Four genomes

A nuclear family gets its nuclear DNA sequenced. What can it tell us?

With sequencing technology going dramatically down in price and up in speed, and routine individual genomes within sight as a matter of routine medical practice, one group of researchers decided to sequence the DNA of two parents and their two children to see what we can gleen from such ultimate-detail data.

One thing to note is that the sequence of an individual's genome is static data. Once done, for whatever price, that is it- it does not have to be redone again, unless the original error rate was excessive. This work claims accuracy of 99.999%, which seems sufficient for most needs. At three billion base pairs, this amounts to 3,000 errors, which isn't nothing, but is very small.

On the other hand, the interpretation of this data is highly dynamic. As we learn more about how human biology works, how genes turn into cells, organs, behaviors, and about how the astronomical numbers of human genetic variants affect these traits, we can keep going back to our genomes to learn more about ourselves.

The paper makes several basic observations, improving data that had been approximated by other means. For instance, the human mutation rate turns out to be ~70 mutations per generation. Considering that roughly 2% of the genome codes for proteins, and no more than 30% of the genome involves gene-related DNA at all, (introns, promoters, etc.), this is a pretty modest mutation rate. We are all mutants, but the chances of something disastrous occuring are relatively small, as is seen in the phenotypic real world as well.

The researchers are able to map the recombinations that happened on each chromosome in each gamete that produced each child, in detail. Just over half occurred at what are called recombination hotspots, sprinkled along each chromosome. This remarkable process of recombination mixes things up genetically, insuring that what each child gets is not just a roulette selection of whole chromosomes from the respective grandparents, (which is what would happen in the absence of recombination), but a unique patchwork assembled out of both grandparent's chromosomes, insuring that each human is highly unique, and that, over long periods of time, genes get selected on their own merits rather than living and dying based on the many other gene variants with which they co-habit their chromosome.

The putative reason to do all this sequencing was to track down two rare and severe genetic diseases afflicting both children, and this complete sequencing offers several technical advantages for such a hunt. Firstly, the accuracy of each of the full sequences is increased by having the others to compare with. Shared variants are likely to be real, while unique ones can be explicitly resequenced to double-check. Assembling these sequences from the small individual reads that form the basis of all DNA sequencing is a huge computational effort, always helped by having a comparison base of maximally similar data.

Secondly, the density of this data makes finding disease-causing genetic variants much easier. In typical studies of genetic associations, a population of affected patients is studied, with comparison to a control group, randomly selected from the population. There will be a very large number of genetic variants among all these people. Ferreting out the variants or regions of variation that happen more frequently in the affected group is thus very difficult. In a family group, on the other hand, while the parents presumably have no special genetic relationship to each other, the group as a whole will have far lower numbers of stray variants, decreasing the search space substantially.

In this case, the researchers find that since two diseases they are interested in, present in both children but absent in the parents, appear to show recessive genetics, they can throw out 78% of the sequences, and, from the recombination map, focus on those bits of the children's genomes that are identical between them and heterozygous in the parents (22%). The variants also must be rare, based on the rarity of the syndromes (primary ciliary dykinesia and Miller syndrome), allowing them to throw out variants known to be common from other population genetic variant studies. This allows them to winnow down the disease candidates to four variant genes, as opposed to the dozens that would have resulted from a more typical gentic disease association study.

Personalized medicine is coming our way- it will combine sequence analysis of our genomes (in addition to molecular analysis of cancer biopsies and the like) with the developing knowledge of just what the sequence means- knowledge that is only in its infancy right now.

• The genetics of grooming.
• The dark heart of the Democratic party.
• A double-dip, on the way.
• Religion, shmeligion.
• Bill Mitchell quote of the week, regarding Greece and its suffering brethren in the Euro:

"If I was in charge of one of these nations I would announce next weekend (when the banks are closed) that I was introducing a new currency, defining all Euro debt liabilities in the new currency and let the foreign exchange markets value that currency on the Monday morning.

I would withdraw any semblance of central bank independence (that is just another democratic insult) and I would expand the budget deficit immediately by introducing a Job Guarantee.

Then by Tuesday, I would start repairing the confidence of private spenders to get the economy rolling again.

And after a relatively short time I would notice that economic growth was gaining speed, private spending was returning, unemployment was low and … the budget deficit was falling.

Then I would send an open invitation to the citizens of Germany to abandon the teutonic ship and head south (or west)."

What is labor's share?

How does labor's share of income and wealth happen? (Forgive me, this is sort of a thinking-aloud and lengthy post.)

In our time, large increases in productivity are going everywhere but to the laborers who are doing the work- to the financial sector, to capital, to government, and especially to the rich in the form of income and wealth inequality. Why is this, and what can be done about it? I will discuss a hierarchy of processes that affect this balance, from the easily understood to the more arcane.

(Please see a recent NYT story for a discussion of this inequality, with useful graphics.)

- Direct conflict: strikes, unionization, union-busting
One method of altering the share of income going to labor is to agitate directly for that increased share. Unions are the primary vehicle of pro-labor agitation, and in their heyday made America a much better place, with a more-equal distribution of income and other advancements in workplace decency. Conversely, antiunion government policies ("right-to-work" laws, strike breaking assistance, and race-to-the-bottom tax breaks for business relocation) and corporate agitation have the reverse effect. Since the 60's, antiunion agitation by large employers like Walmart, Ronald Reagan, and many others has been markedly more effective than pro-union activity. Thus, on balance, this effect has contrbuted to decreasing the labor share of GDP in recent decades.

- Labor markets:
Theoretically, the labor market lets employers bid for available labor, and in flush times, even for unavailable labor, poaching from other employers. Conversely, it lets workers bid for acceptable workplaces and higher salaries. In the aggregate, employers have to pay labor enough to staff the enterprises from which they can then reap excess profits and value. What limits labor supply, and what sets the price?

Conventional theory claims that it is productivity that ultimately sets the labor price.. that employers hire workers at the market wage rate until the marginal profit per extra worker reaches zero, assuming that the last worker is less productive in the enterprise setting than the first one.

A more realistic scenario might be that employers have certain models of how to run their enterprise at a certain scale with a minimum amount of labor. They hire that labor at the prevailing wage, then pursue productivity gains that allow them to eliminate those individual employees representing the lowest profit to wage ratios. The employer has no interest in hiring to the limit of marginal utility, since that is a waste of effort and profit in an organized business model which is not, typically, infinitely expandable. Thus there is no need to clear the labor market from an individual employer's perspective, and nor does pay in a given company necessarily rise to the level of productivity. In aggregate, however, new enterprises will hopefully be founded to employ marginal labor, depending on a variety of cultural and governmental settings, discussed below.

Businesses also have a variety of other advantages in the labor market. One is assymetric information, where a culture of secrecy surrounds salaries outside the HR department, putting applicants at a severe disadvantage. Secondly, employees tend to be more loyal to companies than the reverse, valuing stability for personal reasons and setting themselves up for undervaluation. Thirdly, in the internal competition to be a high profit-to-wage employee, the profit side of the equation is highly flexible, in the form of extra time spent, creative effort, and other contributions (though the reverse might also be cited, in Dilbert fashion, with pointless meetings, personal activities, self-dealing, and other drags on profit). On the other hand, pay is highly inflexible, raised only in the most notoriously grudging manner.

I'd rate this process as tending toward lowering the labor share as well, though it is perhaps the only process of those discussed here that can lead to wage gains when the stars are all aligned, which it to say, when enough entrepreneurs and businesses have pending business needs and credit available to bid up salaries. This happened most recently during the late Clinton years, not due to that administration's economic policies, but mostly due to the techno-cultural ferment of the computer and internet boom which raised productivity even faster.

