Thursday, April 30, 2020

science news 30.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.



astrobiology

4-billion-year-old nitrogen-containing organic molecules discovered in Martian meteorites

Newly discovered exoplanet dethrones former king of Kepler-88 planetary system


evolution

Bizarre 66 million-year-old fossil from Madagascar provides clues on early mammals

New fossils rewrite the story of dinosaur evolution and ecology -- and change the appearance of Spinosaurus
Scientists have long opposed the idea that dinosaurs lived in aquatic habitats. Now, an international team of researchers, supported by the National Geographic Society, has discovered unambiguous evidence that Spinosaurus aegyptiacus, the longest predatory dinosaur known to science, was aquatic.


conservation

Thousands of miles of planned Asian roads threaten the heart of tiger habitat
This reminds me of my feature on the world with 2 billion cars (open access).

Tuning into dolphin chatter could boost conservation efforts

Simulated deep-sea mining affects ecosystem functions at the seafloor


biomedical

Antibodies from llamas could help in fight against COVID-19



Scientists were inspired by antibodies produced by this llama, named Winter, to develop their antibody against SARS-CoV-2. Winter is four years old and still living on a farm in the Belgian countryside operated by Ghent University's Vlaams Institute for Biotechnology.
Credit: Tim Coppens


sustainability

Upcycling spongy plastic foams from shoes, mattresses and insulation
The material known as polyurethane foam, in the chemical lingo.

Heat-friendly microbes provide efficient way to biodegrade plastic
PET, this time.

Engineers make a promising material stable enough for use in solar cells
A Purdue University-led research team has found a way to make halide perovskites stable enough by inhibiting the ion movement that makes them rapidly degrade, unlocking their use for solar panels as well as electronic devices.

humans

Evidence of Late Pleistocene human colonization of isolated islands beyond Wallace's Line

Deformed skulls in an ancient cemetery reveal a multicultural community in transition
That's in the settlement of Mözs, today's Hungary, established around 430 AD.


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From the news media:

Wednesday, April 29, 2020

science news 29.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.



astrobiology

Hubble watches comet ATLAS disintegrate into more than 2 dozen pieces


evolution

Micro-CT scans give clues about how hero shrews' bizarre backbones evolved


ecology

Study reveals important flowering plants for city-dwelling honey bees

Understanding deer damage is crucial when planting new forests


Life on the edge

Arctic wildlife uses extreme method to save energy
Birds in Svalbard shut down their immune system in the arctic winter to save energy, apparently. Don't try this at home.

Shrinking instead of growing: how shrews survive the winter



The common shrew is a survivor: to save energy, it does not hibernate, but simply becomes smaller.
Credit: Christian Ziegler


humans

Two-person-together MRI scans on couples investigates how touching is perceived in the brain


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From the news media:

Iceland tested 12% of its population for coronavirus and spotted the outbreak in the faraway Austrian ski resort Ischgl before anybody else did. Interview with the prime minister, Katrín Jakobsdóttir

Meanwhile, in countries that didn't do so well, the official hospital deaths are only the tip of an iceberg of additional deaths - analysts at the Financial Times are now looking at the excess deaths over the long-term seasonal average and some of these results are quite scary.



Monday, April 27, 2020

a crisis of touch

Open Archive Day

One of the collateral problems arising from the covid-19 pandemic is the fact that the distancing dramatically reduces opportunities to experience touch with other humans, as for instance, V (the artist formerly known as Eve Ensler) has pointed out in the Guardian recently (I really liked her suggestion that all the mad female grooming culture is just serving as an excuse to get a regular dosis of gentle touching).

See also this feature in Wired magazine on skin hunger.

Even before this pandemic, some have argued that western societies were becoming more touch averse and that this was having a negative impact on our mental health, as I reported in my feature from last April, which is now in the open archives. With distancing measures likely to remain necessary for months if not years, one can imagine that these problems will become even more serious.

Are we losing touch with our world?




The human sense of touch is important for well-being, but current trends in society tend to discourage touching behaviours. (Photo: andreas160578/Pixabay.)


Sunday, April 26, 2020

stuck inside

new tag: covid19

The death cult that is the populist right is beginning to clamour for an end to the UK's restrictions (it's hardly a lockdown as people around here go out and about as they please), so let's check the maths, shall we?

In the last seven days (18.-25.4.) the UK's hospital deaths went up by 4855, that's 694 per day, roughly 700. I don't trust that figure as it may well be capped by test availability and hospital availability, i.e. more people have died but haven't been tested, and/or didn't get hospital treatment when they needed it, but sadly it's the best figure we have available. So what does it tell us?

Assuming around 1% mortality and 3 weeks from infection to reported death, this tells us that around the 1st of April, 70,000 people caught the disease every freaking day. This figure is hopefully going down as long as we keep that r value below 1, but if you look at all the lovely data from lots of different countries on the Financial Times analysis page, it is typically going down very slowly. Part of the reason being that even without going out, the people unaware that they're infected will still pass it on to eg one other person in their immediate sphere, hence the r values of just below one that have been reported eg in Germany.

So if we're very lucky, and this is just a guess based on the FT curve for Italy's recovery, the rate of new infections has gone down by half this month, so we might see 35,000 new infections daily around now. With the restrictions in place. As authorities are failing to get tests up to 20,000 people per day, there is no way we could keep the spread contained if we start from this level.

Give it another month, and we might be at 17,000, and by then the govt. may have figured out the logistics and the science of testing people and chasing up their contacts, and test them too, so my guess would be, if handled well (what are the chances of that happening?), the UK could ease restrictions and return to test and trace approach at the end of May.

Obviously, if the deatheaters win the argument and lift restrictions now, we're back on the old exponential with an r significantly greater than 1, so it will be six-figure death counts and/or another lengthy lockdown.

Takehome message: As the fall in cases is much slower than the rise, every day lost in doing something may cost a week more spent in lockdown. Same is true for every day coming out of lockdown when we don't really have the ways and means of keeping the spread under control.





