Implications of Charles law in a biological matrix: farts

See note 3 for source.

Maggie Koerth-Baker has a great piece up at the 538 blog: "How Big Is A Fart? Somewhere Between A Bottle Of Nail Polish And A Can Of Soda."  It's well researched, digging into the biomedical literature with verve.  And it's great that she gives the answer a context, it's easier to visualize a bottle of nail polish than a 17 ml blob for most people, me included.

I'm not at all surprised at what you can find in the primary literature (I tracked down papers on exploding people and deuterated dogs¹ for my introductory chemistry class last spring). The piece is the first in a series Science Question From A Toddler, though I suspect that people somewhat past the target age group (5 and under) would be interested in the answer to this question, too.

In a footnote Koerth-Baker suggests that farts in the body would be smaller because the gas would be compressed inside the body.  But the pressure inside the human colon is the same as atmospheric pressure.  Farts and burps keep it that way. What's different is the temperature, higher inside the body by about 30^oF (17^oC).  Gases expand at higher temperatures. You can use Charles' law to figure out by how much the volume changes with changes in temperature:  V2=(T2/T1)V2

The researchers measured the volume of the farts at room temperature (I read the paper!), so the volume of a fart should be slightly larger in the body than the reported numbers by a factor of (310/293) or about 6% larger.  So how big is a fart?  Just before exit, it's about the size of a 14 ounce ketchup bottle for the largest one in the 1997 study.

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The details of the experiments are fascinating.  The technique for quantitatively² capturing flatus in the bathtub is elegant, and while a significant improvement over the method used for the studies in the 1860s³ you have to wonder how they got volunteers for either experiment.  And speaking of volunteers, the assessment of the "flatus perception threshold" was done by delivering 100 ml of an odorant mixture "from a large 250ml syringe in about 1s, 1 meter beneath the nose of the panel members, mimicking a flatus emission."

And just in case you don't think this is serious stuff: "The common tendency to treat rectal gas as a humorous topic has obscured appreciation of the complex physiology that underlies the formation of this gas." Suarez et al. American Journal of Physiology  272, G1028-G1033 (1997).

1.  The physiological effects of drinking heavy water, D₂O, on dogs.  If you've ever wondered what would happen if your poured that little vial of D₂O into your coffee, the answer is not much.  It's not great for the dogs as a steady diet, but a sip or two won't hurt.
2.  The fancy chemistry term for "we got all of it!"
3.  See the figure, from Tangerman, "Measurement and biological significance of the volatile sulfur compounds hydrogen sulfide, methanethiol and dimethyl sulfide in various biological matrices" Journal of Chromatography B, 877,  3366-3377 (2009).

Science at Play

The Chemical Heritage Foundation in Philadelphia's latest exhibit is called "Science at Play" — and even if you can't get to Philadelphia, you can browse some of the materials on Tumblr, including animated videos of experiences — good and bad — with chemistry kits.

When my kids were young, I encouraged them to play with science stuff.  I wanted them to be willing to get messy, to make mistakes, to think about stuff where it wasn't perfectly clear what was going on and to begin to understand that protective gear wasn't a ritual or a costume, but part of thinking through how to reduce risk.  That you could make your own equipment.

Though kits have gotten far more tame over the years — no more uranium ore or instructions for making ammonia in your hand — there are still commercial kits that let kids play not only responsibly, but productively, with chemistry.  The new MEL kits that Todd Bookman's piece on chemistry kits for The Pulse (listen here - full disclosure, I was interviewed for this segment) highlights are particularly cool in that they plug into another important skill for budding scientists:  how to share your work.  The kit comes with a lense that you can snap over a cell phone camera, giving you an up close look at what you are doing, and enabling you to share it via social media.

But as important as kits are, I think the ad hoc experiences of doing science are equally critical.  They hone the ability to read instructions (and reveal how much is not revealed in the methods sections of any science communique), encourage a sense of scale and quantitation (how much is 1 gram of something, as opposed to pour in this packet) and help novice scientists get comfortable with tinkering to build apparatus when they don't have exactly what they need. And when tackling a new research problem, do you ever have precisely what you need?

While you can make do with measuring cups and kitchen scales, I'm with the Chemical Heritage Foundation's Erin McLeary, who notes the appeal of having the real stuff in your hands.  These days you can easily and inexpensively acquire a few real beakers, graduated cylinders and other lab equipment -- along with gloves and other protective gear.

