Monday, August 3, 2015

The Hellgrammite

Messing around in the Patapsco River yesterday I found one of these, about three inches long. Hellgrammites are the larvae of Dobson flies. Very freaky looking, and I'm told their bite is very painful. They are said to live only in fairly clean water, which I suppose is a good sign about our stretch of the Patapsco.

Former U.S. Ambassadors to Israel Support the Iran Deal

More support from professionals for the nuclear deal with Iran:
July 27, 2015

Dear Speaker Boehner and Minority Leader Pelosi:

As former United States ambassadors to Israel and former Under Secretaries of State, we have worked throughout our careers to strengthen and deepen the bonds between the United States and Israel. Our firm instructions in every administration we served, reflecting American national interests and values, were to help assure Israel's well-being and safety.

It is our commitment to this enduring objective of American policy that motivates us now to write in support of the Joint Comprehensive Plan of Action (JCPOA) reached by the five permanent United Nations Security Council members plus Germany (P5+1). We are persuaded that this agreement will put in place a set of constraints and monitoring measures that will arrest Iran's nuclear program for at least fifteen years and assure that this agreement will leave Iran no legitimate avenue to produce a nuclear weapon during the next ten to fifteen years. This landmark agreement removes the threat that a nuclear-armed Iran would pose to the region and to Israel specifically.

We acknowledge that the JCPOA does not achieve all of the goals its current detractors have set for it. But it does meet all of the key goals required for high confidence. . . .  We see no fatal flaws that should call for the rejection of this agreement and have not heard any viable alternatives from those who oppose the implementation of the JCPOA.

Those who advocate rejection of the JCPOA should assess carefully the value and feasibility of any alternative strategy to meet the goal of better protecting the security of the U.S. and Israel and more effectively prevent Iran from acquiring a nuclear weapon. The consequences of rejection are grave. . . .
The Administration must make clear that it will remain the firm policy of the United States during the agreement and beyond, to prevent Iran from acquiring a nuclear weapon by all necessary means.

During the implementation period of the JCPOA, it is essential that Israel remain assured by the Administration of the enduring and unequivocal American commitment to its security and well-being. The prevention of a nuclear-armed Iran must remain a highest priority of U.S. policy in the Middle East.


R. Nicholas Burns, former Under Secretary of State for Political Affairs and Ambassador to NATO
James Cunningham, former Ambassador to Israel
William Harrop, former Ambassador to Israel
Daniel Kurtzer, former Ambassador to Israel
Thomas R. Pickering, former Under Secretary of State for Political Affairs and former Ambassador to Israel
Edward S. Walker Jr., former Ambassador to Israel
Frank G. Wisner, former Under Secretary of State for International Security Affairs and Under Secretary of Defense for Policy
By and large, the more people know about the deal, the more likely they are to support it.

Hellenistic Bronzes at the Getty

The Getty Museum is mounting an amazing exhibit of bronze sculptures from the Hellenistic and Roman worlds, 330 to 30 BCE. Above, Head of a Poet. Lots of amazing stuff from museums in Italy; I wonder if this was part of the deal when the Getty returned all that stuff that turned out to have been looted?

Portrait of Aule Meteli, 125 to 100 BCE.

Portrait of a Man, c, 100 BCE.

Boy Removing a Thorn from his Foot, c. 50 BCE.

This one goes by the informative title Head of a God or Poet, first century BCE.

Sleeping Eros. More at the Getty's web site.

The Translator's Sleepless Nights

From an interview with novelist and translator Juan Gabriel Vásquez:
You’ve translated the work of John Hersey and Victor Hugo, among others. What’s the most challenging aspect of translation for you? Has translating changed your approach to reading fiction in translation?

The most challenging aspect of translation, particularly when working with a book you love, is learning to be unfaithful to the original. Doing a little violence to a sentence you love is hard, and many sleepless nights can be caused by it. As for the second question, the answer is yes. Knowing firsthand how translation works, I’m unable now to read just any Chekhov or Kafka: I have my favorite translators too. Also, I try to read in languages that are closer to the original. I read German literature in English (Sebald by Michael Hulse) but Italian literature in Spanish (Claudio Magris by J. A. González Sainz).

