"I Think the Second Amendment is There For a Reason."

A Senator alludes to insurrection against the state he is sworn to uphold.

This is not a new phenomenon. Before the Civil war, many senators and other politicians from the South tried their best to undermine the federal government, going so far as to capture armories and other supplies for the looming conflict. Today, a similar mind-set arises from similar sources- the Southern and Southern-inspired strategists of "State's rights" and a new decentralized feudalism. On guns, their argument is that the free ownership of guns allows the insurrectionists a fair chance against a totalitarian state, much as the original colonists waged a guerrilla war against Britain.

One first question is - in what way is our democracy defective? Does it over-represent the totalitarian, state-centered interests? Only if one construes those to be represented by the Republican party, ironically. Does it over-regulate and construct collective and long-term interests against the wishes of short-term greed and small-minded ideologues? Yes, it certainly does, but we have the "democratic" process to thank for a dramatic pushback, in the form of unchecked spending by corporate and other greedy interests, flame-throwing conservative media, plus the Russian government. It is hard to see where these complaints can find purchase, in such an atmosphere.

A second question is, even supposing that our state is or could be tyrannical in some irremediable way, where does one draw the line on armaments? What arms are valid for this hypothetical use, and which are not? We all seem to agree that nuclear bombs are not proper for civilian use. But why? Is it that the danger they pose is far beyond what is reasonable to put into the hands of one person, without some organized institutional oversight? Is it that we do not want to live in a MAD society, each armed to the teeth, in a petrified defensive crouch, waiting to see what the next madman will do?

This logic applies down the line to other military weapons, naturally, given that our fellow citizens (even presidents) are not to be relied upon to be uniformly sane and good-natured. Great firepower implies great danger and great responsibility. Where do machine guns fall in this scale, for that is what the semi-automatic and other assult-style weapons amount to? Obviously, in light of the many mass shootings in the US over recent years, they fall into the dangerous class of weapons that should be restricted to organizations with structured oversight. That, of course, was the original meaning of the second amendment, with its justification through an organized, state-supporting milita, something which has been lost on our Supreme Court, not to mention our rabid gun nuts.

The Civil war should have disabused our home-grown insurrectionists from any notion of armed resistance against whatever bogeyman they make the "guvmint" out to be. People power is the only effective power. They can never win without a political movement. Their arms are merely a fascistic decoration, not an effective form of policy. That we let off the Bundy gang so lightly was a travesty, both legally and politically. But their intended revolution against government control of government lands never took off on a popular, armed basis, and now is being accomplished from the inside, in the new administration, via the "democratic" process.

There is a mental health issue afoot, and it is that people with military-grade guns are mentally ill, as are open-carriers and other maximalist acolytes of the NRA. These attitudes are uncivil, insurrectionary, and deranged. The idea that others will be politically and socially intimidated by their weapons and various forms of rage is absurd and insulting, apart from spineless politicians, who don't seem to understand the first thing about our constitution, their duties, or statehood in general.

• Pakistan is still at it. Not even Trump lies quite like the Pakistanis lie.
• An infrastructure nothing burger.

Too Damn Many People

We are in a population crisis.

Virtually every serious crisis we are experiencing now, from anti-immigrant attitudes, to climate change, lack of housing, homelessness, inequality, warfare, drought, desertification, traffic, scarcity of natural resources, and loss of wildlife, share a common root cause of overpopulation. Like any wonderful thing, it is the dose that makes something great turn into something less great.

The top line of damage is of course environmental destruction. In the last 50 years, the population of wild animals has fallen by half. CO2 in the atmosphere has doubled, which promises an eon of pain for the biosphere. The oceans are awash with trash, and all habitats from the arctic, to prairies, coral reefs, and rainforests are either being directly destroyed by humans and / or are being impaired indirectly by our global effects.

Summer arctic sea ice in dramatic decline.

Politically and socially, the idea that Europe should welcome millions of refugees from Africa and the Middle East, driven themselves by environmenal degradatation and overpopulation, and the conflicts they generate, is creating an understandable backlash. Just as global heating is reducing water and arable land, populations are growing all over these regions due to a modicum of medical and agricultural technology, combined with lack of human development. But is further human development the answer? From an environmental perspective, hardly- while development typically reduces birth rates, it explodes appetites and capacities to degrade the ultimate resource- the Earth- its minerals and biosphere.

An example is China. China carried out one of the most important environmental policies of all time when it instituted the one-child policy. It was, thanks to its draconian nature, effective in keeping population growth under control. Now China has a billion more people than the US, but it could easily have been two billion, in far more miserable condition. It played a big role in enabling the ensuing economic development, which has made China the biggest emitter of CO2 in the world, and generated countless other environmental problems, of global as well as local scope. They are building coal-fired power plants at a breakneck pace, and will be almost doubling worldwide coal-fired power capacity over the next decade or two. This is not driven by population, but by development of existing populations.

We are living far beyond the carrying capacity of the Earth, and our long-term choice is to either live sustainably or to have fewer people. Both seem impossible options, given that true sustainability is far more arduous than what any country has attempted to date, and is very hard to envision. Carrying capacity has many different aspects, from aesthetic features that come with a healthy biosphere, to critical minerals, water supply and agricultural capacity. Each of these has different relations to human population, and different elasticities based on our needs and technology. But we can safely say from the many ways we are degrading the global environment that we are well beyond many individual capacities, especially those that pertain to the biopshere in general, and animals other than ourselves.

Population is unfortunately, precisely the area where we care least about others. Our desires for family and legacy are very personal, often construed as a human right of some sacred or sovereign nature. But summed over the globe, it amounts to another tragedy of the commons, where my chastity merely makes room for someone else's profligacy.

There is no population bomb in the traditional sense. The agricultural technology we have, and the economic systems that drives its use, will insure all can be fed to some degree. There is a bomb, however, in a larger environmental sense. The degradation of the biosphere by humans is a slow-motion attack, as though several nuclear bombs were unleashed every year, rendering large areas uninhabitable, and sprinkling the rest of the globe with all sorts of trashy, choking fallout. These bombs are going off steadily and silently, year in and year out, till we will end up living in a global trailer park.

• Sectarianization?
• Economic injustice? We are great again.
• Very little wage growth here. Economic graph of the week:

Touch the Pressure Sensor

The revealing structure of one pressure-sensing protein complex.

