Slime: a natural history

Susanne Wedlich.
Slime: a natural history.
Granta. 2021

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Slime is ubiquitous in living systems: as glue holding bacterial mats together, as lubricant allowing us to swallow our food, as both glue and lubricant excreted by slugs and snails to travel on, and much much more.

In this fascinating book, Wedlich explores all things slime (or mucus, or even biological aqueous hydrogel to sound more formal, if less attention-grabbing). She covers our human reaction to slime (the ick factor), and its role in art and culture; the physics of slime and how it can be both glue and lubricant; slime in organisms, particularly bacteria; the role of slime in the origin and evolution of life; and the place of slime in our ecosystems. This is all utterly fascinating, with new revelations on nearly every page. I had thought I knew at least something about the various major processes in biology: after reading this, I feel as if I have discovered a whole new kingdom.

I learned a lot, not just about organisms and evolution, but unexpected aspects like the role of slime in deserts and sea surfaces, and how climate change threatens the delicate balance of this almost unrecognised but crucial component of our biome. Highly recommended.

[Disclaimer: I was given my copy of this, in preparation for my hosting a discussion with the author during the York Festival of Ideas 2022.]

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For all my book reviews, see my main website.

festive hats

Out for a walk this morning, I spotted that someone has made a festive decoration for a pillar box:

The base is knitted/crocheted; the decorations are felt-work.

I looked out for the next pillar box I passed, and sure enough:

Here the carol singers are also knitted, and some have clearly had a little too much mulled wine.

Thanks, mystery yarn-bomber, for raising a smile!

sequestering carbon, one Christmas at a time X

His ’n’ hers Christmas presents:

another year, another tree

Due to a variety of circumastances, we got our tree a bit later than usual this year.  The first place we went had only four tiddlers left.  Fortunately, the next place had a decent one.

thick ice

It has been below, or around, freezing for a while now, and there’s a lot of ice around.  Today I noticed that the ice in one of our garden water tubs has expanded about 1cm above the rim of the tub.

Looking at it, I wondered how thick the ice was in total, to give that amount of expansion.  And then, could I calculate the thickness from just this observation?  And could I calculate it without knowing the height of the tub?

So I drew a sketch:

On the right is the liquid situation: water to the brim of the tub (which it was before the freeze).  On the left is the current situation, the top x units of water frozen to make x+d units of ice.  That does indeed look independent of the depth of the tub (unless maybe it is all frozen, which I doubt).

Let’s assume both the ice and water are at 0°C.  Wikipedia tell us that ice has a 9% increase in volume over water, which means that d = 0.09 x.

Since the observed d = 1cm, this implies that x = 11cm (much less than the depth of the tub, so no need to worry about it being frozen through), and so the whole ice layer is about 12cm (nearly 5 inches) thick.

That’s a thick layer of ice!

that's no cat!

Caught on our webcam around lunchtime today.  

Reviewing the images, we initially thought it was the neighbour’s ginger tom Trevor, as he likes prowling round our garden.  But it looked a bit weird.

Then, a few shots further on, we could see its thin legs, and it turned its head.

It’s a deer!  In our garden!  We are not in the countryside: we are surrounded by houses.  Where did it come from?  Where did it go, after it trotted past the car?

sequestering carbon, several books at a time CXXVI

 It's been a while since the last update, so there are rather more in the pile than usual:

Theoretical Computer Science for the Working Category Theorist

Noson S. Yanofsky.
Theoretical Computer Science for the Working Category Theorist.
Cambridge University Press. 2022

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I have been wanting to dip my toe in the sea of category theory for a while now, but have not found a suitable entry point. The books written for mathematicians are impenetrable. Those written for computer scientists lose me in the detail. When I came across this one, a book about computer science, written for category theorists, I was intrigued. I was reminded of a colleague of mine who collected foreign languages: he would learn them by reading a text he knew well in the language he wished to learn (memory offers up the thought it was Macbeth, but it may have been a different Shakespeare play). Maybe I could similarly learn the foreign language of category theory by reading about a topic I know, when written in that language? Especially since the book is a brisk 130 pages.

So, I am definitely not the target audience (being a computer scientist rather than a category theorist). And yet I feel I have learned more about category theory from this book than from any of the others I have tried. Not enough to be fluent, but enough that I can see what the concepts are, how they are put together, and how they can help illuminate a subject.

