I spent the better part of this afternoon rigging up my personal electronic notebook using MediaWiki 1.16 on my MacBook. I downloaded the alpha version of MediaWiki (1.16alpha) because I wanted SQLite search support, although I'm not even totally clear on whether or not I need that.

The only reason I'm writing this post is because getting the Biblio extension on MediaWiki was pretty troublesome. Actually, for the most part, everything went smoothly, per the instructions. But I was hung up on an error that the Biblio extension gave me. It uses NuSOAP, which is apparently deprecated or something, and doesn't work well with PHP 5.3. I was getting the following warning:

Warning: attempt to modify property of non-object at [path/to/nusoap.php] line 4151.

I addressed this warning by commenting out line 4151, which on my file is this:

$this->schemas[$ns]->imports[$ns2][$ii]['loaded'] = true;

And I replaced it with the following:

$list2[$ii]['loaded'] = true;

At the very least, it removed the warning messages and the script still executes fine. So I've almost convinced myself that my correction is fine. Please let me know if you believe otherwise. I just wanted to put this out there for anybody else who may run across this and need a quick fix. Please let me know if you think this patch of mine is not the best way to fix it!

Filed under science

Posted by H. C. Hodges at 8:15 PM | Permalink | Comments (8)

This BBC report sounds pretty neat. Scientists in Hawaii have hit magma rather than oil, allowing them for the first time to study the liquid rock in place, rather than as lava flows.

Apparently this was released at the 2008 American Geophysical Union annual meeting, which is taking place here at Moscone, where ASCB is also being held right now.

Filed under science

Posted by H. C. Hodges at 6:45 PM | Permalink | Comments (8)

As some of you know, my old Titanium PowerBook G4 (an ancient relic of 2002), died back in April. It gave me a solid 6 years before giving up the ghost, but, thankfully, I had heard that Apple was just about to release a new laptop with a completely new design. So I waited. And waited. I finally got the new MacBook (Late 2008 model) in October, and the 13" aluminum unibody construction is incredible! I love every aspect of it except for the glossy screen, which I am surprised to report that I have gotten used to it very quickly and I usually don't even notice it now.

However, the screen contrast on the new MacBook left something to be desired (as has been reported elsewhere). After some searching, I found that (Ctrl-Opt-Cmd-,) and (Ctrl-Opt-Cmd-.) will decrease and increase the contrast, respectively. That made it a little better, but I still yearned for blacker blacks and richer dark colors... perhaps I was spoiled because I use the 23" Cinema Display on a PowerMac in lab.

It seems obvious now, but the solution was to calibrate the LCD display. Under System Preferences, go to "Displays" and click the "Color" tab. Select "Calibrate," and then check "Expert mode." This will allow you to really calibrate the gamma and color temperature of the display. If it sounds scary, no worries, because it only involves you adjusting two knobs until the color and contrast of your screen looks right. You do this a few times and then save the results. It's very easy, and if you aren't happy, you can always go back to the factory defaults!

When it arrived from the factory, my LCD display had less contrast and had lower color temperature. By comparison, grays were more yellow-red, and are now more blue, which seems to me truer color. The contrast is also much better. Give it a try if you think your display could be improved.

Filed under technology

Posted by H. C. Hodges at 9:40 AM | Permalink | Comments (7)

I always prefer going to vote on Election Day rather than mailing in a ballot. There's something about standing in the booth and marking on the paper that makes me feel like my vote really counts. Voting is one of my favorite rituals, a rite of secular democracies that is open to all citizens, where participation allows you to help decide the future and meet your neighbors. It's great.

This year is the first year that I've ever had to wait in line to vote, and I wait I did, for almost an hour this morning. I cast my vote for Obama, and while I am cautiously optimistic, I am also nervous as hell.

Here's to hoping that America makes the best decision today; may we finally shake up the Republican party and its openly hostile anti-intellectual tendencies.

Filed under berkeley · california · culture · education

Posted by H. C. Hodges at 2:08 PM | Permalink | Comments (2)

I wish there were a market on Intrade for the Nobel Prizes. Two years ago, I wrote a post in which I expressed that Roger Tsien and Marty Chalfie should win the Nobel Prize in Chemistry for their work in GFP. Today, that became a reality.

The two are newly minted Nobelists, along with Osamu Shimomura, for their work with GFP, which is used basically in all of biochemistry, molecular and cell biology and genetics. Kudos to all of them for their well-deserved win.

Filed under biology · chemistry · science

Posted by H. C. Hodges at 3:22 PM | Permalink | Comments (2)

Although I've never been one to be a conspiracy theorist, I find myself unable to accept the government line on the anthrax story. I spent a couple weeks working in Fort Detrick at the NCI-Frederick Cancer Research & Development Center, and ate lunch with the civilian and military scientists in the cafeteria. We continue to work in collaboration with a lab there in Fort Detrick. Although I'm not really close to the story, I feel closer to it than I ordinarily would, and it has certainly drawn my attention.

As of yet, no physical evidence has been produced regarding Bruce Ivins' guilt. And now, he has died under mysterious circumstances. Conveniently, upon his death, the FBI immediately announced that they were "closing in" on him and were "about to seek indictment." This smells very strongly to me of scapegoating, and with Ivins' suicide, it actually looks downright creepy. You'll note that the first anybody heard about Ivins' death was in connection with the case. The FBI didn't let notice of his death leak out without telling in the same breath that he was a suspect and that they were "closing in." It looks too suspicious to me to assume the government is being forthright.

If you recall, the anthrax scare occurred right after the September 11 attacks, and were used partly in the justification to go to war. For the interested, I highly recommend Glenn Greenwald's Salon piece, where he discusses the role of ABCNews in breathlessly reporting government-leaked misinformation about the anthrax scare.

The government already sought one scapegoat, who later sued to the tune of $5 million. Was Bruce Ivins another easy target for blame? I don't know, but if he was innocent, then the scary thing is that this could have happened to any government scientist.

Also: Be sure to check out John McCain on David Letterman's show in October, 2001, spreading rumors that the anthrax attacks may have originated in Iraq. He uses that opportunity, barely one month after 9/11, to announce that Iraq was already being planned for "phase 2." Please do not vote for him.

UPDATE: The FBI has released grand jury documents regarding their case against Bruce Ivins. They can currently be found here. A slightly more accessible collection of documents is available at The Smoking Gun. While their case does make Ivins look suspicious, the science that they describe in the documents indicates that all of their case was circumstantial. I doubt that this would have been enough to get a conviction, and I remain concerned that the FBI is apparently closing the case without physical evidence to indicate that they have the perpetrator.

UPDATE: I was quoted by the Associated Press as part of an article on persistent skepticism on the anthrax story.

Filed under biology · science

Posted by H. C. Hodges at 3:45 PM | Permalink | Comments (1)

The news from Nature (free access) is that a terrorism suspect in the UK has been denied access to college-level chemistry and biology classes. The judge has decided that the classes would put the suspect in a "substantially stronger position" to carry out terrorist attacks.

This has to be about the stupidest, most disgusting, anti-democratic and anti-intellectual ruling ever made. I am shocked that an economically advanced country like Britain could place access to basic education off-limits to suspects of any crime. In addition to the presumption of guilt, the government has basically said that if they think an individual might become or might have been a terrorist, then it has the right to limit that person's education. This ruling is really short-sighted and shameful.

More on this at the BBC, who says that the UK government could place these sorts of restrictions "on anyone the secretary of state has reasonable grounds for suspecting is involved in terrorism or terrorism-related activities."

Filed under biology · chemistry · culture · education · science

Posted by H. C. Hodges at 10:43 PM | Permalink | Comments (2)