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 Post subject: from current journals as of 2016 12 12
PostPosted: Mon Dec 12, 2016 9:09 pm 
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Article
Why Sinuhe Ran Away
Back in the Archives, our Swedish correspondent Sprengtporten mentioned Finnish author Mika Waltari during a discussion of The Complete Royal Families of Ancient Egypt. Waltari’s historical novel The Egyptian was his first international success, and was eventually made into a movie. (Wikipedia notes this was the first Finnish-language novel to be made into a Hollywood movie, and also that The Egyptian was the best-selling foreign novel in the US until passed by The Name of the Rose (I find that rather dubious, but who am I to doubt Wikipedia?))

At any rate, Waltari’s The Egyptian follows the adventures of Sinuhe, a doctor in the court of Akhenaten. There is an actual ancient Egyptian Story of Sinuhe, with vague plot similarities to Waltari’s novel. The Story of Sinuhe was apparently a popular text Egyptian schoolchildren used to practice their reading and writing; there are many copies available.

The Egyptian version is set in the reigns of Amenemhat I and Senusret I. Sinuhe is a palace official, serving in the royal harem. While on campaign in Libya (which at this time was anywhere west of the Nile Delta) with the Crown Prince Senusret, he overhears a conversation between Senusret and some messengers. He’s terrified by what he hears and flees, heading east into the Levant. Here he becomes a courtier to one of the minor kings of the area, eventually acquiring lands and a family, and defeating a local champion in a David-and-Goliath type duel (although Sinuhe uses a bow instead of a sling). However, news comes to him from Egypt that whatever made him run away is no longer an issue, and he returns to a royal welcome.

The issue here is: What did Sinuhe hear that made him panic and flee? There’s a lot of evidence that Amenemhat I, the first king of the 12th Dynasty, was a usurper, taking the throne from the last king of the 11th Dynasty, Montuhotep IV (and there’s some less convincing but still plausible evidence that Montuhotep IV was also a usurper, or at least not a direct descendant of Montuhotep III). In a “prophecy” attributed to Amenemhat I’s reign it’s noted that his mother is from the extreme south of Egypt (interestingly, there’s no mention of who his father was); the implication is that she was not of the nobility); the “prophecy” is supposed to be from much earlier but stylistically it dates from Amenemhat I’s reign, and the conclusion of Egyptologists is it was fabricated to justify succession to the throne by a Pharaoh with dubious antecedents. Finally, there’s a piece of “wisdom literature” (The Instructions of Amenemhat) in which it seems like the narrator, Amenemhat I, is “speaking” to his son from the afterlife – after being killed in a harem conspiracy. Thus the conclusion is the message brought to Senusret was that his father had been assassinated; even though Senusret was Crown Prince, Sinuhe must have feared that the succession would be in dispute and officials of the former regime, like him, might be in danger; thus he took off for the boondocks. There’s a possibility, of course, that he might have been involved in the conspiracy himself.

Natural History December 2016 – January 2017
The Subterraneans
A popular article on geomicrobiology – bacteria that live in deep rock formations. These were discovered as early as the 1920s, but it took a while to convince microbiologists that these were not surface bacteria carried down by drilling equipment. The most interesting one to me is Candidatus desulforudis, a bacterium that runs (sort of) on nuclear power. This requires a little more explanation, which I had to look up elsewhere, since it isn’t explained in the article. C. desulforudis is an obligate anaerobe that uses sulfate ion instead of oxygen as an electron acceptor. However, what’s available in the mine is sulfide, not sulfate – but there’s enough uranium in the mine to split water to hydrogen and hydroxyl ions. The hydroxyl ions can combine to form hydrogen peroxide, which then oxidizes sulfide to sulfate. Thus the bacterium is not using nuclear power as a direct energy source (the way photosynthetic organisms use sunlight), but it couldn’t survive without uranium – or at least radioactivity – in its environment.

Geology December 2016
Sulfur-oxidizing bacteria prior to the Great Oxidation Event from the 2.52 Gya Gamohaan Formation of South Africa
What we have here is microscopic spherical (well, originally spherical) thingies from a deep-water chert. The authors interpret these as sulfur-oxidizing bacteria similar to the extant Thiomargarita. Photographs show the assumption that the things are living organisms is fairly convincing; the conclusion that they are something like Thiomargarita based on more assumptions but still plausible. The coccoid cells are large, there are a few other coccoid bacteria this big but they are photosynthetic and have a more complicated cell wall then what is seen here. Plus the geological setting is pretty clearly deep, aphotic sediment and analysis shows abundant sulfur and sulfur compounds. These would be the oldest sulfur-oxidizing bacteria known. (I note we’ve run into Thiomargarita before)
Slow net sediment accumulation sets snowball Earth apart from younger glacial episodes
The authors compare sediment deposited during the Sturtian and Marinoan glacial periods and conclude it was deposited at much slower rates – 4 to 15 times slower – than Phanerozoic glaciations, even adjusting for things like duration, latitude, and distance from ice margin. They note most Phanerozoic glacial sediment was deposited during interglacial melt periods, and conclude that for some reason these were fewer during “snowball Earth”.

GSA Today December 2016
A Novel Plate Tectonic Scenario for the Genesis and Sealing of Some Major Mesozoic Oil Fields
We’ve had various threads on petroleum genesis. The authors of this article (GSA Today is mostly a news organ for the Geological Society of America, but publishes one article each issue, usually on something “popular”) contend that the Ghawar oil field (the world’s largest) resulted from Saudi Arabia being in the Intertropical Convergence Zone back in the Jurassic, resulting in lots of biological activity forming petroleum precursors. Then plate tectonics took it rapidly south into the “arid tropics”, where deposition of carbonates and anhydrite sealed the oil reservoir until ARAMCO showed up.

Scientific American December 2016
Science Agenda
Bringing Up Baby, Helping the Economy
Scientific American argues that paid family leave will benefit the US economy, noting that the FMLA allows for 3 months of unpaid leave for private employers with more than 50 employees, or public employers; thus about one half the US workforce is ineligible. The claim is that infant mortality is reduced by about 10% with family leave, there is an increased rate of breast feeding, and the emotional health of the parents improves. It’s noted that Scientific American offers 10 days of paid leave.
Advances
The Brainy Big Cats
The “social intelligence” hypothesis suggests that social animals have more cognitive ability than solitary ones; they supposedly need to figure out things like who is a friend and who is an enemy within the group. In the subject case, it’s noted that lions outperformed tigers and leopards on a test involving pulling on a rope to open a box full of raw meat. Of the twelve lions tested, seven solved the problem on their own and four solved it after watching another lion do it.

American Scientist November-December 2016
Sightings
Hungry Little Beasts
A fire whirl is a tornado-like vortex of flame; on land, they’re usually seen in forest fires. However, researchers at the University of Maryland noted an unusual phenomena in a video of a fire whirl; it evolved to a spinning, blue flame that was highly efficient. The video was of a fire after a lightning strike on a whiskey warehouse in Kentucky which had dumped Jim Beam into a nearby lake, and the blue whirl was burning on the water surface. Laboratory experiments (one of which set thing back a while after they used a little too much fuel and burned down the laboratory) showed the proper combination of fuel and rotation would create a stable, low-emission flame that might be used to clean up oil spills. As yet the blue whirls are still pretty mysterious.
Perspective
The Fate of Channel Island Foxes and Isle Royale Wolves
We had a thread on the wolves of Isle Royale National Park, which will probably soon disappear due to inbreeding. The population of grey foxes on the Channel Islands of the California Coast would appear to face a similar problem; the animals are highly inbreed, with the 494 San Nicolas foxes suffering from a heterozygosity index of 0.14-0.19. (Heterozygosity index is the genome-wide heterozygosity per 10K base pairs); the effective population size for the San Nicolas foxes is 2.1 (a single male/female pair of foxes would have an effective population size of 2.0). In comparison, mainland foxes have a heterozygosity index of 12.0 and an effective population size of 109. Although the other Channel Islands have larger populations and more heterozygosity than San Nicolas, they all have much smaller heterozygosity indices and effective population size than the mainland. However, the Channel Island foxes show no sign of deleterious results from inbreeding, which puzzles biologists.

Science 18 November 2016
News
Experiment to raise dead blocked
The Indian Council on Medical Research has blocked clinical trials of ReAnima, a proposal to inject brain-dead patients with mesenchymal stem cells and peptides plus transcranial laser brain stimulation and medial nerve stimulation. Critics noted the treatment has not been tested in animals and might distress family members.
Animal travel ban paralyzes labs
The two major Spanish airlines refuse to carry laboratory animals; in mainland Spain this apparently doesn’t cause problems but it is threatening biomedical research in the Canary Islands. The official airline reason is “safety” – escaped mice might damage cables – but the European Animal Research Association believes the airlines caved in to pressure from animal rights activists.
News in Depth
No need to apply, Dutch science academy tells men
The Royal Netherlands Academy for Arts and Sciences – KNAW – will not admit any men in the 2016 (ten new members) and 2017 (six new members) elections. Currently 87% of the 556 KNAW members are men. Marcia McNutt, president of the US National Academy of Sciences, commented “I don’t think we would do that; other people might feel the women elected this way somehow did not meet the same standards as their male counterparts, or even other women elected through the regular process”. However KNAW president José van Dijck says the process will be just as rigorous as always.
Engineered crops should have it made in the shade
Research
Improved photosynthesis and crop productivity by accelerating recovery from photoprotection
If there’s too much sunlight, plants invoke a process named nonphotochemical quenching (NPQ); chloroplasts just dump the excess photons. However, although NPQ can be raised in minutes it takes hours to turn off. The University of Illinois has engineered tobacco plants to improve the NQP shutdown time; test plant yields increased by 14% to 24%. Note and paper.
Insights
Fixing carbon unnaturally
Research
A synthetic pathway for the fixation of carbon dioxide in vitro
The most common carbon fixing cycle (i.e., the plant process that converts carbon dioxide to plant biomass) is called the Calvin cycle, aka the RoBisCO cycle, because the key enzyme is ribulose 1,5-bisphosphate/carboxylate. Five other natural carbon fixing cycles are known; the most efficient is the 3HP-4HB cycle. A new synthetic cycle, CETCH (I won’t go into what the initials stand for) is 4.3 times as efficient as the 3HP-4HB cycle and 37 times as efficient as the RoBisCO cycle; the enzymes for the CETCH process come from a plant, humans, and 10 microbes. It’s noted that transferring the CETCH cycle to a microorganism will be difficult; however the process can use either sunlight or electricity as an energy source. Note and paper.
Revealing the dynamics of a large impact
Research
The formation of peak rings in large impact craters
Recent drilling into the Chicxulub has confirmed some model predictions and confounded others. In particular, seismic velocity in the “peak ring” is low, leading to speculation that rocks here were either from near the surface or severely deformed. Drill cores, however, found peak ring rocks to be deep basement granites that were only moderately deformed. It’s speculated that the low seismic velocities are either caused by large-scale deformation features (dikes, faults, etc.) or by subtle features that haven’t been recognized yet. The scale of events is pretty dramatic – a range of mountains higher than the Himalayans is raised and collapses in the first three minutes after impact; a fluidized central peak forms and collapses in minutes 3-4, and everything “shakes down” in minutes 4-10. Note and paper.

Science 11 November 2016
News
Clinical trials go unpublished
An automated tracking system, TrialsTracker, found that nearly half of clinical studies done in the last 10 years have never been reported in a peer-reviewed journal.
Luxembourg eyes asteroid mining
The Grand Duchy of Luxembourg is investing €25M in Planetary Resources, a Redmond, Washington startup hoping to launch an asteroid prospecting mission by 2020. Luxembourg has also partnered with Deep Space Industries of Mountain View, California; both Planetary Resources and Deep Space Industries have established their European headquarters in Luxembourg. Who knows, maybe Monaco?
Court clear supplement sleuth
(Appended to an earlier thread)
Early farmers expanded dogs’ diet
DNA sequencing finds that dogs have genes for processing starch, while wolves do not. Now DNA analysis of 7000- and 5000-year-old dog bones showed the genes had developed that early, predating the development of dog breeds.
By the numbers
It had been thought that most black-market elephant ivory came from old government stockpiles, but C-14 dating of seized illegal ivory shows 90% comes from recently killed elephants – i.e., poaching.
Features
The lost Norse
According to this article, conventional wisdom is that Norse Greenland failed because the farmers stubbornly clung to traditional livestock raising instead of shifting to marine mammal hunting like the natives. Recent studies, however, suggest the Greenland Norse were adapting but failed anyway. The peak European population in Greenland was around 3000, mostly in two settlements (“Western” and “Eastern”; both were on the west coast of Greenland but the Eastern Settlement was further south and east). The Western Settlement was depopulated by 1400; the Eastern Settlement lasted until around 1450. The idea that “the Norse destroyed their environment” was popularized by Jared Diamond in Collapse. However, recent analysis of trash middens and burials suggest that the Norse were doing quite well up until the onset of the Little Ice Age; that they were careful managers of the soil and the few trees that grew in Greenland; and that they conducted an extensive trade in walrus ivory. Although it seems like there was some conflict over resources in the Western Settlement, people from the Eastern Settlement seem to have simply emigrated back to Iceland.
Insights
Leprosy in red squirrels
Research
Red squirrels in the British Isles are infected with leprosy bacilli
We had recent thread about the decline of red squirrels in the British Isles (I'd link to it but I'm out of urls); it now turns out that they are also a host for Mycobacterium leprae, which had previously been known only from humans, nine-banded armadillos, and mouse foot pads. Note and article.
Policy Forum
Precaution and governance of emerging technologies
The eight co-authors all argue that the “precautionary principle” is unjustly criticized, claiming that critics believe it will always lead to suppression of new technologies. They argue that this is not always the case and that “targeted precaution” should be embraced, specifically citing “gene drive” as a technology that should be covered by the precautionary principle. They provided no examples of cases where the precautionary principle has not lead to suppression of new technology.


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 Post subject: Re: from current journals as of 2016 12 12
PostPosted: Tue Dec 13, 2016 3:07 pm 
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Joined: Fri Apr 04, 2008 10:45 am
Posts: 8205
setnahkt wrote:
The issue here is: What did Sinuhe hear that made him panic and flee?


[flash]https://www.youtube.com/watch?v=92gP2J0CUjc[/flash]

Quote:
Scientific American December 2016
The Brainy Big Cats
The “social intelligence” hypothesis suggests that social animals have more cognitive ability than solitary ones; they supposedly need to figure out things like who is a friend and who is an enemy within the group. In the subject case, it’s noted that lions outperformed tigers and leopards on a test involving pulling on a rope to open a box full of raw meat. Of the twelve lions tested, seven solved the problem on their own and four solved it after watching another lion do it.


The problem with this hypothesis is the brainlessness of my clowder.

Quote:
Science 18 November 2016
News
Experiment to raise dead blocked
The Indian Council on Medical Research has blocked clinical trials of ReAnima, a proposal to inject brain-dead patients with mesenchymal stem cells and peptides plus transcranial laser brain stimulation and medial nerve stimulation. Critics noted the treatment has not been tested in animals and might distress family members.


"Whose stem cells?"
"Why, my own, of course."
"Of <i>course</i>."

Quote:
No need to apply, Dutch science academy tells men
The Royal Netherlands Academy for Arts and Sciences – KNAW – will not admit any men in the 2016 (ten new members) and 2017 (six new members) elections. Currently 87% of the 556 KNAW members are men. Marcia McNutt, president of the US National Academy of Sciences, commented “I don’t think we would do that; other people might feel the women elected this way somehow did not meet the same standards as their male counterparts, or even other women elected through the regular process”.


"Other people." But not you, Ms. McNutt?

Quote:
Science 11 November 2016
News
Clinical trials go unpublished
An automated tracking system, TrialsTracker, found that nearly half of clinical studies done in the last 10 years have never been reported in a peer-reviewed journal.


My impression is that publication is required by some funding agencies now even for negative results. But that's clinical trials, which may not be the same as "clinical studies"?

Quote:
Policy Forum
Precaution and governance of emerging technologies
The eight co-authors all argue that the “precautionary principle” is unjustly criticized, claiming that critics believe it will always lead to suppression of new technologies. They argue that this is not always the case and that “targeted precaution” should be embraced, specifically citing “gene drive” as a technology that should be covered by the precautionary principle. They provided no examples of cases where the precautionary principle has not lead to suppression of new technology.


"No examples." Do tell.


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 Post subject: Re: from current journals as of 2016 12 12
PostPosted: Wed Dec 14, 2016 12:18 am 
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As far back as the 1950's there was concern that the failure to report studies with high complication rates or low cure rates would skew the belief in medical goodness.

"Science 11 November 2016
News
Clinical trials go unpublished
An automated tracking system, TrialsTracker, found that nearly half of clinical studies done in the last 10 years have never been reported in a peer-reviewed journal."


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 Post subject: Re: from current journals as of 2016 12 12
PostPosted: Wed Dec 14, 2016 4:38 pm 
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Joined: Fri Apr 04, 2008 11:22 am
Posts: 1019
KGB wrote:
setnahkt wrote:
The issue here is: What did Sinuhe hear that made him panic and flee?


[flash]https://www.youtube.com/watch?v=92gP2J0CUjc[/flash]

Quote:
Scientific American December 2016
The Brainy Big Cats
The “social intelligence” hypothesis suggests that social animals have more cognitive ability than solitary ones; they supposedly need to figure out things like who is a friend and who is an enemy within the group. In the subject case, it’s noted that lions outperformed tigers and leopards on a test involving pulling on a rope to open a box full of raw meat. Of the twelve lions tested, seven solved the problem on their own and four solved it after watching another lion do it.


The problem with this hypothesis is the brainlessness of my clowder.

Quote:
Science 18 November 2016
News
Experiment to raise dead blocked
The Indian Council on Medical Research has blocked clinical trials of ReAnima, a proposal to inject brain-dead patients with mesenchymal stem cells and peptides plus transcranial laser brain stimulation and medial nerve stimulation. Critics noted the treatment has not been tested in animals and might distress family members.


"Whose stem cells?"
"Why, my own, of course."
"Of <i>course</i>."

Quote:
No need to apply, Dutch science academy tells men
The Royal Netherlands Academy for Arts and Sciences – KNAW – will not admit any men in the 2016 (ten new members) and 2017 (six new members) elections. Currently 87% of the 556 KNAW members are men. Marcia McNutt, president of the US National Academy of Sciences, commented “I don’t think we would do that; other people might feel the women elected this way somehow did not meet the same standards as their male counterparts, or even other women elected through the regular process”.


"Other people." But not you, Ms. McNutt?

Quote:
Science 11 November 2016
News
Clinical trials go unpublished
An automated tracking system, TrialsTracker, found that nearly half of clinical studies done in the last 10 years have never been reported in a peer-reviewed journal.


My impression is that publication is required by some funding agencies now even for negative results. But that's clinical trials, which may not be the same as "clinical studies"?

Quote:
Policy Forum
Precaution and governance of emerging technologies
The eight co-authors all argue that the “precautionary principle” is unjustly criticized, claiming that critics believe it will always lead to suppression of new technologies. They argue that this is not always the case and that “targeted precaution” should be embraced, specifically citing “gene drive” as a technology that should be covered by the precautionary principle. They provided no examples of cases where the precautionary principle has not lead to suppression of new technology.


"No examples." Do tell.


I'm just going to ditto every comment you made, especially the last.

Quote:
They argue this is not always the case


By inference, that means it usually is.


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