Field of Science Combined Feed

Music and fractal landscapes

Gianluigi Filippelli — Sat, 25 May 2013 15:39:00 +0000

For the #towelday I publish the paper by Richard MacDuff extracted from from "Dirk Gently's Holistic Detective Agency" by Douglas Adams

Music & Fractal Landscapes from Jamie Shoard on Vimeo.

Mathematical analysis and computer modelling are revealing to us that the shapes and processes we encounter in nature—the way that plants grow, the way that mountains erode or rivers flow, the way that snowflakes or islands achieve their shapes, the way that light plays on a surface, the way the milk folds and spins into your coffee as you stir it, the way that laughter sweeps through a crowd of people—all these things in their seemingly magical complexity can be described by the interaction of mathematical processes that are, if anything, even more magical in their simplicity.
Shapes that we think of as random are in fact the products of complex shifting webs of numbers obeying simple rules. The very word “natural” that we have often taken to mean “unstructured” in fact describes shapes and processes that appear so unfathomably complex that we cannot consciously perceive the simple natural laws at work.
They can all be described by numbers.
We know, however, that the mind is capable of understanding these matters in all their complexity and in all their simplicity. A ball flying through the air is responding to the force and direction with which it was thrown, the action of gravity, the friction of the air which it must expend its energy on overcoming, the turbulence of the air around its surface, and the rate and direction of the ball’s spin.
And yet, someone who might have difficulty consciously trying to work out what 3 × 4 × 5 comes to would have no trouble in doing differential calculus and a whole host of related calculations so astoundingly fast that they can actually catch a flying ball.
People who call this “instinct” are merely giving the phenomenon a name, not explaining anything.
I think that the closest that human beings come to expressing our understanding of these natural complexities is in music. It is the most abstract of the arts—it has no meaning or purpose other than to be itself.
Every single aspect of a piece of music can be represented by numbers. From the organisation of movements in a whole symphony, down through the patterns of pitch and rhythm that make up the melodies and harmonies, the dynamics that shape the performance, all the way down to the timbres of the notes themselves, their harmonics, the way they change over time, in short, all the elements of a noise that distinguish between the sound of one person piping on a piccolo and another one thumping a drum—all of these things can be expressed by patterns and hierarchies of numbers.
And in my experience the more internal relationships there are between the patterns of numbers at different levels of the hierarchy, however complex and subtle those relationships may be, the more satisfying and, well, whole, the music will seem to be.
In fact the more subtle and complex those Relationships, and the further they are beyond the grasp of the conscious mind, the more the instinctive part of your mind—by which I mean that part of your mind that can do differential calculus so astoundingly fast that it will put your hand in the right place to catch a flying ball—the more that part of your brain revels in it.
Music of any complexity (and even “Three Blind Mice” is complex in its way by the time someone has actually performed it on an instrument with its own individual timbre and articulation) passes beyond your conscious mind into the arms of your own private mathematical genius who dwells in your unconscious responding to all the inner complexities and relationships and proportions that we think we know nothing about.
Some people object to such a view of music, saying that if you reduce music to mathematics, where does the emotion come into it? I would say that it’s never been out of it.
The things by which our emotions can be moved—the shape of a flower or a Grecian urn, the way a baby grows, the way the wind brushes across your face, the way clouds move, their shapes, the way light dances on the water, or daffodils flutter in the breeze, the way in which the person you love moves their head, the way their hair follows that movement, the curve described by the dying fall of the last chord of a piece of music—all these things can be described by the complex flow of numbers.
Thatís not a reduction of it, thatís the beauty of it. Ask Newton.
Ask Einstein.
Ask the poet (Keats) who said that what the imagination seizes as beauty must be truth.
He might also have said that what the hand seizes as a ball must be truth, but he didnít, because he was a poet and preferred loafing about under trees with a bottle of laudanum and a notebook to playing cricket, but it would have been equally true.
Because that is at the heart of the relationship between on the one hand our “instinctive” understanding of shape, form, movement, light, and on the other hand our emotional responses to them.
And that is why I believe that there must be a form of music inherent in nature, in natural objects, in the patterns of natural processes. A music that would be as deeply satisfying as any naturally occurring beauty - and our own deepest emotions are, after all, a form of naturally occurring beauty...

Tree pruning - man with a machete

The Phytophactor — Sat, 25 May 2013 13:44:00 +0000

Pruning trees correctly is a skill; pruning trees well is an art. When you see a person, OK, in this case it will always be a man, heading toward a tree with the intent of pruning it and he's carrying a machete, nothing good will come of this. No connection exists between pruning and a machete. Most certainly the tree will suffer and more than likely the machete wielder will injure themselves in the bargain, and yes, TPP hears some of you out there saying, he got what he deserved. Anybody who desides to use a machete to prune a tree knows so little about pruning, or the use of a machete, that they should not be allowed near either one. To someone who knows pruning, you can see the results of bad pruning decades afterwards, tsk, tsk. Now of course taking a machete away from someone may not be easy. But maybe they can be distracted by that shiny new saw!

Styrofungus, mycolastic - saving us from styrofoam

The Phytophactor — Sat, 25 May 2013 13:04:00 +0000

To interplanetary archeologists our particular civilization will probably be know as the "styrofoam makers". Styrofoam and its cousin polystrene (those white coffee cups, packing "peanuts", and fast-food clam-shell containers) are for all their convenience almost forever because nothing out there has the enzymes needed to decompose this stuff, so it tends to last, and accumulate. Worse, when it does eventually breakdown, polystrene breaks down into its monomers, styrene, a know carcinogen. On one hand you have to admire our bravery in drinking and eating out of these containers, but ignorance is bliss, so pass the asbestos platter and let's eat! These foamy plasticy things are great because of their strength and very light weight, so each and every one of us has unpacked something we bought that had those foamy form-fitting inserts to hold the object in place in the center of a carton. While excellent for this particular use, this is stuff has to be on the top 10 list of least green products. Wouldn't it be nice if someone found a substitute product? Well, a couple of guys out of RPI (Rensslaer Polytechnic Institute) are growing a fungal based alternative. The basic recipe is plant waste material (think shredded corn stalks) and a fungal mycelium, a bit of the filamentous body of a fungus that you typically don't see because it's growing under ground or in dead wood. Add water put into a form and the mycelium grows until it fills the space. Dry it out and voila, you've got a tough, light packing material custom-made to pack that Italian espresso maker you've ordered online. The best thing is that this biomaterial will break down quickly. The product is being made by Ecovative Design, sort of a nifty name. TPP learned of this via an article in the New Yorker published about 2 weeks ago. Wonder if it would make a good soil additive because if so we could begin to solve the peat moss problem at the same time. Remember this slogan, "Better living through fungus."

