Sunday, October 06, 2013

thoughts on Science's predatory journal sting

I commented on this discussion on the American Chemical Society's LinkedIn page, but I know LinkedIn posts don't stay up for long, so I thought I would preserve it here for posterity.

The post was about this story from NPR, reporting on a piece in Science about a sting to expose predatory journals.

Here's my comment:

"The fatal flaw of the spoof study was that it lacked a negative control, but so too did this piece of stunt journalism.  Maybe he told too many coworkers about his project to be able to send it to Science, but what about Science Translational Medicine, Nature, The Journal of Biological Chemistry, etc. etc.?  It's true that the rate of acceptance of the spoof paper among open access journals was shockingly high, but if he's going to make the claim that this is a problem with open access and not with publishing in general, he really needs the traditional publisher control.  Any sort of argument that traditional publishers don’t have the same financial incentives to publish bad papers as open access journals that charge publication fees, and therefore are unlikely to accept the spoof study, is cute, but is not science.  Besides, many subscription-based publications, such as The Journal of Biological Chemistry, also charge publication fees, too, and have the same financial incentive to publish as many papers as possible.

"Predatory journals are an important issue, and I’m glad he’s raising awareness about it, but I’m not convinced this was the best way to do it.  In particular, I’m puzzled as to why he pretended to be from Africa.  He says “My hope was that using developing world authors and institutions would arouse less suspicion if a curious editor were to find nothing about them on the Internet”, but I thought the whole point was to reveal that editors of some journals don’t even bother to do even the most basic homework on the papers submitted.  By deliberately making the manuscript difficult to read, he undermines his claim that “This sting did not waste the time of many legitimate peer reviewers.”  I fear that this sting could very well erode trust in the scientific process, and might make Western journals even more suspicious of papers submitted from developing countries, simply because they are from developing countries."

Monday, September 16, 2013

phrase of the day: inter alia

The phrase of the day is inter alia:

[Latin, Among other things.] A phrase used in Pleading to designate that a particular statute set out therein is only a part of the statute that is relevant to the facts of the lawsuit and not the entire statute.
Inter alia is also used when reporting court decisions to indicate that there were other rulings made by the court but only a particular holding of the case is cited. (The Free Dictionary)

"The control of biological function by light is enabled, inter alia, by the incorporation of molecular photoswitches into biomolecules and bioactive compounds.

 - Willem A. Velema et al., "Optical control of antibacterial activity", Nature Chemistry doi:10.1038/nchem.1750 (published online

Friday, August 30, 2013

molecule of the day: anisomycin

The molecule of the day is anisomycin:

It's a natural product from Streptomyces that inhibits protein translation in eukaryotes.  It can be used to determine whether a phenomenon depends on protein synthesis.

Wednesday, August 28, 2013

Thursday, August 22, 2013

word of the day: schliere

The word of the day is schliere:

Etymology:  German, < regional Schliere (feminine) striæ, streaks, corresponding to Schlier (masculine) marl, < early new High German schlier (masculine and neuter), < Middle High German slier mud, related to Middle High German slier, sliere ulcer, < Old High German sclierrun (dative plural). 
b. A zone or stratum in a transparent medium whose density differs sufficiently from that of the surrounding medium for it to be detectable by refraction anomalies, usu. in consequence of pressure or temperature differences or composition inhomogeneities. (OED)

"With the introduction of the phase plate into the schlieren optical system and the development of double sector cells and synthetic boundary cells along with refinements in theory, great strides have been made in the accuracy of the determination of sedimentation coefficients (for a detailed account of these developments see reference 2)."

 - Howard K. Schachman, "Deductions from Hydrodynamic and Thermodynamic Measurements", Brookhaven Symposia in Biology 13:49 (1960)

Wednesday, August 21, 2013

word of the day: collimate

The word of the day is collimate:

Etymology:  < ‘collīmāre’, an erroneous reading, found in some edd. of Cicero, of Latin collīneāre, < col-, com- together + līnea line, līneāre to bring into a straight line. 
2. trans.
a. To place or adjust (a telescope) so that the line of sight is in the required position; to place (two telescopes, lenses, etc.) so that their optical axes are in the same line.
b. To make parallel, as a lens, the rays of light passing through it. (OED)

"General attrib. uses of pl. schlieren, with reference to an experimental method for the observation and recording of schlieren in transparent media, in which the specimen is illuminated with a collimated beam of light, and the diffraction pattern resulting from localized refraction of light rays by the schlieren is photographed or displayed on a screen."

 - OED

Friday, July 05, 2013

word of the day: timbal

The word of the day is timbal:

Etymology:  = modern French timbale (1646 in Hatzfeld & Darmesteter), Italian timballo , Spanish timbal , Portuguese timbal , timbale , substituted for, and apparently altered from, earlier French attabale (Cotgrave 1611), Italian taballo (Florio 1611), Spanish atabal , Portuguese attabale , see atabal n. It is not clear in which language or under what influence the change was made (perhaps in Italian, which had already dropped initial a): compare the French alteration of tabour to tambour. The spelling tymbal was apparently due to the influence of cymbal. 
1. Entomol. A membrane (resembling a drum-head) in certain insects, as the cicada, by means of which a shrill chirping sound is produced. (OED)

"The live cicadas he'd set loose in the church apparently had stagefright and refused to sing, although one perched on a microphone, as though to lip- (or timbal-) synch."