The sensation of touch is perhaps the most elemental, and the most wide-spread, in nature. And detecting pressure doesn't just function in conscious sensation, but in all sorts of other processes such as, proprioception in muscles and joints, kidney function, red blood cell shape maintenance, blood pressure regulation, pain, bone maintenance, cancer cell invasion, neural development, and embryonic development generally, where bulging, shape changes, and migration are all guided by mechanisms that sense pressure inside and between cells.

Thus it is no surprise that we have numerous pressure sensors in our genomes, of various types. The sensors involved in hearing (TMC1 and TMC2) are different from a series of sensors involved in touch, (TREK-1), which are different from those responsible for organ shape and development. One thing they all share, however, is that they are cation channels. That means that deformations in the membrane they lie in, or other attachments they may have, get translated into a rush of potassium or calcium ions, out of or into the cell, respectively. This leads either to direct membrane depolarization (potassium ions), or signal propagation (calcium) via other proteins and channels.

A recent paper (review) detailed the interesting structure of PIEZO1, which is in a recently-discovered family of mechano-sensors that function in organ development and maintenance, conduct cations, mostly potassium, when activated, and directly (though briefly) depolarize membranes they reside in. While all membrane proteins are affected by membrane stretching, and there are simpler ways to translate mechanical stress into channel opening, PIEZO1 shows a rather intricate structure that allows exquisite sensitivity and control of its channel.

Top view, and side views of the PIEZO1 mechanosensory ion channel. In cells, the top faces the cytoplasm.

The first thing to notice is the dramatic, classic, maybe even Star-Treky, triskelion structure adopted by the trimeric protein. The authors note that they did not even see the entire protein, and that there should be twelve more helices extending out on each arm beyond those here that we can see, which are flapping in the breeze, so to speak. Second is the knot of protein in the center, above the plane of the rest of the structure. The actual channel is deep within the convergence zone of the three arms, so is far away from the protein knot, which extends intracellularly. This structure was derived from electron microscopy, which has begun to overtake X-ray crystallography as a method for structure determination, and the authors provide an averaged overview of what they were looking at, below.

Averaged electron micrographic view, without the inferred atomic modeling shown above. Scale bar is 10 nm.

Here, the arms are looking much more like a membrane interface, and the structure as whole clearly forms a cup that pre-deforms the membrane in a way that then makes the detection of membrane stretching even more sensitive than it would otherwise be. The authors spend much of the paper showing that this is the case- that in artificial vesicles, one can see PIEZO1 deforming the local membrane quite dramatically. One can easily see how this would make membrane stresses easier to sense.

Model of the channel (gray) surrounded by key protein structures, including negatively charged Glutamic acid (E) at the most constricted point, where opening is predicted upon membrane tension.

As for the actual channel, they provide a structure that narrows down to nothing at the bottom (E2537, showing the red negatively charged ends of glutamic acid). Clearly their model is of a closed version, which makes sense given the relaxed conditions used for visualization. Opening awaits some stretch on the overall structure that will pull these protein structures apart slightly, but not too much- enough to allow a four Ångstrom opening, as estimated from studies of the channel's conductance.

Another key part of the structure is the long helix running from the bottom, near the ion channel to about halfway along each triskelion arm. They seem to be key "beams" that transmit leverage from tension-induced membrane flattening towards the center nexus where this channel constriction is so obvious. As the authors put it ("TM" refers to transmembrane alpha helix domain, of which there are 38 in all per monomer):

"At first consideration a force directed along the triskelion arms toward the center of the trimer, associated with flattening of Piezo’s arms, might be expected to constrict the pore further. However, given that TM37-38 are domain-swapped relative to TM1-36, such a force will more likely push the ‘swapped’ pore-lining helices away from the center and open the pore."

That is to say, the beam helices at so long and subtly connected to the pore that they push cross-wise from the three directions, pulling the channel open instead of pushing it closed. This putative mechanism helps to some degree also to isolate the pore from the activating force, limiting its opening so that it can be ion-selective and have high, but limited, conductivity while open, all with super-high sensitivity. There are examples of stretch activated channels from bacteria whose function is to relieve turgor pressure stress, and whose opening is virtually unlimited under stress, becoming completely non-selective in what they allow through, which is very effective for their stress-relieving role.

This is a beautiful and informative structure. It shows yet again that underlying the magic and mysteries of biology is always structure and chemistry. Defects in these types of channels are responsible for a wide range of problems. Complete deletion of this gene (PIEZO1) in mice is rapidly lethal soon after the heart begins to beat, since the nascent vasculature is deranged, not being able to sense fluid pressures. The same gene is key for neural cell development and pathfinding. It also plays a central role in helping red blood cells know and regulate their pressure status, which is key to their function and survival as they squeeze through tight spots and get jostled by turbulent flows.

• On neoliberalism. With an example.
• Afghanistan- not going so well. Reminiscent of Vietnam, the countryside is slipping away, due to pervasive corruption.
• Things are not working so well here, either.

Vietnam: the Good Fight

Maybe not wise or practical, but morally, Vietnam was justified, especially in hindsight.

It was culturally traumatic, and militarily disastrous. It was a collossal mistake and soure of bitterness for decades. The Vietnam war remains a touchstone of shame and division in the US; a toxic and momentous legacy in Vietnam itself. I saw the first several episodes of Ken Burns's treatment of how we got into that war, and found it very interesting, historically. The documentary's tone was drenched with sadness and tragedy. But it also let some significant facts leak in.

The problem was that the government of South Vietnam was a mess. It was essentially a successor state to the French colonial regime, while the government of the North was the successor of the successful independence fight, led by the communists / Viet Minh. The North capitalized on its credibility with effective PR, and before you know it, the South was overrun with Viet Cong and related insurgents, sympathisers, and agents, especially in the rural areas. And all seem to agree that Ho Chi Minh would have won the re-unification elections that were never held. But the North was not all it seemed. It was also a brutal communist state- a predator state. According to Wikipedia:

"The Socialist Republic of Vietnam, along with China, Cuba, and Laos, is one of the world's four remaining one-party socialist states officially espousing communism. Its current state constitution, 2013 Constitution, asserts the central role of the Communist Party of Vietnam in all organs of politics and society."

