Unqualified Offerings

By Thoreau

University of Washington researchers have developed a computer game that folds proteins. Yes, really.

Protein folding is a tough problem. You’ve got this long chain of amino acids, and somehow they come together to take on a particular shape. And they do this every time a cell produces the protein. You’d think that a long chain of molecules would try all sorts of random configurations, but somehow they always form the same pattern. It’s hard to understand why, because all of the molecules are interacting with each other in very complicated ways, so you have to solve an equation that could involve hundreds or thousands of forces. Some computers are having luck folding a few proteins, but it’s slow.

The researchers theorized that people are very good at playing games and picking out the most efficient way to do something. Good gamers intuitively know which traps to avoid. So they designed a game where you try to fold up a molecule into the most stable shape (the one where the forces all cancel and the energy is at a minimum). They tested it on some proteins with known structures, and they got good results. Now they’re trying proteins with unknown structures.

So to all my students, I say “Go and play more video games! Do something useful for science!”

I predict that we’ll start seeing research article titles like “PWNAGE of Matrix Metalloprotease 9 Structure!  SW33T!” by DoneGeneMaster11 et. al.

By Thoreau

I’m sure that Claire is dead. Maybe she died after being lured to Jacob’s cabin. Maybe she died in the attack on The Others’ Village and what we saw for the last 2 episodes was her ghost. Or maybe she died in the plane crash and what we’ve been seeing the entire time is her ghost. I don’t know. The one thing I do know is that Claire is as dead as her father. Why else would she be in Jacob’s cabin with her dead father, happy and smiling, unconcerned with the fact that she isn’t with her bay-bee? Truthfully, the past few episodes have been Claire’s best ones since her flashback last season. It’s not that I don’t like the character or the actress, but she’s been woefully underused for a few seasons now. The few times that they gave her good material she did great, but they’ve given her so little. Finally, though, she’s at the center of a big mystery.

Overall, it was a good episode. Very little about Jack and the love triangle, lots of action and mystery on the boat. I was surprised when we learned the boat doctor’s fate this episode. I figured that the mystery of the boat doctor would be one of those things that Lindelof and Cuse would promise to address “in season 5″ and then they forget about it. Keamy is an awesome villain, although I do wish they’d confirm that the thing on his arm is a heart rate monitor rigged to explosives. Also, I hope that Michael and Desmond aren’t forgotten. Desmond needs to find his Penelope, even if he has to kill 200+ suitors to get to her!

The flashbacks weren’t exactly earth-shattering (is it really news that the Island is interested in Locke?), but they were appropriate. The biggest mystery in the flashbacks was the last one, where the black guy named Abaddon talks to Locke. In the flashbacks, Abaddon appears to be working on the same agenda as Richard Alpert, who is one of The Others. However, in another episode we saw Abaddon working with Naomi, the woman from the freighter who landed on the island last season. That would suggest that Abaddon is with Widmore, not the Others. Also, he went to Hurley in the asylum, seeking info. It could be that Abaddon has changed sides, or that Abaddon serves an agenda separate from the Others and Widmore.

Anyway, I liked it. And I am optimistic that next week we will get some awesome action.

By Thoreau

I just got an email from the top student from my grad school research group.  He’s now a professor at a very prestigious research university.  And he just emailed me with a research question.

And I think I can solve the problem.

By Thoreau

Today at Hit and Run, they link to an article by Steve Chapman regarding McCain and Iran.  I’ve had my issues with some of Chapman’s columns on economic matters, but on foreign policy he makes some points that are as salient now as they were in 2003.

Amid all the war hysteria, it was easy to forget containment worked against Stalin and Mao — both unbalanced dictators with nuclear weapons. They were far more formidable tyrants with dreams of world domination. Yet we managed to preserve our security without pre-emptive war.

For that matter, containment had worked against Saddam Hussein. In the 12 years after the first Gulf War, we kept him in a box, where he was no threat to us or his neighbors. In 2002, he even had to accept the return of United Nations weapons inspectors — who found no weapons of mass destruction because, thanks to our efforts, he had none.

…

The claim is that the Iranians are too crazy to be deterred from using nukes against Israel or giving them to terrorist groups to use against us. One common trait of governments and their leaders is an overriding desire to survive. If Iranian nukes are ever used for aggression, the regime can be sure Iran will be, as Hillary Clinton so vividly put it, “obliterated.”

I tried to raise all of these points in 2002 (no, I wasn’t in the blogosphere back then) and any hawk that I talked to just brushed them aside.  They acted like there was something wrong with me, like I just wasn’t “getting it.”   A lot of Americans have since come to their senses, but there’s a contingent that still doesn’t grasp these basic points, and I fear that they hold far too many of the cards.