TMI Friday: Batteries should NOT be included

The Defective Brain — Fri, 24 May 2013 12:24:00 +0000

There are some days when you have to ask yourself, just what is the deal with men. I don't mean our general demeanour, or the pretensions of superiority over other genders. No, I'm talking about the strange things that men decide to do when left alone for too long.The men who happily dangle their members inside bottles, or in reach of the spinning blades of a vacuum cleaner not thinking of the consequences.
With this in mind, we arrive at a case study by Bedi et al, where they describe the case of an elderly gentleman who was referred to them from a nursing home. He had been experiencing extreme pain during urination. A year previously, he had a similar problem. On that occasion, it was found that he had stuffed a pen lid inside his penis.
Now, one shouldn't make assumptions about people. Just because he had abused the elasticity of his urethra before was no reason to suspect that it had happened again. He could be experiencing difficulty urinating for a whole number of important medical reasons.
Then he pissed out a rusty Triple A battery.
And he still had trouble urinating ! This is when the nurses at the home realised that they needed to get help from doctors.
An X-ray revealed the source of the problem. Two batteries were still lodged in the man's urethra. Meanwhile one of the residents of the home for the elderly is wondering why the remote stopped working.
So how do you pull these batteries out ? The surgeons decided to use special endoscopic forceps to pull out the batteries. Endoscopic forceps are essentially long tubes with jaws on the end (for grasping things).
They had to insert these forceps up the urethra to grasp at these batteries.
Upon being presented with these batteries, the man admitted to jamming these batteries up his urethra four weeks earlier whilst masturbating. The train of thought which led him to put lead in his pencil may in fact be similar to all of the other male "thrill seekers" who decide to risk their genitalia for the sake of sexual gratification. But even after reading all of these articles, that trainwreck of thought is completely unknown to me.

Bedi N., El-Husseiny T., Buchholz N. & Masood J. (2010). 'Putting lead in your pencil': self-insertion of an unusual urethral foreign body for sexual gratification, JRSM Short Reports, 1 (2) 18-18. DOI: 10.1258/shorts.2010.010014

Ants Reveal How to Build a Tunnel You Can't Fall Down

Elizabeth Preston — Fri, 24 May 2013 09:01:00 +0000

It's hard to keep your footing in a steep tunnel made of loose dirt while others are scrambling around and over your body. Harder still in pitch blackness. That's why fire ants build tunnels that will catch them when they fall—a strategy human engineers might want to steal.

"Slips and missteps are likely a constant, recurring feature of life underground," says Nick Gravish, a graduate student in Daniel Goldman's rheology and biomechanics lab at Georgia Tech. Yet ants have to traverse their tunnels quickly, especially when there's a colony emergency like a flood or destruction by a gardener's spade.

To study how ants engineer their tunnels, Gravish brought the fire ant Solenopsis invicta into the lab. Invasive to countries around the world and packing a nasty sting, these South American ants deal out plenty of hardship. But Gravish was interested in how they handle adversity themselves.

First, the ants were put into "laboratory soil" (actually tiny glass balls) to dig. Researchers took x-ray CT scans of the resulting tunnels and found that no matter the moisture of the "soil" or the size of the glass beads, ants dug circular tunnels of approximately the same diameter. That diameter was just a little bit more than the length of their bodies, not counting legs or antennae.

This suggested that the diameter of the tunnel was crucial to the fire ants. To see how well the ants moved within these tunnels, the researchers recorded video of them climbing as fast as they could. ("We startled them into climbing at high speed by exhaling gently into the nest," Gravish says.) They saw that ants were able to navigate their tunnels quickly, reaching speeds of more than 9 body lengths per second. They also saw that sometimes the ants slipped and had to recover their footing.

In addition to their tunnels, the researchers recorded ants climbing in vertical glass tubes. To get a better idea of how ants corrected their falls, the scientists jolted the tubes to knock the ants off the walls while they were climbing. (If you enjoy videos in the falling-bugs genre, this study generated several new additions. Here's one video of several ants falling and stopping themselves.)

Now the reason ants build tunnels so close in diameter to their own body length became clear. Ants responded to a fall by spreading all their appendages wide and waiting until they jammed to a stop. "One of the coolest things we found was that fire ants used their antennae to brace themselves," Gravish says. While falling, the ants turned these delicate sensors into extra load-bearing limbs.

When the glass tube width increased to 1.3 times the ants' body length, the strategy began to fail. The tunnels ants built themselves had an average diameter of just 1.06 times their body length, the authors report in PNAS. It seems fire ants put most of the responsibility for stopping falls on the tunnels themselves. After that, all a plummeting insect has to do is stretch out its limbs.

Gravish likens this strategy to the way humans build stairs. Steps are engineered to fit our bodies. If they're too tall or short, we struggle to use them (or maybe just fall down them). But with the right design, our environment works with us to get us where we're going.

This strategy could inspire how we design robots for confined spaces such as search-and-rescue zones, Gravish says. For instance, "falling is usually considered a failure mode for a robot." But fire ants seem to use little falls to descend more quickly through their tunnels. If engineers knew the size of the cracks and crevices in a disaster area, they might be able to send in many inexpensive robots designed to tumble through those spaces—rather than one very expensive robot built to keep its footing.

What about humans ourselves: would we benefit from building tunnels that were only as wide as our head-plus-torso length, like the ants? Gravish points out that fire ants often fall many body lengths before catching themselves, making this not such a great strategy for people. "Ants have a robust exoskeleton," he says. "We humans are quite soft in comparison."

Images: ant in tunnel by Laura Danielle Wagner; ants falling by Gravish et al.

Gravish, N., Monaenkova, D., Goodisman, M., & Goldman, D. (2013). Climbing, falling, and jamming during ant locomotion in confined environments Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1302428110

Porcelain Fans

noreply@blogger.com (Christopher Taylor) — Thu, 23 May 2013 07:22:00 +0000

Mature specimen of Rhapydionina deserta, from Loeblich & Tappan (1964).

Calcareous foraminiferans have been featured on this site before: planktic floaters, living stars, microscopic jelly moulds and gigantic reef-formers. All these forms have belonged to the group of calcareous forams known as the rotaliids. Today's subject is another group of forams, the Rhapydionininae, belonging to a different calcareous group, the Miliolida. Miliolids may have shell walls made of calcite like the rotaliids, but differ in the wall structure: while the walls of rotaliids are glass-like and porous, those of miliolids are structured like porcelain. Phylogenetic studies of forams have not placed the miliolids close to the rotaliids, and the two groups seem to have evolved their secreted shells independently (Sen Gupta 2002).

