Jonathan Coulton’s Re Your Brains. Be sure to lis­ten. Con­sider buy­ing some songs.

[via Scalzi’s blog]

I’m fin­ish­ing up (and sig­nif­i­cantly revis­ing) some code I wrote for a research project this semes­ter. More of the details of the project and results over the next few weeks, but in the mean­time, some very neat tools and pack­ages you may find interesting:

• Net­workX
• pypars­ing — a class library for text pro­cess­ing in Python
• pydot
• pya­gent
• Sci­en­tific Tools for Python wiki

Could a really, really, really flu­ent speaker of Old Eng­lish, or maybe Klin­gon, or Esperanto or Volapük, affect an authen­tic accent? As in: an accent when speak­ing English?

If so, I would give a lot to hear a record­ing of the elic­i­ta­tion para­graph read by one of those folks who wouldn’t nor­mally be expected to appear on the list.

I won­der some days what we think we’re test­ing in acad­e­mia. This is not merely the usual harp­ing about giv­ing or get­ting grades, nor merely another thing about whether test­ing instru­ments are valid, and nor what sorts of gen­er­al­iza­tion they can inform. Not even revis­it­ing my hare-​​brained ideas on multi-​​objective grading.

Just what it is we actu­ally test, and what we think we’re testing.

I’ve had an impor­tant les­son slammed painfully home this week. I’m one year into a entirely new dis­ci­pline (indus­trial engi­neer­ing), after 20+ years’ com­fort­able suc­cess in another cou­ple (the­o­ret­i­cal biol­ogy, and what in hind­sight was appar­ently “not-​​industrial” engi­neer­ing): all my plan­ning esti­mates are off by a fac­tor of 4x or 5x. I suck at deadlines.

But I’ve sucked at dead­lines, like, for­ever. A lot of peo­ple in the Uni­ver­sity do. Look at the aca­d­e­mic blogs, and much of what you’ll read is com­plaints about “Oh, my, I have so many meet­ings!” or, “Can you believe my stu­dents can’t do every­thing I tell them to?!” I’m still con­vinced that the demo­graphic who sur­vive to become pro­fes­sors are exactly those who’re best at post­pon­ing things to the knife-​​edge of the last minute, with­out push­ing them too often or too far over the edge into reg­u­lar tar­di­ness. And like those folks, I’ve never been very tardy. Well, as such. Sure there are some papers I’ve wished I could give another edit, some thoughts left for fol­lowup papers, some deeply abbre­vi­ated dis­cus­sions. But gen­er­ally I get the job done.

Because I have a strong sense of the effort required. I know the stuff: domain knowl­edge takes lit­tle or no time for me to dredge up. Regard­less of the domain. I was, after all, employed as a Know-​​it-​​all. And along with “all”, I also know how to write. So I’ve got­ten pretty good through the years at weigh­ing these strengths against the rel­a­tive com­plex­ity of the tasks I’m assigned. Yeah sure, that’s a kind of lazi­ness. This is the point where I can remind you that all the best engi­neers are intrin­si­cally lazy, that it’s the dri­ving force in the field.

But this year I suck. All my esti­mates are off, and all my work suf­fers because of it. Not because of this new “yes, really math­e­mat­ics means indus­trial” engi­neer­ing domain knowl­edge I need to learn; maybe it takes me twice the time to dredge up some long-​​ignored fact about lin­ear alge­bra or matrix mul­ti­pli­ca­tion, but what’s an extra ten min­utes? No, what’s off is my abil­ity to communicate.

I spend all my time edit­ing. I spend extra time,not my own, edit­ing. And re-​​editing. Not just “Did that sen­tence make sense?” or “Do I under­stand that word?” but also “If I use this com­mon­place term, will the reader know what I’m talk­ing about?” or “To me this is the first obvi­ous step. If I were them, would it be?”

The words make sense, but maybe not to the reader: my use of “fit­ness land­scape” and “auto­cor­re­la­tion struc­ture” come to mind as recent exam­ples that have proven I’m from Mars. Or I under­stand the word, but not in the same way as the reader: “com­plex sys­tems” and “data min­ing” come to mind. Obvi­ous rules of thumb and tools I always use, unthink­ingly, in every case—like ran­dom sam­pling the search set of an opti­miza­tion prob­lem, or sav­ing a record of every solu­tion tested so I can watch progress of an ongo­ing search.… well, I may as well have invoked Marx or done a lit­tle inter­pre­tive dance. And at the same time, the con­sumers of my prod­ucts are watch­ing for cer­tain sig­nif­i­cant pass­words, and they’re just not com­ing. Because I’m not see­ing the cues, the raised eye­brows, the head tilted, the mut­tered “…and—?”

