September 2006

The Cell is Like Tron!

At least that’s the impression I got from this quite spectacular animation. (Via Shtetl-Optimized.)

The Inner Life of the Cell Animation

Admittedly, real biological molecules would be quite a bit more densely packed, and there would be a lot less smooth motion and a lot more jaggedy fluctuation. Either that, or there’s an awful lot of spooky-action-at-a-distance going on inside cells.

After you’re done being amazed, you could do worse than check out the lecture notes for Scott Aaronson’s class, Quantum Computing Since Democritus. And when you’re done with those, here are some videos of Feynman lecturing on QED in New Zealand. (Thanks to Ed Copeland for reminding me of these.)

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Torture and Permanent Detention Bill Passes

The Senate has voted 65-34 in favor of S. 3930, “A bill to authorize trial by military commission for violations of the law of war, and for other purposes.” Here, “trial by military commission” means that, if you are an unlawful enemy combatant, you have no right to a trial by your peers or any other basic protections of the Bill of Rights. (Who counts as an “enemy combatant”? Whomever the government says. Even U.S. citizens who haven’t even left the country, much less engaged in combat? Yes.) And “other purposes” means torturing people.

I remember when Republicans used to look at government with suspicion. Now the motto of the Republican Party is “Trust us, we’re the government, we know what’s best and we don’t make mistakes.”

I have nothing to add to the discussion that hasn’t been said by more expert people elsewhere. I just wanted it on record, if the internet archives last a thousand years and I’ve been cryogenically preserved for the same length of time, that I was one of the substantial number of people who thought the bill was repulsive and anti-democratic. It will go down in history as one of those sad moments when a basically good nation does something that makes later generations look back and think, “What made them go so crazy?”

I can just quote other people. Jack Balkin:

The current bill, if passed [as it just was], will give the Executive far more dictatorial powers to detain, prosecute, judge and punish than it ever enjoyed before. Over the last 48 hours, it has been modified in a hundred different ways to increase executive power at the expense of judicial review, due process, and oversight. And what is more, the bill’s most outrageous provisions on torture, definition of enemy combatants, secret procedures, and habeas stripping, are completely unnecessary to keep Americans safe. Rather, they are the work of an Executive branch that has proven itself as untrustworthy as it is greedy: always pushing the legal and constitutional envelope, always seeking more power and less accountability.

Almost all the Republican Senators, of course, voted for the bill, Lincoln Chafee being the lone honorable exception. As Glenn Greenwald notes,

During the debate on his amendment, Arlen Specter said that the bill sends us back 900 years because it denies habeas corpus rights and allows the President to detain people indefinitely. He also said the bill violates core Constitutional protections. Then he voted for it.

Most Democrats were against (although not all, sadly). Hillary Clinton:

The rule of law cannot be compromised. We must stand for the rule of law before the world, especially when we are under stress and under threat. We must show that we uphold our most profound values…

The bill before us allows the admission into evidence of statements derived through cruel, inhuman and degrading interrogation. That sets a dangerous precedent that will endanger our own men and women in uniform overseas. Will our enemies be less likely to surrender? Will informants be less likely to come forward? Will our soldiers be more likely to face torture if captured? Will the information we obtain be less reliable? These are the questions we should be asking. And based on what we know about warfare from listening to those who have fought for our country, the answers do not support this bill. As Lieutenant John F. Kimmons, the Army’s Deputy Chief of Staff for Intelligence said, “No good intelligence is going to come from abusive interrogation practices.”…

This bill undermines the Geneva Conventions by allowing the President to issue Executive Orders to redefine what permissible interrogation techniques happen to be. Have we fallen so low as to debate how much torture we are willing to stomach? By allowing this Administration to further stretch the definition of what is and is not torture, we lower our moral standards to those whom we despise, undermine the values of our flag wherever it flies, put our troops in danger, and jeopardize our moral strength in a conflict that cannot be won simply with military might.


Russ Feingold
:

Habeas corpus is a fundamental recognition that in America, the government does not have the power to detain people indefinitely and arbitrarily. And that in America, the courts must have the power to review the legality of executive detention decisions.

Habeas corpus is a longstanding vital part of our American tradition, and is enshrined in the U.S. Constitution.

As a group of retired judges wrote to Congress, habeas corpus “safeguards the most hallowed judicial role in our constitutional democracy — ensuring that no man is imprisoned unlawfully.”

Mr. President, this bill would fundamentally alter that historical equation. Faced with an executive branch that has detained hundreds of people without trial for years now, it would eliminate the right of habeas corpus.

