here goes:

Simulatability and Bifurcation --- information theory at critical points

There is an interesting link between bifurcation theory and computability. In the vicinity of a bifurcation, two systems (i.e. same underlying physics, but at different positions in parameter space) maybe very close in one sense (i.e. in parameter space), but behave very differently. At some point (i.e. the bifurcation), we might believe that it becomes a good philosophical question whether or not the system can be simulated by any sort of computer. It becomse a question of whether underlying reality really is simulable. For example, if we believe that there is some underlying minimum length scale, and that quantum mechanics works on a lattice with finite values etc., then a quantum computer would, in principle, be able to simulate the system right up to the bifurcation point (in fact, in this situation, I don't think the bifurcation point really exists, except in an abstract manner: the system is definitely on one or the other side of the bifurcation). If, however, we don't believe that physics is limited in this fundamental way, it seems that such systems are not simulable when the parameters are directly on the bifurcation point. This is because at these points, an error at any length scale produces an enormous qualitative difference in behaviour: the long time behaviour of the system is no longer even statistically predictable (By this I mean that the system is non-ergodic, so we can't even predict which part of its phase space it will be sampling: this is the difference I'm trying to draw between this and chaos theory --- in chaos theory, you can at least say that the system will get arbitrarily close to any point in an appropriately chosen space, i.e. between to KAM surfaces. Here, we can't even say that: in chaos, we're talking about an initial condition which lies right on the boundary between two chaotic attractors which go to completely different parts of phase space.) (Hmmm... intuition is suggesting some link to Chaitin's omega numbers here...).

So, the question "Is reality simulable by any finite state system?" is something which really becomes important near a bifurcation, where all length- and time-scales become relevant.

Something interesting: we could say that for values of parameters not on a bifurcation point, reality really is simulable: perhaps this is another possible definition of a bifurcation? There is also the question of noise in the system. In essence, bifurcations indicate a breakdown in the slaving principle of synergetics: degrees of freedom which could be ignored away from the bifurcation can no longer be ignored as we approach it. What was, putatively, a relatively low-dimensional system suddenly has a plethora of non-ignorable dimensions, each of which play an important role in its future behaviour. Also, noise in any one of these dimensions can no longer simply be "added" to obtain a gaussian or whatever by the central limit theorem. Now, they act in a more complex way. Perhaps this is the origin of 1/f noise: we need a "different" central limit theorem for noise near a bifurcation point? Noise in some DoFs will act on one time-scale, others on different time-scales and the result is 1/f noise?

However, in any case, it seeems to me taht the discussion of bifurcation is the important question for computability and the physics of information. Can systems near a bifurcation point, in principle, be simulated? Or is there a fundamental limit to their simulation? I think it is wothout-doubt possible to simulate systems which are even an infinitesimal distance from such a point, but when they are directly on the bifurcation, it becomes a different story.

(Ideas on where to go with this:

- Really, when I talk about "simulable", I mean "efficiently simulable": there is a
relationship between distance from the bifurcation in parameter space, and the
Space/Time efficiency of a simulation procedure. As one approaches the
bifurcation, the Space/Time costs of accurate simulation diverge, and efficient
simulation is impossible.

- Noise: I guess strictly speaking, the boundary in phase space between two attractors when the system is at a bifurcation point in parameter space will (most likely) take on fractal characteristics. Noise has the effect of smearing out this fractal below a certain length scale (time is implicit in determining this length scale --- it's a complex interaction between the speed of recession of the system from the boundary, and the strength of the noise). There's also the origin of the noise to consider: is it just some artifact of the openness of the system? Or does it stem from the underlying irreducibly random nature of quantum mechanics? Is it necessary to treat these two situations differently? (yes) What is the criteria for deciding between them? What about quantum chaos?)

Other works to think about in the light of this view, and pointing to this view:

- Robert Rosen: "On Life Itself" and "Essays on Life Itself" --- Rosennean
complexity. Rosen's definition of a complex system is one which does not admit a
computable model. This would seem strange for a quantum-information theorist:
they believe that the laws of physics themselves admit a computational model, and
hence any system obeying them must be simulable (i.e. The Church-Turing-Deutsch
principle). However, Rosen's point is that this is not so obvious. On any one
length scale, a suitable slaved system is simulable... but are the underlying
rules of the universe simulable?

- Bertrand Russell: The Analysis of Mind --- He makes a brief comment at one point
that living systems display a profound characteristic --- a very small change in
part of the system produces soon produces a very large change in the gross system,
and does so in a controllable way (i.e. not like chaos). For example, a few
neurons firing in the brain (very little mass or energy transfer) produces an arm
movement (comparitively massive energy release). Much like pushing down on the
handle of a dynamite-trigger causes half of a mountain to collapse. There is a
great amount of energy bound up in the system which can be controlled by a very
small subset of the system. Hence, the system must be sitting very close to some
sort of bifurcation at all times. How does it manage to stay there? What is the
way in which it stabilises itself? Does this have any bearing on mental
disorder? Dynamical diseases i.e. epilepsy? Are "consciousness" and "free will"
examples of the breakdown of simulability? Quatnum chaos and general relativity:
do they enter? Roger Penrose: do you have a case?

- Per Bak: Self Organised Criticality --- this might be one way of maintaining a
system close to a critical point.

2004-10-25T13:14:00.000+10:00

And the second thing I had to say today.

Abstraction, Mathematical Maturity and Biology

I've been reading the book "Essays on Life Itself" by Robert Rosen recently, and in it, he has brilliantly described something I feel myself, but haven't been able to put so eloquently. That is on the idea of abstraction and modern mathematics.

Mathematics is a language --- it is a language that allows us to describe, very efficiently, certain observations about the nature of the universe. But more than that, it is tailored towards abstraction. An example: geometry. Geometry is the description of the underlying logic of space. For example, how points in space relate to one another. There are certain rules which suggest things like "rotating all of space doesn't really cause a fundamental change in the relationship between the objects you are dealing with". Similarly, translating all of space leaves the relationships amongst the objects unchanged. These properties can be expressed with the help of algebraic structures known as groups. For example, any rotation you can perform on a space can be considered an element of a group. Groups which are of interest to geometers are those which describe the operations one can perform on a space without affecting the relationships one is really interested in (i.e. between two lines, or three points, or whatever). This has, in relatively modern times, allowed for a different way of looking at geometry --- these "transformation groups" are not bound to any particular space. For example, Cartesian space does not have a monopoly over the ideas of rotation and translation --- these are abstract objects which can be studied in their own right, and are equally applicable to other spaces with appropriate properties. What's more, the study of these groups can allow one to "pull down" their properties to the level of any space they can be applied to, allowing one to gain "for free" knowledge about that space.

This idea of abstraction is a powerful thing. Of course a Cartesian geometer isn't going to be too happy about it... Cartesian space is his (or her) playground. He's not going to like it if an algebraist comes along and says: this is how it really works, I've studied the underlying group structure of your space, and everything you can say about it, I've already said. I just need to pull it down to your level.

I imagine the geometer would thing the algebraist was an arrogant prick, and would tell him to go and jump off the nearest building.

The unfortunate thing is that while the idea of abstraction is very powerful, few people seem to understand it. This isn't true in mathematics, of course: it is essentially (as I see it) the mainstay of the field --- "mathematical maturity", apparently, comes when one realises that it is the similarities between apparently different objects which are interesting. (For example, that the symmetry group of elliptic curves is somehow related to the taylor expansion of the zeta function, or whatever it is.... that monstrous moonshine thingy! Or that the algebraic structure of knots is somehow related to transfer functions in condensed matter physics, or that ... etc.)

