Field of Science Combined Feed

Religion is halfway between an fact and an opinion - according to kids and adults

noreply@blogger.com (Tomas Rees) — Sun, 19 May 2013 20:58:00 +0000

Is it possible for two people to disagree, and for both to be right?

Well it depends, of course, on what they're disagreeing about. If it's a matter of fact ('Dinosaurs are extinct'), then the answer is 'no'. On the other hand, if the discussion is about what flavour of ice cream is best then, well we are probably going to have to agree to differ.

But is religion a fact or an opinion? And do kids draw the same distinction as adults? To find out, Larisa Heiphetz (a psychologist at Harvard University in the USA) and colleagues quizzed 100 children about a faraway planet, Tamsena.

The children of planet Tamsena have a lot of conflicting opinions about things like the spirit world ("All of the invisible spirits on Tamsena live under the ground" vs. "All of the invisible spirits on Tamsena live in the tops of the trees"), matters of fact ("The first king of Tamsena was called Benjamin Smith" vs. "The first king of Tamsena was called Daniel Jones"), and matters of opinion ("Mankala is the most fun game to play" vs. "Ubuthi is the most fun game to play").

The kids were asked whether or not the two Tamsenites could both be right about these matters, or if only one of them could be right. They asked 37 adults (average age 27 years) the same questions.

The results suggested that, although seemed to be a trend with increasing age, the same pattern of results was seen in all age groups.

While most people believed that only one person can be right about factual questions, most also believed that both could be right about matters of preference.

And questions involving mystical beings were half way between the two.

Interestingly, there seemed to be a trend towards ambivalence with increasing age - although this wasn't really confirmed statistically. It looks like older people are more likely to accept that there are many issues about which multiple opinions may be correct (or, at least, about which it's not possible to tell).

So that's a fantasy planet? What about questions about the real world?

Well they did a similar study but instead involving real questions of fact and preference, and about religion. They got pretty much the same results, although a little less clear cut (that's probably because having some knowledge of the answers to the questions helped the children to judge whether they were matters of fact or opinion).

Heiphetz and colleagues conclude that:

Children as young as 5 years seem to represent other minds as capable of containing conflicting beliefs. Additionally, around the age of 7 years, children become more likely to say that two people whose preferences conflict can both be right. This developmental shift may reflect children’s increasing experience with contradictory preferences as they begin elementary school and learn to navigate the conflicting preferences of their peers.

So it seems that children do have to learn (or develop the ability) to understand that differences of opinion can be legitimate.

But at every age, both children and adults seem to agree that religion occupies some kind of half-way house between fact and opinion!

Heiphetz, L., Spelke, E., Harris, P., & Banaji, M. (2013). The development of reasoning about beliefs: Fact, preference, and ideology Journal of Experimental Social Psychology, 49 (3), 559-565 DOI: 10.1016/j.jesp.2012.09.005

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

Garden Sunday

The Phytophactor — Sun, 19 May 2013 18:23:00 +0000

Today May 19th, really seems like the first full-fledged day of summer. The temp is in the upper 80s; thunderstorms threatened half the day. Yesterday the daughter of long-time friends got married in a delightful, non-traditional ceremony outside on a lake. Utterly charming. The neighbors' lovely daughter is graduating from high school today at the top of her class. How nice. Their dogs still bark too much. And today the Phactors are busily getting the gardens into summer mode. The herb garden was easiest, but no lemon grass is around. How do you live without lemon grass? We cannot imagine such deprivation, but Thai basil was in good supply. Colorful birds were around all day: gold finches and scarlet tanagers; how nice. Planting of the kitchen garden got off to a good start, but the peas are probably too late to be a really good crop. Unfortunately the lily pond filters needed cleaning and it's a terrifically messy job washing the green-brown bio-slime out of everything. Quite a number of early summer plants started to flower; Sinocalycanthus, tulip tree, golden chain tree, Niellia, beauty bush, and more. Now to construct a nice summertime supper: spicy fried chicken livers on fresh greens with a soy sauce-sesame oil dressing. And it's a good thing we got ourselves going because in another month the Phactors' garden is part of a garden tour. Contact TPP if you want confidential information about the tour.

Bioengineers go retro to build a calculator from living cells

Sun, 19 May 2013 09:11:03 +0000

Scientists in the US have developed a calculator from living cells, using old-fashioned analog programming. Their hope is that the technology could be used in the future to program cells to kill cancer.

Researchers have previously built electronic circuits using living cells. They achieved this by forcing living cells to behave in binary (digital) systems. But this is not energy efficient. And many cells are required to implement simple functions that transistors, the basic units of electronic circuits which are ten times smaller than a cell and more reliable, can perform.

Instead analog technology, which uses not just two states like digital but many, could be used to make cells do more complex tasks. Rahul Sarpeshkar, of the Massachusetts Institute of Technology, realised that chemical reactions inside a living cell are also analog in nature.

Chris Myers at the University of Utah, who like Sarpeshkar is an electrical engineer working on biological systems agrees. “Natural systems are more analog than digital,” he said. “They are also a million times more power efficient than our electrical systems despite using very poor components that produce lots of noise.”

Sarpeshkar, whose work has been published in the journal Nature this week, chose the bacteria Escherichia coli, commonly known by its abbreviation as E. coli, to make his calculator. For building it, he needed to create a way to input numbers, a program to execute the calculations and a way to count the output. All three of those functions would occur in living cells via chemical reactions.

The program for performing calculations was coded in synthetically made plasmids, which are circular DNA molecules, and injected into the bacteria. These plasmids, also called genetic circuits, have the ability to turn certain genes on or off. This starts a cascade of chemical reactions, eventually leading to the production of proteins.

Sarpeshkar’s E. coli cells were designed to produce proteins tagged with a fluorescent dye in response to the plasmids. These proteins could then be “counted” based on the amount of light they emitted when a laser activated the dye. Their calculator could perform addition, division and power-law computations.

Sarpeshkar’s aim is not to build computers using cells. That would be an inefficient use of the technology. Instead, Sarpeshkar said, “In the future, we may build more complex circuits that ‘compute’ whether a cell is cancerous or not and destroy it if it is.”

There have been preliminary studies where genetic circuits put into bacteria can communicate within a population of cells. That population can then sense their environmental condition and decide to perform a response. This means Sarpeshkar’s plan to kill cancer cells using cells that can compute may not be as far-fetched as it might seem.

This article was first published on The Conversation.

Friday Fabulous Flower - Yellow tree peony and friend

The Phytophactor — Sat, 18 May 2013 14:28:00 +0000

Next to magnolias and other magnoliales TPP's favorite flowers are tree peonies, and among those nothing is better looking than my yellow tree peonies. This particular plant is about 4 feet tall and 4 feet in diameter. This year it has a couple of dozen of these huge yellow flowers. This year the bastard balm (yes, that's its common name), one of the showier members of the mint family was in full bloom at the same time so everyone gets a two-fer to make up for some of the Friday's missed. As this is being typed the peony is about 6 feet to my left just below the window, and the floral fragrance, such that it is, a hard to describe floral muskiness is quite evident. Eh, you don't grow them for their fragrance. The yellow-flowered tree peonies routinely flower several days behind the white and pink flowered ones. TPP has one of the Itoh hybrids with yellow flowers but they just aren't as commanding a presence. They lack the red highlights in the center. The hybrids are hardy, fast-growing, and vigorous, but they still seem as light beer is to a full-bodied lager.

Fiddling while Rome burns - climate edition

The Phytophactor — Fri, 17 May 2013 13:32:00 +0000

"So why are we behaving like this?" asks Martin Wolfe of the Financial Times.
"A second reason is opposition to any interventions in the free market. Some of this, no doubt, is driven by narrowly economic interests. But do not underestimate the power of ideas. To admit that a free economy generates a vast global external cost is to admit that the large-scale government regulation so often proposed by hated environmentalists is justified. For many libertarians or classical liberals, the very idea is unsupportable. It is far easier to deny the relevance of the science."
It will be interesting to see the reaction to a commentary that really hits the nail on the head.
HT to Gravity's Rainbow.

Tacky is as tacky does

The Phytophactor — Fri, 17 May 2013 13:22:00 +0000

Garden gazing balls (even when the size of the one in Millennium Park), plywood cutouts of some one bending over in their garden, and, yes, especially, garden gnomes are tacky, as are plastic ducks and deer. Sorry, that's just the way it is. Not even the fact that after 100 years the Chelsea Garden Show is allowing celebrity decorated garden gnomes to be auctioned for charity changes the fact that they are tacky. You have to take a large hop, skip, and jump to get from tacky to whimsical, which in gardens is actually OK. Now you may ask how do you know what's tacky and what's whimsical? A fair question, and the answer is simple enough: something has to be a bit clever, a bit creatively odd, a bit tastefully fanciful to be whimsical, and you know it when you see it. Mostly you do not get whimsy ready made; it has to be transformed from ordinary, so there's a chance that a gnome decorated by Elton John just might make the grade to whimsical, or like Liberace, it may end up just wildly, fantastically, grandly tacky, but tacky nonetheless. Hope this raises a lot of money for a worthwhile charity because how else could Chelsea bear the indignity?

TMI Friday: Taking it to third base ..literally

The Defective Brain — Fri, 17 May 2013 12:32:00 +0000

The variety of foreign bodies in the rectum tests a surgeon's ingenuity to solve a myriad of geometric puzzles

So begins Major PT Mcdonald's 1976 paper, in which he has to deal with a patient with a somewhat unique problem.
The patient, a 49 year old baseball fan, who had serious trouble with his bowels ever since the Oakland A's won the world series in 1974. The doctors examined him, and noticed

" a firm, fixed, round object barely palpable which was lodged high in the rectum"

It was a baseball. To celebrate the Oakland A's victory, he had his sexual partner force the hardball up his rectum, where it got lodged. Unable to get any purchase on the surface of the ball, retrieval seemed impossible.
Thus it was left to the surgeon to figure out how to get the ball out. They drained the man's bladder using a catheter to take some of the pressure off the baseball. They tried to hook the ball, and drag it out as you would a particularly large fish. But this anal fishing expedition was for naught, as they only managed to rip some of the skin from the baseball.
They then decided that perhaps a better way of extracting the ball was through using obstetrics forceps. For those of you who don't know, these are generally used to deliver babies. So they pumped a little bit of air around the baseball, and tried to use the forceps to grab the ball.
It didn't work. They realised what the problem was. The baseball had travelled up through the pelvic arches, and after it had done so, it had become swollen with fluid, and become lodged in the pelvis.
It was a dire situation. The surgeon decided to cut into the man's abdomen to get access to the baseball. It was still stuck fast, and he needed to get some grip on the surface. So he skewered the baseball with a corkscrew, and tried to use it to pull it out. It still wasn't enough. So he got an assistant to stick their fingers up the patients arse from the other end whilst also pulling on the corkscrew, and with " a force enough to lift the patient off the table", popped the baseball out.

McDonald M.P.T. & Rosenthal C.D. (1977). An unusual foreign body in the rectum—A baseball report of a case, Diseases of the Colon & Rectum, 20 (1) 56-57. DOI: 10.1007/BF02587455

An Ecotourism Vacation

Jessica M. Budke — Fri, 17 May 2013 01:33:00 +0000

The end of the school year has me thinking about summer vacations and I have just added a new location to my vacation wish list. The Cape Horn region of southern Chile and Argentina sounds like an amazing place to visit! The area has high levels of bryophyte diversity and a beautiful landscape of waterways and islands. Unfortunately my summer vacation plans do not include the Cape Horn this year. Instead I have been reading a book all about ecotourism of the miniature forests and imagining myself there.

Miniature Forests of Cape Horn: Ecotourism with a Hand Lens (2012) by Bernard Goffinet, Ricardo Rozzi, Lily Lewis, William Buck, and Francisca Massardo.

This book makes it easy to imagine you are far away in the Cape Horn. There are many full color photos of the landscape and a up close photos of the plants. They also identify the many species of mosses, liverworts, hornworts, and lichen that live in the Cape Horn region. The book has text in both English and Spanish, as you can tell from the cover.

For some of the species they describe interesting structures, such as the lamellae on the leaves of the Polytrichaceae.

