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).

A universal hotness manifold

Slothful thermometers.

I'm working on a column for Nature Chemistry about temperature, prompted by the incredible collection of early thermometers and thermoscopes at the Museo Galileo in Florence.  (Can't get to Florence and visit it and the amazing gelato spot Perché no! — they have an incredible online virtual tour of the exhibitions.)

The question of how one can be assured that two objects, well separated in space and/or time, would be in thermal equilibrium with each other should they be brought into contact — that is, can you be sure that two objects are at the same temperature —  is not quite as simple as it sounds.

First you need a measuring device, then you need to agree on a way to quantify the output of the device.  And it would be nice if your colleague who lives across an ocean could set up her apparatus in such a way as these quantities are the same.  In another words, you need a calibrated thermometer.

There's a wild and wonderful history to figuring out how to create this basic piece of lab equipment, including what you mean by zero, how big should degrees be, and how to to tell if water is really boiling.  But my favorite find is in a paper by mathematician James Serrin, in which he defines a thermometer by formally stating the zeroth law of thermodynamics [1]:

Manifolds, M, marked in with L, hotness levels (the black
enamel dots).  Or,17th century Florentine degree thermometers.

"There exists a topological line M which serves as a coordinate manifold of material behaviour. The points L of the manifold M are called 'hotness levels', and M is called the 'universal hotness manifold'."

I'm trying to imagine standing up in front of a classroom of students and talking about hotness levels.

And those slothful thermometers?  They tell the temperature by little balls that float or sink...slowly, very slowly.  Lazily, you might say.

Just reading the paper brought back memories, the collection of conference papers this quote is pulled from are reproduced from typed (double-spaced, with a typewriter!) manuscripts, complete with the typos you might expect before word processors and spell check arrived on the scene ("physcis").  In the late 1970's this was one way to inexpensively and rapidly get proceedings and reviews into print.

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1.  "The concepts of thermodynamics" in Contemporary Developments in Continuum Mechanics and Partial Differential Equations. Proceedings of the International Symposium on Continuum Mechanics and Partial Differential Equations, Rio de Janeiro, August 1977, edited by G.M. de La Penha, L.A.J. Medeiros, North-Holland, Amsterdam, p. 416.

Chemists are wildly polysemous

STO-3G//STO-3G calculated Raman spectrum of arsole

A few months ago this BBC news report - about the evacuation of a building because of a volatile compound got chemists on Twitter talking about language, particularly those words that mean one thing to chemists and something quite different to the rest of the world.  (Thanks @NatalieFey_NLS, ‏@stephengdavey and @stuartcantrill!) Like volatile (high vapor pressure vs. explosive) or to my mind the most overexposed chemical example and the inspiration for far too many t-shirts: mole.  One thing led to another, or at least, one comment by @stuartcantrill led to my Thesis column in  this month's Nature Chemistry.

Is RT retweet or 2.5 kJ/mol?

This piece was pure fun to write.  I enjoyed crowdsourcing examples of chemical double meanings. (List of 200 examples is here.) By far the favorite mechanism of formation for chemists is polysemy, where words share a common ancestor, but the meanings have drifted apart.  Take flush, as in flush a column, or flush a toilet or  flush game or even a straight flush.  All these senses derive from the Latin fluxus for flow.  (Don't see the connection to poker? The OED suggests you think of a flush as a "run" or flow of cards.)

Sometimes the two meanings sit close to the surface for chemists, other times we are pretty blind to the lexical ambiguity.  My youngest son is toying with the idea of a chemistry major, and when I read him examples from the list, he was quick to note both senses for many words: cell, salt, aromatic.  But when I got to molar, he wanted to know what else it meant beyond the concentration of a solution.  "Teeth?" I suggested.  He face palmed.  Whether he majors in chemistry or not, we've already messed with his mind.

Polysemy is productive — as the linguists would say — not just in terms of the language, but of new chemistry.  We ought not to discourage lexical play in chemists (not that one has much control over language in any case, IUPAC's gold book notwithstanding) it gives us a rich set of images to draw on and as I said in the essay, "we can't look for what our language doesn't let us imagine."

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Read the essay here. ($)

What is the half-life of a tweet?

My tweets apparently have a half-life of about two hours, but I have no idea if that's unique to me.  My spouse is new to Twitter and as I was showing him how he could see some data about his tweets, I noticed that the graph of the data looked familiar.  Probably because I taught chemical kinetics twice last year (in pchem and general chemistry).

