Travels Through the Golgi

A brief introduction to one of the more intriguing organelles of eukaryotes.

One of the star organelles of eukaryotes is the Golgi apparatus- great name, elegant structure, and mysterious function. Sharp-eyed readers might have spotted one in last week's post about coronavirus replication, though that virus mostly circumvents the Golgi apparatus in its trip through the secretory system to infect more people (going directly from post-endoplasmic reticulum vesicles to the exterior). This week, using a recent theoretical paper, we will delve into the nature and rationale of the Golgi apparatus.

What we do know is that the Golgi organelle is where a lot of protein processing happens. It is the major way-station from the endoplasmic reticulum (ER)- where proteins destined for the membranes, vesicle organelles, and exterior of the cell are synthesized- to their final states and destinations. So it both directs traffic, and also directs post-translational modifications like glycosylation, sialylation, and phosphorylation, by way of short sequences, or addresses, on the individual proteins. And all this is done via a series of vesicle budding and fusion events, since it is vesicles that carry proteins from the ER to the cis face of the Golgi, and onwards from the ends of each Golgi stack to the next (medial and trans) stacks of the Golgi, and thence off to destinations like the plasma membrane and lysosome. For example, insulin is a secreted protein, translated into the ER. Its key disulfide bonds form in the ER, but its cleavage into two interconnected peptides happens in the Golgi, after which it is stabilized and stored in secretory vesicles, ready for release when glucose signals arrive at the pancreas. These processing steps often have to be done sequentially. For example, sialylation can only happen after the core glycosylation has happened. This gives some direction and rationale to the gradual and stepwise nature of the Golgi transit / processing system.

Electron micrograph (right) and schematic (left) of a Golgi apparatus, with ER-originating vesicles entering from top, and secretory vesicles leaving from the bottom, towards the plasma membrane and exterior of the cell. The story is one of vesicles, both for inputs and outputs, but also as the carriers of traffic between the various internal stages, or cisternae, of the apparatus.

We also know that the key enzymes of the Golgi, which carry out the protein processing and regulate the apparatus's own stability, are often membrane proteins, have their own addressing system, and engage in retrograde (i.e. backward) vesicular transport, which keeps them localized to the stack where they are supposed to stay, against the general flow of proteins going forward through the apparatus. There is also a special set of switch-like GTPase proteins, called Rab proteins, that control some aspects of Golgi form and function, and additional proteins, GRASPS and golgins, which all affect Golgi structure, by mutational studies. There are also cytoskeletal interactions, as the Rab proteins appear to regulate the activity of specialized myosins that are motors on actin, and dynein/microtubule activity as well. These at very least help to orient the Golgi with respect to the source (ER) and destination (exterior) locations, but may have more intimate roles in the shape of the Golgi and the paths that its voluminous vesicle traffic takes, within its compartments, and externally.

So there are many clues and ideas, but as yet we do not know fully how this structure forms and maintains itself- why do stacks form at all? Are the stacks stable, or do their pancakes progress and mature, like a slow conveyor belt from cis to trans, with new ones forming behind? A recent paper tries to synthesize past theories and evidence to come up with a unified model of self-organization for the Golgi. Unfortunately, it struggles to even represent the golgi, let alone explain it, so I will summarize briefly.

They set up a few relations- the preference vesicles generally have to fuse with similar membranes, the maturation of each membrane micro-domain and locations near it through time, as processing of the nearby proteins (both on the membrane surface and within the vesicle) takes place, and the formation of vesicles out of such matured subdomains. From these more or less empirical premises, they develop a model that they can tune on several parameters- the budding rate, the fusion rate, and the rate of purification of nearby domains, thus the purity of budding vesicles, with regard to stages of secretory processing. Vesicles of mixed purity can fuse in either direction, retrograde or anterograde (forward with the next cistern of the Golgi apparatus). But the more pure the segregation of components is at vesicle budding sites, (and indeed within the budded vesicles, while they are underway), the more forward-biased the whole process becomes. This leads, with certain parameters, to a reasonably realistic, if highly abstract, model of the Golgi.

Author's general model of the substructure of the Golgi apparatus, and some alternate models of traffic flow. Here the direction is turned around, with ER proteins arriving from below. Models that propose wholesale maturation and movement of Golgi sub-compartments are unlikely to be true, in light of genetic experiments that dissociate and tie down portions of the Golgi to mitochondria, and find that their character remains stable. PM = plasma membrane; TGN = trans-Golgi network; ERGIC = endoplasmic reticulum- Golgi intermediate compartment.

All this simply follows from their assumptions and modeling. For instance, it is entertaining to see that raising the budding vs fusion rates can cause vesicle sizes to decline, leading to a flurry of tiny vesicles. Whether this modeling helps account for the features of known actors and mutants, of which there are many that affect Golgi structure and function, is claimed, but not easy to evaluate. In the end, it would probably be much better to address the actual molecular function of these proteins, and place them in a biochemical network of interactions and regulation, to build an explicit model of what is going on, rather than one that treats the Golgi as an abstraction. Reconstitution of Golgi activity from pure components, which would be the ideal method, is likely to be extremely difficult, given its great complexity. Genetics will doubtless remain the main tool.

• Fear and the conservative mind.
• Ditto.

Sanctum Sanctorum of the Coronavirus

Why is the coronavirus wrapping itself in so many vesicles?

One of the most notorious jokes in molecular biology lectures is, when starting the discussion of DNA replication, to place a fig leaf over the cartoon of the replication fork- the moment when one strand of DNA becomes two. It works on many levels, and signifies the importance of this most central event and structure. Coronaviruses never use DNA- they are RNA viruses exclusively. But RNA replication is processive just like DNA replication. Since RNA occurs only in one strand, rather than DNA's two strands, however, copying has to happen in two stages, first to a negative strand copy, then back to a positive strand copy, which goes into new virions. Amplification naturally can happen along the way as well.

A remarkable characteristic of coronaviruses and virtually all other positive strand RNA viruses is that they generate a complex and novel population of membrane structures and vesicles in cells. It is in or on these vesicles that their RNA replication takes place. There is a whole new vocabulary of membrane entities made, like convoluted membranes, zippered endoplasmic reticulum, reticulovesicular network, double membrane spherules, and double membrane vesicles. The last of these (called DMVs) is where viral genomic RNA replication takes place.

Vesicles and other membrane structures induced by coronaviruses. The large double-walled structures are called DMV, or double membrane vesicles. The tiny vesicles around them are called DMS or double membrane spherules. And the mess labeled CM (including a few clear spherules) stands for convoluted membranes. These are all induced by viral infection and viral RNA replication seems to happen in or on the DMVs.

These membranes are created by some of the earliest protein products the virus encodes- the nsp3, nsp4, and nsp6 proteins. The figure shows one possible structure of nsp6, which is thoroughly integrated in membranes, by virtue of the hydrophobicity of its transmembrane segments. But how this structure leads to membrane curviture and DMV formation is not at all clear. A paper from 2014 developed a drug that binds and disrupts the function of nsp6, which dramatically reduced the formation of DMVs, and viral replication.

Schematic prediction of the transmembrane structure of viral protein nsp6.

