building better bacteria

The Scientist | Researchers from the J. Craig Venter Institute have developed a technique for generating modified strains of bacteria with novel, genetically engineered properties, they report online today (August 20) in Science. The advance could help scientists tweak microorganisms to more efficiently produce biofuels, the researchers say.

"I think it's an important and interesting advance," said James Collins, a bioengineer at Boston University who was not involved in the study. "I suspect this will turn out to be quite important for bioengineering and bioenergy systems."

Last year, Venter, an author on the paper (and a member of The Scientist's editorial board), reported that he and his collaborators had created a synthetic bacterial genome and cloned it into a yeast cell. However, they were unable to transfer the genome into a cell that would use the genetic code to produce a functioning version of the organism. In the current paper, the researchers present a technique for doing just that.

The Venter team first cloned the genome of the bacterium Mycoplasma mycoides into a yeast cell. They then altered the genome, using the myriad tools available for yeast gene manipulation. In the procedure's trickiest step, they transplanted the yeast-bound bacterial genome into a closely related bacterium, Mycoplasma capricolum, coaxing it to "take this bacterial genome and boot it up" and generate their mutant strain, said Sanjay Vashee, a synthetic biologist at the institute and the corresponding author on the paper.

The hurdle Vashee and his team had to overcome to achieve this feat involved bypassing the bacterial equivalent of an immune system -- essentially a collection of restriction enzymes. These enzymes, thought to have evolved to chew up the genomes of viruses infecting bacterial cells, were preventing the successful transplantation of the modified M. mycoides genome into wild-type M. capricolum. So the group developed two fixes, which together solved the problem: First, they inactivated M. capricolum's restriction enzymes. Then, they chemically modified their mutant M. mycoides genome where these enzymes typically cleave the genomes of intruders.

Decades of research on yeast genetics have yielded the know-how to do extensive genomic manipulations in yeast, but that capability doesn't exist for other microorganisms. "There are so many organisms in nature that we cannot manipulate," said Vashee. "If we can extend this -- and put those genomes into yeast, to manipulate them there -- we've got a new technology that can bring genomics to a wide host of organisms." (Vashee noted that the current study was conducted in a natural Mycoplasma genome -- not the synthetic genome the group assembled last year.)

The Race

Craig Venter on the great race;

"We've been digitizing biology, and now we're trying to go from that code to designing biology. We've tried various approaches, paring it down to basic components, digitizing it, now we're trying to ask: can we regenerate life or create new life out of this digital universe? The pace of digitizing life has been increasing exponentially. Our ability to write genetic code has been growing more slowly. Turns out synthesizing DNA is difficult. In a biological system the software builds its own hardware, but design is critical, and if you start with digital information, it has to be really accurate. How do we boot-up a synthetic chromosome? We can do a transplant of a chromosome from one cell to another and activate it. We may be about to create a new version of the Cambrian explosion, where there is massive new speciation (the formation of new and distinct species) based on this digital design. We have now a database with about 20 million genes, and we like to think of them as the design component of the life of the future. We now have techniques to do combinatorial genomics, to build a robot that can make a million chromosomes a day.

We're now focusing on fourth-generation designer fuels. Curent biofuels aren't the solution. The only way that biology can have an impact on fuel without increasing the price of food, it's to start with CO2 as the feed stock -- create new energy out of CO2, and we think we will have something within the next 18 months. Future uses of this technology: increase the basic understanding of life; replace the petro-chemical industry; become a major source of energy; enhance bioremediation. We're changing the evolutionary tree with new bacteria and species."

I suspect that this memetically recursive path is the ONLY viable path out of the evolutionary bottleneck. Because of the choices made on large institutional and cultural scales, I begin to doubt whether or not this path will be explored hard enough and fast enough to make the difference that it could make. This is where the world should invest its space race fervor.

Stem Cell Breakthrough

So we're doing the family chitchat over dinner yesterday evening, and my daughter is on about how much more opulent her lifestyle will be than the one she currently enjoys with her mother and I. This child has been versed in the realities, so it's a humbling parental reality check to witness all those carefully sown facts disintegrate into nothingness in the face of peer and media information onslaught (consensus reality).

Anyway, not wanting to harsh her thanksgiving mellow with my own somber outlook on what's around the signpost up ahead, I ask her if she's on top of this week's big news in the life sciences? Thankfully, both children are very interested in biology and I've made a point of trying to steer them in the direction of computational biology, genomics, and so forth, because this area has an exceptional concentration of new institutional investment in these disciplines, and, they have easy access and extensive potential exposure to folks working in this fundamentally important area;

To help explain this, we turn to Kenneth Miller, a cell biologist and professor at Brown University. He also serves as an adviser to the NewsHour's Science Unit.

Well, Ken, let's start with the science here. What does it actually mean to reprogram cells?

KENNETH MILLER, Cell Biologist: Well, what it means to reprogram cells, builds upon essentially a trick. And it's a trick that our own reproductive cells pull off when a sperm and egg unite to form an embryo.

The cells in an adult body -- skin cells, muscle cells, nerve cells -- are sort of at dead ends. In other words, that skin cell is going to remain a skin cell; that muscle cell is going to remain a muscle cell.

But our reproductive cells have the ability to go back to stage one, form a single-celled embryo, and then grow into every one of the tissues and cells in the body. That reprogramming is something that happens with us normally between each generation.

What developmental biologists have longed to understand is how that reprogramming takes place. And what this development means today is that we are a little bit closer to understanding how to switch on the reprogramming, take one of our adult cells, trick it into thinking it's part of an embryo, and hopefully get that cell to develop into cells that we really need to repair or to heal the body.

JEFFREY BROWN: And this work came out of studies that were done on mice, right? We talked about it on the program when that was done. So what's the advance here?

KENNETH MILLER: Well, the advance here, on one hand, the advance isn't much. In other words, you could minimize it. You could say, back in June, three laboratories reported that it was possible to pull this feat off, of taking an ordinary adult cell, sticking a few extra genes in it, and reprogramming it to become an embryonic stem cell, and that was done in one species, mice.

The development today is now it's been done in another species. And you might say, "Big deal." But that other species happens to be human beings, human cells. And now it's getting close to having direct application in hospitals and in laboratories.

You never know. Maybe we are on the cusp of the singularity and Moore's Law applied to the quantum computational apparatus of life itself will unlock a bounty and a utopian rather than dystopian future for this child of mine dreaming of opulence....,

I - Is the Establishment Reviving Eugenics?

On Sunday, the New York Times published one of the most deeply embarrassing articles I have ever read. This article was so bad that it should have never even had a chance of seeing the editorial light of day. Let me get this point out front and let's be perfectly clear about the focus of my concerns. My liminal awareness suggests to me that this was an intentional move by a very important element of the U.S. media Establishment that has demonstrated a long-standing pattern and praxis of promulgating "scientific" racism to support another and geographically local element of the U.S. Establishment which was recently humiliated by its trusted employee James Watson's clumsy ideological disclosure of some of its institutional and Establishmentarian ass.

THE NY TIMES has a science reporter, Nicholas Wade, who makes very similar claims, using rhetoric that is much less provocative. In Wade’s recent book, BEFORE THE DAWN, he writes: “Over the course of many generations the peoples of each continent emerged as different races” (181). And he later suggests that Jews “may be genetically more intelligent” than other races (that is, other groups, he regards as “races”; see pp. 252-56). Let me say that I believe that Watson and Wade have every right to express their views; I believe in free speech, almost with no limits. But when Watson and Wade say such things, there ought to be ample opportunity for others to lay out the factual and logical errors in their arguments and conclusions. This paper calls attention to Watson’s provocative claims about human races, but when will THE NY TIMES provide space to those who disagree with the more soberly expressed, but in many ways convergent, views of its reporter, Nicholas Wade?

Tell me till you're blue in the face that Watson's views were unknown to the board of trustees at Cold Spring Harbor (and don't be fooled because they host this "Never Forget" archive) and that Wade's pseudo-scientific essentialism is unknown to the NY Times. Cause if you truly believe that, I've got some stories to tell you about Santa Clause and his elves and some swampland to sell you at a firesale discount....,

Such categorical violations of editorial standards for journalistic integrity, scientific validity, and source accountability have to have had a subtextual motivation. That the "grey lady" which has a track record for supporting "scientific" racism would carry it is bad enough. However, this piece of propagandistic garbage was put on the wire and uncritically repeated far-and-wide by such media chains as McClatchy - which themselves never paused to exercise editorial standards for integrity, accountability, and validity.

It took up half of page 8 in the front section of the Kansas City Star as a Sunday Health and Science feature with the even more ridiculous title Geneticists worry data could fuel racial prejudices. That something like this was promulgated far and wide suggests to me that elements in the U.S. Establishment have taken the decision to resuscitate and legitimize eugenics in the U.S.. First and foremost let me be clear that I believe that big money is the prime mover behind this effort. Highly credentialed negrodemics are staging protests in support of genetic racial pseudo-science because there's a buck to be made off of it.

Pharmaceutical and genomics companies have $trong in$entives to grease this pseudo-science on the skids of public awareness and acceptance. However, it never hurts to kill multiple birds with one stone - and to the extent that race remains a vital lever in the U.S. Establishment's system of governance - why not cast fundamental and scientific doubt on the human worth of Black folks - while you set the stage for raking in the big bucks? Isn't this exactly what happened in the entertainment industry in 1988 when organic and politically conscious HipHop was sacked in favor of the race pornography of gangsta RaP. (Rhyming and Posing)

Individual Genetic Variation 5X Greater Than Thought

The First Diploid Sequence of an Individual Human: The highly accurate sequence suggests that our genetic code is five times as variable as we thought

SOURCE: "The Diploid Genome Sequence of an Individual Human" Samuel Levy et al.
PLoS Biology 5: e254

RESULTS: Genomics pioneer Craig Venter and his colleagues have generated a highly accurate sequence of Venter's genome, one that includes the DNA sequences inherited from both his mother and his father.

WHY IT MATTERS: The genome sequence generated by the Human Genome Project, the massive, distributed effort to sequence human DNA that was completed in 2003, was a milestone in the history of biology. But the DNA sequence produced by the project represented just one set of chromosomes (every human has two sets, one inherited from each parent), and it drew on DNA samples from many individuals. As a result, it didn't reflect some of the variability between individuals. ­Venter's diploid genome suggests that genetic variation between individuals is approximately 0.5 percent, not the 0.1 percent that earlier sequencing projects suggested.

METHODS: In the new study, researchers used a method of gene sequencing called Sanger sequencing. The method is more expensive than newer approaches, but it generates longer strings of DNA that are easier to assemble into a complete genome.

NEXT STEPS: Venter and his colleagues plan to add phenotypic information, such as medical records and physical characteristics, to the database housing his genome. This will allow scientists to begin analyzing an individual's genomic information in the context of his or her actual traits.

Don't Take it Personal...,

In the last several months a potential new tool for diabetes prevention has come to market. A test developed by the Icelandic genomics company deCode Genetics and marketed to consumers by San Francisco-based DNA Direct determines whether people carry copies of a genetic variation that can greatly increase the risk of developing type 2 diabetes. Diabetes is the result of a complex mix of genetic and environmental factors. But recent genomic studies have identified several genetic variations that contribute heavily to the disease. The one that exerts by far the biggest influence occurs in a gene called TCF7L2, which was discovered by scientists at deCode in 2005; almost 20 percent of people with type 2 diabetes carry two copies of the high-risk version of the gene. These people are thought to secrete less insulin, a crucial hormone that signals cells to store glucose for energy. A single copy of the varia­tion somewhat increases the risk of contracting the disease, and two copies double the risk, regardless of other risk factors.

The Genetic Information Non-Discrimination Act, which would prohibit discrimination in employment or insurance on genetic grounds, is still lounging in the Senate, despite presidential support and a whopping margin (420-3) in the House of Representatives.

Do you really imagine that there's anything about you that "our" governing aristocrats consider inviolable?

Remember, what, it's all about...,

Synthetic Genomics

The popular view in the British press; Imagine if the engineers of 18th-century Britain could have foreseen the consequences of industrialisation. If they had been warned that it would bring untold wealth and comfort to millions, but would also disrupt human communities, lead to a terrible escalation of war and huge environmental degradation, how then would they have weighed the massive and momentous consequences? And how are we going to? In a couple of decades we could have a nature to organise entirely as we like - the scientist Freeman Dyson suggested black-leaved forests for more efficient use of sunlight in an article on synbio in a recent New York Review of Books. We could be busy creating our own biodiversity to replace the one we will have lost. We might have a "new, improved nature" which is more efficient in meeting our needs and ensuring the survival of future generations: is that a threat or a promise of salvation? And who are we going to trust to make that judgment call?

The governance blueprint at the JCVI; Synthetic genomics combines methods for the chemical synthesis of DNA with computational techniques to design it. These methods allow scientists and engineers to construct genetic material that would be impossible or impractical to produce using more conventional biotechnological approaches. For example, using synthetic genomics it is possible to design and assemble chromosomes, genes and gene pathways, and even whole genomes.

Scientists foresee many potential positive applications including new pharmaceuticals, biologically produced (“green”) fuels, and the possibility of rapidly generating vaccines against emerging microbial diseases. However, as with many technologies, there is the potential for misuse and accidents.

Designing ways to impede malicious uses of the technology while at the same time not impeding, or even promoting beneficial ones, poses a number of policy challenges for all who wish to use or benefit from synthetic genomics. The report presents governance options that attempt to reduce security- and safety risks without imposing undue burdens on researchers, industry, or government.