Archive for COVID-19

a journal of the plague year [almost gone]

Posted in Books, Kids, Mountains, pictures, Travel with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , on January 23, 2021 by xi'an

Read The stars are legion, by Kameron Hurley, which I brought back from Gainesville last year. Although I cannot remember why I bought the book, it must have been a “recommendation” on Amazon… The story is part unusual, part classical, with a constant switch between the two major characters [viewpoint].  And between different times. The style is complex, maybe too complex, as the universe is slowly revealing itself, through the perception biases of the characters. Including (spoiler!) one with multiple memory erasures and two attempts at recycling. Stars are actually (spoiler!) space-ships with some possibly organic elements that are decomposing (and showing the steel skeletons), with also apparently organic smaller vessels to travel between ships or fight between clans. Some of the ship inhabitants are mutants, possibly for being unprotected from space or ship radiations (although the control and propulsion of these ships is never mentioned), possibly because they are perceived as such by different groups in the ships, à la Huxley’s Brave New World? And there seem to be only females on-board, with all of them getting (mysteriously) pregnant at one time or another, rarely giving birth to children (associated with driving the ships? creating new ships?) but rather to other organic entities, apparently contributing to keeping the ship alive. All this is quite creative, with a powerful theme of power versus motherhood, but the story-telling is just too messy for me to have enjoyed it. The more because the type of subterranean universe where characters wander from one level to the next and discover supremely different ecosystems at each level never appealed to me. Since I read Verne’s Voyage au Centre de la Terre. (And I suddenly remembered dropping out of an earlier Hurley’s book.)

Cooked (the last remaining) pumpkin risotto with (legal) Lapsang tea, which worked out rather nicely, albeit loosing most of the Lapsang flavour. Had a week of (pleasant) cookie flavour home fragrance while my wife was preparing cookies for the entire family. Cooked a brunch with my son on the last Sunday of 2020, once again with Lapsang as drink. And had a Michelin take-away with my mom in Caen, since all restaurants remain closed till an unknown date. Which proved a great choice as it was surprisingly good, once out of the (potato starch) package.

Watched Season 2 of the BBC His Dark Materials series. Still impressed by the high level of the show (and enjoying it even more as I had forgotten basically everything about The Subtle Knife!) Except for the dark matter physicist turning to I Ching to understand her empirical experiment… But it remains a great series (esp. when mostly avoiding bears.) Also rewatched a Harry Potter film with my daughter, The Order of the Phoenix, which I found rather poor on the whole, despite a few great scenes (like the Wesley twins’ departure) and the fabulous rendering of the petty bureaucratic evil of Mrs. Umbridge throughout the film. And a part of The Half Blood Prince. Which sounded much better by comparison.

“It slowly dawned on me that it’s possible for the wise men who run your life for you to see disaster coming and not have a plan for dealing with it”

Read another K.J. Parker’s book, “How to rule an empire and get away with it“, sequel to “Sixteen ways &tc.” Light (mind-candy) but enjoyable bedside reading. Somewhat of a classical trick where a double becomes the real thing, if not in a Kagemusha tragic style.

For a resilient and recovery year

Posted in Kids, pictures, Travel with tags , , , , , , , , , on January 1, 2021 by xi'an

a journal of the plague year [december reviews]

Posted in Books, Kids, Mountains, pictures, Travel with tags , , , , , , , , , , , , , , , , , , , , , , , , on December 19, 2020 by xi'an

Read only a part of a Brandon Sanderson’s novel, Steelheart, that I found incredibly terrible (given the achievements of the writer). With a few cardboard characters, incl. the (compulsory) nerdy teenager with unique skills and a David Copperfield childhood (also named David) and cartoonesque villains with superpowers. Until I realised, while looking at its Wikipedia page, that this was intended as a (very?) young adult novel… And did not try to finish the book (first of a trilogy) before leaving it in the exchange section in front of our University library.

Cooked (and enjoyed) a fennel and (local) honey tarte tatin and a broccoli polenta with Vacherin (cheese). Made several rye breads as I find them easier to knead and bake than other flours, once I found that I could get fresh yeast by the gram from my favourite bakery.  Fell into a routine of cooking winter vegetables, like pumpkins, butternuts, and cabbages, Jerusalem artichokes (a pain to peel!) and (expensive) tuberous chervil. Plus the available mushrooms.

Watched a few episodes of the Korean drama Two Cops (투깝스), more for the scenes showing bits and pieces of Seoul, than for a very thin and predictive plot. Following a radio broadcast mentioning Carol Reed’s The Third Man as one of the best movies ever—although I had read Greene’s novel a long while ago—, I tried to find it online but ended up instead watching for the first time Fritz Lang’s Die 1000 Augen des Dr. Mabuse,  which is his third Mabuse film and the last film he shot (in 1960). While the harsh lights and grainy surveillance TV screens, along with absolutely everyone smoking, put some perspective to the story, connecting post-war West Germany with its immediate past, I did not enjoy much the acting, which sounded very artificial, and the plot was quasi-nonexistent.