An even older paper from 2008 did the original work that identified the double membrane vesicles as the site of RNA replication. They took high resolution electron micrographs of infected cells, and stained for the presence of double-stranded RNA. This showed up very distinctly in the DMV structures. A more recent paper followed this up by short time course labeling with radioactive RNA precursors, so that newly made viral RNA would show up . These results were less clear, but labeling is roughly around the DMV structures. 

DMV structures are full of double-stranded viral RNA, indicating a core role in replication.

Brief labeling by radioactive nucleotides to find the location of replication gives ambiguous results, but points to DMVs. Note the beautiful electron micrograph of mitochondria (mm) and other cellular & viral structures. ER is endoplasmic reticulum, RO is replicative organelles (of the virus, which includes DMVs), and VCR stands for virion-containing region.

One major motive for the virus to hide its replication and replication products inside DMVs is that cells have various defenses that are triggered by double stranded RNA, and by RNAs that have non-cellular caps. Coronaviruses contain several enzymes to make cell-like caps on its RNA products, but still, hiding them entirely is probably a safer approach. Their replication requires double-stranded RNA at least transiently, and typically quite a bit builds up. On the other hand, DMVs also present significant problems. Are these vesicles completely closed to the cytoplasm? If so, nucleotides for replication would be difficult to come by. Also, what ultimately happens to the RNA hidden inside? None of this is clear yet. The recent paper makes a case that DMVs all have small openings to the other structures or the cytoplasm, but previous studies disagree.

Thus more work is needed, to validate this drug as something that could be used in humans, to figure out how and even where replication of the viral RNA really happens, why positive strand RNA viruses are so reliant on membrane-linked replication systems, how the viral proteins like nsp6 drive formation of these membrane structures, and what the life cycle of these structures is- what the fate of all this packaged RNA might be. The original model of coronavirus replication was that RNA replication takes place freely in the cytoplasm, and the N (nucleocapsid) protein joins it to make proto-viral genome packets. These bud into the endoplasmic reticulum, at sites where the M and S (spike) proteins have been concentrated in proto- envelope membrane regions. These enveloped buds then comprise complete virions that are exported by normal cellular pathways through the vesicular secretion system in large vesicles that bud with the plasma membrane to release the new viruses. But the extra complexity of the DMVs throws this simple schema into doubt. For such a tiny quasi-life form, coronaviruses do a huge amount of damage, and present a lot of mysteries.

• We are heading into a lawless state.
• Notes on satanic democracy.
• Oh, we took the money and fired the workers anyhow.
• Lindsey Graham, taking the high road.
• A gene for bigger brains.

The Gift

How to be thankful, without anyone to be thankful to.

Remember back when Barack Obama told business leaders that "you didn't build that"? He meant that they didn't build all the public goods that their businesses relied on- the roads, the legal system, the military defense, the regulatory bodies creating fair playing fields, the educational system. Businesses make it their business to be as myopic as possible, feeding off "business models" that foist as much cost onto others- workers, the government, the environment- as amorally possible. That is the only way to survive.

We all are a little like that, with tunnel vision focused on what we need, what we can get, and what we can do. Sometimes it is all one can do merely to survive in a world that seems so difficult, competitive, even hostile. But at the same time, who and what are "we"? Is our next need the full measure of our place in reality? Our focus on doing and on agency is a highly misleading aspect of consciousness. It presupposes a gazillion things that we have no agency over, couldn't even if we tried, and couldn't understand in any case. We didn't make our bodies, for one thing. This biology that we think we are so familiar with is, to biologists, incredibly inscrutible. The trillions of cells, billions of neurons, gajillions of molecules, all work away in obscurity to make us go. But are we thankful? Rarely. We didn't make them. We don't even understand them, and a century or two ago, we really, really didn't understand them. They are utterly alien. Yet they are also us.

The story goes similarly with everything else about us- the flow of time and fate, the universe we live in. All these are, at a fundamental level, still hardly understood. Where did all the energy of the big bang come from? What did it expand into? Why did it cool into the particles of physics? Are there other universes? No idea. And even if we had an idea, we weren't there and didn't make it happen. We are recipients, not actors, in this most vast drama. We should not be distracted by the competitive social systems we live in, and the pressing difficulties of life, to forget that we, as the conscious "I" of an individual human, are mysterious feathers floating on rivers of unplumbed unconscious depths, in a rich forest of abundance, on a planet mild and pleasant, in a universe that rendered these provisions in fantastic plentitude, to us and possibly to countless other worlds as well.

The lilies of the field, well, they toil quite hard, actually, in their own way. But that may not be apparent to the homilist, and took some science to figure out.

There needn't have been an intention behind all this- to conjure a cosmos, and evolve life. Indeed, it is rather unlikely given the little we do know. At any rate, we have speculated long and hard enough to know that more speculation isn't going to get us very far, or obtain any brownie points. We are, regardless, the benificiaries of these gifts. This is a, perhaps the, fundamental religious feeling- thankfulness for the infinite powers and entities that we embody, experience, and rely on, yet have precious little understanding of- the mysterium tremendum.

Does this all imply god? No. God is a rather pathetically inferred solution to, or better yet, an anthropomorphization of, this mystery. As social beings, and products of families, we in a primitive state might naturally ascribe the vast mysteries that undergird our existence and far outstrip our conceptions to a personified father figure (or mother, if one's society happens to be matriarchial). No error could be more obvious. Science has served to push the boundaries of mystery a little farther out, from a choking fog where virtually everything is obscure, to a view that goes billions of light-years across the universe. What all this has shown is, that as far as we can see, mechanism is the rule. Our bodies are mechanisms. The universe is a mechanism. Diseases are not the vengeance of jealous gods, nor is the weather. The inference of god has not held up well over time- not well at all. Yet that does not mean that we shouldn't be thankful for the gifts we receive, which are so rich on our life-giving planet. Nor that we shouldn't strive to pass them on rather than destroying them in the current moment of greed, by our thoughtless overpopulation and immiseration of this world.

• Another soul eaten by the president.
• And his base... the truly demented.
• The ideology of business naturally shoots itself in the foot.
• Failure of public management angers some.

Cliques of Civilizations

Huntington's "Clash of Civilizations", twenty five years on.

Is America great again, yet? Well, that didn't turn out quite as promised. China is ascendent as never before, having vanquished a virus that we simply can not get our heads around. China is also putting the screws on its neighbors, assimilating Hong Kong, building island bases in the South China sea, ramping up soft power efforts in its Belt and Road and other diplomatic initiatives, and slowly building the sphere of influence that it merits as the largest nation in the world. In comparison, we are a laughing stock, our incompetent leadership high and low exposed for all to see.

It is quite a different world from that of Francis Fukuyama's "End of History", which imagined that international conflict would disappear with the close of the Cold War and the march of liberal democracy across the globe. Instead, while democracies did advance significantly in the first post-cold-war decade, progress since has stalled. An alternate model of governance has taken root out of the communist ashes- an authoritarian capitalist fusion of the Russian and Chinese types.

Numbers of democracies rose after the Cold War, then plateaued.

