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 Post subject: from current journals as of 2017 05 21
PostPosted: Sun May 21, 2017 9:52 pm 
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Location: Broomfield, Colorado
I have been remiss in journal review duties since I’ve been busy moving Mom.

Paleobiology Issue 2 2017
Relating Ediacaran fronds
The authors note cladistic analysis has never been applied to Ediacaran organisms, proceed to do so, and conclude that the traditional phyletic taxonomy groupings (Arboreomorpha, Eriettomorpha, Rangeomorpha) are correct, which is interesting if anticlimactic.

Archaeology May-June 2017
From the Trenches
The Third Reich’s Arctic Outpost
There was a German meteorological station on Alexandra Land (which in turn is part of the Franz Joseph Land archipelago) from 1943 to 1944; the Kriegsmarine built it to radio weather information to U-boats operating against the Murmansk convoys. It was off-limits to Russian archaeologists – or anybody not Soviet military - until after the fall of the USSR. Recently Russian archaeologists have found the base and collected various artifacts.
Article
The Blackener’s Cave
Surtshellir is a lava tube cava in western Iceland. The cave figures in a number of Icelandic legends; it was supposedly occupied by a giant, a band of outlaws, and a group of heretic bandits. Archaeologists found considerable evidence of human activity but it’s all fairly mysterious. About 100 yards in there’s a drystone basalt wall fifteen feet high and spanning the entire 40-foot width of the cave. The blocks weigh four tons. This was obviously a major undertaking, especially since it had to be done with artificial illumination, but there’s no real clue as to who built it and why; there’s a legend mentioning a “fortress” in the cave and this would certainly fit, but one would think a fortification would be built closer to the entrance. A side branch has an oval enclosure, 22 by 11 feet, also made of drystone basalt blocks. Nobody has any good idea what this is either, but one archaeologist speculated it is the “oldest standing Viking structure in the world”. Finally, another side branch has a bone pile, now diminished by looters from an original circle 12 feet wide and a few feet deep. The bones are estimated to be the remains of over 200 animals, and have been thoroughly and meticulously smashed into tiny pieces; radiocarbon dates are 890-930. One hesitates to use “ritual objects and structures”, but that seems like a reasonable bet.
One + One = Forty-Nine
The Egyptians mummified lots of stuff. People, of course, but also bulls, cats, ibis, hawks, baboons, crocodiles, and shrews. In some cases, the mummification was less than meticulous; there’s a human mummy that has what appears the be the remains of the embalmer’s lunch (duck) stuffed into the body cavity, and another one where X-rays show a skull and both lower legs but the rest of the body is made up of sticks and packing made to look human after bandaging. This particular article concerns crocodile mummies. CAT scans show some of the mummies a built up from parts; the particular one illustrated has two juvenile crocodiles and 47 baby crocodiles packed together and wrapped to form one “adult” crocodile mummy. Researchers propose two theories: either the embalmers were commissioned to make a crocodile mummy and just grabbed whatever was at hand, or there was some sort of ritual significance in combining crocodiles of different age. I’m for Theory 1, but concede we know so little about Egyptian religion that Theory 2 is possible.
When the Ancient Greeks Began to Write
Relevant to the recently reviewed Empires of the Word. The Greeks conceded that they learned the alphabet from Phoenicians. However, Phoenician, like most Semitic languages, didn’t write vowels; the Greeks couldn’t write poetry without vowels; and thus the Greeks invented them by adapting Phoenician consonants that didn’t have a Greek equivalent. (There was even earlier, Bronze Age Greek writing using Linear B, but that’s syllabic rather than alphabetic; Linear A might be Greek; it uses the same symbols as Linear B but can’t be translated; there’s an even earlier hieroglyphic writing from Minoan Crete but that can’t be translated either; and finally there’s a thing called the Phaistos Disk with a bunch of symbols carved on it that don’t seem to relate to anything else). This article concerns excavations at Methone in northern Greece, which revealed the earliest Greek writing (i.e., using Greek alphabetic script rather than Linear B) dating from around 735 BCE. The inscriptions are scratched on pottery; one says “I am the cup of Nestor, a joy to drink from. Whoever drinks this cup, straightway that may the desire of beautiful-crowned Aphrodite will seize”. This apparently refers to passage in the Iliad, describing a cup owned by Nestor, which would indicate familiarity with Homer.

American Scientist May-June 2017
Infographic
The Chemistry of Ironing
Plant-based fabrics are mostly cellulose. The cellulose chains are crosslinked with hydrogen bonds, which keep them parallel and flat. Washing the cloth temporarily breaks the hydrogen bonds; as the cloth dries they reform but now the cellulose chains are wrinkled and the hydrogen bonds hold them that way. Ironing breaks the bonds again while flattening and smoothing the cloth, so when they reform again it’s unwrinkled. Permanent press fabrics use chemical bond cross-linkers, urea-formaldehyde resins or dimethylol dihydroxyethylene urea; these break down eventually to Internet-scary formaldehyde, so other cross-linkers are being researched.
Engineering
Slide Rules: Gone But Not Forgotten
Henry Petroski specializes in the history of simple things: silverware, paper clips, pencils. Slide rules are perhaps a little more complicated. I never had a really good Pickett or Keuffel and Esser or Post (although I coveted one) but made do with a cheap plastic one. It was a double-log trig duplex, though, and I practiced with it and an instruction book until I was confident using all the scales. It’s still in a desk drawer somewhere. Petroski notes the original John Napier device was called a “calculating table”, and incorporated multiple scales that slid back and forth in a book-like holder; there was a desk-mounted cylindrical slide rule patented in 1881 that used multiple folded scales and was the equivalent of a 30-foot long linear instrument. Petroski notes that one thing the slide rule did was force the user to figure out where to put the decimal point, and thus have an order-of-magnitude estimate of the answer before calculating; electronic calculators don’t do this and naïve users sometimes come up with ridiculous answers.
Article
Anyone Can Become a Troll
Researchers analyzed 16 million comments on CNN.com and found two key factors in “trolling” (they note their use of trolling includes both general unpleasant comments plus personal attacks). The first factor is the troll’s mood; this was tested in an experimental group, plus the observation that trolling peaks on Monday and the observation that people who troll in one discussion are more likely to troll in a second. The second factor is discussion context; if a discussion starts with a “troll” remark, subsequent comments are likely to be trolls. It was also noted that these situational factors were much better predictors of trolling that a person’s previous trolling history, leading to the article title that anyone can be a troll if they’re in a bad mood or are tempted. (A poster child for this – she’s actually shown in the article – is Isabella Sorley of Newcastle, UK. She had no previous history of abusive comments and is described as “polite” by interviewers, but late one night (she comments alcohol use was involved) she Twittered a death threat to a member of Parliament and ended up sentenced to twelve weeks in prison.
Replaying Evolution
Article author Zachary Blount is one of the principle experimenters on the Long-Term Evolution Experiment; this takes Escherichia coli cultures, incubates them in the lab, and every 24 hours transfers a 1% aliquot to another container; every 500 generations an aliquot is extracted and frozen. This has been going on for about 65000 E. coli generations. At about generation 33,000, once of the 12 cultures developed the ability to use citrates as an energy source in addition to glucose. (Citrates had been provided to the cultures to add in iron uptake, not as an energy source). Blount uses this to discuss Stephen Gould’s concept of “contingency” mentioned in Wonderful Life; the idea if you “replayed the tape” of evolution things would come out very different. The citrate metabolism ability was traced backward using the frozen aliquots; the series of mutations that enabled citrate metabolism started at about generation 20000, and that cultures started after this generation were more likely to evolve a citrate metabolism ability. Blount eventually traced the exact series of five mutations that made citrate metabolism possible; a crucial one involved duplication of a stretch of DNA that coded for citrate transport; without this further evolution in the direction of citrate metabolism was actually harmful, because it interfered with the cells normal, non-metabolic use of citrate. Blount’s general conclusion about the meaning of this as a demonstration of contingency isn’t that clearly stated; of the 12 cultures only one developed (so far) the citrate metabolism ability, suggesting that it really was an example of “contingency”.

Skeptical Inquirer May-June 2017
News and Comment
Chicken Acceleration? APA puts Imprimatur on Credulous Psi Book
The American Psychological Association has published Transcendent Mind: Rethinking the Science of Consciousness. This includes description of an “experiment” with a “psychic” who, by going into what appeared to be “an altered state of consciousness”, converted unfertilized eggs to live chicks in nine minutes; a woman who could make gold foil materialize on her body, and an interview with Richard Feynman, conducted by séance. The chicken and gold foil demonstrations could not be duplicated under controlled conditions. In the Feynman “interview”, it was proposed to identify the spiritual entity by asking a physics question, so “Feynman” was asked the value of the fine structure constant. After considerable delay, the medium decided that it involved the capital letter M and the number 0.08.

Nature 11 May 2017
This Week
Clause for concern
Nature notes troubling interference from funders with scientists studying addiction. Not corporate funders, like the tobacco industry, but government funders. The gist is that research that appears to show government policies aren’t working gets suppressed. I imagine this could apply across the political spectrum.
Blurred lines
In a sort of vague counterpoint to the above, Nature circumspectly suggests that not all government and public criticism of science is unjustified. The particular examples cited are cuts in environmental programs – not necessarily motivated by science denial but possibly by a desire to reduce overall government spending; distrust of GMOs, not necessarily motivated by science denial but by distrust of corporations; and defunding some programs, not necessarily motivated by science denial but by a desire to spend government funds more efficiently.
Seven Days
Dead flowers
A shipment of daisy type specimens, some dating to the 18th century, sent from the National Museum of Natural History in Paris to the Queensland Herbarium in Brisbane was “accidentally” destroyed by Australian customs officials. The problem seems to have had several sources; the herbarium sent a description of the samples to the wrong email address; the Paris museum listed the value of the samples as “$2”; Australian customs incinerated the samples (as is normally done with low value items that are not properly documented) before the time limit expired. Museums worldwide have responded by suspending all specimen exchanges to Australia until things are clarified.
News Feature
The secret war on counterfeit science
A Chinese scientist, looking for a cheap way to print labels for specimen vials, walked into a local print shop and asked for a demonstration of a label-printing machine. He was shocked when the shop owner proudly pulled out a sheet of labels he had printed for another customer; they were counterfeit labels for expensive antibodies produced by the American companies Abcam and Cell Signaling Technology. Further investigation disclosed a counterfeit chemistry ring that was selling diluted or just plain wrong reagents. A number of Chinese and Western scientists interviewed noted that the counterfeit reagents had ruined and delayed research. Immense profit margins and China’s cumbersome import bureaucracy are blamed.

Science 5 May 2017
News in Brief
Call to retract microplastics paper
Sweden’s Central Ethical Review Board has called on Science to retract a paper that appeared in June 2016 on the effect of microplastic on fish larvae. The paper was found to contain fabricated data. The CERB also faulted Science for failing to enforce its open data policy. See “Fishy business” from the 24 March Science below.
News in Depth
Mauritius invites primate research labs to set up shop
Supplying long-tailed macaques for primate research has long been an industry on the Indian Ocean island of Mauritius. (The macaques are an invasive species on the island, having been introduced from India in the 18th century; the ones sold for research are from breeding colonies, not wild-caught. In the face of animal rights groups applying pressure on airlines ban flying primates from source countries like Mauritius, the country has proposed setting up its own primate labs to be used by foreign researchers. The usual people are outraged. It’s noted, though, that China has already set up elaborate primate research centers and Mauritius, with a less-developed infrastructure, will have to compete with those.
New crop pest takes Africa at lightning speed
The fall armyworm Spodoptera frugiperda, a New World pest, was first noted in Nigeria in January 2016. By November 2016, it was found in Niger, Benin, Togo, Ghana, Cameroon, and São Tomé and Principe. By February 2017 it was found in Mozambique, Zambia, Malawi, Zimbabwe, Namibia, Botswana, and South Africa; by April it had turned up in the Democratic Republic of the Congo, Rwanda, Uganda, Ethiopia, Kenya, Burundi, Tanzania, and Swaziland. The insect specializes on maize; in Zambia about 8% of the crop was destroyed. There is the usual enthusiasm for natural controls.

Scientific American May 2017
Advances
A spare hand
Some people have lost practical function in a hand due to nerve damage. Austrian surgeons are trying a technique where a bionic prosthetic hand is connected to the patient’s forearm and hooked up to a set of undamaged nerves, which were not involved in controlling the “real” hand but which can be pressed into service with practice. Once the patient is good enough at controlling the bionic hand, their hand is amputated and replaced with the bionic one. Creepily illustrated.
Article
Strange News from Another Star
In 2014, Tabetha Boyajian reported an unusual discovery from the Kepler satellite. Star KIC8462852 (more conveniently dubbed “Tabby’s Star” or “Boyajian’s Star”) displayed unusual brightness variations. Kepler was designed to pick up planetary transits; Boyajian’s Star had dimming characteristic of transits – but they dips were irregular in timing and duration and therefore not due to an orbiting planet. A number of theories were proposed: a disk of gas or dust around the star; swarms of comets; a dust cloud in the interstellar medium; intrinsic variation; a nearby black hole. All of these have some sort of fatal flaw in explanation. A last suggestion is an alien megastructure (which, of course was the one picked up by the MSM); the aliens are in the process of building a Dyson Sphere or a Ringworld around the star.

Proceedings of the US Naval Institute May 2017
We Must Change the Way We Name Ships
The author notes that there are US Navy vessels named after a Congressman implicated in the Abscam scandal (LPD-26 John P. Murtha) and an unrepentant segregationist (CVN-74 John Stennis) but none after Richard Best, who sunk the Akagi at Midway, or Ernest Evans, who was captain of the USS Johnston and lead it in its death ride off Samar in 1944. (He concedes there were vessels named after Best and Evens but they have been decommissioned). He proposes a return to more or less the system used in WWII:
  • Carriers – famous US naval vessels, battles, national regions, national ideals
  • Cruisers – cities with a population greater than one million and/or State capitals
  • Destroyers, frigates, and other surface combatants not cruisers or littoral combat ships: - US Navy or Marine recipients of the Medal of Honor or the Navy Cross.
  • Littoral Combat Ships: Cities with a population less than one million and which are not the State capital or among the three largest population centers in the state.
  • Attack submarines: Fish and other real or fictional sea creatures
  • Ballistic missile submarines: States
  • Amphibious ships and other vessels used primarily by the USMC: Marine battles
  • Other vessels: Mythical creatures not used by attack submarines, signatories of the Declaration of Independence, US astronauts
I personally approve; however I find the proposal unlikely to gain any acceptance with Congress. As Hyman Rickover (SSN-709 Hyman G. Rickover) famously pointed out, “Fish don’t vote”.

Nature 27 April 2017
Seven Days
Google health study
A Google spin-off, Verily, has announced Project Baseline, which will study 10000 volunteers with wearable sensors, smartphones, and regular clinic visits.
Fake peer review
Springer is retracting 107 papers from Tumor Biology after finding that they had been accepted based on fabricated peer-review reports. All the papers were by Chinese authors. The Chinese state-run People’s Daily blamed the scandal on lax punishment for academic misconduct and pressure to publish.
News in Focus
Stem-cell bet faces big test
We’ve had some threads about the California Institute for Regenerative Medicine before. This was created by a ballot initiative in 2004 in response to restrictions on Federal funding for stem-cell research by the Bush administration. The saga of the CIRM illustrates the perils of politics in science finding. The CIRM was initially funded with $3G. Most of that money has run out, and the CIRM has yet to produce any “cures” (although some clinical trials are scheduled for 2020). Critics note that the CIRM lacks “strategic focus”, and that some of the scientists vetting proposals had conflicts of interest. Supporters of the CIRM plan another ballot initiative for 2020.
News and Views
Unexpected early signs of Americans
Letter
A 130,000-year-old archaeological site in southern California, USA
This made the MSM, usually as some variant on “Early Native Americans were contemporaries of Neandertals”. Claims for very early people in the New World have been made before; possibly the most famous is the Calico site in California, which none other than Louis Leakey pronounced as authentic. Now comes another site from California, the Cerruti Mastodon Site, which I expect will eventually end up being debunked too. But there are just a few things at Cerruti that are intriguing. At the Calico site, “artifacts” were picked out of flood gravels. When examined in isolation, they really did look like Oldowan stone tools. The catch was the high energy environment made lots of cobbles and pebbles with chips take out of them and if you went through enough of them it was possible to find ones that resembled Oldowan tools. On the surface, the Cerutti site seems similar. There are mastodon bones, the bones have been fractured, the fractures are spiral (which, it is argued, means they were done in fresh bone), and there’s a couple of good-size chunks of andesite which are supposed to be a hammer and anvil for breaking bones. The catch is the site is 130700 ± 9700 years old; Nature says the dating is “rigorous’. According to conventional archaeology, AMHs would have just started diffusing out of Africa at that time, and they would have had to sprint pretty fast to get to California. I can think of a lot of natural ways to break fresh mastodon bone, and I’m not sure the contention that only fresh bone breaks in a spiral pattern is actually proven. Thus the initial response is there’s something wrong here; the dating is wrong or the interpretation of human-caused bones factors is wrong, or both. But there’s a catch. As mentioned, the “hammer” and “anvil” rocks are big chunks of andesite. The excavators carefully screened the area, a found a bunch of little chips of andesite, which could be fitted back into the “hammer” and “anvil”. And those chips are not randomly distributed in the site, but form a fan-shaped pattern with the apex at the putative anvil stone: what you might expect if the mastodon bone was laid on the anvil and then somebody brought the hammer stone down on it, with their own body blocking the spread of stone chips “backwards”. There have been a number of other sites here and there around the world that purport to show mammoth or mastodon bones fractured by human agency; pachydermologists note that extant elephants curious about the remains of their species and will sometimes pick up bones, transport them, and trample on them (possibly breaking them). But there’s no report of them hitting bones with a hammer stone. Thus I remain pretty dubious – but not completely dubious. Note and technical paper.

Science 21 April 2017
News in Depth
A New Neglected Crop: Cannabis
Plant biologists note that now that 44 states have some form of marijuana legalization, the plant is ripe for studies to improve pharmacological effects, growth rate, and fiber content. However many studies cannot be conducted because of legal restrictions. It will be amusing if the hippies finally accept genetic engineering because it gets them cheaper highs.
Society labels harassment as research misconduct
The American Geophysical Union has voted to include sexual harassment in its definition of research misconduct. Critics note that research misconduct is unique to the scientific profession, while sexual misconduct is inappropriate in society at large; and that investigation techniques for sexual harassment are different from those for research misconduct; supporters note that sexual harassment interferes with the scientific enterprise and thus should be classed as research misconduct.
Insights
Rewiring metabolism under oxygen deprivation
Everything about naked mole rat biology is strange. It turns out now that naked mole rats are unique among mammals in being able to tolerate low oxygen levels, recovering completely from 18 minutes of anoxia. They apparently do this by switching to a fructose-based metabolism (glucose metabolism is regulated by phosphofructokinase and stops when no oxygen is available for this step; fructose can enter the chain “downstream” from phosphofructokinase, and metabolism continues, albeit slowly). One puzzle yet is how naked mole rats deal with lactate accumulation, a byproduct of anaerobic metabolism; the other vertebrates that can function anaerobically are cyprinid fishes and two genera of turtles. The fish clear lactase by conversion to ethanol and diffusion out the gills; the turtles buffer excess lactate in their blood by extracting calcium carbonate from their shells. Nobody knows what the naked mole rats are doing with it. The comment about turtles using calcium carbonate from their shells intrigued me; “ostracoderms” (the group is polyphyletic) are early fishes with a heavy bony exoskeleton, usually described as “armor”. The problem has always been there doesn’t seem to be anything they needed to be armored against; they have no jaws themselves and show up in the fossil record before the big eurypterids. It’s been suggested off and on over the years that the “armor” had some other purpose; perhaps the fish were using it for anaerobic metabolism? I’ll have to check with some vertebrate paleo people.

Science 14 April 2017
News
Canada ice cores suffer meltdown
On April 2 a freezer failed at the Canada Ice Core Archive at the University of Alberta in Edmonton and 180 of the ice cores were lost, including 15 meters of ice core from Mount Logan and 22 meters from Baffin Island. The cores were valued at $US 500K to 1M each,
23andMe disease risk tests OK’d
The FDA is allowing the genetic testing company 23andMe to give customers information on risk for certain diseases – mentioned are Parkinson’s disease and Alzheimer’s disease )the FDA had previously allowed 23andMr to inform customers if they were carriers for cystic fibrosis). The FDA had previously opposed giving out this information because of fears customers would act without consulting a doctor.
Pachyderm panspermia
Birds are the prime seed dispersers, carrying them up to 300km before redeposition; however, a graduate student studying elephant dung found that savanna elephants can move seeds up to 65km. The short note says this is important in maintaining genetic diversity in the savannah. I wonder how well mammoths did? Or for that matter, dinosaurs?
Insights
An AI stereotype catcher
Research
Semantics derived automatically from language corpora contain human-like biases
Researchers have tweaked existing word association software to look for gender, age, race and ethnicity bias in text. The software looks for word associations – pairs within 10 words of each other; and example given was the proximity of “male” to “president”, “leader”, “director”, “boss”, “chief” and “executive” and the proximity of “female” to “subordinate”, “aide”, “helper”, “assistant”, “co-worker” and “employee”. The juxtaposition of the article above – the FDA being terrified of consumers getting access to their own genetic information – with this one – software that anybody can use to analyze written text for evidence of putative racism, sexism, etc. – is interesting. Note and article.
Research
Enhancement of Zika virus pathogenesis by preexisting antiflavavirus immunity
Mice with antibodies to flaviviruses – such as West Nile Virus and dengue fever – are more prone to sever consequences if subsequently infected with Zika virus. This “antibody enhancement” has been demonstrated with other diseases before but it was unknown if Zika virus was affected. The authors note this should be taken in to consideration when designing flavivirus vaccines. I heave a sign – the research is interesting and important and one more thing antivax nutbars can seize on.

Nature 6 April 2017
News and Views
Large rise in carbon uptake by land plants
Letter
Large historical growth in global terrestrial gross primary production
One of the numerous inputs to carbon dioxide models is the rate of uptake by land plants for photosynthesis. A new proxy involves atmospheric measurement of the trace gas carbonyl sulfide, and it indicates that Gross Primary Productivity increased by about 31% from 1900 to 2013. The way this works is carbonyl sufide is produced at the ocean surface by organic sulfur reactions, and destroyed by uptake by land plants. Since the ratio of carbonyl sulfide to carbon dioxide use by plants is known and predictable the rate of carbon dioxide uptake by plants can be estimated by carbonyl sulfide concentrations in ice cores. Gross Primary Productivity had been expected to increase with increasing carbon dioxide, but the amount of increase was unknown; the 31% increase estimated by the carbonyl sulfide proxy is on the high end of previous estimates, which ranged from 55 to 52%. Note and technical paper.

Science 7 April 2017
News in Depth
Relics of the first Americans?
“Western stemmed points” have been known for years; they’re made by a core-flaking technique, where the knapper breaks successive flakes off a prepared core. They’re kind of crude looking, but practical; there’s no particular reason to spend a lot of effort on stone point if you’re probably going to lose it by using it. Up till now western stone points have been languishing in museum collections. But recently somebody pointed out that there’s some stratigraphic evidence that this style is very old, that they are found all along the Pacific Coast of North and South America, and that a few have been found in Kamchatka and Japan. Thus it’s possibly they were part of the toolkit of the hypothetical people that reached the Americas by moving along the coast.
Cell-like giant viruses found
Article
Giant viruses with an expanded compliment of translation system components
Giant viruses were discovered in 2003; they are much bigger than most viruses; in fact some are bigger than some bacteria. They also have an unusually large genome; some have as many as 2500 genes (since viruses live by coopting the cellular machinery of their hosts they don’t need a lot of genes; there are a couple of viruses known that get by with two). This has lead to the suggestion that they represent a fourth domain of life (the others being Archaea, Bacteria, Eukaryota); perhaps not by themselves but maybe they infected a now-vanished host. Researchers in Austria sampled sewage sludge for viral genomes and stitched together DNA fragments showing a continuous sequence between much smaller, “ordinary” viruses and the giant viruses; giant viruses apparently go big by incorporating genetic material from their hosts. While interesting, there are skeptics; in particular it’s noted that nobody has taken the bits of loose DNA and assigned them to a particular virus, and nobody knows what the hosts are for these things. Note and technical paper.
China aims to sow a revolution with GM seed takeover
The Chinese public has always been skeptical of GM foods; one farmer interviewed says “everybody knows they are bad for you”. With the Chinese government purchase of Syngenta, that will change; already the state TV network has announced it will no longer run advertisements with unproven claims for GM and non-GM foods, and the agriculture ministry has announced a streamlined approval process for biotech crops. Bt corn and herbicide-tolerant soybeans are expected to be planted by 2020. It’s noted that some farmers are already planting smuggled GM seeds.

Natural History April 2017
Samplings
Colorful Language
An Australian team investigated color terms in the Pama-Nyungan language family, using cladistic phylogenetic methods; they were testing a model that predicted color terms would increase over time, and that the colors would be added in order: black and white; red; green, yellow and blue; brown; pink, purple, orange and gray. The predicted order was confirmed; however the prediction that color terms would increase with time was not, with some languages losing color terms.
Article
Lost then Loved: The Case of the Tasmanian Tiger
The last know Tasmanian tiger (Thylacinus cynocephalus), Benjamin, died in the Hobart zoo on September 7th, 1936. Bounties had been place on thylacines since it was believed they preyed on cattle; however there were no recorded cases of this and analysis of the jaws suggest they had a relatively weak bite and would have been most suited to small animals. Claims of sightings persist, mostly from northeast Tasmania; however there have been no photographs, footprints, hair samples, or any other hard evidence. Hope persists; enthusiasts note a couple of other Australian animals, Gilbert’s Potaroo and the Night Parrot, were rediscovered in remote parts of the country after being judged extinct.

Egyptian Archaeology Spring 2017
Living Color: the Met Museum’s Temple of Dendur
The Aswan Dam flooded a number of Egyptian monuments, the most famous being the Temple of Rameses II at Abu Simbel, which was painstakingly cut out the rock and reassembled high enough above its original location to be out of the water’s reach. Most smaller temples were abandoned to the water, but some were donated to countries financing the effort; the temple at Dendur was given to the United States and awarded to the Metropolitan Museum of Art in New York. Visitors to Egypt are used to seeing the temples in natural stone color, but it’s know from traces of paint that they were originally brightly colored. The Met has reconstructed the color scheme of the temple of Dendur from remaining paint traces and analogy to other temples with paint traces, and has set up a projection system to allow the temple to be seen in its original color.

Science 24 March 2017
News in brief
An ethics code for studying the San
The San people of southern Africa have issued an ethics code researchers must follow. The San are a popular subject for anthropological research since they are one of the few remaining hunter-gatherer peoples. The code requires researchers to let communities read their results before publication, and “give back” to the San community, either monetarily or in educational and job opportunities. Researchers are generally supportive but note restrictions on reuse of data may make it hard to replicate studies.
Monsanto authorship probe
A group claiming exposure to Roundup gave them non-Hodgkin’s lymphoma claims that a paper co-authored by New York Medical College pathologist Gary Williams was actually “ghost written” by Monsanto employees. A Monsanto spokesman responded “ghost writing” is an inappropriate way to describe scientific collaboration.
News in depth
Tweak makes U.S. nukes more precise – and deadlier
The article claims warheads in U.S> ballistic missiles have been fitted with a new fuze that allows more precise control of detonation height, and thus more likely to destroy a target missile silo. The usual people claim this is “destabilizing” and will provoke a new arms race with Russia.
News Features
Fishy business
There was a stir in the MSM a while back about plastic microbeads, used in some cosmetics, and their supposed deleterious effects on fish embryos and larvae. These results prompted a number of NGOs to call for a ban on microbeads, and some governments complied. The study was done at the Swedish Ar Research Station on Gotland. However, two other researchers at the station claim the study is “a complete fantasy”: they were at the research station at the time and saw no sign of such a study being done; they found Facebook photos of one of the researchers at a restaurant in Stockholm at the same time she was supposed to be on Gotland doing the study. The whistleblowers investigated further and found that the microbead study would have required simultaneous use of 30 1-liter aquaria, but the microbead lab only had three; some juvenile fish were supposedly collected in a bog 65 km away but the catch was not recorded in a log book as required. The whistleblowers sent questioning letter to Science (where the microbead study was originally published; when Science asked for the raw data they were told it had been on a laptop that was stolen a few days earlier. Uppsala University (which runs the Ar station) investigated and found no misconduct; the whistleblowers appealed to the Central Ethical Review Board in Stockholm, whose expert came to a completely different conclusion: the lead researcher in the microbead study could provide no evidence proving she was actually on Gotland during the time claimed; she had kept no lab notebooks; and her ethics permit to conduct the study wasn’t granted until a month after the study was supposedly complete, was for a different field station, and for a different study design. Investigations continue.
Insights
Genes, environment, and “bad luck’
Reports
Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
A 2015 study concluded that about two thirds of cancers could be explained solely by the number of stem cell divisions in the various tissues examined – or, simplifying, were due to “bad luck” rather than genetic or environmental factors. There was immediate backlash. The original authors have now done another study noting the same correlation in cancers from outside the United States. A note by a biostatiscian comments that the study would not be able to distinguish a hypothetical environmental carcinogen that increased the risk of all cancers by the same proportion – but also that the original paper didn’t make this claim. (The statistical note is not a summary of the research paper).

Newsletter of the Society or the Study of Egyptian Antiquities Spring 2017
The Nudity of Cats and What It Reveals
Seldom do you run across Egyptology papers with such intriguing titles. Further, I googled the author – Jennifer Miyuki Babcock – and she’s a comic book artist studying to be an Egyptologist. Interesting combination. The ancient Egyptians were fond of cartoons of anthropomorphic animals – a lion and a goat playing senet, a mouse acting as vizier, etc. These are usually drawn on ostraca – more or less flat pieces of white limestone – rarely on papyrus, which was too expensive for cartoons. Babcock has examined these cartoons – she notes there are 78 known – and finds something interesting – while the mice, dogs, etc. in the cartoons are usually shown wearing human clothes, the cats (with one known exception) are always naked. Babcock presents a couple of theories. One suggestion is the ancient Egyptians were fond of “topsy-turvy” stories, where paupers become rich and nobles become poor, for example. The naked cats subservient to clothed mice may be an example of this; the only humans shown naked in Egyptian art are children, the poor, and exotic dancers. Another idea is the cartoons may reference oral traditions – fairy tales or fables – that’s no longer accessible; perhaps the Egyptians had the equivalent of Aesop’s or La Fontaine’s fables and these cartoons reference those. Interesting but not testable.

Science 10 March 2017
News in Depth
Blackouts cast Australia’s green energy in dim light
South Australia is heavily committed to renewable energy; to be fair the state has lots of wind and sun and not much in the way of fossil fuel. However, the power grid was designed for conventional energy. Two blackouts in six months have led to criticism of the renewable effort. The first blackout, in September 2016, was blamed on a severe storm that blew down power lines; however, it’s conceded that the second, in February of this year, was a result of underestimating peak power demand and overestimating wind availability; a natural gas backup generating facility couldn’t ramp up to speed in time.
Features
Making waves
A profile of microbiologist Penny Chisholm and her research on the cyanobacterium “species” group Prochlorococcus. The bacterium is so small it was discovered by flow cytometry giving a chlorophyll signal where none was expected, rather than conventional microscopy (in 1988); it wasn’t cultured until 2000; yet it is suspected to be responsible for about 5% of the planet’s total photosynthesis. There are numerous different strains of Prochlorococcus, which is why “species” is in quotes above; Linnean taxonomy doesn’t work very well with bacteria. The different strains are adapted to various ocean conditions; although an individual cell has about 2000 genes that “pangenome” is estimated at 80K.
Insights
Policy reforms to update chemical safety testing
The 2016 reform of TSCA called for the EPA to adopts “alternative testing strategies” (ATS) for evaluating new chemicals. ATS are supposed to speed testing – which industry would presumably like – and reduce animal testing – which enviros would presumably like. The ATS process calls for identification of Adverse Outcome Pathways – identifying ways the chemical could affect various molecular pathways; then in vitro testing on cell lines, they computer modeling, then “integrating evidence”; then regulation. The authors note that although the EPA is required to “facilitate” ATS, it isn’t actually required to adopt it; however it’s also noted the EPA will be unlikely to meet time deadlines set in the 2016 TSCA act unless it uses ATS.
Yeast genome by design
Research article
Design of a synthetic yeast genome
Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyonf
”Perfect” designer chromosome V and behavior of a ring derivative
Deep functional analysis of syn11, a 770-kilobase synthetic yeast chromosome
Bug mapping and fitness testing of chemically synthesized chromosome X
Engineering the ribosomal DNA in a megabase synthetic chromosome
3D organization of synthetic and scrambled chromosomes
Project Sc2.0 proposes to generate a synthetic eukaryote cell by building synthetic chromosomes. Software is used to design the chromosomes which are then “swapped” with a “native” chromosome. So far, six of 16 chromosomes in the yeast Saccharomyces cerevisiae have been replaced by synthetic counterparts. My short description here doesn’t do justice to the procedure; I don’t know enough about DNA synthesis to fully understand what’s going on. Note and research papers.
Scalable-manufactured randomized glass-polymer hybrid metamaterial for daytime radiative cooling
The material is polymethylpentene with embedded silicon dioxide microspheres backed with a silver reflective coating. (Other plastics can be used but aren’t quite as efficient; the material is transparent without the reflective backing). The idea is solar radiation is reflected by the by the backing, but the material emits infrared through “window” wavelengths where the atmosphere is transparent; in tests cooling power is 93 W/m² (i.e. radiated infrared minus absorbed solar). The test material was manufactured in 300mm wide strips at 5 m/minute. The authors note there have been no tests on long-term outdoor durability.
The geologic history of seawater pH
Since ocean acidification is a thing now, the authors take a stab at the long term history of seawater pH. The tentative conclusion, based on modeling and some proxies, is that pH was arounf 6.5-7.0 in the Archean, gradually rising to today’s values. They concede a lot of unknowns, such as the partial pressure of carbon dioxide in the ancient atmosphere and exchanges between carbonate and alkaline rocks and seawater.

Nature 9 March 2017
Seven Days
Emissions toll
(Appended to an earlier thread)
Pollution deaths
Apropos of the above – in which models claim the “emissions defeat device” in Volkswagen Diesel engine software caused 1200 excess pollution deaths in Europe – another set of models claim 570K worldwide deaths of children under 5 due to air pollution, and another 361K from “unhygienic conditions”. Models are useful, but I’m not sure how much. I suspect the best use is to generate testable hypotheses, but too often the models are an end in themselves.
Mould money
Alexander Fleming is thought to have made a number of glass and plastic disks containing mold from the original Penicillium chrysogenium culture; one sold at auction recently for £11874. I have an investment going in my refrigerator.
News in focus
Psychologists push for open data
Gert Storms is an editor at the American Psychological Association’s Journal of Experimental Psychology: Learning, Memory, and Cognition. Storms was asked to resign his position when he invoked a personal policy of rejecting submitted papers if the authors do not share their data or explain why they can’t. The journal’s head editor claims this policy is unfair to authors and is in conflict with APA guidelines (the journal “asks” paper submitters to share data but does not require it); Storms refuses to resign saying there is way too much sloppy science in psychology. A number of prominent psychologists have sided with Storms.
News Features
A matter of time
This one made the MSM; it sounds like something out of a Dr. Who plot. An ordinary crystal has a pattern of atoms that repeat in space; a “time crystal” has a pattern of atoms that repeat in time. I confess I don’t understand the physics here; it seems it’s not the spatial position of the time crystal atoms that is repeating but their spin state. Time crystals were first proposed in 2012 as a pattern of atoms in their lowest energy state that would cycle continuously; it was proved that this can’t happen. However, a variant – where a group of atoms get a periodic laser “kick” – does work; the system maintains a repeating pattern that is not synchronized with the incoming kick. The best analogy one of the physicists could come up with was “It’s as if you were plaing jump rope, and your arm went around once but the rope went around twice”.
The shared past that wasn’t
The article focuses on “fake news”, such as the “Bowling Green Massacre”, but there’s a little side snippet on the “Mandela Effect” – the belief that Nelson Mandela died in a South African prison in the 1980s (sometimes the 1990s). rather than 2013. People recall seeing the funeral on TV, speeches by politicians, and a fight over book rights. Some can be disabused of the notion, although they express puzzlement over their false memories; in others attempts at debunking just strengthen their resolve and they insist the “Mandela” that became President of South Africa was a clone or actor. There is a similar effect with the cartoon The Berenstain Bears, with many convinced that the original name of the show was The Berenstein Bears and that it was changed (one subtheory is that there is an alternate universe with Berenstein Bears, and somehow we all unconsciously slipped into the Berenstain Bears one). It’s been shown it’s relatively easy to plant false memories in individuals – leading to some rather nasty criminal cases – here there’s a discussion of group false memories, with discussion participants reinforcing their memories of things that never happened.
Show drugs work before selling them
This article caused something of a twinge in my libertarian world view. The Administration has proposed weaker regulatory standards for drug approval, and the article notes that libertarian economists generally agree. The poster children for drug regulation are those injured by thalidomide in the womb; the libertarian counterargument is that while the harm caused by “bad” drugs is quickly obvious, the harm caused by withholding “good” drugs from the market is invisible (although the article doesn’t mention it, metformin – approved in Europe decades before it was approved in the US – is a case in point). The libertarian argument is that the market will quickly adjust to promote “good” drugs and eliminate “bad” ones; the authors counter that there’s another category “safe but useless” – and cite homeopathy preparations as an example. We had a thread a while back about “right to try” laws, with terminal patients given access to drugs that haven’t gone through the complete approval process; a counter to that was the observation that most drugs – IIRC 4 out of 5 that have made it to Stage III trials – turn out to be useless.
Letter
Earth’s first stable continents did not form by subduction
Very early (4 – 2.5 Ga) continental crust is composed of tonalite-trondhjemite-granodiorite (TTG) and exhibits what’s interpreted as an “arc signature”, similar to continental crust formed by subduction of basalt at island arcs. This paper argues that this interpretation is incorrect, and the TTG crust was actually formed by partial melting of a previously existing basaltic crust, facilitated by much higher mantle temperatures and thermal gradients, and without subduction being necessary.
Smithsonian March 2017
A Pox on History
A toddlers’ body interred sometime between 1643 and 1665 in the crypt of a church in Vilnius, Lithuanian has yielded the oldest definitive smallpox genome. “Molecular clock” analysis produced a considerable surprise: the original smallpox virus appeared in the late 16th or early 17th century AD. This raises the question – if earlier reported plagues weren’t smallpox, what were they? In particular, what was the disease that devastated Native American populations in the 1500s? The researchers suggest it was an earlier variant of the variola virus; Europeans supposedly had developed immunity to the virus but Native Americans had not. Then this strain mutated to the deadlier form in Europe. The argument seems strained.

KMT Spring 2017
Queen Nefertari’s Knees?
Nefertari was the first “Great Royal Wife” of Rameses II; she’s often confused with Nefertiti (the element nfr means “beautiful” in this context, thus it’s a common element in Egyptian female names). Her tomb, QV66, was excavated in 1904; a pair of bandaged legs broken off above and below the knees were discovered and have been languishing in the Museo Egizio in Turin ever since. However, they are now being examined by a multidisciplinary team; so far the results are they belonged to a 40-50 year old person, carbon date to the 13th century BC, and have a wrapping technique consistent with other mummies from the 19th dynasty. Thus while it can’t be proved the knees belong to Nefertari, the circumstantial evidence is pretty consistent with that attribution.

Science 6 January 2017
News in brief
Escaped pets could save endangered species
While a number of wild animals are heading for extinction, the exotic pets trade has transferred many to new habitats where some escape and go feral. As an example, the yellow-crested cockatoo is critically endangered in its native Indonesia but a feral population is thriving in Hong Kong. Researchers have identified 49 species of birds, mammals, and reptiles in this category, and suggest capturing some, screening them for disease and parasites, and returning them to native habitats.
News features
The burning question
The law of unintended consequences strikes the Paris Accords. According to the rules, burning wood is carbon-neutral; a wood-burning power plant can claim zero carbon dioxide emissions. Therefore, power plants in Europe are harvesting trees in North Carolina, pelletizing the wood, and shipping it to European power plants. As you might expect, input-output models of this are all over the map, with the pros claiming zero emissions and the cons arguing that when things like transportation costs and the reuse of logged land are considered wood burning actually produces more carbon emissions than coal.

Science 23 December 2016
News in Depth
XPrize finalist mull payloads to the Moon
The $20M prize winner must land a privately funded probe on the moon, move 500 meters (the lander can move or it can release a rover), and send back pictures. There is a $4M bonus for sending back pictures from an Apollo landing site; a $4M bonus for unambiguous discovery of water on the lunar surface; and a $1M bonus for sending back pictures from an unmanned lunar probe landing site. In contention are SpaceIL, from Israel; Moon Express, from the US; Synergy Moon, from the US; Team Indus, from India; and Part-Time Scientists, from Germany. SpaceIL and Moon Express will meet the movement requirement by “hopping” with the lander’s thrusters; the others will release rovers. All carry some sort of scientific payload (although the prize does not require one); however the Synergy Moon proposal is a little dubious, a holographic projector that will display artworks on the Moon (the team claims this will also study whatever thin atmosphere exists).


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 Post subject: Re: from current journals as of 2017 05 21
PostPosted: Mon May 22, 2017 12:04 pm 
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Thank you Set.

I laughed at your biofuel pelletized wood note. People burning this product can be very vague about the location of the source of their fuel supply.

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 Post subject: Re: from current journals as of 2017 05 21
PostPosted: Tue May 23, 2017 2:58 pm 
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Quote:
The Blackener’s Cave
Surtshellir is a lava tube cava in western Iceland. The cave figures in a number of Icelandic legends; it was supposedly occupied by a giant, a band of outlaws, and a group of heretic bandits. Archaeologists found considerable evidence of human activity but it’s all fairly mysterious. About 100 yards in there’s a drystone basalt wall fifteen feet high and spanning the entire 40-foot width of the cave. The blocks weigh four tons. This was obviously a major undertaking, especially since it had to be done with artificial illumination, but there’s no real clue as to who built it and why; there’s a legend mentioning a “fortress” in the cave and this would certainly fit, but one would think a fortification would be built closer to the entrance. A side branch has an oval enclosure, 22 by 11 feet, also made of drystone basalt blocks. Nobody has any good idea what this is either, but one archaeologist speculated it is the “oldest standing Viking structure in the world”. Finally, another side branch has a bone pile, now diminished by looters from an original circle 12 feet wide and a few feet deep. The bones are estimated to be the remains of over 200 animals, and have been thoroughly and meticulously smashed into tiny pieces; radiocarbon dates are 890-930. One hesitates to use “ritual objects and structures”, but that seems like a reasonable bet.


Well, it's not like rituals weren't important to most ancient peoples. And many modern.

Quote:
Relevant to the recently reviewed Empires of the Word. The Greeks conceded that they learned the alphabet from Phoenicians. However, Phoenician, like most Semitic languages, didn’t write vowels; the Greeks couldn’t write poetry without vowels; and thus the Greeks invented them by adapting Phoenician consonants that didn’t have a Greek equivalent.


Interesting.

Quote:
Anyone Can Become a Troll
Researchers analyzed 16 million comments on CNN.com and found two key factors in “trolling” (they note their use of trolling includes both general unpleasant comments plus personal attacks). The first factor is the troll’s mood; this was tested in an experimental group, plus the observation that trolling peaks on Monday and the observation that people who troll in one discussion are more likely to troll in a second. The second factor is discussion context; if a discussion starts with a “troll” remark, subsequent comments are likely to be trolls. It was also noted that these situational factors were much better predictors of trolling that a person’s previous trolling history, leading to the article title that anyone can be a troll if they’re in a bad mood or are tempted. (A poster child for this – she’s actually shown in the article – is Isabella Sorley of Newcastle, UK. She had no previous history of abusive comments and is described as “polite” by interviewers, but late one night (she comments alcohol use was involved) she Twittered a death threat to a member of Parliament and ended up sentenced to twelve weeks in prison.


I find this definition of "troll" idiosyncratic. I understand a troll to be someone who enjoys lobbing hand grenades into a crowded living room and watching everyone scramble for the exits and/or fight each other to fall on the grenade. In other words, someone who stirs up trouble at a web site simply for the perverse entertainment of getting a rise out of people.

Quote:
Chicken Acceleration? APA puts Imprimatur on Credulous Psi Book
The American Psychological Association has published Transcendent Mind: Rethinking the Science of Consciousness. This includes description of an “experiment” with a “psychic” who, by going into what appeared to be “an altered state of consciousness”, converted unfertilized eggs to live chicks in nine minutes; a woman who could make gold foil materialize on her body, and an interview with Richard Feynman, conducted by séance. The chicken and gold foil demonstrations could not be duplicated under controlled conditions. In the Feynman “interview”, it was proposed to identify the spiritual entity by asking a physics question, so “Feynman” was asked the value of the fine structure constant. After considerable delay, the medium decided that it involved the capital letter M and the number 0.08.


<facepalm> I'm about convinced we still don't have a legitimate science of the human mind. Shakespeare understood the human psyche better than these clowns.

Quote:
Nature notes troubling interference from funders with scientists studying addiction. Not corporate funders, like the tobacco industry, but government funders. The gist is that research that appears to show government policies aren’t working gets suppressed. I imagine this could apply across the political spectrum.


You think?

Quote:
The secret war on counterfeit science
A Chinese scientist, looking for a cheap way to print labels for specimen vials, walked into a local print shop and asked for a demonstration of a label-printing machine. He was shocked when the shop owner proudly pulled out a sheet of labels he had printed for another customer; they were counterfeit labels for expensive antibodies produced by the American companies Abcam and Cell Signaling Technology. Further investigation disclosed a counterfeit chemistry ring that was selling diluted or just plain wrong reagents. A number of Chinese and Western scientists interviewed noted that the counterfeit reagents had ruined and delayed research. Immense profit margins and China’s cumbersome import bureaucracy are blamed.


My own theory is that Chinese reagent counterfeiters are to blame. But incentive structures do influence people.


Quote:
Article
Strange News from Another Star
In 2014, Tabetha Boyajian reported an unusual discovery from the Kepler satellite. Star KIC8462852 (more conveniently dubbed “Tabby’s Star” or “Boyajian’s Star”) displayed unusual brightness variations. Kepler was designed to pick up planetary transits; Boyajian’s Star had dimming characteristic of transits – but they dips were irregular in timing and duration and therefore not due to an orbiting planet. A number of theories were proposed: a disk of gas or dust around the star; swarms of comets; a dust cloud in the interstellar medium; intrinsic variation; a nearby black hole. All of these have some sort of fatal flaw in explanation. A last suggestion is an alien megastructure (which, of course was the one picked up by the MSM); the aliens are in the process of building a Dyson Sphere or a Ringworld around the star.


Yeah, this one is a real puzzle. I remain skeptical that it's space aliens.

Quote:
Springer is retracting 107 papers from Tumor Biology after finding that they had been accepted based on fabricated peer-review reports. All the papers were by Chinese authors. The Chinese state-run People’s Daily blamed the scandal on lax punishment for academic misconduct and pressure to publish.


<i>Blink blink.</i> Earlier today I found myself taking Trump's side against a <i>National Review</i> columnist. And now I find myself actually agreeing with the Chinese state press. What's this world coming to?

[quote]
News and Views
Large rise in carbon uptake by land plants
Letter
Large historical growth in global terrestrial gross primary production
One of the numerous inputs to carbon dioxide models is the rate of uptake by land plants for photosynthesis. A new proxy involves atmospheric measurement of the trace gas carbonyl sulfide, and it indicates that Gross Primary Productivity increased by about 31% from 1900 to 2013. The way this works is carbonyl sufide is produced at the ocean surface by organic sulfur reactions, and destroyed by uptake by land plants. Since the ratio of carbonyl sulfide to carbon dioxide use by plants is known and predictable the rate of carbon dioxide uptake by plants can be estimated by carbonyl sulfide concentrations in ice cores. Gross Primary Productivity had been expected to increase with increasing carbon dioxide, but the amount of increase was unknown; the 31% increase estimated by the carbonyl sulfide proxy is on the high end of previous estimates, which ranged from 55 to 52%. Note and technical paper.
[quote]

Good news. But look for the usual suspects to find a reason to call it bad news.


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 Post subject: Re: from current journals as of 2017 05 21
PostPosted: Wed May 31, 2017 6:50 pm 
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Quote:
I remain skeptical that it's space aliens.


You would stand against the concensus of the Internet?

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