Some people spend their holiday vacations catching up on reading, or spending time with relatives. I like to take a day and devote it to fixing up my web pages, which tend to get sadly neglected over the year. (The erratum page for my book is embarrassingly out of date, I really should fix that.) This year I sat down and made a list of my favorite blog posts ever, from the heady and innocent days of Preposterous Universe to the practiced maturity of the blog you see before you today. Actually I tended more toward the “potentially useful” than simply my favorites. I think the Anatomy of a Paper series was the best of this year — much of my recent blogging has been of the short throwaway variety, but occasionally I work up the energy for something more substantive.

Interestingly, I still don’t know what to think about blogging in general. I read them all the time, and can’t seem to stop myself from posting even when things get busy. (It’s the quality that deteriorates, not the quantity, it seems.) But the technology is still quite new by any sensible standards, and the kinks have yet to be worked out. In the blogs I read, there seems to be some degree of shaking-out going on — the more successful blogs are ones where there are at least a couple of posts every day, and that’s a hard rate to keep up. It either means that you become a professional blogger, or at least a semi-professional for whom blogging takes up a majority of your attention. (As already admitted, I can’t seem to stop blogging, but at the same time I can’t really imagine devoting more than half an hour a day or so to the practice.) And very few people, of course, have quite so many novel and interesting things to say, so we find a lot of repetition or reacting to stories generated elsewhere. Some of the more casual and informal voice of the earlier days may be being lost. There’s no necessary reason for this, given the easy access to newsreaders like Bloglines or Google Reader — one could certainly imagine subscribing to an eclectic collection of provocative and unpredictable bloggers who only post a few times per month. But how do you find them? I think there’s a great opportunity out there for clever aggregators, who can figure out an efficient way to collect the best of what is already going on throughout the blogs and bring it to the appropriate readers.

Science blogging, I think, still has yet to find its comfort zone, despite the growing numbers of impressive science bloggers. There are important questions about how to you conceive of your audience, the best way to conduct research discussions in a public forum, and how to deal with comments generally. We’ve talked a little bit about this before — here, here, here — but I think this is a conversation that is very much ongoing. A sadly effective demonstration of the difficulties can be found in the Garrett Lisi thread, where everyone (including me) got snippy and annoyed at everyone else. The real problem there, in my judgment, was not the occasional bits of rudeness or nonsense, but the insistence on responding to the rudeness and nonsense, making the thread about the meta-conversation instead of sticking to the actual conversation. It’s pretty elementary internetology that the best way to deal with low tone is to raise the tone by being relentlessly high-minded, but that’s a strategy that requires almost everyone to go along for it to work. Or to have someone who is willing to spend their time carefully moderating hundred-comment threads, which our blog doesn’t have. Of course we could be very dramatic, requiring that commenters register, or disallowing anonymity entirely. Those sound like drastic steps that would likely change the feel of the blog beyond recognition. In any event, we’re still trying to balance our goals of conducting interesting conversations about ideas in a public forum, without actually spending much time on it — we’ll see how it goes.

And we have a Facebook group. Still don’t know what to do with that, but it’s great to see pictures of some of our regular readers. Happy New Year to all!

A few internet tidbits to keep you going through the intra-holiday blogging lull.

• The World’s Smallest Website! Seriously, this website is not only extremely small, it probably has a lot more interesting stuff than yours does. You should be ashamed.
• How interesting is your IP address? Mine is prime, which is nice, but it makes a terrible poker hand.
• Cosmic Variance Calculator. Sometimes, you just want to calculate your cosmic variance. By Michele Trenti, based on this paper.

Back when my oldest kid was 2.5 and planning her Halloween costume (a guaranteed-to-terrify “pink monster princess”), she pointed out that “last year, I was the one who was scared, but this year, I’m going to scare both those guys!”. I knew that one of the guys had to be our neighbors’ friend Pete, who’d unknowingly traumatized her with a rather horrific mask the previous year, but I was stumped about the other. I asked who the “two guys” were, and she replied, “Pete…and SANTA”.

Her relationship with Santa has thus always been, well, complicated. She’s fascinated, and troubled, and yet remains devoted to the idea of Santa. As she nears 7, she oscillates between a deep suspicion that her parents are somehow complicit and a joyful hope that Santa is as real and bountiful as he’s always been (with the latter state taking the lead as Christmas morning approaches). Over the last year, I watched her pragmatic, rationalist core battling the idea of a magical figure who somehow figures out the ultimate just-in-time logistics delivery problem, and I thus was not sure that her belief in Santa was going to survive till December. It did, but with an increasing number of tests and conditions, as she remembered what Santa’s handwriting looks like, and is sharp enough to notice if Santa uses any familiar wrapping paper.