Samuel Huntington wrote his "Clash of Civilizations" in response to Fukuyama, offering a conservative, realist view of history as continuing apace in the post-cold-war era on a very traditional basis- that of civilizations, rather than of ideologies. Donald Trump seems to have read (or skimmed, or heard about, or heard about "people" talking about) Huntington with some attention, since his instincts hew quite closely to Huntington's views. Rather than liberal democracy resplendent and ascendent, Huntington proposes that the new world order will be a traditional sphere-of-influence model, centered on the core civilizations of the world- Western, Chinese, Orthodox, Indian, and Islamic. Africa is so far behind that it does not count seriously in Hungtington's scheme, though that may change a few decades on. The Catholic/Hispanic cultures of Central and South America also do not count for very much in his scheme. These civilizations are based on different religions and ethnic histories, and are centered on core states. The US is the core state of the West, (though the EU may take over that role sooner than anticipated!). Russia is the core state of the Orthodox / Slavic civilization, India is virtually the only Hindu state, and China clearly leads the Sinic or East Asian world.

The Islamic world lacks a clear core or leading state, with Saudi Arabia, Iran, Turkey, and Pakistan all in contention, a contest that is still nowhere near resolution, and involves starkly different visions for the future of Islamic culture. Islam is a special case not only for its lack of a central or core state that can lead and moderate its civilization at large, but also for its general lack of effective governance, and its peculiar historical position of having had its golden age almost a millenium ago, after which the West gained progressive, and eventually overwhelming, superiority. The bitterness this engenders has not been channeled, as in the Asian tigers, into competition and often superior performance vs the West, but rather into regression, grievance, fundamentalism, and a rededication to its own cultural superiority. Thankfully, Huntington forecasts that by about now, the demographic bulge of Islam, which had been fueling much of its internal discontent and violent lashing-out, would moderate and lead to a less combative general culture- a prediction that I think is slowly coming to pass.

One of the most interesting themes of Huntington's thesis is the clique-like banding together of nations with similar civilizations. Unlike the American ideal of international affairs, where all people everywhere just want democracy and plenty of shopping, Huntington sees nations aligning on cultural terms, like people do in many other settings, like high schools, religions, neighborhoods, and so much else. The Balkan wars are, for Huntington, exhibit A. Each contestant was backed by its cultural kin among the larger countries, with the Muslim Bosnians supported by a variety of Muslim states from Saudi Arabia to Iran, the Orthodox Serbs supported by Russia, and the Catholic Croats supported by Germany, particularly the German Catholic church. Likewise, in the first Gulf war, Huntington writes that, while several Muslim countries were, under Americal pressure, part of the military alliance against Iraq, the Arab street was uniformly anti-West and pro-Saddam. His description of these sentiments and how they sapped their government's respective resolve about the war and its aftermath was sobering, and should have given the next Bush administration pause in its headlong rush into its own crusade against Iraq.

Another corollary of the civilizational world as Huntington sees it is that some cultures are odd nations out. Japan is a prime example. Clearly, Japan exists in the Chinese general sphere of influence. But Japan has been closest to the US since its defeat in World War 2, has adopted many Western attitudes and practices, a highly functional democracy among them. It also, through its wartime and pre-war imperialism, has earned the virtually undying hatred of China and Korea, among other countries in the region. What will its future be like in a world where China takes prime position over all of East Asia? Can it band together with anti-Chinese fellow coutries like Taiwan, Vietnam, South Korea, and Australia to create a balancing anti-Chinese bloc? That looks generally unlikely, partly due to negative US leadership, and partly due to the obvious problems it entails, ending in some kind of vast war.

China's sphere and local conflicts.

What China wants as the regional, even global, leader, is actually quite unclear. The history of Korea is instructive in this regard. China has been Korea's big neighbor for at least 2,000 years, and has repeatedly enforced vassalage, favorable trade, and cultural exchange. But it never took over and tried to exterminate Korean culture the way the Japanese did before World War 2. China clearly seeks control over some of its fraternal cultures, like the Tibetan and Uyghur, and now Hong Kong and ultimately Taiwan. But Vietnam? What China wants out of other nearby cultures such as Vietnam, Korea, and Japan is not entirely clear, and some kind of vassalage relationship may suffice. Perhaps seeing the Yuan as the reigning currency, along with other clearly friendly military and trade relations would be enough for long-term stability.

More darkly, some nations in Huntington's system are "torn", in that they partake of more than one culture and therefore face diffcult conflicts, internally and externally. Yugoslavia was an obvious example, but there are many others. Turkey is one, in that it has for decades tried to enter the EU and be a Western country. But with increasing Islamization, this is increasingly off the table, and Turkey is moving towards leadership as a modernizing influence within Islam rather than being a little fish in the EU and lapdog of the US security establishment. Russia has also made its definitive choice, after centuries of conflicting sentiments about the West, turning against a possible turn to NATO and the EU in the post-Soviet moment, and retrenching as leader of the Orthodox civilization. Was it ever realistic to think that Russia might become a normal, Western parliamentary democracy, after its communist collapse? Perhaps not, though our wretched economic advice surely didn't help.
 
Huntington closes on very Trumpian themes, warning that increasing Hispanic immigration to the US may make us into a "torn" culture, less cohesive in international and other terms. Multiculturalism is clearly the enemy. He spins a truly bravura dystopian scenario towards the end of the book, where China and Vietnam spark a world war (with some blundering US intervention) that spirals out of control, Russia and India allying with the West. The US is hobbled, however, by Hispanic dissention, which causes a lack of fighting resolve, and we settle for negotiation! Yikes!

Much of what Huntington wrote was quite precient, especially in the turns that both China and Russia have taken against the West and towards rebuilding their traditional geographic and cultural spheres of influence in clearly civilizational terms. He warns against American universalism- the idea that everyone wants what we want, we just have to invade their countries and give it to them. That way lies imperialism, pure and simple. And his warning about unity in the US is significant. We need to continue to expect and encourage assimilation of immigrants, not social and political balkanization. But it turns out that the principal risk of disunity in the US comes from the native rich, not the foreign poor. The logic of hyper-capitalism and its related ills of political and media corruption has created a plutocratic class that treats the rest of the country as a vulture capitalist project- a place for tax breaks, pet politicians, flagrant propaganda, and walled compounds served by a feudal workforce. That is what is killing our institutions and destroying our standing in the world.

• Sunk costs and lost souls- Trump's enablers.
• Such as Sessions. But GOP voters are just as complicit.
• Should Australia be independent?
• Man or woman?
• The rich getting richer...
• Small steps in the right direction.

A Crisis in Public Management

What is the common thread between the US SARS-Cov2 crisis and the Black Lives Matter movement? Dysfunctional public management.

It is curious how the George Floyd crisis came up during the Covid 19 pandemic. Were people a little stir-crazy? Perhaps. Were people fed up with the callous culture war being waged from the White House? Definitely. But I think there is more to connect these crises- deep problems in American public management. Our problem with the pandemic speaks for itself. While many other countries, large and small, have eradicated this virus and proceeded to re-open their economies, (Canada, New Zealand, Singapore, China, Taiwan, to name a few), we obviously have not, and continue to lead the world in new cases, day in and day out. What is wrong?

