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 Post subject: from current journals as of 2017 07 10
PostPosted: Mon Jul 10, 2017 7:25 pm 
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American Scientist July-August 2017
First Person: Sheila Jasanoff
This is an interview with a professor of “science and technology studies” at Harvard. Her concerns are about the ethics of human germline editing. I was originally inclined to dismiss this as neoLuddite wowwoo, but she does make some interesting arguments about subtle effects; I still think she’s wrong but there are things to think about. She notes if you ask most people “if a new technique could be developed that would cure a condition causing early death in children or an irreversible condition in adults, should it be?’ most would say “Yes, of course”. However, she cites the idea that disabled people who have genetic illnesses (because their germlines weren’t edited in time) will now been seen as people who “should have been eliminated”. This might well be true, but the solution is to educate people about the condition, not eliminate the technology.
Sieve filters salt from seawater
A graphene sieve has been developed that will pass water molecules but not salts; this requires pores less than 1 nanometer. The problem of the sieve swelling in sea water was solved by an epoxy coating.
The two faces of nanotechnology
A review article on nanotechnology, starting out with a success story: the BIND-014 treatment uses a nanoparticle encapsulating the powerful chemotherapy drug docetaxel. The particle will only bind to a tumor, and then releases the drug. Although the example patient was apparently cured of metastatic ovarian cancer with this treatment, other results were mixed; the author notes many nanotechnology firms have folded (although overall nanotechnology profits continue to grow). The article describes the process for making nanoparticles as more like mechanical engineering than chemistry; in conventional chemistry, random motion brings molecules together and they bind to promote the lowest level of free energy. Nanotechnology positions reactants in “nanojigs” on a “nanoconveyor” and presses them together to assemble; I’m not sure this is really how it works but I suppose I have to take the author’s word for it. We had a thread on the possible deleterious effects of nanotechnology, and the article confirms the possibility, noting that nanoparticles have toxicological properties that are difficult to predict and potentially different from macro scale substances. As yet no nanomaterial with such deleterious properties has been identified, although there are lab reports that carbon nanotubes can cause various lung problems if inhaled (there is no epidemiological data to back up these studies as yet).
Bright Light or Blight Over Brighton
Henry Petroski describes “British Airways i360” (so called because it was funded by the airline), an observation tower in the resort city of Brighton, England. The tower has a number of unusual features; it has the largest height-to-diameter ration of any tower in the world (i.e., it’s extremely slender). A annular elevator brings tourists to the top of the 162 meter tower; each trip is called a “flight”. The structure has some pretty serious antivibration features to deal with wind. Some locals and architects criticized it as a “blight” on the Brighton skyline, but it’s been very successful financially.
Reexamining Lyell’s Laws
Charles Lyell introduced the uniformitarian principle in geology in 1830; this was the idea that all geology can be explained by application of the same processes geologists saw every day – gradual erosion and gradual mountain building. Lyell’s approach was in opposition to previous catastrophic theories – that geology was the result of the Biblical Flood, or massive volcanic eruptions, or encounters with comets. The article, authored by New York University biologist Michael Rampino, argues that Lyell was “fundamentally wrong” and catastrophes like the K-Pa asteroid impact are indeed important to geology. I’m going to turn around and say Rampino is “fundamentally wrong”, quoting Ambrose Bierce’s definition of “accident” from The Devil’s Dictionary:
Accident n.: An inevitable occurrence due to the action of immutable natural laws.

“Catastrophe” could have the same definition; asteroid motions are predictable; we just don’t see impacts on human time scales. On astronomical time scales, they happen with statistical regularity; there’s no essential difference between a grain of sand falling into a river and being carried out to a delta and a rock the size of a county hitting the Yucatan; it’s just a matter of scale.

Natural History July-August 2017
Gray Seals and White Sharks Meet Anew
There have been some threads about great white sharks (Carcharodon carcharias) being seen outside their “normal” range, a situation often attributed to climate change or some other human meddling. This article suggests that is correct in a sense; the human meddling involved was harvesting of gray seals (Halichoerus grypus), which were almost eliminated from New England (both Maine and Massachusetts paid bounties on them) until they were extinct as a breeding population in the United States (there were still gray seals breeding on Sable Island). It is suggested that the seals were a major prey item for great white sharks (seals are in other parts of the world) and sharks went elsewhere when the seals disappeared. It’s documented that both shark sightings and sightings of bitten seals have increased; the authors caution that a lot of the sightings come from commercial fishermen, and “fishing effort” has decreased, and therefore there may actually be even more great whites than estimated.

Sky and Telescope August 2017
News Notes
Cosmic Lens Provides Unique View
Type 1a supernovae are “standard candles” for astronomical distance measurements; they have a known intrinsic maximum luminosity; thus the apparent maximum luminosity allows calculates of the distance. A new supernova, SN2016geu, didn’t follow the rules; it turned out to be gravitationally lensed into a classic “Einstein cross”. Light from each of the four images took a slightly different time to get to Earth; that can be used to calculate the universe expansion rate, since you don’t have to assume that to calculate the distance to the supernova.

Science 30 June 2017
Déjà vu for U.S. nuclear waste
The authors, at George Washington University and Stanford, decry the U.S. performance on nuclear waste disposal and suggest an independent agency run by utility companies. It’s noted U.S. utility users pay $0.001/kWh for a nuclear waste disposal fund, which now contains $35G; the money hasn’t been used for waste disposal but instead offsets Federal debt. The authors note other nuclear countries – Canada, Finland, Sweden and Switzerland – use the utility-managed approach. They somewhat disingenuously note that “sustained opposition can derail projects”.
News in brief
Yellowstone’s grizzlies off endangered list
The Department of the Interior delisted Yellowstone grizzlies (grizzlies in the lower 48 outside Yellowstone are still on the list). The usual suspects are outraged. We had a related thread before, concerning wolves rather than grizzlies; in this case biologists commented keeping animals on the list after recovery “impugns the ESA and gives ammo to those who dislike the Act.” Even Science is a little disingenuous here, commenting that removing grizzlies from the list puts them under control of State wildlife agencies in Idaho, Montana and Wyoming and “could lead to legal grizzly hunting seasons”. Since only animals within Yellowstone National Park are off the list and hunting is prohibited in the park this is highly unlikely.
Neolithic stone ring site holds new surprise: a buried square monument
Avebury is the largest stone circle monument in the UK – much larger than Stonehenge. Excavations were underway in 1939, were abandoned due to WWII, and have now been resumed, showing a surprising square monument in the middle of the circles. This is unusual for Neolithic sites.
News in depth
Stem cell approach for cataracts challenged
Of some personal interest, since I had cataract surgery last week. The article reports success with stem cell replacement for infant cataracts. These are a difficult problem for conventional cataract surgery – removal of the natural lens and replacement with a plastic one – since a new lens starts to grow from the stem cells remaining behind in the lends capsule, resulting in an obstructive clump behind the implant. Since infants need vision – or at least light reaching the retina – for proper brain development, the traditional approach has been to remove the cataract and the lens capsule, then provide a replacement lens later. However, a Chinese team has claimed that they can restore a lens just by removing the cataract-ridden one and letting the remaining stem cells grow a new “perfectly formed, intact, transparent lens”. However, lots of ophthalmologists are dubious, claiming that a similar approach was tried as far back as the 1970s and never worked; others say the regrown lenses are cloudy (since they likely have the same mutation as the removed ones) and take too long to regrow. The Chinese team say they can solve both these problems.
Europe’s top court alarms vaccine experts
The European Court of Justice, not exactly known for scientific rigor in its decisions, has just rendered another one that is head-slappingly nuts, deciding that a French patient’s multiple sclerosis was caused by hepatitis B vaccine (the patient has since died from MS complications (the lawsuit was filed in 2006; the patient died in 2011; his family continued the suit). The article notes the decision was “jargon filled”, but the gist is that the burden of proof for medical product liability shifts from the plaintiff to the defendant, and “any abnormal and serious damage” to a recipient is reason to find a vaccine defective, regardless of population-level benefits.
European bee study fuels debate over pesticide ban
A cocktail of toxins
Country-specific effects of neonicotinoid pesticides on honey bees and wild bees
Chronic exposure to neonicotinoids reduces honey bee health near corn crops
A two-year field trial in the United Kingdom, Germany and Hungary yielded inconsistent results for neonicotinoid pesticides; honeybees did just fine in Germany but were harmed in Hungary (the UK bees had trends similar to Hungary, but not significant). Wild bees had “depressed reproductive potential” in all three countries. The usual parties have the expected comments. Note, longer note, and two full-length papers.
Policy Forum
Help, hope, and hype: Ethical dimensions of neuroprosthetics
We’ve had some threads about brain-controlled prosthetics before, including a link to a remarkable video that shows a quadriplegic pouring a liquid into a cup, picking up a stirrer form a container, and stirring it, all controlled by visualizing the results through a computer interface. The authors note that the devices may advance to the point that they are semiautonomous – making the source of an action difficult to identify. A hypothetical case might be a prosthetic advanced to the point where the user could initiate a whole series of actions just by thinking about the start of the sequence – for example, looking at a cup and thinking “pick that up” would initiate a whole series of action in the prosthetic without the user having to think “open hand – extend arm – rotate hand – close hand – retract arm”. Such a sequence might be perfectly appropriate if the target is a cup but much more problematical if the target is a baby. If something bad happens, is the prosthetic manufacturer responsible, or the user, or both? Another concern is “brainjacking” – if signals to a device are transmitted by WiFi, can a hacker intercept and take over?
Review Summary
Cellulosic biofuel contributions to a sustainable energy future: choices and outcomes
It’s noted that biofuels are part of almost all climate change mitigation scenarios, even though that actual benefits are unclear. Among the questions are: if planted on existing croplands, will biofuels increase food prices? Will they lead to the establishment of new croplands elsewhere? Will biofuel planting diminish biodiversity? Will biofuels need more water than the vegetation they replace? Will they need more nitrogen? It’s explained that appropriate choice of biofuel crops for their environment will solve these difficulties.
Estimating economic damage from climate change in the United States
This one made the MSM, usually as some variant of “climate change will hit Trump voters hardest”. The 12 co-authors, scattered around various institutions, assume a “business as usual” model for climate and predict results for the years 2080 to 2099, by county. Temperature, rainfall, carbon dioxide fertilization, “cyclone intensification”, and sea level rise are considered. As series of choropleth maps by county display the results: Agriculture yield (gains for the Pacific Northwest, losses for the South); Mortality (people die younger in the South, live longer in the North; Maine, Vermont and New Hampshire do very well); Energy expenditure (bad for the South); Low-risk labor (people who work inside) – mildly bad everywhere; High risk labor – very bad everywhere; Coastal damage – bad on the Gulf and Atlantic; Property crime (bad in the North; the explanation is cold suppresses property crime); Violent crime (bad everywhere); and total county GDP change (counties in the northern tier have increase of up to 13%; the South and Southwest have decrease up to 28%; Georgia looks really screwed.

Nature 29 June 2017
This Week
Image rights
According to the editorial, one in five images in published papers in the life sciences have been digitally manipulated. The Liebniz Institute on Aging recently reprimanded Karl Lenhard Rudolph for “failure to supervise his research group” when it found 8 “high-impact” papers with manipulated images. He was required to publish corrections, one paper was retracted, and is banned from funding for three years. Nature notes that some journals check all images, while others don’t check any; Nature runs “random spot checks” but is reviewing its practices.
This Week
Paper pirates
We had a thread on the Sci-Hub scientific paper pirate site. A New York district court awarded Elsevier $15M in damages for copyright infringement by Sci-Hub. The note observes it’s extremely unlikely Elsevier will be able to collect, given that Sci-Hub is based in in Kazakhstan, is a one-woman operation, and the operator is in hiding.
Evolution dropped
The Turkish high school curriculum is dropping evolution from the biology requirement, and total biology teaching will be dropped from three to two hours per week. Religion and ethics instruction will get the extra hour.
News in focus
Air-gun blasts kill plankton
Marine seismic surveys use “air guns” to provide the seismic signal; these emit a pulse of air (which the article calls a “blast”). It’s been known for a long time that these bother marine mammals, but now studies off Tasmania find that they kill copepods and planktonic larvae, out to at least a radius of 1.2 kilometers (that’s as far as they were sampled).
Water loss in plants mismeasured
Plants have pores, called stomata, that allow carbon dioxide to enter the plant for respiration – and allow water to leave. In the past, botanists have assumed that all water loss was through stomata, and used water loss to estimate CO₂ consumption and primary productive (since direct CO₂ measurements are difficult). However, research – originally done in the 1980s but receiving little attention until recently – found that there is significant water loss directly through the cuticle. This means, in turn, that the CO₂ concentrations inside plants have also been overestimated, which has implications for primary productivity calculations – and thus climate models.
Taxonomy: retain scientific autonomy
A response to an earlier thread about taxonomy and conservation. The correspondent notes “…taxonomy is an independent scientific discipline, not a service provider for conservation biologists and policymakers”, and that a species description is not different from any other scientific hypothesis and it is up to the taxonomic community to accept or reject the hypothesis.

Science 2 June 2017
News in Depth
Deep in a mine, earthquake gold awaits
There have been previous attempts to drill into an active fault, most recently the Alpine Fault in New Zealand. Now a previously unknown fault in South Africa is inviting another attempt. The fault produced a M5.5 earthquake in 2014 – the largest in South Africa in 50 years – and has the salient advantage that it runs below the world’s deepest mine, the Moab Khotsong; the drillers will only have to go an additional 750 meters to get to the fault from Level 95 in the mine. (It’s possible the earthquake was induced by mining operations, but unlikely; the mine has induced some small quakes in the past, but this one was not on the same level as the mine; was perpendicular to other faults; and is strike-slip, unlike previous induced quakes).
News Features
The Post-Op Brain
“So and so has never been the same after the operation” is a pervasive comment. The syndrome is called POCD, for Post-Operative Cognitive Decline; the evidence is anecdotal, and some anesthesiologists deny it exists. To further complicate things, there’s also anecdotal evidence that patients become mentally sharper after some operations, particularly bariatric surgery for obesity. Studies are underway, but it’s noted that many of the patients claiming POCD were elderly people in for heart surgery, and the mental decline may have started long before the operating room.

Science 12 May 2017
News in depth
Pinpointing HIV spread in Africa poses risks
In 1999, a geneticist in Scotland was served with a warrant demanding the HIV viral sequence data for one of his subjects. This matched the viral sequence from a woman he had had sex with – and whom he hadn’t informed of his HIV positive status. He was convicted and sentenced to 5 years in prison for “reckless conduct”. There’s an effort underway in Africa to sequence HIV from more than 12000 patients; this will allow identification of individuals who have spread the virus and “hot spots” for virus transmission. There’s concern that the test subject will be targets for law enforcement – homosexual behavior is illegal in many of the countries involved – and/or subject to blackmail if their identities are revealed. The project is making every effort to keep the data anonymous, but, as one put it, are in an “ethical minefield”; the project has great promise for health benefits but also might get some of the participants killed or imprisoned.
Pocket-sized sequencers start to pay off big
The cost and size of DNA sequencers is rapidly decreasing; for about $1000, you can now buy a device about the size of a cell phone that sequences DNA by reading distinctive changes in current as the bases pass through nanopores. The devices take multiple passes to sequence a complete genome, but the record is about 1/6 of a bacterial genome in a single pass. A researcher commented “Very, very soon anyone could sequence a genome anywhere”.
Policy forum
Myriad take two: Can genomic databases remain secret?
Myriad Genetics lost a Supreme Court case, invalidating its patents on BRCA1/2 genetic variants, which increase the risk of breast cancer. Myriad still has a large and proprietary database of genetic variants that it maintains under trade secret law, and thus continues to dominate the BRCA1/2 testing market. Last year, four individuals seeking access to personal data filed suit against Myriad under the HIPAA (supported by the American Civil Liberties Union), seeking four categories of data; the authors of this article, all at the Center for Medical Ethics at Baylor, say the suit constitutes an attempt to do an “end run” around trade secret law by forcing release of individual data that would be proprietary in the aggregate. The dueling laws are the HIPPA, which allows patients access to “individually identified information related to that patient’s health condition and care”; while the 2016 Defend Trade Secrets Act allows Federal lawsuits in cases of improper acquisition and disclosure of trade secrets. The raw data isn’t so much a concern; it’s the proprietary algorithms Myriad developed to interpret the data, which might arguably be considered “records necessary to interpret data” under HIPPA. The authors suggest, as you might expect, regulatory involvement, by giving the FDA authority to set a time period for “exclusivity” of diagnostics tests.
Review summary
Poor human olfaction is a 19th-century myth
The myth was promulgated by Paul Broca, who decided that the human olfactory system is impoverished at the expense of free will; Sigmund Freud later picked up on this and decided human weak olfaction contributed to mental illness. Here it’s pointed out that while the human olfactory system is proportionately smaller than many other mammals, it’s absolute size is larger; and human versus animal performance on olfactory tests depends strongly on the range of odors tested, with humans outperforming rodents and even dogs with some odors.

Nature 13 April 2017
Seven Days
Martian moon plan
The Japanese and French space agencies have announced a plan to bring back samples from Phobos and Deimos. The Japan Aerospace Exploration Agency will launch the craft in 2024 with an Earth return in 2029. The CNES will provide mission support, including and infrared spectrometer to scan for interesting minerals on the moons’ surfaces.
How the lizard gets its speckled scales
A living mesoscopic cellular automaton made of skin scales
Everybody has probably played John Conway’s Game of Life at one time or another; just in case you haven’t, it works by setting up a grid of “cells”, with each cell having an arbitrary initial state of “on” or “off”. With each cycle, a rule is applied turning cells “on” or “off” based on a mathematical function; in the original game this was relatively simple; an “on” cell was “live”, an “off” cell was “dead”. With each cycle any live cell with fewer than two live neighbors became “dead”; a “live” cell with two or three “live” neighbors remains “live”; a “live” cell with more than three “live” neighbors “dies”, and a “dead” cell with exactly three “live” neighbors becomes “live”. The “game” (not really a game”) makes fascinating patterns that move through the grid. The “Game of Life” is a specific example of a general category of “cellular automata”. Now herpetologists have discovered that the scale pattern of the ocellated lizard (Timon lepidus) obeys the rules of a cellular automata; chemical signals diffuse through the scales and cause color patterns dependent on the adjacent scales.


 Post subject: Re: from current journals as of 2017 07 10
PostPosted: Wed Jul 19, 2017 3:56 pm 
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Location: Surfing thru Cyberspace
Can someone explain how sieves work? In the case above, the sieve is selectively allowing the water molecules to squeeze through the opening in a single-file train of water molecules, leaving the salt behind. But why doesn't the salt molecule (or ions of Na and Cl) clog the opening of the sieve? I can't get this idea out of my head, so please help me see the light.

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


 Post subject: Re: from current journals as of 2017 07 10
PostPosted: Wed Jul 19, 2017 11:59 pm 

Joined: Fri Apr 04, 2008 10:45 am
Posts: 8205
scoob5555 wrote:
Can someone explain how sieves work? In the case above, the sieve is selectively allowing the water molecules to squeeze through the opening in a single-file train of water molecules, leaving the salt behind. But why doesn't the salt molecule (or ions of Na and Cl) clog the opening of the sieve? I can't get this idea out of my head, so please help me see the light.

My guess? The Na and Cl are, in fact, frequently plugging up the pores. But thermal motions tend to quickly jar them loose, particularly since they're almost always surrounded by a shell of water molecules (attracted to their ionic charge) that makes them effectively much larger than individual Na, Cl, or water molecules.

 Post subject: Re: from current journals as of 2017 07 10
PostPosted: Thu Jul 20, 2017 12:30 pm 
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Joined: Fri Apr 04, 2008 12:03 pm
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Location: Surfing thru Cyberspace
That helps a little. But I can see two such forces at work - the action of the water going through the sieve creates a flow (the train wants to keep going and the hydrogen bonds allow that to happen) but such a flow would have to bring along some of the ions, sucking them into the entry-point, clogging the sieve. But for how long?

The other force is the movement of the body of water being filtered. With enough agitation, I can see the salt ions being moved out of the way regularly. So I guess if we're looking at a micro-scale, the individual holes might get clogged and cleared regularly, but on a macro-scale the water is flowing pretty well as long as the movement in the body of water is enough to keep things moving. OK, now I'm better with the concept.

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


 Post subject: Re: from current journals as of 2017 07 10
PostPosted: Thu Jul 20, 2017 2:40 pm 

Joined: Fri Apr 04, 2008 10:47 am
Posts: 345
I'm unclear on how this is any different than Reverse Osmosis, besides being graphene instead of a plastic membrane. Does the sieve not require significant pressure on the seawater side to produce meaningful flow? I found a CNN article that was rather useless, and it linked to the actual paper. Which of course would only let me preview the 1st page. I didn't see any references to pressures, just the size of the "holes".

This might be an advance over current membrane technology, but it's still going to be energy intensive. Not like you'd be able to dip a graphene straw in the ocean and drink clean water from it.

 Post subject: Re: from current journals as of 2017 07 10
PostPosted: Fri Jul 21, 2017 6:38 pm 

Joined: Fri Apr 04, 2008 10:45 am
Posts: 8205
I don't see a difference, either. Unless electrical power rather than PdV work is being supplied to effect the separation; I haven't read the article closely.

And, of course, it will require just as much energy supplied as electrical power as when it's supplied as PdV work. I was musing this morning on why we call it Gibbs free energy; t'aint nothing free about it.

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