the "to don't" list

As part of a research project I’m currently involved in, we are developing a simulation of a particular theory of genetic regulation.  We are building the simulation in an “agile-ish” manner, in that we are producing a minimal functionality “version 0”, and are then going to add further biological-relevant functionality incrementally once v0 is released.

Being as agile as possible, we are adhering to the YAGNI (you ain’t gonna need it) principle, and implementing strictly the bare minimum needed.  However, this being research, we keep talking about, and getting excited about, all the potential later versions.  In order not to get confused about what goes in v0, and to document the good ideas for later versions, we've instituted a to don’t list.  This is a place to record these ideas that are not going into v0, but which we may, or indeed may not, use later.

We are developing our simulator using the CoSMoS approach, which enjoins us to list the assumptions we are making, as material for the argument that the simulator is “fit for purpose”.  The (negation of) the to don’t list forms a very nice source for assumptions we might not have thought of otherwise.  If the to don’t list has an item “do X”, it means v0 hasn’t done X, and so there is the assumption that X is not necessary for v0 (and potentially, for every other version, if we never decide to implement it).

So, in research meetings around the whiteboard, as well as saying “YAGNI” when someone comes up with an idea, we now say “that’s one for the to don’t list”.

sequestering carbon, several books at a time XXVII

Surprisingly, a batch of all non-fiction this time:

I've been after Aczel’s Non-Well-Founded Sets for a while, and finally a second hand copy popped up at a not-too-ridiculous price.

A colleague at work was enthusing to me about Scala in general, and Horstmann's Scala for the Impatient in particular, so I decided to find out what the fuss is about.

Begon et al’s Ecology is there as potential source material for realistic ALife simulations.

film review: The Hunger Games (2012)

I haven’t read the book yet, so this is the review of the film alone.

We are in a dystopian world, many decades in the future.  For no readily apparent reason 12 hunger-riven Districts must annually send two “tributes” to play in the Hunger Games, a gladiatorial fight to the death where only one survives, broadcast as a Game Show in the downtrodden Districts, and also in the Capitol where the effete rich people live. When Kaitness Everdeen’s younger sister is chosen by lottery as the female tribute for District 12, she volunteers in her place.

There are few surprises here in this long film (142mins) (what, you mean you hadn’t predicted the rule change at the end?), but it is relatively well made, and once the Games begin, quite engaging, with some clever little touches like the fire cloaks, and the wasp nest, and avoiding the mines.

Jennifer Lawrence makes a good Kaitness: competent, resourceful, determined, and scared. Importantly, there is a reason Kaitness can realistically compete despite not having trained: she’s been using a bow to hunt in the woods for food for her family. (But why do these film archers never collect their spent arrows? And how do they keep walking around with their bow drawn?)

The scene with the apple in the pig’s mouth is amusing (if predictable), yet surely those people would have been protected better: has no-one in the past 70-odd years of the Games ever attempted something similar? And of course Kaitness wins.

But nothing else in the world changes. Even if I didn’t already know, I’d suspect a sequel.

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For all my film reviews, see my main website.

book review: Sense and Sensibilia

J. L. Austin.
Sense and Sensibilia.
Oxford University Press. 1962

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As it says on the front cover, this book is “reconstructed from the Manuscript Notes by G. J. Warnock”. Versions of these notes span several years of giving the set of lectures, from 1947–1958. Warnock provides a preface describing the reconstruction approach. Being based on lectures, the book does have a nicely conversational style.

The conversation is about Austin’s response to certain philosophers (mostly Ayer and Price, but also, to some degree, Warnock himself, amusingly enough) and their approach to perception. I don’t know what the current state of the philosophy of perception is, but this book is worth reading just as an illustration of how Austin goes about eviscerating others’ arguments.

The sense one gets is that Austin is exasperated by his colleagues’ oversimplification and possibly deliberate obtuseness when investigating certain aspects of this, and other, philosophical problems. He doesn’t mince his words. (Is this style a feature of the words being spoken in a lecture, rather than written in a book or paper? I don’t know; but given this was reconstructed from Austin’s own written notes, I suspect not.)

[p3.] My general opinion about this doctrine is that it is a typically scholastic view, attributable, first, to an obsession with a few particular words, the uses of which are over-simplified, not really understood or carefully studied or correctly described; and second, to an obsession with a few (and nearly always the same) half-studied ‘facts’. (I say ‘scholastic’, but I might just as well have said ‘philosophical’; over-simplification, schematization, and constant obsessive repetition of the same small range of jejune ‘examples’ are not only not peculiar to this case, but far too common to be dismissed as an occasional weakness of philosophers.) The fact is, as I shall try to make clear, that our ordinary words are much subtler in their uses, and mark many more distinctions, than philosophers have realized; and that the facts of perception, as discovered by, for instance, psychologists but also as noted by common mortals, are much more diverse and complicated than has been allowed for. It is essential, here as elsewhere, to abandon old habits of Gleichschaltung, the deeply ingrained worship of tidy-looking dichotomies.

I had to look up Gleichschaltung: a term used by the Nazis for “forcible coordination”; this appears to be a rather savage criticism to apply to a philosophical style!

In the first half Austin carefully picks apart the way “common mortals” use terms like “looks”, “looks like”, “looks as if”, “appears”, “appears like”, “appears as”, “appears as if”, “seems”, “seems like”, and so on. He teases apart subtle distinctions, to demonstrate that the philosophers who lump these all together under one restricted meaning are missing most of the richness of meaning, and hence being led astray in their subsequent philosophising.

Then in the second part, he picks apart use of the word “real”, here criticising Ayer in particular for using the word too fluidly, not recognising its multiple meanings, conflating them, and hence causing confusion.