But words are cheap, and nobody stepped up to filibuster the bill. Democrats, as usual, put their fingers to the wind and decide to be spineless. The calculation seems to be that they won’t look sufficiently tough if they come out strongly against torture. They don’t get it. “Tough” means that you stand up for what you believe in, and that you’re willing to fight for it if necessary. How are you supposed to keep the country safe when you’re afraid to stand up to demagoguing Republicans? People know this, which is why it’s been so easy to paint Democrats as weak.

The “tough” stance of the Bush administration has taken Iraq, a country that formerly opposed al-Qaeda, and turned one-third of it over to al-Qaeda, in the process fueling Islamic radicalism and making the threat of terrorism significantly worse. If that’s what you get from “tough,” I’ll stick with “smart” and “principled” any day.

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Quantum Mechanics Made Easy?

I was recently asked to recommend a good popular-level book on quantum mechanics. I don’t think I know of any, at least not first hand. We had a whole thread on the Greatest Popular Science Book, filled with good suggestions, but none specifically about quantum mechanics. A quick glance through amazon.com reveals plenty of books on particle physics, or even specific notions like quantum computing, but not one book that I could recommend in good conscience to someone who just wants to know what quantum mechanics is all about. It is the greatest intellectual achievement of the twentieth century, after all.

There are some books that either come close, or might very well be perfect but I’m not familiar with them. In the latter category we have The Quantum World by Ken Ford, and David Lindley’s Where Does the Weirdness Go? These might be great, I just haven’t read them. I’m sure that the Mr. Tompkins books by George Gamow are good, since I love One, Two, Three… Infinity (and Gamow was a genius), but I haven’t actually read them. Feynman’s QED is another classic, but focuses more on quantum electrodynamics (duh) than on QM more generally. David Deutsch’s The Fabric of Reality is a fantastic book, especially if you are curious about the Many-Worlds Interpretation of quantum mechanics; but I’m not sure if it’s the best first introduction (I haven’t looked at it closely in years). And David Albert’s Quantum Mechanics and Experience is great for a careful philosophical account of what QM is all about, but again maybe not the best first exposure.

Any suggestions? Not for a good book that is related to quantum mechanics or perhaps mentions it in a chapter or two, but for something whose major goal is to provide a clear account of QM. Surely there is something?

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Libya Planning to Execute Nurses and Physician

Declan Butler, a reporter at Nature, is calling for scientists to follow the lead of Lawyers Without Borders in speaking out against the sham trial of the “Tripoli Six.” There is also an urgent editorial in Nature calling for action.

Tripoli Six

Five Bulgarian nurses (Valya Chervenyashka, Snezhana Dimitrova, Nasya Nenova, Valentina Siropulo, and Kristiyana Valtcheva) and one Palestinian doctor (Ashraf al-Hajuj) had been sentenced to death by firing squad for infecting more than 400 children with HIV at the al-Fateh Hospital in Benghazi in 1998. The Libyan Supreme Court ordered a retrial after international outrage at the unfairness of the original proceeding. During that trial, Luc Montagnier of the Pasteur Institute in Paris and Vittorio Colizzi of Rome’s Tor Vergata University analyzed the viruses from the children, concluding that they had mostly been infected before the health care workers ever arrived in Libya. This testimony was thrown out in favor of a study by Libyan doctors. It seems likely that the cause of the infections was poor hospital hygiene, which doesn’t reflect well on the Libyan government.

The medics have now spent five years in jail, during which two of the nurses were raped. Muammar Gaddafi’s government has demanded $5.5 billion in compensation if the prisoners are freed. As the Nature editorial says, scientists should be speaking out against this travesty of justice:

The scientific community has also been relatively silent on the case, perhaps in the hope that it would be sorted out by diplomacy. But the latter has not proved to be the case, and scientific leaders need to use all their influence urgently, as the fate of the medics will be sealed in the coming weeks. It is time not only to save the doctor and nurses, but also to defend a common vision of science and law in establishing the truth, above all other imperatives. Meanwhile, Gaddafi has the opportunity to put this affair behind him by giving the six an immediate pardon.

International pressure was crucial in forcing the original retrial of the six health-care workers; Bill Hooker has information about places to contact with expressions of concern. Anyone with a blog or other platform can help by spreading the word.

Thanks to Janet for the pointer.

