The marriage thing

 politics  Comments Off on The marriage thing
Sep 122007
Recently released data from the Census bureau reports a surprising jump over the past 6 years in the percentage of people aged 20-29 who have never been married, for both males and females. This is not an entirely unexpected development, but rather serves as an exclamation point over a trend that has been developing for many years. People are getting married and having kids later and later, postponing these events until they are settled and have stable careers. The corollary to this is the increase in the occurrence of cohabitation before marriage.

This may not be anything to get particularly worked up about. Although the trend may lead to delayed childbirth, there’s nothing intrinsically wrong with waiting until your 30s to get started on a family. People with a few more years as a single may have more time to find that special someone.

On the other hand, the decline of marriage may contribute to the existing trend of professional women waiting later and later (in some cases too late) to have children. The increasing cost of childcare makes single-motherhood almost completely untenable for women in some advanced professions (a young postdoc’s salary will barely cover daycare in some places). Of course many cohabiting couples are models of fidelity notwithstanding the lack of vows, and a responsible father will contribute his fair share to the family. However, the formal arrangement probably brings some sense of security and commitment with it.

Of course there are factions that will react with utter terror and alarm to this situation, namely the family values pundits. The trend toward increasing cohabitation (living in sin!) is taken as a sign of moral decline; this will be added to that weight. They are likely to be most affected in this regard by anecdotes of people choosing cohabitation as a way to avoid the messiness of divorce. Probably divorce is a contributing cause to the current trend; witnessing their parent’s travails may have put some of the twentysomething population off the idea of marriage. The irony here is that the “Focus on the Family” crowd have been frothing after the wrong culprit for so long. The real danger to the institution of marriage isn’t gays who want it; it’s straight people who don’t.

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.

Oh damn that is so freaky

 biology  Comments Off on Oh damn that is so freaky
Sep 072007
There’s a lovely little article in this week’s Nature about how moray eels eat their dinner (subscription required). Like nearly all fish, the moray has a second set of jaws in located in its throat, called pharyngeal jaws. The vast majority of fish use suction to transport food from the outer part of the mouth to the pharyngeal jaws. In morays, however, the suction is known to be weak, raising the question of how these particular predators manage to eat large prey. The answer, as it turns out, is a strange alternative mechanism: the pharyngeal jaws lunge forward to seize food in the moray’s mouth and pull it into the throat, as shown in the radiographs below (arrow indicates pharyngeal jaws).

This unique approach to the problem is a fascinating story in biological structures. I, however, could not help but be reminded of another organism that has a mouth inside its mouth:

Spongiform theology

 religion  Comments Off on Spongiform theology
Sep 072007
I have just finished reading a couple of books by John Shelby Spong, once Episcopal Bishop of Newark and long a voice against the literal interpretation of the Bible. Spong’s viewpoint really appeals to those who, like myself, view the Bible as containing principles of virtue rather than recitations of fact. The unfortunate thing about Spong’s writing, besides his preacher’s penchant for repetition, is that it appeals to those who, like myself, view the Bible as containing principles of virtue rather than recitations of fact. For very different reasons, Spong’s books probably will not convince an atheist that there is anything of particular value in the Bible, and they certainly will not convince a Biblical literalist that it should be read as the epic myth it is.

The second point I take first because it is easier. Spong spends a fair amount of time in Rescuing the Bible from Fundamentalism going over some of the easiest-to-find contradictions in the Bible, and he repeats some of these in The Sins of Scripture. It’s fair to point these out, but mere contradictions will never compel fundamentalists to change their approach to the Bible. Nor will their minds be changed by some of the “terrible texts” Spong quotes in Sins. Nobody ever remembers that Lot offered up his daughters to the mob as a gang-rape alternative, or that he later through incest fathered two nations with them. No, all anyone ever remembers is that God destroyed Sodom for being home to a bunch of gays, and then they go on about how Lot and his family were spared because he was moral. Nor will the fervent quoter of Old Testament purity laws feel any compulsion to renounce his wool-blend suit. And when he tries to get out of that by saying that the New Testament eliminates the old laws (a position he did not hold two minutes earlier when he called homosexuality an abomination), he will nonetheless admit to no obligation to tell his wife to shut up each time they enter a church. Consistency is not a thing fundamentalists require of themselves; thus they are unlikely to require it of their holy book.

