The New York Times tells the story of Fayçal Ziraoui, a 38-year-old French-Moroccan business consultant who "caused an online uproar" after saying he'd cracked the last two unsolved ciphers of the four attributed to the Zodiac killer in California "and identified him, potentially ending a 50-year-old quest." Maybe because he said he cracked them in just two weeks. Many Zodiac enthusiasts consider the remaining ciphers — Z32 and Z13 — unsolvable because they are too short to determine the encryption key. An untold number of solutions could work, they say, rendering verification nearly impossible.

But Mr. Ziraoui said he had a sudden thought. The code-crackers who had solved the [earlier] 340-character cipher in December had been able to do so by identifying the encryption key, which they had put into the public domain when announcing their breakthrough. What if the killer used that same encryption key for the two remaining ciphers? So he said he applied it to the 32-character cipher, which the killer had included in a letter as the key to the location of a bomb set to go off at a school in the fall of 1970. (It never did, even though police failed to crack the code.) That produced a sequence of random letters from the alphabet. Mr. Ziraoui said he then worked through a half-dozen steps including letter-to-number substitutions, identifying coordinates in numbers and using a code-breaking program he created to crunch jumbles of letters into coherent words...

After two weeks of intense code-cracking, he deciphered the sentence, "LABOR DAY FIND 45.069 NORT 58.719 WEST." The message referred to coordinates based on the earth's magnetic field, not the more familiar geographic coordinates. The sequence zeroed in on a location near a school in South Lake Tahoe, a city in California referred to in another postcard believed to have been sent by the Zodiac killer in 1971.

An excited Mr. Ziraoui said he immediately turned to Z13, which supposedly revealed the killer's name, using the same encryption key and various cipher-cracking techniques. [The mostly un-coded letter includes a sentence which says "My name is _____," followed by a 13-character cipher.] After about an hour, Mr. Ziraoui said he came up with "KAYR," which he realized resembled the last name of Lawrence Kaye, a salesman and career criminal living in South Lake Tahoe who had been a suspect in the case. Mr. Kaye, who also used the pseudonym Kane, died in 2010.

The typo was similar to ones found in previous ciphers, he noticed, likely errors made by the killer when encoding the message. The result that was so close to Mr. Kaye's name and the South Lake Tahoe location were too much to be a coincidence, he thought. Mr. Kaye had been the subject of a report by Harvey Hines, a now-deceased police detective, who was convinced he was the Zodiac killer but was unable to convince his superiors. Around 2 a.m. on Jan. 3, an exhausted but elated Mr. Ziraoui posted a message entitled "Z13 — My Name is KAYE" on a 50,000-member Reddit forum dedicated to the Zodiac Killer.

The message was deleted within 30 minutes.

"Sorry, I've removed this one as part of a sort of general policy against Z13 solution posts," the forum's moderator wrote, arguing that the cipher was too short to be solvable.

NASA has released a new video explaining the complicated, hour-long process required for the Mars rover to take a selfie (which was actually a composite of 62 separate images stitched together).

And meanwhile, CNN reports that its Ingenuity helicopter completed its eighth flight this week, "and even got a software update to fix an annoying issue that impacted some of its previous outings." On its latest outing, Ingenuity flew 525 feet (160 meters) to the south and southeast to a new airfield. This was the copter's third flight of the operations demo phase, in which Ingenuity is proving its usefulness as an aerial scout without interfering with the Perseverance rover's science mission — searching for evidence of ancient life on Mars... Ingenuity continues to do well, and the team is planning for more flights that will push its capabilities. And the helicopter is doing even better now that its troublesome "watchdog" software issue has been fixed. That was deployed before the eighth flight...

Ingenuity is also due for a navigation computer software update that will fix the issue that occurred during the chopper's sixth flight. Images captured by the navigation camera, which feed into the helicopter's navigation computer, had timing delays. Those images help Ingenuity to track its location, among other critical factors during flight. When the incorrect times and images were associated, it caused the chopper to wobble in the air. Ingenuity was able to land safely, but the team wants to prevent the issue from happening again so the chopper doesn't spiral out of control. It's also why the helicopter didn't capture any color images during its last two flights.

Ran Balicer leads an expert Covid-19 advisory panel for the Israeli government. Friday he shared some troubling news with the Wall Street Journal: "The entrance of the Delta variant has changed the transmission dynamics," said Prof. Balicer, who is also the chief innovation officer for Israel's largest health-management organization, Clalit.

About half of adults infected in the outbreak of the Delta variant of Covid-19 in Israel were fully inoculated.