Over lunch today, while waiting for my car to be serviced, I decided to explore the kinetics of my tweets.  I used data from the first 10 hours after I posted a tweet, and used tweets that had several hundred total impressions and few retweets.  Using five data sets from the past month, I fit the tweets to linear models for 0th, 1st and 2nd order kinetics.  R² values suggest that a 1st order model is most appropriate, with a rate constant of 0.35/hour, which translates to a half-life of 2.0 ± 0.4 hours.  I'm curious if that's relatively constant for me, or whether it's characteristic of other parameters, but time is up.

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Perhaps because I'm writing this outside in a park, I'm reminded of an infamous problem about the temperature dependence of the chirp rate of male snowy tree crickets in many general and physical chemistry texts.  A discussion of the phenomenon (first recorded in the late 19th century, and not true of cricket everywhere) can be found in Thomas Walker and Nancy Collins. “New World Thermometer Crickets: The Oecanthus Rileyi Species Group and a New Species from North America.” Journal of Orthoptera Research 19 (2010): 371–376. 

Ephemeral Elements

The late 19th and early 20th centuries were hotbeds of elemental discoveries (literally and figuratively). New elements came — and on occasion went. Some were known elements in unknown guises, such as previously unrecognized allomorphs. Others, like didymium, weren't elements at all, but mixtures of as yet to be identified elements (in this case neodymium and praseodymium). Some were more ephermeral than others.

Yesterday I ran across a description of the discovery of a new element in an 1890 issue of Chemical News: damarium, oddly enough reported in the Notes & Queries section and not among the research papers. The report of the gaseous element, collected in Damara Land (present day Namibia) was a bit over the top, even for a time when flowery prose was in style in scientific papers: "One of the party had in his hat a branch of a shrub, which in a very short time lost its green colour and assumed a violet blue..."

One contemporary report assumes it is a hoax, but several sources were not so quick to dismiss the claim, particularly in a period when elemental identity was in flux. At least one commenter wondered if it might be "helium" — an element as yet undiscovered on earth.

I wonder if it's worth tracking down the original cite if I can (the Chemiker Zeitung is available on microfilm at the Othmer). Ah...Google books has it here.

German chemical humor or not? What do you think?

Two thousand mockingbirds

I'm writing final exams for two intro chem courses. I try for a light touch brush of humor on at least a couple of the questions, it's stressful enough without every question probing deeply important things.

Some useful (in this context) unit conversions:

2000 mockingbirds = 2 kilomockingbirds
10^-6 fish = 1 microfiche
454 graham crackers = 1 pound cake
10 millipedes = 1 centipede
10 monologs = 5 dialogues
2 monograms = 1 diagram
8 nickels = 2 paradigms
10^-2 mental = 1 centimental

Have more to suggest?

Writing Science: Punch Lines

"When a thing is funny, search it carefully for a hidden truth." George Bernard Shaw

How seriously should we take science? Is science inherently funny - are those odd spots where truth is hidden? Can science be humorous without being a caricature? Do you have to be a scientist to get the joke? What role might humor play in teaching science? And for that matter, why are words with a hard c sound (like cryogenic) funny?



Readings

Brian Malow - superb stand up science comedy
The Big Blog Theory - the science behind the humor on The Big Bang Theory

Periodic table humor.

XKCD a comic strip which carries the warning: "this comic occasionally contains strong language (which may be unsuitable for children), unusual humor (which may be unsuitable for adults), and advanced mathematics (which may be unsuitable for liberal-arts majors)." And apparently unsuitable for high school students, it's blocked as "adult content" where I'm on the web. I'm in the high school nominally supervising the theater tech crew as they construct a set. Don't ask about the decibel level!)

Men of Mystery (subscription only) Taking on the stereotypes of science: why are scientists drawn as guys in white coats with bad hair? M.M Francl, Nature Chemistry, 2, 68-70 (2010).

Writing Science: The Short and Sweet of It, Titles and Tweets

We're thinking about writing short bits of science with style and precision: titles and tweets, abstracts and blog posts.

What makes a great title? One theory (here) suggests great book titles should be PINC ("pink"): make a promise, create intrigue, identify a need, and/or describe content.

Are there other things that titles should do in a science piece (be it blog post, tweet or scholarly article)? How would you prioritize these for different audiences, different genres?

Should an abstract tease? Is there a place for wit in the formal scientific literature? When? How? Who? Is it OK for someone of Paul Wender's stature to indulge?