Rhapydionina liburnica, from Loeblich & Tappan (1964).

The Rhapydionininae were defined by Loeblich & Tappan (1964) as a group of miliolids with a conical test composed of broad chambers stacked one on top of another (the overall shape being kind of like a fan or an ice-cream cone), with each of these chambers subdivided by internal septa into multiple chamberlets (the difference between a 'chamber' and a 'chamberlet' being that the latter are not completely divided from each other by the walls). The opening of the test took the form of a sieve-like array of pores at the top end. However, subsequent researchers have discovered that Loeblich & Tappan's definition was inadequate. Rhapydioninines start life growing as a flat spiral, with growth becoming linearised at maturity. However, it turns out that not all Rhapydionininae become linear; some retain their juvenile coiling into maturity (Vicedo et al. 2011). At least some species are believed to have both a linear megalospheric form and a coiled microspheric form. To explain, forams can be divided between microspheric forms, in which the first chambers of a new test are much smaller, and megalospheric forms with larger initial chambers. In those relatively few forams whose life cycles have been studied in detail, these two forms correspond to an alternation of generations, with a mostly microspheric asexually-reproducing generation giving rise to the generally megalospheric sexually-reproducing phase. Loeblich & Tappan's (1964) concept of rhapydionines, therefore, would have potentially placed members of a single species into separate families.

Diagram of internal structure of two adult chambers of Cuvillierinella, from Vicedo et al. (2011). Key to abbreviations: ap f = apertural face, c chl = cortical chamberlets, flo = floor, m chl = medullar chamberlet, prp = preseptal space, rpi = residual pillars, s = septum, sl = septulum.

Rhapydionines are best known as fossils, with a definite range from the Upper Cretaceous to the mid-Eocene (Loeblich & Tappan 1984). Believe it or not, whether there are still rhapydioninines in the world is something of an open question. Loeblich & Tappan (1964) listed two Recent genera in the Rhapydionininae, each represented by only a single known specimen. Ripacubana conica was originally described from sand deposits in Cuba; however, Loeblich & Tappan (1964) suggested that Ripacubana may actually represent what has been referred to as a 'zombie taxon'. Some of you may be familiar with the palaeontological concept of a 'Lazarus taxon', where a species disappears from the fossil record only to reappear at a later date. What has actually happened in these cases is that the species had only become locally extinct, but survived in some other locality that has not been preserved, subsequently recolonising its old range. A 'zombie taxon', however, is one that has genuinely become extinct at the earlier date, but its fossilised remains have since been transported into a younger sediment deposit, giving the impression that it survived later than it did*. In the case of Ripacubana, it is difficult to know just how long a foram shell buried in sand has been lying there.

*Identifications of Lazarus taxa also have to be on the look-out for 'Elvis taxa': where the more recent population does not in fact represent the same species, but a different species that has convergently evolved similar features.

Craterites rectus, from Loeblich & Tappan (1964).

Loeblich & Tappan (1964) did not express the same reservations about Craterites rectus, described from a beach on Lord Howe Island east of Australia. Craterites was later separated as its own subfamily by Loeblich & Tappan (1984) on the basis of its being attached to the substrate, and so differing from other free-living Rhapydionininae. Nevertheless, they kept the two subfamilies together as the family Rhapydioninidae, so Craterites may still be the only known survivor of the rhapydioninine lineage. However, with only one known specimen, the details of the internal structure of Craterites remain unknown.

REFERENCES

Loeblich, A. R., Jr & H. Tappan. 1964. Treatise on Invertebrate Paleontology pt C. Protista 2. Sarcodina, chiefly "thecamoebians" and Foraminiferida, vol. 1. The Geological Society of America and The University of Kansas Press.

Loeblich, A. R., Jr & H. Tappan. 1984. Suprageneric classification of the Foraminiferida (Protozoa). Micropaleontology 30 (1): 1-70.

Sen Gupta, B. K. 2002. Modern Foraminifera. Springer.

Vicedo, V., G. Frijia, M. Parente & E. Caus. 2011. The Late Cretaceous genera Cuvillierinella, Cyclopseudedomia, and Rhapydionina (Rhapydioninidae, Foraminiferida) in shallow-water carbonates of Pylos (Peloponnese, Greece). Journal of Foraminiferal Research 41 (2): 167-181.

Naming a viral disease around the world

Connor Bamford — Thu, 23 May 2013 02:48:00 +0000

OK so I need a little help.

I am a final year PhD student studying the molecular biology of mumps virus. As part of my final written thesis I would like to include an historical aside to mumps virus and the disease. In particular I would like to know how different societies have named the same set of characteristic symptoms: swollen salivary glands and testis. (Of course there are others, such as meningitis and many infections are asymptotic but lets not be confusing.)

For this I need diverse and global input from as many people as possible. So if you have a name in mind, add it to this spreadsheet.

I have filled it in with a couple of known names to me.

Mumps - characteristic unilateral salivary gland swelling. What do you know this as?

Flower parts and then some

The Phytophactor — Wed, 22 May 2013 14:10:00 +0000

Most if not all of the readers of this blog know their basic floral parts. Generally there's a perianth in two whorls, sepals and petals, and then there's the androecium composed of a whorl of stamens, and lastly one or more pistils. But not all flowers are so constructed. So here's Calycanthus, Carolina spice bush. It has a lot of floral parts. Perhaps you've never taken one of these flowers apart, part by part to have a look see, but TPP just loves taking flowers apart to see what makes them tick. Not only does this flower have lots of parts to some extent they grade one into another and don't fall neatly into the usual categories.
Below the flower is a pair of bracts, leaves of reduced size. One is shown. Then you start peeling off the perianth parts which are not differentiated into sepals and petals. They are longer and greener at first (l-r, top to bottom in order of removal), and then they get broader and purple-red. They are all spirally arranged. As the perianth moves inward the parts get smaller and more curved. The tip becomes yellow in color (row three, 4th one). After the 31st perianth part (the number you find may vary), the next part is abruptly smaller, a stamen, which is not your typical stamen in form, no filament, sort of a chunky version of a perianth part with two pair of microsporangia. These continue to spiral inward and downward into the receptacle. In this flower there were thirteen stamens. The next parts were too small to easily remove so what remains in this image is the top of the receptacle with a transitional stamen-pistil and then the rest of the pistils.

The pistils are sort of semi-embedded in the receptacle, each pistil topped with a creamy-white stigmatic area. It's hard to know how many there are 14-15, because the small vestiges are probably not viable and barely visible light areas. The spiral of parts continues with the pistils getting smaller, which you can see starting with the largest pistil at about 5 o'clock (reddish structure is the base of a stamen, white oval inwardly adjacent is the largest pistil), then the next biggest one is at about 10 o'clock, and so on. Altogether there are 60 floral parts, often a multiple of 3, but often off one or two as well. Maybe now you understand why textbooks illustrate flowers with simple things like a lily as if it were typical. This is a flower for advanced learners, so take your shoes off and get to counting the parts! Enjoy.