For others, cool interactions, such as the flies that are attracted to moss capsules and disperse the sticky spores are featured.

Overall I think that it is a great book. I may be a little biased since I know two of the authors quite well (Goffinet was my PhD advisor and Lewis was my labmate at the University of Connecticut). I think that the book is a great outreach tool and I hope that many people will take them up on visiting the area to see the amazing miniature plants.

Red bud fracking instead of hydraulic fracking

The Phytophactor — Thu, 16 May 2013 13:38:00 +0000

Hydraulic fracking is quite an issue just now in Lincolnland. One of the key issues is how much water must be used to fracture deep sediments. This is one of those things where industry wants to pretend the resource is free, the water is free, without an environmental cost. It would be nice if there were an alternative to using water to fracture those deep sediments. Then came this idea. Plant red buds, lots of them over the sediment you wish to fracture. Based upon the effort needed to pull a tiny red bud seedling from the ground and the length and depth of its root penetration, by the time the red bud stem reaches about the diameter of your finger, it's roots should have penetrated the sediments in question and simply pulling the red buds will certainly fracture the sediments in question. This is a simple extrapolation of the finding that 3-4 inch tall red bud seedlings, some with the cotyledons still attached, have a root penetration somewhere around a mile and a half based upon those TPP has pulled. By the time you notice red bud seedlings, they are already too deeply rooted to pull even if you have a weed wrench. Hmm, that's the problem obviously, nothing we've invented can pull up such roots. Drat! So close to a solution.

"Fool Me Twice, Shame on ME," Says Sea Slug

Elizabeth Preston — Thu, 16 May 2013 10:14:00 +0000

"Simple" is often a compliment in the human world, used to describe low-fuss dinners or closet solutions. When scientists use "simple" to describe an animal, they mean something more like, "That sac of goo has no business acting clever." An especially simple creature—a sea slug—recently demonstrated that despite its humble resources, it can learn from experience and form new hunting strategies. Smaller goo sacs, beware.

Despite its squishy stature, the sea slug Pleurobranchaea californica is a killer. It roams the sea and swallows whatever appealing morsels are in its way. Being blind, it can't tell how tasty its prey looks—or doesn't.

It can't see, for example, the flashy coloration of the "Spanish shawl" nudibranch (Flabellina iodinea). If it could, it might guess that those bright pink and orange hues are a warning: Flabellina is not nice to eat. It steals stinging cells from its own prey (such as corals and anemones) and stores those stingers in its bristles.

Rhanor Gillette, a neuroscientist at the University of Illinois, Urbana-Champaign, observed that not only do Pleurobranchaea slugs spit out Spanish shawls, but they seem to remember and avoid the animals in the future. To study how well the predatory sea slugs learn their lesson after tasting Flabellina, he and graduate student Vanessa Noboa set up a meet-and-greet between the two species.

In tanks, the large, hungry sea slugs encountered the smaller nudibranchs. Researchers recorded how long it took for Pleurobranchaea to take a taste, then waited for the slugs to change their minds and turn away from their potential prey. (Here's a great video of a Pleurobranchaea attempting to Hoover up a Flabellina, then spitting the animal back out. While the big slug pivots away in disgust, the little one does its "Don't eat me" dance like nobody's watching, which is true.)

On the first day, this interaction happened five times. By the end, most of the Pleurobranchaea slugs were much slower to take a taste of the Spanish shawls, or were ignoring them altogether. Twenty-four hours later, the sea slugs were still reluctant to approach Flabellina. Even after 72 hours, they remembered what they'd learned. Gillette and Noboa report their results in the Journal of Experimental Biology.

Since the predatory slugs seem to sniff something in the water that makes them turn away, the researchers think the noxious Spanish shawls give off a distinctive warning odor.

Gillette says the sea slugs have a decent memory, considering their elementary nervous system. "In these experiments their memory is strong at 48 hours," he says, "and in unpublished work we've seen savings up to a week, so it's not bad." (Oddly, some slugs had to be removed from the experiment because they didn't mind the taste of the stinging Flabellina at all. They sucked it up just like any other food.)

Learning from an unpleasant taste experience, then using that memory to change one's hunting strategy, is "a real cognitive trait," Gillette says—in other words, a "goal-directed use of knowledge." The Pleurobranchaea slugs learned to avoid the smell of Flabellina, although they continued to eat a related, non-stinging species without hesitation.

Being able to change their feeding strategy is a good thing, since these slugs are generalists. Everything in the path of their oozing is a potential meal. "More specialized animals, say sea-slugs that may munch on a particular kind of sponge, may not need to employ such learning abilities," Gillette says. For a hunter like Pleurobranchaea, the decisions aren't so simple.

Noboa, V., & Gillette, R. (2013). Selective prey avoidance learning in the predatory sea-slug Pleurobranchaea californica Journal of Experimental Biology DOI: 10.1242/jeb.079384

Image: Rhanor Gillette.

A Critical Period for Learning Language?

GamesWithWords — Thu, 16 May 2013 08:30:00 +0000

If you bring adults and children into the lab and try teaching them a new language, adults will learn much more of the language much more rapidly than the children. This is odd, because probably one of the most famous facts about learning languages -- something known by just about everyone whether you are a scientist who studies language or not -- is that adults have a lot less success at learning language than children. So whatever it is that children do better, it's something that operates on a timescale too slow to see in the lab.

This makes studying the differences between adult and child language learners tricky, and a lot less is known that we'd like. Even the shape of the change in language learning ability is not well-known: is the drop-off in language learning ability gradual, or is there a sudden plummet at a particular age? Many researchers favor the latter possibility, but it has been hard to demonstrate simply because of the problem of collecting data. The perhaps most comprehensive study comes from Kenji Hakuta, Ellen Bialystok and Edward Wiley, who used U.S.A. Census data from 2,016,317 Spanish-speaking immigrants and 324,444 Chinese-speaking* immigrants, to study English proficiency as a function of when the person began learning the language.

Their graph shows a very gradual decline in English proficiency as a function of when the person moved to the U.S.

Unfortunately, the measure of English proficiency wasn't very sophisticated. The Census simply asks people to say how well they speak English: "not at all", "not well", "well", "very well", and "speak only English". This is better than nothing, and the authors show that it correlates with a more sophisticated test of English proficiency, but it's possible that the reason the lines in the graphs look so smooth is that this five-point scale is simply too coarse to show anything more. The measure also collapses over vocabulary, grammar, accent, etc., and we know that these behave differently (your ability to learn a native-like accent goes first).

A New Test

This was something we had in mind when devising The Vocab Quiz. If we get enough non-native Speakers of English, we could track English proficiency as a function of age ... at least as measured by vocabulary (we also have a grammar test in the works, but that's more difficult to put together and so may take us a while yet). I don't think we'll get two million participants, but even just a few thousand would be enough. If English is your second (or third or fourth, etc.) language, please participate. In addition to helping us with our research and helping advance the science of language in general, you will also be able to see how your vocabulary compares with the typical native English speaker who participates in the experiment.

--------
Hakuta, K., Bialystok, E., & Wiley, E. (2003). Critical Evidence: A Test of the Critical-Period Hypothesis for Second-Language Acquisition Psychological Science, 14 (1), 31-38 DOI: 10.1111/1467-9280.01415

*Yes, I know: Chinese is a family of languages, not a single language. But the paper does not report a by-language breakdown for this group.

Average weather

The Phytophactor — Wed, 15 May 2013 21:20:00 +0000

Weather people like to tell you how much below or above average the current weather is. Of course here in the great midwest of North America this is largely complete crap. You can average the weather data, but there is no average weather around here. Basically you go from too cold spring weather to summer instantly, and then back and forth a few times more. It just depends upon what particular weather front is winning the push and pull battle as they cross the plains. Three days ago the heat was on in our house because the temps at night were in the 30s. Now it's in the 80s and you have to turn the heat off and get the window screens in place. Ceiling fans get turned on in the bedrooms just a couple of days after you needed a blanket. Plants have to be tough to deal with such weather. On the good news side, cold weather has kept our field work in check and we're only running about 2 weeks late, and a few plants have had some prolonged flowering because of the cool nights. On the bad side, grass is growing like crazy and TPP doesn't like to mow. New street trees, a red oak, a swamp white oak, and an Accolade elm have been planted (by the city) to replace two huge white ash trees that had to be taken down because of emerald ash borer. Now some rain is needed. April was real wet, but May has been dry, oh, and you can average their rainfall amounts, but it's never just average. Welcome to a continental climate.

A New Non-mammaliaform Eucynodont from the Ischigualasto Formation of Argentina

Bill Parker — Tue, 14 May 2013 21:23:00 +0000

Martínez, R. N., Eliana Fernandez, E., and O. A. Alcober. 2013. A new non-mammaliaform eucynodont from the Carnian-Norian Ischigualasto Formation, Northwestern Argentina. Revista Brasileira de Paleontologia 16: 61-76. doi:10.4072/rbp.2013.1.05

Abstract - The record of non-mammaliaformes eucynodonts from the Carnian-Norian Ischigualasto Formation is diverse and abundant, including a medium to large size herbivore and small carnivores. Here is described a new small eucynodont from the Ischigualasto Formation, on the basis of a partial skull. The new taxon is characterized by palatal process of the premaxilla extending posterior to the level of the first postcanine; deep and large maxillary laterodorsal fossa that opens at the level of the root of the upper canine; and postorbital bar diverging posterolaterally at very low angle (35.6°) from the anteroposterior axis of the skull. Results from a phylogenetic analysis supports the new genus placement as a probainognathian eucynodont, more derived than Probainognathus Romer, and more closely related to Ecteninion Martinez, May & Forster and Trucidocynodon Oliveira, Soares & Schultz than to any other eucynodont. Ecteniniidae is proposed as a new clade including the new genus, Ecteninion and Trucidocynodon, and in the phylogenetic hypothesis represents the sister-group of Prozostrodontia (Prozostrodon Bonaparte & Barberena, Tritylodontidae and Mammaliaformes). Additionally, the new taxon from the Ischigualasto Formation shows that the Scaphonyx-Exaeretodon-Herrerasaurus biozone has similar cynodont diversity than the supposedly contemporaneous Hyperodapedon Assemblage Zone of Santa Maria 2 Sequence, in Southern Brazil.

Pollination success - waiting, waiting.

The Phytophactor — Tue, 14 May 2013 13:23:00 +0000

TPP's apple and pear trees have flowered, and it wasn't the absolute best weather for flowering, and we had a close call the other night with a low temperature near freezing, so now just waiting to see if we have pollination success. Last year an early spring and a late freeze combined to nuke the entire upper midwest apple crop. It was grim. Had to have northern spys shipped in from NY. It's just a tad to early to judge whether the pollinators did their job or not. Plenty of crab apples were in flower too, so lot's of nearby pollen sources, and no crab apple pollen will not affect the apples, just the apple offspring (seeds). The pear tree did not flower well, so the display might not have been big enough for good pollination. Combination of drought and bunnies required redoing most of the raspberry bed this week as well, and this was after giving up on the blue berries. In the process discovered that the neighbors property adjoining ours is raising a bumper crop of garlic mustard. Each year their seeds repopulate our gardens, so no matter how zealously the Phactors weed, we get more. Does the military sell surplus flame throwers? TPP will attempt to widen the weed-free zone along the fence line (on their side!) one way or another. But guess we're to gardening as Cub fans are to the Cubs, always hopefull, often disappointed.

Countries with a state religion also have fewer political and civil freedoms

noreply@blogger.com (Tomas Rees) — Mon, 13 May 2013 21:55:00 +0000

It's fairly common for a national government to explicitly favour one particular religion or sect. This support can take many forms - financial, political, or legal - but the common factor is that the dominant religion gets a helping hand from the state.

Now it probably wouldn't be too much of a surprise to learn that states inclined to interfere in religious expression are also more likely to place a controlling hand on political and civic freedoms, However, proving that relationship is not so straightforward.

Just defining "State Religion" is tricky enough. Several teams have created scorecards for country freedoms, but they disagree over the number of countries that have a state religion (somewhere between 48 and 75).

Even so, Steven Kettell at the University of Warwick in the UK, has pored over these statistics and come up with some interesting findings.

