Lab News [original papers]

The forgotten medieval habit of 'two sleeps'
By Zaria Gorvett
10th January 2022
For millennia, people slept in two shifts – once in the evening, and once in the morning. But why? And how did the habit disappear?
[...]
https://www.bbc.com/future/article/20220107-the-lost-medieval-habit-of-biphasic-sleep

The sci-fi genre offering radical hope for living better
By David Robson
14th January 2022
In these times of cynicism and despair, is 'hopepunk' the perfect antidote? David Robson explores radical optimism, and why it matters.
[...]
https://www.bbc.com/culture/article/20220113-the-sci-fi-genre-offering-radical-hope-for-living-better

Spent 2 Hours Looking For This At The Natural History Museum (London):
Totally Worth It

False banana: Is Ethiopia's enset 'wondercrop' for climate change?
Scientists say the plant enset, an Ethiopian staple, could be a new superfood and a lifesaver in the face of climate change.

The banana-like crop has the potential to feed more than 100 million people in a warming world, according to a new study.

The plant is almost unknown outside of Ethiopia, where it is used to make porridge and bread.

Research suggests the crop can be grown over a much larger range in Africa.

"This is a crop that can play a really important role in addressing food security and sustainable development," said Dr Wendawek Abebe of Hawassa University in Awasa, Ethiopia.
[...]
https://www.bbc.com/news/science-environment-60074407

Welcome to the OneZoom tree of life explorer...
An interactive map of the evolutionary links between all living things known to science. Discover your favourites, see which species are under threat, and be amazed by the diversity of life on earth.
[...]
https://www.onezoom.org

Steve Gschmeissner [age 71] is one of the world’s leading scanning electron microscopists. Meet a highly skilled professional using a wonderfully realistic microscopic technique. His coverage of the microscopic world is comprehensive and wide ranging, including bacteria, human and animal tissues such as blood, nerves, bone and hair cells, pests, parasites and pond life, electronic circuitry and nanotechnology. His greatest contribution is an unrivalled collection of difficult to access cancer cells. SPL is the exclusive representative of his collection. We are proud to share the news that our contributor, scanning electron microscopist Stephen Gschmeissner, has been awarded the prestigious 2021 Lennart Nilsson Award.
https://stories.sciencephoto.com/portfolio/lennart-nilsson-award-2021/
https://stories.sciencephoto.com/portfolio/steve-gschmeissner/
https://www.sciencephoto.com/set/3657/steve-gschmeissner-finding-the-unexpected

Scientists raise alarm over ‘dangerously fast’ growth in atmospheric methane
As global methane concentrations soar over 1,900 parts per billion, some researchers fear that global warming itself is behind the rapid rise.







https://doi.org/10.1038/d41586-022-00312-2

[...]

Monocytes - type of white blood cell that can transform into macrophage or dendritic cell
Macrophages - devour dead cells and living enemies, coordinate defences and heal wounds
Mast cells - filled with tiny bombs that containing potent chemicals that cause local inflammation
Dendritic cells - like an intelligence officer, it gathers samples from dead intruders
Natural killer cells - hunt two types of enemies: cells infected by viruses and cancer cells
Neutrophils - all-purpose weapons system engineered to quickly deal with enemies especially bacteria
Eosinophil - causes inflammation, battles parasites, activates other cells
Basophil - like mast cells and eosinophils, they prolong an allergic reaction
T cells - they do many things including orchestrating other cells and killing cancer cells
B cells - produce antibodies and activate other cells
[...]
https://www.bbc.com/news/health-60171592

The urine revolution: how recycling pee could help to save the world
Separating urine from the rest of sewage could mitigate some difficult environmental problems, but there are big obstacles to radically re-engineering one of the most basic aspects of life.
Chelsea Wald











Nature 602, 202-206 (2022)
https://doi.org/10.1038/d41586-022-00338-6

The Head and the Heart

The head is stately, calm, and wise,
And bears a princely part;
And down below in secret lies
The warm, impulsive heart.
[...]
Yet each is best when both unite
To make the man complete;
What were the heat without the light?
The light, without the heat?

— John Godfrey Saxe, 1898
https://www.poetrynook.com/poem/head-and-heart

An ancient link between heart and head — as seen in the blobby, headless sea squirt
The vital connection between body parts provides insight into the evolution of vertebrates’ closest kin.
Amy Maxmen
[...]

