Clash of civilizations

It's the White House vs the State Department vs the Military vs USAID vs Marines vs Army, vs Pakistan, vs ... oh yes, Afghanistan! A review of Rajiv Chandrasekaran's book about our war in Afghanistan.

Washington Post reporter Rajiv Chandrasekaran's "Little America" is highly painful reading. Almost every sentence is about some stupidity by which we shot ourselves in the foot in Afganistan during the recent surge. (A boiled down version of Chandrasekaran's points.) This was the time when we finally really "got it", when we really understood the lay of the land, had a non-deluded president in charge, and put the right resources in play. Yet the accomplishments have been meagre, to say the least.

The Marines have cleaned up Helmand province for the moment, but Eastern Afghanistan has languished and overall security is little better. And Pakistan? It responded to our surge by egging the Taliban into a surge of its own, while preventing any negotiations. Some ally! More importantly, though, the long game seems nowhere in sight. The (Afghan) government is as corrupt and incompetent as ever, and the Taliban waits in Pakistan to move right back in as soon as the US leaves. The Afghan army and police, which were supposed to be trained and ready to replace the US forces, are nowhere near ready, filled with unmotivated clock punchers (and abusers of their fellow citizens) with little logistical apparatus.

What happened? Well, for one thing we continue to be befuddled by the Afghan culture. The surge was all about installing district-level governance that would provide the services, at least some of which the Taliban was so famed for: quick justice, local policing, schools, and agricultural aid. Is that what the Afghans wanted? Is that what President Karzai wanted?

It turns out, no- that is not what they wanted. The Afghans already had a governance structure in the form of a very hierarchical tribal / warlord system. Each woman has a male who controls her, each family has its male head, or elder, and each family has its tribal council of elders with a commander, and each tribe fights tooth and nail with other local tribes to put its man in charge as the local warlord. Afghans are educated in the school of social power in a way that we in the west can hardly even conceive of any more, despite all our technological power (exhibit A: Obama's weirdly absent negotiating skills).

It is, however, as old as humanity, from ancient Greece and beyond- a life of constant warfare and power struggle. The West has made a long journey through the Roman legal system and medieval constitutions like the Magna Carta (with detours through the Tudors!) to arrive at the Nobel prize-wining EU. Our children are plunged into some of this primitive schooling in junior high, but we diligently try to civilize them out of it as soon as possible.

However Afghanistan has been on a different road, one strangely abetted by the militant bigotry of Islam. And its people (at least those in power, who have the guns and typically the most highly honed conception of how to screw others) were and are apparently not ready to make this fast-forward transition to a non-tribal system of "good governance" as we understand it.

Chandrasekaran presents an interesting example, portraying president Hamid Karzai's brother Ahmed Wali Karzai as Hamid's answer to governing Kandahar, which went quite well, except that the Taliban was all over the place. It was a beautiful bit of corruption, served the local population to some degree, kept a superficial peace, and displayed Hamid Karzai's evident disinterest in taking on the Taliban in any direct way or providing western-style governance. While he vociferously complained about Pakistan harboring the Taliban, he didn't seem to have much problem with Taliban on his own doorstep, and indeed threated to join the Taliban himself in one particularly unhinged press conference.

Why? Perhaps because when all is said and done, Pashtun tribal solidarity, which the Karzais share with the Taliban, trumps the national interest, and certainly trumps the interests of the US. In any case, after working for years to sideline Ahmed Wali for his corruption, putative drug interests, and ineffectiveness vs the Taliban, the US finally started working with him late in the surge, with postive effects, at least until he was assassinated by the Taliban. Who's the boss now?

Another theme of the book is the peace negotiations with the Taliban that Richard Holbrook in particular was keen on, on the theory that our surge gave us the time of maximum power to extract a reasonable peace deal. But the surge also had a deadline, allowing the Taliban to simply wait us out and reap the rewards of what they sensed to be the continuing gross incompetance of the Afghan government, helped along by a few choice assassinations.

This is one place where I think the book goes off the rails. It goes into excruciating detail about why the negotiation idea failed. Holbrook was hated by the rest of the bureaucracy, Pakistan wouldn't let the Taliban negotiate, the military didn't want to hear about it, much rather playing with its toys and killing people. Etc. and so forth. But the basic idea is not questioned, and the distinct impression is given that these talks were some brilliant solution that died a bureaucratic death.

But to me such negotiations were a non-starter, and I agree (reluctantly) with the military on this one. Doubtless Holbrooke had sugarplum-like visions of his personal heroics at Dayton (on the post-Yugoslav war) and the Paris negotiations (on the Vietnam war), which explains his desire to put himself at center stage. But I think the parallel with Vietnam is uncomfortably and instructively close.

We never gained anything by our negotiations to end the Vietnam war. The brutal truth is that the North took over the South, and the US lost about 60,000 soldiers and the local countries well over a million people. The only thing the negotiations proved (by confidence-building measures like bombing pauses and the like) was that the US had civilian control over the military. Which is not an insignificant point, but not one likely to impress an enemy which had a sanctuary from which to attack, an incredibly effective quasi-religious ideology (including a healthy dose of nationalism) that motivated its own citizens and infected those of the enemy, and which faced a terminally corrupt and incompetent government in the South. And which, incidentally, had perfectly effective civilian control over its military as well.

Sound familar? But instead of working with the time-honored governing structures of Afghanistan, such as they are, (and they are typically extremely corrupt), our armed forces cleared areas in horribly painstaking fashion, only to wait for a "government-in-a-box" that never arrived, or if it did, was an ineffective token, ignored by all. Nor did pouring money into the zone alter the fundamental situation, since the long game was always about politico-military power.

The Counter insurgency (COIN) strategy was a fundamentally political strategy, aiming to turn the resident populations away from the Taliban and towards the government. But we had in mind a fundamentally different government (something from Switzerland, perhaps!) than the Afghans themselves had, and fundamentally different from what they are willing to provide on the long term. Perhaps we were spoiled a bit by Iraq, which, while tribal in significant areas, also has a long-standing central state and bureaucratic tradition (several millennia old, indeed) that enabled us to eventually hand off power to someone, despite our many blunders.

In Afghanistan, however, that someone is Hamid Karzai, who has proven himself to be a disaster, solidly in the Afghan tradition of tribal politics and small-minded corruption, utterly uncomprehending of the possibilities of western-style governance where power is heavily restricted so that it can be channeled into lawful, productive, and legitimate pursuits, not zero-sum feuds and wars. Our neglectful treatment of him during the Bush administration also left him with little choice but to run his country the old-fashioned way, rather than through a modern state system that had some chance to appeal to the lowest and most populous rungs of the society, rather than the warlord caste.

In any case, here we are, at the end of the surge, with the Taliban bloodied, but convalescing peacefully in its Pakistani resorts, with the Afghan government hated almost as much as the Taliban, and with the Afghan army a shell of whatever it was supposed to be, to conduct the coming civil war.

Chandrasekaran is most enamored of the advice of one of his well-fawned sources, diplomat John Weston, who thought the surge was misguided in its temporary nature. Better to commit smaller forces for the long term- as long as it might take to protect the core of the Afghan state and wait for the Taliban fires to burn themselves out. The Afghans have been whipsawed so often by one strategy after another, from boots on the ground to light footprints to no-nation-building to yes-nation-building to surges to COINs, etc.. they are exasperated and sick of us, not to mention their own civil wars.

