Human evolution- drifting, not sweeping

Our genomes indicate relatively few genetic sweeps in the last 100,000 years.

Despite the lack of a medical revolution from our knowledge of the human genome, as yet, other fields are being revolutionized, including the study of human evolution. The ability to compare complete genomes from people of different lineages generates vast amounts of digital comparative data that can transform pre-history into history of a sort.

Humans are virtually clones, compared to most other organisms which have far greater genetic variation. Our genetic variation is small due to the very small population sizes we seem to have had for much of our evolutionary history, (perhaps even due to severe bottlenecks), leading to the genetic Eve/Adam reconstruction of single ancestors dating to maybe 250,000 years ago.

Since that time our genetic variation has been increasing apace, with most modern-day variation residing in Africa and much less outside, due to the later migration of small populations out of Africa, perhaps 50,000 to 90,000 years ago, combined with very limited interbreeding with resident homo cousins like the Neanderthals.

This variation (caused by mutation, then reduced by selection and drift) is the mother lode- it tells us which populations are more related to others, it generates the traits that differ between populations and between individuals, and it carries traces of the selective process itself, which is the focus of the current paper.

Imagine a strongly beneficial mutation arising that, say, provides complete protection against some disease like the plague. This mutation resides on, say, chromosome 8. After an epidemic of plague, all members of the (now reduced) population have this new mutation- the others have been killed off. (In the parlance, this mutation has now been "fixed" because there are no competing alleles at its locus.) This means also that all members of the population share the same chromosome 8 in its entirety. This has been a selective sweep, carrying along whatever other variation resided on that copy of chromosome 8 that had the disease-protecting variant, good or bad. This kind thing can bring along and expose recessive traits like the royal haemophilia, and it dramatically reduces genetic variation of this chromosome in the population, which can be tracked for tens of thousands of years.

On the other hand, imagine another trait with less dramatic effects. Perhaps which slightly reduces the severity of psoriasis in those who have condition that due to other factors in the genetic background. This trait may be beneficial in a few situations, but will never sweep itself or its neighbors to predominance or completion in the population. It will drift along, gradually rising in percentage within the population (if it has no untoward side effects, which would be rare, given the networked nature of the genome, actually). The key point is that the slowness of this process allows recombination to have its say.

Recombination happens on every chromosome in every generation, swapping parts of its arms between those inherited from each parent. Roughly speaking, the location of such swaps is random and at least one happens on every chromosome per generation, so very gradually over time, each gene variant in a population becomes neighbors with variants of nearby genes other than those it was born with. After roughly 200,000 years for humans, this mixing should be essentially complete and the variant tends to be no more associated with than the neighboring variants it was born with than one would expect by chance.

Crossover recombination, which happens on each chromosome, at least once per generation, mixing up the genetic variants on chromosomes throughout the population.

That process is what this paper was interested in- figuring out whether there were any islands of unusually low variation that bespeak selective sweeps by highly beneficial gene variants over the last few hundred thousand years in humans. The authors hail from something called the "1000 genomes project", though they only have 179 genomes to their name in this paper, claiming that is enough to start sifting through the available variation. They consider three sub-populations: Yoruba of Africa (YRI), European (CEU), and Asian (CHB+JPT). The goal was to find whether over the time since these populations split, (roughly 100,000 years for YRI vs the other two, and 23,000 years for CEU vs CHB+JPT), any gene variants went from low percentage to become fixed (i.e 100%) in only one lineage.

Unfortunately, most of the more statistical data presented in this paper is stunningly hard to interpret and present. I also doubt that it means as much as they make it out to mean. But I will take a stab with one emblematic graph. Skip the next paragraph if you are in a hurry!

For this graph, the authors have isolated all exons of the human genome and conceptually centered them at the X-axis midline. Then across the local region, (X-axis in centimorgans, a unit of genetic distance), they graph on the Y-axis the diversity of the populations they have sampled. This tends to be lower in highly conserved areas like exons and higher in outlying areas. This diversity is normalized to (divided by) the difference between the canonical human genome and the sequence of rhesus monkey, which should in principle cancel out the variations due to conservation of protein-coding genes and other typically conserved elements.  Note that the diversity of the African population samples (green) is substantially higher than that of the European (orange) or Asian (purple) population samples. The authors argue that the central troughs are signs of specific directional selection that has affected the human linage differentially from the normal maintenance or purifying selection that would have been in common between the human and rhesus genomes. The main result is that the troughs they see are very narrow- signs that this directional selection dragged along very little of the surrounding genomes, where diversity remained high. Which is to say- genetic sweeps were very uncommon, on average.

The main result, aside from the sorts of somewhat dubious graphs shown above, was that there are very few fixed differences between their sampled populations- only four fixed amino acids in the entire genome that differ between the African and European population samples. For comparison, there are about 40,000 human-specific fixed amino acid changes between chimpanzees and humans (split for 5 million years), of which 10 to 20% are estimated to be selectively significant. So one would have expected to see 800 fixed changes in the 50,000 to 100,000 years since the African/European split.

Unfortunately, the authors focus on amino acid changes, (apparently out of convenience), totally missing the more important and frequent loci of evolutionary change in regulatory regions. They are only seeing the tip of the iceberg, really, and don't have or offer a good idea how big the whole iceberg is. Additionally, a small amount of genetic flow between populations, as might have been transmitted through the bordering regions of North Africa and Arabia, could have severely reduced the fixation of variants that had otherwise become established in their respective geographic regions.

Nevertheless, this illustrates the overall tiny level of genetic difference among contemporary human populations. It also implies that whatever evolution and differentiation was going on in the protein-coding regions they focus on, it was almost entirely confined to slowly jiggering the frequencies of alleles present in a population rather than rapid revolutionary replacements of an old gene variant with a shiny new gene variant. Even with the limited genetic variation that humans posess, significant phenotypic variation is evidently possible with virtually no population-level 100% differences. This undoubtedly reflects complex traits influenced by many genes whose interrelations make change both slow and genetically hard to track.

"An important implication is that in the search for targets of human adaptation, a change in focus is warranted. To date, selection scans have relied almost entirely on the sweep model, either explicitly (by considering strict neutrality as the null hypothesis and a classic sweep as the alternative) or implicitly (by ranking regions by a statistic thought to be sensitive to classic sweeps and focusing the tails of the empirical distribution). It appears that few adaptations in humans took the form that these approaches are designed to detect, such that low-hanging fruits accessible by existing approaches may be largely depleted."

So, human evolution seems to have slowed down in recent times, at least with regard to sweeps by strongly beneficial variants. I would guess that this is due to our rapidly increasing population sizes over this time, which tends to preserve variation and forestall fixation, at least on a short-term basis. It may also be a testament to our frolicsome tendency to interbreed widely, preserving variation in the face of wars, famines, diseases, genocides, and calamities generally.

• Republicans are seeking even less regulation over the financial industry, in service to crony capitalism.
• Ditto from Krugman ... on mortgage fraud and other criminal activities. 
• Victimization narratives know no bounds, really.
• Fascinating analysis of self control, anarchy, religion, and conservatism.
• Guess who is on the wrong side in Africa?
• More on financial fraud:

"Indeed, accounting control fraud is finance's “weapon of choice” in much of the developed world because it is the superior solution to the tradeoff between the risk of being sanctioned for looting and the rewards from looting. Even the most powerful bank CEO faces a grave risk of being imprisoned if he sticks his hand in the till and steals $10,000. If, instead, he uses accounting control fraud to loot the bank of $50 million he has an excellent chance of never even being prosecuted."