However, in the field of biology, the story is completely different. People who wish to understand principles seem to be looked on as sad cases, or even as dandy dreamers, who can't add anything of worth to the field! It seems to me that there is an active dislike of people who wish to look for similarities between all forms of life, instead of emphasising differences. And that is, in some regards, fair enough: someone who has devoted his or her life to sorting through shark entrails for tapeworm (for instance), doesn't want to be told that what they're finding can be inferred by looking at taperworms which have already been studied --- "what an upstart!" they'd say. This sort of thing has happened so many times: for example, Arthur Winfree, of circadian-rhythm fame, applied the ideas of mathematical topology to the understanding of biological rhythms. He proved (using elementary arguments, as far as topology is concerned) a certain fact about biological clocks. The idea is very simple:

Given that we live in an environment which displays certain periodic properties (i.e. day-night and the cycle of the seasons), it would be advantageous for an organism to be able to anticipate these periodic signals and modify its behaviour appropriately. Thus, biological clocks have evolved: for instance, typically, one's metabolism begins to wind down at night to conserve energy (assuming you're not a possum or something). However, the clock system has developed in such a way that external cues can reset the clock to keep it in sync with the environment: the environment is not strictly periodic, so the clock can't just blindly tick away at a constant rate. Typically, for the circadian cycle (circadian meaning "roughly as long as a day"), this is achieved through a light-sensitive mechanism. For example, daylight triggers the production of certain compounds in the retina and pineal gland, which modify the phase of the underlying clock, and get it in sync. (There are other resetting cues as well, such as temperature variations, but we'll focus on light.)

Anyway --- what Winfree did was abstract from any particular clock in order to say something about clocks in general. In effect, he proposed that a clock can be modelled by one parameter, its phase (in fact, by two parameters: he included amplitude... however, for this argument, we only need phase), which is periodic, and in an idealised clock, maintains a constant rate of change. External influences can then perturb this rate, speeding it up or slowing it down. The size of this effect may in turn depend on the phase of the clock when the influence was applied. For example, if you imagine having an analogue clock with a weight tied to the minute hand (just pretend the clock had no hour or second hand: we're only interested in one of the hands), then for times before 30 minutes, the hand would be dragged down, and the rate of change would be increased, while for times after 30 minutes, the hand would also be pulled down, and the rate of change would decrease (because the hand is trying to move up). Hence, the effect of the influence is a function of the phase of the clock. We can turn these influences into "stimuli" by only applying them for a certain period of time: for instance, suppose we only put the weight onto the clock hand for 1 minute, then we might find that if we applied this "stimulus" at a phase of "10 minutes", then when the stimulus was over, the clock would read "11 minutes and 30 seconds" as opposed to "11 minutes", while if we applied the stimulus at 50 minutes, we might find that when the stimulus was finished, the clock read "50 minutes and 30 seconds" as opposed to "51 minutes": The stimulus acts as a function, mapping each phase of the clock before the stimulus was applied to a corresponding phase after the stimulus has been applied.

Mathematically speaking, we are currently dealing with a toroidal space: we can express our mapping by a curve plotted onto the surface of a doughnut. This is because it maps between two periodic spaces: the initial and final phase of the clock. On our doughnut shape, the initial phase of the clock might be represented by the angle around edge of the doughnut (i.e. think about the numbers of the clock written directly on the doughnut, with the clock's hands sticking through the hole! :) ) and the final phase by the angle around the "tube" of the doughnut.

Winfree noted that there are several qualitatively different types of mappings on a torus, which are characterised by the number of times the line describing the mapping goes "through the hole" in the doughnut: mathematically, this is called the "winding number". If the line goes through the hole exactly once, we have an example of a clock which is still functioning pretty much normally: to see this, imagine applying a stimulus which "does nothing" --- the final phase is equal to the initial phase, and the line describing the function moves around the tube of the torus in exactly the same way as it winds around the hole in the center of the doughnut: hence, it goes through the hole exactly once. Similarly, suppose we only applied the "weight" to the hand of our clock for a very brief moment --- that wouldn't produce much of a change in the behaviour of the clock, so we wouldn't expect the curve on our doughnut to differ much from the case where "no stimulus" was applied. As we increased the amount of time for which the weight was applied, we'd expect the line to get stretched more and more. However, we would also expect it to stay continuous, so while it might get stretched out of shape quite a lot, it should still wind through the hole in the doughnut exactly once.

But what if the weight was applied for so long, that the minute hand ended up at 30 minutes no matter what its initial phase when the weight was first applied? In this case, the line would no longer wind through the hole in the doughnut: we have a qualitatively different effect on the clock.

The thing that Winfree noted was that, if this was to happen, then there must be some special combination of stimulus strength and initial phase where the line describing the effect of the stimulus on the clock "breaks"; becomes discontinuous. To see this, imagine the line winding around the doughnut as a loop of string (i.e. its ends are tied together): if the string goes through the hole once (like when "no stimulus" or a "weak stimulus" is applied), then there is no way to get the string off the doughnut without cutting it --- i.e. without making it discontinuous.

Winfree's insight was that if there was a biological clock which, for different stimulus strengths (perhaps different intensities of light?) showed phase-mapping functions which were of two different types( i.e. for a weak stimulus, threaded through the hole, but for a sufficiently strong one, did not), then there had to be a particular combination of stimulus strength and phase for which that biological clock stopped working; for which its behaviour became undefined (corresponding to the point where the "string was cut").

Mathematically, the argument is extremely simple, but the consequences for biological systems are profound.

The thing that I find sad is that for many years, no one would believe him! When he finally proved his point (in an absolutely beautiful experiment which generated some amazing patterns by measuring the hatching times of fruit flies, of all things! :) ), it started up a huge industry with biologists specialising in one animal or another showing that their system, too, displayed this amazing property! I think there are possibly many situations like this, where people refuse to even listen when someone has something to say, which has been arrived at by some theoretical considerations, simply because, well "How can they know? They haven't been crawling around in shark guts for 25 years".

I can certainly understand why people would feel this way. What I'd like to work out is how this perception can be changed, an how more widespread, fruitful interactions between theory and experiment can be achieved in biology. In particular, in the more high-level, systems biology. I'm sure that in many places, such interactions are occurring, and with gathering momentum. However, I've also read about people who's careers have been destroyed by politics on the part of the "old-guard", who can't understand the value of theoretical, as well as practical research. However, my intention here is not to gripe about this, it's really to try to understand what it is, as an aspiring theoretical biologist, I can do to change the situation!

I think in part, the language used by people such as myself can be damaging to our cause: facts which we regard as self-evident can not be assumed in this context. Also, I think that the reticence we have for getting our hands dirty can be damaging: how can we expect to say something of value about any system if we haven't had any experience with the difficulties of making measurements, or performing experiments on that system? It's pie-in-the-sky time if we refuse to acknowledge those difficulties.

On a slightly unrelated, and more divergent note, I think this situation mirrors something that goes on in the brain itself. Research has indicated that there are two distinct modes of information processing in the brain: "bottom-up" and "top-down". Bottom-up is concerned with details: in the visual system, with taking all the information delivered by the retina, and gradually piecing it together from its smallest components. This seems to me to be analogous to the old school of biological thought: "The devil is in the details". Meanwhile, there is also a flow of information in the opposite direction: from higher levels of the brain down. The brain theorises about the environment it's in. It builds models, makes guesses, enforces its ideas of reality onto the information it receives.

The intriguing thing is that neither of these processes, by themselves, is sufficient for survival. The world provides far too much information to our visual system for it to be able to unambiguously interpret it by looking only at the details it gathers from the retina. Heck, the world is three-dimensional, while our retina is only two-dimensional. That's a lot of ambiguity already. We need to have a skeletal theoretical structure by which to interpret the information coming in, in order to disambiguate it. Similarly, however, many experiments have demonstrated that our model-building approach has its weaknesses: the attentional blink effect, and visual stimuli such as "my wife and my mother in law" by Boring, show that we are capable of completely ignoring information that doesn't fit into our currently dominant world-view. This takes on an even more menacing front when we look at the simplistic world-views which dominate the religious fanatics of the world, and the harm and destruction these can cause.