But this assumes that the Taliban were not winning the war and were not gaining territory, and that some modest level of special forces, advisors, and a few other coalition forces could do what they had spent the previous decade not being able to do, which was to put the Afghan government on its feet in some form. The surge has surely helped that process, mostly by increasing the Afghan army and police (another long story of bumbling, waste, and incompetence...). And perhaps also by clarifying all around what each side really means by governance.

It is horrifying to read about the wasted lives, wasted limbs, wasted time, wasted money, ignorance, and mismanagement that has been brought to bear on Afghanistan. That is not to say that other institutions of the West, like finance, or our political system, are paragons of good management. But in Afghanistan we are faced with the most elemental contest of power with extremely experienced and ideologically strong adversaries, which deserves much better from our Western intellectual capacities than what we have so far deployed. We were plunged into a maelstrom of political complexity, and bringing along only one tool- EU-style governance- while admirable in some respects, was also deluded.

Our capability to change foreign cultures is limited. If we really wanted to set up a democracy with women's rights and secular governance for all in Afghanistan, we would have had to shave off the entire top of the social system and sit on the county with about 3 million soldiers for a decade or two (for a country of ~35 million) till our bright new modern generation of Afghans came of age. Social revolution takes work. Pursuing the same aims with fewer resources was doomed, unless there was a local mechanism to sponsor it. That was not Hamid Karzai, or anyone else we were working with who had any power.

On the other hand, just tipping the balance of existing social dynamics, (and blowing things up), as we did for the Northern Alliance to let it topple the Taliban ... that was easy. But then we decided that despite the light footprint, (lightened even more by our diversion to Iraq), we didn't want the Northern Alliance to rule the country outright, and indeed wanted the trappings of a democracy, women's rights, and modern administration. But didn't want to do nation-building. It was completely incoherent, with only the excuse that powerful Afghans were happily lying to us the whole time about how they naturally shared our aims if only they could share our money for a little while.

It is a country whose national sport is civil war. Pakistan knows this well, and happily encourages more to keep Afghanistan weak. A cynic would say that we should do the same, except that weakness in the last instance equates with Al Qaeda sanctuary, given the history and remaining strength of the Taliban. So we need to pick and choose what part of the social system to support, and which to combat (very little of it, necessarily). We also need to be better at knowing whom to trust and how far- a difficult job when we (still) know so little about the culture, fatally undermined by our one-year-and-gone tours of duty for virtually all the relevant personnel.

We have been schizophrenic in this task, as we fatally over-estimate what we can accomplish and continue to have precious little appreciation of the true aims and capabilities of the Afghans. I hope this book helps make these points to our policy makers, though at this point the die is mostly cast, as we await the coming battle between the Afghan government and the Taliban this year or next.

• Why so many whackos on the loose? Blame Reagan.
• Where religion is weak, atheism is weak.
• Theology is dead ... long live spirituality.
• Spinoza- killer of theology, originator of the modern perspective.
• Japan prepares the big guns against deflation.
• Krugman considers the robot end-point.
• Where are those concealed guns-for-protection when you need them?
• A lengthy history of New Deal Keynesian Mariner Eccles.

"He assiduously cautioned FDR to eschew a course of action that many economists have suggested Japan dolefully followed in the 1990s. “If we spend some every year, but not sufficient to give the required stimulus to private expenditures,” Eccles wrote in a prophetic memo in early 1935, “we can build up a large debt and still not be out of the depression.”"

What a real right to work would look like

It would start with a right for everyone to actually work, and get a decent living for it.

The recent GOP push to double down on their agenda for the rich and powerful by passing "right-to-work" laws was a typical instance of their love of Orwellian language, not to mention their utter corruption by the rich. It was really about whether a company should be faced with a unified, organized workforce, (i.e. a union shop), or not. Whether companies have an unbridled right to put people out of work.

I have plenty of problems with unions. They are clumsy, highly unfair, and in the public sphere have generated reprehensible corruption. It is a poor mechanism to foster labor power. But if no other way is offered, it is better than nothing.

What might be a better way? The most appalling aspect of our current economic crisis is that millions of people are being crushed- unions do not care about the unemployed, and nor does anyone else. They are forgotten, and after about six months, no one even wants to see their resumes.

The Fed has long been more concerned about inflation than unemployment, (though in fairness it is doing more about unemployment than most central banks around the world), and one of our political parties takes positive glee in celebrating the success of the successful and moralizing about how the victims of this downturn have no one to thank but themselves, so get out there and find a job, even when there are five or more applicants for every opening. Republicans cater to one interest- the rich, whose power over workers has been ironically and horrifyingly increased by the mismanagement of our economy by the fabulously rich and corrupt.

So the first ingredient in a humane economy is to provide work and income to anyone interested in working. This is well within the government's power to provide. We have crying needs for infrastructure renewal, ecological restoration, sustainable power, child care, not to mention the normal needs of any municipality- general cleaup, care for public properties, housing for the homeless, health care for the elderly, and a million other needs. (My prior, more extensive treatment of this concept, including how one pays for it.)

How much should this kind of program pay? It should pay a living wage, which would be at least one and a half times the current poverty level. It should be available to anyone who asks, with the condition that it is real work, and the person can be fired for cause just as at any private sector job.

This would transform our society, from one based on fear of the employer, to one where everyone reasonably willing is welcome to work in a dignified manner. Private employers then would have to bid over this base level of income and in addition have to offer reasonable working conditions in order to get employees. Would that be a terrible or dangerous situation? No, though prices for services currently provided by the underpaid would certainly go up. Concomitantly, the need for welfare and incarceration (and probably mental health care and homelessness), would go dramatically down, if everyone had access to some basic level of dignified existence.

In addition, health care and pensions should be decoupled from the particular employer you work for, (or union you are a member of), but instead be universal. The pension "system" is phenomenally unfair, with no rhyme or reason to which employers offer them (fewer all the time, understandably) or not. Ideally, we would double social security for every worker, and do away with all private pension contracts, since they are unreasonably forward-looking commitments for corporations having much shorter time horizons. The only way to do this kind of thing fairly is to make it a modest, but universal program. Then it would be up to individuals to save for their retirements, over and above this decent minimum.

Beyond this, I would envision a much more vibrant job market, where workers are continually plugged into a market system that matches employers with candidates. The current online systems are OK, but I think the scope can be quite a bit more broad, as sort of a merging of linkedin with monster in a way that would convince employers to use this kind of service routinely and uniformly, as well as encouraging third-party matchmakers to actively roust up options for those not actively looking for work. Right now, only the least relevant and often diversionary postings seem to occur on these systems. In any case, once the power of employers over the health care, pension, and income of the worker is mitigated in these ways, we would see much more mobility in the workplace- more power in the hands of employees.

Proceeding along in my fantasy of an ideal employment world, the taboo of income secrecy would also be broken, and companies would all operate with open books, so that everyone's cards are on the table. This would eliminate a great deal of inequality and subterfuge, and again put a little more power into the hands of employees.

• Inequality of income has essentially nothing to do with marginal productivity or ability, and everything to do with power.
• Do we need unions for labor to have power? A very good discussion of the union shop.
• Full employment is going to be the next progressive narrative.
• We have a problem with guns. And gun control does work. And why is the right wing intent on jumping the shark?
• Self-medicating with weapons, which translate to more killing.
• A (second) Republican recession is brewing. Why do they have any economic credibility left?
• And it looks like they will be shutting down the government too, shortly.
• On how we are like Rome as it went from republic to autocracy.
• Summers on the unjustness of the tax system- now he is progressive, when he has no power!
• Krugman beats on the utterly bankrupt right wing economics.
• Google is the boss of you.
• Doomsday for Afghans, coming soon.
• Galbraith reviews the economic landscape.
• Bill Mitchell economics quote of the week, on the dominant modeling method in mainstream economics, quoting of Robert Solow:

"A thoughtful person, faced with the thought that economic policy was being pursued on this basis, might reasonably wonder what planet he or she is on. An obvious example is that the DSGE story has no real room for unemployment of the kind we see most of the time, and especially now: unemployment that is pure waste."

