Apr 302008
It’s becoming increasingly clear to me that an emerging requirement for scientists is that they possess a laptop computer in addition to any desktop. It just seems to be an essential feature for giving talks at conferences and (crossing fingers) for jobs. For whatever reason it seems like you just can’t ever trust that your presentation will ever work on somebody else’s computer. Plus, on the rare occasions that I travel it might just be convenient to have one. So, I’ve decided to purchase a laptop, and would like some advice based on personal experience or whatnot.

The requirements I have are pretty basic. I don’t plan to do any heavy computational lifting or gaming with this machine. I need it to be capable of word processing, running Powerpoint (or equivalent), displaying images, and accessing the web. It also needs to work smoothly with external projectors (this used to be a problem with Macs; is it still?), have good battery life, and be hardy enough to get knocked around in a plane or in my car and still function well. I would strongly prefer that it not put out enough heat to neuter me if I have the misfortune to actually use it in my lap. Obviously, since this will be a secondary computer, I want it to be relatively inexpensive, not much more than my rebate check if I can help it.

So, any recommendations? Are there any Macs that fit the bill, or are they all in the way too expensive zone? Are the Dells (Vostro, Inspiron) a suitable option, or are they also too pricey? Does HP make any laptops that won’t burn your pants right off? Can laptops running Linux deal with LCD projectors?

Apr 232008
Our 500, that is. As I related in previous posts, our 500 MHz spectrometer was hamstrung by the signal from a local HDTV broadcast and subsequently had to be moved to a space in the basement of one of our research buildings. This process took about a year, because that space first had to be renovated, and in fact the last upgrades to the space won’t be finished for several days yet. But the 500 has moved into its new digs, (hopefully) finished quenching, and is ready to work. So yesterday I finally was able to collect an HSQC on it for the first time in many months.

So, here’s the spectrum I got:

For comparison, here is the last HSQC taken before we stopped using it. Obviously, this is of a different protein, but both spectra were taken using the same probe on samples with the same concentration, at the same temperature. I countoured them identically. The only difference here is that the protein in the spectrum below has much better relaxation characteristics than that in the spectrum above. In theory, this should produce much better signal to noise. Oh, and also that when I took this spectrum I was also receiving data about cubic zirconium.

This is really good news for a couple of reasons. The first is simply that we have another magnet, and that allows us more flexibility in scheduling. No more fighting when people want 9 days of NMR time next week. The second thing is that, for a variety of reasons, some experiments just work better on a lower-field magnet. In particular, I have some experiments that are sensitive to chemical shift anisotropy and REX; using a lower-field magnet attenuates both these problems.

Apr 152008
Maybe you know someone who has been suckered in by the numerous distortions, outright lies, and malevolent accusations of the “documentary” Expelled, starring famous bore and Nixon speechwriter Ben Stein. Perhaps even you have been convinced by its “startling” array of important “facts” about the “controversy” between the scientifically useless design conjecture and staggeringly successful evolutionary theory. If so, I urge you to direct your credulous friend (or yourself) to Expelled Exposed, a website devoted to debunking the lies of this appalling propaganda flick. Even if you favor a creationist viewpoint I think you will find it highly disturbing how freely the creators of this film distort the truth to favor their views.

In addition, for general knowledge on debunking the claims of creationists you should check out The Panda’s Thumb, TalkOrigins, TalkDesign, TalkReason, and the National Center for Science Education.

Also, New Scientist has an excellent article up featuring 24 misconceptions about evolution. Read it.

Also check out some other articles about the film and its marketing:
Biologist PZ Myers, interviewed in the film, is expelled from a screening of Expelled. But they let Dawkins in.

An animation in Expelled was ripped off from Harvard University and XVIVO. It should be noted that famous cdesign proponentsist William Dembski was for a long time in the habit of stealing this film to display in paid lectures.

Expelled tries to draw a line between belief in evolution and anti-Semitism. Interestingly, one of the creationist scientists they interview is the anti-Semite Maciej Giertych.

Apr 112008
That cool breeze you felt this morning blew in from the icy recesses of the underworld, the result of a sudden climactic change that occurred because labmate and occasional commenter Wladimir Labeikovsky successfully defended his thesis on the interaction of tau with prolyl isomerase Pin 1 yesterday. He now has his Ph.D., a sure ticket to worldwide fame and fabulous wealth. Congratulations to him on bringing a successful conclusion to a long graduate career, and looking good in a suit. Hit the jump for pictures.

Wlad cleans up nice, doesn’t he?

Wlad still laughs at Dorothee’s jokes.

Little known fact: as part of your training for grant applications, you must successfully break a piñata in order to receive a Ph.D. in biophysics. The piñata in this case is full of candy and Skyy vodka sample bottles.

Here’s a view of the party afterwards. Nothing says “science” like a bunch of folks standing around drinking.

Wlad attempts to murder a committee member with a champagne cork.

Here we see Wlad’s adorable godchildren during the brief time that they were not covered in frosting.

Enough said.

By the way, I would appreciate it if whoever received my worldwide fame and fabulous wealth in error would forward them to me promptly.

Apr 032008
Discount Thoughts turned eleventy-one with that last post, which I think is an excellent time to shake up the structure of this annoying little site. I’ve decided to kiss the keywords list goodbye and revamp the links. I’ve replaced it with a non-exhaustive list of keywords and the most popular posts (relative to my other posts) from the last month or so. The list of papers (formerly headed as “Shameless Self Promotion”) has been removed and will now exist only in this post. Let me know what you think of the changes.

“Solution Structure of Polymerase μ’s BRCT Domain Reveals an Element Essential for Its Role in Nonhomologous End Joining”

“Dynamic Coupling and Allosteric Behavior in a Non-Allosteric Protein”

“Role of Structural Plasticity in Signal Transduction by the Cryptochrome Blue-Light Photoreceptor”

“Long-Range Dynamic Effects of Point Mutations Propagate through Side Chains in the Serine Protease Inhibitor Eglin c”

“Increased Rigidity of Eglin c at Acidic pH: Evidence from NMR Spin Relaxation and MD Simulations”

And some contact information, rendered in my native language:
Email : clarkson dawt emm double yew at geemail dawt cawm
Speak it to learn my address.

Also in this post: the Discount Thoughts lexicon!

bafmodad (baf mō dad) — In a video game, an object which is not of any intrinsic use but which must be obtained in order to advance the plot. The Medallions from Ocarina of Time are a classic example. The bafmodad is conceptually related to the cinematic MacGuffin. Term invented by Jerry Holkins and Mike Krahulik as a corruption of the name of an actual item from Starfox Adventures.

cameralepsy — The repeated recrossing of a boundary between two camera fields of view. Generally occurs in games which have fixed cameras and camera-relative controls. If the smallest angle between the cameras is > 120 degrees, there is a high probability of a cameraleptic seizure, which can only be cured by ceasing to move or (in games like Grim Fandango) changing the control scheme.

disingenue — A person, often famous, who falsely claims that his or her bad deeds are due to the influence of poorly chosen friends.

magibabble — The fantasy equivalent of Treknobabble, magibabble is pseudoscientific, jargon-filled dialogue concerning technicalities of magical physics that will either cause the destruction of the world, allow the heroes to save the world, or both. Excessive use of magibabble is a particularly common sin of fantasy RPGs. The emphasis on jargon is a critical feature of magibabble. Ordinary myths and legends often hinge on some technicality of magic, but they are not examples of magibabble because the rules are explained in plain language. Magibabble is typically used to disguise plot holes or laziness.

tatropmr (tä trōp mər) — The Abstract Transcendental Realm Of Perfect Mathematical Relationships, a nonexistent place which is frightfully dull, rather difficult to comprehend, and not inhabited by natural laws. All those who fundamentally misunderstand the process and meaning of science are eternally condemned there. First identified by Paul Davies, also the first to be publicly damned to it.

the turtles — A key problem with many arguments for creationism or intelligent design is the turtles: specifically, the fact that they go all the way down.