Lately, Republicans have been on a tear against government funding for clean energy. The fact that yet another company backed by federal loan guarantees — Beacon Power, a flywheel storage company — just filed for bankruptcy won’t help matters. And, today, the Energy Department’s watchdog, Gregory Friedman, is telling Congress that the agency was ill-equipped to hand out the $35 billion gusher of stimulus money it received two years ago. Way back in 2005, there was a broad consensus in Congress that the government had a role to play in funding new alternative-energy sources. Now? Not so much.

(Koichi Kamoshida/Bloomberg)

Now, there are a few caveats here. As my colleagues have reported, clean-tech investments can be very volatile, in part because projects like solar farms are so capital intensive. Sometimes, timing is everything, and it can be hard to spot long-term trends by glancing at a few quarters. Just today, for instance, Ernst & Young announced that venture-capital investment for clean tech actually rose 73 percent over the past year to $1.1 billion, as money flowed into energy storage and renewables. Plugging that number into Third Way’s charts would make the picture look somewhat less dire.

When I asked Third Way’s Josh Freed about this, he noted that the uptick in the third quarter of 2011 was encouraging. “However,” he added, “looking under the hood, we have some serious concerns. First, the move to later stage investments is not reversing, so we still have fewer new companies with access to capital to scale up; second, the bottom is likely to drop out of the federal investment side of clean tech.” Venture capital, he notes, tends to follow federal investment. If Congress decides to withdraw support for alternative-energy technologies, private investors will start to edge away, too.

One thing to note about the Energy Department’s much-dissected loan guarantee program, however, is that it also tended to focus on large, well-established firms (some of the biggest loan guarantees went to giant companies like Ford and Georgia Power). In part, that’s because — as we’ve seen with Solyndra — trying to lavish too much money on overly risky start-ups tends to lead to political blowback. “Even if, by some miracle, the government could make good business decisions void of political influence, such programs are still doomed to failure because the public and media won’t allow for even one loan or investment to fail,” argues clean-tech venture capitalist David Gold.

There’s not really an easy solution here. As David Victor of UC San Diego and Kassia Yanosek of Tana Energy Capital recently wrote in Foreign Affairs, plugging this “commercialization gap” — bringing novel clean-tech ideas to market — is particularly tricky because “the costs are greater and the best policies require government agencies to work alongside private actors without undermining market competition.”

That’s part of the reason why the two authors also predict a coming “crisis” for clean energy in the United States, especially with the stimulus expiring and a price on carbon unlikely. The vast majority of clean-tech investments are currently pouring into well-established technologies: installations of rooftop solar photovoltaic panels, for instance, have been booming thanks to a Treasury grant program that’s soon set to expire. But as for newer, more innovative energy technologies — the things that, as California is discovering, we may need to drastically curb emissions? There’s less reason for optimism there.