So every­thing I do needs to be edited. Four times, five times. I’ve learned the hard way that it may as well be blank, as handed in unin­ter­pretable. Indeed, it’s because I’ve so deeply mis­un­der­es­ti­mated the amount of social edit­ing required, that yes­ter­day I was forced to turn in a paper—one that I was orig­i­nally very proud of—mostly blank.

Crip­pled. What am I going to do, fac­ing a strict dead­line and already hav­ing spent two weeks and 30 hours straight work­ing on it, leave a skele­ton of head­ers for all the beau­ti­ful things I have in my head but left myself no time to com­mu­ni­cate? Even though I’d eas­ily pass them along in a face-​​to-​​face con­ver­sa­tion, or writ­ing to an old col­league? All it would take is a few moments and a few choice turns of famil­iar phrase. Which I can’t use; when I do use them, when I write a com­plete and cogent account of some inter­est­ing things I’ve done, still the cues are not there, and what I get is another “…and–?”

So my final report for this class was a piece of embar­rass­ing crap. If I were given it, I’d throw it away half-​​way through. But then, I didn’t even get halfway through writ­ing it; who knows, maybe that could play out in my favor.

As I heard Dr. Dan Got­tlieb say on the radio, there’s noth­ing more painful than see­ing your­self help­less to aid some­body you love. I know all about that. It’s also true, though to a lesser extent, about something you love doing.

Because, I sup­pose, the stuff is you.

Which-​​all sends me down the dispir­it­ing spi­ral, and starts me think­ing about the nature of grad­u­ate pedagogy.

When a stu­dent is being tested, to suc­ceed they need to (1) rec­og­nize the explicit and tacit expec­ta­tions of the ques­tioner, (2) obtain (recon­struct or recall) the domain knowl­edge and raw facts nec­es­sary to answer the explicit ques­tion, (3) con­struct a plan for a cogent response, and then (4) exe­cute and con­vey that response with the appro­pri­ate for­mal­ism and idioms. This is true in edu­ca­tion from the ele­men­tary level to the pro­fes­so­r­ial job talk: Some­body poses a chal­lenge to you, and your response will be judged not merely on its fac­tual con­tent but also on the degree to which it com­mu­ni­cates your mem­ber­ship in a joint com­mu­nity of practice.

In my new domain with its weird idioms and cul­tural assump­tions, my first response to hear­ing many ped­a­gogic utter­ances is typ­i­cally a mix of

1. “Oh, cool, I’ve never thought of that!”
2. “Uh huh, sure. Get to the point.”
3. “Why would any­body in their right minds con­sider that reasonable?”

Think­ing back to my days as an instruc­tor, and talk­ing after the fact with my pro­fes­sors here, surely they have the same set of responses to my (and other stu­dents’) work prod­uct. What dif­fers from case to case is the pro­por­tion of the time spent in the first and last ones. We’re all brim­ming over with domain knowl­edge; what dif­fer­en­ti­ates us is dis­ci­pli­nary frame­work, cul­ture, confidence.

On the sub­ject of con­fi­dence, briefly: it gets far too much respect in acad­e­mia. Unlike knowl­edge or expe­ri­ence, con­fi­dence has a dan­ger­ous Goldilocks-​​curve type of non­lin­ear­ity. Nei­ther too lit­tle nor too much is a good thing. Treat con­fi­dence warily.

The goal of higher-​​level edu­ca­tion is to build con­fi­dence in the instruc­tor that the stu­dent is spend­ing increas­ingly more of the time in the sec­ond phase of “Uh huh, sure. Get to the point,” and less in “Oh, cool, I’ve never thought of that!” The last one is always unde­sir­able, both in the stu­dent and in the instruc­tor, except in the rare occa­sions when somebody’s out­side their discipline.