 - Nick Paumgarten, "Brood dude", 24 June 2013 The New Yorker

Thursday, July 04, 2013

word of the day: aspic

The word of the day is aspic:

aspic, n.1 
Etymology:  < French aspic asp, < Provençal aspic , unexplained derivative of Latin aspid-em , nominative aspis : see asp n.2 
1.a. By-form of asp n.2, used chiefly in poetry. 
b. attrib. 
c. fig. 
2. transf. ‘A piece of ordnance which carries a 12 pound shot. The piece itself weighs 4250 pounds.’ C. James Mil. Dict. 1816. (Perh. only French.) (OED)

aspic, n.2
Etymology:  < French aspic (in huile d' aspic vulgar form of huile de spic) for spic, < Italian spigo the Great Lavender, originally Spikenard, = Old French espic < Latin spīcus (in medieval Latin) Spikenard, doublet of spīca spike.
The Great Lavender or Spike ( Lavandula Spica), a plant from which a volatile aromatic oil is obtained. (OED)

Etymology:  < French aspic. Littré suggests its derivation < aspic asp, because it is ‘froid comme un aspic,’ a proverbial phrase in French. 
A savoury meat jelly, composed of and containing meat, fish, game, hard-boiled eggs, etc. Also attrib. in aspic-jelly. (OED)

"His painting 'A Visit from the Old Mistress' (1876) reports on the state of the nation a decade after 'Prisoners'.  A lone figure of authority, in this case a stony white dowager, faces three antagonists: variously unwelcoming black women, in head scarves, one of whom holds a child.  The interloper evidently must bargain for services that used to be her perquisite.  She may get them, but with no conceivable abatement of the festering memories and the interminable consequences of slavery.  The painting's shadowed tones and ruddy hues suspend the scene in an aspic of anguish."

 - Peter Schjeldahl, "The seething hell: portraying the Civil War", 3 June 2013 The New Yorker

I have no idea what that means.  Is it literally the color of an aspic (meat jelly)?

Wednesday, July 03, 2013

word of the day: rangy

The word of the day is rangy:

Etymology:  Probably partly < range n.1 + -y suffix1, and partly < range v.1 + -y suffix1. 
1. orig. U.S. 
a. Of an animal: adapted for or capable of ranging; having long limbs and a lean body.
b. Of a person: tall and thin, with long limbs. 
c. Of a plant or tree: tall and spindly with long branches, or a long stem or trunk; (of a branch, etc.) long and thin. 
2. orig. and chiefly Austral. Mountainous, hilly. 
3. Chiefly N. Amer. Of a place: having room for ranging; spacious.
4. Of great scope or compass; expansive, broad, wide-ranging. (OED)

"But Homer's most important efforts, like 'Prisoners', are quiet, singling out persons within uniforms.  Of special note is 'The Bright Side' (1865), in which four black Union teamsters relax outside a tent, from which another pokes his head, clenching a pipe in his teeth and glaring at us.  Here are men of rangy dignity, defying any objectifying gaze."

 - Peter Schjeldahl, "The seething hell: portraying the Civil War", 3 June 2013 The New Yorker

No, I still don't know what he means.  "Wide-ranging"?  But what does that mean when applied to dignity?

Tuesday, July 02, 2013

word of the day: ambrotype

The word of the day is ambrotype:

Etymology:  ? < Greek ἄμβροτος immortal (? imperishable), or perhaps amber n.1 and adj., + type n. 
The name given in U.S. to a photograph on glass, in which the lights are produced by the silver, and the shades by a dark background showing through. (OED)

"'The Civil War and American Art' complements another show at the Met, 'Photography and the American Civil War', which opened in April with a theatrical profusion of vintage prints, stereographs, ambrotypes, and tintypes, notably from the studios of the pioneering photojournalist Mathew Brady and of Alexander Gardner, a former Brady staff photographer who set up in competition with him."

 - Peter Schjeldahl, "The seething hell: portraying the Civil War", 3 June 2013 The New Yorker

Monday, July 01, 2013

word of the day: casuistry

The word of the day is casuistry:

Etymology:  < French casuiste (Spanish casuista , Italian casista ), < Latin cāsus case

The science, art, or reasoning of the casuist; that part of Ethics which resolves cases of conscience, applying the general rules of religion and morality to particular instances in which ‘circumstances alter cases’, or in which there appears to be a conflict of duties. Often (and perhaps originally) applied to a quibbling or evasive way of dealing with difficult cases of duty; sophistry. (OED)

"Aside from staged eccentricity, freak tourism, and eye-popping spectacle, Ripley trafficked in anachronism, hyperbole, and casuistry."

 - Jill Lepore, "The odyssey: Robert Ripley and his world", 3 June 2013 The New Yorker

Sunday, June 30, 2013

word of the day: verglas

The word of the day is verglas:

Etymology:  French, < verre verre n. + glas (modern French glace ) ice: see glace n.1

n. the phenomenon of rain freezing as it falls and forming a glassy coating on the ground, trees, etc.

"In 2008, he climbed the Nordwand in two hours and forty-seven minutes - less time than it takes to watch 'Cloud Atlas'.  The style was pure, too: he waited until a storm had left fresh ice and covered old tracks, and he used no ropes or protection of any kind - just crampons and ice axes, in a technique called dry-tooling.  Later, he repeated the climb for a film crew, doing pitches over and over, waiting for the setup of each shot, and the footage of him dry-tooling verglas, and running up near-vertical snowfields, where one mistake could mean a mile-long plunge, brought him international renown."

 - Nick Paumgarten, "The manic mountain: Ueli Steck and the clash on Everest", 3 June 2013 The New Yorker

Sunday, June 16, 2013

word of the day: belay

The word of the day is belay:

Etymology:  Old English bi- , belęcgan < Germanic *bilagjan, in Old High German bileckan , bilegen , modern German belegen , Dutch beleggen ; < bi- , be- prefix + lagjan , in Old English lęcgan to lay v.1
5.a. Naut. To coil a running rope round a cleat, belaying pin, or kevel, so as to fasten or secure it; to fasten by so putting it round. Said especially of one of the small ropes, used for working the sails. Also in Mountaineering. (OED)

"After an hour, Steck and the others reached the level of Camp 3, where they would have to traverse the face to get to their tent, which meant they needed to cross over the fixed line.  They chose a spot where four Sherpas were at the belay, below the lead fixer, and moved slowly past them, taking care, Steck says, not to touch the ropes with their crampons or to kick chunks of ice onto the Sherpas working below."

