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Archive for July, 2009|Monthly archive page

Protein folding is fun and games, and more

In Uncategorized on July 28, 2009 at 3:25 am

Despite the obvious advantage of having humongous amounts of computing power at one’s disposal, it seems that some problems’ solutions yet rely on humans’ puzzle-solving machinery, and our ability to recognize patterns that elude our hard drives. How our neural circuitry takes the leaps of logic that it does is another question, but since the capability is available, the win-win situation should be capitalized on–you get the satisfaction of solving a puzzle, and scientists get a candidate folded structure for a protein, for which the only available structural information is the primary sequence.

Gamers unravel the secret life of protein,” John Bohannon (Wired Science)

From inside the beltway: watching Waxman et al working the fields

In Policy on July 28, 2009 at 3:24 am

This summer in DC, we live in interesting times. Not only are we unusually likely to hear gunshots on the national mall, or fear imminent and deadly collisions on the Metro – oh no. The greatest fears, the looming things that fill my life as an intern with fear and trembling, come from the throats of House Agriculture Committee members, the ominous lineup at a hearing, the writings of renowned Princeton professors. Environmentalists look at the House climate bill, its massive, morning-of-vote manager’s amendment, Senate stirrings, and “aspirational” G8 emission reduction targets in awe. I have found myself open-mouthed at my computer screen and the television. “They must know what that means,” I’ll say, until the next shortfall, the next halfhearted compromise – “or don’t they?”

All around my ideological corner, we are alarmed. But for policymakers all around this fine city, global climate change seems – at most – just a wave to ride.

My area of expertise when it comes to wave-riders lies in the agriculture sector, where the waves are quite crowded. Biotech, ethanol, organic, you name it – if it’s ag, it wants a piece of the climate legislation pie*. And boy, is ag ever eating well.

Ag’s slice of Waxman-Markey (or HR 2454, or just “the House cap-and-trade bill”) comes in diverse flavors. First, unlike practically every other sector of the economy, agriculture’s greenhouse gas emissions – which amount to over 7% of national emissions (see EPA GHG inventory) – are not to be reported, regulated, or capped. This, on its own, is an apparently arbitrary** boon to agribusiness that many environmentalists likely find reproachable.

Additionally***, rural electrical cooperatives would receive a considerable portion of cap-and-trade permits for free under the House bill – understandable, given that co-ops are nonprofit organizations serving vast swaths of America.

But wait! Most of ag’s pie slice consists of juicy offsets. If an agriculturalist did; happen to reduce his or her emissions under Waxman-Markey, he or she could have those reductions verified as offsets and sell them to businesses in capped sectors in place of emissions allowances. In other words, ag can make money doing what other sectors have to spend money doing.****

What constitutes an offset? On the official list, introduced in an amendment by House Agriculture Committee Chairman Collin Peterson (D-MN), are plenty of organic practices, such as cover cropping and reduced fertilizer application, along with more expensive no-till methods and waste digesters. Some claims are legitimate and some are questionable, but so far, regardless of scientific validity, ag has gotten practically everything it’s asked for.

I cordially invite you to take a look, for instance, at recent and past research on the usefulness of no-till agriculture to the end of carbon sequestration in soils. You can find an interesting discussion of that controversy over on the Climate Progress blog. The current, very erasable bottom line is that we don’t really know if no-till does any good so far as climate is concerned – but there it is on the list, emblazoned by Chairman Peterson because, yea verily, this pie is tasty.

All that said, inside the beltway, we are quite aware that health care is the issue of the day. The Senate will not finish markups on its climate and energy legislation until September. With whatever additional time is allotted – I hazard that additional time will be allotted – the legislation will hopefully come to a vote and become law (or not) in time for the Meeting of the Parties to the Kyoto Protocol in Copenhagen this December. There’s still a lot of room for change to occur – probably negative change, from an enviro’s perspective, since the Senate ag bloc is even stronger than that in the House. The slice will grow larger or, if you prefer, the wave-riding will not cease.

But Science in Society is about the interface between science and policy – in essence, about trying to collapse the difference between what is usual, probable, and political and what is right. So I encourage you to do your own research on the provisions of Waxman-Markey, and on the activities of the Senate, and get in touch with your congresspeople accordingly. This is your country, your planet, and – let’s face it – your lifetime that will see the impacts of this legislation. Don’t let lobbyists or the party line gobble it up.


*Please excuse my abominable mixed metaphor. They happen to the best of us.

**Of course, nothing is arbitrary. Chairman Peterson assembled a voting bloc containing enough farm state Democrats to kill Waxman-Markey if concessions to ag were not made. Well, shucks – politics.

***There is yet another flavor of ag handout pie, and that flavor tastes of corn starch and burnt rainforests. Yes indeed, everyone’s favorite climate controversy: bioenergy. It is a topic deserving of its own post, so I will tell you about it later. Promise.

****If it sounds like I’m needlessly ragging on hapless small farmers, please consider that the vast majority of America’s agricultural products are made by large-scale, industrial agribusiness. Very few quaint red farmhouses have been harmed by my enviro-vitriol.