Congratulations all around, especially to Jin-Der, who has done a fantastic job of making this project work. Although we were the first to observe ribosome activity in real-time, there is so much yet to come!
]]>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!
]]>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.
]]>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.
]]>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.
]]>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.
]]>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.
]]>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."
]]>Where I live, there are hard-core organic farms, as well as conventional super-farms. Local organic farms in the Central Valley compete directly with agro-giants to sell all sorts of foods, from grapes to garlic, avocados to artichokes. So despite the strong "anti-organic" sentiment that I held when I arrived here, I have slowly begun to question whether or not large conventional monocultures are the way to go.
Just as a bit of background, I went to an ag school for college; I graduated from the College of Agriculture and Life Sciences at Texas A&M University. I'm comfortable thinking about the business of agriculture, and I'm also a biochemist, so I'm not exactly a grungy, anti-biotech hippy. Anyhow, let me break down the chief reasons why I think the conventional wisdom is wrong about organic farming.
Myth 1: Organic farming is inefficient while conventional farming is a modern marvel.
The data shows otherwise. This article in the journal Science [subscription required], shows that organic farming is 80% as efficient in terms of crop per acre, and it is overall more energy efficient than conventional farming, owing to reduced fertilizer, energy and pesticide usage. Another study from Cornell researchers concluded that crop yields from organic and conventional farms were identical, while organic farming resulted in better soil quality at the end of the study. Therefore, if there are differences in the crop yields between conventional and organic farms, they are minimal and inconsistent. Broad claims that organic farming is significantly less efficient are simply untrue, according to the scientific literature.
Myth 2: Conventional farming really doesn't use that much pesticide.
The National Academies, the scientific advisers to the U.S. President, have published a review, entitled The Future Role of Pesticides in U.S. Agriculture (which you can read online!). In 1997, over 567 million pounds of pesticide active ingredient were used on U.S. crops (p. 46), which corresponds to over two pounds of pesticide per person, given the U.S. population in 1997. That's over two pounds of solid pesticide active ingredient per person per year.
Over 60% this pesticide usage comes in the form of herbicides. The clever part about organic farming isn't the patchouli smoke blown at the butter lettuce every morning. The clever part of organic farming is that there are physical methods of preventing growth of contaminating weeds, rather than chemical methods involving herbicides. Instead of spraying atrazine and glyphosate on an acre of lettuce seed, the lettuce is grown from individual sprouts protected from weeds in a greenhouse until they have grown enough to be ready for planting in the earth. Once planted, they have a great head-start relative to any weeds, so few weeds gain the upper hand. In other words, it's similar to the way you'd do it at home, since few would want to go spray atrazine all around their backyard lettuce.
Similar techniques exist for other plants. The organic methods are very simple, and they're not hippy magic. At its heart, organic farming is simply about using physical means to prevent crop failures, rather than chemical means. And although this currently requires more labor, it results in reduced pesticide and energy usage, as well as reduced runoff of synthetic chemicals into important water supplies.
If anyone has evidence that conventional farming really is significantly more efficient, please let me know!
]]>First spread out the steamed rice to steam off a little bit; you never want to make fried rice with really wet rice or it gets gummy. Dice the kimchi to small pieces about 1x2 cm, and cut the steak into thin slices about the same size. Melt 1 tbsp butter on a pan then stir fry the beef. Quickly add the black pepper, then take the beef off the pan and onto a plate before it's fully cooked (there should still be some red in it, but very little). Melt 1 tbsp butter in the pan again and then add the diced kimchi. Let it cook just until the green parts are starting to look dark and the white parts soften and turn clear, then take it off the heat and onto a plate. Cook the rice in two batches if need be... to each batch, melt 1 tbsp butter in a large pan, then add the rice and stir constantly. To each batch, add half of the kimchi, half of the kimchi juice, and half of the beef; stir on medium heat until everything is cooked. Salt to taste and mix again. Turn off the heat, add 1/2 tbsp sesame oil to each batch, stir and eat.
- 3 cups steamed rice (preferably from a rice cooker)
- 16 oz (450 g) kimchi (in its own juice)
- 4 oz (120 g) lean steak
- 4 tbsp butter
- 1 tsp salt
- 1 tsp black pepper
- 1 tbsp sesame oil
Optional: serve topped with a fried egg.
Yield: makes 3+ servings.
Delicious!
]]>Carlos José Bustamante
Jeff is the 'most outspoken member' of Citizens for Retiring the Penny. Below is the segment from the show:
Congratulations all around, especially to Jin-Der, who has done a fantastic job of making this project work. Although we were the first to observe ribosome activity in real-time, there is so much yet to come!
]]>On behalf of Ryan, age 1 and three quarters, we thank you in advance.
I knew right away that it was a conservation effort, so rather than tossing it in with the junk mail, I set it aside to read later. I finally opened it and read about the "ClimateSmart" program, which offered:
For about $5 a month, you can make the energy that you use "climate neutral" by investing in environmental projects that absorb or reduce greenhouse gases.
I was a bit skeptical because of the constant use of scare quotes every time the phrase "climate neutral" was used in the mailer. Turns out, this program is not exactly like green tags, or carbon offsets. As I read at Grist, the ClimateSmart program is not at all a way of purchasing renewable power, and doesn't support programs to create, support or expand renewable power. If you are considering joining the PG&E ClimateSmart program, do read these two posts at Grist:
]]>This would of course require Jeb Bush to run in 2016, followed by Chelsea in 2020. Hell, we could keep this up for a second generation if required!
America did away with kings and queens over two centuries ago. Right?
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