So if you're looking for an interesting and unique gift for a kid interested in science, try assembling a small kit and including the instructions and materials for a couple of experiments.  For starters, extracting DNA from dried peas or copper electroplating (yes, it uses something you shouldn't eat - don't and wash your hands) or even the infamous water electrolysis (sans smoldering splint and thereby less risk of singed eyebrows).  Offer to help supervise or be the videographer.

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To read more of what I've written about chemistry kits and doing chemistry outside the laboratory see:

"Homemade Chemists" in Nature Chemistry
"Felony Science" at Slate
"Handheld Chemistry" on the blog, about the making of ammonia in your hand

From the portals of hell to built-in fire protection: intumescents

A friend posted the link to this demonstration, wondering if it was safe. (Do listen to the children in the background - their cries of "kraken" at 1:02 are worth it.  Science is great fun!)

The caption that came with it noted that it was a mixture of ammonium dichromate ((NH₄)₂Cr₂O₇ )and HgSCN (mercurous thiocyanate).¹ Mercury and chromium, probably not something you want to eat I told my friend. The whole thing made me curious, just what were those tentacles come out of the burning pile? And what chemical reactions were driving it?

It's a coupled set of decomposition reactions. The volcano comes from the decomposition of ammonium dichromate

(NH₄)₂Cr₂O₇(s) → Cr₂O₃(s)+ N₂(g)+ 4H₂O(g)

The reaction produces a lot of heat, which makes the particles being thrown off by the rapid expansion of the two gases (nitrogen and water vapor) glow.

The heat then triggers the decomposition of the mercury compound:

2 Hg(SCN)₂(s) → 2HgS + 4CS₂ + carbon nitrides

The erupting tentacles are an example of intumescence², a property of mercury thiocyanates noted long ago by the venerable Friedrich Wöhler³. It's a well known demonstration, often called Pharaoh's Serpents. Many material intumesce when heated, and thus produce their own insulation.  Some passive fire protection systems rely on this property of polymers, by which they essentially rapidly produce their own insulating layer upon heating, or by swelling up to block air ducts to prevent smoke and other gases from spreading too quickly through a ventilation system.

It works with mercuric thiocynate as well (Hg(SCN)₂) — by some accounts even better — and better yet if you toss a bit of potassium nitrate and a bit of fuel in the form of sugars. In other bits of historical trivia, the mercuric thiocyanate was originally made by the aptly named Otto Hermes. The sale of mercuric Pharaoh's Eggs ceased after some kids ate them with deleterious (fatal) effects.

If you just want to see the snakes minus chromium salts or mercury - try this demonstration based on calcium gluconate instead or check out pyrotechnic expert Tenney Davis suggestions in the Journal of Chemical Education.

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1.  From the Latin verb "to swell" — related to thumb and tuber (as in root vegetables like potatoes)

2.  The chemist who showed in 1828 that compounds made by nature do not have some "vital essence" that distinguishes them from the same structure crafted by a chemist from inorganic (never living) materials.  Something the Food Babe and hawkers of 'bioidentical' hormones do not get.

Read more:

Brian Clegg at Chemistry World.  A paper on the demonstration from Journal of Chemical Education in 1940, by Tenney Davis of MIT who taught courses in explosives way back when ($).

Formaldehyde: not just for dead things

Next spring I'm teaching a course on the physical chemistry of food while a colleague is teaching a course on the analytical chemistry of foodstuffs.  Among other science texts we'll be using John Coupland's Introduction to the Physical Chemistry of Food, but I'm also collecting short pieces to put some of the work into a historical and social context.

These aren't actual biological specimens preserved
in formaldehyde, but Halloween decorations.  

Though these days we tend to think of chemists as the untrustworthy creators of toxic, artificial everything, the systematic training of chemists was driven in part by the desire for the public to know what was in their food and water.  In 19th century Britain, hundreds of chemists made their living testing the purity of everything from butter to well water.  So when the Food Babe tells you there is something "yucky" in your food, the reason we know it is there is some chemist developed a careful protocol for its analysis, and other chemists tested the material.

Molecular structure
of formaldehyde

I've been thinking about formaldehyde, one of the simplest organic molecules (to a chemist, organic means made up mostly of carbon and hydrogen atoms, and has nothing to do with whether the molecule is synthetic or natural or...). Last year, formaldehyde, which is a preservative, was in the news because Johnson & Johnson had agreed to remove it from baby shampoo, though as Matt Hartings and Tara Haelle clearly pointed out in a piece at Slate, it was in such low concentrations that it posed no risk to babies (who, they point out, themselves contain substantial amounts of formaldehyde.)