Sunday, August 2, 2015

Hacking Ribosomes

Ribosomes are one of the many molecular wonders that make life as we know it possible. These are the tiny factories where proteins are made; a bacterial cell contains around 20,000 ribosomes, but there may be as many as 10 million in a rapidly growing mammalian cell. (In the images above, the dark dots are ribosomes; this is all you can see of them with an electron microscope.)

Understanding in detail the structure and function of the ribosome has been one of the great triumphs of microbiology; the 2009 Nobel Prizes were given to people involved in this work.  Ribosomes are about 2/3 RNA and 1/3 protein, snarled together in a fiendishly complex shape. Bacteria and eukaryotic cells (cells with a nucleus) have distinctly different ribosomes, and one thing we learned from the recent work is that some antibiotics work by clogging bacterial ribosomes.

The process of making proteins in a cell goes like this:
1) the instructions for making the protein are transcribed from a DNA molecule to a molecule of messenger RNA (mRNA);
2) the mRNA molecule carries the instructions to a ribosome;
3) the ribosome assembles the protein.
If you want more detail than that, the British Society for Cell Biology has it.

For what follows you need to know that each ribosome actually has two parts, which in eukaryotes are called 60s and 40s. The smaller piece binds to the mRNA, while the the protein is assembled on the larger piece. The two halves do not have to stay together; in fact they often come apart and recombine with other pieces.

From the time that we first discovered what ribosomes do, scientists have imagined taking over this amazing machinery to make custom proteins or other molecules. You can get cells to make new proteins by altering their DNA, the way we get yeast to make vanilla and so on. But this only works if you can find a gene for that protein that will work in your target cell's genome. This excludes many proteins that one might like to make, including completely novel, unnatural ones. Which is why there is continued interest in directly hacking the ribosome.

So for a decade now scientists have tried creating mutant ribosomes and inserting them into cells, hoping that the cells would then produce the desired proteins. But because the two halves come apart and recombine with others, the hacked ribosomes kept combining with native ribosomes in failed combinations that could make neither the natural nor the hacked proteins, and the cells stopped growing or even died.

And now this week's news:
The solution, Mankin and Jewett's team decided, was to marry together two engineered subunits. It was unclear whether the approach would work: it was thought that ribosomes exist in two distinct units because it is necessary for their function.

The researchers used a strand of RNA to tether the large and the small subunit together, toiling for months to get the length and location of the link just right so that the machine could still function. “We certainly came close, several times, to saying ‘OK, biology wins',” says Jewett.

The team screened its tethered ribosomes in Escherichia coli cells that lacked functioning RNA, and eventually found engineered ribosomes that worked well enough to support some growth, albeit slow. They then tested their platform to confirm that a tethered ribosome could operate side-by-side with natural ribosomes.

The result unlocks a molecular playground for bioengineers: by tethering the artificial subunits together, they can tweak the engineered machines to their liking without halting cell growth.
I don't know that this discovery will end up being very important; I simply find it amazing that we understand life at the molecular level well enough to do things like this.

The Paw Prints of a Roman Cat

Not long after the Roman conquest of Britain, a cat walked across this roof tile while it was drying . Dog prints are much more common on bricks and tiles, but that probably says more about the environment of brickyards and construction sites than taste in pets.

A Vaccine for Ebola

Great news from Africa, where our cleverness with molecular biology has finally given us the advantage over an awful scourge:
A highly unusual clinical trial in Guinea has shown for the first time that an Ebola vaccine protects people from the deadly virus. The study, published online today by The Lancet, shows that the injection offered contacts of Ebola cases 100% protection starting 10 days after they received a single shot of the vaccine, which is produced by Merck. Scientists say the vaccine could help to finally bring an end to the epidemic in West Africa, now more than 18 months old. . . .

The vaccine, first developed by researchers at the Public Health Agency of Canada, consists of the Vesicular Stomatitis Virus (VSV), which causes disease in livestock but not people, with the Ebola surface protein stitched into it. 
Not only was the vaccine created in a hi-tech way, it was tested using advanced techniques in public health:
The decision to start the trial was taken in October, but it didn't get off the ground until March. By then, Ebola cases had already begun to plummet, and they were scattered across a large area in Guinea. To show efficacy in a standard randomized controlled trial, the researchers would have had to enroll far more people than was feasible.