I think the main thing that is wrong is that our public health officials do not know what they are doing, and do not even conceive of the problem correctly. Their ambition has been to flatten the curve to reduce hospital congestion. This sentences us to, at best, a continous slow burn of viral cases, spiraling up when people get too careless, and quieting down after lockdown rules are re-instituted. It is clear that public officials completely lacked the ambition to fully contain and eradicate the virus. Doing that would require mobilizing an army of contact tracing and containment deputies, and enforcing quarantines on traced contacts, possibly with phone-based apps. We in Northern California had an ideal opportunity during the April-May time frame to fully control the virus. But did we? Not at all. The public officials contented themselves with testing and publicizing the daily trickle of cases, and having the police close public parks and other venues of congregation. Never was eradication even in the conversation, nor the appropriate powers and staff contemplated, as far as I can tell. Then, when the economic cost of even these half-hearted lockdown and distancing measures became too much, we re-opened, with the natural result of a rising tide of cases.

By not even conceiving that they should and could mount a total eradication campaign, our officials, from the local to the national levels, gave up before the game even began. And why was there this complete lack of ambition? First, we have not been used to this kind of disciplined, society-wide activity. Our social, not to mention political, system, is so atomized and uncohesive, dedicated to individualism, that an actually effective Chinese-style lockdown seems to have been inconceivable. But still, Canada has managed it at least partially- our closest neighbors, geographically and culturally.

Another obvious issue is the lack of a coherent health care system. The public health portion of it is an atrophied vestige, devoted more to bureaucratic stasis and policy quibbling than to actual intervention, uncertain whether it is a safety net for the poor, or a guardian for everyone. Higher officials should have realized that the given infrastructure would be and remains completely unable to mount the effort needed- which is thorough testing, contact tracing, and enforced isolation of contacts. A new organizational infrastructure needed to be built immediately, which was done in other countries, but not here. This is an obvious failure of public management, both in imagination and in execution.

In China, green means go.

Just as the pandemic shines a ghastly light on our public health organizations, the death of George Floyd, and the many prior cases of brutality and murder shines a similar light on another sector of public management- the police. Most police do great work in difficult conditions. Problems arise from a (large) sub-culture of callous disregard, inherited from Jim Crow and other authoritarian elements, combined with weak public management. One issue is unionization. Public employee unions have been toying with the electoral system for decades, running influential campaign ads and altering local elections and public policy to suit their interests. No wonder that we now have a public pensions crisis, absurdly early retirements, double dipping, secrecy for key records, and a litany of other abuses of the public purse and trust. Policies that make it virtually impossible to fire public employees are only one part of the problem, but one that is most central to the George Floyd case. Unlike the situation in public health, the rogue policemen are overzealous, rather than under-zealous. But the management issue is similar- who runs these organizations, do they have the full public interest in mind, whom do they serve, and do they have effective control over their employees? Answers to these questions are not pretty.

We are faced with two brands of corruption when it comes to public management. One is the Republican brand, which hardly cares about the public interest at all, only private interests. Anything they can do to drown the govm'nt in the bathtub, and allow natural feudalism to reign, giving social and economic power to the powerful, is OK with them. This means supporting white power and a traditional racial hierarchy, attracts sympathetic authoritarian types to police forces, and then winks at their indiscretions in enforcing the "natural" order.

The other is the Democratic brand, which cares so much about public service that it gladly ties itself up in knots of bureaucracy and procedure (and pensions, and consultants, and politically correct meetings, due process, and translators, and environmental review, and...) ending up incapable of accomplishing anything, or holding anyone to account. The Democratic brand is also pro-union, adding a whole other level of dysfunction and mismanagement to an already difficult situation. To bring in yet another example, the California high speed rail project is an object lesson in this style. Tens of billions of dollars have been poured down a bureaucracy dedicated to good pensions, due process, poor land acquisition practices, and continual underestimation of the fiasco they are participating in. The expected path of this train now looks more like an amusement park ride than a bullet train, and will only go from Los Angeles to somewhere in the central valley. As a citizen, it is incredibly frustrating to watch this waste and ineffectiveness.

The countries that have been most successful against Covid-19 have been the most cohesive societies, either by nature or by authoritarian force. Cohesiveness correlates with good public management, since it represents shared objectives and understandings about values and ways of doing things. Cohesiveness helps smooth the way between ideals and implementation. The US stands, clearly, as one of the least cohesive societies in the world, particularly after the trauma of the current administration. Is there strength in diversity? Up to a point. But there is more strength in unity.

• We are not good at collective action, at least these days.
• Public health.. what is that? Is it safety net care for the poor, or is it health for everyone?
• Thoughts on building better public institutions.
• Happy thoughts on the current administration.

How's Your Relationship With Jesus?

Review of American Gospel, Christ Alone- an evangelical hate letter to prosperity- and happy-gospel televangelists.

As an atheist, my relationship with Jesus is not very good. I regard him as historically questionable, and if a real person, then wildly misinterpreted and inflated by the subsequent mythological process that resulted in Christianity and Islam. Oh, and also dead, really most sincerely dead. But just for fun, I watched a film provided by my library- American Gospel, Christ Alone. It features a parade of mostly white evangelical male pastors excoriating the prosperity gospel- the Joel Osteins, Benny Hins and Creflo Dollars of televangelism. They get rather worked up- Why? Aren't there actual atheists and heathens about, or sick and destitute to help? As usual, internecine conflict is the most bitter (remember early Christianity, or the refomation and counter-reformation). It is about an attention market where conventional evangelicals, Baptists, etc. compete perhaps mostly closely and intensely with this other theology that is so uncomfortably close to their own. Though Mormons come in for a few potshots as well, as do Catholics.

For, did Jesus die for your sins, or your happiness? Is faith enough, or would a donation help? It is a fine line, really. Even if one takes the conventional, Lutheran attitude that faith alone, scripture alone, and Christ alone are sufficient for salvation and whatever else is putatively desirable in worshipping and satisfying god, why do we want to satisfy god at all, or want salvation, or want our sins redeemed? Might that be to make us happy? To be righteous, better than one's neighbor, part of the tribe, and to have that great insurance policy, heading to the big family reunion in the sky? There is no getting around the happy part of the gospel. It is supposedly good news, not bad. And the parts that are difficult, like giving up one's family and possessions, and waiting in penance for the end of the world? Well, who takes that seriously? Not the evangelicals.

Creflo Dollar freely misinterprets the Bible. "Provision" is no part of the original. Rather, the kingdom is heaven, and the very next verse is.. "Sell your possessions and give to the poor. Provide purses for yourselves that will not wear out, a treasure in heaven that will not be exhausted". But do the Evangelicals take this rank communism seriously either? Hardly.

The prosperity gospel may be gauche and low class, aimed like a heat-seeking missile at the downtrodden who need something a little more concrete to hope for than snooty biblical correctness and heavenly rewards. But it is not so far from the original message of Christianity, which offered a tight-knit community along with the sugarplums of heaven in return for the acceptance of Christ as one's totem in opposition to all the other totems available, particularly the official ones of the Roman Empire. And those early Christian communities were no monastaries. They were full of normal people, including merchants, who benefited from the commercial networks and moral creeds taking shape in this church. While the creed had an ideal of communism and anti-materialism, in practice it quickly came to an appreciation of money as a beneficence, for clergy, and for alms and other good works. Does that make money good?