First off, he confirmed that countries with a state religion really do have substantially lower than average levels of political rights and civil liberties. This was chiefly down to countries with a Muslim majority, which are disproportionately likely to have fewer freedoms and also a state religion.

They also have higher levels of "social regulation" of religion - meaning that there are informal, unofficial barrier confronting other religions and favouring the state religion. They also have higher levels of religious persecution.

However, the striking thing was that, whereas general social and political freedoms were higher in nations with greater human development (a mix of wealth, health and education), there was no relationship between human development and the presence or absence of a state religion. There was also no connection to religious diversity or religiosity in general.

That lead Kettell to conclude that:

...the lower levels of freedom found in countries with state religions may have less to do with their particular socio-cultural conditions, and more to do with the institutional mechanics of state religions themselves. Given that the entire point and purpose of a state religion is to support the promotion of one particular religious perspective over other world-views, and given that this objective invariably involves the provision of various financial, legal and political privileges, it is not hard to see how these dynamics can lead to the curtailing of political and religious freedoms.

So, state religion and freedom: cause or effect?

The question matters, because religious protectionism is on the rise in the West. If such protectionism actually leads to other infringements of civil liberties, we could be in for a rough time.

Kettell, S. (2013). State Religion and Freedom: A Comparative Analysis Politics and Religion, 1-32 DOI: 10.1017/S1755048312000600

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

Poison for pain, the homeopathic way

noreply@blogger.com (Steven Salzberg) — Mon, 13 May 2013 20:43:00 +0000

At my local mega-grocery store last weekend, I happened to stroll down the aisle dedicated to homeopathic treatments. I saw shelf after shelf of brightly colored packages, all claiming health benefits. Most of these "medicines" were not cheap.

Amazing. To an average shopper, all of these products look like real medicine. The packaging is similar, the claims are similar, and it's all on display at a respectable grocery store. The difference, though, is that none of these products do what they claim to do. Thanks to a special exception for homeopathy created all the way back in 1938, none of the claims on these medicines need to be tested. The homeopathy aisle is an organized, state-sanctioned scam.

The 1938 law was the brain child of a U.S. senator, Royal Copeland, who happened to be a homeopath. Sen. Copeland inserted language into a major food and drug law that declared homeopathic preparations to be drugs. It also allowed homeopaths themselves to maintain the official list of these drugs, called the Homeopathic Pharmacopeia. Talk about the fox guarding the henhouse! Thanks to aggressive lobbying by homeopaths, homeopathic ingredients are not subject to the normal review required of real drugs. Most importantly, homeopathic drug makers do not have to prove their products are effective.

Homeopathy is based on the long-discredited beliefs of Samuel Hahnemann 200 years ago. Hahnemann thought that "like cures like," as long as you dilute the substance sufficiently. Thus caffeine will cure sleeplessness, poison ivy extract will cure an itch, and paralyzing plant toxins will cure pain. None of this is true.

The other key principle of homeopathy is that the more you dilute something, the stronger its effect. This is not only wrong, but it is exactly the opposite of what really happens. Greater dosage levels, unsurprisingly, have stronger effects. In Hahnemann's defense, science wasn't very far along when he came up with these notions.

Real medicine moved on long ago. But homeopathy persists, because there is money to be made - lots of money.

Back to my grocery store. Several shelves were filled with something called Topricin(R), which claims to relieve pain. Sounds like a medicine, right? Real drugs often use "cin" or "in" in their names because the word "medicine" itself ends with that sound. Clever! In front of me I saw Topricin for pain, Topricin foot cream, even Topricin for children. The Topricin packages and the company's website proclaim, in big letters, "Ideal Pain Relief", and in slightly less big letters: "Safe. Effective. Free of Side Effects." It also claims:

"Topricin's 11 homeopathic medicines are proven to be safe and effective for the elderly, pregnant, children, pregnant women and all skin types. Experience Topricin's relief for damaged muscle, tendon, ligament, and nerve tissue."

This is simply not true. It even seems to go beyond the bounds of what the (very weak) FDA regulations allow. The website specifically claims that Topricin is effective for arthritis, back pain, bruises, bursitis, fibromyalgia, minor burns, tendinitis, and more.

Well, what is it? Let's look at just two of the homeopathic ingredients in Topricin:

Belladonna 6X................. Treats muscles spasms, night leg cramps
Heloderma 8X................. Relief of burning pain in the hands and feet

Belladonna for pain? Belladonna is one of the most toxic plants known to man. Eating just a few small berries is lethal. And the one study I could find showed that it has no clinical effect when used in a homeopathic preparation. That's lucky for unwitting consumers: if it wasn't so diluted, Belladonna would make them very sick indeed.

Heloderma? That's the venom from a gila monster. Although rarely fatal, it causes severe pain, bleeding, nausea, and vomiting. This is not something I would take for pain - and I certainly would never give it to children.

I know that Big Pharma is often guilty of deceptive marketing, and I've criticized Pharma many times. But CAM ("complementary and alternative") pharma is every bit as bad. Big CAM takes advantage of generous laws to make medical claims with impunity, often skirting as close as possible to what the law permits. And the Big CAM companies profit handsomely in the process. Everything on the Topricin package - the name, the packaging, the claims - is designed to make the consumer think that it is an effective pain treatment. It's not. It's a modern package of snake oil.

How to Convince People WiFi Is Making Them Sick

Elizabeth Preston — Mon, 13 May 2013 10:05:00 +0000

All it takes is an antenna on a headband. If you've got a breathless video report on the dangers of wireless internet connections, that will help your case. It doesn't take much, though, to turn an ominous hint into a real headache.

Some people consider themselves sensitive to electromagnetic fields. They report symptoms such as burning skin, tingling, nausea, dizziness, or chest pain, and they blame their malaise on nearby power lines, cell phones, or WiFi networks. A recent Slate article described such people moving to a remote West Virginia town where radio-frequency signals are banned. (The town is within the U.S. National Radio Quiet Zone, an area that's enforced to keep signals from interfering with radio telescopes there—telescopes that work because they receive the radio-frequency signals constantly hitting our planet from space.)

There's no known scientific reason why a wireless signal might cause physical harm. And studies have found that even people who claim to be sensitive to electromagnetic fields can't actually sense them. Their symptoms are more likely due to nocebo, the evil twin of the placebo effect. The power of our expectation can cause real physical illness. In clinical drug trials, for example, subjects who take sugar pills report side effects ranging from an upset stomach to sexual dysfunction.

Psychologists Michael Witthöft and G. James Rubin of King's College London explored whether frightening TV reports can encourage a nocebo effect. They recruited a group of subjects and showed half of them a clip from a BBC documentary about the potential dangers of wireless internet. (The BBC later acknowledged that the 2007 program was "misleading.") The remaining subjects watched a video about the security of data transmissions over mobile phones.

After watching the videos, subjects put on headband-mounted antennas. They were told that the researchers were testing a "new kind of WiFi," and that once the signal started they should carefully monitor any symptoms in their bodies. Then the researchers left the room. For 15 minutes, the subjects watched a WiFi symbol flash on a laptop screen.

In reality, there was no WiFi switched on during the experiment, and the headband antenna was a sham. Yet 82 of the 147 subjects—more than half—reported symptoms. Two even asked for the experiment to be stopped early because the effects were too severe to stand.

Witthöft says he expected to see a greater effect in people who had watched the frightening documentary. This wasn't the case overall. Instead, the movie mainly increased symptoms in subjects who described themselves beforehand as more anxious.

"It suggests that sensational media reports especially in combination with personality factors (in this case anxiety) increase the likelihood for symptom reports," Witthöft says.

Plenty of symptoms were reported without the sensationalist TV show, though. The antenna on the head, the researchers' allusion to a "new kind of WiFi," and the instructions to monitor their bodies closely were enough to trigger symptoms in many people who watched the other video.

Witthöft points out that his study would have been stronger if there were a third group of subjects who didn't wear the "WiFi" headband at all, but were simply told to pay attention to their bodies for 15 minutes. This kind of attentiveness might trigger symptoms on its own.

Still, Witthöft says, "I think the high percentage of symptom reports nicely shows how powerful nocebo effects are."

Though the researchers set out to show how irresponsible reports in the media can trigger a nocebo effect, they ended up showing how easy it is to make a person feel sick with just a a prop and a few choice words. Even a National Radio Quiet Zone can't protect against that.

Witthöft, M., & Rubin, G. (2013). Are media warnings about the adverse health effects of modern life self-fulfilling? An experimental study on idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) Journal of Psychosomatic Research, 74 (3), 206-212 DOI: 10.1016/j.jpsychores.2012.12.002

Image: Scott Beale/Laughing Squid (via Flickr)

Living in an Imperfect World: Psycholinguistics Edition

GamesWithWords — Mon, 13 May 2013 10:00:00 +0000

You, sir, have tasted two whole worms. You have hissed all my mystery lectures and been caught fighting a liar in the quad. You will leave Oxford by the next town drain. -- Reverend Spooner.

There is an old tension in psycholinguistic (or linguistic) theory, which boils down to two ways of looking at language comprehension. When somebody says something to you, what do you do with that linguistic input? Is your goal to decode the sentence and figure out what the sentence means, or do you try to figure out what message the speaker intended to convey? The tension comes in because presumably we do a bit of both.

Suppose a young child says, "Look! A doggy!" while pointing to a cat. Most people will agree that technically, the child's sentence is about a dog. But most of can still work out that probably the child meant to talk about the cat; she used the word doggy either due to lack of vocabulary, confusion about the distinction between dogs and cats, or a simple speech error. Similarly, if your friend says at 7pm, "Let's go have lunch," technically your friend is suggesting having the midday meal, but probably you charitably assume he is just very hungry and so made a mistake in saying "lunch" instead of "dinner".

For a variety of reasons, linguistics and psycholinguistics have focused mostly on decoding sentences rather than intended meanings. This is important work about an important problem, but -- as we saw above -- it's only half the story. PNAS just published a paper by Gibson, Bergen, and Piantadosi that addresses the second half. Gibson and Bergen are at M.I.T., and Piantadosi recently graduated from M.I.T., and like much of the work coming out of Eastern Cambridge lately, they take a Bayesian perspective on the problem, and point out that the probability that the speaker intended to convey a particular message m given that they said sentence s is proportional to the prior probability that the speaker might want to convey m times the probability that they would say sentence s when intending to convey m.

This ends up accounting for the phenomenon brought up in Paragraph #2: If the literal meaning of the speaker's sentence isn't very likely to be what they intended to say ("Let's go have lunch", spoken at 7pj), but there is some other sentence that contains roughly the same words but has a more plausible meaning ("Let's go have dinner"), then you should infer that the intended message is the latter one and that the speaker made an error.

So far, this is not much more than a restatement of our intuitive theory in Paragraph #2. But a Gibson, Bergen and Piantadosi point out that a few non-trivial predictions come out of this. One is that you should assume that deletions (dropping a word) are more likely than insertions (adding a word). The reason is that there are only so many words that can be dropped from a particular sentence, so even if the probability of accidentally dropping a word is low, the probability of accidentally dropped a particular word isn't all that much lower. So if the intended sentence was "The ball was kicked by the girl", and the speaker accidentally dropped two words, the probability that the speaker happened to drop "was" and "by", resulting in the grammatical but unlikely sentence "The ball kicked the girl" is not so bad. However, suppose the intended sentence was "The girl kicked the ball", what are the chances the speaker accidentally adds "was" and "by", resulting in the grammatical but unlikely sentence "The girl was kicked by the ball"? Pretty much zilch, since English contains hundreds of thousands of words: There is pretty much no chance that those particular words would be inserted in those particular locations?

The authors present some data to back up these and some other predictions. For instance, if listeners are given reason to suspect that the speaker makes lots of speech errors, they are then even more likely to "correct" an unlikely sentence to a similar sentence with a more likely meaning.

There's plenty more work to be done. There are plenty of speech errors out there besides insertions and deletions, such as substitutions and the various phonological errors that made Rev. Spooner famous (see quote above). Work on phonological errors shows that speaker are more likely to make errors that result in real words (train->drain) than non-words (train->frain). Likely, the same is true of other types of errors. Building a full theory that incorporates all the complexity of speech processes is a ways off yet. But the work just published is an important proof of concept.