- Immigration and trade policy:
Another broad influence on the macroeconomic settings and on labor power in particular is immigration policy, or lack thereof. While legal immigration is relatively balanced and doesn't lead to overall distortions in the employment market, illegal immigration has huge effects on the lower end of the labor market, essentially removing the wage floor for unskilled workers. The enormous tide of illegal immigration from Latin America is great for employers, who bid down unskilled pay to minimum wage and below, with under-the-table arrangements, and other means of keeping menial work not only underpaid, but distasteful. The upshot of this process is the typical mantra that such immigrants "do work that citizens don't want to do".

The alternative to importing and underpaying labor is offshoring work to low-wage countries. The usual theory of comparative advantage would say that we gain from this exchange, freeing domestic labor for higher-value pursuits, while getting advantages of trade. This only works when domestic labor is actually employed in higher value pursuits- something that is not the rule, needless to say. Scandinavian countries take a strongly supportive role in labor mobility, sponsoring serious retraining for displaced workers, leading to real jobs in such higher-value industries. The lesson is that the state has an important role to play in making such economic freedom for companies work for the labor force and country at large.

At any rate, our immigration and trade policies have been strongly on the side of decreasing labor's share of income, winking at a flood of low-skilled immigration, and providing trade agreements that favor US businesses, occasionally consumers, but never labor (NAFTA, for example).

- Macroeconomic policy:
A key insight of Keynes was that demand leads to production. Enterprises don't produce what doesn't sell, and they can only sell to someone who has money to spend, which was earned or was given by the government. Collapses in aggregate demand, such as we see currently as the private economy swings from excessively high indebtedness and consumption to higher saving, lead directly to lower production, and thence to a spiral of deflation unless the state (which prints the money, after all) steps in to fill the demand gap. The state ideally supplies money up to productive capacity, also funding the increased private saving and leakage via the trade deficit while also keeping aggregate demand afloat.

The stimulus package of the last year was a step in this direction, but clearly not enough, as unemployment remains painfully high and we head into what looks like a double-dip recession. High unemployment leads naturally to a lower wage share of GDP, as employers can bid lower for workers, as well as employing fewer overall.

On the long term, macroeconomic settings have critical effects on this balance, as the Federal Reserve's fundamental directive makes clear- "maximum employment, stable prices, and moderate long-term interest rates". Have they been pursuing maximum employment? I don't think so. Recent decades have seen the decline of Keynesianism and the rise of monetarism, after the inflation, stagflation, and resource shocks of the 70's led economists to pitch full employment under the train in favor of fighting inflation. The chosen weapon was high interest rates, which choked credit and business formation, lowering employment in what was generally viewed as "necessary pain" to wring inflation (in the form of escalating wage demands) out of the economy. All this was quite effective on the inflation front, but what of employment? Maximum employment has been reinterpreted as NAIRU, or the rate of unemployment consistent with low inflation. What unemployment is that? Well, it is very difficult to say. Could be 5%, or 10%. Right now, we have low inflation, so we could be at the NAIRU- no one really knows.

The fact is that there is no analytical method to determine the NAIRU. It is whatever unemployment rate has been consistent with low inflation in the past, and might change at any time, depending on cultural, technical, or other factors. It is a chimerical construct allowing policy makers to accept some arbitrary amount of unemployment as good rather than bad. But there are other ways to skin the cat of inflation, rather than through unemployment. Employment is very high in Japan while inflation remains very low, probably due to a high savings rate that keeps aggregate demand relatively low. The US in the 50's and 60's also had consistently high employment with low inflation, until the Vietnam war and other compounding fiscal and resource problems led to rising inflation in the 70's.

In that time period the US probably benefitted from consistent export surpluses which allowed rising private net saving with low government debt (i.e. even without government deficits, the private economy gained net financial resources from trade that it could save). Now that our trade balance is consistently in deficit, the government has to continually replace that leakage with deficit spending, leading to accumulated government debt, pending eventual re-alignment of our trade position. (Debt which is not bad, by the way. Who worries about our 28 trillion of accumulated private debt, compared to the 10 trillion of public debt? No one.)

At any rate, the Fed has focused on wringing out residual inflation over the last thirty years, accepting substantial levels of unemployment and underemployment along the way. The Fed has been pilloried for keeping interest rates too low in the last decade, fueling the housing boom with easy money. I would disagree. The Fed was partially at fault, but not for low rates- those were fine, general inflation being quite dormant. Rates are a very blunt instrument, penalizing all businesses and workers for the sins of one sector in this case. No, the Fed's fault lies in lack of regulation, both of the mortgage industry, and of the high-finance industry, which created such an Everest of fraudulant "instruments". Its laxity was driven by ideology, assuming that markets self-correct and that active and adversarial regulation is unnecessary. They do self-correct, but not in a timely fashion. After all, Ponzi schemes self-correct as well, eventually! The Fed was established to mitigate this kind of destructive self-correction that was recurrent in the 1800's, and it failed spectacularly in that role.

High interest rates are a drag on business and labor, but more pernicious for labor, since while the number and size of businesses can go down during a recession, the population can't- it keeps going up, leading to the agony of unemployment, as well as the market effects noted above where wages are bid down to the lowest level necessary to hire the desired worker. I.e., the labor share of a shrinking GDP decreases. This is one reason why most economists take economic growth as such an automatic good- even though growth may represent unsustainable resource use, pernicious monetization of human needs, and counterproductive activities of many other kinds, the basic need for employment is only met in a setting of economic growth.

The Fed was also at fault for persistently calling for federal fiscal discipline and balanced budgets, via ideologs like Alan Greenspan. It was this fiscal discipline, briefly expressed as federal budget surpluses, which drove the private economy into high debt which has now imploded. Government spending has to cover leakages from the private economy- leakages like trade deficits and net savings to government bonds which reduce money available for consumption. With the economy in perpetually high trade deficit, and the dollar not adjusting due to its special position as the world's reserve currency, (among other reasons), far more government deficit spending was needed to keep the private economy from consuming out of private debt as has happened over the last decade. Issuing government debt for all these deficits was also not necessary- debt is purely a monetary operation to guide interest and inflation rates, and is not required to directly "fund" government spending.

- Cultural settings of education and optimism:
Now I transition from what is economics (loosely construed!) to what is practically theology. Entrepreneurs create jobs, combining inspiration, skills, labor, and capital into new ways to fulfill human needs. Apple Computer is a great example of a persistently entrepreneurial operation, which keeps coming up with new businesses- ways to transform mundane materials and engineering talent into satisfied human desires and economic flows.

Entrepreneurs need a variety of external ingredients, principally labor with the education or skills to realize a new vision, and capital. If capital is scarce, as it is right now, then labor excess is not going to make up for it, unless its price is bid dramatically down, perhaps to garage start-up levels. Conversely, all the money in the world isn't going to make an Apple Computer- it takes education and more broadly a culture of technical innovation, even geekery. This is what makes urban environments so productive relative to rural ones- labor's share is higher in dynamic urban environments because the balance of entrepreneurs with the necessary ingredients for job creation is high, compared to the labor pool, leading to economic growth. In rural areas, wages are low, but that is not enough to offset the lack of an educated labor pool flexible enough and concentrated enough to turn its hand to many different value-creating ideas.

But not all urban environments are dynamic, and this is California's achilles heel looking to the future. Our schools have dropped to among the worst in the nation, as we have counted on the cultural / physical climate and the UC system to attract bright people from elsewhere to employ a workforce which is heading toward unskilled labor due to demographic and immigration trends. As California becomes increasingly dysfunctional politically, educationally, and economically, entrepreneurs may lose access to the requisite concentration of skills and eventually the sense of optimism to keep building high-tech businesses in the state. This would seriously impair not only economic growth, but also, given a lower rate of business formation and job growth, labor's share of the economy.