• How's that trickle-down economics doing?
• Cello quartet? Yes!
• Bill Mitchell quote of the week:

"It doesn’t take too much to know that if a nation sacrifices millions of dollars of potential income per day because it keeps millions of its citizens unemployed that it is not using its resources optimally. When you do the sums there is no greater inefficiency than mass unemployment."

Plato is unreal

Abstract ideas are our creations, however much we want to make them into absolutes and deities.

"Platonism describes idea as prior to matter and identifies the person with the soul. Many Platonic notions secured a permanent place in Latin Christianity." - Wiki

As a non-philosopher, it may be slightly presumptuous to dismiss the founding philosopher. But something really needs to be said. Plato and his school were obsessed by the abstract- by forms and ideas. The idea(!) is that abstractions are real-er than real, since we need ideas to make sense of sensations. They paid homage to the soul as the ideal figment of man, and to idealized forms of the universe as the shape or expression of god. Christianity, formed out of the meeting of Greek philosophy and Jewish theology, lapped all this up, treating Plato as a church father who led the way towards making the metaphysical and the supernatural into respectable intellectual topics. But Plato was wrong.

Who makes forms? Nature doesn't. Nature can (sometimes) be described using formal mathematics. We can abbreviate its vast clockwork using abstract ideas. But they are only helpmeets and makeshifts to make up for our paltry cognitive capacities. They are our creations, confined to our minds and writings. We discover them in the sense of developing those ideas the most efficiently describe large collections of phenomena. But we don't discover them in the sense of going to Antarctica to discover new equations. They are found in our heads, and there they remain.

It is frankly bizarre that people could get so carried away with the power of abstract thought, (their own or that of others), that they project these powers onto the universe at large, characterizing it as a giant computer, or as a "thought" of a deity. And go far as to deprecate the very reality they are faced with, regarding it as less real than the true realities that are hidden behind in the shadowy realms of mathematics, celestial spheres, simplifying concepts, and the rest.

What does this amount to? It is the oldest form of thought in the book- magical thinking, which sees hidden forces, agents, spirits in all the vexing phenomena of our world. This is not to say that phenomena can't be analyzed ... where would we be without germ theory, geology, or Newtonian physics to make sense of the bewildering chaos around us? But never have we come face to face with what we most desired and feared- that vengeful deity or merely conscious being that, to be frank, sprang entirely from our own imagination.

Plato cleaned this up in his image as forms rather than gods, but the same process was at work- the projection of human capabilities and motivations on the canvas of reality. So, isn't the quest of physicists for a grand unified theory of everything an indication that he was on the right track? Wouldn't the ultimate reduction of physical reality into, say, an enormous Lie group, or a tiny string, vindicate the Platonic position? No it wouldn't, because such an abstraction, enormous as its explanatory power would be for us, wouldn't change the reality before us.

Biology has taught us the dangers of casual projection in place of detailed empirical engagement when dealing with bizarre, even alien, technologies. How much more inscrutable is the fabric of the universe? Whatever its cause and nature, it would be madness to assume that it follows the outlines of psychological projections which have been consistent over millennia, persistently invoking a thinking, emotional, sentient, powerful, intelligent, and caring, etc... being.

If forms were really the real reality, then we should be able to stretch reality into new shapes by altering those forms. Admittedly, this is the ultimate magical thinking, but it follows directly from the Platonic argument (as well as all the related theologies of prayer, intercession, etc.). If, on the other hand, the forms we use to describe reality are mere desiterata of our mental mechanics while reality exists outside them, not caused by form or embodying form, but capable (sometimes) of being represented through forms and formalisms... then the empirical reality is what we get, adamantly resistant to formal manipulation.

And what is the cause of this reality that we can abstractly understand by our formalisms? Is it something / someone which thinks, and whose thoughts actually conjure reality in elegant mathematical relations? This again is a projection from our mode of understanding onto the world. Biology has taught us the dangers of casual projection in place of detailed empirical engagement when dealing with bizarre, even alien, technologies. How much more inscrutable is the fabric of the universe? We simply have no idea what its ultimate cause is or was. While we can be thankful that it exists, there is no reason to think that there is anything cognizant at its core, let alone cognizant of us, much as we may wish to please it and understand it.

• A historian goes viral on the GOP.
• Notes on age discrimination.
• Extreme rhetoric, irresponsible politics, and concealed weaponry- precursors to political breakdown.
• GE- Not only pays no taxes, but gets money back from the IRS. A study in corruption.

"The company reported worldwide profits of $14.2 billion, and said $5.1 billion of the total came from its operations in the United States. Its American tax bill? None. In fact, G.E. claimed a tax benefit of $3.2 billion."

... "... have pushed down the corporate share of the nation’s tax receipts — from 30 percent of all federal revenue in the mid-1950s to 6.6 percent in 2009."

• Disaster theology, Japan edition.
• Bill Mitchell quote of the week, courtesy of Joseph Stiglitz:

"The fact that countries with central banks that were not independent performed so much better than some of those that were—partly because the latter were “cognitively captured” by the financial markets that they were supposed to regulate—should perhaps lead to rethinking of doctrines concerning central bank independence."

Memory on my mind

Memory storage in the brain happens simultaneously in the hippocampus and cortex.

Despite the continuing hold that supernaturalism, soul-ism, and related theistic sentiments have over much of the population, to those scientists working on the mind and consciousness, its physical nature is obvious and underpins a rich program of research.

One key to consciousness, of course, is memory, which, along with direct sensation, emotion, and whatever else bubbles up from unconscious processes, make up its contents. Sensations as well are now understood not as mechanical readings of outside input, but as template-filling exercises strongly structured by our prior experience and expectations- i.e., our memories. And emotions are increasingly characterized to have complex hormonal and anatomical sources within the brain, also strongly tied to memories, many of which are themselves unconscious.

For instance, in the paper under review this week, rats learn about what is good to eat or not by smelling the breath of another rat who has just eaten that food. Give one rat some tasty, aromatic cinnamon, and its housemates rapidly learn about it as well, and remember that goodness (if that is what the first rat thought about it) for the rest of their lives. We are all each other's taste testers, apparently!

Memory formation is currently theorized to begin in the hippocampus as short-term storage, before being deposited in the cortex for long-term storage. This model arose from studies of humans and other animals with lesions indicating that if the hippocampus is absent or disconnected, no memories form at all, while if its connections to the cortex are severed, no long-term memories are formed, though prior long-term memories are retained and short-term memories form briefly (weeks to months) as well. Some forms of immediate short term, or working, memory (like recalling phone numbers and word lists) escape this effect and are not dependent on the hippocampus at all.

The transfer mechanism between the hippocampus and the cortex is currently believed to involve sleep and dreaming, where memories are replayed, perhaps in substantially speeded-up form, reinforcing their connections and salience in the cortex.

"Replay of encoding-related activity during phases of sleep has emerged as a core mechanism for driving the structural changes within the hippocampal-cortical neuronal networks."

And what is the ultimate physical engram of memory? This is thought to be the neuronal synapse, whose structure is plastic over long and short time spans, and whose structure / connection is reinforced by electrical activity in the basic Hebbian learning hypothesis. This current paper also engages in some molecular wizardry to manipulate synaptic structural change and thence either enhance or cancel memory formation in rats.

