Sunday, July 30, 2017

Back from Western NY

https://www.nytimes.com/2017/07/29/opinion/sunday/texas-childbirth-maternal-mortality.html?_r=0
This is a commentary by Kristof about health care in America and specifically about Dr. Lisa Hollier, an obstetrician-gynecologist, who is campaigning for better health care for women and abortion law reform. The medical journal Obstetrics and Gynecology reports that the US ranks below every nation in the Organization for Economic Cooperation and Development, except for Mexico, in maternal mortality. Around the world maternal mortality has been reduced by almost half since 1990; the US is a notable exception, where maternal deaths have become more common.





https://www.nytimes.com/2017/07/29/opinion/sunday/when-life-on-earth-was-nearly-extinguished.html This is an article in the Sunday Review by Peter Brannen about mass extinctions. Brannen has a new book called "The Ends of the World." There's more to the title but it is about the "big five" mass extinctions and about large scale volcanism as the driver.  There is also a special issue of the journal Paleogeography, Paleoclimatology, Paleoecology, whose readers probably call it PPP. In the special issue, the point is made that volcanic releases of carbon dioxide "may have helped drive many of the most extreme die-offs in the earth's history."  Brannen calls the US exit from the Paris Agreement "hare-brained" and mentions that we are on pace for a 4 degree Celsius warming of the earth by the end of the century.


https://www.nytimes.com/2017/07/28/opinion/greenhouse-gas-emissions-trump-funding.html This is a commentary in the NYT about a U of Colorado science center lab that houses a high-precision mass spectrometer that is able to detect fossil fuel contribution to carbon emissions, a critical aid to reducing these emissions. The Boulder lab is one of the few labs with the equipment that is capable of precise enough measurements. The lab was also dedicated to monitoring global greenhouse gasses exclusively. In fact, if the proposed budget cuts to climate science are approved, the whole national greenhouse gas monitoring program may be at risk.




http://www.bbc.com/news/world-australia-37211349 This is an article from BBC news reporting that after ten years of administering the HPV vaccine, the death rate due to cervical cancer has decreased 50% . In the US the cervical cancer vaccine has not achieved the approval rating as elsewhere and the results are not as spectacular. There are still several thousand women who die from cervical cancer in the US. The vaccine given protects against two strains and is being replaced with a vaccine the protects against nine strains. Some types of oropharyngeal cancer - the cancers inside the mouth that are caused by these viruses.


Professor Ian Frazer at work in a hospital laboratory

https://www.nytimes.com/2017/07/31/well/no-crying-over-dry-eyes.html This is an article from the NYT about the perils of "dry eye" also known as keratoconjunctivitis sicca, which sounds more serious. Eye drops, sold over the counter, are mainly methylcellulose, but they prevent burning and protect the eye after sun exposure and long hours at the computer. Which brings up the functions of tears, the components of which include 1,500 proteins (who knew?). I'm going to start using my eyedrops today.


https://www.nytimes.com/2017/07/31/science/dogs-shelters-adoption-behavior-tests.html  This is an article from the NYT about the unreliability of dog obedience testing trials which determine whether the shelter dog is euthenized as a danger to people. Personal note: I adopted a shelter dog newly returned by the adopters after clamping its mouth (no blood) on a child's hand. The dog did nip a couple of people in the twelve years we had her (who were entering out house) but certainly would have been euthenized.  There is serious scrutiny being given the shelter tests which are now regarded as poor predictors of whether the dog will be violent since one of the false negatives (negatives can be considered worse for people than false positives because the positives are killed) resulted in a death. One of the points made in the article relates to the shelter environment itself as evoking aggression. One test of dog-on-dog aggression showed that dogs reacted more aggressively to a fake dog than a real one. Shelter staff could carefully observe the interactions between the dog and other dogs and shelter employees in order to make the life-or-death decision.




https://www.nytimes.com/2017/08/02/opinion/fda-smoking-nicotine.html This is an op-ed piece by Robert Proctor, a science historian, about nicotine addiction.A fascinating statistic: if the rate of present consumption of cigarettes continues until 2015, 17 million more Americans will die of tobacco-related illnesses. I wonder what the statistic would be if if no one smoked any more cigarettes. I always wondered why nicotine in consumables wasn't made illegal (tobacco lobby) and this article answered my (naive) question. The FDA is barred from requiring the removal of nicotine from cigarettes but they can mandate the reduction by 99%, so they are minimally, or non- addictive. The Goldilocks optimum is between 1 and 2 percent, by weight, which is addictive. Reducing by a factor if ten would make it very difficult for cigarettes to become addictive, and, if addiction did result, not hard to quit.

http://abcnews.go.com/Technology/wireStory/scientists-id-tiny-prehistoric-sea-worm-50-head-49013050 This is a piece from abc news about a report in Current Biology about the identification of the 4 inch long capinatator praetermissus fossil from the Cambrian explosion about 541 milliuon years ago. Scientists say these fossils are so different from any previously found that they represent not only a new species but a new genus, a grouping larger than species. It is an ancestor  of the worm grouping called arrow worms, which are abundant in the world's oceans.
In this illustration by Marianne Collins/Royal Ontario Museum shows a Capinatator praetermissus. Long before dinosaurs roamed the Earth, a bizarre creature swam the seas, a miniaturized prequel of “Jaws.” The Capinatator didn’t even have a face. Inst

https://www.nytimes.com/2017/08/02/science/gene-editing-human-embryos.html  This is a report from the NYT of a Nature  report on the use of a novel gene editing technique to remove a deleterious mutated gene from a human embryo. As used in the genetic engineering of human beings, this technique has received widespread scrutiny as it may lead to a new type of eugenics, in which people would pay for the inclusion of certain culturally valued traits and the exclusion of less valued ones. Scientists at the Oregon Health and Science Institute along with colleagues successfully fixed a mutation that affected the heart and leads to sudden death.



https://www.nytimes.com/2017/08/07/health/atheists-religion-study.html?_r=0 A report in the NYT about a study published in Nature Human Behavior about people's beliefs about religion. People were given a questionnaire asking them to indicate their religion (or lack thereof) and, given a description of a sociopath with gory criminal details provided, asked whether this person was religious or non. Overwhelmingly, most people chose "non." This is contrary to the actual religious affiliations of serial killers who have been studied, who are sometimes religious believers and sometimes not.




https://www.nytimes.com/2017/08/07/climate/climate-change-drastic-warming-trump.html The NYT obtained a copy of a climate change report saying the average US temperature has risen steeply since 1980, directly contradicting the assurances of President Trump and his cabinet. The report is a special section of the National Climate Assessment and the National Academy of Sciences has signed off on it but the president hasn't viewed it, or agreed to release it yet. A small difference in the global temperature makes a big difference. "The difference between a rise in global temperatures of 1.5 degrees Celsius and one of 2 degrees Celsius, for example, could mean longer heat waves, more intense rainstorms and the faster disintegration of coral reefs."


http://www.ledger-enquirer.com/news/business/article165833912.html This is an article from the inquirer about the attempt by the Army Corps of Engineers to keep an invasive species of carp out of the Great Lakes.  I have just completed a book called "The Life and Death of the Great Lakes" on the subject. The Asian carp abounds in the Mississippi and its tributaries but it would not take much to breach the barrier into the Great Lakes. The plan to restrict the invading fish includes technologies such as underwater noisemakers, electronic dispersal barriers (the book said that they already have the latter) and a new lock, costing $275 million. These measures would protect the Great Lakes fishing industry.

https://www.forbes.com/sites/judystone/2017/08/06/germs-on-your-kitchen-sponge-get-a-grip/#6cf94fb9746e This is an article from Forbes in response to a study publicized by the NYT cautioning people about the germs in their sponges. Forbes finds that the few microorganisms that survive sterilization  recolonize the sponges. One of the bacteria, Acinetobacter, causes infections in people who are in the ICU. There was no salmonella or campylobacter or other organisms that cauxe food poisoning. Conclusion: if you want to worry about catching an infection from an object: worry about your cell phone. In a study of 200 hospital workers, 95% of the phones carried nosocomial (hospital-acquired) infections, including MRSA.


https://www.nytimes.com/2017/08/09/science/dinosaurs-flying-mammals-squirrels.html?_r=0 Article by Carl Zimmer in the NYT reporting a Nature study of flying mammals in the Mesozoic, the Age of Dinosaurs, done at the University of Chicago.  In the 1990's paleontologists found entire fossils of mammalian skeletons containing even impressions of skin and hair. These and other newly found fossils allow scientists to draw in previously unknown branches of the mammal family tree. One skeleton, Volaticotherium, appears to have been able to fly.


https://www.nytimes.com/2017/08/10/health/gene-editing-pigs-organ-transplants.html  A report in the NYT of a Science publication about the increasing possibility of using pig organs in human transplantation. Piglets were created that had human organs with their DNA edited to remove diseases, like the pig version of the HIV virus and other retroviruses, that could be transferred to the human recipients of the transplants. This is an important development and carries forward the treatment of diabetes patients with pig pancreas cells and heart valves from pigs rescue heart disease sufferers. Animal rights activists should not be more concerned than they are with the many pigs raised for the human diet.

Sunday, July 9, 2017

In July

http://blogs.plos.org/scied/2017/06/28/the-trivialization-of-science-education/ This is a blog entry by Mike Klymkowsky about the trivialization of science education. Klymkowsky, a professor at the University of Colorado- Boulder, revs up the large engines including Socrates and Richard Feynman in his plaint about the abdication by colleges of their role in students' science literacy. Since most colleges and universities do require non-majors to take at least one science course with associated lab, does this requirement build in students a scientific vocabulary and understanding of methodology in order to approach and evaluate scientific issues critically? The fact that it does not has serious consequences to meaningful, as opposed to pretend, learning.




http://www.philly.com/philly/opinion/20170710_Poor_math_skills_lead_to_bad_politics_and_policy.html  This is an opinion piece from the Philadelphia Inquirer about math illiteracy. in 2003, the National Assessment of Adult Literacy  calculated that 1 in 5 Americans couldn't compute their weekly paycheck or a restaurant tip. The opinion piece suggests that the fact that our technologies can help us with some of these things makes us even more math-illiterate. The 2 million dollar error in the 2018 budget submitted by OMB is an example.


https://www.nih.gov/news-events/news-releases/scientists-replay-movie-encoded-dna
OK so I don't really understand this. This is a link to an NIH news release about a movie encoded in and played from human cells. In a report featured in this week's Nature, Seth Shipman and his group were able to insert into bacterial cells and retrieve from the cells the image of a human hand. After doing this they inserted one frame at a time into bacteria 5 frames of translated DNA of a racehorse in motion movie and then they sequenced the DNA to reconstruct the movie. They intend to use the DNA as a "molecular recorder" to study the brain.
For the first time, a primitive movie has been encoded in – and then played back from – DNA in living cells. Scientists funded by the National Institutes of Health say it is a major step toward a “molecular recorder” that may someday make it possible to get read-outs, for example, of the changing internal states of neurons as they develop. Neuroscientist Seth Shipman, Ph.D., of Harvard Medical School, explains the study.

https://www.washingtonpost.com/news/speaking-of-science/wp/2017/07/13/human-evolutions-biggest-problems/?utm_term=.a9a227f64517 This is a position piece from the Washington Post about Trump's explanation, written with a ghostwriter, of how high-status males with "kick-ass attitudes" (like Trump) "who didn't give a crap about what other people in the tribe thought" were able to have "top models" and the most beautiful women. The writer makes the point that "prosociality", caring about the tribe, enabled Trump's ancestors to survive. Trump also says that this is how it always was and will be but the writer again corrects him that nothing about evolution "always was and always will be", since evolution is not static.

https://www.nytimes.com/2017/07/12/well/move/high-intensity-workouts-may-be-good-at-any-age.html This is an article from the Well Column about how short, high intensity workouts (called interval training) are good for any age. This new study reported in the blog centers on older organisms. Mice equivalent to over 65 in human life span were "coaxed" through interval training (little treadmills). The mice that had done the interval study were in some ways "younger" than at the beginning of the trial. They had greater endurance and more muscle mass than the control animals.


http://www.latimes.com/science/sciencenow/la-sci-sn-larson-ice-sheet-20170713-htmlstory.html An article from the LATimes about the loss of an iceberg the size of the state of Delaware in Antarctica's Larsen C Ice Shelf. But a UCIrvine glaciologist reports that this is only the beginning. This collapse could possibly lead to the loss of the entire shelf, which may be decades away.



https://www.nytimes.com/2017/07/14/nyregion/seabird-deaths-long-island.html This article in the NYT is about an observation by a wildlife pathologist from the NY Department of Conservation about a type of shorebird that has been found dead on LI beaches in increasing numbers, an unusual observation. The great shearwaters nest on the of the world's most remote islands in the south Altantic before migrating to the waters off New England and Newfoundland. The bird carcasses, when autopsied, were thin and anemic, which leaves the question: why is their health so poor? Since these birds are very rarely seen, gliding up the Gulf Stream, and, after feeding in the Caribbean, passing Long Island, why were they off course? Possibly winds forced the birds over land.



https://www.nytimes.com/2017/07/17/health/india-south-asia-castes-genetics-diseases.html?_r=0 This is a NYT article reporting from a Nature Genetics publication about residents of Andhra Pradesh and Telangana in South Asia who can die if administered muscle relaxants due to a mutation in their DNA. An analysis of 2,800 people belonging to 260 South Asian groups showed 81 groups that had lost genetic variation more extreme than Ashkenazi Jews and Finns due to genetic isolation and interbreeding. This lack of genetic variation is due to what is called the founder effect, when a population expands from a small group of founders with resultant genetic similarities which can cause a high incidence of the inheritance of rare diseases.


https://www.nytimes.com/2017/07/11/well/live/the-gentler-symptoms-of-dying.html A NYT article about how organ failure, preceding death, shuts the brain down. Each of the major organs, according to the physician reporter, has the ability to shut the brain down, evoking symptoms not as readily discernible to a witness as the classic death rattle. The exception is "terminal lucidity", as described by biologist Michael Nahm, in which case there is a brief state of clarity preceding death.




https://www.theatlantic.com/technology/archive/2017/07/toaster-a-bit-more-button/534312/ From the Atlantic, a paean to the Breville toaster. The writer says that this device makes toasting bread "more quantitative".  He references the "a bit more" button, which allows the bread to raise up and have its degree-of-toastness appreciated.  This design element is part of the new culture which responds to the user experience, or "UX". To follow: coffins (just kidding.)
A Breville toaster with the "A Bit More" button