This, two decades after the fall of the Soviet Union, and four and a half since the end of the American War (Vietnam War). This is a durable system! While Vietnam has lately followed China's lead in adopting limited capitalism, we should not imagine that it is a free or prosperous country. It remains very much in the totalitarian camp.

At the time, the US had just been through a similar war, in Korea, another tough slog defending the South from a blitzkrieg by the North. In that case, the US and the South were successful, and now South Korea has transformed into a happy, rich country, exporting K-Pop off an assembly line that seems to have no limit. Meanwhile, North Korea has remained stable in its way- stably dictatorial and desperately poor.

These are the conditions that the US was consciously defending South Vietnam from, and we were very right to do so. Unfortunately, the French had so thoroughly loused things up, between their import of Catholicism, their moral blindness in denying the Vietnamese what they had themselves had just fought World War 2 to regain, their futile war in Vietnam, and their organization of the South under Emperor Bao Dai and Prime minister Ngo Diem, that propping up the South proved impossible. The US did not want to replicate the colonialism of the French, just to keep the South out of the communist hands. But as it turned out, we would have had to do so and run the whole country, indeed on a rather brutal basis, if we really had wanted to save the situation. The problem was never military, but political- the people of the South were so mistreated by their government that their will to fight, in the myriad ways one has to fight in a civil and a guerrilla war, had dropped to zero.

So I think we should recognize that the US was doing a noble and proper thing in this war. Leaving the South defenseless, or cutting and running after we had gotten involved, would have been expedient, but not morally good. However, in hindsight, those would have been the wisest policies, saving everyone a great deal of death and waste. But that is a different point, both from the moral perspective, and given that hindsight comes too late. We can grant that many people, not least of whom were John Kennedy and Lyndon Johnson, recognized to some degree the bad, almost futile situation they were getting into. But while we can doubt their wisdom in not following their own analyses with greater discipline and political courage, their moral purposes were not bad ones.

• The status of our inequality.
• The big ripoff- dollars can immigrate for free!
• Selection for psychopaths.
• Criminal? Yes.
• Burger King explains net neutrality.
• What is wrong with pharmaceutical research? And why isn't science = engineering?

Measuring Genetic Fitness

Yes, it is a thing, and is quantitative. But it can be hard to measure, especially when genetic epistasis enters the picture.

Biological fitness is often thought about in nebulous terms, as unquantifiable, even taboo. But in genetics, it has a specific and quantifiable meaning- the likelihood of a gene, organism, or other unit of study to make it into the next generation. For example, an antibiotic resistance gene may have very high fitness in a bacterial population under antibiotic pressure, and also confer high fitness on its host organism as a whole. In those terms, fitness is measurable and quantifiable, especially for tiny laboratory organisms which reproduce quickly, have relateively few genes, and are easy to measure and manipulate. But it can be very difficult to evaluate elsewhere, and not just because organisms like us reproduce slowly and have lots of genes.

Fitness as a concept typically applies to deviations such as mutations, or sub-populations or sub-species, against a background of normal (i.e. wild-type) gene / whole population. It a measure of difference from the norm. The wild-type organism would have a fitness of 1, and a mutant with, say, a fatal developmental defect, has a fitness of 0. For a population, the collection of all fitness values is called the fitness landscape, the average being 1, but the deviations being very significant, as we know from our own populations. The population having some complex landscape of more and less fit individuals evolves through time with more fit genotypes gaining population share, and less fit genotypes (by definition) declining. One of the major functions of sexual reproduction is to continually re-arrange the fitness landscape to a more diverse and dispersed state by mixing and recombining genotypes, so that much of the deleterious mutational load of the population ends up segregated to low-fitness craters in the landscape, and is disposed of efficiently. But the same token, beneficial alleles can be more rapidly combined to reach fitness peaks.

A notional fitness landscape, from low (blue) to high (red). Populations with sex/recombination (a, right) have a much faster path to fitness peaks within this landscape. Note also that this is a very additive landscape, without epistatic or other complex genetic effects.

When considering the fitness value of individual genes and their combinations, the starting assumption is that they will be additive. That is, the quantitative fitness value for, say, an altered hemoglobin that allows survival at higher altitude will be independent of, and additive with, the fitness value for being able to consume yak milk in adulthood, via changes in lactase enzyme expression. But the fitness of one gene often affects that of others, an interaction that geneticists call epistasis. If I have a genetic propensity for alcoholism, and also a genetic propensity to liver failure, the combination, while conceptually and mechanistically independent, may end up far more lethal than either one would be alone. One extreme form of epistasis is synthetic lethality, where two mutations that are individually tolerated turn lethal when they occur together. Since everything in organismal biology is to some degree connected with everything else, epistasis is very common, and thus fitness values or, similarly, disease prognostic effects that we might be interested to determine for various allele variants, (i.e. mutations), as seen increasingly in the diagnostic clinical setting for humans, can be very tricky to estimate.

A recent paper advanced the measurement of fitness in complex genetic situations and from practical forms of data. It is naturally difficult to measure fitness across whole genomes and populations. Typically, an observation is made of relative fitness for an isolated gene/allele, where one mutation outcompetes another, in a shared genetic background (using model organisms). This ranking or rank-order style of data is far more accessible and thus more common than are detailed calculations of absolute fitness. This is true for single genes, and even more true for complex combinations that may exhibit epistasis. Yet the rank-ordering of fitness for alleles, genotypes, organisms, or other entities remains a very rich source of information, which the authors exploit to find novel epistatic effects.

Epistasis = ( w00+w11) - (w01+w10), where fitness is "w", and the genotypes are 00 (wild type), 11(double mutant) and 01, 10 (each single mutant). Epistasis, i.e. the deviation from additivity, can be positive or negative, and is quantitative to the extent that the fitness values they are based on are quantitative. The figure below gives a very simple example that indicates epistasis between two loci on the basis of very minimal fitness data.

Depiction of two known rank-order fitness relationships, and a conclusion of epistasis from such minimal / partial data. Arrows point towards higher fitness, and show ranks, in a rock-paper-scissors kind of sequence. Highest fitness is at the top, and least is at the bottom. We can already see that something is not additive, as one of the single mutants is more fit than the double mutant, while the other single mutant is more fit than the wild-type. If all effects were additive, the advantageous 01 mutation would not make the 11 double mutant less fit than the 10 single mutant.

