The Holy Brotherhood

Nobody who’s anybody walks in LA.

The Missing Persons song got it right: nobody walks in LA.

It’s time to renew my visa, which means a flight to Los Angeles to render myself to the French consulate tomorrow morning (you are assigned to one consulate or another depending on where in the US you live–mine is in Los Angeles), which means that I spent three hours this afternoon photocopying every @#$% document that the application requires, arranging them all in my little French plastic sleeve in the exact order in which they appear on the instructions page on the consulate web site, imploring the poor lady at FedEx to take my mug shot in such a way that I might appear adorable, or at least not hideous; and walking.  Possibly the Missing Persons lyrics should have been “nobody who’s anybody walks in LA,” ’cause I wasn’t actually the only one. There was the enormously, enormously, enormously obese white woman wearing a halter top and a muumuu, sitting in front of a house that must have cost several million dollars (I shit you not), with all of her belongings in three very chaotic-looking shopping carts, singing softly to herself.  The black lady of my age or so sitting at an empty table in Starbucks, staring at nothing, her lips silently moving as her legs twitch like… well, I suck at analogies, but the poor lady’s legs twitched non-stop.  The oddly-well-groomed-despite-wearing-shorts-and-sneakers-with-tube-socks white guy of my age or so pacing the sidewalk with a blank canvas under his arm, becoming increasingly agitated as he stops by my table again and again to ask if it’s not the case that the car parked in front of the cookie shop is there illegally.  The thin black woman of my age or so (what the fuck is going on with the people my age in LA??) sitting on a bench, waving her hands and having an animated conversation with someone visible only to herself; on her lap is a checklist on which is written חֶבְרָה קַדִישָא, which is Aramaic for “The Holy Brotherhood,” which is the term for a Jewish volunteer burial society.  (Just don’t fucking ask why I can read Aramaic well enough to catch things written on random strangers’ checklists, OK?)

The streets of Paris are full of beggars (see this post for information on why that’s the case, and why it has been the case for centuries).  What the streets of Paris are not full of, though, is vulnerable psychotic people.  Why?  In the United States, we have no national health care system.  In France, there is a national health care system.  Want to know which other first-world countries don’t have national health care systems?  None.  And what are the Republicans hot to do?  Get rid of the closest to national health care that we’ve ever been able to get.  Vote in 2018…

The folks at the consulate were super-nice, and I’m happily re-established in Paris–legal until the end of April, yay!


English notes

I shit you not: I’m not kidding you; I’m telling you the truth.

The basic principle of shopping in a market

Expecting everyone in the file d’attente behind me to be groaning at my idiocy in not being prepared to pay, I dug out my wallet and started digging through it frantically.  “Relax, it’s Sunday,” said the nice lady behind the counter. 

The basic principle of shopping in a marché (market) is this: look for the longest line, and get in that one.  If there are lots of little old ladies in it: all the better.

So, it’s my turn at the chosen fromagier’s kiosk, and madame is weighing my little Vacherin.  Because there are tons of people in line behind me, I’ve got my money right there in my hand, waiting to pay as soon as I have the goods in hand.  Seulement voilà (the thing is), when the fromagière tells me the price, it turns out to be twice what I thought I remembered from last year.  Expecting everyone in the file d’attente behind me to be groaning at my idiocy in not being prepared to pay, I dug out my wallet and started digging through it frantically.  Relax, it’s Sunday, said the nice lady behind the counter.  (If it’s in italics, in happened in French.  But, this gentleman in line behind me, this lady–I don’t want to inconvenience them.  

Oh, no–madame is right, it’s Sunday.  No one is in a hurry, said the gentleman.  He smiled.  The lady behind him smiled.  The fromagière smiled.  even smiled.  I got my Vacherin, said au revoir to everyone, and walked away.  Have a good Sunday, said the fromagière.

Explain to me again why you think that French people are rude??