There was a long tangent in this film about health and sickness. The prosperity preachers generally have a sideline in faith healing. Which is likewise low-class and disreputable. Evangelicals, in contrast, portray themselves as demurely thanking god for everything good that happens, and if in the mood, thanking for the trials and tribulations as well, all without expecting that prayer is going to help. Nothing so gauche as a transactional prayer! But lo, what happens after every tragedy and in every evangelical church? Thoughts and prayers go out to those in hardship, with a wink-wink that god presumably must be paying attention, big as "he" is. It may not be as callous as selecting the not-very sick for dramatic faith healings and speaking in tongues, but the principle is exactly the same. We pray, and someone should listen, and all that should lead to results, in a the world we want to see, hopefully here, but if not, then hereafter.

So, high or low, it is all equally nonsense in the service of personal comfort and mass psychotherapy, whether one has the fancy degrees to go with one's Biblical references or not. The film is positively crawling with citations- cherry picked quote after quote, to say (among many other things) that faith alone is sufficient, no dollars required to enter into heaven. But the televangelists have plenty of quotes too, and so do the Jews! Rather contrasting belief systems can all draw from the same well, and all the rhetorical hellfire and brimstone isn't going to resolve these endless contradictions. Second, and more important, what on earth does god want? That is what this whole drama is about. But after a god treats his originally chosen people with derision and scorn, then issues himself in human form to conduct some rather cryptic repentence preaching, and then has himself killed in grisly fashion in order to show the world that he is the soverign king of all creation... Well, no wonder there are various interpretations.

It is not a focus of this film, which is full of self-righteous pastors, but religious people often proclaim the inscrutability of god. And that would be a good place to leave the subject, rather than saying in one's next breath what god wants, how we miserable sinners are both so important to him (always him!) that we have to do what he or she says, but at the same time how complete he or she is, great, omnipotent, and omniscient, needing nothing whatsoever. The sheer idiocy of these contradictions and paradoxes are generally meant to cow the humble sinner under the eagle eye of the charismatic pastor. Heaven forbid that a thought enters one's head. For, back in the day, pastors used to be the most educated and intellectually capable members of society. Similarly, American protestantism has settled on having a "personal" relationship with Jesus, or, if one wants to be ambitious, with god. The therapeutic value of meditation, mantras, and lucid dreaming are real enough. But communing with dead people, voids, and imaginary friends? Really? It is a method of mass and self-hypnotic propaganda- pure nonsense.

So, spew vitriol on each other as much as they like, but what we are seeing here is simply upper-class versus lower class charlatanism at loggerheads. Conventional pastors uphold conventional (reformed) understandings, like our sinning depravity and undeserving natures that can only be saved by faith and repentence - that is what god wants. Since their parishioners tend to be well-to-do, conservatism is quite sufficient for this world, and faith can be directed mostly at the next. (Plus, the collection plates fill up without any crass appeals to transactional prayer.) But the unconventional pastors speak to a more downtrodden demographic. Sure, they prey on their hopes and dreams, but they also strengthen those hopes by saying that god is not the disinterested, damning character you hear about in mainline churches. No, he is powerful, and healing, and helpful.

The film ends with the wife of the producer proclaming that despite her many health woes, (which she wouldn't dream of asking god to fix!), she knows Jesus is in her heart, and that makes her super-happy. That, and having a delightful house, husband, and kids. Oh, and a tube sticking out of her nose, presumably for oxygen, and some more tubes out of her insides, for feeding. But thankful for all the clever people who researched the feeding mixture, and invented the tubes, and manage their sterility, and who performed the operations, and who serve her at the hospital? Not a word about all that. It is Jesus in her heart that she is thankful for. And by the way, they could use some money.

• Enter your prayer request here, and god will answer.
• BBC looks askance.
• Christianity Today is alarmed. And no, God does not want you to be happy.
• Treatments for Covid-19 will probably save us before a vaccine does.
• People who know, know creeping fascism.
• Recessions are damaging and unnecessary.
• What it is like working for a weasel. Or being an idiot.
• History and Henry Wallace.
• Why aren't the gun nuts equally vociferous about women's rights against state interference on their most personal and significant actions?

Atlas of Political Correctness

An appreciation of Cloud Atlas. (Spoiler alert!)

I recently happened across the 2012 film "Cloud Atlas", which must be one of the baggiest films ever made. Even reading the plot on the Wikipedia page leaves one befuddled. Yet it was great fun to watch, clearly an actor's feast and treasury of tropes and cultural references, six films packed into one. It is typical for science fiction films now to have huge ambitions and let plots go wild, sacrificing coherence for short-term motivation and effects. No reference to 2001 here- that would have been a harsh comparison, and overly optimistic.

The ensemble of actors get to play many roles, some have parts in each of the six stories set in different time periods. But no one crosses type. The good characters are always played by one set of actors, the bad guys by the other set. Nurse Noakes of the prison-like nursing home, in an inspired bit of cross-dressing, is played by Hugo Weaving, who also plays the killer Bill Smoke and the future executioner Boardman Mephi, among others. This helpfully keeps at least the good-guy/bad guy valence coherent, even as the rest of stories hop-scotch about wildly in time and place.

And what places! There is a matrix-like high-tech future dystopia, and even more dystopian low-tech lord-of-the-flies future beyond that, a seventies streets-of-San Francisco, Victorian shipping, wartime England, and the present. A grab-bag of well-worn settings, vivified by enthusiastic acting and propulsive, if perforated, plots.

Everything is confused. This DVD cover hints at the sprawling mess the Wachowski brothers attempted to bring to the screen.

So what is it about? Each story has a basic good versus bad armature, whether of vast world-spanning oppression countered by a Zion/Keanu Reeves-style resistance, an oil industry plot to blow up a nuclear reactor, countered by a journalist, or an evil Hugh Grant who tries to lock up his brother in a nursing home, which the latter escapes in a crazy escape and chase sequence. The various worlds / times are tenuously linked by readings from their respective pasts. The farthest future uses a climactic speech from the Zion-like resistance as its scripture. The Zion resistance watches the nursing home caper for entertainment. And so forth. The real connections, however, are the politically correct tropes of contemporary movie making. The heroes are all good, the villains are all bad, and each is ready identified (cue music) whatever the age we may be in.

The relentlessness of this good/bad dichotomy easily knits the whole thing together even without an identifiable plot, yet is also a glaring philosophical weakness. We watch movies to be uplifted and gain some hope in a difficult world, and generally expect and deserve a happy ending. But films such as these prompt the question of why... Why are bad people so common throughout the ages? Why do they dominate epoch after epoch, world after world, when every single person in the audience is cheering for the good characters, not the bad? Isn't there something deeper to be said? Indeed, isn't this easy, Zoroastrian / Manichean dramatic dichotomy damaging to a mature understanding of the world and of ourselves?

