The Problem With Atheism

Bernard Mandeville and the impossibility of getting along without lying.

We live in a little cloud of lies. From the simplest white lie and social protocol for hiding unpleasantness, to the universal belief that one's own family, city, country are better than the other ones, untruth is pervasive, and also essential. Vanity, optimism, a standard set of cognitive biases.. are opposed to the reality principle. The economic commonplaces which are, as Keynes noted, unknowningly derived from some defunct economist. Our unconscious is resolutely irrational. Euphemism, humor and swearing are ways to refer to truths that are difficult to bring up in straightforward fashion. But more serious truths are the more deeply hidden. Such as death, the final stop on everyone's trip. Full-on honesty and truth? No one wants that, or could live with it.

Many thinkers have plumbed these depths, from Machiavelli to Freud. Bernard Mandeville was one, profiled in a recent BBC podcast. His most enduring (and brief) work was the Fable of the Bees, which portrays a society much like Britain's, rife with greed, ambition, corruption, and crime. Due to moralist complaints, god decides to make this hive moral and good, upon which everything promptly goes to pot. The economy, previously held up by a love of luxury, collapses. Courts and lawyers have nothing to do, clothing fashions fail to change. The traders leave the seas for lack of demand, and the military succumbs for lack of population. The hive ends up resembling one truly composed of bees, and goes to live a hollow tree, never to be heard from again.

"Those, that were in the Wrong, stood mute,
And dropt the patch'd vexatious Suit.
On which, since nothing less can thrive,
Than Lawyers in an honest Hive."
... 

"Do we not owe the Growth of Wine
To the dry, crooked, shabby Vine?
Which, whist its shutes neglected stood,
Choak'd other Plants, and ran to Wood;
But blest us with his Noble Fruit;
As soon as it was tied, and cut:
So Vice is beneficial found,
When it's by Justice lopt and bound;"

His point, naturally, was that vice is both natural and to a some extent the underpinning of national greatness and economic vitality (given some beneficial management). Greed is good, as is irrational optimism and ambition. Mandeville was also a famous anticlericalist in his day, but that is another story. It was a classic contrarian point, that what we fight tooth and nail to vanquish or hide has, in reality, a role to play in the national character and success, for all its embarrassment. And that we routinely lie, to ourselves above all, to hide the truth of reality so that we can go on our way from one day to the next.

"My aim is to make Men penetrate into their Consciences, and be searching without Flattery into the true Motives of their Actions, learn to know themselves."
- Bernard Mandeville, in Free Thoughts on Religion, the Church, and National Happiness.

What is our most florid and communal lie, but religion? This is the salve of social togetherness, moral self righteousness, and imaginary immortality. It is the finely tuned instrument that addresses alike our private fears and social needs. And atheists know it is completely, utterly wrong! But what is the point of saying so? Religions have been corrupt, abusive, greedy and murderous from time immemorial- they have many faults. But untruth is not a flaw.. it is the reigning feature of this imaginative confection, providing the credulous a full belief system to support a positive and hopeful self-image, (not to mention conventional authority!), so important to happiness, providing the more skeptical an endless labyrinth of theological puzzles, while providing even the most skeptical or apathetic a social institution to call home.

So why go around ripping the clothes from believers, crying that their cherished narratives of meaning are senseless- that they should go forth theologically naked? It is a serious question for atheists, going to the heart of our project. For Freud, after all, repression had a positive function, and was not to be comprehensively cleared away, root and branch, only pruned judiciously. Lying is indeed integral to mature social functioning. Clearly, untruth is not, by itself, an unacceptable portion of the human condition. This implies that atheists need to be generally gentle in approach, and selective in what they address directly- the most significant outrages and injustices perpetrated by religions, of which there is no shortage. When religions invade the territory of science, making bone-headed proclamations about biology and geology, that clearly crosses such a line. And likewise when religions insinuate themselves into governmental institutions, bent on seeking power to foist their beliefs and neuroses on others.

The so-called arrogance of atheists consists of their opposing / exposing the cherished verities of others as false. Such arrogance is of course not unknown among religious believers and zealots either, and for much more modest cause. The secular state settlement of the West has forced religions to forego armed conflict and state violence in the pursuit of their truths and enemies. Atheists should take a page from this success to lead by example and humor, rather than frontal assault, even rhetorically.