Taking this to more loci and complex relations, the authors venture into Dyck numbers, graph isomorphism, Walsh coefficients, and other obscure methods to organize these rank analyses, and come out with computationally easy ways to analyze all this for any number of loci, to help geneticists make sense of what patchy / partial data they may have at hand.

Antibiotic resistance shows clear epistasis. Among four mutations relevant to antibiotic resistance in the TEM-class of bacterial antibiotic resistance gene, (a beta lactamase common in hospitals, in E. Coli, H. influenzae, and N. gonorrhoeae), having all mutations (TEM-50) is most resistant and thus most fit, but surprisingly, no single mutation (TEM-84,-19, -17, -33) confers better resistance than having none at all. But honestly, one didn't need a computer to figure this out.

"Although we have applied our method here only to fitness, any other continuous phenotype of interest can be analyzed in exactly the same manner. The fitness landscape w is then replaced by a more general genotype-to-phenotype map. For example, rather than using it as a fitness proxy, one may be concerned about the drug resistance phenotype itself and its genetic architecture."

We will soon have our complete genomes at hand as a normal part of our medical record. This will uncover an ever-growing list of deviations and oddities, whose significance will be the subject of many decades of study. The work above is just one of many kinds of methods that will be attempting to make sense of our genetic variations, with the goal of peering into our medical and inter-generational futures.

• Climate change is fast, but too slow for us. Or are we too slow for it?
• "The best way to reduce the public debt ratio is to stop issuing debt."
• The kind of things Trump is looking for.
• Analogies between agriculture and manufacturing, in the annals of economic efficiency.

Theory of the Predator Class

A review of Thorstein Veblen's "The Theory of the Leisure Class."

The Occupy movement seems so long ago. The most durable movement to come out of the 2008 economic crash seems, in retrospect, to be the Trumpian revisionists- the Tea Party / Santelli Republicans who alchemized a total breakdown of financial markets and lack of proper regulation into a movement to hobble government even more, and increase inequality over its already breathtaking levels.

The fight between the predators and the prey, however, is perennial, from our most ancient records of Greek cities, between the oligarchs and the demos. The last century saw the most vociferous and ideological movement against inequality and aristocracy, in the form of communism. Sadly, that turned out almost as badly as the royalist/aristocratic/capitalist propaganda portrayed- an appalling recreation of status-ridden tyrannies, with the added insult of thorough-going inversions of truth, in the name of a worker's paradise.

But before all that, in 1899 Thorstein Veblen published a classic critique of the aristocratic system and its capitalist derivatives, whose leaders he called the "leisure class". It laid the foundations of institutional economics, was a scathing re-analysis of the class and economic system of the time, and prefigured many later developments, such as feminism and our continued inability to distribute our enormous wealth equitably with the consequence that the vast majority remain highly dependent on jobs and salary for sustenance, living more or less hand to mouth. Unfortunately, his writing is quite pedantic. But it is also archly sarcastic, so much so that it becomes a sort of a comic masterpiece. Here he describes the role of religion and its various officers and adherents as an example of economic (not to mention intellectual) waste sponsored by the aristocratic elements of society:

"While belief is by no means confined to the leisure class, that class to-day comprises a disproportionately large number of believers in the occult sciences of all kinds and shades. By those whose habits of thought are not shaped by contact with modern industry, the knowledge of the unknowable is still felt to be the ultimate, if not the only true knowledge."

The leisure class is in Veblen's system the predators of society, lineally decended from the owners, kings, chiefs, and nobles of yore. They live by the work of others. Their need to show status is not reflected in useful activities or service to the collective, but in waste- the waste of time, of money and especially of other people's time, which all goes to show their power and position. Their servants are dressed just so, their wives do not labor and conduct futile charitable activites. Their religions are devoted to a supernatural leisure class which lives even more wastefully than they do, intermediated and officered by an utterly useless class of theologians and priests. Their scholarly institutions are likewise based on theological origins, study useless things, (Veblen's time period was the late 1800's), and adopt finely graded and conservative ceremonies of punctilious status, all to show the capacity of the sponsoring and attending aristocrats to waste prodigious amounts of time and resources.

The sad part of all this is that the aristocratic class leads the society in a ladder of wasteful emulation. Like the British royal family, or its more modish incarnation in the James Bond character, the class with little to do but waste its time forms the inescapably rivetting spectacle and model of the ideal life, and thus what the lower classes should aspire to. Naturally, this is abbetted by native greed and ambition, for all aspire to be not just like the leisure class, but part of it. This leads to endless consumption and living beyond one's means, ironically sabotaging the very goal of gaining the wealth required to gain entry. In this way, the upper classes unconsciously collaborate with the middle and especially lower classes in a conservatism that perpetuates an invidious system.

"From this proposition it follows that the institution of a leisure class acts to make the lower classes conservative by withdrawing from them as much as it may of the means of sustenance, and so reducing their consumption, and consequently their available energy, to such a point as to make them incapable of the effort required for the learning and adoption of new habits of thought. The accumulation of wealth at the upper end of the pecuniary scale implies privation at the lower end of the scale."

While historically, the predator class served as the warrior class, gaining land and wealth for the group as a whole, that function is now (with any luck) in abeyance. Thus their predatory instincts are turned exclusively inward, towards engines of capitalist fleecing, of government corruption, and the like, in order to maintain wealth and status. That they would receive the free sanction of a democratic people to run roughshod over the land, as happened in 2016, may be unimaginable to contemporary intellectuals, but might not be to Veblen himself, who had a relatively pessimistic view of human nature and institutions, including its tendency towards conservatism.

• Our economy in a few graphs
• Whence Capitalism?
• Krugman gets a little pessimistic too.
• "There have been two striking developments in economics over the last thirty years. First, a major theoretical revolution occurred in macroeconomics (from Keynesianism to Monetarism and beyond). Second, unemployment and broader labour under-utilisation rates have persisted at high levels."

A Moronic Foreign Policy

Trump accomplishes the opposite of what he claims. But Putin would be so proud!

Is America great again? Apparently, we are getting there very fast, even faster than orginally envisioned, according to our President, who is also a very stable genius, with an extremely large button. But for some reason we are also a world-wide laughing stock, headed by a moron whose erratic spleen is vented daily on Twitter, who can't read more than a few sentences at a time, who lies compulsively, and whose wanna-be mobster management style is pathetically at odds with any trace of professionalism. His vision of greatness seems to be letting corporations and the rich (such as himself) run roughshod over everyone else. How long that will play with his base is anyone's guess. But the worst consequences of Presidential intelligence and temperament (or lack thereof) are, as usual, on foreign policy.