This may sound a little strange: a book picking apart the meaning of a few words? But it is wonderfully readable, and gives an insight into deep and clear thought processes. And the exasperated style enlivens it considerably.

[I must confess that, although I had appreciated that the title is a pun, I had not appreciated quite how delicious a pun it is until, glancing at the cover, I misread the author!]

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For all my book reviews, see my main website.

quantum Zeppelins

Benjamin Russell, Susan Stepney.
Zermelo Navigation and a Speed Limit to Quantum Information Processing
Physical Review A, 90, 012303, 2014.  doi:10.1103/PhysRevA.90.012303
(also available from quant-ph arXiv:1310.6731)

Inspired by the Graf Zeppelin’s circumnavigation of the world, Ernst Zermelo posed his navigation problem back in the late 1920’s: given a Zeppelin travelling at constant speed relative to the air, and given a wind that can vary in time and space, what is the optimal way to steer the Zeppelin to reach its destination D in minimum time?

Mathematicians have, in the way of mathematicians, been generalising this problem.  Now there are results for general differentiable manifolds, not just mere Euclidean space.

Taking what seems to be an unrelated tack, one thing we are interested in is ultimate speed limits in quantum computers.  These speed limits come from physical constraints on the speed with which a quantum system can move from one state to another.

Here’s the connection to Zeppelins: Quantum mechanics can be expressed geometrically.  In the paper, we cast the quantum speed limit problem as a (generalised) Zermelo navigation problem.  The manifold is given by the special unitary group SU(N), and the wind is given by the time-independent “drift Hamiltonian” (what the quantum system would do if it wasn’t being controlled).  The system is affected by both this drift Hamiltonian and some specific control Hamiltonian (the analogue of the Zeppelin's engine).

We consider the case where the control Hamiltonian is also time-independent (the Zeppelin is steered in a fixed manner).  This allows us to calculate the optimal time taken to reach our desired D, a specific target quantum state.  From this general closed-form result (if you want to see what it looks like, see the paper!), we can then calculate specific times for our specific quantum setups and specific target quantum states.

This particular approach gives us the optimal time, but does not give the actual control Hamiltonian needed to achieve that time.  It’s like knowing that there is a direction you could steer your Zeppelin to reach your destination in a day, that you can't get there any faster than that, but you have no idea which direction to go.

Finding the optimal control (the direction) that achieves the optimum time: that’s the next paper!

bimodal June

June, with its longest day, has come and gone.  So we have seen maximum possible solar power for this year, if not maximum actual.  Here is a view of the power generation per month:

The horizontal time axis runs from 3:00am to 9:00pm GMT (no correction for summer time: this is all sun time!). The vertical axis runs from zero to 8kW.  Here the black line is the mean generation at that time, averaged over the month.  The orange regions indicate the minimum, lower quartile, median, upper quartile, and maximum generation at that time, over the respective month.

The daily power production per month is:

(For an explanation of these violin plots, see the May solar power post.)  There are several things interesting about this plot.

1. June is (slightly) bimodal.  We had mostly either dull days or sunny days, with fewer intermediate days.
2. The June minimum is significantly higher than previous months: even the dull days weren’t that dull.  In fact, the June minimum is about the same as the January upper quartile: three quarters of the January days were duller than the dullest June day.
3. The June maximum is less than the May maximum, which is less than the April maximum.  We never had an all clear day in June.  Here are the maximum days for each month (where the black line shows the production on that particular day):

We suspect that there is a second effect causing this reduction, too.  These later very sunny days not reaching the peak generation around noon may be due to temperature effects: solar panel power output decreases at higher temperatures.  The orange maxima shown were achieved on a range of different days with spiky production, due to scudding clouds, which will have reduced the temperature.  We await a hot summer to see if this effect continues.  We’re not sure how many years we will have to wait for a hot summer, of course…

change blindness

I went to a fascinating seminar by Professor Stephen Tipper last week.  It was about how perception (mostly vision described here) and action deeply influence each other.  There were lots of fascinating examples (with predictions backed up by clever experiments):

• Moving your finger clockwise or anticlockwise can change the apparent rotational direction of some flashing spots.

• Merely looking at a picture of a footballer v a tennis player activates your foot or hand mirror neurons respectively (although I personally didn’t even recognise the photos!).

• Watching someone perform a movement fluently v more awkwardly can affect your emotional response to them positively or negatively respectively (does this mean my left-handed self shouldn’t write on a whiteboard in front of my predominantly right-handed students?).

One aspect that caught my attention was the illustration of change blindness: how quite large changes in a scene are completely invisible, until eventually seen, at which point they cannot be unseen.  One of the examples shown was "couple at dinner".

The version above is taken from a webpage on a talk by J. Kevin O’Regan  and Alva Noë.  It seems to be flashing slower than the example in the talk, and I can’t tell if it still works, because now that I know the change, I can’t unsee it!  However, that page has several other examples, which did all work for me.

After talks like this, I never want to trust anything I see again!  But what really caught my attention about the change blindness segment of the talk was a seeming contradiction between what I was witnessing here, and something I’ve experienced before.  A blink comparator is used in astronomy to  to detect planets and other rapidly moving bodies.  Two images of the night sky are switched back and forth, and any object moving against the essentially motionless stars leaps out to the viewer.  How can a blink comparator work if we suffer from change blindness?

I asked Stephen about this after his talk.  The answer: it’s all in the timing.  The blink comparator blinks faster than do the change blindness images.  Blinking fast enough engages our motion detectors; blinking slower does not, and we become change blind.

Amazing.