Relishing Osmosis

Tomorrow is a day for iconic cooking. Turkey. Stuffing. And of course, cranberry sauce. At a dinner a few years ago, a friend produced an odd silver implement and asked the gathered group of foodies just what we all thought it might be. Would you believe a jellied cranberry server - just the right size, she pointed out, to cut the canned jelly! Turns out that serving pieces for jellied sauces, like tomatoes and cranberries pre-date the Ocean Spray cans, but it was a fun puzzle regardless.

For me, the whole question of canned or homemade sauce is moot, since I prefer cranberry relish. I make it by running a bag of cranberries and a whole orange through the food processor, then adding sugar to taste. Since it's best made ahead, so the flavors can blend, I made a batch yesterday afternoon when I went home for lunch between office hours. Straight from the food processor the relish is whitish, dry and pretty bitter. Stir in the sugar and not only does it become sweet, but a ruby syrup begins to appear.

This is a (literally) beautiful example of osmosis in action. The high concentration of sugar outside the cell walls of the finely chopped orange and cranberry mixture encourages the water within the cells to pass through the cell membrane to bring the concentrations inside and out into equilibrium. The sugar and cellular contents are too big to cross the membrane, so the best the poor cells can do is to dump their water out creating that lovely syrup. The process intensifies the flavors of the berry and orange bits as well, since they are essentially "dried".

After a day of cooking and now kitchen scrubbing, my fingers are wrinkled. [This is an osmotic process as well, in this case, the water is crossing the cell membranes into my cells, causing the out layer of skin to get larger, and wrinkle.] Or perhaps, not! As David Bradley points out in the comments to this post, the wrinkling of the skin on your fingers after prolonged immersion in water is not particularly well understood. My reading of the literature suggests that osmosis plays at most a small role.

Weird Words of Science: stochastic

I'm teaching a graduate course in mathematical modeling of natural processes. Many math modeling techniques rely on the random numbers and are more generally known as stochastic algorithms. A simple example is numerical integration. We used numerical integration techniques to the value of pi by (virtually) throwing darts at a circular target embedded in square (figure). The ratio of hits inside the circle to the total hits is pi/4. Stochastic comes from the Greek stochastikos "to take a guess", which itself derives from stochos - "target", so the target image above is apt.

Weird Words of Science: MythBusters at the Beach

We're on vacation this week, "down the shore" as they say in these parts. My cable deprived kids are enjoying evenings watching MythBusters and Nick. The episode du jour is Grenades and Guts, in which the myth that drinking a liter of Diet coke and eating a pack of Mentos will make your stomach explode is busted. In the process, the team wondered if the muriatic acid in the stomach was somehow blocking the usual spectacular reaction.

Muriatic acid is better known to chemists as hydrochloric acid. It gets its name from the Latin for brine - muria. It was also sometimes called marine acid, again calling to mind its briny origins (though the eytmology of marine is different than that of muriatic, the former comes from the Latin for sea, mare).

The first synthesis of hydrochloric acid is attributed to Jabir ibn Hayyan around 800 CE. Mixing oil of vitriol (sulfuric acid) and common salt (sodium chloride), produces hydrochloric acid: HCl.

Tin tears

Tin cries. Not tears, but when tin is bent it elicits a peculiar sound called by metallurgists a "tin cry". Indium also lets out a scream when deformed, as Michael Cassidy pointed out in an earlier comment.

You are hearing the sound made by a phase transition, a change in the structure of the metal at the atomic level. Indium in its crystalline form is tetragonal, when bent, the mechanical stress induces "twinning" in which sections of the crystal become mirror images of adjacent planes. Twinning plays a role in mechanical failure of metals subject to stress, the research literature goes back roughly a century.

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Listen to a recording of indium "screaming" made by Theodore Gray at the WGBH studios. It's an unnerving sound, more like a crackling than a scream.

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The photo is courtesy of David Hammon in the physics department at the University of Vermont.

