The end of my toenail

I observed with fear the headline of Wired's "The end of theory." After all, theory is what distinguishes us from the apes, right? I couldn't bring myself to read it, but it popped up again on El Reg. Basically, the thesis is that by mass observation and correlation, no model (i.e. theory of causation) is necessary. Key quote from Reg:

"Would Anderson be willing to help test a drug that was based on a poorly understood correlation pulled out of a datamine?" Timmer challenges, apparently unembarrassed to be seen in flagrante putting an ad hominem argument. Of course not, which is why we test on guinea pigs. (And why should Anderson be first?)

But if anything, this is a reason Anderson could use. With sufficiently good correlations, it might finally be possible to spare guinea pigs, chimpanzees, or rats trial by laboratory testing.

Question: Where would those correlations come from? Sole Possible Answer: Mass observation of humans exposed to random doses of random chemicals.* It's not just Anderson that would be testing it. Note also that a good pharma shop will have thousands to millions of different drugs on the shelf.

Quote two:

Yet increasing computing power, both in hardware and statistical analysis algorithms, can still bring forth useful correlations, and new interesting discoveries. Anderson cites Craig Venter's DNA sequencing: having done with sequencing individuals, "in 2005 he started sequencing the air. In the process, he discovered thousands of previously unknown species of bacteria and other life-forms."

"The opportunity is great", he adds, because "correlation supersedes causation, and science can advance even without coherent models, unified theories, or really any mechanistic explanation at all."

Well done Craig! Anyway, what's a species? How does DNA sequencing work? Why would DNA sequencing tell you that you've found a new species? What's DNA? Obviously, in order to know that you need to perform a ligation reaction on an air substrate, amplify with phiC31 rolling circle replication, and sequence via CV's secret method, your species must either: A. Have a theory as to how ligation, phiC31, and DNA sequencing work or B: Run around performing random chemical reactions on the atmosphere until something repeatable yet awesomely variable comes in.

Don't get me wrong, this mass observation stuff is great, but a theory provides so much more direction.

*: But, you say, couldn't you just test the blood/urine/semen of people that recover from or are immune from disease X and then correlate some common factor as the cure? 5-FU! Many drugs derive from naturally occuring compounds, but virtually no drugs are in the form / dose / route that could reasonably occur. Sure, some workers might be exposed to fluorine gas in an industrial accident, and some of them might have cancer, and some of those cancers might regress, but in order to get enough N, you'd have to engineer fluorine leaks all over town (and that stuff is NASTY).

OK, so you figure out that nucleoside analogues are great. But you find that only some of them work on cancer, while others work on HIV (you do subscribe to the germ theory of disease, right?). Is there some way to figure out which ones are more likely to work? Well, if you have a theory of DNA, and DNA polymerization, and recombinant DNA technology it just so happens that if you add the right fraction of some goo that kills bacteria to a mixture of factors that contain something significant for allowing human cells to grow [which you produced by heating human cells in a reaction well with some random chemical strains that you synthesized, then heated it, then cooled it, then heated it, then cooled it, and so on {in a chain} 30 times {a number you hit on randomly} ] with something that allows the bacteria to survive when you add that mold extract that a technician dropped the fertilizer in one day, then treat the bacteria with that one solution and fractionate them, you can try to use one of those fractions to do something similar to that heating/cooling thing (EXCEPT YOU MUSTN'T HEAT IT) in the presence of various nucleoside analogs, and perhaps so many mice won't have to die.

What is 538 trying to tell us?

Is it just me, or does this seem to suggest Virginia as the key state in the election?

Revenge of the Cavendish

I was trying to decide whether to rename "The Banana" as "Pudding," so I checked on Google Trends:

Surprisingly, Pudding jumps up near the end of every year - Thanksgiving and Christmas presumably. The surprising this is that Banana tracks with it...

Celebration Guns

There's no good way to come at this.

Reading Spencer Ackerman's blog, I come across a column in which gun rights people are upset with the Republican party. The pro-gun people are upset with the Justice Department because it argued in favor of continuing gun restrictions in the D.C. v. Heller case. In the column he references, one quote stuck out:

As the gun grabbing Brady Campaign acknowledges, such a finding by the Supreme Court could open the door to striking down as unconstitutional most, if not all, of the victim disarmament laws on the books.

Emphasis mine. I was tickled by that characterization of gun laws. It reminded me to write the rest of this post, which was originally hung on a gaffe that Mike Huckabee made at the NRA national convention a couple of weeks ago. A clatter was heard during Huckabee's speech, to which he joked:

“That was Barack Obama, he just tripped off a chair and someone pointed a gun at him and he dove for the floor.”

Barack's gun-phobia is presumably linked to the possibility of assassination, but it could be a more banal, if not benign fear. Michelle Obama (in response to a question about assassination):

I don't really lose sleep over it. Because the realities are that, you know, as a black man, you know, Barack can get shot going to the gas station...

She took a lot of flak for that. Reading the words on this page, I can see why. The flat invocation of blackness is weird.* But the invocation of gas station sends a tingle up my spine. I remember one night my first summer in Hyde Park, gassing up the van at the ill lit Mobil on 53rd. The station was flanked on both sides by dark apartment buildings. On the opposite side of the street was a park,** empty. A man riding by on a bicycle abruptly turned in and started calling to me. And I thought, "O.K. this is going to be my first time getting mugged." And I checked my pocket. "Hey," said the man, "are you ready for the anatomy test tomorrow?" It was SDS.***

So, when Michelle Obama talks about a black man pumping gas, I fill in the blank "on the South Side of Chicago," an area where you really could get shot while pumping gas.*4

Which brings me to my last meditation. Amadou Cisse. Cisse was a graduate student in Chemistry at the University of Chicago. I never met him, but his death is still a subject of discussion. Without sources or verification, this is how it went down: Two guys borrowed a car from their neighbor with the intention of going clubbing. However, they realized that they were short on money. No big deal, they figured, we'll just get some off those rich students at the UofC.*5 First they mugged two students coming out of the biology / med school lecture building, and netted a pen. Coming back south, they threatened a professor near 60th and Woodlawn, who ran away as they shot at him (and missed). They continued west, finally running into Cisse near 61st and Ellis. Cisse was coming back from lab, had no money, wasn't even carrying his wallet. They got frustrated, so they shot him.

No. Seriously.

This takes me back to the D.C. gun ban. Chicago also bans handguns, which the murderers used. A lot of people have said a lot of very intelligent things about guns. I have something not very intelligent to add:

If someone were mugging me, and God came down and said, "You can either have a gun in your pocket, or $40," I know that with one of those options, I'm guaranteed to walk away.




*: Is it? The murder rate and murderer rate are much higher in blacks than whites. Concurrently, black on black murder is way more common than black on white or the reverse. This isn't to say Barack is likely to get murdered at the BP in Gunbarrel...

**: A couple years later, gangs of malicious 12 year-olds would ambush students cutting through that park after school and steal their electronics.

***: SDS is a white guy, so, you see, I'm not racist. I'm afraid of everyone in the dark.

*4: A takeoff of the infamous survey question from Freakonomics "How does it feel to be poor and black on the South Side of Chicago."

*5: We don't think of ourselves as rich, of course, but as people with well-off parents (yup) or very few expenses (yup), we tend to walk around with iPods (nope) laptops (sometimes) or other saleables (yup).

60% Cancer, 20% Parkinson's Prevention, 20% Pure Pleasure*

I was listening to Dan Carlin's podcast, Mad about Torture, and after the apparently controversial bit about hating torture** he talks about the idea that fat people are using all the oil to move their fat butts around and eating all the food, therefore increasing food prices for people abroad.***

I'm not going to talk about that.

I'm going to talk about cigarettes. In the '90s Phillip Morris did a study in the Czech republic indicating that cigarette smoking is a net positive for government revenue. I suppose there's a debate about healthcare costs, but if someone dies before the age of 65, they get no social security, whereas if they die at age 90, they suck up a lot.

This phenomenon is enhanced in the U.S. by private insurance. If someone dies before 65, they don't get Medicare at all, and private insurance pays for it.

So: Cigarettes = Gov't saves money. Private insurers hosed.