- Conclusion:
Now, it could be that capital and high earners have in all truth become more important than labor to the production of GDP in the US, deserving their higher and growing share. Perhaps with rising automation and other technological conveniences, the marginal product of low-skill labor has declined, while the leverage of high-creativity and capital-intensive work has increased. Perhaps the ceaseless winner-take-all nature of many professions has properly segregated very high producers from the riffraff, now unsupported by blanket protections they might have enjoyed in the past like unionization and conveyer belt-like promotion and seniority systems. We may have transitioned to an Ayn Rand-ian meritocratic system which has finally uncovered the true relative worth of various economic actors, both human and monetary.

However, I doubt that is the case. First principles would indicate that with rising wealth, the economic value of that wealth as capital should decline relative to the labor which is the true source of creativity in employing it. The more wealth we pile up, the less useful each increment is in funding productive activity. Thus one suspects that the evident higher returns to wealth in recent times are a form of rent, perhaps due to rampant financialization and excessive private indebtedness that has afflicted the US economy in recent decades.

Secondly, inequality between high and low earners is very hard to defend if one takes our educational system seriously, since it cranks out broad classes of certified people for the various professions and other pursuits. While there are surely fine differences in personal characteristics that make people variously productive after such training, they are unlikely to correspond to the differentials of hundreds-fold present in today's business pay structures. Not in any linear fashion, at any rate. Far more likely is that these markets are defective, either because of intrinsic problems of tournament-like markets, or because executives defeat market mechanisms by collusion, misappropriation of shareholder equity, etc., while using the same markets to consistently underpay employees.

• A little harmless dreaming on the economic left.
• Back to the barricades in Europe?
• A brief little labor primer.
• Larry Summers even gets it, seemingly.
• How science works.. by critique and experiment.. somewhat unlike theology.
• Mr. Bully kindly requests that we bomb Iran.
• Revolving door sleeze under Ken Salazar.
• We may be headed for a double-dip super-recession.

Note to fish: We can't see you!

The sea of slaugher keeps getting worse.

The current oil spill in the gulf of Mexico has been a tragedy of errors, none of which are more appalling than the out-of-sight, out-of-mind attitude taken towards sea life. News reports uniformly fear damage that might happen if the oil hits the shoreline, and breathe a sigh of relief if the mess appears to wash out into the Atlantic.

Adding insult to injury is the use of delicately named "dispersants" in the hundreds of thousands of gallons, in order to reduce the unsightliness of oil on the ocean's surface. Apart from the incenstuousness of BP insisting on using chemicals that it has a financial interest in, the whole idea is fundamentally troubling. ToxicA + ToxicB = ?less toxic situation?

Corexit (what a great name- as though this material was going to make a problem go away) is a mix of soaps and solvents, themselves toxic to all forms of life, doubtless more so the more one relies on water to live. It contains:

- 2-butoxyethanol, used as solvent in paints, inks, and cleaning products like Simple Green.

- Sulfonic acid, a kind of soap, which, well, let wikipedia tell the story:

"Sulfonic acids are typically much stronger acids than their carboxylic equivalents, and have the unique tendency to bind to proteins and carbohydrates tightly; most "washable" dyes are sulfonic acids (or have the functional sulfonyl group in them) for this reason."

- Propylene glycol, which is relatively non-toxic, being used in drugs and animal feed.

- And other proprietary ingredients, probably of a detergent-like nature.

It is hard to imagine that fish would like this material. But who cares about fish? For many kinds of wildlife, (birds, mammals, some fish), it is good to get oil off the surface where they spend a great deal of time, and where we like to go bird-watching. But adding further toxic, and ironically petroleum-derived chemicals to the disaster mix presents increased problems for everyone else in the ocean.

• Some links on the oil-dispersant mess.
• The beauty of Jellies and other denizens of the deep.
• Palau asks to have its ocean back.
• Bill Mitchell quote of the week:

"Unemployment is about a lack of jobs. If the private sector will not create enough jobs then there is only one sector left in town that can. Hellooooo! Its called the government sector.

They can do it directly (that is, hire the workers themselves and put them to work advancing public purpose – rebuilding community and environmental infrastructure; providing personal care services; etc). There is never a shortage of work – just a shortage of funding to pay the wages.

They can also do it indirectly by stimulating the private sector via tax cuts or targeted spending. Both approaches have advantages and disadvantages but the net effects are always overwhelmingly positive."

(Noting as usual that a fiat currency-issuing government can provide funding without limit when inflation is low.)

Bullying Iran

Perhaps the US should take a breather from its vilification campaign against Iran.

US foreign policy can get curiously ossified at times. Our stance toward Cuba is an example, which after the trauma of the Bay of Pigs and Kennedy's assassination, seems to have drifted into auto-pilot, not thinking too hard of what would be best for our interests, let alone what would be best for Cuba and the region.

Likewise, we seem to be carrying on a long-term grudge against Iran, dating from their Khomeini-ite revolution. It is frankly embarrassing to see the US try to bully Iran, to little avail, on its uranium processing and nuclear weapons policy.

Barack Obama took a promising tack when he first come into office. His reduction of pressure resulted in a deep destabilization of the Iranian government during its fraught elections. The equation is clear- the more pressure we apply, the more recalcitrant the Iranian government is, and the more support it gets at home, squeezing just a little more mileage from those tired old great Satan slogans. Bullying by the biggest country on the block never looks very good.

But now, the Obama administration has tacked back to a campaign of vilification, with embarrassing speeches by Hillary Clinton at the UN about how terrible Iran is, and how the nuclear non-proliferation agreement is not a residuum of neo-colonialism, but the self-evident and permanent apotheosis of universally accepted international relations.

Unfortunately, it is all too transparent where this change in policy comes from- it comes from our symbiotic relationship with Israel, which is running scared over a nuclear threat from nearby governments that hate it. It is also a neocon hangover from the Bush years and before. It also comes from our own difficulties with Iran's role in Iraq and Afghanistan, on the borders of both of which it sits, and with Islamism in general.

What are the risks? First is the risk of Iran actually carrying out its threats of wiping out Israel with a nuclear bomb. I think it should be clear that the chances of this, even when Iran does aquire a bomb, are minuscule. The history of nationalistic and diplomatic bombast is a long and painful one, but rarely reflected in action. Iran, even while indulging in clownish rhetoric, has shown a pattern of measured power projection, including provocations on its borders and through its Shiite friends in Lebanon and Palestine. Its relationship with Syria was mostly strategic, when it was mortally threatened by their mutual neighbor, Iraq. The unanticipated benefit of gaining Arab street cred by irritating Israel via its Hezbolla clients was purely gravy.

Not to mention that Israel has plenty of deterrent capability in the form of nuclear bombs of its own, hopefully well-protected from attack, and quite a bit more to the point, from its own rather numerous religious crazies. So I'd assign this prospect to pure fantasy. As far as terrorist appropriation of such a weapon goes, we are into this scenario pretty deeply already with Pakistan, with no accidents to date. I'd rate Iran better run, with better technical and cultural coherence than Pakistan, and thus estimate that Iran could control its bombs at least as well.

Second is the risk of Iran rising to become a true regional hegemon, supplanting US influence to some extent. This is a more serious threat, and certainly has Saudi Arabia quaking in its boots, as well as Israel. The ironic aspect of this is that the more we bully Iran, the more credibility it gains, both at home and in the Arab world. On the other hand, the more doctrinaire its policies- the more theocratric and economically closed it is- the less likely it will gain and consolidate this kind of influence. The more open it is and accepting of modernizing influences, the more successful it will be economically and culturally in what is, after all, a rather diverse Arab world and one that is majority Sunni.

So I would see this threat as self-limiting, which to say that insofar as Iran is dangerous, it will not be attractive to others in the region, whatever its purely military power. Israel serves as an example, having all the military power one could hope for, yet hardly being a hub of local cultural or political influence, for obvious reasons. The only influence it does have is not due to its military power at all, but due to its democratic system which serves at least in form as a counter-example to all others in the region.