Daily deaths smoothed out over 7-day window, screenshot grabbed from the Financial Times today. (The page changes daily while keeping the same URL, so there isn't any other way of referencing a specific dataset, other than screenshot and paste, I'm afraid.)


PS from the day (12. or 13.3.) when I heard one of the govt. science guys mention herd immunity and realised they were attempting to drive us over a cliff, I had the suspicion that Dominic Cummings was hiding behind a curtain and telling them what to say. Yes scientists disagree on details and the best strategy, but that idea, which would easily lead to 400k unavoidable deaths, plus a malus of those produced by capacity overload, was so illiterate it could only come from the delusional brains of Cummings and kind of deatheaters he's trying to promote. This weekend, revelations from the Guardian, based on several whistleblowing members of the Sage advisory committee, have confirmed my suspicion that DC was indeed an active participant in Sage meetings.

Saturday, April 25, 2020

jigging on

So in month two of the plague year I've found my way through the pair of minuets from the first cello suite, which is one of the easiest movements in the suites, so I reckon it's all uphill from here. I really love the first repeat of the second minuet to bits, I could play that all day and am developing a kind of deja vu illusion in that I am wondering if that tune hasn't been used in some French chanson that I used to know as a child. Maybe not, but somebody should have made a song out of that one.

Anyhow, upwards and onwards to the gigue of the first suite (movement 1.6).

The video of Patrycja Likos is a helpful starting point as she plays the movements very straight and the fingerings are clearly visible at all times. One could almost learn the piece just by copying her moves.

For a slightly more engaging performance and more artistic videography (I should do a blind test to rule out the possibility that it is the videography that tricks me into finding this performance more engaging), try this recording from Denise Djokic.

And then consider the helpful hints from Inbal Segev. She's done a short tutorial (or two in some cases) for every single movement, which is quite something.

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

Every other day I still listen to the complete first suite on soundcloud by Mischa Maisky. (I also have the complete suites by Rostropovich on CD but am beginning to spot artistic choices in there that I don't like that much. Will definitely buy Segev's recording when Blackwell reopens.)

Oh, and I ordered a study book about the first suite online which should arrive next week. Watch this space.



I like reflections and bridges ... and I sometimes take random photos of our family cello, which now come in handy.

Friday, April 24, 2020

science news 24.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


astrobiology

Promising signs for Perseverance rover in its quest for past Martian life
New research indicates river delta deposits within Mars' Jezero crater -- the destination of NASA' Perseverance rover on the Red Planet -- formed over time scales that promoted habitability and enhanced preservation of evidence.




NASA's Mars Perseverance Rover, expected to launch in July 2020, will land in Jezero crater, pictured here. The image was taken by instruments on NASA's Mars Reconnaissance Orbiter, which regularly captures potential landing sites for future missions.
Credit: NASA/JPL-Caltech/ASU

Researchers use 'hot Jupiter' data to mine exoplanet chemistry
After spotting a curious pattern in scientific papers -- they described exoplanets as being cooler than expected -- Cornell University astronomers have improved a mathematical model to accurately gauge the temperatures of planets from solar systems hundreds of light-years away.


evolution

Ocean biodiversity has not increased substantially for hundreds of millions of years -- new study

Fossil frogs offer insights into ancient Antarctica

Jurassic Park in Eastern Morocco: Paleontology of the Kem Kem Group

Giant teenage shark from the Dinosaur-era

Coronaviruses and bats have been evolving together for millions of years


conservation

North Atlantic right whales are in much poorer condition than Southern right whales


biomedical

Novel coronavirus detected, monitored in wastewater
Love a bit of wastewater-based epidemiology.


sustainability

Zero-emissions Boston could save 288 lives and $2.4 billion annually: BU study


humans

Icelandic DNA jigsaw-puzzle brings new knowledge about Neanderthals
An international team of researchers has put together a new image of Neanderthals based on the genes Neanderthals left in the DNA of modern humans when they had children with them about 50,000 years ago. The researchers found the new information by trawling the genomes of more than 27,000 Icelanders. Among other things, they discovered that Neanderthal children had older mothers and younger fathers than the Homo-Sapien children in Africa did at the time.

Women's faces in Time Magazine throughout history
In a paper published in Journal of Cultural Analytics, an interdisciplinary group of researchers used machine learning to extract 327,322 faces from an archive of Time magazine issues dating from 1923 to 2014. Titled the Faces of Time project, findings reveal that more images of female faces were presented during eras where women took on an increased participation in public life, and fewer images were shown during periods characterized by a backlash against feminism.

Health impacts of pollution upon indigenous peoples

To combat COVID-19, behavioral pitfalls must be addressed



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From the news media:

Thursday, April 23, 2020

science news 23.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


earth

Evidence for plate tectonics on earth prior to 3.2 billion years ago


ecology

Disappearing Alaskan sea ice is significant for Arctic marine ecosystem
A new study shows that plant materials originating in Arctic sea ice are significantly incorporated into marine food webs that are used for subsistence in local communities of the greater Bering Strait region. The research has the potential to demonstrate the importance of sea ice ecosystems as a source of food in Arctic waters in Alaska and beyond.