Readings

• "Wit" and "Abstracts" Pierre Laszlo, Communicating Science: A practical guide. Springer 2006. p 56, p. 2
• The art(?) of scientific abstract writing From In the pipeline, Derek Lowe
• Four strategies for creating snappy titles. Michael Hyatt
• Writing a scientific paper, From Research to Manuscript: a guide to scientific writing, Michael Jay Katz, Springer, 2006. pp 113-114
• Referee's quotes, Environmental Microbiology (2010) 12(12), 3303–3304

Writing assignment #3
Write 5 tweets pointing colleagues to recent articles in the field (give me title/ref for the article); In 50-100 words comment on the construction of your tweet in light of the criteria you have developed for a good science tweet.

Writing Prompt for the day
Write a series of possible titles for the abstracts below. When you get stuck, move to the next abstract! Five minutes. (Click on the links to see the title the authors chose.)

A. Human infants face the formidable challenge of learning the structure of their social environment. Previous research indicates that infants have early-developing representations of intentional agents, and of cooperative social interactions, that help meet that challenge. Here we report five studies with 144 infant participants showing that 10- to 13-month-old, but not 8-month-old, infants recognize when two novel agents have conflicting goals, and that they use the agents’ relative size to predict the outcome of the very first dominance contests between them. These results suggest that preverbal infants mentally represent social dominance and use a cue that covaries with it phylogenetically, and marks it metaphorically across human cultures and languages, to predict which of two agents is likely to prevail in a conflict of goals. Science 331, 477-480 (2011)

B. The effect of environmental change on ecosystems is mediated by species interactions. Environmental change may remove or add species and shift life-history events, altering which species interact at a given time. However, environmental change may also reconfigure multispecies interactions when both species composition and phenology remain intact. In a Caribbean island system, a major manifestation of environmental change is seaweed deposition, which has been linked to eutrophication, overfishing, and hurricanes. Here, we show in a whole-island field experiment that without seaweed two predators—lizards and ants—had a substantially greater-than-additive effect on herbivory. When seaweed was added to mimic deposition by hurricanes, no interactive predator effect occurred. Thus environmental change can substantially restructure food-web interactions, complicating efforts to predict anthropogenic changes in ecosystem processes. Science 331, 461-463 (2011)

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).

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H/T to Dr. Lisa!

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!

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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...)

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!

Sex and the scientist

(Cross posted at my other blog.)

I am in the midst of writing an essay for Nature Chemistry - about why people are so curious about stereotypes of scientists, but seem less so about other fields. There is the DAST (draw a scientist test), but not as far as I can discover similar instruments to assess the images of other professions. Where are the DATTs (draw a teacher test) and DACTs (draw a chef test)? On the other end of the cultural spectrum there is the Big Bang Theory.

The earliest anthropological study I can find dates to the late 1950s and is by Margaret Mead (yes, that Margaret Mead) and Rhoda Metraux under the auspices of the AAAS. They analyzed thousands of essays, drawn from a set of 35,000 written by US high school students. The 1 page essays were written in response to one of three prompts. Prompt I read "When I think about a scientist, I think of..."

What took my breath away was Prompt II (italics are not mine, but as given in Mead's original paper - Science 126, 384-390 (1957)):

If you are a boy, complete the following statement in your own words.
If I were going to be a scientist, I should like to be the kind of scientist who...

If you are a girl, you may complete either the sentence above or this one:
If I were going to marry a scientist, I should like to marry the kind of scientist who..."

Math Man points out that I did both.

UPDATE: So there is a draw-a-teacher test (DATt) (H/T to Neil who commented on drawing God - another area that has been explored by educators and psychologists)

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Images are from K.D. Finson, J.B. Beaver, B.L. Cramond, "Development and Field Test of a Checklist for the Draw-A-Scientist Test" School Science and Mathematics 95, p. 195 (1995).

How to tell if you're really a chemist

You pronounce unionized as UN-ionized not union-ized.
When you hear the word mole, you don't think of an animal.
Milli is a prefix, not a girl's name.

This Sceptical Chemist blog post suggests a new test to tell if you're really a chemist. What do you see when you look at this illustration by Joon Mo Kang? If the first things you see are five bonds to carbon, and three bonds to a hydrogen, you're a chemist. If that's all you see - you are really a chemist.

A couple of chemists missed the point of the illustration so completely they wrote to the NY Times to let them know of their chemical illiteracy. Another blogger was also vexed by the nonsensical molecule.

I'll admit it -- I saw five bonds.