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)

slang.

 

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

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

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.

“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.

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."

"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.

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.)

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.

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

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

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

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

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

acronym of the day: S.E.O.

The acronym of the day is S.E.O.: "search engine optimization":

"“Girls” has been attacked, and lauded, and exploited as S.E.O. link bait, and served up as the lead for style-trend pieces, to the point of exhaustion."

 - Emily Nussbaum, "Hannah barbaric: 'Girls', 'Enlightened', and the comedy of cruelty", 11 & 18 February 2013 The New Yorker

word of the day: gormless

The word of the day is gormless:

Etymology:  < gaum, dial. < gome n.² notice, understanding + -less suffix.

orig. dial.

Wanting sense, or discernment. (OED)

"Of the Old and New People of Willesden I speak; I have been chosen to speak for them, though they did not choose me and must wonder what gives me the right. I could say, “Because I was born at the crossroads of Willesden, Kilburn, and Queen’s Park!” But the reply would be swift and damning: “Oh, don’t be foolish, many people were born right there; it doesn’t mean anything at all. We are not one people and no one can speak for us. It’s all a lot of nonsense. We see you standing on the balcony, overlooking the Embassy of Cambodia, in your dressing gown, staring into the chestnut trees, looking gormless. The real reason you speak in this way is because you can’t think of anything better to do.”"

 - Zadie Smith, "The Embassy of Cambodia", 11 & 18 February 2013 The New Yorker

word of the day: Abernethy biscuit

The word of the day is Abernethy biscuit:

Etymology:  Probably < the name of John Abernethy, British surgeon (1764–1831), who is said to have developed the biscuit as an aid to digestion.

More fully Abernethy biscuit. A hard biscuit flavoured with caraway seeds. (OED)

"One Bruichladdich whisky—the “classic” twenty-two-year-old expression—promises to deliver a dizzying chain of sensations: “sweet yellow fruits, drizzled with honey and crushed almonds”; “freshly picked summer flowers”; “custard cream and toasted barley”; “banana bread and vanilla fudge”; “marzipan”; “Abernethy biscuit”; “marine citrus meringue.""


 - Kelefa Sanneh, "Spirit guide: Reinventing a great distillery", 11 & 18 February 2013 The New Yorker

word of the day: tatty

The word of the day is tatty:

Etymology:  < tat n.⁵ + -y suffix¹.

colloq.

1. Of a person, an animal: untidy, disreputable, ‘scruffy’. Cf. tatty adj.¹ 

2. Of clothes, decoration, etc.: shabby, tawdry, cheap. 

3. Of a place or a building: badly cared for, neglected, run down.

4. transf. In other miscellaneous uses. (OED)

"The walls were tiled with awards and citations, and next to his computer sat a tatty thesaurus, which he uses to write the digressive essays that form the basis for the company’s official tasting notes."

 - Kelefa Sanneh, "Spirit guide: Reinventing a great distillery", 11 & 18 February 2013 The New Yorker

word of the day: hawser

The word of the day is hawser:

Etymology:  apparently Anglo-Norman hauceour , < Old French haucier to hawse v., hoist; in reference to the original purpose of a hawser. 

Naut. 

a. A large rope or small cable, in size midway between a cable and a tow-line, between 5 and 10 inches in circumference; used in warping and mooring; in large ships now made of steel.  (OED)

"At about five-fifteen in the afternoon, the hawsers began to snap as the surge lifted the boats above the piers."

 - Ian Frazier, "The toll: Sandy and the future", 11 & 18 February 2013 The New Yorker

Ondansetron study

I am very pleased to see the article “Ondansetron in Pregnancy and Risk ofAdverse Fetal Outcomes” in the New England Journal for two reasons:

1.  Drugs generally aren’t tested on pregnant women during clinical trials, so for most drugs (and food additives: see the recent FDA warning on SimplyThick), we just have no idea whether they’re safe for pregnant women or not.

2.  This is a negative result (no difference between the women who took the drug and the control).  Many journals are biased against publishing negative results, because they’re thought to be uninteresting, but knowing that a drug is safe is actually really important, so I’m glad that it’s prominently featured in the journal and on their web site.