My pet theory about the human nose: breastfeeding

Bjørn Østman — Wed, 22 May 2013 12:08:00 +0000

Why is the outer nose shaped as it is? Why don't humans just have two holes in the face, rather than this protuberance that we care so much to have the right shape of?

Here's the best illustration I've seen of my pet hypothesis:

Imagine that little baby had two holes rather than a nose. It would suffocate. That huge breast would block the air intake, making it impossible to breastfeed. But when the baby's nose is pushed from the front, slits are formed that enable the baby to still breathe through the nose.

In other words, humans have a proboscis so that they can breastfeed.

Some support: Cows, dogs, and cats have a slit to the side, making them able to breathe when their noses are blocked form the front.

A caveat: Snub-nosed monkeys have no external nose, but just two holes. Admittedly, they probably breastfeed. I wonder how they do it. They also sit with their faces downwards when it rains, to prevent rain from entering their nostrils. I wonder if the olfactory abilities of these monkeys are reduced?

More on the variation of nose shapes in humans and the evolutionary origin of the human nose, but nowhere can I find anyone suggesting a link between nose-shape and breastfeeding.

VerbCorner: A Citizen Science project to find out what verbs mean

GamesWithWords — Wed, 22 May 2013 08:00:00 +0000

Earlier this week, I blogged about our new VerbCorner project. At the end, I promised that there would be more info forthcoming about why we are doing this project, about its aims and expected outcomes, why it's necessary, etc. Here's the first installment in that series.

Computers and language

I just dictated the following note to Siri

Many of our best computer systems treat words as essentially meaningless symbols that need to be moved around.

Here's what she wrote

Many of our best computer system street words is essentially meaningless symbols that need to be moved around.

I rest my case.

The problem of meaning.

I don't know for sure how Siri works, but her mistake is emblematic of how much language software works. Computer systems treat and Computer system street sound approximately the same, but that's not something most humans would notice because the first interpretation makes sense and the second one doesn't.

Decades of research shows that human language comprehension is heavily guided by plausibility: when there are two possible interpretations of what you just heard, go for the one that makes sense. This happens speech recognition like in the example above, and it plays a key role in understanding ambiguous words. If you want to throw Google Translate for a look, give it the following:

John was already in his swimsuit as we reached the watering hole. "I hope the tire swing is still there," John said as he headed to the bank.

Although the most plausible interpretation of bank here is side of a river, Google Translate will translate it into the word for "financial institution" in whatever language you are translating into, because that's the most common meaning of the English work bank.

So what's the problem?

I assume that this limitation is not lost on the people at Google or at Apple. And, in fact, there are computer systems that try to incorporate meaning. The problem there is not so much the computer science as the linguistic science.** Dictionaries notwithstanding, scientists really do not know very much about what words mean, and it is hard to program the computer to know what the word means when you actually do not know.

(Dictionaries are useful, but as an exercise, pick* definition from a dictionary and come up with a counterexample. It is not hard.)

One of the limitations is scope. Language is huge. There are a lot of words. So scientists will work on the meanings of a small number of words. This is helpful, but a computer that only knows a few words is pretty limited. We want to know the meanings of all words.

Solving the problem

We've launched a new section of the website, VerbCorner. There, you can answer questions about what verbs mean. Rather than try to work out the meaning of a word all at once, we have broken up the problem in a series of different questions, each of which tries to pinpoint a specific component of meaning. Of course, there are many nuances to meaning, but research has shown that certain aspects are more important that others, and we will be focusing on those.

I will be writing a lot more about this project, it's goals, the science behind it, and the impact we expect it to have over the coming weeks. In the meantime, please check it out.

----
*Dragon Dictate originally transcribed this as "pickled", which I did not catch on proofreading. More evidence that we need computer programs that understand what words mean.
**Dragon Dictate make spaghetti out of this sentence, too.

The Wool Plants

noreply@blogger.com (Christopher Taylor) — Wed, 22 May 2013 06:02:00 +0000

Vegetable lamb, as illustrated in The Travels of Sir John Mandeville (ca 1360).

Medieval legend in Europe spoke of a strange animal that could supposedly be found far off in central Asia: the vegetable lamb. According to legend, this was an animal much like an ordinary sheep except that it grew directly from a plant, to which it remained attached by the umbilical cord. The vegetable lamb would sustain itself by grazing on nearby vegetation but when this was depleted, as the lamb could not move away from the plant to which it was attached, the lamb would die. How such a pointlessly self-defeating organism was supposed to persist does not appear to have concerned the medieval lexicographers; presumably it was supposed to be allegorical of something.

Opening fruit of Gossypium hirsutum, photographed by B. P. Schuiling.
Part of the reason for the legend's persistence, however, was that there was indeed a form of 'wool' that came from a plant: cotton. The cotton genus Gossypium comprises about fifty species found in tropical and subtropical regions around the world (Wendel et al. 2010). Members of the genus vary from herbaceous perennials to small trees. The genus is divided into four subgenera, most of which are geographically distinct. The subgenus Gossypium is found in Africa and Arabia, subgenus Sturtia in Australia, and subgenus Houzingenia in the Americas. These three subgenera between them include the diploid cotton species; the fourth subgenus Karpas is also found in the Americas but differs in containing tetraploid species. Genetic evidence indicates that the subgenus Karpas arose at some point in the very recent past (within the last one or two million years) from a single hybridisation event between a species of subgenus Gossypium and one of Houzingenia, probably as a result of some chance dispersal event from Africa. Gossypium seeds seem well suited to dispersal: seeds of the Hawaiian Island species G. tomentosum have apparently germinated after being kept immersed in artificial seawater for three years (Wendel et al. 2010)! This same predicection for dispersal has resulted in the tetraploid species rapidly becoming widespread despite their recent origin, and in producing two species in remote locales: the Hawaiian G. tomentosum is directly related to the mainland G. hirsutum, while the Galapagos G. darwinii is sister to the mainland G. barbadense.

Levant cotton Gossypium herbaceum, photographed by H. Zell.

Commercial cotton is grown from four species of Gossypium, which may have each been domesticated independently in prehistoric times. All Gossypium species produce seeds with a covering of fuzzy hairs, but seeds of the two Old World diploid species G. herbaceum and G. arboreum also possess an outer layer of longer, flatter hairs that can be woven into thread. It was one of these two species, or possibly some now-extinct close relative, that made the crossing over the Atlantic to become one ancestor of the tetraploid species; as a result, the tetraploid species also possess these long outer hairs. Two of the tetraploid species, G. barbadense and G. hirsutum, were also domesticated, and the latter of these is now by far the most abundant cotton species in cultivation*.

