Monday, March 08, 2021

save the vaquita

There have been quite a few features about Homo sapiens recently(Covid, conspiracies, pollution and such like), so I was keen to get back to some endangered animals, and a faithful reader from Mexico suggested to look at their local endangered cetacean, the vaquita porpoise. It so happened that the vaquita just had a high quality genome sequence out, which led to the surprising conclusion that the species, although reduced to a population of fewer than 20 individuals, doesn't have any genetic problems. The only thing that has to happen is that the illegal fishing (for other species, but killing vaquitas as they're the same size) needs to stop.

Adding to that, I also looked at other genome and genetic diversity data of other cetacean species, to see how they're coping these days, including humpback whales recovering after a close brush with extinction.

The resulting feature is out now:

Cetaceans balancing on the brink

Current Biology Volume 31, Issue 5, 8 March 2021, Pages R215-R218

Restricted access to full text and PDF download
(will become open access again one year after publication)

Magic link for free access
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The vaquita porpoise (Phocoena sinus) is the most endangered cetacean, but a genome study suggests that it may still recover if the threat of gillnet fishing is removed. (Photo: Paula Olson/NOAA.)

Monday, March 01, 2021

jigging into spring

Plague Year(s) Bach Project, 13th month

I enjoyed learning the Sarabande in D minor in February, which was a perfect match as the piece has 28 bars, so I've been able to stick to my established speed of memorising a bar per day (skipping some of the troublesome chords which I can always fit in later). I do feel the sadness and the strength in that one.

Staying in the second suite, I'm now tackling the gigue, which has a few bars more, so I might end up with another fractionally memorised movement, let's see how it goes.

Some helpful links:

I'm starting with Inbal Segev's musings, as always, and I found a few recordings of the whole D minor suite, (with timestamps for the gigue in the link to take you there directly) from:
Ariana Kashefi
Eva Lymenstull
Misha Maisky
Laurens Price-Nowak

I'm also adding these videos to my youtube playlist "cello repertoire".

After 12 months with 329 practice days and 347 bars memorised, the list now looks like this (parts 2 upwards make up my revision rota, with the two most recently learned movements being revised on alternating days, and the others in a separate cycle):

1) movements I've studied for a month, then put aside for now
1.1. Prelude
1.2 Allemande

2) movements memorised in a significant part
1.3 Courante (2/3)
2.5 Minuet I&II (1/2)
3.4 Sarabande (1/3)

3) movements memorised in their entirety
1.4 Sarabande
1.6 Gigue
2.4 Sarabande
3.6. Gigue

4) movements memorised and synchronised with metronome
1.5 Minuet I&II
3.5 Bourree I&II

5) watch this space ...

... like a briiiiiidge over troublllllled water ...

Monday, February 22, 2021

something in the air

With all the worries about airborne viruses these days, we shouldn't forget that the air that we breathe in our cities isn't all that healthy in normal times either. Recent reports based on 2019 data provided detailed mortality burdens for pollution on a state level for India and for cities in Europe, so I rounded these up along with some studies on what parts of the body are damaged by pollution (spoiler alert: possibly all of them), for my latest feature which is out now:

A breath of deadly air

Current Biology Volume 31, Issue 4, 22 February 2021, Pages R161-R163

Restricted access to full text and PDF download
(will become open access again one year after publication)

Magic link for free access
(first seven weeks only)

Air pollution is affecting the health of most people around the globe, but problems are particularly severe in megacities, such as Hyderabad, India, shown here. (Photo: Daniel Dara/Unsplash.)

Sunday, February 14, 2021

spa break

#lostcities episode 9: Bad Nauheim

We're approaching the end of the series and coming to cities which I actually remember from my childhood. Memories left me with a soft spot for Bad Nauheim, even though when I was there as a child everybody was about a hundred years old and seeking spa treatment for some horrible diseases. My great-grandmother and great-aunt lived in a crumbling art nouveau villa which I've raved about before, and which in the whole series is the only property to mourn. Although the Frankfurter Str. is the main through road and quite noisy, the location is quite central and within walking distance of the railway station and the historic spa facilities. Cafe Bienenkorb in the Hauptstrasse is another reference point I remember.

