Field of Science

Calm amino acids

It's the time of the year when I covet both energy and calm. A young friend sent me the link to these mints, which promise both in a single package. The secret ingredient is L-theanine (structure shown at left), a naturally occurring amino acid found in Camelia sinensis. Interestingly, the dried, fermented leaves of Camelia sinensis are what I use to brew my preferred pharmacological concoction to decrease stress and increase alertness: tea.

Some amino acids (roughly 20) are used by biological systems to build proteins (the working machinery of cells). The basic structural motif of any amino acid has a carboxylic acid group (COOH, which occurs in molecules like acetic acid, aka vinegar) along with an amine group (NH2 — certain amines are responsible for the characteristic odor of fish) as shown here:

Theanine is not one of the twenty plus amino acids used to construct proteins. There is some evidence that it works synergistically with caffeine to enhance cognitve performance, while moderating some of caffeine's less desirable effects.

So…do the mints work as advertised? I've no idea, but browsing the literature suggests that my students might reap some benefit from the multiple cups of tea I drink while grading their exams. A calm, but alert grader can't be all bad!

Related posts:

Where does the name amine, and hence amino acid come from?
How old are whales and what does this have to do with right and left handed amino acids

Oprah's take on quantum mechanics - and mine

I was checking my blog stats (read seriously procrastinating folding the laundry) and noticed that one of the search terms that was sending surfers to my other blog was "Oprah's take on quantum mechanics". She has one?

I promptly popped it into Google to see what would come up. I had to know.

I found out. The Law of Attraction. Think and you can change what happens. Proven by quantum mechanics. The Quantum Cleanse. (Don't ask - you don't want to know.)

Somehow the word "quantum" manages to sound simultaneously mysterious and scientific, and so people attach it to things that they want to sound simultaneously mysterious and scientific. Like diets and the power of positive thinking, or even theology.

I named my personal blog "Quantum Theology" as a play on the two fields I'm trained in: quantum mechanics and theology. Recently a friend of almost forty years wondered just exactly what was quantum mechanics - just what do I do for a living? Repair broken quantums?

When I say something is quantized, I don't mean it's mysterious, I mean that only certain values are allowed, and nothing in between. A good everyday example is your shoe size. You are a 5 or a 5 1/2, but never a 5 1/6. Off the rack shoes (are there any other kind these days?) are quantized.

To a physicist or physical chemist, a quantum is a fixed portion of energy. (The word was coined by Max Planck in 1900.) Quantum mechanics considers the interaction of energy and matter on the atomic level. What happens when light hits an atom? Why is it that only certain amounts of energy can be absorbed? How is it that matter can behave as a particle, and as a wave? Evidence that matter could behave like a wave suggested to Erwin Schrodinger that he could write an equation to find a mathematical description of this behavior.

So what is it I actually do? I use quantum mechanics — specifically solving Schrodinger's handy little equation — to predict the structures of molecules and their energy, then use that information to think about what molecules might exist, or how hard it would be for them to react and what products are likely to form. Right now I'm exploring molecules that are uncomfortably twisted - and topologically "interesting" (Moebius strip molecules).

My name is Bond.....

Ionic Bond. Taken, not shared.

I caught this pun on a t-shirt at an ACS meeting a few years back. In that same vein In the Pipeline is highlighting this paper in ChemBioChem: Live-Cell Imaging of Cellular Proteins by a Strain-Promoted Azide–Alkyne Cycloaddition. Don't see the connection? Check out the abstract:

Live and let dye: Three coumarin-cyclooctyne conjugates have been used to label proteins tagged with azidohomoalanine in Rat-1 fibroblasts. All three fluorophores labeled intracellular proteins with fluorescence enhancements ranging from eight- to 20-fold. These conjugates are powerful tools for visualizing biomolecule dynamics in living cells.

The NY Times blog on applying to college mused today about the perils of being overly cute on college applications, I wonder what advice they'd give to journals on this score?