These so-called breakthrough cases — defined as positive Covid-19 test results received at least two weeks after patients receive their final vaccine dose — are broadly expected as the Pfizer vaccine is highly effective but not 100% foolproof, according to Mr. Balicer. Israeli health officials are optimistic that even if the variant does spread, evidence from countries such as the U.K. indicate the vaccine will prevent a large increase in severe illness and hospitalizations that plagued the country's health system in previous outbreaks. Israel has recorded only five severe cases in the past 10 days, Prof. Balicer said, but whether more will emerge is too early to tell....

Dr. Tedros Adhanom Ghebreyesus, director-general of the World Health Organization, said the worrisome variant is now present in 85 countries.
Several countries appear concerned that fully vaccinated people could still spread the Delta variant. Israel's government just reimposed safety measures (including an indoor-mask requirement), according to the Journal. And Sydney, Australia (the country's largest city, housing more than 5 million people) "will enter a hard two-week lockdown on Saturday night..." reports CNN, "as authorities try to contain a fast-spreading outbreak of the highly infectious Delta coronavirus variant." More than a million people in downtown Sydney and the city's eastern suburbs were already under lockdown due to the outbreak, but health authorities said they needed to expand that after more Covid-19 cases were recorded, with exposure sites increasing beyond the initial areas of concern.
Meanwhile, CNBC reports: The World Health Organization on Friday urged fully vaccinated people to continue to wear masks, social distance and practice other Covid-19 pandemic safety measures as the highly contagious delta variant spreads rapidly across the globe. "People cannot feel safe just because they had the two doses. They still need to protect themselves," Dr. Mariangela Simao, WHO assistant director-general for access to medicines and health products, said during a news briefing from the agency's Geneva headquarters. "Vaccine alone won't stop community transmission," Simao added. "People need to continue to use masks consistently, be in ventilated spaces, hand hygiene ... the physical distance, avoid crowding. This still continues to be extremely important, even if you're vaccinated when you have a community transmission ongoing."
CNN reports that the U.S. Centers for Disease Control and Prevention also "warned that there is a small chance a fully vaccinated person could still get infected if they're exposed." "Current data suggest that COVID-19 vaccines authorized for use in the United States offer protection against most variants currently spreading in the United States. However, some variants might cause illness in some people even after they are fully vaccinated," CDC spokesperson Jade Fulce told CNN in an email on Friday. While Covid-19 vaccines are effective, Fulce said no vaccine is "100% effective at preventing illness." And with millions of people getting vaccinated against the virus, some who are fully vaccinated "will still get sick if they are exposed," Fulce said.

"However, people with breakthrough infections may get less severely ill or have a shorter illness than they would have if they had not been vaccinated."

An anonymous reader quotes a report from The New York Times: Researchers have found evidence that a coronavirus epidemic swept East Asia some 20,000 years ago and was devastating enough to leave an evolutionary imprint on the DNA of people alive today. The new study suggests that an ancient coronavirus plagued the region for many years, researchers say. The finding could have dire implications for the Covid-19 pandemic if it's not brought under control soon through vaccination. "It should make us worry," said David Enard, an evolutionary biologist at the University of Arizona who led the study, which was published on Thursday in the journal Current Biology. "What is going on right now might be going on for generations and generations."

Over generations, viruses drive enormous amounts of change in the human genome. A mutation that protects against a viral infection may well mean the difference between life and death, and it will be passed down to offspring. A lifesaving mutation, for example, might allow people to chop apart a virus's proteins. But viruses can evolve, too. Their proteins can change shape to overcome a host's defenses. And those changes might spur the host to evolve even more counteroffensives, leading to more mutations. When a random new mutation happens to provide resistance to a virus, it can swiftly become more common from one generation to the next. And other versions of that gene, in turn, become rarer. So if one version of a gene dominates all others in large groups of people, scientists know that is most likely a signature of rapid evolution in the past.

In recent years, Dr. Enard and his colleagues have searched the human genome for these patterns of genetic variation in order to reconstruct the history of an array of viruses. When the pandemic struck, he wondered whether ancient coronaviruses had left a distinctive mark of their own. He and his colleagues compared the DNA of thousands of people across 26 different populations around the world, looking at a combination of genes known to be crucial for coronaviruses but not other kinds of pathogens. In East Asian populations, the scientists found that 42 of these genes had a dominant version. That was a strong signal that people in East Asia had adapted to an ancient coronavirus. But whatever happened in East Asia seemed to have been limited to that region. The scientists then tried to estimate how long ago East Asians had adapted to a coronavirus. They took advantage of the fact that once a dominant version of a gene starts being passed down through the generations, it can gain harmless random mutations. As more time passes, more of those mutations accumulate. Dr. Enard and his colleagues found that the 42 genes all had about the same number of mutations. That meant that they had all rapidly evolved at about the same time. "This is a signal we should absolutely not expect by chance," Dr. Enard said. They estimated that all of those genes evolved their antiviral mutations sometime between 20,000 and 25,000 years ago, most likely over the course of a few centuries. It's a surprising finding, since East Asians at the time were not living in dense communities but instead formed small bands of hunter-gatherers.

