2020-05-23

Bad beekeeping 2020

In the absence of any very exciting news (Cummings good! (no-one wants to talk about that) or Cummings bad! (everyone wants to talk about that)) I thought I'd record the bees. It has been a warm - or at least sunny - spring, and so they dutifully swarmed. This was fortunate, as a friend is starting beekeeping and wanted a swarm.  Walking down to the hives one sunny lunchtime I could clearly hear the hum, and see them dancing in the gap between some trees; an hour later they weren't, and so I deduced they had settled, and wandering o'er the banks of the stream I found them, conveniently at ground level, somewhat less conveniently on various sticks barely above the mud on the riverside.

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The stream isn't the dump this view suggests. However the bees are as irritatingly badly placed to be scooped up as the pic suggests. All the dry sticks need to be broken off and since they snap jerkily, that upsets the girls.

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We came back with a big cardboard box and after cutting back the sticks mostly and not disturbing the bees too much, I scooped them into the box which is easier to say than to do, and we hoped for the best: there's an awkward time when you can't tell if the queen is inside or outside, and whether the stream of bees is heading towards settled or needing recapture.

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Happily, they had settled, and a little later were taken away to their fine fresh new home (from which they decanted, but not far, and my friend recaptured them with no help from me).

After that my occasional run to Grantchester revealed that the rape fields were fading which is the sign for the spring recolte, and after an extensive period of nettle-chopping and other weeding the hives were fit to be seen to.

The first revealed - again, alas - a birds nest in the eaves. Will they never learn? It had three cute little eggs in it. I felt guilty, but Google Lens tells me these are of the Great Tit and it clutches in 12s, so perhaps these were just failures that didn't take. Anyway, I destroyed the nest and later repaired the mesh. See here for the eggs. See here for the hole in the gauze.

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Inside... about half the frames were capped and that seemed good enough. On a first go I didn't explore the lower super; you can have too much of a good thing. Also there was a small amount of brood in the middle. How did that get there? Tut. So I thought I'd let the lower super sort itself out, somehow.

That was enough excitement for one day, but happily the next was sunny too so onto hive #2. This initially looked like it had gone solid, but that was illusion, it was mostly fine. And just like the first hive it seemed quite well populated, so I'm slightly puzzled as to which had swarmed. This too I managed to deal with quite efficiently, and put the newly emptied frames under the remaining full super, which I left for later. Spinning it all out the honey extractor was full, and I then recalled that I didn't have any jars left, so taking off any more supers can wait for Thornes' finest to deliver.

General view. Hive #1 straight ahead, hive #2 R, spare super and roof hanging around just in case they feel like swarming into it; and spun frames awaiting replacement in hive #2.

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Hive #2: formerly top, now spun, super put back on, and the formerly lower, still unharvested, super off to the R on top of the green box awaiting replacement on top. All the comb standing up will have to be removed before replacement.

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Inside hve #2 top super before it came off. You can do this "properly" with bee excluders, but I don't bother with that, and just remove it frame by frame, carefully brushing away bees as I go.

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As I scraped off the upstart comb from the now-top super it went into the box together with the attendant honey; so afterwards I let them have it back. Side note: when I took off another super a week later, they had completely removed all the honey and the wax too.

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There's a video on Youtube of tapping off the spun honey.

Update


A week or so later I took off the (now) upper super on Coppertop. Here are the frames. And then put on the spare super I had lying around, having painfully but pleasantly (do I mean painstakingly?) having recovered enough frames for it, and re-sat the spacers. And this is afterwards.

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Lot marks


For my memory:

* '20B - 2020 (duh), from the Blue Bowl.
* '20T - 2020, from the Tub.
* '19H - 2019, from the tub that Miranda used, melted out, hence "Hot".
* '20S - 2020, Second lot (currently in the tub) from the second super on Coppertop.

2020-05-11

Coronavirus days: OUR PLAN TO REBUILD: The UK Government’s COVID-19 recovery strategy

EXrjSOLWAAI2Qd4 Or, "I read this stuff so you don't have to" you lucky people. My pic is an example of the govt's almost comic innumeracy.

