A Program for Response to Climate Change

 environment  Comments Off on A Program for Response to Climate Change
Sep 112007
The recent news that polar bears might disappear by 2050 shouldn’t really shock anyone, but it does serve as a reminder that the global warming policies being proposed by our political elites are failures-in-waiting. That the Republicans have presented a suite of jokes as policy proposals is par for the course, but the Democratic approaches are equally weak. Most of them advocate cuts in greenhouse gas emissions, but that ship has already left port — no cuts made over the next 40 years can prevent global warming, they can merely limit it. That’s still a noble goal, and carbon cuts should be made, but the belief that we can do something to stop warming and then all will be well is fundamentally misguided. What we need and deserve to see from our candidates is not just their promises to reduce emissions, but their plan for mitigating global warming’s impact.

Climate change will alter the temperature schedule and rainfall levels in many agricultural regions, producing novel climates in some portions of the country. Water may become scarce in some areas of the country now thickly populated. Sea levels will probably rise, threatening coastal regions. As supplies are exhausted, petroleum prices will begin to increase, making the modern suburban lifestyle less tenable for the middle class, especially when those price increases percolate through every other sector of the economy.

The response has to be multifaceted and nimble — years of effort have not yet yielded any certainty on the precise effects of warming on the environment. So it would be a mistake for anyone to plan on the basis of any particular model. However, there are general steps that could be taken for preparedness.

Agricultural research and readiness
: The United States has a plethora of agricultural universities, and now is the time to strengthen their research programs, with the aim of producing hardier, more efficient strains of our workhorse foods. Make use of the powerful techniques developed in the study of human health and bend them to the study and improvement of plants. Technical development should also be a focus: particular attention should be paid to the devising of more efficient irrigation systems. Pest control and topsoil management should also be priorities. Existing technologies should be pushed into use wherever possible; agricultural schools should be used as distribution centers to help local farmers put novel techniques into use. The government should take an active role in helping farmers adapt to the changes in local climate. The Department of Agriculture, in conjunction with local agricultural universities, should help farmers change what they grow and when they grow it so as to maximize productivity. This will have to come at the expense of tradition, and I’ll miss Chilton County peaches if they have to go, but it’s better for the food supply and better for the farmers if they’re growing crops suitable for the climate they’re experiencing.

Alternative fuels: By which I do not mean biofuels. In fact, biofuel initiatives should be abandoned immediately, not only because cutting forest to make way for biofuel monocultures is harmful to the environment, but also because biofuels will not substantially help carbon balance or warming in the long term. The simple fact is that burning biofuels is still burning something, and the additional CO2 and NO2 released during their cultivation will seriously diminish their potential to affect global warming. A recent (non-research) article in Science (subscription required) points out that sequestration of carbon in forests is superior to the use of biofuels from the pure greenhouse-gas perspective. Moreover, using arable land for biofuel monocultures will be a losing proposition when climate change stresses the food supply. Food prices in the United States and Mexico have already suffered some disruption from the proposed use of ethanol; when food itself starts being difficult to come by, the growing of corn for fuel (or even animal feed) is likely to be untenable.

If biofuels are to be used, then it ought only be when they can be produced exclusively from the refuse of existing food crops (cellulosic ethanol from cornstalks, for instance). Barring this, the government should enforce increasingly stiff fuel-efficiency requirements while pushing forward on research into non-carbon fuel sources for transportation. Simultaneously, every effort should be made to reduce the amount of automotive traffic required in everyday life…

Re-urbanization: Cities are crowded, messy, polluted, and filled with crime, but suburbs sprawl, destroy forests, promote excessive use of automobiles, and spread vile environmental impacts over a large area. As forests are our best friends in the fight against warming, anything that destroys them must be anathema. However, there is no way that any mandate of the government could shove everyone back into the cities. Rather, the government must work diligently to support the cities in their efforts to call people back by reducing crime and producing more family-friendly spaces. At the same time, the cities themselves must be revamped so that they are more environmentally friendly. “Green” buildings must be economically encouraged or enforced by statute. Public transit must be made as attractive and efficient as possible. Suburban sprawl must be curtailed, by inviting the nation back into the cities if possible, by forbidding further development in wooded areas if necessary. Increased property taxes encourage living in small spaces while providing additional revenues to support urban redevelopment.

Water Policy: Water management beyond the local level has largely been ad hoc up to this point, but with increasing populations in some major urban areas stressing the water supply of multiple states or large regions, a comprehensive higher-level policy must be put in place. The government should provide assistance to those wishing to move away from areas experiencing significant strains on the water supply, and help develop economic opportunities in areas where water is plentiful in order to make such moves desirable.

Disaster preparedness: One likely consequence of the development of novel climates is the destruction of the previous climates. In cases where temperatures rise and rainfall decreases, this will probably take the form of extensive forest fires. Even now it seems like every year brings a record number, and it’s probably not because so many kids are playing with matches these days. The government will need to come up with a comprehensive plan for dealing with these fires without completely exhausting the men and women who fight them on our behalf. Trying to imagine and then plan for every possible contingency is a good way to get completely lost in details, but nothing DHS and FEMA have done since the Katrina disaster suggests that they have grown more nimble or capable. These agencies should be shaken up from top to bottom, and if necessary FEMA should be removed from the bloated and apparently completely ineffectual DHS.

This isn’t everything that such a plan needs by half, and by this time next week I may have 3-4 more headings of components that are necessary. But it’s telling that even the most environmentally conscious candidates seem to have only thought of one.

Mr. Deeds goes to town

 boo  Comments Off on Mr. Deeds goes to town
Sep 112007
I hate the idea of submitting a paper to Proceedings of the National Academy of Sciences because if you get rejected you feel especially bad. Despite its relatively high impact factor, PNAS puts out a fair amount of garbage, and sometimes you feel like you’re reading a dumping ground for the bad ideas of big names. Case in point is a paper from the lab of Eugene Shaknovich that just showed up in pre-publication form. Shaknovich is famous for performing simulations of proteins that rely on a reduced or “lattice” representation, and in the interest of full disclosure I’ll admit that I’m highly dubious of this method. In this case, however, I’m relatively certain that the simulation produced a correct answer, for reasons that should become obvious as we go along.

Deeds et al. are out to address what seems like a fairly interesting problem of specificity in protein interactions. Most experiments performed in biomolecular laboratories make use of highly overexpressed proteins in relatively pure environments. This allows us to obtain quality information about the details of particular proteins and their interactions. However, what happens when we put these proteins into the cell at relatively dilute concentrations? If we consider a particular pair of interacting proteins, A and B, we know that their specific binding is strongly energetically favored. However, A and B probably have the potential to interact nonspecifically with many other proteins. If A and B are at relatively low concentration, and the cellular milieu is crowded with millions of these potential nonspecific interactions, can we be sure A and B will find one another?

To address this question, Deeds et al. construct their typical lattice models with two “proteins” that have a designed interaction, and simulated a situation in which up to 90% of a 3d space is populated by random “proteins” that have a small potential to interact with the targets. They let the systems equilibrate, and then take a look at the kind of interactions that are occurring. The findings are truly revolutionary, as you can see from the figure below. At low temperatures (A), the random interactions (blue) predominate when nonspecific-binding proteins are the larger component of the system. As the temperature increases slightly, to a point above the ‘melting temperature’ of random complexes, the designed, ‘specific’ interactions (black) begin to play a larger role, even at low ‘concentrations’ of interacting proteins. Finally, as the temperature really climbs, the specific interactions start to dominate the milieu.

So basically what Deeds et al. have discovered is that when the energy available from heat is enough to break random interactions but not specific interactions, then at equilibrium specific interactions are highly favored even if there is an awful lot of opportunity to bind randomly. On the other hand, if the temperature of the system is too low to break up random-binding events, then random binding dominates when most of the proteins are nonspecific binders. This is not a surprise, and hardly qualifies as a conclusion at all, even less so when you consider that this is a simulation (and thus that unsurprising results are likely to result directly from the assumptions used) and not an experiment on real proteins. This seems more like a control for some other experiment using this same system that derives some surprising conclusion.

Deeds et al. go on to make some important predictions from their discovery that energetics dictate binding (who knew kT could be so important?). For instance, they point out that in crowded protein-protein interaction experiments like the yeast two-hybrid screen there may be a lot of false positives, which must come as shocking news to any yeast two-hybrid researchers who have never read any papers or protocols about yeast two-hybrid screens, nor even Wikipedia. They also recommend using techniques that don’t rely on overexpression, but the fact is that almost any molecular biologist would prefer it if he could answer questions using experiments that involved no overexpression. None of this is new, and to treat the insight as novel because some simulation showed it is just insulting.

In the end, this is a paper about a control, and not even a particularly well-written one. Don’t get me wrong; it isn’t bad for what it is, and I don’t blame Shaknovich for trying to get it published in the best journal he could find for it. This is not bad science, but it doesn’t tell us anything new, doesn’t present a novel technique with wide application, or really provide any other reason to appear in a broad-based journal. I can and do blame PNAS for allowing in something that really ought to have been relegated to a specialized journal. And I will blame Shaknovich for the condescending tone of the discussion, in which he descends from his lofty computational height to tell us poor experimentalists “interesting implications” that we already knew. Too often, simulations get a bad rap from experimentalists, but this sort of paper, which will leave a bad taste in the mouth of anyone unfortunate enough to spend time reading it, makes that attitude seem justified.