University of Oxford scientists are trialing giving Ivermectin to people with Covid symptoms to see if it can keep them out of hospital. The BBC reports: The Principle study will compare those given the drug to patients receiving the usual NHS care. The drug has become controversial after being promoted for use across Latin America and in South Africa, despite being so far unproven. Previous studies of Ivermectin have generally been small or low quality. Most commonly used to treat parasitic infections such as river blindness, spread by flies, Ivermectin has also been shown to kill viruses in petri dishes in the lab -- although, at much higher doses than would usually be prescribed to people.

Dr Aurora Baluja, an anaesthesiologist and critical care doctor, said Ivermectin was often being given in parts of the world where there are high incidences of parasitic infections. Covid patients who are also fighting a parasitic disease at the same time would be likely to fare worse and that might explains some of its seemingly positive effect. Though there have been some early "promising" results from small and observational studies, Principle joint chief investigator Prof Richard Hobbs said it would be "premature" to recommend Ivermectin for Covid. [...] The Oxford team said they had selected Ivermectin to be included in the trial because it was "readily available globally" and known to be relatively safe (although, like most things, it can be toxic at very high doses). People aged 18-64 with an underlying health condition or experiencing breathlessness, and anyone aged 65 or over, can sign up to the Principle study within 14 days of having Covid symptoms or receiving a positive test. "All in all, though, the most compelling reports of ivermectin's effects seem to come from the smallest and least controlled samples (all the way down to anecdotal results) while the larger and more well-controlled trials tend to produce equivocal evidence at best," writes Derek Lowe, a medical chemist working in the pharmaceutical industry. "My current opinion is pretty much exactly that of the WHO guidance: I do not think that the current evidence is strong enough to say that ivermectin is a useful therapy for coronavirus patients. I know that there are quite a few studies out there in the literature, but they suffer from various combinations of small sample size, poor trial design, not enough data reported, and (in many cases) inconclusive statistics."

Should people on their deathbeds be allowed to try anything to save themselves? Should the entire world be allowed to practice self-care on a grand scale? These are some of the questions American author, journalist, and podcaster Matt Taibbi poses in an article via Substack. He argues that ivermectin "has become hostage to a larger global fight between populists and anti-populists."

UPDATE (2/18/2021): CNN reports "The antiparasitic drug ivermectin doesn't prevent severe disease from Covid-19 any more effectively than symptom management and close observation by medical professionals, according to a study published Friday in the journal JAMA Internal Medicine." In fact, slightly more patients in the ivermectin group went on to need extra oxygen compared with those who took a placebo, though the difference was not statistically significant.... [T]hey also looked at whether patients needed to be hospitalized, had to go on a ventilator, needed intensive care or died from their infections. There was no meaningful difference in outcomes between the group that took ivermectin and those who got the placebo treatment.

It was a randomized-controlled trial, the gold standard of medical research, in which researchers test an intervention against a placebo....

In addition to the fact that ivermectin didn't work, people who took it had more side effects than those who didn't, and sometimes those side effects were severe, including heart attacks, anemia and diarrhea that led to shock.

A simple blood test that can detect more than 50 types of cancer before any clinical signs or symptoms of the disease emerge in a person is accurate enough to be rolled out as a screening test, according to scientists. The Guardian reports: The test, which is also being piloted by NHS England in the autumn, is aimed at people at higher risk of the disease including patients aged 50 or older. It is able to identify many types of the disease that are difficult to diagnose in the early stages such as head and neck, ovarian, pancreatic, esophageal and some blood cancers. Scientists said their findings, published in the journal Annals of Oncology, show that the test accurately detects cancer often before any signs or symptoms appear, while having a very low false positive rate.

The test, developed by US-based company Grail, looks for chemical changes in fragments of genetic code "cell-free DNA (cfDNA)" that leak from tumors into the bloodstream. The Guardian first reported on the test last year and how it had been developed using a machine learning algorithm a type of artificial intelligence. It works by examining the DNA that is shed by tumors and found circulating in the blood. More specifically, it focuses on chemical changes to this DNA, known as methylation patterns. Now the latest study has revealed the test has an impressively high level of accuracy. Scientists analyzed the performance of the test in 2,823 people with the disease and 1,254 people without. It correctly identified when cancer was present in 51.5% of cases, across all stages of the disease, and wrongly detected cancer in only 0.5% of cases.

In solid tumors that do not have any screening options "such as esophageal, liver and pancreatic cancers" the ability to generate a positive test result was twice as high (65.6%) as that for solid tumors that do have screening options such as breast, bowel, cervical and prostate cancers. Meanwhile, the overall ability to generate a positive test result in cancers of the blood, such as lymphoma and myeloma, was 55.1%. The test correctly also identified the tissue in which the cancer was located in the body in 88.7% of cases.