Additionally, the real problem with Iran's nuclear ambitions is local- with its volatile neighbors. It isn't the US that needs to worry about Iran's bomb. We have plenty of distance and bombs of our own. If we had our diplomatic wits about us, we would let the local powers (i.e. Saudi Arabia, Egypt, perhaps Iraq) take the lead, and have them ask the UN for relevant sanctions, etc. One could even imagine a common front between those countries and Israel, if Israel hadn't completely alienated everyone in the region. The nascent denuclearization movement in the Middle East is such a local initiative, and the US should support it rather than torpedoing it at the behest of Israel.

Compared to the risks, what are the opportunities? The grand prize is obviously flipping the Iranian state from its Khomeini-ist system to something more democratic and less militant. Any other opportunities pale in significance, such as prying Iran away from Russian influence, or cutting Iran's oil revenue by restricting trade and establishing green energy, etc. Such an enormous change came very close to happening in the last election cycle. The population seems deeply interested in such a resolution, though it is hard to tell what the true proportions of sentiment are. All of our policy should be aimed at promoting this process. As noted above, our bullying has the opposite effect, consolidating the current state, and accentuating its interest in getting exactly the weapon at issue. Unless we have a big stick to wield, (and we don't), we'd be better off speaking softly.

Our policy should be to speak the truth and engage where we can. We should not recognize the current state as legitimate, since it is not (ditto for Afghanistan, unfortunately). We should also not sign off on nuclear treaty compliance that doesn't exist. But our target should be the vast population that yearns for modernity and for a voice in the context of a fully autonomous and democratic Iran. We needn't encourage Iran to build a bomb, but should at least recognize their desire for such a deterrent, beset as they are with US forces on both sides, and having faught a catastrophic war just 25 years ago. Israel, for its part, would be better off mending its own wretched relationships with the Palestinians and the rest of the Arab world rather than egging us on to foolhardy diplomatic/military adventures.

Iran is a historically rich, sophisticated country with plenty of its own problems, like rebellious minorities, a corrupt and ideologically rotten elite, and energy needs that may outstrip its pace of energy development. The Khomeini-ist state is an unfortunate problem, for its subjects as much as for us. But it has shown a good deal of practicality over the years, and ultimately can't win against its own people, as they are increasingly aware of conditions and trends outside their country, and of their own power. It seems a good deal more fragile than, for example, the Chinese government, due to its internal complexity and an ideology that has diverged substantially from that of the public at large.

The risks are small, and the opportunities are large. My prescription would be to pursue quiet containment against the government of Iran while accentuating democratic, open principles at every turn in public, as we should universally in our foreign policy. We should promote travel between our countries, as well as non-sensitive trade and other exchanges. The enormous Iranian expatriate community in the US would probably welcome such an approach and be an important medium of improved relations as well as cultural change.

• Who cheerleads for more bullying? What a feud. After the kindness of Cyrus, you would think they would be a little more grateful.
• Afghanistan- still coming unraveled.
• ...or perhaps not so much. Shalizi on Afghanistan- wealth of links, etc., including a detailed political network analysis.
• Evolution- still a dirty word.
• The Euro is on its death-bed. Dissolution, or pan-European government and fiscal policy- that is the stark choice.
• More on the Euro.. mentioning its trend toward pre-Keynesianism. Why aren't we doing more post-Keynesianism here in the US?
• A Keynesian prescription for Britain.
• More on criminal, er, financial, racketeering.
• Big government fights back against free information.
• God is here .. at minute 26.
• Bill Mitchell quote of the week, speaking of Europe particularly:

"So a classic mainstream argument that unemployment is caused by excessive real wages and government regulations. If you took time and analysed the shift to profit share over the period he analyses, you will realise that productivity was running ahead of real wages. So where was the real wage overhang?"

Protein theology

I critique a scholarly article from the "intelligent design" camp.


One of the wonders at the heart of modern biology is our knowledge of protein function and structure. The fact that the linear genetic code produces protein molecules that spontaneously fold into complicated shapes, wander off to various corners of the cell, and then spontaneously do their complicated functions like metabolic reactions, holding things together, filtering ions, or replicating DNA. etc.- it is mind-boggling, and a little magical.

But it all had to come from somewhere, and I ran across a recent paper that takes up the issue. This is from a creationism house journal, BIO-Complexity, put out by the Discovery Institute. They have their own peers, thus this is darn well a peer-reviewed journal! Accompanying it is an honest-to-goodness experimental article, where the experimenters strive to not observe a phenomenon that they theorize doesn't happen .. and succeed!

Alright, sarcasm aside, the article, "The case against a Darwinian origin of protein folds", by Douglas Axe, is well-written and mildly interesting, though I take a highly critical attitude. It is a review- no new theories are proposed, let alone tested. He lays out (using the royal "we" throughout) the difficulty of protein domains arising from nothing, and claims to make a strong case that this was impossible within the Darwinian paradigm (presumably including early chemical evolution in the broader Darwinian theory).

Domains are the structural units of proteins- the smallest portions that fold by themselves and sometimes function by themselves in doing whatever, like catalyzing a reaction. Typically, proteins are composed of several domains, whose connection is critical in, for example, activating the catalytic activity of one domain in response to binding a regulatory chemical by another. The definition can be vague, since very small proteins (called peptides) may have important functions (like hormones) despite being unable to maintain a coherent fold/shape on their own. One might say they are protean! And there are large proteins that amount to very large domains, not easily broken down conceptually into independent folding / functioning sub-domains.

Axe spends quite a bit of time using average protein size statistics to marvel at the improbability of any protein-sized, or even domain-sized unit of protein sequence arising de novo. If we have 20 amino acids, and the average protein is 300 amino acids long, that amounts to 1E390 possible combinations. Finding the one of these that is a modern protein is like, well, it is simply impossible, there being only 1E150 particles in the entire universe, 4E20 microseconds since the big bang, etc. He likens it to finding a gemstone in a Sahara desert to the Nth power, and other elaborate comparisons.

Even if one cuts the search space down to the size of a domain, (average modern size ~ 100 amino acids), these numbers are astronomical, though Axe does not go into this correction in detail. But obviously, the origin of proteins at the dawn of life has never been hypothesized to involve the sudden appearance of 300 or even 100 amino acid-long enzymes for oxidative phosphorylation. This is a straw man from top to bottom.

Why is he and his community fixated on it? It seems to follow a model of a deity trying desperately to design our proteins from above, stabbing away over billions of years and uncounted quadrillions of organisms before getting it just right in the case of homo sapiens. If one lays out the premises explicitly, they dissolve before one's eyes. But with the ID community, all this is implicit as a religio-political "wedge" project, not a serious intellectual endeavor.

Over in the actual scientific community, the origin of protein coding capacity is commonly assumed to have extremely modest beginnings, as an extension of the RNA world, when RNA had the primary replicative and catalytic ability. This modest catalytic ability might then have been abetted by tiny peptides, painfully assembled by a set of primitive RNA enzymes, and then extended to slightly longer protein chains, which eventually and competitively, through their vastly superior chemical abilities, relegated RNA to what is now its mostly informational role. Indeed, the protein-translating ribosome remains a thoroughly RNA machine, using strings of mRNA as the template code, tRNA- mounted amino acids as the building blocks, and a catalytic core of rRNA for polymerization. This sort of gives the game away right there, if one cares to look.

The original genetic code is also likely to have had fewer than the 20 amino acids that are universal today. The messiness of this genetic code, with some amino acids encoded by only one of the 64 codons, and others encoded by six, indicates some late additions and jerry-rigging to the system. And since the code's establishment, more amino acids have come into use through chemical modifications, either before the amino acid is incorporated (selenocysteine), or afterwards (hypusine).

