Thursday, December 30, 2010

Bits and Pieces - December 30, 2010

A good explanation of why the courts shouldn't even be hearing the state cases against the individual mandate of the Affordable Care Act.

Another of the difficulties in comparing today with the Middle Ages. And I'm wondering which part of the Middle Ages Parag Khanna thinks we're going into: the High Middle Ages of the 12th century, the dreadful 13th and 14th that Barbara Tuchman writes about, or the warlike 15th. Or something else.

Emptywheel gives those geeky young men much more attention than I'm inclined to. Check her out if you're trying to figure out who said what about whom. More from Blake Hounshell and Felix Salmon.

A couple of really good posts on American grand strategy by Stephen Walt and John Mearsheimer. I'd like to write more about these, but we'll see how much snow remains to be shoveled tomorrow.

What's the rational math for cost-benefit decisions?

Every explanation I read about human irrationality when it comes to wagers seems to treat $6 like the 6 on a die. As if money was for spending right away or for stuffing mattresses--as if interest didn't exist and rates didn't prevail, and as if there were no prospective element of the value of a win or the harm of any given loss. This is not the rationality they teach and recommend in business school classes, I'll wager; yet I wonder to what extent they've developed a math for it, whether that math has pithy principles or lessons by analogy to the bell curve or binomial distribution; and whether it might have something to teach or learn from biological competition, in which the currency likewise is non-inert and prospectively oriented.

How to Make a War

There has been a certain amount of self-contratulation across the Web on how Israel built a worm and avoided shooting war with Iran. Plus Mossad won't confirm or deny the various murders in Iran of nuclear scientist, just smiles that Cheshire cat smile.

According to Richard Silverstein, Mossad kidnaped, some months back, an Iranian Revolutionary Guards general, who wound up in an Israeli prison, where he died recently. There is the usual argument about suicide or murder that ensues when someone dies in captivity under less-than-public circumstances.

Now, according to Silverstein, the Israeli Defense Force has circulated a letter to its reserve officers that they may be targets for Iranian hit men. Not too surprising that Iran might learn some lessons from this not-war, including lessons that Israel would have preferred they not learn.

So let's say that some Israelis are now blown up, selectively or not, and Mossad claims that the perpetrators can be traced back to Iran. How many rounds of that before Israel has to bomb Iran? In self-defense, of course.

Wednesday, December 29, 2010

Historical Analogies

Parag Khanna provides a nice analogy between 2011 and the 13th century. (Not the 12th, as he gives it; not with Marco Polo and Ibn Battuta.) He leaves out a lot: the role of religion in particular and the Crusades.

Things started breaking up in Europe in the 13th century. Partly it was an attempt, in France, anyway, to bring the country under the king, but it took a religious cast in an attempt to exterminate heretics in the south. In fact, things came apart so badly that by the 14th century, European society was in tatters and plague-ridden. And the Templars, heroes of the Crusades, were found to be corrupt and were dissolved, the leaders burned at the stake.

One of my hobbyhorses; lots more to say, but no time just now.

Reading list:
Parzival, by Wolfram of Eschenbach
A Distant Mirror, by Barbara Tuchman

Moving on to the Next Stage

The Obama administration has announced that it will continue on the nuclear road mapped out in Barack Obama's April 2009 Prague speech, its Nuclear Posture Review, and the New START negotiations. They plan to put ratification of the Comprehensive Nuclear Test Ban Treaty (CTBT) before Congress next year, to propose a way forward on a fissile material control treaty in the Conference on Disarmament, and to begin to negotiate with the Russians on tactical nuclear weapons.

During the Senate's debate on New START, a number of Republicans criticized the treaty because it didn't address tactical nuclear weapons. It was never intended to, of course. But, backing the administration's longer-range plans, the Republicans inserted language in the Senate resolution of ratification to begin talks on those weapons next year. So one might think it would be hard for a rightwing organization like the Heritage Foundation to criticize those talks, but no!
Baker Spring, an analyst at the Heritage Foundation and a critic of New Start, said it would be better not to get into a new round of talks. “The imbalance in tactical nuclear weapons is very worrisome,” he said, “but I do not think the U.S. should enter into negotiations on these weapons, because it has no cards to play.”
Not that they were right on anything about New START. The Armchair Generalist picks up on this too.

One of the benefits of New START, not so much discussed in the Senate debate, is that it renormalizes arms control talks between the United States and Russia. Continuing this kind of contact allows issues to be raised and, potentially, solved outside the glare of the press so that nobody has to lose face. But the next talks will be difficult for a number of reasons.

The Russians have about 3000 tactical nukes, and we have about 300. Many are full-up bombs to be delivered by aircraft, but they are not associated with delivery vehicles as the strategic nuclear weapons covered by New START are. So they will have to be counted individually. This is likely to require some sort of identifier for each nuke, with some possibility of allowing the other side to see more of the weapon than the weapon's owner would prefer. New START takes a small step in this direction by counting, explicitly, the warheads on missiles. The inspectors will actually see the warheads, encased in a reentry vehicle.

The Russians also see those tactical nukes as equalizers for American and Chinese conventional power. This may be a more difficult issue than counting warheads, but it is also a next step in arms control. As the numbers of nuclear weapons go down, conventional arms become more important and will also be an issue as other nations are brought into the negotiations.

Getting the CTBT ratified will be interesting. The Senate will be slightly more Republican than the one that ratified New START, and Jon Kyl, who helped to defeat CTBT ratification in the 1990s, will be itching to do it again and regain face with those who think nuclear explosions are a good idea. Those numbers, however, seem to have decreased since the last time around. The big question will be how much Kyl and McConnell have been damaged with their Republican colleagues by their fruitless opposition to New START.

For a fissile material control treaty, there's another "just say no" player: Pakistan, which has been stonewalling discussion on such a treaty in the Conference on Disarmament like forever. It will be useful for the United States to provide a proposal. I have my doubts as to the usefulness of such a treaty. The United States and Russia have surpluses of weapons fissile material; we're burning it in reactors to get rid of it. China is increasing its nuclear stockpile very gradually and may have as much weapons fissile material as it feels it needs. So a treaty to end production of weapons fissile material would primarily affect India, Pakistan, North Korea, and possibly Iran and Israel. None of them are going to sign on to anything like that any time soon. There may be some value, however, in a forum for discussing the subject and in inspection regimes developed to verify such a treaty.

Tuesday, December 28, 2010

No, I'm Not Comfortable With Geeky Young Men Making News Decisions For Me

I keep wondering what is in the Wikileaks cables that haven't been released and the reasoning behind the order of release. I've been told, and it seems to be on the interwebs somewhere, that Wikileaks negotiates with their chosen news organizations to decide on every day's releases.

But news organizations also fall out of Wikileaks favor. The New York Times irritated Julian Assange before enough started happening that any number of newspapers now may have printed the equivalent of what the Times did that irritated Assange. And I think the Guardian, or another European paper, may now be on the s***list too.

I'm not following the stories very closely, although I am alert for explanations when they appear, having missed them early on. Assange has written a number of pieces on his philosophy, if it can be called that. It seems to be that governments and wars are wicked, and the clear light of day will end the wickedness. At the same time, he seems less than willing to face the Swedish charges against him in the clear light of day, although he has accepted an invitation to write about his life, no doubt with the same level of censorship he has displayed in his responses to the Swedish charges and his method of releasing the cables.