It seems to me that the most effective, but simultaneously, the most difficult, line to walk in this struggle between high- and low-level is precisely in the middle ground: where theory and experiment inform one another; where they constantly debate. Historically, heterodoxy has often been indicative of an underlying problem in the current dogma, however, it has also, almost always been met with oppressive dismissal. Why is it that we can't learn from our past mistakes and try to take a more balanced view on these issues? If a theory is shown to have a weakness, that does not in any way take away from its value: all theories are bound to be wrong at some level --- their value is not only in the hypotheses they spawn, but in the debate they foster. Suppressing an idea because it does not conform to currently accepted theory is a dangerous thing to do.

Anyway --- that's enough from me for now.

Alex: I'll write up some maths demos sometime soon! :)

BTW: I'd really love to hear some comments on what I've written, positive or negative, from anyone who's interested. If anyone has any other friends who might be interested in reading what I've got on here, feel free to give them the URL.

2004-10-18T21:53:00.000+10:00

I'm not really going to write anything today. Just going to put up a list of topics that I'd like to write an entry or two on in the future. If anyone wants to hear my point of view (or if I don't have my own point of view, then my favourite perspective) on any of them, feel free to leave a comment, and I'll get to that one first!

(1) The brain from a dynamics perspective (a hopefully comprehensible version)
(2) Biological clocks
(3) "Bootstrapping" and abstraction
(4) Language, thought and politics (yes, I do like Orwell)
(5) Mathematics demonstrations for school kids
(6) Semantic biology, path dependence (and hacking)
(7) Current favourite books
(8) Aiki, music and life
(9) Favourite words, phrases and quotes

hmm.. there are others I would put up, but I'm not sure I'd be able to come good if someone actually wanted me to write something about them (i.e. ethics, religion/spirituality), so that'll do for now.

wheee... off to sleep and dream of rain...

2004-10-18T01:10:00.000+10:00

WARNING: This post is unlikely to make any sense. You will probably decide that Duncan is a raving lunatic on the basis of it (if you haven't already). You have been warned. (though that being said, any comments are welcome).

Well --- it's really too late for me to be writing stuff on here now. I should be sleeping.

Unfortunately, I got really excited today about an idea I've had for my phd. I've been reading a lot recently (well... ok --- not just recently. Heck. I'm always reading). In particular, about nonlinear dynamics and its application to the brain. There has been a big movement over the past 8 years or so looking at chaotic dynamics, and self-organised criticality in neural networks. Some really interesting work has been done showing that EEG recordings, time-perception, fMRI recordings and a whole raft of other things show "1/f noise". 1/f noise is essentially the fingerprint of self-organised criticality (which I'll get around to explaining at some point, but not now! In fact, at the moment, I'm probably going to be about as clear as turkish coffee).

Anyway --- I'm thinking that there is some sort of a link between bipolar-disorder and the way in which activity in the brain organises itself. (ok --- so that's a completely obvious statement). In particular, I think that comparisons of EEGs from bipolar and normal subjects will be revealing. There are a number of reasons why I think this, though none of them are really well enough developed to be put into words at the moment.

In particular, right now I'm trying to build up a model (or at least a mud map) of perceptual rivalry based on self-organised criticality. The vague picture I'm getting at the moment is that for a stimulus with multiple interpretations, there are a number of mutually exclusive classes of activity, which sort of "compete" for dominance. (nothing profound there; that's one of the standard models for perceptual rivalry.) The interesting part is that each of these classes of activity, by itself would be attain SOC, but thanks to the inherent instability of the stimulus, they aren't able to reach the stable (if critical state), and are continually knocked down... Kind of like trying to build a building with gravity constantly changing direction. Or something like that. As a result, collapses occur with more regular timing (i.e. not strictly 1/f: we now actually have a characteristic time-scale), due to a sort of generalised renewal/competition process. (If SOC only was involved, we'd expect to see scale-free behaviour). Anyway --- the reason I think this is interesting is that different brain-structures (i.e. in different individuals) would support differently behaved SO critical states. The properties of any particular class of perceptual rivalry would be mirrored by other phenomena in the same brain. This sort of thing has been observed repeatedly: perceptual and other oscillations are coupled over a huge range of time-scales, time-perception differs in a systematic way for "fast" and "slow" switchers, efference copy is much greater in slow switchers (i.e. the brain "remembers" what it has done for longer) etc. etc.

One of the more fascinating aspects of perceptual rivalry in slow switchers is that adjacent rivalrous stimuli tend to become coupled, and switch in sync. This is consistent with some work done by a fellow (can't remember his name) in Canada, who has been modelling mood via SOC (damn it! why'd he have to have the same idea!? :) ), and has found that the *dimensionality* of a system is the key parameter in determining its behaviour. Here, dimensionality is related to the number of lateral connections a neuron has with its neighbours. Very suggestive.

Anyway --- now that I've blathered out those thoughts (trust me, in my head they're a lot more coherent, I just can't quite express them yet...), I think I'll go to bed.

2004-10-14T17:20:00.000+10:00

This is an unfinished poem I started writing *ages* ago, when I arrived at the Brisbane international airport to fly to Norfolk island, only to find out at the check in desk that my passport had expired a week or two ago (Maybe by posting this up here, I'll actually finish it sometime...):

-------------------------------------

It was early, eyes were bleary, and silence ruled the dark.
The moon had pressed her face behind the clouds.
Morning's light was far from showing
four friends' faces there aglowing ---
excitement flushed, though weary as a taxi tried to park.

Bags were shoved and pushed and loaded, the trunk door slammed down hard.
We piled into the car, a gutsy mess.
"To the airport's where you'll take us
where I hope they don't mistake us
for terrorists, shake us down and put us under guard."

The cab careered and cornered, taxi drivers do that well...
screeching down the eerie empty roads.
And while you'll find it unexpected,
Even though *I* had directed,
we arrived on time, and clambered out into the terminal.

Two hours of waiting later, in that garish ghastly hall
A hostess graced our presence with her smile.
Her nasal voice requested
that our passports be inspected,
I handed mine out proudly... but pride comes before a fall....

(Cue Menacing Chord)

While we jumped and joked and jostled, the hostess did her check
opening our tiny grey-blue books
All was going fine
'till she cast her eyes on mine:
Her grin slid from her face, 'cause something weren't correct!

"It seems, sir, that your passport ain't a passport any more
You're holding there a useless little book.
You see passports can expire
with consequences dire
you won't be flying now, no matter how much you implore."

-------------

2004-10-12T20:51:00.000+10:00

Well. It's been a bloody long time since I've written anything in here. I don't really know why. Things have been changing and not changing so quickly that I've felt like there's been nothing to add.

I just thought I'd add to the general feelings around Australia concerning the election. How the hell did Howard get back in? More than get back in, how did he manage to get the balance of power in the SENATE as well?

I know that it's not right to think of people who vote differently to me as being stupid. I also know that it's not true: people who voted for the liberals are not stupid in general. But still, I simply can not understand how someone could. If anyone has any insight into the matter, please fill me in!

Ok --- I'll admit, I do have some understanding. It's pretty easy to see why people might get nervous about a growth in interest rates. (though I still don't understand what it is that makes them rise: I thought the reserve bank set the interest rate? Surely all one could really say was that there is a chance interest rates will rise under a particular set of policies?)