Now, the government introduces cigarette taxes, with the idea that they're going to recoup the added costs that smokers cause the government. Remember, those costs are illusory. But, the taxes will cause some people to stop smoking, which will increase government costs, which will be offset by cigarette taxes****

So: Cigarette taxes = Gov't increases spending and revenue (no idea which is greater). Private insurers save money.

It follows that: Smoking Ban = Gov't increases spending with no consummate increase in revenue. Private insurers go to the bank (increased tax revenue?).


Therefore, a cigarette tax is a win, win, win, win, lose situation (gov't, insurers, quitters, smokers, smokers).




*: via VKP, actually cigarettes are a mixture including emphysema, prevention of Crohn's
disease, various cancers, and asbestos, in addition to the ingredients presented above.

**: Apparently some people thought he was pro-torture 'cause he projects a very manly image. I don't know, I just started listening 'cause I wanted more podcasts. Anyway, one of my great formative experiences was reading The Gulag Archipelago. I swore when I read it that I would fight against any government that resurrected those principles. I have to say that an America in which citizenship and fair skin may or may not protect you from getting kidnapped, taken to a black site, disappeared and tortured to death deserves fighting.*****

***: It's the old mother's standby - how can you leave food on your plate when children in India are starving. As far as I can tell, the world food price increase is a result of more numerous meat eaters everywhere, thick and thin, combined with biofuels, and agricultural subsidies in the West.

****: Yes, I realize that cigarette taxes are local and medicare and social security are national. I'm assuming that since governments are always passing around responsibility / grants, it's fungible. Feel free to correct me.

*****: But, you say, It's just a few people. IT ALWAYS STARTS SMALL. Part II of The Gulag Archipelago talked about the establishment of the Gulag in the Solvetsky Islands in the 1920's, and how it started small, and now the original camps were replaced by voleyball courts. Sick stuff, kids.

Obama Must Name VP Nominee NOW!!!

Via Matt Yglesias:

New HRC campaign rationale -- Obama might get shot and killed before formally securing the nomination, so she may as well stay in the race!

...
Specifically (from NY Post MY links to), "We all remember Bobby Kennedy was assassinated in June in California."

The thinking being that if Barack gets assasinated now, the Democrats would nominate Sen. Clinton. The only way to avoid this is if Obama names his VP nominee now. While I can't think of any examples of nominees being assassinated, surely the VP nominee would take the top slot?

Creativity = Synthesis

Once upon a time, I was worried that I wasn't creative. All I did was take two things that existed and put them together, sometimes in an unusual way. My friend Marc said "But, J, that is what creativity is."

Haha haha haha what?

I just finished Flyboys. I would have thought a WW I period piece about fighter pilots had real potential. Perhaps it does...

I think I'm usually pretty generous to movies, and don't even notice many of the things that others gripe about. I noticed them in Flyboys. Let's start with the utterly inhuman portrayal of the Germans. Surely, after Downfall we can stand for all of our enemies to have more than 1 dimension. Not a single German word is translated and the 'honorable' German seems more random than deliberately noble. The SWAT-esque ransacking of a French house seems unlikely to impractical.

Move past the 'Real World' rainbow of American stereotypes that make up the protagonists. Forgive the magical learning of English by the female love interest. Pay no attention to the 'one of these guys is a spy' plot that unspools and wraps up, tensionless, in the space of 15 minutes. Feel relieved when the 'hero' American is supposed to get court martialed, and instead gets a medal. Accept the fact that the EXACT wound that kills 'gruff, experienced, but heart of gold' American pilot is not only survived by 'hero' American, but he is able to do aerobatic maneuvers, and shoot 'super-evil' German guy with a pistol at range while flying, and survive.

Whenever characters need to be interacting in the background, or chattering, or filling dead air, they laugh. They always laugh. Everyone in the movie is constantly laughing, but no one ever tells a joke. This 2:30 epic movie was done so cheaply that they couldn't even pay a guy to throw in chatter about the latest cinemas, or whores, or whatever.*

Of course, this happens in other shows as well. The episode of The Tudors I'm listening to right now, for instance. But it usually doesn't rise to my level of notice.

* In all fairness, it's not as bad as the soundtrack of On the Beach.
1. Waltzing Matilda Overture
2. Waltzing Matilda piano only
3. Waltzing Matilda sung by drunk guys
4. Waltzing Matilda flute only
5. Waltzing Matilda variations

One saving grace of OTB is that they seem to realize how annoying it is when the captain yells at the drunks singing WM.

Hardy Heron

One of the things I love about running Ubuntu is that every 6 months I get a 'new' operating system. This time, it's the upgrade to Ubuntu 8.04, codenamed Hardy Heron.

I've done this once before (7.04->7.10) and the experience is the same - on the day of the release, you click the upgrade button, hang around while it downloads all the new files, and then reset to a new system.

Here's the thing - everything still works after the reset, and you get a couple of new features. Of course, this is considerably better than Windows.

Being a partial Linux fanboy, I trolled around for sites talking about the upgrade (there were several about new features as they were announced) and came across this piece on the Linux Format site. Other than it's blahblah writing style, I paused when I read:

...as an LTS (Long Term Service - pe) release... [Hardy Heron] will be supported for three years... to give corporate users the reassurance that they are getting something stable. However, having said that, the release cycle for this version was the normal six month cycle, so there's been no surface change to the work rate that has gone into the Hardy Heron ... To be honest, when the delay to Dapper was announced, it communicated that Ubuntu and Canonical were committed to delivering a quality release. Looking at it this way, Hardy feels like just another notch on the bed head of Ubuntu, which is a shame.

Are they saying that because the release was delivered on time, that means It wasn't significant? When a game company, or a filmmaker delays a release date, it usually means something's going wrong.* As a student, when I ask for an extension, the product is usually far from my best work. Would the author feel better if he knew the product wasn't available 'til 9 AM central time, a full 15 hours into the Grenwich mean time day? Also, see what I mean about the writing? Doughy, doughy, doughy (I admit this isn't often my best work, but I hope I'm not that bad)

Of course, that sentiment contrasts with:

The development of Ubuntu has not let up since 6.06 (the last LTS -pe) got out the door, with some impressive releases that have lead up to this point in time.

So they have been working on this LTS for more than six months... right? From my perspective, it seems like what makes an LTS and LTS isn't the work that's put into it before release, but whether it is Supported over the Long Term.

The Linux Format article also included a discussion of some theoretical interest

With the 6.06 release, Kubuntu (Ubuntu + the KDE environment**) was classed under the LTS banner; however, with the advent of 8.04, this is not the case due to the... recent release of KDE 4. ...KDE 4 was [considered] too new to be... stab[le]... for a[n] LTS release, [and it would be ] difficult to... support... KDE 3.5 over the next three years. This is... understandable, but...inconsistent as Ubuntu 8.04 ships with Firefox 3 Beta 5... with which we've had minor stability issues.

I invite you to read the tortured original. My opinion? Apples and Oranges. Firefox may be the most used program on my computer (and probably most others) but it is just a program. KDE is an environment, several programs that run in that environment, and the toolkit used to add programs to that environment. Instability there has much wider ramifications. A downgrade to Firefox 2.x*** is easy. A downgrade to KDE 3.5 may be impossible.

This also has something to do with the fact that Ubuntu releases occur 'like clockwork' not only 6 months after one another, but also 1 month after the most recent GNOME release. Since Ubuntu is coordinated with GNOME, that means it's not coordinated to KDE.

Presumably, the customer also matters. I'll probably upgrade to Ubuntu 8.10 in October. A smaller number of critical users and servers will be the ones still using Hardy Heron in 2013. It makes sense to get them all on the same platform to decrease duplication.

Also, screw KDE. I did a test install on my laptop, and it ran slightly faster than Windows Vista. Even my tower stalled a bit. If Ubuntu is going to be the desktop Linux, it should, you know, run on computers people actually use.****

*: I'll make no mention of Windows since, as far as I can remember, no version has ever been released on time

**: KDE = K desktop environment**2, as opposed to the Gnome environment that comes standard with Ubuntu.

**2: Environment = does not translate into Windows world, but do you know how all windows, buttons, menus, icons, text fields etc. in Windows look the same? And how all the windows, buttons, menus, icons, text fields, etc. on a Mac look the same between programs, but always different from Windows? That look and feel is the 'environment.' Also part of that environment is a standard set of programs akin to Notepad, Windows Media Player, Paint, Calculator, Internet Explorer.