[...]
Nature 602, 380-382 (2022)
https://doi.org/10.1038/d41586-022-00413-y

Abrupt emissions reductions during COVID-19 contributed to record summer rainfall in China
Abstract
[...] [we] show that the abrupt emissions reductions during the pandemic strengthened the summer atmospheric convection over eastern China, resulting in a positive sea level pressure anomaly over northwestern Pacific Ocean. The latter enhanced moisture convergence to eastern China and further intensified rainfall in that region. Modeling experiments show that the reduction in aerosols had a stronger impact on precipitation than the decrease of greenhouse gases did. We conclude that through abrupt emissions reductions, the COVID-19 pandemic contributed importantly to the 2020 extreme summer rainfall in eastern China.

Quelques illustrations :

A tour of the evolution of minds
Philip Ball
An informative guide takes in archaea, birds, primates and more — overconfidently.
[...]
The book offers an admirable survey of how minds might comprise modules that control simple operations, which are combined to solve complex problems of survival. For instance, a bacterium can move towards food sources thanks to motor systems that switch between directional swimming and random tumbling, depending on how it senses nutrient concentrations changing in its environment. In this way, a spatial problem acquires a temporal solution — how does the situation now compare with a moment ago? — and the microbe acquires a memory of sorts.

A rat finding food in a maze breaks down a visual scene into component features of edges, foreground and so on. And there’s more: the rat mind holds a complex internal representation of the world against which to compare sensory input; it is constantly checking this inner map. The authors lean here towards the ‘free-energy minimization’ model proposed by neuroscientist Karl Friston and others, in which organisms strive to shrink the mismatch between expectation and experience.

Ogas and Gaddam take a very broad view of mind as “a physical system that converts sensations into action”. At face value, this grants a mind to thermostats and robots as much as to living entities. “A mind responds. A mind transforms. A mind acts,” they write. But the same is true of many machines. What, then, distinguishes a mind? If it’s sentience or awareness, the authors give a confusing picture. They say the “self-awareness” of an amoeba is “piddling” — and later seem to deny this quality to all organisms except vertebrates.

[...] Since the late 1960s, Grossberg has developed the idea that consciousness arises from ‘resonance’ between specific modules of the brain. Ogas and Gaddam are vague about what resonance means here, beyond saying that the modules amplify and prolong each other’s outputs, and they give the reader little indication of what empirical evidence exists to support the idea. Grossberg’s theory is provocative and stimulating, but, couched in the abstract mathematical framework of dynamical systems theory, it remains contingent on his supposition that “all conscious states are resonant states”. I’m not convinced it amounts to the revolution that the authors assert.

There are many other proposals for what consciousness is and how it arises. Better-known is global workspace theory, championed in the past three decades by Bernard Baars, Stanislas Dehaene and others. They present consciousness as a phenomenon of information exchange in the brain, positing that awareness simply ‘ignites’ once certain criteria in the interaction of brain circuits are satisfied. Their corollary is that this would apply to any information-processing circuits with the correct architecture. Others, including neuroscientist Anil Seth, suspect that consciousness might be supported by only certain kinds of entities — as far as we know right now, ones that are alive. Ogas and Gaddam jump the gun, in my view, when they suggest that Grossberg has all the answers.

There are other instances in which they present contentious ideas with certainty. For all of the minds they discuss, much remains open. They write that birds didn’t develop language “because they don’t have hands”, but in fact it’s still debated whether gestures helped lead to the origin of language. They state that insects have no consciousness, when there is good reason to suppose that bees, at least, have many of the mental attributes associated with consciousness, such as foresight and the ability to imagine. Even bacteria are not the simple automata portrayed here; other researchers describe bacterial behaviours in the language of cognition.

The structure of a progression from the seemingly simple minds of bacteria and amoebas to the complex ones of primates makes narrative sense, but recalls the outdated image of evolution with humans at the apex. Our minds do excel in certain respects, most obviously in developing language and complex culture — but in dexterity, vision, navigation and more, other species eclipse us. There is more than a hint that evolution is striving to a particular end in Ogas and Gaddam’s suggestion that, once early single-celled organisms acquired the ability to sense and move, “the royal road to consciousness beckoned”.
[...]
There is plenty to like in Journey of the Mind. It is so often informative and entertaining that it feels mean to cavil. But the book exemplifies a persistent problem in popular science, in which pet theories are presented with too much confidence and too little context. Readers deserve the full picture — less definitive and satisfying, perhaps, but ultimately more honest and illuminating.

Nature 603, 221-222 (2022)
https://doi.org/10.1038/d41586-022-00652-z

The paradox of how antidepressants are tested
By Andy Extance, 16th March 2022
Mental health has never been so important, yet antidepressant drug trials typically exclude those who need help most. Now regulators and some researchers are asking if there needs to be a change in how these drugs are tested.
[...]
https://www.bbc.com/future/article/20220315-the-paradox-of-how-antidepressants-are-tested

Beauty and wonder of science boosts researchers’ well-being


Coloured scanning electron micrograph of Ectopleura larynx, a sea creature related to jellyfish. Biologists reported seeing beauty in complexity and pleasing colours or shapes. Credit: Jannicke Wiik-Nielsen/Science Photo Library

Scientists’ ability to experience wonder, awe and beauty in their work is associated with higher levels of job satisfaction and better mental health, finds an international survey of researchers.
[...]

[...]
The survey found that, overall, scientists reported moderately high levels of well-being, with 72% saying they were mostly or completely satisfied with their jobs. But there were significant disparities. Women reported higher levels of burnout than men, and 25% of postgraduate students reported serious levels of psychological distress, compared with just 2% of senior academics. “Students are in a pretty bad place,” says Dickerson. “And I worry this narrative is being normalized. It shouldn’t be swept under the carpet.”

Vaidyanathan says he did expect to see a difference in mental health between tenured faculty and students — but he didn’t expect it to be so profound. And although the majority of those surveyed seem to be coping with work stress, it is important to pay attention to those who are struggling. “We can’t dismiss those concerns as trivial,” he says.
https://doi.org/10.1038/d41586-022-00762-8

Rapid adaptation in fruit flies
University of Pennsylvania - March 17, 2022
Evolution is normally considered to be a gradual process, unfolding over long timescales. But new findings show that widespread physical and genomic adaptation to the environment can occur within just weeks.
[...]
https://www.sciencedaily.com/releases/2022/03/220317143723.htm

Topsy Turvy a écrit:
Scientists’ ability to experience wonder, awe and beauty in their work is associated with higher levels of job satisfaction and better mental health, finds an international survey of researchers.
[...]

[...]

C'est rigolo, les biologistes aiment la complexité et les physiciens la simplicité Very Happy

The complete sequence of a human genome
[...]
To finish the last remaining regions of the genome, we leveraged the complementary aspects of PacBio HiFi and Oxford Nanopore ultralong-read sequencing to assemble the uniformly homozygous CHM13hTERT cell line (hereafter, CHM13) (17). The resulting T2T-CHM13 reference assembly removes a 20-year-old barrier that has hidden 8% of the genome from sequence-based analysis, including all centromeric regions and the entire short arms of five human chromosomes. Here, we describe the construction, validation, and initial analysis of a truly complete human reference genome and discuss its potential impact on the field
[...]
https://www.science.org/doi/10.1126/science.abj6987

Global population is crashing, soaring and moving
Josie Glausiusz
From Japan to Yemen, India to Ukraine, rates of births, deaths and displacement are reshaping nations.
[...]
The twenty-first century “is less a story about exponential population growth than it is a story about differential growth — marked by a stark divide between the world’s richest and poorest countries”, she writes.


How far will global population rise? Researchers can’t agree

In Latin America and the Caribbean, eastern and southeast Asia, Europe and North America, Australia and New Zealand, the total fertility rate (TFR), or average number of children a woman is likely to have in her lifetime, was below replacement level (around 2.1 children per woman) in 2020. By contrast, sub-Saharan Africa’s population is set to increase sixfold this century; its TFR is 4.72, down from 5.88 two decades ago. In Nigeria, children and adolescents are half of the population.
[...]
A 2021 report projects that by 2045, one-quarter of the Japanese population will have dementia (N. Nakahori et al. BMC Geriatr. 21, 602; 2021). As more people exit the labour force than enter it, wealthy countries worry about how to preserve economic growth. To soften the economic blow of ageing, Sciubba presents four options: raise retirement ages, cut benefits, push more people in the country to work or increase immigration.

She focuses at length on immigration. Only 2–4% of the world’s people live outside their country of origin, but between 2000 and 2020, according to the United Nations, the number of international migrants and refugees who had fled conflict, crises, persecution, violence or human-rights violations doubled from 17 million to 34 million. (This was all, of course, before Russia’s invasion of Ukraine forced more than four million refugees to flee the country.) Most of those compelled to move by the end of 2020 were internally displaced, as Sciubba notes. Between 2008 and 2020, an average of 21.8 million people per year had to move within their countries because of weather-related disasters, such as floods or wildfires.
[...]
Thanks to humanitarian intervention, global health campaigns, vaccination and improvements in sanitation, deaths from communicable diseases and famine fell abruptly in the decades before the COVID-19 pandemic. Deaths from HIV declined by 51% from 2000 to 2019, with the use of antiretroviral therapy saving millions of lives. Starvation in countries such as Yemen (or Afghanistan in 2022, where more than half the population is “acutely food insecure”, according to the UN World Food Programme) is not solely the result of population increase. It is often the outcome of economic sanctions and, in the case of Yemen, the bombing of infrastructure including markets, roads, ports, farms and water pipelines.

“A good health foundation makes countries far more prepared for the unexpected,” Sciubba concludes. With the right political will and with humanitarian intervention, it seems, people can turn the tide on disease and war.
Nature 604, 33-34 (2022)
https://doi.org/10.1038/d41586-022-00926-6

The awake ape: Why people sleep less than their primate relatives
Ancient humans may have evolved to slumber efficiently — and in a crowd
By Elizabeth Preston 04.28.2022
[...]

[...]
https://knowablemagazine.org/article/society/2022/why-people-sleep-less-than-primate-relatives

The tale of the domesticated horse
The beloved animal has shaped human history over millennia, just as people have influenced its evolution — but only recently have scientists discovered exactly when and where it went from wild to tame
By Amber Dance 05.04.2022
[...]

[...]

[...]
https://knowablemagazine.org/article/living-world/2022/tale-domesticated-horse

Quelques comparaisons en illustrations :

Monkeypox goes global: why scientists are on alert
Max Kozlov
(...)
What researchers can tell from this preliminary genetic data is that the strain of the monkeypox virus found in Portugal is related to a viral strain predominantly found in West Africa. This strain causes milder disease and has a lower death rate — about 1% in poor rural populations — compared with the one that circulates in Central Africa. But exactly how much the strain causing the current outbreaks differs from the one in West Africa — and whether the cases popping up in various countries are linked to one another — remains unknown.

Answers to those questions could help researchers to determine whether the sudden uptick in cases stems from a mutation that allows monkeypox to transmit more readily than it did in the past, and whether each of the outbreaks traces back to a single origin (...). DNA viruses are better at detecting and repairing mutations than RNA viruses, which means it’s unlikely that the monkeypox virus has suddenly mutated to become adept at human-to-human transmission, MacIntyre says.

Still, for monkeypox to be detected in people with no apparent connection to one another suggests that the virus might have been spreading silently — a fact that Andrea McCollum, an epidemiologist who heads the poxvirus team at the US Centers for Disease Control and Prevention in Atlanta, Georgia, calls “deeply concerning”.

Unlike SARS-CoV-2, which can spread without causing symptoms, monkeypox does not usually go unnoticed when it infects a person, in part because of the skin lesions it causes. If monkeypox could spread asymptomatically, it would be especially troubling, because it would make the virus harder to track, McCollum says.

Another puzzle is why almost all of the case clusters include men aged 20–50, many of whom are men who have sex with men (MSM). Although monkeypox isn’t known to be sexually transmitted, sexual activity certainly constitutes close contact, Rimoin says. The most likely explanation for this unexpected pattern of transmission, MacIntyre says, is that the virus was coincidentally introduced into an MSM community, and has continued circulating there. Scientists will have a better idea of the origin of the outbreaks and the risk factors for infection once an epidemiological investigation — which can take weeks and involves rigorous contact tracing — is complete.
(...)
Nature 606, 15-16 (2022)
https://doi.org/10.1038/d41586-022-01421-8

Waking up to monkeypox
(...)
It is frustrating to see the same pattern repeating itself again. Attention is only paid when certain diseases hit high-income countries—exemplifying our collective failure to properly address “epidemic preparedness” and “global health,”—though they are nominally on top of our agenda with the covid-19 pandemic. It also illustrates the double standard applied to how people’s health is valued between wealthy countries and the rest of the world.

Since the disease mostly occurs in remote areas, there is a very large iceberg underneath the small tip that we see and that is recorded, both in terms of the real numbers and the health impact of the disease. Mortality for the cases that come under observation is higher for infections recorded in the Congo basin (11%, including the Central African Republic) than the West-African clade (4%).
(...)
Nakoune E, Olliaro P. Waking up to monkeypox. BMJ. 2022 May 25;377:o1321. doi: 10.1136/bmj.o1321. PMID: 35613732.
https://www.bmj.com/content/377/bmj.o1321