LS9, a startup using synthetic biology to produce a renewable petroleum product, says it has secured Bill Haywood as its CEO to lead the company’s transition from research and development into production. The three-year-old company has been led by President Bob Walsh, who joined in July 2007, and before that Doug Cameron had the role of acting CEO, who at the time was also the Chief Scientific Officer at Khosla Ventures (though has since joined Piper Jaffray as Chief Science Advisor. LS9 is based in South San Francisco (update: recently moved from San Carlos, Calif.), and has raised at least $20 million from Khosla Ventures, Flagship Ventures and Lightspeed Venture Partners.

Update: We had a long chat with Haywood, who says the company is planning on creating a demonstration facility in the later half of 2010 that will be able to produce 2.5 million gallons of biofuel per year. LS9 will also be looking to raise a funding round of $75 million to $100 million in the first or second quarter of 2009.

LS9 is one of several biofuel startups using synthetic biology and genetics to develop biofuels that are more energy-dense than current first generation biofuels, require less energy to produce and can be distributed through the existing petroleum infrastructure. LS9 makes microbes that can convert fatty acids into hydrocarbon-based biocrudes and industrial chemicals. Other startups with similar aims include Craig Venter’s Synthetic Genomics and Amyris Biotechnologies.

We haven’t heard much from LS9 over the past year, and likely it was heads-down proving the technology worked. Now that Haywood has joined, the company says it will be shifting into commercial production. Haywood was previously senior VP of refining for Tesoro Petroleum, and he has more than 30 years of experience in the fuels manufacturing business.

We worried last week that the credit crunch would hurt cleantech, and especially ethanol. Now this week there are two more additions to our ethanol death watch map, Visions Fuels in Iowa and Oklahoma Sustainable Energy, embedded below. In both cases the financial crisis on Wall Street was blamed for drying up investments.

View Larger Map The capital-intensive business of ethanol production is getting hit hard as project financing slows to a trickle, and we expect to add more pins to our map. This could be the end for Vision Fuels, which announced today it had to cancel its Des Moines plant and lose a nearly $1 million deposit. Vision Fuels had originally planned on building three plants but abandoned plans for the two other plants in July.

Unfortunately, it’s not as if the developers who moved earlier and got funding before the collapse are fairing much better. Record corn prices and tumbling oil prices are squeezing already thin margins for grain-ethanol producers. Citigroup thinks three-quarters of all U.S. ethanol plants are at risk of closing.

In a separate twist, nepotism, conflict-of-interest laws and Missouri state politics have stalled incentives for an ethanol plant in Missouri.