Fusion Weapons from chemistry notes

Fission weapons discussed above are ultimately limited in their destructive capability by the sheer size a subcritical mass can assume -- and be imploded quickly enough by high explosives to form a supercritical assembly. The largest known pure fission weapon tested had a 500 kiloton yield. This is some thirty-eight times the release which destroyed Hiroshima in 1945. Not satisfied that this was powerful enough, designers developed thermonuclear (fusion) weapons.

Fusion exploits the energy released in the fusing of two atoms to form a new element; e.g. deuterium atoms fusing to form helium, ²H + ²H = ⁴He₂ , as occurs on the sun. For atoms to fuse, very high temperatures and pressures are required. Only fusion of the lightest element, hydrogen, has proven practical. And only the heavy isotopes of hydrogen, ²H (deuterium) and ³H (tritium), have a low enough threshold for fusion to have been used in weapons successfully thus far.

The first method tried (boosting) involved simply placing ³H in a void within the center of a fission weapon, where tremendous temperatures and high pressures were attendant to the fission explosion. This worked; contributing energy to the overall explosion, and boosting the efficiency of the Pu fissioning as well (fusion reactions also release neutrons, but with much higher energy).

Because ³H is a gas at room temperature, it can be easily 'bled' into the central cavity from a storage bottle prior to an explosion, and impact the final yield of the device. This is still used today, and allows for what is termed 'dial-a-yield' capability on many stockpiled weapons.

Multistage thermonuclear weapons -- the main component of today's strategic nuclear forces -- are more complex. These employ a 'primary' fission weapon to serve merely as a trigger. As mentioned above, the fission weapon is characterized by a tremendous energy release in a small space over a short period of time. As a result, a very large fraction of the initial energy release is in the form of thermal X-rays.

These X-rays are channeled to a 'secondary' fusion package. The X-rays travel into a cavity within a cylindrical radiation container.

The radiation pressure from these X-rays either directly, or through an intermediate material often cited as a polystyrene foam, ablates a cylindrical enclosure containing thermonuclear fuel (shown in blue at left); this can be Li²H (lithium deuteride).

Running along the central axis of this fuel is a rod of fissile material, termed a 'sparkplug'.

The contracting fuel package becomes denser, the sparkplug begins to fission, neutrons from this transmute the Li²H into ³H that can readily fuse with ²H (the fusion reaction ³H + ²H has a very high cross-section, or probability, in typical secondary designs), heat increases greatly, and fusion continues through the fuel mass.

A final 'tertiary' stage can be added to this in the form of an exterior blanket of ²³⁸U, wrapping the outer surface of the radiation case or the fuel package. ²³⁸U is not fissionable by the slower neutrons which dominate the fission weapon environment, but fusion releases copious high energy neutrons and this can fast fission the ordinary uranium.

This is a cheap (and radiologically very dirty) way to greatly increase yield. The largest weapon ever detonated -- the Soviet Union's 'super bomb', was some 60 MT in yield, and would have been nearer 100MT had this technique been used in its tertiary. Again, to control the yield precisely, ³H may be bled from a separate tank into the core of the primary, as shown in the hypothetical diagram on the left of a modern thermonuclear weapon.

This primary/secondary/tertiary or multistage arrangement can be increased -- unlike the fission weapon -- to provide insane governments with any arbitrarily large yield.

Fusion, or thermonuclear weapons, are not simple to design nor are they likely targets of construction for would-be terrorists today.

Many aspects of the relevant radiation transport, X-ray opacities, and ultra-high T and D equations-of-state (EOS) for relevant materials are still classified to this day (though increasing dissemination of weapons-adaptable information from the inertially-confined fusion (ICF) area may change this in time). Keeping such information classified makes good sense.

Source: Simpelthiniking.com

What do flamingos, Cheetos and Quantum Chemistry have in common? from chemistry notes

The vibrant colors of flamingos and Cheetos are both the result of related carotenoid dyes. Carotenoids (named for the vegetable in which they were first found!) are based on a linear conjugated diene skeleton, and provide nature with many colorful accents. Canthaxanthin, for example, is fed to captive flamingos to produce their characteristic pink color (a similar pigment found in brine shrimp does the same favor for wild flamingos). Astaxanthin is responsible for the characterstic color of lobsters. Canaries, whose signature color is a greenish yellow, can be turned red if they are fed paprika during their molt. The new feathers will grow in orange-red.

If you're tired of only changing the color of your hair, you can try for a pumpkin look for fall. The compound that gives this class of vegetable pigments its name - β-carotene - when consumed in large quantities by humans, will turn them orange. [Really, but don't try this at home! It was observed clinically in Britain during WW II when food shortages led some people to include large amounts of carrots in their diets.]

If you thought the bright color of Cheez-Whiz and Cheetos was artificial -- it's not. Bixin or annatto, a natural pigment used for centuries, is the source of that unforgettable orange. Researchers have recently elucidated the biochemical pathway for the synthesis of bixin and are pursuing genetic engineering approaches to its bulk synthesis in tomatoes [Florence Bouvier in Science, 300:2089-2091, June 27, 2003].

What does this all have to do with quantum chemistry? A very simple quantum mechanical model, the particle in a one-dimensional box, can be used to predict the color of conjugated dyes.

Cranky Numbers: From the 3rd grade to Fermat's Last Theorem from chemistry notes

What's the connection between 3rd grade math and Fermat's Last Theorem? My 3rd grader comes home with problems that ask him how many ways he can write a number, such as 4, prompting him to list such expressions as: 1+3, 2 x 2, and 8÷2. If you restrict the list to sums of non-negative integers, the list is short and finite: 0+4, 1+3, 2+2, 1+1+2, 1+1+1+1. The number of sums in the list is called the partition number; the fourth partition number is thus 5. A patient 3rd grader (if such existed) could find the partition number of any integer. Partition numbers are handy if you are a 3rd grade teacher making up problems to occupy your students or a particle physicist.

If you looked at a list of partition numbers (the first 20 are: 1 2 3 5 7 11 15 22 30 42 56 77 101 135 176 231 297 385 490 627 more), you might notice that starting with the 4th partition number (5) every 5th number is divisible evenly by 5. Beginning with the 5th number (7), every 7th number divided evenly by 7. Perhaps not surprisingly, every 11th number after 11 is also divisible evenly by 11. The pattern ends there, but not the mystery. Indian mathematician Srinivasa Ramanujan recognized the patterns almost 100 years ago, but it took almost 40 years before Freeman Dyson explained them by inventing a function which he called the rank. Dyson's rank only explained the 5 and 7 patterns, roughly another 40 years would pass (is there a pattern here?) before the invention of the crank would account for the 11's.

As it turns out, there are more sequences buried in the list of partition numbers, you just have to know where to find them (a pattern based on those divisible by 13 begins with the 111,247th partition number). It also helps to have some of the techniques in number theory developed by Andrew Wiles to prove Fermat's Last Theorem. A proof that such patterns will exist for any prime number larger than 3 was published this year by Karl Mahlburg, a graduate student in math at the University of Wisconsin.

Extract DNA in your kitchen from chemistry notes

When my kids think of DNA, they think of the classic picture of the double helix. But what does DNA really look like? A lot depends on how you look at it, and since most of us don't have a good scanning tunnelling microscope at home, we can't get pictures that look like this one from Lawrence Berkeley Labs.

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With a bit of patience, you can extract DNA in your kitchen, and see what the long polymer strands look like in the aggregate! The Genetic Science Learning Center at the University of Utah has developed a protocol for extracting DNA from split peas. Last summer my kids and several of their friends spent a morning in our kitchen pureeing peas and extracting the DNA. The white threads at the top of each test tube are the DNA. A great rainy day project - even if you don't have kids.

Building better ice cream and popcorn - who says physical chemistry is useless? from chemistry notes

Physical chemistry, which I teach, has a certain reputation among chemistry majors: as difficult, dull, mathematically intensive, time consuming. There is even a bumper sticker that says "Honk if you passed p-chem!" When you are looking at the Maxwell relations in thermodynamics, it seems hard to imagine that p-chem has any impact on your daily life at all. But in reality, researchers at Purdue University are hot on the trail of better microwave popcorn and using physical chemistry to do it. [See Role of the Pericarp Cellulose Matrix as a Moisture Barrier in Microwaveable Popcorn; Agung S. Tandjung, Srinivas Janaswamy, Rengaswami Chandrasekaran, Adam Aboubacar, and Bruce R. Hamaker; Biomacromolecules].

Unpopped kernels in your popcorn are a pain, particularly when your kids pick them out and leave them in the living room! It turns out that unpopped kernels are even more of a problem in microwaved popcorn (is there any other kind anymore?). The key to getting popcorn to pop is is the structure of the outer hull (the pericarp), which is made of a biological polymer (which is why this was published in the journal Biomacromolecules). Pericarps in which the cellulose polymers exhibit a strongly crystalline structure pop better. The researchers used differential scanning calorimetry and x-ray crystallography to study the pericarp.

Prefer ice cream with your movie? Erich Windhab, at the ETH in Zurich (where Einstein once worked), used physical chemistry and physics to figure out how to make a smoother, richer ice cream - with fewer calories. You can now buy ice cream made with this process (Edy's Grand Light where I live). [See the article by Robert Kunzig in the June 2004 issue of Discover]

The physical chemistry of the flu from chemistry notes

Fifteen different types of hemagglutinin, a protein embedded in the surface of the influenza virus, have been identified in influenza viruses, tagged as H1, H2 and H3, etc. H1, H2 and H3 have all been found in human viruses, the others are principally found in avian reservoirs. The binding of hemagglutinin, to glycoproteins on a cell's surface prompts the cell to engulf the virus, thus allowing the virus to hijack cellular mechanisms for its own reproduction. Chemical and biological studies suggest that hemagglutinin binds in a helical form, while it is generally in a random coil configuration in solution. Thermodynamics and statistical mechanics can be used to study the shift. pH appear to be a critical factor in the helix-coil equilibrium for this protein.