Genome junk: the history and usefulness of transposons

Why do we have so much, and bacteria so little? Because a junkyard has its uses.

The role of junk in the human genome continues to fascinate, since there is so much of it- perhaps 98% of the total. I reviewed some recent work that described how active much of this junk is, getting transcribed to RNA and bound by proteins of various sorts, though honestly, this may be more smoke than fire.

Another way to understand junk DNA is from a broader evolutionary perspective, which is what Nina Fedoroff offers in a fascinating recent review (sorry, not even a free abstract). The problem is that many workers (e.g. Richard Dawkins) have thought of this junk as parasitic, such as transposons of various sorts which carry protein-encoding genes and other sequences needed to replicate and pop themselves around the genome. (Much of the junky DNA arises more straightforwardly as errors in replication that pile up as boringly repetitive sequence.)

Transposons certainly have this capacity of propagation, but what Fedoroff focuses on is that eukaryotes have had these transposons and related junk from the very beginning. Bacteria are afflicted by them too. In addition, eukaryotes have had, from the beginning, various mechanisms inherited from bacteria which counteract transposon proliferation, such as the recently discovered micro-RNA mechanisms. One simple mechanism is homologous DNA recombination, which can delete duplicated DNA segments, even as it can also create them.

(Incidentally, introns, which are the junk that lie between the exons that encode our proteins, also were there from the very beginning, and possibly before, being descended from primordial transposable RNAs.)

So it has all been an ecosystem present from the beginning, and the reason why eukaryotes such as ourselves have a lot of junk (and plants have even more) is not that DNA transposons have become more infectious or diabolical, but that advanced organisms have relaxed their surveillance over this aspect of their genomes, for other reasons.

Sizes of genomes, from various species. Bacteria occupy a distinctly tiny range, (bottom), while genome size increases roughly with organismal complexity. Some plants (and amphibians) have allowed another order of magnitude amount of DNA in their genomes. The actual gene content of these genomes is much less variable than the gross DNA size shown here, ranging from about 3,000 genes to perhaps 45,000 genes. So the gross size at the higher end reflects "junk" elements almost exclusively.

One reason is that active shuffling of genomic elements can be highly advantageous, enabling faster evolution for larger organisms with longer generation times than bacteria. Unlike the highly compact arrangement in bacteria, our genes are modular pastiches of broken-up exons and far-flung regulatory elements whose duplications and rearrangements sometimes lead to cancer, but can more rarely also lead to the evolutionary innovation we are so familiar with from economic theory- Marx's "creative destruction".

Plants are a prime example of this. Barbara McClintock was amazed to see the variegation of maize, as shown by stunning varieties all over the American landscape.

Well, some of this variegation is driven by transposons, which hop in and out of the relevant pigmentation genes and their regulatory regions with abandon, and earned McClintock an Nobel prize for her assiduous, astonishing work bringing this to light in the 1940's and 50's, long before the molecular revolution in biology.

Now we know some of the molecular details, and they are pretty hard to believe. Fedoroff  offers a diagram of one locus of about six genes, from various maize strains (each row is a different strain). Each of the colored triangle insertions are transposons, and one can see in some cases they have piled up with time, one inserting within another.

A dramatic history of transposon (colored triangles) insertion into a six-gene segment of the maize genome. (The bronze locus, encoding an anthocyanin pigment in kernels.) Each row shows a different strain, from widely varying origins. Coding regions are the crayons in yellow, with exons dark, and the introns light. Click to see at full magnification.

There is a direct connection between the apparent physical plasticity of plants, including an ability to respond to many environmental conditions, and their genomic plasticity. Maize was clearly selected by prior generations of Americans to have additional flexibility to meet a variety of aesthetic and functional needs.

The only question then is why all life forms have not availed themselves of such genomic plasticity. Plants have a particular need, not being able to respond to the world via nervous systems or locomation. But wouldn't bacteria be in the same boat? Yes, but they are trapped in a world of even more cut-throat competition, where the margins of victory and defeat are razor-thin, proportional to their microscopic size and especially their infinitesimal cell volume. A maize plant can lose a few seeds to mutation and still succeed, but a mutation in a bacterium presents a much more immediate threat.

Additionally, any extra DNA spent on junk is a metabolic cost- a cost high enough to prevent bacteria from accumulating much of it. A maize plant can gain large amounts of DNA without it being a significant metabolic load- due to its high cell volume, its DNA is a tiny fraction of its biomass. And this in turn, combined with a lack of recombination via sex and lack of modular gene units like exons, limits bacteria's ability to adapt to environmental challenges via genomic change. Instead, they rely on a great deal of promiscuous quasi-mating, infection, and DNA transfer from related and unrelated microorganisms to acquire new codes and traits, like antibiotic resistance. If evolution had stopped with bacteria, our planet would have an ocean alive with a bacterial soup, (and an atmosphere of oxygen), but few other signs of life.

It is a sort of ironic comment on this world of maximal competition and insufficient cooperation that bacteria have to resort to infecting and stealing from each other to advance even a small amount in evolutionary terms. We, on the other hand, are blessed with a much richer fund of internal diversity to draw on, which has (slowly) contributed to the development of multicellularity, terrestrial colonization, skeletons, (both animal and plant), cognition, sociality, and so many other complex biological bequests.

• A novel model of gene duplication, as more fodder for evolution.
• On the other hand, conifer genomes appear to be more stable, but keep plugging along anyway.
• You can fight climate heating.
• Job creators busy creating fewer jobs.
• What happens when the value of labor goes to zero?
• Economic value of revolving door corruption in the US.
• Afghanistan remains hopelessly corrupt. Leaders seem to be planning for return of the Taliban- the only entity with any spine.
• Al Qaeda is back, feeding on the nexus of Islamic bigotry and hatred of the US.
• Lying about Santa is OK. About god too?
• Children are narrative-driven. Do adults have to be as well?
• Platitude O' the day provides a model of theology.
• Spinal-watch: will the White House hold out for good public policy?
• The sick thought process of the anti-abortion forces. "Becoming like children", indeed.
• Really, cell phones are OK for your brain.
• Hadn't heard of Bon Iver before...
• Nor of Lianne La Havas.
• Bill Mitchell quote of the week, from his quiz:

"5. Premium Question: The Australian National Accounts data came out this week and the federal government maintained its assertion that the annualised growth rate revealed (3.1 per cent) was around the trend established over the last decade (3.2 per cent). They reaffirmed their policy aim, which is to keep real GDP growth at that trend rate. If labour productivity grows at 1.5 per cent per annum and the labour force grows at 2 per cent per annum and the average working week is constant in hours, then this policy (if successful) will see the unemployment rate rising." A: true

If fish could scream

Does anyone care about overfishing?

As a preview of global biosphere destruction, (the big show, so to speak), the wanton destruction of fisheries around the world is a fair example, though many others can be cited. A common resource is plundered by commercial interests with a focus on efficiency, but little thought to tomorrow.