Complicating the problem are another group of geeky young men at Wired magazine (via). Apparently Kevin Poulsen, a senior editor at Wired, has material pertaining to Bradley Manning's conversations with Adrian Lamo, another geeky young man who seems to have been working for the government. Poulsen is releasing this information as he sees fit.

Are you following this? I'm not sure I am.

You can argue that Assange and Poulsen are doing the same sort of thing that Bob Woodward does, except Woodward does it in best-seller books. I've not found Woodward's leaks all that compelling or praiseworthy, either.

The whole thing reminds me of the unpleasant late-adolescent men I've known, who have all the answers to the world's problems and are going to inflict them on me. This particular bunch seems to have possession of some stuff that may be interesting, but they also seem to be determined to deal with it their way.

Monday, December 27, 2010

Community Organizing Shows Some Results

I’ve argued that President Obama is using community organizing tactics as part of his presidential strategy. The country is divided, the Congress has been powerless, and dialog among political positions is poisonous. How would a community organizer bring people together?

One of the principles of community organizing is to enable and encourage people to do the things only they can do for themselves. It’s not up to the President to pass legislation through Congress or to make our discourse civil. It’s up to Congress, the voters, us.

Exhortation has its limits. Preachers have limited appeal today. So the argument for the President’s bully pulpit is far too optimistic. In fact, the suspicion of authority figures and the readiness of the political opposition to take words and phrases out of context makes the bully pulpit potentially counterproductive. Part of that suspicion, too, comes from promises made and not kept. Better not to promise any more; political campaigns demand it, and Obama has a campaign backlog.

So Obama has limited his speechmaking to allow the rest of us to figure out what we need to do. Buy-in is always better if the buyer thinks it’s her idea.

And it’s working. Dennis G. at Balloon Juice links to the long lists of accomplishments halfway through President Obama’s first term. I’ll add in David Ignatius’s accounting of foreign policy successes. Health care reform, the New START Treaty, two new Supreme Court justices, straightening out some of the many messes the Bush Administration left behind. The record seems to be comparable to that of Franklin Roosevelt or Lyndon Johnson.

I’m reading David Halberstam’s War in a Time of Peace, about the 1990s wars in the former Yugoslavia and the US response to them. The book starts with the George H. W. Bush administration, but it is mostly about the Clinton administration. Halberstam focuses on the response to the war, but the context of domestic politics and disorder within the administration is provided as well.

We won’t have the same sort of look at the Obama administration for a few years yet, but they appear to be far ahead of the Clinton administration in fulfilling campaign promises and doing what they set out to do.

Dennis G. looks at the disappointment of some on the left with Obama and suggests that it’s because Obama’s reality conflicts with the expectations of the disappointed ones. I tend to agree that what Dennis proposes is part of that reaction, but I would add that the disappointment is that Obama is making us think and work for ourselves, not handing us solutions on a silver platter. Handing over the work to the people suited to doing it frequently provokes griping, particularly when they have become accustomed to something else. But Congress got with the program, all the way through its extremely productive lame duck session.

So Obama and his cabinet can move forward on the issues not dealt with or not completed. Global warming, Guantanamo, bringing the economy back to full health. And it sounds like they’re ramping up for it. The administration is already addressing, by regulatory means, carbon dioxide emissions and remuneration for doctors discussing end-of-life directives with their patients, left out of the health care reform legislation because of the Republican-generated hysteria over “death panels.”

Republicans are vowing to fight the regulatory agencies, but they have been weakened by the lame duck successes. The administration peeled off thirteen Republicans who care more about national security than Republican fantasies, in the face of the Senate minority leader’s determination to vote against New START. And the Senate remains majority Democratic. Changes to the filibuster rules are likely, which will further weaken the Republicans. None of that is necessarily transferable to the House, but perhaps the Republican leadership there will recognize that it is making itself look foolish, or the voters will see it and pull things back on track.

That’s another community organizing precept. Don’t go head-to-head with opponents. Give them the opportunity to go to their extremes and alienate potential supporters

Additionally, ordinary people are beginning to speak up. The controversy over grabbing grandma’s junk at TSA checkpoints hasn’t gone away. The unfairnesses in the financial system continue to provoke anger. Some of the crazier Tea Party aberrations were thoroughly rejected in November’s election.

I’ll disagree with Steve Clemons. The successes aren’t centered on Obama. If his game is picking up, it’s because it takes some time in community organizing to get everyone on the team and to let those who don’t want to be self-destruct. I’m looking forward to 2011.

Fire and Ice

Some say the world will end in fire,
Some say in ice.
From what I've tasted of desire
I hold with those who favor fire.
But if it had to perish twice,
I think I know enough of hate
To say that for destruction ice
Is also great
And would suffice.
--- Robert Frost, 1923

Daniel Little looks at hate groups on the political right and wonders what motivates people to join or originate these groups. I’m also wondering why there seem to be more of groups like this on the right than on the left. They’re not absent on the left, but there are fewer of them. Prime time in the United States for left hate groups seems to have been the late 1960s and early 1970s.

After the now-mandatory holiday clash with a rightwing relative, I would extend those questions to why otherwise intelligent people can sign on to absurd propositions. This particular difference had to do with the idea that the preamble to the New START Treaty limits the US ability to develop missile defense. Or that strategic missile defense works. It’s not hard to find factual material on these issues, along with others (like the existence of Barack Obama’s birth certificate). Or why it seems to be a cluster of absurd things. The efficacy of missile defense has no connection with where Barack Obama was born, although if he is a Kenyan anticolonialist marxist socialist, then he may well be undermining America’s development of missile defense.

It’s possible that listening and reading only to material selected for its agreeability with preconceived notions disables the critical capability of one’s brain. Or that the cluster of rightwing beliefs provides emotional support for people who need it. But that brings us back to Little’s questions, because a large element of this belief system seems to be hate and fear. Fear of anyone who is different that morphs into hate. Argumentation that morphs into bullying. The form of too many rightwing arguments is to start by accusing the other party of holding a variety of loathsome beliefs, followed by an absurd claim, devoid of proof, and a demand that the other party prove that the claim is false. This often amounts to proving a negative.

That’s the famous epistemic closure widely discussed earlier in the fall, but what I’m interested in is what predisposes a person to that epistemic closure and what motivates them to hold it so tightly.

Monica A faces hate in herself.
I have had two deaths in my immediate family, one was the man I considered to be like my father. My uncle was killed in a car accident the Sunday following Easter. The person responsible was sentenced to four years in prison. It was the most he could get.

I was prepared to hate the man responsible for the rest of my life. I was prepared to do whatever it took to exact a measure of retribution for the loss (making sure everyone he came into contact knowing that he had committed this crime), but all of that changed with a simple gesture. My cousin walked over to the man that had taken his father, extended his hand and forgave him. Could any of us had done such a thing? Could we have shaken the hand of man responsible for our father's death?

I was taken aback when I learned of this. How could I continue on my path? My family are devout Christians. In the face of this horrible event they have chosen to forgive. I cannot be vengeful in the face of their forgiveness, but where do I put my hate? Where do I put the energy it took to hate this man? Where does my life go from here?
Hate, of course, takes a great deal of energy to sustain and can devour the hater. There are larger reasons, as well, for forgiveness.
when the requisite conditions are met, forgiveness is what a good person would seek because it expresses fundamental moral ideals. These include ideals of spiritual growth and renewal; truth-telling; mutual respectful address; responsibility and respect; reconciliation and peace.
Monica A is dealing with a one-to-one personal relationship between herself and the man who caused the car accident. The haters Daniel Little is discussing hate on a more general, institutional level: blacks, homosexuals, people who aren’t like us. Is that the same kind of thing? Can it be resolved by forgiveness?