The interesting finding in this paper is that cortical involvement is key for this type of memory in rats from the very start, not just after some weeks of residence in the hippocampus, as the prior theory had it. To figure this out the experimenters used a somewhat shocking technique of injecting the respective areas of the rat's brains with an inhibitor of synaptic transmission (CNQX) for various windows of time. So, if they blocked the hippocampus at the start of the 30-day period, no memory of the food smell occurred at the end. Conversely, if they blocked the frontal cortex in the second half of the 30-day period, the memory was reduced by half. Some key experiments are diagrammed below:

Direct brain injection of a synaptic transmission inhibitor (red) vs control fluid (gray) into the orbital frontal cortex at the time of learning (day 0) eliminates long-term memory (30 days) of the social food interaction (this time with cumin), but not the short-term memory (7 days).

Double learning test, where one inhibitor injection eliminates memory of the taste learned simultaneous with drug, but not the one learned a week beforehand.

What they found was that blocking nerve transmission in the frontal cortex during the early time (days 0 to 12) also dropped memory formation by half at the end of 30 days. They claim from this that the hippocampal-first model of memory formation may be incomplete, and perhaps nascent cortical memory is laid down at the very start, during or after the original experience, but requires reinforcement over the ensuing weeks from the hippocampus to become a long-term memory.

"This finding identifies early cortical tagging as a potentially critical process reponsible for the progressive embedding of enduring memories within cortical networks."

The experimenters supported their theories on the cellular and molecular levels by mapping synaptic morphology and numbers, intracellular golgi complex concentrations, and histone modifications in among  neurons otherwise tagged as active in the dissected rat brains, all of which are known to correlate with memory formation. They claim that the single learning trial (of 30 minutes) conducted in each experiment significantly increased measurements of these indexes in their rat's brains. Which perhaps goes to show that these rats, housed in individual plexiglass cages, were leading stultifyingly boring lives otherwise!

In addition, they applied drugs locally into the cortex that are known to alter memory formation at the cellular level, (either inhibiting or activating histone modification enzymes) at selected times; in this case at the same time as the learning session. Memories established by the social food preference learning exercise could be eradicated (or enhanced) by this pharmacological intervention, showing that while the hippocampus is sufficient for memory recall at early times (1 to 2 weeks), memory formation in the cortex depends not only on late events, but early ones as well.

Test of memory enhancement with sodium butyrate (inhibitor of histone deacetylases). Injection into the orbital frontal cortex at the time of learning significantly enhances the same type of memory that the synaptic inhibitor eliminated, thirty days later.

The main message I took from this is that the study of memory is getting remarkably detailed. Theories are becomming more refined, spanning from the behavioral and anatomical to the molecular levels, and are tested with more intricate and bizarre methods. The results are consistent with mechanistic theories of memory storage and retrieval, while being disputed and adjusted in many details as experiments go on. It is amazing, really to see this progress.

One has to ask, however, what goes on in rats getting cortical infusions of a synapse blocking agent? Were they conscious? Were they even alive? Apparently so, but these methods seem rather extreme and prone to a lot of unintended consequences. The methods section of this paper reiterates that the drugs were precisely delivered in quite small amounts. And their location and activity were verified on autopsy by staining the brains for gene expression patterns characteristic of neural and synapse activity.

In the end, a great deal remains unknown. Assuming that the Hebbian model is basically correct, how are the network engrams (i.e. memories) called up at will? Does any associating thought or sensation lead the brain to re-animate the stored memory, injecting into the stream of active thoughts? Does calling it up automatically reinforce it, or does something else have to happen, like new cognitive or emotional associations? What is the form of sleep/dream replay that reinforces memory between the hippocampus and the cortex? And of course, how do memories relate to consciousness- do they "enter" it, or do they constitute it?

• Basic brain anatomy video.
• Nuclear disaster, or climate disaster?
• We need a Tobin tax, and not just on currency speculation.
• Are scientists ready to take over the mantle of spirituality in the West?
• Bill Mitchell ... Writes a fine piece in the Nation.

"Under the gold standard governments had to borrow to spend more than their tax revenue. But since 1971 that necessity has lapsed. Now governments issue debt to match their deficits only as a result of pressure placed on them by neoliberals to restrict their spending. Conservatives know that rising public debt can be politically manipulated and demonized, and they do this to put a brake on government spending. But there is no operational necessity to issue debt in a fiat monetary system. Interestingly, conservatives are schizoid on the question of public debt: public borrowing provides corporate welfare in the form of risk-free income flows to the rich because it allows them to safely park funds in bonds during uncertain times and provides a risk-free benchmark on which to price other, riskier financial products."

You can't take it with you

A modest proposal: tax estates at 100%

It always strikes me as funny how Republicans cry on about freedom, the opportunity society, and everyone pulling themselves up by their own bootstraps and getting only what they work for & deserve. But when it comes to their own children, no expense or trust fund is spared. The principle of individualism takes a back seat to a distinctly socialistic distribution of wealth without regard to merit or virtue, the criterion of blood trumping all others.

While this is without question instinctive and in accordance with the most hallowed aristocratic traditions, it hardly accords with the professed ideology of the right, which celebrates the self made, the entrepreneurs, the innovators, the up-from-poverty Horatio Alger stories. Leaving aside the typically dubious methods of acquiring such nouveaux riches, the vieux riche are rather the opposite- unemployed, coddled, Paris Hilton ... need we say more? The best that can be said by way of justification is that they share some of the genes of the originating generation, if one sets store by that kind of inheritance. Or that they faintly echo the dreams of their progenitors, who, despite being dead and gone, deserve our continuing gratitude.

So in order to supply all the character-building and innovation-encouraging opportunities heretofore denied to children of the rich, I'd propose that all children start life out of the same gate, provided with all the opportunities we can collectively and fairly give them, along with the healthy need to take advantage of them. Each would make his and her own way in the world. In short, each would have to work.

We could begin to provide this opportunity by making the estate tax 100%, eliminating the corrupting influence of inherited wealth. Such a tax should net upwards of $200 billion per year. Perhaps not quite the vast sums we need to fund the whole government, but a definite boost to programs needed to provide all children the opportunities and education needed to have a proper start in life. Gifts and other forms of intergenerational transfer would likewise be prohibited over nominal levels, to make the playing field of life as fair as possible. While I am at it, elementary and secondary schooling would become similarly egalitarian, with private schools either eliminated or opened to all students without financial restriction.

The last century has seen a truly remarkable sea change in the opportunity structure of higher education in the US and Europe. Academic and personal merit has gained substantial ascendance over breeding and money. Trust fund students still get inordinate attention, but financial aid has enabled high achievers from all backgrounds to get excellent educations in the finest schools, with meritocratic standards like standardized test scores opening many doors to the unpropertied and un-networked.

A no-inheritance revolution would extend this opportunity-generating process, making our society fairer, more focused on the many public goods involved in providing opportunity to the young, and better able to nurture and benefit from everyone's talents. It would also make us less susceptible to the kind of entrenched power that flows from old money- from the creeping re-establishment of aristocracy, if you will. The New World should lead the way in repudiating this inherited vestige of Europe- one of its very worst traditions.

Indeed, a thousand years hence, this may be one of those things that people look back at in sage disappointment, as we do at slavery in ancient Rome. That we prideful "moderns" still adhered to the old rules of blood inheritance, ate the carcases of dead animals, and burned fossilized carbon till we choked on it.