 - Nick Paumgarten, "The manic mountain: Ueli Steck and the clash on Everest", 3 June 2013 The New Yorker

Saturday, June 15, 2013

word of the day: serac

The word of the day is serac:

Etymology:  < Swiss-French sérac, originally the name of a kind of white cheese; the transferred application was doubtless suggested by similitude of form. (OED)

"By the end of the month, they were established at Camp 2, at 21,300 feet, beyond the top of the Khumbu Icefall, a tumbling portion of the Khumbu Glacier mined with crevasses and seracs."

 - Nick Paumgarten, "The manic mountain: Ueli Steck and the clash on Everest", 3 June 2013 The New Yorker

Friday, June 14, 2013

word of the day: sclerotic

The word of the day is sclerotic:

Etymology:  < medieval and modern Latin sclērōticus (medieval Latin in feminine form sclerotica n.), < late Greek *σκληρωτικός having the property of hardening, pertaining to sclerosis or hardening, < σκληροῦν : see scleroma n. 
A. adj.1 
1.a. Anat. In sclerotic coat, sclerotic membrane, sclerotic tunic = B. 1 
.b. Of or pertaining to, or connected with the sclerotic coat of the eye. sclerotic bone, sclerotic plate = sclerotal n.; sclerotic ring, the ring formed by the sclerotic bones of the eyeball.
 2. Of medicines: Adapted to harden the tissues.
3. Pathol. Of or pertaining to sclerosis; affected with sclerosis. 
4. Bot. Hardened, stony in texture. sclerotic cells, grit-cells or sclereids; sclerotic parenchyma, grit-cells or stone-cells in pears, etc.
5. fig. Unmoving, unchanging, rigid. (OED)

"The V.A. is a sclerotic and overwhelmed bureaucracy; it barely has the resources to maintain its current level of health coverage, let alone expand it."

 - Nicholas Schmidle, "In the crosshairs", 3 June 2013 The New Yorker

Thursday, June 13, 2013

word of the day: nystagmus

The word of the day is nystagmus:

Etymology:  < post-classical Latin nystagmus a rapid involuntary movement of the eyeball (F. Boissier de Sauvages Nosologia Methodica (1768)) < ancient Greek νυσταγμός nodding, drowsiness < the base of νυστάζειν to nod, to be sleepy ( < the same Indo-European base as Lithuanian snūsti (stem snūd-) to begin to doze, grow drowsy) + -μος, suffix forming nouns.
1. Involuntary, rapid, oscillating movement of the eyeballs (most commonly from side to side); an instance or type of this. (OED)

"Just before 2 A.M. on March 5, 2010, Kyle was driving alone in central Dallas, near Love Field, when he lost control of his truck and crashed into a wooden fence, nearly ending up in someone’s swimming pool. A policeman found Kyle with 'bloodshot eyes, slurred speech, breath smelling of alcoholic beverage, unsteady balance and nystagmus.' Kyle told him, 'I’m stupid. I was drinking and driving. I missed the turn. It was my fault.'"

 - Nicholas Schmidle, "In the crosshairs", 3 June 2013 The New Yorker

Wednesday, June 12, 2013

word of the day: salmagundi

The word of the day is salmagundi:

Etymology:  < French salmigondis (in the 16th cent. salmiguondin, salmingondin), of obscure origin. 
1. Cookery. A dish composed of chopped meat, anchovies, eggs, onions with oil and condiments. (OED)

"'Colin Quinn Unconstitutional' is a salmagundi of alternative history (George Washington loved 'setting fires in barns and torturing animals'), mordant rumination ('No praying in school - unless some kid is shooting up the school'), and arresting analogy (he likens the separation of powers to the Three Stooges, with Moe walloping Curly when he gets out of line)."

 - Tad Friend, "On closer inspection: framers unframed", 3 June 2013 The New Yorker

Tuesday, June 11, 2013

word of the day: ambit

The word of the day is ambit:

Etymology:  < Latin ambit-us a going round, a compass; < amb- about + -itus going, < ī-re to go. 
1. A circuit, compass, or circumference. 
2. esp. A space surrounding a house, castle, town, etc.; the precincts, liberties, ‘verge’. 
3. The confines, bounds, limits of a district.
4. fig. Extent, compass, sphere, of actions, words, thoughts, etc. (OED)

"Two years earlier, in a commencement address at Xavier University, he discussed the importance of being able 'to see the world through the eyes of those who are different from us—the child who’s hungry, the steelworker who’s been laid off, the family who lost the entire life they built together when the storm came to town.'  He went on, 'When you think like this—when you choose to broaden your ambit of concern and empathize with the plight of others, whether they are close friends or distant strangers—it becomes harder not to act, harder not to help.'"

 - Paul Bloom, quoting Barack Obama, "The baby in the well: the case against empathy", 20 May 2013 The New Yorker

Monday, June 10, 2013

word of the day: biff

The word of the day is biff:

Etymology:  Imitative.
1.a. trans. To hit, strike. Also to biff (a person) one. 
b. fig. To deal a blow to, to refute, to ‘stump’ (see also quot. 1895). 
c. To throw. Also intr. Austral. and N.Z. 
2. intr. To go, proceed. Esp. with off, to leave, depart. 
3. The verb used adverbially with go, in the sense of ‘with a violent blow’.  (OED)

"Are you about to get busted for a zero-to-sixty presumption of intimacy? Biffed by a stranger’s unaccountable rage? Anytime you are approaching an ambush point, Social Trapster will flare red, and suggest an alternate route: 'Ixnay on the oopidstay, this person was involved in the making of that film!'"