*In case you were wondering, no-one seems to have suggested that the island species related to the two American domesticates might have been human-dispersed.

Sturt's desert rose Gossypium sturtianum, from here.

Other diploid Gossypium species do not possess this longer outer hair layer, only the inner short layer, and are not sources of commercial cotton (though hybrids with some of these species have been used to breed desirable genetic traits into the commercial species). In one group of Australian species (the section Grandicalyx) found in the Kimberley region of northern Western Australia, the hair layer has become very sparse and the seeds are almost hairless. These seeds also possess fatty bodies called eliosomes that are attractive to ants, and the plants are dispersed by having hungry ants carry their seeds away. Grandicalyx species are seasonal herbs, dying off above ground during droughts only to resprout from their thick root-stock. Other Australian species include the Sturt's desert rose Gossypium sturtianum, the floral emblem of Australia's Northern Territory.

Gossypium gossypioides, from here.

As with other plant groups, hybridisation appears to have been a recurring factor in the evolution of Gossypium. The diploid Gossypium species have been divided between eight genome groups, hybrids between which are generally not viable (though not unknown: the parents of the tetraploid lineage, for instance, belonged to separate groups). However, genetic studies of some Gossypium species have identified discrepancies where a species may possess the nuclear genome of one group, but the chloroplast genome of another. For instance, the North American species G. gossypioides resembles other New World species in its nuclear genome, but has chloroplasts related to those of G. herbaceum or G. arboreum (which it may have acquired as a result of the same hybridisation event that produced the tetraploid species*). This phenomenon, which has been called cytoplasmic introgression, may have arisen in cotton through a process called semigamy. Semigamy is a particular form of apomixis (reproduction without fertilisation) in which sperm and egg cells fuse cytoplasmically, but their nuclei remain distinct (Curtiss et al. 2011). These nuclei will eventually be segregated by cell division, resulting in offspring that are mosaics of male- and female-line genomes. Over time, selection or drift may produce a homogenous population that retains the nuclear genome of one ancestor, but the cytoplasmic heritage of the other.

*The American parent of the tetraploids has more usually been identified as G. raimondii, a South American species, but G. raimondii is the direct sister species of G. gossypioides. It may be that G. gossypioides is the true parent of the tetraploids, or it may be that it too is derived from G. raimondii or its parent stock).

REFERENCES

Curtiss, J., L. Rodriguez-Uribe, J. McD. Stewart & J. Zhang. 2011. Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L.) through comparative microarray analysis. BMC Plant Biology 11: 49.

Wendel, J. F., C. L. Brubaker & T. Seelanan. 2010. The origin and evolution of Gossypium. In: Stewart, J. McD., D. Oosterhuis, J. J. Heitholt & J. R. Mauney (eds) Physiology of Cotton pp. 1-18. Springer.

How dumb is too dumb? We still don't know!

The Phytophactor — Tue, 21 May 2013 13:09:00 +0000

A very excited out-of-work sports caster called TPP on the phone last night. “Now’s the time!” And after reeling off the current set of anti-Obama sound bites asked me to sign a petition in support of Sarah Palindrone (someone who sounds just as dumb forward as backward) running for the Senate from Alaska. Oh, yes, and a little donation to the effort would be nice too. However the response that TPP wanted to leave was not an option.

Now this raises quite an interesting question about politics that this recording could not answer. How dumb is too dumb in ‘Mercan politics? TPP figured that we’d bottomed out and people would come to their senses after electing Reagan. This shows TPP's political acumen. And then along comes W who made Ron sound and look like a Rhodes Scholar. In the next election cycle, the afore mentioned Palindrone was given way more attention than anyone with so little to say and so little reason to say it and who will then say it anyways with so much dumbth should ever be given. And she hasn’t improved. Perhaps it was Gov. Perry of Taxes who so lowered the bar that Ms. Palindrone’s IQ rose in comparison because now some near breathless people want her in the Senate.

"The mind of this country, taught to aim at low objects, eats upon itself." Ralph Waldo Emerson offered that observation in 1837, but his words echo with painful prescience in today's very different United States (from an old WashPo article). What would Ralph think now about our virulent mixture of anti-intellectualism, anti-rationalism, ideology, and low expectations? There are smart capable people in the USA, but almost none of them are electable in this era of you-can’t-be-too-dumb politics.

The Even Earlier Discovery of Antibiotic Resistance

The Defective Brain — Tue, 21 May 2013 12:00:00 +0000

So about a month ago, I wrote about how amazing it was that penicillin resistance was discovered as early as 1940, two years before it went on general sale. But whilst researching that article, I realised that Sulphonamide drugs entered the market long before penicillin, with their discoverer, Gerhard Domagk, being nominated for a Nobel prize in 1939. He had been tasked by Bayer pharmaceuticals to test out a gargantuan number of dye molecules to see whether they could kill off bacteria, and in the process , stumbled across the first antibiotic.
You may recall from the previous instalment that Heinrich Hoerlein was the man to recruit Gerhard Domagk into Bayer. Heinrich Hoerlein was a talented chemist, who had specialised in developing dyes for wool. How did this dye maker end up working to create one of the most important pharmaceuticals that the world had seen up until that point ? Why was it that when Bayer decided to devise new treatments against bacterial disease, they focussed on the compounds used to colour clothes ?