The reason that she couldn’t quite give up Santa yet is simple. At this point, Santa makes her happy. Deeply, contentedly happy. On some level she knows that the mechanics of Santa go against everything else she understands about how the world operates. And yet, the idea that there is still a little bit of magic that might operate in her very own life makes her giddy.

As adults, even the most rational of us sometimes make small concessions to that joy in letting ourselves believe in something wonderful, but not sensible. When I bowl, I firmly believe that absurd amounts of body english after the ball has left my hand are key to keeping the ball out of the gutter. I obviously “know” that this can’t possibly help, but it makes me really happy to indulge my belief that it does. I have friends who have chants that will make parking spaces open up, who carry umbrellas to prevent it from raining, or who have magical articles of clothing that are critical to the success of their favored sports team. All of these beliefs are obviously absurd, but satisfying nonetheless.

Which in the end, is why I typically stay out of the God vs the Atheists discussions in the blogosphere. I am soft enough of heart to take no pleasure in trying to argue people out of something that makes them deeply happy. I find no evidence for what they believe, and I profoundly disapprove of any attempt to institutionalize those beliefs beyond an individual church/synagog/mosque, but I just cannot build up a big head of steam to fight against individuals’ believing in something that helps them cope with life’s frustrations, tediums, and cruelties. I am not blind to the evils that have been visited upon us in the name of organized religion. Yet, individually, there are many people whom I value and love who also take comfort from believing in God. Individually, their belief causes no harm to anyone. They still support teaching of evolution in schools, and don’t abandon free will in favor of waiting for God’s Will to be manifest. They will still be friends with a godless heathen like myself. While this “mostly harmless” manifestation is not true for all religious individuals, it dominates in those that I know personally, making me loathe to engage in sweeping criticisms of theists, even while I struggle with concerns about the impact of invasive institutionalized religion.

I won’t defend my tolerance with well-reasoned arguments, since I have none. Other writers and readers of this blog have given this topic far more rigorous thought than I. Instead, the tolerance grows out of the same inkling that it would feel a bit small for me to take away my daughter’s belief in Santa before she was ready to stand without it.

Have a peaceful holiday, everyone. If you’re not feeling especially peaceful, perhaps this bit of groove from Rosko Mercer can help you along.

Audio and artwork via the Love Unlimited sound system.

Atrios is right, this is pretty amusing:

“Who is your favorite author?” Aleya Deatsch, 7, of West Des Moines asked Mr. Huckabee in one of those posing-like-a-shopping-mall-Santa moments.

Mr. Huckabee paused, then said his favorite author was Dr. Seuss.

In an interview afterward with the news media, Aleya said she was somewhat surprised. She thought the candidate would be reading at a higher level.

“My favorite author is C. S. Lewis,” she said.

If Aleya had been keeping up with blogs, she would have been less surprised at Huckabee’s reading level.

Lurking behind the debate over the high energy physics budget is a meta question that rarely gets addressed head-on: in a world with many things that we would like to do, but limited resources to do them, how do we decide what questions are interesting enough to warrant our attention? This question arises at every level. If we have a certain number of dollars to spend on particle physics, how much should go to the high-energy frontier and how much to smaller-scale experiments? Within fundamental science, how much should go to physics and how much to biology or astronomy or whatever? And it’s not just money: within a university, how many faculty positions should go to historians, and how many to archaeologists? Within philosophy, how many logicians do we need, and how many ethicists? It’s not even an especially academic question: which book am I going to bring with me to read on the plane?

There are a number of issues that get tied up in such considerations. One is that certain activities simply require certain resources, so if we judge them sufficiently interesting to be pursued then we need to be prepared to devote the appropriate resources their way. A colleague of mine in condensed-matter physics was fond of complaining about all the great small-scale physics that his community could do if they only had half of Fermilab’s budget. Which is undoubtedly true, but with half of Fermilab’s budget you wouldn’t get half the science out of Fermilab — you wouldn’t get anything at all. If that kind of particle physics is worth doing at all (which is a completely fair question), there is an entry fee you can’t avoid paying.

