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08 October 2006 Blog Home : October 2006 : Permalink

Science Bloggy Thoughts

From time to time I like to spend a while reading a number of the scientific blogs and magazines to see what I'm missing. One thing that spurred me on to do this again this weekend was the Gene Sequence X Prize.

On October 4, 2006, the X PRIZE Foundation announced the launch of its second prize — the Archon X PRIZE for Genomics. The $10 million cash prize has been created to revolutionize the medical world. The launch was attended by visionaries and entrepreneurs from around the globe who recognize the significance and impact that the Archon X PRIZE for Genomics will have on the fields of medicine and research.

What I found most interesting is why this is still a problem. I mean we sequenced the human genome back in 2000 yes? Well Gnxp has a crisp explanation of why that lay asumption is WRONG.

One broader question overall is: why do we need a new method for sequencing? Sanger sequencing has gotten us this far, shouldn't a little more miniaturization and automation get us where we need to be? The answer, in a word, is no.

As I see it, the problem with both 454 sequencing (one of the top candidates to be the next major sequencing technology) and Sanger sequencing is their ability (or lack thereof) to handle large repeats. Here's what I mean:

First, note that sequencing is not the same as looking at a DNA molecule and reading on down. Sanger sequencing gets you about 600 bases at a time, so you first need to break the genome up into pieces of that size, sequence them all, then put them back in order. In 454 sequencing, you break the genome up into piece of about 1000 bp, but you only can read about 200 of them. Note that the human genome is composed of somewhere around 3.3 billion bases.

Now imagine you have a stretch of 3000 bases on chromosome 5, and another identical stretch on chromosome 11. If you're sequencing 600 bases, you have no idea that there are two copies of that sequence in the genome-- all you see is a bunch of identical sequence. The only thing you can do is sequence the same genome over and over again and hope that one of your 600 bp reads overlaps both some unique sequence from one chromosome and some of your repeat, allowing you to anchor it down. Of course, there are computational methods for resolving repeats that have gotten much better in the past few years, but the larger the repeat, the harder it is, and you still have to generate a lot of sequence-- off the top of my head, I'd guess you need something like 10X coverage (meaning for a 3.3 billion bp genome, you have to sequence 33.3 billion bases) to successfully resolve most repeats. That's a lot.

Although given this sort of problem with current technologies John Hawks' question "how are they going to test the accuracy of the reconstucted genomes?" is rather critical.

Other fun bioscience related news includes the Pinker/Lakoff grudge match, ably commented on here, and a couple of examples of dodgy use of facts, one by the Intelligent Design (ID) iots and one by a paleontologist who ought to know better.

Moving on from biosciences to physical ones and there are a numebr of straws in the wind that, IMO, make it increasingly likely that the world's "oil addiction" can be cured. Firstly Popular Mechanics highlights an improved hydolyzer i.e. the production of hydrogen by electrolysis of water:

Bourgeois's prototype electrolyzer cuts the equipment cost of using electricity to grab hydrogen from H2O. The key was replacing tooled metal with a moldable, high-tech GE plastic called Noryl, saving on materials, manufacturing and assembly. The result? A kilogram of hydrogen — the energy equivalent of roughly a gallon of gas — that costs $3 instead of the current $6 to $8. "I could imagine a small box that sits on-site making hydrogen for a factory," Bourgeois says. "Eventually, even filling stations may make their own hydrogen."

Combine this with recent improvements in solar cells (economist article summarizing) and you get a way to store solar power in a useful form that can be readily transported.

Finally the space race seems to be heating up which is interesting, and, critically IMO, it is becoming mroe and more of a private sector challenge. That isn't to deny the dangers of space travel though as slashdot highlights the atmosphere does provide us with a lot of protection.

I despise l'Escroc and Vile Pin