Celebrating a new linux user!

Today, the linux world has a new member. A student with whom I work received a linux laptop today, a great little machine from System 76 [1]. In celebration of the open-source goodness of linux, I list a few of my favorite applications and plugins for linux and open-source software.

  • OpenOffice.org 2.0: MUUUUUUUUCH better than OpenOffice 1.0, which drove away an entire generation of physicists it sucked so bad. While we can never replace LaTeX in the scientific community, the drag-and-drop ease of OO.org 2.0 makes rapidly assembling talks very simple. They also look darn good, once you realize that the key to good slide design is STYLES, STYLES, STYLES. Here are a few OO.org 2.0 tips for physicists: to get some simple Feynman diagrams for your slides, download Orhan Cakir’s .doc file with some diagrams embedded in it, which you can use in your own documents: http://science.ankara.edu.tr/~ocakir/PSFDO_v1.tar.gz. When using the equation editor, remember that “%” is just like “\” in LaTeX, so to make a Greek character like “\alpha” use “%alpha”. Need to do an exponent? + and – are operators in the editor, and expect arguments on either side. To do something like 10^{-4}, you need to do one of the following: 10^{{}-4} or 10^{“-“4}.
  • Plugins for Firefox: Firefox is great because it can be extended by the user, for free. I recommend the following plugins: AdBlock, for stripping banner ads out of pages; ScribeFire, for remote editing of a blog; Download Statusbar, to get rid of that f&@#ing annoying pop-up download window; Sage, for reading RSS news feeds; and Session Manager, for more intelligent saving of the state of your browser, for easy recovery after a crash.
  • Claws Mail: Once called “Sylpheed-Claws”, because it was the cutting edge CVS branch of the stable “Sylpheed” e-mail client, Claws Mail is the mature end result of the “claws” development effort. Using the GNOME-style widget set, it’s super-fast, supports POP, IMAP, and local mail, and has a suite of plugins for syncing with a pocket PC, training a Bayesian Spam Filter, viewing postscript files inline in the e-mail. This is perfect for physicists. In Ubuntu, it’s still called “sylpheed-claws”. I recommend “sylpheed-claws-gtk2” for a better-looking client.
  • Trick out your desktop! Find tons of themes for KDE or GNOME at http://www.kde-look.org and http://www.gnome-look.org. Want sweet rendered images? Checkout my old favorite: http://digitalblasphemy.com/freegallery.shtml.

Enjoy these picks, new users everywhere!

[1] http://www.system76.com/

Science without Ethics, Ethics without Religion, Religion without Science

At one of the first Republican Presidential candidate debates, three of the contenders raised their hands when asked if they do not believe in evolution. These were Tom Tancredo, a Congressman from Colorado, Senator Sam Brownback, and former Governor Mike Huckabee. Since then, they’ve been clarifying their position [1]. This is not a surprise – they weren’t allowed at the debate to “take a position”, merely raise their hands if they didn’t believe. That’s not debate, and that format is insulting to the intelligence of Americans. Putting that aside, all three have said that their positions are compatible with science.

However, it’s interesting to ask what they mean by “science”. What do they think “science” means? Science is, at its most functional essence, a process by which a hypothesis is posed, an experiment is conducted to collect data about the natural world, and that data is used to test the hypothesis.  Huckabee feels that his belief in scripture is not in conflict with science, which is good because they really seem to be two things that have little to do with one another. Science is a process, while scripture is a collection of stories which have passed through many human hands and purport, though it has been translated, re-translated, and miscopied, to be the “word of God”. Scripture relates to a personal belief system, while science is a common practice by which facts about the natural world can be established. Trying to force science into personal belief, or personal belief into science, cheapens both.

One thing I thought was very telling about a person like Huckabee was the following paraphrased statement: “Huckabee argues that voters don’t care about evolution — they ask about things like gas prices, health care, college tuition and Iraq.” [ibid.] This statement already shows the short-sightedness of this kind of politics. In fact, evolution has a direct bearing on many of these things, because evolution is a general framework for understanding how new forms arise from old ones, how environment influences development, how social order is established. Another way to read this statement, which has even more dangerous implications, is that voters don’t care about science. In that case, all four of the above have something to do with science.

What do I mean by this? Well, gas prices are connected to energy policy, and a sound energy policy makes efficient use of existing resources, invests money in R&D for future resources (some of which may not pay off), and provides incentives to adopt existing alternative energies. Certainly, good science and good policy go hand-in-hand on this one. Health care, and in particular the development of new drugs for solving common but “non-sexy” diseases, are directly related to evolution. The challenges faced by this nation as relates to obesity (diabetes, etc.), diseases of aging (which have a huge relevance to the baby boomers), and re-emerging diseases (TB, for instance), can only be addresses by a society committed to the principles of evolution. As for college tuition, how can you have a society committed to the principles of evolution if you cannot educate them? And as for Iraq . . . well, if more of an actual honest process, and a review of the process, had been applied to the motivation for the war, maybe we wouldn’t be up to our hips in this quagmire.

Today, as I was browsing in Barnes and Noble, I saw Sam Brownback’s book, “From Power to Purpose”.  One chapter (“Miracles of Science”) dealt with science. I thought that one of the passages in that section was very telling not only of Sen. Brownback’s understanding of science, but also religion. At one point, he said that there are people out there who don’t think that ethics should have anything to do in the practice of science (who are these people, I wonder?). He then immediately talks about religion as ethics, as if religion is the only thing that informs ethics. This all suggests that Brownback lacks both an understanding of science and a deep reading of scripture. I find it fascinating that evolution is an example from science which begins to give us a basis for ethics that doesn’t come from an old book. It teaches us that in systems based on cooperation (like a society), there is a benefit to those who would cheat (for instance, be lazy and let the others in the society do the work) but that benefit is limited. This is because eventually the society collapses (too many cheaters) or backlashes against the cheats. Cheating, an “unethical” behavior,  has an evolutionary advantage on the small scale, but on a large scale causes collapse or retaliation. One can weigh the benefits of cheating, but also recognize the consequences of doing it for society, and all without reference to an angry superbeing.

There is a famous saying attributed to Einstein that “Science without religion is lame, religion without science is blind.” That’s a fine sentiment, and for Brownback I’d like to take it further: ethics without religion is functional, religion without ethics is dangerous. To equate religion and ethics is ridiculous. If they were synonyms, then it would be fine to have sex with your father [2], something with modern religions tend to frown upon. Please note two things: first, evolution gives us a rational basis to frown upon incest, as it tends to accentuate bad genes and thus promote genetic diseases; second, the story of Lot occupies the same book of the Bible as the creation story that some tend to take so literally, begging the question: where do they draw the line?

[1] http://www.usatoday.com/news/politics/election2008/2007-06-07-evolution_N.htm
[2] The Story of Lot

Dreaming of Taus

The mad rush to the summer conferences is almost over, and while I am still trying to wrap up the research projects I’ve been working on for many months, I am thinking ahead to other projects that I’d like to start in the autumn. The BaBar experiment offers many opportunities to study the building blocks of the universe. My thoughts have, of late, turned to the many possibilities offered by the charm quark and the tau lepton. For many years, I’ve used both of these subatomic particles as a means to an end. I’ve use mesons from charm quarks to help constrain the decays of one B meson, so that I can then use the tau to study very rare final states of the other B meson. However, there are so many other possibilities with these under served subatomic particles.

In recent years, most of the new states of matter that have been discovered have been excited states of the charm quark when its paired with another quark. The tau, heaviest of the leptons, is like the Hadrian’s Wall of particle physics; what lies beyond is the wild unknown, the realms of the world yet unenclosed in the empire of our knowledge. The beauty of these two building blocks is that the collider at SLAC is a factory for them, just as much as it’s a factory for the b quark (its primary goal). For every 10 pairs of b quarks, we make 9 pairs of tau leptons and 13 pairs of charm quarks.

When I get started considering some potential new projects, I like to think about many things. The physics motivation is only part of it for me; that is, the (possibly shakey) theoretical motivation for doing the project in the first place. Does the project have implications for the Standard Model? Does it have implications for physics scenarios that lie beyond the Standard Model? If it only has relevance to the Standard Model, is it still interesting? Many people prize this part of the thinking above all others. In other words, if it’s not interesting to theorists then it’s not going to be read about when its published, and therefore not worth doing. I think this is narrow-minded. Why should experimentalists not be free to play around with an interesting project, just because theorists fall asleep when the topic is mentioned? Should we really be beholden to the “sexy topic whimsy” of theorists?

I’m being a bit extreme here, but only in response to what sometimes seems like the opposite extreme in my experimental colleagues. The other part of my thinking is to look ahead to the analysis itself. How will I reconstruct the decays of the subatomic particles? Are there new uses for old kinematic variables, discriminants based on momentum and energy, that can be applied here? Are there new variables that I could develop that would be the real killer, the thing that will really discriminate between the target process and the possible backgrounds? What are the backgrounds? Are there processes that are easily removed? Are there processes that are so similar to the target final state as to be “irreducible” – that is, impossible to remove, no matter how smart you are?

I’ve spent part of my weekend mulling over these things for the charm quark and the tau lepton. Consequently, my dreams have been filled with lists of numbers, lists of final states, the kinematics of backgrounds. The character, Charlie, from TV’s “Numb3rs” sees the math in real-time, as he’s thinking about a problem or is presented with another topic that suddenly has relevance to his problem. I dream about it. I woke up twice this morning, realizing my last thoughts were about lists of numbers and decay modes streaming past my eyes.

This is not an uncommon phenomenon. To me, it signals a mental obsession with a problem, something my brain wants to chew on at night. Sometimes I event wake up with new ideas. Sometimes I just feel like shit in the morning because I’ve been dreaming about taus. If you want to learn more about this phenomenon, check out the Radiolab special on sleep [1].

[1] http://www.wnyc.org/shows/radiolab/episodes/2007/05/25

Standing for Nothing

I finally had a chance this week to listen to the Senate testimony of Dr. James Holsinger, the President’s choice for Surgeon General. It’s taken me a few days to digest and form some impressions. I’ll try to communicate them here.

My most global observation is that Holsinger stands for nothing, except maybe that kids shouldn’t be fat. However, there were many occasions when he was asked questions like, “Give an example of something you feel strongly about, and how you would resist pressure from the President to speak against that topic.” Of course, Senators were interested in hearing him talk about something sexy: homosexuals, stem cells, etc. I would have settled for opinions on regulating “herbal supplements”, or even on the effect of smog on human health. Whatever. Holsinger always responded with something like, “I don’t want to get into hypotheticals.”

The premise of this response is funny, and frustrating. Holsinger seems to imply that he can’t give an example, until it actually happened to him. But in order for it to happen, he’d have to have already been Surgeon General. Cripes. It’s almost as good as listening to Attorney General Gonzalez sneak into and out of each lie. Clearly, just as Galileo held the opinion, hypothetically, that the Earth goes around the sun, and was allowed by the Pope to publish his “Two New Sciences” based on that, Holsinger could have spoken hypothetically about stem cells at no cost to his nomination. What’s he afraid of?

The less obvious point is that by doing this, we find a nominee that stands for nothing. He made strong statements about several things, most notably that science should speak in matters involving science, and that the patient matters more than the doctor’s philosophy. However, it’s really quite impossible to judge the man unless he can speak passionately about an issue. His greatest passion was about childhood obesity, but if that was passion he was showing then this man is about as moved as a lead brick in a cool breeze.

One of the funnier moments of the whole thing was a performance by Senator Ted Kennedy. In some of his first questions, the Senator
singled out that unpublished paper of Holsingers about homosexual sex. What was amusing was his focus: the bibliography. Senator Kennedy pointed out that the bibliography contained sources unused in the body of the paper. He noted that this is unusual in a scientific paper, and quizzed Holsinger about his motives for including uncited sources. Wow. Who knew that the Senate was a form of peer review?