Hemagglutinin is often used as the immunizing agent in flu vaccines. The 1957 flu virus that was inadvertently included in a set of controls recently sent to 5000 labs around the world was type H2N2 (N refers to the type of neuroamidase - another protein found on the surface of the virus). The avian influenza circulating in Asia recently is type H5. While occasionally humans have contracted this form of the virus, it has not spread person to person, however the lack of general human immunity to H5 worries public health officials. The hemagglutinin found in the influenza virus from the 1918 pandemic is similar to avian forms of the protein. Over 12,000 people died from contracting the 1918 virus in Philadelphia alone in a one month period. World War I was raging in Europe, but the total US combat deaths in that war, staggering as they were at the time (53,513) were dwarfed by the number of Americans who died in the 1918 epidemic: 850,000.

Microscopic terrorists hijacking our cells should worry us at least as much as human terrorists - and indeed homeland security considers a flu pandemic to be a potential catastrophe.

What came between slipsticks and calculators? from chemistry notes

"The Curta is a precision calculating machine for all arithmetical operations. Curta adds, subtracts, multiplies, divides, square and cube roots... and every other computation arising in science and commerce... Available on a trial basis. Price $125."

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From an advertisement in the back pages of Scientific American in the 1960s. The cost is nearly $700 in 2002 dollars -- about the same price as Mathematica. Curtas sell on e-Bay for thousands of dollars these days.

I found one of these while cleaning out a drawer in an old piece of furniture inherited from my husband's family. Its purpose was a mystery, until an article in Scientific American on the history of these calculating machines. What did we do before calculators and symbolic algebra code? There was paper and pencil, log tables, slide rules (based on logarithmic principles and called a slipstick by the geeks of the time!) and calculating machines based on rotating drums. The most sophisticated of these mechanical computers was the Curta. Developed by Curt Herzstark while he was imprisoned in Buchenwald by the Nazis, this small drum shaped calculator was capable of 11 digit accuracy. For comparison, a slide rule has only 3 digit accuracy and a TI-83 graphing calculator has 14 digit accuracy (even though it only displays 10!).

Got a headache? from chemistry notes

Several painkillers in the class of COX-2 inhibitors have been pulled from the market lately (Vioxx), and now there are questions about the cardiovascular safety of some of the NSAIDS (non-steroidal anti-inflammatories), a class believed to be generally cardioprotective, if hard on the stomach. Millions of people take baby aspirin to stave off heart attacks.

Acetylsalicylic acid (aspirin) is the oldest member of the NSAIDS. It has been used for over 100 years for pain, fever and inflammation. Until 1915 aspirin was only available by prescription. Bayer Aspirin was the first drug ever to be marketed in tablet form. It was first marketed in 1899 as a powder, but by 1900 aspirin was being compressed into a water-soluble tablet. This new method eliminated the need to package individual doses in paper bags and thus cut costs by half. Aspirin is consumed in a variety of ways. The French prefer suppositiories to pills, the Italians take fizzy forms akin to Alka-Seltzer and the British seem to like aspirin powders that can be dissolved in water.

One purple pill is much like another from chemistry notes

One purple pill is much like another, perhaps even more than you might think. You can't open a magazine these days without seeing an ad for "the purple pill", Nexium. The original purple pill, Prilosec, was the number one selling prescription drug in 2001. A proton pump inhibitor, it stopped the production of acid in the stomach at a different step than earlier heartburn drugs such as Zantac. Patent protection for Prilosec expired that year, and Nexium was introduced with much fanfare. The FDA approval was based on the argument that Nexium was more effective than Prilosec. Now for the chemistry trivia: Nexium is exactly the same molecule as Prilosec.

To understand the relationship between Nexium and Prilosec, you need to know that many organic molecules come in mirror-pairs. The molecules have exactly the same structure, but are mirror images of each other. Your hands are a good example of this kind of mirror pairing, and in fact the chemical term describing this phenomenon, chirality, comes from the Greek for hand.

Many biological systems show a preference for one mirror image over the other. For example, all the proteins in your body are made up of amino acids which exist in these mirror pairs. Naturally occurring proteins all use only one of the two mirror images, called the L form. Perhaps the most striking example is that of spearmint and caraway oils. Rye bread and spearmint gum taste very different, but the molecules responsible for the taste are identical except that they are mirror images of one another.

Back to Nexium and Prilosec. The active compound in Prilosec is omeprazol, which comes in two forms, R-omeprazol and S-omeprazol. The R and the S come from the Latin for right and left - just like the hands - and indicate that this is a pair of identical mirror images. Both R-omeprazol and S-omeprazol are effective in reducing heartburn, but S-omeprazol is about 4 times as effective as the R form. Prilosec contains a 50/50 mixture of the R and S forms, Nexium is pure S. So 20 mg of Prilosec is equivalent to 12.5 mg of Nexium (10 mg of S + 10 mg of R/4). The prescribing literature on Nexium obscures this fact, giving a new name to S-omeprazol: esomeprazol. Get it? "es"omeprazole.....

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If you want to learn more about chirality, check out Prof. Jean-Claude Bradley's organic chemistry lecture. Lecture 16 introduces chirality. The lecture is available as a podcast or streaming video.

Hazy days from chemistry notes

In my part of the country, it's seriously allergy time. My car is covered in a green haze, and my eyes and nose are running like they're in the Penn relays. The ads promise me "Claritin clear" days if only I would take 10 mg of loratadine. One ad features an allergy sufferer who takes only the brand-name version (Claritin) to be sure that he gets exactly what his doctor used to prescribe. Viewers are cautioned that some other allergy medications might make you drowsy and shows a box with the word diphenhydramine circled in red. It all vaguely implies that if you don't take Claritin itself, you might get something that will put you to sleep. If you know your chemistry, you might realize that diphenhydramine is actually the generic name for Benadryl (which can in fact make you drowsy). If you take Benadryl, generic or otherwise, you could drift off to sleep in the middle of that critical meeting. But if Claritin doesn't make you sleepy, neither will any generic brand of it. Bottom line: if it says loratadine on the box - it's the same stuff your doctor used to prescribe as Claritin. No need to buy the brand name box.

Both loratadine and diphenhydramine are H1 blockers. They bind to a particular type of histamine receptor, and sit there. An overabundance of histamine, released in response to an allergen leads to the woes of pollen season. If the histamine can't get into the receptors, it can't make you miserable. Interestingly, histamine production also plays a role in acid reflux. Several good heartburn drugs (Zantac and Tagamet) are H2 blockers.

Nuisance or Nobel? from chemistry notes

Bryn Mawr's Center for Science in Society hosted a discussion of gender and science earlier today. Al Albano showed a short clip from Nova on Naomi Halas, who got her Ph.D. in physics at Bryn Mawr. Have things changed? Are women generally seen as potential Nobel laurates, or nuisances? Certainly they are better than in Goeppert Mayers's day!

Maria Goeppert Mayer is one of the few women to have won the Nobel prize in physics or chemistry (trivia question - who are the others?). She was cited for her work on the structure of the nucleus. Though she received her Ph.D. from the University of Goettingen in 1930 and worked on the Manhattan Project during World War II, her first full time paid position was at the University of Californai at San Diego in 1960! She had often worked at the same institution as her husband (a chemist), and hiring rules at the time forbade spouses from having faculty positions at the same place. At the beginning of her career, many places considered her a "nuisance". Her early work in chemical physics was with Herzfeld on the colors of organic molecules (see my earlier post on Cheetos, flamingos and quantum chemistry).

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Winning the prize wasn't half as exciting as doing the work itself.

Maria Goeppert Mayer
Nobel Prize winner in physics (1963)

How old is a whale? Chirality has a clue... from chemistry notes

Helis the whale is summering in Philadlephia. Spotted a couple of weeks ago as far north in the Delaware as Trenton, and then again this week in the Schuylkill River, biologists speculate that Helis has come to enjoy the warm (relatively speaking) waters in his old age. Beluga whales typically range much further north than the Delaware Bay, and Helis comes from the St. Lawrence River estuary. He has been observed there since 1986, which means he must be at least 20 years-old, but is probably closer to 30 years old and nearing the end of his life. How do you tell how old a whale is? How long do they live? Humans are among the longest-living mammals, with a life-span on the order of 100 years. Human ages can be verified by consulting birth and census records. Whales are also apparently very long-lived, but discovering the age of a whale is a somewhat more daunting task and the life-spans of most whale species have not been established.

In the case of belugas like Helis, longitudinal observations of populations provide an answer. Individual whales are identified, then followed for their lifetimes, the cetacean equivalent of the US Census. Many whale populations are not regulars in rivers, and not so easily followed -- what then? The concept of chirality again comes into play as chemists and biologists try to answer the question.

The ages of some whales, such as blue whales and fin whales can be determined by counting the layers of ear wax in their inner ears. [Really!] These whales have an apparent life-span similar to that of humans, between 80 and 100 years. Bowhead whales, which live north of the Artic circle, are still hunted in limited numbers by the Inuit. Since the early 1980s, several clearly ancient harpoon heads have been found embedded in modern bowhead whales. The types of points recovered had not been used since the late 19th century, suggesting the whales were more than 100 years old. Inuit oral histories also supported a long life span for these whales, as multiple generations of hunters described encountering the same whale.

There are two forms of the amino acid aspartic acid, R and S. Amino acids are the building blocks of proteins. The S form os aspartic acid is what is found in naturally occuring proteins. Over time, some of the S form will turn into the R form, a process called racemization. The degree of racemization of aspartic acid in the lense of the eye has been used to find the ages in 20 different species, including humans. Ages were obtained for 48 different whales, one which had an apparent age of 211 years [Can. J. Zool. 1999, 77, 571-580], making the bowheads the longest living mammals known!

Global Freezing from chemistry notes

It's May and there is a chance of frost tonight in Philadelphia. It's been cold and damp here, which made me think of Kurt Vonnegut's novel, Cat's Cradle, where the whole world was in peril of freezing (or at least all the water).