To understand how this state of affairs occurred, we need to go back further in time to the 1800s, and look at bacteria. If we were to do this in this era, we would need to get a good microscope. Bacteria tend not to be visible to the naked eye. So let us look down our microscope, what would we see ?
We would probably see tiny transparent blobs. This could mean that we either have lots of bacteria, or are looking at some air bubbles. There are various legends of scientists proclaiming that they have found an entirely new type of bacteria, only to later realise that this bacteria was nothing more than a bubble of air in the wrong place at the wrong time.
This is where dyes become important. The odds are that you are wearing clothes which have undergone the dye process. A dye works by chemically binding to the surface of whatever you want coloured.
A number of scientists of that era began to work on dyes that bind to cells, allowing them to be more easily seen under a microscope. This allowed scientists to see that bacteria came in all sorts of shapes and sizes, and that different species were associated with different diseases.
One of the pioneers of this research was a man named Paul Ehrlich. His PhD had been dedicated to studying how aniline dyes, which had previously only been used for fabrics, could actually be used to colour cells. He also noticed that dyes he used would colour some cells differently to others. Some cells would take up a lot of the dye, whilst others would not and remain transparent. At the age of 24, using the new "staining" techniques, he had managed to discover a new type of cell, known as a Mast cell.
A lot of his scientific achievements could be tracked down to the one simple question he asked himself when he saw this effect: Why did some cells take up more dye than others?
He theorised that cells took up specific nutrients, and that receptors on the surface of these cells played a crucial role in this process. Different cell types have different receptors on their surface. some of these receptors allow dye molecules to enter the cell, and some do not. The reason that different cells "stained" differently was due to the different receptors on their surfaces.
He suggested that toxins on the surface of the bacteria bound the receptors on the surface of the host during infection. In response, the host cell would secrete these receptors to flood the toxins on the surface of the bacteria, thus neutralising them. He called these secreted receptors antibodies.
Whilst this is far from our modern understanding of antibodies, it was a crucial step in the right direction, and he would be credited as one of the founders of immunology as a result of it.
He also suspected that bacteria also had receptors which they used to ingest dye molecules. He noted that some dyes were taken up by bacterial cells, but not human cells. He suggested that this was because the dye molecules resembled nutrients that the bacteria eat. If he could manufacture the chemical structures of these dye molecules to include poison, then he could have a chemical that kills of bacterial cells, and leave human cells alone. He termed these chemicals "Magic Bullets".
In 1904 came his first breakthrough, with a compound, known as Trypan Red, due to it's colour, and sucess for treating mice infected with trypanosomes. Whilst this was useful as a proof of concept, Trypan Red only worked against the types of trypanosomes that infect mice, but not those which attack humans
It was while he was working on this problem that researchers at the Liverpool School of Tropical Hygiene, Anton Breinl and Harold Wolferstan Thomas, discovered that a compound known as Atoxyl, though to be non-toxic for humans, could kill off trypanosomes. From 1906, a number of expeditions to Africa took it with them to protect themselves from the Sleeping Sickness caused by these organisms. Robert Koch, one of the founders of microbiology, used it to treat patients on the shore of Lake Victoria. It became incredibly popular at the time.
Intrigued, Paul Ehrlich investigated this wonder drug, in addition to the other dye based drugs he was developing. During the course of his research, he noticed a worrying trend. After prolonged therapy with these drugs, the resistance of the trypanosomes to these chemicals increased, until they were completely resistant to the therapy. He coined the term "fastness" to describe this trait in bacteria. The fact that he had observed this "fastness" occurring in response to such a broad range of chemicals suggested to him that this was an inevitable event.
Ehrlich was unexpectedly energised by this discovery of resistant organisms. This was because of the finding that once an organism became resistant compound, it was also resistant to chemicals with the same shape and structure. This provided evidence for his fledgling theory of surface receptors which bind to specific chemicals based on their shape and structure.
But his discovery of resistance put him on a crash course with Robert Koch, who had not observed this effect, and thus disputed that it had ever occurred outside of the lab. The main differences were that Robert Koch used much higher doses of Atoxyl than Ehrlich. Either way, Atoxyl was fast falling from popularity. Patients treated with it would go blind due to its severe side effects. A study in 1910 would show that it merely halted progression of trypanosome disease, and that patients were no better off using it.
Ehrlichs lab was still screening drugs to fight off pathogens, and it came across compound 606, a derivative of atoxyl that not only had less severe side effects, but had proven utility against syphilis.
This was marketed as Salversan, and became an important drug in the fight against syphilis, and was used up until the 1940's, when penicillin replaced it.
The discovery of these drugs, and the apt demonstration that dye molecules could make good antibiotics cemented his place in history. One of his assistants, Wilhelm Roehl, would go on to head a research department at Bayer. It was he who would recruit a Dye chemist, Heinrich Hoerlein, to find the next big drug.
So whilst Ehrlichs theory of "magic bullets" would live on, and laid the foundations for the discoveries of Domagk and Fleming, what happened to his theories on antibiotic resistance ?
There were a number of weaknesses in Ehrlichs theories that a number of researchers called into question. Ehrlichs theories of antibiotics and antibiotic resistances were too simplistic. He posited that for each compound, there was a single path to resistance through the mutation of a single receptor. But we know that bacteria and other pathogens can adapt to antibiotics in multiple ways. This made it difficult to replicate his results, and even more difficult for him to explain why they didn't replicate. The rules he had set out for explaining antibiotic resistance did not always hold true. The disparity observed between his experiments of Atoxyl, and of Kochs experiments did not help his case.
This apparent wooliness would mask the threat of antibiotic resistance as a merely theoretical phenomenon. It would for the next 30 years be regarded as a curiosity that would never pose a threat to people.
Over a hundred years after Ehrlich's initial observation of antibiotic resistance, we have a slightly different perspective on his discovery than his contemporaries.

References

Gradmann C. (2011). Magic bullets and moving targets: antibiotic resistance and experimental chemotherapy, 1900-1940, Dynamis, 31 (2) 305-321. DOI: 10.4321/S0211-95362011000200003

Titford M. (2010). Paul Ehrlich: Histological Staining, Immunology, Chemotherapy, Laboratory Medicine, 41 (8) 497-498. DOI: 10.1309/LMHJS86N5ICBIBWM

Casanova J.M. (1992). Bacteria and their dyes: Hans Christian Joachim Gram, Historia de La Immunologia, 11 (4) DOI:

Ehrlich P. Address in Pathology, ON CHEMIOTHERAPY: Delivered before the Seventeenth International Congress of Medicine., British medical journal, PMID: 20766753

Kaufmann S.H.E. (2008). Immunology's foundation: the 100-year anniversary of the Nobel Prize to Paul Ehrlich and Elie Metchnikoff, Nature Immunology, 9 (7) 705-712. DOI: 10.1038/ni0708-705

Even People Without Synesthesia Find Colors in Music

Elizabeth Preston — Tue, 21 May 2013 10:40:00 +0000

It’s time to stop scoffing at the synesthetes: linking music to colors is totally normal. It’s not really about the notes, though. Researchers say the colors we find in music are actually the colors of the emotions the music makes us feel.

Synesthetes are people whose sensory experiences overlap; they most often link letters or numbers to certain colors. Music-color synesthesia, in which hearing music triggers the colors, is rarer. In fact, when Stephen Palmer and Karen Schloss at the University of California, Berkeley, set out to do a pilot study of music-color synesthetes, they couldn’t find any. So instead they began looking at the connections between music and colors in everybody else.

As part of a larger study called the Berkeley Color Project, Palmer and Schloss included questions about music. Participants saw a grid of colors while listening to 18 brief clips of classical pieces, and chose the colors that were “most consistent” and "least consistent" with each selection.