The US has been leader of the free world, and the industrialized world, since World War 2, and arguably since World War 1. We have been the indispensible nation, the leading economy, and the leading culture of the 20th century. We faught a drawn-out and bitter Cold War with the main ideological and geopolitical adversary, communism, which ended with the latter's complete implosion. Russia has reconstituted itself along Tzarist lines, while China has reconstituted itself along similar capitalist/authoritarian lines, but without the personality cult at the top, at least until the current president, Xi Jinping. These former communist countries have learned from each other, and from the West, to arrive at their current blend of corrupt, Orwellian one-party rule, combined with substantial personal and business freedoms. And China is growing at a clip that will make it the largest economy and leading world power in a matter of decades, if not years.

This is the current competition that we face as a governing model- one that is attractive to smaller countries like Pakistan, the Phillipines, Iran, and many others. It is a time of flux, and our leadership, while not as central as in the fight against communism, remains critical if real democracy is to supplant fake democracy. Yet our current administration is pedaling as fast as it can in the wrong direction. It is itself beholden to Russia for its existence, and the President conveys his admiration for Vladimir Putin as often as possible. It embodies precisely the same style of corrupt, authoritarian, nepotistic, and predatory tendencies as the countries we least want to emulate.

In foreign policy, this administration has been sending a lot of mixed signals. This on its face is bad foreign policy, and contributes directly to a decline in global leadership. But it is understandable, as a war plays out within the White House between the President's terrible instincts, and the obvious interests of the US as represented by his hand-picked military policy staff, by a withering State Department, and by whatever other sane people remain. So we have been making enemies on a daily basis. The President promised that he would solve the Middle East, and the Israeli-Palestinian problem. Who knew that meant giving Israel whatever it wants, and giving the finger to any notion of a peace process? The pissing match with North Korea has been both futile and contemptible. We have relinquished whatever slight claim we ever had to leadership on global warming. The sudden attack on Pakistan, while eminently understandable, was also unnecessarily bombastic. The attacks on NATO and Europe, though since reeled back by his handlers, have been very damaging to the notion that the US has anything futher to do with the future of Europe. Mexico? Don't even ask.

In sum, we are retreating from greatness on a daily basis, becoming a smaller, petulent actor on the world stage, at a time when our values are under the most subtle attack, and when competing models of governance have found new footing after the communist debacle. We seem to be rushing to join them, rather than standing for enlightened values of truth, decency, and equality.

• A spirited foreign policy debate between a trump-is-not-so-bad person, and a we-are-going-to-hell person.
• Trump is an asset ... to someone.
• We have now taken the measure of our man.
• Opposite of helping the working class.
• Immigration is another part of the class war.
• Restore Net Neutrality- join a vpn system.
• How bad is facebook?

A Crime Against Humanity

Climate protection is the moral issue of our time.

One Christmas book that came my way was "Facing Climate Change", by Jeffrey Kiehl. It is a Jung-meets-the-climate-problem book. Evidently we should all hug a tree and get in touch with our Selves. It is, in short, preaching to the choir, and that in the gentlest possible way.

While the problem is principally psychological, the climate problem will take more aggressive thought and action to solve. At the same time, it is soluble. A recent New Yorker article focused on negative carbon- ways to remove CO2 from the atmosphere, which is what we need to have any hope of keeping biospheric catastrophe at bay. It will take country-sized infrastructures and improved technologies to solve, but is solvable. Given the collective will to solve it, there are plenty of policy and technical tools at our disposal.

The main problem is neither technical nor depth-psychological. It is moral, and reminds me of slavery in the US, and the resulting Civil War. Both sides knew it was wrong, and both sides benefitted from it economically. One side had the moral fiber to stand up and say that slavery was wrong, so wrong that it needed to, at least, be confined to the South, and ideally, abolished as an institution. The abolitionists were viewed as extremists and whackos at the time, unrealistic, weak, and sentimental. The other side prevaricated, rationalized, and ultimately fought tooth and nail to keep that system of incredible rapacity, greed, and injustice intact.

We are all implicated in climate change. We all know it is real, even if CO2 is invisible and its consequences relatively nebuous and distant. Denial, among the denialists, is but a stage of grief, for the greedy and wasteful freedoms we all grew up with and would like so much to maintain. The current Trumpian moment is one last hiatus from reason and responsibility, the dead end of an old and immoral regime. The US limped on for decades through the slavery crisis, reaching compromise after compromise, in hopes of saving a divided nation from the bloodbath that came. We have so far limped through two and a half decades, more or less, from the time when global warming was widely recognized, with analogous, if less heated, controversies, denial, and compromises.

Temperatures, decade by decade, and getting hotter.

Thankfully, addressing climate change will not require a war. Those poor nations most affected by it are far more likely to yearn to join the polluters than they are to start a war agaist them. In the US of the eighteenth century, the slaves likewise did not revolt in any successful way- the issue was not pressed by its victims, but by morally engaged onlookers- the abolitionists. Those economic interests most entwined with fossil fuels, at least in the US, are not politically independent, and while their corrupt influence is enormous, they are not unreachable by democratic governance.

What we need is a clear moral statement about the matter, in the vein of Uncle Tom's Cabin. That novel cast a new, brutal light slavery as it had never been lit before- as morally depraved and unsupportable by any civilized person. Climate change is a crime against the biosphere and against future generations of humanity, of vast proportions. We are slowly destroying whole ecosystems and ways of life, and robbing our children, en masse and comprehensively, of a healthy biosphere.

Al Gore started the process with his "Inconvenient Truth". It established the problem as undeniable, and moved many people with its moral urgency. But evidently we need more- a more compelling statement of the impossibility of being a moral person while denying climate heating or leaving it to someone else to solve. Most Americans agree, generally, but not with the urgency that leads to voting or action, and those who are most powerful seem to be most irresponsible on this front. Thus we are very close to a tipping point, and defining the issue with greater moral clarity could push us towards action.

Polar bears can help, but images and anecdotes are not enough.. there has to be a stronger comprehensive narrative around the issue.