Silver linings

Yesterday I had a round of minor surgery. When all was said and done, the surgical site was cauterized with what a nineteenth century physician would have called "lunar caustic" -- silver nitrate to a modern chemist or physician. I have to admit my first geeky thought was, "how does that work?"

Silver nitrate has been used for a long time as a cauterizing agent. In 1826 John Higginbottom, a British physician wrote An essay on the application of the lunar caustic in the cure of certain wounds and ulcers. My physician used a solution of AgNO₃, Higginbottom almost certainly used a solid mixture of silver nitrate and silver chloride, but other than that the basic treatment protocol hasn't changed in almost 200 years. Higginbottom notes that the application "smarts" and I would guess that it must have. I felt it, even with a good local anesthetic. The good 19th physician also prescribed adjuvant therapy ("I took away ten ounces of blood and administered purgative medicine") which my physician sensibly eschews!

So why is the stuff called lunar caustic? The caustic part is obvious, silver nitrate is an effective oxidizing agent for organic molecules, including biomolecules. Alchemists associated silver with the moon, its Latin name, argentum derives from "white, shining".

Perils of Summer 2: Mephitis Squared

It's war on my dad's farm: humans versus Mephitis mephitis, night time maneuvers complete with chemical weapons. Currently the skunks hold the high ground.

Last night my brother's dog threatened a skunk, with predictable results. The collateral damage included my shoes and feet. The Reverend's Wife produced a bottle of something guaranteed to elminate the smell and we decontaminated me and the dog on the lawn. I was more cooperative about being hosed down. The odor was overpowering, and even after twice deskunking me, my kids swore I still smelled of skunk.

Skunk musk is a mixture of low molecular weight thiols, sulfur containing compounds that have the basic structure ☐-S-H (where the box represents a functional group, such as methyl or butyl), and related compounds called thioacetates. Most thiols have a characteristic, and awful, odor. (Thioacetates don't smell quite so badly.) The simplest thiol is methane thiol, also known as methyl mercaptan, which is used to spike methane (natural gas) so that leaks can be detected. (Methane is actually odorless.) Humans can detect thiols at very low concentrations, less than 1 ppm, which explains why my kids could still pick up the odor.

Skunk odor can be neutralized by converting the thiols to less odiferous molecules. One way this can be accomplished is by reacting the thiols with hydrogen peroxide, which oxidizes the thiol to a sulfonic acid ( ☐-SO₃H), which has virtually no odor. Bleach (a strong oxidizing agent) will work as well. A similar technology is used to remove thiols from industrial waste water, where the thiols are converted to disulfides ( ☐-S-S- ☐), which are oils that separate easily from the water.

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Mercaptan comes from the Latin mercurium captans, something that seizes or captures mercury. Sulfur reacts very effectively with mercury, and one way to clean up a mercury spill is to sprinkle sulfur on the mercury. Thiol is Greek for sulfur.

If you need a recipe to remove skunk odor, try Humbolt's list. I can personally vouch for the effectiveness of the pet/human version. Note that tomato juice is not particularly effective.

1-para-methen-8-thiol is an uncharacteristically and pleasantly scented thiol more commonly known as grapefruit mercaptan.

More demystified chemical perils of summer...

Urrrrrr - it itches!

The spring was cold and so the itch to get outdoors once the warm weather arrived was hard to resist. As moms will tell you, scratching just makes the itching worse, and scratching even metaphorical itches can raise welts. Ask anyone who has heeded the siren call of summer and ended up with hives, or worse yet, encountered a patch of poison ivy.

My niece and I took a tour last week of the Mutter Museum in Philadelphia which has a great collection of wax models of dermatological pathology, used for teaching students in the days before slides and PowerPoint, including hives or urticaria. The name comes from the Latin for nettle, and the resulting skin wheals certainly bear some resemblance to nettle stings (as my youngest can attest after a close encounter with that plant). Histamine leaking from mast cells in the skin is responsible for hives' principal misery - itching.

