The glass is both half empty and half full today for Amyris.

Amyris -- a UC Berkeley spin-out that coaxes genetically modified yeast to secrete designer hydrocarbons and medicines -- sold 5.3 million shares for $16 a share in an IPO, below the $18 to $20 price it anticipated in an S-1 filing with the SEC on September 13.

However, the stock is now trading at $17.44 a share. In other words, it's up. Not bad for a company that chronically loses money. While the stock has only been trading for a few hours, if the trend holds, Amyris could possibly avoid the fate of many greentech IPOs -- namely, a below-the-water price. For example, Codexis, which generates enzymes for biofuels, went public at $13 earlier this year, and it now hovers around $9. A123 Systems started at $13.50, went up to $20 and is now in the $9 range. On the other hand, Tesla Motors, which went public at $17, trades now at $21.

Amyris hopes to produce a wide variety of fuels from organisms concocted in the laboratory. Under ordinary conditions, yeast secrete alcohol. To get them to secrete hydrcarbons is a twist on nature that increases the value of the output. CEO John Melo in late 2008 talked about producing biodiesel for $2 a gallon with the process, which also emits far fewer greenhouse gases than regular diesel production.

The company has also struck deals with Brazilian companies to produce fuel in South America. Because the fuel produced in Brazil will be a hydrocarbon and not ethanol, it isn't subject to tariffs when brought to the U.S. The company has also discussed putting plants in Alabama.

Now, here is your ugly reality moment. Oil sells for around $75 a barrel and many startups and the investors that back them have discovered that getting to market is a time-consuming, cost-intensive endeavor. Range Fuels and Mascoma, among others, have experienced delays and continue to spend large amounts of time fundraising. Amyris itself has raised $244 million from investors.

As a result of the difficulties of making it in the fuel space, many companies have branched out into producing oils or chemicals for industrial concerns or food producers. Aurora today confirmed a story we wrote a month ago that suggested the company was retreating from trying to produce fuel to make omega-3s for the food industry instead.

Amyris can also do this. The company has developed organisms that can generate a synthetic version of artemisinin, a malarial medicine. Natural artemisinin grows in mangrove swamps in China and can be costly to harvest. The Bill and Melinda Gates Foundation gave Amyris $40 million a few years ago to develop the drug. Even if sold to governments at bargain rates, the synthetic arteminisin would sell for tens, if not hundreds, of dollars a gallon. Malaria is not going away and no one else can make this, unlike biofuels. Why the company doesn't concentrate on that remains a mystery to me. 

Nonetheless, the company has emphasized fuel in recent years. In December, it paid $82 million to Brazil's São Martinho Group for a 40 percent stake in an ethanol mill project that the parties hope will be operational by 2011 or 2012. The Brazilian company already controls three ethanol plants that make about 600 million liters (158 million gallons) of ethanol per year.  Soon after, it entered into agreements with three other Brazilian companies -- Acucar Guarani, Bunge Limited and Cosan -- to produce ethanol and high-value chemicals. 

The company had 2007 sales of $6.1 million, 2008 sales of $13.9 million and 2009 sales of $64.6 million.  The profits from those years were...just kidding: the company lost $11.7 million in 2007, $41.8 million in 2008, and a whopping $64.4 million in 2009. It lost $36 million in the first half of this year. That big jump in revenue in 2009, however, came because the company booked, and then resold, ethanol from other companies. It had nothing to do with a biological breakthrough. We heard about the proposed public offering back in February and Amyris filed its first S-1 in April.