Elemental Audio Visual

A chemistry friend shared this cover of Lehrer's classic litany of the elements:

It's worth the 85 seconds it takes to watch! The subtext is fascinating....when the elements flash by you can see the alternate searches Google is proposing. The searches for oxygen bars, I get, but how many people really need to know the price of lutetium? ($5.89 per gram for 99.9% pure lutetium metal here, or $13.99 per gram for "used" on eBay — your choice, act fast if you want to bid, though).


H/T to Dr. Lisa!

Urban Myths of Chemistry Redux: The Enantiomers of Thalidomide

A few months ago I mused about the persistence of an urban myth of chemistry - the meaning of the p in pH. The musings grew into an essay which appeared in Nature Chemistry in August. [Urban legends of chemistry, Nature Chemistry 2, 600 (2010) - caveat, you or your institution need to have a subscription]. The in vivo behavior of the enantiomers of thalidomide turns out to be grist for another persistent myth.
"Ryoji Noyori, who shared the 2001 Nobel Prize in Chemistry for his contributions to asymmetric synthesis, uses the tragedy of thalidomide to open his Nobel lecture: 'A compelling example of the relationship between pharmacological activity and molecular chirality was provided by the tragic administration of thalidomide to pregnant women in the 1960s. (R)-Thalidomide has desirable sedative properties, while its S enantiomer is teratogenic and induces fetal malformations. Such problems arising from inappropriate molecular recognition should be avoided at all costs.'

A close reading of these tales raises more than a few flags. Details differ — was thalidomide marketed for depression or insomnia or morning sickness or to prevent miscarriage? (No, yes, yes and no.) Here is another urban legend of chemistry — with multiple authoritative sources, varying in detail, superficially reasonable, persistent — and with an incredibly compelling plot line. Yet it's not true — as even the tellers acknowledge on occasion. Both forms are teratogenic when administered, as they rapidly racemize in vivo.

Why would chemists pass on urban legends (and ones known to be false, at least in part)? Carl Jung suggested that 'no intellectual formulation comes near the richness and expressiveness of mythical imagery'" ....[read the rest at Nature Chemistry]

Prof. Israel Agranat (whose paper about chiral switches I reference in the essay) wrote me to share that it's not only chemistry textbooks in which these myths circulate. He pointed me to examples, including this one, from the law literature:

Citalopram is a racemate... Such molecules are called chiral (from χειρ, a hand) because, like a pair of hands, they are mirror images which cannot be completely superimposed on each other. They are conventionally designated (+) and (-). It has been well known for many years that, despite their similarities, the two enantiomers may bind to different proteins and produce different biological effects. The most notorious example was thalidomide, which consisted of a (+) enantiomer which was effective to prevent morning sickness in pregnant women and, unknown to the consumers, a (-) enantiomer which was teratogenic and caused severe birth defects." — excerpted from Lord Hoffman's decision of the England and Wales Court of Appeal in the Escitalopram oxalate (Cipralex, Lexapro in the US) patent litigation, H. Ludbeck A/s vesus Generics (UK)
So why do we pass on the legends? My short answer is that resistance is futile!

Better Labs and Gardens: Culinary uses for a rotovap

What kind of lab is this? An anonymous commenter came close with "Biochem/Natural products isolation? "

It's a kitchen. The clue is on the cabinet where it says "3 TBS Sugar". Read here how chef Dave Arnold of the French Culinary Institute in NYC got Buchi to tweak a rotovap for some cool chemistry in the kitchen.

I'm fairly sure the stuff in the beaker is mint.

A Night in the Museum

When I was in elementary school we lived in a small town outside of Chicago. The local rec department had a terrific summer program, drop-in arts & crafts, boating lessons and field trips galore. My favorite trips (besides the outings to Cubs' games) were to the Museum of Science and Industry - what I called the "push-button" museum for all the interactive exhibits. I could go again and again...and did. We were on our own in the museum, something that is probably unthinkable in these hypervigilant days, trusted to return on time to our yellow school bus for the long trip back home.

When I read From the Mixed-Up Files of Mrs. Basil E. Frankweiler I didn't dream of running away to the Met in New York, I dreamed of hiding out in the Museum of Science and Industry. I would have slept in the U-boat.