"With just over half of the U.S. population fully vaccinated against COVID-19, and two-thirds having received one dose, a clear and unambiguous trend has emerged," writes Slashdot reader quonset. "Not only have deaths plunged from approximately 3,400 per day in January to roughly 300 per day now, 98% to 99% of all COVID-19 deaths are now from people who aren't vaccinated." MarketWatch reports: An Associated Press analysis of available government data from May shows that "breakthrough" infections in fully vaccinated people accounted for fewer than 1,200 of more than 853,000 COVID-19 hospitalizations. That's about 0.1%. And only about 150 of the more than 18,000 COVID-19 deaths in May were in fully vaccinated people. That translates to about 0.8%, or five deaths per day on average.

The preventable deaths will continue, experts predict, with unvaccinated pockets of the nation experiencing outbreaks in the fall and winter. Ali Mokdad, a professor of health metrics sciences at the University of Washington in Seattle, said modeling suggests the nation will hit 1,000 deaths per day again next year. In Arkansas, which has one of the lowest vaccination rates in the nation, with only about 33% of the population fully protected, cases, hospitalizations and deaths are rising. "It is sad to see someone go to the hospital or die when it can be prevented," Gov. Asa Hutchinson tweeted as he urged people to get their shots.

The discovery of a huge fossilised skull that was wrapped up and hidden in a Chinese well nearly 90 years ago has forced scientists to rewrite the story of human evolution. Shmoodling writes: Analysis of the remains has revealed a new branch of the human family tree that points to a previously unknown sister group more closely related to modern humans than the Neanderthals. The extraordinary fossil has been named a new human species, Homo longi or "Dragon man," by Chinese researchers, although other experts are more cautious about the designation.

"I think this is one of the most important finds of the past 50 years," said Prof Chris Stringer, research leader at the Natural History Museum in London, who worked on the project. "It's a wonderfully preserved fossil." The skull appears to have a remarkable backstory. According to the researchers, it was originally found in 1933 by Chinese labourers building a bridge over the Songhua River in Harbin, in China's northernmost province, Heilongjiang, during the Japanese occupation. To keep the skull from falling into Japanese hands it was wrapped and hidden in an abandoned well, resurfacing only in 2018 after the man who hid it told his grandson about it shortly before he died. Details are published in three papers in The Innovation.

SpaceX is "shooting for July" to launch the first orbital spaceflight of its Starship rocket, company president Gwynne Shotwell said Friday. From a report: "I'm hoping we make it, but we all know that this is difficult," Shotwell said, speaking at the National Space Society's virtual International Space Development conference. "We are really on the cusp of flying that system, or at least attempting the first orbital flight of that system, really in the very near term," Shotwell added. SpaceX has conducted multiple short test flights of Starship prototypes over the past year, but reaching orbit represents the next step in testing the rocket. The company in May revealed its plan for the flight, which would launch from the company's facility in Texas and aim to splash down off the coast of Hawaii. Starship prototypes stand at about 160 feet tall, or around the size of a 16-story building, and are built of stainless steel -- representing the early version of the rocket that Musk unveiled in 2019. The rocket initially launches on a "Super Heavy" booster, which makes up the bottom half of the rocket and stands about 230 feet tall. Together, Starship and Super Heavy will be nearly 400 feet tall when stacked for the launch.

Hmmmmmm writes: China aims to send its first crewed mission to Mars in 2033, with regular follow-up flights to follow, under a long-term plan to build a permanently inhabited base on the Red Planet and extract its resources. The ambitious plan, which will intensify a race with the United States to plant humans on Mars, was disclosed in detail for the first time after China landed a robotic rover on Mars in mid-May in its inaugural mission to the planet. Crewed launches to Mars are planned for 2033, 2035, 2037, 2041 and beyond, the head of China's main rocket maker, Wang Xiaojun, told a space exploration conference in Russia recently by video link. Before the crewed missions begin, China will send robots to Mars to study possible sites for the base and to build systems to extract resources there, the official China Space News reported on Wednesday, citing Wang, who is head of the China Academy of Launch Vehicle Technology.