If we simply cheer for the good, and from such flacid moral exercises believe we are good, doesn't that lead right to the moral blindness that these movies try so strenuously and earnestly to "address"? Doesn't it contribute to various unwoke blindnesses like white priviledge and American exceptionalism? Unless we interrogate our own involvement in evil, the needs and compromises we routinely make, which lead through the many white-washed, green-washed, and theo-washed institutions of greed and tribalism to all the bad effects we decry in the world around us, we have not gotten very far.

• Language of fascism.
• Our position as most feudal country in the developed world.
• Lessons in Ebonics.

The Silicon Age

This magical element brings us the modern age- in computation, and in power.

In geologic terms many regard the current epoch as the Anthropocene, based on our various far-reaching (and often obscene) effects on earth's biosphere and geology. But where are we in the sequence of cultural epochs, starting from the stone age, and continuing through the bronze and iron ages? This somewhat antiquated system of material culture-based divisions seems to have petered out with the iron age, about 500 BC. What came after? There was certainly a technological hiatus in the West (and perhaps elsewhere) around the dark ages, where iron remained the most advanced material, though one might make a case for concrete (a Roman invention, with extensive use in antiquity), glass, or porcelain as competitor, though the latter never had the broad impact of iron.  The industrial age was perhaps founded on steel- the new material that brought us well into the twentieth century, until we hit the atomic age, an age that did not age well, sadly, and seems to be headed for the scap heap- one that will be radioactive for eons.

Now we are clearly indebted to a new element- silicon. That it is the magic ingredient in computers goes without saying. But now it is also providing the power for all those computers, in its incarnation as solar cells, as well as light for our lives, as efficient LEDs. It is incidentally intriguing that silicon resides just one row down, and in the same column, from the central element of life- carbon. They have the same valence properties, and each have unusual electronic properties. For silicon, its magic comes from being a semiconductor- able to be manipulated, and in switchable fashion, from conducting to insulating, and back again. A magic that is conjured by doping- the peppering-in of elements that have either too many valence electrons (phosphorous; n for negative) or too few (boron; p for positive). Too many, and there are extra electons that can conduct. Too few, and there are positive charges (holes) that can conduct similarly.

Charge and electrochemistry across the p-n junction.

At the interface between n and p doped zones something amazing happens- a trapped electrical charge that forms the heart of both transisters and solar cells. The difference in composition between the two sides sets up conflicting forces of diffusion versus charge. Electrons try to diffuse over to the p doped side, but once they do, they set up an excess of electrons there that pushes them away again, by their negative charge. Holes from the p doped side likewise want to migrate over to the n doped side, but set up a similar zone of positive charge. This zone has a built-in electric field, but is also insulating, until a voltage going from p to n, which squeezes this zone to smaller and smaller size, making it so narrow that charge can flow freely- the diode effect. The reverse does not work the same way. Voltage going from n to p makes this boundary zone larger, and increases its insulating power. This, and related properties, gives rise to the incredibly wide variety of uses of silicon in electronics, so amplified by the ability to do all this chemistry on precisely designed, microscopic scales.

Solar cells also use a p-n doping regime, where the bulk of the silicon exposed to the sun is p-doped, and a small surface layer is n-doped. When a photon from the sun hits the bulk silicon, the photoelectric effect lets loose an electron, which wanders about and meets one of two fates. Either it recombines with a local atom and releases its photon energy as infrared radiation and heat. Or it finds the p-n junction zone, where it is quickly whisked off by the local electric field towards the positive pole, which is all the little wires on the surface of solar panels, taking electrons from the n-doped surface layer. The p-n interface has a natural field of about 0.6 volt, which, when ganged together and scaled up, is the foundation for all the photovoltaic installations which are taking over the electric grid, as a cheaper and cleaner source of electricity than any other. Silicon even plays a role in some battery technologies, helping make silicon-based solar power into a full grid power system.

Solar power is scaling to provide clean energy.

Silicon gives us so much that is essential to, and characteristic of, the modern world. Like carbon, it is very abundant, not generally regarded as rare or precious. But that doesn't mean it lacks interest, let alone importance.

• Green hydrogen- a way to use all that excess solar.
• Generic drugs from India and China: rampant fraud.
• Meanwhile, an outstanding article describes the slow destruction of US pharmaceutical and public health capabilities.

The Music in my Head

Brain waves correlate with each other, and with cognitive performance.

This is a brief return to brain waves. Neural oscillations are low-frequency synchronized activity of many neurons, from the low single Hz to 50 or 100 Hz. They do not broadcast information themselves, as a radio station might. Rather, they seem to represent coalitions of neurons being ganged together into a temporary unified process. They seem to underlie attention, integration of different sensory and cognitive modes, and perhaps subjective "binding". A recent paper provides a rare well-written presentation of the field, along with a critical approach to correlations between waves coming from different places in the brain. They also find that strength of oscillatory coupling correlates with cognitive performance.

The issue they were trying to approach was the validity of cross-frequency coupling, where a rhythm at one frequency is phase-coupled with one at a higher frequency, at some integer difference in frequency, like 1:2. (In other words, harmony was happening). Such entrainment would allow fundamentally different cognitive processes to relate to each other. They study two different types of correlation- the straight frequency coupling as above, and a phase-amplitude coupling where the amplitudes of a higher frequency oscillation are shaped to resemble a lower frequency wave. This resembles AM radio, where the high-frequency radio signal "carries" a sound signal encoded in its rising and falling amplitudes, though its frequency is completely stable. This latter form of coupling was more difficult to find, analyze, and in the end failed to have significant functional consequences, at least in this initial work.

Cartoons of cross-frequency couplings (CFC, aka harmonies) that were investigated.

The authors' first goal was to isolate gold-standard couplings, whose participating waves come from different locations in the brain, and do not (respectively) resemble contaminating similar waves inherent in the complementary location. After isolating plenty of such cases, they then asked where such phenomena tend to take place, and do they correlate with function, like performance on tests. They used resting brains, instead of any particular task setting. This makes the study more reproducible and comparable to others, but obviously fails to offer much insight into waves as they are (if they are) used for critical task performance. Resting brains have an ongoing hum of activity, including a well-known network of waves and frequency couplings called the default mode network. Going past the authors' statistical analysis of maximally valid correlations, they found a variety of "hubs" of cross-frequency coupling, which had an interesting nature:

"In α:β and α:γ CFS, the α LF hubs were observed in PFC and medial regions that belong to the default mode network [29] or to control and salience networks in the functional parcellation based on fMRI BOLD signal fluctuations [94–96]. This is line with many previous studies that have found α oscillations in these regions to be correlated with attentional and executive functions [14–19]. In contrast, the β and γ HF hubs were found in more posterior regions such as the SM region and the occipital and temporal cortices, where β and γ oscillations are often associated with sensory processing"
Alpha, beta, and gamma are different frequency bands of neural oscillations. CFS stands for cross-frequency coupling. LF stands for the low frequency partner of the coupling, while HF stands for the high frequency partner or source. PFC stands for the prefrontal cortex, which seems to be a locus of relatively low frequency brain waves, while the sensori-motor (SM) regions are loci of higher-frequency activity. This is interesting, as our brains are generally filters that gather lots of information (high frequency) which is then winnowed down and characterized into more abstract, efficient representations, which can operate at lower frequency.