Indeed, I sus­pect the proper way of think­ing of a dis­ci­pline is like a bio­log­i­cal species, which is dif­fer­en­ti­ated by repro­duc­tive bar­ri­ers. In acad­e­mia, it’s not about the fuck­ing, but about think­ing the other peo­ple are fools. If they’re time-​​wasting fools, they’re in another dis­ci­pline. (And if they’re in another discipline.…)

Yet I find I often say that bit about, “Why would any­body in their right minds con­sider that rea­son­able?” My instruc­tors report they say it a lot about me. Not sur­pris­ingly, this leads to increased pres­sure in test­ing situations.

The point being: We often seem to for­get how impor­tant issues of prag­mat­ics and cul­ture are in the ped­a­gogic cycle. Instruc­tors know the damned answer. The older the stu­dent is, the more con­fi­dence the instruc­tor should have that the stu­dent also knows the damned answer. What an advancedin­struc­tor should be doing is look­ing for cues that some­where in that stranger’s head is a cul­tural frame­work and body of knowl­edge that together will suf­fice in the future. Maybe (for some weird rea­son we shouldn’t dwell upon) that grad­u­ate stu­dent won’t end up being a pro­fes­sor… I sup­pose… but in the mean­time, a men­tor should be see­ing numer­ous cues that the stu­dent will soon be able to talk the talk, even out­side this pro­tected, nur­tur­ing creche that is grad­u­ate school.

So, two objec­tives: knowl­edge and communication.

I’m think­ing back to years spent grad­ing intro biol­ogy stuff—and for that mat­ter some of the man­u­scripts I’m sent for peer review—and reflect­ing on the “mem­ory dump” pat­tern that we all know and love. The canon­i­cal “mem­ory dump” appears on the face of it as a blind list­ing of facts, and we’re tempted to see it as a clear demon­stra­tion of fail­ure to syn­the­size knowl­edge. I won­der, though, if the author of a “mem­ory dump” might be feel­ing chal­lenged in the com­mu­nica­tive aspects of the process. In con­ver­sa­tions, where they can read cues and adjust the flow of talk on the fly, they never get a chance to spew ran­dom facts. [Well, most don’t.] They come over as “smarter”. Thus it is con­fus­ing when we encounter a stupid-​​sounding list, an essay that dances around the sub­ject and never gets to the point.

When we test knowl­edge, we are also test­ing accul­tur­a­tion. When we embark on an assigned task, to suc­ceed we need not merely know, but demon­strate the knowl­edge, and for that mat­ter show we have the abil­ity to do so with facility.

And when we are given a test, an essay, a report, a man­u­script to review, and it’s full of gaps and holes, what then should we infer?

What do we test, exactly?

1. My Mom has sleep apnea. I do too. My Dad did, too, worse than any­body I’ve ever heard. A lot of peo­ple do, it seems.

   The Uni­ver­sity Health Ser­vices have a fancy clinic now, just down the street from our house, where they will fit you with a fancy CPAP machine that you will wear every night for the rest of your life and it will pos­si­bly make you bet­ter, so your risk of heart dis­ease is lower because you don’t wake up so much in the night.

   The sleep apnea thing is a huge growth indus­try, clearly. It’s a simply-​​described con­di­tion with a broad range of pos­si­bly seri­ous detri­men­tal med­ical effects, and it’s often treat­able. Made for wind­fall prof­its: Soon it will be clear that you’re being self­ish and hog­ging med­ical effort if you don’t get treated. Think of the sav­ings that could be passed on to treat real dis­eases, if only we mouth-​​breathers didn’t clog up the health­care pro­fes­sion with our triv­ial problems.

2. An over-​​produced glossy six-​​color flyer shoved in every grad student’s mail­box (what? maybe 5000 of them?) the other day pointed out that over 30% of grad­u­ate stu­dents seek help for depres­sion or stress-​​related syn­dromes. That makes sense to me; seems a lit­tle scant, frankly.

   When I was a Biol­ogy grad stu­dent at U Penn, there came a point where my cohort sud­denly looked across the lunchtime bitch-​​table at one another, and some­thing in folks’ eyes made me call out, “Any­body not tak­ing anti­de­pres­sants here, now, raise your hand.” And we all sat there rais­ing our eye­brows at each other. Not our hands.

   I’m not depressed but merely stressed these days. I find I don’t get depressed much any more, per­haps because now I am old and like many old peo­ple I have much more ratio­nal first-​​hand expe­ri­ence of how much worse it can be. The inim­i­cal evil of the world, the relent­less march towards the grave, &c &c. Sure there’s some stress, but… stress, well, that’s just an extra dose of cor­ti­sol and some insom­nia. Every­body knows older peo­ple sleep less.