This was initially available as a PDF from the publishers site. I downloaded, and started active reading, which involved annotating the PDF with questions, thoughts, and ideas. (I come from a generation where annotating an actual physical book is Not Done.) I did skim a few of the more technical parts, but did read the whole thing. I then bought a hard copy.

As well as having a better understanding of Category Theory, I have a new perspective on theoretical computer science: the subset of functions that comprise computable functions is somewhat ugly to formalise.

This is the first in a series of Cambridge Elements: shortish works on Applied Category Theory. This one is highly recommended: I will be looking out for the others.

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For all my book reviews, see my main website.

Covid-19 diary: booster 2!

I got my (now annual?) booster jab today, along with a flu jab.  It was the now familiar efficient conveyor belt approach, with stations providing stickers and checking names, socially distanced queueing, and medical history questioning.  This included: “have you had Covid?”, “Yes, over four weeks ago”, which is long enough to be okay.  In fact, I booked this slot for my jab while I had Covid, as this was when I was contacted to come in.  If only I had been contacted a little earlier!  (Still, at least I now know Covid affects well-vaccinated me like a cold, and not worse.  Well, the current variant does, at least.)

I had the Pfizer jab in my left arm, and the flu jab in my right arm.  I again got a “young person’s flu jab” – because I'm still under 65.  Apparently the over-65 flu jab is higher dose, which may be why my other half had a reaction last year and I didn't.

Geek Sublime: writing fiction, coding software.

Vikram Chandra.
Geek Sublime: writing fiction, coding software.
Faber & Faber. 2013

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Chandra writes novels, and also writes software. Here he explores the fundamental differences between these two forms of writing, and whether software developers, in striving for ‘beautiful code’, can really be considered to be producing ‘art’.

In this discursive writing on the topic, we learn why Chandra believes the answer to be ‘no’. In particular, the process is so different. Writing is hard; it is a conscious anguished-filled ‘hell’, where every word is sweated over. On the other hand, although programming is also hard, it is hard in a different way: it requires a depth of concentration, and the developer can get lost in the process, unconscious of time passing, trying just one more thing. (Oh, how I recognise this description!) He doesn’t say whether the writing of this book was more like the hell of fiction, or the flow of programming.

We also learn a lot about the differences between Indian and Western philosophy and approaches to art. And one thing I learned was how the Indian philosophy explains how one can enjoy reading about something that one might never enjoy directly experiencing:

[p114] The pleasure of rasa comes from the meta-experience of experiencing oneself experience the stable emotions.

That is a sentence that will definitely resonate with programmers!

An interesting different look at programming, and art, through a non-Western philosophical lens.

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For all my book reviews, see my main website.

all good things come to an end

The final day and a half of the Erice Unconventional Computing workshop were also good, but without photos.

The Tuesday was also scheduled 9am to 7:10pm, but due to some unfortunate cancellations, we had “free” time from noon until 5pm.  A small group of us took the opportunity (moving leisurely from the gelato shop, to a Pizza restaurant, to the conference refreshment room) to sketch out a 20 year research vision, and a shorter term research plan, based on our previous work plus what we had learned at the workhop itself.  Next we have to consolidate the ideas, and write some research proposals (oh, and do the research if we win the funding, of course).

Tuesday evening was the workshop dinner, in the posher of the various restaurants we have been exploring, and not the standard set menu either.

Wednesday was only a half day, and mostly a discussion session of what we had learned, and what to do next.  A slot for andother workshop in 2024 has already been booked, so that’s something to look forward to!

The drive back to Palermo airport was in the light, so I could see some of the scenery I missed on arrival.  Since my flight wasn’t scheduled until 9:45pm, I had the oipportunity to experience the airport cuisine.

The flight was delayed. Surprise.  Not as bad as the over 3 hour delay on the way out, but "only" an hour and a half.  This meant I was passing through Stansted at 1:30am, rather than just before midnight as planned.   The drive home was also longer than planned, since the motorway was closed for roadworks, and I had to use the back roads.  So I got home at 3am, rather than the 1am I was hoping for.  Still, at least I didn’t have to get up early this morning to go to a workshop!  Hopefully I’ll be less zombie-like and sleep deprived tomorrow.

All in all, a great workshop, with excellent talks and ideas and conversations, plus gorgeous weather, and delicious gelato.  If only one could be at these places without having to travel.

excursion to Segesta

The early morning weather has been getting clearer each day, and this morning I could actually see a, still slightly hazy, view from my room window when I got up.