Spencer Ackerman on the wages of torture.

By Thoreau

Ever worry that it’s a bad idea to beam radio signals into space in hopes of making contact with aliens?  Ever worry that they might take those radio signals as an invitation for some interplantary pre-emptive democracy-building?  Well, fear no more:  If aliens detect our electromagnetic transmissions, the signal they’re most likely to detect is the radar that we’ve been using to search for planet-destroying asteroids.

Tim F. explains the economics of bombing "training camps" in Iran or elsewhere:

If training camps are anything like the ‘training’ or ‘camps’ that I’ve seen those places are mostly dirt with targets set a long distance away from the muddy spots where people kneel to shoot at them. Obstacles are made out of unpainted plywood and the barracks make your freshman dorm look like the Hilton. Building one of those would cost, what, $50k? It would take about five days to build another one using minimally skilled labor. A cruise missile costs a a million. A big GPS-guided bomb dropped by a stealth plane at night can’t cost that much less, and I doubt that the time and resources spent to ensure that the rest of our planes could overfly Iran without playing dodge-the-missile would come cheap either.

Of course, as Tim explains, it gets worse.

By Mona

In the process of researching a totally unrelated (I swear!) topic, I ran into this:

There has not been a scientifically definitive physiology of female anatomy until quite recently but strange images from its ambiguous history still haunt the common imagination and impact on women’s self image. None is stranger than the female womb.

[…]

.

“Hysteria” is derived from the Greek word for uterus.

.

[…]

.

A …treatment evolved in the 19th century, when hysteria became a veritable epidemic, especially in the white middle classes. The doctor massaged the genitals until there was a healing convulsion and moist spasms (an orgasm by any other name), which relieved the patient for a while – until the next appointment. Hysteria was considered chronic and incurable, requiring ongoing treatment.

By Thoreau

Nice article on why the brain takes so much energy and what it does with it.

It’s worth noting that TSA screeners require far fewer calories than the rest of us

Roger Kaplan’s "argument" that we seize "the oil fields" in the American "Spectator" today is a whole "tree" full of presents for the connoisseur of meanness and "idiocy" on your "guest list." I particularly enjoy the unselfconsciousness that lets him include the following in his article:

Let the stupids talk to the stupids . . .

Oh by all means! But keep doing it where the rest of us can hear you.

Kaplan argues that we should "seize" the oil fields like Lincoln and Douglas did in 1858. This will lead to no end of benefits on Kaplan’s planet, where the last five years have not shown everyone how impractical it is to secure oil production and transportation infrastructure in the absence of broad social consent at every stage of the supply chain, and where the basic economics textbooks elucidate a principle called "The Law of Supply and Dammit I Can’t Remember the Other Part I Could Swear It Was on the Tip of my Tongue a Minute Ago!"

Seriously, if you love high-falutin’ lunacy, read the whole thing.

Gareth Porter unredacts part of the classified war plans from late 2001 quoted in Doug Feith’s new book:

Rumsfeld’s paper was given to the White House only two weeks after Bush had approved a U.S. military operation in Afghanistan directed against bin Laden and the Taliban regime. Despite that decision, Rumsfeld’s proposal called explicitly for postponing indefinitely U.S. air strikes and the use of ground forces in support of the anti-Taliban Northern Alliance in order to try to catch bin Laden.

Instead the Rumsfeld paper argued that the U.S. should target states which had supported anti-Israel forces such as Hezbollah and Hamas. It urged that the United States "[c]apitalize on our strong suit, which is not finding a few hundred terrorists in caves in Afghanistan, but in the vastness of our military and humanitarian resources, which can strengthen the opposition forces in terrorist-supporting states."

Feith describes the policy outlined in the paper as consisting of "military action against some of the state sponsors and pressure – short of war – against others."

. . .

Gen. Wesley Clark, who commanded the NATO bombing campaign in the Kosovo War, recalls in his 2003 book Winning Modern Wars being told by a friend in the Pentagon in November 2001 that the list of states that Rumsfeld and Deputy Secretary of Defense Paul Wolfowitz wanted to take down included Iraq, Iran, Syria, Libya, Sudan, and Somalia.

Clark writes that the list also included Lebanon. Feith reveals that Rumsfeld’s paper called for getting "Syria out of Lebanon" as a major goal of U.S. policy.

When this writer asked Feith after a recent public appearance which countries’ names were deleted from the documents, he cited security reasons for the deletion. But when he was asked which of the six regimes on the Clark list were included in the Rumsfeld paper, he replied, "All of them."