I honestly don't understand how anyone can see Howard as a *strong* leader. How did he get labelled with that honour? The impression I get is that it was due to his treatment of refugee issues, not saying sorry to the stolen generation, and committing Australia to that most glorious of oxymorons, the war on terror. I don't think that pandering to fears of a generally undereducated majority at the expense of general human rights, refusing to acknowledge a great smear on Australia's past, and triumphantly leading the country to an illegal war should qualify someone as a strong leader. I really would like to know how he got that title.

It seems like people think that strength is equivalent to sabre-rattling. I'd have thought that people like Mandela, Ghandi and Jesus were better role-models for strength. And now we have a government who believes that it is justified to launch attacks preemptively, admittedly only as a last option... but then, the war on Iraq was certainly the only possible option, wasn't it?

So far, the only people I've heard from who did vote liberal did so because they felt that "Howard was strong" or that "Interest rates would rise if they didn't". One particularly bright spark, talking on triple J about costs of education for students said (paraphrasing) "So what if hecs fees go up? the Howard government is going to cancel compulsory student union membership, which is instant cash-in-hand, and much more relevant to students than higher hecs fees". What the fuck?!?!? So in a 4 year degree, you pay about (at uq) $1000 in student fees over the entire course of the degree. I'm not sure how much of a strain a 25% increase in hecs puts on someone, but my guess is that it's a helluva lot more than $1000. Of course, what I'd really like to see is compulsory student union fees abolished as well --- or at the very least, have *some* decent union politics.

Anyway... Just wanted to get some of that out. I certainly don't make any claims to being a highly informed voting member of the public, but I think I have at least a modicum of intelligence.

On a more positive note, I had a nice day today. Aiki training was good. I learnt a bit more about electrophysiology. Read another 10 pages of "The Count of Monte Cristo" to Elise... we've been reading our way through that together for the last 2 weeks or so... it's good fun.

Anyway. I'm going home.

2004-07-22T17:57:00.000+10:00

Today; more on this idea of changing to RAships instead of continuing with a phd....

I had a chat to Ben over lunch; his suggestion was somewhat different --- to continue with the phd, but approach lots of different people, asking whether they have some small projects that require some sort of maths or physics; perhaps John Maddick, or Joe Woolf (I believe is his name; the guy in Sydney working on physics of sound...). Ben said that this is what he would have done if he'd known about it at the beginning of his phd.

It's strange; while I was talking to Ben, the whole thing made sense, seemed possible... but when I got back to my room, things felt different.

What's the problem??

I think I'm sort of locking myself off in a little square at the moment... I feel nervous about approaching people, because I feel like I'd need to bring them some sort of idea... that's not true though. I feel a little weird, because the whole thing seems like such a game --- maybe that's the best way to think of it? What are the reasons I don't feel like I can follow Ben's suggestion?

(1) Maybe I don't really believe that I'm "good" enough to have something to offer --- That's a little strange... it's sort of on the right track: I think I can offer little insights, but I feel less than confident that I could actually complete a project...
(2) Maybe it seems like it would be too much fun...?

I'm sort of struggling with these inbuilt ideas of what a phd is, and of what "life" is, neither of which are at all correct, but both of which have power over me.

I guess the thing to do is to ask.

So... there's
John Maddick: His stuff on genetics and "junk DNA" is fascinating
Hugh Possingham: I was really interested in the decision theory aspects of his work, and also in the work Nadiah was doing
Geoff Dromey: He's already offered RAship work using his genetic design idea
The dude in France with "The Continuator" --- that'd be a cool thing to work on....
Guy: Continuing on with multistable perception
Gerard: He'd have projects coming out of his ears....
Michael Nielsen: Same thing....
Conrad and other folk in physiology: What could be done here with modelling?
Perry Bartlett and the other QBI folk: Like what Kirsten was working on
Pankaj

What I don't really understand is how to tie all this into a phd.... It'd all be fascinating, but how could it fit together? Ben was of the opinion that it didn't matter .... maybe I could chat to Michael Neilsen about that....

2004-07-21T08:57:00.000+10:00

Right --- after two fantastic weeks (attending a workshop and acting as a team guide at the international biology olympiad) which I'll post about sometime later, I'm beginning to think that maybe I shouldn't be doing a phd right now....
What I'm thinking of doing instead is working short term (say 3 months at a time?) stints as a research assistant in as many different areas as I can.... then I could choose to just go travelling for a while if I wanted.... or follow up on different areas of interest....

Is this really a good idea? I don't know..... it turns out that I can still apply for an APA in the future if I drop it within 6 months of starting, so that's not really a problem (I hope... ). I guess in some ways it'd be a bit unfortunate if I opted out of my phd now - I've only just handed in my proposal, and now, theoretically, I can get on with the fun part --- i.e. actually doing some research. Except that at the moment I just don't have any motivation to do so. There are so many other more interesting things to do.

I guess one thing to think about is whether when I start doing an RAship, will I just have the same difficulties I'm having now? It's all well and good thinking "I'm going to do something different", but once I've started, it probably won't stay "something different" for long. Perhaps what I really need to do is stick with my phd, and really get into it???

One thing I'm not going to do is rush in to this; I seem to do that too often, and almost invariably regret it (there are one or two notable exceptions...)

What do I have to do to really follow up on this idea and think it through?
I guess talking to as many people as I can is one thing.... If anyone who actually reads this has any comments, I'm all... eyes, I guess.... The people who come to mind are:
- Jack, Hugh Possingham, Guy, Uli, Olivia, Danielle, Catherine, Luke, Michael, Donald, the folks, Lachie, Elise, Pankaj, Halina et al, Brett, Allan, Ben, Don, Geoff ...lots of people...
- Find out about the APA; how difficult is it to get a second time? What other options are there?
- Where could I do this work? Which areas would I like to try out?

In any case, I'm not going to act (other than to find some information) until Jack gets back and I have a chance to talk to him. So in the meantime, I will try to really work on my phd, and get some research done. Ok. So the first things to do there are to understand the stimuli Guy has programmed, write my own, design and implement the experiment and get in some test subjects.

Cool. I'm going to get on with that.

Any comments?

2004-06-27T00:49:00.000+10:00

A strange, but distantly familiar feeling has been creeping up on me in the last couple of days... I think it's called "enjoyment", and I think that except for afew isolated incidents, it's been somewhat absent from my life over the last while...

I think it's return has coincided with me being irresponsible. While I should be writing a stupid research proposal, I have instead spent a goodly number of hours in the following manner:

1) Downloading heaps of python source code, packages, examples: Yes, for about the 25th
time in my life, I'm going to learn to program again!
2) reading a big textbook on artificial intelligence
3) playing classical music on the piano, and trying to memorise it, not just sight-read (I'm learning 'Rhapsody in Blue' now: it's fun :) wheeeeeee!!!)
4) reading pulpy sciencefiction/fantasy books
5) cleaning the house

And it's been fun. The next revolutionary thing I'm going to try is organising a barbeque, and ringing my friends on a regular basis. How the hell did I ever let work get so much in the way of life like that???

2004-06-24T19:01:00.000+10:00

I haven't written in here for a while, and I won't write much now, but here's an interesting scenario courtesy of N. Hanson:

Johannes Kepler and Tycho Brahe are standing on an early morning hillside awaiting the dawn. When that moment finally comes, they both turn toward the east, and, looking in the same direction, they see..... what?

Anyway... I'm going home now.

2004-06-02T09:55:00.000+10:00

Garr. Another great day begins, as great days often do, with a dawn naginata class. (I think I now have more posts about naginata than anything else...) I actually got around to doing a bit of practice for it this week, so I was actually able to do the techniques! Yay!
Today, that involved going through the naginata kata (a series of set movements which sort of "showcase" the general principles behind using the weapon) first in a step-by-step sort of way, and then "under movement".