Would inequality remain? Huge amounts would indeed remain, from social and professional networks to more or less enriching home environments and genetic endowments. The advantages of the advantaged would still be incalculable. But perhaps without unearned and undeserved wealth to look forward to, all children would on average have a brighter future, and children of wealth could embody those values their class so prizes, of self-reliance, ambition, and hard work.

• A plan for progressive taxation.
• How rich can someone get? And what is the point?
• How one aspect of privatization screwed up the mortgage industry and fleeced the public.
• Afghans are in negotiation with this?

"Over the past several years, the Taliban have savagely attacked tribal leaders who oppose Taliban rule in the tribal areas and the greater northwest [of Pakistan]. Tribal opposition has been violently attacked and defeated in Peshawar, Dir, Arakzai, Khyber, and Swat. Suicide bombers have struck at tribal meetings held at mosques, schools, hotels, and homes."

• Pakistan is on fire ... and Islam as the fuel.

"The religious fanaticism behind our assassinations is a tinder-box poised to explode across Pakistan," -Zardari 

• Skidelsky on Ricardo, Osborne, and austerity.
• GOP knows no bounds in meanness towards the poor and unfortunate. The rich are the only ones you can trust with money, after all!
• Bill Mitchell quotes of the week:

"In relation to today’s blog we should understand that government deficits are the norm and they generally never pay back their debt (overall).

...

These economists essentially lead sad professional lives. They bunker down in their offices and doodle away with mathematical models that are largely banal representations of some obscure untested assumptions about human behaviour and motivation which the other social science disciplines and relevant research show to be inapplicable."

And:

"The only “pressing policy question” relating to “fiscal space” is that there are millions of people unemployment who could be engaged productively generating income and feeling better about themselves.

Unfortunately, that is not the “hotly debated topic” and that is because economists like this lot have a completely warped sense of priorities and a mistaken understanding of how the monetary system actually operates."

Socialism - Si!

We live in a socialist country and have for a long time.

One of the many scarewords of the right is "socialism". Obama is a socialist, Nancy Pelosi is socialist, Government reform of health care is socialism, except for Medicare, which is OK. However what we should really be worried about is totalitarianism, not socialism. The banks didn't mind a bit of socialism over the last few years, nor does the miltary get dinged for its entirely socialistic structure and practices. No, the danger is the health of our political system, which the right has done far more to damage in recent decades than anyone else.

The "socialism" debate is really about more or fewer public goods. Socialism is all about public goods provided on the basis of citizenship or other merits like educational potential. In contrast, Laissez faire is all about private goods sold to those willing and able to pay... the highest bidder. There is no question that laissez faire is a great way to distribute many goods- those that are exclusive, privately enjoyed and consumed, with no further socially redeeming qualities. Like toothpaste.

The right-ward view, most thoughtfully expounded by Friedrich Hayek, maintains that private goods are the most important, and every attempt to provide goods in non-laissez faire fashion ultimately fails because "government is the problem" ... it is inefficient, sclerotic, corrupted, etc. Corporations could never exhibit such blemishes. Corporations are always cleansed and policed by Darwinian competition, while the state's ultimate regulation, by its voters, appears to these thinkers to be untrustworthy and ineffective- fundamentally less effective than the discipline of the market.

Such proponents grit their teeth and accept the necessity of a bare minimum of public goods- police, military, maybe a legal system. But they are deeply suspicious of every good that could conceivably be furnished in private fashion. A gold-based currency is only one of the most signal and bizarre examples. There are many others- oil companies should be private, as should postal services, power companies, educational institutions at all levels, drug testing, and pensions, to name a few.

The US has, however, never taking this view terribly seriously, and painstakingly raised itself out of bare laissez faire conditions by establishing public schools, a social security system, public research institutions, public roads, regulatory bodies, and countless other public goods. The question is not whether we might become socialists, but how much socialism we decide to practice.

Herewith, a few more of the great American public goods:

• The Panama Canal
• WWII (our side)
• The space program
• The Louisiana purchase
• Public broadcasting
• Rural electrification
• The internet
• Hoover Dam
• Railroad surveys and land grants
• Social Security
• The abolition of slavery
• National Parks
• Public elementary and secondary education
• Public colleges and universities

The fact is that public, common goods are the very foundation of our greatness in commercial, not to mention other, spheres. There is no question that US worker productivty, which all sides recognize as the fountain of future prosperity, depends in very large measure on public goods devised or supplied by the government- education, roads, legal structures, the internet, academic research, military security, sound money, ... the list is endless. Even an economic safety net is essential to maintain individual social and work potential, according to some!

To take a concrete example, the inefficient redundancy of the US cell phone industry is traceable to the ideological abdication of rational regulation and public provision. Due to a laissez faire approach to cell phone infrastructure, we now have four or more providers building totally independent national networks on conflicting technical standards, each with poor coverage.

We could have had a common carrier policy where single technical standards were used, common tower systems were installed, by the government directly or by a publicly regulated consortium like electric or other utilities, and different companies allowed to sell service in whatever form they wished. This would have created advantageous competition on an optimal technical and infrastructure basis (upgraded as needed, on a national scale).

Similarly, the TV cable and landline phone industries still labor under monopolistic and overly privatized structures due to the inability (for ideological reasons) of our government to grapple with the common goods and network aspects of these industries. Now we are slipping behind countries with more vigorous governments, mostly in Asia, more willing to provide public goods.

Health care is a similar problem, where purely private markets are simply defective and unworkable- for insurance, for treatment, and for larger social objectives. Obamacare, as the right likes to call it, is not only an important increment to public goods for US citizens, but is going to do more to reduce long-term deficits than any amount of token budget-cutting of parks and PBS by the Republican House.

Now, one asks.. what is the role of safety net, income support and similar redistribution schemes in this conception of government? Aren't they the opposite of proper government infrastructure provision? Well, it depends how you look at it. If happy, secure, and educated workers/citizens are the goal of a prosperous society, then such provisions certainly are part of the infrastructure picture- social, not physical. If cowed, cheap, and deskilled workers are the goal, then they are not. It is our choice.

Such social supports are broadly enabling in several ways. First, in giving workers some security that they and their parents are not going to be discarded at the end of their working lives, they enable somewhat more worker mobility and flexibility- a large advantage in an ever-changing economy. By providing income during economic downturns, they provide the automatic stabilizers needed to counteract the business cycle and prevent the kind of long-term unemployment we are looking at right now.

And insofar as they combine with progressive taxation, they also counteract the socially corrosive ratchet of the rich getting richer, which is inevitable in the laissez faire system and happens increasingly the more laissez it is, up to the limit of feudalistic serfdom + aristocracy. There is simply no way that total laissez faire ends up constructing a remotely egalitarian society. Socialism is required.

As an aside, it is notable that state and local taxation systems in the US are broadly and strikingly regressive, averaging twice the taxation relative to income on the bottom 20% as on the top 1%. Not a single state has a truly progressive system. Thus the Federal role needs to be that much more progressive to accomplish these social goals.

At the same time, Hayek had an important point, which is that key motors of private enterprise- the ability to address private needs by capitalizing on novel ideas, founding and growing companies, and meeting freely expressed demand in a stable, impartial legal system- that is all critical to both economic prosperity and personal liberty. But the key point is that markets are only part of the picture- they are by themselves inefficient and not broadly beneficial. They need a vast array of public goods to reach their potential, and beyond markets, we as citizens and humans need yet more public goods to reach our full human potential.

So government is not the problem. It is a solution, very often the only solution, to many of our most important problems.