In the novel Vonnegut proposes a new solid form of water, Ice IX, which is more stable that liquid water at "normal" pressures and temperatures. Once released into the world at large, it would catalyze the conversion of all liquid water to this solid form - permanently! Some analyses of the text suggest that Vonnegut's brother (who had a Ph.D. in physical chemistry from MIT) might have seeded this idea. Ice IX was not actually discovered until 1968, about 5 years after Cat's Cradle appeared (and doesn't catalyze the conversion of liquid water to a solid form).

We tend to think of only 3 phases of water: ice, liquid water and steam, but there are many forms of ice, each with a particular structure. Ice IX is stable at high pressures (several hundred atmospheres) and low temperatures. The pressures and temperatures of various forms of ice are summarized in a phase diagram here.

Hal Clement had a story called "Phases in Chaos" where the protagonist relied on his recall of the phase diagram of water to negotiate a complex extraterrestial undersea environment. You never know when you'll need to know a bit of physical chemistry!

Measuring height with a thermometer from chemistry notes

Phase diagrams can be plot devices in more than one sense. In the mid-nineteenth century, the British empire was anxious to map the lands north of India. The British and the Russian were engaged in a "Great Game", in which geographical information was but one of the prizes, as each sought to expand their area of control in Asia. Unfortunately for the British, the emperor of China had closed the borders with India to foreigners, under penalty of death. More than one British surveyor perished in attempts to cross the border and map Tibet. Eventually Thomas Montgomerie of the British Survey hit upon recruiting well-educated Indians as clandestine surveyors whose cover identity would be that of itinerant lamas.

The "pundits" were given extensive training over two years and learned to use a sextant, measure altitude by boiling point determination (This is an application of the Clausius-Clapeyron equation: as altitude increases, atmospheric pressure decreases and the boiling point of water decreases in a known relationship) and to walk a measured pace. Pundits counted their paces with the traditional rosary carried by holy men; their rosaries had been altered to contain only 100 beads instead of the usual 108 and a single circuit of the beads was equivalent to a traverse of 5 miles. Observations were recorded on the papers inserted into their prayer wheels.

One of the first pundits was Nain Singh, who at 33 and headmaster of a school in the Himalayas was recruited along with his cousin Mani Singh to survey Tibet. Singh walked thousands of miles in his mapping ventures, and the maps constructed from his survey were the best available until well into the 20th century. On his third and last survey journey, Singh traveled more than eight months from Leh to Lhasa to map the trade route. His measurement of the altitude of Lhasa using measurements of the boiling point of water were accurate to within a hundred meters. Singh retired after this journey to train other pundits. He was well recognized for his feats by many geographical societies and the government of India in his later years. If this all sounds vaguely familiar, it may be because Rudyard Kipling drew heavily on the events around the "Great Game" in his novel, Kim.

The Culture of Science: The Tangled Bank from chemistry notes

Visit The Tangled Bank, an eclectic bi-weekly guide to science writing on the web. Buridan's Ass is this week's host. My lateral take on left versus right is highlighted there and can be found at One Purple Pill is Much Like Another and How Old is a Whale? below.

If you've ever wondered what an epicycle is, visit the Canadian Cynic to find out. (Though if you played with a Spirograph as a kid, turns out you already know what an epicycle is!). Orac Knows' field guide to poster sessions is a great read as well! Check out the Tangled Bank to discover lots more...

Thermodynamics of Spring from chemistry notes

Rumor on the playground this evening was that the weather is warming (they're predicting 80F for Monday!). As Art Carey's recent article in the Philadelphia Inquirer points out, water temperatures will lag behind. Chuck Sutherland, an avid sea-kayaker, points out the perils of cold water. The article notes that cold water will lower your body temperature 25 times faster than cold air, as anyone who's ever jumped in a cool pool can attest!

So, why is cold water "colder" than cold air (at the same apparent temperature)?

A little statistical thermodynamics is a help here. What we sense on the macroscopic level as heat, at the microscopic level is the result of molecular motion. The faster a herd of molecules moves, the "hotter" they are. To move energy from one set of molecules (say, those in your skin) to another (those in the water) requires a collision. This is why a thermos works, by making a near vaccum, where there are very few molecules to collide, you reduce heat transfer. The more collisions, the more heat gets transfered. The density of molecules in liquid water is about 1000 times higher than that in air, leading to more collisions in any given period of time and so increased heat transfer.

Weird Words of Science 1 from chemistry notes

virial

The virial equation provides both a general form for an equation of state for gases or liquids, as well as a connection (through its coefficients) to the microscopic level intermolecular forces experienced by the atoms and molecules. The equation of state can be used (along with other information) to arrive at a phase diagram. The Latin root of the word is vir which is a plural form of vis or force.

Physical chemists are quite fond of the virial expansion, as this quote might suggest:

"The virial expansion is one of the cleanest-cut developments in the subject of statistical mechnics." Condon and Odishaw in the Handbook of Physics, 1967.

Sweet secrets from chemistry notes

No one wants to run the cotton candy machine at the school fair, and now I know why. The plant booth is serene under the trees, the bake sale treats are neatly packaged up, even the lemon mom has only sticky hands. I am covered in pink, blue and violet spun sugar from head to foot. Really, I was seeing the world through rose colored glasses. And it gave me a lot of time to muse about sugar -- why is it so sticky?

What my recipe book calls sugar a chemist calls sucrose (or in very formal situations: [beta]-D-fructofuranosyl [alpha]-D-glucopyranoside). The stickyness of sugar is related to its hygroscopic nature (it will pick up water out of the air), which is a function of its molecular structure (for example the polar nature of the groups on the surface of the molecule - lots of OH groups.) and the physical form of the sugar (why cotton candy noticeably more hygroscopic than granular table sugar).

Biologically, the stickyness of sugar has certain advantages, as an article in Journal of Molecular Biology last year suggests.

And yeah - I'll do the cotton candy again next year!

Weird Words of Science 2 from chemistry notes

bra
A term coined by Dirac in 1947 to describe a vector in a function space that represents a wavefunction's complex conjugate. Kets are the notation for the corresponding vector representing a wavefunction. The words come from splitting "bracket", since when combined, the notation for looks like a bracket. "We shall call the new vectors bra vectors, or simply bras, and denote a general one of them by the symbol < |, the mirror image of the symbol for a ket vector." P. A. M. Dirac in "Principles of Quantum Mechanics"

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I've been working on a paper today, and included an equation using bra and ket notation (which I find generally easier to follow than the intergral notation), which is what brought this to mind -- either that or it was the laundry I was folding!

Science in the Kitchen 2: Jello lasers from chemistry notes

Last year my physical chemistry students and I attempted to design and build a dye laser from scratch. This is both easier and harder than you think. Several papers and an excellent web site provide background information and plans, but a good deal of patience is required to achieve an actual laser pulse. Limited time led to limited success for us.

Lots of different dyes will lase and you see the occasional reference on the web to Jello and whiskey lasers. These sound like urban legends, but in fact are not. Arthur Schawlow, who shared the Nobel Prize in physics in 1981 with Townes for building the laser, shows you can make Knox gelatin lase. See "Laser Action of Dyes in Gelatin", T. W. Hansch, M. Pernier, A. L. Schawlow, IEEE Journal of Quantum Electronics, January 1971, pp. 45-6. Interestingly, the longevity of the laser improves if you jiggle it.

Weird Words of Science 3 from chemistry notes

quantophrenic
A term used for an obsession with and exaggerated reliance upon mathematical methods or results. (Source Oxford English Dictionary). For a long time, chemists considered quantum theorists (of which I am one) to be quantophrenics. The following quote summed it up well: "Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry. If mathematical analysis should ever hold a prominent place in chemistry - an aberration which is happily almost impossible - it would occasion a rapid and widespread degeneration of that science." Auguste Comte, Cours de Philosophie Positive, 1830. Fortunately, quantum chemists persisted, and the methods they developed to treat chemical systems have become powerful tools for chemists in many areas.

The Invisible College from chemistry notes

I spent part of today preparing for a talk for I'm giving at Drexel on Wednesday, for their E-Learning Lecture Series. Jean-Claude Bradley (whose lecture is linked to the posts on chirality) is my host. He's been constructing on-line courses in chemistry, that are also taught in real-time. By the end of term, most of the students are not present in the classroom, but are invisible in some sense to the lecturer. The web allows us to construct an invisible university, where neither chronological nor spatial constraints apply to the community of scholars.

This is nothing new. In the 17th centure, Robert Boyle, whose name we associate with the inverse relationship between pressure and volume, was part of an institutuion known as the Invisible College. The Invisible College was group of natural philosophers working in England, which Boyle joined in the 1650s. This group eventually became the Royal Society of London for Improving Natural Knowledge, still operating nearly 400 years later.

Interesting tidbits about Boyle: He identified himself as an alchemist and believed that base metals (such as iron) could be "transmuted" into more precious metals such as gold. The study of the properties of gases is the precursor of "scientific chemistry", and was an active field in the 17th century (think balloons!). Even though general chemistry books refer to Boyle's Law, it is also attributed in some texts (principally in Europe) to Mariotte. Boyle authored The Skeptical Chemist, where he encouraged experimentation and observation, and Some Considerations Touching the Usefulnesse of Experimental Natural Philosophy, where he strongly supported the teaching of experimental science in schools (if you don't enjoy lab, blame Boyle).

Multiple Personalities 1: Wrists and snow from chemistry notes

Decoding the eponyms of science and medicine offers a quick history lesson. The same names sometime surface in multiple contexts. Some are Renaissance men, others come out of scientific dynasties (think the Thompsons) , still others are just cases of "mistaken identity" (Fischer projections and Fischer carbenes).

Today is the birthday of Marcel De Quervain, a Swiss geologist who has done significant work on the physical properties of snow. A recent paper on the application of manure (really!) to snow and its effect on the melting of the ice pack refers to De Quervain's work.

If you have wrist problems, you may have heard of Fritz De Quervain who in 1895 described the tenosynovitis that bears his name.