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Gibson, E., Bergen, L., and Piantadosi, S. (2013). Rational integration of noisy evidence and prior semantic expectations in sentence interpretation Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1216438110

Please don't smoke the tomatoes!

The Phytophactor — Mon, 13 May 2013 09:57:00 +0000

How ya doin New Yawk? The NY Boys in Blue busted a rooftop marijuana growing operation except it turned out to be tomatoes. Yes, tomatoes. Which of course are grown for their berries not their smokable leaves. This is a good thing because the smoking tomato leaves is way worse than smoking tobacco leaves, both nightshades, and similar enough that you can graft tomatoes onto tobacco root stock and grow some high nicotine tomatoes (not recommended for several reason taste being the primary one), however you will not get tomato hornworms on them. Like most nightshades, the green foliage of tomatoes contain one or more of the tropane alkaloids, primarily hyoscyamine. It's not good for you when ingested, and European so well knew this that the edibility of tomatoes was very much in question when newly introduced from the New World. The rooftop gardeners were turned in by the building super who said it was marijuana. The police never checked it out (good police work, boys) and came busting in on the tomato patch. As stupid as this sounds, these be city boys. People so far removed from the production and source of their food that they probably thought tomatoes grew on trees. TPP remembers a college friend from Brooklyn who recoiled in total revulsion once he actually saw, up close, first hand, where milk comes from. He was also incredulous about the actual size of a cow. "Tings like dis belong in zoos!" If his remark is recalled accurately. So from TPP's perspective, in their vegetative state, neither the super nor the cops could be expected to make an accurate ID of any plant foliage. Wonder what they'd pay for doing some plant ID work for the NYC police?

Blue lawn to green slime

The Phytophactor — Sun, 12 May 2013 08:43:00 +0000

A month ago a large portion of our lawn was a carpet of blue scilla. It took decades for the scilla to multiply so prolifically, and it's a wonderful and lovely harbinger of spring. What could be the problem? A month has passed and lawns need mowing. The blue lawn is now a verdant thicket of green scilla leaves, but they mow right? Sort of. The leaves of scilla contain a considerable amount of mucilage and moisture. The discharge from you mower is basically green slime. Generally the best strategy is to simply wait until the scilla leaves begin to yellow and fade before mowing the densest parts. Even where the scilla isn't solid, it can get so slippery, you can barely get enough purchase to push the mower! Ah, well, nothing's perfect.

Friday Fabulous Flower - Fern-leafed Peony

The Phytophactor — Fri, 10 May 2013 18:03:00 +0000

Several years ago a long-time employee of TPP's favorite neighborhood garden shoppe was offering us several perennials at significant discounts rather than trying to over winter them and sell them the next spring. And three fern-leafed peonies (Peonia tenuifolia) were among the lot, at least 3 pots labelled as such. They were a bit slow to get started but now all three produce 2 foot high mounds of very finely dissected foliage. Their single flowers are bright scarlet red, one at the end of each aerial shoot, and they are the earliest of the peonies, even beating the tree peonies by a week. Unfortunately, while very handsome, the flowering display does not last long, but then again, few flowering displays do. The foliage remains attractive enough, so do think of putting these into a middle position is a partly shady bed. They particularly look great in the morning sun. Actually just checking the data, and our Japanese peonies flowered at the same time, a woodland, herbaceous perennial. Something tells TPP he's done this as a FFF before, but so what.

Upcycling rather than recycling

The Phytophactor — Fri, 10 May 2013 15:21:00 +0000

Alternatives to waste, alternatives to over consumption, alternatives to filling more land-fills are always welcome ideas, and here's a very nice and interesting video of upcycling in Greece. Now TPP figures that many of you are pretty conscious of and maybe even conscientious about recycling. Further many of you are in one way or another associated with universities. Now where else would be a better place to initiate the concept of upcycling than in a university town? You've got the arty types. You've got the techie types. You've got the junk generating types! And they all need jobs and cash. Upcycling isn't exactly a new idea.
TPP grew up with old New England farmers who never threw out anything. When you needed something, you visited your junk pile, found some bits and pieces, and built it. The manner, and the creative way these people upcycle is impressive and shows what some imagination can do? So pass this on; upcycle it so to speak.

TMI Friday: Using a Bottle for a Throttle

The Defective Brain — Fri, 10 May 2013 14:32:00 +0000

Today we once again must again take a look at men who take incredible risks in order to find new and grotesque methods of masturbation. You have been warned.

This week, the object of their fascination is.. the plastic bottle.

In the grand scheme of things, at least the plastic bottles don't have spinning blades inside them, so in theory, these individuals are better off than those who turn on the vacuum cleaner for stimulation.

The first case we shall be examining comes from 2004, when a 27 year old man in India was admitted to hospital with a peculiar problem. His penis was stuck in a hard plastic bottle. There apparently were no attempts at an excuse, just the simple explanation that he had attempted to use it for masturbation. They called in the hospital carpenter to cut away the bottle *very* carefully using an Iron cutting saw. After 15 minutes of struggle, the bottle was removed.

In 2009, a 77 year old man in Singapore was admitted into hospital with complaints of blood in his urine, and difficulty urinating. Initially he wasn't forthcoming about his case history, for reasons that will soon become clear. You see, one week previously he had pushed a 1.5 litre bottle over his genitals, and got stuck. Over the next 3 days, he managed to cut away most of the bottle. But he still couldn't remove the neck of the bottle, despite attempts at lubricating it with soap. The surgeons managed to pry off the bottle neck with scissors, and they managed to repair some of the damage, but he died 3 days after admission.

The third case we will look at came from 2010 , and also occurred in India. A 47 year old man came in 14 hours after attempting to masturbate himself with a plastic bottle. That in itself is not the hair raising part of this case. We are told that the bottle neck was placed in such a position that it was impossible to access with a normal cutting device. So what did they use ? A soldering iron. Think about that. They mitigated the heat somewhat through adding cold saline in order to regulate the temperature. Still, it's not exactly a pleasant thought.

The final case I'll be talking about involves a 58 year old man. His flatmate called an ambulance for him after recognising that he was behaving oddly. But he sent them away, claiming that he didn't have anything wrong with him. Two days later his flatmate found him dead. The autopsy revealed that his genitals had been constricted with a plastic bottleneck. This bottleneck had cut off the circulation to this region, and allowing parts of his genitals to begin decaying. This lead to bacteria entering the bloodstream, and eventually caused multiple organ failure.

So how could these people stick their members into such small openings, and then get stuck. In order to answer this, we must examine how the penis works. Essentially it is a balloon filled with blood. To become erect, arteries dilate in order to increase blood flow. However, if the veins that take the blood out of the penis are constricted, by say, a plastic bottleneck, then blood takes longer to escape, and so it swells up and gets stuck. This can actually be very dangerous. when the circulation is cut off, it can become gangrenous and in severe cases of penile strangulation, the only option is amputation. this is not even the worst case scenario, as we have seen, if this is not dealt with as soon as possible, then there is a risk of death.

Penile strangulation appears to have a higher body count than men who stick their appendages into the whirling blades of a vacuum cleaner !

References

Jain S., Gupta A., Singh T., Aggarwal N., Sharma S. & Jain S. (2004). Penile strangulation by a hard plastic bottle : A case report, Indian Journal of Surgery, 66 (3)

Ooi C.K., Goh H.K., Chong K.T. & Lim G.H. Penile strangulation: report of two unusual cases., Singapore medical journal, PMID: 19296009

Shamrao Kumbhar U., Dasharathimurumu & Bhargavpak (2011). Acute penile incarceration injury caused by a plastic bottle neck., International Journal of Biological & Medical Research, 2 (4)

Morentin B., Biritxinaga B. & Crespo L. (2011). Penile strangulation: report of a fatal case., The American journal of forensic medicine and pathology, PMID: 22101437

Extinction is forever - A close call for an ebony

The Phytophactor — Fri, 10 May 2013 09:41:00 +0000

Islands are evolutionary laboratories providing genetic isolation of any organism that disperses there with the result that new and novel species often arise that grow no where else. Then there are those species (just 1) that build boats so that they may disperse more easily, and bring with them their pigs and goats, much to the detriment of endemic species that arose in isolation from such organisms. Here's a story of a near brush with extinction, the St. Helena's ebony. Long thought extinct, two bushes were found growing on a cliff beyond the reach of grazing goats. With the assistance of Kew Gardens, this species' extinction has been forestalled for now, by using these two survivors to propogate new plants, something not easily done without today's biotechnical tools. Without botanical gardens with such conservation programs the situation around the world would be much worse. Of course, what difference does such a species make? Why should we care? Why should we expend so many resources rescuing this tree? Maybe next time the species will be something really important, and knowing how to do it would be a good thing. And who are you to judge this species of no consequence? And to give you some idea what TPP means, parochial dolts, unfortunately dolts put in charge of higher education, wonder why we "waste" time and money teaching our students about rain forest as if all that matters, or should matter, takes place within the non-biological borders of Lincolnland.

Chemistry, fluid dynamics and an awful radioactive mess

noreply@blogger.com (Wavefunction) — Fri, 10 May 2013 01:19:00 +0000

When it comes to handling radioactive waste the Hanford site in western Washington state is the opposite of a role model. Ever since its reactors started producing the plutonium which was used in the Nagasaki bomb, Hanford has been generating waste with little foresight and responsibility. It has the dubious honor of being the most contaminated radioactive site in the country.

Scientific American has an article which gives an idea of how truly awful the problem is. It's not just that there's a lot of waste or that it's everywhere. It seems like the waste basically conforms to the devil's definition of the word "heterogeneous" and takes a form representing the average nuclear chemist's version of hell:

"Overall, the waste tanks hold every element in the periodic table, including half a ton of plutonium, various uranium isotopes and at least 44 other radionuclides—containing a total of about 176 million curies of radioactivity. This is almost twice the radioactivity released at Chernobyl, according to Plutopia: Nuclear Families, Atomic Cities, and the Great Soviet and American Plutonium Disasters, by Kate Brown, a history professor at the University of Maryland, Baltimore County. The waste is also physically hot as well as laced with numerous toxic and corrosive chemicals and heavy metals that threaten the integrity of the pipes and tanks carrying the waste, risking leakage.

The physical form of the waste causes problems, too. It’s very difficult to get a representative sample from any given tank because the waste has settled into layers, starting with a baked-on “hard heal” at the bottom, a layer of salt cake above that, a layer of gooey sludge, then fluid, and finally gases in the headspace between the fluid and the ceiling. Most of the radioactivity is in the solids and sludge whereas most of the volume is in the liquids and the salt cake."

"Plutopia", by the way, is a very interesting book. In any case, the waste problem at Hanford looks like it will engage the services of every conceivable kind of chemist, engineer and fluid dynamics expert that I can imagine.

"All of these considerations contribute to the overall problem, which can be summed up in one word: flow. To get to the glass log stage the waste has to travel through an immense labyrinth of tanks and pipes. It has to move at a fast enough clip to avoid pipe and filter clogs as well as prevent solids from settling. This is quite a challenge given the multiphasic nature of the waste: solids, liquids, sludge and gases all move differently. The waste feed through the system will be in the form of a “non-Newtonian slurry”—a mixture of fluids and solids of many different shapes, sizes and densities. If the solids stop moving, problems ensue."

The article also talks about two serious concerns; the possibility that enough plutonium in the waste could build up to trigger a chain reaction (although one which in bomb parlance would be a "fizzle") and the possibility that the heat and radiation could split water up and lead to a buildup of hydrogen. For now these concerns are about unlikely events and are secondary in any case to the much more important problems of Sludge Management and the Battle against Viscosity. Just tells you how important it is to nip problems with reactor waste in the bud before they turn into a godforsaken headache for future generations.