Here is another public good to possibly add to the list above:

• A solution to global warming

The biggest challenge of our time is a clear public goods challenge- that of climate change. The long-term harms of CO2 acrue to everyone worldwide, while the present benefits acrue to whoever has the wherewithal to purchase and use fossil fuels (much of which many, like our roads, are themselves public goods). Rational policy would price these harms into our use now, making it gradually prohibitive versus all the private motivations that would lead us down the garden path to an unacceptable future.

One can liken this crisis to that of the US civil war, so ably covered by the historian's series in the New York Times. The civil war was a crisis of greed, in a nation of greed. The South knew that the future was not on its side, neither morally, economically, nor technologically. The slave trade had ended completely. Territories were increasingly resistant to the idea of expanding slavery. Southerners were living in the past- a Roman past, if one wants to be specific, more flagrantly inegalitarian and cruel than even the feudal model of medieval Europe. Out of sheer greed, the leading figures of the South thought it wise to shut their borders, maintain the peculiar institution, and hope that they could continue their barbaric ways, selling cotton to a world that had otherwise turned its back on slavery.

With global warming, we know what needs to be done. We know the stakes. We know that we won't have fossil fuel forever in any case. Yet we (the US political system, and the right in particular) keep our heads in the sand, hoping that it will all blow over somehow.

Well, it won't, and while the earth is heating up, animals are going extinct, and the weather gets worse, we are dithering, as the US did in the decades leading up to the Civil War, extending compromises against fate, engaging in morally dubious alliances to preserve this peculiarly addicting institution. For this too is at base a moral question- whether we leave a world hopelessly compromised and diminished from how we found it. The earthworms won't care. It is our human posterity that will care, and curse us for our profligacy.

• Tom Tomorrow, on punishing success.
• Meanwhile, what is going on in Wisconsin? It used to be such a nice state.
• Whence labor and progressive politics, without unions?
• Orwell wouldn't be so proud.
• Some more coverage on income inequality.
• The mind-boggling scale of the foreclosure crisis.
• Curiouser and curiouser, in the Catholic church.
• Are the Saudis next?
• Platitude of the day outdoes himself.
• Some good clues in Afghanistan.
• Bill Mitchell quote of the week:

"My profession is a total disgrace and our arrogance leaves us blind to reality. The latest survey by the National Association for Business Economics reinforces how far removed from reality my profession is. They think the most pressing problem in the US at the moment is the deficit and the public debt and downplay the importance of the entrenched unemployment. When pressed to explain this crazy set of priorities they invent a fantastic (as in fantasy) narrative about the dangers of deficits (which are?) and emphasise that unemployment is largely a voluntary choice by the individuals involved. The academic members of the profession teach their students this nonsense. They talk about the virtues of efficiency but ignore the huge losses that arise from unemployment.

...

The problem is that it is the likes of these characters who were incapable of seeing the worst recession in 80 years that was looming up before them but who are now lecturing us from behind the desks of their secure jobs that the deficit is the number one problem."

Ambassador from the Taliban

Review of "My life with the Taliban" by Abdul Salam (Mullah) Zaeef

Ever wonder what it's like on the other side of the news? What it's like to be a mullah? What it's like to help found the Taliban? What it's like to win a civil war? What it's like to be an ambassador? What it's like to be invaded by the US? What it's like to be taken prisoner by the US and rot in Guantanamo? If so, this is your book.

Deciding on today's title was quite difficult. Zaeef's book is so full of rich and ironic themes that many titles suggested themselves. I will pepper in some of the alternates as I go along.

Abdul Salam Zaeef grew up in rural areas in southern Afghanistan around Kandahar, attending madrassas, (thus becomming a talib, then a mullah), joining the Mujahideen against the Soviets, briefly running a mosque (thus becomming an Imam), helping to found the Taliban movement that took over most of Afghanistan, and rising to become its ambassador to Pakistan. After the US invasion, he was imprisoned and eventually shipped to Guantanamo for years of imprisonment, finally ending up as a private citizen in Kabul (under close supervision) in his early forties, writing his memoirs.

His story is well and briskly- occasionally movingly- told. Orphaned at a young age by his parent's deaths from illness, (his father was a minor Imam), then at age seven ripped from his younger sister by her arranged marriage, inspired at age fifteen to join the mujahideen and partipate in Afghanistan's brutal wars, and later shockingly abused by the US, he has plenty to be bitter about. The hold of a victimization narrative couldn't be stronger. The US is always killing women and children, while the Taliban is always seeking peace and friendly accord. [Studies in narcissism, Taliban division].

In Jungian terms, he seems quite unfamiliar with his own shadow side, which embodies the inevitable opposite of our positive qualities. Each of us has an individual shadow side, which we tend to project onto others rather than own up to ourselves. Cultures, too, take on communal shadow sides. The work of psychotherapy, in this school, is partly to bring the shadow to consciousness so that the individual can withdraw the shadow projections and start dealing with reality in more constructive ways, than simply to hate and trample on some object of projection- the scapegoat. So I would suggest that Afghanistan undertake a few decades of mass Jungian analysis(!). [Shadow over Afghanistan].

In fairness, principal policy makers in the US were hardly more reflective, as exemplified by the recent memoirs of Donald Rumsfeld and George Bush, both out to generally dreadful reviews. I would bet that, for an adventurous book club, the Rumsfeld memoir would make an intriguing pairing with Zaeef's!

But there is also love- specifically Zaeef's love of study, love of Islam, and love of his comrades in the great war against the Soviets. [We happy few, we Taliban]

"May God be praised! What a brotherhood we had among the mujahedeen! We weren't concerned with the world or with our lives; our intentions were pure and every one of us was ready to die as a martyr. When I look back on the love and respect that we had for each other, it sometimes seems like a dream."

Indeed, he recalls some earlier childhood preparation:

"We led our armies into fierce battles, slaying our enemies to defend our kingdoms. We ruled our land just like ministers and kings, at times demanding tax for the right of passage, or negotiating deals and truces. I think this is what all children do around the world."

I don't recall doing this, personally. At any rate, he also proclaims love of the Afghan people, and even includes a sugary plea to the US for better understanding in his preface and again at the end, accompanied by some other good advice.

"The world should realize how bad the situation for Afghans is, and how oppressed they are. People should be kind and compassionate to them."

His love of Afghanistan manifests in the crucial pivot of the book, in 1994, when the demobilized taliban faction of mujahideen around Kandahar, (one of many factions), with Zaeef in the lead, decide to take matters in their own hands against the local warlordism and banditry. They elect Mullah Omar as their leader, and set up a political network of mullahs that ousts each minor bandit in turn, gathering popular support and eventually taking complete charge of the area, including Kandahar. If the story ended here, (summary), it wouldn't have been such a bad turn of events. Zaeef doesn't say much about it, but the Taliban went on to fight a brutal war for the rest of the country, ousting the nascent regime of Massoud and Rabbani in Kabul (with the help of 20,000 Pakistani soldiers and floods of Saudi money).

The unasked question is- why? Why fight for the whole of Afghanistan, taking so much foreign support, committing massacres, and terrorizing the population? What was the big difference with the Northern alliance, headed by Burhanuddin Rabbani and Ahmed Shah Massoud? Why did the Taliban suddenly  become so bloodthirsty? Both sides were Muslim. Both were Afghan. Both had had plenty of war and suffering. The answer is they had fundamentally different views of Afghanistan's future- theocratic or democratic:

To take a quote from Shah Massoud:

"The Taliban say: 'Come and accept the post of prime minister and be with us', and they would keep the highest office in the country, the presidentship. But for what price?! The difference between us concerns mainly our way of thinking about the very principles of the society and the state. We can not accept their conditions of compromise, or else we would have to give up the principles of modern democracy. We are fundamentally against the system called 'the Emirate of Afghanistan.'" ... "There should be an Afghanistan where every Afghan finds himself or herself happy. And I think that can only be assured by democracy based on consensus."