Surface feeding could provide more than just snacks for New Zealand blue whales

New bat species discovered -- cousins of the ones suspected in COVID-19


conservation

More protections needed to safeguard biodiversity in the Southern Ocean

Caribbean coral reef decline began in 1950s and 1960s from local human activities



Staghorn coral can form dense groups called 'thickets' in very shallow water, providing important habitat for other reef animals, especially fish. Elkhorn coral, along with staghorn coral and star corals built Caribbean coral reefs over the last 5,000 years.
Credit: NOAA


biomedical

Structure-based design of antiviral drug candidates targets SARS-CoV-2 main protease


food and drink

Sweet potato microbiome research important first step towards improving yield
Despite the importance of sweet potato, little is known about the sweet potato microbiome. ;A plant's microbiome profoundly impacts its health and development,' explains Brooke Bissinger, an entomologist who recently published a study on sweet potatoes in Phytobiomes Journal. 'We sought to better understand the sweet potato microbiomes by characterizing it within and between actual working farms.'

sustainability

Windows will soon generate electricity, following solar cell breakthrough
Semi-transparent solar cells that can be incorporated into window glass are a 'game-changer' that could transform architecture, urban planning and electricity generation,

Portland State study finds bike lanes provide positive economic impact


humans

What protects minority languages from extinction?
A new study by Jean-Marc Luck from Paris and Anita Mehta from Oxford published in EPJ B, uses mathematical modelling to suggest two mechanisms through which majority and minority languages come to coexist in the same area.
The maths comes from studies of the ecology of predator-prey relations, apparently. Slightly worrying for speakers of minoritised languages. But on the plus side, there are clues as to what kind of attractiveness can help the languages survive.


dystopian futures

Who's a bot and who's not
The big philosophical question of our age: Am I a bot? What if I fail to click all the squares that contain traffic lights. Does that make me a bot?

How we end up 'confined' on YouTube
Researchers have studied recommendations from a thousand YouTube videos on different subjects, thereby running through half a million recommendations. Their results show that contrary to the algorithms of other platforms, which seem to promote the exploration of novelty and serendipity, YouTube's is actually an exception, generating a number of confinement phenomena.

Interesting point that. I did notice that YouTube bots knew me a lot better than those of other platforms even when I wasn't using it all that much - presumably because they actually measure how much time you're willing to spend with a given video, whereas other formats often only have clicks to count. I don't let them confine me to one box though, I make sure I feed them with wildly different material in a dozen different languages to keep them guessing and to keep the recommendations varied.



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From the news media:




Wednesday, April 22, 2020

science news 22.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


astrobiology

ASU scientists lead study of galaxy's 'water worlds'
In seeking to learn more about Neptune-like exoplanets, an international team of researchers, led by Arizona State University, has provided one of the first mineralogy lab studies for water-rich exoplanets.


ecology

Expansion of world's cities creating 'new ecological niches' for infectious diseases

Lizards develop new 'love language'
Free from the risk of predators and intent to attract potential mates, male lizards relocated to experimental islets in Greece produce a novel chemical calling card.



This is a male Podarcis erhardii, the Aegean wall lizard.
Credit: Colin Donihue


nanoworld

Cool down fast to advance quantum nanotechnology
An international team of scientists have found an easy way to trigger an unusual state of matter called a Bose-Einstein condensate. The new method, recently described in the journal Nature Nanotechnology, is expected to help advance the research and development of quantum computing at room temperature.


biomedical

How SARS-CoV-2 gets into respiratory tissue -- and how it may exploit one of our defenses

A new biosensor for the COVID-19 virus
This one is based on RNA-sequence recognition and detection by surface plasmon resonance. In yesterday's news collection there was one based on whole virus detection by antibodies and electronic sensors.


food and drink

Coffee changes our sense of taste


climate change

North pole will be ice-free in summer
Summer Arctic sea-ice is predicted to disappear before 2050, resulting in devastating consequences for the Arctic ecosystem. The efficacy of climate-protection measures will determine how often and for how long.


sustainability

Penn Engineering's new scavenger technology allows robots to 'eat' metal for energy


humans

Study sheds light on unique culinary traditions of prehistoric hunter-gatherers

Human pregnancy is weird -- new research adds to the mystery
University at Buffalo and University of Chicago scientists set out to investigate the evolution of a gene that helps women stay pregnant: the progesterone receptor gene. The results come from an analysis of the DNA of 115 mammalian species.



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From the news media:

Financial Times (open access): Coronavirus could help push us into a greener way of life. For all its horror, the pandemic may change our habits when nothing else could.

Tuesday, April 21, 2020

science news 21.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.



astrobiology

Exoplanet apparently disappears in latest Hubble observations
What scientists thought was a planet beyond our solar system has 'vanished.' Though this happens to sci-fi worlds (like Superman's home planet Krypton exploding or the Death Star's attack on Alderaan), scientists seek a plausible explanation. One interpretation: instead of a planet, it could be a dust cloud produced by two large bodies colliding.


evolution

Promiscuity in the Paleozoic: Researchers uncover clues about vertebrate evolution
By looking at the DNA of living animals, researchers from the Okinawa Institute of Science and Technology Graduate University, alongside an international team of collaborators, have revealed early events in vertebrate evolution, including how jawed vertebrates arose from the mating of two different species of primitive fish half a billion years ago.

Oak genomics proves its worth
A landmark 10 article collection published in the April 16 issue of New Phytologist helps clarify the evolution of oaks and identify key genes involved in oak adaptation to environmental transitions and resistance to pathogens. It also addresses the implications and history of oak hybridization, and traces genomic evidence for an estimated 56 million years of oak evolution.


ecology

Spores, please!
Black poplar leaves infected by fungi are especially susceptible to attack by gypsy moth caterpillars. A research team at the Max Planck Institute for Chemical Ecology found that young larvae that fed on leaves covered with fungal spores grew faster and pupated earlier than those feeding only on leaf tissue. The results shed new light on the co-evolution of plants and insects, in which microorganisms play a much greater role than previously assumed.



A gypsy moth caterpillar (Lymantria dispar) relishing the spores of Melampsora larici-populina a rust fungus that has spread on a poplar leaf. The new study shows that the insect is not only herbivorous, but also fungivorous, that is, likes to feed on nutrient-rich fungi.
Credit: Franziska Eberl, Max Planck Institute for Chemical Ecology

Rare video captures humpback whale nursing behaviors in UH Mānoa research

Ants restore Mediterranean dry grasslands

A new mouse of the Peromyscus maniculatus species complex (Cricetidae) from the highlands of central Mexico
Researchers analysed specimens collected in 1968 using both molecular and morphological criteria and concluded they represent a new rodent species. (Link to the abstract provided by the authors.)


nanoworld

Self-aligning microscope smashes limits of super-resolution microscopy

Scientists uncover principles of universal self-assembly


biomedical

Cost-effective canopy protects health workers from COVID infection during ventilation
I imagine this could be important - with all the breathing support given, there must be a considerable risk of viruses being blown around ...