My brother Pat (who I think I could have counted on to be my co-conspirator in such an adventure) sent me an announcement for a competition to spend a month living my all time favorite museum. Alas, I'm not on sabbatical, and am so committed for the fall that there is no way I could go, even if I could survive the competition. But a girl can dream, can't she?

Photo of The Museum of Science and Industry, Chicago, IL. Photographed 9 April 2006. © Jeremy Atherton, 2006. Used under CC license.

Better Labs and Gardens: A challenge

I've been doing some research for home renovation projects this summer (new cabinets for the kitchen) and came across this quiz to determine "your decorating style". (For the record, I don't have one!) It got me thinking about lab spaces and how they reflect the work done in them, as well as the scientists.

Labs and research spaces have a certain aesthetic to them. Biochem labs have a different "style" than synthetic labs than laser labs than...right down to a preferred palette of wall colors (for some reason, I associate white with biochem labs, black or deep blue with laser labs) and what sort of signs you'll find on the doors going in (eye protection required) and going out (did you remember to fill the trap?).

Take a look at the bench in the photo and see if you can correctly identify the research field. Organic, inorganic, or....

Look for the answer tomorrow!

Is your lab an architectural or decorating wonder? Could we identify your field from a photo of your bench or lab? Want to play? Send me a photo.

Link to the photo will come tomorrow (otherwise I'd give away the answer...)

Fiat Lux 1: On Fire for Quantum Mechanics

My sailboat's name is the Fiat Lux — "let there be light" in Latin — drawing from both my theological and scientific personae. I sail a Laser, an Olympic class racing dingy, which is an apt boat for a quantum mechanic. The ability to amplify light by stimulating an existing emission process was first predicted by quantum mechanics, then the apparatus to actually do it was built. Laser is really an acronym: Light Amplification by Stimulated Emission of Radiation. The radiation is electromagnetic radiation, not the radioactive radiation.

There's been a smattering of conversation about light production around my house this weekend between sailing the Laser, setting off fireworks and observing fireflies. One of my teen guests wondered how the fire in fire flies was different from the fire in fireworks. All light is not created in quite the same way....though there are some fundamental similarities.

There are really two fires in fireworks, the thermal explosives that send them skyward, and the "rockets red glare" — the glittering burst of color in the sky. The heat from the thermal explosion (usually blackpowder or a similar substance) is what trigger the colors.

If you ever done a flame test, putting a solid substance or a concentrated solution on a wire loop and placing it in a flame to see what color is produced, you've done the same chemistry. The extreme heat excites electrons in an atom or molecule, and as they fall back down to their lowest energy, or ground state, emitting a photon (a bit of light) that just exactly matches the difference in energy between the excited state and the ground state. An orange flame meant you had sodium on the wire, while a violet flame suggested potassium. More properly this technique is called atomic emission spectroscopy.

For atoms the picture you usually see in a high school text of this process is of a ladder, where electrons are shown moving from rung to rung. The larger the distance between the two rungs (or states) the higher the energy of the photon emitted. If the distance corresponds to photons in the visible region, you see a color, otherwise you have to use something fancier to figure out the energy of the photons being released.

Different atoms have different spacings between states and so the colors they emit when heated to high temperatures are likewise different. There are in fact many states, and so many types of photons can be emitted, but few are in the visible region.

If you click here, you can see a simulation of the photons you'd expect to see when an excited sodium atom returns to the ground state. Are you surprised that sodium can be used for yellow-orange in fireworks? Some urban legends suggest that lead (or radioactive barium) are used in fireworks, but if you look at the line spectrum of lead you can see why it can't be true -- there is no rung to rung jump in lead that corresponds to a visible photon. So a lead firework would be invisible! (Lead used to be used to make the fireworks "crackle"...)

(And it's true that barium salts are used in fireworks, but they are not radioactive. There are no naturally occurring radioactive isotopes of barium.)

Read more:

An article at C&E News on the chemistry of fireworks

Related posts:

Jello lasers
Romancing the stone (lasers in the plot line of a romance novel)

Image from Wikimedia.

Warning, Dr. Smith! Warning!