***: Firefox 2.x is probably the least stable program on my computer, a comment I have heard from other Ubuntu users.

****: Part of the age-old battle in the linux community. The desktop people have traditionally lost because most of the people paid to work on linux are using servers and other high-end machines.

Disambiguation page

Hopefully you're not too focused on Aliza Shvarts. The Yale art student who claims to have repeatedly artificially inseminated herself and induced miscarriage and is using the resultant blood / products of conception in an art installation.*

via Andrew Sullivan, I see this quote:

It creates an ambiguity that isolates the locus of ontology to an act of readership. An intentional ambiguity pervades both the act and the objects I produced in relation to it. The performance exists only as I chose to represent it. For me, the most poignant aspect of this representation — the part most meaningful in terms of its political agenda (and, incidentally, the aspect that has not been discussed thus far) — is the impossibility of accurately identifying the resulting blood. Because the miscarriages coincide with the expected date of menstruation (the 28th day of my cycle), it remains ambiguous whether the there was ever a fertilized ovum or not. The reality of the pregnancy, both for myself and for the audience, is a matter of reading.

First, I can think of several ways of accurately identifying the resulting blood, including whether or not there was a fertilized ovum, and whether Shvarts used 'abortifacient herbs.' Shvarts obviously isn't up on her PCR or mass spec.*** Furthermore, the ambiguity on my part exists because something has been artificially concealed from me, but it is not ambiguous to Shvarts. Therefore it is inappropriate to say "it remains ambiguous." IT is not ambiguous. IT is determined. Apparently, Shvarts did not determine whether she had conceived prior to inducing abortion, so that fact is ambiguous. But the cat and mouse over whether this is a prank, a Sokol affair against science, that's definitive.


*: Not related to the point of this post, but my opinion is:
1. Yuck
2. Moral revulsion, possibly tied to my aesthetic revulsion - if an human conceptus has one iota of rights derived from being human then it deserves not to be created for the sole purpose of being aborted for art.
3. Scientific skepticism - what is the success rate for DIY artificial insemination? What is the success rate for 'abortifacient herbs'? What are said herbs?
4. Puzzlement - Why use DIY artificial insemination instead of ordinary sex? Various explanations have been offered, usually based on the romantic preferences of Shvarts or her 'fabricators'** I speculate there is some sort of feminist message a la "A woman needs a man like a fish needs a needle-less syringe." But considering the 'message' which as far as my untrained mind can discern is about the arbitrary control of society over the body of its female members, I would think cruising for roofies would be more meaningful, though perhaps less reliable.
5. Side note that this is exactly what pro-choicers don't need.

**: WTF?

***: Polymerase chain reaction to genotype the blood. Conceptus-containing blood would include 'DNA fingerprints' that are not present in the... artist. Mass spec would identify foreign compounds in the blood. If it were me, I'd spring for sequencing the albumin gene, on the probability that it's actually chicken or cow blood.

I was wrong, sort of.

The final polls had it 43% Obama, 49% Clinton. Of the 8 percent undecided, I figured all 8% would go to Obama. So 2% went to Obama and 6% went to Clinton - a neoclassical Bradley.

CNN has it at - Clinton 55%, Obama 45%

Since 10% is the magic over/under, get out/stay in number, it's worth going into further...

Clinton: 1,258,245 to Obama: 1,042,297... type type type... calc calc calc.... 9.4%

I'm so pithy.

Pennsylvania prediction

I got a bad feeling in my stomach today. Not the rumble of too much 'better-living-through-chemistry' Kosher for Passover coffe cake, no. Barack Obama is going to lose Pennsylvania. Badly.

The voters of Pennsylvania aren't plugged into my narrative. They're going to vote for the candidate they think is best prepared. I can't decide whether to congratulate them for focusing so closely on what matters to them, or damn them for conducting their election in a vacuum, which is exactly the same thing.

RCP has Barack with 43% vs. Clinton's 49%. Consider the lesson of New Hampshire, where undecideds broke almost entirely for Clinton, giving her those extra 8000 votes. Consider Texas, where voters that made up their minds in the last 24 hours overwhelmingly went for Hillary. Those 8 percent of faux fence sitters will swing to Clinton.

Barack loses by 14.

See you in August.

Several birds

I see that John McCain opposes a bill to improve educational benefits for troops because it might hurt retention rates. I also have an idea that would increase retention rates. And I have an idea that would decrease American troop casualties. And I have an idea that would save more than 10 times what McCain would save by cutting the $51 billion of earmarks he has identified.

By strange coincidence, they are all the same idea.

12 years ago, I thought girls were gross

And aparently, 12 years ago, Barack Obama held positions so liberal that they "won’t even fly with a large number of Democrats, let alone in a general election"

Evidence:

The evidence comes from an amended version of an Illinois voter group’s detailed questionnaire, filed under his name during his 1996 bid for a state Senate seat.

Late last year, in response to a Politico story about Obama’s answers to the original questionnaire, his aides said he “never saw or approved” the questionnaire.

They asserted the responses were filled out by a campaign aide who “unintentionally mischaracterize(d) his position.”

But a Politico examination determined that Obama was actually interviewed about the issues on the questionnaire by the liberal Chicago non-profit group that issued it. And it found that Obama – the day after sitting for the interview – filed an amended version of the questionnaire, which appears to contain Obama’s own handwritten notes adding to one answer.

emphasis mine. So Barack Obama filled out a questionnaire twelve years ago, then forgot that he filled it out. Perhaps they might follow up with whether he might have, you know, changed his mind since then?

Barack Speech

The Clintons are elated because Barack Obama is being forced to give a major, very well covered and publicized speech about race, religion, and his personal connections to Rev. Wright.

What they don´t know is that Barack Obama gives an outstanding speech, and that the three things Barack Obama speaks about best are race, religion, and Barack Obama.

Wait... they don´t know that?

A Bit of Veiled Conceit*

Quick, what is Michal Kleinlerer (the woman)´s profession?


If you looked at that toothsome smile and guessed ´toothpaste model´ you´re exactly wrong! She´s an orthodontist. As in the old joke about the barber with the worst haircut in town, if you need some molars out, you should look at the competition.

I was originally going to make fun of her for padding her dental school application with one of those ridiculous Masters in Medical Studies,** when I glanced at the photo and BAM!

Speaking of dpp target genes (of which BAg of Marbles is one), Dr. Kleinlerer has a hit on Google Scholar, where she studied the role of the activin receptor III in skull development. I suppose one peer reviewed abstract isn´t bad for a year of masters work. And the abstract is from ´07, which means she did it after her ortho school.

Shenkin, the groom also has some research chops, and I was able to dig up this study on cavities and second-hand smoke.

So I´ve completely failed to make fun of these people, while simultaneously distracting myself from plant development for an hour.

sorry.

*:The idea of making fun of people in the NY Times Weddings section is from Zach at Veiled Conceit on hiatus for the last 3 years.

**: Many people who are not accepted to medical school on the first go-around because of a lack of research experience or a low college GPA apply to these programs. Some teach the first year of medical school, with the possibility of transfering into the second year, some are serious research programs (though I am suspicious of any research whose pace is controlled by the clock and not the internal logic of the data), and some are an expensive waste of time. I frequently assume the latter case.

Open Access

A couple of months ago, there was a paper published in Cell describing a way to turn skin cells into stem cells. Personally, I think it´s crap - using four modified HIV strains to induce multipotency? And they demonstrated said multipotency by immunofluorescence for so-called signature proteins? Nonsense.

Here... see for yourself.

Oh, wait, you probably can´t, not unless youŕe willing to pay $30 for the privilege. While scientists churn out new information every month, most of it is behind terrifyingly high subscription walls. If youŕe at a cush research institution like this one, they pay ungodly fees for unlimited access, but if youŕe at Drake, or a civilian, just interested in an article about your illness or trying to understand the latest scientific fad, then youŕe stuck with your nose to the glass.

But, I hear you say, many magazines are subscriber only. Certainly theyŕe under no obligation to give away their product for free? Am I just trying to guilt them because itś about medicine?