Axe never recognizes such realistic accounts of the primitive origin of proteins, however. He also assumes that successful proteins have to approach modern levels of efficiency, making any path from one folded form to another folded form (there are an estimated ~2000 classified folds) impossible, none in between being likely to have a well-honed function. Here again he fails to recognize the wider spectrum of hypotheses available. Many proteins have unstructured regions- floppy areas that may adopt structure only when binding some other partner, or adopt alternate structures under different conditions. Such alternate folding lies at the heart of Alzheimer's disease and prion diseases.

While one optimized folding structure is unlikely to turn into something completely different and coherent through direct evolutionary selection, there are many other resources for the emergence of novel domains, such as these floppy sections of working proteins, or random DNA segments that do not, for the moment, code for genes, or various fusions of working proteins (a fertile source of cancer), or duplicated coding genes with no selective constraints at the moment. Many accidents have happened to genomes over time.

Axe cites experiments showing that proteins can switch readily between quasi-stable folds, an important precursor to these innovations. But he dismisses such cases as not competitive in the modern Darwinian landscape. When a novel function is at issue, however, how primitive is too primitive? Some function is doubtless better than none, and that is how new functions (and structures) gain a toehold in the Darwinian paradigm. The starting point for any evolutionary optimization path is not an already-optimized functional protein, but one with any function at all, however glimmeringly small, compared to the lack of that function in competing organisms. This will often be an off-beat mutation of an existing protein conferring a novel, if weak, activity.

The idea that one sequence out of all 1E390 sequences is the one that evolution must find, and in a hurry, is fallacious in another way as well. All of phylogenetic analysis is based on the wide variation of sequences, to the point that functionally and structurally similar proteins may have no detectable similarity in their linear sequences. We have essentially no idea how big a swath of sequence space any function might require, even when it is optimized. Evolution certainly never samples all of it- that we can agree on.

But does it have to? No, it obviously does not. One of the wonders of molecular biology is that, as sequences were accumulated in databases, many of them turned out to be related to each other, elegantly recapitulating the phylogenetic tree that Charles Darwin had first sketched out so tentatively to extraordinary depth and detail. In addition to clearly tracking the divergence of species by the divergence of their homologous genes, this method also found countless deeper relationships- families of proteins that had diverged at ancient times from single ancestors through duplication, first sharing functions, but often diverging in function as well. Unfortunately, as indicated above, relationships between linear sequences go back only so far before becoming unrecognizable, despite being truly ancestral, so the full story of ancient protein domain diversification can not be revealed in this way.

Axe notes that every organism harbors, in addition to critical genes that are highly conserved, a population of others with no detectable relationships. A bold hypothesis from his perspective would be that it is these proteins that are the most important, showing that god remains at work, creating new protein structures for critical cellular functions, as has been his habit through the ages.

Unfortunately, another hypothesis is quite a bit more likely. These proteins are, in point of fact, the least important ones of the organism, prone to rapid mutation and divergence to the point of unrecognizability. These, in turn, might be exactly the kinds of proteins that generate new structures, folds, and functions, if they can outrun complete inactivation through mutation, yielding up the novel folds that the author seems so perplexed by.

Indeed, I'd suggest that the known collection of protein folds is reasonably definitive and represents the limited number of ways that small domains can fold coherently. The vast remaining unexplored sequence space is unlikely to add much, just as it is unlikely to add new secondary structures to the venerable alpha helix and beta sheet, due to basic physico-chemical constraints.

If Axe and his peers are interested in doing a real service, they would help save the huge fund of bio-diversity (including protein diversity) we are squandering by the day, rather than pursuing faux-science whose philosophical destination would indicate that god might be happy to reverse our degradation of the natural world with a wave of his magic wand. So, no worries!

• Russell Doolittle speaks on these statistics (at about minute 47) in a general history of bioinformatics.
• What are we all descended from? One original life form, seemingly.
• Up with the pill.
• The Obama iApocalypse.
• Carbon capture? You've got to be kidding- another techno-boondoggle. 

Religion: not so bad after all!

A paper discusses the correlations between large societies, market behavior, and world religions.

Humans have a difficult relationship with truth. We love it, we seek it, we respect it. We habitually claim to have it long before we really do. And in our heart of hearts, we also fear it. One fearsome truth is death. Another is the meaninglessness of existence. It is the highest irony that to escape such truths, humans have created countless other fibs, fantasies, and scams. Oh, what a web we weave!

The premier purveyor of these self-deceptions has been shamanism/religion, which may provide hope for transcendent justice, visions of a god-filled world of mythical drama, life after death, complex justifications for social power relations, social cohesion, and generous amounts of meaning. Can we live without it? That is the question of this secular time, when our self-consciousness has been raised to excruciating heights via evolutionary biology, existentialism, psychoanalysis, and other myth-shattering ideas.

Historically and pre-historically, we have not lived without it. Every society has harbored some kind of religious system, though some contemporary societies appear to have, perhaps for the first time ever, lost its services. From the simple beginnings of superstition and animism to the ever-more fantastic products of theology, we have experienced a crescendo of communal imagined meaning, charming to look back on as myth and fable, and still a matter of vibrant belief in some quarters.

Where do we go now? Will knowledge and self-knowledge keep undermining mythical sources of meaning and ultimately banish religion (the secularization hypothesis), or will religion (or some other ideology) tease (or force) the genie of consciousness back in to the bottle of blissful communal ideology? The answer lies not in any analytical framework, but in human nature- whether we continue to cultivate knowledge and value truth over comfort, and whether functional communal meaning can be devised in the absence of myth and surrender to the many shamans of our time- herbal healers, theologians, nationalist revolutionaries, Islamists, etc.

That digression was by way of introduction to a paper in a recent issue of Science, which offers a rationale for the tremendous parallel growth of "world" religions and world population. "Participation in a world religion is associated with fairness, although not across all measures. These results suggest that modern prosociality is not solely the product of innate psychology, but also reflects norms and institutions that have emerged over the course of human history."

As is usual in so-called social science, most of what they have to say is far from novel. I mean, how much of human culture is "innate psychology" in any case? It is essentially impossible to disentangle culture from innate psychology, other than wild-child cases, which indicate that we are cultured virtually to the core.

Anyhow, the authors make the case that the modern cosmopolitan culture depends on dramatically different norms than the typical hunter-gatherer band of prehistory, which we see modeled in some respects in surviving human indigenous cultures, and perhaps in some small way in the small-band stucture of chimpanzee society. The new norms of mass society are characterized by an ability to trust complete strangers and treat them fairly- to buy/sell food from them, to join them in political action, to join companies with them, to "Friend" them- to do all the things that make our large societies run smoothly (until fraudulent actors take advantage of everyone's accentuate-the-positive trust and take the economy to the cleaners!).

Paired with that trust is a new norm of punishment- punishing violators of the first norm even though the individual punisher may not directly benefit- combined the practice of broadcasting the (bad) reputations of violators. One critique I would have is that it is hard to imagine that these tendencies are specific to large societies. Small societies have extremely strong reputational mechanisms, (gossip), and while typically distrustful of outsiders, have carried on trade with immesely distant partners as far back as archeologists have been able to trace.

Small societies are typically very fair among themselves- positively socialistic on an extended family model. So the question may be much more the sense of membership that people have in increasingly large and abstract communities (e.g. nationalism) than any changes to the psychology of group behavior.

At the heart of paper are a set of experiments, done with the hapless members of widely varying societies all over the world, from hunter-gatherer (Hadza) to blue-collar (Missouri). The first core experiment is to give one person some money, and ask him or her to share it with a second person. Both are apparently brought face-to-face, though the article is unclear on this point. The amount shared is up to the first person exclusively (this is called the dictator game). The authors take higher sharing to imply higher "fairness", and sharing ranges from half (rare) to none (also rare).