Step-by-step is fun (especially some of the later "ground clearing" techniques), but under movement is so incredibly cool I thought I'd freeze. Basically, you pair off with one person playing the part of an attacker, and the other a defender, and then move around each other, the attacker (we call him the "Nage" in Aiki) looking for a moment when the defender's (the "Uke's") focus breaks to launch an attack.

Uke, meanwhile, attempts to lure Nage into an ill-timed assault: the whole thing becomes a big psychological game....

Fantastique.

And now I've arrived back at uni and after a relatively uneventful walk in from the car, a stereotypically "nice" cup of tea, my brain is prepared to get on with writing my research proposal. Right, brain?

2004-05-25T17:08:00.000+10:00

It's not obvious to me what is meant by "perception". Is it as simple as just "building an internal representation of the external world"? I don't know that I believe that. By perception, do I only mean "that which is consciously perceived"? (Ooooh... luverly and circular...) i.e. including the internal world; thoughts; emotions? What on Earth is perception?

Sometimes, when I stare at something, I can have the sudden recognitions that I haven't consciously taken it in at all. Like driving a car and finding you've gone the last 10 km without any memory of the outside world. (To take a common example...) But when you try to catch yourself out at it, it is, of course, impossible; it's only something you can look back on and remember: "I was staring at something, but I have no recollection of actually seeing it." What is your conscious experience made up of during those times? are you even conscious? Would you call that experience an experience of perception? or is perception something that can only come from outside?

I guess that's the point of the "ecological approach" to perception or the... what was it?.... perception-from-action idea --- you go to make an action, and what you perceive and experience is directly linked to that action. The parts of it that aren't consciously motivated, and the sensations which may be important for those parts just don't reach consciousness. So what is perception??

anyway... time to go.

2004-05-17T22:32:00.000+10:00

Just a quick little glob from me today.

I've decided to start a music listening group. It just hit me today that I've effectively written music out of my life at the moment, and I think its lack is beginning to take its toll....

So, I figure it'd be fun to advertise/organise a group of people to get together every couple of weeks, sit around a table with nibblies and a sound system, and have each person choose and research a bit about a piece of music each week. Then we could each keep a CD with mp3s of the pieces we've listened to and the notes written up by the person who made the selection.

I'm not sure yet whether I think it would be better to focus on just one style or musical period at a time, or to just have a big mixture. Or maybe we could try to have a big variety of genres represented each week.

I know that I want to listen to a lot more Jazz, and a lot more Baroque/early classical music at the moment, and really get to understand what I'm listening to. Right down to chord changes and voicings (one day...)

Anyway...

It's late now, so I'm heading bedward. Yay

2004-05-07T18:31:00.000+10:00

Ooops.... one more thing before I go....

My office-cohabitor has recently been out to Lamington National Park, and was quite bemused by strangler figs; in particular, how the roots sent down from the sapling (if that's the correct term for a strangler) are able to fuse together when they contact each other. Isn't the outermost layer dead? How do the roots recognise one another?

A bit of internet searching revealed that the process was called "anastomosis", and that it also occurred in the circulatory system of animals or something, and also that strangling vines are often coated with some sort of adhesive --- maybe that allows the vines to recognise one another?

One other interesting factoid that came out of the internet search is that ancient people living in South America used to make living bridges across rivers by tying together several roots from figs on opposite sides of the river; these would eventually fuse, and make a bridge! I don't know whether I believe them at the moment... I would have expected the roots to need to be of the same genetic stock??! Mind you --- people can make babies....

It'd be cool to take some sections from near the fusion point of a strangler fig. I wonder what the internal structure of the wood would be like?

(This rambling Duncan will now go home.)

2004-05-07T17:43:00.000+10:00

I saw a really interesting talk today, on "Parondo's Paradox". It concerns a bizarre situation in game theory, where by playing two losing games in alternation, the resulting "combination" game is actually a winning one!!

When I say "losing" or "winning" games here, I'm talking about gambling games (for instance, calling heads or tails on a coin toss) which are weighted so that in the long run, you either lose more than win, or vise versa (i.e. the coin is weighted towards tails, and you're only allowed to place your money on heads).

In fact, in the simple version of Parrondo's paradox demonstrated in the talk, one of the two losing games was simply a weighted coin toss: the probability of winning was 1/2-(a little bit), and the complementary probability of losing was 1/2+(a little bit). The other game was a little more complicated, and allowed the creation of something known (I think) as a "stochastic ratchet"... it's a little difficult to explain how this works without the benefit of pictures (I'm too cheap to pay for web hosting...)... but here goes...

These ratchet things rely on an underlying asymmetry in one of the two games: the way you play the game is dependent on your current state (in the case of gambling, on the amount of money you have in your pocket... ok, so that's not a very likely thing to have happen.... though I guess in the financial world, that's the point of lawyers and accountants...). In the particular example shown during the seminar, if the number of dollars you have does not divide evenly by 3, then you are given a coin weighted against you (just like the coin for game number one, but possibly with slightly different probabilities), and if your current currency collection does divide by three, you are actually given a coin weighted *for* you.

If the probabilities are chosen carefully for the second game's two coins, it can be shown (using Markov chains, if anyone's interested...) the second game can also be made to be a losing game.

The cool thing is that if you now happily wander between the two shifty gentlemen who would be tending to these games, betting on one then the other, you actually end up making money.

Ok.

I'm going to stop now, because I'm tired, and I want to go home. The details for how this works are also eluding me at the present time. But before I bog off, the reason I think this is particularly interesting from where I'm sitting is that my phd project seems to be related to this paradox in some way:

Two hemispheres, two cognitive styles = two different strategies.

In most cases, neither strategy will be a winning one: the left, goal oriented, "I rock the world" strategy may work when you're in a safe environment, but as soon as there are things a little tougher and nastier than you, life-expectancy drops rather rapidly. Big scary lions don't tend to care when you tell them how cool you are. (I think that'd be a fair definition of a losing strategy....)

While the other "right hemisphere" strategy of waiting and watching, noting every discrepancy, and jumping at every slight change in the environment is also unlikely to be all that effective. You can't stay in your cave all day... well, I guess you could, but you'd eventually starve. (Or maybe the lion would find you... I doubt he'd care much if you jumped when you saw him...).

However, by mixing the two behaviours up, perhaps a more sensible, winning strategy can be developed?

The researchers studying Parrondo's paradox have also studied different methods of switching between the two games: just alternating and playing game 1, then 2 etc., switching randomly (i.e. playing 1 several times, then deciding to go to 2 for a while, all at the whim of a coin toss), or making the transitions between the games on the basis of a *chaotic* sequence. I'm not sure entirely what that means, but the fellow giving the seminar mentioned that when chaos is used as the driving force, one seems to be able to do the best of all the methods of switching.

Unfortunately, studies of binocular rivalry (my area) suggest that it is not chaotic (apparently -- I haven't actually read the papers yet: that's this weekend's job). But who knows? I've seen some other research suggesting that it contains "scaling" properties like those seen in avalanches and a whole cast of other phenomena. Perhaps also has some sort of evolved "Parrondo optimising" significance?

Oh well.

It all seems pretty cool anyway!

Tschuss!

2004-05-04T21:08:00.000+10:00

I was thinking about dying in the car on the way home today. Not the suicidal I hate life kind of dying, but just dying in general.

It seems strange to me that things actually die. By themselves. Without any external factors (like bricks or anything...). Why should things die?

I remember reading somewhere that dying is kind of built into the system. Something triggers cells to just sort of wear out. (You'll note, reading this, that I'm talking about an area of science that I know pretty much nothing about. Oh well. I'll just muddle along. If anyone reads this who actually *knows* something about the subject has something to say, tell me!)

Anyway.... it seems to me that there are two reasons why organisms would die: a reduction in cell regeneration with time, or an inbuilt "your turn now" trigger.

So why would the first of these things happen? Doesn't each cell in an organism have a complete copy of the DNA? if that's the case, why can't the body just constantly regenerate? Maybe there's more information needed than is just stored in the DNA code; maybe the actual 3d structure of the DNA is important too... I remember hearing somewhere that while the list and order of the base pairs in a cell's DNA might be identical to another cell's, the coils and folds of the molecule can be different. Would that result in ultimate failure of the body?

Maybe death by lack of regeneration occurs for another reason. I guess that having a flawless copy of DNA doesn't necessarily mean that the organism's self-regulating system is able to find exactly what needs fixing. How on earth does it know what to fix in other situations?? what would separate the aging process from those other situations??

Taking an evolutionary point of view, I guess the question of "natural death" has never really come up before (at least for humans).... life was always such a dangerous occupation in the past, we've never really had a life expectancy long enough to worry about dying from natural causes. So maybe whatever the slow degeneration is, it just hasn't been relevant for the forces that have shaped our development.

And what about the idea that there's a death trigger built into our bodies? That seems really weird. What would be the evolutionary advantage of such a thing? I guess it would speed up the process of evolution in benign environments... is that necessarily a good thing? no, that makes no sense. Isn't evolution a blind sort of process? It's irrelevent whether something would be good for a species' long term survival... what matters is the differential advantage it gives to an individual, right?

(7/5: Ok... that was bullshit.... "speeds up evolution in benign environments"? What was I smoking?! :) )

Hmm...

I gotta go for dinner now, but one final thought was.... maybe something which is still under evolutionary selection in humans (at least in developed countries) is the age at which one can still successfully breed?? The age at which we tend to have children would have increased dramatically over the last couple of thousand years, I'd have thought... Are more people tending to have children at much-advanced ages??

Anyway..
Gotta go.

I know that this stuff hasn't really been well thought out, but if anyone has any ideas, email me! I'm keen to try to care less about how stupid what I say seems to the outside world, and talking about something I know nothing about seems to be an ideal way to start!

------------------------

7/5: Thanks for the email!

Some points pointed out to me by someone who knows a lot more about this than I do!:

One assumption you made is wrong
"A flawless copy of DNA"
As a cell divides, mistakes occur in DNA replication. Heaps of them. Most of them get fixed, but not all. I suppose it's a good idea for a cell line to stop dividing after a certain number of iterations, otherwise it would all turn cancerous or something. Oh yeah. That's precisely what happens when it starts dividing furiously. Right.

Hmm --- yup. I definitely should have thought of that (especially considering I've spent quite a bit of time over the last few years thinking about how to save information from corruption and decay in quantum computation....)! I hadn't realised that that was where cancer actually came from!

What I was thinking of, I think, was the amount of redundancy in the body: so many cells with so many copies of the DNA... but, of course, any new repair cells have to come from somewhere, and there are always going to be transcription errors...

So anyway, to stop this happening, or so my understanding goes, each DNA molecule has a lifespan. There are telomeres at the ends of chromosomes. These get slowly eaten end-first. When they're all eaten up, the cell can't divide anymore, and the useful DNA gets eaten or something. And something. Hmm. never mind that. Look up telomeres and tell me what you find. Try proper journals, not pop-sci things. They make a mess of it all.

Yah --- I haven't looked up telomeres, but funnily enough, straight after writing the first post, I noticed about 6 nature articles, a nature review issue, a slashdot article and a whole heap more about aging, dying and telomeres. Makes sense having an inbuilt time-bomb in cells I guess. I wonder whether the "strength" of the telomeres is different in different parts of the body, depending on the number of times those cells need to divide or something.

Anyway, you're right. Once you get beyond a certain age, all your eggs or sperm are mutant, because of errors in DNA replication as they get made.
So there's no point in having babies anymore because they'll likely be mutants.
So there are these old folk hanging around that can't have kids and are competing with the young folk for food.
So they die, so that the young folk with the pristine DNA can pass it on better.

Another article I noticed today was exactly on that topic. Apparently that was suggested by some guy way back just after Darwin suggested his theory. However, people then noticed that animals tended to die before they'd be competing with their offspring anyway, and the fellow died muttering "death is an evolutionary perversion" or something along those lines.

Of course, with all good theories, it seems to be making a comeback: a prize was awarded recently to a mathematician-turned-biologist who is working on aging, and is finding the original "no competition" idea more and more tempting.

Ok. That was fun.

Anything else?

2004-04-22T21:14:00.000+10:00

After a few days of not enough sleep and the accompanying depression, I'm back to feeling good again today. I never understand why I let that happen.

Anyway --- I'm feeling inspired. Jack got back from the US yesterday, and this afternoon gave a talk I'd love to see again. He is such a fantastic speaker. Sailing around from fish on Prozac, anti-depressive US agression-in-the-water and cauliflower cortices to diffusive identity disorder, Tibetan monks and oscillating blue meditators in Spain. My god what a trip.

And this morning, I finally got around to organising an ECG of Tamyka while she was running. Hopefully got some decent results; she had two short periods of flow, and managed to get split records of both of them. Who knows, maybe my phud will really take off now?

On top of that, I ran into Clair (don't remember the last name), a girl I tutored two (three?) years ago. She made me jealous; she's just spent the last 3 months rock-climbing in Thailand. That's cool.

Ok. There's a note in my room from Elise, and dinner to eat, and sleeping to do.

Have fun world.

2004-04-08T18:03:00.000+10:00

I really like crows.

I've found that most people are very divided when I mention that: I've never found anyone whose opinion on crows is half-hearted. My English teacher considered a rifle to be the perfect answer to the question posed by a crow.

My brain fizzled today for a while, probably after I tried to read a book full of depressing examples of the symptoms of schizophrenia in far too short a period of time. Luckily, I was interrupted halfway through, but the resulting shock to my brain was still enough to leave me in a daze for the next 3 hours, until I was saved by a crow. It was drinking from the fountain up outside the SSH library, cawing and chuckling to itself, and being followed conspicuously by a pair of ibii.

After that, everything went very smoothely. I played frisbee for most of the afternoon, and ran into an old physics/maths aquaintance who's resently got himself a postdoc in the maths department at the university of Bristol. Anyway --- we spent a pleasant hour or so discussing spectral graph theory, and how graphs can actually represent quantum systems in a very natural way. He has an idea to try to understand the underlying Hilbert space representation of Quantum field theories by using simple, run of the mill, 2nd year math graphs. Well --- ultimately taken to some sort of continuum limit. Still, I think it sounds like a fascinating idea. I'd been thinking along similar lines, but with much less sophistication when I was looking at quantum chaos last year.

Ahh. I think I'm going to miss theoretical physics during this phd. I don't think there'll ever be too much call for representations of quantum field theories in neuroscience.

2004-04-07T17:49:00.000+10:00

Beauty.

I just read your post, and I found what you wrote very interesting. In my mind, beauty is something you can search for, perhaps, but when you do, what you find --- the particular experience of beauty --- is never exactly what you set out for. It's something that sneaks up on you. (or on me, since I'm talking about my thoughts...) It's a momentary thing; perhaps with enough zen mastery, or when one forgets to think, a moment can stretch out; but the experience --- the instant when you catch your breath, or feel yourself begin to expand --- for me only seems to last until I acknowledge it. Then it becomes an academic appreciation... I'm not sure that's a problem? For me perhaps, with the anaesthetised, scientific language I typically describe my thoughts in, an experience loses more than for someone who's intuition for the emotional, descriptive side of language is stronger.

I guess that's why I usually refrain from saying anything to myself about what I'm seeing or feeling (though that depends on mood, of course!) --- unless I'm with someone else: then I want them to share in what I'm seeing. Maybe that's a selfish attitude to take?

It's interesting. For me, this brings back some memories of the discussion in Pirsig's "Zen and the Art of Motorcycle Maintenance" --- the difference between romantic and classical beauty --- the joy of direct experience, and then the joy of finding a connection, or seeing behind something. The latter seems related to this analysis of experience --- I reckon it'd be pretty hard to find underlying connections without some work at conceptualising things --- but perhaps the sensation of beauty one gets when a deep, or unexpected connection is seen is fundamentally the same as the first-sense experience? A momentary glimpse of "rightness".

Hmm..

Right. That'll have to do for now. Gotta go and meet me mum!

2004-04-06T09:23:00.000+10:00

Well. I just found I'd I've made a bit of a mistake. Jack sent me an email the other day regarding testing a little fellow with our machine, and putting me in contact with someone who turns out to be his mother. Me, being my usual tactless self, without thinking of the fact that this was possibly his mum, sent back an email asking her if she "knew anything more about (insert name of kid here) than was in the email?". I guess it's not that big a thing, but if you're worried your child is bipolar, and you happen to be an eminent researcher yourself (another thing I wasn't aware of...), the last thing you probably want is some whippersnapper of a phd student asking if you want to meet up for coffee, and whether you know anything about your own son.

Gar. I feel like an idiot. It's much easier to deal with one-dimensional projective measurements. They don't have feelings.

On the upper side, I'm currently out at Prince Charles (or as I keep saying to increasingly confused people, "Charles Sturt") hospital, and about to learn how to use a holter ECG. That will make me happier. And I think now I'll spend some time finding out exactly how they work. I guess that's one of the plusses of being in a hospital library, and studying things medical.

I wish they played different music though.

2004-04-04T16:56:00.000+10:00

Hmmmm harrung hmph chup chup schmup yup. That'll do for now. (sounds from someone just awaking from the semi-catatonic state induced by spending far too long on the internet....)

2004-03-31T15:47:00.000+10:00

Today was pretty darn good, and promises to become better: Elise, Morena, Myles, Murray (lots of Ms) and Naomi are coming over for dinner. That will be good. It's going to be a mexican smorgasboard of delectable delights. Followed, (I'm assuming, and given the crowd), by dancing, singing, guitar playing, drum bashing and playing 4-player Gauntlet on the XBox.

I think it will be fun. Yes.

I also had Aiki this morning --- more Naginata. Getting up at 5:30, changing into a sweaty gi and waving around a heavy wooden implement has never been more satisfying. This week, we were practising (excusing my Japanese spelling...) Happo Giri, or "eight-directional form", with 2 opponents. It's great! You get to whirl around in circles with a big spiky stick, while scaring away other people with big spiky sticks.

While that probably doesn't make it sound too entertaining, you really should trust me. We were focusing on timing in particular this morning, and when you get it, you just feel awesome.

Yeah. Awesome.

2004-03-29T16:50:00.000+10:00

Don't really feel like writing right now, but since the reason I started doing this is to learn to write when I don't feel like it, I will bravely soldier on in the face of adversity, and achieve my goal of posting a bit more rubbish on the internet. I think I'm off to a good start.

Gar. I think I'll stop now. I want to go and play a guitar.

Tschuss peoples.

2004-03-26T17:13:00.000+10:00

I love the ads I get at the top of my blog.... currently they're suggesting that I'm a fat, tired phd student who doesn't know how to dissertate... (I obviously have no trouble making up words...)

How rude.

Oh well.... I imagine at some point I'll try to convince whatever webbot has actually managed to find its way here that I'm a flower-eating lesbian hyperchondriac, with a taste for fine cheese and who lives for her pet elephant, Thelma.

That would make for strange advertising. Unfortunately, at the moment, all I really want to do is sleep. and eat.

I'll leave off the learning to dissertate for a while.

2004-03-25T18:16:00.000+10:00

Goodbye 25th of March 2004.

That was a pretty good day on the whole. I woke up at about 6:00, dreaming about crashing starship enterprises, a strange planet full of talking trees, and the screams of children (which moved around in packs, and sometimes sounded like nightmares, and sometimes just sounded excited)... a bit on the trippy side. However, I have decided to write my dreams down at the suggestion of my friend Ben, who swears that it's a great way to start lucid dreaming which sounds like a whole lotta fun.

The rest of my day was slightly less exciting. Jack tested a bipolar student, while I watched on, making the occasional not-so-well thought out comment. I got a little depressed at the amount of stuff I need to know, but talked it through with Jack, and now feel a whole lot better.

Not much else to tell really, except that I think I'll go and see "Once apon a time in Mexico" sometime soon. It may be a completely crap movie, but still, the idea of a posse of flamenco-guitar playing assassins wandering about sounds like just what I need. No more crashing starship enterprises for me, thank you my screwed-up subconscious.... (hell, I don't even watch star trek... Grumble grumble...)

2004-03-24T16:15:00.000+10:00

Well --- it has just hit home that I'm doing a phd, and as a result, may actually have to work for a change.

I have to have a thesis proposal + literature review done in a month or so, and I'm really not sure how to go about it. Ugh. I'm also beginning to get the picture of what is meant by "independent research" --- it kind of feels like my supervisor expects me to know how to do research, and what experiments to do, before I've realised we're actually considering doing experiments in the near future.

And phding is such a lonely profession. Maybe that's just my fault though. I seem to spend most of my day sitting in a dingy office wondering how best to start assimilating a massive mound of papers, while trying to design experiments.

Oh well.

All that aside, I think things will ultimately get alot better --- once I work out how best to work, and get myself properly organised. Ok. I will now end this entry, before I get depressed. I think perhaps a sleep-lacking weekend is at the bottom of this. Time to get back to work.

2004-03-19T17:28:00.000+10:00

I'm tired. This week has not been a good one for sleep. The Equinox celebration for Aiki last night was a little too much fun, so I didn't end up getting home until after 12:30, and after quite a bit of sake and homebrew... Still, those Vietnamese salad roll things worked out brilliantly, and as a side effect, I've found a great little gourmet market which is actually NEAR my house. So that's good. I imagine it will save me quite a bit of time in the future.

Anyway --- my tiredness is probably more a convergence of the fact that I got up at about 6:00 this morning to jog/walk up Mt. Cootha with my great uncle, and the seminar I just went to at the IMB on cloning mice from olefactory neurons. It was pretty damn interesting, but my lack of genetics knowledge (in particular, of terminology) meant that I missed a lot of it. Still, I'll probably try to read the associated paper.

The rest of the day was pretty good --- Gran, Great Uncle Martyn and I did 2 cryptic crosswords at breakfast, which was fun. I spent my time in at uni mostly fiddling with the data from yesterday's epic data-entering effort. Looking through the results and the survey sheets again certainly drove home to me how important good experimental design is. In this case, quite a bit of data was, at least in my opinion, compromised because the forms to be filled in were a little bit ambiguous --- it just shows how easy it is to make a mistake like that!!!

Garr. Anyway --- I'm tired. So I'm going home now. mmmm. Sleep....

2004-03-18T13:40:00.000+10:00

Arrrrgh! My back hurts!

It's amazing how typing in the data from 111 surveys can eat time and vertebrae. Ugh.

Still, they're all in now, so that's good. Now I just have to hope that the way I've represented the data allows it to be analysed!

Um... anyway --- other than data-entering (and watching the survey being done), today has not involved all that much. I did meet the other Olivia --- or Liv, to minimise confusion. She's currently doing her third year of science (after having already done a degree in fine arts), and is doing a project with Jack on auditory rivalry. Sounds interesting :) Well --- she will be doing it, after having sat the GAMSAT. Silly medical exam things.