Diagnostic biosensor quickly detects SARS-CoV-2 from nasopharyngeal swabs
Now, researchers reporting in ACS Nano have developed a field-effect transistor-based biosensor that detects SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19, in less than one minute.
This could definitely become very important.

Corona and air pollution: How does nitrogen dioxide impact fatalities?


food and drink

Chocolate 'fingerprints' could confirm label claims
The flavor and aroma of a fine chocolate emerge from its ecology, in addition to its processing. But can you be certain that the bar you bought is really from the exotic locale stated on the wrapper? Now, researchers are presenting a method for determining where a particular chocolate was produced by looking at its chemical 'fingerprint.'
As a parent, I am thinking that "chocolate fingerprints" may be creatiing the wrong impression ...


sustainability

Faster-degrading plastic could promise cleaner seas
To address plastic pollution plaguing the world's seas and waterways, Cornell University chemists have developed a new polymer that can degrade by ultraviolet radiation,

Aquaculture at the crossroads of global warming and antimicrobial resistance


humans

Origins of human language pathway in the brain at least 25 million years old


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From the news media:

Monday, April 20, 2020

hope and comfort

Three weeks ago, my guess of what people may want to read right now, close to the peak of the pandemic in many places, just past it in some, and I went for something on finding hope and comfort by reconnecting with nature.

So I've covered some conservation success stories, along with examples of how nature can cheer us up in difficult times. And perhaps most importantly, my hope that this pandemic will scare humanity into doing something effective about climate change.

All of which is out now:


Finding comfort in nature

Current Biology Volume 30, Issue 8, 20 April 2020, Pages R329-R331

FREE access to full text and PDF download



As the COVID-19 pandemic limits the contacts and movements of people, reconnecting with nature may offer comfort and ways to a more sustainable future. (Photo: Sippakorn/Pixabay.)

Sunday, April 19, 2020

chronicle of a disaster foretold

I need a bit of clarity about the disaster unfolding here and when and why and who knew what.

For me personally it is easy to reconstruct - I was in Germany from 5.-14.3., where case numbers were three days ahead of the UK, and where media pay a lot more attention to what happens in other EU countries such as Italy, so I had a bit of a headstart in awareness. Around March 13th, when I heard the govt. advisors mentioning herd immunity, I did the back-of-the-envelope calculation. 66 million people x 60% infection rate needed for herd immunity x 1% mortality = 396,000 people dead unavoidably. Plus avoidable deaths of those who don't get access to a ventilator when they need one. Might be as many again, so could be anything up to 800,000.

It was a complete horror show to watch how it took the government another 10 days to realise that a six-figure number of casualties would look bad on all of their CVs, until they made a screeching U-turn. In these 10 days, infections went up by a factor of 10, and the deaths went up from 30 to 330. Based on China, I calculated that after lockdown, deaths still rise by two orders of magnitude (30 to 3000 in China's case). So my expectation for the UK is 33,000. We're well on track to reach this figure. Changing course 10 days earlier would have saved 90% of these, i.e. 30,000.

So, considering that it took me nothing more than two simple multiplications to realise the govt was driving us over a cliff, I am really curious about who knew what and what they are going to say in their defence when they end up in court for killing 30,000 people by gross negligence. Based on my own notes from the events of the past weeks, and on today's comprehensive reports in the Sunday Times (paywalled but there are copies floating around on social media) and in the Observer, I've drawn up a simple timeline of how we got into this mess.

covid-19 timeline

2016 Pandemic preparation exercise Cygnus finds health system would collapse, naming many key problems including shortage of ventilators and PPE. Recommendations resulting from the analyses were never implemented.

31.12.2019 China alerts WHO that several cases of an unusual pneumonia had been recorded in Wuhan.

22.1.2020 WHO begins daily briefings on new coronavirus disease
UK government convenes first meeting of its scientific advisory group for emergencies (Sage) to discuss the virus

24.1. Chinese experts report in the Lancet new coronavirus disease with 800 confirmed cases and confirmed human-to-human transmission.
First Cobra meeting considering the virus happens without Johnson, chaired by Hancock who says risk to UK is low.

29.1. First cases identified on British soil: two Chinese nationals in York.

30.1. UK govt. raises risk from low to moderate. WHO raises highest level of alert.

31.1. Johnson speech on Brexit Day.

3.2. Johnson speech at Greenwich: “There’s a risk that new diseases such as coronavirus will trigger a panic and a desire for market segregation that go beyond what is medically rational to the point of doing real and unnecessary economic damage.”
”Humanity needs some government somewhere that is willing at least to make the case powerfully for freedom of exchange, some country ready to take off its Clark Kent spectacles and leap into the phone booth and emerge with its cloak flowing as the supercharged champion of the right of the populations of the Earth to buy and sell freely among each other.”


7.2. Chinese doctor reprimanded for his early warnings dies of the disease. His death is also reported in the UK.

13.2. Cabinet reshuffle. Matt Hancock remains health secretary.
Johnson goes on 2-week half-term holiday at Chevening.

19.2. Champions League match Atalanta Bergamo v Valencia at Bergamo acts as a major spreading event, setting up new hotspots of infection in Valencia as well.

21.2. Italy imposes lockdown on many northern cities

25.2. Johnson returns to London for fundraising event, the Winter Party.

26.2. John Edmunds and colleagues present a scenario to govt. advisors that predicts 380,000 deaths and need for 220,000 intensive care beds. Their report emphasised the urgent need for a lockdown.

