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Comment Scientific writing doesn't have to be opaque! (Score 2) 160

My favorite discussion of this topic is The Science of Scientific Writing. The authors' basic argument is that most people think science is hard to read because the ideas are complex; but instead, scientists can convey their ideas clearly by meeting the structural expectations of the reader.

For example, readers expect the subject of the sentence to be the subject of the story you're telling. They expect old information to come before new information. They expect the end of the sentence to be the "stress position", and for information there to be emphasized.

It is not overstating matters to say that this article has forever changed the way I write scientific prose. Highly, highly recommended.

Oh, and the other takeaway? It's not that science writing is opaque by necessity -- it's just that many scientists write poorly.

Comment Facilities that people could use, but don't? (Score 2) 291

I work in an academic genomics laboratory, and our tech staff are on the lab meeting rotation schedule. What they generally spend that time doing is presenting tutorials on interesting things you can do with our computational and networking infrastructure. For example, our admin implemented a really slick remote access server (Sun-branded, I think) and it was a nice chance for him to give a live demo of something that, at this point, a lot of us find useful. (Also a good chance for him to show us that he was earning his keep!) I agree with your assessment, though - avoid the utilization charts.
United States

Submission + - US Research Open Access In Peril (

luceth writes: Several years ago, the US National Institutes of Health instituted a policy whereby publications whose research was supported by federal funds was to be made freely accessible a year after publication. The rationale was that the public paid for the research in the first place. This policy is now threatened by legislation introduced by, you guessed it, a Congresswoman who is the largest recipient of campaign contributions from the scientific publishing industry.

Comment Re:Yes! (Score 1) 65

Well, it was just installed a few weeks ago - hasn't seen a whole lot of use yet, so not too many experiences on which to base an opinion. A single run costs ~$400 (an order of magnitude less than an Illumina Hi-Seq run!), but only gets you 10-20 million bases of sequence. (A human genome has ~3 billion bases, and you need ~10-fold coverage to make sure you get each base. In the Nature paper, they sequenced Gordon Moore's genome - and it took about 1000 chips to do it.) There's some talk of using it to QA libraries before a Hi-Seq run - for $400, I think that makes a whole lot of sense. I'm not sure that talking about Illumina approaching the magical $1000 genome is quite on target, either. The other thing most people don't talk about is read length - an Illumina run will get you enough sequence, but it's only in 50-100 base chunks. Reassembling an entire 3 billion base genome (6 billion if you consider both haplotypes!) is either extremely difficult, or actually theoretically impossible, depending on who you ask. The $1000 genome X-prize is to sequence a single genome, for $1000, in one week, to the quality standards of the original Human Genome Project (1 error in 1000 bases, IIRC). To do that, you're going to need long-range sequence data. I think that the nanopore sequencing approaches, that read a single piece of DNA for hundreds of thousands of bases at a stretch, have a much better shot at getting there in the next few years. The other interesting thing about the Ion Torrent PGM is that the magic happens on the disposable chip - and that can be upgraded without the rest of the machine (sensor interface, fluidics) changing. The next generation of chips is spec'ed to produce 10x as much sequence, and it's already sampling at early access laboratories like Baylor and MIT.

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"Text processing has made it possible to right-justify any idea, even one which cannot be justified on any other grounds." -- J. Finnegan, USC.