Pepsi is reformulating Diet Pepsi to take out the artificial sweetener aspartame. The Food Babe is crowing that she and her army have forced Kraft to remove the so-called coal tar dyes (e.g. tartrazine/FD&C Yellow 5), to be replaced by natural colorings from spices.  What does all this have do do with formaldehyde?

From the Food Babe's 'campaign' literature.

To start with those natural colorings - at least one of them used in the UK version of mac and cheese, beta-carotene, isn't extracted from natural sources but synthesized from petroleum feedstocks (just like those coal-tar dyes).  One of the starting materials:  formaldehyde. The other natural colorings on the table — annatto, turmeric and paprika — are not quite what you might think either.  While you might imagine shaking in some spices from a quaint bottle, the spices themselves are not used as colorants, the colorants are extracted using organic (not that kind of organic, the chemist's kind of organic) solvents, such as ethyl acetate.  It's unclear to me why these colorants, particularly beta-carotene pass muster with the Food Babe.


Aspartame is sometimes vilified because it is metabolized into methanol and formaldehyde in the body.  Which it is.  You already contain a lot of formaldehyde, about 12 milligrams per liter of fluid in your cells.  One source is metabolism of the amino acids, particularly, serine and glycine (in naturally occurring proteins), from which your body scavenges methyl groups (CH₃) to pop on to various structures.  Aspartame is a very tiny protein, so the same pathways that produce methanol and formaldehyde from natural sources, dismantle aspartame to yield methanol and formaldehyde, though the amounts produced are tens of times lower than what comes from eating apples and fish.

Because formaldehyde occurs naturally in foods (about 5 mg per serving in some fruits, fish is also high, pectin containing fruits such as apples add significantly to the amount of formaldehyde ingested), our bodies have a mechanism for dealing with it, we process about 60 to 100 grams of formaldehyde a day and do so quickly.  Formaldehyde has a half-life of about 1 to 2 minutes in the body.

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Why are those spices colored?  What does it have to do with quantum mechanics, flamingos and canaries?  Read this post, the very first one written for the blog,  to find out.

References
EFSA report on endogenous versus exogenous sources of formaldehyde.
EFSA review of curcurmin, a component of turmeric, which had been suspected of being genotoxic.

Chemophobia: The Boy with a Thorn in His Joints

I'm at ScienceOnline2013 where Carmen Drahl and Dr. Rubidium just finished running a terrific session on chemophobia: how can we bridge the gap between "better living through chemistry" and ads for "chemical-free sleep aids." The thrust of the session was not how to convince people chemistry and chemicals are good, but more about how to inject nuance into the public conversation. Chemicals have risks and benefits — and of course, are unavoidable. But we current view chemical as synonymous with toxic, hazardous, unnatural or just plain bad.

What are the roots of this cultural shift? Can understanding these help scientists and writers communicate more clearly and in the end help people not only understand what is in their "stuff" — chemicals, it's all chemicals — but give them tools to work with and make decisions about the materials that make up the world — chemicals. As @docfreeride (ethicist Janet Stemmwedel) noted at another session yesterday, we can agree on facts, and still make different decisions based on them.

Today's New York Times has a perfect example of the various ways chemophobia presents in the Magazine: The Boy with a Thorn in His Joints. The piece chronicles Susannah Meadow's search for an effective treatment for her son's rheumatoid arthritis. She agonizes about the decision to give him methotrexate (which in high doses is used in anticancer treatment) and turns to alternative treatments, in particular four-marvels powder. There are intense arguments with the pediatricians and with her husband over the issue. I was struck by two things in this piece. First, the language Meadows uses to limn the controversy, and second her ignorance, not so much of the chemistry that is in your face (methotrexate), but of the ways in which chemistry is couched in alternative cultural schemes(four-marvels powder).

It makes me wonder how chemophobia is linked to the language we use to talk about it. It can be nearly impossible for an non-chemist to figure out what methotrexate is (beyond "a chemical"). The very name sounds harsh. Four-marvels powder is easy to parse: a powder with four effects. Its name rings with hope.