Any relation? Not to my knowledge. Connections? You can aggravate your De Quervain's tenosynovitis if you ski...in the snow

Philatelic takes on famous scientists of this era (and others) from chemistry notes

Earlier this month the USPS released a new set of stamps honoring four scientists: "some of the greatest scientists of our time, their pioneering discoveries still influence our lives today," according to John F. Walsh of the U.S. Postal Service's Board of Governors. Well, maybe! The four scientists are Barbara McClintock (geneticist), Richard Feynman (physicist), Josiah Willard Gibbs (thermodynamicist) and John von Neumann (mathematician/computer scientist). McClintock, Feynman and von Neumann are all more or less our contemporaries (their careers covered much of the last century)-- but Gibbs has been dead more than 100 years and I certainly would not count him "of our time".

Gibbs' name is familiair to almost any chemistry student - through the Gibbs free energy. J. Willard Gibbs (1839-1903) was the son of a Yale professor of sacred scripture, and himself worked at Yale. Gibbs was not paid a salary for the first 9 years of his job at Yale. It was only once he had a job offer from Johns Hopkins University in Maryland that Yale began to pay him. He gained little recognition for his work during his lifetime mainly because of his inability to communicate his ideas so that others could understand the concepts he was discussing.

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With thanks to Tony Addison of Drexel for pointing me to the stamps.

I Wish I'd Made You Angry Earlierfrom chemistry notes

Yesterday was Max Perutz's 101st birthday. Perutz won the Nobel in 1962 for his work in x-ray crystallography. I recently found a collection of essays he'd written (I Wish I'd Made You Angry Earlier: Essays on Science, Scientists, and Humanity and given the family history (both of my husband's parents were crystallographers of some note) picked it up to read.

The title essay is about Perutz's graduate research, where he and a colleague come close to unlocking the secret of the α-helix. Two things struck me in this essay. First was the origin of the terms α-helix and β-sheet. Bill Astbury, a crystallographer working with the Wool Research Associate in England had taken two crystal structures of a sample of kertain. The first diffraction experiment (the α sample) showed a simple and characteristic diffraction pattern, the β experiment, done after heating and stretching the sample gave a different pattern. Astbury concluded that the first pattern must arise from a coiled structure, the second from straight strands of amino acids laid out in a repeating pattern. Thus, theubiquitous α-helix and β sheet.

Perutz and Kendrew tried to crack the problem of figuring out just how the amino acids wound into the coil by building a model using a broomstick with nails hammered into to indicate the repeat (5.1 A). Even with all the sophisticated computer visualization (literally) at my fingertips, there is something about a tangible model that beats it all, even if I end up resorting (as I have) to using chickenwire. A few years ago, I solved a structural mystery by making a paper-doll like model of the molecule of interest.

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The title? Pauling and Corey solved the mystery of the α-helix before Perutz and Kendrew. Reading the paper so angered and frustrated Perutz that he was able to design and execute the crucial experiment that proved beyond a doubt that Pauling and Corey were correct. Bragg, Pertuz's Ph.D. advisor told him that he'd wished he'd make him angrier earlier!

Better Breathing Through Chemistry from chemistry notes

Dr. Andy has posted about the marketing of an asthma control assessment by Glaxo-Smith-Kline (who not coincidently markets Advair as a treatment for asthma). I haven't seen any of the commercials, but I fairly sure my 8 year old has. He showed up in the kitchen last week and asked if he should take a test about his asthma and take it to his doctor. His asthma is mild and well controlled and I simply reminded him that if he had questions about it, he could ask at his next check-up. I wondered where he got the idea about the test, and since I don't watch TV, it took Dr. Andy's blog to point me in the right direction. The marketing is effective.

Last night sleep here was interrupted, in fact, by an asthma attack. Things resolved well using albuterol, but at 3 am I couldn't help wondering what I would have done 100 years ago, besides worry. Turns out inhalation devices for the treatment of asthma have been around since the 19th century at least. See examples here. Albuterol, a β-agonist, dates to the 1970s and is the most commonly used inhaled agent in its class in the United States. On the molecular level, it activates the β-2 receptor on the muscles surrounding the airways, relaxing them. It is fast acting, which was certainly a benefit last night. The structure is relatively simple.



The molecule is chiral and albuterol is marketed both as a single stereoisomer and (most commonly) as the racemic mixture.

Crestor, grapefruits and Italian towns have what in common? from chemistry notes

In the current issue of the journal Circulation, there is a study supporting concerns that Crestor (known to chemists as rosuvastatin) is riskier than other statins. When you take most statins you can't drink grapefruit juice, which sounds like an odd prohibition, but for which there is a biochemical basis. Crestor is unusual, in that grapefruit juice does not affect the metabolism of the drug. So what is it in grapefruit juice that mucks up the behaviors of the statins?

Imbibing grapefruit juice (but not orange juice) raises the blood levels of the statins, making them more potent in terms of lowering cholesterol, but also more toxic. A component of the grapefruit juice apparently inhibits an enzyme responsible for the breakdown of the statins in the liver. One possible culprit is bergamottin.

If you drink Earl Grey tea, scented with oil of bergamot, this name may seem familiar to you. Etymologically, bergamottin is derived from the same source as bergamot, both stem from a citrus tree Citrus Bergamia , named for a town in Italy, Bergamo, where such trees presumably grow.

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The cholesterol-lowering statins were first isolated from molds. The first (Lovastatin aka Mevacor) was isolated in the 70s from Aspergillus terreus .

Weird words of science 4 from chemistry notes

statins Anyone who reads the newspaper, listens to the news or watches TV will clearly associate the word statin with cholesterol, but in fact the source of the common name of this class of drugs comes from another biochemical pathway entirely. The suffix -statin was coined in 1973 in an article in Science by Brazeau: "We propose to name the peptide described here somatostatin, from somato(tropin), a pituitary factor affecting statural growth, and stat(in), from the Latin 'to halt, to arrest'." The cholesterol stopping statins were isolated around the same time (there are trends in scientific names, just as there are in baby names) and made use of the new suffix. A quarter century later in common use we've forgotten that there are other statins, such as somatostatin and nystatin, with no structural or theraputic relationship to the profitable cholesterol lowering agents.

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For an intersesting take on trends in baby names, see Freakonomics, serialized here at Slate.

Made from sugar, so it tastes like sugar from chemistry notes

I was reading the South Beach Diet book the other night (never mind why!) and noticed that the author recommends (without giving an explicit brand name) an artificial sweetener derived from sugar. A friend on the diet will only use sucralose, saying that the only one that "works right" with the diet. (The SB book itself says it doesn't matter, it's just personal preference.) A recent ad campaign claims, "Made from sugar so it tastes like sugar". As a chemist, I read this and cringe!

Sucralose is made by chlorinating sugar, that is replacing 3 of the 8 hydroxyl (OH) groups with chlorine atoms. [Ed: Yes, I know, chlorine gas, Cl₂ is poisonous, but this doens't mean that anything contains a chlorine atom is a poison, despite the claims here. But that's another post!] Such a substitution can utterly change the properties of the molecule, including it's taste. For example, replacing the OH group on ethanol (the alcohol we drink) produces an effective refrigerant (it's used as a local anesthetic, in fact), but not a good drink! An even smaller change, the inverting of two groups on the molecule that makes up spearmint oil, changes it into caraway oil (and you certainly would never say that mint tea tastes like rye bread). Bottom line, there is no reason that any given derivative of sugar will taste anything like sugar!

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Much is actually known about the molecular characteristics necessary for sweetness.

Maxwell's demon from chemistry notes

James Clerk Maxwell was a Scottish mathematician and physicist. He is perhaps most famous for his extension and refinement of Faraday's equations describing magnetic and electric fields. He reduced the necessary set of equations to four simple partial differential equations, the eponymous Maxwell equations, publishing the work in 1873.

He also worked in thermodynamics, lending his name to another set of four key differential relationships (the Maxwell relations). He also independently derived the Boltzmann distribution of the kinetic energies of gas molecules. Maxwell's demon, a "finite being" who opened a door between to a box of molecules, letting them in and out depending on the amount of energy they had was a rhetorical device Maxwell used to show that entropy and heat flow were, at their core, statistical phenomena.

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Lord Kelvin (aka William Thomson) applied the demon tag, Maxwell used the term "finite being"!

The French Connection: Napoleon and Laplace from chemistry notes

The Laplacian is a scalar (not a vector) differential operator that appears in important equations in physics and chemistry, such as Schrodinger's wave equation.



The operator, and the quintessential equation it appears in are named for Pierre-Simon Laplace, an 18th century French mathematician, who made critical contributions to the development of calculus and classical mechanics. The Laplace equation
appears in Laplace's Treatise on Celestial Mechanics, however, it was not original to Laplace, having been known for almost a half century.

Chemists typically write the Laplacian using the symbol ∇, however, some mathematicians will use Δ instead. Since chemists associate Δ with "change in" or "heat", depending on context, the source of the preference is obvious! The Laplacian can be constructed for higher dimensional spaces. The symbol used for the operator in 4-dimensions (called the d'Alembertia after another French mathematician of the 18th century, the quarrelsome Jean Le Rond d'Alembert) is . I presume the symbol for the Laplacian in 5-D would involve a pentagon?

What do Laplace and d'Alembert have to do with Napoleon Bonaparte? Laplace was appointed by Napoleon to the Ministry of the Interior, but removed from his post in less than a year for what Napoleon later wrote was his habit of bringing "the spirit of the infinitely small into the government." Napoleon was 14 when d'Alembert died, as far as I know, there is no direct connection.

The Hidden Women of Science from chemistry notes

The Chronicle of Higher Education has an article this week on the election of a record number of women to the National Academy of Science, the obstacles women face, and a forum on issues related to women in science. The words "women in science" tend to bring up the image of Marie Curie, Dorothy Hodgkins or, in a peevish moment, Larry Summers. These are not the women in science I'm thinking about. It's the hidden women, the women behind the scenes that fascinate me. The truly hidden women of science are the wives of the scientists who make it possible for them to work 80+ hours per week and still play golf.