With slavery, the logical end point was clear, even though it was also highly unpopular- the full enfranchisement and integration of African Americans into American society. With climate change, arbitrary lines have been drawn, but need to be periodically re-drawn as we spew our way through CO2 concentration limits and temperature thresholds. Two degrees? Or two and a half? This is one more way that this problem is devilishly easy to ignore and evade. The accords that have been reached so far, in Kyoto and Paris, have fallen far short of what is needed, and the only way to change that is through moral suasion- making it morally impossible to do otherwise than what is responsible to our future selves and progeny.

• Regulations? We don't need no stinkin regulations.

Pterosaurs

Yes, they really did fly- the amazing world of pterosaurs.

National Geographic recently had a beautiful spread on pterosaurs- those ungainly creatures that nobody thought could fly, until, apparently, we realized they really did fly. Indeed, they ruled the skies for over 160 million years- far longer than birds have. They operated a good deal like bats, with wings of membrane spread between modified fingers, which also stretched back to their legs. But a crucial difference is that, unlike bats, pterosaurs used only a modified fifth finger to carry the outside of the wing. The other fingers made up a strong hand about mid-wing that could be used for walking and lifting off. Thus pterosaurs were much better walkers than bats, and could also lift off from a standstill more effectively.

Reconstruction of the largest known pterosaur, Quetzalcoatlus, as tall as a giraffe, from the late Cretaceous.

What remains astonishing is how much apparent weight these animals carried, especially in front. The largest known pterosaur, Quetzalcoatlus, weighed about 440 pounds and had an enormous head. The head may have been quite thin, but, with neck, takes up roughly half its length. All pterosaurs tended to have large heads, and frequently added remarkable crests or horns, as if snubbing their beaks at aerodynamics. But looks are deceiving, since, like the toucan's bill, pterosaur crests and bones are hollow, very thin (1 mm), and thus were very light. The classic Pteranodon, with a crest almost as long as its enormous bill, is estimated to have weighed only 25 pounds, easily carried by a wingspan of 25 feet. Whether they could have carried off the hapless Zara Young is another matter.

Beautiful specimen of Rhamphorhynchus, from the Jurassic, with impressions of wing and tail membranes.

What is almost as compelling as the fossils of pterosaur bones are fossilized trackways, which show them in action. Over thirty walking tracks have been found, and one paper even describes what the authors interpret as a landing track. Typical pterosaur walking tracks show the heavier hind feet on the inside, and the wing/hands much more lightly on the outside. At each stride, the rear feet pull up roughly parallel to where the wing/hands have just left (b, in the figure). In these novel tracks, which begin abruptly, there are only hind feet for two strides, before the wing/hands appear. Secondly, the first hind feet tracks have elongated claw marks. Thirdly, the first two or three hind foot track sets are parallel and show a very short stride, different from typical walking gaits, of which the rest of this track is an example. These characteristics all lead to the idea that this pterosaur was landing, and hopped a couple of times with both feet before transitioning to a walking gait.

150 million year-old tracks from France. Top is an interpretation of the middle tracks, as evidence of landing. Below is a typical walking sequence and interpretation from the same location / source. The scale bar at bottom is 10 cm, so this pterosaur was relatively small.

This is not new work, dating from 2009, but the message is still a little hard to wrap one's head around- that tens of millions of years went by with these incredible creatures carrying on the battle for survival, with great success, and high style as well.

Nyctosaurus gracilis, reconstructed, from the late Cretaceous.

• A dumber nation- Thanks, Scott Pruitt!
• Xmas notes on another flying life form.

Structure of the Polytene Chromosome

Fly researchers have had a special microscope on their genetic subject for a century. Now we know why.

The DNA of our cells is enormous, and at the same time it is microscopic. Our 3 billion basepair genome is six feet long. Yet each of our cells contains a copy that is exquisitely wrapped up and so difficult to observe that it took X-ray crystallography and decades of experiment and inference to divine its true nature. Fruit fly researchers had a significant head start, however, with their recognition that a few fly cells make a form of their genome that can be observed with relative ease.

A "squash" of Drosophila polytene chromosomes. The upper left inset shows condensed normal mitotic chromosomes for comparison- they are very small. What do the bands signify?

Polytene chromosomes are made by larval insects in their salivary glands, apparently for the purpose of amplification of gene expression. Rather than develop ways to super-express the salivary protein products they need so much of from the usual single DNA copy, these cells re-duplicate their DNA many times, (about 1000-fold), while keeping it joined in a sort of synaptic alignment, which would normally only be apparent during cell division. They can then express selected genes to high levels with less regulatory effort. These "on" genes are apparent as puffs in the chromosomes when they are prepared with special stains and visualized under a regular microscope.

A "puff" of opened and expressing DNA is visible at upper left. The three panels are 1: staining with a general fluorescent DNA dye (green) along with a specific red dye targeted to a gene of interest (red; see arrows- this was a DNA-primer-based detection, so quite direct). 2- the customary orcein / Giemsa stain for visible light microscopy. 3- a light filter specific for the fluorescent red dye in the first panel bring out its locations.

The great Red Book of Drosophila genetics offers a comprehensive mapping of genes with respect to the "cytology" of these polytene chromosomes. The figure above was prepared by modern molecular biology reagents, which makes locating a gene of interest easy. But before all that, genetic mapping was done by tracking visual changes in the polytene chromosomes and mutations that befell gross genetic loci and had phenotypic consequences, such as re-arrangements of DNA that cut a gene in half. Decades of such work, correlated with more standard genetic mapping by recombination, resulted in a dense roadmap of genetic markers distributed along the characteristic banded pattern of the Drosophila polytene chromosomes.

But why were the polytene chromosomes banded in the first place? What were these landmarks that everyone relied upon? A recent paper re-opens this issue and links the interband zones (the lighter areas in both the green-stained and the orcein-stained preparations above) to the specific molecule function of transcriptional insulation. "Bands" are richer in DNA, while the interbands have less DNA. What do they have instead? Evidently proteins, of a particular sort.

Genes are packed pretty tightly in the DNA of our genomes, and are regulated by sites in the DNA that are typically nearby and upstream with respect to the direction of transcription. But "nearby" could mean tens of thousands of basepairs away. Thus it has been found that a great deal of looping goes on to bring such distant regulatory sites close to the gene start site where they have their effect. This naturally raises the question of why such regulatory sites don't just loop over to some other gene distant on the chromosome, or even on a different chromosome. In the tight confines of the nucleus, such things are doubtless quite possible.

Enter the "insulator". These appear to be special proteins that bind DNA situated between gene regions, keeping the regulatory apparati of each functionally distinct. The authors of this work reviewed the field and then carried out new crosslinking experiments that track genome-wide which DNA segments are close to others, or to specific proteins. That means that they essentially "froze" the 3-D structure of the DNA relationships with a chemical that promiscuously crosslinks any DNA or proteins close to each other. They then cut and joined those proximate DNA segments to each other with ligase, and sequenced the junctions at large scale to determine all the junction points.

The fact is that polytene chromosomes are sort of blown-up representations of normal DNA in the nucleus, which is normally not just randomly jumbled about, but is arranged in loci and loops organized around gene regions. That means that this kind of experiment, which was conducted on early Drosophila embryo cells, and not on the salivary cells that generate polytene chromosomes, is looking at the native looping and regional structure in normal cells, at least at that particular developmental stage, which will have its unique pattern of genes turned on and off.

They found it was easy to discern topological structure in these nuclei, just as others have before. Specific regions of DNA are in close contact, while others are not. It is not a random jumble. More importantly, there are a set of about 5,000 zones that had high local interaction, but less interaction with others- they termed these topologically associated domains (TADs). The boundaries between these correlate with other work finding high accessibility to DNase, and finding proteins bound that are called insulators. Yet other work on the polytene chromosomes found that they exhibit about 5000-6000 visible bands, the borders of which are again highly accessible to DNase, and the sites of insulator protein binding.

The hallmark of insulator proteins is that when DNA sites for their binding are engineered between enhancers and the gene they typically regulate, they tend to cut that communication. The mechanism behind this is not clear yet. It could be because looping is a progressive process, starting locally and scanning out to the nearest gene, in a kind of sewing machine model.

In any case, the authors draw on all this work to put the pieces together, and claim that polytene banding, as detected by DNA and other stains, show this structure at the visible level, with topological gene units housed in the dark bands, and the light units housing intergeneic segments, with insulators in between. Since Drosophila has almost 16,000 genes, this indicates that many of these topological units house multiple genes, an example of which is the homeobox complex, where complex and coordinated regulation extends over several nearby genes.

Correlation between polytene banding and cross-link contacts, in one segment of the genome. Banding is on top, and cross-link contacts are show in color. The crosses form out of topological localities with high internal contact rates, and lower external contact. At bottom is shown a gene track of the region from Flybase. Blue vertical bits are exons.

Correlation between polytene banding and cross-link contacts, in one segment of the genome. Banding is on top, and cross-link contacts are show in color. The crosses form out of topological localities with high internal contact rates, and lower external contact. At bottom is shown a gene track of the region from Flybase. Blue vertical bits are exons.

This is problably not news to the field, which is why this paper was buried in an obscure journal, but it is nice to see new methods make sense of quite old historical problems, and to recognize that we were looking at significant and functional genomic features all the time, from the first staining of these giant chromosomes in 1881.

• Greed as a religion- good or bad?
• For workers, or against them?
• Does this corruption know no bounds?
• One woman's story, of unconscious and conscious secrets.
• For Christmas, I would like to be a corporation.

Native American Cleansing, Army-Style

Review of Keith Murray's "The Modocs and Their War".

It was a brief national sensation during the Grant administration, but now a forgotten episode in the ethnic cleansing of the West. A tiny band of obscure Native Americans in Northern California resisted the US army for a year, engaging over ten times their own numbers, turning whole army units into demoralized fleeing cowards. A splinter group of the Modocs, numbering about 65 fighting men, were induced to go to a reservation in Oregon around 1865, but naturally found the experience unappealing, and decided to return to their native lands. With the US distracted by the Civil War and its aftermath, they were left alone for several years, while the settlers that were encroaching on their lands threw up increasingly bitter complaints.

Lava beds at Tule lake

One feature of these native lands, around Tule lake on the border with Oregon, are lava beds with very rugged topography. While barren, these also make excellent natural fortifications. The Modoc band, with their leader Captain Jack, made thorough use of them to hold off a determined Army attack on January 16 and 17, 1873, inflicting about 50 casualties while suffering none of their own. In fact, the Modocs throughout this episode ran circles around their enemies in tactics, logistics, scouting, and intelligence. In contrast, the Army of the West was a notorious home to cast-offs and hirelings, with little motivation and very great expense. There was an actual F-Troop involved, bringing quite appropriately to mind the old TV show about Western Army incompetence and corruption.

Eventually, the Army brought in hundreds of soldiers, plus units of friendly Native Americans, and hunted the Modocs down after they had thoroughly exhausted their supplies, not to mention their shaman's spiritual powers. Four of the leaders were hanged, and the rest shipped off by train to a reservation in Oklahoma, where the Modoc nation survives, barely.

I highly recommend this book, which dates from 1959. It is painstakingly researched, clearly told, and well-, sometimes sardonically, written. Murray reflects on the failings of the US Army, when faced with highly motivated and guerrilla resistance. He reflects:

"When the student of the Indian troubles turns from men or events to generalizations, he is struck with the obvious fact that the most serious aspect of the Modoc War was that the government had clearly learned nothing from its experience. Even while Captain Jack was awaiting execution at Fort Klamath, the civil government of Oregon expressed concern over the actions of certain Nez Percés of Joseph's band living in the Wallowa Valley of northeastern Oregon" .. which then led to similar mistreatment, broken promises, incompetence, and a long and tragic war of resistance.

The portents for Vietnam are alarming here, not to mention the displacement and mistreatment of the Palestinians. But to stick to domestic affairs, the overall dynamic was one of moral turpitude and greed on a national level, which the Army was put in a hopeless position to manage and mitigate. While the (Northern) US is justly proud of its moral position in the Civil War, its position towards Native Americans was one of ethnic cleansing, not to say extermination. The press of manifest destiny and the homesteading / settler movement encroached relentlessly on Native American lands. Treaty after treaty was signed, then ignored or reneged, boxing Native Americans into smaller and smaller reservations. We may call them concentration camps. They are on the worst possible land, in the most remote corners of the nation.

Territories of the Nez Percé. Green shows original treaty lands,  while the inner orange shows what they are left with today.

