This article is the last in a 5 part series by Alexis Madrigal, coming to us via Spot Us. Read part I here, part II here, part III here and part IV here.

Dozens of companies up and down Silicon Valley are hard at work rethinking the gasoline that's powered internal combustion engines since Henry Ford oversaw assembly lines. They're designing and growing fatty algae whose bodies are filled with oil that just so happens to mimic diesel fuel. They're using genetically-modified bacteria to munch tires and sugar cane into petrol. Anything that contains carbon, they reason, can be turned into a liquid hydrocarbon with the right combination of chemical process and engineered microbes. They call these experiments advanced biofuels, and they, we're assured, will be better for the environment than ethanol.

And yet, for all the press, all the beautiful minds at work on the best science, the ultimate success of the enterprise might rest in the crusty industrial checklist of the logistics situation. Trains, trucks, and the people who connect one to the other could have as much of an impact on the market as the particular molecular manipulations that produce the right fuel.

Some advanced biofuels claim to fit neatly into certain pieces of the current liquid fuel distribution system, but until they're actually produced at scale, it won't be possible to know how many devils will need to be exorcised from the details.

"Everybody is excited about cleantech and having some wiz bang widget, but it doesn't matter if you're talking about algae or jatropha biodiesel or switchgrass cellulosic ethanol," says Iyer of Primafuel. "None of it matters unless you can get it to market."

To get to market, the fuel will have to go through the Crocketts of the world. The companies producing the fuel will have to interact with the Kinder Morgans, the farmers, and the Mike McDonalds. Do green venture capitalists, recently converted from the IT ranks, have contacts in these areas? Do Berkley molecular biologists want to spend their time getting dirty in the industrial parks of the exurbs?

In the solar industry, the schism between purists and those like VC-backed Ausra, which put a former fossil fuel power plant executive at the helm, continues to grow. Who better to get a power plant built, the Ausra officials told me, than someone who'd built a few, no matter how fossilized its fuel?

It's a split that Iyer's company is keenly aware of. When I first met Iyer in a San Francisco bar last winter, he spoke passionately about the difficulties of connecting the current and future fuel distribution networks. The challenge is not, however, just the nozzles and tanks, but the people who control them, too.

Iyer, who is of Indian descent, noted that he's not the guy they send to sell their services to biofuel producers in the largely white, rural regions of the Midwest. Take a look at the company's website: you won't see the words "green" or "environment" anywhere.

The highly pragmatic approach extends beyond their branding. Though their prospective Sacramento biodiesel plant will produce some of the cleanest fuel in the nation, it will also provide a terminal for unit-trains filled with old-school ethanol and tanks to store all types of biofuel.

The facility is the type of infrastructure that could allow California to satisfy its current demands while allowing it the flexibility to incorporate better fuels as they come along. It would increase the energy security of the Bay Area and San Joaquin Valley without locking the region into ethanol use forever.

This flexible execution and ideology is the only way that Iyer thinks his company can build a big enough tent to convince a host of skeptical groups -- investors, regulatory agencies, refiners, environmentalists -- to support the same plan for the future of fuel.

"At the very highest level, it's our vision that this facility enables a wide range of low carbon fuels making it into the marketplace," Iyer said. "The challenge is that in order to justify investing more than $100 million in steel and concrete, you need to ensure this facility can start up on time."

Primafuel is doing what it can to make sure that happens. They've picked up a California Air Resources Board grant and a Davos Technology Pioneer award. They've made it most of the way through the environmental permitting process and are in the final stages of negotiating a complex financing package. If all goes well, they'll break ground in the last quarter of this year and be operational by the end of 2009.

"It is a market changing investment," Iyer maintains, but it isn't one that many companies are eager to make. Squeezed on one end by Big Oil companies and on the other by consumers unhappy with high gas prices, companies in the fuel distribution business don't get to innovate through iterations. There's no beta for a rail terminal, and a fail whale for the gasoline system wouldn't be cute.

In other words, if we want alternative fuels and electric vehicles to transform the century-old car and society with it, we can't take Lincoln's proverbial advice: we have to change fuels in midstream.