An SF fan from the moment I discovered Heinlein's Have Spacesuit -Will Travel in the minuscule public library in the small (population 2500) Midwest town I grew up in, it's probably not a surprise that I would have been an avid watcher of SF on TV. When I get various 'urgent warnings' in my inbox, I often hear the Lost in Space robot's voice in my head, "Warning, Dr. Smith! Warning!"

A few days ago, this warning about the dangers of taking business cards from strangers appeared. Take one of these drug laden cards in your bare hands and soon you will be easy prey for swindlers and worse. Is such a thing possible? Can you be drugged against your will by briefly touching a drug?

In principle, yes. Unbroken skin, though a good way of keeping your insides in, is not an absolute barrier to molecules entering the body. Some molecules — such as DMSO — are better at getting in than others.

When I teach mathematical modeling, one topic we look at is ways to model diffusion. An application that many of my students find interesting are passive drug delivery systems that capitalize on diffusion. In other words - patches. To me this warning sounds like a folkloric riff on drug patches. In fact, delivery through a patch is a pretty complex system, it's not just a matter of soaking the equivalent of a gauze pad in a drug and taping it to your arm.

The drug cocktail purported to be on the business cards is burundanga - a mixture of two plant alkaloids, atropine and scopolamine. Both can be administered through the skin, when I had surgery a couple of years ago, the anesthesiologist use a scopolamine patch to manage my post-op nausea. But he didn't hand me a "don't throw up" card to hang onto for a few minutes in pre-op - that patch he applied behind my ear was a marvel of pharmaceutical engineering!

Burundanga has been used criminally but by slipping into a victim's food or drink. Incidental contact with atropine or scopolamine won't incapacitate you — though the prescribing information for the scopolamine patch points out that you should avoid touching the patch and then your eyes - resulting in dilated pupils and blurry vision.

Scopolamine was used as an amnesia inducing agent during labor and delivery in the 60's. I suspect Betty Draper's halucinations during labor and delivery on Mad Men (The Fog, Season 3, episode 5).

Image is of belladona, from which atropine and scopolamine can be extracted.

Climate Change Skeptics

Paul Krugman has a piece on climate change on his blog at the NY Times. One commenter responds:

"One thing they are "gong" [sic] to do is point out that if the ppm increase in atmospheric CO2 is solely due to man-made combustion of fossil fuels, laws of chemistry and physics have been violated. For every molecule of carbon, two molecules of oxygen are consumed. Therefore, if the rise in CO2 is due to such combustion, then we should observe a decrease in atmospheric O2 by a factor twice as great. I have seen no evidence to suggest that global O2 is decreasing at all." (H. Muhlphart )

Ouch! My response:

No law of chemistry and physics has been violated by assuming that the increasing CO2 comes from combustion of fossil fuels. The reason no decrease in O2 is "noticed" is because the loss due to the formation of carbon dioxide is very small compared to the total amount of oxygen. If you increase the amount of CO2 by 100 ppm (more or less what's predicted in the next 50 years), the decrease in O2 is from 209,460 ppm to 209,360 ppm. That's the equivalent of being at the top of less than a 30 foot hill. You certainly don't notice any change in the oxygen levels between the basement and second floor of a house, do you?

And I didn't even bother with the notion that carbon dioxide "eats" two oxygen atoms no matter what carbon source you make it from - fossil fuel or respiration. Or that it's one carbon atom to one oxygen molecule. At this level of understanding of the basic science, you are not simply not entitled to an opinion on the matter.

Chemical Urban Legends: pH

What does the p in pH stand for?

The term pH has been in use for more than a century. It is a logarithmic measure of the hydrogen ion concentration ([H+]): pH = -log10[H+]. (Technically, there aren't bare protons (H+) floating around in solutions, but that wasn’t known when pH was introduced!) The original symbol used by Sorensen was pH+.

Theories vary as to the origin of the p - most agree it means power but whether in Latin, French or German, seems in dispute. Thinking it would be either French or Latin as the original paper was published in French, I was surprised to find that it's neither, though the legend is both old and persistent. By 1920, many authors were assuming that it meant “power”, but Jens Norby returned to the original sources and points out that it was the arbitrary choice of the letters p and q for two variables in the work-up of the experimental data. The variable p eventually ends up in the formula arrived at for the concentration of the hydrogen ion.