Juan Cole also considers some of the factors that may be involved with hating homosexuality in particular, emphasizing religion. I would go further back the logic chain and ask why some people use religion to justify their hates. The biblical citations used to justify discrimination against homosexuals, for example, hardly bear the weight of that justification.

And then we have the trivialization of hate, which indirectly serves to support those in hate groups. The people discussed in this article are pathetic, but hardly worthy of hate. If they are widely hated, as the article claims, then perhaps there is no harm in institutionalizing hate in the groups that Little discusses. Do reporters hate the people listed in the article?

Saturday, December 25, 2010

Friday, December 24, 2010

The Trouble With Wikileaks

I've seen all too many stories based on the cables being portioned out by Wikileaks that report somebody telling somebody else about a third party as though it were fact. Here are three from today.
This is why Wikileaks is so crucial: A June 2009 cable from France, days after the great Cairo speech of Obama, in which the Israelis are said to claim a secret deal with the US for settlement growth.
That story goes on to quote the cable:
MFA Middle East Director (Assistant Secretary-equivalent) Patrice Paoli informed POL Minister Counselor June 18 that Israeli Defense Minister Ehud Barak told French officials in Paris June 15 that the Israelis have a "secret accord" with the USG to continue the "natural growth" of Israeli settlements in the West Bank.
A French official said that Ehud Barak claimed a "secret accord" with the USG to continue Israeli settlements in the West Bank. Let's unpack that. How did the French official know this? Did he hear Barak? Was it a rumor? If Barak said that, was he claiming something that didn't exist? Joking? Exaggerating? This piece of information has passed through at least two people.

Israel destroyed a Syrian nuclear site in 2007, former U.S. Secretary of State Condoleezza Rice said in a cable to diplomats, Yedioth Ahronoth reported Friday.
It is the first official confirmation that Israel was involved in the attack, the newspaper said.
I think I would save the phrase "official confirmation" for announcements from the government. "Confirmation" would have been sufficient. This is not surprising news, given the unofficial confirmations involving cheshire-cat smiles and refusals to comment. It's a more direct piece of information than the first example, though. The quote from the cable I find more interesting is
destroyed the nuclear reactor built by Syria secretly, apparently with North Korea's help
Note the word apparently. That could denote uncertainty or it could be a bureaucratic tic.

And Colum Lynch points out the problem with the report that Egypt was offered a nuclear weapon. That link doesn't quote the cable, but my recollection is that I had a number of questions. How would Maged Abdelaziz know this? His response to Rose Gottemoeller's asking of that question is quite vague. There weren't any specifics about who was offering, either. My impression was that it might have been the Russian government or it might have been someone else.

Most of the cables are like this: a tantalizing bit of information, with little confirmation. Because so much of the media is treating the revelations themselves as the news, the real stories are being missed. Any of these three might be made into a real story by further investigation along the lines of the questions I've asked. But that would be a lot more work, and most of the cables would be found to contain less news than their release is being treated as. Unfortunately, many readers will retain that Egypt was offered nukes by Russia or that the United States has a "secret accord" with Israel.

Tracking Santa

If you'd like to keep track of Santa Claus's travels today into tomorrow, NORAD and the Los Alamos National Laboratory both offer sites for doing that.

Meanwhile, Christmas in what has been called the Holy Land.

And not a good day for dinosaurs. Speaking of which, one of the traditions is persecuting wrens.

It's always seemed to me that we hardly need the alternative celebrations around this time of the year. Christmas is a holiday that replaced the Roman Saturnalia, festooned with the tree and holly trimmings of pagan northern Europe, and Santa Claus, whose roots go back to paganism, mostly of the northern Europe variety, grown into the symbol of today's consumer capitalism.

So have a happy holiday, however you'll be spending the weekend! Me, I hope to get some more thoughtful posts and other stuff written along with the festivities.

Thursday, December 23, 2010

Shaman's Greeting

The sun rose in glory today and kissed the clouds.

We can now be assured that the sun has escaped Ilmarinen's forge and will move away. Find a spot on the horizon, watch it every morning when the sun rises, and you will see that the sun is moving toward summer, however the storms may come for the next month or two.

Now we may celebrate.

Wednesday, December 22, 2010

New START Ratified, 71-26

The New START Treaty was ratified by the Senate by a vote of 71 to 26. Thirteen Republicans decided that national security was more important than party politics. Vice President Joe Biden presided over the vote.

Fred Kaplan has probably the best analysis of the politics of the ratification. He sees Jon Kyl and Mitch McConnell as the big losers. It will be interesting to see what effect this might have on the next Congress.

Particular credit goes to the Republicans voting to ratify the treaty:
Alexander, R-TN
Bennett, R-UT
Brown, R-MA
Cochran, R-MS
Collins, R-ME
Corker, R-TN
Gregg, R-NH
Isakson, R-GA
Johanns, R-NE
Lugar, R-IN
Murkowski, R-AK
Snowe, R-ME
Voinovich, R-OH

Full vote here.

Shaman's Greeting

The sky is bruised again today.

That is all.

Tuesday, December 21, 2010

Shaman's Greeting

[Play while reading]

The sky was bruised this morning in the direction of sunrise. This can only mean that the sun has become caught in Ilmarinen's forge.* The sun has been headed in that direction for some months now, despite our warnings and supplications. The struggle spread across the southern sky. Ilmarinen released the sun, but made it promise to return tonight. I guess it was inevitable when the water refused to freeze in the birdbath, now for two nights. Three ravens flying overhead have told me what is needed, though.

The sun can be untangled only if the Senate passes the New START treaty. The great sage Eisenhower told us many turnings ago that we were on a path that could lead to the sun's capture, and now we are facing that terrible prospect. The next few days will be critical. I will continue to report.

Now I return to my hut. We all must pass the next few days in penance, in streets and stores crowded with demon-possessed people.

*Or Wotan's, Vulcan's, Hephaestus's. I'm an inclusive shaman.

Monday, December 20, 2010

Bits and Pieces - Followup Edition

Everything Troutsky wanted to know about classified information, from the Congressional Research Service.

Stan Collender rounds out my post on why scientists aren't Republicans.

Kevin Drum gets Mitch McConnell's position on New START right.

Adam Serwer nicely summarizes the GOP position.

Added later: Jeffrey Lewis rebuts some things being said by Republican senators that irritated me, too.

GOP senators concede arms treaty will secure enough votes to pass. I'm not counting them chickens yet, though.

A good overall summary.

In new news,

Rapid change in Inner Mongolia. Nice photos.

Iran is cutting its gasoline subsidies. The sanctions are pinching.

And some celebration of the season:

New Russian military uniforms.

The paleontological twelve days of Christmas. I thought they came after Christmas. Never mind.

Added later: A toy I probably won't have time to play with.

Astronomy 101

I have seen more scrambled explanations of the solstice and lunar eclipses in the press this week than I would have imagined. I saw one and blew it off, then another, and finally Richard Cohen in the New York Times:
WHAT is the winter solstice, and why bother to celebrate it, as so many people around the world will tomorrow? The word “solstice” derives from the Latin sol (meaning sun) and statum (stand still), and reflects what we see on the first days of summer and winter when, at dawn for two or three days, the sun seems to linger for several minutes in its passage across the sky, before beginning to double back. [emphasis mine]
The Santa Fe New Mexican had something on Saturday about the sun and the moon and the earth being opposite each other. (It's gone to recycle limbo in the garage.)