Observations on the final week of a semester

The Phytophactor — Thu, 09 May 2013 15:37:00 +0000

The end of a semester and the possibility of graduation for some, survival for others, puts a lot of strain on the system. After many years on a university campus you sort of get used to a certain amount of manic activity and stressed out behaviors. And there are other hallmarks that the semester is nearly over. Let's see what we have. A fellow just ran down the hallway screaming and throwing papers every which way. Hmm. Based on the papers, perhaps he was happy to be done with this particular chemistry class, one way or another. Presumably done in such a manner as to never need those notes again. A corner of our staff parking lot was vacant because someone had tossed a rather largish TV out of an apartment window, and it sort of exploded upon impact. Perhaps they were aiming at someone's car (faculty?)? Perhaps they had finally figured out that its addictive nature had caused them to spend more time with reality shows than with the reality of studying. Perhaps it was a physics experiment done as a final project. A student sporting a rather deep tan shows up to explain why they haven't had time to finish their final paper yet. Hmmm. A student stopped by to say goodbye and introduce TPP to their parental unit, show them the greenhouse, and try to impress them with how much they had learned. Those exams haven't been read yet, but it's a good bet they did pretty well. A student who seemed to have steadfastly ignored by advice all semester stopped by to see if they could get a letter of recommendation. TPP explained his perspective that would have to be part of his letter; they seemed surprised that you just didn't write how nice they were. Four cars of studenty looking people, no one of which seemed to know which way they were going, were in wrong lanes, going opposite ways, and everyone was yelling at everyone else. This is why TPP never rides to campus on his bike until the crazies have gone home. Grades get posted for a big introductory class in a hallway display case. The first student to arrive looks up their grade and gestures with a fist, yelling, "Yes!"; the second arrives, looks, and breaks into tears. That's the long and short of it. A nicely dressed young lady is strolling through the quad taking pictures; with all the crab apples in flower, the campus does look lovely. Piles of refuse are growing upon the curbs and around apartment dumpsters. It looks a lot like the aftermath of a flood or some other natural disaster. Years ago it was the custom among out students to haul ruined, or just slightly used, furniture out into an intersection and torch it. This custom was frowned upon. Still the amount of waste is appalling; the concept of recycling has not caught on and slum-lords throw out everything left behind. Garbage cruisers are having a big time, which is the only sort of recycling going on. Fast food delivery is going on every where. One place near campus has bike delivery to anywhere on campus, fast! Yes, a semester is coming to an end; you can tell.

Happy Blogday! Help Me Rename This Site

Elizabeth Preston — Thu, 09 May 2013 09:34:00 +0000

Inkfish is three years old today!

One great thing about blogs that doesn't apply to real three-year-olds is that you can change their name and appearance at will. I'm getting tired of "Inkfish"—too mysterious, too many creepy arms. Too much guilt about mistakenly calling octopus arms "tentacles" on occasion.

So I'd like to give the blog a new name and a new look. Below are several directions I'm considering. I hope that you, readers, will weigh in.

**********

Welcome! You Probably Got Here by Googling Your Juice Cleanse Symptoms
Tagline: Or Searching for Ionic Foot Detox Reviews
Alternate tagline: I Write About Other Stuff Too. Check It Out When You're Less Hazy
Banner art: a weeping woman with her feet in a small tub of brown water. Foregrounded, a glass of kale juice with a party umbrella.
Inspiration: juice cleanses, foot detox, everything else.

Why I Couldn't Hang Out Last Night
Banner art: a blogger on a couch in a dark room, gently lit by the glow of the laptop screen.
Inspiration: purely fictional.

Every Study About Penguins
Banner art: penguins.
Alternate art: not penguins. Irony could increase my readership among hipsters.
Inspiration: penguins, penguins, penguins, penguins, penguins.

The Loom
Banner art: portrait of Carl Zimmer.
Inspiration: trying to lure Bing users who are searching for Carl Zimmer's blog, The Loom.
Potential complication: lawsuit.

Animals with Things on Their Heads
Banner art would be a rotating selection of photos: crabs wearing GPS devices, pigeons carrying cameras, penguins with earmuffs, and this seal.

Inspiration: animal stalking, pigeons.

Girl That Poops Flowers
Alternate title: Most Inconvenient Moments to Have Narcolepsy
Banner art: a mouse that's quiet—too quiet.
Inspiration: unusual internet searches addressed at the help desk.

Adventures in Bodily Fluids: An Ongoing Quest to Make My Grandmother Admit She Doesn't Love Everything I Write
Banner art: the empty vanilla ice cream bowl I considered using to illustrate a story about sperm-eating flies.
Inspiration: see above.

**********

Please leave your votes in the comments (or just say hello). Thanks for your help, and thanks as always for reading!

5-8-13 Fibonacci day

The Phytophactor — Wed, 08 May 2013 20:55:00 +0000

The infamous Fibonacci series is recalled on this May 8th, 2013, part of the series which is constructed when each element is a sum of the previous 2 elements in the series. So 1 - 1- 2 - 3 - 5 - 8 - 13 - 21 etc. Lots of things in biology are arranged in helices, spirals, which can be described in terms of a Fibonacci series. This has been around a long time because, Fibonacci was actually Leonardo of Pisa (not of Vinci), who must have been one hell of a mathematician. This is just about all TPP knows about this other than some of the flowers whose development he has studied involve Fibonacci spirals describing the arrangement of multiple parts. Such dates don't come around very often, so glad some math geek was around to point it out.

Post semester clean-up and end-of-the-semester rant

The Phytophactor — Wed, 08 May 2013 14:35:00 +0000

In addition to grading and grades, followed by tears and gripes, TPP's research lab and teaching classroom/lab are basically a pit. The debris left over by a semester of student work is considerable. Fortunately disposable petri dishes may just be disposed of. OK, this isn't green, but it is ultra convenient. Bits and pieces of student research projects either get removed or discarded as well. Much of it was recycled material anyways. Glasswear gets washed. The refridgerator, oh, this can be very scary. Maybe you've never had a lab fridge, but you don't want to put your lunch in there, although ours is safe for food, safe in a certified sense. All sorts of slides and specimens must find their way back to there respective homes, their cabinets, drawers, and cupboards. Most people have no idea how much of this stuff it takes to teach botany labs, but it takes up more space than the classroom itself. This is why it's so helpful when a facility manager declares that "they [biolog] have plenty of room if they'd just throw out all the junk the keep around." Yes, "all the junk" we use to put biology into the hot little hands of students. "All the junk" that makes us a university not a high school. Remind me again why faculty must tolerate such morons? Students come into two flavors with respect to general lab cleanup; those who take care of their own messes and trash, and those who expect someone else to follow them around and deal with it. Whose apartment would you want to visit? The fun part is rediscovering things you had sort of forgotten about. It's like re-discovering a toy you hadn't played with in a great while. Some things have for unknown reasons taken a beating like the four balls of clay used to demonstrate a tetrad of spores and the fomation of trilete scars on the spore wall following meiosis. Yes, clay. What do you use? Fortunately it can be remolded. And lastly you have to make a list of supplies and commodities that got used up so that when the new budget year arrives, and if some budget actually arrives with the new year, you can get replacements. Lab stools dropped like flies having demonstrated that their have a 12 year useful half-life; exactly half the stools broke during the last 2 semester. Wonder if we can get some new stools or continue to display a stool/chair museum. This is the latest outrage in misguided and phoney baloney cost accounting. Since the lab classroom is only used by our department, buying furniture for the lab is the dept's responsibility. OK you can understand this, but, and this is a big BUT, the dept never gets any of the revenue the teaching generates. So no tuition money to buy stools exists in the dept, but it's the dept's responsibility. It must take the combined intellects of at least 3 assistant provosts to think of stuff like this. Oh, so now TPP is back to grading.

On synthesis, design and chemistry's outstanding philosophical problems

noreply@blogger.com (Wavefunction) — Wed, 08 May 2013 12:38:00 +0000

: Chemists need to move from designing structure - exemplified by this synthetic receptor - to designing function (Image: Max Planck Institute).

Yesterday I wrote a post about a perspective by multifaceted chemist George Whitesides in which he urged chemists to broaden the boundaries of their discipline and think of big picture problems. But the article spurred me to think a bit more about a question which I (and I am sure other chemists) have often thought about; what’s the next big challenge for chemistry?

And when I ask this question I am not necessarily thinking of specific fields like energy or biotechnology or food production. Rather, I am thinking of the next outstanding philosophical question confronting chemistry. By philosophical question I don’t mean an abstract goal which only armchair thinkers worry about. The philosophical questions in a field are those which define the field’s big problems in the most general sense of the term. For physicists it might be understanding the origin of the universe, for biologists the origin of life. These problems can also be narrowly defined questions that nonetheless expand the understanding and scope of a field; for instance in the early twentieth century physicists were struggling to make sense of atomic spectra, which turned out to be important for the development of quantum theory. It’s also important to note that the philosophical problems of a field change over time, and this is one reason why chemists should be aware of them; you want to move with the times. If you were a “chemist” in the sixteenth century the big question was transmutation. In the nineteenth century when chemistry finally was cast in the language of elements and molecules the big question became theconstitution of molecules in the form of atomic arrangements.

Synthesis is no longer chemistry’s outstanding general problem

When I think about the next philosophical question confronting chemistry I also feel a sense of despondency. That’s because I increasingly feel that the great philosophical question that chemists are going to face in the near future is emphatically not one whose answer they will locate in the all-pervasive activity that always made chemistry unique: synthesis. What always set chemistry apart was its ability to make new molecules that never existed before. Through this activity chemistry has played a central role in improving our quality of life.

The point is, synthesis was the great philosophical question of the twentieth century, not the twenty-first. Now I am certainly not claiming that synthesizing a complex natural product with fifty rotatable bonds and twenty chiral centers is even today a trivial task. I am also not saying that synthesis will cease to be a fruitful source of solutions for humanity’s most pressing problems, such as disease or energy; as a tool the importance of synthesis will remain undiminished. What I am saying is that the general problem of synthesis has now been solved in an intellectual sense (as an aside, this would be consistent with the generally pessimistic outlook regarding total synthesis seen on many blogs.)

The general problem of synthesis was unsolved in the 30s. It was also unsolved in the 50s. Then Robert Burns Woodward came along. Woodward was a wizard who made molecules whose construction had defied belief. He had predecessors, of course, but it was Woodward who solved the general problem by proving that one could apply well-known principles of physical organic chemistry, conformational analysis and spectroscopy to essentially synthesize any molecule. He provided the definitive proof of principle. All that was needed after that was enough time, effort and manpower. If chemistry were computer science, then Woodward could be said to have created a version of the Turing Machine, a general formula that could allow you to synthesize the structure of any complex molecule, as long as you had enough NIH funding and cheap postdocs to fill in the specific gaps. Every synthetic chemist who came after Woodward has really developed his or her own special versions of Woodward’s recipe. They might have built new models of cars, but their Ferraris, Porches and Bentleys – as elegant and impressive as they are – are a logical extension of Woodward and his predecessor’s invention of the internal combustion engine and the assembly line.

A measure of how the general problem of synthesis has been solved is readily apparent to me in my own small biotech company which specializes in cyclic peptides, macrocycles and other complex bioactive molecules. The company has a vibrant internship program for undergraduates in the area. To me the most remarkable thing is to see how quickly the interns can bring themselves up to speed on the synthetic protocols. Within a month or so of starting at the bench they start churning out these compounds with the same expertise and efficiency as chemists with PhDs. The point is, synthesizing a 16-membered ring with five stereocenters has not only become a routine, high-throughput task but it’s something that can be picked up by a beginner in a month. This kind of synthesis might have easily fazed a graduate student twenty years ago and taken up a good part of his or her PhD project. The bottom line is that we chemists have to now face an uncomfortable fact: there are still a lot of unexpected gems to be found in synthesis, but the general problem is now solved and the incarnation of chemical synthesis as a tool for other disciplines is now essentially complete.

Functional design and energetics are now chemistry’s outstanding general problems

So if synthesis is no longer the general problem, what is? My own field of medicinal chemistry and molecular modeling provides a good example. It may be easy to synthesize a highly complex drug molecule using routine techniques, but it is impossible, even now, to calculate the free energy of binding of an arbitrary simple small molecule with an arbitrary protein. There is simply no general formula, no Turing Machine that can do this. There are of course specific cases where the problem can be solved, but the general solution seems light years away. And not only is the problem unsolved in practice but it is also unsolved in principle. Sure, we modelers have been saying for over twenty years that we have not been able to calculate entropy or not been able to account for tightly bound water molecules. But these are mostly convenient questions which when enunciated make us feel more emotionally satisfied. There have certainly been some impressive strides in addressing each of these and other problems, but the fact is that when it comes to calculating the free energy of binding, we are still today where we were in 1983. So yes, the calculation of free energies – for any system – is certainly a general problem that chemists should focus on.

