WYSIWYG

Panther's gone.

Mon, 21 Dec 2009 02:16:51 GMT

She was holding more or less steady last night, but as of early this morning and throughout the day she went into serious decline, and there was really no other choice. Her last hour was spent in as much comfort as we could give her, and she was surrounded by people she loved and who loved her. A long and good life, and a very nearly painless death.

Everyone be extra nice to your pets tonight.

Panther update

Sun, 20 Dec 2009 00:09:27 GMT

She's hospitalized again, probably at least for the weekend. The immediate diagnosis is dehydration and hypothermia; her temperature on intake was 96 F even, which would be rather on the low side for a human and is extremely low for a cat. She's been drinking plenty of water, and not urinating any more than normal, so we really don't know where the dehydration came from. As for the hypothermia, she was curled up in one of her favorite warm spots last night, but if she got cold and wasn't able to move to the bed ... hell, we don't know. It's a mystery at this point.

Current (as of a few hours ago) labs show severely elevated kidney values, somewhat elevated liver values, and slightly elevated pancreas values. Her body is trying really hard to do something, but we don't know what. It's a good possibility that this is all secondary to the dehydration, but it's also possible that her kidneys are failing and that's the root of the problem. We won't know until she's been pumped full of fluids for a while. Hopefully we should get the results on another round of labs around midnight.

Thank you for the well-wishes, everybody.

Panther's back legs are hardly working.

Sat, 19 Dec 2009 14:28:06 GMT

On our way down to VRCC. Wish her luck, everybody, okay?

Schumer and "bitch" -- on words, and the meaning of words

Fri, 18 Dec 2009 17:55:17 GMT

Most of my writing these days is scientific, and in scientific writing, and academic writing generally, we try to be as detached as possible. Scientists themselves are anything but detached -- we're not Frankenstein, neither are we Spock -- but that's the way the journal game is played. And this is probably a good thing.

I'm also an occasional writer of fiction, and there of course the rules are different. A good fiction writer doesn't try to load every word with emotion, since "purple prose" is not a compliment, but the emotion is there. A story that doesn't make the reader feel something is a lousy story. I'd go so far as to say that a journal article that doesn't make the reader feel something is a lousy article, too; the author just has to be very careful about how those emotions are evoked. In my academic writing, I try to bring my skills as a novelist to bear, but in a muted way.

All of which boils down to this: I spend a lot of time thinking about words. Not just the definitions of words, but their meanings, which encompasses what you'll find in the dictionary and a whole lot else. What we mean when we use a word is more than the sum of its parts.

Recently, Senator Charles Schumer (D-NY) used the word "bitch," and he wasn't talking about a female dog of proven fertility. This Salon article describes the affair nicely (and Googling for "Charles Schumer" brings up a large number of stories if you want multiple perspectives) and it drew the predictable anti-PC PC response: "Stop whining! 'Bitch' isn't even an insult any more! Women get to call men 'dicks' all the time, so turnabout's fair play!" Etc.

My letter, written before the flood really began, also drew the inevitable ire of the anti-PC PC crowd. It's a fairly short letter, and please go read it if you want to, but the key line is this:

If a black person makes you angry, do you say "nigger?" If a Jewish person makes you angry, do you say "kike?" I'm guessing not.

A number of responses pointed out that women use the word "bitch" all the time, often as a point of pride. Yes, they do, and that's where we get into meaning. Personally I'm not fond of this usage of the word ... but I'm a man, and my opinion on this matter really doesn't carry that much weight. It is, in fact, almost precisely analagous to the black use of "nigger" or the gay use of "queer." As a straight white man, I don't get it, but it's just not my business. And a straight person who calls a gay person "queer," or a white person who calls a black person "nigger," or a man who calls a woman "bitch," is still pretty much an asshole.

Men call each other "bitch," too, but the use of this fact as a defense of Schumer is just bizarre. It's an insult between men precisely because of its female meaning; the idea is that the worst insult you can apply to a man is to compare him to a woman. The implied threat of sexual domination comes in there too -- "in prison, you'd be my bitch" and the like. It manages to combine sexism and homophobia in a perfect storm of macho stupidity.