A recent paper summarized the sorry state of global fisheries, which they divide into two groups: "assessed", which were the subject of previous work by the authors (and the UN food and agriculture organization) in well-known fisheries such as the Bering sea, and "unassessed", comprising everything else around the world, of which there are thousands, large and small. The bottom line, surprise surprise, is that most fisheries around the world are depleted and, even in economic terms let alone ecological terms, are abused and declining.

Figure from the prior work, showing each of the "assessed" fisheries. Estimates of actual catch (u, blue circles); ratio of actual population to the population at maximum  sustainable yield (B/Bmsy, green triangles). Bands are also provided for catch levels consistent with msy (upper light blue), and levels consistent with rebuilding a depleted fishery (lower dark blue). The California current fishery seems to be the only one being managed back to some semblance of health, with New Zealand evidently undertaking a similar course. In contrast, the Newfoundland region has collapsed.

There are a few terms of art used here. One is biomass (B), the total quantity of fish in the sea, of the species of interest. Then there is maximum sustainable yield (msy), the yield available yearly in an optimally (from the managers and industry's perspective) managed fishery. How much pain and suffering are being inflicted.. how much ecological damage is being done in collateral damage to countless non-"fishery" species ... I think no one really wants to know. Also, fisheries managers tend to use a baseline of maximal yield from personal experience or other recent memory, not from the often enormously higher baseline of natural abundance predating human exploitation entirely. This is a general problem in appreciating losses in our standard of living, with respect to the natural world.

Status of various fisheries around the world, where "assessed" are relatively well-studied and -managed.

Even among assessed fisheries, "63% have a biomass below what would produce maximum sustainable yields". The main finding is that the unassessed fisheries are in much worse shape, which is a bit surprising, since they are not the prime economic hunting areas. But they are also less regulated and less organized. There is open season, more or less, on sharks in the open ocean.

Status estimates for a few "unassessed" fisheries.

It is a testament both to the failure of classical markets & the free market ideology that this is happening, and a call to international government with global purpose and teeth. Classical economists might make the point that this simply makes the case for "fencing-in" these commons and investing them with property rights that lead to sustainable resource extraction. But our experience with tree farms and other kinds of farming (see the Dust bowl) says clearly that environmental values always get short shrift in such systems. Not to mention that fish are mobile resources, making such fencing problematic even conceptually.

Needless to say, everyone would be better off in the long run if we could control our corporate ideologies and greed in the short run. Sadly, perhaps the best mechanism is put large regions of the ocean entirely off limits to commercial fishing. Simple, but a reflection of how more intricate rules by which we try to manage and regulate "free" markets are simply not up to the task of preserving what is obviously the common good.

• Can a fish even be seen? Death and fish in the movies.
• The scientific consensus on global heating has been too ... modest.
• Bob Costas, on guns.
• "The wealth of the Walton family – which still owns the lion’s share of Walmart stock — now exceeds the wealth of the bottom 40 percent of American families combined."
• Gambling pays ... those in the house.
• Forget the dollar coin- how about if we phase out all coins? Indeed, all cash?
• Class war, continued.
• A soap opera, filmed from Middle Earth.
• Bill Mitchell quote of the week..

I told an SBS Radio journalist today who was asking why the Government refused to lift the unemployment benefit despite admitting themselves that it is below the poverty line that the Government was deliberately impoverishing the unemployment but at the same time refused to create the macroeconomic policy settings necessary to generate sufficient jobs.
The way they defend that irresponsible and unethical policy stance is to claim the current unemployment rate is full employment. The dirty way out that governments of both political persuasions have employed since they became infested with the lies of neo-liberalism.

and...

The rise in acceptance of Monetarism and its new classical counterpart was not based on an empirical rejection of the Keynesian orthodoxy, but was according to Alan Blinder in 1988 “instead a triumph of a priori theorising over empiricism, of intellectual aesthetics over observation and, in some measure, of conservative ideology over liberalism. It was not, in a word, a Kuhnian scientific revolution”.

Thomas Nagel: in search of his mind

Unfortunately, he is looking in all the wrong places, following his intuition.

Philosophy is in a bad state. All problems with any hope of resolution have hived off to other fields. Its star scholars are not taken seriously in the wider culture, other than the occasional charismatic performance artist, like Zizek. It is left ruminating on the perennial "big questions", worshipping at the altar of Plato, and claiming to be the last redoubt of reason and critical thought in an ever more classical-averse culture.

Which is odd, since the ultimate resource and criterion of the contemporary philosopher appears to be his or her own intuition. Each defends her intuition with whatever rhetoric and precedent she can bring to bear, and criticizes that of other philosophers, though with the decorum appropriate to an ecumenical community of not-very-rational belief systems with little hope of resolution or reconciliation. If it were up to me, their academic departments would be renamed Departments of the History of Philosophy, and they would give up any pretense (doubtless owing to physics-envy) of doing "research" or of making "progress".

"The best we can do is to develop the rival alternative conception in each important domain as fully and carefully as possible, depending on our antecedent sympathies, and see how they measure up. That is the more credible form of progress than decisive proof or refutation." - Nagel on doing philosophy.

This week's example is Thomas Nagel, whose recent book, "Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False", sets out his intuitions on several topics, and follows them out to their cracked conclusions. (Hat tip to Darrell for suggesting it.) At least he claims to be an atheist- one intuition I can agree with. But on every other count- on consciousness being non-material, on reason being inexplicable by evolution, on moral realism, and on the (lack of) explanatory power of evolutionary theory generally, he would rather overturn our understanding of the cosmos than give up his favorite intuition.

Nagel writes very well, and is apparently one of the most eminent philosophers of our day. The book is brief and clear. Unfortunately, this brutally exposes his arguments in a way that other philosophers typically, and perhaps wisely, avoid. Take intelligent design (ID). Nagel makes it clear that he is no fan of theism or theistic explanations of biology. But he takes the intelligent design critique pretty much at face value, with horrified sprinklings of "chemical accident", "random chance", "dead matter", "accidental mutation", and "purely chemical" in his argument. Speaking of ID proponents: "They do not deserve the scorn with which they are commonly met. It is manifestly unfair." Following this school, he doubts not only the capacity of chemistry to explain the origin of life, but of mutation and natural selection to explain the profusion of life's diversity, particularly the origin of his own amazing mind.

"In the present intellectual climate such a possibility is unlikely to be taken seriously, but I would repeat my earlier observation that no viable account, even a purely speculative one, seems to be available of how a system as staggeringly functionally complex and information-rich as a self-reproducing cell, controlled by DNA, RNA, or some predecessor, could have arisen by chemical evolution alone from a dead environment."

All this has been discussed ad infinitum elsewhere, and I hardly need to go into detail. But it is shocking to see this as a founding idea by a leading philosophical academic. Does he also impugn geology as a mere tissue of hypothesis, incapable of really telling us what went on in the Archean era? No. We can't all study the eternal and time-reversible particles of physics, and have to make do with the best theories we can muster and with the evidence at hand. He reserves his incredulity for biology because, as we all know, biological organisms are astoundingly complex and it is, to this armchair philosopher, incredible that evolutionary theory is equal to such astoundingness.

"I realize that such doubts will strike many people as outrageous, but that is because almost everyone in our secular culture has been browbeaten into regarding the reductive research program as sacrosanct, on the ground that anything else would not be science."

