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 Post subject: from current journals as of 2015 10 10
PostPosted: Sat Oct 10, 2015 7:57 pm 
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Science 2 October 2015
News in brief
Syrian researchers to make first seed bank withdrawal
The Svalbard Global Seed Vault on Spitsbergen stores seed varieties that are duplicates of seeds from a number of agricultural research centers; the intent was that if global or regional conflicts or disasters destroyed one of the other seed banks it could be restored from Spitsbergen (it being assumed that Spitsbergen wouldn’t be involved in war or disaster). The International Center for Agricultural Research in the Dry Areas (ICARDA), formerly based in what used to be Aleppo, has made the first ever seed withdrawal from Spitsbergen and will attempt to re-establish its seed banks in Lebanon and Morocco.
Cancer test draws FDA warning
(Appended to a previous thread).
Climate pledges not enough to curb global warming
A nonprofit says the current national commitments to cut GHGs are not enough to keep global warming below the magic 2°C level by 2100; instead temperatures will rise 3.5°. (This is, of course, assuming that the countries that have pledged actually come through). If there are no changes in GHG emissions (“business as usual”) Earth is expected to warm 4.5° C.
Minister accused of plagiarism
Plagiarism detection software has tapped German defense minister Ursula von der Leyen’s 1990 PhD dissertation as plagiarized on 27 of 62 pages. Von der Leyen denies the charge. It’s noted that “at least a dozen” German politicians had have degrees revoked after plagiarism detections, including two former cabinet ministers – previous defense minister Karl Theodor zu Guttenberg and education minister Annette Schavan. As a side I note Ursula von der Leyen is a gynecologist, which seems an odd background for a defense minister.
News in Depth
Europe’s rifts over transgenic crops deepen at key deadline
(Appended to an earlier thread)
Perspectives
Safer fuels by integrating polymer theory into design
Research Reports
Megasupramolecules for safer, cleaner fuel by end association of long telechelic polymers
Researchers are investigating polymer additives to jet fuel that will reduce misting – and therefore fuel/air explosions – in crashes, but will not interfere with fuel pumping or vaporization in engines. The problem thus far has been shear degradation during routine handling. So far promising bench-scale candidates are α,ω-di(di-isophthalic acid) polycyclooctadiene and α,ω-di(di(tertiary amine)) polycyclooctadiene. “Telechelic” polymers have reactive end groups that quickly recombine if broken by shearing.
How stable are food webs during a mass extinction?
Research Reports
Community stability and selective extinction during the Permian-Triassic mass extinction
The authors set up “plausible” food webs for the life of the Karoo Group in South Africa and tested how stable they would be during mass extinction. The PTr extinction seems to be unusual in that small plants, small herbivores, and small amniotes were preferentially affected; most other extinctions had more effects on large organisms than small ones. It’s noted that in more recent food webs, the large herbivores feed on grasses; since there were no grasses in the Permian there was a stronger correlation between the size of plants and the size of herbivores (and therefore their predators) than there is now.
Research Reports
State shift in Deccan volcanism at the Cretaceous-Paleogene boundary, possibly induced by impact
(Appended to an earlier thread)

Nature 1 October 2015
This Week
Testing times
The editorial discusses the Volkswagen scandal. I don’t know exactly what Volkswagen did, other than devise a way to determine if a car was undergoing an emissions test and adjust engine performance accordingly. I heard – no confirmation – that the tests were done on a dynamometer, and the Volkswagen “defeat device” was software to detect steering wheel movement; if there were no constant, minor steering adjustments it was assumed there was no driver. Could be. At any rate, the article notes the test fraud was discovered by the International Council for Clean Transportation, described as a “non-profit … counterweight to the influence of the global automobile and energy industries in policy debates”. The ICCT gave a $50k grant to the University of West Virginia Center for Alternative Fuels, Engines and Emissions that discovered the fraud; Nature notes that the EPA had a R&D budget of $537M and the European equivalent had a $371M budget yet it was this relatively small entity that found test fraud apparently going back to 2009. I find myself pretty annoyed with Volkswagen, of course, but the scandal points out a major problem with environmental regulations (and perhaps government regulations in general); the regulatory agencies spend a lot of time and effort writing them but very little verifying that they are being followed.
News in Focus
Gene-edited pigs to be sold as pets
The Chinese research institute BGI has developed a strain of pigs that only weigh 15 kilograms as adults using a gene-editing technique that disables one of two copies of the growth hormone receptor gene in fetal cells. Pigs are a popular research animal due to their dietary similarity to humans, but full-size pigs cost more and require larger drugs doses in tests. As a side business, BGI will over the pigs as pets (current price is around $1600 but that will be adjusted when they figure out what the demand is). Pigs can be ordered in a variety of coat colors and patterns, which BGI will also set with gene editing. The usual parties are outraged to the point of incoherence.
News Feature
Mountain Battle
(Appended to an earlier thread)
Comment
Build imprecise supercomputers
The author, Tim Palmer, notes that a great deal of the electrical power used by supercomputers – the next generation of machines is supposed to consume 100 megawatts – goes to correct errors, such as thermal noise and cosmic ray strikes. He argues that reducing power by a factor of four will only result in a 1% increase in incorrect computations. I would be somewhat more confident in his claim that imprecision is tolerable if he wasn’t a professor of climate physics at the Oxford Modeling and Prediction Center.

Natural History October 2015
Samplings
Gut Reaction
The coffee berry borer, Hypothenemus hampei, is able to tolerate caffeine levels that would kill most insects (as an aside, a lot of plants use caffeine as a pesticide; however some use it as a pollinator attractor in nectar; bees apparently enjoy getting a buzz). At any rate the caffeine resistance turns out to be due to a gut bacterium (Pseudomonas fulva) that metabolizes caffeine. It’s suggested the discovery may be useful for coffee pest control strategies.

Proceedings of the U.S. Naval Institute October 2015
Cuba, the Coast Guard, and Chaos
To my surprise, the Coast Guard has had “a man in Havana” for 15 years, coordinating drug traffic interdiction with the Tropas Guardafronteras. The article notes that with the re-establishment of diplomatic relations, there will be a lot more traffic across the Florida Straits, possibly making it harder to interdict drug traffic. According to the article, the average Cuban income is the equivalent of $20/month; it’s suggested the drug cartels may find it fairly easy to corrupt ordinary Cubans.
Be Prepared for Maritime Drones
A general warning that various nation states may be using unmanned underwater vehicles and unmanned surface vehicles for military reconnaissance, and drug cartels may use them for delivery. The article mentioned a vehicle I had never heard of before, the Slocum Glider (named in honor of Joshua Slocum). The general class of underwater gliders use physical differences in water (usually thermal, but potentially density as well) as a propulsion method. As a result, the vehicles are essentially passive sonar proof.

Science 25 September 2015
News
Stings and pee: the Ig Nobels
One of this year’s IgNobel prizes went to a PhD entomology student at Cornell, Michael Smith, who evaluated the most painful places to be stung by using himself as a test subject. The winners were the upper lip, inside the nose, and the shaft of the penis. Other prizes went for the discovery that the amount of pain felt while driving over a speed bump is an excellent predictor of the severity of appendicitis, and the observation that various mammals, ranging in size from dogs to elephants, take 21 seconds to urinate, independent of their bladder size; the discoverers named this phenomenon “The Golden Rule”.
U.K. application to edit embryos
(Appended to an earlier thread)
News in Depth
Sleuthing sheds light on STAP cell fiasco
(Appended to an earlier thread; out of urls but should show up in current topics)
China’s island building is destroying reefs
By dredging and filling, China has converted several of the Spratly reefs (which China calls the Nansha Islands) to full-fledged islands. An air photo example of Fiery Cross reef shows a barely awash atoll in 2006; in 2015 it has a 3000-foot airstrip, a deep harbor, and numerous buildings, including fuel tanks. Environmentalists are aghast.
Features
Ecology’s tough climb
Starting in 2000, the NSF began working on NEON (National Ecological Observatory Network). There would be 20 “core” and 17 relocatable terrestrial sites, and 20 core and 14 relocatable aquatic sites. Each terrestrial site would consist of a tower, with environmental sensors at various heights, and a utility shed to provide power and collect data. The towers were to be stacks of modular segments. Each aquatic site would have solar powered buoy taking automated water samples and shore-based hydrological and meteorological sensors.
NEON is apparently just a hair short of a fiasco. The project is 18 months behind schedule and $80M (out of $434M) over budget. The scientific staff has had a gruesome turnover rate; the article interviews participants at scientific levels from director to field worker; all the interviews expressed a high level of dissatisfaction with the way NEON was run. The “observatory director” complained that despite the title he had little influence over how the network was being build or the activities of the scientific staff; he left the position after less than a year; he was one of five who have held the director position and resigned since 2007. At one point the entire scientific advisory panel considered a mass resignation on the grounds that despite their status as “advisors” no one was listening to their advice. A low level employee interviewed, the site manager for a the NEON station near Gainesville, Florida had a masters in biology and initially was enthusiastic about the job; she resigned after five months in frustration, saying her bosses discouraged her from showing any initiative or using her knowledge. The Puerto Rico site was abandoned after two security guards were murdered.
The factors the article quotes are probably familiar to anyone who’s ever worked on a large project. The funding source, NSF, is used to working with projects – observatories and space missions are given as examples – that have a fixed single goal. The NEON scientific staff expected to have to adapt at each site; NSF wanted a single design for everything. The project managers found it was impossible to recruit ecologists that had any experience in facility design or engineers that had any experience in ecology – they didn’t exist. There was a “festering” disagreement over whether a NEON site was operation or not; the scientists wanted the site considered operational as soon as it was generating data, while the NSF didn’t consider a site operational until it had data available on line. The difference seems trivial, but its noted that until the site was officially “operational”, money for running it came out of the construction budget rather than the operational budget; that led to cost overruns in construction (there’s no explanation as to why the available data couldn’t go online quickly; I can think of some, though). Finally, the NEON management group was cited by Congress for spending management funds on “inappropriate” activities; the one cited is a Christmas party. Another major hurdle was intergovernmental infighting. NEON doesn’t own any of the sites; as a result any work requires numerous permits from the various Federal, state and local agencies involved. A manager noted that network construction required “5 to 10 times more” permits than was planned for and was a huge drain on resources. One NEON component, STREON (Stream Experimental Observatory Network), proposed adding various things to streams (phosphorus and nitrogen are what’s mentioned) and/or removing various aquatic organisms to see what would happen. The environmental permitting “hurdle” for this proved to be too high and STREON was abandoned. The permitting process for Alaska and Hawaii has proved to be so onerous that NSF proposed dropping NEON sites there, ecologists “reacted with horror” and the proposal was dropped. NEON managers remain cautiously optimistic, hoping to have 60% of NEON operating by September 2016 and the entire network running by 2017.
Insights
Extreme weather, made by us>
Repeating something that everybody but the media, the public, politicians and environmental activist community knows, the article notes that no particular extreme weather event can be established as due to anthropogenic climate change. It’s noted that historical data is not adequate to justify claims for things like hurricanes or heat waves as due to AGW. The authors caution it’s still meaningful to ask if (for example) the frequency of hurricanes will increase with climate change, just not to claim that any particular hurricane is due to climate change.
Female genital cutting is not a social coordination norm
A “social coordination game” is one where all the parties have an incentive to match strategies. It’s conventional wisdom that female genital cutting in areas that practice it fits the social coordination game theory; the incentive involved is finding husbands for daughters. If marriageable men will accept uncut girls, there is no incentive for families to have their daughters mutilated; however once a significant fraction on men demand mutilated brides everybody will have to do it. The research tested 45 communities in the Sudanese state of Gezira and found the social coordination model falsified. The model predicts a discontinuity in cutting rates, with some communities at low or zero and some at high or complete. Instead the data show a linear trend from lowest to highest rates. The researchers didn’t find an alternate explanation, although they suggested several: religious obligation; a way of clearly marking gender; a signal of sexual fidelity that will bring high status husbands; underestimation of the health problems associated with genital cutting.

Nature 24 September 2015
This Week
Ecological impact of crops drops
Researchers at UCSB found that the freshwater impact of maize and cotton crops in the US has decreased by 50% over the last decade, mostly because of the use of genetically modified plants that use less pesticide. However the impact from soybeans has increased by a factor of 3 due to the spread of an invasive pest and consequent impact. The note implies “impact” is not strictly direct use of water, but contamination by fertilizer and pesticide runoff and processing and transportation water uses.
Features
The Big Peek
A 2011 study investigated the question “How much does good teaching help students?”. The researchers went back to the 1980s and took students that had been randomly assigned to “average” or “high” quality teachers between the ages of five and eight. The study then investigated their current status in annual earnings, university attendance, retirement savings, home ownership, and marriage. The students with high quality teachers outperformed the others as expected. I can imagine a lot of confounding factors, but that’s not the point of the article; the researchers had access to tax returns. I had no idea it was possible to access tax returns for social studies at all; the article quote a researcher as saying “It should be hard to get access to data, but it’s very important that such access be made possible”. The article cites other examples of such use of big data; the Danish study that firmly refuted the link between MMR vaccine and autism was based on the ID number that each Danish citizen uses when they access the national health care system. In a more controversial case, the Target firm used a teenage girls’ purchase records to deduce she was pregnant, and began mailing her coupons for baby products; this was the first her parents knew of it.
Comment
Democracy is not an inconvenience
Sociologist Nico Stehr warns climate scientists not to become disillusioned with democracy because of impatience with slow government action on climate change. Good to have that reassurance.
Cannibis
The “Outlook” subject for this issue of Nature; sponsored by a pharmaceutical company, interestingly enough.
The cultivation of weed
It’s noted that the genetics of marijuana are complicated. Since research has been fairly difficult, there have by fewer genetic studies than for tobacco or wine grapes (although it’s cautioned that tobacco is often used as a model organism independent of its production of a psychoactive drug).
Research without prejudice
Israel is in the forefront of cannabis research. American researchers note that in the U.S., cannabis is still a Schedule A drug, which means it has no medical use; therefore the Federal government only allows research into what harm it might cause, not possible benefits. Several researchers have therefore transferred their study programs to Israel, where a prominent Orthodox rabbi recently ruled marijuana was kosher.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Sun Oct 11, 2015 9:37 am 
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Quote:
...a prominent Orthodox rabbi recently ruled marijuana was kosher.


Not being conversant with Jewish dietary laws, my mind still went places with this, from sellers adding a 'Kosher' label to the product, to users having to separate it from non-dietary-compatible foods.

There seem to be a lot of horrified or aghast interest groups represented here.

Quote:
Democracy is not an inconvenience


:shock: Someone has to say that? Oy!

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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Sun Oct 11, 2015 7:46 pm 
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Quote:
Sociologist Nico Stehr warns climate scientists not to become disillusioned with democracy...

Climate scientists or climate activists?
Quote:
...a prominent Orthodox rabbi recently ruled marijuana was kosher.

Especially if you just smoke it. However doesn't it put you at risk of violating dietary rules if you develop a need to snack when your decision making processes are debilitated?

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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Sun Nov 01, 2015 8:40 pm 
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setnahkt wrote:
Nature 24 September 2015
Comment
Democracy is not an inconvenience
Sociologist Nico Stehr warns climate scientists not to become disillusioned with democracy because of impatience with slow government action on climate change. Good to have that reassurance.


Nature 15 October 2015
Correspondence
Climate justice more vital than democracy
Three academic from Denmark submit a letter to the editor criticising the above, claiming that democracy can be used be elites to reinforce their positions and goals, and that policy makers should use social justice considerations instead of democracy in efforts against climate change. Good to know that "social justice considerations" cannot be used by elites to to reinforce their positions and goals.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Fri Nov 27, 2015 10:13 pm 
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setnahkt wrote:
Nature 1 October 2015
This Week
Testing times
The editorial discusses the Volkswagen scandal. I don’t know exactly what Volkswagen did, other than devise a way to determine if a car was undergoing an emissions test and adjust engine performance accordingly. I heard – no confirmation – that the tests were done on a dynamometer, and the Volkswagen “defeat device” was software to detect steering wheel movement; if there were no constant, minor steering adjustments it was assumed there was no driver. Could be. At any rate, the article notes the test fraud was discovered by the International Council for Clean Transportation, described as a “non-profit … counterweight to the influence of the global automobile and energy industries in policy debates”. The ICCT gave a $50k grant to the University of West Virginia Center for Alternative Fuels, Engines and Emissions that discovered the fraud; Nature notes that the EPA had a R&D budget of $537M and the European equivalent had a $371M budget yet it was this relatively small entity that found test fraud apparently going back to 2009. I find myself pretty annoyed with Volkswagen, of course, but the scandal points out a major problem with environmental regulations (and perhaps government regulations in general); the regulatory agencies spend a lot of time and effort writing them but very little verifying that they are being followed.


Earth November-December 2015
Comment
Pipe Dreams: What We Have Learned From the Volkswagen Clean-Diesel Scandal
The authors note that the scandal provided "important lessons" about consumer behavior, markets, and the temptation to cheat. In particular consumers don't want to sacrifice performance for environmental considerations; Volkswagen used that in a commercial that compared a VM Jetta with a Toyota Prius. The article also noted a discrepancy between how much consumers say that are willing to spend to protect the environment and how much they actually spend.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Fri Nov 27, 2015 11:09 pm 
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setnahkt wrote:
The article also noted a discrepancy between how much consumers say that are willing to spend to protect the environment and how much they actually spend.


This is called "revealed preference" in economics. Been known for some time now.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Sat Nov 28, 2015 6:42 pm 
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Journalists, despite being human and despite participating in an economy, always seem amazed when people behave the way human behavior and economic theories predict.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Sat Dec 26, 2015 7:13 pm 
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setnahkt wrote:
Science 25 September 2015
Features
Ecology’s tough climb
Starting in 2000, the NSF began working on NEON (National Ecological Observatory Network). There would be 20 “core” and 17 relocatable terrestrial sites, and 20 core and 14 relocatable aquatic sites. Each terrestrial site would consist of a tower, with environmental sensors at various heights, and a utility shed to provide power and collect data. The towers were to be stacks of modular segments. Each aquatic site would have solar powered buoy taking automated water samples and shore-based hydrological and meteorological sensors.
NEON is apparently just a hair short of a fiasco. The project is 18 months behind schedule and $80M (out of $434M) over budget. The scientific staff has had a gruesome turnover rate; the article interviews participants at scientific levels from director to field worker; all the interviews expressed a high level of dissatisfaction with the way NEON was run. The “observatory director” complained that despite the title he had little influence over how the network was being build or the activities of the scientific staff; he left the position after less than a year; he was one of five who have held the director position and resigned since 2007. At one point the entire scientific advisory panel considered a mass resignation on the grounds that despite their status as “advisors” no one was listening to their advice. A low level employee interviewed, the site manager for a the NEON station near Gainesville, Florida had a masters in biology and initially was enthusiastic about the job; she resigned after five months in frustration, saying her bosses discouraged her from showing any initiative or using her knowledge. The Puerto Rico site was abandoned after two security guards were murdered.
The factors the article quotes are probably familiar to anyone who’s ever worked on a large project. The funding source, NSF, is used to working with projects – observatories and space missions are given as examples – that have a fixed single goal. The NEON scientific staff expected to have to adapt at each site; NSF wanted a single design for everything. The project managers found it was impossible to recruit ecologists that had any experience in facility design or engineers that had any experience in ecology – they didn’t exist. There was a “festering” disagreement over whether a NEON site was operation or not; the scientists wanted the site considered operational as soon as it was generating data, while the NSF didn’t consider a site operational until it had data available on line. The difference seems trivial, but its noted that until the site was officially “operational”, money for running it came out of the construction budget rather than the operational budget; that led to cost overruns in construction (there’s no explanation as to why the available data couldn’t go online quickly; I can think of some, though). Finally, the NEON management group was cited by Congress for spending management funds on “inappropriate” activities; the one cited is a Christmas party. Another major hurdle was intergovernmental infighting. NEON doesn’t own any of the sites; as a result any work requires numerous permits from the various Federal, state and local agencies involved. A manager noted that network construction required “5 to 10 times more” permits than was planned for and was a huge drain on resources. One NEON component, STREON (Stream Experimental Observatory Network), proposed adding various things to streams (phosphorus and nitrogen are what’s mentioned) and/or removing various aquatic organisms to see what would happen. The environmental permitting “hurdle” for this proved to be too high and STREON was abandoned. The permitting process for Alaska and Hawaii has proved to be so onerous that NSF proposed dropping NEON sites there, ecologists “reacted with horror” and the proposal was dropped. NEON managers remain cautiously optimistic, hoping to have 60% of NEON operating by September 2016 and the entire network running by 2017.


Nature 17 December 2015
This Week
NEON Inc. out
The NSF has dropped NEON, Inc. as the contractor for NEON sites after hearing that the project was $80M over budget. A new contractor hasn't been selected yet.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Mon Jan 11, 2016 11:09 pm 
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setnahkt wrote:
setnahkt wrote:
Nature 1 October 2015
This Week
Testing times
The editorial discusses the Volkswagen scandal. I don’t know exactly what Volkswagen did, other than devise a way to determine if a car was undergoing an emissions test and adjust engine performance accordingly. I heard – no confirmation – that the tests were done on a dynamometer, and the Volkswagen “defeat device” was software to detect steering wheel movement; if there were no constant, minor steering adjustments it was assumed there was no driver. Could be. At any rate, the article notes the test fraud was discovered by the International Council for Clean Transportation, described as a “non-profit … counterweight to the influence of the global automobile and energy industries in policy debates”. The ICCT gave a $50k grant to the University of West Virginia Center for Alternative Fuels, Engines and Emissions that discovered the fraud; Nature notes that the EPA had a R&D budget of $537M and the European equivalent had a $371M budget yet it was this relatively small entity that found test fraud apparently going back to 2009. I find myself pretty annoyed with Volkswagen, of course, but the scandal points out a major problem with environmental regulations (and perhaps government regulations in general); the regulatory agencies spend a lot of time and effort writing them but very little verifying that they are being followed.


Earth November-December 2015
Comment
Pipe Dreams: What We Have Learned From the Volkswagen Clean-Diesel Scandal
The authors note that the scandal provided "important lessons" about consumer behavior, markets, and the temptation to cheat. In particular consumers don't want to sacrifice performance for environmental considerations; Volkswagen used that in a commercial that compared a VM Jetta with a Toyota Prius. The article also noted a discrepancy between how much consumers say that are willing to spend to protect the environment and how much they actually spend.


Nature 7 January 2016
Seven Days
Volkswagen sued
The DOJ sued Volkswagen on January 4, 2016, claiming 600000 Volkswagen, Audi and Porsche vehicles had been fitted with "defeat devices". Still no explanation as to exactly what the "defeat devices" were.


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 Post subject: Re: from current journals as of 2015 10 10
PostPosted: Thu May 26, 2016 10:01 pm 
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setnahkt wrote:
Nature 24 September 2015
Cannabis
The “Outlook” subject for this issue of Nature; sponsored by a pharmaceutical company, interestingly enough.
The cultivation of weed
It’s noted that the genetics of marijuana are complicated. Since research has been fairly difficult, there have by fewer genetic studies than for tobacco or wine grapes (although it’s cautioned that tobacco is often used as a model organism independent of its production of a psychoactive drug).
Research without prejudice
Israel is in the forefront of cannabis research. American researchers note that in the U.S., cannabis is still a Schedule A drug, which means it has no medical use; therefore the Federal government only allows research into what harm it might cause, not possible benefits. Several researchers have therefore transferred their study programs to Israel, where a prominent Orthodox rabbi recently ruled marijuana was kosher.


Science 29 April 2016
AAAS News & Notes
Marijuana policy patchwork not based on science
The AAAS sponsored a Neuroscience and Society event; participants expressed frustration with current legislation on marijuana. Twenty-three states and the District of Columbia currently allow some use of marijuana for "medicinal" purposes, despite what the AAAS panel called a lack of studies demonstrating medicinal properties; part of the problem is that as a Federal Schedule I illegal drug, marijuana is legally defined as having no medicinal properties. While it's theoretically possible to study marijuana, the process is "very, very difficult".


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