Instead, they opted for a design called ring vaccination, in which only contacts of new Ebola patients, as well as the contacts' contacts, were vaccinated. The rings, or clusters, were randomized; in 48 of them, vaccination occurred as soon as possible after the detection of the Ebola case in their community. In the 42 other clusters, the vaccination teams came to give the shots three weeks later. The researchers then counted the number of new Ebola cases in each ring; because they weren't sure how long it takes for the vaccine's protection to kick in, they only included cases that occurred at least 10 days after vaccination in their primary analysis of the data. There were zero such cases among the 2014 people who were vaccinated right away, and 16 among the 2380 who got the shot 3 weeks later. That translates to 100% vaccine efficacy, at least in this study, the researchers write.
Still waiting to here the results of another vaccine that is also being tested this year, but rumor has it that we may soon have two effective vaccines to choose from.

Leon Battista Alberti's Renaissance Churches

Leon Battista Alberti (1404-1472) was one of the leading architects of the Italian Renaissance, designer of many famous buildings and also author of the age's most popular theoretical treatise on the subject. His first church was the never completed Malatesta Temple in Rimini -- Malatesta sounds deeply sinister, but it was really just the name of the project's patron. (How, though, did a noble family get a name that sounds like bad news or false witness?) As with most of Battista's projects, the church was begun long before his time in a different style, and he was called in to enlarge it and transform it into something up-to-date. Construction began in 1450.

Sadly Signor Malatesta fell afoul of the pope, was excommunicated, and suffered a steep decline in his fortune, so he had to abandon the project. Among the elements never built was the dome Alberti designed; and in fact although he designed other great domes, none was ever built.

By the standards of the time Alberti was learned in classical studies -- he could read both Greek and Latin and spent many years studying Roman architecture all across Italy. In fact his great theoretical work, De Re Aedificatoria, was published before he actually designed any buildings. What I like about Alberti's work is that while he knew how to work in a completely classical style he chose not to do so, enlivening his work by varying the classical orders and adding charming touches like the angel medallions above.

Alberti's most famous work, the facade of Santa Maria Novella in Florence (1458-1471). This was another remodeling job; the lower floor of the facade was already in place, with the entrances, before Alberti was called in.

Therefore you often see only the top displayed in architecture books, like this. I don't know that I like this church very much, but it is certainly striking and original. Since I am a novelty-loving modern, I do occasionally want to see something different than the Romanesque or the Gothic, and as I said I like the way early Renaissance architects played with classical forms rather than regurgitating them.

The church of San Sebastiano in Mantua. In this case Alberti planned the church from the ground up, but on the other hand he never got to see it finished. Some of what you see is modern, including the stairs. But the radically simple facade seems to be Alberti's own.

Alberti's last church was Sant' Andrea in Mantua, where construction began in the year of his death. Notice the varying heights and styles of the pilasters, the variations in the window treatments,and so on.

The main doorway.

The barrel-vaulted room of the nave. This was built after Alberti's death, so we don't really know how closely it matched his vision, but it is certainly one of the most Roman-looking buildings of the age.

As I said, not my favorite buildings, but remarkable in their own way.

Thursday, July 30, 2015

Alison Syme, Willow

Willows have long been associated with death and mourning; but I was surprised to discover, from reading Alison Syme's Willow (2014), how far back this association goes.

At least to ancient Egypt, where the myth says Osiris was drowned in a willow casket, and where the sites where his dismembered pieces landed were all marked by willow groves. Here, a pharaoh makes an offering of willow branches in a temple of Hathor at a place called Nikentori, with means willow-earth.

Syme thinks the association of willows with both death and fertility springs from the ease with which willow twigs spring back to life if planted in the earth. Even, old, dried-out looking branches will sometimes take root and grow. These pictures show the planting and eventual appearance of the Auerworldpalast in Germany, a living structure made by sticking willow withies into the ground and letting them take root.