Another said something about the earth adjusting its tilt.

And some have noted that the full moon and the eclipse are happening at the same time. Quelle surprise!

The New Mexican formulation seemed to be a clumsy translation into words of what the writer might have understood. Cohen simply doesn't understand, nor do those seeing the earth adjust its tilt or being amazed at the conjunction of full moon and eclipse.

So let me explain lunar eclipse and winter solstice.

A lunar eclipse happens when the moon enters the earth's shadow. So the sun, earth, and moon are lined up. Usually at full moon, the moon is above or below the earth's shadow, so not every full moon is an eclipse, but every lunar eclipse is at a full moon.

And here's how it will look at various times, earth's shadow indicated.

Diagrams from Our Universe and Sky and Telescope.

Now the solstice. Cohen has the derivation right. It's about the sun standing still. Sort of.

The earth is tilted in its orbit. That tilt remains in the same orientation relative to the solar system, which means that it points more or less toward the sun at different times. At the solstices, the tilt is toward or away from the sun. At the equinoxes, it is at right angles to the sun.

[From Boquete Weather.]

So what does that have to do with the sun standing still?

Well, the sun doesn't stand still. It keeps doing what it's been doing all year and before that. We know (I think) that the sun doesn't actually move around the earth to provide day and night, but rather that the earth's rotation makes it look that way. So if we start with the fall equinox (from the Latin for equal night, because the day and night are of equal duration), then as the earth moves toward the winter solstice, the sun rises a little later every day and sets earlier. If you watch the sunrise, you can seen the sun rising a bit further south every day. It also sets a bit further south. On the solstice, that changes. The sun then rises and sets a bit further north every day after the solstice, and the days get longer.

So on the winter solstice, the sun stands still in its journey south.

"[T]he sun seems to linger for several minutes in its passage across the sky, before beginning to double back." And just what had you ingested before you saw that, Richard Cohen?

Update: Props to The Guardian for getting it right!

Sunday, December 19, 2010

Don Van Vliet, 1941-2010

Photo by Anton Corbijn

"Breaks my heart to see them cross the sun
Grain grows rainbows up straw hill,
Breaks my heart to see the highway cross the hill...."

Senate Debate on New START Treaty

An amendment to the treaty itself offered by Senator Jim Risch (R-ID) is being debated as I write. Amending the treaty (rather than the resolution of ratification) will require new negotiations with Russia, essentially from scratch. In effect, voting to amend the treaty is voting to destroy it.

I keep wondering why the opponents of the treaty want to enter future history books as the people who damaged an improving relationship with Russia, who wanted more and more nuclear weapons, undermining any arguments that the United States can make against North Korea and other nuclear wannabes. I also can't understand what future they are looking to, whether a more unstable world is really what they want.

Jon Kyl has a reputation going: he'd like, I suppose, to add another notch to his anti-treaty belt after helping to defeat ratification of the Comprehensive Nuclear Test Ban Treaty in the 1990s. But isn't that less important than world stability, backing away from the nuclear brink?

It's hard to regard these people as rational and grant them any other motivation than the most limited vision: political victory, in a strictly win-lose world.

Joe Cirincione says that not all Republicans are siding with the extremists and the treaty will be ratified when the final vote is taken.



From Pres. Obama's "Organizing for America" email:
Moments ago, the Senate voted to end "Don't Ask, Don't Tell."
When that bill reaches my desk, I will sign it, and this discriminatory law will be repealed.
Gay and lesbian service members -- brave Americans who enable our freedoms -- will no longer have to hide who they are.
The fight for civil rights, a struggle that continues, will no longer include this one...
But this victory is also personal.
I will never know what it feels like to be discriminated against because of my sexual orientation.
But I know my story would not be possible without the sacrifice and struggle of those who came before me -- many I will never meet, and can never thank.
I know this repeal is a crucial step for civil rights, and that it strengthens our military and national security. I know it is the right thing to do.
Politically, Sen. Lieberman got the win. So what. He has atoning to do in the name of his own piddling opportunistic legacy. This is the pragmatic president's work, however. There are obvious failures, at least in the short term, but the victories, subtle and grand, are adding up to a great presidency, two and a half years in. He's not a crass pragmatist; he's a philosophical pragmatist.

From Pres. Obama's "Organizing for America" email:
But the rightness of our cause does not guarantee success, and today, celebration of this historic step forward is tempered by the defeat of another -- the DREAM Act. I am incredibly disappointed that a minority of senators refused to move forward on this important, commonsense reform that most Americans understand is the right thing for our country. On this issue, our work must continue.
The US Senate's place in history. The coming 112th Congress won't step in the direction of basic decency partly because anti-immigrant demagoguery helped many of them get elected. But in the end they're on the slippery back end of the vaunted "arc of history." Despite his harsh statements about DREAM, I think Lindsey Graham knows this. "Comprehensive immigration reform" is a crucial conversation to be had by sane people, it must be admitted, regardless of whatever dog whistles some may think that phrase possesses. The tragedy, of course, is in the second-class treatment of human beings who view themselves as de facto American, while the anti-immigration faction jerks them around with specious claims about what it means to be de jure American.

This reminds me that I still need to produce that post on the Republican's capture of moral relativism....


Friday, December 17, 2010

Bits and Pieces - New Start Edition

European foreign ministers say "ratify New Start." Unfortunately, this seems likely to harden Republican opposition.

Quotes from the senators from Tennessee.

A bit of political analysis. The Republicans asked to offer amendments but are just using up time. More here. And here. If Congress amends the treaty, it would have to be renegotiated with the Russians. However, the Senate's ratification statement could be amended.

Meanwhile, in other news

President Obama has been criticized for not making everything all right all by himself. Now the complaint is that he's not involving enough of us. But the voters seem to have more sense than the pundits.

During the BP blowout last summer, Governor Bobby Jindal of Louisiana, one of the Republican Party's up-and-comers, wanted sand berms built to protect the coast against the oil. Scientists and engineers said it was a dumb idea. Now the data is in, was a dumb idea. Reason #592 why scientists are not Republicans.

What if they turned off Niagara Falls? Via.

Another Reason Why Scientists Aren't Republicans

Steve Benen reminded me yesterday.

The United States government still does not have a budget, three months into the fiscal year. The Republicans are considering holding their breath, turning blue, and shutting the government down altogether.

Many scientists work for the government. Other scientists can look on in horror or schadenfreude, according to their temperaments.

Practically any job, and that includes scientific research, requires a modicum of continuity. The federal budget is supposed to be approved before the beginning of the fiscal year. After Congress approves the budget, there are other decisions to be made and paperwork to be done down the line in the departments before the money flows to the scientists. So budget approval somewhere in the early summer would be ideal. IIRC, the budget bills came up in Congress about that time, and the Republicans obstructed. So, in order to keep the government running, a continuing resolution was passed in September.

A continuing resolution says "keep spending money pretty much the way you did last year." But projects may be expanding or contracting, and the scientist managing a project has to make some guesses about how the budget will go. Simply because there is a logic that a project will expand or contract does not mean that Congress will fund it that way. If a project is expanding, every month under a continuing resolution means less progress toward the expanded goals. If a project is contracting, every month under a continuing resolution means an even lower budget for the rest of the year. You can even calculate (as scientists are wont to do) situations in which, when the budget comes in, it's all spent already and everyone on the project has to be laid off until the next year.

