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."

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 15 September 201)

molecule of the day: anisomycin

The molecule of the day is anisomycin:

(PubChem)
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.

molecule of the day: dipicolinic acid

The molecule of the day is dipicolinic acid:

It's a chelating agent, used, for example, in this paper.

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)

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

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

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)?

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?

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

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

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.
 (OED)


"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

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

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

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

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.

Med.

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

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

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

word of the day: biff

The word of the day is biff:

Etymology:  Imitative.

slang.

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

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