• BBC to continue spouting religion.
• Silicon valley has its religion as well- a sort of Stockholm syndrome.
• But lies in politics.. is there no limit?
• Hate is in the textbooks, in Saudi Arabia.
• Euro countries are not independent.
• 5G to rule them all.
• Heredity counts for a lot.. more than parenting.
• The labor market could run much, much better.

Three Rings to Rule Them All

Condensins, cohesins, and SMC5/6: a family of ring-shaped protein complexes that keep chromatin organized, compacted, and generally under control.

Each of our cells contains a meter of DNA, scrunched up to microscopic proportions. This DNA is particularly visible during mitosis, when it is neatly condensed into chromosome brushes, which get pulled and segregated in the remarkable ballet of cell division. We also know that topoisomerases, which can cut this DNA, either nicking on one strand to allow unwinding, or on both strands to allow strand passage (to uncatenate or untangle as needed), are central players in keeping this mess under control, at least in a passive sense. But obviously, to make neat chromosomes, and for countless other tasks, some of which will be described below, more than topoisomerases are required. Another class of proteins called SMC (structural maintenance of chromosomes) supplies some of the lariats, knots, and other rope tricks that are needed to keep our nuclear DNA going in the right direction, and has been the focus of quite a bit of recent progress.

Bacteria generally have one SMC protein, but we have six, paired into three functional ring-shaped complexes: condensin, cohesin, and SMC5/6  (no clever name, unfortunately). They were originally found to function, respectively, in the condensation of mitotic chromosomes, in the cohesion of sister chromatids, and in DNA repair. The SMC proteins pair up to form large rings, of about 50 nm, have an ATPase activity which has been recently found to function as a motor along DNA, and associate with a bunch of other proteins to regulate their activities. It is generally believed that the rings they form can encircle one or two strands of DNA, to provide the pairing and looping functions to be described.

Cartoon of how cohesin encircles both daughter strands of replicated DNA, to keep them paired until the critical separation point in mitosis.

For example, cohesins glue together daughter strands after DNA synthesis, so they do not float apart, but can be carried along as pairs into mitosis, and then separated at the right time (anaphase) with a dose of protease which cleaves the cohesin ring. Mutant cohesins cause DNA tangling and loss of proper segregation at cell division, leading to mutations and thence to death, cancer, etc. But having sister DNAs close together is convenient for other reasons as well. If one gets a mutation, homologous repair can use one strand of the good copy to directly invade the bad one, and after excising the bad portion, encode the repair. In fact, the various SMC complexes have somewhat overlapping functions, so some can fill in for defects in the others.

Electron micrographs of purified condensin, showing the structure of a ring with large blobs (containing ATPase and other accessory proteins) at one end (customarily the bottom) and a smaller blob on the other side where the two SMC proteins also dimerize (called the "hinge" region). Bar is 100 nm.

Condensin is the main driver of chromosome compaction, looping, and transcriptional domain establishment. Ultrastructural studies of mitotic chromosomes have long shown that mitotic chromosomes are composed of loops- variably sized and perhaps of multiple levels. Condensin has perhaps been the best studied of the SMC family, with beautiful recent work (also here) showing that it forms loops by pumping DNA through its ring structure. In the experiment shown below, a single molecule of DNA, fluorescently labeled, was attached to a surface at both ends. Then a flow was set up in the ambient fluid, towards the top right. When cohesin protein (purified from yeast cells) was added, along with ATP, it selected a site on the DNA, then started forming a collar and pumping out the free portion of the DNA, forming a little loop. At the end of the experiment, several minutes down the line, this cohesin complex spontaneously let go, allowing the DNA back into its original state, waving freely in the flow.

A single DNA molecule in a fluid flow cell, anchored at two points (red circles), shown through time as it is bound by one codensin molecule, which forms a little pumped loop within a few seconds.

Such looping is not only relevant for mitotic chromosome structure, but also for transcription. Genes are driven by regulatory protein binding sites, "enhancers", that can be very far from the core coding portion of the gene- often tens of thousands of base pairs away. How does such an enhancer know which gene it is supposed to enhance? It has gradually become clear that genes are surrounded by a zone of isolation with "insulator" DNA sites on the boundaries. Cohesins have recently been shown to be key creators of these zones, binding to the boundary sites and pumping out the intervening DNA, isolating one loop from its neighbors, at least with respect to processively scanning searches by DNA binding proteins, and also with respect to mega-complex fomation by the enhancers of each zone.

