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Daniel Dvorkin

[ website | The Parlor ]
[ userinfo | livejournal userinfo ]
[ calendar | livejournal calendar ]

Oh, if only [22 Jan 2010|10:57pm]
[ mood | impressed ]

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The worst threat to intellectual property EVAR [19 Jan 2010|11:50am]
[ mood | amused ]

http://go-to-hellman.blogspot.com/2010/01/offline-book-lending-costs-us.html

2 comments|post comment

Here I stand; I can do no other. [18 Jan 2010|06:23pm]
[ mood | determined ]

It's the wrong Martin Luther for the day, I know, but it seems appropriate.

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Things have really gone downhill since Faust's day [15 Jan 2010|08:11pm]
[ mood | amused ]

The Devil's letter to Pat Robertson. If Haiti really made a pact with Old Scratch, man, they got a lousy contract.

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What the internet is for, part the nth [14 Jan 2010|10:06pm]
[ mood | giggly ]

http://www.firstpersontetris.com

2 comments|post comment

Panther's gone. [20 Dec 2009|07:18pm]
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.
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Panther update [19 Dec 2009|05:11pm]
[ mood | worried ]

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.

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Panther's back legs are hardly working. [19 Dec 2009|07:29am]
[ mood | scared ]

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

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Schumer and "bitch" -- on words, and the meaning of words [18 Dec 2009|10:56am]
[ mood | thoughtful ]

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.

Read more... )

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My semester is over. [17 Dec 2009|06:51pm]
[ mood | tired ]

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.

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I have presented my paper to the Society ... [14 Dec 2009|09:33am]
[ mood | tired ]

... 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.

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There's cold in them thar hills (again) [05 Dec 2009|11:58pm]
[ mood | tired ]

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!

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Evolution in six easy steps! [03 Dec 2009|07:16pm]
[ mood | amused ]

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Handy refutation of oft-heard propaganda. [02 Dec 2009|02:10pm]
[ mood | pleased ]

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.

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Charles Darwin: The Most Evilest Man Ever [29 Nov 2009|01:13pm]
[ mood | impressed ]

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

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For those who are wondering what I actually do ... [29 Nov 2009|11:21am]
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.
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Okay, so why am I spending the time again? [29 Nov 2009|12:57am]
[ mood | amused ]

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?

4 comments|post comment

I'm doing SCIENCE! [29 Nov 2009|12:51am]
[ mood | pleased ]

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!

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Turkey Day is a go [26 Nov 2009|01:50am]
[ mood | cheerful ]

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. ;)

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Panther update [23 Nov 2009|11:51am]
[ mood | exhausted ]

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.

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