29.2. Johnson and Symonds at Chequers, release baby news.

1.3. Meeting of Sage, Dept. Health and NHS sees evidence from Italy suggesting 8% of people infected will need hospital treatment (up from 4-5%), raising concern re NHS ability to cope.

2.3. First Cobra meeting on coronavirus attended by Johnson, after he missed the previous five. Battle plan drawn up including plans to establish Nightingale field hospitals.

3.3. Johnson says he still shakes hands with everybody, including Covid-19 patients.

7.3. Johnson attends Rugby match at Twickenham.

9.3. Italy extends lockdown to the whole country.

10.-13.3. Cheltenham Festival goes ahead with 250,000 visitors, encouraged by govt.

11.3. WHO declares global pandemic.
Champions League game Atletico Madrid v Liverpool goes ahead in Liverpool and 3000 Atletico fans attend although Spain is already beginning lockdown measures.

12.3. Johnson at press conference: “More families, many more families, are going to lose loved ones before their time.”

13.3. UK govt. moves from contain to delay phase – emphasizing hygiene measures, but giving up contact tracing and systematic testing. Patrick Vallance, the govt. chief scientific advisor discusses herd immunity as part of the government's strategy.

18.3. School closures announced. Last day of school: Fri 20.3. ?
Pubs and restaurants also to close at the end of business on 20.3.

23.3. UK govt announces stay at home order for following day. Official hospital deaths announced by that day: 335, with more than 20% daily increases, tracking Italy’s curve with 2 weeks delay.

1.4. According to Doris Ann Williams, ceo of British In Vitro Diagnostics Association cited in the Sunday Times, this was the date her organisation was first approached by the govt. to help scale-up of testing.
The British Healthcare Trades Association (BHTA) was ready to help supply PPE in February — and throughout March — but it was only on April 1 that its offer of help was accepted.



This illustration shows the ultrastructural morphology of the novel coronavirus responsible for the 2019–2020 pandemic of the COVID-19 coronavirus disease. (Photo: Alissa Eckert, MS, Dan Higgins, MAM.)

PS after writing this it occurred to me that March 21st was the 100th day after the election. Is this the worst 100-day record of any government ever?

Some links:

Polly Toynbee's analysis on the situation after the Sunday Times report.


UPDATE 5.5.2020:
The Guardian has published an extensive report with a timeline on 30.4. From this I learned that the Chief Medical Officer, Chris Whitty, said on March 3rd (at the press conference where Johnson said he was shaking hands with everybody) that in a worst case scenario 80% of the population could become infected and 1 % might die. Nobody seems to have done the multiplication which would have shown a result of 528,000 deaths (still not including those to the health system collapsing under the overload).

Also from the Guardian report, a couple of quotes from Patrick Vallance, 13.3.: “Our aim is to try and reduce the peak, broaden the peak, not suppress it completely,” Vallance explained on BBC Radio 4’s Today programme: “Also, because the vast majority of people get a mild illness, to build up some kind of herd immunity, so more people are immune to this disease, and we reduce the transmission. At the same time, we protect those who are most vulnerable to it. Those are the key things we need to do.”

Asked on Sky News what proportion of the population would need to become infected to achieve herd immunity, Vallance replied: “Probably about 60% or so.”

Saturday, April 18, 2020

oxford pubs

Oxford pubs
Dave Richardson
Amberley Publishing 2015

How very ironic to read a book about Oxford pubs while all of them are closed for a few months. But hey, finally I have the time to catch up with the reading.

So from the Amberley series of local interest books (they also have one about the Oxford waterways), here come the pubs, 38 of them. They come in four parts: centre, north, east, and further afield. Within each section, they are ordered alphabetically, which doesn’t make much sense, especially as there are often connections and comparisons to be drawn between pubs that are located close to each other.

The author appears to have visited each one (possibly in the company of photographer Phil Gammon) and had a good chat with the landlords, and found out about the history, which generally gives a good impression of what the place is like even if you don’t know it. I know more than half the pubs included, so I can calibrate my expectations on those and get a very clear impression of what the others are like. It’s also fascinating to read up on the ancient history of places you know.

Strangely though, the one and only reason why I know that many pubs isn’t even mentioned in the book, not once. It’s folk sessions (aka pub sessions or also Irish sessions, even though I tend to prefer the non-Irish ones). When the pubs aren’t closed, there are about 18 such sessions happening in Oxford every month (and there would be loads this weekend for the Folk Weekend), where everybody (including even me) can walk in and play along. This modus operandi isn’t widely understood by the general public (and even the bar staff). Hence, when the author mentions that music is being played eg at the Half Moon on certain nights, he doesn’t seem to realise the nature of the beast. On a similar note, one group of people that has probably kept quite a few pubs afloat over the difficult years isn’t mentioned at all: Morris dancers.

The author seems to like his pubs quaint and old-fashioned, unspoiled by progress, as he likes to say, but as progress offers so much entertainment in the comfort of your own home, it is easy to see that they are struggling to reinvent themselves in various ways. Here’s hoping they come back after this coronavirus crisis, so I can play some more wrong notes in public.



PS at 14.99 RRP, these books are a bit steep for 96 pages (with lots of colour photos though) - but I think they are available from The Works at less than half price.


Update 23.4. Pubs may be among the last businesses that will reopen, and will probably need substantial help to survive, reports the Guardian this week.

Friday, April 17, 2020

biofoundries feature

I didn't really know what biofoundries were until I was asked to write a feature about them, but it turns out they are research centres combining synthetic biology (which I've covered before so phew, that's something I can cling to) with artificial intelligence (ditto). So all good, I just had to connect a few more dots, which is my favourite pastime.