Massoud was a committed democrat, and had progressive ideas about running Afghanistan, which were just coming to fruition after the civil war he fought from his position as defense minister in Kabul, against a variety of Islamists and other former mujahideen. Note also how Massoud mentions women as part of the democratic polity, something Zaeef never does. Zaeef hated him, as he describes upon hearing the announcement of a post-commnist government:

"Why did he appoint Massoud? Why would he take a decision like that? I knew [president] Mr Mujaddidi was a jihadi leader, who himself had fought against the Russians and the Communists. He had suffered and sacrificed in the name of God. Why would he now do something that would cause even more suffering? What was in his heart? In a split-second my happiness left me, my eyes turned red form the tears that came pouring down my cheeks and my cry turned into a scream."

Why indeed? I can only speculate, since Zaeef doesn't reveal his motivations (and may not know them, really). Massoud had certainly suffered and fought no less than the other mujahideen. Indeed, his northern region of operations was on the Soviet border. Perhaps it was simple tribalism, with Zaeef as a Pashtun shocked to hear of Tajiks (Massoud and Rabbani) running things. [Blood is thicker than religion]

But I think religion was actually more important. Zaeef seems to have had his heart set on the new government being a theocracy rather than a pluralist/democratic government that seemed to be excluding Islamist elements. His mujahideen faction in the war was the taliban- students from madrassas, mullahs, and others who chose an Islamist organization over the many other tribal and party-based mujahideen groups. A big part of their anti-communist motivation reacted to the Communist's aggressive modernization, in terms of women's rights, expropriation of large landholders, de-emphasis of religion, and the like. Clearly Zaeef was not alone, since the country promptly fell back into civil war, mostly due to the exclusion of, and brutality by, another Islamist group, the Hezbi Islami, or HIG.

Perhaps even more significant, Massoud and Burhanuddin Rabbani were Sufis, and there are few internecine hatreds so bitter as that between fundamentalist Sunnis and Sufis, who turn many of the violent and retrograde facets of Islam on their head. Sufis are accommodators, modernizers, and mystics. They are the anti-fundamentalists.

It is a sad story. We all operate from a position of great compassion for the people of Aghanistan and recognition of their right of self-determination. We can accept that Afghan revolutionaries and freedom fighters deserve high respect. They are Afghan. They sacrificed everything to free their country from the Soviets. They come from the people whom they seek to govern. Who are we from the West in comparison, when it comes to running Afghanistan?

But then one views the fruits of their efforts in self-government. The warlord period after victory over the Soviets was a Darwinian bloodbath. The Taliban's own rule, however effective in imposing brutal control, was a nightmare of a different sort. And finally, the Taliban's current efforts are once again singularly brutal and horrifying as they use mafia tactics to re-impose their rule over the poor people of Afghanistan. Has the cultural implant from the West over the last decade been enough to guide Afghanistan to a better future once we leave in a few years? It is very difficult to say.

But let us return to Zaeef's story. Mullah Omar gave him several ministerial posts in the new Taliban government (styled an emirate, under Omar as the Emir, I believe), culminating with the post of ambassador to Pakistan, easily Afghanistan's most important foreign mission, and eventually its only contact with the outside world. [Diplomat, mullah, patriot]. Zaeef characterizes Pakistan well, as the two-faced nation:

"Pakistan, which plays a key role in Asia, is so famous for treachery that it is said they can get milk from a bull. They have two tongues in one mouth, and two faces on one head so they can speak everybody's language; they use everybody, deceive everybody. They deceive the Arabs under the guise of Islamic nuclear power, saying that they are defending Islam and Islamic countries. They milk America and Europe in the alliance against terrorism, and they have been deceiving Pakistani and other Muslims around the world in the name of the Kashmiri jihad. But behind the curtain, they have been betraying everyone."

"The wolf and the sheep may drink water from the same stream, but since the start of the jihad, the ISI extended its roots deep into Afghanistan, like a cancer puts down roots in the human body; every ruler of Afghanistan complained about it, but none could get rid of it."

It is fascinating to hear about Zaeef's time as Ambassador, trying to ride the raging bull of the Taliban's international relations. He was a perfect person for the role, completely committed, yet soft-spoken and highly insightful when convenient. One of the greatest difficulties arrives in the form of a fatwa that damns and encourages the assassination of any Muslim who fights against the Taliban (as Musharraf and Pakistan were doing at the behest of the US). [Fatwa of the damned]. In the end, after the Islamic Emirate of Afghanistan is ushered off the stage, Zaeef was, for good measure, personally betrayed by the Pakistanis, who imprisoned and handed him over to the US. [US respects diplomatic immunity. Not!].

This part of his story is deeply troubling, indeed mortifying, to read as a US citizen. We've all heard about the horrors of the US's foreign prisons as well as Guantanamo. The stupidity of treating people in bestial fashion, of expecting them to break under torture, of driving them insane, not to mention the moral depravity ... there is no sufficient way to characterize it, other than to recount it in detail, as Zaeef does for us here. [US respects human rights. Not!].

"Each brother who spent time in Camp Five [Guantanamo] looked like a skeleton when he was released; it was painful to look at their thin bodies. When Abu Haris returned from the camp, I did not recognize him; there was no resemblance between the man who had been taken away and the body that was returned. I was so scared by his appearance that sometimes I would even dream of him and wake up screaming. May almighty Allah release all Muslim brothers in good health and save them from the hands of the pagans and cruel people."

Not only have we made countless enemies in the Islamic world through this despicable behavior, we have hardly gained any information that we couldn't have through perfectly cordial conversations (this book, indeed, is a testament to Zaeef's willingness to talk!). And we have subverted our own legal system and standing in the international system, rendering Guantanamo's imates more hardened, more difficult to repatriate, and impossible to prosecute in any rational way.

Now Zaeef is back in Kabul, essentially under government watch and quietly twiddling his thumbs. But he has also apparently resumed his role as interlocutor for the Taliban, being whisked to Britain recently to confer with their foreign office.

For regular Afghans, the Taliban are unwelcome, as is the current fully corrupt Karzai government, as is the contest between the US and both of the above. What should we do? Zaeef's prescription is to go with the Taliban, which represents traditional and Islamic values from his vantage as a Kandahari and fundamentalist Mullah:

"Americans should know that they are no longer thought of as a people of freedom and democracy. They have sown the seeds of hatred throughout the world. Under their new banner they have declared a war on terrorism and terrorists, but the very term 'terrorist' is of their own making. The jihad against them will never stop as long as America doesn't take steps to correct its mistakes"

"Secondly, eliminating the word 'jihad' from the curriculum of the schools and some other subjects is extremely worrying. Jihad is a central concept within Islam, and understanding it is an obligation of every single Muslim."

"It is astonishing that after eight years, with tens of thousands of troops, warplanes and equipment, and a vast national army, facing down some estimated ten thousand insurgents, leaving some two-thirds of the country unstable, that foreign governments still believe that brute force is a solution to the crisis. And still they send more troops. The current conflict is a political conflict and as such cannot be solved by the gun."

