Biofuel companies may be getting it right this time, learning some lessons from ethanol's failures. When I say that, what I mean is they're not focusing on fuels at all. Companies such as Amyris (Nasdaq: AMRS), Solazyme (Nasdaq: SZYM), and Rentech (AMEX: RTK) are often lumped into the biofuels category because that's what people understand, but that's probably not where their future is.

Each company, in its own way, is finding ways to diversify their potential products beyond biofuels. Since biofuels will likely suffer from the same problems that ethanol did, a lack of feedstock or an increase in feedstock prices if biofuels became successful, this is a wise move for these companies.

A new business model
The new model these companies are using focuses first on making high-value products instead of trying to take over the world with volumes of biofuels.

Amyris says it is focusing on existing scale and high-value products made from current strains, which includes cosmetics, plastic additives, and flavors and fragrances. This will allow the company to diversify into higher volume lubricants and fuels in its new plants. The problem right now is that increased volumes of diesel and other high-volume products have put a damper on margins.

Rentech, which has its sights set on biofuels as well, actually makes most of its revenue from nitrogen fertilizer. It's the fertilizer business that drives results right now and keeps the company solvent.

Solazyme's products can be used to make everything from makeup to food products to jet fuel. This is a diverse base that the company hopes to draw a number of product lines from. Dow Chemical (NYSE: DOW) and Unilever have partnered with the company to make products such as soap, detergent, and de-icing materials. These products have higher margins than fuel, but will they grow fast enough?

Why I'm cautious
Unlike many of my Foolish friends, I'm much more worried about these biofuel stocks, in particular Solazyme. The company makes oil from algae using a variety of feedstocks. It is very proud of powering a U.S. Navy destroyer, a Maersk cargo ship, and the first U.S. commercial flight on biofuels with United Airlines. But what's to keep this company from going to way of ethanol?

Solazyme uses "low-cost plant sugars" such as sugarcane, switchgrass, corn, and forest residue. I feel like I've seen this movie before. Sugarcane and corn are already used for biofuels, so why reinvent a failed square wheel? A number of other feedstocks are named, but these sources of energy must grow from somewhere, and ethanol showed that a cheap feedstock can become expensive when you try to scale up production.

You would think a company like this would at least be growing like a weed, like Amyris is. But Solazyme saw revenue fall 35.7% in the fourth quarter. Product revenues are barely big enough to mention. Yes, the company has a joint venture with Bunge (NYSE: BG), which could produce a massive amount of oil, but the financial terms aren't known so it's hard to judge the impact.

Some will say that I don't understand the model, just like I didn't understand Energy Conversion Devices, Ener1, or A123 Systems. All of these companies relied on hope in their business plans, just like Solazyme does: hope that the market will grow quickly, hope that raw material costs won't rise, hope that production plants aren't more expensive than planned, and most importantly hope that they won't run out of cash before all of these things take place. Hope is a tantalizing thing, but it doesn't often make a good investment.

Foolish bottom line
It's far too early to say that any of the emerging biofuels companies will be successful or even survive. Losses have been piling up, and the companies face a lot of the same challenges that ethanol faced in its early days. Without government support long term, I don't see this ending differently unless these companies can make nutritionals, health sciences, or lubricants a big market in a short amount of time.

I've watched too many companies built on cool technology and a lot of potential fail to make it over the last few years to buy into biofuels stocks right now. My contrarian view even leads me to make an underperform call on Solazyme over the next three years. I just don't think the company will ramp as quickly as expected and its big cash cushion will burn up quickly.

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