But it would seem to me that this has little to do with fairness, and perhaps more with how prosperous and generous people feel- how generous they can be with the amounts of money at play in the experiment, and how connected the feel with their partners. The amount was set at one day's local wage, which seems like a well-controlled level. But one day's wage may represent quite different values to people with either no reserves, living hand-to-mouth, or with substantial financial reserves, access to credit, and other cultural supports (social security, etc.) that allow higher generosity. The values involved may also be different if money represents the common currency of all facets of life, as it does for us, or if it represents inessential luxury values for getting occasional tools and decorations. In different societies, money, even if numerically similar in value, may be quite differently valued. It is very hard to understand why the experimenters imagined their games where truly comparable across cultures.

The following graph shows how well the US stacks up in what I would term generosity in the dicator game, and how this value correlates with what the authors term market integration- the percentage of calories in the diet that are bought rather than self-gathered or grown.

This graphed relation is detectable- market integration correlates with generosity (though the spread is obviously very broad indeed, with the unintegrated Au of New Guinea approximating maximal levels). Generosity was less strongly correlated with membership in world religions, though here the statistics were extremely poor. Virtually all the subjects were members of world religions (the only group with less than 50% membership was the Hadza [0%], while the Au had 100% membership).

Further experimental setups explored punishment tendencies, and I won't get into them here, though the interesting conclusion from the authors is that "... we find that world religion is associated with significantly (P<0.05) more punishment, though market integration reveals no such relationship". Well, surprise, surprise! As one can tell just glancing at the religious landscape, though religious hierarchies may be loath to punish their own members, they are hotbeds of outwardly-directed punishment in defense of their moral "standards", and in support of (indeed expression of) their own cultural power.

One has to note as an aside that these anthropologists utterly ignore the validity of any religious doctrine they are dealing in. Moonies, Islam, Mormonism- it is all the same to them, as though they were looking at ants obeying a pheromone-laden queen. They are far above this fray, with the implication typical in academic circles that the validity of such doctrines is not worth considering.

So, if one takes this work seriously, the conclusions are that some mix of using money-based markets (i.e. buying food), and being nominally part of a world religion each account in some part for increased individual buy-in to the norms of large societies. As unifying ideologies, religions offer just such social norms, bringing disparate people into deeply meaningful community membership which carries with it the punishment of black sheep as well as love and devotion of loyal members. The world religions, by definition and by a sort of natural selection, have specialized in servicing large populations by way of organizational hierarchies, viral spreading memes, and strategic good-cop/bad-cop deployment of both violence and love.

On the other hand, it might simply be the actual act of trading and carrying on the day-to-day activities of larger societies that clues everyone in to the benefits of a new paradigm of higher trust and punishment (i.e. duties of citizenship, like jury duty, respect for legitimate authority, etc.). This realization is then cultivated formally and informally as it is in our schools and preschools, with the result that religion, while helpful in some areas of poor schooling/cultivation (such as striving Pentecostals in Latin America), is less helpful in the setting of a deeply educated and cosmopolitan modern secular culture, indeed impeding greater trust development by its parochial divisiveness, not to say occasional literal terrorism.

• Fascinating segment on North Korea as an effective cultural belief system.
• POTD takes on the British election.
• Morality- present from the start.
• Shutting off the thinking process.
• The Bushies made an oopsie.
• The deep tension between borders policy and social policy.
• Interesting take on what the Fed has been up to.
• Do we need some kind of wildlife reservation for ex-financiers?
• This modern world, in financial engineering.

A nervous switch

The structural basis of nerve conduction: voltage gated ion channels.

One of the grails at the junction of neurobiology and structural biology has been the physical basis of gating in voltage-gated ion channels. A recent paper seems to have cracked the problem for one of them, the potassium (K+) channel.

Nerves conduct impulses quite differently than do electrical wires. There are places where nerves are heavily wrapped with insulation (myelin) and electric pulses race along almost like they do through a wire, but those segments are very short, and the pulse still consists of a small voltage difference across the membrane, between inside the cell and outside, not a difference in voltage between one end of the wire and the other end, as in copper wires.

All the action is at the membrane, and it is driven by an interesting cast of ions and ion channels. Some channels pump ions against their natural gradients (using ATP) to maintain the resting state of the nerve cell. This state is high K+ inside and high sodium (Na+) outside (see animation here). Other channels then use this primed rest condition to propagate the transient nerve impulse, also called the action potential or spike. This begins with a rapid opening of Na+ channels to create a reversal in voltage, then closing of those channels, followed by rapid opening of K+ channels to bring the voltage back to the original state, then a brief refractory period, and then back to rest, ready to fire again.

The voltage reversal, or "spike" of an action potential induces nearby Na+ and K+ channels to do the same thing, unless they have just fired, in which case they are in their refractory period. It is the properties of these channels that gives the nerve impulse its form and forward direction. The nearby Na+ and then K+ channels fire because they are "voltage-gated", meaning that they are turned on by a small change of membrane voltage (another crude animation). In this respect, they are similar to transistors, which use a small voltage to regulate a larger current running through the main conduit.

Biologically, this is a very special type of ion channel control, different from other means of controlling channels, such as binding specific chemicals, temperature, light, or touching structures on other cells. Once open, the channel is passive, letting Na+ or K+ through as fast as it can, but also selective, having just the internal shape and electrical fields to allow that one ion through and no others.

When the membrane potential changes again, due the channel's own effects (high voltage flips another voltage gate to inactivate the Na+ channel while flipping the K+ channel on; then the low voltage re-established by the K+ channel closes it as well). All of which brings the local voltage back down a little below its resting state, with the Na+ and K+ channels closed again.

The current paper describes the physical mechanism of voltage gating of the K+ channel. Naively, one would think that a little charged lid might cover it at one end, but that isn't the case. What happens is that a long protein helix sitting next to the channel slides up through the membrane, levering an attached helix against the bottom of the channel, allowing it to open. The positive charge of this helix gives it its sensitivity. The authors begin by solving an X-ray crystal structure of the K+ channel with its voltage sensor in place, in the open position.

Let's start with images of the channel core in its open and closed positions. Imagine the membrane going horizontally through the picture, with the channel peeking out at top (outside of the cell) and bottom (inside).

The open form (O) is the structure they solved for this K+ channel protein from rat. The closed form (C) is a structure they model based on structures from similar channels (but solved without the voltage gating mechanism) in their closed forms. The potassium ions (tiny green dots) are in the center channel arriving from the outside, whether the bottom end is open or closed. It is only the bottom of the channel that changes shape substantially when closed- tightening into a sort of pucker. This structure can be seen in three dimensions at the protein databank (use the Jmol view tool, which gives full 3-D control and other animation/drawing options [closed form]).

The red helix at the bottom is a key piece of the voltage sensor, but not the whole thing. The sensor occurs in four copies around the channel, which is why there are four helices. Four proteins make up this structure, each contributing one-fourth of the core channel structure, but each contributing one voltage sensor on the periphery. The next structure shows the whole thing they solved- voltage sensors (two shown in red and gray) plus the open channel (blue).

You can see that the voltage sensor (S4) links to the channel bottom through the small helix S4-S5. Leverage up or down in the red sensor communicates to the channel through this linkage. The helices S3b and S4 are the most active parts of the sensor, which the authors deduce must descend dramatically through the membrane to physically push the S4-S5 helix to the other orientation and close the channel.

Then next image is the voltage sensor up close, showing the details of how these helixes fit together. Note that these structures are shows as "ribbon diagrams", only schematically showing the path of the protein backbone. There are many other ways of visualizing atomic structures, based on what one is interested in seeing.