What you have to understand is, 9/11 was like Christmas for these people. It was the happiest day of their lives. To them, the only dreary aspect was that they had to make at least a show of responding directly to the conspiracy that murdered three-thousand Americans on the way to doing what they really wanted, which was remake the entire Middle East in their image.

In turn, the US invasion of Iraq was the nicest present Osama Bin Laden ever got. Bin Laden and the national-greatness conservatives probably all send each other cards.

I’ve got a couple new, campaign-related pieces on The Art of the Possible, including my Indiana and NC predictions, and a couple of older pieces way down below the monumental Glenn Greenwald interview Mona linked to yesterday. My plan this week is: I want you reading AOTP anyway; so between now and Friday, I’m not going to tell you when I’ve put up new material there. It would warm my heart if you would be so kind as to check for it. Then, starting Friday, I will return to my usual linky exhibitionism.

By Thoreau

The unstoppable juggernaut that is the Ministry for State Security is bound and determined to protect America from a dire over-supply of construction workers, for fear that any one of them might secretly be plotting to scam Osama Bin Laden.  (Only in America would that be a crime.)

However, they’ve run into a snag:  The fence would divide habitat occupied by endangered jaguars.

I propose a steel cage match between a jaguar and one of our fearless defenders in the Ministry for State Security.

I know that some of our commenters (including people that I like, not just our good comrade from the Ministry for State Security) are in favor of a wall to keep out immigrants.  If this were just about immigration, well, that would be one thing.  You know where I stand, I know where you stand.  But this is about DHS, and I hate them with a bitter passion.  Perhaps the immigration restrictionists and I can find some common ground here:  Since DHS is a bunch of dunces, surely it would be better if immigration policy were handled by, well, just about anybody else.  Whether you favor a tougher policy or a more open policy, I think we can all agree that DHS will find a way to screw it up, and probably piss off both sides in the process.

In the mean time, as long as DHS is involved with this, I’m rooting for the jaguars.

By Thoreau

Even a TSA screener.

Look, it would be one thing if the only people able to get guns past the TSA were the super-secret ultra-skilled undercover inspectors (and I’m sure that they’re ultra-skilled because otherwise the feds would never, ever hire them!). But apparently getting a gun past the checkpoint is so easy that even a TSA screener can do it. Which means that we are completely defenseless, because even Spinal Tap’s drummer has at least a 30 IQ point advantage over your typical TSA screener.

The TSA, of course, is declining to comment on what consequences, if any, were faced by the screener. They cite privacy regulations, and I’m sure that they’re telling the truth because nobody in the TSA would ever just make shit up. I mean, if you can’t trust the people who believe that my shampoo is a deadly threat, then whom can you trust? What I do know, however, is that if some dude named “Abdullah” were found with a gun in the airport his face would be all over the news, and Comrade Chertoff would be assuring us that our Fatherland is safe thanks to the arrest of this dangerous terrorist. Well, either that or he’d be in a KGB prison in Poland. (See why I make the commie references?)

If the TSA can’t actually prevent any idiot off the street from bringing guns into the airport, maybe they could at least let me board a plane without the indignity of showing my papers at a checkpoint while being searched. If you can’t protect my life, then respect my privacy. Or at least let me keep my 4 ounces of toothpaste?

In this blog’s continuing quest to shake your sense of the world to its very foundations, I notify you that a New York Post film critic, writing in Pajama’s Media, laments Iron Man’s anti-Americanism. In comments on Julian Sanchez’s site, who provides our via, old friend of the blog Franklin Harris writes

I picture the neoconized right wingers running around, screaming like the aliens in “Invasion of the Body Snatchers” whenever they encounter something that offends them.

In the reviewer’s defense, he brings a lighter touch to his version of political correctness than Michael Medved typically does. Which reminds me! (For you, Loyal Reader, I am listening to Medved’s review as I type!) Holy crap! He reviews it as a movie! And he recognizes its virtues too. And declines to carp about the politics. Now my sense of the world has been shaken to its very foundations . . .

By Thoreau

The point of the lab was to characterize a meter.

Lab instructions: 1) Setup your circuit so that when the voltage measured over here is 3V, the needle on that meter is at its maximum reading. Get that? Needle at max means 3V over there.

2) Turn down the voltage over there, and see if the needle reading matches it.

My explanation: “So, if you turn down the voltage to half its original reading, so now it’s 1.5 V instead of 3 V, the needle should be reading half its original value. And if you turn down the voltage to 1/3 its original reading, so now it’s 1 V instead of 3 V, the needle on the meter should be reading 1/3 of its maximum value. Check to see if it’s right. And check a few other voltages, to make sure the two values always agree within a few percent.”

Student question: “So what formula do we plug this into?”

Of course, to be fair, the needle was hard to read. It is very vibration-sensitive, and after they asked me these questions I started pounding my head into the table in hopes of making the pain go away. So the needle was jumping all over the place.

By Mona

GG: I think that many liberals have become much more skeptical of government power and the notion of trusting government leaders as a result of the abuses of the last eight years. Obviously, there are some of them who will quickly lose that skepticism and distrust if there is a Democrat in the White House, but — while recognizing this is just speculation — I honestly believe that’s a minority. I think the radicalism of the last eight years in terms of expansive government power has engendered a real political realignment and made liberals and libertarians far more natural allies than libertarians and those on the Right.

The Stiftung is right: the Grady Hendrix piece on Iron Man the icon in Slate is almost cosmically bad. It’s like, if you uttered the words "state capitalism" at Hendrix he would gape like anal porn. Wha-? State Wha-?

Reed Richards might have been the Objectivist avatar five-minutes’ web surfing has deceived Hendrix into thinking Stark was, except that Richards’ creators were not Objectivists. As for Tony Stark, the military-industrial complex was just not a Randian enterprise. And the anachronism of not just Hendrix’s comics history but his American history is farcical. The Vietnam War was not unpopular in 1963. Marvel’s "young-people demographic" wasn’t a nation of little hippies then; they were mostly the kids that would become hippies in about five years. Tony Stark was conceived as Mister Public-Private Partnership - Mister Public-Private Partnership in things that explode. There’s a quiet, gutsy moment in the cave at the beginning of the movie where Shaun Toub’s Yinsen let’s Tony Stark understand that he is far from the first person to have pieces of Stark Industries shrapnel tunneling toward his heart, and by no means the most innocent person to be in that position. It’s a truth the 1960s Iron Man never showed. The early Iron Man had one customer for that shrapnel, and that customer paid well.

By Thoreau

Delaware is opening the very first charter high school devoted to preparing students for careers in Fatherland Security.  Yeah, good luck getting kids to attend a school where you can’t bring soda or other liquids into the lunch room.

OTOH, the curricular option in “professional demolition” should be useful for the FBI’s efforts to grow their own terrorists.  Obtaining terrorists on the black market is hard, and the homegrown hydroponic version requires water (no go at the checkpoints) so this high school is the logical next step.

By Thoreau

As I mentioned, somebody from the Ministry for State Security decided to show up and debate us. Some of the most interesting things that our good comrade had to say were:

1) “We know all kinds of stuff, man.”

What I am, however, is on the inside; I know things you don’t. I know things you never thought of. I know things that I can’t talk to you about, on grounds of losing my job and going to jail.

I’m sure that our good comrade is indeed required to not divulge some of what he or she is told. What our good comrade has not yet realized is that just because they tell you something is secret, that doesn’t mean they’re telling the truth. And even if what they are saying is true (perhaps especially if what they are saying is true) that doesn’t mean that the rest of the world doesn’t already know it. I won’t ask the loyal worker and peasant to divulge what he or she was told, because I don’t really want to see one more person go to Gitmo–not even a TSA person. However, I’ll bet that if it ever comes out, it will turn out to either be false or underwhelming.

2) “Yes, we know that terrorists don’t need to attack planes.”

Even if something weren’t, and it, say, detonates at the checkpoint and kills all of us… well, at least it didn’t get on a plane. Sucks for us, but TSA would’ve still called it a success for not detonating on the plane and killing citizens - and that, they remind us, is what life insurance is for.

This was stunning to me. I’ve long feared that eventually a terrorist will get some explosives and blow himself up in an airport security line. What do you do then? Have a security line before the security line, so the terrorist blows himself up somewhere else? Or else maybe a terrorist will blow himself up in a shopping mall, or some other place where there are a lot of people and not many metal detectors. And a free and open society will always have such vulnerabilities.

I won’t pretend that it’s completely trivial for a terrorist to blow himself up and exact maximum casualties. Planning matters. Good bomb construction and timing and location matter. Psychological preparation matters. Keeping some operational secrecy beforehand matters. But, at the same time, while it may not be trivial, it’s not exactly rocket science either. The very fact that this hasn’t happened tells me something. It tells me that we are not actually up against a horde of ready, willing, and able suicide bombers. It tells me that the threat is far too small to justify however many tens of billions we spend allegedly fighting terrorism. So far, it appears that most of the “terrorists” caught since 9/11 have been losers, some of whom the FBI actually had to coax into planning attacks.

Anyway, it is stunning to hear our good comrade from the TSA admit that if terrorists really want to blow shit then they’ll blow shit up.  What he doesn’t realize, though, is that the fact that this hasn’t really happened much means something.