As you'd expect, there's revisionism in Bojo's foreword: That price could have been higher if not for the extraordinary efforts of our NHS and social care workers and had we not acted quickly to increase the capacity of the NHS... On 3 March we published our plan... OK, so the idea he's trying to push is that it's all Very Grave, but we've done Jolly Well, and it is All as Planned. But that plan contains no reference to lock-down. Or care homes. And whilst praising the NHS etc. always gets lapped up by everyone, he's trying to drag himself along on their coat-tails. Continuing I said we'd take the right decisions at the right time is, in retrospect, clearly wrong, so he is unable to learn even with hindsight1. Testing: the govt is still lying about the number of tests - having nailed its colours to the mast it cannot change now - but even their figures show less than 100k a day for the past week.

Having got that snark out of the way, I'm afraid that the actual plan itself is not mad, indeed their main problem is to try to disguise how bleedin' obvious it all is - do we really need to pay all these expensive people for this? There's still no attempt at any kind of numerical cost-benefit analysis, just an implicit hand-wavy one: fewer people might die if we continued the lock down, but then again the economy would suffer, and anyway are people going to take much more of this? That last is a valid consideration: even if your only concern was to save lives, some relaxation reduces the risk of an explosion.

If you'd rather read someone else's take then the Graun has a pretty straight summary. Update: they also (now) have If we follow Boris Johnson's advice, coronavirus will spread by David Hunter (professor of epidemiology and medicine at the University of Oxford). Excellent. Someone prepared to make a prediction.

The timelines are vague, as they should be: The next chapter sets out an indicative roadmap, but the precise timetable for these adjustments will depend on ... monitor closely the effect of each adjustment, using the effect on the epidemic to gauge the appropriate next step. Initially, the gap between steps will need to be several weeks, to allow sufficient time for monitoring. However... this response time may reduce.

There is a very tiny nod to regionalism: Restrictions may be adjusted by the devolved administrations at a different pace in Scotland, Wales and Northern Ireland because the level of infection - and therefore the risk - will differ. Similarly in England, the Government may adjust restrictions in some regions before others: a greater risk in Cornwall should not lead to disproportionate restrictions in Newcastle if the risk is lower. But their heart isn't in it, and it isn't included in Step One.

The Beeb's report on all this pulls out "advice for people to wear face coverings on public transport and in some shops" which is sensible of them; this is in the Govt doc but not nearly so obviously - making it too obvious would raise the embarrassing question of why it wasn't suggested much earlier2.

Step One


Anyway, where do we start? For the foreseeable future, workers should continue to work from home rather than their normal physical workplace, wherever possible... All workers who cannot work from home should travel to work if their workplace is open. Which seems almost sensible to me. The bit that isn't sensible is not considering whether people should travel to work on public transport; I wouldn't go on the Tube at the moment myself. Somewhat later they say everybody (including critical workers) should continue to avoid public transport wherever possible, which is all very well but if it isn't possible you're stuffed if you follow their rules; they keep trying with Social distancing guidance on public transport must be followed rigorously; it will be interesting to see how that gets enforced; clearly they haven't quite worked this one out as they say appropriate guidance... will be published this week.

Schools aren't to re-open, but as they note actually schools are open, for some categories of children, and they urge more children who would benefit from attending in person to do so, which appears to be a sensibly disguised way to push up school occupancy without going too high.

Going outside is less restricted - in England; the idiots in Wales are still in panic mode, sadly -, and it looks like the bloody stupid bit where the rozzers nick you for sunbathing is out.

Step N


Step Two won't be before the 1st of June: more school opening, more bizniz, some sporting events. And then the vaguer Step Three won't be before the 4th of July.

Stay Alert


It's a bit shit. isn't it? Pretty well everyone agrees on that. I hate living in a country where every policy has to have some associated fuckwitted slogan. Unfortunately the crit - at least as reported in the Graun - is not "this is all rather wanky" but that the “stay alert” messaging is “too vague” and that “more precision is needed”. Which is about as useless as the govt's slogan. But the Grain needs to attack the govt plan for something, since they're Tories, and it doesn't want to put its ass on the line by suggesting any substantive changes (update: and neither does the opposition). Incidentally, while having Bojo spout off on Sunday while the doc wasn't available until today was a bit shit too. Or was it? How much in the great scheme of things did that actually matter, except to the chatterati?

Notes


1. FWIW, I ran the Cambridge Half Marathon on the 8th of March, and would have been annoyed had it been called off, so I'm not claiming any great foresight for myself.

2. Actually they make excuses for this, and international quarantine, on p22, but I don't find their excuses plausible.

Refs


What can we learn about the COVID fatality rate from Guayas? - JEB
* Americans Didn’t Wait For Their Governors To Tell Them To Stay Home Because Of COVID-19 - 538
Boris Johnson’s new covid-19 campaign falls flat - Economist

2020-05-09

Coronavirus days: regionalism, modelling, hypocrisy, global warming

MVIMG_20200508_160649 Let's start with Neil "Bonking" Ferguson, who said: "I accept I made an error of judgement and took the wrong course of action. I acted in the belief that I was immune, having tested positive for coronavirus and completely isolated myself for almost two weeks after developing symptoms. I deeply regret any undermining of the clear messages around the continued need for social distancing." This is interesting, in the light of claims to be "following the science". It would appear that his scientific advice is that, if you've had the virus you're immune so contact is permissible. As far as I can tell he believes his error was "undermining the message" rather than his scientific judgement. This then recalls... The Climate Change Hypocrisy Of Jet-Setting Academics? No, not that one, but the linked Climate chickenhawks.

But perhaps his scientific judgement was correct. Of course in the fervid atmosphere of the UK that is no proof against charges of hypocrisy, as should have been bleedin' obvious to him. Which leads me on to regionalism. Or, that the current one-size-fits-all policy is, errm, how about "non-optimal from a theoretical point of view". The rates of infection in the country vary wildly by region, with the general pattern being that outside the plague-pits of large cities things are fairly OK. And using hand-waving density arguments, that would likely be true with less lockdown. Unfortunately the centralised response we have appears to be unable to think about this; R4 this morning were desperately worried that even the smallest divergence between England and Wales might be confusing. Perhaps it might confuse their tiny minds but I think people could cope. The USA gets to experience this more directly I think, since the States are responsible for themselves, and this is good. Closer to home, we're going to see changes in Europe as an example - for either good or ill - to us.

One Adam Kucharski sticks up for NBF Twatting There seem to have been some misconceptions about how COVID science is done and how it helps inform decision making. As we clarify here, it's a large collaborative effort... and linking to their doc (arch). Which includes inter alia In early March 2020, the emerging consensus amongst scientists involved in this country-wide consultation was that SARS-CoV-2 was circulating widely in the UK, it was capable of causing substantial hospitalisations and fatalities, and that in the absence of drastic social distancing measures, the healthcare system would rapidly become overwhelmed in the same way that it had been in Northern Italy at the time. Although new studies and data have since emerged, this consensus has not changed. But there are problems there. Firstly the idea that little has changed revises away rather large changes in doubling time, as JA noted. And secondly, if the govt is "following the science" and the science in early March was such, why did we lock down so late? The answer of course is that rather important things did change, most obviously their belated revision of the doubling time.

Incidentally, SM points to the list of meetings which contains lots of interesting but frustrating minutes; it would be good to pore over those some time - but even better for someone else to do it and synthesise their timeline. Having browsed a couple I found myself frustrated because there are raw statements not backed by any references.

Moving now onto models, consider the Imperial model. Obviously at a superficial level, because I know little about it, but I did find We modified an individual-based simulation model developed to support pandemic influenza planning to explore scenarios for COVID-19 in GB. The basic structure of the model remains as previously published. In brief, individuals reside in areas defined by high-resolution population density data. Contacts with other individuals in the population are made within the household, at school, in the workplace and in the wider community. Census data were used to define the age and household distribution size... This model has been a bit crap overall, because as JA has so elegantly demonstrated, they fucked up the calibration by not doing any. Indeed this seems almost a textbook illustration of how useless it is to have an elaborate model capable of simulating fine-grained detail when important controlling parameters aren't know. As a country-aggregated simulation it appears almost comically inappropriate. And yet for what I want them to do - modelling regionally-varying degrees of lockdown / isolation - it could be quite appropriate; but the little buggers aren't doing that.

Global warming


Richard-the-Betts Twit “Like in the Covid pandemic, timing [of climate action] is critical to prevent devastation. If you wait until you already have a serious problem, then it is too late. Unlike with corona, sea-level rise cannot be stopped for many centuries", riffing on Sea levels could rise more than a metre by 2100, experts say. I disagreed, on the grounds that there's no exponential growth of temperature. In a thrilling continuation, RAB hit back with But there is a very long lag in sea level response. If we wait until we've seen (say) a 50cm rise before doing anything, we'll be committing future generations to substantially more, but so far he has no response to Well that's part of the point: the lag really is very long indeed. There is some limit beyond which it is not worth planning: Should we care about the world after 2100?

Bees


Ah, my picture: a swarm from one of my hives. They flew off not very far and collected themselves on the muddy bank of a local brook. We collected them into a large cardboard box and tookthem away; Mac reported that they swarmed again this morning, but he seems to have re-collected them again.

Another view


From Kal.
   

2020-05-07

Coronavirus days: the Imperial model, impartially consider'd

But not by me, I hasten to add.

Quiz: to be taken before you get to the end. Who is this, and why is he relevant?

The story so far: Imperial have some kind of epidemic model that was used to predict, errm, stuff1. After a bit people, predictably (arf!) enough, said "where's your source code" and Imperial said "errm, it's a bit of a mess actually, hang on a mo" and after a fair while and heavy massaging from folk in the private sector that turned an unreadable unmaintainable 15k single-file model bearing a powerful resemblance to S+C's MSU code into something that could be seen in public without too much embarrassment, they put it onto Github2. I even poked around in there for a bit before realising I didn't know how to look at Github, and getting bored.

But! Other people have looked, and are unimpressed. This is no great shock I think. The people I found were "Lockdown Sceptics" who, despite their sensible but derivative motto Stay sane. Protect the economy. Save livelihoods, are probably a bunch of nutters; they also have a dreadfully slow website. They have a post (arch) called Code Review of Ferguson’s Model.

Most of the post is about non-determinism. This is interesting (though probably no great flaw) and I'll get to it in a moment, but first a few other things they pick out. The first is the absence of any kind of tests, which seems a fair point. Writing tests is tedious and often neglected even in the Real World, so it is unsurprising that a bunch of amateurs didn't bother. Another is poor documentation of some parts; and again, meh, so it goes. let's go back to the interesting part, non-determinism.

There are a number of meanings for this that need to be disentangled. In running such a model, you probably want to run a pile of runs with similar but perturbed initial conditions and do some averaging of the results. In this sense the model is intended to be "stochastic", and that's fair enough.  However, with a given random seed, you would rather like the model to be repeatable. It appears to be rather shaky at this. The first problem looks to be parallelism. This comes up in GCMs too, and indeed way back when I said:
There are two sorts of repeatability: you run the model again, and you get *exactly* the same results down to the last bit. This is call bit-reproducibility. Or, you run the model again, and you get *scientifically* the same result (the same climate; probably the same response to forcing within statistical error) but the exact details of the weather differ. Because the climate is chaotic (in the sense that small initial perturbations rapidly amplify) and GCMs reproduce this well, if your model diverges even slightly from bit-reproducibility it will diverge strongly from it, because the details of the individual weather will be totally different. But the climate (statistics of the weather) will be the same.
So you can see Repeatability of GCMs for more. The problem with the parallelism stuff if that the easy way to implement it leads to numbers coming back from other processors in a different order, and so inevitably the exact last few bits of floating point calculations don't quite match. If you put effort in you can avoid that, at the cost of slowing the thing down a little3. Imperial's solution appears to be running the model single-threaded, instead (but because they didn't really care about repeatability, and had no tests to pick up problems, they still had repeatability bugs even in single-threaded mode).

If you look at the report, the non-repeatability looks to produce a pretty big difference. However, I rather suspect this is like GCMs: if you look at output after one month after a trivial perturbation, it will look very different even though the long-term climate is the same. What that report / pic appears to show is sensitivity to when the initial perturbation starts to grow. This might be a problem; but it might not (I think you'd need to see a whole ensemble of runs to see what it is supposed to look like).

So overall I think the criticism in scientific terms isn't exciting. As a lesson-for-our-times I think "when you look behind the curtain of just following the science you'll see some messy stuff" will do. Or even Laws are Like Sausages. Better Not to See Them Being Made.

The East is Red


Interestingly, seen from one bug report, people are shamelessly using the concept of "Red Team" in this context. It's almost as though the concept is sensible and helpful, when used in good faith.

Update


The fight for the soul of the Imperial model continues. Nurture has Critiqued coronavirus simulation gets thumbs up from code-checking efforts which (once you remove the goo and dribble) amounts to pointing out CODECHECK certificate for paper: Report 9: impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand. March 16, 2020 which looks to be part of a commendable effort to re-run codes leading to publication by Stephen J. Eglen; and they have, and get the same answers (in the stochastic sense).

Meanwhile Bryan Lawrence has a somewhat unconvincing defence in On scientific software - a beginning.

Refs


The Imperial College code - ATTP

Notes


1. I'm a big-picture man. Don't bother me with details.

2. I've been re-reading Proust.

3. The Met Office / Hadley Center are not a bunch of amateurs and did put the effort in. Incidentally, one reason for wanting the reproducibility is rare bugs where you model blows up. If you don't have reproducibility, you can'r re-run with extra debug to get to the same point and see the failure more clearly, so you're pretty well stuffed for debugging.





2020-05-06

Predictions are overrated?

IMG_20200506_100300 Sabine Hossenfelder has a blog post (via Not Even Wrong) asserting that Predictions are overrated. Obviously, in PW's words, the naive view that you can evaluate a physical theory simply by the criterion “Does it make predictions?” is wrong; but SH goes too far in dissing predictions.

Happily, after all the physics, which they definitely know more about than me, SH comes on to climate models:
Another example where this misunderstanding matters are climate models. Climate models have correctly predicted many observed trends, from surface temperature increase, to stratospheric cooling, to sea ice melting. That’s an argument commonly used against climate change deniers. But the deniers then go and dig up some papers that made wrong predictions. This, so their claim, demonstrates that really anything is possible and you can’t trust predictions.
This is naive to the point of being wrong. Most importantly, most climate modelling - well, especially the IPCC - has been careful to talk of projections rather than predictions. The outside world hasn't been great at picking up that nuance, but it is there, and needs to be considered if you're attempting some scientific evaluation rather than a political one. That we don't know the value of climate sensitivity is well up front, and clearly century-scale predictions of climate evolution aren't possible without that. Secondly, some of the predictions she mentions - sea ice melting is the most obvious - are ones where the models have done a fairly poor job, other than getting the sign right. And thirdly, there's a variety of models predicting different things, and they can't all be right.

How you should evaluate the credibility of the climate modelling community / scientists / effort, based on past "predictions"? Clearly, picking any one "prediction" at simply verifying that is wrong. You need to look at more of an amalgam, like the IPCC. As to the kinda question "should we trust them now, based on what they said in the past?" you need to look at how the predictions were presented. If you could find multiple frequent cases where people confidently published clear predictions which were subsequently proved wrong, then you would indeed mark them down. Since that isn't actually the case, you don't.

And then there's the point, which SH notes that we have moved on to arguing about the integrity of scientists and the policies of their journals instead about science. If you're talking about denialists, then yes, you're talking about "integrity" and sociology of science, not about actual science. What if you're actually interested in evaluating the science? Then I still think the ability of the models to make predictions matters. In this case it's hard to say quite what we mean by "the science" - all the subcomponents like radiative transfer theory are effectively "unit tested" to borrow from software engineering, but those aren't the bits we're evaluating; in terms of GW, "the science" means that integrating them all together within a GCM (a) works and (b) captures enough of the physical world to say something useful. Without something in the way of prediction, I don't see how that's possible. Where generally you allow "prediction" to include predicting the past; i.e. temperature evolution over the 20th century.

SH proposes instead What, then, is the scientific answer for the climate change deniers? It’s that climate models explain loads of data with few assumptions. Which is nice, but never convincing, unless you believe it anyway. It isn't convincing because it isn't clearly true from the outside: you can't tell that they have "few" assumptions (hence, it is a useless answer for denialists themselves, and not much use when in front of an audience of the general public). Worse, the statement isn't even meaningful; GCMs have lots of "assumptions" in them, measuring "few" or "lots" in any meaningful way would be a difficult task in itself. This is why predictions are good: they don't require looking inside the black box. Perhaps it is just her rhetorical question that's wrong: if she'd asked, What, then, is the scientific answer for the climate change scientists? it would make some sense, but still be hard to evaluate.

Just to be clear, I don't think there's an absolute answer. Trying to evaluate a scientific theory and coming up with an opinion as to whether it is likely true or not isn't a science. There's a question of how much weight you give to predictions versus other factors. But making good predictions is generally so hard, anything that can predict correctly gets a lot of weight.

2020-05-02

Coronavirus days: would most covid-19 victims have died soon, without the virus?

20200502_GDC100-Artboard_1 Asks The Economist. And the answer (as always) is no. Somewhat to my surprise and against my prejudices. But matching other studies I think I recall seeing elsewhere. But this one comes with a rather nice pic, which I share with you.

So each decade-group from 60 on up has about the same contribution to total deaths; proportionately more of the 90+ group die of course, but there are fewer of them to start with. And the x-axis is number of long-term conditions, so I think all you really see there is that 60 year olds have 1-2, and every decade adds a couple of conditions, on average. The y-axis being years lost we see that 90 year olds only lose a year or so, but the 60 year olds much more, and the average is about a decade.

When easing lockdowns, governments should open schools first


Another Economist headline that could perhaps have been answered with no, if it were a question. But it isn't, it's a policy prescription. The suggestion seems to be based on three ideas: that they appear to be less prone to catching and passing on covid-19; that loss of schooling is damaging; and that kids seriously get in the way if you want to work.

Minor disclaimer: I have a daughter in her last year of school. She would have gone on study leave on the 7th of May had this fuss not happened, so school is over for her. The only intervention that could matter is re-instating exams, but I'm fairly sure the govt nailed its colours to the No mast early, so that won't happen; because it would now be unfair to change the system.

I think the kids-don't-get-it-or-spread-it argument is weak, largely from lack of evidence (and slightly less so due to what I feel is implausibility) at this point, so relying on it seems poor. That loss of a term or two's schooling is a disaster is also I think weak; although that may be coming from a nice-middle-class perspective, where if Darling Daughter asks about divisions of particles in the Standard Model, I can at least offer a useful discussion.

I'm rather more sympathetic to the problem of getting people back to work while the kids are under foot. I think I'd solve this regionally: if you look at maps of the disease, some areas - most obviously big cities - are plague pits and much of the rest of the country is mostly free. So, re-open schools in such areas on a trial basis, see how it goes, would be my plan. Possibly do something complicated, if you want to keep the numbers down, like have half the pupils come in on odd/even days.

But I'd definitely re-open garden centers first. And book stores, and cafes; all with some density restriction, if required. And large offices and factories that can meaningfully impose distancing.

2020-05-01

Coronavirus days: saving the planet demands sacrifices just as Covid-19 does

IMG_20200428_165609 An interesting article in the FT by Tim Harford, Saving the planet demands sacrifices just as Covid-19 does (arch), which links Covid and GW more usefully than previous attempts. The best line I think is The pandemic is giving us a taste of what an end to growth might look like. Which is aimed at the many environmentalists [who] nod along with Greta Thunberg’s sentiment about “fairy tales of eternal economic growth”. You can weasel about this as "of course this wasn't planned and it would be better if we planned it" but I don't believe that - apart from anything else, Covid shows how poor any central planning attempt is likely to be. As to the actual question, see my How much would we have to adjust our lifestyle to stop global warming?

As you see from my pic, the premature eternal summer is over. In other news, my cat has an Instagram account. And it rather appears that some people need to read stuff like Price Signals, Price Gouging, and Philanthropy.