Not Just Beer -- Yeast Factories For Everyone!

The Venter Institute has just published a PNAS paper detailing their work to turn beer yeast (Saccharomyces cerevisiae) into multi-use factories. These yeast factories can be made to crank out components for completely artificial organisms which the Venter Institute are developing. Artificial organisms that can make synthetic fuels, valuable chemicals and chemical feedstocks, new pharmaceuticals -- a veritable cornucopia of biologically produced treasure.

Senior author Clyde Hutchison added, "I am astounded by our team's progress in assembling large DNA molecules. It remains to be seen how far we can push this yeast assembly platform but the team is hard at work exploring these methods as we work to boot up the synthetic chromosome."

Venter and his team continue to work towards creating a living bacterial cell using the synthetic genome sequence of the Mycoplasma genitalium bacteria.
_AFP

More from Green Car Congress:

The JCVI team continues to explore the capacity for DNA assembly in yeast, and the various applications of this particular method. They conjecture that a variety of combinations of DNA molecules and genetic pathways could be manufactured in yeast, in essence turning yeast into a genetic factory for specifically designed and optimized processes. This advance is being used by scientists at the company SGI in making next generation biofuels and biochemicals more efficiently. _GCC

Venter's team is not the only group working on the genetic transformation of organisms to create biofuels. This Al Fin Energy piece describes the work of the Chromatin-Monsanto alliance.

A South Korean scientific team has just completed the sequencing of the genome of a Korean scientist Kim Seong-jin, as the genomics revolution spreads worldwide. The tools of genomics will soon be inexpensive and ubiquitous enough so that garage hobbyists will be able to sequence various genomes, and experiment by inserting gene stacks -- "artificial chromosomes" -- into plants and animals.

Scientists Creating New Life? Why Not?

High school kids do it all the time in the back seats of automobiles. It may finally be time for over-educated researchers to start doing something that remarkable, for a change?

...a lab led by Jack Szostak, a molecular biologist at Harvard Medical School, is building simple cell models that can almost be called life.

Szostak's protocells are built from fatty molecules that can trap bits of nucleic acids that contain the source code for replication. Combined with a process that harnesses external energy from the sun or chemical reactions, they could form a self-replicating, evolving system that satisfies the conditions of life, but isn't anything like life on earth now, but might represent life as it began or could exist elsewhere in the universe.

While his latest work remains unpublished, Szostak described preliminary new success in getting protocells with genetic information inside them to replicate at the XV International Conference on the Origin of Life in Florence, Italy, last week. The replication isn't wholly autonomous, so it's not quite artificial life yet, but it is as close as anyone has ever come to turning chemicals into biological organisms.

"We've made more progress on how the membrane of a protocell could grow and divide," Szostak said in a phone interview. "What we can do now is copy a limited set of simple [genetic] sequences, but we need to be able to copy arbitrary sequences so that sequences could evolve that do something useful."

By doing "something useful" for the cell, these genes would launch the new form of life down the Darwinian evolutionary path similar to the one that our oldest living ancestors must have traveled. Though where selective pressure will lead the new form of life is impossible to know. _Wired

Everyone will be wanting to ask, "Yes, but what does it actually do?" Just creating a living cell from spare parts would certainly be a first, but what do these particular scientists plan to do as an encore?

We understand what Craig Venter and his merry band of biochemists, geneticists, and microbiologists are trying to do: they are trying to overturn the entire balance of energy on the human planet of Earth. Venter and his crew plan to create organisms that create fuel--and to become the world's first trillionaires in the process. That is the type of over-riding ambition and hubris that I can respect.

Creating artificial cellular life in the lab will be incredibly useful for bio-science and biotech, of course. Each artificial cell is a powerful bio-model platform, for testing every little function of the cell--and perhaps inventing new ones. It is a profound area of study, in itself. But Venter plans--once again--to do an "end around", bypassing the masses of scientists huddling in the center of the field. He intends to go all the way to the endzone via one Hail Mary pass.

Exciting and most interesting times for the biologically trained.

Artificial Cells, Synthetic Biology, Revolutionary Life Forms

Living cells are able to thrive miles below the earth and the sea, and can survive transit through the vacuum of space. While we are waiting for nanotechnology to come of age, some revolutionary biologists are learning to design novel life forms almost from scratch--life designed for specific human purposes.

The people who are defying Nature's monopoly on creation are a loose collection of engineers, computer scientists, physicists and chemists who look at life quite differently than traditional biologists do. Harvard professor George Church wants "to do for biology what Intel does for electronics"—namely, making biological parts that can be assembled into organisms, which in turn can perform any imaginable biological activity. Jay Keasling at UC Berkeley received $42 million from Bill Gates to create living microfactories that manufacture a powerful antimalaria agent. And then there's Craig Venter, the legendary biotech entrepreneur who made his name by decoding the human genome for a tenth of the predicted cost and in a tenth of the predicted time. Venter has put tens of millions of dollars of his own money into Synthetic Genomics, a start-up, to make artificial organisms that convert sunlight into biofuel, with minimal environmental impact and zero net release of greenhouse gases. These organisms, he says, will "replace the petrochemical industry, most food, clean energy and bioremediation."

Source

Many of the things that Drexler, Merkel, and Freitas expect out of future nanotechnology can be accomplished in the nearer term by specially designed life-forms. Biology has an evolutionary head start of billions of years over nanotech. While Crick and Watson made their earthshaking discoveries in the mid-20th century, equivalent foundational discoveries for workable molecular assembly nanotech have yet to be made.

It is certainly true that a mastery of biology possessed by malevolent individuals could endanger all life on earth, it is more likely that such a mastery would be used to move industrial and chemical processes to cleaner and more sustainable forms.

Complexity: When Computer Models Simply Will Not Do

Biological systems are too complex to be well-modeled by computers, currently. Medical personnel are on the front lines, saving lives. Society requires a far higher level of certainty of results from medical research than can be achieved by today's computer models.

Most biological models make use of lab animals such as mice or rats. But increasingly, acellular models are used. A fascinating type of biochip that allows placing various cellular components on a silicon dioxide surface--connecting them by microfluidic channels--promises to provide increasingly ingenious acellular models for biomedical research.

Now, in a major breakthrough, a group of researchers at the Weizmann Institute of Science in Israel, led by Roy Bar-Ziv, in collaboration with Margherita Morpurgo from the University of Padova in Italy, have designed a molecule affectionately called the “daisy” that is able to bind genes onto chips in miniature patterned arrays.

Bar-Ziv and co-workers have been able to use the daisy to pattern tiny regions of double-stranded DNA onto silicon dioxide surfaces. Indeed, these immobilized genes are able to conduct their business on patterned silicon substrates without the need for living cells. These biochips can act as protein microtraps, selectively trapping specific proteins from crude cell extracts with high spatial resolution. Moreover, the gene sequences immobilized on the biochips can be used for the on-chip production of proteins by transcription/translation processes such as those occurring within cells.

Bar-Ziv and his colleagues have also demonstrated the integration of these systems with microfluidics. Integration with flow systems is of interest for the fabrication of miniature assembly lines on chips, wherein proteins can be synthesized on the chips and transported to their final destinations through microfluidic channels.

In a remarkable demonstration of the utility of the daisy approach, the researchers have patterned two different genes as alternating stripes on a biochip. The protein synthesized on one stripe diffuses to the second stripe where it regulates the synthesis of a second protein. More complex artificial gene circuits can be envisioned by extending this protocol, and thus the biochips may be able to carry out complex cascaded information-processing functions, mimicking those in living organisms.

Source.


While computer modeling may be sufficient for political organisations such as the IPCC and Greenpeace to predict an apocalyptic future for the earth, for down-to-earth bio-researchers who absolutely must provide reliable results, computers are simply not good enough. But bio-engineers, bio-physicists, and molecular biologists working with nanotechnologists are growing increasingly clever in designing useful models that do not use lab animals.

It will be many years before biomedical research no longer needs to sacrifice large numbers of lab animals for the saving of human life. But it is encouraging to see the creation of "artificial cells" on silicon, and it is fascinating to contemplate the possibilities they offer.

Synthetic Biology: When Genetic Engineering Goes Ballistic

At the moment, what passes for genetic engineering is mere pottering. It means moving genes one at a time from species to species so that bacteria can produce human proteins that are useful as drugs, and crops can produce bacterial proteins that are useful as insecticides. True engineering would involve more radical redesigns. Source.

Those of you who thought Craig Ventner was washed up and retired to his island home, may be in for some disillusionment. Instead, Ventner is well-connected with venture capital, and in the forefront of the revolutionary movement known as synthetic biology.

In the short run such engineering means assembling genes from different organisms to create new metabolic pathways or even new organisms. In the long run it might involve re-writing the genetic code altogether, to create things that are beyond the range of existing biology. These are enterprises far more worthy of the name of genetic engineering than today's tinkering. But since that name is taken, the field's pioneers have had to come up with a new one. They have dubbed their fledgling discipline “synthetic biology”. Source.

The potential payoff from achieving mastery over the life-mechanisms of even simple cells, is difficult to overstate. That is why more and more smart money venture capitalists are being drawn to the bright lights of the field.

Dr Ventner reckons he will be able to synthesise a working bacterial genome from scratch within two years. More complex genomes, of the sort that make plants, animals and fungi, will take longer. But they, he thinks, should be possible within a decade. Even this definitive erasure of the distinction between the living and non-living worlds is not, however, the most radical idea in synthetic biology. Some people want to go beyond the toolkit that evolution has provided and create biological systems that work with a chemistry that is not found in natural living things. Source.

Here is an interesting close-up look at this year's Synthetic Biology 2.0 conference from Synthesis blog. Read the linked post, then click around to read descriptions of the entire conference. You may find, as I did, that the comments can also be interesting.

A good place to go to acquire an understanding of what synthetic biologists are doing, is the Santa Fe Institute. Abstracts of a few SFI papers on synthetic biology can be found here, here, here, and here. There are a lot more available, along with the full text pdf files.

If you think you understand the world, you are wrong. If you think you know what tomorrow will be like, based upon what yesterday and today were like--you had better stock up on alprazolam. This roller coaster is almost to the top of the first hill.

New Reports on Synthetic Biology

Biosingularity Blog links to an exciting suite of articles in The Scientist. These articles discuss different aspects of the revolutionary new quest to build artificial living cells. Go here for the starting point, then follow the links to the other stories.

Craig Ventner (pictured above), is a prominent part of the The Scientist discussions. He is famous for accelerating the project to map the human genome, and now wants to be the first to synthesize a living, reproducing cell. Different researchers are working on various approaches to synthetic cells.

Thanks to Snowcrash at Biosingularity for the link.

Creating living, reproducing cells, is one way to learn about the necessary mechanisms of life that have evolved over billions of years. It may be the best way to learn to improve on those mechanisms, in the long run. The hit or miss methods often used in biological research have worked well in discovering the various pieces of the puzzle. We know that the puzzle has more pieces than we have in the box. We also know that the pieces, once we know we have them all, will have to be put together in certain ways, or the puzzle will not "work."

Fortunately there are many tricks that have been learned over the years in science, engineering, information science, etc. that should come in handy in the many variations of the assembly process.

Synthetic Biology Incorporated

An article at Biosingularity blog announces the formation of Synthetic Genomics, Inc., another Craig Ventner startup. Given the successful track record of Dr. Venter's enterprises, the prospects look pretty good for SGI.

Quoting from Biosingularity:
The ability to make extensive changes to the DNA of a chromosome, assemble it, and insert it into an organism is in its infancy, and the capability to assemble chromosome length strands of DNA will be key to the success of the company. Synthetic Genomics, Inc. is developing new scientific processes to enable industry to design and test desired genetic modifications. Using the genome as a bio-factory, a custom designed, modular “cassette” system will be developed so that the organism executes specific molecular functions. Synthetically produced organisms with reduced or reoriented metabolic needs will enable new, powerful, and more direct methods of bio-engineered industrial production.