The modern form pH was introduced in 1920, "as a matter of typographical convenience".

For the full explanation, see Jens G. Norby, The origin and the meaning of the little p in pH, Trends in Biochemical Sciences 25, 36-37 (2000). The illustration is a selection from the original paper: Sorensen, Compt. redn. du Lab. de Carlsberg 8 1-168 (1909).

Open Laboratory 2009

Open Laboratory 2009 - a juried anthology of the best of the science blogosphere from last year has appeared. Edited by scicurious, it's available here. I have a piece in it - a cleaner version of this post on the use of helium to preserve documents. I'm fascinated with the interplay between web and print that ultimately produces this volume.

Want a copy? Order one -- or if you're feeling lucky, de-lurk and leave a comment before March 5th and I'll draw a winner at random. The rest of the pieces look great - on everything from the flu to charismatic megafauna (whales and chimps) to the statistics of human milk production.

Nobel Conversations

I vividly remember the first time I met a Nobel Prize winner. I was a graduate student in my 3rd year, and Roald Hoffman had recently won the Prize in chemistry (1981). A group of us went up with our research advisor (who had worked with Hoffman as an undergraduate) to hear him speak at a symposium at USC. On the drive up we were briefed as to behavior - do not speak unless spoken to. Frankly, we were happy enough to be out of the lab as well as treated to lunch (and to a terrific speaker). Lunch was at picnic tables in an outdoor courtyard - the grad students all clustered at a table on the edge. Imagine our surprise (and delight) when Hoffman joined us at the table, and spent lunch asking us what we were doing for research, and what excited us most about chemistry. I, at least, left with the sense that I was an interesting part of the chemical community -- even if a very junior one.

The Noble organization and Honeywell are offering the opportunity to anyone to ask a question of Nobel winners. The next live broadcast is Tuesday, March 2 at 11:15am (-6hrs GMT), when you can hear Robert Grubbs, who won the chemistry prize in 2005 for his discovery of olefin metathesis (a method to rearrange carbon-carbon double bonds using metal catalysts). I wrote my oral exam proposal on olefin metathesis in 1982 - I was fascinated then, and am still, with these atomic level architectural changes.

The best part? You can ask questions - email them to or go through Twitter or Facebook.

Are scientists palatable?

In the early part of the 19th century, the word scientist had yet to be coined. As the scope of materials and phenomena that natural philosophers and historians dealt with increased, there was a growing sense that these terms were inadequate to describing the task of this new breed of inquirers. In the 1830s, the British Association for the Advancement of Science explored potential candidates, but ultimately rejected various proposed terms, including scientist:
"Philosophers was felt to be too wide and too lofty a term,..; savans was rather assuming,..; some ingenious gentleman proposed that, by analogy with artist, they might form scientist, and added that there could be no scruple in making free with this termination when we have such words as sciolist, economist, and atheist — but this was not generally palatable."
The need remained, however, and a decade later, William Whewell, a philosopher and biologist pushed the issue again: “We need very much a name to describe a cultivator of science in general. I should incline to call him a Scientist.” This time it stuck.

Once the name stuck, an image quickly became attached -- wild hair, lab coats and odd apparatus all became part and parcel of what it means to be a scientist. My most recent Thesis columnin Nature Chemistry -- Men of Mystery -- takes up popular images of scientists, and considers the impact the images might have on public discourse about science.

UPDATED: See Snail's Tails post about philosophy and philosophical instruments. The ad for the "philosophical instrument makers" is fascinating!

Science blogging at its best: Open Laboratory 2009

In 2006, Bora Zivkovic brought us the first edition of Open Laboratory, a print collection of the best science blogging of the year. Now in its 4th year, the 2009 edition, guest edited by scicurious at Neurotopia is going to press soon. A record 760 posts were nominated, winnowed down to fifty by scicurious and her panel of judges.

One post of mine (The Pressure to Preserve) will be included! While you're waiting for this edition to come out, I heartily recommend browsing the earlier editions. Who says scientists can't write?