I experimented with panoramic settings to get a great, if slightly curvy, view from the tearoom window.

Then down to the lecture room, where today’s schedule of talks started at 8:30am, but finished 1pm, as today is excursion day.  We all piled on to a coach, which took us to the even more historic site of Segesta.

As we arrived at the entrance, we could see a hint of the Doric wonders to come.

the top of the temple just visible above the trees

But first, we hopped onto a shuttle bus (that for some reason was called free, yet cost 2Euro) that took us up to some ruins and a Greek theatre.  Both the acoustics and the view were fabulous.

We inspected various ruins for a while, then hopped back on the shuttle bus to take us back down the hill.  The winding trip down gave us several glimpses of the temple from a distance.

Once back down to the entrance, it was only a short walk up to the temple itself.  (Despite not being far, I needed a short stop part way up, due to post-Covid lack of puff.)

wow !

The roof hasn’t fallen down: it was never erected.  The temple was never completed, and has stood like this for two and a half thousand years.  Signs of partial completion include no internal structures, lack of fluting on the columns, and the construction “knobs” on the base stones, used for attaching ropes.  These construction signs are not visible on completed temples, as they would have been chiselled off to give a smooth final finish.

Unlike the ruins up the hill, the temple was never dismantled by the locals for its stones, as it is “too remote”.  (Mind you, the ruins up the hill aren’t all that accessible, either!)

The temple is 6 columns wide by 14 columns long, breaking the standard “n by 2n + 1” formula.  It was difficult to get a good shot of the side, due to the length.  Panoramic view gives a weird curve.  But I eventually managed to get far enough away, taking care not to hurtle down into a chasm, to take a normal shot of the entire side view.

wow !!

a view from below

fearful symmetry

Back down to the entrance, and just time to get a gelato before piling back onto the coach, and back to Erice.

a walk around the town

Sunday at the Erice workshop is another packed schedule: 9am until 7:10pm (with again the 9pm-11pm poster session).  Despite the long days, we do get scheduled a 2 hour lunch break.  Lunch is available at a selection of the many restaurants, and there is a workshop set lunch: a plate of pasta and sauce, followed by a plate of meat and green salad.  After ordering, it takes a while to arrive, because it is gloriously, freshly cooked.  (Hence the need for 2 hours.) However, today I wanted a look around the town, so skipped the restaurant option, and just had a cheese and salami roll from the local catering, before setting off with a colleague to explore.

Narrow streets led down past a bell tower to a walk around the perimeter, with views of castles and the rest of the town just seemingly growing directly out of the rock.

bell tower glowing in the sunshine

castle growing out of the rock

castle close up

the whole town just growing out of the rock

On our way back up to the venue for the afternoon session, we passed a gelato shop, realised what we had seen, retraced our steps, and went in.  I had the most amazing and darkest chocolate ice cream I’ve ever seen.  I think we’ll be visiting there again.

an old town

Although it is a Saturday, we had a full schedule of talks, timetabled 9am to 7:40pm, then a poster session after dinner!

After getting a full night’s sleep, I have been feeling a lot more alert today.  Apart from when some boiler or fridge rattles for a few minutes, my room is utterly silent: thick stone walls and essentially no traffic contribute to this.

On the way up to breakfast in a different building, I took this photo of the corridor out of the building where my room is:

gorgeous

My room is just around the corner from the main conference venue, which has this magnificent entrance:

The streets are all paved with this form of cobbling.  After hundreds of years of wear, it is somewhat slippery.  That’s not a problem on level surfaces, but most streets in Erice slope dramatically.

This is the street up to the breakfast room, and tonight’s poster session; many streets are much steeper than this.  I picked my way up it carefully, to have a look at the posters, then picked my way back down again even more carefully.