Let's take it chronologically, though, this is what happened:

After fleeing from Königsberg (see episode 6) and rejoining the rest of the family in the sticks, my great-grandfather remembered that he quite liked the spa town of Bad Nauheim where he had spent time as a reconvalescent decades earlier. In July 1945 he moved there, initially to a room in Frankfurter Str. 26. By November he had moved to Frankfurter Str. 12 (the villa mentioned above), found space for the family, and started relaunching his trade with textiles. He died in March 1950, however, aged 66. My great-grandmother stayed at that address until she died in 1972. My great-aunt had continued the textile business until 1960, then bought the property with funds from the compensation for the lost factory in Königsberg. At that point she gave up on the textiles and operated a bed-and-breakfast for spa guests, but she hadn't inherited the business sense of her father, clocking up debts to wipe out the value of the property.

When I was visiting there as a child, we used to make fun of the fact that my great-aunt changed the layout of the flats all the time, so the running joke was that the loos are now where the kitchen used to be. Which may explain where the money went. She also hired a carpenter to build shelves for a customised floor-to-ceiling library (which I inherited, so mustn't grumble) and had a habit of taking taxi rides everywhere.

Of the town, I remember the swimming pool which included a heated outdoor basin even in winter (maybe not the most sustainable thing on climate grounds). I also went ice skating there (I believe Bad Nauheim used to be successful in ice hockey) and saw a lot of the historic spa buildings, like the ones in the post card below. Funnily enough I don't remember the lake at all, maybe that was too far, being on the other side of the town.

Re-visiting the town in 2010, I found the town layout built around the spa rather than a proper town centre slightly odd, but then again, the sheer wealth of art nouveau architecture that survived there makes up for that. Although it's still relatively small (amazingly, in 1970, only 14,000, but now upwards of 32,000), I could walk around a few days just looking at the houses. And it does have direct trains to Frankfurt, if one gets fed up with the small town thing.

Bad Nauheim 1956 (still looked very much the same when I spent time there in the 1970s). Source

#lostcities series so far:

  1. Elberfeld / Wuppertal 1919 - 1961
  2. Strasbourg 1901 - 1908
  3. Minden 1903 - 1952
  4. Tangermünde 1888 - 1916
  5. Rheydt 1923 - 1935
  6. Königsberg 1935-1945
  7. Aachen 1936-1940
  8. Idar-Oberstein 1940-1962

Thursday, February 11, 2021

some viral stories

Quite Covic-heavy this round-up of German pieces, with the variants covered in December (just before the issue exploded) and the vaccines in February (see the cover below), as well as a tongue-in-cheek appreciation of the dog-led diagnostics. Other topics available include soil biodiversity, ammonia emissions from human skin, and protein crystals found inside the glass needles of marine sponges.

The Covid stories are on open access, and some of the others appear to be too, not sure why.

Ausgeforscht: Wir Emittenten
Nachrichten aus der Chemie Volume 68, Issue 11, November 2020, Page 98
Access via Wiley Online Library

Der Stammbaum der Pandemie
Nachrichten aus der Chemie Volume 68, Issue 12, December 2020, Pages 64-65
FREE access via Wiley Online Library
related content in English: Pandemic genomics

Verflixt verschachtelt
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Pages 87-88
FREE access via Wiley Online Library

Der Covid-Schnuppertest
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Page 114
FREE access via Wiley Online Library

Biomineralisation: Im Innern der Glasnadeln
Chemie in unserer Zeit Volume 55, Issue 1, February 2021, Page 12
Access via Wiley Online Library
related content in English: Sponges feature

Impfen gegen Covid-19
Nachrichten aus der Chemie Volume 69, Issue 1, January 2021, Pages 50-53
Access via Wiley Online Library
related content in English: Vaccines feature

cool cover of the Feb issue of Nachrichten aus der Chemie, although not quite a representation of how the vaccines work ...

Monday, February 08, 2021

vaccines revolution

By mid January, a year after the novel coronavirus was formally identified and sequenced, eight new vaccines of three different types were approved in full or in emergency mode by at least one country. So I though this was a good time to have a look at how this miracle happened. Especially here in the UK we're still rubbing our eyes a bit as it is about the only aspect of the Covid response that has worked better than expected (so far).

As part of the special treatment for Covid related information, my feature has been available as an open access preprint for the last two weeks, but today it is officially out in the proper format, and still on open access:

How to develop 8 vaccines in 12 months

Current Biology Volume 31, issue 03, pages R101-R103, February 08, 2021

access to full text and PDF download
This is currently on open access as part of the general Covid-19 info policy from Cell Press. Should that change, it will become open access again one year after publication

Any problems with the link above, try the:

Magic link for free access
(first seven weeks only)

Although the new vaccines have materialised at record speed, they have been tested as thoroughly as any previous vaccines. (Photo: Lisa Ferdinando/US Secretary of Defense (CC BY 2.0).)

Looking ahead, I do hope that the success story of vaccine developments also translates into successful elimination of the disease, but it's too early to start victory celebrations. One thing I worry about here in the UK is the large gap between first and second dose which produces two problems:

1) patients feeling somewhat protected by the first dose increasing their risk behaviour may very well overcompensate the extent of protection they have. So if their infection risk is reduced by a factor of 2 but they are having 3 times as many risky encounters, they may in the end be more likely to catch it. So the only relaxing (of rules and precautions) should be happening as a function of second doses given, not of first ones.

2) having a vast population partially protected and still exposed to the virus could be a breeding ground for mutants resistant to the vaccine.

So, in the UK in particular, given how Johnson's government has mishandled and amplified the first and the second wave, I wouldn't rule out the possibility that they are cutting corners again and thereby facilitating the third wave.

PS In nerdy note-taking news, this feature completes 10 years since I started writing a feature for every issue of CB. Since issue 4 of 2011, there have been 235 features in 240 issues, so it worked out quite nicely, even if I say so myself.

Saturday, January 30, 2021

sadness and strength

Plague Year(s) Bach Project, 12th month

Ariana Kashefi recently played the D minor suite in a lockdown livestream and explained that it represents sadness and grief with an underlying sense of strength and courage. So I guess it's perfect for lockdown number three and the beginning of plague year number two. And to properly wallow in the sadness bit, I'm now moving on to the Sarabande.

Some helpful links:

I'm starting with Inbal Segev's musings, as always, and I found a few recordings of the whole D minor suite, (with timestamps for the sarabande in the link to take you there directly) from:
Ariana Kashefi
Eva Lymenstull
Misha Maisky
Laurens Price-Nowak

I'm also adding these videos to my youtube playlist "cello repertoire".

In January, I learned the second minuet of the D minor suite (there were some scary chords that put me off the first minuet). It took me just over 21 days to memorise its 24 bars, which inspired me to check if the rate of 1 bar per day of practice is typical and indeed it is: since March 15 2020 I have clocked up 300 days of practice and managed to memorise 311 bars. I should check how many bars the six suites have overall, but I suspect three years won't be enough to learn them all.

I spent the rest of the month memorising what was left of the Gigue in C, and learning to play the Bourrees in time with a metronome, so with all these improvements, the list now looks like this:

1) movements I've studied for a month, then put aside for now
1.1. Prelude
1.2 Allemande

2) movements memorised in a significant part
1.3 Courante (2/3)
2.5 Minuet I&II (1/2)
3.4 Sarabande (1/3)

3) movements memorised in their entirety
1.4 Sarabande
1.5 Minuet I&II
1.6 Gigue
3.6. Gigue

4) movements memorised and synchronised with metronome
3.5 Bourree I&II

Heinrich at last September's socially distanced slow session in Florence Park.

PS: predictably, I couldn't resist doing the maths, I think the total is 1933 bars, so learning all at one bar per day would take five years, three months and two weeks. Realistically though, I've spotted quite a few bars in suites 5 and 6 that I definitely won't be able to get into my head.

Wednesday, January 27, 2021

entering plague year 2

The novel coronavirus started spreading in the UK around this time last year, so we're now entering the second year. And we've passed 100,000 deaths even by the most conservative metrics used by the government. And with the new vaccines and the new variants, the second year will be a completely different game, although I'm not confident the UK government will handle it much better than the first one.

Oh and my new feature on the development of the vaccines that are now being used is out as a preprint, free access here, the regular publication date will be Monday Feb 8th. I'll do a proper blog post for it then.

Might be a good time to round up the Covid-related contributions from the first year:

Features

Blog entries

I'm a great fan of the Corona cover art of Der Spiegel, this is issue 03 of 2021.

Links

This Guardian editorial concludes: "the story of Britain’s pandemic will long serve as a monument to bad government."

See also the very depressing video summary from Led by donkeys.

Monday, January 25, 2021

marine marvels

It has almost become a January tradition (since Fantastic species and where to find them in 2017) that I start the year writing a light-hearted feature on the wonders of the natural world. So this years it's all about sponges:

Magical mysteries of marine sponges

Current Biology Volume 31, Issue 2, 25 January 2021, Pages R51-R54

Restricted access to full text and PDF download
(will become open access again one year after publication)

Magic link for free access
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Many sponges have hidden mineral skeletons, but glass sponges have their glass structures on display, like this Venus’ flower basket (Euplectella aspergillum) found in deep waters of the Pacific. (Photo: NOAA Okeanos Explorer Program, Gulf of Mexico 2012 Expedition (CC BY 2.0).)

PS Last year's "fantastic" feature was about evolutionary lineages losing or gaining legs when they change their way of locomotion:

Step changes in evolution

It is now in the open archives.

Where you'll also find the first feature of last year, about life after the anthropocene.

Saturday, January 23, 2021

gemstone town

#lostcities episode 8: Idar-Oberstein

Fun fact: All four of my grandparents lived at Idar-Oberstein for some time, although never more than three of them simultaneously. By the time I was born, however, two had died and the other two moved to the countryside, 30 km away from the town. Which is why it pops up in my list of cities that we lost touch with.

Much like Wuppertal, but on a ten-fold smaller scale, Idar-Oberstein is the result of a merger of two towns squeezed together in a river valley. The merger of Idar and Oberstein occurred soon after that of Barmen and Elberfeld, in October 1933, producing a new town of just over 32,000 residents, on the river Nahe (semi-famous for its vineyards). The little creek separating the two parts is the Göttenbach, and a high school serving both towns was located near that boundary and called the Göttenbach-Gymnasium. Which is what brought my paternal grandparents there in 1951. They lived in Hauptstraße, literally just across the road from school (which was in the building now occupied by the municipal administration, which you can see here).

Postcard: Hauptstraße Idar Oberstein, 1953, looking towards a well camouflaged Felsenkirche. It is more conpicuous in recent photos where it is painted white. This is the street where my paternal grandparents lived until 1960, although I’m not sure whether the relevant building appears in this shot.
Source

The maternal grandparents came there from Aachen in 1940, which looks like a strange move for a customs officer, but I am told my grandfather was transferred to a department involved in policing alcohol duties, so that sounds fun. Unfortunately, he was then called up for the war and didn’t come back. My grandmother died in Idar-Oberstein in 1962, less than two years after the other grandparents had moved to the sticks.

Idar-Oberstein in the post-war years was under French occupation control. I read that the authorities weren’t all that keen on prosecuting Nazi criminals. Instead, the Grande Nation relied on its cultural charms, with French being taught at the high school and French culture being supplied in abundance. I hear Jean-Paul Sartre and Simone de Beauvoir stayed there for a night in 1948 and watched an opera performance.

Desperate to create more space for cars, the town planners made the river Nahe disappear under a lid in the 1980s – they should have taken up the idea of Wuppertal and built a suspension railway above the river! Since the Nahe has disappeared, the remaining attractions of the town are now the Felsenkirche, a tiny church implausibly popping out of a vertical cliff face, where various people got married, and the museum of gems and minerals celebrating the long tradition of gemstone processing and trading. Links with Brazil are particularly strong, as many migrants from the region went there and sent minerals back. So you get to see lots of massive agates and amethysts hailing from Brazil but handled in Idar-Oberstein.

#lostcities series so far:

  1. Elberfeld / Wuppertal 1919 - 1961
  2. Strasbourg 1901 - 1908
  3. Minden 1903 - 1952
  4. Tangermünde 1888 - 1916
  5. Rheydt 1923 - 1935
  6. Königsberg 1935-1945
  7. Aachen 1936-1940
  8. Idar-Oberstein 1940-1962

Monday, January 11, 2021

post-truth is pre-fascism

Four years ago, ahead of the inauguration of a certain US president, I warned of the dangers of a post-truth world. After the November 2020 election that voted him out I wondered what we have to do to get some sense of truth back, after the world has become used to being flooded with toxic lies. Conspiracy theories not only disturb political process, they may also jeopardise the response to the Covid crisis.