The reason that I hadn’t boughten a Vacherin for a year: it’s a winter cheese.  (Boughten discussed in the English notes below.) Yes, cheeses have seasons, and this one shows up around the time that the days start to get depressingly short and you wonder whether or not you can find last year’s gloves.  According to my copy of Marie-Anne Cantin’s Guide de l’amateur de fromagesIl est de nos jours un des rare fromages saisonniers.  (The kid at the fromagerie that I usually go to–it’s about a 20-second walk from where the firing squads used to do their thing up against the wall of the Fermiers généraux, as recently as 1871–told me one day about some of the tricks that are now used to get sheep to produce milk outside of the lambing season.  It’s not cruel, but not exactly appetizing, either.)

epicea_commun
Picture source: http://www.haussimont.com/

Also known as Mont d’or, I think it’s hyper-bon, and apparently a lot of other people do, too, because at this time of year, it’s stocked more heavily than anything else.  As you can see in the photo (taken on my kitchen table), it comes in a box (and it must come in a box), and the box is made of épicéa (spruce) (and it must be made of épicéa).  Cantin says that it’s from the spruce that the unusual taste of a Vacherin comes.

As you can see from the picture, a good Mont d’or has undulations on the surface–des vagues (waves), Cantin calls them.  It’s a very soft cheese, to the point that if you a buy a larger one, it typically comes with a wooden spoon–indeed, you can just scoop it out, and it spreads easier than butter.  (One of my friends insists that the only way to eat a Mont d’or is to pour some white wine on top, put it in the oven for a bit, and then pour the melted cheese over boiled potatoes.  Cantin sees it my way, though, and what my friend doesn’t know, won’t hurt her.)

In the time that it’s taken me to write this post, I’ve eaten approximately 25% of my Vacherin, and you know what?  I don’t care.  The other day I calculated how many more weekends I have to live: 680.  Probably sounds morbid, but it inspired me to work not more than, say, 30 minutes all of this weekend, which happens, like, never–did you calculate how many weekends you have left yesterday, and if not, what did you do this weekend?  Carpe diem, baby!


French notes

l’épicéa (n.m.) : spruce.

le vacher : cowherd.  Le vacherin était autrefois le fromage des vachers.  As Cantin explains this: back in the days, comte was made in the mountains while the cows did their summer grazing.  In the winter, the cows would be back in the stables, and the milk quantity and quality decreased.  Additionally, the roads could impassable.  So, rather than taking the milk to a cheese-maker, the farmers made their own cheese out of it–hence Vacherin being a vacher’s cheese.


English notes

boughten: yes, boughten is English.  More commonly, it’s bought, but you will run into the boughten form in some dialects–the Midwest and the Northeast, mostly, I think, although I couldn’t swear to that.

quote-no-memory-of-having-starred-atones-for-later-disregard-or-keeps-the-end-from-being-hard-robert-frost-230318
Picture source: http://izquotes.com/quote/230318
boughten
Picture source: bittersoutherner.com
1280x720-zoe
http://www.dailymotion.com/video/x2yaza1

 

A day in the life of a puppy

There was a leaf and I sniffed it and there was kibble and I peed and I took a nap and there was a bird and I barked at it and we played King of the Hill and I peed and I took a nap and…

J’ai bien reçu cet SMS du chiot d’un pote aujourd’hui :

yavê une feui é jl’é reniiiphlé é yavê dé krokè é sétè miam miam et pui jé fê pipi é popo et pui jmesui fê un peti som et pui jé fê pipi et pui yavê un ouoyzo et jé hurlé trê férossmen et ysanètalé et pui on a jwé roy de la montanie et pui jé fê un peti som et pui jé fê pipi é pui ma seur m’a bouskulé et jé di “iapiapiap” é pui on a rennniphlé un ballllon é pui on a jwé loup-garou é pui jé fê pipi é pui jmsui fê un peti som et pui jé fê pipi

Nul en ponctuation mais il se débrouille pour bien exprimer ce qui lui passe quand même, hein ?