Needless to say, he has no better theory to offer, other than vague intimations of teleology and "mind". Nagel made his mark as a philosopher of mind, and retains a Platonic view (oh, that disastrous philosopher!) that the mind can not be reduced. His intuition is that subjective experience is fundamentally separate from, incommensurate with, and irreducible to, material existence. This attitude is what creates the dilemma, the need to question evolutionary theory, and the pining for some way to make of the mind a cosmic explanatory principle. It is not unusual to see this quest among new age cranks, but among scholarly philosophers? What millenium are we in?

(Parenthetically, one of his finest passages is on this divide between materialism and Platonic idealism:  "After all, whatever one's philosophical views, so long as there is such a thing as truth there must be some truths that don't have to be grounded in anything else. Disagreement over which truths these are defines some of the deepest fault lines of philosophy. To philosophers of an idealist pursuasion it is self-evident that physical facts can't just be true in themselves, but must be explained in terms of actual or possible experience. just as it is evident to those of a materialist pursuasion that mental facts can't just be true in themselves, but must be explained in terms of actual or possible behavior, functional organization, or physiology.")

He sees himself in search of a middle way, between the non-explanatory assertions of theism, and the insufficiently explanatory, but irritatingly hegemonic, claims of scientific materialism / naturalism. What does he find when he goes down his intuitive road, which apparently (and inexplicably) also puts him in search of transcendence(†)?

Here are a couple of summaries of his program:

"the respective inadequacies of materialism and theism as transcendent conceptions, and the impossibility of abandoning the search for a transcendent view of our place in the universe, lead to the hope for an expanded but still naturalistic understanding that avoids psychophysical reductionism. The essential character of such an understanding would be to explain the appearance of life, consciousness, reason, and knowledge neither as accidental side effects of the physical laws of nature nor as the result of intentional intervention in nature from without but as an unsurprising if not inevitable consequence of the order that governs the natural world from within. That order would have to include physical law, but if life is not just a physical phenomenon, the origin and evolution of life and mind will not be explainable by physics and chemistry alone. An expanded, but still unified, form of explanation will be needed, and I suspect it will have to include teleological elements."

"The implausibility of the reductive program that is needed to defend the completeness of this kind of naturalism provides a reason for trying to think of alternatives- alternatives that make mind, meaning, and value as fundmental as matter and space-time in an account of what is. The fundamental elements and laws of physics and chemistry have been inferred to explain the behavior of the inanimate world. Something more is needed to explain how there can be conscious, thinking creatures whose bodies are composed of those elements. If we want to try to understand the world as a whole, we must start with an adequate range of data, and those data must include the evident facts about ourselves."

At best, (i.e. in his most sane moments), he suggests that some new principle might make the usual evolutionary paradigm make sense. To explain this, I can offer the analogy of quantum mechanics. Some enzymes make use of electron tunneling, one of the more obscure aspects of the quantum world. This was not because some brainiac designer chose the most esoteric way to accomplish a difficult task, but because all aspects of natural reality are at hand in the evolutionary toolkit, ready to happen and be selected as means to success.

Likewise, Nagel would imagine that consciousness and especially the human style of rich consciousness demands some new element in reality, in addition to that of which we are already aware, which could close out the account of how subjectivity and mental activity broadly happen as part of the physical brain at the pinnacle of otherwise reasonably understood developmental and evolutionary processes.

But, critically, he has no idea what this new element might be. It might be some cosmic pan-psychism, or dark matter, or ... there is nothing there, no alternative hypothesis worth the name. He hammers on the point that to him, it "seems" that the mind is non-reducible, and uses that as his premise for all else in the book, including his vast project to destabilize if not overturn all of modern science, and introduce teleology into the cosmos.

"I am drawn to a fourth alternative, natural teleology, or teleological bias, as an account of the existence of biological possibilities on which natural selection can operate. I believe that teleology is a naturalistic alternative that is distinct from all three of the other candidate explanations: chance, creationism, and directionless physical law. To avoid the mistake that White finds in the hypothesis of nonintentional bias, teleology would have to be restrictive in what it makes likely, but without depending on intention or motives."

If you have ever taken physical chemistry, this line of argument is laughable. The possibilities that chemistry presents are well-known, and are pitilessly random. If some bias were present in the collisions of gasses and the jumbling of molecules, we would know about it by now... it is a topic of great interest, deep theory, and astonishing technological achievement.

Being charitable, one can say that, despite his bomb-throwing attempt to boost book sales, his suggestion in minimal terms is merely that nature is not yet fully understood, and something new may come along to explain minds and other pet philosophical issues (i.e. counter-materialist intuitions). In principle, this is fine. No one pretends that everything is understood in naturalist terms. Even in physics, despite the amazing completeness of the standard model, capped off by the Higgs boson discovery, there are clearly holes, such as dark matter and dark energy, not to mention the arrow of time and the origin of the cosmos.

So the real question is not whether naturalism is incomplete as a general philosophy or has explained everything, but whether it is wrong, (according to Nagel's subtitle: "almost certainly false"), whether there are in any particular instances a different and better hypothesis available, and in the specific case of biology, whether "something new" is needed at all to explain the mind/brain connection or anything else. I think not, and no work among those actually studying these issues points in this direction.

It is important to pay attention to the circumstantial evidence in this field and in biology generally, which points uniformly in materialist directions. Nothing we have learned about the brain so far (admittedly, not very far) has violated physics or materialism. Our thoughts happen at speeds acceptable under normal physics, lesions in the brain destroy thoughts and abilities ... it all makes sense. Do we have a full explanation of consciousness? Not yet, but at this late date, it strains credulity that our intuitions are telling us anything important about it. We need to follow evidence rather than intuition.

But Nagel will have his intuition, first and foremost:

"It seems conceivable, for any Ω, [the observable, objective properties of the brain], that there should be Ω without any experience at all. Experience of taste seems to be something extra, contingently related to brain state- something produced rather than constituted by the brain state. So, it cannot be identical to the brain state in the way that water is identical to H2O."

(Note the extremely heavy lifting done by the word "seems", moving the argument from a fanciful thought experiment to "cannot".)

Is what he is doing science? Well, perhaps, but not very good science. He is, as part of the intelligent design community, expressing doubts about the reigning theory. But without specific disproof, and without a better theory, these attacks are foolish. They are based on bare incredulity in the teeth of a great deal of countervailing direct and circumstantial evidence. My take on this assertion is that given a brain with all the structures, electrical activities, and hum of a working brain, (i.e. it would be alive), its subject would necessarily have experiences. Not only that, but that reproducing such experiences in artificial computers is something whose accomplishment is just a matter of time.

So far, we have not given a fig about the internal experience of computers, which contrasts sharply from the forces of evolution, which put motivation, continuity, and unity of conception and action foremost, thus leading understandably to computational machines that represent their output internally rather than on a printer. In any case, all studies of our cognition are consistent with its computational character, up to the point of subjective experience.

Lastly, once Nagel gets into the weakest point of his argument- his intuition that moral values are objective, (i.e. moral realism or value realism) which conveniently makes another argument for cosmic teleology. He admits, however:

"So I am in agreement with Street that, from a Darwinian perspective, the hypothesis of value realism is superfluous- a wheel that spins without being attached to anything. From a Darwinian perspective our impressions of value, if construed realistically, are completely groundless. And if that is true for our most basic responses, it is also true for the entire elaborate structure of value and morality that is built up from them by practical reflection and cultural development ... Nevertheless, I remain convinced that pain is really bad and not just something we hate, and that pleasure is really good, and not just something we like. That is just how they glaringly seem to me, however hard I try to imagine the contrary, and I suspect the same is true of most people. ... Indeed the disposition to ascribe an illusory objectivity to plainly contingent, response-dependent norms, of language and custom, for example, seems to be typical of humans, and quite useful."