And does more correlation in the resting state mean better brain performance when doing tasks? These authors claim that yes, this is the case:

"CFS between θ–α with β–γ oscillations (θ–α: β–γ CFS) and CFS between β and γ oscillations (β:γ CFS) showed significant positive correlations with scores on Trail-Making Tests (TMTs), which measure visual attention, speed of processing, and central executive functions, as well as with Zoo Map Tests, which measure planning ability (p < 0.05, Spearman rank correlation test, Fig 8). Intriguingly, negative correlations with the test scores were observed for CFS of α and β oscillations with higher frequencies (α–β:γ) and for γ:Hγ CFS in the Digits Tests measuring WM performance.
...
These results suggest that in a trait-like manner, individual RS CFC brain dynamics are predictive of the variability in behavioral performance in separately measured tasks, which supports the notion that CFC plays a key functional role in the integration of spectrally distributed brain dynamics to support high-level cognitive functions."
RS refers to the resting state, of the subjects and their brains.

It is exciting to see this kind of work being done, gaining insight into information processing in the brain. It is an opaque, alien organ. Though it houses our most intimate thoughts and feelings, how it does so remains one of the great tasks of humanity to figure out.

• For fun, what do these frequencies sound like?
• We still need answers.
• ... not a corrupt whitewash.
• The fat blue line.
• Plus a few lies.
• Tables are turning.
• How did all these little Hitlers pop up?

Eating the Wild Things

Despite humanity's long tradition of eating wildlife, it is high time to rethink it as a practice. 

The coronavirus outbreak certainly gives one pause, and time to think about what we are doing to the biosphere and to ourselves. It also makes one wonder about the wisdom of killing and eating wildlife. I have been reading a book about a different disaster, the struggles of the crew of the ship Essex, back in 1820. This Nantucket-based factory ship was hunting whales in the middle of the Pacific when, in an ironic, yet all too-rare turn of events, a huge male sperm whale rammed and sank the mother ship as the smaller whaleboats were out killing its relatives. Months of drama, extremity, and cannibalism ensue, (for the humans), after which a fraction of the crew survive to tell the tale. It seems to us now bizarre, and beyond wasteful, that street lights in Nantucket were lit with whale oil, and that people would sail all over the world's oceans just to kill whales for the oil in their heads and blubber. Humans have an instinct for survival, and for the most concentrated source of various goods, and, whether under the colors of capitalism or simple greed, think little of externalizing costs, no matter how brutal and far-reaching, whether eating each other, "fishing out" some rich source of food, causing extinctions, or setting Charles island of the Galapagos ablaze in an inferno (another episode that occurs in this ill-starred history). One must be "hard" in this business of living, after all.

Well, we can do better. Now, two centuries on, we are still abusing the biosphere. Some ways are new, (climate change, plastics, insecticides), but others are old, such as over-fishing. Factory ships are still plying the great oceans of the world, vacuuming up wild animals so that we can eat them. And not just do they derange whole ecosystems and litter the oceans with their waste, but they also kill a lot of innocent bystanders, euphemistically called "bycatch"- sea turtles, albatrosses, dolphins, whales, etc. Albatross populations are in steady decline, from very low levels and heading towards extinction, for one main reason, which is the fishing industry.

This simply has to stop. It is a tragedy of the commons, on a collossal scale, all for the atavistic desire to eat wild animals. Human overpopulation, coupled with technology, means that no wild animals stand a chance in an unregulated environment- not in Africa, not in Brazil, and not in the international oceans. We are killing them by a thousand cuts, but do we also have to eat them, as the final indignity and form of waste?

If we want to save the biosphere from utter impoverishment, humanity needs a change of heart- an ethic for keeping the wild biosphere wild, rather than running it like so much farmland, or so much "resource" to be pillaged, whether "sustainably" or not. Obviously, eating meat at all is a fraught issue- ethically, and environmentally. But surely we can agree that wild animals, and wild ecosystems, deserve a break? Conversely, where we have so screwed up ecosystems by eliminating natural predators or introducing invasive species, we may have to kill (and yes, perhaps eat) wild animals in systematic fashion, to bring back a functional balance. Go to town on feral hogs, boa constrictors, Asian carp, etc. (But try to do so without poisoning yourselves and the evironment with lead.) The point is that we are stewards of this Earth now, like it or not, and ensuing generations over the next hundreds and thousands of years deserve an Earth with a functioning biosphere, with some semblance of its original richness.

• Lying is a weapon of war.
• It's the same old Pakistan.
• Astronomers take a whack at the virus.
• What to do after the protests. And then prohibit public employee unions from corrupting political campaigns. And then prohibit all other special interests from corrupting campaigns as well, for good measure.

Iran: Object Lesson of the Enlightenment

Review of Iran: A Modern History, by Abbas Amanat. Part 2- the contest between autocracy, democracy, and theocracy.

Has history ended? Did all countervailing ideologies give up and yield to democracy as the universal form of government and does peace now reign? Apparently not. Indeed, democracy is embattled in many areas as it has not been in decades- even in the US, whose institutions are under sustained attack by a renascent autocratic / plutocratic coalition. Iran has exemplified the contest between the ideals of democracy, human rights, state stability, authority, and religious sentiment in ideologies of government over many centuries. It has been positioned at some remove from, though in durable if not tragic contact with, the European cultures that fostered the Enlightenment in all its aspects. What has been their impact, and what are we to make of the current result?

Amanat provides a magisterial overview of Iran's recent history, (recent meaning since 1500, which leaves out a vast portion going back to antiquity and beyond), focusing on its political systems as they range between autocracy and revolution, growth and decline, consolidation and decadence. Iran was heavily influenced by Europeans starting in the mid-1800's, as the great game got underway. While Russia was unapologetically autocratic, making its menace clearly lineal with previous contests against other invaders, Britain, and later the US, brought a new level of hypocrisy as imperial powers founded on Enlightenment ideals and practices, which were, however, not for foreign consumption.

The Qajar monarchy in the 1800's managed a weak position relatively well, keeping Iran intact and largely sovereign, if also continually corrupt, indebted, and backward. But finally, the modernist winds were too strong, and a constitutional revolution established a constitutional monarchy and parliament in 1906, then again in 1909. This parliamentary system never fully found its footing, however, tussling with the Shah for power, and buffeted through disastrous invasions and occupations during world war 1. It was sort of a Weimar Republic, never attaining full power in military or political terms.

But it embodied the idea of a Western-style, constitutional, democratic system. The addition of an Islamic advisory council was an afterthought and never seriously implemented during this era, since the ulama, or community of clerics, was generally content with its long-standing role of loose collaboration with the secular power, tending to a narrow sector of jurisprudence over religious, business, and personal matters, on a somewhat freelance basis. While the Shi'i clergy had occasionally led protests and fostered limited political activism in the face of gross injustices and suffering from their base among the small merchant class and urban poor, the idea of becoming a full partner in government, or its comprehensive adversary, did not cross their minds, since government was fundamentally unclean and not worthy of theology, short of the return of the twelfth Imam. The clerics were also fully invested in the somewhat corrupt system, having gotten quite rich from their segment of the economy.