I wrote a feature about this in the first week of December, writing about the strange beliefs of Republicans in the past tense, half hoping they might get bored of crazy conspiracies by the time the article comes out. Unfortunately, the opposite has happened and they decided it might be a good idea to storm the Capitol and try to prevent the completion of the official election process. A very good analysis of what happened, with just the right amount of references to Weimar Germany, is in this essay by Yale historian Timothy Snyder - from which I borrowed the title of this blogpost. Snyder makes the point that, on top of all the small and medium sized lies, the big lie that Trump won the 2020 election and had the presidency stolen from him could continue to bind his fanbase in their perceived victimhood and serve a future fascist coup like the Dolchstoss-Legende about the end of worldwar I served the Nazis. Trump might be too incompetent to lead that coup himself, but somebody else now patiently waiting in the wings could take over his devoted fanbase and use it for a successful putsch.

Now I'm somewhat less optimistic that the problem can still be fixed in the US, and if it can't the fallout will be catastrophic for the rest of the world as well, if only because raving lunatics around the world will feel encouraged to try the same. But to feed the small hopes we still have here are some thoughts on how to bring back a bit of reason.

Recovering a sense of reality

Current Biology Volume 31, Issue 1, 11 January 2021, Pages R1-R3

Restricted access to full text and PDF download
(will become open access again one year after publication)

Magic link for free access
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The denialists in the photos we had available in December looked comparatively sane compared to the photos from last week! Demonstration of denialists protesting against Covid restrictions in Leipzig, Germany. (Photo: Roy Zuo/Wikimedia Commons (CC BY-SA 4.0).)

Saturday, January 02, 2021

a city on the border

#lostcities episode 7: Aachen

Aachen is still there, physically, just lost to my family who left it behind. Today a city with 250,000 residents, it is doing quite well out of its technical university and the historic sites linked to Charlemagne who was crowned emperor there on Christmas Day 800. Located close to the point where the borderlines between Germany, the Netherlands and Belgium meet, it is also terrifically well connected with the high speed trains from Frankfurt and Cologne stopping there on their way to Paris or Brussels.

Aachen Hauptbahnhof in 1938, with the Haus Grenzwacht (which ironically never was the customs office although its name seems to suggest some sort of border protection function, but I think it refers only to it being an unusually high tower block for its time and close to the national border, so I suspect from the top you could probably see Belgium and the Netherlands. The Hauptzollamt is behind the viewer's back.
Source.

My grandfather worked at the customs office, and got moved around frequently, typically being relocated to a new city each time he got promoted. By the time he was posted to Aachen in January 1936, he had an official car and more than 100 people to boss around so it was kind of a last hurrah before the war from which he didn’t return.

When you step outside the main station, the former main customs office (Hauptzollamt) is on your left, it is now a listed building and looking very well kept, although I couldn’t find a postcard of it. Instead, the one above shows what may very well have been the view from his office window. The family lived in Mariabrunnstraße, just a block away from the Hauptzollamt and still close to the railway line. The street is a cul de sac for cars but has a footpath passing under the rails.

Although I have stayed at Aachen a couple of times and visited the sites mentioned, I haven't formed much of an attachment. One issue I have with the place is that I am missing the structure provided by a decent river. There is some water flowing from the Elisenbrunnen in the city centre and the area around that is ok, and the cathedral is an UNESCO World Heritage Site of course. I am also slightly spooked by the fact that the relevant time frame falls entirely into the Nazi era, so one can imagine the spirit prevailing in the main customs office, which by then would have been cleared of anybody who didn't go with the flow.

A modern photo of the Hauptzollamt (2014).
Source: Wikipedia

#lostcities series so far:

  1. Elberfeld / Wuppertal 1919 - 1961
  2. Strasbourg 1901 - 1908
  3. Minden 1903 - 1952
  4. Tangermünde 1888 - 1916
  5. Rheydt 1923 - 1935
  6. Königsberg 1935-1945
  7. Aachen 1936-1940
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