Note once again the work that "seems" does here, and the excruciating work Nagel must do to deny the sensible model in favor of his intuitions, even being aware that his intuitions are perversely well-accounted for by the Darwinian theory. It is a breathtaking piece of philosophy!

He believes that, based on his intuitions about each of these issues, he has demonstrated the necessity of some non-physical explanations that go beyond the scientific / materialist / naturalist paradigm. I think these arguments are poorly founded in the extreme, and by the weight of current evidence incorrect on every count, even putting aside his failure to offer a competing model of any detail. It is high time to put intuition-based philosophy, not to mention intuition-based science and cosmology, out to pasture.

---

† Note on transcendence...

"Evolutionary naturalism implies that we shouldn't take any of our convictions seriously, including the scientific world picture on which evolutionary naturalism depends.
I will defend these claims in later chapters, but here let me say what would follow if they are correct. The failure of evolutionary naturalism to provide a form of transcendent self-understanding that does not undermine our confidence in our natural faculties should not lead us to abandon the search for transcendent self-understanding. There is no reason to allow our confidence in the objective truth of our moral beliefs, or for that matter our confidence in the objective truth of our mathematical or scientific reasoning, to depend on whether this is consistent with the assumption that those capacities are the product of natural selection."

Firstly, I think he confuses two cases- the case of moral concepts versus the other cases of mathematical and scientific concepts. Under evolution, morals are not objective, thus we should indeed be a bit more humble about our innate faculties and prejudices in this regard. Whatever our intuitions, it would be more accurate as well as helpful in practical affairs if we gave up the idea that morals are objective, particularly our own morals.

On the other hand, the idea that evolutionary theory destabilizes our other senses and especially our ability to accurately do math is simply wrong. No one questions that math is hard. We are not natural mathematicians, at least beyond the number of our fingers. But what we do have are ways to validate our work, looking for logical consistency and forms of calibration that supply the critical perspective that we innately may lack, on both mathematical and scientific issues.

More generally, we have evolved to possess general computational power. That means that we have not only, say, a graphics card (i.e. a visual system) dedicated to visual processing, but also a completely general ability to do logic on any topic we wish, typically assisted with language, pencil, paper, or other devices. This frees us mentally to analyze any question of interest and critique that analysis, devising fully logical answers (i.e. proofs) given a set of premises. These premises may be faulty or unfounded, but that is a separate issue.

So while our visual accuracy is perhaps dependent on the quality of our evolution, (with color-blind people being barred from certain perceptions in the absence of modern technologies, for instance), our logical perception is not dependent on the specifics of our wiring. It may go terribly slowly, but with enough work, we can come up with definitive answers that, yes, transcend our native perceptual abilities. That is the whole point of science and math.

So I do not think Nagel's premises are correct. His quest for transcendent self-understanding also is misguided. If he means a well-founded, objective scientific understanding that is correct within the bounds of current knowledge (i.e. will be ony be extended rather than disproven, in the sense of Einstein's work), then we already have such an understanding in many areas, particularly of biology. If he is pining for a religious perspective on the cosmic mind and its teleological principle, he is barking up the wrong tree entirely.

• Others are more sympathetic to Nagel. Others, not so much.
• Meanwhile, brains are pointing the way for computers.
• But if you want to leave the thought process entirely, try positive thinking. Great post on irony, perversity, and New Thought.
• Yes, our infrastructure is really crumbling.
• Corruption, Citizens United, and Rome.
• Inequality even worse after the great recession.
• Karzai, official head of corruption.
• Corruption in international commercial law.
• QE vs anti-QE ... perhaps it comes out in the wash.
• Beyond religion, with the Dalai Lama.

White house not burning

Not even smoldering... Johnson & Kwak's miss-titled book on the federal debt.

Simon Johnson and James Kwak have written "White House Burning", about how to solve the putative crisis of US federal debt. It is a very mature discussion of the federal budget, deserving to be read by everyone even remotely interested. They pursue a generally liberal line, working diligently to explain and defend the great insurance systems of the New Deal and Great Society. Since they open with a lengthy history of US budgets, focussing on the war of 1812- which, as usual, was not paid for out of pocket but on credit- they allow themselves to refer to the burning of the White House in that era; not something that turns out to have anything to do with our current predicament or even with the federal debt in general.

Buring or not burning aside, their main point ends up as an enormous let-down from the title which promised a more hyperbolic FOX-newsy polemic. They close:

"Most Americans, we think, are made better off by programs that require insurance contributions today but provide protection against unforeseeable and unavoidable risks in the long term. The question we leave you with is this: Are you and your family willing to face these risks alone, not knowing what will happen in the future, or do you want to live in a society that will protect you from misfortunes that lie beyond your control? For this is what the debate over the national debt boils down to, and its outcome depends on you."

That is great, and they have done a great service in cutting through much of the smoke that characterizes this debate, most egregiously exemplified by the claim that the federal government is "broke".

US federal debt, past and future. Blue shows the projection under current law where the Bush tax cuts expire.

But I think some rather acrid smoke remains wafting about even after reading this book, and deserves some critique. They are remarkably imprecise about the risks and problems of the debt, even as they are remarkably precise in their prescription- debt held at 50% of GDP over the long term. They dutifully refer to the Reinhart & Rogoff work on all sorts of state debt histories, and which sets the dangerous red line at 90% of GDP. But then Johnson and Kwak mention that many of those historical cases were utterly unlike the currency-issuing, debt-in-our-own-currency, floating-exchange-rate system that we have in the US.

Johnson and Kwak put a great deal of weight on our position as the world's reserve currency, and that other parties in the international system may someday tire of lending us endless money so that we can go on domestic, or worse yet, blundering international escapades.

"In the long term, either the voting public will ensure that the national debt is brought down to a sustainable level, or bond investors will do it for us, as they are doing to Greece and Ireland."

They also reflexively mention Greece and Ireland as bogeymen examples of debt gone wrong, which is simply unforgivable, given the vastly different constraints they are under as euro countries- without floating exchange rates to their main trading partners, or their own fiscal policy or currency. Europe tried to hide the fact that the euro had transformed each of its countries from a sovereign state into a federal province, in monetary terms. But that fact has now come to light in unpleasant ways.

Most curious of all is Johnson & Kwak's limp handwave towards Japan, which comes up in only one parenthetical sentence:

"The fourth, [enumerating countries with debt levels over 100%], Japan, has been able to maintain high levels of government debt because it has a high household savings rate and there is little competition from private sector businesses to borrow money."

That is it! Here is a country that has gone through a very similar real estate boom and crash decades before we did, is going through just the demographic transition we are planning for in the coming decades, and carries a national debt of roughly 200% of GDP. One would think they could devote a few more words and brain cells to the question of whether the situation of Japan is truly sustainable, and if so, why it is or is not a model for our own situation. For one thing, it indicates that the whole reserve currency issue is something of a red herring.

As I have mentioned some time back, Japan is the confounding case, which conventional-wisdom economists keep telling us is going to blow up any minute. Yet it fails to blow up. I think the reason is that it is time to come to grips with the nature of post-capitalism and the new role that the Federal debt can play as another in the set of grand insurance schemes offered by the federal government.