"How much longer will foreigners who fail to understand Afghanistan and its culture make decisions for the Afghan nation? How much longer will the Afghan people wait and endure? Only God knows. One again, I pray for peace. Once again I pray for Afghanistan, my home."

One can easily draw out the many contradictions at work here. Zaeef prays for peace, but believes in jihad (real jihad, not some namby pamby Sufi spiritual jihad). He believes arms can not solve the political problems of Afghanistan, but apparently hasn't communicated this insight to his brethren in Pakistan.

This kind of self-blindness makes our common goal of preventing civil war and anarchy in Afghanistan extremely difficult. Perhaps mass psychotherapy won't be possible. Perhaps the Pashtun code and Islamic religion are both fundamentally violent. Perhaps the Afghan government is impossibly corrupt. Perhaps Pakistan is a relentlessly meddlesome and deceitful neighbor. Perhaps democracy doesn't map effectively onto the tribal and hierarchical social structure of traditional Afghanistan, which restricts the effective franchise only to the upper (male) tier of landholders/power brokers. (A bit like colonial America, come to think of it). It isn't going to be easy or pretty getting out of Afghanistan, but the surge of democratic sentiment sweeping the Muslim world has to make one hopeful.

• An interview with Abdul Zaeef.
• Sample of news conference in Pakistan, as ambassador and in denial.
• Some recent Talib propaganda.
• Someone else's review of this same book- taking a rather dim view, really.
• Complete rot at the top in Afghanistan.
• So Karzai hates us, naturally, and bumbles along.
• Hitchens flays the "human rights community".
• We are talking to the Taliban.
• Appreciating the dark side of our archetypal narratives.
• Historians sort of agree with Mullah Zaeef.
• A little history of Libya.
• USA is number... er ... 31.
• Non-islamic terrorism ... yawn ...
• Lincoln puts his foot down.
• Screw the workers!

"Recall that in recent years, we've witnessed two separate debates over two types of taxpayer-subsidized laborers. First, we saw a brief argument over how much taxpayer money should pay government-sponsored bankers on Wall Street. Now, we're having a more prolonged discussion about how much taxpayer money should pay public employees in our schools, police departments, fire departments and infrastructure agencies."

• Bill Mitchell quote of the week:

"The IMF helped cause the crisis. It has no credibility in lecturing us on what we should do to resolve it. Its notions of fiscal sustainability are based on meaningless financial ratios. It talks about being worried about jobs and poverty but then forces agreements on nations which unambiguously cause a loss of jobs and increasing poverty."

An inconvenient future

A review of the geological record (i.e. our climate crystal ball) points to a torrid Earth

As we all know, climate change is already here and affecting our lives. Extreme weather, hotter average temperatures, desertification, coral bleaching, wildfires ... on and on it goes. The biosphere is in crisis, and we will bear substantial costs, though probably not the extinction that is the fate of so many of our fellow organisms. A recent story told of a polar bear who took off from shore with her cub towards the pack ice, only to find it over 400 miles away, herself emaciated and her cub dead.

A recent brief review in science (news stories here, here) laid out the trajectory where we headed, using Earth's climate 35 million years ago as its benchmark. CO2 was at roughly 1000 ppm at that time, compared to the roughly 400 ppm we are at now. The recent preindustrial level was roughly 280 ppm, and assuming we are near peak oil, and nowhere near peak coal, business as usual gets us to 1000 ppm CO2 by 2100 (which equals 0.1% of the atmosphere).

CO2 trajectories under various scenarios of public action.

One can not overemphasize how big these changes will be. The paper discusses them in terms of °C, (as most scientists do), which for US readers has a seriously diminishing effect, reducing the absolute values as well as using unfamiliar units. So I will convert all values to Fahrenheit (which incidentally is just as foreign an invention as the Celsius scale, only by a German rather than a Swede!). The paper assumes that CO2 is the main variable forcing climate change, which is consistent with everything we know to date about these geologic eras. It also synthesizes various geological markers of the temperatures and CO2 concentrations which the author and others have spent their careers studying.

Ancient climate data. Top- inferred CO2 concentrations, averaged in green. Bottom, glaciations & ice caps, which are absent at >~800 ppm CO2.

On average, earth was 29° hotter then than it is now. The tropics were 14° hotter (averaging 99.5°), while the poles were 32° warmer, averaging 73°. One can imagine that any kind of polar ice cap is not possible under these conditions. Miami Florida currently has an average annual temperature of 76°. The hottest average annual temperature ever recorded was 94° in Dallol, Ethiopia, in the 1960's.

Getting to these levels will probably take some extra time beyond 2100, due to lags in the climate system, principally the time it will take to melt the South Pole. But one can see that this is a world we do not want to live in. Everyone would want to move to the poles, where there is, frankly, not a lot of room. After the South Pole melts, sea levels will be roughly 230 feet higher than they are now.

Antarctica, melted.

While climate changes like this took millions of years in past epochs, we are imposing this change in a matter of two hundred years, far faster than our fellow earth inhabitants can evolve to keep up. After already causing one extinction event by our prehistoric hunting of large animals over several continents, followed by our destruction of many wild populations in historical time, we will shortly cause another of even more breathtaking scale by our CO2 emissions.

CO2 levels over more recent times, the last 400,000 years.

Once CO2 is at these levels, natural processes will take tens of thousands of years to return it to normal. So we had best come up with atmosphere purifying methods quickly, whether or not we manage to achieve policy changes that reduce our emissions.

These are conservative estimates, since the sun was 0.4% dimmer back in the Eocene era that we are talking about. But, being drawn from our actual climate past, they are very plausable predictions, not dependent on complex modelling and other types of forecasting (which tend to be conservative, actually). Earth has been there before, and while life surely flourished in the Eocene, it was not in the same places as it is now, and was not even the same life that exists now. We are heading into a far, far different world.

It is easy to blanch at this prospect and adopt a deer-in-the-headlights state, each individual being such a small part of this vast and cataclysmic problem/solution. That is why it is particularly important to raise climate change to the top of the political/economic agenda, more so than it is to perform individual mitigation, however laudable. Our collective economic and political structures need to take this seriously before any of our actions can be truly effective.

• Our buildings can be efficient.
• Lamestream smearing - called "reporting" by Washington Post.
• Doing the lord's work in Iraq.
• A long view of values-based imperialism.
• Who is more moral- right or left?
• Lasik- you takes your chances.
• A lone voice cries out against deficit hysteria.
• Jefferson Davis, also doing god's work:

"Reverently let us invoke the God of our fathers to guide and protect us in our efforts to perpetuate the principles which by his blessing they were able to vindicate, establish and transmit to their posterity. With the continuance of his favor ever gratefully acknowledged, we may hopefully look forward to success, to peace and to prosperity."

• Bill Mitchell quote of the week:  A graph, which speaks for itself.

• Plus a bonus quote from FDR:

"We know now that Government by organized money is just as dangerous as Government by organized mob."

A flowering of RNA

Curiouser and curiouser: down the genomic rabbit hole with regulatory RNAs

One of the biggest molecular biology stories of the last decade was about RNA. The more we look, the more functions biologists find for RNA in the cell. We thought we understood RNA decades ago- the floppy and unstable molecule used in only three places- as rRNA, forming the structural scaffold of the translating ribosome; as tRNA to link amino acids to their codons during protein translation; and as mRNA- the message translated from DNA into RNA, which likewise enters the ribosome to serve as the template for translation.

That was it- nice and neat, with three functions all centered around translation. It was surprising enough to find out that the rRNA was not just a scaffold, but actually the catalytic center of the ribosome- further evidence for the centrality of RNA in that way-back eon when DNA hadn't been invented yet, before the full advent of life as we know it.

But RNA has kept turning up in the oddest places over the last decade or two, clearly not willing to be neatly boxed up and put on the shelf of molecular biology knowledge. A flood of new prefixes and other variations tell the tale:

miRNA
ncRNA
lincRNA
snoRNA
piRNA
mirtron
RNAi
Xist

Clearly things (or people) are going a little nuts. No one knew about these RNAs before because they are typically small, or of modest significance. Small genes, especially of non-coding RNAs, are hard to find, since with the flood of genomic DNA sequence, we use trained computers to find genes by traditional rules, which prominently include the genetic code to conceptually translate DNA to proteins, and statistics to decide whether a gene is "real" or not (i.e. large). But nature is not so tidy, and doesn't need any stinkin' rules. It makes things up as it goes along.

The central "dogma" of DNA -> mRNA -> protein still holds for most functions of the cell. The new RNAs don't make structures in the cell, but regulate other genes, adding to an already elaborate network of control. They control, but don't stick around.

A recent paper in science (reviewed here; general review) provided a fascinating example of one of these RNAs in action, operating in that eternally interesting pathway that plants have to figure out whether to flower or not. First off, I should say that this pathway is not fully understood. The actors are only gradually coming into focus, and this paper is just one scene in a long-running production.

Vernalization is the process by which plants sense the alternation of cold to warm in order to flower properly in the spring, when we all want our daffodils to bloom. No winter, no tulips, crocuses, or other delightful flowers. The model plant used in this paper and elsewhere is the small weed Arabidopsis thaliana. We can assume that its processes more or less generalize to all plants, especially to most temperate flowering plants.

A central gene the vernalization process is FLC (flowering locus C), which represses a battery of other genes involved in flowering by repressing their transcription. It is a central regulator, and typifies the very common motif of repression, which often occurs in extensive circuits of double-negatives. Biological circuits are logical, but that doesn't mean they are intelligently designed!

Anyhow, FLC is usually on, repressing the whole flowering razmatazz in most tissues and at most times. During extended cold temperatures, however, FLC is turned off in gradual, progressive fashion in selected tissues, which, when maintained as temperatures rise again, allows flowering. This shutoff of FLC has to be maintained through many cell divisions, as the flower grows, so its mechanism has to be quite robust. A central question, then, has been how FLC is turned off in response to cold in the gradual way required to sense the winter season. And that is what this paper is about.

Prior papers showed that FLC is turned off by a venerable mechanism known as the polycomb system, named for the fruit fly where it was first found to have subtle effects on the male sex comb (don't ask!). Polycomb proteins form large complexes linearly spread over the chromatin (DNA plus histones, etc.) and also chemically modify histones, shutting off nearby genes in a permanent fashion- just the thing when you are, say, a skin cell, and don't ever want those liver genes turned on again. Polycomb proteins are used frequently in developmental processes once final decisions have been made. Their repression is carried along through mitosis to progeny cells, as required by the vernalization and flowering process.

Prior work also found one gene (VIN3) that is necessary (though not  sufficient) for establishing FLC repression in cold temperatures, as well as other genes encoding proteins of the generic polycomb complexes which are required to maintain the repression once temperatures rise again. VIN3 is another transcriptional regulator, making this whole story rather humdrum and typical, so far.

But the thing about polycomb proteins is that they don't glomb onto a zone of chromatin and do their thing without some extra help ... they need direction from RNA guides, whose sequence directly mates with the complementary DNA and then attracts the polycomb proteins. Only in the last few years has this necessity for RNA been realized, opening a new field looking for such guide RNAs all over the genome that service these developmental repression processes. The VIN3 protein may help turn the FLC gene off, but it can't by itself set up more durable repression by the polycomb complexes. And that is where the new paper comes in, finding an RNA, (named COLDAIR), which is encoded by the first intron within the FLC locus itself, and which seems to guide polycomb repression of FLC.

COLDAIR non-coding RNA is transcribed from the first intron of the FLC gene. VRE stands for "vernalization response element", which is a DNA site controlling transcription of COLDAIR, presumably by binding activating proteins.

The researchers show that COLDAIR is essential for the vernalization process, is expressed at the right time, and associates with the polycomb proteins as hypothesized, both in the test tube and in plants. They somewhat acidly note that a nearby RNA found by others (COOLAIR) neither has any known role in vernalization (by deletion or other functional test) nor associates with polycomb proteins, despite a proposed role in the process. The current authors had found COLDAIR by intensively searching through the FLC gene for stray transcription products appearing under the right conditions, hypothesizing that as a subject of a polycomb repression process, such an RNA would be required to direct its location/nucleation. COLDAIR is about 1100 bases long- very long for minor regulatory RNAs in general, but typical for these polycomb complex guide RNAs.

Expression of relevant genes during vernalization, expressed as number of days of cold temperature (V) or warm (T).

How all these dots connect isn't entirely clear, unfortunately. What regulates the expression of the COLDAIR RNA at the right time and place in response to cold temperature isn't known. What connects VIN3 protein binding and repression (and local histone de-acetylation) with COLDAIR RNA expression or recruitment is also not known, though it is likely that VIN3 represses FLC transcription directly and partially modifies the local histones. And the details of how RNA in combination with the VIN3 DNA binding protein can guide the polycomb complex growth around the FLC gene is not quite clear, though direct triplex formation between the RNA and the DNA duplex is a leading theory.

While a work in progress, the polycomb story is most interesting and general. The master regulators of mammalian body plan development, (capable of cutting off limbs, digits, and vertebral segments when misexpressed), the HOX genes, are regulated in a similar fashion, turned off in various areas of the body by the polycomb system using locally produced guide RNAs, similar to what is described above. (Landmark paper.) Indeed it is becoming apparent that our cells are full of stray RNAs that may add substantially to the count of "genes" in the human genome. These don't code for protein components of the physical body, but regulate how other genes operate, lending support to the theme that our complexity arises less out of the hardware of what we are made of, and more out of the vastly complicated (though also quite junky) software controlling how, where, and when the limited number of pieces are put together.

• Some GOP commentary on Egypt.
• GOP announces new climate strategy: Abandon Earth.
• Does anyone do background checks at Freddie Mac?
  
• A bit of ham & jazz.
• Bill Mitchell quote of the week: (Quote taken from a recent report criticizing the economists at the IMF, showing how ideologically blind they were and remain, here in regard to Iceland.)

"In spite of a banking sector that had grown from about 100 percent of GDP in 2003 to almost 1,000 percent of GDP, financial sector issues were not the focal point of the 2007 Article IV discussions. The massive size of the banking sector was noted, but this was not highlighted as a key vulnerability that needed to be addressed urgently. Instead, the IMF worried about the possibility of overheating, and the staff report was sanguine about Iceland’s overall prospects. For example, the headline sentences in the staff appraisal were “Iceland’s medium term prospects remain enviable. Open and flexible markets, sound institutions … have enabled Iceland to benefit from the opportunities afforded by globalization.” The report presented a positive picture of the banking sector itself, noting that “the banking sector appears well-placed to withstand significant credit and market shocks” and “[B]anks took important steps over the past year to reduce vulnerabilities and increase resilience.”"

• Lastly, we are all Egyptians this week, with high hopes for the future.