As Andy Pollack paraphrased Venter in the New York Times, "These watermarks, Dr. Venter noted, contain coded messages. Sleuths would have to determine the amino acid sequence coded for by the watermarks to decipher the message." Functionally, the watermarks distinguish the synthetic genome from its natural counterpart. The Genbank sequence for the modified Mycoplasma synthetic genome contains five of these watermarks, and speculation has flown about what they were, as Venter refused to disclose them to press.

In response to a phone call from Wired Science, David Wheeler and Tao Tao of the NCBI checked into the genetic sequence submitted by Venter's Institute and found the watermarks hidden in plain sight. For the first time, we reveal the five coded messages that will go down in history as embedded in the first synthetic genome ever created after the jump.
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Such viruses would be one of the first potential applications of the emerging field of synthetic biology, which aims to design and build useful biomolecular systems.

The researchers at the Massachusetts Institute of Technology and Boston University have already demonstrated one such virus. They say they believe many more viruses could be created to target different species or strains of bacteria.

"Our results show we can do simple things with synthetic biology that have potentially useful results," said MIT-Harvard doctoral student Timothy Lu, who led the research with Boston University Professor James Collins.

The work -- supported by the U.S. Department of Energy and the National Science Foundation -- is reported in the July 3 issue of the Proceedings of the National Academy of Sciences.

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They have already successfully demonstrated one such virus, and thanks to a "plug and play" library of "parts" believe that many more could be custom-designed to target different species or strains of bacteria.

The work, reported in the July 3 Proceedings of the National Academy of Sciences, helps vault synthetic biology from an abstract science to one that has proven practical applications. "Our results show we can do simple things with synthetic biology that have potentially useful results," says first author Timothy Lu, a doctoral student in the Harvard-MIT Division of Health Sciences and Technology.

Bacterial biofilms can form almost anywhere, even on your teeth if you don't brush for a day or two. When they accumulate in hard to reach places such as the insides of food processing machines or medical catheters, however, they become persistent sources of infection.

These bacteria excrete a variety of proteins, polysaccharides, and nucleic acids that together with other accumulating materials form an extracellular matrix, or in Lu's words, a "slimy layer," that encases the bacteria. Traditional remedies such as antibiotics are not as effective on these bacterial biofilms as they are on free-floating bacteria. In some cases, antibiotics even encourage bacterial biofilms to form.

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This idea came up in conversation with Pat Mooney of the ETC Group in regards to an article I'm writing about the regulation of synthetic biology -- not just the "Will it kill us all?" angle, but how regulators and the public can shape this emerging field in a way that ensures its benefits to society.

Pat mentioned something I'd not heard about before: two years ago, the UK convened juries on nanotechnology. They brought together randomly picked people to grill nanotech researchers about what they were doing, how they were doing it, and what it all meant.

The scientists were initially skeptical, and understandably so. If I were a nanotech researcher at the time, I would have worried that discussions would be hijacked by overblown Gray Goo-type fears. But the conversations ended up being quite productive.

Scientists reassured the public that they wouldn't accidentally ruin the world. The public encouraged scientists and the government to take precautionary safety measures, and -- just as important -- to think about what sort of projects deserved high-priority funding, and how to make sure that the products would be accessible and affordable. The suggestions they made weren't legally binding, but they helped inform how nanotech research in the UK was conducted and guided.

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As an analogy, take nanotechnology: on the nano scale, materials take on new, sometimes quantum physical properties, meaning they could pose unexpected health risks. Likewise, a genome built from scratch (and perhaps with new building blocks, beyond A, C, T and G) could be harder to evaluate than a well-known bacteria with a single gene tweak.

On the other hand, maybe current regulations are perfectly sufficient. The important thing is that regulators think about this now, because the field is exploding -- and, if a quick round of press office calls is anything to judge by, they're not. Press officers at the EPA, FDA and US Patent Office all had to ask what synthetic biology is. (The NIH officers weren't in the office, but the agency has at least hosted talks on possible bioterror applications. That's only a small aspect of synthetic biology regulation, but it's a start.)

Not that this means people at the various agencies haven't thought about synthetic biology (and the press people were very helpful about looking to see.) But at the very least there aren't any formal programs to consider regulatory approaches. This is troublesome in every case, but particularly so at the Patent Office, where an overly-broad approach to intellectual property -- for example, granting exclusive patents not just on a technique for building a genome that performs some function, but on the very idea of building a genome to do that function -- could stunt research.

I'm currently awaiting some calls back. Hopefully they'll tell me that, yes, they really have thought about all this....

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Venter’s goal in transplantation of the genome from one species of bacteria into another bacterial species is to help take carbon dioxide out of the atmosphere, with the eventual hope of helping clean up the atmosphere and reducing the United States’ dependency on petroleum products.

Many scientists are calling Venter’s accomplishment a very important step for eventually creating the first synthetic life form.

As a further step, Venter is also working toward synthesizing the entire genome—which consists of a length of 580,000 DNA units--of the parasitic bacterium called Mycoplasma genitalium. It is considered the smallest free-living bacterium (that is, able to live outside a host).

If Venter is able to produce the first synthetic life form out of the Mycoplasma bacterium, his research team will validate human ability to control the mechanism of a living organism through synthetic biology, a more difficult form of genetic engineering, which does not just move genes into bacteria but actually controls them for a specific purpose.

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Working at a central lab facility in the San Francisco Bay Area, researchers will create new forms of life that will produce ethanol with unprecedented efficiency. This field of science -- synthetic biology -- will be used to make crops that are extremely tough and productive. Optimized plants will push the limit of fuel production per acre of land. The same laboratory techniques will be used to design organisms that convert plant material into fuel in the most cost-effective manner possible.

Biodiesel and ethanol are currently the two leading types of liquid biofuel. Ethanol can be blended with gasoline to make a somewhat clean-burning fuel called E85.

Fermenting sugar is the easiest part of making ethanol. Humanity has been adept at this for millennia, but there is still a lot of room for improvement. Most microbes die when the alcohol concentration in a tank gets too high. Stronger microbes will be able to work longer and possibly break down a wider variety of substances to make fuel.

Brazil is far ahead of the United States in biofuel production. In Brazil, ethanol is easy to make because the juice of sugarcane crops can be directly fermented. Many crops in the United States are low in sugar but very high in the carbohydrate cellulose, which must be turned into fermentable sugar. That transformation is a costly and expensive process. Researchers at JBEI will design new organisms and enzymes to convert cellulose to sugar as efficiently as possible.

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This year, the team is preparing another entry in the exclusive competition, which will be held in November. They are studying the pathway of lipid production with the ultimate goal of designing machines that can cause plants to produce more or less oil. If successful, this technique could develop alternative plants for energy production. Earlier this month, they received the DNA package from MIT with which they’ll do their work.

Victor Ho, a doctoral student in biochemistry, said the team is working to design a way to shorten the time needed to analyze whether a particular genetic process has occurred.

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In the laboratories of the Venter Institute, in Rockville, Maryland, scientists have made the first steps towards building a lifeform from scratch. Welcome to the world of synthetic biology, where entirely new species of viruses or bacteria are designed and created in order to perform useful functions - for example to convert plant matter to fuel or to digest pollution. The aim is to select desirable genes from existing species and string them together to create artificial cells.

The race is now on to create the world's first entirely synthetic organism, and it appears that the Venter Institute - named after Craig Venter, the bio-entrepreneur who mapped the human genome using his own DNA as the template - is leading the way.

The institute has filed an application for worldwide patents on what it believes are the 381 essential genes needed to make an organism.

This "mycoplasma laboratorium" has not yet been created, but already the ETC group has coined a catchy moniker for it. "Goodbye Dolly... Hello Synthia," exclaimed their press release, calling for the patent applications to be rejected on several grounds.

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Other scientists who did not participate in the research praised the achievement, published yesterday on the Web site of the journal Science. But some expressed skepticism that it was as significant as Dr. Venter said.

His goal is to make cells that might take carbon dioxide out of the atmosphere and produce methane, used as a feedstock for other fuels. Such an achievement might reduce dependency on fossil fuels and strike a blow at global warming.

“We look forward to having the first fuels from synthetic biology certainly within the decade and possibly in half that time,” he said.

Richard Ebright, a molecular biologist at Rutgers University, said the transplantation technique, which leads to the transferred genome’s taking over the host cell, was “a landmark accomplishment.”

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