But more deeply, the problem is that there is no intrinsic property of “interestingness” that we can compare across different academic questions. Questions are not interesting in and of themselves; they are interesting to somebody. If I happen to not be interested in the American Civil War, and a friend of mine thinks it’s fascinating, that doesn’t mean that one of us is “right” and the other “wrong”; it just means that we have different opinions about the interestingness of that particular subject. It’s precisely the same kind of personal decision that goes into preferences for different kinds of music or cuisine. The difference is that, unlike CD’s or appetizers, we don’t consume these goods individually; we need to make some collective decision about how to allocate our intellectual resources.

People pretend that there are objective criteria, of course. The standard battle lines within physics are drawn between research that is “fundamental” and research that is “useful.” I was once in the audience for a colloquium by Steven Weinberg, back in the days when we were still planning on the Superconducting Supercollider, and he was talking about why particle physics was worthy of substantial investment: “People sometimes object to the way we speak about particle physics, objecting that we give the impression that it’s more `fundamental’ than other fields. But I think it’s okay, because … well, it is more fundamental.” Contrariwise, I’ve heard condensed-matter physicists wonder with a straight face why anyone in the general public would be interested in books on string theory and cosmology. After all, those subjects have no impact at all on their everyday lives, so what is the possible interest?

In reality, there is no objective metaphysical standard to separate the interesting from the uninteresting. There are a bunch of human beings with different interests, and we have the social task of balancing them. A complication arises in the context of academia, where we don’t weigh everyone’s interests equally — there are experts whose opinions count for more than those on the streets. And that makes sense; even if I have no idea which directions in contemporary chemistry or French literature are interesting, I am more than willing to leave such questions in the hands of people who care deeply and have contributed to the fields.

The real problem, of course, is that sometimes we have to compare between fields, so that decisions have to be made by people who are almost certainly not experts in all of the competing interests. We have, for example, the danger of self-perpetuation, where a small cadre of experts in an esoteric area continue to insist on the importance of their work. That’s where it becomes crucial to be able to explain to outsiders why certain questions truly are interesting, even if the outsiders can’t appreciate all the details. In fundamental physics, we actually have a relatively easy time of it, our fondness for kvetching notwithstanding; it’s not too hard to appreciate the importance of concepts like “the laws of nature” and “the beginning of the universe,” even to people who don’t follow the math. Making a convincing request for a billion dollars is, of course, a different story.

Sadly, none of these high-minded considerations are really at work in the current budget debacle. High-energy physics seems to be caught in a pissing match between the political parties, each of whom wants to paint the other as irresponsible.

The White House and congressional leaders exchanged barbs Tuesday over who was to blame for the Fermilab impasse. Lawmakers said the Bush administration’s tight overall budget targets tied their hands, while a spokesman for Bush’s Office of Management and Budget said the Democratic leaders could have met the targets by cutting back on other discretionary elements of the budget.

Durbin said the $196 billion required for the wars in Iraq and Afghanistan left little room for budget maneuvering.

“We were left with stark choices: reduce funding for high-end physics or cut money for veterans; reduce spending at Fermilab or eliminate funding for rural hospitals,” Durbin said in a statement Tuesday.

Sean Kevelighan, a spokesman for the administration’s Office of Management and Budget, said Congress could have chosen instead to take more money from the $9.7 billion worth of earmarks designated for lawmakers’ projects.

“The choices were up to the Congress,” Kevelighan said.

As annoying as academia can be, politics is infinitely worse.

The news from Capitol Hill this week is terrible. Congress has finally passed an omnibus spending bill for Fiscal Year 2008 – this is a bundled package of 11 appropriations bills that fund the operation of our government. The House of Representatives passed the bill on Monday, the Senate on Tuesday, and now it is being prepared for the President’s signature. We have been under a continuing resolution since 1 October, 2007, which is the start of FY08, and had been welcoming the end of the stand-off between Congress and the President so we would have an actual budget for the year. That was last week. This week, we wish we could be funded via a continuing resolution all year long, just like last year.

In short, this omnibus spending bill is at best disappointing, and at worst a total disaster, for science funding in the US. Overall, the research agencies all received a meager increase in their budgets (roughly 1% for NIH, 2% for NSF, 3% for NASA, and 2% for the DOE). That’s disappointing because these increases don’t keep up with inflation, are far, far short of the Administration’s request and the American Competitiveness Initiative, and won’t support all the scientific projects in the pipeline.