A recent look at Princeton's cadre of science faculty, which is reasonably representative, one might presume of the larger cohort of top research universities, reveals that the majority of male faculty enjoy a stay at home spouse. None of the female science faculty are so blessed. On the face of it, this is not surprising, since the bulk of women with doctoral degrees are married to highly educated spouses. In these days, men (highly educated or not) do not frequently choose to stay out of the job market and work in the home. Women have more freedom to make such choices in the current social millieu. So what? So, the guys with spouses who work at home have staff. Someone to coordinate the school activities, the after school activities, the errands, the house repairs (who stays home for the plumber, eh?), the grocery shopping, car repairs, cooking, cleaning. Yes? In households where both work, say as science and math faculty, someone still must do those chores! And these things do take time. Outsourcing is expensive, particularly for younger faculty, and in some cases just not easily accomplished. (Again, who stays home for that plumber? Our toilet was stopped up for a week until one of our schedules was open enough to allow for someone to be here for the extended period of time required. I was trying to submit a paper, and my session timed out twice while I was trying to help the plumber identify the object that was stuck in the @#$% thing.)

So when we think about women in science, we must realize that much of the top-ranked academic research enterprise depends very heaviliy on the unpaid labor of women -- in science.

Book Meme (from Snail's Tales) from chemistry notes

Aydin tagged me last week, but I haven't had a chance to respond until now.

Number of books I own: The collection is hovering around 5000 volumes and I've committed to a "one in-(at least) one out" philosophy, so that is its size for the foreseeable future. There are no more walls to put bookshelves against - so unless we convert the kids' room to compact shelving (and don't think I haven't dreamed about it!)...this is it.

Last book I bought: Spirit of Fire by Ursula King. A biography of Teilhard de Chardin, a Jesuit paleontologist and theologian.

Last book I read for the first time: I wished I'd made you angry earlier. This series of essays by Max Perutz, a Nobel prize winning x-ray crystallographer is wonderful to dip into. I didn't read them in order, but opened it up at random to find yet another gem. There is an essay about Haber, Germany and the war effort, and another one about the discovery of the α-helix.

Four books that have influenced me:
Lady with a Spear by Eugenie Clark. Women in science, working your way through school, and adventures in the Pacific, this book has it all. Dr. Clark's sheer joy in the science comes through, and even though I didn't end up as an oceanographer, I think I take as much pleasure in my work as she does in hers.
The Seven Storey Mountain by Thomas Merton. The courage to change your life, or let it be changed in dramatic and sometimes, difficult ways. The book that inspired me to begin praying the Liturgy of the Hours on a regular basis.
The Liturgy of Hours
Marie Curie by Eve Curie. When I was younger, it was such a romantic tale -- fainting in a garret, so entranced by the science that she didn't eat (or couldn't afford to!) ; meeting her husband, another scientist. When I was older, coping with being a young widow...

Five bloggers to tag:
Respectful Insolence
The Examining Room of Dr. Charles
Geeky Mom
See Jane Compute
Scrivener

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I cross posted this on my other blog (Quantum Theology).

Glow in the Dark Kid from chemistry notes

"Mom, is it OK for me to go back to school?," asks my 11-year old wounded road warrior. We're driving back after getting his shoulder x-rayed - he broke my tail light (and his pediatrician suspects, his clavicle) after hitting my car with his new bike.

"Sure you can go back to school, why not?" "I'm radioactive now, aren't I?" "Ah....well, actually you are, but not from the x-ray!"

Slate magazine's Explainer column last week looked at the radioactivity of everyday materials in "Is Cat Litter Really Radioactive?". (The short answer is yes.) People living in the US are exposed to roughly 360 millirems of radiation a year. Most of this is from naturally occurring sources, such as cosmic radiation and radon (and cat litter). About 10% of the exposure is from your own body, which contains measurable amounts of carbon-14 and potassium-40, both are which are radioactive. Your basic banana contains about 47 μg of potassium-40. Crash Kid's x-ray probably exposed him to less than 10 mrems, about what he gets every year from flying to visit his grandparents in California. To put this all in perspective, an acute dose of 50,000 mrem could give you radiation sickness.

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Oh...the fracture is limited to the tail light!

Why can't a woman be more like a man? from chemistry notes

A post on Harvard's new $50M initiative for women in science by a woman in IT, brings to mind Henry Higgin's lament in "My Fair Lady": Why can't a woman be more like a man?

Progressive Indian-American Woman notes

. Seems to me they want to spend $50M to get more women and minorities in. But they are not really looking towards changing their system. Indeed there isn't really even an awareness that they might need changing. It is still a case of "how can we make you more like us?", rather than "women, what do you need so that you can strike a balance?"

On this coming Friday, I get a chance to speak on these issues at the Cosmopolitan Club in Philadelphia.

Film Studies from chemistry notes

In the late 19th century, Wilhelm Roentgen discovered the x-ray. X-rays are light, with very short wavelengths (on the order of 10s of Angstroms) relative to visible light (on the order of 1000s of Angstroms). Roentgen was experimenting with various materials to see what might be opaque to the new rays by placing samples in front of a barium platinocyanide screen which fluoresced on contact with x-rays. When putting a block of lead in the way, he noticed the skeletal image of his own hand on the screen. Roentgen published a paper less than 2 months later detailing his discoveries, but it turns out that the first x-ray image had actually been made two years before at the University of Pennsylvania, and filed away, its significance unrecognized by the researchers there.

The new rays were all the rage - as an article in McClure's magazine shows. Many of the images in the article were produced at the Urania in Berlin by Spies. The Urania was a scientific theater, where spectators paid to see new scientific discoveries (and other interesting phenomena) demonstrated and explained. The x-ray at the top of this post is of Professor Spies' wife's hand.

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Science as performance -- a new funding model? Set up the lab, train a guide and sell tickets to the latest new discovery.

The Topology of the Tangled Bank from chemistry notes

The latest edition of the Tangled Bank is up at geomblog. The emphasis is on math and physics blogging, but there is plenty for biology fans as always.

Elements of Trivia 1 from chemistry notes

How cultured is your chemistry? Test your knowledge!

What element takes its name from the Greek for lead? (Hint: It's not lead and was used in medieval illuminated manuscripts.)

Weird Words of Science 5 from chemistry notes

secular If you look up secular in most dictionaries, the only definition given is "non-religious" or "of the world". Hunting a bit deeper yields an astronomical meaning, coming from Roman usage where a secular event is one that happens once in long period (such as century). [The Latin root is saeculum, "age".] Astronomers refer to long-period effects as "secular" effects. The secular effects in an orbit can be found by finding the roots of the secular determinant, which has the same form as the determinant that arises in quantum mechanics' linear variation theory. The physicists working on linear variation theory noticed the similarity in form and used the same term.

The "Productivity Puzzle" and the "Impact Enigma" from chemistry notes

Remarks as part of a panel presentation on women in science, prompted by Larry Summers' remarks on the paucity of women in science for a joint meeting of the Cosmopolitan Club and the Franklin Inn club in Philadelphia.

I will confess to a guilty pleasure, I keep a blog. It's called the Culture of Chemistry, and for the most part it is a gentle riff on popular culture through the eyes of a chemist. Last week I posted a short piece called "The Hidden Women of Science" -- and overnight the number of readers quadrupled. The post was prompted by an article in the Chronicle of Higher Education about the record number of women elected to the National Academy of Science this year and reads in part:

"The words "women in science" tend to bring up the image of Marie Curie, Dorothy Hodgkin or, in a peevish moment, Larry Summers. These are not the women in science I'm thinking about. It's the hidden women, the women behind the scenes that fascinate me. The truly invisible women of science are the wives of the scientists who make it possible for them to work 80+ hours per week and still play golf.

A recent look at Princeton's cadre of science faculty, which is reasonably representative, one might presume, of the larger cohort of top research universities, reveals that the majority of male faculty enjoy a stay at home spouse. None of the female science faculty are so blessed. So what? So, the guys with spouses who work at home have staff. Someone to coordinate the school activities, the after school activities, the errands, the house repairs (who stays home for the plumber, eh?), the grocery shopping, car repairs, cooking, cleaning.....

So when we think about women in science, we must realize that much of the top-ranked academic research enterprise depends very heaviliy on the unpaid [and unacknowledged] labor of women -- in science."

The post provoked various comments on my blog and the blogs of others, by both men and women. One male computer scientist frankly acknowledged that his wife's willingness to take on these tasks made it possible for him to spend the hours necessary; a male English professor notes that he does the same so that his wife can make partner in her law firm, and that reading my commentary he realized that he was a "man of the law" in the same way; a woman computer scientist wondered why (with respect to Harvard): "there isn't really even an awareness that they might need changing. It is still a case of 'how can we make you more like us?', rather than 'women, what do you need so that you can strike a balance?'"

I'd reframe Nandini Pandya's comment and ask, what do we - men and women both - need to be successful, productive and well-balanced scientists without recourse to the hidden women of science (or the missing men of law!).

A couple of years ago I gave a paper at a international conference. There had been an after-dinner talk - the first given by a woman at this meeting in its 30-year history. Afterward, a clump of chemists lingered by the elevators, dissecting the talk, when suddenly an older colleague blurted out that science was, he thought, "a grim life for a young woman." He went on to say that you could neither do enough science to be taken seriously, nor take adequate care of your children, so it is rather a lot of drudge work, without any chance of reward. I certainly had not found my life to be "grim" at all. I enjoyed what I did as a chemist and as a parent. I am a successful scientist - tenured, promoted, on a list of highly cited scientists - and had managed much of this while raising two young sons who seem to be turning out reasonably well. (My kids read about this in an essay published this month and my youngest was aghast that anyone would think that a scientist could not be a great Mom - who else has a mom that can help you extract DNA in your own kitchen). Let's just say that my adversary's response, "Well, la-di-da for you!" did not exactly encourage further serious discourse on the issue. I hate to say it, but he does have a point: and one that is supported by research.

