word of the day: obviate

The word of the day is obviate:

Etymology:  < classical Latin obviāt-, past participial stem (compare -ate suffix³) of obviāre to act contrary to, to go against (late 2nd cent. a.d.), in post-classical Latin also to meet (Vulgate), to withstand, oppose, prevent (5th cent.) 

1. trans.  

a. To meet and dispose of; to circumvent, do away with, remove (a difficulty, need, etc.); to prevent or avoid by anticipatory measures.

b. To anticipate, forestall. Obs. rare.

2. trans. To meet, encounter; to withstand, oppose. Obs. 

3. trans. To lie in the way between. Obs. rare.

"The endotherm asymmetry at 13 mole % GD1a suggests a phase transition which is more complex than a simple first order transition.  (Fig. 6 1B, 1C, also see ref. 34.)  It also obviates the possibility that a new species, such as mixed micelles, is formed in the dispersion (as was suggested for egg PC: GD1a dispersions having more than 10 mole% GD1a."

 - Barenholz et al., "Characterization of micellar and liposomsal dispersions of gangliosides and phospholipids", Advances in experimental medicine and biology 125:105 (1980)


Of course, knowing the meaning of this word is not enough to help me decipher this sentence: it would be nice if this paper actually had a Figure 6 1B and 1C.

Molecule of the day: trinitrobenzenesulfonic acid

The molecule of the day is trinitrobenzenesulfonic acid (TNBS).

It's often used to neutralize peptide terminal amino groups, but will react with any primary amine, and can also be used to measure the bilayer integrity of membranes containing phosphatidylethanolamine:

(Sadly, the "submitted" reference appears to have never made it into print.)

word of the day: lyotropic

The word of the day is lyotropic:

Etymology:  lyotrop- (in lyotrope adj.) + -ic suffix: see -tropic comb. form.
Physical Chem.  1. Associated with the change of internal pressure of a solution from that of the solvent which is caused by the solute. lyotropic series, a series in which ions are arranged in order of their lytropic effects, esp. their ability to cause precipitation of a lyophilic sol.   
2. Of a mesophase: having its phase transitions readily effected by a change of concentration. Also applied to the mesomorphism exhibited by such a mesophase. (OED)

Perhaps this definition from Case Western is a little more helpful:

"Liquid crystals come in two basic classifications: thermotropic and lyotropic . The phase transitions of thermotropic liquid crystals depend on temperature, while those of lyotropic liquid crystals depend on both temperature and concentration."


"The gangliosides, which are part of the lipid bilayer of the membranes differ in their lyotropic behaviour from the phospholipids and cholesterol which constitute the main components of the membrane.  The membrane phospholipids have two long hydrophobic chains, an interface region and a relatively small inogenic head group.  They are classified as 'non-soluble swelling amphipaths, implying that they do not form micelles but disperse spontaneously in water, forming bilyaered multilamellar large liposomes (MLV) or, upon ultrasonic irradiation small unilamellar vesicles (SUV).  In contrast, the gangliosides are 'soluble amphipaths' which form micelles in water.  The fact that, in spite of their two long hydrophobic chains the gangliosides are classified as 'soluble' amphipaths is explained by their large and highly negatively charged polar head group."

 - Barenholz et al., "Characterization of micellar and liposomal dispersions of gangliosides and phospholipids", Advances in Experimental Medicine and Biology 125:105 (1980).


I'm pretty sure they meant "ionogenic" instead of "inogenic".

I also have an irrepressible desire to look up the authors and mail them each a copy of Lynne Truss's Eats, Shoots, & Leaves.

molecules of the day: filipin and amphotericin B

The molecules of the day are filipin:

(PubChem)









and amphotericin B:

 (PubChem)

They're antibiotics that work by associating with cholesterol and thereby altering membrane structure.  (Not clear to me why that would select prokaryotic over eukaryotic cells: any ideas?)

word of the day: monotectic

The word of the day is monotectic:

The reversible transition, on cooling, of a liquid to a mixture of a second
liquid and a solid.  (IUPAC Compendium on Chemical Terminology)


"An equimolar mixture of dilauroyl phosphatidylcholine and distearoyl phosphatidylcholine, which shows a monotectic behaviour, is hydrolysed at all temperatures."