Across Europe there is a widespread ritual in which young men welcomed spring by whipping young women to encourage fertility, and except among the Romans -- who used whips of wolf skin, hence lupercalia -- this was almost always done with willow branches. In many places the branches had to be covered with catkins for the ritual to work. As with other pagan symbols of rebirth, the willow was attached to Easter; across eastern Europe what I call Palm Sunday is Willow Sunday.

Mythmakers, poets and painters have found the association irresistible. Besides their striking form, willows dwell in the liminal place along the water's edge, where they can overlook drownings like Ophelia's:
There is a willow grows aslant a brook,
That shows his hoar leaves in the glassy stream.
Therewith fantastic garlands did she make
Of crow-flowers, nettles, daisies, and long purples,
That liberal shepherds give a grosser name,
But our cold maids do dead men's fingers call them.
There, on the pendent boughs her crownet weeds
Climb'ring to hand, an envious sliver broke,
When down the weedy trophies and herself
Fell in the weeping brook. . . .
Some digital scholar figured out that willow is the plant most often mentioned in classical Chinese poetry, beating out even plum blossoms:
Whether the willow can love or not,
It is always dancing,
With a beauty that shakes the kingdom. . . .
Willow comes in hundreds of species, some of which hybridize freely, creating a muddle that has long frustrated taxonomists. True weeping willow is Silex babylonica, native to China. From there it spread across Asia, arriving in the Middle East by the medieval period and in Britain in the 17th century. It was instantly popular with gardeners all across Europe, since its lovely weeping form fit so perfectly with the mythical associations of willows.

Besides the myths, Syme also deals with the practical importance of willows, both in medicine (aspirin comes from willow bark) and in making baskets. Baskets were economically vital until recent times. One detail: during World War I, the British government commandeered the island's whole output of willow branches to make baskets for things like artillery shells and homing pigeons.

Willow is an interesting book, short and with lots of great pictures. I read it in a day and mostly enjoyed it.

Yet I found it vaguely dissatisfying. Yes, willows are woven all through the folklore of the northern hemisphere, from the groves of Hades where Persephone languished to Old Man Willow and Buffy the Vampire Slayer's best friend, Willow. But one could write an identical book about many other plants: oak, rowan, holly, rose, mistletoe, and probably many more. Instead of just a list of places that willows appear in myth and art, I want to understand the relationship between the mythic and natural worlds. Do all plants that are so prominent in the lives of traditional peoples cross into their stories? Are the same stories told about different species of tree and shrub, or do some species have stories all their own? What does it all mean?

The human fascination with the growth of plants runs deep. Plants feed us, shelter us, and spring from the ground in a miraculous way, growing from tiny seeds or cast off pieces. Sometimes, looking at plants and thinking about them, I have felt the power of rebirth in a deep way, and been filled for a few moments with something that felt like understanding, only to have it fade away a moment later, like a rainbow, or dew in the sun.

The Mathematician Plays Chess with the Devil

From an article on math prodigy turned Fields Medal winner Terry Tao:
The true work of the mathematician is not experienced until the later parts of graduate school, when the student is challenged to create knowledge in the form of a novel proof. It is common to fill page after page with an attempt, the seasons turning, only to arrive precisely where you began, empty-handed — or to realize that a subtle flaw of logic doomed the whole enterprise from its outset. The steady state of mathematical research is to be completely stuck. It is a process that Charles Fefferman of Princeton, himself a onetime math prodigy turned Fields medalist, likens to ‘‘playing chess with the devil.’’ The rules of the devil’s game are special, though: The devil is vastly superior at chess, but, Fefferman explained, you may take back as many moves as you like, and the devil may not. You play a first game, and, of course, ‘‘he crushes you.’’ So you take back moves and try something different, and he crushes you again, ‘‘in much the same way.’’ If you are sufficiently wily, you will eventually discover a move that forces the devil to shift strategy; you still lose, but — aha! — you have your first clue.

Wednesday, July 29, 2015

Artifacts from along the Anacostia River in Washington, DC

I mentioned a while back that I have been involved in a project to go through old artifact collections from along the Anacostia River in Washington, DC. These are really old collections picked up mainly in the 1870s and 1880s. Most were surface finds. As this collection shows, back then you could fill a box in an afternoon without bothering to pick up any broken junk. These spear points probably date mainly to between 2000 and 1000 BCE.

Sherd from the neck of a pot made between 1200 and 1500 CE. This is what we call Potomac Creek pottery. This is a rather famous sherd because this is the one that Smithsonian archaeologist William Henry Holmes used to illustrate the type in the report where he gave it the name Potomac Creek,back in 1891.

Stone axes.

And more points. There is a ton of stuff (literally, I would guess) in the Smithsonian's collections from the Anacostia, but much of it is labeled only "Anacostia River," not enough to say where it actually came from. We focused only on collections that we could locate more precisely, and still there are thousands of artifacts like these.

The Hard Scientific Problem of Hamster Happiness

Is your hamster happy? How would you know? Well, you might try this experiment designed to measure whether a hamster's level of depression is affecting its judgment. The idea is that depressed animals have a bias toward pessimism, happy ones toward optimism:
Recent developments in the study of animal cognition and emotion have resulted in the ‘judgement bias’ model of animal welfare. Judgement biases describe the way in which changes in affective state are characterized by changes in information processing. In humans, anxiety and depression are characterized by increased expectation of negative events and negative interpretation of ambiguous information. Positive wellbeing is associated with enhanced expectation of positive outcomes and more positive interpretation of ambiguous information.
According to this study, hamsters who live in "enriched" environments are 12% more likely to interpret ambiguous signals in a positive way, i.e., are more optimistic, than those who live in a Spartan environment.

Who says science isn't taking on the hard, important problems?

Pluto, Getting Clearer

As the hi-resolution photographs from the Pluto flyby are gradually transmitted back to earth, we see Pluto in more and more detail. Above, mosaic of the whole planet(oid) at twice the resolution of the famous image from July 12.

The true color photographs NASA releases are made by combining two different types of data. New Horizons' main camera works in black and white, generating images like this one and the one below. That decision was made because 1) it's really dark that far from the sun, and the scientists wanted the maximum possible resolution, and 2) color images take a lot more bandwidth to transmit, and the scientists were not certain they would have good enough communications with the spacecraft to download everything. But color information is collected by a different instrument, and that color data can be algorithmically added to the black and white photos. So eventually we will see all of these detail shots in color, too.

Now That's Street Art

A cooperative of artists known as the Germen Crew transformed this neighborhood in Pachuca, Mexico from drab (below) to explosive.

More views below.

Tuesday, July 28, 2015

About that Armed Citizenry

Every time a lunatic opens fire in a theater or school, fans of guns say that it wouldn't have happened if more people were armed. The National Gun Victims Action Council arranged a study to see what would happen if average citizens with guns actually encountered crisis situations:
They recruited 77 volunteers with varying levels of firearm experience and training, and had each of them participate in simulations of three different scenarios using the firearms training simulator at the Prince George's County Police Department in Maryland. The first scenario involved a carjacking, the second an armed robbery in a convenience store, and the third a case of suspected larceny.

They found that, perhaps unsurprisingly, people without firearms training performed poorly in the scenarios. They didn't take cover. They didn't attempt to issue commands to their assailants. Their trigger fingers were either too itchy -- they shot innocent bystanders or unarmed people, or not itchy enough -- they didn't shoot armed assailants until they were already being shot at.
Gee, that sounds like a great solution. The Post has videos of some of the amateurs in actions.

Demographic Change in Europe

Detailed map from the German government showing population changes in Europe over the 2001 to 2010 period. Click to enlarge.

Some things to note: the large areas of dark blue (= population decline of more than 2% per year) in Albania, Bulgaria, eastern Germany, the Baltic states and rural Greece and Turkey; strong population growth in western France, Ireland, and in rings around many great cities, representing surging suburbs. In general there is much movement from rural areas to great cities, and from east toward the northwest.

Joni Niemelä: Details

Joni Niemelä is a Finnish photographer who specializes in small things viewed from up close. These images are fine, but what really grabs me is the colors. Above, one image from a whole series on the carnivorous plants called sundews. Lots more at his web site and instagram.