But here’s the even bigger challenge that I really want to talk about: We chemists have been phenomenal in being able to design structure, but we have done a pretty poor job in designing function. We have of course determined the function of thousands of industrial and biological compounds, but we are still groping in the dark when it comes to designing function. Here are a few examples: Through combinatorial techniques we can now synthesize antibodies that we want to bind to a specific virus or molecule, but the very fact that we have to adopt a combinatorial, brute force approach means that we still can’t start from scratch and design a single antibody with the required function (incidentally this problem subsumes the problem of calculating the free energy of antigen-antibody binding). Or consider solar cells. Solid-state and inorganic chemists have developed an impressive array of methods to synthesize and characterize various materials that could serve as more efficient solar materials. But it’s still very hard to lay out the design principles – in general terms – for a solar material with specified properties. In fact I would say that the ability to rapidly make molecules has even hampered the ability to think through general design principles. Who wants to go to the trouble of designing a specific case when you can simply try out all combinations by brute force?

I am not taking anything away from the ingenuity of chemists – nor am I refuting the belief that you do whatever it takes to solve the problem – but I do think that in their zeal to perfect the art of synthesis chemists have neglected the art of de novo design. Yet another example is self-assembly, a phenomenon which operates in everything from detergent action to the origin of life. Today we can study the self-assembly of diverse organic and inorganic materials under a variety of conditions, but we still haven’t figured out the rules – either computational or experimental – that would allow us to specific the forces between multiple interacting partners so that these partners assembly in the desired geometry when brought together in a test tube. Ideally what we want is the ability to come up with a list of parts and the precise relationships between them that would allow us to predict the end product in terms of function. This would be akin to what an architect does when he puts together a list of parts that allows him to not only predict the structure of a building but also the interplay of air and sunlight in it.

I don’t know what we can do to solve this general problem of design but there are certainly a few promising avenues. A better understanding of theory is certainly one of them. The fact is that when it comes to estimating intermolecular interactions, the theories of statistical thermodynamics and quantum mechanics do provide – in principle – a complete framework. Unfortunately these theories are usually too computationally expensive to apply to the vast majority of situations, but we can still make progress if we understand what approximations work for what kind of systems. Psychologically I do think that there has to be a general push away from synthesis and toward understanding function in a broad sense. Synthesis still rules chemical science and for good reason; it's what makes chemistry unique among the sciences. But that also often makes synthetic chemists immune to the (well deserved) charms of conformation, supramolecular interactions and biology. It’s only when synthetic chemists seamlessly integrate themselves into the end stages of their day job that they will learn better to appreciate synthesis as an opportunity to distill general design principles. Let the synthetic chemist interact with the physical biochemist, the structural engineer, the photonics expert; let him or her see synthesis through the requirement of function rather than structure. Whitesides was right when he said that chemists need to broaden out, but another way to interpret his statement would be to ask other scientists to channel their thoughts into synthesis in a feedback process. As chemists we have nailed structure, but nailing design will bring us untold dividends and will help make the world a better place.

First published on the Scientific American Blog Network.

Do You Speak Korean?

GamesWithWords — Wed, 08 May 2013 09:30:00 +0000

Learning new languages is hard for many reasons. One of those reasons is that the meaning of an individual word can have a lot of nuances, and the degree to which those nuances match up with the nuances of similar words in your first language can make learning the new language easier; the degree to which the nuances diverge can make learning the
new language harder.

In a new experiment, we are looking at English-speakers learning Korean and Korean-speakers learning English. In particular, we are studying a specific set of words that previous research has suggested give foreign language learners a great deal of difficulty.

We are hoping that we will be able to track how knowledge of these words develops as you move from being a novice to a fluent speaker. For this, we will need to find a lots of people who are learning Korean, as well as Korean-speakers who are learning English. If you are one, please participate.

The experiment is called "Trials of the Heart". You can find it here.

We do also need monolingual English speakers (people whose first and essentially only language is English) for comparison, so if you that's you, you are welcome to participate, too!

Image credit

Just a little bit busy this spring

The Phytophactor — Tue, 07 May 2013 12:47:00 +0000

The end of the semester, the beginning of field season, a publishing deadline, and home gardening are all colliding here in May when the days just don't have enough hours. At the coffee shoppe this morning, at least 5 colleagues were sitting there with piles of papers. Only one of them was in a semi-good mood. What a terrific person she must be. Students want to know their grades, and TPP wants to provide them as soon as possible. However, a bit of patience is a virtue and so is a careful, thoughtful evaluation. Same goes for the field work and gardening. This afternoon will be spent in the field looking for our permanent plots. They are marked in the SW corner by a big spike and a inch and a half numbered aluminum tag. It's hard enough to find them when the prairie has been burned, but this year is didn't get burned. When the plot gets found, a 36-inch pvc pipe is shoved over the spike at the corner. When the vegetation really gets up there, it's hard to even find the pvc. An observant person can be within inches of a tag and not see it. This is sure to be fun. At home, plants are showing up faster than the Phactors can plant them, and it's always good to take time to plant things well and in the best location possible. One particularly well-placed plant is an orange flowered azalea that sits in a nice copse among old spruces, a bald cypress, and big hostas. In flower, it really lights up the space, which faces the street. Yesterday a passer-by noticed it and braked their car suddenly for a better look and almost got rear-ended. That would have been an expensive look. People have actually stopped, parked, and come to the door to ask what variety it is (spicy lights). Just planted a new azalea in the same series that has white and yellow flowers (highlights). TPP will try hard to get some more plant placements like this.

What's the Point of Making This Face When We're Scared?

Elizabeth Preston — Tue, 07 May 2013 09:52:00 +0000

If cartoonists ever pause in their sketching to ponder human evolution, they must feel grateful to the forces that shaped our fear expression. All it takes is a pair of extra-wide eyes to show that a character is freaking out. There may be a point to this expression beyond making artists' lives easier: widening our eyes expands our peripheral vision, and might even help other people spot the cause of our alarm.

"Our lab is interested in the evolutionary origins of emotional expressions," says Daniel Lee, a graduate student in psychology at the University of Toronto—in other words, "why they look the way they do." When we feel afraid, for example, is there a point to stretching out our eyelids and raising our eyebrows to the ceiling?

To explore this question, Lee and his coauthors first asked whether widening our eyes helps us see better. They had 28 volunteers look at a fixed spot on a computer screen while holding their eyes in a neutral expression, an expression of fear, or one of disgust. (Subjects acted out these expressions rather than, say, having a chair pulled out from under them before each trial. Lee points out that emotions themselves may also change our perception, but he wanted to study the effects of widened eyes separate from any psychological effects of fear on the brain. "We coached each participant on how to make fear and disgust expressions based on the Facial Action Coding System," he says.)

Subjects were tested with flashing images on the screen in their peripheral vision. Lee found that people making a disgusted expression—with the eyelids narrowed as in "Ew, get that out of my face"—scored the worst. People making a wide-eyed fear expression scored the best, with a useful field of vision 9% larger than that of people with a neutral expression.

Being afraid, then, may help us gather more visual information about whatever's threatening us in our environment. But does it also help us communicate that threat to our companions?

The researchers next used pictures of models' eyes expressing different emotions to create simplified, graphic eye images. (They didn't use real eyes because those might have conveyed extra emotional information, instead of only varying in wideness.) Subjects saw these eye images flash briefly on a screen, looking toward the right or left by varying degrees. Lee found that when the eyes were wider, subjects had an easier time telling which way they were looking. The results are reported in Psychological Science.

"We believe the widening eyes of fear...[are] a functional response for vigilance toward threat," Lee says. When we're scared, he thinks, widening our eyes helps us to see threats and to communicate their location to our group.

The researchers point out that human eyes are uniquely suited for this kind of communication: we're the only primate with a white sclera (the area outside the iris). In other apes and monkeys, this part of the eye is dark. It's yet another factor that cartoonists, no doubt, appreciate.

Lee, D., Susskind, J., & Anderson, A. (2013). Social Transmission of the Sensory Benefits of Eye Widening in Fear Expressions Psychological Science DOI: 10.1177/0956797612464500

Image: by Tom Check (via Flickr)

George Whitesides on the responsibility of chemists and the future of chemistry

noreply@blogger.com (Wavefunction) — Mon, 06 May 2013 21:14:00 +0000

Catching up on a few articles I had missed, I came across a characteristically deep and wide-ranging essay called "Assumptions" by George Whitesides about science, its future and our responsibility as scientists. It's a very general and kaleidoscopic essay not restricted to chemistry, but the bits about chemistry, its role in understanding the major problems confronting humanity and chemists' responsibility in extending the scope of chemical science are quite thought-provoking:

Chemistry, by its culture, has been almost blindly reductionist. I am repeatedly reminded that “Chemists work on molecules”, as if to do anything else was suspect. Chemists do and should work on molecules, but also on the uses of molecules, and on problems of which molecules may be only a part of the solution. If chemists move beyond molecules to learn the entire problem—from design of surfactants, to synthesis of colloids, to MRI contrast agents, to the trajectories of cells in the embryo, to the applications of regenerative medicine—then the flow of ideas, problems, and solutions between chemistry and society will animate both.

Whitesides is clearly making a plea for chemists to become even more interdisciplinary than what they already are, to pursue not just the development of the solution but its application and integration; his own group provides a remarkable example of chemists, physicists, biologists and engineers working together on highly multidisciplinary problems. It's quite clear that to achieve this interdisciplinary expertise we have to completely break down the traditional barriers between synthesis, structure determination, biology and materials (in this world the professor who rejected my biochemical literature seminar topic because it "did not include any synthesis" would be an anachronism). The next paragraph makes clear the role of the "central science"

As a technology, chemistry has built the foundation from which many of the discoveries of “biology” or “microelectronics” or “brain science” (or “planetary exploration”, for that matter) have grown. There would be no genomics without chemical methods for separating fragments of DNA, and for synthesizing primers and probes, and for separating restriction endonucleases into pure activities. There would be no nuclear ICBMs without methods of refining plutonium, and making explosive lenses. There would be no drugs without synthesis and mass spectroscopy. There would be no interplanetary probes without fuels, and carbon/carbon rocket throat nozzles, and silicon single crystals.

And here's something about what the future of chemistry should be:

Those are the past. What about the future? Chemistry is, still, everywhere: It must be! It is the science of the real world. But to remain a star in the play rather than a stagehand, it must open its eyes to new problems. It is impossible that the human life span will increase dramatically without manipulation of the molecules of the human organism, but understanding this problem will require more than manipulating molecules. Communication between the living and non-living will require engineering a molecular interface between them, but designing this interface will require understanding the nature of “information” in organisms and in computers, and how to translate between them. A society that uses information technology to interweave all its parts requires new systems for generating, distributing, and storing power, but batteries will be only one part of these systems.

Chemistry has always been the invisible hand that builds and operates the tools, and sustains the infrastructure. It can be more. We think of ourselves as experts in quarrying blocks from granite; we have not thought it our job to build cathedrals from them. Whether we choose to focus on the molecules, materials, and tools that are at the beginnings of discovery, or bring our particular, unique understanding of the world to bear on unraveling the problems at the end, is for us to decide. I believe that everything from methane to sentience is chemistry, and that we should reexamine our own assumptions concerning the boundaries of our field. Examining the broader assumptions that follow may provide some stimulus to do so.

Indeed, examining the "broader assumptions" of their field in the broadest sense of the term is what chemists should do. The first paragraph presents a fair sampling of the myriad problems in which chemistry can play a central role. They involve everything from engineering interfaces between computers or electronics and human brains to harnessing the power of chemistry in generating, storing, interconverting and deploying energy in all its forms. I strongly think that the future of chemistry lies in recasting itself as an informational science in the broadest sense. At the level of biology chemistry has already manipulated information in the form of sequencing and genomics; synthetic biology will take this capability to a whole new level. But there are other areas in which chemistry can serve to manipulate information, and part of what Whitesides is doing is challenging chemists to become informational scientists in hitherto unexplored areas like energy and transportation.

The essay ends with a systems-level view of chemistry that every chemist should keep in mind, even as she works in her narrow world of natural products, zeolites, ROMP or kinases.

Because chemistry contributes broadly to the foundations of technology, it is particularly difficult to guess its future impact: a new chemical reaction might be used to make a cancer therapeutic, or a chemical weapon. Some of the opportunities that seem within the reach of investigation, if not within the reach of solution—technologies that might substantially prolong life, or develop new forms of life, or lead to sentient systems that rival us in intelligence—will do both good and harm. At minimum, those of us whopursue these problems should accept an obligation to explain to our fellow citizens fully and clearly what we are doing, and why, and (to the limited extent we can) with what possible outcomes. Humankind will do what it will do, but at least everyone should understand—in so far as is possible—what the choices are, and what the consequences might be. Chemistry, if it takes more interest in (and responsibility for) the full scope of programs—from molecules, to applications, and to influence on society—may be able to use the very breadth of its connections to technology to help in this explanation.

Whitesides Image: Boston.com

The 100th flowering plant Index - 2010-2013

The Phytophactor — Mon, 06 May 2013 20:48:00 +0000

TPP's 1st day of flowering log provides some interesting data. On May 5th, the 100th different plant in our gardens flowered. This is considerably later than a typical year, if such a thing exists. In 2010 the 100th flowering event was reached on April 21st, and in 2011 it came on April 27th. So 2013 is 8 to 16 days behind. However last year was just much abnormal. The 100th flowering event took place on March 25th! It was ridiculous! The 100th flowering event sort of evens things out by taking into account a large number of plants and their reactions to weather events. In general this date is reached in late April, but obviously a great deal of variation occurs with spring weather events. Now if something like the melting of the Arctic ice cap alters the pattern of the jet stream, then things may get earlier or later, depending. Too often we tend to say things, like, it's a late spring, or an early spring, but only when you have some data do you have some real information and the ability to compare. Only wish our flowering log contained several more years of data.

Exploding expertise

Michelle — Mon, 06 May 2013 14:01:00 +0000

How do we decide who to listen to about something chemical? I have a piece in Slate this week (on the brouhaha around the teenager in Florida and the exploding water bottle), and someone in the comments feed there thought to comment on my expertise:

Jack Stephens

The author is apparently ignorant of chemistry. The active ingredient in toilet bowl cleaner is not hydrochloric acid, it is sodium hydroxide. Aluminum and sodium hydroxide react to form hydrogen gas.

16 Hours Ago

from slate.com

· Reply · Like · Flag

Franz Liebkind

Some toilet bowl cleaners (e.g. Lysol's) contain hydrochloric acid in 10-ish percent concentration. It is there to dissolve calcium carbonate deposits (i.e. scale) found in hard water areas. Both HCl and NaOH react with nonbulk Al to produce, among other things, H2 gas. Iirc in the HCl case the reaction should go faster.

Sodium and HCl (or just water!) is much neater and more spectacular. Adolescent pyromaniac curiosity inspired many of us to major in chemistry.

9 Hours Ago

from slate.com

· Reply · Like · Flag

Franz Liebkind

P.S. USGS says that the water from the Upper Floridian Aquifer, which supplies most of Polk County and Bartow, is moderately to very hard.

I just finished a new Thesis column for Nature Chemistry about the ways in which chemists can (or cannot) communicate with general audiences about chemistry. Is it possible to have nuanced conversations using the word "chemical" and chemistry, or has the word itself chemical accreted so many toxic associations that it can't be rehabilitated? Can chemists have a role in these conversations by virtue of their expertise? (Short answers: Problably not, probably yes, probably not.)

A session at ScienceOnline2013 earlier this year still has me thinking about the disconnect between how chemists want to talk about their field ("did you know that everything is chemicals? just look at how this works! isn't it cool?") and how people process the information we are so enthusiastically providing ("she is a working mother who probably feeds her kids fast food five nights a week and can't possibly care about her family's nutrition so why should I listen to what she has to say about the molecular structure of NutraSweet™?") Addressing the deficit in science knowledge may not in fact help people assimilate what they need to know make informed decisions about things chemical.

For a society who in many ways is so keen on credentials (or how else do those online diploma mills spammers make money), social science research suggests we don't necessarily consider purely those credentials into our decision when we decide who is an expert in a given field. Dan Kahan and colleagues at the Culture Cognition Project suggest that we assess expertise through the lens of our cultural and social affinities as much (or more) as we do through objective credentials.

So when it comes to deciding who you should believe about aspartame, you believe Dr. X who is an "nutritionist, aspartame victim and single mother of three boys" (her doctorate comes from an unaccredited online school) not Dr. Y who does research on molecular structure and is the mother of two boys and is not an aspartame victim (her doctorate comes from a top accredited school).

As for the Slate commenter, I'm rather fascinated that someone could generalize from you don't know what is in toilet bowl cleaner (is the subtext here that I would be above cleaning my own bathrooms?) to you apparently know no chemistry. Could you imagine that a well-trained scientist would not think to look this up even if she doesn't do bathrooms? (The police report gives the brand of cleaner, which the manufacturer says contains 20% HCl. Of course, practically it doesn't matter -- both the acid and the base oxidations of aluminum produce three equivalents of hydrogen gas.)

Evolutionary Psychology, Proximate Causation, & Ultimate Causation

GamesWithWords — Mon, 06 May 2013 09:30:00 +0000

Evolutionary psychology has always been somewhat controversial in the media for reasons that generally confuse me (Wikipedia has a nice rundown of the usual complaints). For instance, the good folks at Slate are particularly hostile (here, here and here), which is odd because they are also generally hostile towards Creationism (here, here and here).

Given the overwhelming evidence that nearly every aspect of the human mind and behavior is at least partly heritable (and so at least partially determined by our genes), the only way to deny the claim that our minds are at least partially a product of evolution is to deny that evolution affects our genes – that is, deny the basic tenants of evolutionary theory. (I suppose you could try to deny the evidence of genetic influence on mind and behavior, but that would require turning a blind eye to such a wealth of data as to make Global Warming Denialism seem like a warm-up activity).

What's the matter with Evolutionary Psychology?

What is there to object to, anyway? Some of the problem seems definitional. Super-Science-Blogger Greg Laden acknowledges that applying evolutionary theory to the study of the human mind is a good idea, but that "evolutionary psychology" refers only to a very specific theory from Cosmides and Tooby, one with which he takes issue. And in general, a lot of the "critiques" I see in the media seem to involve equating the entire field with some specific hypothesis or set of hypotheses, particularly the more exotic ones.

For instance, some years back Slate ran an article about "Evolutionary Psychology's Anti-Semite", a discussion of Kevin MacDonald, who has an idiosyncratic notion of Judaism as a "group evolution strategy" to maximize, through eugenics, intelligence (the article goes into some detail). It's a pretty nutty idea, gets basic historical facts wrong, and more importantly gets the science wrong. The article tries pretty hard to paint him as a mainstream Evolutionary Psychologist nonetheless. Interviewees aren't that helpful (they mostly dismiss the work as contradicting basic fundamentals of evolutionary theory), but the article author pulls up other evidence, like the fact that MacDonald acknowledged some mainstream researchers in one of his books. (For the record, I acknowledge Benicio del Toro as an inspiration, so you know he fully agrees with everything in this blog post. Oh, and Jenna-Louise Coleman, too.)

In a similar vein:

This spring, New York Times columnist John Tierney asserted that men must be innately more competitive than women since they monopolize the trophies in -- hold onto your vowels -- world Scrabble competitions. To bolster his case, Tierney turned to evolutionary psychology. In the distant past, he argued, a no-holds-barred desire to win would have been an adaptive advantage for many men, allowing them to get more girls, have more kids, and pass on their competitive genes to today's word-memorizing, vowel-hoarding Scrabble champs.

I will agree that this argument involves a bit of a stretch and is awfully hard to falsify (as the article goes on to point out). And sure, some claims made even by serious evolutionary psychologists are hard to falsify with current technology ... but then so is String Theory. And we do have many methods for testing evolutionary theory in general, and roughly the same ones work whether you are studying the mind and behavior or purely physical attributes of organisms. So, again, if you want to deny that claims about evolutionary psychology are testable, then you end up having to make roughly the same claim about evolutionary theory in general.

Just common sense

It turns out that when you look at the biology, a good waist-hips ratio for a healthy woman is (roughly) .7, whereas the ideal for men is closer to .9. Now imagine we have a species of early hominids (Group A) that is genetically predispositioned such as that heterosexual men prefer women with a waist-hips ratio of .7 and heterosexual women prefer men with a waist-hips ratio of .9. Now let's say we have another species of early hominids (Group B) where the preferences are reversed, preferring men with ratios of .7 and women with ratios of .9. Since individuals of Group A prefer to mate with healthier partners than Group B does, which one do you think is going to have more surviving children?

Now compare to Group C, where there is no innate component to interest in waist-hips ratios; beauty has to be learned. Group C is still at a disadvantage to Group A, since some of the people in it will learn to prefer the wrong proportions and preferentially mate with less healthy individuals. In short, all else equal, you would expect evolution to lead to hominids that prefer to mate with hominids that have close-to-ideal proportions.

(If you don't like waist-hips ratios, consider that humans prefer individuals without deformities and gaping sores and boils, and then play the same game.)

Here is another example. Suppose that in Group A, individuals find babies cute, which leads them to want to protect and nourish the infants. In Group B, individuals find babies repulsive, and many actually have an irrational fear of babies (that is, treating babies something like how we treat spiders, snakes & slugs). Which one do you think has more children that survive to adulthood? Once again, it's better to have a love of cuteness hardwired in rather than something you have to learn from society, since all it takes is for a society to get a few crazy ideas about what cute looks like ("they look better decapitated!") and then the whole civilization is wiped out.

(If you think that babies just *are* objectively cute and that there's no psychology involved, consider this: Which do you find cuter, a human baby or a skunk baby? Which do you think a mother skunk finds cuter?)

These are the kinds of issues that mainstream evolutionary psychology trucks in. And the theory does produce new predictions. For instance, you'd expect that in species where a .7 waist-hips ratio is not ideal for females (that is, pretty much any species other than our own), it wouldn't be favored (and it isn't). And the field is generally fairly sensible, which is not to say that all the predictions are right or that evolutionary theory doesn't grow and improve over time (I understand from a recent conversation that there is now some argument about whether an instinct for third-party punishment is required for sustainable altruism, which is something I had thought was a settled matter).

Riroriro

noreply@blogger.com (Christopher Taylor) — Mon, 06 May 2013 04:42:00 +0000

The grey warbler or riroriro Gerygone igata, photographed by Peter Bray.

The eighteen recognised species of the genus Gerygone are an assemblage of small, drab-coloured birds found mostly in the Australo-Papuan region, with G. sulphurea found in the Malay Peninsula, Indonesia and the Philippines, and G. flavolateralis found in New Caledonia and Vanuatu. These are another group of birds that have tended to draw the short straw in the vernacular name stakes: G. igata, one of the most abundant of New Zealand's native birds, is usually identified by the uninspiring 'grey warbler'. Personally, I prefer the more onomatopoeiac Maori name for these lively little birds: 'riroriro' (it has been suggested in some circles that it could possibly be referred to as the 'grey gerygone'; this proposition shall be treated with the scorn that it deserves). The riroriro and its congeners feed on small insects that they mostly glean from leaves or small branches, generally in the middle to upper canopies (Ford 1985). A certain amount of their prey is caught in the air, while the riroriro and the brown warbler G. mouki of eastern Australia also forage in lower vegetation than other species. The riroriro is also the only Gerygone species known to forage on the ground (Keast & Recher 1997).

Gerygone species build hanging purse-shaped nests; this is a brown warbler Gerygone mouki photographed by Peter.

Somewhat unusually for a decently-speciose passerine genus, the circumscription of Gerygone has been fairly stable in recent years, and the genus has mostly been supported as monophyletic. The only exception of recent times has been the New Guinean G. cinerea, recently reclassified by Nyári & Joseph (2012) as a species of Acanthiza. In the early 1900s, some authors divided Gerygone species between smaller genera (for instance, the Australian ornithologist Gregory Mathews, who never met a genus he couldn't break down). One species so separated was the Chatham Island warbler G. albofrontata, which is something of an island giant compared to other Gerygone species, weighing about 12 g while other species are about 6 to 7 g (Keast & Recher 1997). Unfortunately, the Chatham Island warbler was not included in the phylogenetic analysis of Gerygone by Nyári & Joseph (2012), but it was not identified as significantly separate from other Gerygone species in the morphological analysis by Ford (1985).

The Chatham Island warbler Gerygone albofrontata, from here.

REFERENCES

Ford, J. 1985. Phylogeny of the acanthizid warbler genus Gerygone based on numerical analyses of morphological characters. Emu 86: 12-22.

Keast, A., & H. F. Recher. 1997. The adaptive zone of the genus Gerygone (Acanthizidae) as shown by morphology and feeding habits. Emu 97: 1-17.

Nyári, Á. S., & L. Joseph. 2012. Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae). PLoS One 7(2): e31840.

Religion doesn't seem to protect against depression.

noreply@blogger.com (Tomas Rees) — Sun, 05 May 2013 20:54:00 +0000

In most countries, religious people tend to be happier and less depressed, and it's often suggested that religion somehow provides a happiness boost and protects against depression.

Maybe, so the thought process goes, religious belief alone is enough to perk people up, but even if it doesn't then participating in religious gatherings, and the social support that goes with it - well surely that's got to help.

It's an attractive idea, but the problem is that it's really difficult to unpick cause and effect. Maybe it's simply that depressed people stop being religious. That's certainly what a study that came out last year suggested.

About the only way to tease this out is to follow people over time, and see who gets depressed and who doesn't. That's what Michael King (University College London) and colleagues have done in a recent international study.

They interviewed 8318 patients without depression attending doctor's surgeries in the Chile, Estonia, The Netherlands, Portugal, UK, Spain, and Slovenia. Then they interviewed them again 6 and 12 months later (well, most of them - some, especially the younger and less educated, didn't turn up to later interviews).

They found that significantly more of the participants who actively practised religion (10.3%) or had a spiritual world view (10.5%) experienced an episode of major depression over those 12 months compared with those who had a secular outlook (7%).

Once they'd adjusted for differences in the characteristics of the people in the depressed and non-depressed groups (age, sex, education, employment, social support, past history of depression and country), only 'spiritual world view' (and not active religious participation) remained a significant predictor of future depression. And the country where this effect was strongest was the UK.

Among those who said they were spiritual or religious at baseline, there was a clear relationship between the strength of belief and the risk of depression. That's shown in the figure - while the risk of depression for those who were only weakly religious was similar to the non-believers (at 7.4%), for the strong believers the risk rose to 12.5%.

They concluded that:

Although our main finding of an association between religious life understanding and onset of depression varied by country, we found no evidence that spirituality may protect people, and only weak evidence that a religious life view was possibly protective in two countries (Slovenia and The Netherlands). Finally, there was no moderating effect of religious and spiritual understanding of life on the impact of life events on onset of major depression.

So religion doesn't seem to protect people from depression, and spirituality in the absence of religious affiliation seems to be a positive risk factor - especially in the UK.

That chimes with other studies (including a recent one by King himself [see references below], and one showing that New Agers are particularly prone to delusional beliefs). What does that mean?

Probably only that people who are prone to psychological problems tend to drop out of organised religion...

Leurent, B., Nazareth, I., Bellón-Saameño, J., Geerlings, M., Maaroos, H., Saldivia, S., Švab, I., Torres-González, F., Xavier, M., & King, M. (2013). Spiritual and religious beliefs as risk factors for the onset of major depression: an international cohort study Psychological Medicine, 1-12 DOI: 10.1017/S0033291712003066

King, M., Marston, L., McManus, S., Brugha, T., Meltzer, H., & Bebbington, P. (2012). Religion, spirituality and mental health: results from a national study of English households The British Journal of Psychiatry, 202 (1), 68-73 DOI: 10.1192/bjp.bp.112.112003

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

A quiet, seldom-seen woodland wildflower in these parts - blue cohosh

The Phytophactor — Sun, 05 May 2013 20:39:00 +0000

In over 3 decades of botany here in the upper midwest, TPP has seen blue cohosh (Caulophyllum thalictroides) in the wild exactly twice. As the specific epithet suggests, the thrice compound foliage looks quite like the leaves of the meadow rue (Thalictrum, in the buttercup family). Blue coshosh might be a bit more common that suspected, but it tends to escape notice. Appropriately enough one hides in our woodland behind a screen of bluebells. One of the reasons it escapes notice is that it's purplish-blue hue tends to help it hide. What confuses quite a few people is that the flowers are 3-parted and the same greenish, bluish color as the foliage, however three-parted flowers are common enough among basal dicots. It's a member of the Berberidaceae, and most of the members of the family with which people are familiar are shrubs rather than spring ephemerals. Blue cohosh has quite a reputation as a medicinal plant and was widely used by native americans as an abortive agent atesting to its toxicity, which may explain why it's one thing the bun-buns don't eat.

Osteoderm Microstructure of “Rauisuchian” Archosaurs from South America

Bill Parker — Sat, 04 May 2013 20:52:00 +0000

Cerda, I. A., J. B. Desojo, T. M. Scheyer and C. L. Schultz. In Press. Osteoderm microstructure of “rauisuchian” archosaurs from South America. Geobios (accepted manuscript) doi: http://dx.doi.org/10.1016/j. geobios.2013.01.004

Abstract - In this contribution we analyze and discuss the microanatomy and histology of postcranial osteoderms of a number of “rauisuchians” from different localities of South America (Argentina and Brazil). The studied sample includes osteoderms of Fasolasuchus tenax, Prestosuchus chiniquensis, Saurosuchus galilei and an undetermined rauisuchian from Brazil. The bone microanatomy of the osteoderms is variable: whereas some specimens have a rather compact structure, others show a diploe architecture with a central cancellous core bordered by two compact cortices. Both external and basal cortices are mainly composed of poorly vascularized, fine and coarse parallel fibred bone and networks of interwoven and mineralized fiber bundles. The internal region of the non-remodeled specimens consists of a well-vascularized core in which the intrinsic fibers exhibit important variations (even in the same specimen), ranging from coarse, parallel-fibred to woven-fibred bone tissues. Lines of arrested growth (LAGs) are well recorded in both basal and external cortices. Differences in the bone microstructure (compact vs. diploe) could be related to the age, sex and reproductive status of the sampled individuals. Hence, age estimation based on the count of LAGs in rauisuchian osteoderms appears to be reliable only in the early stages of ontogeny. The bone microstructure suggests that rauisuchian osteoderms were originated through a mechanism that involves both intramembranous and metaplastic ossifications.

Elasticity of the air

Gianluigi Filippelli — Sat, 04 May 2013 19:20:00 +0000

Text extracted from "The magician's own book, or The whole art of conjuring" (1862) by George Arnold

This can be shown by a beautiful philosophical toy which may easily be constructed. Procure a glass jar, such as is here represented. Then mould three or four little figures in wax, and make them hollow within, and having each a minute opening at the heel, by which water may pass in and out. Place them in the jar, as seen in the figure, and adjust them by the quantity of water admitted to them, so that in specific gravity they differ a little from each other. The mouth of the jar should now be covered with a piece of skin or India-rubber, and then, if the hand be pressed upon the top or mouth of the jar, the figures will be seen to rise or descend as the pressure is gentle or heavy, rising and falling, or standing still, according to the pressure made.
Reason for this
The reason of this is, that the pressure on the top of the jar condenses the air between the cover and the water surface; this condensation then presses on the water below, and influences it through its whole extent, compressing also the air in the figures, forcing as much more water into them as to render them heavier than water, and therefore heavy enough to sink.

Mob scene turns ugly!

The Phytophactor — Sat, 04 May 2013 11:31:00 +0000

Mobs can be pretty ugly; unruly mobs even more so. When they all surge in the same direction their energy is like being caught in a tsunami. Kids, senior citizens, small electric vehicles, all get bowled over in seconds as the relentless mob rolls on. An NFL offensive line wouldn't stand a chance. Checked the time; it was still a few minutes before 8 AM, which was when our annual arboretum plant sale was scheduled to begin, but this morning cabin-fevered gardeners were a mob not to be denied as they swarmed into the sale early. When you see two elderly women duking it out, a cane versus a walker, to obtain the last queen of the prairie, you realize that plant sales with limited quantities are not for the faint of heart. There was more pushing and shoving over Amish paste tomatoes, a great favorite, but not worth risking your life over. With impeccable timing, Mrs. Phactor was late to the fray and emerged completely unscathed with several bloodroots for our woodland garden. Gardeners, usually such nice people, show their ugly side at plant sales. Such animals!

Provincialization of Terrestrial Faunas Following the End-Permian Mass Extinction.

Bill Parker — Fri, 03 May 2013 20:48:00 +0000

Sidor, C. A., D. A. Vilhena, K. D. Angielczyk, A. K. Huttenlocker, S. J. Nesbitt, B. R. Peecook, J. S. Steyer, R. M. H. Smith, and L. A. Tsuji. 2013. Provincialization of terrestrial faunas following the end-Permian mass extinction. Proceedings of the National Academy of Sciences (advance online publication)
doi: 10.1073/pnas.1302323110

Abstract - In addition to their devastating effects on global biodiversity, mass extinctions have had a long-term influence on the history of life by eliminating dominant lineages that suppressed ecological change. Here, we test whether the end-Permian mass extinction (252.3 Ma) affected the distribution of tetrapod faunas within the southern hemisphere and apply quantitative methods to analyze four components of biogeographic structure: connectedness, clustering, range size, and endemism. For all four components, we detected increased provincialism between our Permian and Triassic datasets. In southern Pangea, a more homogeneous and broadly distributed fauna in the Late Permian (Wuchiapingian, ~257 Ma) was replaced by a provincial and biogeographically fragmented fauna by Middle Triassic times (Anisian, ~242 Ma). Importantly in the Triassic, lower latitude basins in Tanzania and Zambia included dinosaur predecessors and other archosaurs unknown elsewhere. The recognition of heterogeneous tetrapod communities in the Triassic implies that the end-Permian mass extinction afforded ecologically marginalized lineages the ecospace to diversify, and that biotic controls (i.e., evolutionary incumbency) were fundamentally reset. Archosaurs, which began diversifying in the Early Triassic, were likely beneficiaries of this ecological release and remained dominant for much of the later Mesozoic.

Hear those crispy rice grains calling for help? Snap! Crackle! Pop!

The Phytophactor — Fri, 03 May 2013 13:25:00 +0000

New scientific findings are often fun and interesting, but how some "journalists" write about such things is annoying to the nth degree. Xylem consists of a series of cellulosic tubes and during water stress, the transpirational pull upon the water columns, a force generated by water loss from leaves, can generate air embolisms. In a manner of speaking, xylem gets the bends. A research group has found that formation of these air bubbles makes sounds. Now that's not all that unexpected or surprising. Ever listen to the bubbles of carbon dioxide rising from your carbonated beverage? That hiss you hear is the sound of all those bursting bubbles. If you had sufficiently fine listening devices, and slowed down the sounds recorded, you could probably listen to each individual bursting bubble. Or how about the sound of air bubbles being made in a drinking straw when your sucking has lowered the level of the liquid to nearly the bottom? Now the finding that air bubbles in the tiny xylem "straws" in a tree make a noise when forming is somewhat interesting but mostly because people don't think about trees making any noise. Now here's where the newsy report goes seriously arwy. It's not a "drought distress call" any more than your crispy rice cereal is calling for help to keep from drowning in the milk. Scheesh! This puts this report into a category of bad journalism by making a physical thing that can be explained in a non-technical way into something vaguely anthropomorphic. Was embolism too technical? Or xylem? Where do the find these writers? Oh, yeah, far away from science.