What about "bitch" as a verb, as in "bitching and whining," which was also offered as a defense? This is an example of how bigoted insults become absorbed into our brains without us even realizing it. Anyone willing to expend a moment's thought can figure out the origin of the phrase above, and what's wrong with it ... which doesn't keep a lot of people from saying it anyway, presumably while they're describing their experiencing of jewing someone down while buying a nigger-rigged used car. Hey, at least the guy selling it didn't welsh on the deal!

And yes, we have "dick" and "cracker" and "breeder" and "bible-thumper" and a host of other insults which can be applied to men and white people and straight people and Christians, and these insults are bigoted and ugly and the people who use them are ugly bigots. Fine. But anyone who claims that these words carry the same weight as the words discussed above, that they carry the same level of power and threat, is living in a fantasy world.

Words have histories, and their histories are reflected in their meanings. There was a time, well within living memory in my family, when on almost opposite sides of the world "yid" and "nigger-lover" were serious declarations of intent to do harm; both may seem kind of archaic now, but people died over those words. The people using the words didn't have so much to fear. Who uses the word, and in what context, matters just as much as the word itself.

Schumer strikes me as being, all in all, a pretty decent guy in his political life. In his personal life, he may in fact be a raging misogynist and it doesn't really matter -- to almost everyone in the state of New York, and in the United States as a whole, what matters is what he does on the Senate floor. But he has a brain, and an obligation to use it before he speaks. As do we all.

My semester is over.

Fri, 18 Dec 2009 01:50:06 GMT

Folks can start expecting replies to the backlog of unanswered e-mails and LJ and FB messages this weekend, hopefully. It may take a while.

I have presented my paper to the Society ...

Mon, 14 Dec 2009 16:31:51 GMT

... and the Society did not laugh at me, call me mad, and exile me to my secret mountaintop laboratory¹ in which I would then be compelled to labor for years to show them, show them all! They seemed rather pleased, all in all, actually. Lots of intelligent questions afterwards, which hopefully I answered intelligently, and some helpful suggestions as well.

¹Although if they had been going to do that last bit, this particular conference would have been a good place for it, since we were already halfway up a mountain.

There's cold in them thar hills (again)

Sun, 06 Dec 2009 06:57:24 GMT

Headed up to Snowmass on Wednesday for Rocky '09, which is not, in fact, yet another unnecessary Stallone movie. This will be my first-ever in-person conference presentation. Woot!

Evolution in six easy steps!

Fri, 04 Dec 2009 02:15:26 GMT

Handy refutation of oft-heard propaganda.

Wed, 02 Dec 2009 21:09:56 GMT

Hardcore global warming denialists won't be convinced, of course, any more than creationists will be convinced by fossil evidence or the Moon-landings-were-faked crowd will be convinced by the people who actually walked on the Moon, but this might be a useful collection of shootdowns for the usual canned arguments.

Charles Darwin: The Most Evilest Man Ever

Sun, 29 Nov 2009 20:12:38 GMT

This is beautiful, one of the best capsule refutations of common creationist arguments I've ever seen.

For those who are wondering what I actually do ...

Sun, 29 Nov 2009 18:20:27 GMT

I realize that my last post was a bit obscure; I find that kind of thing amusing when I'm punchy. But for anyone who wants to know more about what I actually do, read on.

One of the basic problems in bioinformatics these days (IMO; others might disagree) is that the low-hanging fruit has been picked. We've done some great things with sequence alignment, microarray expression analysis, etc., but while there is still much to be learned from these approaches and much work to do in improving them, they're becoming pretty standardized approaches these days for specific experiments needed to confirm specific biological hypotheses, rather than the frontiers they used to be.

What is still a frontier is combining these multiple sources of information. Most bioinformatics data is, to put it mildly, noisy. Looking at expression data, say, for a stretch of the genome of any significant size is like trying to reconstruct a theater-quality movie from a snowy image on an old black-and-white TV set. The advantage we have is that we know that all the signals are pretty much coming from the same place -- they're all trying to tell us about the same thing -- and if we can look at the genome from multiple angles, we can figure out more of the underlying truth. Stretching the cinematic metaphor until it screams, suppose that we have not only the fuzzy TV broadcast, but also parts of the script and a few of the props, as well as a giant back-lot warehouse that might ... just might ... contain a high-quality master reel, if we can find it under all the junk.

Specifically, the data I'm working with is microarray expression, transcription factor binding, and sequence conservation, all of which cover the entire genome to a greater or lesser degree. The first is specific to actual genes, the second comes from more-or-less evenly spaced probes across the genome, and the third has base-pair-by-base-pair coverage. But they all feed in to an understanding of the same biological processes, whatever those processes may be

In the particular case of the data I'm working with right now, it's the development of wing shape in D. melanogaster, but it can be anything, in any organism. Specifically, it can be disease processes in human beings, which of course is kind of the ultimate point of the exercise. But flies are a lot easier to breed than people, and ethics boards tend to frown on things like deliberately mutating experimental groups of human subjects, anyway.

So we look at a bunch of flies, some of which have straight wings and some of which have curly wings (I will not descend here into the inevitable flamewar over the politics of insectile racism) and we gather expression and binding data from them, as well as conservation data from melanogaster and various related fly species. The first two types of data are phenotype-specific, i.e., having to do with the specific phenomenon under study. The third is of more general biological significance: highly conserved areas of the genome tend to be those involved in processes which are absolutely necessary for survival, and for a fly, wing development clearly falls into the category.

Expression and binding give us hints as to what parts of the genome are involved. Conservation acts more as a filter. Say a certain gene appears to be more highly expressed in the curly-winged than the straight-winged flies. Is this meaningful? Maybe it is, or maybe it's noise, a pattern of snow on the TV screen that just happens to look like a well-known actor. (And may have more acting talent, too.) If there's lots of transcription factor binding in the area too, that lends support to the hypothesis that something real is going on. And if the region in which this occurs is highly conserved, then we have a solid argument. Otherwise, it's probably time to move on to another region of the genome ... and there's a lot of the genome to consider.

What had me excited last night was this. We have a list of target genes, genes which are thought for various reasons, including direct experimental evidence, to be significant in wing shape development. We also, of course, have thousands of genes which may or may not have anything to do with wing shape development, but probably don't. To have some indication that our method of combing the data actually means something, we want to see the areas of the genome around our target genes identified as significant, along with a very few (but not zero!) of the other genes in the data set. Confirm what we think we know, and then find things we don't know: that, in a nutshell (IMO, YMMV, etc.) is how science works.

And that is what happened last night. I'll be presenting preliminary results of this work at a conference in a couple of weeks; it's good to know I'll be going in prepared. And in the longer term ... this is stuff that matters. I have often regretted leaving patient care for research, or at least looked back on my days of directly saving lives and relieving human suffering with a great deal of nostalgia. But if it turns out that over the course of my entire research career there is one major human disease which we are able to puzzle out, in part, by using methods I've developed ... well, then, I will have done more than I could ever have done as a medic or a physician. And that's pretty much why I made the move in the first place.

Okay, so why am I spending the time again?

Sun, 29 Nov 2009 07:56:21 GMT

The instant I made that last post, I got no less than three of those "order a PhD based on your previous life experience -- no classes or books!" spams. Is the universe trying to tell me something?

I'm doing SCIENCE!

Sun, 29 Nov 2009 07:50:12 GMT

Out of 19 test set genes, 4 were identified as significant (or rather, had significant areas of the genome in their neighborhoods.) By contrast, out of 200 randomly selected genes, only 2 were significant ... and while one of these genes has unknown function, the other is involved in cell adhesion, unsurprisingly, in numerous developmental processes. This is exactly the type of result we want.

Go Team SCIENCE!