The National Survey of Faculty, based at Penn State, compared men and women in the fields of chemistry and English, noting that in both fields at any rank, at any type of institution, women faculty are less likely then men to be married or in committed relationships. The average number of children per woman faculty member is also substantially lower - again regardless of discipline, rank, or type of institution. The survey's authors attribute this directly to "bias avoidance behaviors" in women. Research has shown that time = papers, i.e. productivity (as measured by number of publicationss) is strongly correlated to the number of hours invested in research [M.R. Nakhaie "Gender differences in publication among university professors in Canada" Canadia Rev of Sociology and Anthropology 39 (2): 151-179 May 2002].
Restricting the hours restricts the output, and research shows that what we think is true - is in fact true: restricting the output reduces the chances for promotion. [J.S. Long, P.D. Allison, R. McGinnis, "Rank Advancement In Academic Careers - Sex-Differences And The Effects Of Productivity"] Women know that having a family will cost them, this is the "bias advoidance", both in terms of the hours of domestic work that their male peers not have to invest (men, on average, contribute 10 hours a week to a household, and adding children to the mix does not increase their contribution), and perhaps also in their reputation for academic seriousness. It is a Faustian bargain that women must strike—sacrifice your immortality for scholarly heft.

Scholarly heft is hard to quantify, and we often consider hours worked and papers published as the measure of the quality of the science. Hence Summer's comments that women aren't able or perhaps willing to work the 80+ hours needed. Are they needed? Well, certainly the research suggests they are needed to produce lots of papers. The "productivity puzzle" was proposed in an essay by Scott Long in the early 1990s: why aren't women scientists as productive as men? Recent research has shown that when you account for factors such as prestige of institution, marital status and effort invested (read time) there isn't a puzzle, the differences fade. Which suggests that inherently, women can be successful in science in the traditional way (publish lots of papers), as long as they have the time to invest.

The flip side of the productivity puzzle was the "impact enigma" - women's papers (in biochemistry, the field studied) are cited much more frequently. Why? Even given that the cohort of women studied were in more "marginal" positions, their research appears to be more valued by peers than men's. Is it that each paper must count for more, if you get one chocolate bar a year, it had better be Scharffen-Berger and not Hershey? The jury remains out on the reasons.

President Summers wanted to provoke a conversation, so I will respond in kind and ask two questions:

First, is a model in which depends on "hidden" contributions of women, sustainable in a cultural moment in which women are getting more of the bachelor's degrees than men? Is it fair to those, single parents, singles and women, who do not have access to the same support systems? And, in the end, is this system the most productive for society? My mother-in-law, an X-ray crystallographer, was married to another scientist, and faced productivity issues (a postcard found in her files congratulates her on a productive sabbatical, two sons and a new crystal structure solved). Mildred Dresselhaus, a highly productive and well-regarded materials scientist, at MIT is married to another scientist. If we took one of the two of the pair out of play in either of these partnerships, are we losing more than we are now (since presumably neither partner is as productive as they might be if each had a support staff)? Can we afford to lose 1/2 the pair, when we might have almost two? Certainly the answer to the last is no! To put it more provocatively, would some of Harvard's fifty million dollars be better spent creating a concierge service for faculty, than for more panel discussions?

Second, to what extent do we confuse quantity of publication with quality of work? Is the solution to the "impact enigma" to consider quantitatively the contribution of a scholar's work to the culture at large? If we made the shift to consider impact rather than sheer mass of publication, perhaps then the need for the heavy investment of hours would fade, the hidden women of science (and men of law) could go on to other things and the productivity puzzle would be solved as well!

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Notes

Nandini Pandya has a wonderful essay on these issues being published this week. See her blog at Progressive Indian-American Woman

Christiane Nusslein-Volhard, who won the Nobel prize in Medicine in 1995, is well aware of this issue and is using her prize money to fund household help and childcare for women scientists in Germany. See Lisa Belkin in the NY Times 6/5/2005: "What a Working Woman Needs: A Wife". (Dr. Anna Meadows of CHOP pointed me to this article.)

Some of the material in here comes from an essay I wrote entitled "Elemental MoThEr" collected in Parenting and Professing: Balancing Family Work with an Academic Career (edited by Rachel Hile Bassett, Vanderbilt University Press, 2005) and published this month. Another short excerpt is posted here.

Build your own supercomputer from chemistry notes

I'm enough of a geek to remember the excitement of running my first job on a supercomputer (in 1984 on a Cray X-MP). That machine ran at about 200 megaflops (floating point operations pers second) -- the laptop I'm typing on now is significantly faster. The present generation of supercomputers maxes out in the teraflop range, the current #1 machine is the Earth Simulator in Japan which clocks in at 35 teraflops!

Building and maintaining a supercomputer is an expensive business. There are some cheaper alternatives, such as beowulf clusters and grid computing, that let you spread problems out over a number of machines linked either by cables (the beowulfs) or over a network (grid). SETI@home is probably the most famous grid computing effort. Both methods require some kind of investment in a permanent infrastructure - what if you just wanted a supercomputer for day or two? You could ask for time on at one of the centers, or you could invite some friends with laptops over for pizza and build your own!

The FlashMob team has developed software that lets you link whatever computers you have lying around the house into an ad hoc cluster, run your huge computational problem, then unlink, have dessert and send everyone home. Download the software and give it a try!

The ACS Computers in Chemistry Division (I'm a past chair) and the Philadelphia section of the ACS are hosting an instant supercomputer event September 15 at Bryn Mawr. If you're in the Philly area and interested in computational chemistry, supercomputers, or just want to be able to say that your laptops was once part of a supercomputer, join us! More details coming later in the summer.

Flip-flops and MIPmaps from chemistry notes

Computer speeds are measured in flops and mips. A flop (or flops, more precisely) is a floating point operation per second. These days, teraflop machines define fast (tera = 10¹²), while gigaflop (10⁹)machines can be toted in a briefcase. A mips is a million instructions per second. Both flops and mips are difficult to compare between machines, since both depend on the instruction set used. Better to do a benchmark using something like LINPACK and compare times.

MIPmaps are an entirely different animal. The MIP part of the name is an acronym for the Latin multum in parvo or "much in a small space". MIPmaps are collections of pre-calculated chunks of an image that can be used to speed its rendering at different resolutions (say as you move closer to an object in a game). MIP is sometimes used as a shorthand for MIPmap.

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Floating point numbers are like sand, everytime you move one, you lose a little sand and pick up a little dirt.

Romancing the Stone from chemistry notes

Summer reading should be fun, and not science, but the mystery/romance novel I picked up to read at the swimming pool had a great physical chemistry twist in it. The Paid Companion by Amanda Quick is set in the 19th century and features an evil scientist who believes himself to be the next Newton, working to build a weapon that could destroy London. The penultimate scene finds the heroine in the fiend's underground laboratory, where he shows her the device he has built from 3 red stones (it's implied that they are rubies) and an electrical source. The device produces a thin red beam that chars everything in its path -- what could this be? A laser, perhaps? The word never appears, but those in the know, what else could it be? Physical chemistry is everywhere!

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Last year my physical chem students and I tried to build a laser (a dye laser, not a ruby laser) from scratch, and I now have a much greater appreciation for what it takes to get a working system. Interested in building your own laser in your basement? Directions can be found at Sam's Lasers

Dispatches from the Frontiers of Science from chemistry notes

This week I'm at a Gordon Research Conference (on Chemical Education Research and Practice). These are small conferences, meant to foster informal conversations between active scientists. They were founded 75 years ago by Neil Gordon, a chemist from Johns Hopkins. The ground rules for the conference are that no results may be cited from the conference, (so I can't post about the intriguing work I'm hearing about research in science education this week) so that presenters are encouraged to bring new, speculative, unfinished ideas to the table for active discussion.

I've heard Nobel laureates talk about current work, and sketch out their current thinking on unfinished problems, a rare and wonderful opportunity. Once, I'll admit, I heard a talk from a prominent scientist that repeated work of 15 years before, but generally the talks are interesting, if not all quite at the frontiers of science as Neil Gordon imagined them.

The summer conferences are held in New England at colleges and boarding schools. You stay in the dorms, eat in the cafeteria and have afternoons free to take a hike with colleagues and talk science. I have a friend who calls it summer camp for chemists!

Weird Words of Science 6: adiabatic from chemistry notes

adiabatic Describes a process in which no heat is gained or lost by the system. Comes from the Greek for not (α) through δια) passable (βατωσ). In other words, the heat doesn't pass through. The terms seems to have been coined by William Rankine in 1859.

Decode this one, coined in the 18th century? adiapneustia

Read about science, listen to science, do science! from chemistry notes

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The Scoop on Thawing from chemistry notes

My mom made delicious home-made ice cream. When I was a kid, she made it in a turquoise electric crank machine, the ice had to be chopped up with an ice pick and added, along with layers of rock salt to the bucket. The machine needed careful tending as the motor whirred away, a hot job on what was sure to be a hot day, but the reward for layering in the salt and ice was to lick the paddle.

Stephen Metcalf has a review of the next generation of ice cream makers up at Slate magazine: The Inside Scoop The next generation includes those with built-in freezers and and some with a gel filled canister you pre-freeze -- they still make the ones like my mother used and ones you can use at a picnic to soak up excess kid energy. Metcalf notes that

"More expensive machines contain built-in freezers, with obvious advantages: A built-in compressor maintains a constantly low temperature throughout the freezing process (whereas a gel canister starts to thaw the instant you remove it from your freezer), and consecutive batches can be made without waiting 24 hours for the canister to re-freeze."

There is physical chemistry here -- even though the gel canister does begin to thaw as soon as you take it out of the freezer, it doesn't actually get warmer immediately. As the gel thaws, the temperature remains constant until the thawing is complete. Why? A very simple-minded way of thinking about it, is that all the energy going into the canister goes into melting the gel, so there isn't any "left-over" to raise the temperature. Don't believe me? Take a glass of water and ice and stick a thermometer in it. Wait a while, stir (the stirring is important), and take it again. If all the ice hasn't melted yet, the temp should be unchanged.

TV Science: I Love Lucy #36 from chemistry notes

I'm teaching a one day workshop on chemical kinetics to high school students tomorrow (part of Bryn Mawr's Science for College program). The relationship of the rate of a reaction to it's mechanism (the individual steps that produce the overall molecular transformation) is a key principle underlying the study of chemical kinetics. To explain this, one text refers to the episode of "I Love Lucy" where Lucy and Ethel work in a candy factory (while Ricky and Fred try their hands at keeping house - but that's another post. The candy boxes appear only as fast as the slowest step in the process (Lucy and Ethel wrapping) - reactions go no faster than the slowest step, called the rate determing step (or RDS).