 - J.A.F. Op den Kamp et al., "Action of pancreatic phospholipase A2 on phosphatidylcholinebilayers in different physical states", Biochimica et Biophysica Acta 406:169 (1975).

Word of the day: sessile

The word of the day is sessile:

sessile, adj.




Etymology:  < Latin sessilis sitting down, dwarfed, stunted, < sess- , participial stem of sedēre to sit  

1. Having no footstalk. 
a. Bot. Of leaves, fruits, flowers, or other organs: Immediately attached by the base; not having a peduncle, pedicel, or the like. Hence of a species or variety (e.g. of oak) bearing sessile fruits: opposed to pedunculated. 
b. Zool. Of limbs or organs: Immediately in contact with the structure to which they are attached; having no connecting neck or footstalk. Also of certain animals.c. Pathol. Of morbid growths, warts, etc.: Adhering close to the surface.
2. Of certain animals: Sedentary, fixed to one spot; not ambulatory. Of cells: Immobile. Also in extended use. 
3. Crystallogr. Of a dislocation in a crystal: unable to migrate through the lattice; fixed. (OED)


"This is ridiculous!  Hive queens are supposed to be sessile!"

 - Tarvek, Girl Genius volume 12, page 103, Phil and Kaja Foglio

spider sighting

Found this spider outside my front door yesterday morning:

The community at spiders.us (because, as it turns out, there are people whose idea of fun is looking at other people's grainy cell phone pictures and trying to identify the spiders depicted therein: how did people live before the internet?) identified it as a wolf spider, but I didn't think the eye configuration looks quite right.

Molecule of the day: tripropionin

The molecule of the day is tripropionin:

It can be used as a soluble substrate for pancreatic lipase.

I would probably call it TriC3: a triglyceride of chain length 3.

Sun letter follow-up

On the one hand, the Sun published my letter; on the other hand, their editorial choices reveal that they completely missed the point.

I don't even know why they need to tamper with it at all: it can't be in the interest of conserving space, because then why replace parentheses with two m-dashes and the word "incidentally"?  I think it's quite audacious to start throwing unsolicited adverbs into other people's writing.

But let some good come of this incident: no more will I blame the authors of any idiotic letters I find printed in the Sun, for I know that the editors probably just butchered a letter that had once been filled with subtlety and nuance.

letter to the Sun: liquor store and crime correlation

In which I once again link all of our city's problems to a lack of STEM education:

Dear Baltimore Sun,

The city health officials who plan to strip non-conforming liquor stores of their licenses because of the Johns Hopkins University study linking them to violent crime (“City Targets Liquor Stores”, June 17 [warning: pay wall]) are confusing correlation with causation.  It could be that the liquor stores themselves are not causing the crime, but rather that some other underlying cause is causing both the non-conforming liquor stores and the violent crime.  The distinction is important, because if the liquor stores are not causing the crime, then closing them would not actually be predicted to decrease violent crime, and could even exacerbate it.

As it turns out, property vacancy also correlates with violent crime (for example, Goodstein, Ryan and Lee, Yan Y., Do Foreclosures Increase Crime? (May 2010). Available at SSRN: http://ssrn.com/abstract=1670842 or http://dx.doi.org/10.2139/ssrn.1670842).  If a non-conforming liquor store loses its license, it seems at least as likely that the store will end up as a vacant property than that the owners will decide to open a healthy food store in its place, as the city officials hope.

Before taking away licenses and, as a consequence, closing small businesses (that would furthermore disproportionately impact a particular ethnic group), the city needs to carefully consider the evidence to determine whether the benefits of doing so really are predicted to outweigh the costs.  This story once again emphasizes the importance of having a basic mathematics education (for no student in the first week of an introductory statistics course would confuse correlation with causation), both for our city officials as well as for our journalists.