Turkey Day is a go

Thu, 26 Nov 2009 08:49:53 GMT

Yep, we're doing our Thanksgiving this year. We seriously considered canceling because of the vet emergency, but Panther is doing better and we're not going to let the world beat us down. Anyone who'd like to drop by is welcome to do so, any time after 4:00 or so. Message for directions -- I'll be checking my e-mail, even when I should really be doing other stuff, because you know, I'm like that. ;)

Panther update

Mon, 23 Nov 2009 18:50:57 GMT

She's still in the hospital. There is now no doubt, per the internal medicine vet, that this episode was due to the methimazole OD. And yes, I'm calling it an overdose; doubling the dosage of a chronic medication with profound systemic effects, without reference to how the patient has handled the medication previously, is exactly that. We and Dr. M. are going to have words. Oh yes. Words will be had.

Anyway, she's steadily improving, not out of the woods yet, but getting there. She is eating, the diarrhea's stopped, and her temperature and lab values are headed back toward the normal range. There's some indication of a UTI, which may have been responsible for the fever; I hate to say it, but since everything about her urine was so completely normal up to this point, I kind of suspect a nosocomial infection, i.e. one acquired as a result of hospitalization. I don't blame VRCC for this at all. It sucks, but it just happens (as opposed to doubling the dose of a medication ...)

The agenda: continued IV fluids, bloodwork rechecks, urine culture. The vet is stopping the methimazole completely for 24-48 hours; then we'll go back to her original, well-tolerated dose and maybe try stepping it up, bit by bit, over the course of months. With luck, she'll be discharged tomorrow. Watch this space.

Yeah, it's another one of those weeks.

Sun, 22 Nov 2009 16:38:32 GMT

Panther, our very aged cat, is in the hospital. (VRCC, specifically; for anyone who needs emergency vet care in the Denver area, I heartily recommend them.) Per her regular vet, we recently doubled the dose of her thyroid medication; in retrospect, this was probably too much and I should have pushed back a little harder, talking about stepping up the dose rather than doubling it.

Anyway, last night things started coming out of both ends, and when you're a five-pound, twenty-year-old cat, you don't have a whole lot of reserves. So we took her in, they started her on an IV, and hopefully she'll be discharged this afternoon. Still waiting on some lab reports to know for sure. It's not 100% sure that this is because of the increased dose, but it's a good bet.

So goth_hobbit, rpechmann, and I may not be the most communicative people in the world for the next few days. Still planning on doing Thanksgiving, though. Watch this space.

I wish my papers could be more like this

Sat, 21 Nov 2009 01:01:40 GMT

Parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials

I wonder if Wolf Auto provides a white sheet and pointy hat with your car purchase

Fri, 20 Nov 2009 20:42:26 GMT

http://www.ProgressNowColorado.org/WolfAuto

apologies to anyone who's been waiting for a reply from me ...

Mon, 16 Nov 2009 19:22:45 GMT

Very very busy doing SCIENCE! Hopefully I'll be finishing up the current chunk of SCIENCE! this afternoon, and then I can get around to a bit of (virtual) socializing.

This is one they missed in the Ultimate Showdown of Ultimate Destiny

Sat, 14 Nov 2009 15:08:38 GMT

Okay, the actual story is pretty interesting too. But not even the opening line "E.T. phone Rome" can beat Aliens vs. Popetor: Whoever Wins, We're Saved (coming this summer to a diocese near you.)

About that "thank you to veterans" thing ...

Wed, 11 Nov 2009 19:24:49 GMT

Every November 11th, a whole bunch of people get thanked. I'm not exactly sure how I feel about that.

Every social networking page is filled with posts. Martial poems, particularly "In Flanders Field," get quoted over and over again. Car and furniture dealerships hold sales, announced with bunches of old-fashioned waving-flag banners.

This is not in and of itself a bad thing. I don't mind, and I doubt many of my fellow veterans do either. And yet ...

At the eleventh hour of the eleventh day of the eleventh month of 1918, the guns fell silent on the Western Front. All wars are bad, and some are very bad; the line that had been more or less fixed in place since late 1914 may very well have been the worst ever. The US was, truth be told, a bit player in this; Americans suffered and died, but the scale of the suffering and death which Europe had inflicted on itself is still beyond comprehension. The great feats of endurance and valor which define the best parts of American military history -- Valley Forge, Fort McHenry, Chapultapec, Shiloh, Gettysburg, Belleau Wood, Bastogne, Guadalcanal, Pusan, Chosin, Khe Sanh, Wadi al-Batin -- drop them in the middle of the Somme or Verdun, and they vanish. They become background noise, minor skirmishes forgotten in the main event.

I served honorably, and most of the time with pleasure, for ten years; as an infantryman and as a medic, as a soldier and as an airman, in peace and in war, at home and overseas. My war was bad, because all wars are bad, and it left me with memories I can't shake and will never be able to, memories I could well do without. I can say, without breaking my arm patting myself on the back, that medics and infantrymen are unique in their understanding of what war actually is. Infantrymen do the killing, close-up, whites-of-their-eyes, and most of the dying as well; and medics pick up the pieces, patch up the wounded and comfort the dying, fighting a personal war which is the same in every time and place regardless of which war they're in, which group of evil old men in the halls of power has created the chaos into which terrified kids must descend.

By comparison to the best day in, say, 1916, my war was a walk in the park.

Only for a period of a few months during my entire term of service, between my arrival in Europe and the final disintegration of the USSR, did I actually believe I was defending the Constitution of the United States of America against enemies foreign and domestic. The rest of the time? It was a job. A pretty good job, mostly, sometimes a very difficult job, and occasionally a very dangerous job. A job, not a calling, nonetheless.

And when I did go to war, it was for no noble cause. Not a bad cause, you understand, but not an especially good one either. It was because evil old men far away had decided that once again, it was time for young men and women to die. Like it usually is. 1914-1918 is barely within living memory now, but that lesson should stay with us always.

So, speaking for my fellow veterans: we gladly accept your thanks, and you're welcome. Speaking for myself: you're welcome, but please always try to remember what you're thanking us for.

(x-posted to peacevets)

Sometimes, you have to do what you can

Wed, 11 Nov 2009 02:09:33 GMT

Okay. Money's pretty tight right now, and we really can't justify giving it away. But this is worth it. I made a $1 contribution to each campaign, pretty much symbolic, but it's something.

Because this really matters.

http://www.actblue.com/page/wevegotyourback

"These twenty House Democrats voted AGAINST the Stupak-Pitts pro-life amendment and voted FOR health care reform despite representing districts which lean Republican or are otherwise difficult. They're worthy of your support to show that when they stand up and do the right thing, progressives will have their backs."

Well, I'll be damned ...

Sun, 08 Nov 2009 05:42:11 GMT

... the House passed a real healthcare reform bill, with a (it looks like at first glance) pretty decent public option.

Of course, the price for getting enough of the Blue Dogs on board was an amendment specifically excluding abortion coverage. Grrr. Arrrgh. Even the most ardent anti-choicers don't have a legal justification for this, because HHS abortion coverage is already illegal under the repulsive Hyde amendment. But they just couldn't skip the chance to preach, now could they?

But still. Today is a good day.

Now we'll see what the Senate does. If the Rebublicans are going to filibuster, fine, make them filibuster, make them stand up there and read the phone book to an empty chamber, and meanwhile the Democrats can spend every minute reminding us, over and over, exactly who is blocking reform favored by an overwhelming majority of the American people. And sooner or later, it will come to a vote. Screw the Blue Dogs, screw the Republicans (ah, but I repeat myself) and make it happen with half the chamber plus the VP to cast the tie-breaker if that's what it takes. Make it happen. If Harry Reid can't get this through, it's time to send him to the glue factory.

Also, I was going to contribute to Betsey Markey's campaign next year. Now? She can go to hell.

The kind of thing the internet is for

Sun, 08 Nov 2009 03:50:33 GMT

http://www.3dgalaxymap.com/

It's a fairly memory-intensive Java applet, so if you're on an older computer, watch out. But ... wow. Just wow.

the best thing they could possibly do with it at this point

Mon, 02 Nov 2009 19:54:32 GMT

http://www.tvovermind.com/tv-news/joss-whedon-bids-for-terminator-franchise/12479

Seriously, I was really pissed that they, um, terminated the excellent Sarah Connor Chronicles to make way for that Transforminators piece of shit.