The coronavirus vaccines made by Pfizer-BioNTech and Moderna may have caused heart problems in more than 1,200 Americans, including about 500 who were younger than age 30, according to data reported on Wednesday by researchers at the Centers for Disease Control and Prevention. Still, the benefits of immunization greatly outweighed the risks, and advisers to the C.D.C. strongly recommended vaccination for all Americans 12 and older. The New York Times: The heart problems reported are myocarditis, an inflammation of the heart muscle; and pericarditis, inflammation of the lining around the heart. The risk is higher after the second dose of an mRNA vaccine than after the first, the researchers reported, and much higher in men than in women. But overall, the side effect is very uncommon -- just 12.6 cases per million second doses administered. The researchers estimated that out of a million second doses given to boys ages 12 to 17, the vaccines might cause a maximum of 70 myocarditis cases, but would prevent 5,700 infections, 215 hospitalizations and two deaths. Agency researchers presented the data to members of the Advisory Committee on Immunization Practices, which makes recommendations on vaccine use in the United States. (The scientists grouped pericarditis with myocarditis for reporting purposes.) Most cases were mild, with symptoms like fatigue, chest pain and disturbances in heart rhythm that quickly cleared up, the researchers said. Of the 484 cases reported in Americans under age 30, the C.D.C. has definitively linked 323 cases to vaccination. The rest remain under investigation.

An anonymous reader quotes a report from the BBC: A large facility capable of extracting significant amounts of carbon dioxide from the air is being planned for north east Scotland. The proposed plant would remove up to one million tonnes of CO2 every year -- the same amount taken up by around 40 million trees. The extracted gas could be stored permanently deep under the seabed off the Scottish coast. This Direct Air Capture (DAC) plan is a joint project between UK firm Storegga and Canadian company Carbon Engineering. It's at a very early stage of development -- today's announcement is the beginning of the engineering and design of the plant. A feasibility study has already been carried out and if everything goes well, the facility would be operational by 2026. Storegga say up to 300 jobs would be created in the construction phase. However there are many hurdles, including planning and finance -- and a site for the plant won't be selected until next year. If it does go ahead it would be the biggest DAC facility in Europe and depending on the final configuration, could be the biggest in the world. Why Scotland? The companies cite the country's skilled workforce needed to operate a DAC facility, given their abundant renewable energy sources. The country also has pipelines going out under the sea to allow the permanent burial of the captured carbon.

An array of tiny fossils suggests dinosaurs not only roamed the Arctic, but hatched and raised their young there too. The Guardian reports: While dinosaur fossils have previously been found in the Arctic, it was unclear whether they lived there year-round or were seasonal visitors. Now experts say hundreds of fossils from very young dinosaurs recovered from northern Alaska indicates the creatures reproduced in the region, suggesting it was their permanent home. Prof Gregory Erickson, a palaeobiologist at Florida State University and a co-author of the research, said the discovery was akin to a prehistoric maternity ward, adding it was very rare to find remains of such young dinosaurs because they are so small and delicate.

Writing in the journal Current Biology, Erickson and colleagues reported how they analysed fossils recovered from the Upper Cretaceous Prince Creek Formation in a series of expeditions spanning a decade and involved the use of fine mesh screens to sift sediments. Though remains from dinosaurs have previously been found in the formation, none showed evidence of reproduction. But the new research has revealed the discovery of tiny teeth and bones from young dinosaurs, including those who were just about to hatch or had recently done so. The fossils, dating to around 70m years ago, came from large and small-bodied dinosaurs covering at least seven different types -- including duck-billed and horned dinosaurs. Teeth were also found from a young tyrannosaur, said Erickson, possibly just six months old.

While the findings rule out the idea that dinosaurs only moved north after reproduction, Erickson added that young hatched in the Arctic would have been too small to travel south for the winter. "Given long incubation periods, small hatching sizes, and the short Arctic summer, it is very unlikely the dinosaurs were migrating," he said. The team said the conclusion that the dinosaurs likely lived in the Arctic year-round is backed up by other evidence, including that many of the species have not been found in rocks of a similar age at lower latitudes. At the time that dinosaurs roamed the Arctic, the region would have lacked big polar ice caps and had conifer forests, but the researchers say the creatures still faced harsh conditions, with up to 120 days of continuous darkness in the winter and an average annual temperature of just above 6C.

The storied space telescope that brought you stunning photos of the solar system and enriched our understanding of the cosmos over the past three decades is experiencing a technical glitch. From a report: Scientists at NASA say the Hubble Space Telescope's payload computer, which operates the spacecraft's scientific instruments, went down suddenly on June 13. Without it, the instruments on board meant to snap pictures and collect data are not currently working. Scientists have run a series of tests on the malfunctioning computer system but have yet to figure out what went wrong. "It's just the inefficiency of trying to fix something which is orbiting 400 miles over your head instead of in your laboratory," Paul Hertz, the director of astrophysics for NASA, told NPR. "If this computer were in the lab, we'd be hooking up monitors and testing the inputs and outputs all over the place, and would be really quick to diagnose it," he said. "All we can do is send a command from our limited set of commands and then see what data comes out of the computer and then send that data down and try to analyze it."

At first NASA scientists wondered if a "degrading memory module" on Hubble was to blame. Then on Tuesday the agency said it was investigating whether the computer's Central Processing Module (CPM) or its Standard Interface (STINT) hardware, which helps the CPM communicate with other components, caused the problem. Hertz said the current assumption, though unverified, was that the technical issue was a "random parts failure" somewhere on the computer system, which was built in the 1980s and launched into space in 1990. "They're very primitive computers compared to what's in your cell phone," he said, "but the problem is we can't touch it or see it." Most of Hubble's components have redundant back-ups, so once scientists figure out the specific component that's causing the computer problem, they can remotely switch over to its back-up part.

UPDATE (7/30): All the missing virus sequences have now been published, with their deletion being explained as just "an editorial oversight by a scientific journal," according to the New York Times.

In Slashdot's original report, an anonymous reader quoted another report from The New York Times: About a year ago, genetic sequences from more than 200 virus samples from early cases of Covid-19 in Wuhan disappeared from an online scientific database. Now, by rooting through files stored on Google Cloud, a researcher in Seattle reports that he has recovered 13 of those original sequences -- intriguing new information for discerning when and how the virus may have spilled over from a bat or another animal into humans. The new analysis, released on Tuesday, bolsters earlier suggestions that a variety of coronaviruses may have been circulating in Wuhan before the initial outbreaks linked to animal and seafood markets in December 2019. As the Biden administration investigates the contested origins of the virus, known as SARS-CoV-2, the study neither strengthens nor discounts the hypothesis that the pathogen leaked out of a famous Wuhan lab. But it does raise questions about why original sequences were deleted, and suggests that there may be more revelations to recover from the far corners of the internet.
UPDATE (6/25): The Washington Post notes the data wasn't exactly suppressed. "Processed forms of the same data were included in a preprint paper from Chinese scientists posted in March 2020 and, after peer review, published that June in the journal Small." And in addition: The NIH released a statement Wednesday saying that a researcher who originally published the genetic sequences asked for them to be removed from the NIH database so that they could be included in a different database. The agency said it is standard practice to remove data if requested to do so...

Bloom's paper acknowledges that there are benign reasons why researchers might want to delete data from a public database. The data cited by Bloom are not alone in being removed by the NIH during the pandemic. The agency, in response to an inquiry from The Post, said the National Library of Medicine has so far identified eight instances since the start of the pandemic when researchers had withdrawn submissions to the library.

"This one from China and the rest from submitters predominantly in the U.S.," the NIH said in its response. "All of those followed standard operating procedures."
The New York Times writes: The genetic sequences of viral samples hold crucial clues about how SARS-CoV-2 shifted to our species from another animal, most likely a bat. Most precious of all are sequences from early in the pandemic, because they take scientists closer to the original spillover event. As [Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center who wrote the new report] was reviewing what genetic data had been published by various research groups, he came across a March 2020 study with a spreadsheet that included information on 241 genetic sequences collected by scientists at Wuhan University. The spreadsheet indicated that the scientists had uploaded the sequences to an online database called the Sequence Read Archive, managed by the U.S. government's National Library of Medicine. But when Dr. Bloom looked for the Wuhan sequences in the database earlier this month, his only result was "no item found." Puzzled, he went back to the spreadsheet for any further clues. It indicated that the 241 sequences had been collected by a scientist named Aisi Fu at Renmin Hospital in Wuhan. Searching medical literature, Dr. Bloom eventually found another study posted online in March 2020 by Dr. Fu and colleagues, describing a new experimental test for SARS-CoV-2. The Chinese scientists published it in a scientific journal three months later. In that study, the scientists wrote that they had looked at 45 samples from nasal swabs taken "from outpatients with suspected Covid-19 early in the epidemic." They then searched for a portion of SARS-CoV-2's genetic material in the swabs. The researchers did not publish the actual sequences of the genes they fished out of the samples. Instead, they only published some mutations in the viruses.

But a number of clues indicated to Dr. Bloom that the samples were the source of the 241 missing sequences. The papers included no explanation as to why the sequences had been uploaded to the Sequence Read Archive, only to disappear later. Perusing the archive, Dr. Bloom figured out that many of the sequences were stored as files on Google Cloud. Each sequence was contained in a file in the cloud, and the names of the files all shared the same basic format, he reported. Dr. Bloom swapped in the code for a missing sequence from Wuhan. Suddenly, he had the sequence. All told, he managed to recover 13 sequences from the cloud this way. With this new data, Dr. Bloom looked back once more at the early stages of the pandemic. He combined the 13 sequences with other published sequences of early coronaviruses, hoping to make progress on building the family tree of SARS-CoV-2. Working out all the steps by which SARS-CoV-2 evolved from a bat virus has been a challenge because scientists still have a limited number of samples to study. Some of the earliest samples come from the Huanan Seafood Wholesale Market in Wuhan, where an outbreak occurred in December 2019. But those market viruses actually have three extra mutations that are missing from SARS-CoV-2 samples collected weeks later. In other words, those later viruses look more like coronaviruses found in bats, supporting the idea that there was some early lineage of the virus that did not pass through the seafood market. Dr. Bloom found that the deleted sequences he recovered from the cloud also lack those extra mutations. "They're three steps more similar to the bat coronaviruses than the viruses from the Huanan fish market," Dr. Bloom said. This suggests, he said, that by the time SARS-CoV-2 reached the market, it had been circulating for awhile in Wuhan or beyond. The market viruses, he argued, aren't representative of full diversity of coronaviruses already loose in late 2019.
UPDATE (7/30): When republishing their sequences, the researchers indicated they actually came from January 30, 2020 (and not "late 2019").