An extremely full day, of wonderful talks and posters.  Off for another good night’s sleep, to get ready for more sessions tomorrow (yes, on Sunday!)

view from a conference accommodation window

I am attending the Unconventional Computing workshop an the Ettore Majorana Foundation and Centre for Scientific Culture in Erice, Sicily.  I’ve wanted to attend an Erice event for a long time now, as it is a famous location for scientific conferences.  So I was concerned when I caught Covid, but fortunately I recovered in time.  I arrived at the centre about 3am (due to a more than three hour delay in my flight; thanks Ryanair).  The weather forecast is full sun all week, so I was surprised to see this out of my window this morning:

However, the early morning mist had mostly lifted by the first break.  We trooped up a stone sprial staircase from the lecture room to the tearoom, to be greeted by a most fantastic view: the room is open to the scenery:

The photo just doesn’t do justice to the effect.  The light is amazing.  Going closer to the opening (taking care to avoid falling down the unmarked black steps against the black floor on the way) gives a wonderful view over the historic town of Erice:

Look closely at the roofs, and you will see lines of rocks on the tiles.  Why?

And looking further out we see this magnificent view over the Mediterranean:

After this break, it’s my turn to present, on less than five hours sleep and with a bit of a post-Covid cough. Let’s see how it goes!

oh well

 Inevitable sooner or later, I suppose:

QBism: the future of quantum physics

Hans Christian von Bayer.
QBism: the future of quantum physics.
Harvard University Press. 2016

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Quantum mechanics is notoriously unintuitive, with its “collapsing wavefunctions” or “many worlds” or whatever is added as an interpretation to its weird predictions. Yet those predictions belong to the most accurate physical theory known. 

Quantum mechanics seems to say we have to give up some cherished notion of the world: if we want locality (no “spooky action at a distance”, only local interactions that propagate), we can’t have realism (the idea that there is some definite thing or process there), and vice versa. Quantum Bayesianism lets go of reality, but in an interesting way. 

This brilliant little book takes the reader through a description of the weirdnesses of quantum mechanics, and the interpretation of Bayesian statistics, before applying the latter to the former. 

The key idea of Bayesian, as opposed to frequentist, statistics is that probabilities are about our knowledge of the world (we assign a prior probability to a fair coin toss of 50% of landing heads, because we don’t know all the details of the initial spin, the air currents, etc). Bayesianism defines how to update this prior knowledge (the 50/50 chance) with a new probability once we have further data (anything from more knowledge about those initial conditions, to an observation of how the coin actually landed). So in QBism the probabilistic quantum wavefunction is interpreted as our prior knowledge of the system. This gets around “wavefunction collapse”: we just update our prior with the additional observational data. It gets around “Wigner’s friend”: Wigner has one prior wavefunction, his friend, who has observed more of the the situation, has an updated, and therefore different, wavefunction. The wavefunction belongs to the observer, not to the system. 

Quantum mechanics allows us to calculate the best possible prior from our knowledge of the system. What makes quantum mechanics weird is that a calculated wave function that says a photon has a 50/50 chance of doing something, say, is the best possible knowledge we can have of the system: unlike in the classical case, it is not possible to improve the prediction by having more data about how it was set up. This is why we have to give up “reality”: the wavefunction isn’t “real”, because it is not a property of the system itself, it is just the best possible description of it. There is no underlying “real” system that “knows” what the actual answer will be (unlike the classical coin toss). Once the photon has interacted with something, the system has changed, and we can update our prior with the new observed data. 

This loss of “realism” does not mean QBism denies the existence of a real world “out there”. It instead leads to a startlingly different view of that real world. The world is not a deterministic automaton, set going at the start, trundling along a pre-determined track. It is a world undergoing constant creation by quantum systems (which may include observers) interacting. 

[p208] Understood in this way, the QBist universe is not static but dynamic; less like an intricate clockwork and more like the interior of an evolving star that is not alive in the conventional sense but bubbling with creative energy and continual surprise. It is real but veiled, objective but unpredictable, and substantial but unfinished,

von Bayer writes in a very accessible way. I admit, the sections on the delayed choice and the GHZ experiments could have gone more slowly. But overall, the exposition is brilliant: on quantum mechanics, on Bayesianism, and then on the combination. This book changed my world view.

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For all my book reviews, see my main website.

turning heads

Many minor things have changed for the first time in a lot of people’s lives, due to changing the soverign after 70 years.  His Majesty’s Government; King’s Counsel; His Majesty’s Revenue and Customs; ...  

And the coins will change.  The design of the new 50 pence has been released:

There has been a lot of discussion about the different direction the head is facing.  But that is not a change of a 70-year constancy for some of us.  On 15 February 1971 the UK “went decimal”, changing its coinage from pounds, shillings, and pence to the new decimal coinage.  (If you have ever wondered why people occasionaly say “what’s that in old money?” when asking for something in less confusing units or language, that’s because it was a very common phrase while people adjusted.)