True misery is reserved for those who have contacted Toxicodendron radicans - poison ivy - or a relative. These plants produce urushiol, which binds tightly to proteins in the skin. Molecules like this are called haptens, which comes from the Greek "to fasten". Antibodies don't recognize the small molecule until it fastens onto its target. Then the body reacts, in this case triggering the characteristic linear rash, and keeps reacting until the invader detaches from its binding site.

Despite the similarity in names between urticaria and urushiol, they come from different roots. Urushiol was first isolated from the Japanese lacquer tree - the urushi - by a Japanese chemist, Miyama.

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Other haptens can react with the same sites as urushiol, including substances found in mango skin and fresh cashew nuts, with similar unfortunate consequences.

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Urushiol isn't just a weekend gardener's nuisance, but can cause serious problems for fire fighters in working brush fires in areas such as the California hills, where poison sumac, another urushiol producing plant, thrives. The chemistry gives some clues to helping prevent and treat urushiol reactions. Application of an organic derivative of an absorbent mineral (bentonite) can soak up and trap any oil before it reaches the skin and binds- this is the principal behind the commercial product Ivy Block. Alternatively, something that binds strongly to the urushiol target but is not itself a hapten could act as a preventative. D-Limonene, found in citrus skins, has been floated as a possibility, but I couldn't find any evidence that it works!

Once the stuff has bound, you just have to wait it out. It takes a couple of weeks for the bulk of the urushiol-protein complexes to break down. In the meantime, steroids can reduce the inflammatory reaction and histamine blockers, H1 (like Benadryl) or H2 (Tagamet or Zantac) can provide some relief from the itch.

Indolent Molecules

I heard a colleague talk today at the MidAtlantic Regional Meeting of the ACS about his work with fluoroquinones. These molecules (which despite their name contain no fluorine) fluoresce, that is they "glow" when exposed to light. The process can be short circuited by binding another molecule, a quencher, to fluoroquinone. The research discussed the quenching behavior of tryptophan. Tryptophan is an amino acid, one of the building blocks of proteins. Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.

The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.

Agonists and Allergies

My mast cells are leaking histamine and I am miserable. Histamine is a small molecule that binds to receptors in a wide variety of tissues including, alas, the respiratory system. It happens to increase vascular permeability - in other words, it's causing fluids to leak through my capillilary walls and into my nose. Sigh.

I'm fighting back by taking a histamine antagonist, diphenhydramine to be precise. Antagonists bind to a receptor and block its response, in this case inhibiting the H1 histamine receptors in the respiratory tract (H2 receptors cluster in the gastrointestinal tract - and so H2 antagonist, like Zantac, are used to treat heartburn). Agonists are molecules that bind to a receptor and cause a response. Why would you want to take something that binds to a histamine receptor and provoke a response? Turns out there are a couple of drugs that are histamine agonists, including one for Meniere's disease and another that may have theraputic potential for diabetes.

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What does the term amine have to do with camel dung? Read about it here.

The Carbon Footprint of that Computer

Someone asked me over lunch yesterday if I was worried about global warming. "Worried enough to ride my bike to work through the hills of Bryn Mawr!" was my response. The conversation eventually turned to how much energy computers used - should you turn them off to save energy (and thereby reduce the amount of CO₂ being dumped into the atmosphere)? Their IT support had said to leave the machines on, on the grounds that the amount of energy used to restart them outweighs any savings from turning them off at night. I thought this was not true, and some back of the envelope calculations suggest shutting down from the night (even putting the machine to sleep is not sufficient) is 10 times more energy efficient than leaving it on.

Powering up my machine takes 3 minutes at full tilt. At 120 watts, this uses up about 22 kJ of energy. If I left it in sleep mode all night (at 3.5 watts), it uses 228 kJ. I save about 200 kJ of energy, if I shut it off for the night, rather than just put it to sleep. It comes to about 44 pounds of carbon dioxide a year. It's a drop in the bucket compared to the per capita amount of carbon dioxide produced in the US (19.8 metric tons in 2003) - about 0.1%.

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If you want to check your own carbon footprint, the EPA has a calculator.