 - Karen Russell, "Vision Quest", 20 May 2013 The New Yorker

Sunday, June 09, 2013

word of the day: gnome

The word of the day is gnome:

Etymology:  < Greek γνώμη thought, judgement, opinion; plural γνῶμαι sayings, maxims (Latin sententiae ), < γνω- root of γιγνώσκειν to knows adj.

A short pithy statement of a general truth; a proverb, maxim, aphorism, or apophthegm. Also spec. with reference to Old English verse. (OED)

"Where some scholars are gnomic in style, Nagy piles his sentences high with thin-sliced exposition. ('There are about ten passages—and by passages I simply mean a selected text, and these passages are meant for close reading, and sometimes I’ll be referring to these passages as texts, or focus passages, but you’ll know I mean the same thing—and each one of these requires close reading!')"

 - Nathan Heller, "Laptop U: Has the future of college moved online?", 20 May 2013 The New Yorker

Tuesday, May 28, 2013

molecule of the day: milrinone

The molecule of the day is milrinone:

It's a drug that provides short-term benefits for heart transplant and heart failure patients by increasing heart contractility, but in the long-term it causes arrhythmia.  It inhibits type 3 phosphodiesterases (PDE3s).  Recent work suggests that its target in heart is probably the A isoform (PDE3A) (which is not that surprising given that it's PDE3A that's mostly expressed in heart muscle).

word of the day: inotropic

The word of the day is inotropic:

Etymology:  < German inotrop (T. W. Engelmann 1896, in Arch. f. ges. Physiol. LXII. 555): see ino- comb. form and -tropic comb. form.
Modifying the contractility of muscle. (OED)

"A positive inotropic cardiotonic agent with vasodilator properties."

 - PubChem entry on milrinone

Sunday, May 26, 2013

word of the day: diamanté

The word of the day is diamanté:

Etymology:  French, past participle of diamanter to set with diamonds, to make shine like diamonds.
Material to which a sparkling effect is given by the use of paste brilliants, powdered glass or crystal, etc. Also attrib. (OED)

"In 'Country Girl', O'Brien uses the frame of memory to crop the commonplace out of life.  She loses her virginity in a field outside Dublin, but recalls 'the damp of the grass, a diamanté hair slide that I had lost, the peas that kept slipping off his fork.'"

 - Lauren Collins, "Ink: where she was from", 20 May 2013 The New Yorker

Saturday, May 25, 2013

phrase of the day: wildcat strike

The phrase of the day is wildcat strike:

An employee work stoppage that is not authorized by the Labor Union to which the employees belong.  (

"On a later night, however, they return to lob Molotov cocktails, and a security guard is hurt; to avoid trouble, the friends take off for the summer break, hitching a ride to Italy with a revolutionary film collective in (of course) a VW van.  The sun glares, the strikes are wildcat, and the masses await enlightenment through cinema.  Bliss is it in that dawn to be alive."

 - Anthony Lane, "Battle weary: 'Iron Man 3' and 'Something in the Air'", 6 May 2013 The New Yorker

Friday, May 24, 2013

word of the day: fug

The word of the day is fug:

colloq. (orig dial. and School slang).
A thick, close, stuffy atmosphere, esp. that of a room overcrowded and with little or no ventilation. (OED)

"Instead, they exist in a constant fug that I took for cigarette smoke or tear gas, but that slowly resolves itself into a nimbus of ill-defined needs - a haze of becoming, with the foothills of adulthood starting to loom ahead."

 - Anthony Lane, "Battle weary: 'Iron Man 3' and 'Something in the Air'", 6 May 2013 The New Yorker

Thursday, May 23, 2013

word of the day: logorrhea

The word of the day is logorrhea:

Etymology:  < Greek λόγος word + ῥοία flow, stream (probably after diarrhœa n.).
Excessive volubility accompanying some forms of mental illness; also gen., an excessive flow of words, prolixity.  (OED)

"To be honest, the film is a whiney and logorrheic mess until Stark, after a couple of misadventures, finds himself in Tennessee, just before Christmas, hauling a broken Iron Man suit through the snow like a toboggan."

 - Anthony Lane, "Battle weary: 'Iron Man 3' and 'Something in the Air'", 6 May 2013 The New Yorker

Wednesday, May 22, 2013

molecule of the day: benzopyrene

The molecule of the day is benzopyrene:


It's a carcinogen found in tobacco smoke, among other things, and can be used to induce lung tumors in mice when injected into the peritoneal cavity (tummy), as in this paper, the star of today's Center for Metabolism and Obesity Research journal club.  One of the attendees described it as "that chickenwire compound".

I asked the presenter why, after injecting it into the peritoneal cavity, benzopyrene would cause tumors in the lung (after all, the paper uses a fancy aerosol device to deliver the 3-bromopyruvate (the chemical they were testing to see whether it prevented the tumors from forming), so why not use that to deliver the benzopyrene, too?  Wouldn't that be more relevant anyway for a carcinogen found in tobacco smoke?), and he thought that the authors were just looking at lung tumors and not really interested in any tumors that may or may not have formed in other parts of the body.  I guess intraperitoneal injection is the easiest way to deliver a drug to a mouse, and if it works to produce the desired lung tumors, then good enough?

Reading a bit more, I learned that benzopyrene is actually a "pro-carcinogen": after benzopyrene enters your body, you metabolize it into another molecule, 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene:
which is the actual carcinogen.  It fits into the double helix of the DNA strand, which can cause the DNA to be copied incorrectly and introduce mutations, which can then cause cancer.

word of the day: cadre

The word of the day is cadre:

Etymology:  French cadre frame (e.g. of a picture), also used in sense ‘l'ensemble des officiers et sous-officiers d'une compagnie’ (Littré), < Italian quadro < Latin quadrum four-sided thing, square. 
1. A frame, framework; scheme.
2. Mil.a. The permanent establishment forming the framework or skeleton of a regiment, which is filled up by enlistment when required. Also of an R.A.F. squadron. Also attrib. 
b. The complement of officers of a regiment; the list or scheme of such officers.(After the Indian Mutiny, the cadres of Native Regiments which had been disbanded were kept in the Indian Army List for regulating promotions. In the parliamentary discussions about the amalgamation of the Indian with the British Army, the word was in constant use in this sense.)
 3.a. In Communist countries, a group of workers, etc., acting to promote the interests of the Communist Party; also, a member of such a group; = cell n.1 19.
b. In the People's Republic of China, an office-holder in a Party, governmental, or military organization; also more widely, one who holds a position, esp. in a local organization, school, etc. Also attrib., esp. as cadre school.  (OED)

"As the sharp end of a counter-insurgency strategy, McChrystal's approach resembled the C.I.A.'s Phoenix program during the Vietnam War, when the United States tried, and failed, to suppress the Vietcong by detaining and assassinating thousands of suspected militants and cadre leaders."

 - Steve Coll, "Remote control: our drone delusion", 6 May 2013 The New Yorker

Tuesday, May 21, 2013

word of the day: gravid

The word of the day is gravid:

Etymology:  < Latin gravidus, < gravis burdened, heavy (see grave adj.1, grave n.1 Compare French gravide.
Pregnant, heavy with young.

"Never fear.  I know the difference between
arteries and ardor, arbor and treed,
my bower and a weak-kneed need, a harbor
where one might moor tonight and a port worth
the oars' effort to come ashore for, a bit
part and the serpent's gravid apple."

 - Dora Malech, "To the you of ten years ago, now", 6 May 2013 The New Yorker

Monday, May 20, 2013

word of the day: fer-de-lance

The word of the day is fer-de-lance:

fer-de-lance, any of several extremely venomous snakes of the viper family (Viperidae) found in diverse habitats from cultivated lands to forests throughout tropical America and tropical Asia. (Britannica)

"The rain forests of Mosquitia, which span more than thirty-two thousand square miles of Honduras and Nicaragua, are among the densest and most inhospitable in the world.  'It's mountainous', Chris Begley, an archaeologist and expert on Honduras, told me recently.  'There's white water.  There are jumping vipers, coral snakes, fer-de-lance, stinging plants, and biting insects.  And then there are the illnesses - malaria, dengue fever, leishmaniasis, Chagas'."

 - Douglas Preston, "The El Dorado machine: a new scanner's rain-forest discoveries", 6 May 2013 The New Yorker

Shouldn't that be "fers-de-lance"?

Sunday, May 19, 2013

word of the day: mishegoss

 The word of the day is mishegoss:

Etymology:  < Yiddish meshugas < Hebrew mĕšuggaʿaṯ , use as abstract noun of feminine of mĕšuggaʿ meshuga adj.(Show Less)
Esp. in Jewish usage: madness, craziness; nonsense, foolishness; (as a count noun) a foolish idea; a foible, an idiosyncracy.

"In 1983, around the time that Berman moved to Tuxedo Park, some of his former students received invitations to purchase 'a limited subscriber's edition of a monumental novel'.  It was Berman's magnum opus.  For many alumni, the book - a four-hundred-and-eighty-three-page volume, beautifully published by a former Berman student - is the only window they've had onto their mysterious teacher.  'His whole universe of mishegoss is in there - the art, the music, the literature, the sex', a college professor who has spent many years trying to figure out Berman says."

 - Marc Fisher, "The master: a charismatic teacher enthralled his students.  Was he abusing them?", 1 April 2013 The New Yorker

Saturday, May 18, 2013

word of the day: halt

The word of the day is halt:

Etymology:  A Common Germanic adj.: Old English halt, healt = Old Frisian, Old Saxon halt (Middle Dutch halt, hout, Old High German, Middle High German halz, Old Norse haltr (Swedish, Danish halt), Gothic halt-s < Old Germanic *halt-oz.(Show Less)
arch. and literary.
Lame; crippled; limping. (OED)

"When I asked Berman, who is now seventy-eight, to talk with me, he wrote that he was 'very near death' and that he saw no point in meeting: 'All you would discover is a rather halt old man in deteriorating health.  What you most likely would not perceive is such a person who never in his long life intentionally injured anyone.'"

 - Marc Fisher, "The master: a charismatic teacher enthralled his students.  Was he abusing them?", 1 April 2013 The New Yorker

Monday, May 06, 2013

word of the day: humic

The word of the day is humic:

Etymology:  Latin humus ground, mould + -ic suffix. 
Of or pertaining to humus or mould; present in or of the nature of humus; rich in humus; also, formed or derived from plant remains. (OED)

"Patented Inhibitor Removal Technology eliminates humic substances and other PCR inhibitors."

 - product description for PowerSoil® DNA Isolation Kit from Mo Bio Laboratories, Inc.

Tuesday, April 30, 2013

“I didn’t hear about this experiment until I was a freshman at Brown”

At the Herbert Tabor Research Award Lecture at the American Society for Biochemistry and Molecular Biology meeting, in his talk “Chaperonin-mediated protein folding”, Prof. Arthur Horwich of Yale University and the Howard Hughes Medical Institute opened by regaling us with the story of the famous experiment by Christian Anfinsen.  The hypothesis was that all of the information required for a protein to fold into its three-dimensional shape was encoded in the amino acid sequence.  He tested the hypothesis by treating the protein with urea and beta-mercaptoethanol (BME), chemicals that cause the protein to unfold, then he slowly removed the urea and BME, and amazingly he recovered the protein’s activity, meaning that it had folded correctly.  This is amazing because the number of possible arrangements the protein could assume is huge, and yet it was able to find the right one.  The experiment is elegant, and it won a Nobel Prize in 1972.

It’s a common story to use when beginning a talk on protein folding, but I was more interested by what he said next: “I didn’t hear about this experiment until I was a freshman at Brown”, as if he had expected to have heard about it earlier.

I think this story illustrates the gulf between what scientists expect the public to know and what the public actually knows.  I went to an excellent high school, but my ninth-grade biology class didn’t really discuss biochemistry at a molecular level, and for pretty fair reasons: we didn’t have chemistry until tenth grade, so I’m not sure what would have been gained by talking about the fact that proteins are made of amino acids and the protein folding problem.  In Advanced Placement Chemistry in eleventh grade, we spent a good deal of time on intermolecular interactions, so we probably could have applied those principles to proteins, but it was a chemistry class, not a biochemistry class, so we didn’t.  So even as a definitely more-educated-in-chemistry-than-average student, I, as Prof. Horwich, entered college having never heard of the Anfinsen experiment, or indeed of protein folding.  We scientists would do well to remember that when trying to communicate with the public.

Monday, April 29, 2013

what is the best way to confront misogyny and racism?

Taking an (at least in my opinion) well-earned day recovering from EB2013 and SXMAR2013, I spent a good part of it looking over these entertaining blogs.

I'm a bit torn.  Racism and sexism (like other -isms, capitalism, socialism, etc.) are societal structures that have, over our lifetimes, been cultivated in every one of us (try the Harvard Implicit Association Tests if you haven't already).  I'm not convinced that labeling individuals as "racists" (so that you can then peace out on them) is productive: it implies that racism is something that can be isolated, and exists in some individuals, and not others, and all we have to do to solve racism is to stay away from those bad people.  I'm not the only person who thinks this: I've even heard the hypothesis that a good deal of the racial problems we continue to have in America today can be traced to the fact that Adventures of Huckleberry Finn (a book I love, by the way), which trades in the only-bad-people-are-racists view, is considered the definitive Great American Novel about race and is required reading in many schools, while Uncle Tom's Cabin (a book I haven't read, but this is how the hypothesis goes), which trades in the racism-is-a-structure view, is not.

On the other hand, I'm extremely sympathetic to the idea that denouncing racism and misogyny is more important than considering racists' and misogynists' feelings.  Racism and misogyny are much more offensive than being imperfectly polite while pointing out that people are being racist and misogynist.  And, to paraphrase Prof. Richard Dawkins, when someone calls you "shrill" (or the worse, more specifically misogynist words leveled at MTFOB), what they really mean is that they're unable to criticize the content of your message.

On the third hand: I think tone actually is really important when trying to communicate.  (I've been thinking about this more recently in the context of science communication: starting off with a I've-been-in-school-for-decades-and-know-more-than-you-mortals-ever-will is not a good strategy.)  I don't know if anyone has ever actually been persuaded to change their ways by statements like “FUCK YOU, you piece of shit racist"; maybe something like, "Hey, did you know the word 'gyp' comes from the word 'gypsie' and perpetuates negative stereotypes about certain groups of people being untrustworthy?  No?  But now you do, so now you know when you use that word you might offend people: maybe the word 'swindle' would better convey what you actually mean" would be more effective.  No one has ever regretted taking the high road.

But (and now we come to synthesis): I think it's extremely important not to let the perfect be the enemy of the good.  If someone says something racist or misogynist, I think the most important thing is to speak up: not just to let the person saying it know that that's not cool, but, more importantly, to signal to everyone else who heard that person say the racist or misogynist thing that you don't approve.  If you have to choose between letting the moment slip by because you can't think of the perfectly crafted message, or just spitting something out that, in hindsight, could have been better phrased, choose the latter.  It's pretty likely that the person you're speaking to will get nasty (no one likes being accused of being racist or misogynist), but this is noble work, and the more everyone speaks up, the more socially acceptable it will be and the easier it will be for everyone.

It just takes four words: "Hey, that's not cool."

Friday, April 26, 2013

"Alternative" career panel

Mid-day Saturday, I attended the American Society for Investigative Pathology's 13th Annual Workshop on Graduate Education in Pathology, "We can't all be PIs: preparing graduate students for alternative career paths".

I think panels like these are just wonderful (supporting evidence: this event was extremely well-attended), but I thought the title of the event could have been better.  It's true that we call can't be PIs (principle investigators, or the traditional science professor): in order for it to be sustainable, each PI would, over the course of his or her career, train exactly one replacement.  In fact, many more students and even postdocs are trained than faculty positions are available.  But then this is precisely why "alternative" is not a great word to use here.  People who end up as tenure-track faculty are, in fact, a tiny minority of science PhDs, so it's the academic track that really should be called "alternative".

But also: not everyone wants to be a PI, even if they could be one.  This can be hard for many scientists to imagine (even people who are not, themselves, PIs: I was once at a career fair where an industrial scientist justified his job as "well, being a professor is clearly the best job, but we can't all do that"), but, in fact, not everyone loves doing bench science.  Not everyone loves writing grants.  It's not just that we can't all be PIs: even if we could, not all science PhDs would be happy doing that.  In fact, I think the fact that these sorts of panels are, in my experience, always extremely well-attended, is itself evidence that these sorts of people pursuing PhDs in science, the sort who don't want to be professors, are not that uncommon.  There are many, many important ways science PhDs can contribute to society, but calling these careers "alternative" and saying "we can't all be PIs" doesn't do much to remove the stigma.

It was an admittedly small sample size, so I'm not sure what if anything we can conclude, but I did make the following observation.  The panel had four members, three female and one male.  All three female panel members mentioned that one major reason they chose their careers (over, say, the coveted "PI" role, or even an industrial bench science role) was "work-life balance".  Also, it turns out that all three of the female panelists were married to scientists, of the more "traditional" type (two faculty, one industrial).  Meanwhile, the one male panelist mentioned that after working for a year and a half at a law firm, he started law school at night, while still working full-time at the law firm, with three children.  I don't know what the male panelist's life partner does, but I suspect she's a housewife.

It made me wonder about the degree environment contributes to our "choices" when it comes to work-life balance.  The high school teacher panelist was clearly very happy with the career she had chosen.  But if she had a stay-at-home husband, she may have chosen differently, either because she would have more time to dedicate to a job that required more hours because she could rely on her husband to provide child care, or because she would need a job with a higher salary in order to support her family.  I've heard that the choice of a spouse is the single most important career decision you will make.  I do think one major challenge facing women in STEM [science, technology, engineering, and mathematics] (and, therefore, everyone) is the fact that women in STEM are more likely to have spouses in STEM than men in STEM are.  "Traditional" careers in STEM (like most careers) are still built on the model of employing a breadwinner who has a homemaker at home to take care of things.  This model is not sustainable.

The microbes within us

Shorter thoughts are going to Twitter, but this will be the first in a series of longer posts of thoughts from #EB2013:

Bright and early on Saturday morning I attended the symposium "Managing the microbiome in human GI disease" put on by the American Society for Nutrition.  (The Experimental Biology meeting is made up of six societies: the American Society for Biochemistry and Molecular Biology (the reason for which I was ostensibly attending), the American Society for Nutrition, the American Society for Investigative Pathology, the American Society for Pharmacology and Experimental Therapeutics, the American Association of Anatomists, and the American Physiological Society.  These societies are themselves integrative and interdisciplinary, so any given symposium title could be difficult to assign to which society was sponsoring it.)

The emphasis of the symposium was on inflammatory bowel disease, but as an aside the speakers mentioned recent work on the relationship between obesity and the microbes inhabiting our guts.  For example, you can transfer the bacteria from a fat mouse to a lean mouse, and the lean mouse will gain weight (without changing how much it eats or its physical activity).

I was reminded of this later in the week when I met a graduate student who was researching obesity, but felt that she should move to some other disease for her postdoc, where she could contribute more to potential therapeutics and actually helping patients, since obesity is "preventable".

It got me to thinking about the way that we teach metabolism to the medical students.  We teach them that "calories in - calories out = weight gain", which is true: if you eat less and exercise more, you will lose weight.

But it's also true that for every human cell in your body, there are ten bacterial cells.  Most of these bacteria live in your gut, eating the same food you eat.  The calories they consume and expend are crucially important for how many calories are left available to you .  (The agricultural industry certainly appreciates this fact: they treat their livestock with low doses of antibiotics not to prevent bacterial infection, but to make them gain weight.)  As a society we tend to blame obese patients for making bad choices, but it's not like I chose what kinds of bacteria are living in my gut.

We're just beginning to learn about how specifically our gut bacteria contribute to our metabolism, so maybe that's why we don't want to include that when we teach metabolism.  We're not at the stage where we can tell people to eat certain brands of yogurt to solve certain medical problems (although I do know a scientist who believes he has cured his lactose intolerance by eating yogurt and colonizing his GI tract with the appropriate strains).  But we do know that our microbial communities are extremely important, and I think we're doing our students a disservice when we don't tell them that.

Thursday, April 25, 2013

new Twitter feed

Longer thoughts will continue to be posted here, but for microblogging please see my new Twitter feed @ElizabethJPetro .

(Thought I would prefer the term centi- or deciblogging: 1400-14,000 characters seems more realistic for blog posts than 140,000,000.)

Friday, April 19, 2013

letter to the LA Times: increased or reduced risk of transmission?

Here is the gist of a letter I wrote to the Los Angeles Times:

"Your 17 April 2013 article 'HIV concentrations in breast milk higher at earlier, abrupt weaning' states 'HIV-infected mothers who breast-fed exclusively longer than the first four months after birth had less risk of transmitting the virus to their babies through their milk, researchers said.'

"Here's what the Science Translational Medicine paper actually says about the risk of HIV transmission: 'Viewed from an intent-to-treat perspective, the risk of late postnatal transmission was 7.6% in the group randomized to stop breast-feeding at 4 months and 10.2% in the group randomized to continue breast-feeding (RH, 0.67; 95% CI, 0.39 to 1.15).'

"I.e., HIV-infected mothers who breast-fed exclusively longer than the first four months after birth had an increased risk of transmitting the virus to their babies through their milk."

It's true that HIV concentrations were higher in the milk collected at 4.5 months from the mothers who stopped breastfeeding at four months, but that milk was collected after the babies had stopped drinking it.   It's also true that adherence to the regimen was incomplete, which led to the "excess transmission risk" that the authors mentioned, but the fact remains that the risk was still lower in the group randomized to stop breastfeeding.

I think the culprit here is this sentence from the abstract: "This may explain the reduced risk of HIV-1 transmission associated with exclusive breast-feeding and why early weaning does not achieve the magnitude of HIV prevention predicted by models."  I think what the authors meant by "reduced" here is "reduced compared to what you would expect", but I can only come to that conclusion after having read the entire article.  STM is not an open-access journal: other readers of the LA Times (and, indeed, the science journalist that wrote the article) might not have the same opportunity I have.

Monday, April 08, 2013

word of the day: sui-generis

The word of the day is sui-generis:

Etymology:  Latin.
lit. Of one's or its own kind; peculiar. Also used attrib. †Also illiterately as n., a thing apart, an isolated specimen. (OED)

"But for the sheer density of material and effort, there is nothing like 'The Rose'.  You may not look at it so much as gawk at it, in the chapel-like black chamber, with dramatic lighting, that it commands in the show.  It strikes me as neither good art nor bad but a sui-generis folly that lends itself to mythic reflections."

 - Peter Schjeldahl, "Flower power: A Jay DeFeo retrospective", 18 March 2013 The New Yorker

Sunday, April 07, 2013

word of the day: amatory

The word of the day is amatory:

Etymology:  < Latin amātōri-us of or pertaining to amātor a lover.
A. adj.
Of or pertaining to a lover, to love-making, or to sexual love generally. 
B. n.
A love-potion, a philtre.  [ < Latin amatōrium.] (OED)

"From the beginning, he anticipated attacks similar to those which destroyed Yanin.  He had led a healthy amatory life - he was the object of adoration by many female dancers and countless fans - and it was clear that he had rivals in the company, others who had hoped to lead the Bolshoi."

 - David Remnick, "Danse macabre: A scandal at the Bolshoi Ballet", 18 March 2013 The New Yorker

Saturday, March 09, 2013

word of the day: crotchet

The word of the day is crotchet:
Etymology:  Middle English < French crochet hook, diminutive of croche crook, hook: see crochet n.
I. = crocket n.1 
1. Archit. = crocket n.1 2; also transf. to buds or branches. 
2. = crocket n.1 1. Obs. (Cf. French crochet.) In mod. dial. cratchet = the crown of the head.
II. A hook or hooked instrument. 
3. A small hook, esp. for fastening things; an ornamental hook serving as a brooch or fastening.
4. Surg.a. A hook-like instrument.
b. spec. an instrument employed in obstetrical surgery. 
5.a. A hook used in reaping: see quot. 1833. 
b. A hook fastened with straps on the back of a porter for carrying parcels.  [= French crochet.]
6. A natural hook-like organ or process: spec.a. ‘The tushe, tuske, or fang of a beast’ (Cotgrave)  [French crochet] . 
b. One of the minute hooks or claws on the prolegs of many lepidopterous larvæ.
c. Anat. The hook-like extremity of the superior occipito-temporal convolution of the brain.
III. Derived and figurative senses. 
7.a. Music. A symbol for a note of half the value of a minim, made in the form of a stem with a round (formerly lozenge-shaped) black head; a note of this value. Also attrib. 
b. Often used with playful allusion to sense 9. 
8. A square bracket in typography; = crook n. 7: formerly also called hook. Obs.
9.a. A whimsical fancy; a perverse conceit; a peculiar notion on some point (usually considered unimportant) held by an individual in opposition to common opinion. 
b. A fanciful device, mechanical, artistic, or literary. 
10. Fortification. A passage formed by an indentation in the glacis opposite a traverse, connecting the portions of the covered way on both sides of the traverse. 
11. Mil. ‘The arrangement of a body of troops, either forward or rearward, so as to form a line nearly perpendicular to the general line of battle’ (Webster 1864). Obs. 
12. quasi-adv. Oddly. nonce-use. (OED)

"He became an ever more convinced Copernican, but he had his crotchets.  He never accepted Kepler's proof that the orbits of the planets in the Copernican system had to be ellipses, because he loved the perfection of circles; and he was sure that the movement of the tides was the best proof that the earth was turning, since the ocean water on the earth's surface was so obviously sloshing around as it turned."

 - Adam Gopnik, "Moon man: What Galileo saw", 11 & 18 February 2013 The New Yorker

Friday, March 08, 2013

word of the day: gesso

The word of the day is gesso:
Etymology:  < Italian gesso < Latin gypsum : see gypsum n. 
1. Plaster of Paris; gypsum. 
a. in the native state (obs.). 
b. as prepared for use in painting and sculpture. 
c. A prepared surface of plaster as a ground for painting. 
2. A work of art executed in plaster. Obs. (OED)

"Part of Galileo’s genius was to transfer the spirit of the Italian Renaissance in the plastic arts to the mathematical and observational ones. He took the competitive, empirical drive with which Florentine painters had been looking at the world and used it to look at the night sky. The intellectual practices of doubting authority and trying out experiments happened on lutes and with tempera on gesso before they turned toward the stars. You had only to study the previous two centuries of Florentine drawing, from the rocky pillars of Masaccio to the twisting perfection of Michelangelo, to see how knowledge grew through a contest in observation."

 - Adam Gopnik, "Moon man: What Galileo saw", 11 & 18 February 2013 The New Yorker

Thursday, March 07, 2013

word of the day: tempera

The word of the day is tempera:

Etymology:  < Italian tempera, in phr. pingere a tempera to paint in distemper.
The method of painting in distemper: see distemper n.2 1.
Also the paint used in this method, usu. an emulsion in which pigment dissolved in water is mixed with egg yolk, or any of various gums, glues, or oils.  (OED)

"Part of Galileo’s genius was to transfer the spirit of the Italian Renaissance in the plastic arts to the mathematical and observational ones. He took the competitive, empirical drive with which Florentine painters had been looking at the world and used it to look at the night sky. The intellectual practices of doubting authority and trying out experiments happened on lutes and with tempera on gesso before they turned toward the stars. You had only to study the previous two centuries of Florentine drawing, from the rocky pillars of Masaccio to the twisting perfection of Michelangelo, to see how knowledge grew through a contest in observation."

 - Adam Gopnik, "Moon man: What Galileo saw", 11 & 18 February 2013 The New Yorker