The resulting feature is out now in Chemistry & Industry:

Intelligent Biotech

Chemistry & Industry 84, No. 3, pp 22-25.

access via:

Wiley Online Library
(paywalled)

SCI (members)


Here's a sneaky preview of the first page:

Thursday, April 16, 2020

science news 16.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


earth

Journey to the center of the Earth
In an effort to investigate conditions found at the Earth's molten outer core, researchers successfully determined the density of liquid iron and sound propagation speed through it at extremely high pressures. They achieved this with use of a highly specialized diamond anvil which compresses samples, and sophisticated X-ray measurements. Their findings confirm the molten outer core is less dense than liquid iron and also put values on the discrepancy.


ecology

Human handling stresses young monarch butterflies
People handle monarch butterflies. A lot. Every year thousands of monarch butterflies are caught, tagged and released during their fall migration by citizen scientists helping to track their movements. And thousands of caterpillars are reared by hand or used in classroom demonstrations and outreach events. These activities can provide valuable scientific data and educational benefits for the people participating in them. But how do the monarchs themselves feel about being handled by humans?


conservation

Logging threatening endangered caribou



Cutting down forests means we're also cutting down woodland caribou, says a pioneering study by University of Guelph ecologists showing that logging in Ontario's extensive boreal stands threatens populations of the elusive but iconic herbivore.
Credit: Dr. Tal Avgar


biomedical

New COVID-19 test quickly and accurately detects viral RNA


climate change

Unusually clear skies drove record loss of Greenland ice in 2019


humans

Milk pioneers: East African herders consumed milk 5,000 years ago

Little scientists: Children prefer storybooks that explain why and how things happen



---------------


From the news media:


How Cuba deals with Covid-19




Wednesday, April 15, 2020

science news 15.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


astrobiology

Beacon in space: BRITE Constellation observes complete nova eruption for the first time


earth

'A bad time to be alive': Study links ocean deoxygenation to ancient die-off

Volcanic CO2 emissions helped trigger Triassic climate change


ecology

Flamingos form firm friendships



Flamingo friends
Credit: Paul Rose/WWT Slimbridge


Study points to evidence of stray dogs as possible origin of SARS-CoV-2 pandemic


conservation

A new species of black endemic iguanas in Caribbean is proposed for urgent conservation


nanoworld

Study reveals unique physical, chemical properties of cicada wings


humans

Arduous farm labor in the past means longer working hours today
A new study in The Economic Journal finds that societies with a history of farming crops heavily reliant on labor effort prefer harder work and longer hours.

Autism in males linked to defect in brain immune cells, microglia



---------------


From the news media:

How about some self-isolating animal pictures.

As the current science advisor to the UK govt. has obviously been brainwashed by Dominic Cummings, it is nice to hear from a previous holder of that post, David King.

Also, the Financial Times is still keeping up the good work at the data front.

Speaking of data, I am beginning to get suspicious of the UK death (in hospitals) stats apparently levelling off at around 750 per day. My back of the envelope calculation: if testing capacity = 20k a day (per the David King article above), say 15k are positive, 5% off the positives die (high mortality as only ill ppl get tested), that gives us 750 deaths per day. So are the figures of the last few days capped by test availability? In other words, the daily deaths may very well go on rising, and we'll never know as we don't have the tests available? If that is the case, the excess deaths over long-term average will be the only metric left to assess what's going on.

Tuesday, April 14, 2020

science news 14.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


astrobiology

New formation theory explains the mysterious interstellar object 'Oumuamua


evolution

When fathers are pregnant
Reproduction is still one of the greatest mysteries in nature. Pregnancies are usually carried out by the female sex. Only in pipefishes and seahorses males are the pregnant sex. An international team of scientists led by the GEOMAR Helmholtz Centre for Ocean Research Kiel has deciphered the complex modifications of their immune system that enabled male pregnancy.



Sea horse
Credit: S. Kaehlert, GEOMAR


ecology

Scientists discover bent-toed gecko species in Cambodia

Plant diversity in European forests is declining


biomedical

Loss of smell and taste validated as COVID-19 symptoms in patients, with high recovery rate

Study finds remdesivir effective against a key enzyme of coronavirus that causes COVID-19

Super-charging drug development for COVID-19
Researchers are using cell-free manufacturing to ramp up production of valinomycin, a promising drug that has proven effective in obliterating SARS-CoV in cellular cultures.

New Rutgers saliva test for coronavirus gets FDA approval


dystopian futures

'I saw you were online': How online status indicators shape our behavior


---------------


From the news media:

We are of course, absolutely screwed here in the UK, with the govt. failure of early March now on track to cause the highest death toll of any European country. The one thing we have left to cheer us up is looking at the US. They are so much more screwed than us. Here's a timeline of events and lies from the top.

Monday, April 13, 2020

even harder times for orangutans

Open Archive Day

I am reasonably hopeful that the current coronavirus crisis might scare humanity into doing something about climate change, so it may still turn out saving more lives in the long run than it is costing right now.

However, there may also be collateral damage to the natural world. I heard that the absence of wildlife tourists and rangers has led to an increase in illegal hunting of engangered animals such as rhinos. And there is the risk that the coronavirus, after we have spread it globally, will find some new animals to infect, such as the tiger in the New York zoo. Great apes, for being most similar to ourselves, may be at risk from the disease, and it could even tip some of the endangered species over the brink.

So time to revisit last year's feature about the orangutan, which is now in the open archives:

Hard times for orangutans




still from the banned TV ad "there's a rang-tan in my bedroom" which I mentioned in the feature.

Saturday, April 11, 2020

art for hard times

With museums and galleries now firmly closed and off limits, I have been obsessing about art on twitter a bit, following a few artbots and checking their back catalogues. One of the artists I discovered this way is the British neoclassicist John Godward (1861-1922), who painted lots of very melancholy looking women with mediterranean backdrops. I'm a bit of a sucker for melancholic looking people at the best of times, but now these paintings seem to fit the general mood as well, and I also found lots of people taking inspiration from Godward's paintings and either using them for "mood" posts or recreating their looks.

So here's a little gallery of my favourites, enjoy:




(I haven't made notes of the complete titles, but trying to reconstruct titles from my filenames, we have: 1890 reverie; 1899 letter; 1902 When the heart is young; 1906 tambourine girl; 1906 Violets, sweet violets; 1909 Summer idleness: day dreams; 1918 Lycinna)

Blame it all on this artbot on twitter.

And artrenewal.org has a page with more than 200 of his works.

This website claims it has the complete works (210 of them) but it also has some annoying pop-up ads.

His models included: Ethel Warwick (1882-1951); the sisters Lilly, Harriet and Rose Pettigrew;

PS other artists whose work acquires a new meaning these days include Edward Hopper, whose lonely people look like they may have been quarantined too.

Friday, April 10, 2020

science news 10.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


evolution

Ancient teeth from Peru hint now-extinct monkeys crossed Atlantic from Africa
Four fossilized monkey teeth discovered deep in the Peruvian Amazon provide new evidence that more than one group of ancient primates journeyed across the Atlantic Ocean from Africa. The teeth are from a newly discovered species belonging to an extinct family of African primates known as parapithecids. Fossils discovered at the same site in Peru had earlier offered the first proof that South American monkeys evolved from African primates.


ecology

Black rhinos eavesdrop on the alarm calls of hitchhiking oxpeckers to avoid humans
The kind of story where I read the headline and know it must be in Current Biology (the next one below as well).



This image shows a red-billed oxpecker (called Askari wa kifaru or the rhino's guard) alarm calling on the ear and head of a black rhino in Hluhluwe-iMfolozi Park, South Africa
Credit: Jed Bird


How do mantis shrimp find their way home?
New research in Current Biology indicates mantis shrimp use path integration to find their way back to their burrows after leaving to seek food or mates. That means they can track their distance and direction from their starting point. A series of creative experiments revealed that to do that, they rely on a hierarchy of cues from the sun, polarized light patterns, and their internal senses.


conservation

Canada lynx disappearing from Washington state


nanoworld

Research sheds light on how silver ions kill bacteria


humans

Archaeology: Ancient string discovery sheds light on Neanderthal life
The discovery of the oldest known direct evidence of fiber technology -- using natural fibers to create yarn -- is reported in Scientific Reports this week. The finding furthers our understanding of the cognitive abilities of Neanderthals during the Middle Palaeolithic period (30,000-300,000 years ago).

Aha! + Aaaah: Creative insight triggers a neural reward signal


---------------


From the news media:


How New Zealand kept Covid-19 under control. Other very exemplary stories I've read came from Iceland (where the chief epidemiologist raised the alarm after several ski tourists returning from Ischgl tested positive - it took Austria all of 2 weeks to close the place down, as returning visitors continued to spread the virus across Europe) and from Faroe Islands. Just one island-based country that failed spectacularly on this account.

Thursday, April 09, 2020

science news 9.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.



evolution

New fossil from Brazil hints at the origins of the mysterious tanystropheid reptiles



Life restoration of Elessaurus gondwanoccidens, from the Sanga do Cabral Formation (Lower Triassic), Brazil
Credit: Márcio L. Castro


ecology

Hidden army: How starfish could build up numbers to attack coral reefs

How does habitat fragmentation affect Amazonian birds?
The Biological Dynamics of Forest Fragments Project (BDFFP), located near Manaus, Brazil, began in 1979 and is the world's longest-running experimental study of tropical forest fragments. A new paper in The Condor: Ornithological Applications summarizes four decades of data from the project about how Amazonian bird communities respond to habitat fragmentation, a question as relevant today as ever in light of the recent increase in deforestation in the Amazon.
See also my 2017 feature about forest fragmentation, also covering the work of this project.


nanoworld

House cleaning on the nanoscale

Harnessing the power of electricity-producing bacteria for programmable 'biohybrids'


biomedical

Coronavirus pandemic in Germany: Measures relevant to health

Loss of smell in patient with COVID-19

Potential harms of chloroquine, hydroxychloroquine and azithromycin for treating COVID-19


environment

Vexing Nemo: Motorboat noise makes clownfish stressed and aggressive

Babies in popular low-riding pushchairs are exposed to alarming levels of toxic air pollutants
Quite shocking that we don't appear to know where all those pollutants come from. In the entire press release I couldn't find a single mention of a possible source. The pollutants are just there in the street, must be a natural thing ...



humans


Revolutionary new method for dating pottery sheds new light on prehistoric past
Not about dating sheds, sadly. I would suggest to the PR team to re-read the headline after writing. Maybe a day after writing it.


Earliest humans in the Amazon created thousands of 'forest islands' as they tamed wild plants

Bristol leads archaeologists on 5,000-year-old egg hunt
An international team of specialists, led by the University of Bristol, is closer to cracking a 5,000-year-old mystery surrounding the ancient trade and production of decorated ostrich eggs. Long before Fabergé, ornate ostrich eggs were highly prized by the elites of Mediterranean civilizations during the Bronze and Iron Ages, but to date little has been known about the complex supply chain behind these luxury goods.


Promising advance in depression research
Despite their effectiveness, only 40% of patients respond to the first antidepressant they try. A recent paper in Nature Communication strongly suggests that a particular protein, GPR56, is involved in the biology of depression and the effect of antidepressants. The McGill led research team believe that this protein could offer a novel target for new antidepressant drugs.


---------------


From the news media:


Is this the moment we give up flying?
asks Nicole Badstuber in the Guardian. (I basically gave up in 2010.)

Lancet editor Richard Horton on how the UK govt got the response so catastrophically wrong. He's always worth reading. (My somewhat shorter interpretation is "criminal carelessness".)



Wednesday, April 08, 2020

science news 8.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.




evolution

Coquí fossil from Puerto Rico takes title of oldest Caribbean frog

The evolution of color: Team shows how butterfly wings can shift in hue



Comparison of wild-type brown buckeye and artificially selected blue buckeye wings.
Credit: Aaron Pomerantz


ecology

How wallflowers evolved a complementary pair of plant defenses
Must be one of the perks of being a wallflower.

The link between virus spillover, wildlife extinction and the environment


conservation

Protecting the high seas
Researchers use big data to identify biodiversity hotspots that could become the first generation of high seas marine protected areas.


biomedical
Successful MERS vaccine in mice may hold promise for COVID-19 vaccine


food and drink

Bubble dynamics reveal how to empty bottles faster
Over here in the real world, we just give the bottle a twirl - rotating liquid forms a vortex and clears out 10 times faster, with no need to worry about bubbles at all.


climate change

Climate change triggers Great Barrier Reef bleaching


humans

Students who listened to Beethoven during lecture -- and in dreamland -- did better on test


---------------


From the news media:


An interesting detailed analysis from Reuters of the science advice behind the UK government's (lack of) response. My reading: approaching disaster was clear on March 1, response came >2 weeks too late. Instead of that handshaking remark on March 3 Johnson should have told ppl to keep their distance (and led by example, eg in the setup of his news conference). That would have saved lives.

Meanwhile, the projections from IHME that are currently predicting 66,000 deaths in the UK by August 4th (this page will change with the time, as projections are updated). Here's the Guardian story about it, which will stay. Very impressive how much damage three weeks of criminal carelessness can do.

And the Financial Times continues to have the best daily data visualisation.

Monday, April 06, 2020

debunking stem cell cures

Against coronavirus like against any other kind of medical problem, there are people out there trying to sell you a stem cell cure. Sadly, most of them are on the spectrum from unproven to utter nonsense. In reality, there are only very few proven stem-cell based treatments.

It's been a while since I last covered stem cells, in part I presume, because the progress we've been hoping for since the 00s hasn't materialised quite as fast as expected. This delay between hopes and realisations has in fact helped to the vendors of dubious cures. In my latest feature I revisited the field to do a reality check.

Reality check for stem cell cures

Current Biology Volume 30, Issue 7, 06 April 2020, Pages R287-R289

FREE access to full text and PDF download




Pigs are similar to humans in many ways to the extent that growing human organs in a pig host is a realistic avenue currently under investigation, although many challenges remain. (Image: Kenneth Schipper Vera.)

Saturday, April 04, 2020

stay home play Bach

It may be months before people can go out and play music together (before then we could perhaps launch street orchestras with one parking space per person?), so it's a good time to study JS Bach's unaccompanied works which are a bit like playing chess against yourself, as there are various voices, or solo plus accompaniment, all to be played by one person with one instrument.

In the last two years I found my way through JSB's partita for flute and also his son's response, CPE Bach's sonata for unaccompanied flute, also in a minor. So now, faced with the complete lack of ensemble opportunities, I'm tackling the cello suites, which are a somewhat bigger mountain to climb. I started with the bourrees from the 3rd suite (movt. 3.5), and got the hang of them in a month. (So at one movement per month, the suites will keep me challenged for three years, by which time it will hopefully be safe to play in ensembles again.)

Next stop: the minuets from the first suite (movt. 1.5). I understand this is one of the easiest movements (it has been an exam piece for ABRSM grade 6 at one point). Not sure in which order to proceed after that, but in a forum I've seen a cello teacher suggesting to go through the first suite back to front, so I might do that. Helped by the fact that the second-hand copy of the score I bought at a charity shop for £ 1.50 has fingerings and annotations pencilled in for the entire first suite as well as for movt 3.5. So far these markings have worked very well for me, so I am very grateful to the previous owner for this help.

Recordings and tutorials:

Complete first suite on soundcloud by Mischa Maisky.

Denise Djokic performs the minuets (2012)

Patrycja Likos version is a useful starting point as she performs it straight and the the fingerings are very clearly visible at all times.

Inbal Segev's musings on the first minuet

Inbal Segev's musings on the second minuet
(funny that this has just under half as many views as the video for the first minuet)

The nyckelharpa version







Friday, April 03, 2020

science news 3.4.2020

Today's selection of science news. Links are normally to press releases on EurekAlert (at the bottom end I may also add a couple of newspaper stories). I include quotes from the summary in italics in cases where the title alone doesn't reveal what the story is about. My own thoughts appear without italics if I have any.


astrobiology

Discovery of life in solid rock deep beneath sea may inspire new search for life on Mars


evolution

Fourth new pterosaur discovery in matter of weeks



This is image shows artwork of the Afrotapejara zouhrii.
Credit: Megan Jacobs, Baylor University, Texas

Six million-year-old bird skeleton points to arid past of Tibetan plateau


conservation

Whooping cranes form larger flocks as wetlands are lost -- and it may put them at risk


light and life

Natural sunscreen gene influences how we make vitamin D


biomedical

COVID-19 vaccine candidate shows promise in first peer-reviewed research
still only tested in animals though.


humans

Cocky kids: The four-year-olds with the same overconfidence as risk-taking bankers


dystopian futures

COVID-19 contact tracing apps: 8 privacy questions governments should ask



---------------


From the news media:

On the Saturday 14.3. I travelled back from Germany and was shocked to find that in the UK mass events like the Cheltenham Festival were still going ahead in spite of the virus already spreading out of control, and the science already suggesting that it is also spread by people who don't show symptoms. Now, as the Guardian reports, the impact of Cheltenham is seen in the case stats. In a week, it will be seen in the death stats, which are more reliable. I am keeping the link to the article here mainly because it provides a handy reference of other events that still went ahead on that weekend and shouldn't have, including a Champions League game enabling the spread from Spain to the UK.

On a related note, I read the article in Der Spiegel about how the Austrian ski resort Ischgl became a superspreading centre of COVID-19 mainly because I happen to know the place. Found it both very educational and shocking to read how the relevant people in Iceland spotted the problem on March 1st, and went on to alert other European countries. It took 2 weeks until the place was shut down. English version of the article is here. German original was in the issue 14 page 58.