I also wonder if we worry more about stuff we are familiar with, we've heard more talk on the street about their risks. So we obsess about vaccines, because we hear and read about the side-effects of vaccines, but how many people know anyone who has died of measles? (One of my sister's friends died of measles when I was a child, before there was a vaccine.) So we get in the Times' piece "I was desperate to find a way...without the drugs." pushed up against "[My husband] has always been more comfortable with pharmaceuticals, more trusting in general."

Of course, four-marvel powder is a pharmaceutical, it's just from a different pharmacopoeia — the traditional Chinese — than the one Meadows or her husband is familiar with. Meadows can read the package insert with information on the side-effects of methotrexate, she may be unaware of the routine advice given in Chinese medicine programs (and yes, there are formal academic programs in Chinese medicine, e.g. at Nanyang Technical University) about four-marvels powder (it should never be given to pregnant women, for example, which might make you hesitate before giving it long term to infants or young children).

The session at SciOnline2013 brainstormed about effective ways to help people develop a better sense of nuance around what is a chemical and what are the risks of this particular chemical? What strategies do you think would be most effective?

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!

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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

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?

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.

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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.

Chemistry on Holiday: Science Cookies

'tis the season for baking on the home front. It's been mostly biologically based leavening (yeast) at my house, but some strictly chemical rising has been going on as well. For an interesting mix of chemistry and biology in the kitchen check out Not So Humble Pie's science cookies: zebrafish, drosophila, gel electrophoresis and atoms are on the menu. Something to keep in mind for the next snow day around here...

Feeling quizical?

Pew tracks American's familiarity with the news of the day - my kids took the latest quiz (and each scored in the top quartile for adults and so were quite pleased with themselves). I played with something similar for science...it's definitely NOT rocket science, so if you've any science background at all -- you should score 100%.

If you're looking for the answers - they are here.

Chocolate Math Mystery

My youngest and I are heading into Philadelphia tonight for a chocolate dessert feast, so it seems apt that a friend sent me this bit of mathematical magic this morning - with a plea to explain how it works.

Chocolate Calculator:

This is pretty neat. Don’t say your age; you will probably lie anyway!

DON’T CHEAT BY SCROLLING DOWN FIRST

It takes less than a minute. Work this out as you read.

Be sure you don’t read the bottom until you’ve worked it out!

1. First of all, pick the number of times a week that you would like to have chocolate (more than once but less than 10)
2. Multiply this number by 2 (just to be bold)
3. Add 5
4. Multiply it by 50 — I’ll wait while you get the calculator
5. If you have already had your birthday this year add 1759. If you haven’t, add 1758.
6. Now subtract the four digit year that you were born.

You should have a three digit number

The first digit of this was your original number (i.e., how many times you want to have chocolate each week).

The next two numbers are YOUR AGE! (Oh YES, it is!!!!!)

THIS IS THE ONLY YEAR (2009) IT WILL EVER WORK, SO SPREAD IT AROUND WHILE IT LASTS!

So how does it work?
Expressed algebraically, the procedure if you have had your birthday can be written as:
50 (2n +5) + 1759 - y
where n is the number you chose and y the year you were born

The author asserts that this will produce a number where the digit in the 100's place is n and the remaining digits are your age or 100*n + age. If you have had your birthday this year, your age in 2009 can be written in terms of your birth year, y, as
age = 2009 - y
So the formula should produce 100*n + (2009 - y).

It is trivial (I love saying that) to show that

50 (2n +5) + 1759 - y = 100*n + (2009 - y)

This will not work if your age is greater than 99, but as long as you are younger than that, the last two digits will always be your age even if the number of times you want to eat chocolate in a week is greater than 10 -- so in either case eat all the chocolate you want!

It's Just a Phase

Video Recaps | Full Episodes | Webisodes

Allotropes are all the rage? Or at least sending Conan O'Brien over a very funny edge! The bit was inspired by this article in the NY Times science section. I'm not nearly this riveting when I lecture about allotropes, I've got to admit.

O'Brien gets the chemistry nearly right. My only quibble would be that he calls the different forms (the diagrams are the real thing, by the way) different phases, which they aren't really. They are technically allotropes, different structural forms within the same phase or state of matter. The quintessential example is the allotropes of solid carbon, graphite and diamond and a few others. All that said, when you draw a phase diagram for an element, you show the allotropes on it, and many chemists would characterize the change from one allotrope to another as a phase change.

Oxygen has some fascinating solid allotropes, including one that is a blue solid at room temperature!