Josh was around before too --- he's one of the resident MDPHD students.... the MDPHD is a devilish scheme under which you do both a phd and a medical degree "simultaneously" (it's more 1year of phud, then 1 year of mud etc.) Anyway --- Josh may end up being my partner in crime, if I decide to work on rat embryos to try to find the switch.... (I have a whole heap of ideas for phd projects... one day I'll choose one!)

Ok. And now I'm about to head off to my gran's to cook some snacks and things for this evening's Aiki "solstice celebration" --- I'm not too up on the history or tradition, but apparently, the autumn solstice is meant to be a time when we remember all the ancient fellas who have passed on their knowledge, and led to the school being what it is today. Thus, I am to bring suitable food to this evening's special training class, to be devoured afterwards at Sensei's house. joy. I'm going to make Vietnamese rice-paper salad wraps, I think.

Of course, first of all I have to find out how to make them, and what I need for the sauce etc.

I foresee a long afternoon of rolling salad up into little white sausages....

cheerio!

2004-03-17T18:54:00.000+10:00

Well --- today, I got up at 5:30 am, which I do suprisingly regularly at the moment; on Wednesdays, I have Naginata class at 6:30 for Aiki Tai Jutsu. Had a great time whirling a big stick with a curved "blade" on the end around for an hour, and then headed off into the joys of Brisbane rush hour traffic.

Today was pretty interesting from a research perspective; in the morning, Jack and I (well, Jack really - I "observed") tested a fellow who has an interesting condition in which his olfactory cells haven't moved up high enough into his hypothalamus (Ok --- I'm probably butchering this description, as I wasn't entirely clear on what it all meant...). Apparently, this means that impulses from one side of his brain, associated with movement of one arm are "echoed" and sent down his other arm as well, so any fine movements he makes with his right hand are mimicked by his left! It's apparently made learning to touch type impossible!

Anyway --- the condition is apparently very rare, and Jack was wondering whether we might see some interesting binocular rivalry effects.

The rest of the day saw me reading --- for the first half, a book by a fellow called Winfree, on Biological Oscillators: "The Geometry of Biological Oscillators". It seems very interesting. I've not really got into the details of the biological systems yet, but so far he's used topological arguments to predict what one would see by stimulating biological clocks (such as circadian oscillations) at different "phases", with different stimulus strenghts. I can't really do the subject justice, as my understanding is still very rudimentary, but it does seem very interesting.

The second book I've been browsing is by Richard Ivry and Lynn Robertson; "The Two Sides of Perception", and discusses a theory of hemispheric asymmetry, positing that the difference in cognitive styles can be traced back to differing filters being applied to sensory input sent to the different hemispheres. They suggest that while all "frequencies" (spatial for vision, temporal for aural inputs) are present in both halves, higher level attentional processes divvy out tasks involving high relative frequencies to the left hemisphere and low relative frequencies to the right hemisphere. The "relative" comes in because these attentional processes first make an estimate of the frequency range involved, and then perform the delegation. It seems like an interesting theory in any case.... definitely a book I'll read more closely.

Well... that's it for now. 7:00 pm. Time to go home!

2004-03-16T17:09:00.000+10:00

Hmm... Well --- I got around to this a bit too late today.... I spent the last hour or so wandering from library to library, somehow collecting a massive pile of books as I went. (This tends to happen on these library perambulations.)

Anyway --- Today, I had a good ol' chat to my supervisor about a plethora of vaguely related things. One thing to come out of that is that I'll be involved in my first ever experiment in biology: I'll be handing out forms to a class of undergrad physiology students at 9:00 Thursday morning!

There are other things to tell, but they'll have to wait.

2004-03-15T16:26:00.002+10:00

Back again --- I've just spent a weekend relaxing in a little place called "Buxton", on the Isis river in Queensland (Just near Childers, for the locals), with my folks, my girlfriend and my lunatic of a great-uncle from England. Damn fun; the water was warm, the weather at about the right temperature, and without the life-sucking plague that is humidity (which has been driving me *crazy* for the last few weeks...) and a light breeze suggested that sailboarding would be on the agenda. I was pretty proud of my performance, considering I only get the thing out about once a year. I think I'll have to head out on the water a bit more often.

Either way, now I can jibe, which is a lot more fun than tacking. Woot.

And now I'm back at uni. I made a bit of a half-hearted effort at reading some papers today; some stuff on making single unit recordings from neurons in the extrastriate visual cortex of monkeys, a bit more on "plaid" rivalry and a really interesting bit of work on multistable images....

Which reminds me, I probably should say something about my project!! Well --- it's a little hard to be definite at the moment, since I really don't know... (I've heard this is a common position to be in at the beginning of a phd!), but the overarching theme concerns "neural switching mechanisms":

My supervisor has a theory that many organisms have a neural "switch" which is buried deep in the "hindbrain", and activates and depresses the activity in each of the two hemispheres of the brain alternately. Heaps of research (most famously, on "split brain" patients) suggests that the two halves of the brain, the hemispheres, play very different cognitive roles... it's an idea that's ensnared the popular imagination, as the number of self-help books screaming at us to "release the power of the right brain" attest. Our left hemisphere (or "left-brain") is said to be more analytical and ego-centric, while our "creative" right hemisphere is the home of the intuitive, creative, holistic "you". Less self-helpily, the hemispheres are described as being more "aggressive, goal- and process- oriented" (the left hemisphere), or "cautious, detail- and world- oriented" (the right hemisphere). This is all cool, and some beautiful and inspiring research has been done to show just how cool it is! (I'll go into some of that later).

The problem is that the differing cognitive styles are in a lot of ways incompatible (later on, I'll use the word "complementary") --- one would probably find it downright confusing to be both analytical, and intuitive simultaneously, for example --- but both are useful.

To see this from an evolutionary perspective, imagine one of your paleolithic relatives, let's call him Ugh, who spends his days wandering around the pre-historic plains of Africa. To survive, not only would Ugh have to contend with the rather Ugh-unfriendly wildlife, but he'd also be faced with the task of being succesfully unfriendly to other forms of wildlife, in order to eat. This places him in a difficult position: he can't just wave his spear at everything moving around the place (a "left-brained" response), or freeze everytime something moves (a "right-brained" response). However, both responses are necessary for survival.

One way around this problem is to "switch" between the two cognitive styles --- the hypothesis my supervisor's group has been following up for the past few years.

Whew....

That was more involved than I meant it to be. It's just gone 5:00, so that'll have to do for the moment. Right. 'till later.

2004-03-12T18:10:00.000+10:00

So I now have a blog. A sorry blog at the moment, but a blog nonetheless.

And why have I started it?

There are a few reasons, I guess; the first is just to improve my writing --- at the moment, writing scares the heck out of me, and that's not a good way to be when you're wanting to become a researcher! The second is that I'd like to have some way of recording how I feel and what I do --- you see, I've just jumped in at the deep end of a rather large pool, without having tested the water: After an undergraduate degree in theoretical physics, I've begun a phd in neuroscience. (No, I've never done any biology before in my life...)

So, everything's very exciting, I have heaps of energy, I'm enthusiastic and interested, but I'm sure there are going to be difficulties. I guess that ideally, I'd like this blog to be both a memory for me, and maybe a guide or something for other people wanting to get into research!!

At this end of the process, I sure hope it'll be a positive-sounding guide!

So that's the main reason I'm doing this. Oh --- and of course, I'd like to have the occasional political or philosophical rant, post up a few photos of places and people, and generally just chill out.

Well --- that's enough to begin with.

Cheerio then!

2004-03-09T12:53:00.000+10:00

Well --- here's my first ever post. It won't be long, because JP's talk is on in 5 minutes, but it's here!

Soon I'll get into it more! 'till then, adios!