There is a difference here. When Matthew Yglesias writes an article for The Atlantic, The Atlantic gives Matthew money to write the article. If he needs to go to Belgium to follow the story, they pay for it. If heś a staff writer, they provide him with a computer to write it on and coffee to think with.

Letś say I write an article. My stipend, tuition, insurance, everything, are paid for out of an training grant from the National Institutes of Health. My advisor is paid out of a research grant from the NIH. My equipment is paid for by the same grant. If I have to fly to Belgium to do an experiment, same grant. If I go to a conference, same grant. Itś all paid for by the NIH. Which is to say the U.S. Government. Which is to say, the people.

Keep in mind that when my research gets published, I write the paper. My advisor edits the paper. The peer reviewers brought in by journal are also professors on NIH grants. The editor at the journal and the formatters at the journal are the only ones not paid by NIH.

So, of the expense in producing a scientific paper, greater than 95% is paid for by the taxpayers. I´m not saying screw the journals out of that 5%, but rather the government should spring for the cost of publication and democratize the whole thing.

As wikipedia never tires of reminding me in photo credits:

This image or file is a work of a U.S. Air Force Airman or employee, taken or made during the course of the person's official duties. As a work of the U.S. federal government, the image or file is in the public domain. Subject to disclaimers.

This is from here. While I don mean to imply that I work for the Air Force, or that the current situation is unlawful, I am arguing for the general understanding that documents paid for by the government ought to be public property.

Barack Obama is your new PI*

In re: barackobamaisyournewbicycle.com

Barack Obama is your new PI.

Barack Obama thinks you should start writing your thesis.

Barack Obama said you work too hard.

Barack Obama proofread your grant same day.

Barack Obama went ahead and arranged your committee meeting.

Barack Obama found a protocol for your antibody.

Barack Obama put an awesome paper on your desk.

Barack Obama told everyone to stop coming in on Saturdays.

Barack Obama got 1554 for beer hour.

Barack Obama hired a tech for you.

Barack Obama sent you to a Gordon Conference.

Barack Obama is okay with you coming in at 10:30.

Barack Obama is in his office.

Barack Obama analyzed your data.

Barack Obama knows the perfect lab for your post-doc.

Barack Obama bought you new pipettes.

Barack Obama promised to watch your mice when you went on vacation.

Barack Obama laughed at the joke slide in your lab meeting.

Barack Obama agrees with your hypothesis.

Barack Obama thinks you have adequately characterized your system.

...



*: PI = principle investigator, lab head, research professor, person in whose lab you work

**: Credit ANA, I.

Conspiracy theory

Not being in the Military Industrial Complex, I have limited knowledge...

But a former comrade of mine in international relations suggests the satellite shootdown by the U.S. recently was a response to the Chinese shootdown last year of one of their own weather satellites.

Two pieces of evidence weigh in:

The Navy's stated reason for destroying the satellite was worry about environmental damage from unspent hydrazine in the satellite's fuel tank. Hydrazine is toxic in the sense that if someone is exposed to a lot, they may die, be seriously injured, or have an increased risk of developing cancer. It is not highly lethal (like VX), nor catalytic (like CFC's) nor long-lasting in the environment (like plutonium). There was no statement about where the satellite was likely to crash, so public health exposure is either an unknown or a known unlikelihood. If one looks at this from a strictly environmental perspective, the damage due to not breaking up the satellite must be weighed against the damage due to launching the SM-3, who's solid fuel is not exactly candy and puppy dogs.

What argues against this is that I already assume the U.S. had the ability to shoot down satellites. There's no point in attempting something that everyone already thinks you can do if there's a real chance you might fail. And the op might have failed.

Turnout

Not that I really have time to discuss this, but a lot of people have made a big deal about the high turnout in Democratic primaries (see here for instance).

Bullshit.

The really high turnout in Iowa, New Hampshire, and other early primary states conveys real interest in the election.

High turnout in Hawaii is simply because the primary there has never mattered before. Who is going to turn out to vote after someone has already sewn up the nomination?

Deconvolute that, then Iĺl get excited.

Playground nonsense

I was just listening to the Schmitt/York bloggingheads, and Byron York was saying the proportional allocation system was the electoral equivalent of everybody-wins-don't-keep-score-in-soccer-rah-rah-self-esteem nonsense, as compared to MANLY ROBUST and FAST winner-take-all Republican system. A quick tabulation of Delegates, based on winner takes all the delegates by state, shows Obama CRUSHING Hillary in a MANLY REPUBLICAN RAAARGH fashion, 1396 to 1325.*

Theory, meet reality.

Apparently, the close delegate totals in real life, the close number of states won, the close 'popular vote' insofar as it can be calculated, and the close national polls reflect, amazingly, that fact that Democrats are torn between two vary good choices.

GRRRRRRRRR. MAAAAANLY.

that is all



* Those are the totals if winner takes all, including Superdelegates. If one goes by pledged delegates the totals are Obama: 1093, Hillary: 1075. At this time, the real-world delegate totals are actually farther apart than in Yorkland.

** Delegate counts from Wikipedia, as always.

If you can't be helpful...

I clicked into CNN to a story about polling at Texas that showed Obama very close, but still slightly behind Clinton. There's a link to state by state polling, which I think might help organize my thoughts...

Wow is it bad.

First, I linked to it from a story that says Obama is slightly behind in Texas. The map has him ahead.

Second, it's got states that have already voted. It has Hillary winning Iowa and Obama winning New Hampshire. Hot tip CNN: They had a really, really big poll in New Hampshire, 285,811 people surveyed. Margin of error: 0.

That last NH poll that showed Obama ahead - that's history, not news.

Either clear off the meaningless polls, or replace them with election results.

That is all.

Hmm

I notice a large white space on CNN's delegate counter, perhaps they could use it to display the number of delegates Won and the number of delegates bought. Just saying.

http://www.cnn.com/ELECTION/2008/
screenshot cropped with The GIMP

PatientEtherised, 1 Step ahead of the CW!

CNN has it my way.
But they get some things wrong:
First, they let the Clintons spin them on Ohio and Texas. O&T together are 334 elected delegates. This is only a little more than the 252 remaining to be passed out in February, which the Clinton spin effectively concedes to Obama (not to mention Wanela and Maine, all four of which went for Obama already).

Two, CNN's interest in money is wrongsighted. A winner can always raise more money. The question is, how long can Hillary be behind in elected delegates before the money starts drying up. Or, more realistically, how long can Hillary make up for being behind in elected delegates by having more superdelegates? If Obama can actually surpass Clinton in the total delegate number, look for that to change.

Pro Barack Math

This is how Barack is going to win the nomination:
First, forget the Superdelegates. They're going to line up behind whoever wins the most real delegates. That means that you don't need 2025 delegates to win, you need... 1627, i.e. more than half the 3253 pledged delegates.

Current standings via CNN.com:
Obama 918
Hillary 885

So, Obama needs 709, Hillary needs 742.

The feeling is that Obama is going to do pretty well in all the states until Texas and Ohio (Mar 4). I don't mean 'feeling' as in the Obama momentum lead, I mean that the cynical view, that Obama wins caucus states and states with lots of African Americans, says he should do very well. Those states, Wanela, Potomac primary, etc. are a total of 447 pledged delegates, which is more than all the primaries in March (415) even though March includes Texas and Ohio.

So Obama will definitely be ahead in pledged delegates for the next three weeks... an eternity. And with the anti-superdelegate backlash underway (see Tad Devine's NYTimes Op-ed) Obama's lead in that group will get talked up. If he gets 2/3 of the after-Super-Tuesday delegates (~300), that will make it:

Obama 1218
Hillary 1033

Barack could easily get half of the next 415 delegates (Ohio / Texas / etc.). Why do I say that? Fewer states - more Barack time. Texas is a half-caucus, Ohio is rich in A-A's etc.

Obama 1425
Hillary 1241

Now, at this point, the superdelegates can swing it for Obama, but remember I already discounted them. At this point, Barack needs 202, Hillary needs 386 of the remaining 566 delegates. It's April, and I think momentum comes back into play in a big way.


How is this different from an analysis that says whoever's ahead will win if they get half the remaining votes?