Would Ben Franklin have Blogged? from chemistry notes

Read Carnivalesque #6 at History News Network to see Cliopatria's take on Would Ben Franklin have Blogged?, which cites a Culture of Chemistry piece on Robert Boyle's Invisible College

The Boys of Summer Wear Titanium from chemistry notes

A recent article (first published in the NY Times) notes the popularity of titanium coated necklaces with baseball players. Why? Supposedly it helps them have more energy. The necklaces are made by Phiten, and according to one of their sales representatives:

Everybody has electricity running through their bodies," said Scott McDonald, a Seattle-based sales and marketing representative for Phiten. "This product stabilizes that flow of electricity if you're stressed or tired."

Phiten says their process produces an " aqueous solution of titanium that is considered insoluble in water."

I think what they mean is that titanium metal is not terribly soluble in water (indeed true), their process "carbonizes it" (so now it's no longer the metal and it's conductivity, if you believe that is what is 'stablizing the flow of electricity', changes). If you want to wear non-metallic titanium, try sunblock containing titanium dioxide. It's cheaper, both blocks and scatters UV radiation, and the lotion base will improve dry skin!

The only flow this product is helping is the cash flow of the company selling it!

Oxygen is a blue crystalline solid at room temperature from chemistry notes

Twenty-five years ago I went to a seminar with this intriguing title. The photographs of a deep blue substance trapped in a diamond vise were stunning, particularly in a time when black and white slides dominated the colloquium scene. Things get even more colorful if you explore the phase diagram of oxygen at higher pressures and temperatures (beyond 650 K and 16.7 GPa). A recent paper in Physical Review Letters (PRL 93, 265710, [2004], "New Phase Diagram of Oxygen at High Pressures and Temperatures", M. Santoro, E. Gregoryanz, Ho. Mao, and R. J. Hemley) revealed new solid forms of oxygen. The ε solid phase is a red crystalline form.

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What's a GPa? A gigapascal...or about 10,000 atmospheres.

Read early entrys about phase diagrams and literature.

Organic Synthetic Mystery from chemistry notes

My dad is a retired organic chemist, who suggested we try this reaction. So what does it make?

To a 2-L jacketed round reactor vessel (reactor #1) with an overall heat-transfer coefficient of about 100 Btu/F-ft²-hr add 530 cm³ gluten, 5 cm³ NaHCO₃, and 5 cm³ NaHCO₃ with constant agitation.

In a second 2-L reactor vessel with a radial flow impeller operating at 100 rpm add 235 cm³ partially hydrogenated tallow triglyceride,
175 cm³ crystalline C₁₂H₂₂O₁₁,
175 cm³ unrefined C₁₂H₂₂O₁₁, and 5 cm³ methyl ether of protocatechuic aldehyde until the mixture is homogeneous.

To reactor #2 add two calcium carbonate-encapsulated avian albumen-coated protein followed by three equal portions of the homogeneous mixture in reactor #1. Additionally, add 475 cm³ theobroma cacao and 235 cm³ de-encapsulated legume meats (sieve size #10) slowly with constant agitation. Care must be taken at this point in the reaction to control any temperature rise that may be the result of an exothermic reaction.

Using a screw extrude attached to a #4 nodulizer place the mixture piece-meal on a 316SS sheet (300 x 600 mm). Heat in a 460K oven for a period of time that is in agreement with Frank & Johnston's first order rate expression (see JACOS, 21, 55), or until golden brown.

Once the reaction is complete, place the sheet on a 25 deg. C heat-transfer table allowing the product to come to equilibrium.

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Synthetic method reported in Chemical & Engineering News (C&EN, Jun 19, 1995, p. 100) and attributed to Jeannene Ackerman of Witco Corp.

The 13th Skeptics' Circle from chemistry notes

about Phiten's The Skeptics' Circle is up at Respectful Insolence, hosted by Orac. I'm not the only one skepticaltitanium necklaces.

Sink or swim? from chemistry notes

It's been hot in the coastal foothills of California (afternoon highs ranging from 102 to 107F), and we've been cooling off in the pool and with a steady supply of cold drinks. But the search for truth marches on, even on vacation, and in that spirit we did a little experimentation this afternoon. Does Diet Coke ™ really float, while the high calorie stuff sinks? Not having any on hand, we substituted Diet 7-Up and Sierra Mist (non-diet) and dropped away. Sure enough the diet stuff floats.

Why? The cans are the same size, but the non-diet soda weighs more. Why? Do calories have mass? One of my brothers suggested it was because sugar is a heavier molecule than aspartame (NutraSweet ™). This is true - sucrose weighs in at 342.3 daltons while aspartame comes in just under 300 (294.3 daltons), but not the solution to the mystery. The relative sweetness of the two molecules is the key. You need less than 100 mg of aspartame to equal the sweetness of the roughly 40 g of sugar in the regular soda. Both have the same volume of solution, the sugar one is denser than water and sinks. But wait...why isn't the diet stuff denser than water, too? It should be just a little heavier than just plain water not? True, but the air bubble in the top of the can is just enough to offset it.

A holiday at the intersection of biology and chemisty

I'm on vacation in California taking care of my dad's 10 acre farm while he is out of town. The resident fauna include 2 watch llamas and a small flock of Barbados sheep (self-shearing). When I arrived the flock had 11 sheep - now there are 16. If you're counting (and I am, every morning), that means that 5 new sheep have appeared. Four of them were born in the space of 2 hours a week ago last Saturday in the 107 degree heat of the afternoon. Birth is a messy business, and in the end I sacrified not one, but 2 white t-shirts to the process.

After the biology had settled down and was nursing happily, I turned to chemistry to get the stains out of my shirt. My dad (experienced in these matters) advised no bleach, and soaking in a strong salt solution. Why no bleach? Bleach is an oxidant, and "removes" (or at least decolorizes) many stains by oxidizing the carbon-carbon double-bonds which are responsible for the color. The red color of blood comes from the oxyhemoglobin. Oxidizing the iron in the hemoglobin produces iron oxide - aka rust - not necessarily an improvement on the front of your t-shirt.

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One of the new arrivals.

Astronaut Trainingfrom chemistry notes

The Midstate California Fair is on in town. Last year we went to see friends ride in a roping competition and the bull riding. This year, we did the rides. Crash Kid's undoing was the Gravitron, which runs at 4 G. The ride was developed based on the centrifuge used by NASA for astronaut training. According to Crash and his sib, there is no sense of movement inside, just a feeling of weight and the ability to climb the walls or hang upside down. They also report that while once is fun, twice risks the stability of dinner.

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The Real Thing



Astronaut Walter M. Schirra Jr. prepares to enter gondola of centrifuge which is used to test gravitational stress on astronauts training for space flight. Schirra became the pilot of the Mercury-Atlas 8 six-orbit space mission. Photo is public domain from NASA.

Oil on the waters from chemistry notes

Newsweek's Blogwatch highlights PZ Myers' Pharyngula blog and his altercation with George Gilder. While that post might have inflamed the blogosphere, the same issue considers a publication that recommends casting some calming "oil upon the waters".

A short text box highlights a recent paper (Barenblatt, Chorin, Prostokishin in PNAS Natl Acad Sci. 2005 Jul 27, pre-publication on web) by three mathematicians: "A note concerning the Lighthill "sandwich model" of tropical cyclones". The authors try to show that the maximum wind speeds that can be obtained above water depend on the turbulence of the flow. If you reduce the turbulence of the flow, the winds increase dramatically. They speculate that large water droplets thrown into the air reduce the turbulence and thus result in increased winds. The last paragraph of the article notes that in the distant past, sailors poured oil onto the waters to calm storms. Newsweek notes that a surfactant might work, and you might leave with the impression that oil is a surfactant.

Surfactants (from "surface active agents) reduce the surface tension of a liquid. When the surface tension is reduced, the size of droplets formed from the solution also decreases. So surfacants in theory could reduce the formation of large wind-blown droplets. Oil forms a physical barrier, since oil and water are immiscible, that prevents the water from being touched by the waves. Oil molecules are much heavier than water and less likely to form large stable droplets in the air. So both might work to calm a storm, but in chemically different ways.

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My father spent much of his scientific career making surfactants. They see uses from the prosaic (read the back of your shampoo bottle, see something like sodium lauryl sulfate?) to the exotic (surfactants are used to treat premature babies' lungs).

Working up an appetite for momentum

This week we're "down the shore" as they say around here. We go to the same place each year and my kids have their traditional activities. For example, on the hottest day of the week we're there, we should rent a surrey (a pedicab with two seats and four sets of pedals -- this is not a light weight vehicle) and pedal it up and down the boardwalk for an hour, dodging pedestrians and other cyclists, until the parents (who provide most of the kinetic energy in this event) are soaked in sweat. The ride ends with a short ramp off the boardwalk, which this year Crash Kid was certain he could negotiate without parental assistance. Given his recent history with wheels, his parents were a bit less confident. The conversation quickly turned to momentum, and my spouse noted we had a lot of "m" in the buggy. My youngest thought this might stand for momentum. "Nope, that's 'p'!" his mom replied. Sensibly, he wanted to know why that letter!

Good question, and I'm not sure that I have a good answer for him yet. The lore seems to be that Newton used the term "impetus" in the Principia. Impetus is a Latin import, from petere to seek. Interestingly, the Indo-European root of petere is pter which gives us the Greek pteron (wing), and eventually helicopter. Petere is also the root of the English appetite -- which pedaling that surrey certainly worked up.

If anyone has other ideas about why "p" is used for momentum, I'd love to hear them!

Podcasting

Prompted by a talk last spring given by Jean-Claude Bradley of Drexel's chemistry department, I decided to try podcasting and webcasting my fall course. I submitted the podcast feed to Apple's iTunes, and wondered how many people outside of my course might be interested in listening. More than I might think, as Jean-Claude's post suggests.

