Hail Mary Genome and Motherless Meat — Craig Venter interview

Where are we in the hype cycle of synthetic biology?

My complaint is that there are more books and news articles than there are primary scientific papers. I am probably the biggest critic of the hypesters, because it’s dangerous when fields get overhyped. I was at a seminar last year. The guy speaking was not somebody who works in the field. It was all hype in how you design life forms and there are machines that build them automatically. And I got up and said—I really offended the guy—“Everything you’ve heard is bullshit…”We need more solid science.

Can you explain what the Hail Mary genome is and where we are with it?

It’s funny that that term got out there. We’re trying to design a basic life form—the minimal criteria for life. It’s very hard to do it because roughly 10 percent of the genes are of completely unknown function. All we know is if we take them out of the cell, the cell dies. So we’re dealing with the limitations of biology. If we start with this minimal synthetic cell that we’re designing and building now, you could recapitulate all biology by adding components to that cell. In theory, we could eventually get to humans by adding enough components to that genome…

What’s the most promising thing we can do to curb global warming?

There’s not one thing. Obviously, stopping taking carbon out of the ground and burning it into the atmosphere is the long-term thing that has to be done. The least efficient thing we do is feed cows grass, corn, water, to produce steaks. It’s not sustainable.

I think technology can replace meat from animals. I have a name for our enterprise. It’s called “motherless meat” because vegans have a rule that if it has a mother, they won’t eat it. If we can take the genes that produce meat proteins, take the fat from algae cells, we think we can make healthy meat. It will taste more like meat, and you eliminate the cows and all the processes that we do. I like good steaks, but I like lots of things that aren’t sustainable…

Why haven’t you won the Nobel prize?

It would be fantastic if Ham Smith and Clyde Hutchison and I could share the Nobel prize for the first synthetic life forms, and Ham could be a two-time prizewinner. But I don’t worry about it much. I’ve gotten some pretty nice awards. I’m having trouble finding places to put them all.

One of my idols in science. The man who proved that understanding the capabilities of properly directed computational analysis aids pretty much any and all research.

Yes, it can be phonied up by hustlers; but, that’s true of any process or technology. That has nothing whatsoever to do with the potential value of the tech. Someday, I hope – for example – everyone whining about GM foods learns enough about science to understand the enemy is corporate profiteers and not scientists or the potential of their work.

Austrian algae biofuel-pilot plant to be built in Brazil

The state of Pernambuco in Brazil’s northeast is going to become home to the country’s first algal biomass plant, thanks to an agreement between See Algae Technology (SAT), an Austrian developer of equipment for the commercial production of algae, and JB, one of Brazil’s leading ethanol producers. The plant will produce algal biomass from natural and genetically modified strains of algae.

So far, the cost of producing algae has been the biggest obstacle to bringing algae-based fuel to the market, but SAT has introduced a technology that has brought the price down to about that of ethanol – $0.40 – $0.50 per liter. This is possible because production has been transferred from open air ponds to reactors of up to five meters in height, protecting algae from environmental interference…

The new plant will make the most of algae’s potential. One of the products to come out of it will be feedstock for animals, providing an alternative to soybeans. The process also yields algal lipids that can be used to make biodiesel and biochemicals. Algae are also a source of omega-3. As overfishing has become a serious environmental concern, algae are a more environmentally-friendly source of this nutrient, which is commonly sold as a supplement.

Pilot plant operation; but, you can figure that cost will diminish greatly when they ramp up to serious production.

Sugar beets are potentially better for ethanol production than corn

Sugar beets are a more efficient source for ethanol production than corn for a lot of reasons: they use less land, less water and, they can grown in many regions during the winter where it’s too cold to grow corn.

Sugar beets, which are mostly water, use 40 percent less water for growth than corn does, and require about half as much land, according to oil-industry website OilPrice.com. Also, there’s little waste involved in processing sugar beets to alcohol because much of the waste material can be converted to either fuel or fertilizer.

Finding new sources for ethanol is topical because of both rising federal quotas for renewable fuel and the push by many to cut corn-based ethanol production because of concerns over food shortages, waterway contamination and water and electricity requirements. Late last month, U.S. Environmental Protection Agency boosted its 2012 goals for production of non-corn-based biofuels by about 36 percent. This includes quota hikes for sugarcane and algae-based ethanol and cellulosic biofuels, or biofuels produced from grasses, wood and plants. Could sugar beets be the next reasonable large-scale ethanol crop?

The best bet is so-called energy beets which convert more efficiently into sugars for biofuels rather than human consumption.

Traveling zoo’s crocodile turns orange — WTF?


 
A crocodile, known as Snappy, who lives in the city of Geelong, near the Australian city of Melbourne, has suddenly and unexpectedly turned orange.

The eight foot saltwater crocodile began to turn an interesting shade of orange, causing his keeper Tracy Sandstrom, who runs a mobile reptile display called Roaming Reptiles, to fear for his health.