Molecule of the day: terephthalic acid

The molecule of the day is terephthalic acid:

It's a precursor in making polyethylene terephthalate (PET).  It's in the news because of a new biobased (i.e., sustainable) route to producing p-xylene, which can then be converted to terephthalic acid: the currently used methods produce terephthalic acid from petrochemicals.

More anti-science sentiment in the Sun

A recipe for scones in today's Baltimore Sun (warning: pay wall) includes the words "Tips: I always use aluminum-free baking powder because I don't like the idea of eating metal."

Metals are actually a necessary component of your diet to maintain good health.  This concept is in fact so important that it's what we cover in the very first lecture of the Metabolism course for first-year medical students (here at what U.S. News & World Report considers the second-best medical school in the United States).  Calcium, potassium, and sodium maintain important membrane potentials, and magnesium, iron, zinc, manganese, copper, molybdenum, and selenium are required at the active sites of important enzymes, where they bind substrates, transfer electrons, withdraw electrons, or maintain enzyme conformation.

It's true that aluminum is not on this list (so far!), so if you want to avoid eating it, that's just fine: but please don't avoid it just because it's a "metal".  (Or, heaven forfend, a "chemical".)

Word of the day: emendation

The word of the day is emendation:

Etymology:  < Latin ēmendātiōn-em, noun of action < ēmendāre to emend v.

The action of emending.
1. Correction, reformation, improvement (of life, conduct, etc.). Obs.

2. a. Improvement by alteration and correction; esp. of literary or artistic products, methods of procedure, scientific systems, etc.; a particular instance of such improvement.
b. esp. The correction (usually by conjecture or inference) of the text of an author where it is presumed to have been corrupted in transmission; a textual alteration for this purpose. (OED)

"West's proposed emendations to the texts are couched in the meticulous language of classical scholarship, and take the form of suggestions and proposals; perhaps because Mitchell is not a classicist, he is emboldened to cast West's vision in stone.  His new translation not only deletes passages that West merely brackets or questions but omits even some passages that West thinks were 'expansions' by P himself."

 - Daniel Mendelsohn, "Battle lines: a slimmer, faster Iliad", 7 November 2011 The New Yorker

Word of the day: ouroboros

The word of the day is ouroboros:

Etymology:  < Greek οὐροβόρος, also οὐρη-, devouring its tail

The symbol, usu. in the form of a circle, of a snake (or dragon) eating its tail. (OED)

"The pleasure of the book comes from its descriptive daring -- Billie Holiday's voice sounds 'evacuated'; the evolution of media is envisioned as an ouroboros ('The book bit his tail and became a / disc') -- and from Mackey's refusal to decipher his narrative: 'Nonallegorical ground it / was we stood on.'"

 - "Books Briefly Noted", of Nathaniel Mackey's Nod House, 13 & 20 February 2012 The New Yorker

Word of the day: emolument

The word of the day is emolument:

Etymology:  < Latin ēmŏlŭ-, ēmŏlĭmentum profit, advantage; in most Latin Dicts. said to be < ēmōlī-rī to bring out by effort.
1. Profit or gain arising from station, office, or employment; dues; reward, remuneration, salary.
2. Advantage, benefit, comfort. Obs.

"What had Conn done to Feather that the latter found so unforgivable, irredeemable by emolument, by statements of praise and credit, by the persistent efforts of heartfelt remorse?  What hurt could so engross a man that he would determine to carry it with him to the grave?"

 - Michael Chabon, "Citizen Conn", 13 &; 20 February 2012 The New Yorker

Word of the day: spaldeen

The word of the day is spaldeen:

Origin:
said to be after Spalding  a trademark

 Chiefly New York City .

a smooth, pink rubber ball used in playing catch, stickball, etc. (dictionary.com)

"The paintings -- closeups of manhole covers with their cryptic labyrinthine pattern of raised welts, loving roseate sunsets that turned out to be the sheen and scuff on a spaldeen -- had multiplied; there were so many of them now that the artist had been obliged to carve a trail, as it were, among them, that would permit access to the kitchen table, where David and I now sat down."