   At any rate, I sus­pect the rate of phar­ma­ceu­ti­cally treated depres­sion among the pop­u­lace is rel­a­tively high. Every week get between three and five emails announc­ing “Take Time Off From Your Ph.D.!” and “Wind­ing Down the Stress Lev­els” and “No, Really, Delayed Grat­i­fi­ca­tion is On Its Way To You Some­day Real Soon Now, We Promise” meet­ings from the grad school HQ.

   I am led to con­clude that smart peo­ple prob­a­bly get depressed more than dumb ones. Which makes a kind of sense, in hind­sight. Right? Think of the sav­ings that would result if we all sought treat­ment, and the accom­pa­ny­ing pro­duc­tiv­ity gains if smar­ties just stopped being depressed and stressed, stopped malin­ger­ing. It would fos­ter a new era of… well, something.

   Med­ical break­throughs, surely. Because smart peo­ple, they helped make med­i­cine the rev­o­lu­tion­ary neces­sity it is today.

3. Obe­sity is ram­pant in Amer­ica (includ­ing Canada and some US Pro­tec­torates, I ‘spect). We’re all gonna get vas­cu­lar dis­ease and dia­betes. You’re a bad per­son if you don’t dili­gently exer­cise, eat rea­son­able amounts of bran and pome­gran­ate and spelt wheat, and end up using valu­able resources that could bet­ter be applied to help peo­ple who need it.

   I am led to believe it’s a worse social sin for smart peo­ple to be over­weight. Which makes a kind of sense. Because poor peo­ple are fat, and smart peo­ple aren’t poor. Right? (I’m still work­ing on this one). But think of the sav­ings if we all just took three hours a day and walked around in bright white shoes and officewear, and ate salad at the cafeteria—savings that would ben­e­fit the really sick.

   That’s the feel­ing I got from my recent Health Main­te­nance Exam, at least. “When are you going to get in shape?” Because, my young man, we’re not going to wait for you much longer.

4. I am told that my gen­er­a­tion (“13ers”, also known as Early-​​onset GenX Syn­drome Suf­fer­ers) and those after­wards are prone to get­ting aller­gies and asthma and autoim­mune dis­eases because we didn’t eat enough dirt when we were kids, and now it’s too late to eat dirt because our immune sys­tems have learned incor­rectly that (a) many impor­tant mol­e­cules in our bod­ies look some­thing like the sur­faces of Bad Microbes, and (b) the sur­faces of many ubiq­ui­tous mol­e­cules on the sur­face of Reg­u­lar House­hold Stuff (dogs, books, flow­ers) also bear a strik­ing sim­i­lar­ity to the sur­faces of Bad Microbes, so © our noses are always run­ning and we com­plain fre­quently of seri­ous headaches, and there­fore (d) we’ll need to take pro­phy­lac­tic anti­his­t­a­mines for the rest of our lives.

   I bet the smart kids are more prone to aller­gies. Think of the stereo­type: asth­matic, myopic dweebs. No dirt-​​eating at all as a kid = sickly and sniffly. Stereo­types, as it hap­pens, don’t actu­ally lie that often. Right? So as a par­ent you’re shirk­ing if you don’t take your kids out­side now and then and force-​​feed them some dirt.

   And then spray them quickly with antibac­te­r­ial soap.

   Think of the sav­ings &c &c.

5. And there’s statins. Wow. Biggest-​​selling phar­ma­ceu­ti­cals in the world. We’re all much bet­ter for tak­ing them. Think of the sav­ings in the med­ical com­mu­nity that can be passed on to treat other, more seri­ous patho­log­i­cal con­di­tions. ‘Nuff said.
6. New-​​generation NSAIDs. Aspirin is dan­ger­ous; it might give you tummy trou­bles. Never take aspirin! We should all switch to newer NSAIDs, that are much bet­ter because they’re newer. Sav­ings. Passed on. Think!