Traditionally, capital was scarce, and people who saved found ready takers for their investments. The whole point of capitalism was diverting an investment system that was previously (in all the Victorian novels) almost solely devoted to real estate into an entirely new world of shipping, heavy industry, high technology, trains, and countless other capital-intensive pursuits that have brought us to today's elaborate lifestyle.

But as Johnson and Kwak note of Japan, and as we see around us on all sides, money is no longer scarce. Facebook laughs at its investors and declares it has no idea what it is going to do with its IPO capital. It is probably just going to make its executives and investors rich, not to fund any new employment or other capital- (and labor-) intensive operations. Investors are chasing ever lower returns, and judging from Japan, this is unlikely to end any time soon, even after employment improves and the recession recedes. While the average American may not be saving much, the rich are getting and saving at prodigious rates, saving up about four times GDP in overall wealth in the US.

In this environment, it makes sense for the government to not only provide a variety of social insurance schemes for old-age income and health care, but also a massive banking service, providing what are in essence low-interest extremely safe CDs. The federal government is sometimes called an insurance company with an army attached. Perhaps in the future it will be called a savings bank with subsidiaries in domestic insurance and international policing. The government already insures bank deposits and backstops all those too-big-to-fail banks; why not be the bank?

What is the limit to such banking? The limit is savings desires. When bond holders decide they would rather spend their money than consume it, then real interest rates would go up and inflation might go up as well. As Paul Krugman has pointed out recently, a part of this response, among foreign bond-holders (by far the minority, incidentally) would weaken our foreign exchange rate, which would be beneficial to our export trade and domestic job market. It is an issue we can meet when we come to it. Going by Johnson and Kwak's rule of thumb (debt at 50% of GDP) would obviously not allow this flexibility to serve domestic savings desires.

To me the bottom line is that policy should follow the actual evolution of the economy, and not hold itself to envelope-based and falsely comforting "rules" like the Maastericht 3% deficit rule and these authors' 50% rule.

The cost of the debt is, as Johnson and Kwak allude to, though not with sufficient clarity, the interest that is borne by future taxpayers- a form of redistribution. Might this interest cost become onerous and unfair? Indeed, it might. That is where the inequality and Occupy themes come back into the picture. The debt is generally held by the rich, who have money to save over and above their consumption needs (see Romney, M. W.). This includes pension funds and other large organizations like corporations. So the interest may become a regressive transfer of money in the future from taxpayers to the rich. If the tax and spending code is sufficiently progressive in its other respects,  (like staying away from flat consuption taxes), then the cost comes out in the wash... the rich pay for their own savings benefits in a broad sense.

The interest cost of federal debt is generally the lowest possible interest rate, very near the level of inflation, since due to its full political backing, it has zero solvency risk. But as noted above, if savings desires are truly sated, for instance by a massive demographic transition to old people who consume but do not save, then interest rates even on government debt would rise over the level of inflation, and future taxpayers would face significantly rising real costs on rolling over a large federal debt.

This would be the time to cut federal borrowing & spending, to bring deficits and debt down. But note that the economic situation then would be, unlike today, one of high consumption and low saving. It would be an economic boom, paying richly to those workers who are still young enough to shoulder the load of caring for their elders. Savings would be flowing out of the accounts of the elderly, making it the proper time for the government to reduce inflation by policies including perhaps even running budget surpluses.

So my view is that, as Japan has found, the bond rating agencies don't know anything, and conventional fiscal "rules" are meaningless when one is faced with real economic conditions. The Japanese have been properly feeling their way through a post-capitalist age and I think have arrived at the right policy to support employment, savings, and government services even as enormous demographic and economic shifts have taken place under their feet.

Do we have the policy and political apparatus that could handle such empirically-based economics? Not right now, that is clear. We need a sounder economic theory to have the institutional confidence that we are steering the right, if heretofore unconventional, course. And that, of course, is where MMT economics comes in.

• CBO is not being straight with us.
• James Kwak makes the occupy argument more explicitly.
• Robert Reich chimes in about the deficit.
• Krugman on deficit hawks and bond vigilantes, again.
• The right keeps hating on Social Security. Security of any kind is probably anti-plutocratic.
• Life without power failures and embarrassing infrastructure- can we dream a little?
• Romney's 1% killed the Twinkie.
• Does the 1% tend to exploit workers? Does it want structural advantages and power?
• Clarity on the European crisis.
• Who is surprised that accounting firms are fraudulent and incompetent enterprises? Meg Whitman, and she is doing a heckuva job!
• Are some professions, classes, and personality types not open to evidence?

Humans find some scraps in the genome junkyard

The human genome has a great deal of junk in it, but some junk may be better than other junk.

Humans have been shocked to find out that we have only about 21,000 protein-coding genes, the workhorses of developing and running our tissues. These cover only 2% of the DNA of the genome, so what is going on in the rest of it? Is it just parasitic junk like old retrotransposons, repetitive stutterings, and duplications decayed into pseudogenes?

A large genome evaluation project (ENCODE) has been in the news lately, claiming that perhaps 80% of the genome is actually functional. But that is quite a stretch of interpretation. What they actually found is that this large proportion of the genome is transcribed, typically at very low levels, (detectable with high-technology), or has some other marker of activity like sites where regulatory proteins bind, or signs of activated chromatin, and other features.

It is sort of like saying that cable TV (or Roku, for that matter) has 300 channels, instead of the four or five channels we used to know about in an earlier age. Yet how many of those channels actually count for anything? Perhaps they amount to a lot of garbage, not influencing the larger media and social/political landscape. Perhaps, like FOX, they are putting out a lot of chatter and fluff, but in the end do not help build a greater future...

In biology, regulatory binding and transcription are only the opening steps on the way to gene expression. Only when all the pieces are put together, combining on a real gene whose transcribed RNA gets processed to an mRNA that encodes a protein on the ribosome, and gets transported to the right location, and ... do these regulatory events have effects in the cell and organism.

I think it is likely that, while the regulation of known genes is doubtless quite a bit more complex and distributed than previously realized, (generating the incredibly fine-grained and endless variation that we see among humans), there remains a great deal of junk in the genome, some of which gives rise to biological noise (i.e. transcription and protein binding) whose effect may be minimal.

This was all by way of introduction to a paper that uses this ENCODE data to analyze the genome for signs of recent human evolution, especially of sites which have been newly drafted into use in the human lineage, from what was junk in our ancestors (and remains junk in chimpanzees and other contemporary fellow-species). It is an intriguing story of how genes and regulatory functions may have been fashioned by evolution out of the miscellaneous scraps lying around in the DNA.

An important problem these researchers face is that humans are virtual clones. We have much less genetic variation than other species. We evidently went through narrow population bottlenecks in the recent past (think African "Eve"). The current population of Africa has roughly 1.3 times the genetic variation of all humans outside Africa, due to the extra bottleneck of small groups migrating out of Africa. But human variation is low in any case (a variant every 153 bases in humans, vs every 0.2 bases in other mammals- truly a remarkable difference).

So the researchers turned to mass sequencing of many genomes to assemble enough genetic variation (the 1000 genomes project). This allowed them to map where, across the population, humans have DNA variants. In important areas, there will tend to be fewer variants, and in junky areas, there will be more, since there is no selection for important function keeping mutations at bay (i.e. killing and reducing the reproduction of people carrying variants there).

The second piece of data they use is maps of genome conservation between many mammalian species (26 species, including humans, indicated in blue, below). This allows them to see what has been conserved for a long time. Known genes like hemoglobin will have been around a very long time, be easy to recognize, and be highly conserved, since they do critical work. Most changes in its code are going to be lethal. But elsewhere, most of the genome allows far more leeway and the question is just how much. Are these regions that the ENCODE project identified (indicated in red, below) as being transcribed and sort-of-active important to humans? Or are they still just junk?

