biology (50)

Foxes, Minks, Racoon Dogs...

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Topics: Biology, COVID-19, Education, Research

During the first year of the COVID-19 pandemic, the “[lab] leak” theory gained little traction. Sure, U.S. President Donald Trump suggested SARS-CoV-2 originated in a laboratory in Wuhan, China—and called it “the China virus”—but he never presented evidence, and few in the scientific community took him seriously. In fact, early in the pandemic, a group of prominent researchers dismissed lab-origin notions as “conspiracy theories” in a letter in The Lancet. A report from a World Health Organization (WHO) “joint mission,” which sent a scientific team to China in January to explore possible origins with Chinese colleagues, described a lab accident as “extremely unlikely.”

But this spring, views began to shift. Suddenly it seemed that the lab-leak hypothesis had been too blithely dismissed. In a widely read piece, fueled by a “smoking gun” quote from a Nobel laureate, a veteran science journalist accused scientists and the mainstream media of ignoring “substantial evidence” for the scenario. The head of WHO openly pushed back against the joint mission’s conclusion, and U.S. President Joe Biden ordered the intelligence community to reassess the lab-leak possibility. Eighteen scientists, including leaders in virology and evolutionary biology, signed a letter published in Science in May that called for a more balanced appraisal of the “laboratory incident” hypothesis.

Yet behind the clamor, little had changed. No breakthrough studies have been published. The highly anticipated U.S. intelligence review, delivered to Biden on 24 August, reached no firm conclusions but leaned toward the theory that the virus has a natural origin.

Fresh evidence that would resolve the question may not emerge anytime soon. China remains the best place to hunt for clues, but its relative openness to collaboration during the joint mission seems to have evaporated. Chinese officials have scoffed at calls from Biden and WHO Director-General Tedros Adhanom Ghebreyesus for an independent audit of key Wuhan labs, which some say should include an investigation of notebooks, computers, and freezers. Chinese vice health minister Zeng Yixin said such demands show “disrespect toward common sense and arrogance toward science.” In response to the increasing pressure, China has also blocked the “phase 2” studies outlined in the joint mission’s March report, which could reveal a natural jump between species.

Despite the impasse, many scientists say the existing evidence—including early epidemiological patterns, SARS-CoV-2’s genomic makeup, and a recent paper about animal markets in Wuhan—makes it far more probable that the virus, like many emerging pathogens, made a natural “zoonotic” jump from animals to humans.

Virologist Robert Garry of Tulane University finds it improbable that a Wuhan lab worker picked up SARS-CoV-2 from a bat and then brought it back to the city, sparking the pandemic. As the WIV study of people living near bat caves shows, the transmission of related bat coronaviruses occurs routinely. “Why would the virus first have infected a few dozen lab researchers?” he asks. The virus may also have moved from bats into other species before jumping to humans, as happened with SARS. But again, why would it have infected a lab worker first? “There are hundreds of millions of people who come in contact with wildlife.”

The earliest official announcement about the pandemic came on 31 December 2019, when Wuhan’s Municipal Health Commission reported a cluster of unexplained pneumonia cases linked to the city’s Huanan seafood market. The WHO report devotes much attention to details about Huanan and other Wuhan markets but also cautions that their role remains “unclear” because several early cases had no link to any market. But after reading the report, Andersen became more convinced that the Huanan market played a critical role.

One specific finding bolsters that case, Wang says. The report describes how scientists took many samples from floors, walls, and other surfaces at Wuhan markets and were able to culture two viruses isolated from Huanan. That shows the market was bursting with a virus, Wang says: “In my career, I have never been able to isolate a coronavirus from an environmental sample.”

The report also contained a major error: It claimed there were “no verified reports of live mammals being sold around 2019” at Huanan and other markets linked to early cases. A surprising study published in June by Zhou Zhao-Min of China West Normal University and colleagues challenged that view. It found nearly 50,000 animals from 38 species, most alive, for sale at 17 shops at Huanan and three other Wuhan markets between May 2017 and November 2019. (The researchers had surveyed the markets as part of a study of a tick-borne disease afflicting animals.)

Live animals can more easily transmit a respiratory virus than meat from a butchered one, and the animals included masked palm civets, the main species that transmitted SARS-CoV to humans, and raccoon dogs, which also naturally harbored that virus and have been infected with SARS-CoV-2 in lab experiments. Minks—a species farmed for fur that has acquired SARS-CoV-2 infections from humans in many countries— were also abundant. “None of the 17 shops posted an origin certificate or quarantine certificate, so all wildlife trade was fundamentally illegal,” Zhou and his colleagues wrote in their paper. (Zhou did not respond to emails from Science.)

Call of the Wild: Why many scientists say it’s unlikely that SARS-CoV-2 originated from a “lab leak,” Jon Cohen, Science Magazine

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Interstellar Cellular Membranes...

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Topics: Astrobiology, Biology, Chemistry, Cosmology

The origin of life is one of the great unanswered questions in science. One piece of this puzzle is that life started on Earth 4.5 billion years ago, just a few hundred million years after the formation of the Solar System, and involved numerous critical molecular components. How did all these components come to be available so quickly?

One potential explanation is that the Earth was seeded from space with the building blocks for life. The idea is that space is filled with clouds of gas and dust that contain all the organic molecules necessary for life.

Indeed, astronomers have observed these buildings blocks in interstellar gas clouds. They can see amino acids, the precursors of proteins, and the machinery of life. They can also see the precursors of ribonucleotides, molecules that can store information in the form of DNA.

But there is another crucial component for life – molecules that can form membranes capable of encapsulating and protecting the molecules of life in compartments called protocells. On Earth, the membranes of all cells are made of molecules called phospholipids. But these have never been observed in space. Until now.

First evidence of cell membrane molecules in space, Physics arXiv blog, Astronomy

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The Anatomy of Delta...

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A computer simulation of the structure of the coronavirus SARS-CoV-2.Credit: Janet Iwasa, University of Utah

Topics: Biology, Biotechnology, COVID-19, DNA, Existentialism, Research

The coronavirus sports a luxurious sugar coat. “It’s striking,” thought Rommie Amaro, staring at her computer simulation of one of the trademark spike proteins of SARS-CoV-2, which stick out from the virus’s surface. It was swathed in sugar molecules, known as glycans.

“When you see it with all the glycans, it’s almost unrecognizable,” says Amaro, a computational biophysical chemist at the University of California, San Diego.

Many viruses have glycans covering their outer proteins, camouflaging them from the human immune system like a wolf in sheep’s clothing. But last year, Amaro’s laboratory group and collaborators created the most detailed visualization yet of this coat, based on structural and genetic data and rendered atom-by-atom by a supercomputer. On 22 March 2020, she posted the simulation to Twitter. Within an hour, one researcher asked in a comment: what was the naked, uncoated loop sticking out of the top of the protein?

Amaro had no idea. But ten minutes later, structural biologist Jason McLellan at the University of Texas at Austin chimed in: the uncoated loop was a receptor-binding domain (RBD), one of three sections of the spike that bind to receptors on human cells (see ‘A hidden spike’).

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Source: Structural image from Lorenzo Casalino, Univ. California, San Diego (Ref. 1); Graphic: Nik Spencer/Nature

How the coronavirus infects cells — and why Delta is so dangerous, Megan Scudellari, Nature

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Smart Foam...

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A robotic hand with the AiFoam artificially innervated smart foam, which enables it to sense objects in proximity by detecting their electrical fields and also self-heals if it gets cut, is pictured at National University Singapore's Materials Sciences and Engineering lab in Singapore June 30, 2021. REUTERS/Travis Teo

Topics: Biology, Biotechnology, Materials Science, Polymer Science, Robotics

SINGAPORE, July 6 (Reuters) - Singapore researchers have developed a smart foam material that allows robots to sense nearby objects, and repairs itself when damaged, just like human skin.

Artificially innervated foam, or AiFoam, is a highly elastic polymer created by mixing fluoropolymer with a compound that lowers surface tension.

This allows the spongy material to fuse easily into one piece when cut, according to researchers at the National University of Singapore.

"There are many applications for such a material, especially in robotics and prosthetic devices, where robots need to be a lot more intelligent when working around humans," explained lead researcher Benjamin Tee.

To replicate the human sense of touch, the researchers infused the material with microscopic metal particles and added tiny electrodes underneath the surface of the foam.

Smart foam material gives robotic hand the ability to self-repair, Travis Teo, Lee Ying Shan, Reuters Science

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Quantum Microscope...

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Artist’s impression of UQ’s new quantum microscope in action. Credit: The University of Queensland

Topics: Biology, Biotechnology, Instrumentation, Quantum Mechanics, Quantum Optics

In a major scientific leap, University of Queensland researchers have created a quantum microscope that can reveal biological structures that would otherwise be impossible to see.

This paves the way for applications in biotechnology, and could extend far beyond this into areas ranging from navigation to medical imaging.

The microscope is powered by the science of quantum entanglement, an effect Einstein described as “spooky interactions at a distance.”

Professor Warwick Bowen, from UQ’s Quantum Optics Lab and the ARC Centre of Excellence for Engineered Quantum Systems (EQUS), said it was the first entanglement-based sensor with performance beyond the best possible existing technology.

“This breakthrough will spark all sorts of new technologies — from better navigation systems to better MRI machines, you name it,” Professor Bowen said.

“Entanglement is thought to lie at the heart of a quantum revolution. We’ve finally demonstrated that sensors that use it can supersede existing, non-quantum technology.

“This is exciting — it’s the first proof of the paradigm-changing potential of entanglement for sensing.”

Major Scientific Leap: Quantum Microscope Created That Can See the Impossible, University of Queensland

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Drops in Cells...

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Liquidated3672 (2021), Theodore Lee Jones, CallMeTed.com.

Topics: Applied Physics, Biology, Microscopy, Molecules

A major challenge in cell biology remains to unravel is how cells control their biochemical reaction cycles. For instance, how do they regulate gene expression in response to stress? How does their metabolism change when resources are scarce? Control theory has proven useful in understanding how networks of chemical reactions can robustly tackle those and other tasks.1 The essential ingredients in such approaches are chemical feedback loops that create control mechanisms similar to the circuits that regulate, for example, the temperature of a heating system, the humidity of an archive, or the pH of a fermentation tank.

Theories for the control of biochemical reactions have largely focused on homogeneous, well-stirred environments. However, macromolecules inside cells are often highly organized in space by specialized subunits called organelles. Some organelles, such as the cell nucleus, are bound by a membrane. By contrast, another class of organelles—biomolecular condensates—show the hallmark physical properties of liquid-like droplets, and they provide chemically distinct environments for biochemical reactions.2–4

Such droplets can act as microreactors for biochemical reactions in a living cell (see figure 1). Their liquid nature sustains the fast diffusion of reactants while their specific composition gives rise to the partitioning of reactants in or out of the droplets. In general, the concentrations of reactants inside condensates differ from the concentrations outside. Those differences modify reaction fluxes, which, in turn, can dramatically affect reaction yield and other properties of chemical reactions. Just how such modified fluxes govern the biochemistry inside cells remains poorly understood.

Drops in Cells, Christoph Weber, Christoph Zechner, Physics Today

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Every Tank Has Its Limits...

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Topics: Biology, Planetary Science, Research, Tardigrades

They can survive temperatures close to absolute zero. They can withstand heat beyond the boiling point of water. They can shrug off the vacuum of space and doses of radiation that would be lethal to humans. Now, researchers have subjected tardigrades, microscopic creatures affectionately known as water bears, to impacts as fast as a flying bullet. And the animals survive them, too—but only up to a point. The test places new limits on their ability to survive impacts in space—and potentially seed life on other planets.

The research was inspired by a 2019 Israeli mission called Beresheet, which attempted to land on the Moon. The probe infamously included tardigrades on board that mission managers had not disclosed to the public, and the lander crashed with its passengers in tow, raising concerns about contamination. “I was very curious,” says Alejandra Traspas, a Ph.D. student at Queen Mary University of London who led the study. “I wanted to know if they were alive.”

Traspas and her supervisor, Mark Burchell, a planetary scientist at the University of Kent, wanted to find out whether tardigrades could survive such an impact—and they wanted to conduct their experiment ethically. So after feeding about 20 tardigrades moss and mineral water, they put them into hibernation, a so-called “tun” state in which their metabolism decreases to 0.1% of their normal activity, by freezing them for 48 hours.</em>

They then placed two to four at a time in a hollow nylon bullet and fired them at increasing speeds using a two-stage light gas gun, a tool in physics experiments that can achieve muzzle velocities far higher than any conventional gun. When shooting the bullets into a sand target several meters away, the researchers found the creatures could survive impacts up to about 900 meters per second (or about 3000 kilometers per hour), and momentary shock pressures up to a limit of 1.14 gigapascals (GPa), they report this month in Astrobiology. “Above [those speeds], they just mush,” Traspas says.</em>

Hardy water bears survive bullet impacts—up to a point, Jonathan O'Callaghan, Science Magazine

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Adversary, Friendly, or Neutral...

 

An unidentified flying object as seen in a declassified Department of Defense video, DoD

Topics: Aerodynamics, Applied Physics, Biology, Exoplanets, General Relativity, SETI

May 17, 2019- No, little green men aren't likely after the conquest of humanity. Boyd's piece for Phys.org highlights the reason why the Pentagon wants to identify UFOs: they're unidentified. If a warfighter on the ground or in the sky can't ID an object, that creates an issue since they don't know if it's friendly, adversarial, or neutral.

U.S. Navy pilots and sailors won't be considered crazy for reporting unidentified flying objects, under new rules meant to encourage them to keep track of what they see writes Iain Boyd for Phys.org.

Why is the Pentagon interested in UFOs? Intelligent Aerospace

The Pentagon refers to them as "transmedium vehicles," meaning vehicles moving through air, water, and space. Carolina Coastline breathlessly uses the term "defying the laws of physics." So I looked at what the paper might have meant. The objects apparently exceed the speed of sound without a sonic boom (signature of breaking the barrier). Even though this is reported by Popular Mechanics, they're quoting John Ratcliffe, whose name somehow sounds like a pejorative. Consider the source.

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U.S. Navy F/A-18 flying faster than the speed of sound. The white cloud is formed by decreased air pressure and temperature around the tail of the aircraft.
ENSIGN JOHN GAY, U.S. NAVY

The speed of sound is 343 meters per second (761.21 miles per hour, 1,100 feet per second). Mach 1 is the speed of sound, Mach 2 is 1522.41 mph, Mach 3 is 2283.62 mph. NASA's X-43A scramjet sets the record at Mach 9.6 (7,000 mph), so, it's easy to see where Star Trek: The Next Generation got its Warp Speed analog from. The top speed of the F/A-18 is 1,190 mph. Pilots and astronauts under acceleration experience G Forces, and have suits to keep them from blacking out in a high-speed turn.

A Science Magazine article in 1967 reported the dimensions and speeds for the object were undeterminable. History.com reported an object exceeding 70 knots, or 80.5546 mph underwater (twice the speed of a nuclear submarine, so I can see the US Navy's concern). I found some of the descriptions on the site interesting:

5 UFO traits:

1. Anti-gravity lift (no visible means of propulsion), 2. Sudden and instantaneous acceleration (fast), 3. Hypersonic velocities without signatures (no sonic boom), 4. Low observability, or cloaking (not putting this on Romulans, or Klingons), 5. Trans-medium travel (air, water, space).

When I look at these factors, I don't get "little green men." First caveat: there are a lot of planets between us, and them with resources aplenty. Second caveat: any interest an alien intelligence might have in us is as caretakers of an experiment, or cattle. That's disturbing: ever see a rancher have conversations with a chicken, sow, or steer before slaughter?

My hypothesis (Occam's razor) - these are projections, but of a special kind:

For the first time, a team including scientists from the National Institute of Standards and Technology (NIST - 2016) have used neutron beams to create holograms of large solid objects, revealing details about their interiors in ways that ordinary laser light-based visual holograms cannot.

Holograms -- flat images that change depending on the viewer's perspective, giving the sense that they are three-dimensional objects -- owe their striking capability to what's called an interference pattern. All matter, such as neutrons and photons of light, has the ability to act like rippling waves with peaks and valleys. Like a water wave hitting a gap between the two rocks, a wave can split up and then re-combine to create information-rich interference patterns.

Move over, lasers: Scientists can now create holograms from neutrons, too, Science Daily

This of course doesn't explain the decades of observations, since holograms came into being in a 1948 paper by the Hungarian inventor Denis Gabor: “The purpose of this work is a new method for forming optical images in two stages. In the first stage, the object is lit using a coherent monochrome wave, and the diffraction pattern resulting from the interference of the secondary coherent wave coming from the object with the coherent background is recorded on the photographic plate. If the properly processed photographic plate is placed after its original position and only the coherent background is lit, an image of the object will appear behind it, in the original position.” Gabor won the Nobel Prize in 1971 for "his invention and development of the holographic method." Also: History of Holography

This is purely speculative. I have no intelligence other than what I've shared. It does in my mind, explain the physics-defying five traits described above. It does not explain the previous supposition of sightings since humans started recording history, or trying to hypothesize their sightings in antiquity. Solid objects flying at hypersonic speeds make sonic booms; projections - ball lightning, 3D laser, or solid neutron holograms - likely won't.

If these are projections (adversary, friendly, neutral), who is doing them, and why?

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Ransomware, and Biofuels...

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Continuous improvements in farming and biofuel production technology have helped establish ethanol as a low-carbon fuel.

Topics: Biology, Biofuels, Climate Change, Dark Side, Economics, Environment

The carbon footprint of corn ethanol shrunk by 23% between 2005 and 2019 as farmers and ethanol producers adopted new technologies and improved efficiency, according to a new analysis published in the academic journal Biofuels Bioproducts and Biorefining by scientists at the Department of Energy’s Argonne National Laboratory. By 2019, the researchers found, corn ethanol was reducing lifecycle greenhouse gas emissions by 44-52% compared to gasoline.

Since 2000, corn ethanol production in the United State has increased significantly – from 1.6 to 15 billion gallons – due to supportive biofuel policies. In its study, the Argonne laboratory conducted a retrospective analysis of the changes in U.S. corn ethanol greenhouse gas emission intensity, sometimes known as carbon intensity, over the 15 years from 2005 to 2019, showing a significant decrease of 23%.

The carbon footprint of corn ethanol shrunk by 23% between 2005 and 2019 as farmers and ethanol producers adopted new technologies and improved efficiency, according to a new analysis published in the academic journal Biofuels Bioproducts and Biorefining by scientists at the Department of Energy’s Argonne National Laboratory. By 2019, the researchers found, corn ethanol was reducing lifecycle greenhouse gas emissions by 44-52% compared to gasoline.

Since 2000, corn ethanol production in the United State has increased significantly – from 1.6 to 15 billion gallons – due to supportive biofuel policies. In its study, the Argonne laboratory conducted a retrospective analysis of the changes in U.S. corn ethanol greenhouse gas emission intensity, sometimes known as carbon intensity, over the 15 years from 2005 to 2019, showing a significant decrease of 23%.

This is due to several factors, the analysis explains. Corn grain yield has increased continuously, reaching 168 bushels/acre or a 15% increase while fertilizer inputs per acre have remained constant, resulting in decreased intensities of fertilizer inputs with a 7% and 18% reduction in nitrogen and potash use per bushel of corn grain harvested, respectively. The study also found a 14% reduction per bushel in farming energy use.

The analysis also found a 6.5% increase in ethanol yield, from 2.70 to 2.86 gal/bushel corn, and a 24% reduction in ethanol plant energy use, from 32 000 to 25 000 Btu/gal ethanol also helped reduce the carbon intensity.

“Our study shows that while the corn ethanol industry has experienced significant volume expansion, it has reduced the GHG intensity of corn ethanol through improved U.S. corn farming and ethanol biorefinery operations. Corn yield has increased, and chemical and energy use intensities of corn farming have decreased. In ethanol biorefineries, ethanol yield has increased, and energy use has decreased significantly,” according to the researchers. “Biofuels, including corn ethanol, can play a critical role in the U.S. desire for deep decarbonization of its economy.”

Bonus: I'm not sure Russian criminal elements can hack, or extort us with it.

Researchers add evidence to ethanol’s low-carbon benefits, Jacqui Fatka, Farm Progress

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Biological Fukushima...

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Residents of the Pairaisopolis favela in Sao Paolo wait for meal distribution in the economic crisis brought on by the pandemic. Credit: Alexandre Schneider Getty Images

 

Topics: Biology, COVID-19, Existentialism, Pandemic

 

Note: Many stories are coming out of Seychelles. It is the most vaccinated nation on earth that is seeing rising cases of the Coronavirus due to tourism by Indian elites. We're not going to solve this piecemeal, nor treating each other in our backward, moribund tribal "traditions." This fight is a long haul, and hubris can make it longer, and more painful.

 

To be in Brazil right now feels like being trapped in the middle of a chaotic battlefield, a 14-month-long siege, without anyone in charge on your side of the trenches. Totally surrounded by a lethal enemy that keeps getting closer to you and your family. This biological foe keeps morphing in a way that seems well adapted to infect everyone within reach, showing mercy neither for pregnant women nor for their newborn babies.

 

After 12 months of such brutal biological warfare, more than 390,000 Brazilians have perished; the number of fatalities climbed to more than 4,000 fatalities a day in early April, and the number of new cases per day edged above 100,000, filling hospitals to capacity with tens of thousands of terminally ill patients who occupy all available ICU beds in a country that has one of the largest national public health systems in the world and more hospitals than the U.S. Such a steady tsunami of severely sick patients has led to an unprecedented collapse of the entire country’s health system and the setting of yet another pair of world records in terms of both infected and deceased health professionals. On top of that, the country’s stock of medical equipment and the supplies required to intubate patients in need of respirators to survive are running at a historic low and may run out completely because the federal government simply failed in the process of replenishing the national stockpile several months ago.

 

This, in a nutshell, is the catastrophic and unprecedented hecatomb that Brazil found itself locked in by mid-April 2021. A devastating second wave of the pandemic began to engulf all five regions of the country back in early November 2020. It resulted, in part, from the premature and chaotic relaxation of social isolation measures that had helped at least some regions of the country contain the worst of the initial phase of the pandemic. It worsened because of the large public political rallies that preceded the two rounds of the 2020 national elections, generating a multitude of super spreader events all over the country. And the situation was exacerbated by Christmas and Carnival, the largest national festivity.

 

Brazil’s Pandemic Is a ‘Biological Fukushima’ That Threatens the Entire Planet, By Miguel Nicolelis, Scientific American

 

 

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Panspermia...

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The mysterious object ‘Oumuamua passed through our solar system in 2017. Loeb has suggested it could have been sent by extraterrestrials. (Credit: European Southern Observatory/Kornmesser)

Topics: Astrobiology, Biology, Cosmology, SETI

Life, for all its complexities, has a simple commonality: It spreads. Plants, animals, and bacteria have colonized almost every nook and cranny of our world.

But why stop there? Some scientists speculate that biological matter may have proliferated across the cosmos itself, transported from planet to planet on wayward lumps of rock and ice. This idea is known as panspermia, and it carries a profound implication: Life on Earth may not have originated on our planet.

In theory, panspermia is fairly simple. Astronomers know that impacts from comets or asteroids on planets will sometimes eject debris with enough force to catapult rocks into space. Some of those space rocks will, in turn, crash into other worlds. A few rare meteorites on Earth are known to have come from Mars, likely in this fashion.

“You can imagine small astronauts sitting inside this rock, surviving the journey,” says Avi Loeb, an astrophysicist at Harvard University and director of the school’s Institute for Theory and Computation. “Microbes could potentially move from one planet to another, from Mars to Earth, from Earth to Venus.” (You may recognize Loeb’s name from his recent book Extraterrestrial: The First Sign of Intelligent Life Beyond Earth, which garnered headlines and criticism from astronomers for its claim that our solar system was recently visited by extraterrestrials.)</p>

Loeb has authored a number of papers probing the mechanics of panspermia, looking at, among other things, how the size and speed of space objects might affect their likelihood of transferring life. While Loeb still thinks it’s more likely that life originated on Earth, he says his work has failed to rule out the possibility that it came from somewhere else in space.

Did Life On Earth Come From Outer Space? Nathaniel Scharping, Discover Magazine

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Elephants, Mice, and Clocks...

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Topics: Biology, DNA, Evolution, Research

In her laboratory in Barcelona, Spain, Miki Ebisuya has built a clock without cogs, springs, or numbers. This clock doesn’t tick. It is made of genes and proteins, and it keeps time in a layer of cells that Ebisuya’s team has grown in its lab. This biological clock is tiny, but it could help to explain some of the most conspicuous differences between animal species.

Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged, and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

“I’m interested in biological time,” says Ebisuya, a developmental biologist at the European Molecular Biology Laboratory Barcelona. “But lifespan or gestation period, they are too long for me to study.” The swift speed of the segmentation clock makes it an ideal model system, she says.

These cellular clocks help explain why elephants are bigger than mice, Michael Marshall, Nature

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Lies, Damned Lies, and Statistics...

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Which states have dropped mask mandates and why, Marlene Lenthang, Yahoo News

Topics: Biology, COVID-19, Dark Humor, Existentialism, Mathematics, Politics

Figures often beguile me, particularly when I have the arranging of them myself; in which case the remark attributed to Disraeli would often apply with justice and force: “There are three kinds of lies: lies, damned lies, and statistics.”

Mark Twain, also: https://en.wikipedia.org/wiki/Lies,_damned_lies,_and_statistics

A follow-up to Tuesday's post: VOC...

‘No Thank You, Mr. President’: GOP States Still End Mask Mandates Despite Covid-19 Rise And Warnings From Biden, CDC, Alison Durkee, Forbes Business, April 2, 2021

Having some "fun" with mathematics. It's dark humor for all you young libertarians.

The current US COVID deaths are 573, 988 from https://ncov2019.live/.

The current US population is 332,494,997 from Worldometers.info. Each link updates minute-by-minute, so by the time you read this, these figures will have changed.

(US COVID deaths/current US population) x 100 = 0.17%. Round up to 0.2%.

That's pretty low.

For the "freedom-loving libertarians" spring breaking in Miami, or Fort Lauderdale, Florida, and Corpus Christi, Texas - a thought experiment:

100,000 of you are about to dive into the ocean.

There is a 0.2% = 0.2/100 chance some of you will get devoured by sharks.

100,000 x (0.2/100) = 200 dead spring breakers.

So, out of 100,000 - 200 = 99,800, or 99.8% have a very good chance of not becoming "chicken of the sea," and surviving your spring break. The dilemma is, there will still be blood in the water. Blood that carries pathogens that despite your "Y" swimming lessons and the saline environment, you might ingest red tide, and suffer the consequences.

The problem is, your 0.2% chance is not zero. Under normal circumstances (and pandemics are once-in-a-century "not normal"), there's no libertarian case for this:

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VOC...

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Inside the B.1.1.7 Coronavirus Variant, By Jonathan Corum and Carl ZimmerJan, The New York Times, January 18, 2021

Topics: Biology, COVID-19, DNA, Research

VariantReported cases in the USNumber of Jurisdictions Reporting
B.1.1.716,27552
B.1.35138636
P.135625
Source: CDC

Download Accessible Data [XLS – 738 B]

CDC is closely monitoring these variants of concern (VOC). These variants have mutations in the virus genome that alter the characteristics and cause the virus to act differently in ways that are significant to public health (e.g., causes more severe disease, spreads more easily between humans, requires different treatments, changes the effectiveness of current vaccines).

CDC: US COVID-19 Cases Caused by Variants

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Women's History Month, and CRISPR...

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Topics: Biology, Chemistry, DNA, Nobel Prize, Research, Women in Science

This year’s (2020) Nobel Prize in Chemistry has been awarded to two scientists who transformed an obscure bacterial immune mechanism, commonly called CRISPR, into a tool that can simply and cheaply edit the genomes of everything from wheat to mosquitoes to humans. 

The award went jointly to Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens and Jennifer Doudna of the University of California, Berkeley, “for the development of a method for genome editing.” They first showed that CRISPR—which stands for clustered regularly interspaced short palindromic repeats—could edit DNA in an in vitro system in a paper published in the 28 June 2012 issue of Science. Their discovery was rapidly expanded on by many others and soon made CRISPR a common tool in labs around the world. The genome editor spawned industries working on making new medicines, agricultural products, and ways to control pests.

Many scientists anticipated that Feng Zhang of the Broad Institute, who showed 6 months later that CRISPR worked in mammalian cells, would share the prize. The institutions of the three scientists are locked in a fierce patent battle over who deserves the intellectual property rights to CRISPR’s discovery, which some estimate could be worth billions of dollars.

“The ability to cut DNA where you want has revolutionized the life sciences. The genetic scissors were discovered 8 years ago, but have already benefited humankind greatly,” Pernilla Wittung Stafshede, a chemical biologist at the Chalmers University of Technology, said at the prize briefing.

CRISPR was also used in one of the most controversial biomedical experiments of the past decade, when a Chinese scientist edited the genomes of human embryos, resulting in the birth of three babies with altered genes. He was widely condemned and eventually sentenced to jail in China, a country that has become a leader in other areas of CRISPR research.

Although scientists were not surprised Doudna and Charpentier won the prize, Charpentier was stunned. “As much as I have been awarded a number of prizes, it’s something you hear, but you don’t completely connect,” she said in a phone call with the Nobel Prize officials. “I was told a number of times that when it happens, you’re very surprised and feel that it’s not real.”

At a press briefing today, Doudna noted she was asleep and missed the initial calls from Sweden, only waking up to answer the phone finally when a Nature reporter called. "She wanted to know if I could comment on the Nobel and I said, Well, who won it? And she was shocked that she was the person to tell me."

CRISPR, the revolutionary genetic ‘scissors,’ honored by Chemistry Nobel, Jon Cohen, Science Magazine, AAAS

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Our Flexible Molecule...

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1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and reversible. (Courtesy: Davide Michieletto)

Topics: Biology, DNA, Physics, Polymer Science, Research

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naïve, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment on it, I tried to pipette some of the solution out, but it didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh

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Haplotypes and Neanderthals...

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a, Manhattan plot of a genome-wide association study of 3,199 hospitalized patients with COVID-19 and 897,488 population controls. The dashed line indicates genome-wide significance (P = 5 × 10−8). Data were modified from the COVID-19 Host Genetics Initiative2 (https://www.covid19hg.org/). b, Linkage disequilibrium between the index risk variant (rs35044562) and genetic variants in the 1000 Genomes Project. Red circles indicate genetic variants for which the alleles are correlated to the risk variant (r2 > 0.1) and the risk alleles match the Vindija 33.19 Neanderthal genome. The core Neanderthal haplotype (r2 > 0.98) is indicated by a black bar. Some individuals carry longer Neanderthal-like haplotypes. The location of the genes in the region is indicated below using standard gene symbols. The x-axis shows hg19 coordinates.

Topics: Biology, COVID-19, Genetics, Research

Abstract

A recent genetic association study1 identified a gene cluster on chromosome 3 as a risk locus for respiratory failure after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A separate study (COVID-19 Host Genetics Initiative)2 comprising 3,199 hospitalized patients with coronavirus disease 2019 (COVID-19) and control individuals showed that this cluster is the major genetic risk factor for severe symptoms after SARS-CoV-2 infection and hospitalization. Here we show that the risk is conferred by a genomic segment of around 50 kilobases in size that is inherited from Neanderthals and is carried by around 50% of people in South Asia and around 16% of people in Europe.

Main

The COVID-19 pandemic has caused considerable morbidity and mortality and has resulted in the death of over a million people to date3. The clinical manifestations of the disease caused by the virus, SARS-CoV-2, vary widely in severity, ranging from no or mild symptoms to rapid progression to respiratory failure4. Early in the pandemic, it became clear that advanced age is a major risk factor, as well as being male and some co-morbidities5. These risk factors, however, do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Thus, genetic risk factors may have a role in disease progression. A previous study1 identified two genomic regions that are associated with severe COVID-19: one region on chromosome 3, which contains six genes, and one region on chromosome 9 that determines ABO blood groups. Recently, a dataset was released by the COVID-19 Host Genetics Initiative in which the region on chromosome 3 is the only region that is significantly associated with severe COVID-19 at the genome-wide level (Fig. 1a). The risk variant in this region confers an odds ratio for requiring hospitalization of 1.6 (95% confidence interval, 1.42–1.79) (Extended Data Fig. 1).

The genetic variants that are most associated with severe COVID-19 on chromosome 3 (45,859,651–45,909,024 (hg19)) are all in high linkage disequilibrium (LD)—that is, they are all strongly associated with each other in the population (r2 > 0.98)—and span 49.4 thousand bases (kb) (Fig. 1b). This ‘core’ haplotype is furthermore in weaker linkage disequilibrium with longer haplotypes of up to 333.8 kb (r2 > 0.32) (Extended Data Fig. 2). Some such long haplotypes have entered the human population by gene flow from Neanderthals or Denisovans, extinct hominins that contributed genetic variants to the ancestors of present-day humans around 40,000–60,000 years ago6,7. We, therefore, investigated whether the haplotype may have come from Neanderthals or Denisovans.

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals, Hugo Zeberg, & Svante Pääbo, Nature

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Well Deserved...

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Anthony Fauci has advised seven presidents on public health, most recently serving as chief medical advisor to President Joe Biden. | NIAID

 

Topics: Biology, COVID-19, Research, Science

 

Anthony Fauci – Director of the National Institute of Allergy and Infectious Diseases, an expert on HIV and immunoregulation, and the de facto public face of a science-based recovery from COVID-19 – has been named the winner of the 2021 Philip Hauge Abelson Prize, awarded annually by the American Association for the Advancement of Science to a scientist or public servant who has contributed significantly to the advancement of science in the United States.

 

Fauci is “an outstanding scientist with more than a thousand publications” and “an exceptional public servant, having been at the forefront of the world’s efforts to combat diverse infectious diseases for over 40 years,” wrote Alan Leshner, former chief executive officer of AAAS, in nominating Fauci for the prize. The prize committee cited Fauci’s “extraordinary contributions to science and medicine” and his service that has shaped research and public policy.

 

Anthony Fauci to Receive 2021 AAAS Abelson Prize, Andrea Korte, American Association for the Advancement of Science

 

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2020 Nano Highlights...

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Image source: The article link, but it should symbolize how last year felt to the sane among us.

Topics: Biology, Materials Science, Nanotechnology, Research

Snake vision inspires pyroelectric material design

Bioinspiration and biomimicry involve studying how living organisms do something and using that insight to develop new technologies. Pit vipers have two special organs on their heads called loreal pits that allow them to “see” the infrared radiation given off by their warm-blooded prey. Now, Pradeep Sharma and colleagues have worked out that the snakes use cells that act as a soft pyroelectric material to convert infrared radiation into electrical signals that can be processed by their nervous systems. As well as potentially solving a longstanding puzzle in snake biology, the work could also aid the development of thermoelectric transducers based on soft, flexible structures rather than stiff crystals.

Nanotechnology and materials highlights of 2020, Hamish Johnston, Physics World

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Dark Winter, Brighter Spring...

Topics: Biology, Civics, Civil Rights, COVID-19, Existentialism, Human Rights

I have taken the following vaccines this year: Pneumonia, Seasonal Influenza (Flu), Shingles in two booster shots.

Therefore, I am very likely to take the Coronavirus vaccine either offered by Pfizer or Moderna.

Pfizer is pushing back on the Trump administration's suggestion that the company is having trouble producing its COVID-19 vaccine, saying it's ready to ship millions more doses – once the government asks for them. As the company spoke out, several states said their vaccine allocations for next week have been sharply reduced.

Here's what the key players are saying about a complicated situation:

What Pfizer says

"Pfizer is not having any production issues with our COVID-19 vaccine, and no shipments containing the vaccine are on hold or delayed," CEO Albert Bourla said via Twitter. His company says it has completed every shipment the U.S. government has requested.

"We have millions more doses sitting in our warehouse but, as of now, we have not received any shipment instructions for additional doses," Pfizer said in a statement.

The company also noted that in the past week, it shipped 2.9 million doses of the vaccine it developed with BioNTech in what is widely seen as a breakthrough in the nation's fight against the coronavirus.

Pfizer Says Millions Of Vaccine Doses Are Ready, But States Say Shipments Were Cut, Bill Chappell, NPR

Unlike the 1918 pandemic, I don't think it will take us a decade to come to some sense of normalcy. I am concerned, from a cultural perspective, that the vaccine spreads equitably.

We have a reason to be suspicious. The Tuskegee Experiment happened over four decades, affected hundreds of lives, allowing syphilis to infect men, women, and children. It makes trusting authorities with our lives a bit problematic. As I've said, if it helps anyone reading this entry, I will take the vaccine. I would like to get back to some sense of normalcy.

The revelation of the recent Russian hacks is the equivalent of a Cyber Pearl Harbor. Our nuclear triad material, three states (including Austin, Texas), the Central Intelligence Agency, Treasury, NASA, Commerce, et al. This is a stickup. Think the city, lights: sewage. Like a burglar, we could all be held hostage by a foreign power. To paraphrase a false claim attributed to Nikita Khrushchev, Putin could literally "bury us without firing a shot."

The shenanigans of the current obtuse, malignant, narcissistic, and incompetent administration will come to an end. Vaccines will go out, modeled by an incoming administration that like previous democratic ones before them, have to shovel the country out of the smoldering ruin that the previous republican one left the country in. They will, of course, delay vaccines, they will of course, try to sabotage on the way out. They are the steroids equivalent of Clinton-to-Bush removing the W keys, and costing the government approximately $15,000. It was disappointing and sophomoric. This stunt is petty, malevolent, and deadly. We have crossed the Rubicon of 300,000 dead Americans. At a rate of a 9/11 per day, we'll reach 400,000 by inauguration. Delay during a pandemic will kill more Americans, but I guess that's not a big concern to a malignant narcissist.

But I am hopeful for a brighter spring.

Mango Mussolini can do a lot of damage in 33 days, but it's 33 days at noon when he loses access to the nuclear football, he loses the presidential immunity that protects him from an indictment, not that Letitia James, Cyrus Vance, SDNY, or EDNY are bothered by his threats of family and self pardons. His crimes in New York are state felonies, likely involving inflating his wealth, or decreasing it when it suited him. We'll likely find out he's not as rich as he claims to be. He cashed a series of diminishing value checks sent as a gag by Spy Magazine, proving himself a bit player in the New York Real Estate market. He'll need every penny he's grifting from his deluded followers to stay out of prison. Not that I'm sympathetic: but grift on this constant level has to be exhausting, and depleting of finance, and bodily constitution.

The evil energizer bunny has to run out of gas sometimes. His tweets will reach a limited audience. Cities that haven't YET gotten paid for his previous rallies will refuse to book him. He's proposing bringing back The Apprentice because his "power" is his celebrity, and that dwindles quickly without cameras on you constantly. He can call it Apprentice, 2024: Finding a Vice President (a tacit admittance Pence didn't help him win re-election). Several sources say Twitter might finally remove him, not the conviction to "do the right thing," just that if his followers dwindle, they have no one to gather metadata from for marketing purposes. It's business, and a one-term president probably isn't good for the bottom-line.

That's all fine and good, Donald unless you're spending your evenings at Riker's. Maybe they'll station you at the Queens Detention Complex. He can see the old neighborhood, while the rest of us heal from his madness. We will get through this.

That's it for this year. See you in January 2021.

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