Am I say­ing I think we’re a bunch of whin­ers? No. These are all real prob­lems, espe­cially the just plain con­stant pain one—my Mom suf­fers from ter­ri­ble osteoarthri­tis, for instance, and NSAIDs give her the abil­ity to walk around a bit. Depres­sion sucks, is dan­ger­ous, is more ter­ri­ble in a way than all the oth­ers, because you watch your­self being sick and unable to do any­thing about it. Heart dis­ease, dia­betes, sleep­less­ness, are all actual Bad Things. I’ve watched sev­eral peo­ple die badly from dia­betes and its complications.

Nobody should suf­fer any of these prob­lems or risks. Nobody any­where. We are not—the sick ones—whiners.

Alas, we all do suf­fer these prob­lems. If not these, then some other ones. Don’t get me started on cancer.

An under­re­ported sta­tis­tic I have not read lately, pre­sented here as a reminder: nearly 100% of patients seek­ing med­ical treat­ment even­tu­ally die.

How can we stom­ach that? Why doesn’t any­body do some­thing about it?!

What I’m prod­ding with my Short Stick here is some­thing about our col­lec­tive atti­tudes. Cul­ture. Tacit assump­tions, implicit under­stand­ings. I don’t know whose in par­tic­u­lar. Doc­tors? Sure. They are, in gen­eral, igno­rant over­worked habit­u­al­ists who have so lit­tle time to lis­ten to details or think about con­se­quences that they often as not end up mis­treat­ing their patients. That is, pre­scrib­ing any­thing just to get the patients off their backs.

And the patients, well, they’re stuffed so full of risk aver­sion that they imme­di­ately seek advice and treat­ment and solace for any com­plaint, includ­ing (as noted in (2) above) over-​​complaining and Gen­er­al­ized Life Dif­fi­culty. They want surety, and feel betrayed when some­thing goes wrong that isn’t imme­di­ately replaced or refunded under their implicit War­ranty Ser­vice Agreement.

And then it hits me: This is how reli­gions get started.

Look at it. Think about it.

We have the over­whelm­ing desire for sim­ple, effec­tive solu­tions to ubiq­ui­tous prob­lems. We have a har­ried spe­cial class, who by dint of his­tor­i­cal con­tin­gency and a few early suc­cesses have become the class explic­itly charged with pro­vid­ing solu­tions for those prob­lems. But inevitably they’re unable to cope with the world’s diver­sity, entropy’s insid­i­ous cre­ativ­ity. So these peo­ple, they focus on low-​​hanging fruit, and increas­ingly point out how much more work they could get done if peo­ple just went through a few sim­ple rit­ual moves: statins, CPAP machines, salad not fat, just plain aspirin is now Bad For You. And the obser­vant pop­u­lace, and the major­ity of the spe­cial­ist priest­hood, don’t have the time or incli­na­tion to actu­ally think about what hap­pens in the end. What hap­pens to every solace-​​seeker, no mat­ter what they try. They shunt old and sick peo­ple off to spe­cial tem­ples, for prepara­tory purifi­ca­tion cer­e­monies involv­ing res­pi­ra­tory support.

Those sick folks, they’ve gone to A Bet­ter Place. Some lucky few come back, briefly, and tell thank­ful tales of the wonders.

But they always go back, in the end. Back to the place we don’t see them.

Reli­gion is not a symp­tom of irra­tional­ity. Irra­tional­ity takes hold of all of us, no mat­ter what. We are not ratio­nal beings. Indeed, the mod­ern sci­en­tific atheist’s ten­dency to decry irra­tional reli­gios­ity so flies in the face of facts as to be reduced to an artis­tic act of Grand Irony. Pre­scrip­tivist Phi­los­o­phy as Per­for­mance Art.

Reli­gion is a robust cul­tural sys­tem, a cul­tural attrac­tor that sucks in soci­eties whole­sale. Look at how far it’s pro­gressed, in just the last 100 years or so. In the case of Med­i­cine, I mean.

So many con­verts. So many ads in all the mag­a­zines. “Ask Your Doctor.”

It thrives because any priest­hood inevitably fails when asked to work on the Really Hard Stuff. So it adapts by play­ing to our inher­ent pain-​​avoidance, trot­ting out the old favorite solu­tions of seques­tra­tion and denun­ci­a­tion of prob­lem­atic facts, eli­sion of com­plex­ity, denial of diversity.

Reli­gion thrives because we are built to clas­sify, but made to over-​​generalize.

Of course, it’s more com­pli­cated than that. But we don’t have time to go into that now.