In fact, Spong does plenty in both these books to alienate the literalist, not least his contention that Paul was gay. I regard his case for this as interesting but not compelling; the literalist will probably regard it as deeply insulting. Spong takes it as inspiring, and I can see how some literalists could view it that way, but my impression is that the typical fundamentalist uses the Bible as a post hoc justification for existing homophobia, and thus would regard the theory as entirely negative no matter what it implies about the saving power of Scripture.

So much for the fundamentalist. Spong’s approach is almost entirely a loss. He comes closest to speaking to them when he points out that figurative or symbolic speech is a significant feature of Jesus’ teachings. If the literal words of God are to be understood figuratively, shouldn’t we look at “the word of God” the same way? But Spong doesn’t do much with this point. He also in a few spots implies that viewing the Bible as inerrant and all-truthful makes it a part of the Godhead and is therefore idolatry. Again, he does not build on this point. Perhaps these aren’t very strong (though I find them pretty compelling), but I feel that isn’t his reason for shying away from them. The real reason is that his target audience is not fundamentalists who might be swayed by this approach. He’s targeting people who already question their faith, or who have lost it by exposure to the fundamentalists. But does his work actually speak to these people?

In the end, I think it does not, or at least it will not call anyone to religion. Indeed, Spong makes it clear that what he seeks is a “religionless Christianity” or a “Christian humanism”. He wishes to strip away the idea of a corporeal resurrection, a literal creation of the world, and a unique set of religious laws handed down through time. But without these things, what is Christianity? What are you stating when you say “I am a Christian, but I don’t believe in the resurrection of Christ or that he was really the son of or consubstantial with God or that he died for my sins”?

Spong thinks it means something to say that, but what? That you agree with most of the things Jesus says in the gospels, except for the ones that are about God? If that’s it, then you’re just reading the gospels as third-hand philosophical dialogs, like a copy of a copy of some illiterate fisherman’s recollection of a reading of Phaedo. Jesus takes the role of Socrates, dispensing wisdom and ultimately getting killed by his enemies for no good reason, and why bother? Reading the Bible as philosophy just makes you a worse Humanist, because there’s no derivation of the New Testament’s truly revolutionary principle other than to say it comes from God’s love.

If you are coming to Christianity from without, what does believing in this add to your life other than useless dogma? If you are fleeing Christianity from within, what is there in this approach to bring you back into the embrace of the church? Nothing and nothing. There are better places to find a message of love for one another, undiluted by the racism, sexism, and absurdity that mar the pages of the Bible. If you already believe in loving your neighbor, why clutter that up with the baggage of Christianity? And if you feel that a logical derivation from first principles doesn’t support loving your neighbor, what about Christianity will convince you? Spong’s approach doesn’t give anyone a reason to join Christianity or even just stay. Whoever you are, there’s nothing in it for you.

Spong is right about one thing: Jesus had a revolutionary message for his day, one even most Christians today barely acknowledge and almost never put into practice. And the more loudly they proclaim their Christianity the further away from this message they usually are. This idea, running very much against the prevailing thought of the day, so transformed those who adopted it that they dressed his life up in the raiment of myth. That myth has swallowed the reality, and grown so large that the original message is suffocating to death beneath a blanket of hatred and mindless dogma and dead-hearted “Christians” carrying signs that say “God hates fags”.

If you take it literally, the story of Jesus is a superstitious morass no self-respecting empiricist could really believe. Taken figuratively, it is a story about how the enormous power of Jesus’ message can transform a person, not only in his dealings with others but also in his feelings about himself. Does the message have this power because God was within Jesus, or because God is within us? Does the resurrection mean that a dead man rose up, walked on water, and flew off into the stratosphere, or does it mean that God and Jesus are reborn within us every time we accept the message and live it out?

Spong doesn’t seem to answer these questions, and really, I’m not sure he wants to try. In the end, these books are of value, because they illustrate that a man can hold on to faith while acknowledging that his holy texts are human documents that exist in time, not divine writs that exist beyond it. He does much to explain the historical context of the different books of the Bible, and their role in the evolving story of Judaism and Christianity. But Spong’s vision for the future of Christianity is a road down which no true believer will go, nor any non-believer need go.