Before 1971, there were coins from multiple reigns in circulation (and for a while after, since the old one shilling / new 5 pence and the old 2 shilling (florin) / new 10 pence coins coexisted for a while).  As children, we enjoyed finding the occassional very old coin.  Here are some pennies I found in my change in the 60s, and kept as souvenirs:

old pennies: Victoria, Edward VII, George V, George VI, Elizabeth II

So we knew the heads faced in different directions.

Coin designs didn’t change as much then, either:

only a subtle change in Britannia from 1907 to 1962

The main change was the amount of Latin, and the amount of its abbreviation, on the front.

So, the head has turned once more.

Mind. Blown.

 Wow.  Just ... wow.

JWST view of Neptune

The more I look at this, the more staggered I get.  I remember when pictures of Jupiter had less resolution.  These truly are the days of miracle and wonder.

nobody minded the spider

For all the reasons discussed earlier, I watched the state funeral of Elizabeth II yesterday on TV.  My parasocial relationship and mental model definitely got updated, if only partially for now.  

While watching the ceremonies, I realised why I actually appreciate these kinds of  displays of ceremony and pagentary: I'm a fan of what is known as "competence porn".  I usually get this from reading fiction; it's rare to see something done so well in real life.  (Having oodles of money thrown at it helps, but is certainly not sufficient.)  Although I did think that the funeral music accompanying the processions seemed a little ... jolly ... at times.  Maybe it's the brass band instruments.

Also while watching, at one point I said: "is that a spider?"  Yes, it was, crawling bemusedly on the card on the wreath.  I am not the only one who noticed.  

So, the end of an era.  And the world goes on as before.

 

view from a hotel window

I am in Venice, attending a workshop being run by the European Centre for Living Technology.  This is my first time in Venice, and the weather is glorious.  And the lack of traffic makes it very peaceful (except for the 8am and noon bells).

By hanging out of my hotel window and looking round the corner, I have a lovely view.

The opposite view from the corridor by my room is even better:

There are, of course, numerous canals, mostly quite narrow:

but occasionally quite large:

The workshop venue is equally spectacular:

So, my first visit, but hopefully not my last.

On parasocial relationships, and updating mental models

I came across a new term recently: parasocial relationship.  These are “one-sided” relationships,  where person A invests some degree of time, energy and emotion in following the life of person B, yet person B is unaware of even the existence of person A.

In these relationships, person B is typically some celebrity enough in the news that person A can easily follow them.  But person B may even be fictional: people can look forward to book sequels or new TV seasons so that they can “spend more time” with their favourite characters.  More dedicated fans may even write “fan fiction” to this end.

Parasocial relationships have been categorised into three levels: (1) entertainment-social, with normal fan-like following of news; (2) intense-personal, with feelings to the point of obsession; (3) borderline-pathological, with addiction-like fantasies and behaviours.  

I would say there is also a level 0, more a form of acquaintanceship, due to existing in a culture where news of the other cannot be avoided, so they necessarily become familiar over time.  

An aspect of relationships is that we humans build mental models of our world that include models of these other people (and models of ourselves, and models of their models of us, and…).  Most of the people in our own mental model are our specific friends, relatives, colleagues, and acquaintances, plus a sea of famous people, and a sort of background of undifferentiated extras.  We each use our own model to predict and anticipate events and behaviours, and so need to keep it up to date and as correct as is needed for us to function in the world.  Differences between our model and the real world may be due to a faulty model (eg, I completely misunderstood X’s motivations), or may be due to a change in the world (eg, Y has died).  Then our model needs to be updated.  But this takes time, and it can be jarring or upsetting for us when our model keeps making incorrect predictions, for example because it is assuming that a person who has recently died is still alive.

A combination of a parasocial acquaintanceship and an uncorrected mental model can possibly explain why one feels upset, or discomforted, or just plain off balance, when a famous person dies.  A famous person such as Queen Elizabeth II, for example.

So, I will be watching the funeral.  Partly to help update my mental model through forced correctional input (when will it stop being totally weird to hear people saying “the King”?)  And partly to grieve the end of a parasocial relationship (level 0+) that I have been engaged in for over 60 years.

low moon rising

The very low moon is peeking through the streetlights around the carpark.  Shot on my Pixel4a in "night" mode, 2x zoom, cropped, but otherwise untouched.

21:43 BST