The researchers suspected that a connection between music and color, if there was one, might be emotional. So they separately asked their 48 subjects how happy, sad, angry, calm, strong, weak, lively and dreary each piece of music was. Subjects answered the same emotional questions about each color. (If you’re the kind of person who hates attributing personality traits to color swatches, you would not have enjoyed this study.)

There were 18 music samples, representing every possible combination of 3 composers (Bach, Mozart, Brahms), 3 tempi (fast, medium, slow), and 2 modes (major or minor). The Andante movement of Bach's Brandenburg concerto in F major, for example, was Bach/major/slow.

What emerged from this sea of lively Mozart and sad burnt-orange was a clear pattern. People linked uptempo and major-key music to colors that were warmer (yellower), lighter, and more vivid. Pieces with a slower tempo or in a minor key provoked the opposite colors: cooler (bluer), darker, and less saturated.

Additionally, music that was both slow and in a major key tended to be greener. And although there wasn’t a difference between Mozart and Bach, Brahms—a Romantic composer who wrote the most recently of the three—leaned more to the slow and minor colors.

To learn whether this consistency was strictly cultural, Palmer and Schloss found a collaborator at the University of Guadalajara who wanted to repeat the experiments with Mexican subjects.

The researcher, Lilia Prada-León, “initially complained that she didn’t want to study classical music because her Mexican participants don’t listen to that music much,” Parker recalls. “She wanted to do it with mariachi bands, which we may still do sometime later.”

Despite Prada-León's hesitation, the results from her Mexican subjects fit snugly with the results from Americans. “The pattern of results for tempo, mode, and composer were remarkably similar,” the authors write.

Also similar were the emotional ratings that Mexican and American subjects gave the musical selections, as well as the colors themselves. The emotions linked to each piece of music matched the emotions linked to that music's colors. This suggests that music itself doesn't make most people think of color. Instead, music triggers emotion—and that emotion is linked to a certain set of colors in the mind. The results are published in PNAS.

Out of the eight emotions in the original list, only four were needed to explain the results: happy, sad, strong and weak. Happier and stronger colors were associated with upbeat, major-key tunes, while weaker and sadder colors were tied to slower, minor-key pieces.

So what does all this tell us about actual synesthesia?

Palmer says his group has now repeated a version of their experiments with real music-color synesthetes (after finally rounding some up). The results looked different. While non-synesthetes chose different colors depending on the tempo of a piece of music—even if it was the same musical line artificially sped up or slowed down—synesthetes didn't.

"My current opinion is that synesthetes’ color experiences arise from direct mappings from sound to color," Palmer says. In their minds, emotions don't act as the middleman. However, "non-synesthetes’ color associations are indirect and do involve emotional mediation."

But when researchers asked synesthetes to choose the colors that were most "emotionally consistent" with the music, rather than the colors they experienced in their minds, the synesthetes picked out the same colors as everyone else. Additionally, when researchers altered melodies just enough to change them from minor to major, synesthetes—like everyone else—"chose happier colors," Palmer says.

There may be some common ground after all between synesthetes and others. The two groups probably won't agree, though, on the color of the mariachi music playing there.

Images: top by tanakawho (via Flickr); bottom Palmer et al.

Palmer, S., Schloss, K., Xu, Z., & Prado-Leon, L. (2013). Music-color associations are mediated by emotion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1212562110

Citizen Science at GamesWithWords.org: The VerbCorner Project

GamesWithWords — Tue, 21 May 2013 06:30:00 +0000

What do verbs mean? We'd like to know. For that reason, we just launched VerbCorner, a massive, crowd-sourced investigation into the meanings of verbs.

Why do we need this project? Why not just look up what verbs mean in a dictionary? While dictionaries are enormously useful (I think I own something like 15), they are far from perfect. For one thing, it's usually very easy to find counter-examples even for what seem like straight-forward definitions. Take the following:

Bachelor: An unmarried man.

So is the Pope a bachelor? Is Neil Patrick Harris? How about a married man from a country in which men are allowed multiple wives?

At VerbCorner, rather than trying to work out the whole definition at once, we have broken meaning into many different components. At the site, you will find several different tasks. In each task, you will try to determine whether a particular verb has a particular component of meaning.

If you are interested in what words mean and would like to help with this project, sign up for an account at http://gameswithwords.org/VerbCorner/. Participation can be anonymous, but we are happy to recognize significant contributions from anyone who wishes it.

I will be writing a lot more about this project, it's goals, the science behind it, and the impact we expect it to have over the coming weeks. In the meantime, please check it out.

Open letter to a new president

The Phytophactor — Mon, 20 May 2013 12:55:00 +0000

Dear New President,
Welcome. TPP has lost track of exactly how many presidents this university has had in his academic career here; that's because most of them were pretty forgettable. You always remember the good ones (exactly one) and the really terrible ones (my first), but most of them were inbetween. If they managed to do one or two good things before moving on we considered ourselves lucky. Our last one has done quite a few good things, mostly on the financial and PR side of things, areas where presidents tend to be pretty influential. Try to do the same. Most of the administration is competent and tries to help you do your job. At times the business office and provost seem bent on the opposite, mostly by failing to understand that a university does not actually run like a business. This will not be a rant about the provost's pseudo-business policies other than if you want units to be financially responsible for everything then you have to give those units the fiscal resources they generate. You're not a new president and you've been around the block a few times, so it's no news to you that coaches and ADs lack institutional loyalty, period. So why do they always get golden parachutes when they stiff the university? My advice is hire a lawyer that knows how to write a contract that will screw anybody that screws the university. Glad you got a raise in salary; boy, those northeastern state colleges must really pay crap for top administrators if coming here to Lincolnland is a good fiscal move. While on this subject, us faculty could use a decent raise, all of us; it's been a good long time since we had one of those and believe it or not, we got expenses. Makes TPP wish it were as easy to move on as it is for administrators, coaches, and ADs. It's hard to know where exactly you should start. Everyone, like TPP, will offer you advice. Us old-timers know what the bad old days were all about, so don't change anything that's actually working. However, you need to do something positive to get the ball rolling, so here's my advice: get us some decent ice cream in the student union. How can you be any kind of half-way decent academic institution without ice cream? And not that frozen yogurt stuff that can't make up it's mind if it's a health food or not, we been there, tasted that, and voted with our pocket books. It folded. There's no shortage of good ice cream locally (have them tell you about Carl's), but the rent in the student center is such that a good business man knows a bad deal when they see it. So screw the money, we need ice cream. This would be a good way to make your mark on the university and improve the institution. TPP has been complaining about this for over 2 decades, and clearly lacks any clout what so ever. Hope the move goes well. You got a lot to learn about the great midwest and Lincolnland in particular. People out here didn't even know what bagels were when TPP arrived all those decades ago. Lots of people from up East don't like it here. They get depressed when they go outside the city limits and experience the maize and soybean desert. Well, that's all for now. Truly your success matters to us and you can count on us to let you know how you're doing.
Best regards, TPP.