So if you're intersted in following a quantum chemistry course, subscribe to the podcast through iTunes, or go to Chemistry221 where you can get both the podcast and a webcast.

Replacing the Blackboard: Using Mathematica to Teach Modern Chemical Kinetics

In a talk I gave today at the American Chemical Society fall national meeting, I argued that moving the teaching of physical chemistry beyond what can be done on the blackboard or with pencil and paper can alter not only course pedagogy, but profoundly change course content. Analytical solutions to the differential rate equations often receive the bulk of the attention in an introductory physical chemistry course. Does this reflect the current practice in the field? Should this be the emphasis students take away? I think not. In response I developed a Mathematica based document for teaching chemical kinetics which builds on the traditional framework of analytical solutions, but develops numerical methods in concert, rather than as a special topic and shows how these numerical methods can be used to explore more exotic reactions, such as those that oscillate, or even exhibit chaotic behaviors.

Resources mentioned in the talk, which I promised to post here are:

• POGIL:Physical Chemistry: A Guided Inquiry: Atoms, Molecules, and Spectroscopy, R. S. Moog, J. N. Spencer, J. J. Farrell; Houghton Mifflin: Boston, 2004.
  
• Physical Chemistry Online: Chem. Educator, 5 77-82 (2000) Deborah Sauder,* Marcy Towns, Betty Derrick, Alexander Grushow, Michael Kahlow, George Long, Danny Miles, George Shalhoub, Roland Stout, Michael Vaksman, William F. Pfeiffer, Gabriela Weaver, and Theresa Julia Zielinski
  
• Physical Chemistry in Context
  
• SymMath archive at Journal of Chemical Education
  Physical Chemistry, Metiu

Walking the tightrope: finding the timeless fundamentals in the context of modern physical chemistry

Today was a busy day, I gave another talk at the American Chemical Society meeting. This talk highlighted the ever present tensions in the physical chemistry curriculum between the expanding scope of modern physical chemistry and the timeless fundamentals. It was well summed up by one of my predecessors at Bryn Mawr - in 1913:

“The contributions to knowledge in the domain of physical chemistry have increased with such rapidity within recent years that the prospective author of a general textbook finds himself confronted with the vexing problem of what to omit rather than what to include.” - Frederick H. Getman, 1913

Can the curriculum be updated to include modern examples without compromising the basics? The NSF grant mentioned in my profile is for a new set of materials for teaching introductory physical chemistry that tries to bridge this gap. The materials draw from the recent primary research literature to illustrate key principles in multidisciplinary contexts. For example, the kinetics of first order reactions, illustrated in many current texts by a paper from 1921 reporting the rate of decomposition of gaseous N2O5, can be covered instead by following the racemization of amino acids used in the last decade to date archeological samples.

Resources mentioned in the talk, which I promised to post here are:

Talk less, they learn more

• Using the pause procedure to enhance lecture recall. [Ruhl, K. L., Hughes, C. A., & Schloss, P. J. (1987, Winter). Teacher Education and Special Education, 10, 14-18]
  
• The importance of lecture in general-chemistry course performance [Birk, J.P., Foster, J. (1993) J Chem Ed 70 179]
  
• Departing from Lectures: An Evaluation of a Peer-Led Guided Inquiry Alternative [Lewis, S.E., Lewis, J.E. (2005) J Chem Ed 82 135]
  
• From Traditional to Radical [J. N. Spencer, Thought and Action, The NEA Higher Education Journal, XVII, No. 2 Winter 2001-2002]
  
• A Guided Inquiry Chemistry Course [J. J. Farrell, R. S. Moog, J. N. Spencer, J. Chem. Educ. 1999, 76, 570-574
  

Do less, they learn more

• Effects of lecture information density on medical student achievement [Russell. I.J., Hendricson, W.D., & Herbert, R.J. (November, 1984). Journal of Medical Education, 59, 881-889]
  

Other resources:

• POGIL:Physical Chemistry: A Guided Inquiry: Atoms, Molecules, and Spectroscopy, R. S. Moog, J. N. Spencer, J. J. Farrell; Houghton Mifflin: Boston, 2004.
  
• Physical Chemistry Online: Chem. Educator, 5 77-82 (2000) Deborah Sauder,* Marcy Towns, Betty Derrick, Alexander Grushow, Michael Kahlow, George Long, Danny Miles, George Shalhoub, Roland Stout, Michael Vaksman, William F. Pfeiffer, Gabriela Weaver, and Theresa Julia Zielinski
  
• Physical Chemistry in Context
  
• SymMath archive at Journal of Chemical Education

Oure termes so lerned and queynte

Whan we be ther where we shul exercise
Oure elvish craft, we seme wondrous wyse,
Yet wil I telle them, as they come to mynde,
Though I can not them set right in their kind;
As sal armoniak, verdegres, boras;

Geoffrey Chaucer, "The Canon's Yeoman's Tale" in The Canterbury Tales

Protein chemistry seems like a hot area, but the name given to the basic building blocks of proteins - amino acids - is in fact quite "queynte".

Chaucer's junior alchemist tries to impress the other pilgrims on the road with his knowledge of the terms of his "elvish craft", treating fellow-travelers to a free-associating litany of chemical names, herbs and equipment. Some terms remain familiar to modern chemists, who still ply their trade with vials and crucibles and can pull potassium carbonate off their shelves, others have left their traces in the learned terms of today. Traditionally, the earliest known production of what Chaucer calls "sal armoniak", or ammonium chloride, was from the burning of camel dung in the temple of Jupiter Ammon in what is now Libya – hence "sal ammoniac" or salt of Ammon. This term is the root for "amine" and eventually "amino acid".

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See the whole Chaucerian litany in either Middle English or Modern English here. Want the full medieval experience? Images of the full text of two 15th century versions can be found here. You can read the Canon's Yeoman's Tale in (almost) it's original form thanks to the British Library.

Unnatural Amino Acids

Thirty years ago, it was assumed that all amino acid residues in naturally occurring polypeptides were in the L-form. We now know there are a few exceptions. For example, some polypeptide antibiotics found in fungi incorporate D-amino acids. It is thought that in most cases the peptide is synthesized with all L-amino acids, subsequently individual amino acids undergo enzymatically catalyzed epimerization. Only one such epimerase has been identified to date. The serine epimerase found in the venom of the funnel web spider, Agelenopsis aperta, selectively inverts the configuration of Ser-46 of the substrate omega-agatoxin-TK, leaving the other serine residue at position 28 untouched.

That the Programmer may Return to being a Mathematician

The solution of differential equations has taken on an entirely new dimension in the 75+ years since Erwin Schrodinger proposed approaching the description of matter waves using PDEs. The solution of many differential equations can now be found numerically, using computers. Grace Hopper, who graduated with a BA in math from Vassar, a women's college, in 1928. She worked on her doctorate in math at Yale and returned to Vassar as a professor of mathematics in 1931. During WW II she joined the waves and was assigned to the team running the Mark I - an early digital computer. Her work there eventually led her to design the first compiler - a translator which turns the "natural" language of the programmer into the binary code that the computer can read. Hopper hoped that then "the programmer may return to being a mathematician." The development of widely used symbolic algebra programs such Mathematica and Maple can be traced to Grace Hopper's work. Legend has it that Grace Hopper is the one who coined the term "bug" for problems with a computer, after pulling a moth out of one of the machines

Quantum Chemistry in the Time of Cholera

Slate magazine notes that occasional cases of cholera have been reported in the Gulf states, suggesting that the bacteria Vibrio cholerae is alive and well in that area. Recently, a group at Universtiy of Washington [O'Neal, Claire J., Jobling, Michael G., Holmes, Randall K., Hol, Wim G. J.
"Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP"
Science 2005 309: 1093-1096]has used x-ray crystallography to probe how the cholera toxin provokes such massive diarrhea when it takes up residence in the human gut. A figure from the paper shows how the overall 3-dimensional structure of the toxin changes when an activator protein binds to it. Protein chemists use the term "allosteric" to describe these mechanisms.

The picture is what interests me. I lectured on Monday about the probability density that you can compute using quantum mechanics (ψ*ψdτ). You can also measure the density experimentally using x-ray techniques, as Hol's group did for the cholera toxin. These sorts of pictures don't actually show the full density function, but a surface of constant electron density, usually around .002 e/bohr³, which seems small. A bohr is very small (0.529 x 10^-10 )meters, so this corresponds to about one mole of electrons (on the order of 10²³!) per cubic inch. This sounds like a lot, until you realize it's about the same as the number of electrons in a teaspoon of water!

The University Senate is not a Bath House

Mathematical Physics Seminar: Professor Hilbert, with the assistance of Dr E Noether, Mondays from 4-6, no tuition.

Winter 1916-17 catalog, University of Gottingen

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Emmy Noether was one of the greatest mathematicians of the 20th century - indeed of any century. Born in 1882 in Erlangen, Germany, where her father was a professor of mathematics at the university, she is known for her work in ring theory and non-commutative algebras. Her work in the theory of invariants proved essential to Einstein in formulating his general theory of relativity. In the late 19th and early 20th century, women were not permitted to officially matriculate at German universities, though they could petition individual professors to attend their classes. Noether attended courses at Erlangen, then at Gottingen, receiving her Ph.D. from Gottingen in 1907. She returned to Erlangen to assist her father, but continued her own mathematical work (much of which was published in the papers of others). In 1915, Hilbert (yes, real analysis and quantum afficiandos, that Hilbert - of Hilbert space) persuaded her to return to Gottingen. Though Gottingen refused to appoint her officially to the faculty there until 1919, Noether taught courses by having them advertised under Hilbert's name. Hilbert argued strongly for Noether's addition to the faculty, famously proclaiming, "I do not see that the sex of the candidate is against her admission as a Privatdozent. After all, the university senate is not a bathhouse."

In 1933, she fled Nazi Germany, accepting a visiting position at Bryn Mawr College. She died at Bryn Mawr Hospital in 1935; her ashes are buried in the Cloisters at Bryn Mawr.