Here they use the amino acid codes R for arginine, K for lysine (sorry about the confusion, chemists!), F for phenylalanine (green), E for glutamic acid and D for aspartic acid. The charges are critically important- lysine and arginine are both positively charged (blue- R and K), while the acids are negatively charged (red- E and D). In this open channel conformation, lysine 5 (K5) is parked comfortably opposite the negatively charged E and D and tucked under the green phenylalanine (F). Since this structure is otherwise enclosed by the oily membrane (gray bars on the sides), any charge on the protein likes to stick to an opposite charge if it can, and this F-pocket is particularly influential in allowing the positive charges R1 through K5 to ratchet down through the membrane, positive step by positive step.

The model that the authors present is that in response to membrane voltage changing, the string of positively charged amino acids from K5 to R1 descend, twist, and bind sequentially in the E+D+F pocket. This naturally wrenches the S4-S5 helix around and forces the channel closed.

The crux of the work is that the authors look at the structural model (along with decades of prior work in the field), and infer the dynamic action as outlined above. To provide some further evidence, they make a series of mutations of the R1 and K5 amino acids as well as the F position, and measure their electrical effects- what voltage it takes to open the channel, to close the channel, and even voltage associated with movement of the gating charges themselves (the "gating current"). Moving the series of positively charged R and K residues across the membrane reveals itself to extremely sensitive methods while the channel pore itself is chemically blocked.

They find that lysine (K) binds better to the E+D+F pocket than does R, so putting R at position 5 makes the channel easier to close (to move out of the open position), while putting K at position 1 makes the channel easier to keep closed. When both positions are K, the channel is harder both to open and to close, as shown by about 40 ms extra time for each process in the K1K5 mutant (D, below), compared to the R1R5 mutant (A).

Gating currents are measured for selected mutants in the 1 and 5 sites, showing that K on either end makes either opening (first half of trace) or closing (second half of trace) slower, presumably due to enhanced stability of binding in the F-pocket and reluctance to be dislodged.

It is beautiful work, and I can only touch on the surface here. The authors integrate structural and functional evidence in classic fashion, supporting the presented theory of how the voltage gate works in the K+ channel. Since this gating is one of the many pieces of machinery that lie at the heart of nerve function, of brain function, and thus of the mind, it is a worthy quest that has taken decades, journeying from awe and mystery to understanding.

• A little debunking of electromagnetic hysteria.
• Muslim intimidation- unique?
• The power of sigmoidoscopy.
• Another nakedly ideological, and unconstitutional, 5-4 Supreme Court decision.
• Mutation found for a curious neurological trait.

Fraud, high and low

What do religion and financiers have on common? You guessed it.

The financial crisis remains somewhat opaque as books are written, investigations launched, hearings called, and bills paid. How was so much money lost? How can those responsible for the crisis and ransomed by the government keep raking in money, and keep paying themselves bonuses for doing so?

I think it is useful to just call it fraud. The financial industry has become addicted to it. There is no boring way to make tens of billions of dollars in the financial industry- not if one cares about one's "clients". But there are many ways to make that kind of money through fraud (video).

Take, for instance, sub-prime loans. These are the antithesis of boring banking. Standards one would apply when lending one's own money were thrown out the window. Hopeless loans were reaped from ignorant (or, one might say "faith-based") homebuyers, then passed on like hot potatoes through packagers like Goldman Sachs, and on to investors who were kept ignorant of their true temperature by the collusion of agencies who shared in packaging them with crisp, cool triple-A ratings.

Or take the world of derivatives. In a humbler world, a farmer wants some assurance for his corn crop in advance, so enters contracts to sell it at a set price, long before it is harvested. Who takes the other end of that deal? A speculator who has money to invest and judges the weather, the market, and other factors, including the gullibililty and reliability of the farmer. This is certainly a casino of sorts, but if the derivatives are constructed in a uniform way, prices set publicly in a large market, and public interest rules made and enforced by the state, (i.e. the commodity futures markets), this can yet become a reasonably fair transaction.

But if the same derivatives are sold privately, with no public notice of values and terms, let alone an open and competing market or government regulation, the opportunities for fraud are obvious. Why would any suckers let themselves in for such treatment? That remains a serious question, and a legal one as suits begin to be filed. Often it was one bank trying to take other bankers to the cleaners, leading eventually to seizure of the entire system when one bank said "no more", and the music stopped. Or an insurance company like AIG trying to make some easy money defrauding its customers (and now the taxpayers) by printing pieces of paper in the form of insurance policies on esoteric gambles (CDSs) without any money to back them up, based on fraudulent risk "models".

Often the short term payouts to those doing the deals on both ends were generous, as each in essence were playing their own institutions for suckers. In short, many kinds of fraud were at work in the recent meltdown, some based on blind optimism and ignorance, but more based on cynical arbitrage of short-term greed over fulfillment of basic fiduciary, institutional, and ethical duties.

(Incidentally, a somewhat similar arbitrage happens every day in our short-term energy thinking, defrauding future generations of a healthy planet. But that's another story.)


Which brings me to the other major fraudulent institution of our day- religion. Not just your garden variety televangelist huckster or Reverend Dollar. No, the whole kit and kaboodle, from Bible church of Jesus to the Pope in Rome. Each sells over-pumped products to their clients based on false pretenses, all winding up ultimately in the bankruptcy proceedings of the grave.

Right now the focus is on the Catholic church in its frantic coverup and spin over the fraudulent treatment of minors. No need to go into details. But this is not just a case of a few bad apples in the barrel. No, the abusive priests are bad apples, but the culture of the church, indeed the very premise of the barrel itself, is fraudulent from top to bottom.

Orwellianisms flow without end from the mouths of preachers- life everlasting, god incarnated as man, crucifixion as triumph, prayer as efficacious, god as omnigood and omnipotent. As art, their performances are without parallel, conjuring an alternate universe of meaning, justice, and joy. Confined to art, the harm would be minimal. But true to its shamanistic origins, it is a participatory art, playing on the fears and hopes of its subjects, as all cons do, to rope them into the religion meme- to give money, to give time and energy, to spread the meme to others, going door-to-door, if necessary.

(At this point let me put in a good word for one of Herman Melville's greatest works- The Confidence-Man. He portrays in surreal fashion a riverboat going down the Mississippi with a streaming cast of characters, each preying on the other, but with a mysterious protean confidence man at the center who illuminates the hopes and fears of each party in turn, using Kafka-esque indirection and frankness.)

Do religions provide hope to the hopeless? Goldman Sachs also provides hope to its clients, in the form of tangible investments to keep them afloat in retirement, or gain money for other purposes. And sometimes, that hope is even fulfilled, unlike the 100% loss sustained by religious believers, year in and year out.

Do people perform good works under the influence of religion? They do, and that is commendable. Such work makes everyone happier and strengthens communities. Banks likewise make philanthropic gestures for their communities and other good causes. They are also to be commended. Are their motives less pure than those of religion? Both are image-building affairs, translating the goodwill of their members (whether earnest or cynical) into public proselytism, hoping to trade on this good image for more business in the future and stronger buy-in among existing members.

Do religions foster community and happiness all around? Ponzi schemes foster community as well, though these tend to burn out quickly. The Madoff scheme was exceptionally long-lived, nurturing the hopes of a large community of his communicants for over a decade. Religious Ponzi schemes, in comparison, can be perpetual, since they concern an undiscover'd country from whose bourne no traveller returns to expose their fraudulent nature.

More seriously, communities fostered by financial institutions are not inculcated with the belief that those sponsored by other such institutions are fundamentally evil, require proselytization, and are going to the devil if they fail to convert to the true doctrine. The high degree of (false) meaning conjured by religion generates commensurately high commitment, leading naturally to extremism in those it fully captures.

