Why Linux is Alpha and Omega

I'm sure most people remember DEC - Digital Equipment Corporation - that later rebranded itself as the singularly unmemorable “Digital” before being swallowed up by Compaq in 1998, which was itself digested by HP a few years later. But I wonder how many people remember the DEC Alpha chip.

On Open Enterprise blog.

Is Google Running Short of Hackers?

How hard can it be porting Chrome to GNU/Linux? Hard, apparently:

The 2.0 version of the browser was released to developers and includes a number of new features including the begins of an extension strategy for the browser.

Senior Google staffers said, however, that Linux and Mac versions of the browser would only be made available later this year. CNet quotes Brian Rakowski, Chrome’s product manager, who said that the Mac and Linux versions of the browser were now at the “test shell” stage which meant that they could show web pages but are still in a very raw format.

Rakowski said that versions of Chrome for Linux and Mac would likely be made available by the middle of 2009.

Things getting a bit tough in the Googleplex, chaps?

ARMing GNU/Linux Netbooks for Success in 2009

One of the surprises of 2008 was the runaway success of the ultaportable/netbook form factor. Now that systems running Windows XP are available people tend to forget that it was the low cost and small footprint of GNU/Linux that made this category possible in the first place. Without free software, the new machines would have been forced to run Windows Vista, making them too slow and too expensive - and hence failures. It was only because Microsoft saw GNU/Linux walking away with this nascent market that it executed a massive U-turn over Windows XP, and allowed it to be installed on these systems.

On Open Enterprise blog.

Genomics Goes Read-Write

One of Larry Lessig's favourite tropes is that we live in a read-write world these days, where creation is just as important as consumption. Well, hitherto, genomics has been pretty much read only: you could sequence the DNA of an organism, but creating entire genomes of complex organisms (such as bacteria) has been too tricky. Now that nice Dr Venter says he's gone and done it:

A team of 17 researchers at the J. Craig Venter Institute (JCVI) has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0. This work, published online today in the journal Science by Dan Gibson, Ph.D., et al, is the second of three key steps toward the team’s goal of creating a fully synthetic organism. In the next step, which is ongoing at the JCVI, the team will attempt to create a living bacterial cell based entirely on the synthetically made genome.

The team achieved this technical feat by chemically making DNA fragments in the lab and developing new methods for the assembly and reproduction of the DNA segments. After several years of work perfecting chemical assembly, the team found they could use homologous recombination (a process that cells use to repair damage to their chromosomes) in the yeast Saccharomyces cerevisiae to rapidly build the entire bacterial chromosome from large subassemblies.

He even gives some details (don't try this at home):

The process to synthesize and assemble the synthetic version of the M. genitalium chromosome began first by resequencing the native M. genitalium genome to ensure that the team was starting with an error free sequence. After obtaining this correct version of the native genome, the team specially designed fragments of chemically synthesized DNA to build 101 “cassettes” of 5,000 to 7,000 base pairs of genetic code. As a measure to differentiate the synthetic genome versus the native genome, the team created “watermarks” in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity. To obtain the cassettes the JCVI team worked primarily with the DNA synthesis company Blue Heron Technology, as well as DNA 2.0 and GENEART.

From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation.

The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome.

At this stage the team could not obtain half genome clones in E. coli, so the team experimented with yeast and found that it tolerated the large foreign DNA molecules well, and that they were able to assemble the fragments together by homologous recombination. This process was used to assemble the last cassettes, from 1/4 genome fragments to the final genome of more than 580,000 base pairs. The final chromosome was again sequenced in order to validate the complete accurate chemical structure.

But the real kicker was this comment:

“This is an exciting advance for our team and the field. However, we continue to work toward the ultimate goal of inserting the synthetic chromosome into a cell and booting it up to create the first synthetic organism,” said Dan Gibson, lead author.

Yup, you read that correctly: we're talking about porting and then *booting-up* an artificial genome, aka digital code of life.