The disaster occurs in two specific areas, Fusion Energy Sciences and High Energy Physics, which are targeted for deep, roughly 10%, cuts. The cut in fusion research comes about because the bill provides zero funding for the US contribution to ITER. Let me remind you that ITER is the large international fusion reactor that is currently being constructed in France and is funded by international treaty. The US has signed that treaty and was set to contribute roughly $160 M this year. Apparently Congress just doesn’t understand that there are serious ramifications in backing out of an international treaty. Even one dedicated solely to science projects. This jeopardizes future international projects and provides yet further proof that the US is not a reliable partner. I imagine that the DOE Office of Science will find a way, somehow, to restore funding to ITER.

For High Energy Physics, well, the situation is dire, and I am not exaggerating. The numbers are:

This is a reduction of $63.5 M from FY07 and $94 M from the President’s FY08 request. The language specifically targets NovA (a neutrino facility under construction at Fermilab) and the International Linear Collider:

Within funding for Proton Accelerator-Based Physics, no funds are provided for the NOvA activity in Tevatron Complex Improvements. Within Advanced Technology R&D, in the current constrained environment and without a Critical Decision 0 by the
Department, only $15,000,000 is provided for International Linear Collider R&D and $5,455,000 for Superconducting RF R&D.

Since we are already 3 months into FY08, we’ve already spent this much on the ILC and have put money into NOvA.

So, WTF do we do? Even though the $63.5/94 M shortfall is targeted at projects, it’s important to recall that most of this money is spent on salaries. Not equipment or fancy gizmos, but people. Basically, there are two extreme choices on how to handle the shortfall: shut down all of our operating facilities now, today (yesterday would have been better) and halt science output from the US, or fire $63.5 M worth of people. Don’t ask me how you accomplish the latter. The final solution will clearly be a mix of the two. The young physicists, grad students and post-docs, will be hurt the most as funding for those positions will dry up first. Next come the folks who work at National Labs. We’re going to have to start a discussion about closing and consolidating labs.

It will take a little bit for the DOE, lab directors, project managers, advisory panels, etc to formulate a plan, but no matter what they decide, the consequences of this budget shortfall will be drastic and will be felt for years to come. Our science output will be reduced and we will lose good people with valuable talents.

Oh, and just so folks can calibrate, the countries in the European Union spend about $2 B/year on High Energy Physics, roughly $1 B for CERN, and another billion in individual grants. Germany alone has just infused its total science funding with an additional $2 B Euros. The US continues to fall further and further behind.

It has been a dodgy couple of days for news about my part of England.

Yesterday I watched with pride as my hometown football team - Wigan Athletic - scored three goals in the first half against Blackburn. This then turned to horror as they conceded three, with my pride eventually recovering after they pulled a couple back for a scrappy 5-3 victory (first in thirteen games).

Then (via PZ) I find out that the same type of creationist nonsense that we’re forced to waste time and effort fighting in the U.S. is rearing its empty head in England, and in Lancashire no less! As the Observer reports

The AH Trust, a charity set up last year by a group of businessmen alarmed by the direction in which they see society heading, has identified a number of potential sites in the north west of England to build the £3.5m Christian theme park.

The trust claims it already has a number of rich backers who are keen to invest in the project, which will boast two interactive cinemas, a cafeteria, six shops and a television recording studio, allowing it to produce its own Christian-themed films and documentaries.

Oh the horror! What is going on in my home country? And this isn’t just a place to churn out rip-offs of The Passion of the Christ; they have other issues

‘The church in this country is in crisis and many church leaders living in Australia, America and Canada have openly proclaimed that God has left the church in England,’ the trust states on its website.

‘Evolution has falsely become the foundation of our society and we need the television studio to advocate Genesis across this land in order to remove this falsehood, which presently is destroying the church foundation.’

It just brings tears to my eyes. But I’ll end on a note of pride. Even better than Wigan breaking their losing streak at football is to read this about your hometown

The theme park’s anti-evolution bias and its emphasis on Genesis has raised eyebrows among planning officials, according to Jones, who originally wanted to build the park at the site of an old B&Q store but was refused permission by the council.

‘Wigan council slammed the door in our faces. You mention the C [Christian] word, and people don’t want to know,’

It just warms your heart doesn’t it?

‘Tis the season to file your grades, and in that holiday spirit, I present to you my tried-n-true method for normalizing scores for different TA’s in a large class.

The problem is this: When you teach a 300 person class, you typically run it with a single lecturer and multiple TA’s handling sections. The students do labs and problem sets, which are graded by the TA’s. However, not all TA’s are equally benevolent when it comes to grading, which can lead some sections to have lower scores than they should. On the other hand, not all sections are equally on the ball, so maybe their low scores are exactly what they deserve. So, how do you tell the difference between a TA who graded more harshly than average, and a TA that was stuck with somewhat dimwitted students?

The key is to use the exams, which are taken by all the students. Presumably, a student that does well on the exam is probably sharp enough that they did well in their problem sets and labs. Thus, if that student has a lower than expected section score, then there is a chance that too many points were taken away by the TA, compared to the average TA. So, the trick is to make a plot of the student’s section grade divided by their exam grade, ranked by exam grade. When you do so, you’ll find a well-defined sequence which goes towards 1 at the high end (i.e. those top-notch students who ace everything). I tend to make the section work easier than the exams, so for me this ratio goes to larger values for lower exam scores, but another instructor who gives tough assignments but puffball exams might find the opposite. There is a scattering below the main sequence, due primarily to students who did not turn in all their assignments. TA’s who readily accept late assignments tend not to have this tail.

So, if you have a TA who takes off more points then average, you’ll find that all their section points lie below the main trend, particularly at the low-scoring end, where lots of points were taken off. You can see the effect whether or not the TA’s sections were dimmer than average or brighter than average. The plot on the left shows the section-to-exam ratio for the class as a whole (open circles) and one particular TA (solid circles), whose points clearly fall below the mean trend (click on the image for a larger, more readable version):

You can then easily scale the points taken off by some factor to correct them back to the typical TA. Note that it’s critical to do this scaling on the points taken off, not the points earned, because you don’t want to penalize the students who got everything correct; presumably they’d get everything right no matter how tough the TA was. The plot on the right shows what happens to that same TA’s scores after rescaling the points taken off to reflect the kinder-and-gentler average TA. As you can see, it jumps right back onto the mean line.

Pretty cool, huh? You may now go back to your regularly scheduled grading.

I promise I didn’t rig our informal poll, but I won’t pretend that I didn’t like the results. I would have guessed ahead of time that most of the votes would go to Democrats, and most of those would go to Barack Obama, but the margins in both cases were larger than I had anticipated.

The most amazing thing is that Obama actually has a chance of winning this thing. While Hillary Clinton still has a substantial lead in meaningless national polls, Obama is leading in Iowa among likely caucus-goers, 35% to 29%; he is surging ahead in New Hampshire; tied in South Carolina; and could sweep all four early early contests.

There’s still a lot of time (although Iowa is only three weeks away), many chickens remain unhatched, etc. — standard disclaimers apply. And there is that little thing called the general election (where Obama is handily ahead of the Republican field). Still: there is a realistic chance that Barack Obama could be our next President.

But I don’t think that possibility has quite sunk into the national consciousness just yet. In particular, I think there is a moment yet to come when America sits up and says: “Holy crap, we could have a black person as the President of the United States!” For better or for worse — some people will be exhilarated, some will be appalled, some will be scared, some will cry tears of joy. Many pundits will say stupid things, many nasty smears will characterize the campaign. But regardless, it’s hard to exaggerate how extraordinary such an event would be — twenty years ago, a small percentage of political observers would have suggested there was a realistic possibility for an African-American to be elected President by 2050, much less 2008. The history of blacks in the U.S., with the legacy of slavery and the ubiquity of racism and the persistence of poverty, is almost too sprawling and complicated and emotional for any person to really grasp. It would not be hyperbole to describe the election of an African-American President as one of the most significant events in the history of the country.

There are plenty of valid criticisms to make about Obama, he’s certainly not perfect. It would be nice to have a real mandate for universal health care, for example. And, as historic as it would be, the fact that he is black is by itself not a very good reason to support him — having the first black President be a disaster could set the cause of racial justice back many decades. But even if he were a more typical Democratic presidential nominee — you know, a bumbling white Northeastern male who doesn’t use contractions — he would still be a great choice for President. He combines unusual clarity of vision with impressive legislative chops. The major Democratic candidates are not really that different in terms of policy platforms, so the question rightly becomes one of attitude and judgment — who do you want in charge the next time some completely unanticipated event affects the country? I don’t think I’ve ever been so happy to support a candidate.

Who knows? Obama’s campaign could suddenly go up in flames. Or he could get elected President and be terrible; these things are hard to predict. But if he does get elected, the magnitude of the event and what it means for America is difficult to overstate. We’ll have to see what happens.