Which is the higher and which the lower form of fraud is a matter of debate. The culturally conjured symbols of Mammon, or the fervent and ever-unfulfilled hopes preyed upon by the officers of religion? The dollar, as token of the hard work of others, studiously waylaid in the canyons of Wall Street, or the phantasm of life everlasting peddled in every church in the land? Now that secularity has largely brought the temporal power of the church to heel after several centuries of hard work, one has to say that Mammon has the greater power, and poses the greater danger. Yet the fraud of religion is usually more thorough.

• Hitchens on the Pope as criminal racketeer. Who ever suspected?
• Even that nice Michael Ruse has second thoughts about Catholicism.
• The FDIC fights back.
• And even Martin Wolf is looking for radical reform.
• UBS? Fraud ongoing, thank you very much.
• Next up for the church: women.

Apocalypse past

Freezing over and burning up ... it's all there in the geological record.

A recent issue of science had an interesting pair of geology articles, one reviewing knowledge about the dinosaur-killing asteroid of 65.5 million years ago, and the other reviewing whole-earth glaciations of ~700 million years ago, in an era now dubbed the Cryogenian. In short, fire and ice.

I don't have much new to write about either event, but want to bring up interesting points of each and try to increase appreciation of the dynamic earth we live on, whose future livability can not be taken for granted.

The first article, on the 10 km diamter asteroid that hit the Yucatan peninsula, is a review that ties various pieces together to solidify the consensus that the dramatic extinctions of this time were indeed caused by the impact, as were a very distinctive set of geologic layers all over the world. Alternately, extensive vocanism occurring in India around this time over about one million years might have begun the environmental destruction. Yet the authors point out that the asteroid lofted a thousand times the sulfur and other debris into the atmosphere that volcanism did on a yearly basis. There simply is no comparison.

They present a fabulous pair of figures, one mapping sampled sites all over the world, with diagrams of typical geological profiles, and a second with one closely annotated core taken from the western Atlantic.

(Click to blow this up)

The green wave on each profile in B is the iridium signature of this asteroid impact- an element that is extremely rare on Earth and is presumed to have come directly from the asteroid and been deposited all over the world in a diagnostic geologic layer.

The "graded clastic unit" of the first panel in B is debris from the impact, pure and simple, quickly overlain with the dust and ashes that were lofted and gradually settled back down. The latter is all one sees in the farther-away sites (distal) which feature the "ejecta spherules", "Ni-rich spinels", and "shocked minerals", each of which are further impact signatures. The spherules are typically tiny sprays of molten rock from the impact site, the nickle is directly from the asteroid, and the shocked minerals are typically very hard minerals (quartz) from the impact site that were not melted but only scarred and turned into dust by the impact.

(Click to blow this up)

This second figure shows one core from drilling point 207 in the first figure, off Guyana, South America. The first thing to notice is the total break between the bottom and top parts of the sedimentary record. Usually, this would be due to a break in the geologic time line, where the bottom unit had been raised up and eroded for some time before being buried again and overlaid with a different type of sediment. Not here! The break represents continuous stratigraphy during a real change in materials being deposited, from calcium rich before the inpact, through the impact episode, to low-calcium shale above. They do not comment, unfortunately, about the details of this macroscopic difference.

In the middle is 1 cm or so of material from the impact event, mostly rubble and other dust (with spherules, "SP"), topped with a lighter melange blown up in B. This image is a doubtless an X-ray spectrum micrograph false-colored with various elemental compositions (purple- calcite, blue- dolomite, and red, quartz). Each of these minerals comes from the impact site, and panel C shows the cracked nature of the "shocked" quartz "Q". Unfortunately, I don't have the expertise to know what the tan matrix is here.. probably sandstone composed mostly of feldspar- various silicon oxides that make up garden-variety rocks.

This paper would not shock most people, but there have been persistent controversies in the field as various critics tried to come up with alternative scenarios. Catastrophism vs gradualism continues to cause tension in studies of Earth's history! One scare in the literature sampled many organisms through the event horizon and concluded that most of them were declining precipitously well prior to the asteroid impact. Later criticism showed, however, that this conclusion was false, due to statistical errors in sampling that didn't properly account for a sudden boundary of zero fossils combined with spotty deposition up to that point- a boundary that the typical paleontologist (and her software) would interpret as gradual decline of organisms up to that point.

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The other paper of interest describes better dating of events around the period of "snowball Earth"- very roughly from 600 to 750 million years ago- just before the rise of eukaryotes / animals when the Earth was apparently covered with ice sheets down to the equator. Whether the oceans were iced-over as well is still controversial, but the idea is that once glaciers cover a certain proportion of the land, increased solar reflection drove the process to completion at least on land, resulting in a totally locked-in condition for millions of years.

That condition was only reversed when volcanic emissions drove enough CO2 into the atmosphere to cause a run-away greenhouse effect. CO2 is usually eaten up on geological time scales by mineral erosion- combining with calcium and other elements into carbonates (limestone, marble, dolomite, etc.). With the earth covered with glaciers, there was no air-exposed erosion, and CO2 built up without hindrance. The cold temperatures would have inhibited carbon fixation by oceanic photosynthesizers as well. This part of the process is quite well-understood.

Less understood is why the glaciations happened in the first place. The going theory is that the tectonic plate organization at the time happened to be propitious, with all the land masses at middle latitudes. This made erosion particularly active, driving CO2 levels down, (there's that CO2 again- always a problem!), and also increasing the reflectivity of the planet once snow began to accumulate on the land. Having so much land near the equator made the climate very unstable, allowing icy conditions to reach a critical tipping point. I'd also note that at this time, land was not clothed with plants and greenery as it is today, leaving it uniformly open to erosion.

Model of paleogeography circa 750 million years ago.

In detail, these authors work to more closely pin down two separate episodes of long-term, global glaciation, using a lot of uranium/lead mineral dating. The Sturtian was around 716 million years ago, and they synthesize evidence from other workers to say that it lasted at least 5 million years. That is quite a long time! Catastrophic for anything living at the time. This was repeated in the very similar Marinoan glaciation about 635 million years ago.

The figure gives their interpretation of the timing of this era, combined with estimates of when various eukaryotic lineages arose on the right side. All of the lineages before 700 million years ago are microscopic. The metazoa/animals only arrive in yellow at the far top right (indeed, the closest linage to us of all these is the fungi). The dashes symbolize missing data- the time between the two great glaciations is practically devoid of fossils, for instance. Only afterwards do eukaryotic macro-organisms begin to occur, in the Ediacarian epoch.

Some of the largest organisms from ~750 million years ago, predating the Cryogenian. Eukaryotic protists of some sort.

The key data they offer is the carbon isotope ratio between carbon 13 and carbon 12 in the middle graph, which flips wildly between high prior to glaciation and super-low during glaciation. This ratio, drawn from studies on carbonate minerals, (absent from the period of the glaciation itself, understandably enough), is a bit difficult to interpret, unfortunately. It seems to track biological productivity, since organisms tend to fix light carbon (12) in their metabolism in preference to carbon 13. High levels in geologic deposits correspond to periods when a great deal of carbon was biologically removed from the atmosphere, leaving higher ratios of 13C to 12C, then incorporated into carbonate minerals. Deeply negative values, as seen here at the boundaries of these glaciations, indicate low biological fixation and perhaps release of stored 12C-rich carbon from organic burial/storage, as is happening again today as the atmospheric 13C ratio is declining steeply.

The asteroid impact is well-known, but the whole-earth ice ages prior to the rise of multicellular life are not as well known, making them (possibly) interesting to readers. Both show the dynamic nature of earth's geologic and climate system. The ice ages especially accentuate the role of CO2 as the controlling greenhouse gas. With the current anthropogenic CO2 emissions and climate change, we are not going anywhere the earth has not been before at some point, but we are going to places where humanity has never been before, and going there at (geologically) breakneck speed.

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