French notes: You’ll find the names of some dog breeds below.  (I have no idea how one pronounces chow-chow in French.)  One of the delightful aspects of regulation in France: you can call your purebred dog  (le chien de race) anything you want, but its registry name has to start with the official letter of that year.  2017 is N, so look for lots of registry names like Ninou, Nanette, or Nadine until fin décembre, and then lots of puppies named things like Olivier, Odette, or Ourson beginning January 1st…  One of the delightful aspects of the language itself is the occasional presence of names for males and females of a given breed, but the only one that I know off the top of my head is levrette–no limite remarks necessary on that one, but I’d love to hear about others in the Comments section…

races-de-chiens-290540
Picture source: http://www.ikonet.com/fr/ledictionnairevisuel/images/qc/races-de-chiens-290540.jpg
races-de-chiens-290541
Picture source: http://www.ikonet.com/fr/ledictionnairevisuel/images/qc/races-de-chiens-290541.jpg

I woulda figured something Athabaskan…

Since Bigfoot is mostly sighted in Oregon and Washington and was apparently captured in Alaska…

Na-Dene_langs
Pre-contact distribution of the Athabaskan languages. CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=147052

The Athabaskan languages are a family of languages native to North America.  Currently there are about 53 of them left.  They’re spoken in Alaska and northwestern Canada, in pockets of the coastal areas of Oregon and Washington, and in the south-central United States.  Since Bigfoot is mostly sighted in Oregon and Washington and was apparently captured in Alaska, I woulda figured that he would speak something Athabaskan, but apparently not…

I woulda figured explained in the English notes below. #cleaningthebasement

English notes: Colloquially, one meaning of to figure is to guess or to think.  Some examples:

 

 

 

 

Estimate your vocabulary size

When you figure out how to draw a representative sample of language, notify the linguists, because we sure as hell haven’t figured it out…

Want to see an application of Zipf’s Law?  Go to this web site, where you can get an estimate of your vocabulary size in any of 21 different languages.  I don’t know the details of how they come up with these estimates, but as an indicator of their accuracy (or lack thereof), I can tell you that my percentile placement on their English-language test was the same as my percentile placement on the GRE (the exam that you take if you want to go to graduate school in the United States).  It estimated my French vocabulary size at just over 7,600, which seems reasonable–I would guess that I’ve been learning about 3,000 words a year for almost three years, of which I probably forget about a third due to not running into them a second time (Zipf’s Law: 50% of the language that you will run into today consists of words that occur only very rarely–but that do, indeed, occur), which would work out to just under 6,000; add in another 500 for the one semester of French that I took in college (“university” to you French-speakers in the audience) and you get within 10% of their estimate, which seems reasonable.  (According to the web site, this lands me in the top 44% or so–of whom?  No clue.)

https://www.arealme.com/vocabulary-size-test/en/

How would you use Zipf’s Law to do this kind of estimate?  Remember what the curve described by Zipf’s Law looks like:

zipfs-law-curve-https-::medium.com:@ASvanevik:how-i-learned-german-in-30-days-df7b7ff85654
Zipf’s Law: a small number of words occur very frequently, while the vast majority of words occur very rarely–but, they do occur. Credit: @ASvanevik.

One way to use this to estimate a vocabulary size would be to figure out how far to the right (towards 100) a person can “go,” so to speak.  If someone can’t reliably understand words above a rank of, say, 20, there is a massive number of words that they don’t know.  On the other hand, if someone can reliably understand words in the 90-100 range, their vocabulary is enormous.  How do you turn enormous into an actual number?  I have no clue how they do that–quantifying vocabulary size is hugely difficult, and as far as I know, it’s not possible to do it precisely for anyone, even for very, very young children. The SWAG approach would be to figure out the rank at which you stop recognizing words reliably, and then calculate the number of words above that rank. The Devil would, of course, be in the details–what texts would you use to determine your curve? Load those texts heavily with scientific journal articles about linguistics and someone like me would probably do pretty well–load them heavily with scholarly analyses of metaphors for love in Finnish epic sagas and I would probably do pretty poorly. Use a representative sample, you say? When you figure out how to draw a representative sample of language, notify the linguists, because we sure as hell haven’t figured it out…

41bpA-6YEzL._SX345_BO1,204,203,200_
Source: smile.amazon.com

Want to know some of the many technical details that make quantifying vocabulary size more or less impossible, even in principle?  See pages 22-28 of my colleague Elisabetta Jezek’s book The lexicon: An introduction.