The SMC5/6 complex is proposed to facilitate replication by keeping the daughter strands close so that that topoisomerase II can come in and relieve topological tangles.

The SMC5/6 proteins perform yet another function, of facilitating replication. Like cohesins, this complex forms rings around recently replicated DNA. The replication fork is itself enormously complex, but as it works, (probably stationary, being fed in sewing machine fashion), the DNA going in and coming out is continuously writhing about to accommodate its helical twist. Imagine a sewing machine working on fabric with an intense twist of one full turn per ten stitches- it would be quite a challenge to operate. Most of the stress can be accommodated on both sides, incoming and outgoing, by continuously nicking and relaxing by topoisomerase I. Yet it is thought be helpful to keep the two daughter strands in close proximity, to allow stand-passing topoisomerase II to undo more serious tangles, and also to prepare for the long-term use of cohesin which keeps the daughter strands together through interphase and into mitosis.


What is known about how the SMC proteins actually operate? That is still a work in progress. In order for condensin to form DNA loops, it needs at least two functions- an anchor to hold on to one region of DNA, and an ATP-using pump that scrunches the neighboring DNA and feeds it through its ring structure. The anchor is quite well characterized. It needs to be relatively agnostic about the sequence it binds to, but once attached, it must stay put while the rest of the molecule does its work. This is accomplished with a special knotting portion of one of the accessory proteins attached near the ATPase portion of the complex. These proteins form a positive charged groove, ready to bind DNA. Once bound, there is also an unstructured extension of one of these proteins (in green below) that comes down to lock the DNA in place, prompting the authors to call it a "safety belt". This structural shift does not require ATP, but is required before the ATPase nearby can become active.

Structural cartoon of two accessory proteins of condensing (yellow and beige), which form the anchor. This binds DNA non-specifically, and once bound, gets locked in place by a unstructured protein extension and also licenses the ATPase to begin operating to pull neighboring DNA through the ring. The topology of the shown DNA/chromatin is likely wrong.

What is the ATPase doing? It has just recently been shown that it really is a DNA translocase, (partly as shown above), after some years of doubt. It is also remarkably efficient, traversing at a rate of ~70 basepairs per second, and only using two ATP per second, thus covering about 35 bp per ATP. It must be using the length of its ring to make jumps of some kind- a mechanism more reminiscent of actin or kinesin than of typical DNA/RNA translocating enzymes. Researchers working in this field have proposed a couple of models. One is that the ring separates at the base (right, below) to allow the two ATPases of the paired SMC protein complexes to "walk" alternately along the DNA, taking long strides of up to 50 nm. This obviously risks losing whatever is being enclosed in the ring, so is problematic. The second idea (left, below), is that the extended, coiled portions of the SMC proteins somehow fold and unfold in response to ATP hydrolysis at the end, allowing the complex to take half-steps while rigorously keeping the ring closed. It would be difficult to envision how this mechanism works in detail. It may be that more than one ring cooperate, to resolve some of these coordination issues.

Rings composed of two SMC proteins (red, blue) are proposed to walk along DNA using their ATPase activity by two alternative mechnisms. Note that the SMC molecules with blobs on the ends are not symmetrical. The ATPase and other significant accessory proteins and activities of the complex are all on the lower (striped) blob of each SMC protein, while the other blob represents a much simpler "hinge" region of the proteins which dimerize but have no other known functions.

• Capitalism vs community.
• What is wrong with the EU.
• Learning and flexibility as the red/blue divide.
• One electric utility keeps causing devastating fires in California.
• Canada helps parents keep working.

Fight For the Biosphere

The Story of the Earth Liberation Front: If a tree falls.

What is sacred? No one lives without deep values, whether conscious or unconscious. When I recently travelled to a small midwestern town, I was struck by its devotion to its institutions of reproduction- the high school, the church, the football game, the picket fences. Small town American is under perpetual siege from the outside, from the Amazons, Wallmarts, cheap drugs, bombarding media, and changing values. From capitalism in general, though no one would put it that way. Getting young people to stay instead of heading out to the big city or the coast is one challenge. Another is facing a flow of poorer immigrants who do want to come, but who drop the bottom out of the local labor market and are difficult to assimilate. The FOX and Sinclair propaganda channels harp constantly on "traditional values", as though applying a magic incantation against change (even as they and the right end of the political spectrum work to remove what fetters are left on capitalism, and to destroy the public goods & institutions that these communities rely on). No wonder Trump found a fearful and responsive electorate.