But the trauma of the Pahlavi era, broken in the interval between father and son by a hopeful but chaotic constitutional period under Mohammed Mosaddegh, set the clergy- at least some of it- on a more activist path. Both Shahs were dedicated modernizers, dismissive of religion and destructive to the livelihoods and institutions of the clergy. Along with other islamists in the Sunni world like Qutb, they (that is, the less quietist elements, spearheaded by Ruholla Khomeini) started generating a comprehensive critique of modernism, the Pahlavi apparatus, and the West as antithetical to Islam, which it quite obvoiusly was and remains. They found that they still had enormous political power and public sentiment on their side, not among the intelligentsia, but among the common people who had been coming to the mosques, and requesting judgements, and paying their dues all along. All this was seized by Khomeini, who in 1963 gave fiery sermons denouncing the Pahlavi regime, and was duly detained, almost executed, and then exiled to Iraq. The Shah ran an economically successful few decades, but also a brutal secret service and a grandiose view of himself and the dynasty so severely out of step both with native sentiment and with the democratizing / human rights trends in the West, suddenly put on the top of the table by Jimmy Carter.

Faithful Shi'ite Iranians were interested in more spiritual fare than what the Shah offered, and the clerics, through Khomeini, gave them visions of an ideal society, rectified through "dear Islam" to resolve all the injustices and degradations of the Pahlavi era. In return, Khomeini was first elevated to the unprecedented status of "Grand Ayatolla", and then ultimtely to "Imam" status, which had never been done before, the twelfth Imam having been the last of the set, now in occultation. So the revolution rolled on with inexorable power, but also with inexorable revolutionary logic, piling up bodies and hypocrisies as the imperatives of staying in power overwhelmed all other scruples. For example, Amanat mentions with some acidity that, while centuries of Shi'i jurisprudence may not have foreseen the problems of writing a constitution, running foreign policy, or operating a secret service, it had long dealt, and dealt with care and discretion, in contract and property law. But all that went right out the window as the new government "inherited" or expropriated countless businesses and personal properties, took over all major industries of the country, and distributed their management to family members, cronies and loyalists.

Diagram of the Iranian government, from the BBC.

It is through the lens of the constitution and the cobbled institutions that have arisen in Iran that we can see the dialectic between Enlightenment principles and Islamic principles. Khomeini promised a democracy, where power would no longer be monopolized by a somewhat mad Shah. But it also had to be an Islamic democracy, "guided" by the clerics to retain purity and justice. The logic of all this resulted in a thoroughly theocratic state, where there is an interlocking set of instutions all run by the clerics, from the Supreme Leader to the Guardian Council, Assembly of Experts, and Expediency Discernment Council. Each are supervisory, with various veto and appointment powers, leaving the popularly elected parliament with little real power or even representative complexion, since its candidates are routinely disqualified by the Guardian Council for not being conservative enough.

In practical terms, this means that the system maintains just enough democracy to foster some hope and buy-in from some of the populace, while keeping complete control in the hands of the clerics. Will this end in utter corruption of both religion and government? It is difficult to say, but Iran has more of a functional democracy and republican system than many other Muslim countries, which is sadly not saying much. Those who reflect on the very origins of Islam and Shi'ism can readily see that theory of government is not a strong suit of this tradition. I see Khomeini as a demagogue- a Trumpian figure who promised the stars, offered a telling and comprehensive critique of the Pahlavi system, and had a genius for turning a phrase. But he did not promise a coherent and democratic program of governance, rather a messianic dream and relentlessly divisive politics. In the revolutionary process, he always played to the base, favoring extreme positions. A base whose core, there as here, is a religious element of great patriarchial conservatism and dismissive of intellect and compassion. He was fully behind the hostage-taking students, for instance, which solidified support at home while making Iran a pariah abroad.  Hate, of course, was and continues to be central to the Iranian theocracy, from the Great Satan (us), to the little Satan (the Iraq of Saddam Hussein), to the communist Tudeh party, to the Baha'i religion, which they particularly revile and persecute.

At first, the clerics worked with liberals to fashion a written constitution (a significant concession to modernity and Western ideas) and a civilian government. But as time went on, the many contradictions of this approach became apparent, since if the people were given real power, the clerics would lose theirs- that was a lesson of the first constitutions of the early 1900's, and again during revolutionary process in the 1970's and 80's, which saw many contestants for power. The clerics only won due to their cohesion and their ability, time and again, to move the masses with demagogic and messianic appeals.

So the Iranian clerics ended up in unknown territory, creating a government that had no Persian or Koranic precedent, other than putting clerics in charge of everything (including at the top, the monarch-for-life Supreme Leader), and hoping that their own formation, training, and institutions will keep them uncorrupted. At one dire point in the revolution, a hanging mullah suggested that his rather under-supported decisions didn't matter that much, since God would sort it all out in the end, sending those who deserved it to heaven. But by that logic, he should have killed himself first. It is always curious how those who supposedly believe in religion and the glories of its afterlife turn out to have a strong regard for their own lives in the here and now. One would think that meeting one's maker would be a more positive goal, rather than being a mere scrim for power politics in this fallen world.

Iran gets ranked just above China in the democracy index.

Anyhow, Iran has ended up with more torture, more executions, more war, a bigger secret service, a more intrusive state, and less freedom, than the Pahlavi era. It turned out that Islam is not a guarantee of good, let alone moral, governance. Islamic countries generally occupy the lower rungs of the democracy index, and other indexes of development and happiness. This while Islam portrays itself as a religion of peace, of mercy, and of the most exacting jurisprudence and scholarship. The revolutionary government of Iran dabbled in liberalism, and wrote up a semi-democratic constitution, and faced a culture of great diversity and intellectual depth. But in the end, authoritarian logic won out over traditional Shi'i quietism and over most Western trends, creating a sort of Shi'i Vatican writ large, with opaque committees of old bearded men running everything, with additional torture chambers and gallows.

Iran offers an object lesson why the interlocking lessons of the enlightenment are so important- why withdrawing religious projections, drama, and righteousness from the state, in favor of civic secularism, yields a more rational and humane way of life. Why even the most long-standing and cherished religious traditions and "scholarship", while they may serve as selective institutions to weed out the stupid and socially unskilled, are not conducive to the search for objective truth or even a marker of moral superiority.

All that said, the French revolution began with enlightenment principles, which did not prevent a similar revolutionary logic from sending it to appalling depths of brutality, injustice, and authoritarianism. Yet it also spread more liberal, anti-monarchical values throughout Europe during the Napoleonic era, and ended up, after decades of historical development, with true democracy in France and Europe. The whole point of political theory in the Enlightenment was to allow such development via a fundamental humanism and humility in the civic sphere and the state. Its antithesis is messianism of various sorts, from communism to Shi'i theocracy, (even atheist enlightenment, when driven to extremes!), which drives polarization, extremism, and totalitarianism. Iran may yet develop in a softer direction, after what is now forty years of theocracy, but that would take a substantial change of heart on the part of the current ruling class, and perhaps a reduced allergy to Western ideas.

• Happy Quds Day!
• Changing conceptions of masculinity...
• Right wing legal community is going over the deep end.
• It is not clear that California is ready to re-open. Graph of the week: