Everyone is curious to learn how their body works, but understanding the details can often be a daunting task. But a new children's book rises up to meet this challenge, and it does so admirably: Human Body Factory by Dan Green [Kingfisher – An imprint of Macmillan Children's Books, 2012; Amazon UK; Amazon US]

The author compares the human body to a factory filled with different departments (organ systems), each employing hundreds (thousands?) of workers busy with their own special tasks. Although this book does present anatomy, it focuses primarily on physiology -- the function -- of the human body, making it into an excellent companion volume to the book, Build the Human Body by Richard Walker, which focuses mainly on the body's structure. (Read my review.)

Detailed full-colour cartoons make this charming book into the "Where's Wally?" of the human body; where you'll discover amusing details such as the workers in dinghies mixing gastric juices in the stomach with a giant whisk, park rangers on the skin keeping things clean amongst glades of gently swaying hairs and sweat-gland sprinklers, or the worker hurrying to patch up a leaky blood vessel whilst a vampire lurks nearby, holding out an empty pitcher. As you explore the many "departments" that are essential to keep you functioning, you will learn interesting facts to share with your friends, such as what makes pee yellow-coloured, the number of bacteria residing in the average human mouth, and what is the body's largest organ.

Having taught anatomy & physiology in several universities, I was impressed by the accuracy and depth of scientific detail in this book. Despite being targeted to children, this charming book reminds me of Margaret Matt's and Joe Ziemian's excellent "Human Anatomy Coloring Book" that is often a recommended learning supplement for university biology and premed students.

This oversized hardcover is 48 pages long, and includes a glossary and index. A large full-colour poster summarising the material presented in the book is attached to the inside back cover. Shortlisted for the 2013 Royal Society's Young People's Book Prize, this book will provide hours of education and entertainment for children and adults alike! Highly recommended!

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece is slightly edited from the original, which was published on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. As a judge who helped select the 2013 Royal Society Young People's Book Prize shortlist, she also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on her eponymous Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

Sometimes, the best way to learn is to wrap your hands around stuff and ... build it yourself! This perhaps is never more important than when trying to learn anatomy, which is the reason that these courses include models and a "wet lab". But what if you don't have access to squishy things that you can cut up? This is where Richard Walker's accessible model/book kit, Build the Human Body, fills the gap [Templar Publishing, 2013; Amazon UK; Amazon US].

This oversized hardcover book is affixed to a cardboard box that contains 66 slotted pieces to a model of a human body, printed in full colour on heavy stock. The book is 32 pages long and contains full colour diagrammes and a useful index. The model is a 3-dimensional puzzle that focuses mainly on the human skeleton (although major organs are also included). This kit allows you and your child to learn the fundamentals about the human body whilst examining its structure. This kit is an excellent companion to another of the Royal Society's shortlisted books, Human Body Factory by Dan Green, which mainly focuses on physiology -- the function -- of the body. (Read my review.)

The only (potential) problem that I foresee is the size of the book/box: it's taller than the typical bookshelf and also fills up rather a lot of space. And trying to fit the individual pieces back into the box will consume far more time than assembling the human model took, so you may wish to store them in a zippered bag for future use. Either that or never take the model apart after you've finished it.

Shortlisted by the Royal Society's 2013 Young People's Book Prize, this kit beautifully overcomes one of the main challenges for teaching anatomy by embracing a build-it-yourself approach. The book is concise, well-written and engaging and the kit is accurate and educational, and will provide many hours of enjoyment as children and adults work together to build the human body.

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece is slightly edited from the original, which was published on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. As a judge who helped select the 2013 Royal Society Young People's Book Prize shortlist, she also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on her eponymous Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

Did you know that the bamboo lemur consumes enough cyanide daily to kill a human? ...that Paris green paint, which gets its colour from arsenic, was so toxic that it was used as a rat poison as well for painting masterpieces? ...that there is a lump of crystallised carbon (a diamond) that is 3,000 kilometers (1,865 miles) wide that weighs roughly 2.5 thousand trillion trillion tonnes in the core of a white dwarf star in the constellation Centaurus?

If you enjoy learning interesting facts such as these, then you will love Dan Green's informative book, Discover More: The Elements [Scholastic Children's Books, 2012; Amazon UK; Amazon US]. Although this is a children's book, it is so well written and researched that I think most adults will love it, too.

This large flexi-cover book is printed on heavy glossy paper, and is crammed with gorgeous full-colour photographs and rich graphics, clear and concise writing, and large, easy-to-read font. The book starts by describing what elements are and where they came from and then moves on to provide a close-up examination of each element, who discovered it and when, and discusses its historical and contemporary uses. More than just a recitation of dry facts, this lively book tells the story of each element and includes hundreds of remarkable facts that make it a joy to read. It also includes some basic "kitchen science" experiments that illustrate some of the concepts discussed in the book.

The book follows the periodic table groups and each section starts by asking several questions that are answered in the following chapter. I really liked the graphics that show what is happening at the atomic level when a reaction occurs, and I was impressed by the photo series of experiments that appear in this book, so the reader can see what happens when, for example, sodium is added to water. The book has 112 pages and includes a useful glossary and index.

Shortlisted for the 2013 Royal Society Young People's Book Prize, I highly recommend this informative and accessible book for children and for school libraries -- and even for adults who wish to painlessly review the chemistry they either forgot or never had the pleasure to learn.

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece is slightly edited from the original, which was published on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. As a judge who helped select the 2013 Royal Society Young People's Book Prize shortlist, she also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on her eponymous Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

Do you like flaps in your books? Even though I am an adult, I really like books with flaps. So knowing that, it's almost a foregone conclusion that I'd really enjoy Rob Lloyd Jones's new children's book, Look inside space [Usborne Publishing, 2012; Amazon UK; Amazon US]. That this is a children's science book makes it even better.

Have you wanted to explore the International Space Station? Well, now you can because this show-all book reveals the secrets of the space station -- yes, even how the toilet prevents astronauts from floating away when their trousers are wrapped around their ankles! Have you ever wondered what Earth looks like from space? This book shows you.

This hardcover book is filled with plenty of colourful drawings that illustrate all sorts of interesting facts about space -- everything from the birth of a star to what is in the middle of the Milky Way. This book also features a four-page fold-out centrefold of the solar system, complete with flaps so, for example, you can peek at the surface of Mars, see a close-up of Jupiter's Great Red Spot, and learn why spacecraft cannot land on one of the outer "gas giant" planets. It includes plenty of flaps under the flaps, so it contains a lot more information than what first meets the eye. I especially liked the last section, where kids asked space questions and the answer could be found under a flap.

Shortlisted for the 2013 Royal Society's Young People's Book Prize, this well-constructed and engaging book is interesting, accurate and highly interactive and is a wonderful introduction to space for young children.

.. .. .. .. .. .. .. .. .. .. ..

NOTE: This piece is slightly altered from the original, which was written and published by GrrlScientist on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. As a judge who helped select the 2013 Royal Society Young People's Book Prize shortlist, she also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on her eponymous Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

The complete shortlist for the 2013 Royal Society's Young People's Science Book Award.
Image courtesy of the Royal Society.

Are you a scientist who was inspired to pursue your passion after reading a children's book?

As a member of this year's panel of judges, I freely admit that I am jealous of children today – jealous because when I was a child, I had nothing close to this wealth of science books to read. In fact, I cannot remember reading any children's science books in my youth. As it was, from almost the moment I learned to read, I was reading science fiction. The only science-y book I remember reading as a child was Alfred Russel Wallace's engaging The Malay Archipelago, a book that strongly influenced my career choice and inspired my lifelong passion for the flora and fauna of the South Pacific. (I still own that book; it is a treasured friend that has traveled with me across continents.)

I can only wonder how my career choice may have differed if I'd had a mountain of books describing all areas of science available to me when I was young and impressionable. Would I have become a mathematician, as I'd planned during much of my teen years? Or a chemist, as I'd almost done when choosing which graduate programme to enroll in?

In preparation to meet with my fellow judges to choose the 2013 shortlist for the Royal Society's Young People's Book Prize, I read more than 40 children's science books in one month – easily more children's science books than I've read in my entire life up until this point. From this group of books, my fellow panelists and I had to choose the six that we thought were the very best – a difficult task! There were so many good books that our decision was challenging, and the meeting stretched later into the evening than the Royal Society had predicted it would.

"This year's books have shown how science can become the subject of beautiful poems, be the object of wonderful works of art, and all the time stretching minds, young and old, into the 'realms of imagination' and down-to-earth 'model building'," said this year's Chair of the judges' panel, Professor John Goodby FRS.

"Our eclectic collection of books have been truly enthralling, and our decisions on six candidates for 'book of the year' have been incredibly difficult," Professor Goodby continued.

"Now we turn to the real experts in our young judging panels to give us a definitive result."

The six shortlisted books are:

Build the Human Body by Richard Walker [Templar Publishing, 2013; Amazon UK; Amazon US]
The publisher says: The ancient Greeks had it right: "Know thyself." The editors at Silver Dolphin agree and believe that one of the keys to knowing thyself is knowing how the body works. "Build the Human Body" will teach you about the body's building blocks, help you build its framework, and show you how to map the body organs. Have fun while learning, and see the human body like you never have before through colorful illustrations, fascinating facts, and finally building your very own skeleton from the ground up. Everything you need to build your very own human skeleton is right here, ready to assemble at home or to take on the go.
-- This unique set includes a 32-page book full of colorful illustrations and intriguing facts about the human body, plus 66 slotted pieces to build a three-dimensional skeleton.
-- Explore the inner workings of the human body and learn what you're really made of.
"Build the Human Body" offers a unique building and learning experience as you piece together the human skeleton, bone by bone.
My fellow judges and I said: "A hands on, fun kit to help learn about the human body, accompanied by a well-illustrated, concise, clear book." (Read my review.)

Buzzing! by Anneliese Emmans Dean [Brambleby Books Ltd., 2012; Amazon UK]
The publisher says: This book is a cocktail of brilliant close-up colour photographs and fascinating information about the small yet amazing animals, especially bees, butterflies and other minibeasts, that we find in our gardens all accompanied by wonderful poems about the creatures themselves. Anyone from the age of five upwards will be enchanted by Anneliese's extraordinary insights and talent in bringing to life the world of the myriad tiny creatures that crawl and fly about us. Also, they will enjoy her sense of fun and wit, as revealed in her remarkable verse. Written for all young nature lovers, the book encourages readers to appreciate the natural world around them and help protect it. The Foreword is by the Bumblebee Conservation Trust.
My fellow judges and I said: "This book is buzzing with interesting science facts and wonderful poetry. Each page features a different British minibeast that you might find in your back garden, with a funny poem about them." (Read my review.)

Discover More: The Elements by Dan Green [Scholastic Children's Books, 2012; Amazon UK; Amazon US]
The publisher says: Discovering the elements is discovering life itself. What are we made of? What keeps us and our universe in motion? Everything we are, and see around us, and create, is made up of a little over 90 elements, many of which have existed since the beginning of time and space. This book is more than a walk through the periodic table. It explains the tremendous forces of star birth and death that create elements. It chronicles the history of their discovery and the impact of their science on every aspect of our daily lives, from medicine to technology, architecture to the environment. Beautiful photographs and modern graphics make apparently ordinary substances, their extraction and their changes look as extraordinary as they truly are.
My fellow judges and I said: "A good starting point for learning about the topic and full of rocking chemistry! Starting with what elements are and where they come from, the book goes through each element in turn with facts about their discovery and the science about how they impact our everyday lives." (Read my review.)

Don't Flush: Lifting the Lid on the Science of Poo and Wee by Richard & Mary Platt [Kingfisher – An imprint of Macmillan Children's Books, 2012; Amazon UK]
The publisher says: This book is a light-hearted, yet highly informative study of two of the most natural human resources in the world -- poo and wee. Throughout history, the products of our bladder and bowels have helped us to build houses, wash and dye our clothes, fertilize crops, treat illnesses, solve crimes, control pollution and create fuel, energy and explosives. These pages show you how, and tell you some fascinating stories at the same time. Illustrated with brilliantly fun artworks and endearing characters, you'll be entertained by wizards using 'magical urine', soldiers fighting with exploding piles of dung, wee-wielding beauty therapists and much more.
My fellow judges and I said: "A light-hearted but informative look at the science behind the use of poo and wee throughout history to build houses, wash and dye our clothes, fertilize crops, treat illnesses, solve crimes, control pollution and create fuel, energy and explosives. A perfectly disgusting book: Kids will love it!" (Read my review.)

Human Body Factory by Dan Green [Kingfisher – An imprint of Macmillan Children's Books, 2012; Amazon UK; Amazon US]
The publisher says: Human anatomy has never been as entertaining as this look at a day in the busy human body factory. From the CEO sending out orders in the brain to "waste" being sorted and delivered out of the body at the other end, the busy workers who keep everything running smoothly introduce each 'department.' All the major systems are covered, and the ingenious illustrations are packed with humorous details that kids will love to pore over. All of this amazing artwork is backed up with fascinating facts and clear explanations of the body's essential processes. Whether it's toxic signs and workers wearing biohazard suits in the large intestine, lab workers in dinghies mixing gastric juices in the stomach with a giant whisk, or park keepers on the skin keeping things clean among glades of gently swaying hairs and sweat-gland sprinklers, we promise that kids will never think about their bodies in the same way again.
My fellow judges and I said: "This book is intricately illustrated with tiny factory workers who explain how each part of the body works. It is the 'Where's Wally?' of the human body; you keep noticing comic little details such as the workers in dinghies mixing gastric juices in the stomach with a giant whisk! As well as being fun, we were also impressed by the level of accurate scientific detail. (Read my review.)

Look inside space by Rob Lloyd Jones [Usborne Publishing, 2012; Amazon UK; Amazon US]
The publisher says: This is a great fun flap book packed with interesting information about space, and the amazing things that float through it - stars, moons, comets, and the planets of our solar system. Each double-page spread has a stunning colour illustration, and several flaps to lift to find out more about what's going on in the scene - such as what goes inside the International Space Station, how astronauts visited the Moon and what they did there, as well as the history of astronomy, from Galileo to the Hubble Space Telescope.
My fellow judges and I said: "A fantastically interactive book for younger children. Full of flaps to lift (and flaps under flaps) that reveal amazing facts about space!" (Read my review.)

Now that the shortlisted six have been selected, they are at this very moment being boxed up and mailed out more than 100 groups of children across the UK who will make final choice for this year's grand prize winner. So if you are a member of a reading group who is choosing your favourite, these books will be arriving very soon in the post.

The Young People's Book Prize celebrates the best English-language books that communicate science to young people up to age fourteen. These books had to be published in the UK within the previous year.

The winner will be announced on 11th November 2013.

My fellow judges were a witty, clever and supremely qualified group of people whom I was lucky to meet:

• Professor John Goodby FRS – Chemist at the University of York researching liquid crystals.
• Dr Jenny Read – University Research Fellow at the Institute of Neuroscience at Newcastle University researching visual perception.
• Shazia Lydon – Assistant Headteacher at Challney High School For Boys, Luton.
• Simon Watt – Science communicator and presenter of Inside Nature's Giants on Channel 4.
• And yours truly: GrrlScientist - an evolutionary biologist, ornithologist and science blog writer for the Guardian.

The Royal Society and all my fellow panelists are grateful to the generous support provided by an anonymous donor for this very important prize. So now we are turning the show over to the true experts -- children -- to learn their decision!

"WOOT! We can't wait!"

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece was edited slightly from the original, which was posted on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. As a judge who helped select the 2013 Royal Society Young People's Book Prize shortlist, she also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on her eponymous Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

So many of them I hadn’t thought about for years, people from my early years as a doctor. I certainly remembered Syd, because I still cared for his wife. I also cared for his adult his children, who would also have to be struck off. I made a note of it. There was Mary, who was old, toothless and wonderful. She had grown up picking tobacco and cotton and didn’t much like it, but would still go south to visit her sisters and brothers every year at the family home. There was a Holocaust survivor who watched her greatest tormenter executed by an American soldier. There were so many names.

It’s easy to be forgotten when you’re dead, at least by those who weren’t used to your daily presence. I saw these people in sickness and in health, caring for them in the office and the hospital, but went home every day to my own family, putting as much of work out of my mind as was possible. But here they were, on a computer screen, glowing memories, daring me.

So I read each one, tried as hard as I could to remember them, remember the living things about them, remember that Jack liked to play tennis and make love, that Carole hated her kids. I pictured the lives they led while not in my exam room, lives full of the dull facts that make up a day, a life: making tea, having beer with friends at the corner bar, playing golf. Or worse, holding young children, saying long goodbyes to people who would have to grow up without you.

I struck off each name, the bytes disappearing from the list, shortening it significantly. I hoped that people remembered them all, the good, the bad, the silly. I would do my part; I would try. But I will strike them off just the same, making room for the living who need me more.

If you are thinking that date sounds a bit familiar, you’d be right: that jerk is the signal of the massive magnitude 9.3 earthquake that ruptured a 500 km length of the Sunda Trench off the coast of Indonesia on Boxing Day 2004, and unleashed a devastating tsunami.

What’s impressive is that we are seeing permanent deformation of the crust due to motion on a fault (what is known as coseismic deformation) an extremely long way away. As we can see on the map below, the Indian GPS station IISC is some 2,300 miles away, and the Taiwanese station TNML is 3,600 miles away, from the Sunda Trench. And yet, even at that distance, the Sumatra-Andaman earthquake shifted the land beneath these points about a centimetre – a little less for the Taiwan, a little more for India.

The figure above also compares the actual motion observed with GPS (black arrows) with predictions from a model of the Boxing Day rupture (grey arrows). What this figure doesn’t show is the predicted coseismic deformation at places not occupied by GPS stations. Fortunately, a paper just published in the Journal of Geophysical Sciences contains a much nicer visualisation of the output of a similar model. This model – rather mind-blowingly – indicates that the Sumatran-Andaman earthquake rupture directly deformed a sizeable fraction of the Earth’s surface, including Africa, Arabia, the eastern half of Asia, and most of the Americas.

Paul Tregoning and his co-authors have gone on to calculate the cumulative coseismic deformation resulting from all 15 magnitude 8 or greater earthquakes that have occurred since the turn of the millennium on the Earth’s surface. Unsurprisingly, the big three earthquakes in this period – the Sumatra-Andaman, the magnitude 9.1 Tohoku earthquake in March 2011, and the magnitude 8.8 Chilean earthquake in February 2010 – are the major contributors, but the smaller ones fill in some gaps in the southwest Pacific.

Modelled global coseismic deformation due to all M 8+ earthquakes since 2000, from Tregoning et al., 2013

Basically, outside of western Europe and the Arctic Circle, pretty much the entire surface of the planet has been shifted at least a millimetre or two by an earthquake since the turn of the millennium. And this has real world consequences. The interiors of the Earth’s tectonic plates are generally assumed to be rigid and undeforming, and are used as a fixed reference point for measuring deformation at the plate boundaries. The red arrows in the figure above show exactly how much you’d be wrong if you are assuming that for a given point on the Earth’s surface. Even when you’re a long way from a plate boundary, coseismic deformation from distant, large earthquakes is causing your ‘fixed’ reference point to be not so fixed. Spooky tectonic action at a distance, indeed.

References

Corné Kreemer, Geoffrey Blewitt, William C. Hammond, & Hans-Peter Plag (2006). Global deformation from the great 2004 Sumatra-Andaman Earthquake observed by GPS: Implications for rupture process and global reference fram Earth, Planets, Space, 58 (2), 141-148

Tregoning, P., Burgette, R., McClusky, S., Lejeune, S., Watson, C., & McQueen, H. (2013). A decade of horizontal deformation from great earthquakes Journal of Geophysical Research: Solid Earth, 118 DOI: 10.1002/jgrb.50154

Scarlet macaw, Ara macao, in flight.
Image: Tambopata Research Center. [NOTE: This image has been altered; it has been cropped.]

After many years of research into the behaviours, diseases, genetics and life history of scarlet macaws, a team of scientists have taken their studies to the next level. Christopher Seabury, an Assistant Professor of Genetics at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, and Ian Tizard, Director of the Schubot Exotic Bird Health Center and a Professor of Microbiology & Immunology at Texas A&M University's college of Veterinary Medicine and Biomedical Sciences, spearheaded an international collaboration of scientists that sequenced the genome of the scarlet macaw, Ara macao. This work significantly expands the range and depth of research opportunities involving scarlet macaws and other parrots. In addition to important conservation applications, this research may provide insights into the genetics that contribute to key traits of parrots, such as cognitive and speech abilities as well as longevity.

Scarlet macaws are large and showy parrots with brilliant red, yellow and blue plumage and long pointed tails. Endemic to Central and South America, this impressive neotropical parrot occupies a large range from southeastern Mexico throughout the Amazon basin region of Peru, Bolivia and Brazil. Easily trained to do complex tasks and to mimic human speech, wild scarlet macaws have been persecuted by the caged bird trade. Additionally, their preferred habitat of lowland evergreen rainforests makes them vulnerable to deforestation and habitat destruction.

To do this work, Drs Seabury and Tizard and their team obtained a blood sample from an adult female scarlet macaw known as "Neblina" who resides at the Blank Park Zoo in Iowa. A wild-caught parrot from Brazil, Neblina had been seized in 1995 by the US Fish and Wildlife Service after she illegally entered the United States.

Unlike mammals, avian red blood cells are nucleated, so a small sample of whole blood from a bird is an excellent source of DNA for molecular, chromosomal and cytological studies. Some cells were grown in cultures so the intact chromosomes could be harvested and examined whilst DNA was extracted from other cells for sequencing. These gene sequences were then assembled into the complete scarlet macaw genome by Seabury and his team.

Similar to almost all vertebrates, scarlet macaws are diploid; having two copies of each chromosome type, one contributed by each parent. Like all birds except birds of prey (Falconiformes), parrot genomes contain macrochromosomes and a larger number of microchromosomes.

Macrochromosomes are what most people think of when they hear the word "chromosome" and they are the type of chromosomes that are typically found in mammals. Macrochromosomes, which include autosomes and sex chromosomes, are large -- generally more than 40 megabases (Mb) in size (1 megabase is 1,000,000 nucleotide basepairs in length).

Microchromosomes, on the other hand, are very small -- usually less than 20 Mb in size. Due to their small size, microchromosomes are often impossible to distinguish when creating a traditional karyotype, as you see in Figure 1 (larger view):

Figure 1. Consensus Scarlet Macaw (Ara macao) Karyotype.
Scarlet macaw diploid chromosome number is 2n=62–64, as inferred from chromosome counts of multiple cells derived from three individuals, including the sequenced female macaw (Neblina). All investigated scarlet macaws had 22 macrochromosomes, which included 10 pairs of autosomes and the sex chromosomes, and approximately 40–42 microchromosomes. [doi:10.1371/journal.pone.0062415.s019]

Scarlet macaws have somewhere between 62 and 64 chromosomes; including 22 macrochromosomes (10 pairs of autosomomes and two sex chromosomes) and between 40 and 42 microchromosomes.

To identify similar regions between scarlet macaw and chicken macrochromosomes, the team used chromosome painting. This method uses fluorescently labeled chromosome-specific DNA probes that hybridise to complementary DNA regions, thereby identifying macaw chromosome regions that are similar to chicken chromosomes (Figure 2; larger view):

Figure 2. Chicken-Scarlet Macaw (Ara macao) Comparative Chromosome Painting (ZooFISH).
Using chicken flow sorted macrochromosomes (GGA1-GGA9) as well as GGAZ and GGAW, the homologous chromosome segments of the scarlet macaw were established via fluorescent in situ hybridization. [doi:10.1371/journal.pone.0062415.s019]

As expected, the final completed scarlet macaw genome shows similarities to that of the domestic chicken. However, there are a number of important differences, which are to be expected since parrots and chickens (taxonomic order: Galliformes) diverged approximately 122–125 million years ago. For example, several macaw macrochromosomes (1, 6 & 7) show significant rearrangements. The sex chromosome W shows no similarities at all between chicken and macaw, indicating that this chromosome is changing rapidly and thus, has not been conserved across such a large evolutionary distance.

As typical for other avian genomes studied so far, scarlet macaw genomes are smaller than mammalian genomes.

"The final analysis showed that there are about one billion DNA bases in the genome, which is about one-third of that found in mammals," Dr Tizard explained in a written press release.

"Birds have much less DNA than mammals primarily because they do not possess nearly as much repetitive DNA."

Repetitive DNA has no currently known function. The amount of repetitive DNA varies greatly between taxa: for example, more than 50 percent of the human genome is repetitive DNA [doi:10.1038/nrg3117].

According to Dr Seabury, comparing the scarlet macaw genome to other avian genomes will provide scientists with a better understanding of avian biology.

"The Scarlet Macaw Genome Project opens a variety of doors ranging from modern forensics to determining how the macaws utilize their natural habitat and landscape, as inferred from variable genetic markers," said Dr Seabury in a written press release.

In addition to research into evolution and population genetics, and conservation biology applications, what can we learn from the scarlet macaw's genome? First, even though birds have higher metabolisms than mammals, they enjoy much longer life spans than do mammals with the same body mass. In the case of scarlet macaws, adults weigh somewhere between 1000 and 1200 grams (roughly 2.2 pounds), and they reach sexual maturity at 5 years of age, yet their life span rivals that of humans. By comparing avian genomes to those obtained from other animals, it may be possible to identify which genes contribute to birds' remarkable longevity.

Other genes of interest are those involved in heart and cardiovascular fitness, and those that contribute to the risk for diabetes. But perhaps most interesting are those genes involved with cognition and brain size.

"A preliminary analysis of their genome suggests that [macaws] have a lot of genes involved in brain development", said Dr Tizard in a video press release. "Which fits, knowing how smart they are."

Despite differences from humans in brain development and structure, macaws are much like humans: they are very intelligent and live in highly complex social groups. Additionally, when corrected for differences in body size, macaws' brains are twenty-one percent larger than those of zebra finches, Taeniopygia guttata, which are the model system for vertebrate learning and memory. Thus, comparing the scarlet macaw, zebra finch and human genomes could provide greater insight and understanding into important genetic differences in brain development, structure and volume.

NOTE: this piece is slightly edited from the original, which was published on the Guardian.

Sources:

Seabury C.M., Dowd S.E., Seabury P.M., Raudsepp T., Brightsmith D.J., Liboriussen P., Halley Y., Fisher C.A., Owens E. & Viswanathan G. & Tizard, I.R. (2013). A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao), PLoS ONE, 8 (5) e62415. doi:10.1371/journal.pone.0062415.s019

TAMU written and video press releases.

Also cited:

Treangen T.J. & Salzberg S.L. (2012). Repetitive DNA and next-generation sequencing: computational challenges and solutions, Nature Reviews Genetics 13: 36-46. doi:10.1038/nrg3117

Ried T., Schröck E., Ning Y. & Wienberg J. (1998). Chromosome painting: a useful art, Human Molecular Genetics, 7 (10) 1619-1626. doi:10.1093/hmg/7.10.1619 [OA PDF]

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. You can follow Grrlscientist's work on facebook, Google +, LinkedIn, Pinterest and of course, on twitter: @GrrlScientist

Congrats to @Allochthonous for “Best Physics, Astronomy, or Earth Science Post”: http://t.co/em4cxUTWcl

May 14, 2013 10:24 am via webReplyRetweetFavorite

@SciSeeker

ScienceSeeker

Check out the announcement on the ScienceSeeker blog for full details and links to the winning posts in other categories; there’s some good – award winning! – reading there.

My winning entry was my response to the verdict in the L’Aquila trial, where I argued that earthquake safety is about door locks, not fire alarms: in other words, whatever the dubious merits of the trial and conviction itself, it highlights a worrying focus on short-term warnings (which we can’t do) at the expense of long-term preparedness (which we can do, at least in theory).

It’s an important discussion, so in addition to being happy that the work and thought I put into writing the piece has been recognised, it’s nice to think that a few more people who otherwise wouldn’t have read it will end up doing so. Also, in a phase of my life where I’m having to adjust juggling my blogging with several new personal and professional commitments, it’s a nice incentive to keep it up.

Anyway, whilst I bask in the kudos and the shiny glory of my pretty winning badge (and some prize money to help keep my web host hosting), my thanks to ScienceSeeker for organising the awards (and letting geosciences take over the physics and astronomy category after some vigorous feedback on Twitter), the judges for reading and liking, and fellow All-geo blogger Simon Wellings for putting my name forward.

Dung beetle, probably Neomnematium sevoistra, in dry spiny forest close to Mangily, western Madagascar.
Image: Axel Strauß, 2008 (Creative Commons Attribution-Share Alike 3.0 Unported, 2.5 Generic, 2.0 Generic and 1.0 Generic licenses).

Today's video focuses on the dung beetle, those insects in the taxonomic superfamily Scarabaeoidea. These insects share a fondness for feces, subsisting either partially or entirely on animal dung. Scarabs are coprophagists -- shit eaters. There are more than 5000 species of dung beetles, and although they are found on every continent except Antartica, nearly all of them occur in warmer and moister regions of the world. They devote their adult lives to locating, collecting and secreting away the dung of animals. Most scarabid species specialise on the dung of one or a few animal species, and they prefer the droppings of herbivores to those of omnivores, and both are preferred to the turds produced by meat-eating animals.

This specialisation has led to problems. For example, after cattle were introduced to Australia, parts of that continent were plagued by huge swarms of flies that laid its eggs on cow shit during the summer months. Since the resident dung beetles specialised on marsupial turds, cattle poop remained untouched and over the years, vast areas were transformed into a giant, nearly continuous cow pat. Taking advantage of this situation, flies rapidly grew into pestilential swarms. In the 1970s, 20 or so species of African dung beetles were introduced to deal with the problem, which then reduced the number of flies by as much as 90 percent.

Ancient Egyptians celebrated scarabs for their diligence and industry and indeed, a single elephant turd, which can weigh in excess of three pounds (roughly one-and-a-half kilos), is typically dispersed within just a few hours by tens of thousands of these insects. Even today, dung beetles are admired: for example, the New York Entomological Society uses a scarab in its logo, replacing its prized dung ball with the planet Earth -- make of that what you will (right).

Although some beetles simply drag away bits of fresh poop and deposit them in waiting subterranean chambers, many dung beetles form their prized poop into a ball, which they then roll away, pushing with their front legs and using their hind legs to hold the ball as it spins on an invisible axle. Some species work as a team, and in other species, the male does the poop-pushing whilst the female catches a ride on top.

After the dung ball has reached its burial chamber, the female lays one or more eggs inside (this differs between species, of course), and when the larva hatches, it is surrounded by dinner. In some species, the adults remain with the dug ball to protect their growing brood, a form of parental care.

Sometimes, dung beetles get lost, which is probably not difficult when standing on your front legs to push a dung ball around. When this happens, the beetle stops rolling, climbs aboard the dung ball and orients itself by observing the sun, moon and polarised light. At night, they orient themselves using the Milky Way -- making them the only animal (beside humans) to use the Milky Way to navigate [doi:10.1016/j.cub.2012.12.034].

This charming video shows us a little more about dung beetles:

Cited:

Dacke M., Baird E., Byrne M., Scholtz C. & Warrant E. (2013). Dung Beetles Use the Milky Way for Orientation, Current Biology, 23 (4) 298-300. doi:10.1016/j.cub.2012.12.034

You may enjoy this excellent and charming book Merde: Excursions into Scientific, Cultural and Socio-historical Coprology by Ralph A. Lewin [Aurum Press Ltd, 2000; Amazon UK; Amazon US]. Chapter 12 deals specifically with dung beetles. This fact-filled book is amusing and educational and its chapters are just the right length for reading whilst perched atop the porcelain throne.

NOTE: this piece was slightly reformatted from the original, which was published on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. You can follow Grrlscientist's work on facebook, Google +, LinkedIn, Pinterest and of course, on twitter: @GrrlScientist

Sadly, the internet has conspired against us, with not one but two fascinating new sources of procrastination for us. First, we heard about Google Earth Engine’s processing of several decades’ worth of Landsat imagery to produce a 30 year timelapse archive for the entire Earth’s surface. Time Magazine unveiled it to the world, and on the discovery that the whole world (or, at least, the non oceanic parts of it) were accessible at Google Earth Engine, we happily started exploring to find our favourite examples of geological and anthropogenic evolution in action, as the Storify embedded at the bottom of the post demonstrates. Several examples may make it into future lectures.

http://youtu.be/jHz5kMMavas

Then, just when we thought is was safe to return to the internet, Jennifer Wade just had to introduce us to GeoGuessr, which drops you into a random location on Google Street View and asks you to guess where in the world you are. You get 5 turns, and you are scored based on how close you get. Click through at your own risk – it’s very addictive!

Their ideal is the experiment that, in one session, shoots down a claim cleanly and neatly. So let’s bring in dowsers who claim to be able to detect water flowing underground, set up control pipes and water-filled pipes, run them through their paces, and see if they meet reasonable statistical criteria. That’s science, it works, it effectively addresses an individual’s very specific claim, and I’m not saying that’s wrong; that’s a perfectly legitimate scientific experiment.

I’m saying that’s not the whole operating paradigm of all of science.

Plenty of scientific ideas are not immediately testable, or directly testable, or testable in isolation. For example: the planets in our solar system aren’t moving the way Newton’s laws say they should. Are Newton’s laws of gravity wrong, or are there other gravitational influences which satisfy the Newtonian equations but which we don’t know about? Once, it turned out to be the latter (the discovery of Neptune), and once, it turned out to be the former (the precession of Mercury’s orbit, which required Einstein’s general relativity to explain).

There are different mathematical formulations of the same subject which give the same predictions for the outcomes of experiments, but which suggest different new ideas for directions to explore. (E.g., Newtonian, Lagrangian and Hamiltonian mechanics; or density matrices and SIC-POVMs.) There are ideas which are proposed for good reason but hang around for decades awaiting a direct experimental test—perhaps one which could barely have been imagined when the idea first came up. Take directed percolation: a simple conceptual model for fluid flow through a randomized porous medium. It was first proposed in 1957. The mathematics necessary to treat it cleverly was invented (or, rather, adapted from a different area of physics) in the 1970s…and then forgotten…and then rediscovered by somebody else…connections with other subjects were made… Experiments were carried out on systems which almost behaved like the idealization, but always turned out to differ in some way… until 2007, when the behaviour was finally caught in the wild. And the experiment which finally observed a directed-percolation-class phase transition with quantitative exactness used a liquid crystal substance which wasn’t synthesized until 1969.

You don’t need to go dashing off to quantum gravity to find examples of ideas which are hard to test in the laboratory, or where mathematics long preceded experiment. (And if you do, don’t forget the other applications being developed for the mathematics invented in that search.) Just think very hard about the water dripping through coffee grounds to make your breakfast.

“If you’re not on a fault zone, a volcanically active zone, or a tsunami zone, you’re probably in a valley that’s prone to flooding or having things tumble down the hills towards you.”

So opines risk consultant Tony Taig in this excellent article on how the approach to managing seismic risk in New Zealand is changing in the aftermath of the earthquakes that caused so much damage in Christchurch in 2009 and 2010. Of particular note is New Zealanders’ growing realisation that where they build things is just as, if not more, important as how strongly they build them; and that in New Zealand, there is very little ‘where’ that qualifies as truly safe. The article uses the example of Christchurch’s Port Hills region, where the impact of the strong shaking from the magnitude 6.3 earthquake in February 2011 was multiplied by many buildings on top of, and below, steep cliffs that collapsed and loosed heavy boulders during the quake.

This brings up an important facet of how we need to think about the risks posed by earthquakes and other natural hazards to peoples’ lives and livelihoods: assessing the potential impact of these events solely in terms of their size and recurrence interval is only part of the story. Not all severe events are created equal: a magnitude 7 earthquake in the wilds of Siberia is a very different proposition from a magnitude 7 earthquake close to a large city. Or, in a more topical example, the likely destruction wrought by a magnitude 7.8 earthquake is much greater when the rupture occurs 15 km below the surface, as was initially reported for the recent earthquake in southeast Iran, than the 50–80 km depth that it actually seems to have occurred at. It’s all about location, location, location: the worst disasters occur where big natural hazards intersect with places where a lot of us live.

I’ve been toying with how to represent this graphically, by defining events both in terms of their intrinsic severity (with a shallow magnitude 8 earthquake and a 100-year flood being more severe than a shallow magnitude 7 earthquake and a 50-year flood, respectively) and the exposure of human populations and infrastructure (such as cities, roads, and nuclear power stations). In other words, how many of us, and how much of our stuff, are found within the zone impacted? Plotting these two values on separate, orthogonal axes produces a square or rectangle whose area represents the total human impact of an event. A big square means a large impact, of course, but a nice feature of this representation is that it clearly illustrates how if the exposure is large enough, the overall impact of a moderately severe natural event can be just as significant as a more intense event that occurs in an area with less exposure. Conversely, two events of equal magnitude can end up having very different overall impacts, simply by virtue of their different locations.

The total human impact of a natural disaster is controlled both by the severity of the event, and how much of our stuff is in the way (exposure). In an area with high exposure, even a moderate severity event can have a large impact.

But this representation ignores another factor that affects the overall impact of a natural disaster. Compare a magnitude 7 earthquake near a large city with strong building codes and high public awareness (say, Christchurch), and a magnitude 7 earthquake beneath a city with many poorly constructed buildings and limited public awareness (say, Port-au-Prince). The different resilience of the two populations and infrastructures will greatly boost the impact of the latter event compared to the former, even if the exposure of these events is roughly the same. To show this we need another axis: one that represents the variable resilience of different parts of the world to their particular brands of geological destruction. To really work with the other two axes, it actually needs to be the inverse of resilience – ‘antiresilience’ (or the much more elegant ‘vulnerability’, as suggested in the comments below); – so that a small value corresponds to a robust, well prepared area where the impact is lessened. With these 3 axes in play, instead of a square that increases in area with increasing impact, we get a cube that increases in volume.

The resilience of an area to a hazard is also an important control, meaning that events of the same severity can have very different impacts.

Resilience is going to be at least partially controlled by event severity; for example, any building will be less resilient to stronger shaking in a large earthquake than it will be to weaker shaking by small tremors. But the key point is that for events of similar severity, there will be stark differences in the average resilience of buildings in Christchurch compared to Port-au-Prince. Leading to the greatly different impacts we have seen in these cities as a result of magnitude 7 earthquakes. Another way of thinking about this is that there is probably a threshold beyond which any defences or preparations for a natural disaster are totally overwhelmed and antiresilience gets very large, but this threshold will probably tend to be higher in well protected and prepared places.

Let’s consider last month’s seismic events in Iran and China. The magnitude 6.3 Zagros earthquake on 9th April was shallow enough to cause strong shaking in the area close the epicentre. it occurred in an area of fairly low population density, which reduced exposure, but what buildings were there had extremely low resilience to shaking (or high antiresilience). Result: At least 37 dead and almost 1000 injured. The magnitude 7.8 earthquake that struck the other side of the country a week later was more powerful, but also deeper; this reduced the shaking intensity above the epicentre, even though the earthquake was felt over a much wider area. This is also a fairly sparsely populated region with non-earthquake resilient buildings, and reports indicate at least 36 dead and 150 injured, mostly in Pakistan. It seems the impact of the 2 Iranian quakes was roughly equivalent, despite the higher magnitude of the second event – and arguably the stronger earthquake had less impact than the smaller one. Then we have the magnitude 6.6 in China on 20 April. It was shallow, so there was strong shaking, and resilience was again fairly low, but when you factor in the much greater population density in Sichuan Province, it becomes much clearer why the impact of this event – 200 dead, and 11,000 injured – was so much higher.

The earthquake in China was not the biggest in terms of magnitude, but as a shallow event in an area with high population density and relatively low resilience, it was the most significant in terms of human casualties and damage.

So thinking in these terms helps us to understand why it is not always the most powerful events that are the most destructive, if a more moderate event occurs in the wrong location. It can also help us look forward: we can identify the places most at risk from high impact events, by combining our (imprecise) knowledge of the occurrence and likely severity of natural hazards in an area, the exposure to such events, and an assessment of how we and our infrastructure will stand up to them. Obviously I’ve mainly been talking about earthquakes, but I think it will work for other hazards as well.

Magpie.
Image: acrylic painting by Shelli Ogilvy (2008).

Do you wish to share your love of birds, art and books with (your) children? If so, then you will really enjoy the Alphabet Bird Collection, a lovely children's book that was written and illustrated by Shelli Ogilvy [Sasquatch Books, 2009; Amazon UK; Amazon US]. This beautiful book is designed to teach children the alphabet whilst also teaching them a few things about birds.

Suitable for adults to read aloud to young children (ages 3+) or for older children to read themselves (if they haven't already memorised the entire book from frequent re-readings!), each letter is presented on two colourful facing pages in this hardcover book. One page features a painting of a bird whose name begins with the featured letter of the alphabet (see top) and the facing page includes a rhyming couplet about the bird along with a few interesting life history details. For example:

At dusk you might see from under the eve,
Nighthawks hunting, as they bob and weave.

In the evening Common Nighthawks come out to feed. Their large mouths and flying acrobatics can be confused with those of bats. However, their soft call identifies this bird rather than other insect hunters.

Well actually, not to be nit-picky or anything, but I think common nighthawks sound rather like semi-trailer trucks (articulated lorries) that have downshifted when they roar down a steep hill.

My only complaint is the book claims to include a "song" for each bird, written out on a musical scale and presumably representing what that bird's actual song sounds like. Well, the words may represent the bird's song (kinda-sorta), but writing the words on a musical scale is just wrong since different bird species sing different notes -- and this difference is not represented at all accurately even though the musical scale implies that it is accurate-as-written. Another (minor) issue is these birds are all New World species, which means that at least some of them or their relatives cannot be seen in the Old World -- unless, of course, they become desperately lost during migration, which does happen on occasion!

However, that said, I do love this book for its adorable poems and interesting life history information. For example, I was pleased that the author does not refer to gulls as "seagulls" -- a common mistake that many people make. But this book's primary appeal to kids of all ages are its many beautiful and accurate bird paintings. My personal favourites are "L for Loon" (common loon/great northern diver) and "P for Puffin" (horned puffin).

You may be curious which birds the author used to represent those challenging letters Q, X, V and Z? Well, Ms Ogilvy does have birds representing each of those letters, but their identities are something I'll leave for you to investigate. If you (and your relatives) don't have any kids of your own, you might enjoy purchasing this book for your local school library, just so you can enjoy it first!

.. .. .. .. .. .. .. .. .. .. ..

Shelli Ogilvy is an artist and outdoor adventurer who was born and raised in rural Alaska. She has a bachelor's degree in marine biology and has contributed to published scientific research on humpback whales and gray wolves. When not working as a sea kayak guide in Antarctica or as a camping guide in Alaska's Glacier Bay, she paints and pursues other creative activities. Ms Ogilvy primarily works with acrylic paint on either canvas or paper and sometimes combines mediums such as chalk, ink or spray paint. She divides her time between Gustavus, Alaska and Taos, New Mexico. This is her first book.

.. .. .. .. .. .. .. .. .. .. ..

GrrlScientist is an evolutionary biologist, ornithologist and freelance science writer who writes about the interface between evolution, ethology and ecology, especially in birds. She also has a deep passion for good books, especially good science books, which she reviews with some regularity. You can follow Grrlscientist's work on facebook, Google +, LinkedIn, Pinterest and of course, on twitter: @GrrlScientist

.. .. .. .. .. .. .. .. .. .. ..

NOTE: This piece is slightly reformatted to fit this space from the original, which was published on the Guardian.

So are gun deaths. Cigarettes don’t kill people—unless people pick them up and smoke them. Guns also don’t tend to pick themselves up, point themselves and fire. Guns are simply tools that people use, tools that are responsible for more than 30,000 deaths in the US each year. Every one of those deaths were preventable. Suicide made up a large part of these deaths. Not all suicide attempts are successful, but the immediate lethality and ready availability of firearms makes it easier to try and succeed.

People can certainly disagree about the meaning of the Second Amendment, but facts don’t lie: our adherence to one particular interpretation is allowing tens of thousands of preventable deaths every year.

Whatever lawmakers may say, I will continue to ask my patients about gun ownership because it’s important to their health. I don’t tell them not to have guns, but I do ask them about their hobbies, hunting habits, and gun safety knowledge. I also let them know about the statistics that say that owning guns makes you more likely to suffer a firearms injury or death (obviously, really).

As with cigarettes and auto accidents, it’s likely that gun deaths can be prevented by regulation, but to take that step we ned to at least agree as a society that dead children make the question worth debating, examining, and voting on.

It sounds a bit like morning, the same bird calls I expect will wake me. During the heat of the day, there were more woodpeckers knocking, red-winged blackbirds trilling, and black-capped chickadees, my local favorite, making me feel as if I were farther north.

Even with eyes closed, though, I’ll soon hear the evening. Spring peepers will slash through the relative peace, rivaling the cicadas I expect on a warmer week.

I learned a new flower on my walk last week: bloodroot. Despite all my time outdoors, I’ve never noticed it, preferring to keep my eyes out for trillium. The daisy-like flowers were nearly enfolded by a palmate leaf, seemingly birthing them into the spring.

The poison ivy’s not far behind though. The hardiest of hardy’s I’d say. They always look healthy and do not like to be removed. As soon as a bed has been cleared, they appear on a tree trunk, obscuring the bark, daring us to touch.

A cardinal a little ways away seems as happy as I am, enjoying the cool, dry spring air (although I suppose he’s a bit lonely).

The ducks though—the ducks. We have a pair in the backyard, but today, the female was surrounded by a group of drakes—a large group. They splashed, flapped, scooted, and eventually, two of them trapped the female long enough, I suppose, to make suspect the next generation’s paternity.

They can’t ruin this though. It’s perfect, and when I tuck in my daughter, I expect she’ll agree. I’ll never take spring for granted.

Kent Dam with canal lock and towpath behind it, in this undated photo from Kentohio.net.

For 168 years, a dam stood across the Cuyahoga River, under the main street bridge, and impounded water for a couple of miles upstream. In 2004, the dam was modified to let the river be free-flowing through town. The arched stone dam face was preserved but the remnants of a Pennsylvania and Ohio Canal lock structure were removed, creating a narrow chute in the river where once there was a full blockage. After the reservoir drained, some of the sediments were regraded to form a well-signed little heritage park behind the dam.

Looking upstream at the dam in August 2012. In the summer, water is recirculated to a trough at the top of the dam in order to give the illusion of a waterfall. On beautiful spring evenings, like this week, the park behind the dam is filled with people enjoying the weather…or studying.

Looking downstream through an arch of the Main Street bridge at the remaining section of the dam on the right and the former lock, now river on the left. Photo April 30, 2013.

Above the dam site, the river is confined to a fairly narrow bedrock gorge with class 2 rapids. In a few places you can easily get down to it and see some nicely potholed rock in the riverbed. Kayakers call this a pin spot.

Looking upstream from the pin spot on the Cuyahoga in Kent. Co-blogger and the High Albedo geo-dog for scale.

While we were wandering down there a few evenings ago, we met an angler who caught and released two small trout from the river in the space of about five minutes. There was no fish passage around the Kent Dam before it was removed, so I’m taking the trout as a good sign of some ecological recovery in this section of the river. Another good ecological sign has been spotted a few miles downstream. Rebuilding of another bridge over the river in Kent has been delayed so that endangered native mussel beds can be relocated.

Looking downstream from the pin spot between Main St and Crain Ave. Look closely for the angler near the river.

I know that the dam removal decision in 2004 was controversial in the community – generations had grown up with the dam as a local landmark and it was on the National Register of Historic Places – but when I walk along this section of the river, I am impressed not only by the wonderful ecology and geomorphology of this little river that runs through our downtown, but I’m also impressed by the community’s embrace of the free-flowing Cuyahoga. On this day, so important to Kent’s history, it gives me hope that we can overcome the wrongs and divisions of the past and work together to make a better future for both our communities and the world around us.

At the University of Georgia, a group of nutrition professors are investigating how obesity may affect folate metabolism during pregnancy. With an increasingly obese population and folate recommendations based on studies from the 1990s, they surmise that obese mothers may need more folate during pregnancy.

They recently conducted a pilot study of both normal weight and obese women to measure how the recommended dose — 400 micrograms — is metabolized in the blood over 10 hours. The study, published in the International Journal of Obesity earlier this month, shows that there’s a significant difference between the two groups.

Serum folate response follow a single dose of folate (Silva et al, Int J Obesity, 2013)

The researchers administered a dose of folic acid to 16 normal-weight women with a BMI between 18.5 and 24.9 and 16 obese women with a BMI over 30.  Before the folate was administered, fasting serum folate was lower among participants in the obese group, while their red blood cell folate was higher. During the first three hours after folate administration, serum folate levels were 34% lower in the obese women, and the overall folate response after 10 hours was also lower in obese women. 

Area under the curve for serum folate following folate ingestion (Silva et al, 2013, Int J Obesity)

“It’s quite important to determine whether or not this recommended amount of folic acid should be tailored and based on body weight,” said Lynn Bailey, the lead researcher. “In the pharmaceutical arena, many drugs are prescribed based on body weight, but that’s not the case for this vitamin.”

Getting enough folic acid before and during the first month of pregnancy prevents most neural tube defects — birth defects of the brain and spinal cord — that lead to spina bifida, nerve damage, paralysis, or an undeveloped brain. Folate can reduce these rare neural tube defects from about 2 in 1,000 births to about 1 in 1,000, according to the Office of Dietary Supplements.

Bailey, who has studied folic acid, maternal health, and birth defects for more than three decades, has previously published research that shows obesity is associated with an increased risk of having a pregnancy affected by a neural tube defect.

“We really think this research has translational potential because it could result in a change in the way the public health recommendations are defined,” she said. “If it is based on BMI, we could overcome the negative impact of obesity on developing embryos that don’t receive a sufficient amount of folic acid.”

The U.S. Preventive Services Task Force and Office of Dietary Supplements have recommended 400 to 800 micrograms of folic acid for women of child-bearing age since 1996, and USPSTF reaffirmed the recommendation in 2009. Spokespeople from both groups said further research is needed to determine whether a change is warranted. USPSTF reviews recommendations every five years, and folic acid isn’t currently on the list for USPSTF to update.

“To update this recommendation, the task force will examine all available and current evidence on this topic,” said Mark Ebell, a University of Georgia professor of clinical epidemiology and member of the USPSTF. “We must determine the balance of benefits and harms for folic acid supplementation.”

A new Centers for Disease Control and Prevention study, published in the Journal of Nutrition this month, states that though the majority of women do use folate during pregnancy, only half of pregnant women are using the supplement during the first trimester, when it matters most.

“We found the good news that a majority of pregnant women did report taking a supplement, but it was important to look at the breakdown by trimester,” said Amy Branum, author of the paper and staff member at the CDC National Center for Health Statistics. “We wanted to see how many in the first trimester were taking folic acid because it’s a critical period for neural tube defect development.”

Branum and co-workers investigated data about nearly 1,300 pregnant women surveyed from 1999 to 2006 in the National Health and Nutrition Examination Survey, an annual CDC survey used to evaluate health in the nation. Previous analytical studies haven’t tracked folate use and status in particular, especially by marking trimesters through red blood cell data.

More than three-fourths, or about 77 percent, said they used a supplement in the previous 30 days, usually a multivitamin with folic acid and iron. About 55 percent of women in their first trimester took a supplement compared with 76 percent in their second trimester and 89 percent in their third trimester. Red blood count folate status, which indicates the actual presence of folate in the blood, was also lowest in the first trimester and highest in the third trimester.

“It was nice to study recent data of pregnant women,” said Branum, who has researched longitudinal studies about pregnant women in the 1950s and 1960s. “We’re finding ways to use this data and make it useful to the public and medical community.”

Carolyn Crist

Carolyn Crist is a freelance writer pursuing her master’s degree in Health and Medical Journalism at the University of Georgia. She graduated from UGA in 2010 with degrees in newspapers and English and worked as an education and political reporter.

Geokid’s parents welcome her class to the department of Geology.

Then we split up into two groups: the water group and the rock group. First, I was in the water group, and second I was in the rock group. In the water group, we played in the stream table. We found houses and little pieces of grass, and we tried to make a flood, but then we made a dam so the flood couldn’t get into the ocean. The dams got broken because the water could go under the plastic sand. We tried to make new dams, but we also made whirlpools in the ocean. We learned that rivers can go out of their paths and then back into their paths.

Playing with the EmRiver Stream Table.

In the rock group, we looked at rocks or fossils or both and drew a picture. The picture was supposed to help us remember the rocks and fossils. Then we went back to the place where we were going to eat snack, and we looked at fossils and rocks. We got to hold them and study them with magnifying glasses. There was one that was an ammonite, and there was one that floated in water, and there was one that was magnetic. Some had big crystals, and some were made from lots of rocks and pebbles. Then we got the magnets and we did some experiments. We magneted them to the magnetic rock.

The class picks out their favourite rock.

Checking out Psittacosaurus.

Floating rocks, magnetic rocks… smelly rocks?!

Then we ate snack. Snack was rainbow goldfish, and you got a choice from grape juice or strawberry kiwi juice. Then we watched two movies. The first one we watched was “There are fossils rocks in the ground tonight. They’ve been down there for a very long time. They contain the history of life.” And we also watched “I am a paleontologist! That’s who I am. That’s who I am. That’s who I am.” Then we got little bags of rocks from the students in the Kent State Geological Society. And then we back on campus loop.

The students seem younger every year…. although this class is being remarkably attentive!

We were really excited so when we came home we said “Geology Rocks!” My friends learned that geology rocks.

I worked for two months in a summer camp outside of Hendersonville, NC as a camp counselor, teaching kids to ride horses and taking care of the animals. When the camp ended, together with several other counselors, I got into an old Toyota station wagon and drove all the way up to upstate New York. There we stayed a couple of days, cleaning and degreasing the kitchen of another camp owned by the same organization. That was a nice way to earn a little extra money. I needed it. My travelers checks were OK, but running thin. My regular bank checks were useless – with the war on, the bank transfers were blocked.

One of the camp counselors was a student at Brandeis University, just north of Boston. He took me there and gave me food and shelter in his room. He was one of several guys living in a huge fraternity house which in its past life used to be a funeral home. Apparently, the crematorium equipment in the basement was still operational.

I stayed there for a couple of weeks, then went up north to New Hampshire to visit an old childhood friend of mine. We used to ride horses together and now she was a professional horse trainer up there. We have not seen each other for ten years, so she put me on one of her horses to see how my riding improved since the last time she saw me on a horse. I spent about two weeks there, with her trying hard to switch me from European, deep-seat, controlling style of riding to the more free-flowing, fluid American style – something I needed if I was going to stay in the country and work at a horse farm somewhere – probably the only solution for a person whose visa was about to expire and render him an illegal alien.

She opened the latest issue of the Chronicle of the Horse, the professional weekly magazine, and turned to the job ads. She called up about a dozen numbers. She narrowed them to three: “Now you call!”. I did. One job was in Virginia, paid almost nothing, and the owner did not care about my riding – he needed someone to muck stalls. The second one was with Ian Millar up in Canada, but he was just getting ready to go down to the Florida circuit and had no time to deal with my paperwork, passports, visas, etc.

The third one was Shep Welles, down in North Carolina which was familiar place already. He interviewed me for two hours over the phone, asking everything about my riding history, physique, current administrative and financial situation, and more. He was interested, but he had two girls coming to interview next day, so he told me to call again after a couple of days, in case he did not like their riding. I was nervous. My still very stiff European riding could not possibly compare to locally produced riders.

I went back to Boston, waited a couple of days, and called Shep again. He did not like the way the two girls rode (ooops, he has high standards, nervous, nervous!), so he was interested in seeing me. Again, he interviewed me over the phone for two hours, touching on many of the same topics. I had 20 years of experience with horses by then, riding, training, grooming, teaching riding to kids, and working as finish-line judge and assistant handicapper at the Belgrade racecourse. But I was still not confident that my Balkans-style riding would be something he’d like.

Shep was going to give me a chance. If he did not like my riding, I could stay at his place and clean the stalls and he’d find me a job in the area. If he did like me, he would help me with the visa, documents, finances etc. I borrowed some money from my Boston friend and bought Greyhound tickets to Raleigh.

Actually, it was not that easy. This was 1991, no Google Maps, Facebook, iPhones or Twitter. I wrote down the name of the town the way I heard Shep say it. Then I opened an old print map of USA, found North Carolina, and started looking for “Rowley”. Ooops! No such place. But also no town whatsoever that starts with R except Raleigh. So I risked it – I bought a ticket to Raleigh. If that was a wrong spot, at least I’d be in the right state and they could come and get me.

Ellen Mordecai Welles, 1923-2013.

My bus pulled into the Raleigh Greyhound station. An old, dirty, beat-up truck pulled up right next to the bus. Yup, right there, on the platform. Out came a wiry old lady, Shep’s mother, the owner of the barn. But why not? After all, Mrs.Welles was a Mordecai – she was Raleigh before there was Raleigh, she owned the place, she could park wherever she wanted!

I was standing there with my backpack and she looked straight at me: “You must be Bow-rah!”. Yup, it was me. How did she guess?

She threw my backpack on some bales of straw in the back of the truck and motioned me to get in the cabin. I did. Within a microsecond, three Jack Russell terriers were in my face, barking their heads off. “This is Winston, this is Russell, and this one is Jester and aren’t they such good boys!” They kept barking in my face for another ten miles of the ride, until we got to the barn.

Ten miles does not seem such a long drive, but it did for me then. There was never a moment Mrs.Welles ever looked at the road! Why should she? The old truck knew the way by itself! By the time we got to the house, I heard the history of the family, the history of Camp Triton and Triton Stables. We were greeted at the house by two more dogs – huge, ancient Mildred, and tiny, blind Henry. I was shown my room, deposited my backpack there, and looked at all the cobwebs in the rafters – the life is at the barn, after all, so why clean the house when it’s just for sleeping!

Off we went to the barn across the road from the house. Shep was teaching his class – the group of best riders at the stables – so I had to wait until he had time to put me on a horse for an interview. I sat on a bench and watched. I was deeply impressed. Lots of horses in a relatively small ring, yet horses seemed calm and relaxed and happy, jumping with ease and appetite. This was obviously a top-notch establishment.

When the class was over, and the riders untacked, washed and turned out their horses, one of the riders from that class approached me at the bench: “Hi, I am Catharine, you must be the new guy, may I sit here with you?” Of course, of course, why not…. A year or so later, she became my wife. Triton magic!

Shep put me on a wonderful horse, named Time (I think the show name was ‘Time Maker’), a tall, handsome chestnut who was so easy to ride I managed to remember my New Hampshire lessons and ride him pretty smoothly and fluidly, pretending I was an American rider.

The late afternoon is a hectic time at a barn. Horses need to be brought in and fed. I did not know the horses yet, or even where the grain was. But there was something I could do to help – teach a new kid her first ever riding lesson on a pony. Mrs. Welles handed me an old dappled-grey pony (Rosie), and a tiny little child (Heidi) and told me to teach her to post in trot. Which I did. After all, I used to teach riding before and felt comfortable doing it. By the end of the hour, Heidi was posting like a pro.

Apparently, Shep liked my riding. Also apparently, Mrs. Welles liked my teaching. Some years later I heard that the two of them had a somewhat tense discussion over dinner that night – who will get me! In the end, they decided on a Solomon’s solution: to split me up in half. I spent next eighteen months riding young horses in the mornings and teaching beginner riders in the afternoons and on Saturdays.

The very next weekend, there was a horse show at Triton Stables. Everyone came up to me to introduce themselves. “Where are you from?” “Rowley”, I said, in my best imitation of Southern drawl.

And in a sense, that was true. That was my home now.

On occasion, I’d go with Shep to a horse show as a groom. Not to small local shows where he took bunches of ponies – kids and parents went along for those – but to the big shows where he’d take a few young hunters he hoped to show well – and sell – and his old Grand Prix show-jumper Amadeus. We had great times together at such shows, and I did my best to be a good groom, take good care of horses, and make sure that Penny Lane, Tiki Toy, French Horn, Crusader and others were well warmed up for him. And this was serious stuff – I learned so much just watching Shep warm up!

But afternoons were different. Shep was the boss. Yes, we were friends, we had fun, and my riding improved more during those eighteen months than the entire twenty years before it, but he was still The Boss. On the other hand, Mrs.Welles became a new mother to me. I was a stranger in a strange land. Not sure what tomorrow brings, except that there is no going home to the country that soon became seven countries over a decade of bloody wars.

She was a tough lady. Whenever I hear the phrase “tough as nails” I think of Mrs. Welles – she is the epitome of that saying.

But she also had endless love, for all of her family, all of her students, her horses, her dogs and her cats. With six grown kids, what’s a big deal about adding another one? One more or less, doesn’t matter, there was plenty of heart for all of us.

I got away with some things others could not. As a night owl, it was hard for me to get up in the morning. So I’d wake up at the last moment, run down to the barn to help bring in the horses from the paddocks, feed them, clean the stalls if Alvin and Albert had a day off, put the hay out in the fields. But then I’d run back up to the house for…breakfast break! Instead of working! But I needed my calories! I had my big bowl of cocoa puffs, cocoa crispies and coco pebbles (yes, all mixed in) with chocolate milk, perhaps also some toast and jam, I gulped that all fast and ran back down to the barn to ride. I needed the energy to work all day, walking miles taking horses in and out of the fields, riding several young spirited horses every morning and teaching (which means “running after the ponies non-stop”) two or three classes every afternoon. I actually gained weight! Mrs. Welles liked that – she wanted to see me put on some muscle on this skinny body!

I must have been doing something right. I started by teaching one afternoon class with five ponies: Peppy, Flopsie, Blue Eyes, Bella and Rosie. Within months, I was teaching two or even three classes every day, with a dozen horses in each, pulling the summer-camp ponies out of the fields and putting them to work every single day. Apparently, the kids liked it and kept coming back for more and more lessons. Soon we had to split the pre-short-stirrup show class into two, then three, then four divisions – A, B, C and D. Soon after, my students and Mrs.Welles’ students started battling for ribbons in the D class. Sometimes we fought over students – I wanted to keep my best for “just one more horse show” while she wanted to promote them to her more advanced classes. She even let me take one of my students to short-stirrup division before letting her move up to her classes.

And we talked. We talked so much. About horses. And dogs. And kids we taught. And my old life in former Yugoslavia. And the history of her family. And her pride in successes of her other son Jeffrey on the international circuit. And why I was so good with crazy fillies like Penny Lane, Dream Girl, Pharlap and especially the super-sensitive Con Tiki – the last ever horse she herself broke in, and probably my most favorite horse I rode there. And about my new love for Catharine. And so much more. And we laughed. We laughed a lot. And I felt at home.

I can’t believe it all lasted just eighteen months! Catharine and I got married. I was given a green card. Catharine sold her horse (Double Helix, but she called him Watson) so we could buy a car – a stick-shift Volvo station wagon in which I got my drivers license. The first winter, Catharine moved into my room at the Welles house, and we spent a couple of months battling an outbreak of strangles for many hours every day, from dawn late into the dark, trying to help all the poor horses feel better and get well. The second winter, we moved out to Catharine’s place across the street from NCSU. In the end, I quit and had a couple of boring manual jobs for a few months until I started graduate school at NCSU.

But I kept coming back for many years, judging the pre-short-stirrup classes at Triton shows, thus getting to see Mrs.Welles at least a few times a year. My own Jack Russell terrier, Gru (short for Grushenka – the lady of the night from Dostoyevsky novels), ended up living at Triton so I had to visit her every now and then. Our friend Betty Trustman bought a big thoroughbred, Quartermane, so I went to Triton to ride him on Sundays, to get his energy out so he does not buck her off on Mondays. That was about fifteen years ago – the last time I was on a horse.

As we moved farther away and my life got busier, and as Mrs.Welles gradually stopped teaching and got older and began to feel her age, we lost touch. Thanks to Facebook, I reconnected with several other people from Triton, so I could be informed about comings and goings there. So I knew when the barn moved out to Durham county. And I knew when various other things happened.

Several years ago, Mrs. Welles needed a hip replacement. Catharine and I went to visit her at the hospital right after the surgery. Barely out of anesthesia, Mrs.Welles pulled herself up with her own arms, lifted and moved herself from the trolley to the bed. The nurse kept coming and looking at the monitors, apparently not very happy. Catharine, a nurse herself, asked what was the worry. This is where we had to explain that the pulse will never go up as high as expected – Mrs.Welles, after all, was a top athlete in top form, even when she was in her 70s. She had an athlete’s heart.

A couple of months ago, we heard that Mrs.Welles had another stroke and was again in a hospital and not in a nursing home. We went to visit her. She could not speak. It took her a long time and lots of talking to recognize Catharine, and even longer to recognize me. She was squeezing a plush toy piebald pony – looking just like Marco Polo, or Oreo – with her right hand. Suddenly, she pulled herself up, and grabbed my hand. She pinched my hand so hard I thought she’d break my fingers. Decades of working with horses made her so strong that even this close to the end of her life she could still grip harder than I could. Tough as nails to the end…

Avalanches de printemps

An appropriate demonstration on this Earth Day of the power of our planet. But it’s also notable that, except for the last few seconds, which show that this footage comes courtesy of some climbers who were (fortunately) traversing the opposite side of the valley, there was not a human or building in sight. This is a striking contrast with the normal lens through which we view events like this, which is in terms of how they affect us, and our civilisation*. The pictures coming out Sichuan Province in China, in the wake of the weekend’s magnitude 6.6 earthquake, illustrate this quite well.

A landslide blocking a road and bridge in Sichuan province, China. Source: BBC.

This tendency is perfectly understandable, but it does speak to a certain hubris on our part. The (French) commentary to that avalanche video mentions that this is just a normal part of spring in the Alps, as the snowpack warms up. Earthquakes and volcanoes, storms and floods, landslides and avalanches; all of these ‘hazards’ are in a sense, just the earth doing its thing, and have been happening for hundreds of millions of years before humanity was around to menace. Even now, they only become disasters when we get in the way. But we tend to think of it in terms of nature intruding on us, rather than the other way around.

It’s a very strange way of looking at things, really: we create our little civilised bubbles on an active and vibrant planet, and then manage to be continually surprised when reality decides to pop them. As Terry Pratchett’s anthropomorphic personification of Death comments in The Hogfather,

STARS EXPLODE, WORLDS COLLIDE, THERE’S HARDLY ANYWHERE IN THE UNIVERSE WHERE HUMANS CAN LIVE WITHOUT BEING FROZEN OR FRIED, AND YET YOU BELIEVE THAT A…BED IS A NORMAL THING. IT IS A MOST AMAZING TALENT.

A similar sentiment can be found in New Zealand nowadays, as they are forced into an uncomfortable confrontation with the true dangers in their beautiful yet dangerous homeland:

“If you’re not on a fault zone, a volcanically active zone, or a tsunami zone, you’re probably in a valley that’s prone to flooding or having things tumble down the hills towards you.”

I sometimes wonder if our feet-dragging on the issue of climate change doesn’t partly stem from the same detached attitude: we just can’t understand that what we do in our homes and cities can affect the world out there. So my thought for Earth Day is this: if we want to have a long-term future on this planet, we’re going to have to learn that our only hope of rolling with the planetary punches is not a doomed quest to set ourselves outside of nature, but to embrace it, and understand it, and allow ourselves to be shaped by it.

*I think this might actually be changing though, as video cameras in phones, and the ability to easily upload footage, become more widespread.

This is the same region that was shaken by the much larger magnitude 7.9 Wenchuan earthquake on May 12 2008, resulting in tens of thousands of deaths; in fact, that rupture was less than 100 km north-northeast of this latest one. When added to the fact that the focal mechanisms for both earthquakes are also very similar, indicating WNW-ESE compression on a NNE-SSW trending fault, this relative location makes it likely that we are seeing a further rupture of the same fault system that failed in the Wenchuan earthquake – either an adjacent segment of the same fault, or another, similarly oriented fault in the same thrust system.

Location and focal mechanism for M 6.6 earthquake on 20th April 2013 in Sichuan Province China (orange dots include first 12 hours of aftershocks) and the May 2008 M 7.9 Wenchuan earthquake (grey dot). Data from USGS.

The ultimate cause of this earthquake is the continental collision that has produced the Himalayan mountains to the east. As India continues to push into Asia, some of the Asian crust is pushed out of the way upwards, creating the looming heights of the Himalayas and the Tibetan plateau; but some is also being pushed out of the way sideways in the direction of China. The Longmenshan mountains, where all this seismicity is occurring, mark a place where there is a particularly strong bit of Chinese crust – the Sichuan Basin – standing against this tectonic invasion, forcing the eastwards migrating crust to be thrust over it. For more details and some nice explanatory figures, check out Kim Hannula’s post on the tectonics of the 2008 earthquake.

The other question to consider is whether the Wenchuan quake was an influence om the timing and location of this latest rupture. In a discussion on Twitter Eric Fielding pointed me to this July 2008 paper by Parsons et al. that calculated the permanent stress changes on neighbouring and nearby fault segments induced by the Wenchuan rupture: they concluded that it caused the stress to increase on both the southern continuation of the Wenchuan Fault itself, and the parallel Ya’an Thrust that may be a better candidate for the source of the current shaking.

A tectonic map of the Longmenshan thrust system. The accompanying cross-sections of other faults in the area show modelled increases (red) and decreases (blue) in permanent stress resulting from the 2008 M 7.9 Wenchuan earthquake (white star). Orange boxes highlight the southern segment of the Wenchuan Fault and the Ya’an thrust – both possible sources of the latest quake, whose rough location is shown by the orange circle. Modified from Parsons et al., 2008

This makes it possible that events in 2008 did indeed prime the pump for an earthquake 5 years later, in the sense that it added a little bit of extra stress onto the fault that ruptured last night, and caused it to fail earlier than it would have otherwise. However, the reason that there was a stressed fault ready to fail in the first place is the wider tectonic forces associated with the Himalayan collision.

The first survey, available here, is aimed at the general public, and is trying to determine their (e.g. your) opinions about body weight, health, and related policies.

The second study, available here, is aimed at people who work in the treatment of obesity (physicians, nurses, dietitians, psychologists, etc) in order to inform the development of a “Healthy Body Scorecard” for children.

I found out about both of the above studies via the Canadian Obesity Network, which makes this a good time to remind everyone that their 2nd National Obesity Summit will be taking place May 1-4 in Vancouver.  Peter and I liveblogged the previous Summit in Montreal (those posts can be found here), and it was a fantastic experience.  Early bird registration lasts until this Friday (April 19), so if you’re thinking about going now is the time to sign up.  You can sign up for the conference here.

Travis

Location and focal mechanisms of the two recent large earthquakes in Iran. Data from the USGS.

The USGS originally reported the rupture depth for this week’s quake as 15 km, but as more data was analysed the estimate became much deeper, around 80 km depth (other solutions suggest it’s closer to 50 km). This meant that although this quake was powerful enough to shake buildings from Oman to India, the strength of the shaking immediately above the rupture was far less powerful than was originally feared. Although the mud brick buildings common in this region are not particularly resilient to earthquakes, the largest death toll reported so far is 34 people across the border in Pakistan.

The map above shows that both these earthquakes are associated with the collision of the Arabian and Eurasian plates, although there is a transition from a full-on continental collision in the west to a subduction zone (the Makran Trench in the east). However, the focal mechanisms for these two earthquakes are very different, last Tuesday’s M 6.3 indicating northeast-southwest compression and this Tuesday’s M 7.8 indicating northeast-southwest extension. The former is much more in keeping with what you’d expect at a collisional plate boundary than the latter, at least until you remember that the depth of the rupture makes it much more likely to have occurred in the subducted Arabian slab that must exist underneath eastern Iran and western Pakistan, rather than the folded and crumpled Eurasian plate we see on the surface. In fact, as I’ve also marked on the map above, in January 2011 a magnitude 7.2 earthquake with a very similar depth and extensional focal mechanism occurred around 250 km to the northwest of this week’s rupture in western Pakistan. The plot below, modified from Engdahl et al. (2006) shows both of these earthquakes fall within the projected confines of the subducted Arabian plate; the extensional focal mechanisms are probably therefore caused by either the pull of the down-dip slab, or some sort of plate bending effect.

Rough shape of the subducting Arabian plate (shading added by me) based on the earthquake locations of Enghdal et al. (2006), with approximate locations of this week’s M 7.8 earthquake and the very similar M 7.2 event in western Pakistan, Jan 2011.

As I noted in 2011, the northwest-southeast axis of extension is considerably rotated from the north-south axis you would predict for either ‘slab-pull’ on, or bending of, a north-dipping slab, so some other forces may be at play; perhaps the faster collision of India to the east that forms the Himalayas is forcing some kind of lateral buckling of the Arabian slab.

I was also quite interested in last week’s magnitude 6.3, because it was located in the Zagros mountains: the main shock and aftershocks are located right amidst some of the beautiful folds for which the region is famous, traced out in aerial view by resistant limestone ridges.

Location of last week’s M 6.3 in the Zagros mountains, with aftershocks and pretty, pretty folds. Data from USGS.

The Zagros region is also an example of thin-skinned thrusting, where a layer of weak rock – in this case a Cambrian evaporite – acts as a detachment, or décollement, which isolates folding and thrusting in the surface layers from the deeper parts of the crust. As such, you would expect seismicity in this area to be located on this decollement, or on thrust splays propagating up from it. A nice cross section across this region can be found in McQuarrie (2004), and indicates that the 10 km depth of the rupture is close to the decollement depth, but combining the information from the focal mechanism with this section suggests the rupture was on a NE-dipping splay fault. McQuarrie also suggests that most of the faults are associated with the cores of the folds observed at the surface, although it is hard to clearly see this from the aftershock pattern.

Map of Zagros Mountains. Cross-section A-A' is reproduced below. From McQuarrie(2004).

Balanced cross-section through Zagros fold belt in the same region as last week’s M 6.3 Earthquake. From McQuarrie (2004).

So it seems that Iran’s seismic week encompassed both shallow and deep collisional processes, on opposite sides of the country. And tempting as it is to look for some deeper reason for both of these earthquakes occurring within a week of each other, the Bushehr earthquake last week was probably too small and far away to have had any influence on the timing of this week’s rupture.

Obesity is a complex and multifactorial chronic disease that remains a military and public health priority in the United States. Recently, we’ve identified a strong association between obesity prevalence and altitude within the US. Our findings were surprising because they indicated the magnitude of this association was large and the pattern of association exhibited a curvilinear dose response in 500 meter categories of altitude. There was a 4-5 fold increase in obesity prevalence at low altitude as compared with the highest altitude category after controlling for diet, activity level, smoking, demographics, temperature, and urbanization. We published our findings in the International Journal of Obesity (advance online publication doi:10.1038/ijo.2013.5) and presented at the 2013 American College of Preventive Medicine conference.

The process we used is easily reproducible. We combined several publicly available national datasets using statistical software and geographic information systems using the county of residence as a common linkage across datasets. For a basic visualization, Figure 1 shows the Centers for Disease Control and Prevention’s publicly available map with projected obesity prevalence for each county adjusted only for age. This map was created based on similar data as the source for our study, but we used actual self-reported height and weight rather than the modeling shown in Figure 1 and we adjusted for age, sex, race/ethnicity, physical activity compliance, fruit and vegetable consumption, smoking status, employment status, education, urbanization, temperature category and income. By comparison, Figure 2 from http://ned.usgs.gov/ shows the topography of the United States.

Figure 1. Age Adjusted Obesity Prevalence by County. This image was obtained from cdc.gov/diabetes, but this particular map represents obesity prevalence and not diabetes.

Figure 2. A topographical map of the USA (source). Note the similarities with Figure 1.

While it is always important to remember correlation does not prove causation, in this case, we already know hypoxia causes anorexia and weight loss based on well controlled interventional data.  This effect is biologically plausible based on the relationship between hypoxia and leptin signaling, norepinephrine and sympathetic tone, non-erythroid erythropoietin receptor signaling, and the metabolic demands at high altitude.  We hope additional research will help clarify the mechanisms and long term health effect of either high altitude residence or normobaric hypoxia.  These results, showing a large magnitude of association, provide some optimism that this is a worthy line of research.

Jameson Voss

About the Author: Jameson Voss is a third year Preventive Medicine Resident at the Uniformed Services University of the Health Sciences.  His research focus is on obesity. 

Voss, J., Masuoka, P., Webber, B., Scher, A., & Atkinson, R. (2013). Association of elevation, urbanization and ambient temperature with obesity prevalence in the United States International Journal of Obesity DOI: 10.1038/ijo.2013.5

One of the complaints I most often get is from patients who want me to help them out but don’t want to come to the office. This is understandable. Doctor’s visits aren’t free, and with high-deductible plans becoming the norm, more of the cost is the responsibility of the patient.

But there are two very good reasons to practice medicine face-to-face. The first is simply practical: doctors, unlike lawyers and other professionals, cannot bill for time on the phone, email or other sorts of interactions. We simply cannot keep the lights on if people don’t pay for the services we provide. It’s also morally wrong to expect me to work for free. In our culture, payment shows you understand the value of a service.

I do provide free care through a local charity. They send me patients, but not so many that I can’t deal with it financially. Sometimes doctors will work out arrangements with uninsured folks, but when a patient is insured, discounting a visit can lead to legal trouble with insurance companies.

The most important reason to avoid phone-it-in medicine is that it’s “phoning it in”. If a patient needs a long-standing prescription refilled, it can almost always be handled over the phone. But nearly anything else is asking me to use my professional judgement to help a patient. Medically it’s a bad idea.

If you have long-standing hypertension, this needs regular monitoring. Hypertension often worsens over time and treatments need to be adjusted. Asking me to simply prescribe something indefinitely is asking me to practice bad medicine. A visit in person allows me to look for the signs of damage done by hypertension, and to spend the time talking to you about obvious and subtle symptoms.

It’s hard to tell the difference between bronchitis and pneumonia over the phone. Bronchitis doesn’t require antibiotics; pneumonia does. In the office I can listen to the chest and if needed get an x-ray. Sometimes just looking at someone helps tell me how sick they really are.

When your doctor puts off treating you over the phone, she’s doing it for a reason, one that is usually in your best interest.

Today I received an email from the Board—the board which just gave me a 10 year certification—that it ain’t over. After having been assured that my two year of preparation and examination, costing me about $2000 and endless hours, I will now be required to pay the board $200/year and engage in even more busy-work, such as taking quizzes and collecting patient data (oh, and BTW, is there some sort of IRB approval for all this data-gathering? DrugMonkey?)

When the Board implemented the 10 year certification process it grandfathered in members who had been certified by a certain date. This new process has no such provision: after having spent thousands of dollars and hundreds of hours with the understanding that I won’t have to do this again for several years, I’m now told that I will need to keep going.

This will take away from patient time and from other educational activities. Instead of choosing my own educational programs, I’ll have to use that time and money to do modules from the Board.

I know it’s not all that dignified, but I must tell the ABIM: you’ve jumped the shark with this one. Practicing internists don’t have time or money for your bullshit. Please fuck off.

This lovely graphic is done in the style of German scientific illustrator and naturalist, Maria Sibylla Merian (1647-1717), who was selected to be honoured by today's Google Doodle.
Image: Google.

If you love art, then you may know that today is the birthday of one of the world's most talented scientific illustrators, Maria Sibylla Merian (1647-1717). Long before the camera was invented, she acted as the world's eyes by painting stunning and scientifically accurate pictures of flowers and later, of insects.

Although she was one of the world's first entomologists, it's likely you have never heard of her: she certainly is not as well-known as she deserves to be – even among professional entomologists. This sad reality may be the motivation behind Google honouring her with a specially designed Google Doodle today, on the 366th anniversary of her birth in Frankfurt am Main.

Merian was a remarkable individual. Not only was she an accomplished artist, but she was also an excellent naturalist and a bold explorer, too. After separating from her artist-husband, she relocated to Amsterdam with her two daughters and supported her family by selling her paintings. But Merian soon became spellbound by the stunning array of tropical flora and fauna that returning travelers brought with them from the Dutch colony of Suriname, located in South America. Her extraordinary talents and unusual interests quickly gained her numerous invitations to view many of the natural history collections amassed by the wealthy elites of Amsterdam.

Inspired by her passion for flowers and insects (particularly butterflies), Merian was determined to visit Suriname so she could study and paint the local insects and plants from living individuals instead of from pinned or prepared specimens. She worked hard; painting and studying the local collections for eight years before the city of Amsterdam awarded her a grant to travel to Suriname to paint its flora and fauna – an almost unheard of achievement at the time because such grants were typically awarded only to men.

Accompanied by her younger daughter, Dorothea, the women set sail for Suriname in 1699. After two years, Merian fell ill with malaria so she and her daughter cut their work short and returned to Amsterdam. Despite her illness, Merian published her Magnus Opus, Metamorphosis Insectorum Surinamensium, three years later. This beautiful book is filled with paintings of Suriname's plants and animals, especially of moths and butterflies, as well as beetles and spiders, and even paintings of snakes and lizards. Many of these tropical species were unknown to Europeans at the time.

Debilitated by a stroke in 1715 that left her partially paralysed, Merian died a pauper in 1717 at the age of 70. But her passion for insects had changed science forever. Contrary to the prevailing notion of the day that insects spontaneously arose from the mud, Merian discovered this was not at all true. She was one of the first naturalists who actually cultivated live insects, which gave her powerful insights into their natural history and behaviours. Merian was one of the first scientists to learn that many insects go through distinct developmental stages and, through her lavish and accurate paintings, she was the first to document these life stages for the public.

As an artist, Merian's work had a strong influence upon scientific illustration. In addition to the accuracy and realism of her paintings, Merian's pictures of insects were the first to depict all the different life stages and the chrysalis for each species on its particular food plant. Once ridiculed for her fierce independence and for her unladylike devotion to painting pictures of insects, Merian is now recognised as one of the best insect (and flower) scientific illustrators of her day – and indeed, of all time.

This video will give you some appreciation for Merian's beautiful paintings and drawings:

You can learn more about Maria Sibylla Merian's extraordinary life and work in Kim Todd's biography; Chrysalis: Maria Sibylla Merian and the Secrets of Metamorphosis [Amazon UK; Amazon US]. Ian "Birdbooker" Paulsen also tells me that Taschen translated her masterpiece, Insects of Surinam, into three languages (English, French and German) and published it in 2009.

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece was slightly modified from the original, which was first published on my Guardian blog.

.. .. .. .. .. .. .. .. .. .. ..

Follow Grrlscientist's work on her other blog hosted by the Guardian, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

Birders at Magee Marsh boardwalk.
Image: Gunnar Engblom, 2012.

Do you like to watch birds and other animals (or even your neighbours)? If so, then you'll be happy to learn about a wonderful advance in technology that is guaranteed to add thousands if not millions of new "watchers" to those who already enjoy this hobby!

So how did you spend your spring holiday? If you are like me, you might have been squidging around on mudflats with mud threatening to suck your boots off with every step you take, with a pair of 10x50 binoculars that weigh nearly two kilos strapped around your neck, a birds field guide in one of your jacket pockets and your iPhone (in a plastic baggy -- just as a precaution!) in the other pocket, weighed down by a pack filled with two cameras, five lenses and a tripod (I left the 'scope at home). Was I trying to get into the military? No. I was birding -- watching wild birds.

Or maybe you (wisely) sat in your flat, sipping a martini whilst using your fancy binoculars to surreptitiously peer through your window blinds at your neighbours?

Well, whatever you did, if it involved binoculars, then you will be happy to learn about an innovative technology that practically does your watching for you!

After returning from a weekend staggering around in the field, I ran across a video advertising an innovative new binocular that, had I known about it earlier, would have saved my neck and back a lot of aching. Developed by Eagle Optics, this new binocular merges several advanced technologies into a field-friendly watching device. Named the Wild Turkey, this binocular is a welcome first step in making nature watching easier and more comfortable than ever before. Here's the video:

Wow, that helium technology is really wonderful, don't you agree? Now, if only they would upgrade these binoculars so they include an iPhone and a digital camera so I can snap pictures of "my" birds that I can then share with all my pals on twitter! But of course, the camera would have to be high-quality so I can leave the Nikon (and all its stupidly heavy lenses) at home. Which, I suppose, means more helium is needed, too.

Alas, there's no known innovation that can ease mudflat-squidging in your boots, sigh.

.. .. .. .. .. .. .. .. .. .. ..

NOTE: this piece was slightly modified from the original, which was published on the Guardian.

.. .. .. .. .. .. .. .. .. .. ..

Follow Grrlscientist's work on her Guardian blog, and also on facebook, G+, LinkedIn, Pinterest and of course, twitter: @GrrlScientist

It all began at the end of February, when I travelled to La Crosse, Wisconsin to the Upper Midwest Stream Restoration Symposium, which was a really stimulating and vital mix of academics, consultants, and government folks all interested in improving the state of the science and practice of stream restoration. I gave a talk on Evaluating the success of urban stream restoration in an ecosystem services context, which was my first time talking about some hot-off-the-presses UNCC graduate student research, and I learned a lot from the other speakers and poster presenters. While the conference was incredibly stimulating, travel delays due to bad weather on both ends of my trip made for a somewhat grumpy Anne (nobody really wants to spend their birthday stuck in a blizzard in O’Hare), so I’ll be thinking carefully about how to plan my travel to the Upper Midwest during future winters. Nonetheless, the view from the conference venue was phenomenal.

View of the Mississippi River from the Upper Midwest Stream Restoration Symposium in La Crosse, WI. Not shown: bald eagles that frequent the open water patches of the river.

March proper saw me give variations of the restoration talk two other times. On the 15th, I gave it as the seminar for Kent State’s Biological Sciences department, and on the 26th, I gave it at the North Dakota State University Department of Geosciences (more about that trip below). In between, I gave a seminar on the co-evolution of hydrology and topography to the Geology Department at Denison University in Granville, Ohio. Students in that department had just returned from a trip to Hawaii, and a very memorable dialogue occured in the midst of me talking about the High Cascades:

“You’ve seen a young lava flow. What would happen if you poured a bottle of water on it?” “It would steam!” “Not that young!”

Closer to home I also hosted a couple of prospective graduate students, helped interview candidates for a faculty position in our department, and went with a colleague to visit an acid mine drainage site about an hour to the south of Kent. In one fairly small watershed, we were able to tour a number of different remediated and unremediated sites, and it certainly lent a whole different perspective to the ideas of stream restoration and constructed wetlands to look at a landscape irrevocably scarred by mining activities.

Unremediated acid mine drainage flow directly into Huff Run. The orange is iron precipitate.

Constructed wetland as the second stage of acid mine drainage remediation in the Huff Run watershed.

At the end of the month, we finally got our turn for spring break. I ended up with a somewhat epic combination of mounds of work and a big trip to take, possibly the worst combination of the untenured and tenured professor spring break stereotypes (see this PhD comics strip). The first half of the week, I spent in Fargo, North Dakota, home to the famously flood-prone Red River of the North. (I’ve blogged before about why the river so often produces expansive floods.) It was truly fascinating to put my feet on the ground in a place that I’ve read about and watched from afar for years. And my visit was made all the more interesting by my host and guide, Dr. Stephanie Day, a geomorphologist newly at NDSU and who may well unravel some of the Red’s geomorphological peculiarities.

Stephanie Day, Assistant Professor of Geosciences at North Dakota State University beside the Red River in Moorhead Minnesota. The flat surface in the background is the approximate elevation of the land for miles around.

Looking towards downtown Fargo, ND from the river side of the levee.

River’s edge view looking towards downtown Fargo. Snow well over knee deep here on 25 March, by my measurements. As all that snow starts to melt, the water will rise.

There’s a pretty good chance we’ll see a major flood on the Red River later this spring, as the >24″ of snow melts out of the watershed, runs off over frozen ground, and enters the northward flowing river. The Fargo Flood page is the place to go to follow the action, and you can count on updates (and more pictures) here as events unfold.

The latter half of my spring break saw me diagonal across the state of Minnesota to my beloved Driftless Area, back across the Mississippi River, and into the state of Wisconsin. I saw my family, finished paper revisions, and wrote part of a grant proposal. Then I flew home, with nary a weather delay in sight.

If March was a tight, recursive meander of talks and trips to the Upper Midwest, then April promises to be a bit anastomosing with lots of different threads woven together to make another month of scientific delight.

Saturday night she slept over at a friend’s house. When I picked her up, she said, “It’s a really nice spring day. Let’s do something outside. Can we go to the zoo?”

Yes. Yes we can. We went home, had a little lunch, packed a bag with snacks and took off. The zoo is a gorgeous piece of land, with long esplanades, gardens, and of course, animals. She wanted me to use the map, but it was much more fun to wander and let the animals surprise us.

She’s old enough to read the signs and learn about the animals and their habitats, and enjoyed teaching me. More important, she walked. A kid who prefers to sit walked for hours. Near the end of the day she did wear out. I gave her a piggy back ride, and she kissed the back of my head, saying, “I love you Daddy.”

I’m glad she slept in, but I’m ready for her to come down to breakfast.

The last few mornings, the birds have sounded like spring. Cardinal songs are lovely but their incessant, randy singing can get a bit annoying. Blue jays’ musical tones are wonderful little surprises. But my favorite is the black capped chickadee. Its song always reminds me of the wilderness, so I took off onto the trail this morning for my return to running, and with the hope that the birds would provide a sound track.

I didn’t make it very far, but beside a pond I saw a movement in the bush. There it was, a small bird, perhaps just a random little brown thing. Then its small beak opened and out came the remarkably clear “yoo hoo” of my chickadee. Its camouflage is remarkable. Look how its brown body blends into the background, its black and white head mimics the light-dark of the branches and the spaces between.

Cry havoc and let spring the new season!

Actical accelerometer users rejoice! Rachel Colley of the Healthy Active Living and Obesity Research Group at the Children’s Hospital of Eastern Ontario Research Institute has posted annotated SAS files to use for cleaning and combining accelerometry data from multiple participants.

The Accel+ program is free to download:

• User’s Guide (Download)
• SAS Code
  • Step 1: Read and Stack (Download)
  • Step 2: Quality Control (Download)
  • Step 3: Derive Variables (Download)
  • Step 4: Advanced Analysis (Download)

Contrary to the title of this post, the files aren’t foolproof (the HALO site includes a disclaimer to that effect), but they are extremely helpful for folks like myself who know a little bit about SAS, but aren’t experts.  These Accel+ files can also be viewed as essentially companion files to the National Cancer Institute’s publicly available files for cleaning Actigraph accelerometer data.  I really can’t say enough about how great it is that Rachel and her colleagues (Didier Garriguet, Glenn Glover, Elyse Labonte and Janine Clarke)made these files available for anyone who wants to use them.

The casual reader may wonder why I could possibly be so excited about this.

Well, when researchers want to measure physical activity and/or sedentary behaviour, they usually choose one of two approaches.  They can ask people how much time they spend being active and/or sedentary (e.g. self-report), or they can measure it directly using an accelerometer (there are other approaches you can use, but these are by far the most common).

Anyone who has ever used accelerometry data will know that it can be tricky to analyse.

This has to do with 2 basic issues:

1.  Accelerometers provide an unbelievable amount of data

The two major accelerometers on the market (Actigraph and Actical) give a movement “count” for each minute of the day (1440 datapoints/day), and researchers usually collect data for at least 7 days.  If you  have a study with 1000 participants (which isn’t that large as far as epidemiological studies go), you wind up with a file that has 10080000 (1440*7*1000) data points.  That’s for a smallish epidemiological study.  To put this in perspective, you can only fit the data of 4-5 participants into an Excel spreadsheet before you get an error message telling you that you’ve run out of cells.

Let’s say that one of the accelerometers malfunctions – you do not want to sift through 1 million datapoints by hand in order to find it.  As a result of this giant tsunami of data, we tend to use code-based programs like SAS to clean and analyse accelerometer data.  And since these programs are code-based, they require that you literally learn a new language to use them.  So analysing accelerometer data can be tricky, especially for physiologists who don’t have a biostatistics/epidemiology background.

2.  It can be tricky to be consistent across studies

While accelerometer data is “objective”, there are a lot of somewhat arbitrary decisions that need to be made when cleaning the data (they are usually based on evidence, but still somewhat arbitrary).  For example, should you include participants who only wore the accelerometers for 6 hours/day, instead of the requested 14?  Should you include participants who only wore the accelerometer on weekends, but not weekdays?  How should you decide what values constitute various intensitites of physical activity (light, moderate, vigorous), and how do you determine whether a participant is being sedentary, or whether they took off the accelerometer altogether?

If I decide to include all the data, and you decide to only include data from participants who wore the accelerometer for 10+ hours/day over at least 4 separate days, then you and I are going to wind up with a very different values based on the same dataset.  For the true nerds out there, check out this recent paper from MSSE which illustrates just how these minor changes can affect the relationship between movement and health.

Accelerometers come with their own software for downloading and analyzing data, but it doesn’t really work for the purposes of research.  Hence why programs like Accel+ are so incredibly useful.  Playing with these sorts of pre-made files can also be a very good way to figure out how to use SAS, if you’re into that sort of thing.

If you are a researcher who will soon be undertaking an analysis of Actical accelerometry data, download the above files and get analyzing!

Travis

If doctors stop taking medicare patients should they pay back 500k+ CMS http://www.aafp.org/online/en/home/policy/federal/issues/workforce/education.html … invested in training them?

Now, I’m not saying the tweeter thinks this is what should be done, but the premise is so completely wrong that…well, it’s not completely wrong, it’s just mostly wrong.

First, let’s chat about Medicare, the program that insures people over sixty five (and many disabled people). Medicare sets prices paid to doctors based on all sorts of formulas, but due to Congress’s inability to make financial decisions, these fees are unstable, requiring last minute fixes each year. This means that doctors that treat Medicare patients have considerable trouble planning salaries, hiring, capital improvements, and other expenses. Because of this instability and the generally lower fees paid by Medicare, it might make sense for some to simply opt out and stop participating. Medicare patients would still be able to go to the office, but they would have to pay out of pocket.

The interesting question raised by the tweet is this: since Medicare funds graduate medical education (residencies and fellowships) do doctors owe Medicare some sort of obligation?

Work has a value, and ideally the value is assigned at the time someone is hired for their work. If the worker doesn’t agree with the fee, they move on and management is denied her production. Ideally.

The ethic here is analogous to informed consent: contracts should explicitly state the obligations and benefits for both parties. Doctors pay for medical school, and exit with a debt averaging $200,000. They enter residency with the expectation that they will receive a modest stipend, one that usually doesn’t allow for loan repayment but at least pays room and board. To maintain a residency program, hospitals receive money from Medicare, and some of this money is used to pay this stipend (or salary, depending on whom you ask).

Residency is not a benefit given to young doctors: it is an obligation. In return for being taught and supervised, they take care of patient, working long hours and sacrificing years of potential earning and often family life. There has never been an expectation that they owe anyone anything.

This, then, is why I call “bullshit” on anyone who would suggest the system has other hidden obligations. To impoverish young doctors through debt, and then further impoverish them by having them pay for their training not only in service but in dollars is not consistent with how we create doctors in this country.

If we as a society decide that residency and fellowship are really tuition-based services rather than work, that would need to be explicitly agreed upon long before high schoolers enter college and decide to torture graduate students with questions about their organic chem grade.

If doctors are required to become indentured servants to Medicare, it should not be without an explicit understanding.

Hey, whassup!

Welcome back. I’m dusting off the furniture and moving back in—sort of. I’m having a great time writing over at Forbes (and I sincerely hope you’re reading!), but let’s face it: Forbes is a news outlet, and not a great place to put on the personal touches.

So, I’m re-opening WCU here at WordPress for my non-medical bits: family anecdotes, poetic musings, fiction, political rants, whatever. I invite you to follow both blogs for a complete look under the white coat.

Grand Traverse Bay. Yes, it’s that cold.

OK, that came out wrong, but you get what I’m saying.

So the other night my dad and I were talking about the latest cosmology story in the papers. PalKid, always the eavesdropper, asked what we were talking about. How the hell can I explain cosmology—something I barely understand—to a third grader? The first step, I figured, was ‘c’. Without understanding that light has a finite velocity, there’s no way to understand anything else.

As it turns out, third graders are capable of getting it. I started out with explaining how when we turn on the lights, it seems instantaneous but it’s not. Then we moved up to the sun. “It takes eight minutes?”

Then we moved up to nearby stars, and finally the edges of time. It was amazing. The kid soaked it up like a sponge. And then she went back to watching re-runs of Full House.

Anyway, spring is on the way. The blacked-capped chickadees are getting noisy, the robins fat. If the thermometer would just cooperate…

The whitecoatunderground.com domain will from this point forward direct here, and to get to Forbes, plug in my addy there, and thanks for reading.

I’ve met, corresponded with and in a couple cases collaborated with authors of these papers, but I’ve had no input on writing or peer-reviewing any of them.

• B. Allen and M. A. Nowak (2013), “Cooperation and the fate of microbial societies” PLOS Biology 11, 4: e1001549.
  This is an introductory overview of what can happen when ecological and evolutionary processes occur on comparable timescales and feed back upon one another. It summarizes recent experimental and model-building work on the topic, as realised in Saccharomyces cerevisiae.
• J. A. Damore and J. Gore (2012), “Understanding microbial cooperation” Journal of Theoretical Biology 299: 31–41, DOI:10.1016/j.jtbi.2011.03.008 (PDF). PMID:21419783.
  Next, get a grounding in the sorts of complications which arise with real organisms, even tiny ones, and to see how old mathematics isn’t enough for new questions. In video-game terminology, this is where we defeat the Level 1 boss, “relatedness.” Recommended with the proviso that writing the Price Equation using covariance notation, though common, can be misleading. This is mentioned in the text, but it deserves special emphasis.
• B. Allen and C. E. Tarnita (2012), “Measures of success in a class of evolutionary models with fixed population size and structure” Journal of Mathematical Biology, DOI:10.1007/s00285-012-0622-x (PDF).
  This paper builds up in a nice way the treatment of evolution as a stochastic process. It is probably the most mathematical article on this list. The point made near the end about the way the Price Equation is often misleadingly written is an important one.
• M. Perc et al. (2013), “Evolutionary dynamics of group interactions on structured populations: a review” Journal of the Royal Society Interface 10, 80: 20120997; DOI:10.1098/rsif.2012.0997.
  This review article covers what’s known about evolutionary games on complex network substrates, including adaptive networks. It also touches on nonlinearity in payoff functions, which takes us beyond the idea that “assortment” is everything. To continue the gaming metaphor, this is the boss fight of Level 2.
• P. E. Smaldino, J. C. Schank and R. McElreath (2013), “Increased costs of cooperation help cooperators in the long run” American Naturalist 181 DOI:10.1086/669615 (PDF).
  One of many papers which points out the shortcomings of “moment closure” techniques, this also makes a key point about fitness being a question of timescale.
• S. B. Araujo, G. M. Viswanathan and M. A. de Aguiar (2010), “Home range evolution and its implication in population outbreaks” Philosophical Transactions of the Royal Society A 368, 1933: 5661–77. DOI:10.1098/rsta.2010.0270, PMID:21078641.
  Pair approximations done carefully, with acknowledgements of their limitations, too.
• B. Simon, J. A. Fletcher and M. Doebeli (2013), “Towards a general theory of group selection” Evolution (PDF).
  The distinction between type I and type II multilevel selection is crucial, and often crucially overlooked. Simon, Fletcher and Doebeli build quantitative models of an MLS-2 scenario: there are explicit group-level dynamics, but the set of groups is unstructured.
• B. Simon and A. Nielsen (2013), “Numerical solutions and animations of group selection dynamics” Evolutionary Ecology Research, 14: 757–68 (PDF).
  A follow-up to the previous paper.
• P. Bijma and M. J. Wade (2008), “The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection” Journal of Evolutionary Biology 21: 1175–88, DOI:10.1111/j.1420-9101.2008.01550.x.
  In the context of MLS-1 scenarios, and considering only generation-to-generation changes, ideas which sound very different when said in words are mathematically interconvertible, with only linear transformations of coordinates. I put this down here because of caveats about the distinction between MLS-1 and MLS-2, the terminology of “relatedness” versus “assortment” and the solecism of writing the Price Equation with covariances.

Last updated 7 May 2013.

What’s even more interesting is that most seem to have forgotten that basically an identical study had already been published back in 2008 in one of the world’s top medical journals. In fact, we covered this study nearly 5 years ago on this very blog!

That not-so-new study suggested that monetary reward may be a better motivator for behavior change and ultimately, weight-loss, than the commonly touted health benefits.

Here’s the details of that peer-reviewed and published study:

Dr. Volpp and colleagues tracked the weight change in 57 obese individuals (30-70 years of age) who were randomized to either a no-treatment control group or to 1 of 2 financial incentive programs (a lottery incentive group, or a deposit incentive group). All participants were instructed to lower their weight (via diet and exercise) by 1 lb per week for the duration of the 16 week intervention, thus aiming for a total target weight-loss of 16 lbs. Individuals in the incentive groups received their financial rewards on a monthly basis, only if they had met or exceeded their target weight loss (1lb/wk). Those that failed to make the weight-loss goal were merely told how much money they would have received if they had been successful, whereas the control group received no reward regardless of their progress.

Over the course of the 4 month intervention individuals in the incentive groups earned an average of approximately $300, in contrast to $0 awarded to those in the control group. Interestingly, the average weight loss achieved by those receiving a financial incentive was significantly greater as compared to that of the control group (13-14lbs vs. 4 lbs, respectively). Furthermore, only 10% of individuals in the control group versus approximately 50% of those in the incentive groups achieved the target weight-loss of 16lbs.

However, during a subsequent 3-month follow-up, study participants gained back much of the lost weight after the cessation of the financial incentives – a finding which is common to most, if not all, weight-loss intervention studies.

This study extends findings of a previous investigation in which participants who were offered $14 per percent decrease in weight lost about 5lbs, while those who were offered no compensation lost 2lbs during the 3 month intervention.

So how can any of this be applied in the real-world?

The thinking goes – if an overweight individual has previously had trouble adhering to a diet and/or exercise program, investing some of his/her own money may provide a novel incentive to stay on track in order to avoid losing money – the basic concept of loss aversion.  For example, you can hand over $100 to a trusted friend/spouse/family member and sign a contract before embarking on a lifestyle change. This trusted individual is instructed to return the money in full if you achieve your goal, or otherwise to donate your money to a cause that you find distasteful – like the NRA or the Church of Scientology.

More than anything else, its a cute and gimmicky approach to providing incentive for weight loss, and the idea makes for great headlines (as recently illustrated). I’m sure financial incentives can work for some, but this is no obesity panacea.

Peter

1. Hamlet couldn’t have said anything much before the play starts, because he was off at school in Wittenberg.

2. He sees the ghost on the night of the first day in the play where he appears. Not a long delay there. And his reaction to being told “The serpent that did sting thy father’s life now wears his crown” is, “O my prophetic soul!” Or, in a different idiom, “Called it!”

3. He has every reason not to act rashly, because (a) he wants to be King (Claudius “popp’d in between the election and my hopes”), and (b) he can’t trust that the ghost is really his father. “The devil hath power to assume a pleasing shape”, etc. Watch your Star Trek, people! Emo!Hamlet is a comparatively recent invention. Prior to the late 1700s, the standard was to play Hamlet as a chessmaster, a brilliant young man trying to turn a bad situation to his advantage, facing a shrewd opponent.

4. It’s the characters in the play who remark on Hamlet’s “transformation”. That’s why Claudius sends for Rosencrantz and Guildenstern.

Welcome, dear Rosencrantz and Guildenstern!
Moreover that we much did long to see you,
The need we have to use you did provoke
Our hasty sending. Something have you heard
Of Hamlet’s transformation; so call it,
Sith nor the exterior nor the inward man
Resembles that it was.

5. He’s so antisocial that he…has a girlfriend? And, as Claudius says, is beloved by the general populace of Denmark? Indeed, that’s a big part of why Claudius doesn’t have Hamlet killed for stabbing Polonius. As he tells Laertes, he doesn’t want to hurt Gertrude, and in addition…

The other motive,
Why to a public count I might not go,
Is the great love the general gender bear him;
Who, dipping all his faults in their affection,
Would, like the spring that turneth wood to stone,
Convert his gyves to graces; so that my arrows,
Too slightly timber’d for so loud a wind,
Would have reverted to my bow again,
And not where I had aim’d them.

6. He won’t kill his uncle first because he wants to be crowned, not executed; and second, because he wants Claudius damned, not just dead.

A villain kills my father; and for that,
I, his sole son, do this same villain send
To heaven.
O, this is hire and salary, not revenge.
He took my father grossly, full of bread;
With all his crimes broad blown, as flush as May;
And how his audit stands who knows save heaven?
But in our circumstance and course of thought,
‘Tis heavy with him: and am I then revenged,
To take him in the purging of his soul,
When he is fit and season’d for his passage?
No!
Up, sword; and know thou a more horrid hent:
When he is drunk asleep, or in his rage,
Or in the incestuous pleasure of his bed;
At gaming, swearing, or about some act
That has no relish of salvation in’t;
Then trip him, that his heels may kick at heaven,
And that his soul may be as damn’d and black
As hell, whereto it goes. My mother stays:
This physic but prolongs thy sickly days.

7. He jokes bawdily with Rosencrantz and Guildenstern when they appear. They sell him out and were escorting him to his execution.

8. Horatio, an emotionless stoic? The man tries to commit suicide when he sees Hamlet dying.

9. Hamlet is backed into the swordfight (Osric: “I mean, my lord, the opposition of your person in trial”).

10. And, by that point, Hamlet has found that things only go his way when he seizes whatever random opportunities which come by. Hamlet in Act 5 is basically, “Trying to be L in Death Note didn’t work out. Fighting pirates, though, was pretty wicked.”

11. “Lives with his parents his entire life”? Hamlet was away at university in another country.

[deep breath]

OK. Better now.

Circadian rhythms are biological cycles that occur in humans, animals, insects, plants, and even bacteria with a period of approximately (circa) one day (diem). These rhythms are determined internally by a part of our hypothalamus and are synchronized perfectly to our 24-hr days by the sun and other cues. This internal clock mediates daily variation in everything from hormone levels, to sleep/wake cycles, feeding behaviour, thermoregulation, to bowel movements and cardiovascular function, among many others.

It is largely due to these predictable circadian rhythms that risk of a myocardial infarction (heart attack) is significantly highest in the morning (by about 40% as compared to other times in the day). Right as we awake, our cardiovascular system is in the most compromised state –systolic blood pressure and heart rate show the largest upward spike in the morning, blood vessels ability to dilate in response to increased blood flow is compromised (relative endothelial dysfunction), blood clots are more likely to form, and the ability to break them up is at its lowest point in the day. Is it any wonder then, that the first snowfall – shoveled early in the morning by people at risk – always leads to a spike in heart attacks?

Interestingly, the 1hr shift experienced by citizens of many countries (most notably Europe and North America) during the fall and spring in accordance with daylight savings time also has a detrimental effect on cardiovascular risk. The problem lies in the fact that our circadian clock takes time to adjust, and it is best adjusted by changes in day/night or light/dark cycles – not simply the adjustment of our watch. Thus, the few mornings after the clock change our internal clocks are at odds with our watches and particularly in the spring – when one hour of sleep is lost, we wake up with our cardiovascular system being in an even more compromised state than normal.

A 2009 study in the New England Journal of Medicine clearly shows this effect. In the study the authors investigated the number of heart attacks in Sweden the week before and the week after the 1hr clock changes in both the spring and fall. As would be predicted, individuals had an approximately 5% greater risk of having a heart attack immediately after the ‘spring ahead’ clock change compared to the previous week.

The authors rightfully suggest that individuals at risk of cardiovascular complications would be better off changing their clocks more gradually (i.e. by 15 minutes, starting on the Friday before the change). More importantly, avoiding strenuous activity and stress right in the morning may also be a valid suggestion.

An even better strategy from a public health standpoint would be to do away with daylight savings time altogether.

Peter

Abstract:

A stochastic version of the Brusselator model is proposed and studied via the system size expansion. The mean-field equations are derived and shown to yield to organized Turing patterns within a specific parameters region. When determining the Turing condition for instability, we pay particular attention to the role of cross-diffusive terms, often neglected in the heuristic derivation of reaction-diffusion schemes. Stochastic fluctuations are shown to give rise to spatially ordered solutions, sharing the same quantitative characteristic of the mean-field based Turing scenario, in term of excited wavelengths. Interestingly, the region of parameter yielding to the stochastic self-organization is wider than that determined via the conventional Turing approach, suggesting that the condition for spatial order to appear can be less stringent than customarily believed.

See also the commentary by Mehran Kardar.

I’ve written this blog in it’s many forms for a number of years now, at a number of venues. It’s moving day again.

I’ll give details at the new place, but please note that you will so find new posts appearing at the new White Coat Underground at Forbes.com.

“Well, there’s this guy who made a movie about a cute farmboy in the boondocks who never knew his real father, dreams of outer space, fights in a bar full of crazy aliens and then goes up against the evil overlord who killed his father—this really nasty guy with Roman Empire trappings, favorite color black, lots of glowy green energy—and who flies around in a giant ship bigger than anything else in space blowing up planets. He blasts the home planet of one of the heroes early on, so we know he’s serious, and at the end, it’s a race with the clock to stop him blowing up the planet that’s really important. But the good guys win and there’s a flashy award ceremony to wrap it all up.”

“Sounds great! Is there stuff which only makes sense if, like, Fate or Destiny is willing it?”

“Like you wouldn’t believe!”

“Perfect!”

Those of you from the north know the non-sound of snow falling, the “indoors” feeling of sounds after a heavy snowfall. When we do get enough snow around here (my area is in a bit of a snow shadow) I head out on snowshoes a find my self alone in a large metro area, able to enjoy the sounds. The other night I heard howling and yipping, and had no idea whether it was dogs or coyotes (or both).

The frigid weather this past week gave our local landfill-associated ski areas to make a ton of snow. I dragged PalKid out of bed and we’re heading out soon for a day of brief runs on grainy snow. It’s gonna be a blast.

I’ve written a number of times about how a physician must be careful not impose his or her personal beliefs on patients.

Another interesting case has hit the news. The decision of the California Supreme Court hinged on interpretation of state non-discrimination law. I’m not a lawyer, but I do know a bit about medicine and medical ethics. Regardless of law, this doctor’s behavior was wrong. The details are a little sketchy, but an unmarried lesbian woman was denied fertility treatments by a California doctor because the treatment conflicted with the doctor’s faith.
Conflicted with the doctor’s faith. There’s the rub.

This is a particularly perverse form of proselytizing. It doesn’t involve having coffee with an acquaintance and teaching them the Word. It involves a vulnerable individual, who comes to a qualified professional for help, and is turned away because of “improper” living and thinking. In this case, it is disputed whether the patient was denied care because of being gay or because of being unmarried. It doesn’t really matter. Either reason for discrimination is wrong. What matters is that the doctor felt that treating the patient would violate her own religious beliefs.

The measure of whether a treatment is appropriate is whether it conforms to standard of care, is safe, effective, and ethical (non-coercive, etc.). If a patient presents for infertility treatment, and is medically qualified, she should receive the treatment (assuming she doesn’t breed babies for snack food). The American Society for Reproductive Medicine recognizes this in several position statements. One specifically addresses unmarried and homosexual patients:

–Unmarried persons and gays and lesbians have interests in
having and rearing children.
– There is no persuasive evidence that children raised by
single parents or by gays and lesbians are harmed or
disadvantaged by that fact alone.
–Programs should treat all requests for assisted reproduction
equally without regard to marital status or sexual
orientation.

When you decide to become a doctor, you immerse yourself to the neck in ethical problems for the rest of your career. Patients make bad decisions. Other doctors make bad decisions. Ethically grey conundrums pop up on a daily basis. Standards set by professional organizations help to sort some of these out, but not always. The “most wrong” decision in an ethical debate is the cop-out. For a physician to deny a patient care based on their own beliefs is a cop-out, and is a coercive use of their paternalistic powers. This decision doesn’t just deny them your personal services. It may cause permanent psychological harm to the patient. And that’s not what doctoring is all about.

Another doctor in our area specializes in so-called “holistic” medicine. He runs expensive tests that aren’t covered by insurance. Many of these tests are either of questionable significance and utility, or are run in labs widely known for their “variable” quality. He puts his patients on unconventional mixes of medications and supplements, many of which he apparently sells. He and many doctors like him send their patients to “real” doctors to take care of the rest of the patient’s healthcare.

In the first case, the cops caught up with the guy. The fallout for patients will last for a while as the scramble to find new primary care physicians (there’s a shortage, you know), or have to suddenly deal with a narcotic problem after their source dries up.

In the second case, the doctor will continue to collect cash from patient to whom is is very kind, and who get the answers they want from a kind man.

The second doctor isn’t doing anything illegal. He’s practicing bad medicine, outside of the standard of care, but as far as I can tell, he’s not breaking any laws. And his patients love him. He listens, spends time, and tells them what they want to hear. I looked into ways to get this guy investigated, to have some sort of third party look over his practices, but I couldn’t find one. Complaints against healthcare professionals have to be lodged by patients or their agent. As far as I can tell, in this state there is no way for anyone other than a patient to complain about bad doctors.

This makes some sense. If someone opens a practice across the street from me and my patients start fleeing there, who says I wouldn’t call in a complaint just to hurt my competition? (I wouldn’t obviously, and there’s no incentive even if I were a bad guy. There are plenty of patients for all of us.)

But while doctors clearly breaking the law can get caught and prosecuted, doctors practicing obviously bad medicine are pretty safe. Their patients often love them and wouldn’t think of lodging a complaint. Even if every other doctor in the community knows another doctor is bad news, there’s nothing they can really do.

I may not be completely right. Maybe there’s a way to complain to the medical board in this state. Maybe not. I couldn’t find one, and I’ve never heard of it happening.

Doctors get disciplined if patients complain, maybe get busted for breaking the law, maybe get sued if a patient is unsatisfied, but they don’t get investigated for being quacks.

I don’t have a solution to propose that wouldn’t create layers of bureaucracy and put good doctors at risk of false allegations. But there must be some way to deal with quacks. Their work harms patients and makes my job difficult as I try to tease apart what they’ve done to my patients.

I think there is something else that must be said because it is a magnificent demonstration of discipline. With all of the thousands and hundreds of thousands of people engaged in this demonstration today, there has not been one reported incident of violence. I think this is a magnificent demonstration of our commitment to nonviolence in this struggle for freedom all over the United States, and I want to commend the leadership of this community for making this great event possible and making such a great event possible through such disciplined channels.

Almost one hundred and one years ago, on September the 22nd, 1862, to be exact, a great and noble American, Abraham Lincoln, signed an executive order, which was to take effect on January the first, 1863. This executive order was called the Emancipation Proclamation and it served to free the Negro from the bondage of physical slavery. But one hundred years later, the Negro in the United States of America still isn’t free.

But now more than ever before, America is forced to grapple with this problem, for the shape of the world today does not afford us the luxury of an anemic democracy. The price that this nation must pay for the continued oppression and exploitation of the Negro or any other minority group is the price of its own destruction. For the hour is late. The clock of destiny is ticking out, and we must act now before it is too late. 

The events of Birmingham, Alabama, and the more than sixty communities that have started protest movements since Birmingham, are indicative of the fact that the Negro is now determined to be free. For Birmingham tells us something in glaring terms. It says first that the Negro is no longer willing to accept racial segregation in any of its dimensions.For we have come to see that segregation is not only sociologically untenable, it is not only politically unsound, it is morally wrong and sinful. Segregation is a cancer in the body politic, which must be removed before our democratic health can be realized.  Segregation is wrong because it is nothing but a new form of slavery covered up with certain niceties of complexity. Segregation is wrong because it is a system of adultery perpetuated by an illicit intercourse between injustice and immorality.  And in Birmingham, Alabama, and all over the South and all over the nation, we are simply saying that we will no longer sell our birthright of freedom for a mess of segregated pottage.  In a real sense, we are through with segregation now, henceforth, and forevermore.

Now Birmingham and the freedom struggle tell us something else. They reveal to us that the Negro has a new sense of dignity and a new sense of self-respect. For years— I think we all will agree that probably the most damaging effect of segregation has been what it has done to the soul of the segregated as well as the segregator.It has given the segregator a false sense of superiority and it has left the segregated with a false sense of inferiority.  And so because of the legacy of slavery and segregation, many Negroes lost faith in themselves and many felt that they were inferior.

But then something happened to the Negro. Circumstances made it possible and necessary for him to travel more: the coming of the automobile, the upheavals of two world wars, the Great Depression. And so his rural, plantation background gradually gave way to urban, industrial life. And even his economic life was rising through the growth of industry, the influence of organized labor, expanded educational opportunities. And even his cultural life was rising through the steady decline of crippling illiteracy. And all of these forces conjoined to cause the Negro to take a new look at himself. Negro masses,  Negro masses all over began to re-evaluate themselves, and the Negro came to feel that he was somebody. His religion revealed to him, his religion revealed to him that God loves all of his children, and that all men are made in His image, and that figuratively speaking, every man from a bass-black to a treble-white is significant on God’s keyboard.

So, the Negro can now unconsciously cry out with the eloquent poet,

Fleecy locks and black complexion

Cannot forfeit nature’s claim.

Skin may differ, but affection

Dwells in black and white the same.

Were I so tall as to reach the pole

Or to grasp at the ocean at a span,

I must be measured by my soul

The mind is the standard of the man.

But these events that are taking place in our nation tell us something else. They tell us that the Negro and his allies in the white community now recognize the urgency of the moment. I know we have heard a lot of cries saying, “Slow up and cool off.”  We still hear these cries. They are telling us over and over again that you’re pushing things too fast, and so they’re saying, “Cool off.” Well, the only answer that we can give to that is that we’ve cooled off all too long, and that is the danger.  There’s always the danger if you cool off too much that you will end up in a deep freeze.  ”Well,” they’re saying, “you need to put on brakes.” The only answer that we can give to that is that the motor’s now cranked up and we’re moving up the highway of freedom toward the city of equality,  and we can’t afford to stop now because our nation has a date with destiny. We must keep moving.

Then there is another cry. They say, “Why don’t you do it in a gradual manner?” Well, gradualism is little more than escapism and do-nothingism, which ends up in stand-stillism.  We know that our brothers and sisters in Africa and Asia are moving with jet-like speed toward the goal of political independence. And in some communities we are still moving at horse-and-buggy pace toward the gaining of a hamburger and a cup of coffee at a lunch counter.

And so we must say, now is the time to make real the promises of democracy. Now is the time to transform this pending national elegy into a creative psalm of brotherhood. Now is the time to lift our nation. Now is the time to lift our nation from the quicksands of racial injustice to the solid rock of racial justice. Now is the time to get rid of segregation and discrimination. Now is the time.

And so this social revolution taking place can be summarized in three little words. They are not big words. One does not need an extensive vocabulary to understand them. They are the words “all,” “here,” and “now.” We wantall of our rights, we want them here, and we want them now.

Now the other thing that we must see about this struggle is that by and large it has been a nonviolent struggle. Let nobody make you feel that those who are engaged or who are engaging in the demonstrations in communities all across the South are resorting to violence; these are few in number. For we’ve come to see the power of nonviolence. We’ve come to see that this method is not a weak method, for it’s the strong man who can stand up amid opposition, who can stand up amid violence being inflicted upon him and not retaliate with violence.

You see, this method has a way of disarming the opponent. It exposes his moral defenses. It weakens his morale, and at the same time it works on his conscience, and he just doesn’t know what to do. If he doesn’t beat you, wonderful. If he beats you, you develop the quiet courage of accepting blows without retaliating. If he doesn’t put you in jail, wonderful. Nobody with any sense likes to go to jail. But if he puts you in jail, you go in that jail and transform it from a dungeon of shame to a haven of freedom and human dignity.And even if he tries to kill you, (He can’t kill you) you’ll develop the inner conviction that there are some things so dear, some things so precious, some things so eternally true, that they are worth dying for.  And I submit to you that if a man has not discovered something that he will die for, he isn’t fit to live.

This method has wrought wonders. As a result of the nonviolent Freedom Ride movement, segregation in public transportation has almost passed away absolutely in the South. As a result of the sit-in movement at lunch counters, more than 285 cities have now integrated their lunch counters in the South. I say to you, there is power in this method.

And I think by following this approach it will also help us to go into the new age that is emerging with the right attitude. For nonviolence not only calls upon its adherents to avoid external physical violence, but it calls upon them to avoid internal violence of spirit. It calls on them to engage in that something called love. And I know it is difficult sometimes. When I say “love” at this point, I’m not talking about an affectionate emotion. (All right) It’s nonsense to urge people, oppressed people, to love their oppressors in an affectionate sense. I’m talking about something much deeper. I’m talking about a sort of understanding, creative, redemptive goodwill for all men.

We are coming to see now, the psychiatrists are saying to us, that many of the strange things that happen in the subconscience, many of the inner conflicts, are rooted in hate. And so they are saying, “Love or perish.” But Jesus told us this a long time ago. And I can still hear that voice crying through the vista of time, saying, “Love your enemies, bless them that curse you, pray for them that despitefully use you.” And there is still a voice saying to every potential Peter, “Put up your sword.” History is replete with the bleached bones of nations, history is cluttered with the wreckage of communities that failed to follow this command. And isn’t it marvelous to have a method of struggle where it is possible to stand up against an unjust system, fight it with all of your might, never accept it, and yet not stoop to violence and hatred in the process? This is what we have.

Now there is a magnificent new militancy within the Negro community all across this nation. And I welcome this as a marvelous development. The Negro of America is saying he’s determined to be free and he is militant enough to stand up. But this new militancy must not lead us to the position of distrusting every white person who lives in the United States. There are some white people in this country who are as determined to see the Negro free as we are to be free. This new militancy must be kept within understanding boundaries.

And then another thing I can understand. We’ve been pushed around so long; we’ve been the victims of lynching mobs so long; we’ve been the victims of economic injustice so long—still the last hired and the first fired all over this nation. And I know the temptation. I can understand from a psychological point of view why some caught up in the clutches of the injustices surrounding them almost respond with bitterness and come to the conclusion that the problem can’t be solved within, and they talk about getting away from it in terms of racial separation. But even though I can understand it psychologically, I must say to you this afternoon that this isn’t the way. Black supremacy is as dangerous as white supremacy. No, I hope you will allow me to say to you this afternoon that God is not interested merely in the freedom of black men and brown men and yellow men. God is interested in the freedom of the whole human race.And I believe that with this philosophy and this determined struggle we will be able to go on in the days ahead and transform the jangling discords of our nation into a beautiful symphony of brotherhood.

As I move toward my conclusion, you’re asking, I’m sure, “What can we do here in Detroit to help in the struggle in the South?” Well, there are several things that you can do. One of them you’ve done already, and I hope you will do it in even greater dimensions before we leave this meeting.

Now the second thing that you can do to help us down in Alabama and Mississippi and all over the South is to work with determination to get rid of any segregation and discrimination in Detroit,realizing that injustice anywhere is a threat to justice everywhere. And we’ve got to come to see that the problem of racial injustice is a national problem. No community in this country can boast of clean hands in the area of brotherhood. Now in the North it’s different in that it doesn’t have the legal sanction that it has in the South. But it has its subtle and hidden forms and it exists in three areas: in the area of employment discrimination, in the area of housing discrimination, and in the area of de facto segregation in the public schools. And we must come to see that de facto segregation in the North is just as injurious as the actual segregation in the South.  And so if you want to help us in Alabama and Mississippi and over the South, do all that you can to get rid of the problem here.

And then we also need your support in order to get the civil rights bill that the President is offering passed. And there’s a reality, let’s not fool ourselves: this bill isn’t going to get through if we don’t put some work in it and some determined pressure. And this is why I’ve said that in order to get this bill through, we’ve got to arouse the conscience of the nation, and we ought to march to Washington more than 100,000 in order to say,  in order to say that we are determined, and in order to engage in a nonviolent protest to keep this issue before the conscience of the nation.

And if we will do this we will be able to bring that new day of freedom into being. If we will do this we will be able to make the American dream a reality. And I do not want to give you the impression that it’s going to be easy. There can be no great social gain without individual pain. And before the victory for brotherhood is won, some will have to get scarred up a bit. Before the victory is won, some more will be thrown into jail. Before the victory is won, some, like Medgar Evers, may have to face physical death. But if physical death is the price that some must pay to free their children and their white brothers from an eternal psychological death, then nothing can be more redemptive. Before the victory is won, some will be misunderstood and called bad names, but we must go on with a determination and with a faith that this problem can be solved. 

And so I go back to the South not in despair. I go back to the South not with a feeling that we are caught in a dark dungeon that will never lead to a way out. I go back believing that the new day is coming. And so this afternoon, I have a dream.  It is a dream deeply rooted in the American dream.

I have a dream that one day, right down in Georgia and Mississippi and Alabama, the sons of former slaves and the sons of former slave owners will be able to live together as brothers.

I have a dream this afternoon (I have a dream) that one day, one day little white children and little Negro children will be able to join hands as brothers and sisters.

I have a dream this afternoon that one day,  that one day men will no longer burn down houses and the church of God simply because people want to be free.

I have a dream this afternoon (I have a dream) that there will be a day that we will no longer face the atrocities that Emmett Till had to face or Medgar Evers had to face, that all men can live with dignity.

I have a dream this afternoon (Yeah) that my four little children, that my four little children will not come up in the same young days that I came up within, but they will be judged on the basis of the content of their character, not the color of their skin.

I have a dream this afternoon that one day right here in Detroit, Negroes will be able to buy a house or rent a house anywhere that their money will carry them and they will be able to get a job.

Yes, I have a dream this afternoon that one day in this land the words of Amos will become real and “justice will roll down like waters, and righteousness like a mighty stream.”

I have a dream this evening that one day we will recognize the words of Jefferson that “all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.” I have a dream this afternoon.

I have a dream that one day every valley shall be exalted, and “every valley shall be exalted, and every hill shall be made low; the crooked places shall be made straight, and the rough places plain; and the glory of the Lord shall be revealed, and all flesh shall see it together.”

I have a dream this afternoon that the brotherhood of man will become a reality in this day.

And with this faith I will go out and carve a tunnel of hope through the mountain of despair. With this faith, I will go out with you and transform dark yesterdays into bright tomorrows. With this faith, we will be able to achieve this new day when all of God’s children, black men and white men, Jews and Gentiles, Protestants and Catholics, will be able to join hands and sing with the Negroes in the spiritual of old:

Free at last! Free at last!

Thank God almighty, we are free at last!

Genocide is organized, it’s systematic, it’s supported by people in power. It’s aim to to terrorize and murder large groups of people who share a trait. One could argue that many of Stalin’s millions of murders were not genocide as the targets shared little in common other than Stalin wanted them dead (there are obvious exceptions with some Soviet ethnic minorities). Naziism still serves as our best example of genocide.

Once the Nazi regime decided that Jews would be the target, they systematically drove German Jews out of business, destroyed their places of worship, shot them, beat them, put them in rail cars segregating and murdering them. The entire power of the state was set against an ethnic group. The Germans, who a few years before had been reduced to an impoverished country with little military might, built a dictatorship and a powerful military using the consent of the people, terror, murder, and propaganda. The majority of Germans didn’t oppose this. Any ethnic minority who was labelled to die did just that because an entire state was set against them.

Lately, a segment of the US gun-nut population has been (non-ironically) comparing gun control to Naziism. It’s really hard to believe any explanation for this idiocy is necessary, but let’s look at this analogy a bit.

What is the supposed tyranny gun nuts want to oppose? When you break it down, read their literature, much of it is directed at the US government and at President Obama in particular. When he was first elected, guns and ammunition flew off the shelves. People completely lost their shit, if they ever had it in the first place.

Obama and Hitler share one common trait: they started as democratically-elected leaders. Barely, in Hitler’s case, as his terror gangs helped ensure his political opponents were in no shape to oppose him. In Obama’s case, Americans decided they wanted him to be president, not any of the other guys. This happened despite attempts to dis-enfranchise likely-Democratic voters. Because we are a fundamentally stable democracy, elections work.

Guns have never played a part in the maintenance of a democracy in the US. Gun ownership in the colonies, which existed for more than a century before the revolution perhaps made it easier to form an army to oppose the Brits, but really, without the external support of France, without the distances involved, the war would have lasted much longer. The colonies were, fundamentally, un-rulable and the real question was how much blood would have to be spilled to prove it.

The civil war, in which a large number of Americans rebelled against what they saw as an unjust government killed people—lots of people. It destroyed large swaths of the country. And the war was not won because Unionists kept guns at home, but because the industrial north could manufacture sophisticated weapons in large numbers.

The so-called disarming of the population feared by the gun-nuts isn’t happening, and if it did (we can only hope), it wouldn’t change our form of government, wouldn’t change our ability to resist tyranny from home or abroad. If the US government really wanted to become a dictatorship (unlikely to ever happen), disarming the population wouldn’t even be necessary. The navy could simply drop a JDAM on people they didn’t like.

But we do have constitutional protections against dictatorship, and they’ve worked for centuries. We have a tripartite government with checks and balances, we have a military that is forbidden from intervening domestically, and frankly, Americans simply haven’t been interested in tyranny as a form of government and have rejected leaders who were interested in it.

The government doesn’t want your guns. But many of us Americans want better control of the firearms trade, want military-style weapons off the market, and would like to see far fewer than 30,000 gun deaths a year. And because we’re sane, we don’t think that gun control means Obama is going to ship some ethnic group or another to camps and kill them.

America hasn’t done genocide well for a long time. When we nearly destroyed the entire indigenous American population we were un-apologetic, but we’ve managed not to repeat ourselves, and we’re unlikely to in the future.

Here’s an excerpt:

19,000 people fit into the new Barclays Center to see Jay-Z perform. This blog was viewed about 58,000 times in 2012. If it were a concert at the Barclays Center, it would take about 3 sold-out performances for that many people to see it.

Click here to see the complete report.

Abstract: Shearing solutions of fibers or polymers tends to align fiber or polymers in the flow direction. Here, non-Brownian rods subjected to oscillatory shear align perpendicular to the flow while the system undergoes a nonequilibrium absorbing phase transition. The slow alignment of the fibers can drive the system through the critical point and thus promote the transition to an absorbing state. This picture is confirmed by a universal scaling relation that collapses the data with critical exponents that are consistent with conserved directed percolation.

I read this one a while ago in non-arXiv preprint form, but now it’s on the arXiv. M. Raghib et al. (2011), “A Multiscale maximum entropy moment closure for locally regulated space-time point process models of population dynamics”, Journal of Mathematical Biology 62, 5: 605–53. arXiv:1202.6092 [q-bio].

Abstract: The pervasive presence spatial and size structure in biological populations challenges fundamental assumptions at the heart of continuum models of population dynamics based on mean densities (local or global) only. Individual-based models (IBM’s) were introduced over the last decade in an attempt to overcome this limitation by following explicitly each individual in the population. Although the IBM approach has been quite insightful, the capability to follow each individual usually comes at the expense of analytical tractability, which limits the generality of the statements that can be made. For the specific case of spatial structure in populations of sessile (and identical) organisms, space-time point processes with local regulation seem to cover the middle ground between analytical tractability and a higher degree of biological realism. Continuum approximations of these stochastic processes distill their fundamental properties, but they often result in infinite hierarchies of moment equations. We use the principle of constrained maximum entropy to derive a closure relationship for one such hierarchy truncated at second order using normalization and the product densities of first and second orders as constraints. The resulting `maxent’ closure is similar to the Kirkwood superposition approximation, but it is complemented with previously unknown correction terms that depend on on the area for which third order correlations are irreducible. This region also serves as a validation check, since it can only be found if the assumptions of the closure are met. Comparisons between simulations of the point process, alternative heuristic closures, and the maxent closure show significant improvements in the ability of the maxent closure to predict equilibrium values for mildly aggregated spatial patterns.

J. A. Bonachela, M. A. Munoz and S. A. Levin (2012). “Patchiness and Demographic Noise in Three Ecological Examples” [arXiv:1205.3389].

Abstract: Understanding the causes and effects of spatial aggregation is one of the most fundamental problems in ecology. Aggregation is an emergent phenomenon arising from the interactions between the individuals of the population, able to sense only—at most—local densities of their cohorts. Thus, taking into account the individual-level interactions and fluctuations is essential to reach a correct description of the population. Classic deterministic equations are suitable to describe some aspects of the population, but leave out features related to the stochasticity inherent to the discreteness of the individuals.Stochastic equations for the population do account for these fluctuation-generated effects by means of demographic noise terms but, owing to their complexity, they can be difficult (or, at times, impossible) to deal with. Even when they can be written in a simple form, they are still difficult to numerically integrate due to the presence of the “square-root” intrinsic noise. In this paper, we discuss a simple way to add the effect of demographic stochasticity to three classic, deterministic ecological examples where aggregation plays an important role. We study the resulting equations using a recently-introduced integration scheme especially devised to integrate numerically stochastic equations with demographic noise. Aimed at scrutinizing the ability of these stochastic examples to show aggregation, we find that the three systems not only show patchy configurations, but also undergo a phase transition belonging to the directed percolation universality class.

A. F. Lütz et al. (2012), “Intransitivity and coexistence in four species cyclic games” [arXiv:1205.6411].

Abstract: Intransitivity is a property of connected, oriented graphs representing species interactions that may drive their coexistence even in the presence of competition, the standard example being the three species Rock-Paper-Scissors game. We consider here a generalization with four species, the minimum number of species that allows other interactions beyond the single loop (one predator, one prey). We show that, contrary to the mean field prediction, on a square lattice the model presents a transition, as the invasion rates change, from a coexistence to a state in which one species gets extinct. Such a dependence on the invasion rates shows that the interaction graph structure alone is not enough to predict the outcome of such models. In addition, different invasion rates permit to tune the level of transitiveness, indicating that for the coexistence of all species to persist, there must be a minimum amount of intransitivity.

Interesting things the authors observe about their model:

1. A phase transition as a function of invasion rate $\chi$ appears in the lattice simulations which the mean-field approximation doesn’t pick up at all.

2. The pair approximation (first-order correction to the mean field) fails too. I’d like to see this treated in more detail, as I’ve grown used to seeing mean-field approximations fail for spatial lattices, so the interesting question is whether the adjustments on top of them do any better.

U. Dobramysl and U. C. Täuber (2012), “Environmental vs. demographic variability in two-species predator-prey models” [arXiv:1206.0973].

Abstract: We investigate the competing effects and relative importance of intrinsic demographic and environmental variability on the evolutionary dynamics of a stochastic two-species Lotka-Volterra model by means of Monte Carlo simulations on a two-dimensional lattice. Individuals are assigned inheritable predation efficiencies; quenched randomness in the spatially varying reaction rates serves as environmental noise. We find that environmental variability enhances the population densities of both predators and prey while demographic variability leads to essentially neutral optimization.

X. Chen et al. (2012), “Impact of generalized benefit functions on the evolution of cooperation in spatial public goods games with continuous strategies” Physical Review E 85: 066133 [arXiv:1206.7119]. Interesting on a first skim (I’ve done some numerical work on a case analogous to their sharp-cutoff limit, in various population structures).

Abstract: Cooperation and defection may be considered as two extreme responses to a social dilemma. Yet the reality is much less clear-cut. Between the two extremes lies an interval of ambivalent choices, which may be captured theoretically by means of continuous strategies defining the extent of the contributions of each individual player to the common pool. If strategies are chosen from the unit interval, where 0 corresponds to pure defection and 1 corresponds to the maximal contribution, the question is what is the characteristic level of individual investments to the common pool that emerges if the evolution is guided by different benefit functions. Here we consider the steepness and the threshold as two parameters defining an array of generalized benefit functions, and we show that in a structured population there exist intermediate values of both at which the collective contributions are maximal. However, as the cost-to-benefit ratio of cooperation increases the characteristic threshold decreases, while the corresponding steepness increases. Our observations remain valid if more complex sigmoid functions are used, thus reenforcing the importance of carefully adjusted benefits for high levels of public cooperation.

L. D. Fernandes and M. A. M. de Aguiar (2012), “Turing patterns and apparent competition in predator-prey food webs on networks” [arXiv:1207.3424].

Abstract: Reaction-diffusion systems may lead to the formation of steady state heterogeneous spatial patterns, known as Turing patterns. Their mathematical formulation is important for the study of pattern formation in general and play central roles in many fields of biology, such as ecology and morphogenesis. In the present study we focus on the role of Turing patterns in describing the abundance distribution of predator and prey species distributed in patches in a scale free network structure. We extend the original model proposed by Nakao and Mikhailov by considering food chains with several interacting pairs of preys and predators. We identify patterns of species distribution displaying high degrees of apparent competition driven by Turing instabilities. Our results provide further indication that differences in abundance distribution among patches may be, at least in part, due to self organized Turing patterns, and not necessarily to intrinsic environmental heterogeneity.

A. Szolnoki et al. (2012), “Defense mechanisms of empathetic players in the spatial ultimatum game” Physical Review Letters 109: 078701 [arXiv:1207.4786].

Abstract: Experiments on the ultimatum game have revealed that humans are remarkably fond of fair play. When asked to share an amount of money, unfair offers are rare and their acceptance rate small. While empathy and spatiality may lead to the evolution of fairness, thus far considered continuous strategies have precluded the observation of solutions that would be driven by pattern formation. Here we introduce a spatial ultimatum game with discrete strategies, and we show that this simple alteration opens the gate to fascinatingly rich dynamical behavior. Besides mixed stationary states, we report the occurrence of traveling waves and cyclic dominance, where one strategy in the cycle can be an alliance of two strategies. The highly webbed phase diagram, entailing continuous and discontinuous phase transitions, reveals hidden complexity in the pursuit of human fair play.

S. M. Messinger and A. Ostling (2012), “The influence of host demography, pathogen virulence, and relationships with pathogen virulence on the evolution of pathogen transmission in a spatial context” Evolutionary Ecology DOI: 10.1007/s10682-012-9594-y.

Abstract: A major challenge in evolutionary ecology is to explain extensive natural variation in transmission rates and virulence across pathogens. Host and pathogen ecology is a potentially important source of that variation. Theory of its effects has been developed through the study of non-spatial models, but host population spatial structure has been shown to influence evolutionary outcomes. To date, the effects of basic host and pathogen demography on pathogen evolution have not been thoroughly explored in a spatial context. Here we use simulations to show that space produces novel predictions of the influence of the shape of the pathogen’s transmission–virulence tradeoff, as well as host reproduction and mortality, on the pathogen’s evolutionary stable transmission rate. Importantly, non-spatial models predict that neither the slope of linear transmission–virulence relationships, nor the host reproduction rate will influence pathogen evolution, and that host mortality will only influence it when there is a transmission–virulence tradeoff. We show that this is not the case in a spatial context, and identify the ecological conditions under which spatial effects are most influential. Thus, these results may help explain observed natural variation among pathogens unexplainable by non-spatial models, and provide guidance about when space should be considered. We additionally evaluate the ability of existing analytical approaches to predict the influence of ecology, namely spatial moment equations closed with an improved pair approximation (IPA). The IPA is known to have limited accuracy, but here we show that in the context of pathogens the limitations are substantial: in many cases, IPA incorrectly predicts evolution to pathogen-driven extinction. Despite these limitations, we suggest that the impact of ecology can still be understood within the conceptual framework arising from spatial moment equations, that of “self-shading’’, whereby the spread of highly transmissible pathogens is impeded by local depletion of susceptible hosts.

I think “descendant-shading” would be a better term than “self-shading” here, since it indicates more clearly the timescales involved.

S. Heilmann, K. Sneppen and S. Krishna (2012), “Coexistence of phage and bacteria on the boundary of self-organized refuges” PNAS 109, 31: 12828–33. DOI: 10.1073/pnas.1200771109.

Abstract: Bacteriophage are voracious predators of bacteria and a major determinant in shaping bacterial life strategies. Many phage species are virulent, meaning that infection leads to certain death of the host and immediate release of a large batch of phage progeny. Despite this apparent voraciousness, bacteria have stably coexisted with virulent phages for eons. Here, using individual-based stochastic spatial models, we study the conditions for achieving coexistence on the edge between two habitats, one of which is a bacterial refuge with conditions hostile to phage whereas the other is phage friendly. We show how bacterial density-dependent, or quorum-sensing, mechanisms such as the formation of biofilm can produce such refuges and edges in a self-organized manner. Coexistence on these edges exhibits the following properties, all of which are observed in real phage–bacteria ecosystems but difficult to achieve together in nonspatial ecosystem models: (i) highly efficient virulent phage with relatively long lifetimes, high infection rates and large burst sizes; (ii) large, stable, and high-density populations of phage and bacteria; (iii) a fast turnover of both phage and bacteria; and (iv) stability over evolutionary timescales despite imbalances in the rates of phage vs. bacterial evolution.

G. Demirel, F. Vazquez, G. A. Böhme and T. Gross (2012), “Moment-Closure Approximations for Discrete Adaptive Networks” [arXiv:1211.0449].

Moment-closure approximations are an important tool in the analysis of the dynamics on both static and adaptive networks. Here, we provide a broad survey over different approximation schemes by applying each of them to the adaptive voter model. While already the simplest schemes provide reasonable qualitative results, even very complex and sophisticated approximations fail to capture the dynamics quantitatively. We then perform a detailed analysis that identifies the emergence of specific correlations as the reason for the failure of established approaches, before presenting a simple approximation scheme that works best in the parameter range where all other approaches fail. By combining a focused review of published results with new analysis and illustrations, we seek to build up an intuition regarding the situations when existing approaches work, when they fail, and how new approaches can be tailored to specific problems.

C. Reigada and M. A. M. de Aguiar (2012), “Host-parasitoid persistence over variable spatio-temporally susceptible habitats: bottom-up effects of ephemeral resources” Oikos 121: 1665–79. DOI:10.1111/j.1600-0706.2011.20259.x.

We experimentally and theoretically investigated the persistence of hosts and parasitoids interacting in a Metapopulation structure consisting of Ephemeral Local Patches (MELPs). We used a host-parasitoid system consisting of necrophagous Diptera species and their pupal parasitoids. The basal resources used by the host species were assumed to be ephemeral, supporting only one generation of individuals before completely disappearing from the environment. We experimentally measured the host-parasitoid persistence and the effects of local demographic processes in two scenarios: (1) constant occurrence of basal resources at a single site (no dispersion or colonization of other sites) and (2) variable occurrence of basal resources between two sites (colonization of a new patch requiring species dispersal). The experimental setup and findings were then formalized into a mathematical model describing the interaction dynamics in a MELP structure. We evaluated the contribution of several factors to the host-parasitoid coexistence, such as resource allocation probability (probability of resource appearance in a site), variation in resource size and number of sites available to receive resources in the MELP. We found that demographic fluctuations and environmental stochasticity affected the density of migrants, patch habitat connectivity, persistence and spatial distribution of interacting species.

They did experiments! On nonsimulated life forms! With rotting meat and everything!

B. Allen, C. E. Tarnita (2012), “Measures of success in a class of evolutionary models with fixed population size and structure” Journal of Mathematical Biology online before print, DOI:10.1007/s00285-012-0622-x.

We investigate a class of evolutionary models, encompassing many established models of well-mixed and spatially structured populations. Models in this class have fixed population size and structure. Evolution proceeds as a Markov chain, with birth and death probabilities dependent on the current population state. Starting from basic assumptions, we show how the asymptotic (long-term) behavior of the evolutionary process can be characterized by probability distributions over the set of possible states. We then define and compare three quantities characterizing evolutionary success: fixation probability, expected frequency, and expected change due to selection. We show that these quantities yield the same conditions for success in the limit of low mutation rate, but may disagree when mutation is present. As part of our analysis, we derive versions of the Price equation and the replicator equation that describe the asymptotic behavior of the entire evolutionary process, rather than the change from a single state. We illustrate our results using the frequency-dependent Moran process and the birth–death process on graphs as examples. Our broader aim is to spearhead a new approach to evolutionary theory, in which general principles of evolution are proven as mathematical theorems from axioms.

(Last update: 2 December 2012.)

When I was in high school—at a pretty well-supported public school, out in the ‘burbs at the comparatively unimpoverished end of town—I took a “precalculus” class my eleventh-grade year. Most of the advanced-track students I knew did the same thing. (If you’d gotten yourself on the even-more-advanced track back in eigth grade, you took precalculus in tenth.) This was supposed to prepare us for taking the AP Calculus class our senior year, which would allow us to get college credit. Instead, it was a thoroughgoing waste of time. The content was a repeat of Algebra II/Trigonometry, which we’d taken the year before, with two exceptions thrown in. The first, probability, was a topic our teacher didn’t know how to teach. In fact, she admitted as much: “I don’t know how to teach probability, so you’re all going to read the book today.” The second, limits, served no purpose. I’ll explain why in a moment.

I suggest the following: scrap “precalculus” and replace it with a year-long statistics course. This plan has several advantages:

It takes care of the legitimate point raised by Hacker’s op-ed, what he called “citizen statistics.” If we need students to grow up being well-informed, numerate contributors to civilisation, let’s have a class on exactly that. Required reading: Darrell Huff’s How To Lie With Statistics (1954, but we could update it easily).

It’s easier to implement than demolishing all of post-arithmetic mathematics education and trying to invent a replacement. Just swap out one class! We could develop the necessary material comparatively quickly and try it out with a straightforward pilot program.

As an ancillary benefit, the course materials could be put online as OpenCourseWare for the general welfare.

Would replacing precalculus with statistics impair the students who go on to take AP Calculus? I doubt it. In fact, by teaching as much statistics as it’s possible to do without calculus, we’d prepare the way for improved calculus lessons. For example, when it comes time to show what you can actually use integration for, we could teach about probability distributions. Statistics class would, in part, be a precalculus course itself—just one with an actual raison d’être.

And as for the limits lesson, what serious harm could there be in missing one topic which had been shoved disjointedly into a clone of another class, and which everyone sees again the next year anyway? Personally, I’m of the mind that limits make more sense if you see them after the basic ideas of differential calculus. That way, you know what you’re aiming to do and why it matters. (This alternative also tracks better with the subject’s history: Newton and Leibniz came long before Weierstrass.) Otherwise, as a maths professor friend of mine told me, they look like a solution dying to meet a problem.

How did that precalculus class of mine teach us limits? Well, we had to do a lot of worksheets. Bear in mind, I’d already read about the subject in my father’s old calculus textbook (a doorstopper whose size and yellowing reminded me of a dictionary—far thicker than necessary for first learning the subject!). The book started with a healthy dose of examples, comparing a question one could answer with algebra or geometry and a corresponding question you’d need calculus for. Calculus, it said, was algebra and geometry “with the addition of the limit process.” What did “taking a limit” mean? If you had a function $f(x)$, then writing

$$ \lim_{x\rightarrow a} f(x) = L $$

means that you could make the value of $f(x)$ as close to $L$ as you wanted, by choosing $x$ to be sufficiently close to $a$.

Now, in my high-school precalculus class, this translated into plodding through several pages of Xeroxed problems. Almost all of them belonged to one of two types. Either you could get the answer by just plugging in the number $a$, so you weren’t learning anything new and couldn’t see any reason to care, or you had to find the limit as $x$ approached 0 of some hairy thing which looked like

$$ \frac{\sin(2y + x) – \sin(2y)}{x}. $$

If you already knew a little calculus, you could see that all the hairy problems were just taking the derivatives of functions. And knowing a bit about derivatives—I mean, knowing as much as a physics class teaches in half an hour—you could get the right answer every time in two lines of work. Those who didn’t have this pipeline of wisdom floundered for half a page of trigonometry, rewriting things back and forth and ending up with the wrong answer. Of course, for knowing what was going on and getting the right answer every time, we got the red pen: “That’s not how we learned to do this problem in class.”

Come to think of it, most of my fond memories of those years are about skipping class.

What would the curriculum for this proposed statistics class look like? We could do worse, I think, than cover the topics here: data description and summarization, means and standard deviations, measures of correlation, hypothesis testing… Flesh it out with examples of the “citizen statistics” variety—why was the SEC’s pilot study on repealing the “uptick rule” flawed?—and you’d have a full year’s worth. Alternatively, a one-semester introductory course with a strong “citizen statistics” flavour could be a warm-up for AP Statistics the following term. (In my experience, AP classes were so focused on taking the official exam at the end of the year that there was no time to spread out and look at anything which wasn’t easily testable in multiple-choice form.) The key point, assuming most school administrators are like the ones I had to deal with, would be revising the official tangled web of prerequisites, so that students could take AP Calculus without having taken precalculus first.

Incidentally, the professor friend I mentioned earlier is going to be teaching precalculus to college kids this fall, and is hoping to make it a better experience than the class I shuffled through in eleventh grade.

It’s been a while since I’ve felt riled enough to blog. But now, the spirit moves within me once more.

First, I encourage you to read Andrew Hacker’s op-ed in The New York Times, “Is Algebra Necessary?” Then, sample a few reactions:

• PZ Myers, “A modest proposal”
• Melanie Tannenbaum, “Algebra is Necessary: But what about how it’s taught?”
• Cathy O’Neil, “Does mathematics have a place in higher education?”
• Rob Knop, “When Andrew Hacker asks ‘Is Algebra Necessary?’, why doesn’t he just ask ‘Is High School Necessary?’”
• Mike the Mad Biologist, “It’s Not the Algebra, It’s the Arithmetic”
• Dana Goldstein, “On Algebra, High Expectations, and the Common Core” (Hacker conveniently avoids mentioning that “because 48 states and territories are planning to adopt the Common Core, the energy in school reform is tilting very much in favor of algebra”)
• Daniel Willingham, “Yes, algebra is necessary”
• Evelyn Lamb, “Abandoning Algebra is Not the Answer”
• RiShawn Biddle, “Why Algebra Matters (and Why Andrew Hacker is Off-Target)”
• Alexandra Petri, “The end of algebra”
• Mark C. Chu-Carroll, “Mathematical Illiteracy in the NYT” (good summary of Hacker: “There are no valid arguments to support the teaching of math, except for the valid ones, but I’m going to exclude those.”)

I will try to gather a few observations here which I haven’t seen made elsewhere, for the most part.

Towards the end, Hacker’s reasoning gets just bizarre. He keeps emphasising how important “citizen statistics” is. I’m baffled as to how one could teach statistics in any useful way without the material he wants to throw out! Prerequisites: we needz them. “Is Algebra Necessary?” If you want to do statistics or economics, yes, it is.

Quantitative literacy clearly is useful in weighing all manner of public policies, from the Affordable Care Act, to the costs and benefits of environmental regulation, to the impact of climate change. Being able to detect and identify ideology at work behind the numbers is of obvious use. Ours is fast becoming a statistical age, which raises the bar for informed citizenship. What is needed is not textbook formulas but greater understanding of where various numbers come from, and what they actually convey.

OK, so how are we supposed to teach where “numbers come from” and “what they actually convey” when the students can’t manipulate algebraic formulas? That’s like expecting to raise a generation of musicians who’ve never practised a scale.

It’s also nice how he skips past the serious problems we have with infrastructure. You know, schools not being able to buy books any more, and teachers who feel they aren’t capable of teaching even middle-school mathematics—because they aren’t. But saying that teachers need to be trained and books must be bought doesn’t make you a daring iconoclast worthy of a New York Times soapbox, now, does it?

Hacker’s standard for what counts as advanced—and, therefore, unnecessary—mathematics seems to drift from algebra to calculus:

Medical schools like Harvard and Johns Hopkins demand calculus of all their applicants, even if it doesn’t figure in the clinical curriculum, let alone in subsequent practice.

Maybe because doctors need to understand clinical trials, which requires understanding statistics, which in turn requires calculus? (I’m looking at The Cartoon Guide to Statistics, on page 66. Yup, integral sign.) Hey, here’s a radical thought: maybe not enough doctors really get what’s going on with clinical trials, and we’d be better off if more of them knew slightly higher mathematics, instead of fewer?

Of course, in Hacker’s world, everyone knows what they want to be when they grow up, and nobody needs training for anything else in case they want or need to switch to a new job.

It’s not hard to understand why Caltech and M.I.T. want everyone to be proficient in mathematics. But it’s not easy to see why potential poets and philosophers face a lofty mathematics bar.

Philosophers don’t need to know mathematics? Not even mathematics which is hundreds or thousands of years old? What. The. Fuck?

(by Oliver Byrne)

Oh, poor Euclid. Such a fate, and for you who alone have looked on beauty bare….

How many college graduates remember what Fermat’s dilemma was all about?

I’m guessing Hacker is referring to Fermat’s Last Theorem, but I don’t really know. (Nor does anyone else I know who read Hacker’s piece.) It doesn’t really fit the sense of “dilemma.” Fermat stated a problem and claimed that he had a solution. Perhaps the “dilemma” was that he felt compelled to write it down even though he didn’t have space to include his proof? Come on, I’m trying to be charitable here.

I might as well close with this bit from Hacker:

Yes, young people should learn to read and write and do long division, whether they want to or not. But there is no reason to force them to grasp vectorial angles and discontinuous functions.

So: the line is drawn wherever Hacker feels it should. Good to know. (I wonder: if long division is mandatory, what about, say, extracting square roots by hand? My mother learned how to do that in grade school, but I didn’t pick it up until I read the Feynman Lectures.) Incidentally, as a workaday scientist, I work with vectors and discontinuities far more often than I have to use long division. Honestly, I think “the line is broken in two pieces” is a significantly easier concept to get across than the rigmarole of pulling numbers down and multiplying them up and subtracting them down. But, of course, “vectorial angles” and “discontinuous functions” sound awfully intimidating to the proletariat, so let’s just hold them up as examples of what we don’t need to teach!

(by Eugene)

UPDATE (30 July 2012): I notice some people have been finding this blog entry by websearching for “Fermat’s dilemma,” so I figured I should say a bit more about that, following thoughts I developed on Twitter. As I said above, you could, if you really tried, interpret this odd choice of words as Hacker’s trying to be artful. But even if you try to read it that way, it’s sorry writing. In aiming to be evocative, Hacker just comes across ambiguous. You could say that Fermat’s little theorem—not to be confused with his Last Theorem!—embodies a dilemma. The little theorem gives us a test for saying whether a number is prime, but that test doesn’t always work: it can be fooled by a “pseudoprime.” Do we use a fallible test or not? We have a dilemma on our hands! Or, if that sounds like too much of a stretch, take the subject of probability theory, which Fermat and Blaise Pascal jumpstarted back in 1654. They wanted to answer a puzzle posed by Antoine Gombaud, Chevalier de Méré: how should two gamblers divvy up a pot of money if their game-playing is interrupted? Sorting out this kind of dilemma led Pascal and Fermat to probability theory.

See, we give things names in order to identify them, and if you make up your own names for things which already have them, you’re apt to confuse people. Sometimes, when the old terminology is muddled or unclear, a new turn of phrase is just what we need, but this is not one of those times. Hacker throws around big words like “polynomial functions and parametric equations” in order to make algebra sound intimidating, and when he makes up his own terms, he fumbles.

UPDATE (11 August 2012): Another item in the “oh, this is too fun” category. Hacker mocks the notion that being able to prove

$ (x^2 + y^2)^2 = (x^2 – y^2)^2 + (2xy)^2$

can lead to “more credible political opinions or social analysis.” I didn’t say anything about that until now, because I figured the rejoinder was implicit in what I said up top: if you can’t say that

$ (x^2 + y^2)^2 = (x^2)^2 + (y^2)^2 + 2(xy)^2 $

and

$ (x^2 – y^2)^2 = (x^2)^2 + (y^2)^2 – 2(xy)^2, $

and then combine the two and so deduce

$ (x^2 + y^2)^2 = (x^2 – y^2)^2 + 4(xy)^2, $

then actually learning or doing anything with “citizen statistics” will be beyond you. Them’s the breaks. However, there’s something else interesting here, which goes back to Hacker’s low expectations for poets and philosophers. To make things more clear, I’m going to replace $x^2$ with $a$ and $y^2$ with $b$. Then the Equation Mocked by Hacker becomes

$ (a + b)^2 = (a – b)^2 + 4ab. $

If we divide both sides of this equation by 4, we get a restatement of it which is just as true:

$ \frac{(a + b)^2}{4} = \frac{(a – b)^2}{4} + ab. $

And this is the algebraic statement of what Euclid said geometrically in Proposition II.5 of The Elements—which happens to be one of the oldest fragments of Euclid we have a surviving copy of. In fact, since this papyrus fragment was probably written between 75 and 125 CE, it’s likely older than any copy of any part of the Gospels. Rylands Library Papyrus P52, a scrap with a few verses from John 18, is the oldest one of those we’ve got, and it dates to about 125 CE itself.

It’s easy to say that not being willing to learn mathematics cuts one off from intellectual history. But damn, does Hacker ever put a point on it.

Congratulations, Professor Hacker. Your op-ed has earned a negative score on the Pritchard scale.

“Take the mathematical developments out of the history of science, and you suppress the skeleton which supported and kept together all the rest. Mathematics gives to science its innermost unity and cohesion, which can never be entirely replaced with props and buttresses or with roundabout connections, no matter how many of these may be introduced.”

—George Sarton, science historian

When talking of dynamical systems, our probability assignments really carry two time indices: one for the time our betting odds are chosen, and the other for the time the bet concerns.

A parenthesis in an appendix is already a pretty superfluous thing. Treating this as the jumping-off point for further discussion merits the degree of obscurity which only a lengthy post on a low-traffic blog can afford.

MY PRIMARY CONCEIT

Quantum mechanics provides statistical predictions for the results of measurements performed on physical systems that have been prepared in specified ways … I hope that everyone agrees at least with that statement. The only question here is whether there is more than that to say about quantum mechanics.
— Asher Peres

In this note, I shall take a rather strictly ascetic view of quantum physics. I’ll make the lifestyle choice that “quantum states” are encodings of probability assignments for the possible outcomes of as-yet unperformed experiments. Nothing more, but certainly nothing less. The image which floats hazily to mind is of the great unanalyzed diversity of the world teeming on, and when pieces of it come together, novelty happens: there takes place an act of creative generation which belongs to neither participant alone. Quantum theory is, following this lifestyle, a means of coping with and possibly even living well within a world having such a character. It studies the special case of novelty-generating interactions in which one participant is a scientific agent, a complex system capable of sustaining beliefs and entertaining them with varied degrees of fervency.

This leads me to another touchy question of lifestyle choice: personalist probability theory. The lifestyle starts with the idea of an agent which can believe things, and to these beliefs—which are arrayed in well-defined sets—we say the agent can attach a quantitative expression of its fervency in that direction. We impose the normative rule that the agent’s measures of credence be consistent with one another, and we make the dull matter of consistency more entertaining with stories about Dutch bookies or Ferengi bartenders. We say, and I think this is essentially a historical convention, that higher numbers should mean a stronger belief, even though we could just as well say that an agent writing a larger number means that the agent will be more surprised if that event turns out to happen. (Thanks to Claude Shannon, we know that the one convention is just the logarithm of the other.) Even the use of real numbers for degrees of fervency is, to my eye, a convention: if somebody wants to record credences using Conway’s surreal numbers, or with elements from some Lie group, all I can say is “peace be with you in your quest”. The normative standard of consistency will still yield constraints among credence assignments, the difference being that those credences won’t live in the same set as relative frequencies do. And, of course, there’s no guarantee that the exercise will lead to any useful novel structures.

The theory of subjective event weights built up in this way just is, in the same way that Euclidean geometry just is. It provides an imitation of Platonism in the way that all abstract constructions built up from axioms do. But we want to deal with the natural world our species evolved within! Ferengi-book coherence tells us that subjective event weights obey the axioms of “probability”. The natural question is, in those places where we scientists make use of “probability” talk, can we handle those tasks with SEWs? The claim of the Bayesian-statistics practitioner is that the answer is “yes”—and in those cases where it isn’t, the invocation of “probability” is what’s illegitimate, rather than the theory of SEWs.

In many circumstances of interest, quantum theory can be re-expressed solely in terms of SEWs. Though quantum theory is often (and validly) thought of as a generalization of ordinary probability theory to encompass a wider bestiary of mathematical structures, it can also be treated as a specialization of probability theory.

In quantum physics, we take what we think we know about a system, roll it into a density operator $\rho$, and use that density operator to make statistical predictions about what the system might do in particular experiments. But presenting that information as a matrix operator is not always the most illuminating choice. We can actually rewrite any finite-dimensional density matrix as a probability distribution, using the idea of informationally complete measurements. These are generalized measurement procedures (positive operator valued measures, or POVMs) which have an appealing ability: given a probability distribution over the possible outcomes of an informationally complete POVM, we can compute all the statistics which we could have gotten using the density matrix. Such POVMs can be constructed in any finite-dimensional Hilbert space. The nicest variety are the symmetric informationally complete POVMs, known familiarly as SICs, which are known to exist for many values of Hilbert-space dimension and are suspected to exist for the others. With these tools in hand, quantum theory becomes probability plus extra conditions: the bare bones of “SEW theory” are dressed with sinews whose anatomy depends on our doing quantum physics instead of some other theory.

With all that as prologue, then:

I have occasionally bumped into people who seemingly want to interpret all scientific discovery as Bayesian conditioning. I think it was Howard Barnum who said something about seeing science in “broadly Bayesian” terms, but judging from the “cocktail talk” and how people act in some corners of the Internet, not everyone would grant that “broadly”. New experiences always being weighed against our preconceived mesh of ideas? Yes. Holding to different ideas with varying degrees of tenacity? Yes. The clockwork ratcheting up and down of numerical fervencies defined over a “distinct number of consequences”? I doubt it. Even if such a story could be cooked up, involving a stupendously baroque and artificial sample space, what use would it have?

(A better term than “broadly Bayesian” might be “Darwinian”, or better yet just “evolutionary”. It’s been observed a few times that Bayesian updating is formally analogous to a formula in evolutionary theory called the discrete-time replicator equation. Prior probabilities map onto abundances of alleles in a gene pool, and the weight of new evidence maps onto biological fitness. The probability distribution after updating corresponds to the new gene pool composition after natural selection has operated. (Marc Harper describes it more fully in arXiv:0911.1763.) But the scenario modeled by the discrete-time replicator equation is just a tiny part of evolutionary phenomena. It’s even a tiny part of the mathematics developed to date for dealing with biological evolution. Other evolutionary processes could define other modes of inference whose mapping to Bayesian updating is contrived and awkward at best. For a relatively mundane example, I think Jeffrey conditioning is analogous to a discrete-time replicator equation with a mutation effect added.)

What this might mean for quantum theory is the following: were one enamored of a different physics-neutral mode of inference, the Born rule would be an empirical addition to that mathematics, phrased in its terms. (And, I’d guess, probably harder to translate into the vernacular of physics.) There is your realism for you: the extra addition to coherence due to the quantum character of the world must still be there. We’d just be writing down and trying to motivate a different equation for it.

TIME EVOLUTION

The Schrödinger equation in QM and the Liouville equation in classical mechanics are, I think, fundamentally synchronic statements about probability assignments. If I’m willing to gamble that a pendulum has position within some range $\Delta q$ and momentum within some interval $\Delta p$, and if I accept the mechanics lessons I had as a young’un, then my hands are forced: I must price lottery tickets referring to the pendulum at other times in a particular way. Each probability assignment concerning a dynamical system carries two time indices: one for the time the agent makes it, and one for the time of the event or proposition written on the ticket. We could write the former with a subscript and the latter in parentheses, for example:

$ \rho_\tau(q,p,t) $

would be a Liouville density for a one-particle system, a commitment made at time $\tau$ about the world’s affairs at time $t$. The Liouville equation connects $\rho_\tau(q,p,t_1)$ to $\rho_\tau(q,p,t_2)$. The subscripts are the same; it’s a synchronic statement. If I get new information at time $\tau_2$, then I can update the whole joint probability density for all times by conditioning on that new information.

If I keep gaining new information, say at times $\tau_i$, then the Shannon entropy of my Liouville density for the present time will keep decreasing. By evolving my Liouville density at time $\tau_i$ forwards and backwards, I can refine my distributions for what the pendulum will be doing in the future and what it had been doing in the past. Entropy decreasing over time? Yegads! We must be in contradiction with thermodynamics!

. . . except that by that reasoning, the thermodynamic entropy of any classical system we can characterize exactly must be zero, because the Shannon index of its Liouville density is nil! Indeed, the thermodynamic entropy of any simulated system must be exactly zero, because the computer doing the simulation knows where everything is and where all the pieces are going at all times!

Yeah, that’s pretty silly.

What it does mean is that I can extract energy more and more efficiently, and that I can make better and better predictions of how somebody else’s energy-extraction experiment will fare. (And a typical such experiment might well involve timescales significantly longer than those of the oscillations and vibrations within my system itself, so what matters isn’t where it can be in phase space at one particular time, but rather the possible variety in its trajectories over an interval of time—what I think in Jaynesian language is called its “caliber”.)

The way statistical-physics students are taught to relate Shannon entropy with thermodynamic entropy is through the “fundamental assumption of statistical mechanics”: we’re told to assign equal a priori probabilities to all points in phase space which have the same energy. From this starting point, one makes computations until relationships which look like the phenomenological equations of thermodynamics come out. But the starting point is one which should make a personalist Bayesian’s skin crawl! Who mandates a prior probability, and who died and made them king?

It’s only reasonable at all because of an even-more fundamental assumption: that we obtained all our information from highly coarse-grained measurements which could only access aggregate properties like the total energy. If we could make finer measurements in the first place, then we’d have no warrant to assign equal a priori probabilities across the constant-energy surfaces, and we’d have to rethink the “Shannon to thermodynamics” connection in a different way.

It [the Second Law of Thermodynamics] is not a law that dictates how things go by themselves, but rather how they go in response to particular experimental investigations.
— Campisi and Hänggi (2011)

HISTORICAL SCIENCE

In order to have any scientific weight, retrodictions have to yield predictions. Feynman has a bit in The Character of Physical Law where he explains how geologists “talk about the past by talking about the future”. If you dig in the ground where nobody has dug before—if you perform an as-yet-unperformed experiment—you’ll find fossil bones of the predicted kind. If a statement about the Earth’s geological past can’t be made to yield predictions about the consequences of new digging, we’re not talking about dinosaurs anymore— we’re talking about the invisible dragons which live in my garage. It’s fine to write a Bayesian probability $p(v)$ for the speed of the Chicxulub impactor, but if we can’t turn that into expectations for new investigations, why should anyone care?

So, what if we do commit ourselves to the idea that quantum uncertainty is uncertainty about future experiment outcomes? That measurements are not just disturbing, but generative? Then we must conclude that retrodictions are just a nostalgic kind of prediction, statements made thinking of the past which must concern the future to have any scientific content. If we disagree about things which happened in the past and stayed there—so what?! That’s like my housemate and I disagreeing today about the number of eggs laid yesterday by the invisible dragon living in our garage. Possible agreement in the future about experiments which can be done in the future—that’s the key.

Among other things, this affects, I believe, the criteria one uses to judge the compatibility of quantum probability assignments. I suspect that accepting agent experiences as the things beliefs are about changes significantly how important one feels various possible kinds of disagreement are. It appears possible in the quantum world that two physicists can be in sufficient discord that, as they perform experiments, their novel experiences bring them into agreement about the future but not about the past. More specifically, suppose Alice and her friend Bob are interested in a quantum system and each plan to receive word of an experiment performed on it. Prior to the experiment, Alice and Bob each make an assignment of probabilities to the possible experiment outcomes, in the form of a density matrix. When the measurement experiment intervenes on the system and coughs up a result, Alice and Bob update their “catalogues of knowledge” accordingly. It can transpire that the two physicists’ post-experiment density matrices agree, but the conditional density matrices which encode their beliefs about the past are incompatible. A classical analogue of this situation would be the following: suppose that Alice and Bob disagree about which side of a die is up. Alice says it’s a 6, Bob says it’s a 1. The die is rolled in a new experiment and comes up 6. Alice and her friend can come to agree about which side is up after the roll, but the new result changes nothing about their earlier disagreement.

I do not know if this is a serious inconvenience to doing science, or to the ascetic view that quantum states are catalogues of probabilities for possible future experimental outcomes. After all, if we hold fast to that position, then a post-measurement conditional density operator for the past spacetime region must be a probability catalogue for counterfactual experiments—interventions into nature which could have been done, but weren’t. Incompatible conditional density operators for spacetime regions in the past are, in this view, arguments over yesterday’s tomorrow, friction without heat. They’re what you get when “measurements” in your world are, not just disturbances, but acts of generation.

(Leifer and Spekkens write that “because nontrivial quantum measurements always entail a disturbance [...] coming to agreement about the state of the region after the measurement does not resolve a disagreement about the state of the region before the measurement.” To which a justifiable response might be, “Yes, and isn’t it wonderful?” More importantly, perhaps, I don’t like the phrasing of “a disagreement about the state of the region before the measurement.” The choice and arrangement of words seem wrong. I don’t know if it’s a matter of accident or of design towards a goal I disagree with. Doesn’t “disagreement about the state of the region” sound too much like, say, “disagreement about the calorie content of the region”—isn’t it just the phrasing one would choose if one believed that “the state” were a property of “the region”? This feels to me like bad language for any psi-epistemist, radically QBic or otherwise. “The states ascribed by two agents disagree” would be a more forceful and less muddling statement than “Two agents disagree about the state,” I think.)

A new slogan: Confusion about the past is the price we pay for a world of genuine novelty. The inability of Alice and her friend to come into agreement about retrodictions into the past beyond a measurement is, in microcosm, our inability to agree about what happened before the Big Bang.

(For a discussion of retrodictions-as-predictions in a cosmological context, see Schriffen and Wald (2012), section VI. I also think one could productively disagree with Schriffen and Wald’s discussion of thermal equilibration, at the beginning of Section III. To my eye, invocations of “ergodicity” and “mixing” do not resolve the problem of assigning probability distributions over microstates, but rather defer it. (Which is, to be sure, nonnegligible progress from a physicist’s perspective.) They speak of sampling a system at a “random time” during its dynamical time-evolution, which naturally provokes the question: what do you mean by “random time”? You still need some notion of what probability means to give the whole structure of concepts any content. It’s like the old circular, or rather downward-spiralling, conversation between a Bayesian and a frequentist: “If the probability of the coin landing heads is $p$, does that mean there will be exactly $1000p$ heads in 1000 flips?” “No, the number of heads will likely be close to $1000p$, but not exactly.” “What do you mean, likely? That’s the idea we’re trying to define!” And so forth. You could use large deviation theory to write a formula for how the probability of a deviation falls off with the entropy, but you still need to define probability eventually. That is, you’ve deferred the question—in a sophisticated, quantitative, maybe even useful way!—but not answered it.)

ORION DREAMING

The time-reverse of historical science is, in a sense, the issue of “Boltzmann Brains“—you know, complex structures arising from quantum vacuum fluctuations in the distant future of the universe. Supposedly, there should be stupendously more of them in the long (long, long) run than there are beings like we think we are, and from this the cosmologists deduce all sorts of things. E.g., that there exist an infinite number of beings who have all the memories of my brain up to 18 April 2012, including everything I’ve seen from Hubble and WMAP, but then in their memories they wake up from a long dream and return to being a green-skinned dancing girl from Orion.

(Alas, that is the fashion these days, populating the loneliness with shadow selves, frozen in branches of a stupefying state vector, floating in bubbles of spacetime frothed up by eternal inflation, or recorded in the memories of poor delusional Boltzmann Brains. Or, if you want to be particularly trendy, all of the above. Every variation of Hitler winning the war and von Stauffenberg’s bomb going off as planned, never the histories to meet. Every book in the Library of Babel a biography, innumerably many times over. Infinite iterations of Zhuangzi dreaming he is a butterfly; infinite butterflies dreaming they are Zhuangzi. Is this what we got into science for?)

But is that actually a meaningful number to compute, with quantum theory as it stands? What’s the point of asking, “What are the potential consequences to me of my experimental intervention into this phenomenon?” if the phenomenon in question is, by definition, inaccessible, both to myself and to my posterity?

I’ve read at least one cosmology person, Tom Banks, saying that Boltzmann-brainology is “silly.” His position was essentially that we can modify our physical theories in an infinite number of ways consistent with all available data and making the same predictions for all conceivable experiments, but with different numbers of Boltzmann Brains coming out. In addition, any detector sent out to gather data on Boltzmann Brains would disintegrate by quantum fluctuations itself long before it stood a chance of spotting any. . . but I think the issue is more fundamental than that. You’re asking a question which the theory is not prepared to answer! Sometimes, it’s obvious when that happens, like trying to calculate the self-energy of an ideal point electron and getting infinity, but here, people mostly don’t seem to be thinking of that possibility. If they do think the answer is absurd, they try to screw around with general relativity and invent a new cosmology that way.

Maybe physicists are generally accustomed to thinking about “limits to the validity of quantum mechanics”—if they believe any such exist at all—in an unproductive kind of way? Having prematurely excised the active agent, we naturally think “QM might fail for objects larger than the Planck mass” or something like that, rather than “QM is the wrong tool for answering questions divorced from agent experience”.

UPDATE (16 May 2012): I thank Howard Barnum for pointing out a misdirected hyperlink.

Style file:

• utphystw.bst

Example document:

\documentclass[aps,amsmath,amssymb]{revtex4}
\usepackage{amsmath,amssymb,hyperref}

\begin{document}
\bibliographystyle{utphystw}

\title{Test}
\author{Blake C. Stacey}
\date{\today}

\begin{abstract}
Only a test!
\end{abstract}

\maketitle

As indicated, this is only 
a test.\cite{stacey2011,sfi2011}

\bibliography{twtest.bib}

\end{document}

And the example bibliography file:

@TWEET{stacey2011,
       author={Blake Stacey},
       authorid={blakestacey},
       year={2011},
       month={July},
       day={25},
       tweetid={95521600597786624},
       tweetcontent={I find it hard to tell, in some 
                     areas of science, whether I am 
                     a radical or a curmudgeon.}}

@TWEET{sfi2011,
       author={anon},
       authorid={OverheardAtSFI},
       year={2011},
       month={June},
       day={23},
       tweetid={84018131441422336},
       tweetcontent={The brilliance of the word 
                     ``Complexity'' is that it 
                     means just about anything 
                     to anybody.}}

PDF output:

• twtest.pdf

One way to think about it is this: suppose you had to teach a physics class to first- or second-year undergraduates. Could you get all the textual materials you need from Open-Access sources on the Web? Would you know where to look?

What with Wikipedia, OpenCourseWare, review articles on the arXiv, science blogs, the Khaaaaaan! Academy and so forth, we probably already have a fair portion of this in various places. But the operative word there is various. I, at least, would like it gathered together so we can know what’s yet to be done. With a project like, say, Wikipedia, stuff gets filled in based on what people feel like writing about in their free time. So articles grow by the cumulative addition of small bits, and “boring” content — parts of the curriculum which need to be covered, but are seldom if ever “topical” — doesn’t get much attention.

I honestly don’t know how close we are to this ideal. And, I don’t know what would be the best infrastructure for bringing it about and maintaining it. Idle fantasies and pipe dreams!

I’d like to have this kind of resource, not just for the obvious practical reasons, but also because it would soothe my conscience. I’d like to be able to tell people, “Yes, physics and mathematics are difficult, technical subjects. The stuff we say often sounds like mystical arcana. But, if you want to know what we know, all we ask is time and thinking — we’ve removed every obstacle to your understanding which we possibly can.”

I don’t think this would really impact the physics cranks and crackpots that much, but that’s not the problem I’m aiming to (dreaming that we will) solve. Disdain for mathematics is one warning sign of a fractured ceramic, yes: I’ve lost count of the number of times I’ve seen websites claiming to debunk Einstein “using only high-school algebra!” We could make learning the mathematical meat of physics easier, but that won’t significantly affect the people whose crankishness is due to personality and temperament. Free calculus lessons, no matter how engaging, won’t help those who’ve dedicated themselves to fighting under the banner of Douche Physik.

Alchemists work for the people. —Edward Elric

The Who’s Who Among Executives and Professionals
400 West 19th St., New York City, NY 10001

It’s like being in high school and offered a place in an annual poetry anthology! all over again.

Yeah, no.

UPDATE (3 January 2012): I’ve received the same e-mail again, but this time headed by the subject line “Distinguished Women of The Year”.

Here’s an excerpt:

Madison Square Garden can seat 20,000 people for a concert. This blog was viewed about 68,000 times in 2011. If it were a concert at Madison Square Garden, it would take about 3 sold-out performances for that many people to see it.

Click here to see the complete report.

It is a bit like the story of Niels Bohr’s horseshoe. Upon seeing it hanging over a doorway someone said, “But Niels, I thought you didn’t believe horseshoes could bring good luck.” Bohr replied, “They say it works even if you don’t believe.” [source]

I find it interesting that nobody seems to know where this story comes from. The place where I first read it was a jokebook: Asimov’s Treasury of Humor (1971), which happens to be three years older than the earliest appearance Wikiquote knows about. In this book, Isaac Asimov tells a lot of jokes and offers advice on how to deliver them. The Bohr horseshoe, told at slightly greater length, is joke #80. Asimov’s commentary points out a difficulty with telling it:

To a general audience, even one that is highly educated in the humanities, Bohr must be defined — and yet he was one of the greatest physicists of all time and died no longer ago than 1962. But defining Bohr isn’t that easy; if it isn’t done carefully, it will sound condescending, and even the suspicion of condescension will cool the laugh drastically.

Note the light dusting of C. P. Snow. Asimov proposes the following solution.

If you despair of getting the joke across by using Bohr, use Einstein. Everyone has heard of Einstein and anything can be attributed to him. Nevertheless, if you think you can get away with using Bohr, then by all means do so, for all things being equal, the joke will then sound more literate and more authentic. Unlike Einstein, Bohr hasn’t been overused.

I find this, except for the last sentence, strangely appropriate in the context of quantum-foundations arguments.

Gilbert N. Lewis appears to have introduced the word in “The Law of Physico-Chemical Change”, which appeared in the Proceedings of the American Academy of Arts and Sciences 37 (received 6 April 1901).

If any phase containing a given molecular species is brought in contact with any other phase not containing that species, a certain quantity will pass from the first phase to the second. Every molecular species may be considered, therefore, to have a tendency to escape from the phase in which it is. In order to express this tendency quantitatively for any particular state, an infinite number of quantities could be used, such, for example, as the thermodynamic potential of the species, its vapor pressure, its solubility in water, etc. The quantity which we shall choose is one which seems at first sight more abstruse than any of these, but is in fact simpler, more general, and easier to manipulate. It will be called the fugacity, represented by the symbol [tex]\psi[/tex] and defined by the following conditions: —

1. The fugacity of a molecular species is the same in two phases when these phases are in equilibrium as regards the distribution of that species.

2. The fugacity of a gas approaches the gas pressure as a limiting value if the gas is infinitely rarefied. In other words, the escaping tendency of a perfect gas is equal to its gas pressure.

By golly, I wish I’d had this book as an undergrad.

As it was, I had to wait until this past January, at the ScienceOnline 2011 conference. These annual meetings in Durham, North Carolina feature scientists, journalists, teachers and students, all blurring the lines between one specialization and another, trying to figure out how the Internet can help us do and talk science. Lots of the attendees had books recently published or soon forthcoming, and the organizers arranged a drawing. We could each pick a book from the table, with all the books anonymized in brown paper wrapping. Greg “Dr. Skyskull” Gbur had brought fresh review copies of his textbook. Talking it over, we realized that if somebody who wasn’t a physics person got a mathematical methods textbook, they’d probably be sad. So, we went to the table and hefted the offerings until we found one which weighed enough to be full of equations, and everyone walked away happy.

MMfOPE is, as the kids say, exactly what it says on the tin. It begins with vector calculus and concludes with asymptotic analysis, passing through matrices, infinite series, complex analysis, Fourierology and ordinary and partial differential equations along the way. Each subject is treated in a way which physicists will appreciate: mathematical rigour mortis is not stressed, but when more careful or Philadelphia-lawyerly treatments are possible, they are indicated, and the ways in which their subtleties can become relevant are pointed out. In addition, issues like the running time and convergence of numerical algorithms are, where appropriate, addressed.

The sticker put on by the intellectual toy store would read, I think, “Ages: sophomore and up”. The prerequisites which the text effectively expects would be covered by the first year or so of university mathematics. If you’ve made it through Silvanus P. Thompson’s Calculus Made Easy, you’d be pretty well set, though some experience with vectors, in the way which first-year physics courses grapple with them, would also be helpful. The physics content one ought to know before diving in is, likewise, pretty well encapsulated by first-year mechanics and electromagnetism (what I still think of as 8.01 and 8.02).

I wish I’d had this book when we got to 8.03, because it covers just about everything I should have learned then but ended up having to teach myself later. Rather than plodding through a stupefying number of simple examples to “make sure we get the point”, it builds at a reasonable pace so we can reach interesting things and learn material we can actually use to do stuff. (The sophomore-level classes were easily the worst of MIT’s physics curriculum. I don’t know why, but the sentiment was widely shared, and I appreciate an antidote like Gbur’s book, which makes the subject matter not just clear but also interesting.)

The content was chosen with optics in mind. This does not rule out the usefulness of the book for general physics majors, though an instructor would likely benefit by drawing problems from a supplemental source. Students aiming for statistical physics would enjoy applications of Fourier transforms and convolution to probability theory. Those whose interests lean to mechanical or electrical engineering might appreciate the poles-in-the-complex-plane technology being applied to control theory and the study of stability. This is just to say that a book written with a different goal in mind would have turned out different, and that I myself would like to see those topics explained with the same verve.

The level and style of the presentation befits a text written for students who are seeing most of the material for the first time. Fine books have been written which have the feel of a walk through a forest with a worldy-wise teacher, far from any blackboard. They can achieve a conceptual clarity, but the novice reader often wishes there were a few more stepping stones along the path between equations 17 and 18. MMfOPE generally assumes its readers do not need to be reminded “the derivative of the sine is the cosine”, but its paths are well furnished with intermediate steps.

The historical notes, which indicate who discovered what and where theorems came from, are much appreciated. Without making the book a history-of-science monograph, they correct some common misconceptions and convey the impression that history is richer than we often let on, which is a good thing to be aware of. (The author’s experience as a science blogger with an interest in historical quirks shines through here.) Many exercises also point into the literature. Homework problems which begin, “Read the paper by…” will help students learn what facing into The Literature requires (and that sometimes, it stares back into you).

When our paths have intersected, Prof. Gbur and I have got along in a singularly fabulous way. It is therefore with genuine regret that I note the presence of aberrations in the text which may interfere with its reading. Missing factors of [tex]\pi[/tex] are the bane of the working physicist; Zee advises us that the difference between a good theorist and a bad one is that the good one makes an even number of sign errors. None of the glitches I have found in MMfOPE seriously impede understanding. They are of the kind which can only get squeezed out when a text is used in a classroom a few times over, so its odd byways get explored by people who don’t already know what should be on the page. For example, on p. 147, Eq. (5.32) is missing an equals sign after the [tex]A^\dag A[/tex]. On p. 530, [tex]\alpha^2[/tex] is on the wrong side of Eq. (15.165), and this goof propagates for a few equations after that, though without affecting the conclusions of the section. In Figure 14.7 on p. 490, the two panels make sense on their own, but work oddly in juxtaposition; they would be more clear if the curve in part (b) were the derivative of that in part (a).

COI DISCLAIMER: As indicated, I got a copy of Mathematical Methods for Optical Physics and Engineering for free. That said, I have no financial stake in its success.

UPDATE (20 June 2012): Errata are now available at the author’s web page.