Venn diagram of the human genome (the whole black box). The ENCODE project found that most of it (red) is somehow active, either being transcribed to RNA at some low level, or bound by proteins that regulate active genes, etc. "Mb" means thousand base pairs of DNA. The blue part is that which is conserved among mammals, marking it as functionally significant not just in humans, but over a far longer time. Half of this conserved amount was in the "inactive" portion of the ENCODE data, which is certainly odd, and leads to questions about just what the ENCODE folks were looking at.

The answer is a partial one. They found that, on average, the newly found "active" areas of the genome outside known genes and outside areas known to be conserved in other mammals still carried significantly fewer variants than "inactive" areas (non-red). So they seem to have separated quasi-junk from the honest-to-goodness junk.

(Wonk note: But it is important to note that what they regard as conserved among mammals must be a very small proportion of what is actually active and functional in all these species, since the same ENCODE proportion of activity and function would be found in all these other species as well. So I believe they are comparing incommensurate metrics in this paper, and can not really conclude that the selective constraints on ENCODE-specific areas of the human genome are really human-specific rather than long-standing among mammals, if more variable than what is readily captured by typical measures of conservation.)

Graph of human variation, categorized by type of genome element. The axes are two different measures of genome variation. The X-axis is a metric of the density of SNPs, which are single nucleotide (or base) variants in the DNA, which is the same as a single base mutation. The Y-axis is a metric of derived allele frequency (DAF), which cranks the SNP data through an additional analysis to focus on new ones versus ancestral ones. 

I have added red arrows, which point to the ENCODE included and excluded sets among the non-conserved areas of the human genome. The data of the paper essentially boils down to the difference of these two points on the graph, indicating that the "active" designation by the ENCODE project has some functional significance that is reflected in lower-than-average rates of variation (i.e. mutation) in human populations that reflect intra-species conservation, to some small degree. They term this as the "constraint" these areas of the genome are under, from natural selection. 

Other genomic features mentioned in this graph include: "Non-degenerate coding", codes for protein products, and specifically restricted to bases of the DNA that are not in the synonymous part of the triplet genetic code; "UTR", untranslated region, typically immediately leading or following a coding region; CDS, coding sequence, coding for protein or RNA; "Annotated", previously included in atlases of functional genomic elements; "Active chromatin", regions bound by few histones or special histones chemically marked as permissive for transcription; "intron", interrupting portion of genes that lie between the coding pieces and are specially spliced out of the transcribed RNA; "Exon", the coding pieces of a gene that lie between the introns and the UTRs; "Mappable", means pretty much everything- the whole enchilada, whole ball of genome wax.

Everything in this paper is done in bulk: averages drawn over huge areas and over crudely summarized features of the genome. What actually lies within the ENCODE areas that leads to these rather slight findings of selective constraint (and thus presumed biological function) is hard to say, without consulting the much more detailed work done elsewhere in the project. It could be a few important new genes, perhaps coding for non protein-coding RNAs that have become the focus of so much interest recently and which regulate other genes. Or it could be a large cloud of regulatory protein binding sites that tweek the activities of genes lying far, far away, weakening the idea of the gene as a local object on the DNA. Or some new aspect of biology waiting to be discovered. In any case, it reinforces the idea that it isn't how many genes you have, but how you use them that counts- that humans are beneficiaries of an extremely long process of gene-regulatory tinkering, both recently in our own lineage, and through the deep reaches of evolutionary time.

• Related paper on human variation in regulatory regions, finding regions of positive selection, also using the ENCODE data.
• What is open access for academic journals?
• Climate-gasm: California started auctioning cap & trade permits last week.
• Age discrimination is rampant.
• Grass roots youth group promotes class war against self. Hmmm.
• Search and seizure should require a warrant.
• Is the White House under premeditated attack?
• Mad Max in Honduras.

Government furnishes our freedoms

Ironically, anarchy is the state of least freedom, since our freedoms come from politics & organization.

I was reading a book all about how terrible our federal deficits / debt are, by the eminent economist Simon Johnson, (which may come up in a future blog), when he made a trenchant, if tangential, point worth repeating: that much, or even most, of what we value government for is how it increases our freedoms.

We have been taken over in the last few decades by the paranoid psychosis of the right- that the government is always bad- is sending in the black helicopters to take away our guns, and is stealing our money for its nefarious socialist plots and trilateral commissions to make the whole world a Stalinist gulag.

And obviously some governments are indeed bad. Vigilence against overreach is a constant duty. Our bill of rights and whole constitutional process was a bit obsessed by this ideology, making a great show of granting various rights and constraining the capacity and institutions of the government lest they impinge on our "natural freedoms".

But how are our freedoms natural? With all due respect to the French revolution and its animating characters & philosophies, the state of nature is anarchic chaos where the strong may have some freedom, but only until they meet someone stronger. It is a non-state of no rights where predation is the law of the land. Rights only appear when the sufferers of predation band together to demand freedoms they desire, as the nobles under King John demanded in the Magna Carta. No state, no rights.

So the conflict at work in our contemporary right-left divide is perhaps more accurately seen as a contest not about freedom in some abstract sense, but about who is to be free- the predator or the prey? Are corporations to be free to despoil our common bequests? Are corporations to be free to abuse their workers? Are corporations to be free to gain monopolies and abuse their customers? The whole notion of a business plan typically revolves around some way to corner a market with some predatory intent, whether that is through patented innovation, through defacto monopolies like the cable industry, through the closed ecosystems our smart phone makers create, through legal intimidation or under-paying labor, or the like. The financial industry is a study in predation brought to high art, especially in the sub-prime debacle, which appears to have sucked wealth from the bottom of the economic ladder with startling effectiveness:

There are many kinds of freedom- freedom to have a voice, a vote, a job with income, the freedom to change jobs, to health care at reasonable cost, from unwarranted surveillance and intrusion, to practice religion or not, from theft and fraud, to breathe decent air, from fear of foreign invasion, to get an education, and many, many others. In our society, corporations are some of the primary destroyers of many of these forms of freedom, and government (i.e. our society by virtue of conscious moral decisions and communal organization) their originator and prime protector. Even while they are themselves creations of the state and dependent on its legal system, corporations bring enormous fire-power to bear in their predatory fights against each other and against the rest of us, battering down regulations and personal freedoms (think of, say, Facebook) for profit.

That is one reason the election went the way it did. The Republican convention was surreal in its relentless vaunting of freedom for the business and especially the business owner. All hail Mr. Potter! They did not seem to grasp that this might not paint the warm and cuddly image they imagined, but one of class war, where they were aligned, with their exemplary candidate, on the losing side.

• A small example in the publishing and media industry.
• "The Anarchy", in Norman Britain.
• Religion = hyperbole and identity.
• "Top" economists speak ... the profession should be ashamed.
• Anti-science in left guises... GMO.
• Near death, but in heaven. How does that work?
• Skidelsky- does technological unemployment yield leisure to the rich or suffering to the poor?
• The evolution of spirituality away from religion.
• Legalize it ... in Afghanistan.
• Carbon tax or cap & trade?
• Romney: not so gracious, actually. He still seemed a wee bit entitled.
• Dorothy Donegan vamps all over Misty.
• Miscellaneous data of the week: voting patterns of the easily-led: