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 Post subject: from current journals as of 2017 03 06
PostPosted: Mon Mar 06, 2017 7:11 pm 
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Joined: Fri Apr 04, 2008 10:48 am
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Location: Broomfield, Colorado
Scientific American March 2017
STD results in minutes
A walk-in clinic in London, Dean Street Express, self-service STD tests. A client schedules an appointment online, then shows up at the clinic at the appropriate time and gets a test tube and some swabs from a technician (this seems to be the only human contact involved). He/she enters a private room, watches a video showing how to provide samples, and does so. The samples are tested for syphilis, gonorrhea and chlamydia – HIV is on the way – using molecular genetic markers, and the results get texted to a cell phone in 6 hours. The system was developed by Cepheid, a US company; so far clinics have opened in London, Barcelona, Paris, Brisbane and San Francisco.
Make Earth Great Again
A German study tested self-identified conservatives and liberals by offering a small sum they could donate to hypothetical environmental charities. Conservatives were more likely to donate if the message emphasized restoring the Earth to a previous condition; liberals, if the message was preventing future environmental degradation.
It’s Electric – With the Right Mix
University of Pennsylvania researchers have developed a bench-scale process that uses the ionic gradient between salt and fresh water to generate electricity. Others are skeptical, citing too many ecosystem problems with deploying the system in estuaries. However, it’s noted it could work in brine wastewater ponds.
Your Echo Is Listening
Amazon markets Echo home control devices, which in turn support a Siri/Cortana-like interface, Alexa, that responds to voice commands. The commands can be local (“Alexa, turn on the outside lights” or web-based (“Alexa, find local Chinese restaurants”). In November 2015 a murder was committed at James Bates’ house in Bentonville, Arkansas. The Echo is only supposed to record after it hears the word “Alexa”, but sometimes it thinks it hears “Alexa” and starts recording. Police served Amazon with a warrant asking to here Alexa recordings that were made on the night of the murder, hoping that victim or killer had said something that sounded like “Alexa” in the process of strangling or being strangled. Amazon refused. Technofile columnist David Pogue thinks this was a business decision, suggesting that Amazon thought Echo sales would drop if people thought it recording conversations; he doesn’t mention privacy concerns, although he notes that more and more household appliances respond to voice commands. (James Bates was bound over for prosecution for murder based on another technological device; his smart water meter recorded 140 gallons of water used between 1 and 3 AM; police suspect he was washing away evidence).

Science 10 February 2017
Organ concerns spur retraction
A paper on liver transplant safety published in Liver International was retracted over concerns that the livers had come from executed Chinese prisoners. China banned the practice in 2015 but the transplants studied took place before then.
Venezuela’s HIV drug crisis
Venezuela has a shortage of HIV drugs; HIV activists in the country have attempted to get the Global Fund to Fight Aids, Tuberculosis and Malaria to provide them. However the Fund has declined on the grounds that Venezuela is considered a high-income country.
News Features
Rules of Evidence
In 1976 Bio-Test Laboratories in Chicago was found to be falsifying drug test data. In response the FDA instituted the Good Laboratory Practices procedure, which requires extensive auditing and paper trails. Industrial and government labs in the US follow GLP carefully; academic laboratories generally do not. This leads the FDA to discard many academic reports – for example, tests that appear to show very low doses of bisphenol A cause endocrine disruption – in favor of those done by industry laboratories. The academics counter that the GLP procedure involves too much paperwork. A thread from Nature last year noted widespread problems with quality assurance from academic labs I know from personal experience that the EPA is very hyper about sample quality control procedures; whether it’s excessively so is moot.
No Easy Answers
“Building Blocks” is a pre-kindergarten program supposed to teach mathematics skills and embraced by many big city school districts. Science notes it has exactly the same problem as other early intervention programs – like Head Start – initial results are very promising but the supposed gains disappear by the time the children are 6-8 years old and the test group does no better than the control group.
Data for all
Most European countries have centralized data repositories for things like tax and census data. The US does not, due to constitutionally mandated balances between federal, state and local governments. A bipartisan Congressional Committee on Evidenced-Based Policymaking is trying to sort out rules for access to government data. Right now researchers need to make individual arrangements with each federal agency involved. If data already collected was available, there would be huge savings in administrative costs; an example cited is the American Opportunity Study, which is supposed to track intergenerational mobility – education, financial status, etc. – on an ongoing basis. In the absence of existing data, the researchers would have to recruit people and track them over a good part of their lifetimes; with access to existing data the study could be done now. Skeptics note the idea may not be feasible – the example cited is the task of digitizing handwritten names on 1990 census forms so they could be linked to other databases, for which “writing the code has been harder than expected”. There is some lip service to privacy concerns. I’m of mixed feelings; everybody likes “big data” nowadays and certainly there could be some interesting things done. However, examples like the math program for pre-kindergarten above suggest that even if policy makers have abundant data they ignore it in favor of political concerns, and examples like the child health study below suggest that getting that data in a useful format may be harder than people think. I fear data-dredging and HARKing to support whatever policy is politically correct.
Books et al.
Game changers
Two board games – Evolution: Climate and Settlers of Catan: Oil Springs – are reviewed. The first adds climate change to an evolution game; never played it myself so can’t comment much. The second adds oil as a resource to the Settlers of Catan game which I have played. With oil, a player can upgrade existing cities to metropolises or double other resources; however too much oil use can cause environmental disaster and make everybody lose. The reviewer notes the game illustrates the “tragedy of the commons”.