But everyone has their god- communists worshipped the sacred revolution, into whose maw millions were fed. And into the bargain had their trinity of Marx, Engels, and Lenin. To others, capitalism is a glowing, sacred value, and to some extent for good reason. The adoption of capitalism in China has brought about the most massive and rapid transition out of poverty, ever. (Even though the means to get there has been ecocidal technology.)

But these major ideologies and religions are weakening in our time. People are becoming disaffiliated with the cultural structures and institutions that used to cultivate sacred values, whether those of explicit religion or of its various modern ideological substitutes. The balance is often made up, on a personal level, by "nature". This is our instinctive and "natural" religion- the groves of the pagans, the auspicious birds and other animal spirits, the awesome scale and impurturbability of the surrounding vista, not to mention our own mystifying biology.

A fairy ring in a wooded grove.

The dedication to conservatism that pervades small town America is deeply in conflict with respect to this deeper set of values, as well as being counter-historical. A mere six or seven generations back, these lands were peopled by Native Americans, before being invaded by pioneers. These pioneers found, in their westward expansion, an undreamt-of natural abundance of game, fertile soil, and plant and wildlife of all sorts, which they promptly set about chopping down, shooting, poisoning, and generally extirpating. The illusion of stasis upon which rural Americans are so intent on staking their politics belies tectonic shifts to their natural surroundings and supporting ecosystem.

For the world is on fire. It is not just the loss of wolves, and the invasion of exotic species, and the relentless spread of pesticides, and countless other piecemeal assults that are degrading what we imagine to be perennial nature. It is global warming that is making nature itself a shadow of her former self. California has been literally on fire the last couple of years. Seasons are palpably shifting. Droughts are spreading. The Arctic sea ice is dwindling. Corals are dying en masse all over the world. Wildlife has been halved over the last half-century. Forests continue to be burned and clear-cut.

Those who see the sacred in nature are deeply appalled and affronted by all this. In the late 90's and early 00's, the Earth Liberation Front formed to take direct action against this desecration, not just by protesting, but by attacking those responsible for the clear-cutting, especially of old growth forests. The Northwest is full of roads that have a thin screen of trees to shield the innocent driver from vast clearcuts hidden behind. What are called "National forests" are in reality more tree farms than forests.

El Dorado "national forest"

The documentary "If a Tree Falls" is a moving story of a fight in defense of sacred values, against the modern Maloch of the timber industry. Whether this fight is noble or not is one of the themes of the piece. But the timber cutters have another set of values, more in line with the conventional property and rapine program of American capitalism, and get to brand the ELF activists as "terrorists".

The irony of the ELF actions is sadly unmistakable, using fossil fuels like diesel oil to burn down the buildings of the forest destruction complex, (i.e. the forest service and the timber companies), which will be immediately rebuilt using yet more timber. The bulk of the film profiles one of the last holdouts from Federal investigation and prosecution, Daniel McGowan. A pudgy, unprepossessing terrorist indeed, he gradually comes into focus as unshakable in his deep sense of sacred values which are in total opposition to the established order. Likewise, the prosecutors and investigators are profiled at some length, embodying their dedication to the values of law and order under the existing system. Yet they are visibly uncomfortable with what those values ultimately stand for and accomplish in this case.

Capitalism is fundamentally amoral, and exists to serve whatever we as private people want to have. It is a tool, not a value system. If we want houses made of wood, it supplies that wood, no matter the incidental cost to public lands and the animals and plants that live there. If we want electrical power, it will burn the coal to supply that power, and transmit it over fragile lines that regularly cause devastating conflagrations in high winds, abetted by global climate heating. We can not blindly trust capitalism to safeguard our long-term interests, let alone our sacred values, from our short-term needs. That is the work of government. And the last people to whom we can entrust that government are those who own and benefit from the capitalist system.

• Conservation vs conservatives.
• Pakistan shows who its friends are.. the Taliban.
• "Free speech" in Europe is a little different than in the US.
• The media is not so great in Britain, either.
• Facebook remains a cesspool. 
• Burn it up. The destruction of social trust favors Republicans.
• Fellow sleaze, in a completely illegal appointment.
• The US excels in diagnosing and treating rare diseases.
• Economic graph of the week... Left cities are economically more equitable, which is perhaps not saying much.

Economic mobility in various cities, vs overall employment growth.