The Earlier discovery of Antibiotic Resistance

The Defective Brain — Mon, 20 May 2013 12:00:00 +0000

A couple of weeks ago, I wrote about how quickly penicillin resistance was discovered not long before it was distributed to the public, and how even Alexander Fleming noted his worries over penicillin resistance in the closing of his Nobel prize acceptance speech.

But even in the process of researching this article, I realised that I was merely scratching the surface. You see penicillin was not the first antibiotic discovered. If I want to talk about the first discovery of antibiotic resistance, then I will need to tell this story as well.

In 1932 in Germany, a scientist patented an incredibly important discovery, one that would eventually win him the Nobel prize.

Domagk had been working at Bayer pharmaceuticals at the time of his discovery. In the early 1920's, Bayer had begun to experimenting with different methods for treating bacterial diseases. The experiences of World War 1 had left many researchers with the desire to find ways of preventing deaths from wound infections. Domagk had served in World War 1, and had worked in a cholera hospital near the eastern front. He noted the seeming futility of treating patients with infections.

He came to the attention of Bayer pharmaceuticals after Professor Heinrich Hoerlein* had come across his thesis and decided to hire him. Hoerlein believed that dye molecules could be the key to solving bacterial infection.

The chemists at Bayer would synthesise new chemicals, and then send them to Domagk, and he would then test them on whether they could kill bacteria in vitro, or whether they could prevent mouse deaths from Streptococcus infection. Domagk managed to speed up this process to the point where he could test 30 new chemicals every week.

The chemist on the other end of this process was a man named Josef Klarer. He was the one rushing to make the chemicals for testing. He had tried a number of quinine derivatives, but had no luck. However, in 1932, things would change when he decided to make products based off of Azo Dye molecules. His first success came with Kl-695**, which Domagk found to protect mice during an infection, even though it didn't seem to kill the bacteria in the petri dish. But based off of this finding, Klarer modified Kl-695 again and again. Until it came to a red dye compound that was at the time named Kl-730.

Of course, even though this chemical had been proven in mice, it was as of yet unknown whether it would work in humans. But then Domagks daughter fell ill with a streptococcal disease, and desperate, he gave her a dose of the drug, curing her of the disease.

By 1935, Prontosil Red was being trialled internationally, with Leonard Colebrook, himself a frequent experimenter with antibiotics, demonstrating the effectiveness of Prontosil Red in treating pregnant women, albeit with the side effect of turning his patients bright red. Prontosil Red was the first Sulphanilamide drugs.

Such was the success of this drug that he was nominated for a Nobel Prize in 1939. However, at this time the Nazi's were running Germany. They held a dim view of the Nobel prizes due to the previous German to win a prize. Carl von Ossietzky was a pacifist, who exposed the Nazi's breaking of the treaty of Versailles by training an air corp, and won the Nobel peace prize for his opposition to the Nazi's. As a result of this, the Nazi's forbade any German from accepting Nobel prizes

So when Domagk won a Nobel prize, he was immediately thrown in jail for a week by the Gestapo. This was enough to convince him not to accept the Nobel prize until 1947, two years after Fleming.

By this time, Doctors were already discovering the limits of antibiotics. A.J. Cokkinis wrote in 1938

Inadequate dosage and too short a period not only fail to do any good but seem to lead to the development of acquired resistance on the part of the organism to the drug

Amongst the first to analyse these limitations were a group of researchers based at St Mary's, one of whom was Alexander Fleming**. They had discovered that bacteria could adapt to antibiotic concentrations. The same year, Connor Macleod, a researcher based in New York, investigated this in more detail. He discovered that gradually increasing the amount of antibiotics in broth could increase the numbers of resistant bacteria.

Sulfa drugs like Prontosil Red changed the way medicine worked, and laid down the foundations upon which modern medicine would arise. Unlike penicillin, Prontosil and the related sulphonamide and sulphanilamide drugs could be created entirely synthetically from available chemicals.

Bayer's technique for finding drugs could best be compared to throwing spaghetti against a wall until it sticks, testing random chemicals until they produced the effects they wanted. and people say that Alexander Fleming relied on luck ! Bayer appeared to be basing its company policy on it.

But the question remains as to why they decided to use dye compounds as antibiotics, how did they even know it could work. It's not like there was someone before them who discovered antibiotics even earlier...was there ?

To be continued tomorrow........

References
Wollheim Memorial- Phillip Heinrich Hoerlein
Bayer- Gerhard Domagk
Nobel Prize- Gerhard Domagk

Bentley R. (2009). Different roads to discovery; Prontosil (hence sulfa drugs) and penicillin (hence β-lactams), Journal of Industrial Microbiology & Biotechnology, 36 (6) 775-786. DOI: 10.1007/s10295-009-0553-8

Macleod C. & Daddi G. (1939). A ''Sulfapyridine-Fast'' Strain of Pneumococcus Type 1, Proceedings of the Society for Experimental Biology and Medicine, 41 69-71. DOI: 10.3181/00379727-41-10575P

Cokkinis A.J. (1938). SULPHONAMIDE CHEMOTHERAPY IN SURGICAL INFECTIONS--I, BMJ, 2 (4059) 845-847. DOI: 10.1136/bmj.2.4059.845

Gerhardt Domagk: The First Man to Triumph Over Infectious Diseases By Ekkehard Grundmann

* Heinrich Hoerlein would eventually rise up to the managing board of IG farben, which was the conglomerate which ran a number of companies, including Bayer. Originally, it was primarily a dye making company. But it's activities during World War 2 were infamous. It was the company that developed Zyklon B, in the time that Hoerlein served on its board, which is why he found himself at the Nuremberg trials alongside many of the other company directors. It didn't help that at least one of these directors had been conducting experiments at Auschwitz under the direction of the SS. These experiments involved inducing artificial infections deliberately, and then giving the test subject antibiotics to cure the disease. Heinrich Hoerlein was amongst a number of IG Farbens executives who tried to stop the supply of these chemicals once he had found out what the Nazis were doing with them. When this came to light, the charges were dropped, but the reputation of IG Farben never really recovered, and the conglomerate didn't last long after the war, although some of it's constituent companies are still around today.

** Unfortunately the original paper is locked in the vaults of the Lancet, and so I am forced to diminish his role in the discovery of Antibiotic resistance, because there is no way for me to find out exactly what he did.

Religion is halfway between a 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.

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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.

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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.