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Unconscious but Pervasive Bias

I was hoping to actually say something substantive about this, but time is precious these days (and it’s been all over the blogosphere anyway). The National Academy of Sciences has released a report, Beyond Bias and Barriers: Fulfilling the Potential of Women in Academic Science and Engineering. They seem to think that the relative paucity of women in science is not due to differences of innate aptitude, or even to an aversion to hard work and competitive environments, but to systematic biases within academia. Hmm, fancy that. Cornelia Dean in the NYT writes:

Women in science and engineering are hindered not by lack of ability but by bias and “outmoded institutional structures” in academia, an expert panel reported yesterday…

The panel dismissed the idea, notably advanced last year by Lawrence H. Summers, then the president of Harvard, that the relative dearth of women in the upper ranks of science might be the result of “innate” intellectual deficiencies, particularly in mathematics.

If there are cognitive differences, the report says, they are small and irrelevant. In any event, the much-studied gender gap in math performance has all but disappeared as more girls enroll in demanding classes. Even among very high achievers, the gap is narrowing, the panelists said…

The report also dismisses other commonly held beliefs — that women are uncompetitive or less productive, that they take too much time off for their families. Instead, it says, extensive previous research showed a pattern of unconscious but pervasive bias, “arbitrary and subjective” evaluation processes and a work environment in which “anyone lacking the work and family support traditionally provided by a `wife’ is at a serious disadvantage.”

As Bitch Ph.D. says, “I, personally, am expecting the apologies from Larry Summers’ apologists to start pouring in any day now.”

So I have a question. The reason why most of us were upset by Larry Summers is that he was wrong, in a spectacular and potentially damaging kind of way, and the new NAS study supports this (yet again). But, almost without exception, Summers’ supporters pretended that what got people upset was the very idea of raising the possibility of gender-based cognitive differences, and that these people were anti-free-inquiry and afraid of the truth. Steven Pinker was a dogged straw-man-constructor, but there were plenty of others. (See also Lawyers, Guns & Money.)

My question is: was there anyone who was actually upset at Summers for this reason? That is, was there any respectable academic who really came out against even asking whether there were gender-based cognitive differences? To make things precise, I’m looking for (1) actual professors or other academics, not crazy blog commenters and so on; (2) people who explicitly were against even asking the question or doing the research, not people who (quite reasonably) argue that bias and discrimination are much more important factors in explaining the current gender disparity; and (3) did so in response to Summers, not some time back in the 1970’s or whatever. I sincerely want to know, did anyone take that position? I’m sure it wasn’t the position of most of us, strawmen notwithstanding, but given the speed and efficiency with which the fairy tale was promulgated among Summers’ supporters, I can’t help but think that at least one person did say it. There are alot of crazy academics out there who say all sorts of nonsensical things, it shouldn’t be too hard to find someone.

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No True Believer

It’s tough being a scholar sometimes. Just ask Pope Benedict. In the course of a long speech, he took the time to tell a little story about a 600-year-old meeting between two educated thinkers, one Christian and one Muslim. And now he has the whole Islamic world angry at him. His story went something like this:

The Pope’s speech quoted from a book recounting a conversation between 14th century Byzantine Christian Emperor Manuel Paleologos II and an educated Persian on the truths of Christianity and Islam.

“The emperor comes to speak about the issue of jihad, holy war,” the Pope said.

“He said, I quote, ‘Show me just what Mohammed brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached’.”

Benedict described the phrases on Islam as “brusque”, while neither explicitly agreeing with nor repudiating them.

Hey, this is a popular blogging technique! Just link to a story somewhere else, without giving any explicit endorsement. I wonder if Benedict has been reading Instapundit, or Little Green Footballs?

So now apparently Muslims are upset, as they don’t appreciate the linkage between Islam and violence. Personally, I find it unpersuasive to claim that the two are unconnected when so many people persist in connecting them. Also, if your goal is to insist that your religion is one of peace and tolerance? Probably burning the Pope in effigy is not the best way to get that message across.

Burning the Pope in Effigy

The real problem with the Pope’s speech was his claim that violence had no place in true religion (you know, like Christianity).

“Violence is incompatible with the nature of God and the nature of the soul,” the Pope said.

We all know that most big-time religions have many examples of terrible violence in their past, and Christianity is certainly no exception. Even putting aside the many recent incidents, it’s interesting to consider the record that is part of official Church doctrine, as recorded in Scripture. Steve Wells has done the hard work of going through the Old Testament and counting up the death toll for both God and Satan, taking care not to exaggerate by only including those examples for which specific figures are given. (Via Cynical-C.) The final tally:

  • God: 2,270,365.
  • Satan: 10.

This doesn’t include stuff like the Flood, for which reliable figures are unavailable. If violence is incompatible with the nature of God, He sure has a funny way of showing it.