English notes 

hugely: an adverb meaning “very.”  Is it English?  It first appeared in the language in the 12th century (along with archangel, asleep, dittany, lion, whoredom, and welkin–how cool is Merriam-Webster’s “Time Traveler” feature, and WTF is dittany??).  Have you ever come across it before?  Quite likely not–here are the relative frequencies of hugely and very:

Screen Shot 2017-10-20 at 05.47.42
Screen shot from the Google Ngram Viewer.

…but, it’s hard to argue that it’s not part of the language.

Want to see some cool shit?  Click on the version of the graph that you see below.  Do I REALLY think that this is cool?  Yes.  Is that fact related to the shockingly large number of times that I’ve been divorced?  I would imagine so.

[https://books.google.com/ngrams/interactive_chart?content=hugely%2Cvery&case_insensitive=on&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=&direct_url=t4%3B%2Chugely%3B%2Cc0%3B%2Cs0%3B%3Bhugely%3B%2Cc0%3B%3BHugely%3B%2Cc0%3B.t4%3B%2Cvery%3B%2Cc0%3B%2Cs0%3B%3Bvery%3B%2Cc0%3B%3BVery%3B%2Cc0]

Palimpsest upon palimpsest

Dear Dr. Zipf,

Good day to you.  My name is [name removed to protect the guilty] and I am a Ph.D. in [field removed to protect the guilty] at [a hospital which shall remain nameless].  I need to learn how to use natural language processing to process the electronic medical record and provide data that can be used for analysis.  As you are an expert in this field I thought I would email you and ask for your assistance.  Are there any books or training courses out there that can help me learn biomedical natural language processing in a few weeks.   Any help you can provide will be greatly appreciated.  Please let me know.

Warmest Regards,

[Name removed to protect the guilty]


In a few weeks… In a few weeks…


Dear Dr. X,

Biomedical natural language processing is super-simple, and I would be surprised if you couldn’t learn it in a few weeks.  You might find this book helpful:

Cohen, Kevin Bretonnel, and Dina Demner-Fushman. Biomedical natural language processing. Vol. 11. John Benjamins Publishing Company, 2014.

Please let me know if I can be of any further assistance.

Warmest Regards,

Beauregard Zipf, PhD


Dear Dr. X,

The doctoral students in our graduate program typically spend five years learning biomedical natural language processing.  Personally, I’ve spent my entire career learning biomedical natural language processing, beginning with spending a number of years as a medic in the military, where I learned the “biomedical” part. I mostly did physiological monitoring–hemodynamics, electrophysiology, stuff like that.  I later got a bachelor’s degree in linguistics (double major in English, actually), as well as a master’s degree in linguistics, and a PhD in linguistics, which is how I picked up the “language” part.  Along the way I learned to program–the hard way, which is to say by making more mistakes than you could possibly imagine, from the painful to the just plain embarrassing.  (That’s the “processing.”) Since then, I’ve spent years trying to figure this stuff out, and I still wouldn’t say that I know very much about it.  But, hey, you’ve got a PhD in [redacted], so, yeah–you should be able to pick this up in a few weeks.  You might find this book helpful:
 

Cohen, Kevin Bretonnel, and Dina Demner-Fushman. Biomedical natural language processing. Vol. 11. John Benjamins Publishing Company, 2014.

 
Warmest Regards,

Beauregard Zipf, Registered Cardiovascular Technologist, Advanced Cardiac Life Support instructor, EMT, PhD


Dear Dr. X,

  • Are there any books or training courses out there that can help me learn biomedical natural language processing
  •  

What an interesting question–thank you for bringing it up.  When I Googled the words biomedical natural language processing, the first hit I got was this:

 

Cohen, Kevin Bretonnel, and Dina Demner-Fushman. Biomedical natural language processing. Vol. 11. John Benjamins Publishing Company, 2014.

 

Looks like it might be relevant?

 

Best wishes,

Zipf


Hi, Dr. X,

It’s nice to hear from you.  You might find this book helpful:

 

Cohen, Kevin Bretonnel, and Dina Demner-Fushman. Biomedical natural language processing. Vol. 11. John Benjamins Publishing Company, 2014.

 

Please let me know if I can be of any further assistance.
Best wishes,

 

Zipf


English notes
palimpsest:  “writing material (such as a parchment or tablet) used one or more times after earlier writing has been erased” (Merriam-Webster).  Back in the day, writing was mostly done on parchment, and parchment was expensive, so in the monasteries that preserved much of the ancient writing that we have today, it wasn’t uncommon to scrape the ink off of parchment if you didn’t really care about what was written on it, and write something on it that you did care about.  If you’re lucky, though, today we can recover an earlier text from the impressions that it left behind on the parchment, and there are some texts that are only known from a palimpsest.  Wikipedia lists most of Cicero’s De republica, as well as the oldest Koranic variant in existence.

Just in case you were wondering why your rabbit looks like it does

Black lab, yellow lab, chocolate lab, meth lab.

When I’m in the US, I live in the Wild West, and that means rabbits.  Where there are rabbits, there are probably man-eating rabbits, and I hate them.  So, the chart explaining rabbit coat coloration that you see above intrigued me–to survive the man-eating rabbits, you must be able to spot them, and you can’t always rely on seeing their long, sinister ears protruding from the grass, so you need to know their coat colors.  But, how do those particular genes explain the devilishly sly diversity of color and pattern that you see in the illustration?

For context, let me give you the rundown (as I understand it–bear in mind that I’m a linguist, not a geneticist) on Labrador retrievers:

black-lab-yellow-lab-chocolate-lab-meth-lab-nny-e299a4e299a4e299a4e299a4e299a4-12613532
Picture source: https://goo.gl/Zxb4Dk
  • Labs come in three colors: black, “chocolate,” and yellow.
  • Which color they are is determined by two genes.
  • One gene determines whether your hair is black or “chocolate.”
  • The other gene determines whether or not your hair has any pigment (think of pigment as the molecule that actually has the color) at all.
  • If you have the form of the gene (the “allele”) that allows your hair to have a color, then you will be either black or “chocolate” (assuming that you are a Labrador retriever).
  • If you have the form of the gene (the “allele”) that keeps your hair from having any pigment at all, then regardless of which form of the black-versus-chocolate gene you have, you will be yellow–yellow being what a Labrador retriever hair looks like if it doesn’t have any pigment deposited therein.

My point being: you don’t actually need to have a large amount of genetic variability to get a large amount of “phenotypic” variability (in this case, variability in appearance)–actually, very few things are affected by a single gene.  Rather, most traits are affected by a combination of a number of different genes.


OK, so: how do those rabbits come about?  They differ not just in their colors, but in the pattern of those colors.  Here’s a reasonable guess.

The odd data point in that graphic is the Himalayan.  Everybody else is monochrome, but the Himalayan has a color difference between his (I’m pretty sure that rabbits are generically male, probably due to the known viciousness of the man-eating variety–le lapin anthropophage in French, el conejo antropófago in Spanish, Lepus anthropophagos in Latin, I think, but I couldn’t swear to it) extremities and his…well, everything else.

maxresdefault
A Siamese cat with a baby. Note that the cat is not eating the baby—as far as I know, there is no such thing as a man-eating Siamese cat. Picture source: https://www.youtube.com/watch?v=JAC-s8cWJxQ

