Peter Schultz makes mRNA cry.

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I recently heard a presentation on this crazy guy, Peter Schultz, who has engineered bacteria to use para-aminophenylalanine instead of amber codons. The bacteria synthesize para-phenylalanine, have a para-phenylalanine tRNA synthetase, and and insert it with very high fidelity whenever the amber codon is found. The amber codon, which causes the ribosome to stop reading the mRNA when it’s found, is apparently quite rare, and because bacterial mRNAs aren’t as processed as eukaryotic ones, the bacteria get along quite well. I was thinking it would be really keen to make a series of mutants, each of which incorporated a different D-amino acid instead of the L version. Then, analysis of the structures of the D tRNA synthetases, of the ribosome translating the codon, and of the resulting protein could contribute a little information towards answering why we use all L amino acids.

Coincidentally, while I was googling a good link for this story, I found Lagniappe, who just blogged this story about the same time I heard the presentation.

Here’s Schultz’s PDF in JACS.

Derek, if you’re reading this, you’re the number one link at google for para-aminophenylalanine. Kinda funny that I find a blogspot blog as the number one search result for something right after google buys pyra. However, there were only 2 results total, so I only mention this to be funny, not to suggest anything conspiratorial.

Amazing Science – Mind Control Edition

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Sometimes an article comes out with a title that makes me think, “Wait a second. It’s not even April 1st yet.”

Joe Tsien’s NR2B overexpression experiment and John Chapin’s “Rats control robots with minds” were pretty amazing articles, and now Dalle Molle Institute for Perceptual Artificial Intelligence comes out with a technique that can detect “whether you are thinking about a calculation, a place, a colour or even what you want to eat for dinner…but it’s not good enough yet to detect exactly what colour you’re thinking of.” I believe they’re using Bayesian analysis, a great statistical learning technique which I’ve seen being used more and more often, to look for “EEG patterns embedded in the continuous EEG signal associated with different mental states.” Here’s a summary .pdf describing the technique.

Are you a Lunarist?

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Compare and Contrast

Consider that creation vs. evolution shouldn’t even be a debate we’re having. Michael Shermer and the philosophical debates over the existence of god are something I can tolerate, because that’s what philosophers are for, but the idea that we should have a scientific debate about creationism vs. evolution is every bit as ridiculous as a “lunarist” debate would be, except this time Buzz Aldrin can’t help us.

4 MIT professors give science advice to the president.

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No Sense of Place directed me to 4 MIT Professors give science advice to the president. The actual number is 85 and counting, from science personalities nationwide, including such personalities as Craig Venter (who has a great rant), Ray Kurzweil (who goes offtopic, but makes some excellent points), Eric Drexler, and this from Stephen Schneider.

The role of science in the public debate is clear: assess what can happen and what are the odds of it happening. The role of policy�driven by the beliefs of the public�is to make value judgments on how to react to the odds of various possibilities. It will take some major realignment of institutions like the media and congressional hearings apparatus to back away from the model of polarized advocates toward a doctrine of “perspective”:reporting and debating based on the assessment of the likelihood of various events, not giving advocates of extreme opposite views equal time or space.

Anyone who has the media report on their particular topic of expertise, especially if it’s a scientific topic, knows how totally clueless the newspaper or television treatment can be. However, more subtle distortion also exists. Instead of reporting on the different positions of many scientists regarding a certain issue and maybe the relative validity of each postion judged by the number and repute of the scientists holding each position, the stories that get reported force a debate among the two most diametrically opposed views, even when neither is very likely. Ever read anything about Nature vs. Nurture?

My eyes opened wide when I realized how clearly he understands the problems of science debate among the public and the nation. Unfortunately, and perhaps this is the problem, every statement I read declined the hypothetical offer to be science advisor to the president.

First Post!!1!!eleventy1!!

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I promise to never write one of the following two things: excuses for not posting frequently enough or overextended, overwrought metaphors so old and tired they not only fell off the turnip truck last decade, but have been lying in the dirt of the dusty road, getting run over by passing farm equipment and tractors, ever since. You figure out which.