To be serious for a second: my thing about religion is generally not that it’s bad, but that it’s false. The history of religion is far too complex to be summed up as “good” or “bad,” and there are obviously components of both. The Salvation Army, odious discrimination policies notwithstanding, does a tremendous amount of good. Religious people are generally better at donating to charity than non-religious ones (last I heard; I don’t have specific figures, so this could be wrong). And I like a lot of the art and architecture.

The overall effect of religion may be good or bad, I don’t know how to judge. But if you’re going to talk about it (which the Pope is definitely going to do, given his job description), you should at least be honest, including all the ugly parts. Pretending that either Islam or Christianity is all about non-violence and peaceful dialogue is patently false. You can try to say that the episodes of violence are aberrations, not reflective of the “real” religion, but that’s just the No True Scotsman fallacy. What a religion is, for all important purposes, is revealed by what its adherents actually do, for better or for worse. If Pope Benedict had said “We are all fallible human beings, and people of our faiths do not always act wisely, but we should all strive to promote peace over violence within our churches,” perhaps there would have been fewer effigies.

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Philosophia Naturalis

A new physics-oriented blog carnival, Philosophia Naturalis, has just appeared at Science and Reason. Here’s some background explanation. Looks like a great selection of articles.

To celebrate the birth of this new project, I’ll mention this quote from Al Franken, who is contemplating a Senate run in 2008:

There’s all kinds of things that need to be done. Respecting science again. I would like to do a law where no political appointee can change the language of a scientific report without getting the scientists who made the report to sign off on the language change. That’s a law I’d propose on the first day, I think.

Franken brought this up unprompted during an interview with Lindsay Beyerstein. It shows an admirably pro-natural-philosophy viewpoint.

In contrast, we have George W. Bush, who sees his foreign policy as part of a new religious rebirth:

“A lot of people in America see this as a confrontation between good and evil, including me,” Bush said during a 1 1/2 -hour Oval Office conversation on cultural changes and a battle with terrorists that he sees lasting decades. “There was a stark change between the culture of the ’50s and the ’60s — boom — and I think there’s change happening here,” he added. “It seems to me that there’s a Third Awakening.”

The First Great Awakening refers to a wave of Christian fervor in the American colonies from about 1730 to 1760, while the Second Great Awakening is generally believed to have occurred from 1800 to 1830.

Sadly, the one who views his actions through the lens of a titanic supernatural struggle is the President of the United States, while the one who faces up to the real world is a comedian. Draw your own conclusions about the decline of Western civilization.

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Coltrane Variations

Bad PlusThe Bad Plus have a blog! How cool is that? (Via Marginal Revolution.) The BP are a jazz trio consisting of pianist Ethan Iverson, bassist Reid Anderson, and drummer Dave King, known for an energetic and imaginative style that ranges from free jazz to playful pop. Their version of Nirvana’s Smells Like Teen Spirit became quite a hit as these things go, and rightfully so. The blog is called Do The Math, so perhaps they are trying to compete in the nerd-off. It’s fantastic that a working jazz combo (or musicians more generally) have their own blog; anyone know of any other examples?

I haven’t had a chance to explore the blog very closely, but I noticed that they link to a recent NYT article by Ben Ratliff on Jazz at Lincoln Center’s upcoming Coltrane series, in honor of what would have been his 80th birthday. One of the pieces being performed is Giant Steps, an especially interesting tune. Coltrane knew his music theory backwards and forwards, and he put a tremendous amount of thought into composing Giant Steps; rumor has it that it was meant as an exercise for students, but has since grown into a popular standard, in much the same way as Bach’s Goldberg Variations. (Apparently Trane himself decided that it was too mechanical, and didn’t play it very much after the record had appeared.) The solo is based on an extremely rapid series of a particular type of chord changes, now known as Coltrane changes. In the tune, Coltrane plays four notes in each chord (the root, second, third, and fifth) as a series of eighth notes, changing chords every two beats. For those of you keeping score at home, that means each note is played precisely once before moving on the the next chord, not leaving much time for ornamentation. You can buy a whole book of transcriptions of Trane’s different takes of the chorus.

I know you want me to link to an audio file of Giant Steps, don’t you? But I have something even better. Via Wikipedia, here is an animation of Giant Steps by Michal Levy. It’s extremely well done, and the visual representation tracks the music faithfully while adding its own imaginative dimension.

Giant Steps animation

For your obligatory science content, MR also points to a very clever animation of different dimensions, all the way up to ten! (Okay, the mixing of quantum mechanics and the higher dimensions is a little bizzare; but the pictures are nice.) Those MR guys are pretty good linkers, for libertarians.

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