Here’s the danger in becoming a well-known venture capitalist: You may well become the locus for heated debates over cleantech and environmentalism, even when you’re not expecting it. That’s what happened to Vinod Khosla yesterday, when the Wall Street Journal lashed out with a short hit piece on his policies titled “Khosla’s Conspiracy”.

The motivator was a lengthy interview in last week’s San Francisco Chronicle, in which Khosla, asked whether biofuels are driving up food prices, agreed that they are but said the much greater problem is the price of oil used for transportation. He also suggested that a PR campaign has been organized to smear biofuels. That’s where the WSJ took offense:

Spiking food prices, global shortages and Third World riots have managed to elicit repentance from some ethanol evangelists. Not Vinod Khosla…

“Food prices have been going up,” Mr. Khosla conceded. “But there are massive PR campaigns trying to ascribe most of the blame to biofuels.” Apparently “lots of people” are behind the plot, though Mr. Khosla singled out one: “Clearly, the American Petroleum Institute has been very, very concerned about food prices, and you wonder why.”

Gosh. API is a trade group for the oil and gas industry that is radioactive on Capitol Hill. But we didn’t realize that API’s tentacles were wrapped around the World Bank, the International Monetary Fund and the USDA, all of which blame ethanol for inflationary pressures on food prices. …

Like other green venture “capitalists,” Mr. Khosla now claims that corn ethanol is merely a springboard for the cellulosic varieties, which don’t draw on food stocks. Of course, his investments in such fuels also come with their own handsome subsidies. As long as he’s on the federal dole, perhaps Mr. Khosla should take a vow of embarrassed silence.

In short, the WSJ is agreeing that there’s a PR campaign — but thinks that Khosla, rather than the API, is the master manipulator. True enough, Khosla has stood apart for his interest in biofuels, and helped make himself a strike-point for debate with several doozies, like saying last year that many hybrid-electric vehicles won’t make a difference and repeatedly insisting that corn-based ethanol is necessary to create distribution channels for future, next-generation biofuels.

But is the WSJ right in its own implied assertion that food-based biofuels are a villain? Not really. Essentially, Khosla is right: Food often moves hundreds or thousands of miles from where it’s grown to its target market, so quadrupling the price of transportation fuels over a few years’ time would have driven up prices without the help of biofuels. For its own reasons, the WSJ doesn’t deign to address that argument. Khosla, for his own part, has been bright enough to avoid investing in first-gen biofuels like corn ethanol.

To address these points, and some others of his own, Khosla issued a rebuttal, sending it to us and some other news outlets. We’re reprinting it, with editing to take out some less substantive portions, after the jump.

To my surprise, this morning I found myself cited by the Wall Street Journal as a strong advocate of subsidies for food-based ethanol, and as a recipient of “federal dole” who ought to “take a vow of embarrassed silence.” While I appreciate the Journal’s foray into fiction writing (and I’d love to discuss my status on the dole with my accountant, who recently filed my taxes), I would like to clarify a few of the facts and offer a more rounded view of biofuels and ethanol in general.

I have not advocated subsidies for food-based ethanol. In fact, I strongly believe any nascent technology that cannot exist without subsidies beyond an introductory period will not gain market penetration, and is not worth supporting. I have consistently argued that food-based ethanol cannot scale beyond roughly 15 billion gallons or so in the US, and that making a material impact on replacing oil requires cellulosic or other advanced biofuels. The corn ethanol subsidies that exist today were part of the 2005 Energy Bill, a time when I had no contacts with Washington.

Moreover, I look forward to the WSJ’s complaints about oil’s subsidy bonanza, from tax breaks for drilling, loopholes that allow royalty-free offshore oil leases, manufacturing tax breaks, as well as roughly $7 billion in subsidies in the wake of the Katrina disaster. At a recent WSJ Conference, 75 percent of its erudite audience “voted” (rightly) that oil was more highly subsidized than ethanol.

It is clear that corn ethanol has served as a stepping stone for cellulosic ethanol and other biofuels, mitigating risk and establishing a market. As a venture capitalist, I would not have invested in cellulosic without corn ethanol’s partial alleviation of the risks of creating a market, creating distribution terminals, E85 pumps and starting our flex-fuel fleet… Should we not look past our noses to the larger issues of dependence on oil?

While corn prices certainly have some impact on biofuels, their impact is constantly overstated by sources like the WSJ. In fact, they would do well to see what the USDA has actually said on the subject. Yesterday, USDA Chief Economist Joe Glauber noted: “On the international level, the President’s Council of Economic Advisors estimates that only 3 percent of the more than 40 percent increase we have seen in world food prices this year is due to the increased demand on corn for ethanol.” … Have the editors at the WSJ not been reading the press since they cited the USDA as evidence against me in their op ed? I do believe the UN officials they cite are misinformed and have not done a full food and fuel cost analysis.

I know the American Petroleum Institute (API) has previously engaged in campaigns against corn ethanol, but the current campaign is run by the Grocery Manufacturer’s Association. In fact, based on presentations at the recent WSJ conference, the API and I have similar views on next generation non-food-based fuels, though our assessments of timing may differ…

What is responsible for the bulk of the food price increase? Principally soaring energy costs, increasing demand and droughts in certain countries amongst others. The WSJ fails to note the impact of higher energy prices on food prices: A 2007 study by John Urbanchuk at LECG suggests that increases in petroleum prices have 2-3x the impact than increases in corn prices have on the food Consumer Price Index (CPI) alone.

Furthermore, ethanol has played a significant role in reducing costs for consumers elsewhere. Merrill Lynch has estimated that oil prices may be up to 15% higher than current levels if not for ethanol. What impact might the withdrawal of biofuels and higher oil prices have on food prices? As noted in a press release issued by the USDA yesterday: “According to the International Energy Agency, the biofuels production that has been available to the United States and European markets over the last three years has cut the consumption of crude oil by one million barrels a day. At today’s prices, that’s a savings of more than $120 million per day.”

In the recent Farm Bill discussions, I have consistently advocated for higher cellulosic biofuel mandates over subsidies. Mandates reduce the ability of any specific party to manipulate or hinder the market by limiting access to biofuels. With regards to these mandates, I have proposed an adjustable Renewable Fuel Standard (RFS) that can go up or down every year, depending on the availability of cellulosic fuels at a fair market price like $2.50 per gallon (more than a dollar below today’s gasoline prices). Such a “price capped cellulosic RFS” approach protects consumers by offering them an effective ceiling, while offering investors and producers assurance that all cellulosic fuels that are produced at these reasonable prices will be mandated.

My calculations show that it is conceivable that not one additional acre of land may be needed to replace our gasoline under certain circumstances, but even in more conservative scenarios, the amount of land needed is small. Further insurance to ensure that green house gas reductions from biofuels are significant can come from giving incentives (the carrot) to developing countries to reduce deforestation and providing a stick of banning biofuel (and maybe all agricultural exports) from countries that don’t meet deforestation reduction targets.

Criticism of biofuels is certainly fair game (such as palm oil based biodiesel from Indonesia’s rainforest, which actually hurts the environment more than it helps it), but there is an obligation to stick to the facts. Unfortunately, today’s editorial failed to meet even this basic threshold.

It’s worth noting that this isn’t the first time Khosla has had fingers pointed at him. Two years ago, when he was still at Kleiner Perkins, not yet having formed Khosla Ventures, he was accused of conflict of interest by members of the oil industry. His investing style, which often relies on momentum from excitement over new technologies, can also get him in trouble. But here, it looks like he’s right. If you’ve got your own take, feel free to weigh in below.