I am sure that discussions like this are going on in all government-funded laboratories now.

The continuing resolution fun started under the triumphalist Newt Gingrich-led Republicans in the 1990s, climaxed by a full government shutdown. Now the Republicans are promising to do it again.

The Republicans aren't solely responsible for continuing resolutions. But they are the ones playing politics with the budget. Scientists are smart enough to see that.

Thursday, December 16, 2010


Troutsky asks:
classified is a weird term. Perhaps you could give us a post describing the process, what it actually delineates.

How arbitrary is it? How do we know?
I'll comment, based on what I've seen, but my knowledge is not exhaustive. My sense is that every government agency does things its own way and has its own rules. There is some commonality among the Departments of Defense, Energy, and State, although far from complete synchronization.

Rules for classification exist and are called "classification guidance." The rules can change frequently, and amendments to the guidance are sent out from the classification arms of the various departments to the organizations handling and generating classified matter.

Those organizations usually have people who keep track of the guidance and advise others in the organization. Certain people are designated to be able to classify material at various levels. These two sets of people do not necessarily overlap.

People working on sensitive projects must have what they write reviewed for classification, which comes in different shapes and levels. Troop movements, for example, are classified in a different way than nuclear weapons design information.

How arbitrary is it? Hard to say. Some things are fairly clearcut, others not so much. And I have no doubt that, particularly at higher bureaucratic levels, which have less accountability, stuff gets classified because someone would be embarrassed if it got out. I've never seen that, but I have seen how people think. The guidance can also be hard to work through. During the 1990s, a lot of nuclear weapons information was declassified. Now it looks like it's being reclassified. So some of the guidance may be self-contradictory or just hard to interpret and apply.

How do we know? Supposedly there are various checks and balances within the classification system, requests for additional review, that sort of thing. But, of course, all that is part of the classified system and not available to those outside it, or even to those inside it without the "need to know." As long as we have secrets and classification, it will be hard to make the system accountable, and it will tend to grow. Daniel Patrick Moynihan's book, Secrecy, is a good discussion of why secrecy in government should be kept to a minimum.

classified is a weird term. I've always thought so. I suspect it's a euphemism that refers to the various levels of secrecy. So a classifier classifies documents into those levels.

New Start Treaty Debate Under Way

I'm not writing much about the Senate debate on the New Start Treaty. It's about time, it looks like the votes are there (but just barely), and it looks like Harry Reid will call for a vote before Christmas. Ratification would be a nice Christmas present for the world. Y'know, peace on earth, and all that. Although it's possible Republicans are excluded by the qualification "to men of good will."

I'm not writing much because it's all been said. The Republicans will mount their dumb ideas. Jon Kyl will fulminate that there hasn't been enough time (only since last spring), and others (probably repetitively) will argue that it prevents the United States from setting up missile defense, leaves too many nukes in the hands of the Russians, blah blah blah. In contrast, Mitch McConnell has shown a bit of responsibility in quashing the run-out-the-clock requests from Jim DeMint for the entire treaty to be read.

John Kerry is doing a nice job of guiding debate, as far as he is able. Dick Lugar, as always, is a statesman. John McCain even seems to be acting a bit more responsible than he has on other issues.

The procedure for treaty ratification.

Key issues and responses to critics.

A more detailed version of issues and responses.

The Armchair Generalist has a good summary of the action so far.

Page van der Linden on the amendment process. Looks like amendments to the treaty will not be considered, although amendments to the Senate's statement on the treaty will.

On Twitter, @plutoniumpage, @nukes_of_hazard, and @csisponi are worth following.

I'll post more links to helpful material as I find them.

CSIS-PONI is liveblogging the debate.

Nikolas Roth on the complaint that there's not enough time.

Senator Lugar's speech covers all the bases.

Senator Jeff Bingaman's (NM - D) speech has the numbers. h/t to John Fleck)

Wednesday, December 15, 2010

We Need More Thinking

Several issues that haven't been well thought out.

Apparently numerous government-connected organizations are blocking sites containing Wikileaks material, now including AT&T and Verizon. There's a simple reason for this. Classification remains in force, even if classified material is leaked. The proper response for a person with a clearance when asked about it is neither to confirm nor deny. The sheer volume of Wikileaks material is straining this rule, although not very much of the leaked material is actually classified. I've been wondering about the classification status of the rest. Official use only? Nobody who knows is going to say, for that simple reason. Further, getting classified material on an unclassified computer is big trouble, leading to wiping disks and such. That's why government agencies and their contractors (this is probably the reason for AT&T and Verizon's actions, Emptywheel) are blocking the sites. Just visiting the New York Times these days could get your computer nuked.

The Tea Partiers want the government out of everything. They also want honest politicians who aren't on the take. Dana Milbank enlightens us as to the first actions of Tea Partiers who got elected to Congress: hook up with lobbyists. There goes the "honest" part. There is a solution: government funding of elections, private money prohibited. We'll see which precept the Tea Partiers are willing to give up.

Fox defects in the "War on Christmas."

Happy Holidays from Walmart, too!

Scientists, Republicans, and Others

The last week or so, there has been a blogospheric flutter about the finding, in a survey by the American Association for the Advancement of Science (AAAS) that found that, while something around half of those surveyed were willing to admit to being Democrats, the number admitting to having committed Republicanism was in the single digits, and there was a fairly large component of those calling themselves independents.* The simplified version is that hardly any scientists are Republicans. The flutter has been an attempt to find out (or opine on) why.

The simple answer is that scientists, as I've said before, have to believe that an external reality exists, and that that reality is not infinitely malleable to political preferences and general fantasy. Today's Republican Party seems to prefer the malleability thesis. Here is today's evidence on that point, now beginning to ripple through the blogosphere. And of course there is creationism, and, more subtly in Jon Kyl's and Mitt Romney's criticism of the New Start Treaty, the ignoring of the stated purposes and objectives of the treaty or the words that comprise it. Or the nihilism of Republicanism. Scientists tend to believe that what they are doing is making the world a better place, the opposite of nihilism.

Part of the reason I didn't weigh in to the flutter earlier was that I became tired as I read the blog posts. So many errors, so little time, such boring posts to refute them. And I'm talking about the ones I generally agreed with, too. If you are interested in learning something about science or scientists, please ignore what has been written on this poll and its results.

And now comes a "teachable moment," or so at least one blogger thinks. The New Yorker article on "the decline effect" largely treats experiments in psychology. The author tacks a few physics things on the end of the article, but they would have involved knowing something about physical facts and mathematics, and the psychology would be more interesting to his readers. (Or so I imagine the justification going.) That article made me tired, too. I'll just say that psychology is the science most likely to be affected by earlier results, not to mention the statistical effects that the author muddies up. "Teach the controversy," I guess. Right.

Michael Bérubé makes some very good points on how Republicans have taken over postmodernism and reminds us of the Sokal Hoax, in which a physicist served up some crow to the postmodernists in one of their very own journals. Although it doesn't seem to have been his intention, he's provided perhaps the best commentary relevant to why scientists aren't (or won't admit to being) Republicans and why we all need to be more careful, scientists and literature people, even journalists(!) of how we think and write these things out.

*It would be possible to do a lot of googling for this post and make it sparkle with links and numbers, but I doubt that that is necessary. In any case, I'm bummed out enough by this topic that I wouldn't write this post if I had to do that.

It's a New Day

For an instant this sunrise, all the clouds went neon red, then shaded off to pastel.

Debate on the New Start Treaty is supposed to start this afternoon. Rumor has it that the Republicans will insist on having the entire treaty read, which is estimated to take 15 hours.

Basics of treaty ratification here.

Monday, December 13, 2010

Geminid Meteors Early Tomorrow Morning!

The maximum of the Geminid meteor shower should occur early Tuesday morning. There should still be some around on Wednesday, too. This seems to be where they come from, and here's a star map. They should be pretty much all over the sky, though, particularly in the directions you aren't looking at the time. ;-)

And there will be a lunar eclipse the morning of the 21st, the solstice. I'll post more if I find it.

Update (12/14/10): I saw quite a few meteors between 1 and 2 am, the first time this year I've seen meteors during an official meteor shower. There should be some early tomorrow morning, too.

Is There A Conflict?

Hackers tend largely to be young men. Ayn Rand fans tend largely to be young men and those who haven't grown out of it.

So I was wondering, when reading about Anonymous and all those other hackers who believe that information should be free, if those (largely) young men also believe that everyone should be free to make as much money as they can any way they can. And, if so, how they reconcile their right to disrupt others' secrecy and commerce.

Or is this how the Hobbesian war of all against all develops?

Thinking of Building a Bomb?

Just a friendly warning: it's really hard to get it right.

We now have one more FAIL in Stockholm. The guy managed to kill only himself, although it appears his intention was otherwise.

That in the latest in a line of FAILs: the Times Square bomber, the underwear bomber, possibly the toner-cartridge bomber, and there are probably some I'm not recalling.

This is a lot more impressive than the single Weather Underground blow-up of the Greenwich Village townhouse bomb factory in 1970, but that pretty much convinced the radicals that bomb-making was not a good idea. That cottage industry has now been globalized, and it appears that religion may induce more persistance or blindness than simple motives of societal revolution. Or maybe the lesson is that white men (guys?) really (not just legally) can't do WMD.

The Weather Underground explosion also pretty much convinced innocent bystanders (pretty much everyone else) that the bombmakers were turkeys. Of course, nobody had regarded the Weather Underground as an instant hazard across the United States, as we have inflated the jihadi threat today. So I guess it will take a longer string of bomber FAILs to do that.

I haven't ever worked directly with explosives, but I know people who have. The stuff is dangerous: unstable and either too hard or too easy to set off. And the consequences of a mistake, as we keep seeing, frequently are the end of the bomber's career.

Maybe I'm just too impressionable. I had a middle-school classmate who was rumored to keep a jar of nitroglycerine under his bed. He was fascinated by explosives. One day he didn't come in to school and was absent for some fairly long time. He returned with a glass eye, which had a sort of middle-school fascination, but did seem to be a downside of that jar of nitroglycerine.

Sunday, December 12, 2010


Bits and Pieces - December 12, 2010

Giant squid! Video.

I've been wanting to point this out about Obama, but it's more effective coming from a black guy. And, I'll add, you don't get civility by fighting and screaming at people.

This WaPo article about the Cancun agreement
shows one of the less attractive tics of the MSM. All about what the agreement didn't do. Jim Hoagland did the same thing with the New Start Treaty the other day. But negotiation has to start with agreement, so it just might be worthwhile to examine what the countries felt they had in common. Maybe I'll try doing that when I've got time.

Five myths about North Korea.

What Sig Hecker found in North Korea.

Jack Goldsmith on Wikileaks via Kevin Drum.

Wikileaks on Litvinenko, the Russian who was killed with a dose of polonium.

Eduard Limonov, modern Russia's most uncompromising writer and politician.

A speech by Hillary Clinton on Israel and Palestine, which M. J. Rosenberg characterizes as evenhanded.

I'd like to read some of these in more detail and comment on them, but just now I've got another engagement. Maybe tomorrow.

Friday, December 10, 2010

Bits and Pieces - December 10, 2010

Nice summary of links on the arsenic bacteria question.

This map of slavery in the South suggests the answers to a lot of questions about today's US politics.

Postcards from space.

Two Ways of Looking at the Tax Bill

Ezra Klein has provided some nice graphs on the tax bill. Different graphs emphasize different characteristics, so you can pick and choose what you want to be unhappy about. Or happy. It just seems that there are more unhappy people around, or perhaps they are just more vocal. Here's the big contrast. What Democrats get versus Republicans:

And what taxpayers of various incomes get:

Journalism is Not an Attack

Josh Mull posted some thoughts on how the Wikileaks cables and the hacking by "Anonymous" are being framed. War, attacks, bomb-throwing. Josh makes the point that if Julian Assange is going to declare "war" on governments, he shouldn't be too surprised at the response.

Here's the heart of Josh's argument:
But the problem is that war is real. Terrorists don’t leak cables, they murder people. Insurgents don’t campaign for legislation, they kill the foreign soldiers occupying their lands and the puppet governments working for them. It’s not cool to be in their shoes, it’s terrible, the worst thing you can imagine.

War, whether asymmetrical or not, is not something you want to be a part of, not something you want to support like transparency and accountability. It is instead the complete destruction of society and basic human decency. As Ursula K. LeGuin once wrote, war is the opposite of civilization.
Of course, the war metaphors have been around for a very long time. The War on Cancer of the Nixon administration may have been the first governmental non-war war, but violent metaphors have long been attractive.

They make the bearers feel that what they do is important and that it will make a difference. Unfortunately, as Josh points out, war and violence may be neither.

This kind of language probably contributes to today's political polarization. After all, war is about killing your enemies, not conciliating with them.

So maybe we should just drop the war talk, unless we're talking about real war. It will be hard, because the metaphors of violence have penetrated deep into our speech.

Thursday, December 09, 2010

Quote of the Day

Ezra Klein on the failure of DADT repeal:
The diffusion of responsibility that comes from deciding law through complex parliamentary gamesmanship rather than simple majority-rules votes is the problem.

Best Book Meme

It looks like an end-of-year meme is taking hold. So I will join in.

The best book I read all year is Tony Judt's Postwar. Read it.

That is all.

Wednesday, December 08, 2010

Yet More on Those Arsenic-Eating Bacteria

Apparently my questions (here and here) were mild compared to some that are out there.

The more I've cogitated on arsenic being substituted into DNA backbone, the more I've suspected it's highly unlikely, except for an odd one or two in an odd one or two DNA molecules. My highly-developed, highly-qualitative sense of chemistry says that arsenic bonds are more brittle and aren't going to be able to do the things that phosphorus bonds do in DNA. I've also been wondering if some phosphate hadn't crept into some of the nutrient solutions, even when they were nominally arsenate rather than phosphate. It turns out that others have been wondering the same things.

Thanks to Twitter buddy @jfleck, I've discovered Ivan Oransky's blog and the three most relevant posts, here, here, and here. Carl Zimmer summarizes some of the responses at Slate and has a continuing summary at Discover.

Oransky's blog is called "Embargo Watch," which refers to a practice in science journalism of sending out news releases that are not to be made public ("embargoed") until a certain date and time. This allows reporters to do some background digging before they can all burst out of the gate at once with their stories. More than that, it's tied to the conventions of reporting scientific information and peer review.

There is a protocol to publishing serious scientific papers. First, the paper is submitted to a journal, whose editor sends the paper to reviewers who read and criticize the paper. Then the author(s) (usually plural these days) correct the paper as necessary to get the editor to approve it and publish it in the journal. That publication date is the date to which the news releases are embargoed, because the authors are not supposed to speak publicly about their work until it has undergone the entire procedure, ending in publication.

Like a lot of things, this has become more difficult with the internet and our expectations of instant communication. In this case, word got out early that Science magazine had embargoed a NASA-funded paper, and a couple of the words that got out were "life" and "extraterrestrial." In one of the traditions of the internet, there had to be speculation as to how those words might be related and what the news would turn out to be. Oransky's links give the details.

It occurs to me that that speculation is another downside of this concept of embargo. We already have a deficit in scientific credibility incurred by news stories on medical advances that seem to cancel each other out every few months. Coffee prevents Alzheimers disease. No it doesn't. You should have regular mammograms/PSA tests. Maybe not. Blame for the deficit can be spread around. The scientists (and their funders) want to get publicity, which improves their careers and funding. The reporters may be too credulous or get stuff wrong, or both. An embargo adds that round of speculation to the material that, churned together, confuses the story.

Bits and Pieces - December 8, 2010

John Kerry gives clear responses to the Republican lies talking points on the New Start treaty.

Christmas cheer.

And Scrooge.

I'm wondering if Brazil's and Argentina's recognition of a Palestinian state will make a difference. Could, if more countries sign on.

The Democrats in Congress whine that President Obama isn't doing enough to get legislation passed. He negotiates with the Republicans, and then they don't like that. Come on, guys! You're all on the same side, remember? I am getting really, really tired of the whining and bitching by Dems. Making sausage? Art of compromise? Anyone remember those?

Indeed, the compromise could have been better. In a universe where the worst we'd have to deal with would be Blue Dog Democrats. For example, this chart:

From Maxine Udall, Girl Economist, who makes some more good points in this post.


Tuesday, December 07, 2010

Bits and Pieces - December 7, 2010

It's Pearl Harbor Day. Seems to be no big deal in the media, just like the anniversary of John F. Kennedy's assassination. I'm reading Tony Judt's Postwar, and he meditates in one of the last chapters on Europe's disconnection from history. It rang true enough for what I see in America, too. Our common past could unite us.

If we paid more attention to history, we'd see the stupidity of some of the current arguments for "less government." I put that in quotes, because the proponents seem selectively interested in reducing government. Quite unambiguously along the lines of their own financial interests. Dennis G. over at Balloon Juice has been writing about the Confederate Party, and it's hard to see where he's wrong. Ironic that the Republican Party originated to oppose the Confederate Party. His latest post is particularly well done.

And while we're on American politics, I think Michael Tomasky captures the issues around the tax compromise well. I've been thinking of writing a post on the realities of what Obama can and can't do and why it would be ultimatly stupid and self-defeating for him to pick a fight of the kind that some on the left side of the political spectrum would like to see. But I'm working on another longish post, so this will have to do for now.

The latest round of talks with Iran seem to have gone about as well as can be expected. Nobody's saying much, which means that maybe all have decided that they are engaged in serious negotiations rather than political theater.

And Estonia has finally turned up in the Wikileaks documents. No big surprise, like so many of the "revelations." The Guardian has a nicely detailed description of the defense plan for Poland and the Baltic States and how it was presented to Russia. That's what diplomacy is about.

Speaking of Estonia, I'm listening to Klassikaraadio and getting serious about my competency in Estonian in preparation for a trip this summer. If you want to listen, "Kuula reaalajas" is the button to click. "Listen in real time."

Sunday, December 05, 2010


Unspoken Nuclear Weapons

This degree of toadying clearly poses problems for the Americans. The dispatches repeat genuine appreciation of Britain's unique loyalty as an ally. But LeBaron was typically shrewd to call this behaviour "corrosive".

The American diplomats are smart enough to know that buttering up the Americans is a routine which incoming British leaders think they have to perform, and that most of them privately resent it. They do it largely for reasons the state department understands only too well. Britain's "independent" nuclear deterrent flies the threadbare rags which are all that remain of the United Kingdom's lost "Great Power" status. But its manufacture and use are in reality dependent on the supply of American technology and American strategic decisions.
More here.

One might expect the United States to find an arsenal consisting of an estimated 200 nuclear warheads worthy of notice. One might also expect Israelis to take comfort in the knowledge that, alone among nations in the region, they hold at the ready such massively destructive power. Instead, Washington pretends that the Israeli arsenal doesn't exist, thereby opening itself to charges of entertaining a double standard. Meanwhile, Israelis nurse feelings of vulnerability as if the Jewish state were still David surrounded by a host of Goliaths.
And here.

It was easy to believe, once the Soviet Union dissolved, that we didn't have to think about nuclear weapons any more. But they lurk in the back of most international relationships.

More to say about this, but I don't have time just now.

The Russian Military Machine

Russia recently tried to put some new GLONASS navigation satellites into orbit. They've come back down again.

There are a number of ways that this might be spun. One is that this shows that the Russian military machine is becoming so degraded that we don't need no stinkin' treaties. We can just watch them going down the drain.

Another is that this degradation of the military machine is precisely what makes the Russians so suspicious, because they are losing their capability to know what the United States is doing. This, along with their belief that antimissile emplacements in Europe might be used against them, is part of the basis for their desire for treaties. They are willing to share some of their data if we'll share some of ours.

The first spin, of course, is the triumphalist stand that some, Republicans in particular and neocons very specifically, prefer. The problem with it is that Russia still has a fair bit of military might: they can still put their Bear bombers up in the air with nukes, and if a Proton-M with nuclear warheads fired in anger came down in the wrong place, well, so be it. Frightened and suspicious people, outside of communications, can be unpredictable (cf. North Korea).

Alternatively, the current rather rapid decline of Russia's military machine is something we might want to keep closer tabs on via the inspections New Start will provide and something that we don't want Russia to get too upset over. So transparent mutual declines in armaments, via treaties, keep the sides balanced and Russia not quite so frightened and suspcious.

The second course makes a lot more sense to me. And I have to say that I'm surprised at this significant failure while encouraged by Russia's willingness to announce it.

Saturday, December 04, 2010

More on Those Arsenic-Eating Bacteria

I wrote my earlier post after cursorily reading a few of the news articles on those arsenic-eating (not arsenic-based!) bacteria. The questions that have come up inspired me to take a closer look. My main purpose in the earlier post was to recall some similar experiments that I had been close to.

I haven't read the full paper yet. I am usually satisfied to read the dead-tree version of Science magazine, and that won't be here for a few days yet. The paper is available on line, and I have an irrational aversion to registering for sites, especially when that registration failed, something that happened with Science some long time ago. Maybe I'll make a second try later today. The abstract and supporting online material are available, however, and they answer many of my questions while raising a few others.

This post summarizes the science nicely. A number of good questions are also raised in The Guardian's blog on the story. It appears that very little arsenic was incorporated into the bacteria's essential biochemistry. So I won't be seeing the fully-arsenic-substituted DNA any time soon. Not that I expected that.

Arsenic and phosphorus are probably more similar than any two up-and-down pairs of main-group elements in the periodic chart. That allowed the researchers to substitute arsenate for phosphate in the nutrient solutions. Even so, the bacteria bloated up, just as the algae did in deuterated water, a sign of stress. The bacteria would already have had mostly phosphorus in the places where phosphorus should be, with perhaps a few odd arsenic atoms substituted because they had grown up in the very bizarre environment of Mono Lake. The analyses of where the arsenic went are not totally unambiguous, and they show relatively little arsenic substituted for phosphorus at best.

So all the life we know about still consists primarily of carbon, oxygen, nitrogen, hydrogen, sulphur and phosphorus. Arsenic has not been shown to be able to function in the same ways phosphorus does, nor to be able to substitute completely for phosphorus in life containing all those other elements. For similar periodic-chart pairs, carbon-silicon interchange just isn't likely. Silicon can't do all the things carbon can, and its compounds have a nasty habit of being much more mineral-like than carbon's. Oxygen-sulfur is already in the group, although sulfur does different things in biochemistry than oxygen. Selenium has some trace functions. Substitution? Maybe, but probably not important. Nitrogen-phosphorus is part of the life elements, although, again, the functions are different. And we're looking at arsenic.

So, from the abstract,
Exchange of one of the major bioelements may have profound evolutionary and geochemical significance.
Um, yeah. If there's significant exchange, and not just tolerance of the occasional weird atom in an otherwise normal biochemical compound. The evolutionary significance is that extremophiles, the weirdos of the bacterial world, can grow to tolerate arsenic. If you take a chemical rather than a literary view, that's not too surprising because of the periodic-chart relationships I've been talking about. The evolutionary significance is that bacteria can evolve, which we knew anyway. And, in response to anonymous's question, 10,000 years is a long time in bacterial evolution. In just a few decades of antibiotic pressure, we've managed to evolve antibiotic-resistant bacteria. So living in an increasingly saline/arsenical environment could definitely improve tolerance of arsenic.

The Guardian blog has an example of what I think is going too far:
The microbe seems to be able to replace phosphorus with arsenic in some of its basic cellular processes — suggesting the possibility of a biochemistry very different from the one we know, which could be used by organisms in past or present extreme environments on Earth, or even on other planets.
Here's my correction:
The microbe seems to be able to replace phosphorus with arsenic in some of its basic cellular compounds - which could mean that arsenic is involved in cellular processes in place of phosphorus or that it is an obstacle that the microbe has found ways to work around.
I know, mine isn't as exciting.

Friday, December 03, 2010

Bits and Pieces - December 3, 2010

The Death Panels are here - and they're Republican.

How civil political discourse threatens modern conservatism. Or, reality has a liberal bias.

Jeffrey Lewis tries to make sense of the Wall Street Journal's claims of Russian tactical nuke threats. Hint: what I said the other day isn't too far off, but Jeffrey goes into much more detail.

Are We Seventeenth-Century Poland?

Kevin Drum quoting Senator Jeff Merkeley (D-OR):
What's more, the filibuster isn't just a way of requiring 60 votes to pass legislation. Rather, "the filibuster can be thought of as the power of a single senator to object to the regular order of Senate deliberations, thereby invoking a special order that requires a supermajority and a week delay for a vote."
Later, with the rise of power held by Polish magnates, the unanimity principle was reinforced with the institution of the nobility's right of liberum veto (Latin for "I freely forbid"). If the envoys were unable to reach a unanimous decision within six weeks (the time limit of a single session), deliberations were declared null and void. From the mid-17th century onward, any objection to a Sejm resolution — by either an envoy or a senator — automatically caused the rejection of other, previously approved resolutions. This was because all resolutions passed by a given session of the Sejm formed a whole resolution, and, as such, was published as the annual constitution of the Sejm, e.g., Anno Domini 1667. In the 16th century, no single person or small group dared to hold up proceedings, but, from the second half of the 17th century, the liberum veto was used to virtually paralyze the Sejm, and brought the Commonwealth to the brink of collapse. The liberum veto was finally abolished by the May Constitution of Poland in 1791.

Thursday, December 02, 2010

Arsenic, Phosphorus, Not Such a Big Difference

I'm not as impressed as I guess I was supposed to be with this news, and certainly not as impressed as the New York Times headline-writer.
Subsisting on Arsenic, Microbe May Redefine Life
Yes, we don't like arsenic because, as Dennis Overbye nicely explains in that article, it's a lot like phosphorus chemically, phosphorus is essential to life as we know it, and arsenic is enough not like phosphorus to get into its place and bollix things up.

However, poultry farms feed arsenic to chickens, which seems to improve their growth. Lots of things, like selenium, which had a run in health-food stores a while back, may be essential to life in small amounts and damaging in larger amounts. That's even true of iron. So the "poison" label on arsenic isn't that important chemically, although it has a lot of resonance in literature.

But the reason I'm not impressed is that I've seen something very much like this before, up close and personal, my very first introduction to chemical research. Or official chemical research, anyway. I did a bunch of things earlier on my own.

I worked in Harold Strain's laboratory at Argonne National Laboratory. Harold was one of the most skillful separator of plant pigments in the world. He used big (a couple of feet high by a few inches across) columns of packed confectioner's sugar. The plants were mashed up, extracted with light petroleum ether (boils in the palm of your hand), and adsorbed on the column, "developed" with additions of alcohols to the solvent, and then sculpturally scraped, sugar and all, out of the column by color and re-extracted from the sugar. The process typically gave a few milligrams of each pigment. Spinach was a good starter material for the standard pigments.

Those were the days when differences among isotopes were a big deal, nuclear magnetic resonance was new, and it looked like it might give more information about the processes by which chlorophyll converts light into chemical energy. If you had normal chlorophyll and chlorophyll with deuterium everywhere that normal chlorophyll had a hydrogen. Then you could use NMR to watch particular deuterium atoms exchanging with hydrogen atoms and get some of the kinetics.

Deuterium is an isotope of hydrogen. Whereas arsenic is below phosphorus on the periodic chart, deuterium shares hydrogen's box. But, because hydrogen is the lightest element, deuterium is approximately twice as heavy as hydrogen, a much bigger mass difference than between arsenic and phosphorus. This mass difference makes some difference in the chemical reactions of hydrogen and deuterium, although phosphorus and arsenic have greater differences. Further, deuterium is very uncommon, about 150 atoms in a million hydrogen atoms. So how does one go about obtaining chlorophyll with 72 deuterium atoms in place of its hydrogen?

The way it was done by Joseph Katz at Argonne was to grow algae in deuterated water, also known as heavy water, commonly used in certain types of nuclear reactors, and certainly, at that time, used in nuclear research. As Joe told it, the algae didn't like it at first, and got sort of fat and bulgy, a few died, but most eventually settled down and looked pretty much normal. But their chlorophyll was deuterated.

So Joe's lab grew the algae, and then dried and processed them to get a separable extract, which Harold then put on his sugar columns. The deuterated pigments were sealed into glass tubes under vacuum, to be opened for the appropriate experiments. We speculated on how much per pound those pigments were worth. A lot, but not many potential buyers.

Algae are bigger, with more enzyme systems and biochemical conversions than the arsenic-based bacteria. It's probably even up as to difficulty for the little guys to survive in such alien media, though. Which aren't nearly as alien as what other planets have to offer. They're still carbon based. And some of us have seen something very much like that before, although it was a long time ago.

If you google "algae deuterium oxide", you'll find a fair number of publications from Katz's group. Apparently Argonne is still growing stuff in deuterated water. And I think there's a black and white video of me talking about what I was doing in Harold's lab somewhere out there on the intertubes, although I couldn't find it with a quick google.

Update: And we have to add in XKCD's contribution. (h/t to @jfleck)

Further update: More here.