Inequality Spelled the End of Rome

Historian Michael Grant pins the blame for the decline and fall of Rome on economic and social inequality.

We have never had a government by the rich, and for the rich, quite like today. How this could come to pass as a response to one of the most severe financial panics in our history, to financial mass malpractice, and to the Occupy movement, is quite curious. It is perhaps a testament to the innate temperamental conservatism, coupled with the extraordinary power of money in our media and political system. Where are we headed? One way to think about it is to look to history.

Fabulous relief from a late Empire sarcophagus. Rome was about power.

Rome ruled the Mediterranean for roughly five hundred years, from its scrappy beginnings assimilating neighboring city states on the Italian peninsula to its wimpering end at the hands of successive Germanic armies. Some of its greatest gifts were for politics- running a durable, elitist political system with extremely complicated rules, operating a likewise complex legal system, and treating foreign and allied powers with harshness, but also substantial generosity. Throughout its time, inequality was the rule, including slavery at the very bottom. The system was run by and for those at the top- the senators, landowners, and slaveholders. But at the beginning, there was a great deal of civic virtue- it was a republic, and ambition for the public good / growth of the empire often coincided with personal ambition. But defending a static or contracting multi-continent empire is not as much fun. Increasingly, the rich relieved themselves of taxes and public responsibilities, and the burden of supporting the enormous empire fell on the lower classes, in the form of tax-farming.

This is briefly outlined by Michael Grant in his book "A Social History of Greece and Rome". He stresses at some length that the lower classes- the slaves, the ex-slave freedmen, the poor and middling classes- lived quite miserably, and were treated miserably by the system. But they had no political organization or power, and no consciousness of themselves as a class. They were inert, apart from a few riots and revolts which were always local affairs, driven by desperation rather than principle or organization. This has been true through history. Democracy and other revolutions from below are generally not led from below, but by a faction of the rich, engaged in their customary occupation of competing for power at the top. Our founding fathers were not Scots-Irish hillbillies, but colonial aristocrats disaffected from their fellow lords and peers back in Britain.

So Rome was always nervous about its poor and its slaves, but never faced an organized revolution, let alone a Marxist intellectual critique. This allowed progressively worse treatment as time went on, to the point that free Romans chose to become virtual serfs under large landowners rather than face the tax collectors and military recruiters on their own, leading right into the conditions of the medieval period. A state rests on the allegiance and service of its members. If the rich couldn't be bothered to fund its needs, and the poor were hounded to the point of desperation, of what is such a state made?

"Christian writers, too, support the poor, sometimes with passion, but the effect was one again, in practice, non-existent. The destitute had to be content with the assurance that their plight would stand them in good stead in the next life. Christianity, like to many other institutions, has been blamed for its contribution to the fall of the western Roman empire- because it perpetuated the internal social rifts. And there may be something in this, although the main contribution of faith was to establish a focus of loyalty which was not the imperial court, and was not, in fact, of this world. But the fall of the empire was complex. External pressures played a major part. Internally, the main cause was not Christianity, but the gulf between the rich and the poor whom the rich exploited." - Michael Grant, in A Social History of Greece and Rome

What Americans think inequality of wealth should be like, compared with what they think it is, compared (top) with what it actually is. In fact, the top 1% owns over 40% of the wealth and gets one fifth of all income.

While we in the US have only had such antique social extremes in the slave-holding South, the current level of inequality is, in quantitative terms, astonishing and alarming. The trend of our current administration of giving gargantuan tax breaks to the rich, along with countless other gifts of relief from public good regulations, worker rights, and criminal enforcement, means that we are headed not just back through the New Deal into another gilded age, but possibly well beyond. It is hardly the land of the free if so many are economic slaves to others, with homeless beggars on every corner. As Rome evolved from an aristocratic Republic into a more frankly royal Empire, we seem headed in a similar direction, under a new Octavian who has no patience for the weak, the losers, civil society, democracy, or civility. The state exists for winners. Why anyone (who is not rich) follows him is beyond me, but then the lessons of history are usually learned only by those who don't need them.

• Other theories about Rome.
• Making America great would mean... being more like Europe.
• One consequence of inequality? Murder.
• The euro is dying.
• Wildlife is dying.
• Climate change is causing hunger, and not just for other animals.
• Unfinished business in healthcare- the public option, real negotiation, fair pricing.
• Trump and the "sheriff's star". Even Bill Kristol makes a comment.
• Sleazy fraud.
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• How the Fed thinks.