“I thought he was really sick. I thought he was dying,” said Ms Sandstrom.

It turned out the crocodile, who sleeps in a heated bath at night, had been chewing on the water pipes, damaging the filter. This caused the filter to stop working and pH levels in the water to rise.

Experts believe red algae or tannins from fallen leaves which would normally have stayed out of his water due to the filter managed to get in, which combined with the raised pH led to the change in his colour.

In time he should return to his natural green colour.

“There’s no change in his behaviour, his aggression, his territorialism. He’s still a really nasty crocodile,” said Ms Sandstrom.

Har!

No. I do not want one. Even if he had a clock in his belly.

Orange glorp washes ashore at remote Alaskan village – UPDATED

The sudden appearance of orange goo at an Inuit village in northwest Alaska has left experts baffled.

The substance first washed up on the shores of Kivalina, about 625 miles northwest of Anchorage, on Wednesday. It covered most of the harbour, attracting crowds of bemused residents.

On Thursday residents found the orange matter floating on top of the rain buckets they use to collect drinking water.

By Friday, the orange substance in the harbour had dissipated or washed out to sea, and what was left on ground had dried to a powdery substance.

Samples of the orange matter were collected in canning jars and sent to a lab in Anchorage for analysis. Until results are known, Kivalina’s 374 residents will likely continue to wonder just what exactly happened in their village…

Villagers have never seen anything like this before, and elders have never heard any stories passed down from earlier generations about an orange-coloured substance coming into town…

The Coast Guard already has ruled out that the orange material, which some people described as having a semi-solid feel to it, was man-made or a petroleum product.

That leaves algae as the best guess, said village administrator Janet Mitchell.

The concern is if it’s somehow harmful. What will it do to fish, which villagers will soon start catching to stock up for winter, or the caribou currently being hunted, or the berries..?

The village is also about 40 miles from the Red Dog zinc mine, but officials there assured the village the substance didn’t come from them.

Anyone looking for a reincarnation of Rod Serling?

UPDATE: Turns out to be a fungus among us. Perfectly natural.

Marine Phytoplankton in decline over the last century


Using the Secchi disk ca. 1910

Research collected for more than a century is helping Dalhousie University researcher Daniel Boyce in his quest to examine the health of the world’s oceans.

A simple tool known as a Secchi disk as been used by scientists since 1899 to determine the transparency of the world’s oceans. The Secchi disk is a round disk, about the size of a dinner plate, marked with a black and white alternating pattern. It’s attached to a long string of rope which researchers slowly lower into the water. The depth at which the pattern is no longer visible is recorded and scientists use the data to determine the amount of algae present in the water.

More specifically, the research is focused on a particular type of algae known as phytoplankton. This is the first time that significant research has been complied and examined to study the algae levels in the world’s oceans.

Phytoplankton provides food for basically everything in the ecosystem, from fish right up to human beings,” says Mr. Boyce, a PhD candidate with the Department of Biology at Dalhousie. “Phytoplankton is also important in maintaining sustainable fisheries operations and the overall health of the ocean. We need to make sure that the numbers do not continue to decline.”

The researchers found that the number of phytoplankton has been decreasing by a rate of about one per cent per year, for the past 110 years. While this might not seem like a large number, this translates into a decline of about 40 per cent since 1950. In total, just under half a million observations were compiled to be able to estimate phytoplankton levels through the years…

Based on the research collected, phytoplankton levels have decreased in eight out of 10 ocean regions.

Boyce makes the point that we don’t thoroughly understand all the ramifications of such a decline. Wanna bet it doesn’t bode well for our continued existence?

It’s like running out of dirt.

Ghoulish technology for producing Algae Fuel

We cook ‘em and squeeze ‘em.” That’s how LiveFuels CEO Lissa Morgenthaler-Jones describes her San Carlos, Calif.-based company’s process for turning algae-fed fish into oil for fuel using heat and high pressure. It’s a slightly more gruesome way of harvesting pond scum than the mechanical equipment employed by other startups working on algal fuels, but it might be cheaper.

According to a spokesperson for LiveFuels, which was founded in 2006 and announced the kickoff of pilot operations at a 45-acre open pond test facility in Brownsville, Tex., this week, “It’s still being determined just how much less expensive the LiveFuels natural systems process will be compared to traditional mechanical processes, but we do know that current mono-culture process for developing algae require over $1.00 worth of nutrients…just to grow the algae for one gallon of fuel.” That dollar-per-gallon, he said, doesn’t take into account the cost of energy needed to pump thousands of gallons of water in the production process for every gallon of fuel. LiveFuels aims to cut costs by using grazing minnow-sized fish and “a variety of other aquatic herbivores” to harvest algae fertilized by agricultural runoff, and let “ocean currents do its ‘pumping’ for it.” It then plans to make fish meal from the protein solids, and process the remaining oils into either high-value omega-3 oils or fuel.

This process is not without critics who have environmental and ethical objections to raising animals for fuel. LiveFuels also faces technical challenges, such as how to make the system efficient enough to make up for the likelihood that the fish will have to eat more algae than the company would have to harvest directly for the same amount of fuel, notes Greentech Media.

Some investors, however, think LiveFuels has a good shot at making the technology and economics work. The company raised $10 million in May 2007 from David Gelbaum’s quiet Quercus Trust. At the time, LiveFuels reportedly hoped to have its biofuel ready for launch by 2010. At this point, however, the company is still trying to bring down costs.

I like the idea insofar as it produces useful by-products. Not concerned for wee fish souls.

Exxon investing $600 million in making biofuel from algae

Need I repeat myself? Greentech will succeed when and where it’s profitable.

The oil giant Exxon Mobil, whose chief executive once mocked alternative energy by referring to ethanol as “moonshine,” is about to venture into biofuels.

On Tuesday, Exxon plans to announce an investment of $600 million in producing liquid transportation fuels from algae — organisms in water that range from pond scum to seaweed. The biofuel effort involves a partnership with Synthetic Genomics, a biotechnology company founded by the genomics pioneer J. Craig Venter.

Another venture founded in science and technology that papier-mache pundits lampooned as unrealistic and too far ahead of its time.

Despite the widely publicized “moonshine” remark a few years ago by Exxon’s chairman and chief executive, Rex W. Tillerson, the company has spent several years exploring various fuel alternatives, according to one of its top research officials.

“We literally looked at every option we could think of, with several key parameters in mind,” said Emil Jacobs, vice president for research and development at Exxon’s research and engineering unit. “Scale was the first. For transportation fuels, if you can’t see whether you can scale a technology up, then you have to question whether you need to be involved at all.”

He added, “I am not going to sugarcoat this — this is not going to be easy.” Any large-scale commercial plants to produce algae-based fuels are at least 5 to 10 years away, Dr. Jacobs said.

Continue reading

Home foreclosures sprout green pools – can West Nile be far behind?

In the arid Southwest, the backyard pool was the equivalent of the white picket fence: a sign the homeowners had achieved middle-class status. But as the foreclosure crisis emptied neighborhoods, the once-gleaming pools — caked with algae and infested with mosquitoes — became fetid reminders of all that was lost.

One afternoon in Las Vegas, Robert Cole approached a 3,215-square-foot house on Bracken Cliff Court, armed with his chief weapon against the mosquito scourge: a container of silvery fish. A “For Sale” sign advertised the pool and spa out back. You could smell them from the frontyard.

The deck area near the small pool was decorated with red rocks and outfitted with a blue basketball hoop. On the water’s surface, a slick of green algae inched toward a rubber duck.

Cole tossed four fish into the spa and six into the pool, and a few drops of water splashed him. “Ugh,” he grimaced. “I got that nasty stuff on me.”

Cole, 36, is an environmental health specialist with the Southern Nevada Health District. He and six others are charged with stopping the pools from becoming disease incubators. In recent years, as Sin City turned into Foreclosure City, the team has been swamped…

“As the economy went south, the number of green pools went north,” said Chris Conlan, supervising vector ecologist in San Diego County’s Department of Environmental Health, which stages weekly helicopter flyovers to spot rancid pools.

California, Arizona and Florida also rely on Gambusia affinis, or mosquitofish. The inches-long creatures can survive for months in stagnant water, and to them a batch of larvae is a prime-rib buffet.

RTFA. My guess is folks who really didn’t qualify for the mortgages they eventually defaulted on – are also the same who leave the property damaged deliberately or at least conditions like these – a disaster waiting to happen over time.

Just think. We can reintroduce Yellow Fever and Malaria, give West Nile Virus a headstart for the summer.

Am I being too cynical?

Successful test flight of algae-fuelled jet


Daylife/AP Photo by David J. Phillip

A US airline has completed the first test flight of a plane partly powered by biofuel derived from algae.

The 90-minute flight by a Continental Boeing 737-800 went better than expected, a spokesperson said. One of its engines was powered by a 50-50 blend of biofuel and normal aircraft fuel.

The flight was the first by a US carrier to use an alternative fuel source, and the first in the world to use a twin-engine commercial aircraft (rather than a four-engine plane) to test a biofuel blend.

The flight from Houston’s Bush Intercontinental Airport completed a circuit over the Gulf of Mexico, and pilots carried out a series of tests at 38,000ft, including a mid-flight engine shutdown.

“The airplane performed perfectly,” test pilot Rich Jankowski told the Houston Chronicle newspaper.

There were no problems. It was textbook.” Continental Airlines chief executive Larry Kellner described the biofuel as a “drop-in fuel”, which meant that no modification to the aircraft or its engines was required.

The fuel was a blend of algae-derivative and jatropha – which regular readers will know is one of my personal favorites. I’m not certain how far along the production of raw fuelstock has come. Pilot operations and small scale production are still ramping up. But, the rate at which these alternatives are being developed – smack in the middle of a recession – is encouraging.