These are the sorts of tools that change things

by Beige Alert

New players in sequencing debut at AGBT
[Via Genetic Future]

The main theme of this year’s Advances in Genome Biology and Technology meeting should come as no surprise to regular readers: sequencing. Generating as many bases of DNA sequence as quickly, cheaply and accurately as possible is the goal of the moment, and the number of companies jostling to achieve that goal is growing rapidly.

The meeting saw impressive performances from established players in the field, especially Illumina: their new HiSeq 2000 instrument seems to have dug in as the platform of choice for generating vast amounts of high-quality short-read data. Life Technologies seem to be slowly abandoning the research genomics market (already dominated by Illumina) with their SOLiD platform, focusing instead on capturing the clinical sequencing market; they showed some impressive accuracy improvements for their technology.

As I mentioned in my previous post, PacBio largely underwhelmed the audience with their theatrical unveiling of a massive box with quite limited applications, although we’ll have to wait and see how much its specifications improve over the next couple of years. Meanwhile, Complete Genomics gave an understated but seriously impressive series of presentations on their human genome sequencing service; I’ll have more on them in a day or two.

Anyway, in this post I want to focus on the two brand new platforms announced in the emerging technologies session on the last day of the conference: the newcomer Ion Torrent, and Life Technologies’ futuristic quantum dot technology.

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One machine may be cheap enough to do quality control tests on samples before subjecting them to very high-throughput DNA sequencing devices while the other holds the promise of DNA reads on single molecules that extend for the whole molecule – a single read on a single molecule.

We are approaching the era where these can really be clinical lab technologies rather than only research lab tools. That could have a huge affect on how we interact with the medical profession.

[Listening to: Deacon Blues from the album "Citizen Steely Dan 1972 - 1980 disc 4" by Steely Dan]

The fifteen years that shook the world . . . and you were there

by psd

The fifteen years that shook the world . . . and you were there
[Via Effect Measure]

Fifteen years isn’t a long time. Most of us can remember what we were doing 15 years ago. Often it’s the same thing we are doing now, job-wise. Sure our kids were just kids, not adults. But 15 years isn’t a historical epoch. At least not when you are living through it. But the fact is we have gone through a revolution in that period that will seem as profound as the 50 years from 1450 to 1500, the half century after Gutenberg and the invention of moveable type.

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I mentioned earlier about how far we have come in 5 years. Here is a peek at 15 years back. Some people got it totally wrong, laughingly wrong.

How awkwardly incorrect we will be trying to predict what the world will be doing with technology 15 years from now? Web 5.0?

And the gnashing of teeth will begin in

White House Meets With Non-Theists
[Via Dispatches from the Culture Wars]

The Obama administration became the first presidential administration in American history to hold an official meeting and policy briefing with a non-theist organization. The Secular Coalition for America, a meta-organization that includes the Center for Secular Humanism and American Atheists among others, met on Friday with White House officials on matters of concern to the non-religious community.

This is a very good thing and a very welcome development.

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Three. Two. One. The cry that the secular organizations are getting special treatment is ludicrous, as the administration has met with many, many religious groups. As stated, this appears to be first time a coalition of secular Americans has had such a meeting.

I love that In God We Trust.org kept throwing out “Madalyn Murray O’Hare”, who was murdered in 1995 and whose last name was actually “O’Hair”.

But I don’t expect the moaning to extend very far into the consciousness of most Americans. They have more important things to worry about these days.

Scientists singing about science

Snow Day Special: Warbling Scientists on the Newest Symphony of Science

[Via Discoblog]

Scientific superstars like Carl Sagan and Richard Dawkins are sounding better and better. In the series Symphony of Science, creator John Boswell uses the auto-tune program so beloved by R&B and pop stars to tweak such nerdy delights as Carl Sagan’s monologues from “Cosmos,” and sets them to electro-funk music. The result? Highly watchable videos of Sagan and other guest scientists expounding on the magic of the cosmos and our place in the universe. Boswell has put four videos out previously, but here is his latest offering, “The Poetry of Reality.”

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The Symphony of Science series has been amazing to watch and listen to. And it is a amazing display of what creativity can do using modern tools. He remixed videos, added music, made the scientists ‘sing’, and then put the results up for everyone to examine. He now uses Twitter to help him find new pieces of video or to suggest topics. You can even purchase the music on iTunes.

Five, years ago, this would not have been possible. What will another 5 years bring?

A sign that our courts may not have a clue about the proper place of copyright

US Postage Stamp Found To Be Infringing On Copyright Over Statues In US Korean War Memorial
[Via Techdirt]

Last year, we wrote about the appeal in a case involving a US postage stamp which was based on a photograph of the US’s Korean War Memorial in Washington DC. You can see the sculpture and the stamp below:

There were a variety of issues involved in the case, including who actually owned the copyright, but in the end, the interesting question is whether or not this was fair use. The lower court had ruled that this was clearly quite transformative, different in nature, and did not harm the commercial value of the original work (which even the sculptor admitted). Thus it was fair use. To us, and many other experts in fair use, it seemed hard to question that logic, but when it comes to copyright, you can always be surprised by how judges interpret the law.

The Federal Circuit has ruled on the appeal and stunningly decided that this isn’t fair use, claiming that it’s not, in fact, transformative. I’m somewhat amazed — as is law professor Peter Friedman in the post linked here. The two works are quite clearly extremely different, but the court felt that since they both were designed to honor soldiers killed in the Korean War, it couldn’t be seen as transformative. The fact that the photographer took hundreds of images before settling on this one apparently didn’t matter. On top of that, the fact that the snow totally changes the character of the image was dismissed by the court as being just “nature’s decision.” Update: That “nature’s decision” line was really bugging me, and Friedman has updated his post to show it’s bugging him too, so I wanted to write a bit more. If “nature’s decision” makes something non-copyrightable, then it can be argued that all nature photography is not covered by copyright — which goes against pretty much every precedent out there. It’s hard to see how CAFC can make this argument.

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This really seems to mess of the idea of fair use. And, as the post mentions, how in the world can the government spend public money on a memorial and not be the ones that hold any copyright on the memorial?

That is messed up.