Scientists have managed to slow down the atoms almost to a complete stop in the largest macro-scale object yet. The research has been published in the journal Science. New Atlas reports: The temperature of a given object is directly tied to the motion of its atoms -- basically, the hotter something is, the more its atoms jiggle around. By extension, there's a point where the object is so cold that its atoms come to a complete standstill, a temperature known as absolute zero (-273.15 C, -459.67 F). Scientists have been able to chill atoms and groups of atoms to a fraction above absolute zero for decades now, inducing what's called the motional ground state. This is a great starting point to then create exotic states of matter, such as supersolids, or fluids that seem to have negative mass. Understandably, it's much harder to do with larger objects, because they're made up of more atoms which are all interacting with their surroundings. But now, a large international team of scientists has broken the record for largest object to be induced into a motional ground state (or extremely closely to one, anyway).

Most of the time, these experiments are done with clouds of millions of atoms, but the new test was performed on a 10-kg (22-lb) object that contains almost an octillion atoms. Strangely enough, that "object" isn't just one thing itself but the combined motion of four different objects, with a mass of 40 kg (88 lb) each. The researchers conducted the experiment at LIGO, a huge facility famous for detecting gravitational waves as they wash over Earth. It does this by beaming lasers down two 4-km (2.5-mile) tunnels, and bouncing them back with mirrors -- and those mirrors were the objects that the new study cooled to a motional ground state. The photons of light in LIGO's lasers exert tiny bumps on the mirrors as they bounce off, and these disturbances can be measured in later photons. Since the beams are constant, the scientists have plenty of data about the motions of the atoms in the mirrors -- meaning they can then design the perfect counteracting forces. To do so, the researchers attached electromagnets to the back of each mirror, which reduced their collective motion almost to the motional ground state. The mirrors moved less than one-thousandth the width of a proton, essentially cooling down to a crisp 77 nanokelvins -- a hair above absolute zero. The team says that this breakthrough could enable new quantum experiments on the macro scale.

An anonymous reader quotes a report from Scientific American: Few harbingers of old age are clearer than the sight of gray hair. As we grow older, black, brown, blonde or red strands lose their youthful hue. Although this may seem like a permanent change, new research reveals that the graying process can be undone -- at least temporarily. In a study published today in eLife, a group of researchers provide the most robust evidence of this phenomenon to date in hair from around a dozen people of various ages, ethnicities and sexes. It also aligns patterns of graying and reversal to periods of stress, which implies that this aging-related process is closely associated with our psychological well-being.

The researchers [...] developed a technique to digitize and quantify the subtle changes in color, which they dubbed hair pigmentation patterns, along each strand. These patterns revealed something surprising: In 10 of [the 14 participants], who were between age nine and 39, some graying hairs regained color. The team also found that this occurred not just on the head but in other bodily regions as well. "When we saw this in pubic hair, we thought, 'Okay, this is real,'" [Martin Picard, a mitochondrial psychobiologist at Columbia University] says. "This happens not just in one person or on the head but across the whole body." He adds that because the reversibility only appeared in some hair follicles, however, it is likely limited to specific periods when changes are still able to occur. Most people start noticing their first gray hairs in their 30s -- although some may find them in their late 20s. This period, when graying has just begun, is probably when the process is most reversible, according to [study co-author Ralf Paus, a dermatologist at the University of Miami]. In those with a full head of gray hair, most of the strands have presumably reached a "point of no return," but the possibility remains that some hair follicles may still be malleable to change, he says.

In a small subset of participants, the researchers pinpointed segments in single hairs where color changes occurred in the pigmentation patterns. Then they calculated the times when the change happened using the known average growth rate of human hair: approximately one centimeter per month. These participants also provided a history of the most stressful events they had experienced over the course of a year. This analysis revealed that the times when graying or reversal occurred corresponded to periods of significant stress or relaxation. In one individual, a 35-year-old man with auburn hair, five strands of hair underwent graying reversal during the same time span, which coincided with a two-week vacation. Another subject, a 30-year-old woman with black hair, had one strand that contained a white segment that corresponded to two months during which she underwent marital separation and relocation -- her highest-stress period in the year.