1. Obama's lead in the elected delegates will finally get noticed.
2. Obama's lead in elected delegates will widen.
3. Obama's lead in elected delegates will persist until at least the beginning of April.

After two months of consistently being behind, with the realization of another month of being behidn before people were paying attention, I think Hillary finally crumbles.

Gordon is Bi

So, I was watching Prime Minister's Questions yesterday and the new PM, Gordon Brown was emphasizing the need for bipartisanship. Now, I may be an ignorant Yank, but everyone knows that Britain has three major parties. Perhaps one of the Lib dems should mention it at question time:

"Mr. Speaker, is the prime minister aware of the liberal democrats? Because if he isn't the electorate certainly is."

Recently Asked Questions

Q1: When did you take the boards?*
A1: June 1st.

Q2: What was it like?
A2: 6 hours of sheer boredom, followed by an hour of boredom on the 6 bus that was, if anything, even sheerer.

Q3: How did you do?
IF (Q'er = Jose Quintans)
A3a: You tell me. (Unless you file papers to not have your score reported, your medical school and administrators will receive your score 4 to infinity days before you, as they get it electronically and yours is sent via US mail, hence the chance of infinity. You can file to report to them nothing, or merely that you took the test, unfortunately, those papers have to be filed 2 weeks prior to the exam, which I didn't realize until 3 days before the exam.)

Q3a1: Why can't they send you your score some other way?
A3a1: See answer 9

ELSE
A3b: No idea The score haven't come back yet.

Q4: When will you get your scores?
A4: They said it usually takes 3-4 weeks.

Q5: Why does it take so long to grade a computerized multiple choice test?
A5: Because everyone takes a different test they curve how you did versus people who did the same questions 3 weeks before and after your exam.**

Q6: Why can't they compare you to test takers from the previous 6 weeks?
A6: See Answer 9

Q7: It's been more than 4 weeks, why don't you know?
A7: Since June is a peak test taking month it may take them 6-8 weeks to process your score.

Q8: But you just said that normally they have to wait for enough data before sending your score out. If more people are taking the test, shouldn't you get it back faster?
A8: See answer 9.

Q9: WTF is going on?
A9: Either the National Board of Medical Examiners, or you, are a moron. Since the NBME, with their opaque boards and their monopolistic match control my fate for the next 20 or so years, I'm going to go with you. You are the moron.

Q10: Why am I a moron?
A10: Because you asked questions. And this is medical school.



*: Step 1 of the US Medical Licensing Exam

**: I'm actually kind of grateful that they don't have the scores right away simply because then I wasn't even more tempted to rush through the final test blocks.

So what, Ubuntu

About a month ago, I got a new laptop*, which came with Windows Vista. Being one of those people that said, "Oh, I'll never use that pile of kludge," I installed Linux on it. As it happens, there is no single Linux in the same way that there is a single OS X or Windows. Instead, there is a universe of distributions each of which is a collected set of all the bits that make up a functional operating system. I could, if I had wanted to, hand selected and tuned each piece of the operating system and assembled my own 'distro' from scratch... yeah right.**

Eventually I settled on Ubuntu 7.04 x86. Why: 1) Ubuntu 7.04 was the first distro that detected my sound card and my wireless right off the bat. 2) Have to use x86 or you cant run Flash (i.e. no YouTube et al.). 3) Ubuntu is the most popular distro, so I assume it will be decently well taken care of.

Since I'm the first person in my med school class (I think) and the first person in my family to be running Linux, I've been showing off for the past month, and the response I get is "Oh, it's a computer, it works." Having been deprived of the ego satisfaction, I've gotten to feel the same way. After all, what I've got is a rather boring laptop running a collection of programs that are slightly ugly looking knockoffs of the Windows equivalents.

Don't get me wrong, I appreciate that OpenOffice.org can export PDF's at the touch of a button, but it's best feature is that it can edit Word files without screwing up the formatting. Firefox is exactly the same, GIMP is $300 cheaper than Photoshop, if a little underpowered*** I use all of these pieces of software on my Windows computer, and I appreciate them...

But there's no killer app. The closest Ubuntu comes in my experience is apt-get, a program that lets you find and easily install, yes, more free knockoffs of Windows programs.

Maybe in some fields (web servers? security? mathematics?) the programs that everyone wants are written for Linux, but I suspect that you won't see large scale migration at the consumer level until such an app exists for non-computer professional users. Even if Linux programs looked and ran so well that Windows programs looked like the cheap knockoffs, I think people feel more comfortable with something that you buy.

So if any Linux techies are reading this (unlikely) stop chasing the taillights and do your own damned thing.



*: Acer blah blah blah. Basically I wanted a combination of small, cheap, and AMD. I should note that I didn't pick a computer based on
**: Incomplete list of distros I tried: Xubuntu, SimplyMEPIS, Freespire, Fedora Core, Kubuntu, Debian. Note that all of them installed perfectly on the first try from a LiveCD without needing to be told more than what time it was, which is pretty good. Please please don't tell me why each and every one of these is better. I give my reasons above and I'm sticking to them (for the time being).
***: Yes, I've heard of Krita, but as my computer broke down crying when I tried to run Kubuntu, I don't think it's such a hot idea to try out.

Going to take a toilet bowl cruise...

As you may know, I'm taking the USMLE Step 1 tomorrow. Briefly - it's an eight hour computerized test covering the first two years of med school. Oh, and it's $400 to register for it. Here's a nice bit of the rules:

Your entire testing session is scheduled for a fixed amount of time. The computer keeps track of your overall time and the time allocated for each block of the test. At the start of the testing session, you have a total of 45 minutes of break time. This allotment of time is used for authorized breaks between blocks and is also used to make transitions between items and blocks.

I like the bit about my break time being used for transitions. That means I get charged a nickel every time I answer a question, a dime if the computer decides to be slow. It reminds me of the Dilbert* where the Pointy Haired Boss tells the employees that they're banking too much vacation time, so therefore they will be charged vacation time while they're in the bathroom, hence my title, which is a paraphrase of Wally's reaction.


*: Can't find it, otherwise would post, also don't have time, must sleep. An hour of sleep is like an hour of studying, or something.

A Procedural Marriage

Q: Who would marry a surgeon?
A: Another surgeon.

Q: What would the marriage be like?
A: Surgery is a procedural specialty, so I suppose they would have a procedural marriage...

- Marital procedures would commence promptly at 7:00 a.m.
- It might take all day
- There would be a minimum of post-op follow-up
- A third person might be present to administer anesthetics

There would be some problems, of course...

- Each partner would only specialize in a few procedures
- It would be impossible to "go big or go home"* because most procedures would already be home




* The surgeon's motto.
** You might wonder why I did not include my usual throat clearing explanation of why I was thinking about this. Well, I realized such things are rather dull and also there could be professional conflicts.

No, no, I live in...

I have a friend that lives in the west loop. Well, not actually the west loop. He lives west of the west loop, in what one might call the United Center Zone. However, one can't say that one lives in the United Center Zone because to those in the know, it is the equivalent of saying, "I live in a free fire zone."

This is the problem with the neighborhood system in Chicago. The only semi-official demarcation dates back to 1920, with the obvious problems that come from never getting updated. Thus, developers rename areas of gentrification to make them sound like the areas they want them to be, and not like the areas that they are.

I have decided to do the same thing for Hyde Park,* so, with no further throat clearing:

GENTRIFICATION NAMES FOR HYDE PARK:

Academic Village - obvious
Rockefeller Park - after the university's first benefactor
Forefront Beach - after the hospital's ridiculable slogan
Exposition Park- after the 1893 Columbian exhibition
Suchi and Nuchi - Southern and Northern University of Chicago in the fashion of Tribeca
Olympia - in hopes of netting the 2016 games


We'd just have to do something about the food, the groceries, the public transit, the entertainment and we'd do just fine.

GENTRIFICATION NAME FOR THE UofC: Northwestern.



*: Note that, according to the old system, I live in Woodlawn, which is considered even less desirable, but would be contained within my rubric(s).
**: Rejected names: Columbia Park (columbia is always a 'not-nice' part of town), Harpersville (lame), University anything (see columbia) Ferris Pont (weird), Midway anything (association with previously sketchy airport, though I now note that Midway is quite clean and nice looking, also convenient for moi).

Paris Hilton's Nipples

Fiddle: What do you think is the greatest crisis facing the survival of humanity today?
long silence
I: Well, it's not terrorism. On a personal scale, global terrorism is like waking up in the morning and realizing you can't have a bagel because you're out of cream cheese.
Fiddle: I've thought of terrorism as being like Paris Hilton.
I: And Osama bin Laden is Paris Hilton's nipples - popping in and out of view and always garnering far more publicity than they deserve.



All conversations approximate.

Brief Defence of the FDA

I was at the doctor's office today, and for no apparent reason they have The Wall Street Journal. The editorial page is sort of like watching Prime Minister's Questions - a bunch of people who appear to speak the same language look at the an issue in this country and come at it from a completely perverse direction.

Witness Arcoxia! (etorcicoxib)! that ASTOUNDING wonder drug from Merck. The WSJ Op-Ed guys are in a snit because the FDA won't allow the drug to be marketed. Brief summary:

The FDA explained that it didn't see the need for another drug like this. Robert Meyer, director of the FDA's Office of Drug Evaluation II, told reporters that, "simply having another drug on the market" wasn't "sufficient reason to approve the product unless there was a unique role defined." The FDA is supposed to judge whether a drug is safe and efficacious and that's all.

OK. The authors then rip apart the FDA based on this quote. I say the quote is irrelevant.* The question is, is the drug safe and effective for its stated purpose? Answer: Define "Safe and Effective." Some percentage of people taking warfarin will suffer a fatal bleed into their brain. On the other hand warfarin may prevent them from developing fatal clots. There's a balance depending on the purpose. One is more willing to tolerate side effects from potentially lifesaving treatments from those that merely make life more comfortable.**

So, what does etorcicoxib do? Well, it merely makes life more comfortable (who didn't see that coming?). Etorcicoxib is, for civilian purposes, a pain killer. More specifically, as the 'coxib suffix implies, a COX-2 inhibitor. You may remember the COX-2 inhibitors from such debacles as VIOXX!!!

"Wait," Cara said, "didn't Merck also make Vioxx and get sued for a bunch of money."
"Indeed," said I.
"What a bunch of morons," she noted, then dozed off.

To give you the 60 second caricature, when you pop an Aspirin, or Tylenol, or ibuprofen, or Aleve, the drug inhibits two enzymes, COX-1 and COX-2 which are involved in synthesizing a lot of different molecules called prostaglandins that have different effects in different parts of the body. This broad distribution explains the broad effects of the so-called Non-Steroidal Anti Inflammatory Drugs or NSAIDS - a baby Aspirin thins the blood preventing heart attacks and strokes. Tylenol reduces fevers and relieves pain. Step back a moment andc onsider how odd it is that those effects are linked.

Unfortunately, NSAIDS are also a leading cause of gastric ulcers. This effect is presumably because they block COX-1 in the gut, which results in less secretion of protective mucus (mmmm, protective mucus). Also, the anti-coagulating effect is also due to COX-1, perhaps making the ulcers more difficult to heal. Thus were born, THE COX-2 INHIBITORS!!!. Unfortunately, COX-2 inhibitors kill. All of them. And the degree of killing is related to the degree of COX-2 inhibition. It's late, and I'm studying for boards, so I'm just going to have to take what my pharm professors said and whack you over the head with it. I'm sorry. PubMed will work for you as well as me, and is non-essential to my continuing points. Also, the COX-2 inhibitors don't really prevent ulcers, if you look beyond 6 months of use.

Even before the whole Vioxx thing, I was a big hater of the COX-2 inhibitors, because the things were like, three bucks a pill, and I said, "heck, for three bucks a pill, you could take a truckload of Tums." New, older and wiser, I say, "heck for three bucks a pill, you could buy a cratefull of Prilosec OTC" (unsurprisingly this works).

There I go, tarring etorcicoxib with that rofecoxib brush. Why don't we just see how it stands up on its own? As the WSJ says, there was a trial of over 37,000 people that showed that etorcicoxib was safe. I think they're referring to this trial (PubMed ID 17113426 if that doesn't work), which shows that etorcicoxib is about as safe as the NSAID diclofenac, and had fewer ulcers. Diclofenac? Yes, it's a real drug. I'd never heard of it either 'til I came to med school. In my limited exposure, I have yet to meet anyone taking it. Why the comparison with diclofenac, then? It's a stacked deck.*** As the Wikipedia article linked above indicates, diclofenac has 10:1 inhibition of COX-2 versus COX-1, i.e. it is, essentially, a COX-2 inhibitor (note that even the classic COX-2 inhibitors like rofecoxib, celecoxib, and etorcioxib have some COX-1 inhibitory effect). 'Classic NSAID' indeed.

How does etorcicoxib stack up against stuff that people actually take? Well, there's no significant difference there either. Wait, let's actually read a bit of the abstract:

The RRs for thrombotic events were 1.11 (95%CI: 0.32, 3.81) for etoricoxib (N = 2818) versus placebo (N = 1767);

Let me try and translate this: People taking etorcicoxib were somewhere between one third as likely and three times as likely to get a clot as people taking sugar pills. In other news, I weigh somewhere between an Oxford English dictionary and a Honda Accord. My intelligence is somewhere between a ground squirrel and Da Vinci. George Bush's approval ratings are somewhere between 7 and 70%.

Here's the real "money quote."

1.70 (95%CI: 0.91, 3.18) for etoricoxib (N = 1960) versus naproxen (N = 1497).

Translation number 1: The risk of developing a clot was somewhere between a little less than 1 and 3 times as likely in people taking etorcicoxib versus Aleve. Translation number 2: If the study had gone on 3 months more, we would have succinctly demonstrated that our drug kills people.

So, if I'm the FDA, I bounce the drug, not because there's not a marketing niche, but because it's not safe and effective for purpose. On the other hand, I suppose the study has demonstrated a "unique role" for the drug - expensive AND deadly, woo-hoo.

It's past my bedtime, so I'm going to take a final parting broadside at the WSJ, specifically this anecdote:

One patient, Kathleen Slocum, said that her life without Vioxx or other COX-2 inhibitors was "misery." She also pointed out that while over-the-counter analgesics work well for pain relief, the main problem she has had with her severe arthritis is joint swelling and stiffness; OTC analgesics haven't helped her with these problems. Ms. Slocum knows more about her specific needs than the FDA does. Isn't it possible that at least some segments of the population would find that Arcoxia addresses their needs? And remember that the people choosing are self-interested patients and their highly educated and trained physicians.

I should note that 'over the counter analgesics,' with the exception of Tylenol, will take out COX-2 as effectively as any 'coxib, so from a pathophysiologic standpoint, her argument is meaningless. I also note that 'joint swelling and stiffness' are rather vague terms that would be quite susceptible to placebo effect. Perhaps if naproxen were prescription only and 5$ a pill it would be more effective for her. Finally, there's the dodge about knowledgeable patients and highly educated physicians. I would argue that patients don't know what they need, hence they go to doctors and request drugs they saw advertised on TV.**** And I would argue that physicians, my future self included, are vulnerable to the claims of leggy drug detailers, and busy enough that we won't do the legwork that could save out patients. We will assume that if it's FDA approved, it's benefit essentially outweighs its risk in the intended use. So that's what FDA approval had better mean.

*: Key difference between science (or scientistic fields like medicine) and journalism. In journalism, it's all about getting different authorities to give quotes and bash them against each other. Medicine is supposed to be about the evidence.

**: Look, you can argue this, you can say, "But Jeff, isn't there some pain so bad that it makes life not worth living?" And I would say yes, and then I would say, "If you're so concerned about the pain, why not go for narcotics? Or something to address the underlying problem like joint replacement (for osteoarthritis) or REAL immunosupressants (e.g. steroids, methotrexate, cytoxan... for rheumatoid arthritis)?"

***: I'm as pro-pharma (probably more pro) as the next guy. If you look at a pharma trial, you will find that it has been conducted superbly. However, a trial is only as good as the question is asks. Too often, the comparison is against older drugs with known side effects, or they will test higher doses of the company drug versus lower doses of a competitor drug. This isn't always the case, but it's worth looking out for. It also gives me an excuse to stick to reading the abstracts.

****: This makes me think about all the adds Apple keeps putting out for iPods. It's like, everyone that was going to buy one already has one, but they need to keep advertising so people still think that what they bought is cool. I wonder if you could do a study about some drug in a placebo-ey category like anti-depressants and see if it's apparent efficacy waxes and wanes with the amount of advertising surrounding it.

The problem with Watson-Crick base pairing

Is that W and C don't base-pair. You know what works? Goldstein-Crick base pairing.

(Why this should be funny but probably isn't to you: In addition to the A, T, G, and C of normal DNA sequences, other letters of the alphabet are used to designate possiblities, e.g. W = weak, which could be either A or T, so named because they make only 2 hydrogen bonds, as compared to the Strong G-C base pairs which are held together by 3 bonds.)

Psychiatry

We get conflicting accounts of medicine in popular media, in undergraduate biology, and in more research oriented basic science lectures. But it's always good to get the single consensus answer. In CPP this comes from the mouths of practicing physicians specializing in the disease being discussed. Their answer has the advantage of having survived contact with reality, and being relatively accepted by a lot of other medical types you might talk to.

Psychiatry is an area where the gap between popular accounts and practice appears to be the widest. Civilians* throw around diagnoses, or sub-diagnoses or outdated diagnoses with great freedom, assigning fairly serious conditions to (say) celebrities they have never met. As described in psychiatry, life is more complicated. Diagnosis consists of large lists of criteria that patients have to fulfil, e.g. in order for you to be depressed, from this list:

Depressed mood
Energy loss
Anhedonia (lack of pleasure)
Death thoughts
Sleep changes
Worthlessness
Appetite
Mentation changes
Psychomotor

You must have depressed mood or anhedonia and five of the others for most of the day every day for two weeks to qualify those weeks as a depressive episode. This sort of formal rigor is much more appealing than saying, "Hey, this guy is sad, let's give 'im some Prozac."

One of the best parts of this section was that in lab, instead of only reading cases, we had actual patients come in to talk to the class so we could see what it was like. And that's where the nice neat system vanishes. Our bipolar patient was being treated for anxiety, our obsessive-compulsive disorder patient had depression. Our schizophrenic patients seemed to have well behaved disorders, but our recovering alcoholic physician had his ADHD misdiagnosed as anxiety, and got addicted to his Xanax. And if depression was such a difficult diagnosis to meet, antidepressants would not be among the top-selling drugs.

They do teach some things that are pretty easy for me to swallow:
Psychodynamic psychotherapy ("And how does that make you feel?") is reserved for those with lots of time and money.
Cognitive behavioral therapy is pushed, especially for certain disorders where medication is not helpful.

It seems to me that the reliance on medication is partially about efficacy and partially about cost. Consider that you can get a month's supply generic prozac or paxil (fluoxetine and paroxetine) for $4 from Wal-Mart, but that a month's supply of cognitive therapy is $400.




* I realize that this is my first use of this potentially derogatory term to describe non-medicos and another step on my long journey to becoming and asshole physician. Further I recognize that this blog began as an attempt to stymie said journey, and has instead served as a record of it.

More Veiled Conceit*

Peruse this wedding announcement:

"Unknown to Ms. Luft, her skirt had somehow become tucked into her pantyhose. When the elevator door opened, she realized there was a problem. 'I only noticed when everyone in the elevator was staring at my backside,'"

Obviously, this woman is very enamored of her sweet, tight buns or she wouldn't have related this tidbit to the whole planet. Or at least she was enamored of her 16 year old buns. Let's see what Wechter has to say about it:

''I was very attracted to Sara when I first met her... She's got a very engaging personality. I thought about her all the way home.''

Sweet, tight, engaging.

Couples write their own wedding announcements, so one can only wonder why the couple chose to write it this way. Do they want us to read between the lines? Do they figure they have a better shot of getting in if they have a bit of salacious summer camp gossip?

Doing an O&P (That's occupations and parents) we find that their jobs are investment/portfolio types, as are their parents, so, they're standard fare for the NYTWCA. They live in New Jersey, he works in Greenwich, and she works in New York. How miserable. Each of them spends at least 3 hours a day in the car or in transit.

Other than the meeting story, this couple is so aggressively boring that they would normally fly under the VC radar, except for the bride's heavily aftershadowed closing line, '''It was Josh, making sure I got home safely from my flight,'' she said. 'That was when we were 16 years old, and we've pretty much stayed together since.'''


pretty much [prit-ee muhch] adv. 1. After dating for two years dating long distance, they agreed to 'see other people at college.' His banana face

doomed him to four years of sucking face at closing time at the Copabanana. (Slogan: Where ugly girls go to cop banana faces.


I just realized that this icon is probably for an establishment where ugly girls go to cop other sorts of bananas, but I think the point is made). His bitterness increased when in a desperate, drunk dialing rage he called her voice mail and got: "Hi, this is Sar, please leave a message after the tone. If you're calling because you saw my name above the urinal at Tongue and Groove (click for awesome music), please send a head and a body shot to luftballoon@emory.edu. I'm totally stoked to hear from you, bye-ee." His sobbing description of a strange sore on his penis drew out her compassion, and she agreed to get back together... after the penicillin kicked in.

2. He demanded that they stay together through college, but then one day that girl in his Management 318 class showed up with her skirt tucked in her pantyhose. She flew in unexpectedly to surprise him, and found the pantyhose draped over his doornob. "Wechter?" He said over the phone, "I hardly knew 'er." Six years, 14 breakups, and numerous heartfelt conversations later, they give up on dating other people and show the whole world their orthodontic work on the NYTWCA.

3. In order to stay together in college, they lived in Rocky Mount, VA (exactly halfway between University City and Atlanta) and commuted 6 hours in either direction, which makes their current 3 hour commute look like crossing the street. Once she got really sleepy and stayed in a rest stop in North Carolina, so they spent the night apart.

Which do you think is most likely?



*Veiled Conceit is the original idea of 'Zach' at Veiled Conceit
With special help from Cara.

A Little Veiled Conceit*

Veiled Conceit: A glimpse into that haven of superficial, pretentious, pseudo-aristocratic vanity: The NY Times' Wedding & Celebration Announcements

Before we begin this week's edition of Veiled Conceit, I'd like to give small public service announcement:

Do not, under any circumstances let your picture look like this:











Seriously. She's either ridiculously smug, or giving every pretentious male in the U.S. a 'come-hither' look. Maybe both. She was in the Peace Corps. I would say that ex-Peace Corps folk are usually highly pretentious about it, but the one's I know are actually quite nice. damn. She used to fight child trafficking in Nepal, but then she started working for Planned Parenthood, and you know what inappropriate trafficking joke goes here. As for the groom, Bob, he's totally oblivious, although his gaze is oddly mesmerizing.

Update: I just noticed the bride is 35. I swear officer. I know she looks 17, but at least she's old enough to know to lie, right?


Let's go to this week's vows couple, fine art photographer Alex Heilner and his bride to be Amy Scott. Let's look at some of his work, eh? I immediately went for the collection called 'microbes.' The best I can say is that the landscape photos are much better.


a colony of Penicillin Resistant E. statebuilding

It seems that Mr. H is known for his alphabetizing ability, and his annual scavenger hunt. He's also known for his list of desired girlfriend qualities, "An abridged version" said the Sunday Stylez Crew, "would include: brainy, creative, humble, funny, confident and energetic enough to go out every night. And one more thing: 'Hot. That was important.'" Translation: Hot. Re-translation: Hot, and willing to always put Queen II in front of Queen on Fire: Live at the Bowl because I comes before O, or U.

Let's look at the man himself...

Objects in mirror are closer than they appear.

Any middle class pig can photograph himself in the bathroom mirror. But, the car mirror! Genius. Every car commercial every written satirized in a single, digital moment! Couldn't we get a better head-shot, you ask? Well, no. He's a small, Beetle-like figure in wedding picture A, and an out of focus cheek in wedding picture B.


He's definitely "small enough to fit in a guitar case"

According to the article, the couple married themselves, as is legal under Colorado law. What sort of pretentious yuppie Napoleon bullshit is this?



Napoleon: Also small enough to fit in a guitar case.




Buyers Remorse

As always, the real story is in the background...

He and Alex gaze at the same thing far to the right. Is it the open bar? The air conditioner? Or the next item on Alex's scavenger hunt of love? Only time will tell, but statistics say...



Finally, I'm going to try to convince Cara to help me out with a video, which may get updated in below.
Update:


*Veiled Conceit is the original idea of 'Zach' at Veiled Conceit

Top residency choices this week:

1 allergy & immunology 46
2 hematology 44
3 radiology 44
4 aerospace med 43
5 dermatology 43
6 neurosurgery 43
7 neurology 42
8 emergency med 42
9 general surgery 42
10 pediatrics 42

The 3PPS Test

How to do it: Visual examination of the proximal phalanx of the third "ring" finger of the left ("sinister") hand.

Possible findings - documentation:
1. Nil.
2. Ring - describe ring.
3. Ring callus - note.


The upshot is that my frequent failure to perform this simple task has resulted in mockery from my physical diagnosis comrades,

Tofu Cube... OF DEATH!!!

I had a charming case of food poisoning last quarter, which I was able to (thanks to Medical Micro) identify as heat stable staph toxin. I don't want to go into it now, but at the time, I asked my friends who had been at the same restaurant if anyone had the same symptoms, and a friend wrote back that she can't get food poisoning since she doesn't eat any meat.

Contra that, today I noticed a report in the CDC's Morbidity and Mortality Weekly Reports, and they talk about this Chinese couple that got botulism from their fermented tofu.

Anyway, I have extracted below the recipe for TOFU OF DOOM.

The tofu was a commercially packaged product purchased at a retail market. In the home, the tofu was boiled, towel dried, and cut into cubes. The cubes were placed in a bowl, covered with plastic wrap, and stored at room temperature for 10--15 days. The tofu was then transferred to glass jars with chili powder, salt, white cooking wine, vegetable oil, and chicken bouillon to marinate at room temperature for 2--3 more days. Finally, the fermented tofu was stored and eaten at room temperature.


*
Note that I cite MMWR below.

After I dressed this morning...

C: You look like you're going clubbing.
I: Not so much, but I am going to go study clubbing.

The image to the side is of clubbing - bony expansion of the tips of the fingers caused by long-term lack of oxygen, e.g. that caused by smoking or other lung damage.

AIDS drugs cause AIDS I

Yesterday, I was puttering through the hospital when I came across a J, pathologist friend of mine. Whenever I see a pathologist, I always ask to see whatever slide they're working on, which usually results in an interesting story.

J told me about a case from his residency in 1994. A 20 year old man presented to the morgue with multiple Kaposi's Sarcomas in his GI tract. KS is a cancer of an unknown, probably blood vessel cell which is caused by the Kaposi's Sarcoma Herpes Virus (KSHV, HHV8). Prior to 1981, the stereotypical patient with KS was an 85 year old Italian male.

In '94 the stereotypical patient was this patient, a young gay man. Since the cancer was in his digestive tract instead of the skin, he didn't have a chance to get treatment.

Not that there was much treatment.

J kind of breaks off and says, "We don't really see cases like that anymore, not since '96."

Boards question:
A 37 year old male heroin user has noticed multiple 0.5- to 1.2-cm plaque-like, reddish-purple, skin lesions on his face, trunk, and extremeties. Some of the larger lesions appear to be nodular. These lesions have appeared over the past 6 months and have slowly enlarged. The most effective treatment for his condition is:

A. Vincristine, irinotecan, and cisplatin.
B. Valcyclovir, gancyclovir, and foscarnet.
C. Indapamide, metoprolol, and prazosin
D. Zidovudine, lamivudine, and efavirenz.
E. Ticarcillin, clavulanate, and gentimicin.


Tick
Tick
Tick


Correct answer: D. The common thread in all of this is the Human Immunodeficiency Virus, and the cocktail indicated is an ideal treatment. The release of protease inhibitors in 1996 meant that the number of patients with full blown AIDS and AIDS defining illnesses cratered, hence the dearth of KS biopsies.

This brought to mind a story on badscience.net about South Africa's stand against providing AIDS drugs to AIDS patients. For instance at an international HIV/AIDS conference, the South African booth featured that infamous reverse transcriptase inhibitor, the African Potato. Anyway, part of the South African government's argument is that, as the title of my piece indicates, AIDS drugs cause AIDS.

How can we reconcile J's observations with this claim?

Prior to 1987, there were no AIDS drugs in general circulation. One can only conclude that gay men, injection drug users, and hemophilliacs were secretly stealing AZT and snorting it starting in the mid 1970s. Of course the world's known supply was sitting on some lab shelf in Research Triangle Park. The only reasonable explanation is therefore that the Columbian cartels must have stolen the structure and synthesized a bunch of the stuff, and used it to cut the blow.

Explaining the sudden drop of KS after 1996 is relatively trivial. As it turns out, AZT causes AIDS, but the 3TC and Efavirenz are actually antidotes, so as long as people take them as a cocktail, nothing too horrible happens.

Essential resources:
AIDS reappraisal - Wikipedia (it's almost painful how hard they worked to keep this article neutral)
A little piece of history. Check the date.
Hopefully I'll get to address other aspects of the 'reappraisal' in a later piece.

Among my many flaws:

I: I seem to be missing the gene that makes you want to go to a bar, have one drink, and say, "Hey, let's go to a different bar!

She: SRY?

A problem possibly solved

Yesterday we started anemia, particularly the iron, B12, and folate deficiencies. It reminded me of a patient I saw last year who had a very confusing constellation of symptoms, but which I now realize were all anemia caused by a rash that had appeared on his chest 3 years earlier. The rash contained, presumably, rapidly proliferating skin cells and immune cells, which would suck of the folate and B12, both of which are involved in DNA synthesis. This was compounded by the patient's poor eating habit. Now if I could just figure out what the autoimmune condition was.

Something sort of similar is maybe in this paper.

Problem Solving Skills Dos

We're doing CPP&T this quarter, which is the part of medical school where they actually teach medicine. Each lecture takes the following format: "Here's a disease, here's how you get it, here's how you recognize it, here's how you treat it." Then we have lab twice a day, which is a series of cases where patients have the illness and we have to establish differentials and suggest labs and such.

We're also taking Physical Diagnosis, part of which is to run around the hospital, interviewing patients and doing as much of the physical we have learned, then trying to do diagnosis and present them to an attending physician.

It occurred to me today that medicine is very much like school problem solving - you are presented a patient/problem, you attempt to solve it in a stereotyped way based on practice problems of a similar appearance. You either get it right or wrong, but either way, you quickly move on to the next problem. If you do a good or bad job overall, it will definitely matter, but success on one problem, or even one type of problem is not necessary.

This is unlike other areas of work, which I can't think of right now, where either you can't move on, or all your problems are interrelated in ways that are simply impossible to entangle.

Anyway, that makes medicine comparatively comfortable, as opposed to, say, research, where you may be stuck on a problem for years, never knowing if you have the right answer.

The Second Eval

To: Office of Medical Education
Re: Work load of fall quarter

I would like to clarify my position on the course load for this quarter. I strongly believe that the work load for this quarter is appropriate. Therefore, I would have said "Strongly Disagree," but I'm concerned someone would take that as a request to load more work into the quarter, which I feel would be inappropriate.

Keith Ellison and the Hot Tub

Reviewing this I worry that some people will take it the wrong way, but I worry that throwing more words at it will make it worse. So, please interpret my remarks to be inoffensive to Christians, Muslims, and Jews, and if your worldview is relatively close to mine, we will have achieved communication.

As an aside, I do, in real life, know how to pronounce 'coup.'

Overly extensive coverage at... Wikipedia, where else?

Look there's a moose

My friend Sancho began working at Garmin recently and is justifiably proud of their winter ad campaigns. Observe:

"The moose"


Sancho prefers the moose, but I find it's scare tactic ways a little troubling. More realistic of what I would use a NuVi for would be:

"The unibrow"

Why Rumsfeld stuck around so long

On the top, Leo Thomas McGarry, the wise chief of staff cum vice presidential candidate on the West Wing
On the bottom, Donald H. Rumsfeld, the secretary of defense cum ex secretary of defense on CNN.

Scary it took me so long to figure this out.