Nature 9 February 2017
News in Focus
Treaty to stop biopiracy threatens to delay flu vaccine
The Nagoya Protocol treaty dictates that any company using “genetic resources” from a participating nation must negotiate an advance agreement to share profits and benefits. The WHO analyzes “thousands” of flu strains and makes a recommendation (two a year, one for northern hemisphere and one for southern) on how to make that year’s vaccine. Laboratories make the viruses most likely to work available to pharmaceutical companies; they then prepare and distribute vaccines, and finally people get vaccinated. Time pressure is quite tight; the process currently takes about six months; the pharmaceutical company Nature contacted (AstraZenaca) estimated the Nagoya Protocol agreements would take an additional three months, which means vaccines would not be available until flu season was already underway. The US has not ratified the Nagoya Protocol.
US child-health study takes shape
We had some threads on the National Children’s Study, which was supposed to get all sorts of data by tracking 100K children from birth to age 21. The NIH pulled the plug on that study in 2014, due to trouble recruiting participants, formulating hypotheses, and staying within budget (the NCS has spent $1.2G when cancelled). Now a new study, Environmental Influences on Child Health Outcomes (ECHO) is underway; rather than recruiting participants, ECHO will combine existing cohorts. The article doesn’t use the term “meta-analysis” but that seems to be what is intended.
New wave power
Chinese researcher Zhong Lin Wang proposes a new way to make use of wave energy. Existing wave power devices depend on heavy propellers, magnets, and metals coils that must be anchored to the ocean floor and deal with waves that come in random directions and with highly variable sizes. Wang proposes instead to generate power from static electricity produced by “nanogenerators” – little hollow balls made of dielectric plastic, with another little solid ball of dielectric plastic inside. When agitated by waves, each little ball produces a small amount of power – 1-10 mW. Networks are connected, and then connected to shore with a cable. Wang notes the nets don’t have to be anchored and can generate power regardless of the wave direction; he thinks they will be suitable for small islands, coastal villages, etc. He notes but doesn’t go into detail on a lot of potential problems: the nets must be kept out of shipping lanes, cannot entangle marine life, and must not leak.
News and Views
Tiny fossils in the animal family tree
Meiofaunal deuterostomes from the basal Cambrian of Shangxi (China)
It’s OK, I had to look up “meiofaunal” too. But I knew what deuterostomes were. Background: Deuterostomata is a stem group clade – perhaps an Infrakingdom or superphylum if you’re a phyletic taxonomist – of animals. The distinction from Protostomata is how the gut forms; in protostomes first gut opening the embryo develops becomes the mouth; in deuterostomes the first gut opening becomes the anus. Deuterostomes include echinoderms, the hemichordates, and the chordates. There were formerly a number of other invertebrates assigned to the deuterostomes but the advent of molecular taxonomy moved them to the protostomes; thus the deuterostomes are a relatively minor part of the animal kingdom except that since chordates are deuterostomes they are of some personal interest. At any rate, Chinese paleontologists turned up some phosphatic, blobby fossils that would be candidates for a horror-movie creature – there were some pictures in the MSM - if they were somewhat larger – Saccorhytus coronaries is about a millimeter in the long dimension. The feature that makes them deuterostomes is a set of eight openings on little conical protuberances around the mouth: these are interpreted as gill openings. Echinoderms don’t have gill openings, but hemichordates and chordates – including the embryonic you – do. (Note lots of things have “gills” – structures that extract oxygen from water – it’s the gill slits or pores that make hemichordates and chordates).

Nature 2 February 2017
Seven Days
Caffeine-test error
Northumbria University was fined £400K for an error in an experiment testing the effect of caffeine on athletic performance. Instead of giving the students involved 0.3 grams of caffeine, they were given 30 grams. All students recovered. But I bet they were jittery for a while.
News Feature
First Trip To The Stars
The Breakthrough Starshot program, proposing to send a fleet of tiny little probes to Alpha Centauri, is now considering going to Proxima Centauri instead, since the discovery of a planet orbiting that star. Commenters note that it is unlikely that the project will succeed, but the development of capabilities will revolutionize solar system exploration – one saying “We can have next day Amazon delivery. To Mars”.

Paleobiology Issue 4 2016
Ediacaran distribution in space and time: testing assemblage concepts or earliest macroscopic body fossils
Ediacaran fossils are sort of a personal focus of mine. Because they are weird. As mentioned before, it’s not clear what sort of organisms they were, with a variety of contenders ranging from bacterial mats to animal ancestors. At any rate the authors here analyze know Ediacaran fossils and put them in “bins” – there term – based on “assemblage” – grouping of fossil species together; lithology – the kind of rocj the fossils are found in; time – the time interval they are found in; paleoenvironment – the environment (for example, “deep subtidal” or “outer shelf”); and water depth. The assemblages are Avalon, White Sea, and Nama. The Avalon and White Sea assemblages really seem to be distinct; although they overlap in time they are distinct in their environmental and water depth requirements. The Nama assemblage appears to be later in time and far-ranging both geographically and in water depth preferences.

 Post subject: Re: from current journals as of 2017 03 06
PostPosted: Tue Mar 07, 2017 1:03 pm 
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Joined: Fri Apr 04, 2008 12:03 pm
Posts: 1075
Location: Surfing thru Cyberspace
The Echo case intrigues me. We have one of these at home and use it often. I've got it connected through our Harmony remote to control the living room media center and expect to connect lighting soon. When you say Alexa or Echo - or something close to those - it wakes up to start listening. You can see this happen by the blue ring at the top lighting up, showing it's actively listening. I am curious how much it listens without lighting that ring, but haven't delved into that yet (I may not want to know...). Samsung has warned that SmarTvs are listening, too, so you should be aware that not everything is so private anymore.

I don't run. If you see me running, you probably should run, too.


 Post subject: Re: from current journals as of 2017 03 06
PostPosted: Sun Mar 12, 2017 10:32 am 

Joined: Fri Apr 04, 2008 10:45 am
Posts: 3575
Location: Toronto
Environmental Propaganda introduced into a popular board game

But oil is scarce and its use does not come without cost. Using oil produces pollution, as well as climate changing emissions, which bring with them the threat of coastal flooding—and absolute disaster. With the discovery of oil on Catan, its inhabitants face a new challenge: deciding whether the common good is worth limiting oil usage or whether the pursuit of victory is worth the risk of ruin.

Kind of disappointing and somewhat ironic in that the game is generally only played in countries that have reaped the benefits of using oil.

Winter is coming.

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