 - Michael Chabon, "Citizen Conn", 13 & 20 February 2012 The New Yorker

Word of the day: ephebe

The word of the day is ephebe:

Etymology:  < Latin ephēb-us, < Greek ἔϕηβος, < ἐπί upon + ἥβη early manhood.

Ancient Greek Hist.
 Among the Greeks, a young citizen from eighteen to twenty years of age, during which he was occupied chiefly with garrison duty. (OED)

"The summer before his senior year of college, in 1997, he worked as an intern at The Paris Review. James Linville, who was then the magazine’s editor, recalled Rowan as an 'ephebe type, almost Truman Capote-like.'"

 - Lizzie Widdicombe, "The plagiarist's tale: the author of 'Assassin of Secrets' had a secret of his own", 13 & 20 February 2012 The New Yorker


There must be an additional connotation here that I'm not picking up on.

text of a letter I sent to the Baltimore Sun

Dear Baltimore Sun,

Doug Atwell of the Fells Point bar Rye scoffs at chemists ("A new class of cocktails", Feb 29), but perhaps if he knew more about chemistry he would be a better mixologist.

He would then know, for example, that the cooling power of ice cubes comes primarily from the phase transition of melting from solid to liquid, so while it is true that ice cubes with larger surface area chill a drink faster, it is precisely because they are also diluting the drink faster.

High-quality, natural ingredients are no less governed by the laws of chemistry than brightly-colored, synthetic ones are.  Chemistry is not scary, boring, or unnatural; it's a very useful way of understanding how the world works.

Molecule of the day: tyloxapol

The molecule of the day is tyloxapol:

The seminar I went to presented it as a standard lysosome toxin, but a quick search on the interwebs mostly emphasizes its role as a non-ionic detergent, and even searching for "tyloxapol lysosomes" only mentions its use to purify lysosomes (lysosomes readily take up tyloxapol, which makes them more buoyant, which makes them easier to separate from other cellular components by centrifugation (source)).

So perhaps the speaker mispoke, and meant that it was a lipase toxin.  Tyloxapol is apparently also known as Triton WR 1339, which is reported to inhibit lipoprotein lipase (source).

Equal prospects? How do we know?

Saw this story in the Naturejobs Newsletter: "Equal prospects for both sexes in science: Women as likely as men to be promoted, but fewer apply for jobs."

The way Natasha Gilbert seems to be spinning this story is as more evidence for a confidence gap: women don't face discrimination during promotion, and would succeed, if only they would make the effort.

But: is the best way to analyze these data to compare all women faculty to all male faculty (as this study does), or is it better to compare the women to the top 37%* of male faculty, and then see whether there are promotion discrepancies?  I.e., if it's really true that there are all these qualified women out there who aren't seeking faculty positions, who, if only they did, would bump out the bottom male faculty currently getting positions, then wouldn't that model predict that the women who do have the confidence to seek faculty positions are more qualified than male faculty as a whole, and wouldn't we predict women faculty to have a higher promotion rate than male faculty as a whole? Or does confidence not correlate with ability?

Not only would this experiment be hard to do, because I'm not sure what the best way is to identify the top 37% of male faculty, but also, the skills that get you hired might not necessarily get you promoted. (I.e., maybe you yourself were a very productive postdoc, but you turn out to be terrible at managing a lab.)


What do you think would be the best way to measure whether men and women of equal quality are being promoted at the same rate?


*Why 37%?  I got this ballpark figure from the fact that 27% of incoming faculty are women, so 73% must be men.  27/73 = 37.

This calculation is also problematic, though, because it assumes that postdocs are 50/50 women/men, and that those came from a pool of grad students that were 50/50, and those came from a pool of undergrads that were 50/50, etc.  If these ratios are less than 50/50 at earlier stages, then you would predict women faculty to be even more enriched for qualified candidates.  (Unless, once again, confidence doesn't correlate with ability.)  And that's not even considering the quality of the institutions that the postdocs are coming from.  In summary: the proper analysis here would be complicated indeed.