Read Olin Steinhauer’s The Bridge of Sighs, which was his first novel, as I had greatly enjoyed The Tourist. It takes place in an unnamed Eastern European country that could be Moldova (since Hungary and Czechoslovakia are described as West, while Romania is mentioned as another country, but the city could well be Szeged, both for having its own Bridge of Sighs and for being crossed by the Tisa), right after the War, as a Stalinist regime is under construction and a rookie cop, grand-son of a communist ex-hero, tries to navigate the new regime. I really liked the book: it is very well-written, meaning an attention to style and perspective that stays away from the usual endless dialogues in crime novelsand the characters have depth and originality, I enjoyed also the somewhat Mediterranean cum Balkanic feel of this post-war Soviet satellite. And will presumably seek the following volumes from UK resellers…

Bayesian phylogeographic inference of SARS-CoV-2

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , on December 14, 2020 by xi'an

Nature Communications of 10 October has a paper by Philippe Lemey et al. (incl. Marc Suchard) on including travel history and removing sampling bias on the study of the virus spread. (Which I was asked to review for a CNRS COVID watch platform, Bibliovid.)

The data is made of curated genomes available in GISAID on March 10, that is, before lockdown even started in France. With (trustworthy?) travel history data for over 20% of the sampled patients. (And an unwelcome reminder that Hong Kong is part of China, at a time of repression and “mainlandisation” by the CCP.)

“we model a discrete diffusion process between 44 locations within China, including 13 provinces, one municipality (Beijing), and one special administrative area (Hong Kong). We fit a generalized linear model (GLM) parameterization of the discrete diffusion process…”

The diffusion is actually a continuous-time Markov process, with a phylogeny that incorporates nodes associated with location. The Bayesian analysis of the model is made by MCMC, since, contrary to ABC, the likelihood can be computed by Felsenstein’s pruning algorithm. The covariates are used to calibrate the Markov process transitions between locations. The paper also includes a posterior predictive accuracy assessment.

“…we generate Markov jump estimates of the transition histories that are averaged over the entire posterior in our Bayesian inference.”

In particular the paper describes “travel-aware reconstruction” analyses that track the spatial path followed by a virus until collection, as below. The top graph represents the posterior probability distribution of this path.Given the lack of representativity, the authors also develop an additional “approach that adds unsampled taxa to assess the sensitivity of inferences to sampling bias”, although it mostly reflects the assumptions made in producing the artificial data. (With a possible connection with ABC?). If I understood correctly, they added 458 taxa for 14 locations,

An interesting opening made in the conclusion about the scalability of the approach:

“With the large number of SARS-CoV-2 genomes now available, the question arises how scalable the incorporation of un-sampled taxa will be. For computationally expensive Bayesian inferences, the approach may need to go hand in hand with down-sampling procedures or more detailed examination of specific sub-lineages.”

In the end, I find it hard, as with other COVID-related papers I read, to check how much the limitations, errors, truncations, &tc., attached with the data at hand impact the validation of this philogeographic reconstruction, and how the model can help further than reconstructing histories of contamination at the (relatively) early stage.

a journal of the plague year [mo’vember reviews]

Posted in Books, Kids, Mountains, pictures, Travel with tags , , , , , , , , , , , , , , , , , , , , , on December 5, 2020 by xi'an

Read a short manifest [in French], Décarcérer [Uncarcerate] written by Sylvain Lhuissier about the uselessness of the carceral system and the potential alternatives. Much easier to read than Foucault’s Surveiller et Punir, obviously, but the author is also an actor in the construction of such alternatives in France. Most interestingly, he points out that the arrival of the COVID pandemic, with overpopulated prisons being obvious hotspots, led to an almost instantaneous reduction of the carceral population thus brought below its nominal capacity, without a ensuing explosion in criminal activities.

Made a few jars of green tomato marmalade, as there were a few left when I cleaned my vegetable patch. With little sugar and some peppers to stand between marmalade and chutney. And found a bakery cooking kouignou amman almost on my bike path, although the calories input they provide would require a much longer détour..! And also had a long discussion (at a safe distance) with a tea dealer, who made me taste a unique white Pu Ehr from Laos. She also had many tips on Kunming (even though it sounds less and less likely ISBA 2020 will take place there.)

Read a touching novel [in French] by Akira Mizubayashi, Âme brisée [Broken soul], a moving story around music, deracination, lutherie, childhood memories, travelling between France, Japan and China. (Judging from the summaries of his other books, the themes sound central to the author’s work.) 

Watched a few episodes of The Magicians (although Season 1 came out in… 2015!), although I had not much enjoyed the book (volume 1). And found them an improvement, considerably so, with most characters having enough of a depth and flaws aplenty to compensate for the still terrible plot with its Narnia-esque hidden universe. The central characters Quentin and Alice are pleasantly making themselves quite antipathetic. But the inherent dependence on the weak book plot, a growing boredom (and the terrifying perspective of an enormous number of episodes!) made me stop from pursuing the experiment!