For some time, a collaboration of biologists, chemists and physicists centered at the Universities of Oldenburg (Germany) and Oxford (UK) have been gathering evidence suggesting that the magnetic sense of migratory birds such as European robins is based on a specific light-sensitive protein in the eye. In the current edition of the journal Nature, this team demonstrate that the protein cryptochrome 4, found in birds' retinas, is sensitive to magnetic fields and could well be the long-sought magnetic sensor. Phys.Org reports: First author Jingjing Xu, a doctoral student in Henrik Mouritsen's research group in Oldenburg, took a decisive step toward this success. After extracting the genetic code for the potentially magnetically sensitive cryptochrome 4 in night-migratory European robins, she was able, for the first time, to produce this photoactive molecule in large quantities using bacterial cell cultures. Christiane Timmel's and Stuart Mackenzie's groups in Oxford then used a wide range of magnetic resonance and novel optical spectroscopy techniques to study the protein and demonstrate its pronounced sensitivity to magnetic fields.

The team also deciphered the mechanism by which this sensitivity arises -- another important advance. "Electrons that can move within the molecule after blue-light activation play a crucial role," explains Mouritsen. Proteins like cryptochrome consist of chains of amino acids: robin cryptochrome 4 has 527 of them. Oxford's Peter Hore and Oldenburg physicist Ilia Solov'yov performed quantum mechanical calculations supporting the idea that four of the 527 -- known as tryptophans -- are essential for the magnetic properties of the molecule. According to their calculations, electrons hop from one tryptophan to the next generating so-called radical pairs which are magnetically sensitive. To prove this experimentally, the team from Oldenburg produced slightly modified versions of the robin cryptochrome, in which each of the tryptophans in turn was replaced by a different amino acid to block the movement of electrons. Using these modified proteins, the Oxford chemistry groups were able to demonstrate experimentally that electrons move within the cryptochrome as predicted in the calculations -- and that the generated radical pairs are essential to explain the observed magnetic field effects. Hore says "if we can prove that cryptochrome 4 is the magnetic sensor we will have demonstrated a fundamentally quantum mechanism that makes animals sensitive to environmental stimuli a million times weaker than previously thought possible."

Artificial intelligence is to be used to tackle the most deadly parasitic diseases in the developing world, tech company DeepMind has announced. The BBC reports: The London-based Alphabet-owned lab will work with the Drugs for Neglected Diseases initiative (DNDI) to treat Chagas disease and Leishmaniasis. Scientists spend years in laboratories mapping protein structures. But last year, DeepMind's AlphaFold program was able to achieve the same accuracy in a matter of days. Many diseases are linked to the roles of proteins in: catalysing chemical reactions (enzymes); fighting disease (antibodies); and acting as chemical messengers (hormones such as insulin). And knowing the 3D structure of a protein is important in developing treatments for, among others, cancer, dementia and infectious diseases.

Prof Dame Janet Thornton, of the European Bioinformatics Institute, told BBC News: "Most new drugs in recent years have been developed using protein-structural data as one part of the process. "There are, however, many other aspects which need to be taken into account, which, due to lack of data, may not be amenable to AI approaches." But the predictions would be "particularly valuable" for pathogens with unknown protein structures, including some neglected diseases. "Developing new AI approaches for designing such drugs is a new challenge but one to which the new AI techniques can be applied and this holds out great hope for the future," Dame Janet added.

Proof-assistant software handles an abstract concept at the cutting edge of research, revealing a bigger role for software in mathematics. From a report: Mathematicians have long used computers to do numerical calculations or manipulate complex formulas. In some cases, they have proved major results by making computers do massive amounts of repetitive work -- the most famous being a proof in the 1970s that any map can be coloured with just four different colours, and without filling any two adjacent countries with the same colour. But systems known as proof assistants go deeper. The user enters statements into the system to teach it the definition of a mathematical concept -- an object -- based on simpler objects that the machine already knows about.

A statement can also just refer to known objects, and the proof assistant will answer whether the fact is 'obviously' true or false based on its current knowledge. If the answer is not obvious, the user has to enter more details. Proof assistants thus force the user to lay out the logic of their arguments in a rigorous way, and they fill in simpler steps that human mathematicians had consciously or unconsciously skipped. Once researchers have done the hard work of translating a set of mathematical concepts into a proof assistant, the program generates a library of computer code that can be built on by other researchers and used to define higher-level mathematical objects. In this way, proof assistants can help to verify mathematical proofs that would otherwise be time-consuming and difficult, perhaps even practically impossible, for a human to check. Proof assistants have long had their fans, but this is the first time that they had a major role at the cutting edge of a field, says Kevin Buzzard, a mathematician at Imperial College London who was part of a collaboration that checked Scholze and Clausen's result. "The big remaining question was: can they handle complex mathematics?" says Buzzard. "We showed that they can."