Monday, February 25, 2008

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:
Public domain 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.

Sunday, February 24, 2008

Barack Obama is your new PI*

In re:

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.

Saturday, February 23, 2008

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.

Thursday, February 21, 2008


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).


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.

Tuesday, February 19, 2008

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.


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.

Tuesday, February 12, 2008


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.
screenshot cropped with The GIMP

Monday, February 11, 2008

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.

Sunday, February 10, 2008

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
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.