You’ve seen that pattern before–in Siamese cats, for instance.  My understanding is that the distribution–lighter towards the center, darker at the extremities–is related to reduced blood flow in said extremities.  The reduced blood flow gives you a reduced temperature, and that has some effect or another on the deposition of pigment.  (As I said, don’t quote me on this–I’m a linguist, not a Siamese cat expert.)  Looking at the rabbit that way, you wonder: OK, dark on the extremities and light on the rest, but which dark?  Which light?  Why doesn’t the rabbit have the same colors as a Siamese cat, for instance?  (Think of the evolutionary advantage for a rabbit who looked like a cat–it would be soooo much easier to get humans to take you in, in which case if you were the man-eating variety of rabbit, you could just gobble those overly-trusting humans right down.)

I went digging around for evidence for this explanation for the coloration patterns in Siamese cats.  I found a few papers on a group of related temperature-sensitive tyrosinase mutations that are associated with eye color differences in a range of Siamese cats and Himalayan mice and a rare mink discovered on a ranch in Nova Scotia–and with albinism in humans. (As an albino, your likelihood of going blind due to a lack of protective pigment in the iris and the retina is high–and that’s why we spend your tax dollars on studies of Himalayan mice.)  I found a paper on a temperature-sensitive tyrosinase mutation in a human with the following: white hair in the warmer areas (scalp and axilla) and progressively darker hair in the cooler areas (extremities) of her body. I haven’t tracked it down to the fur color question in Siamese cats, though.  Still think I just make this shit up?  Here’s the paper on the mink found on the ranch in Nova Scotia.  I mean, yeah, I make up the zombies and the man-eating rabbits–but, the rest of the stuff is “for reals,” as the kids say.

figure_12_02_05
Picture source: https://goo.gl/jR2r1Y

Look to the left, look to the right: if the colors in the figure are true to life, the Himalayan rabbit extremities are the color of the rabbit to the left, while the center is the color of the rabbit to the right.  (I am cursed to always remember a scene from an autobiography that I read when I was a kid.  The author has been arrested by the NKVD and finds himself in their notorious Lubyanka prison.  Whenever a prisoner is taken from one room to another, the machine-gun-toting guards intone step to the left, step to the right: attempt to escape.  The NKVD were murderous fuckers, and the threat was entirely believable.  Hence: look to the left, look to the right.)  Likely cause of the pattern of the Himalayan: temperature-dependent pigment deposition gradient of whatever pigment the chinchilla and albino rabbits have or do not have.

Yes, I have been known to spend my Saturday mornings looking for scientific literature on the topic of pigmentation deposition in Siamese cats when I could have been taking a walk in the beautiful fall weather.  This is probably related to why I get divorced so often.  French notes below–no English notes today.


French notes

le dépôt: deposition, in the sense of deposition of a substance.  This seems to be what would be used to talk about pigment deposition.  For example:  La synthèse et le dépôt de mélanines continuent jusqu’à ce que la structure interne ne soit plus visible, on parle alors de mélanosome de stade IV.  (biologiedelapeau.fr)  

le gisement: deposit, in the sense of a deposit of minerals, of archeological finds, and the like.  I haven’t been able to find any examples of it being used in a medical or biological context to refer to deposition of pigments in the skin.

c389pistasierc3a9cessivec389pistasiedominante
The same thing that we saw in Labrador retrievers: one gene for color, one gene for pigment deposition, and you get three kinds of coats. Faute d’orthographe: dépot should be dépôt.  Source: Bernadette Féry, http://slideplayer.fr/slide/181167/
exemple3sidc3a9rosehc3a9patiqueaccumulationdepigmentsferriques
With the correct spelling dépôt: Deposition of exogenous or endogenous iron. Picture source: http://slideplayer.fr/slide/5124382/, author unknown.
fig-1-gisement-non-conventionnel-a-gauche-versus-gisement-conventionnel-a-droite
Picture source: Marc Durand, https://goo.gl/3GcDDN.

 

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Source: Alain Muret.