The irony is that only a few decades after the last of the Indian wars, the country woke up, in some very small degree, to its destruction and rapine of its natural inheritance and started establishing national parks to preserve a few of the most beautiful areas. If the Native Americans had been treated with decency and fairness, with large national lands that were protected from the depredations of settlers, we would today have a much more significant system of wild areas, in addition to preserving many more Native Americans and their diverse cultures. We can only be thankful that the freed slaves were not likewise driven onto barren reservations in the West, over trails of tears.

• The lies are the message, and the power.
• The tax bill is an impeachable offense.
• Fraud is now OK.
• Medicare is next.
• Is collusion with Israel worse than with Russia?
• Cable, unbound.

Truth and Enlightenment

What the Enlightenment and Modernity have wrought, and who has problems with it.

As our values of truth and honesty are slipping, it seems worthwhile to review how we got here. People generally have a tenuous relation to reality. What we see through our eyes is only its surface. We can see plants all our lives and yet have no understanding of how they work and how they came to be. Such knowledge has to come through painstaking inference into a mental model, based on clues, experiments, mutations, exceptions, and the like. Humans are champions of inference, as attested by conspiracy theories and religion- ways that our need to for theories of reality outstrips our actual knowledge, sometimes flagrantly.

Historically, there have been occasional periods when intellectuals had the prosperous and calm conditions to make progress on this front, out of the mire of preconceptions, superstitions, and traditions, and into a more measured and rational view of reality. Not that there is ever a perfectly rational view, but there are clearly more and less rational views possible. The ancient Greeks experienced one such period, founding schools of philosophy that lasted hundreds of years, and fostering the greatest scientist, teacher, and thinker of the ancient world, Aristotle. But the greatest such period was the Renaissance and subsequent Enlightenment of Western Europe, when the learning of the ancient world combined with mounting prosperity and technological development to dispell the fog of Christian theology, and made of scholarship an independent, rigorous, and institutional pursuit that continues today.

Painting is an example of this movement. The Renaissance painters learned perspective, and reveled in new powers of realistic portrayal. Realistic painting may now be old-hat, even déclassé, but after the rude iconography of the Middle Ages, it was revolutionary, reminiscent of the incredibly naturalistic statuary of Greece and Rome at their heights. Similar movements in all areas of intellectual life, including science, philology, history, politics, and social thought generally, and philosophy, brought us to modernity, where our relationship to nature is fundamentally transformed, from that of a mystified and dependent spectator, to that of a deeply understanding (if not always respectful) steward. While morals and ethics are not themselves a matter of truth and natural observation, (though they have a lot to do with integrity and honesty), the same truth-finding ethic trained on social institutions brought down, step by step, the superstitious hold of the religio-monarchical system, to the constitutional / social contract systems of today.

Francesco di Giorgio, ~1490, an idealized architectural view.

But some are not happy with this change in perspective. There were obviously losers in this process of cultural and intellectual maturation. Principally religion, which tried mightily to understand the nature of reality, while mediating our relation to it, but couldn't help putting the cart of dogma and power ahead of the horse of intellectual integrity. For honesty and truth begin in the method of getting there. True humility, not the false and preening humility of putting one's god before all other gods and considerations, is the first step to being able to even see the subtle stirrings of nature, and then to follow them out. Charles Darwin was orginally intended for the parsonage, but as he unfurled the relentless mechanism of biology, and experienced its stabs in his own life, he ended up an evident atheist, woken up to a more sober, mature, and we might say enlightened, view of our nature and situation.

Reality isn't always pretty. Facing it takes fortitude and work. Thus the astonishingly durable, if slipping, hold of religion into this, the twenty-first century. Thus also the attraction of fake news and con artists, not to mention religion. Far easier to have comfort and hope in false and familiar beliefs than to accept uncertainty and ignorance, and do the work required to resolve them, even partially. Who would have thought that, at the so-called end of history, when the US won the cold war, and spread its blend of capitalism, relative freedom, and intellectual ambition across the world, that such moral rot would set in here at home, with our plutocrats, (with the connivance of Russia, of all things!), standing at the head of an army of resentful religious traditionalists, straining every nerve to spread distrust, small-mindedness, and lies over the land?

• Intellectuals- the first targets of authoritarians and fascists.
• And State is the department of intellectuals, at least till now.
• Which country takes the cake for lying?
• But our Republicans are in contention as well.
• What's the matter with Kansas.. will soon be the matter with the rest of us.
• ... Until the revolution.

The Purpose-Driven Pastor

Robert Price answers Rick Warren, in The Reason-Driven Life.

We are all seekers for purpose and meaning. But what happens if someone has the answer? We react, naturally, with a good bit of suspicion and skepticism. For we know instinctively that this search is not only difficult and unlikely to yield definitive answers, but also highly personal. Those peddling pat answers and coookie-cutter solutions may have confidence, but rarely have true answers.

So it is with Rich Warren and his book The Purpose-Driven Life. This has been a fundamentalist staple now for one and a half decades, with sales to rival the Bible itself. "You Were Planned for God's Pleasure." Wow! But what pleasures God? Well, now that we are done with sacrificing chickens and committing genocide, it seems that God is most pleasured by people joining fundamentalist churches like Rick Warren's, imagining they are abasing themselves before God, while lording it over all the sorry sinners who haven't gotten the message. Then they are sent out to spread the word and get more people to join up. Warren's ultimate message is to be a drone for the church: "You Were Made for a Mission". As Robert Price quotes:

'World-class Christians are the only fully alive people on the planet.' The outrageous arrogance of this insane boast never seems to dawn on him. Eric Hoffer has Warren pegged: 'The impression somehow prevails that the true believer, particularly the religious individual, is a humble person. The truth is that the surrendering and humbling of the self breed pride and arrogance. The true believer is apt to see himslef as one of the chosen, the salt of the earth, the light of the world, a prince disguised in meekness, who is destined to inherit the earth and the kingdom of heaven too. He who is not of his faith is evil; he who will not listen shall perish.'

But Robert Price isn't just taking pot-shots. He is a post-fundamentalist, biblical scholar, and church-goer, as well as an atheist. He has great respect and love for the Bible, enabling a critique that makes Warren's literalism and pretensions to a biblical foundation ludicrous. Time and again, citations that seem so pat are exposed as far more complex, even contradictory, both among themselves, and to the points Warren is making. Warren quotes: "He is a God who is passionate about his relationship with you" Exodus 34:14. But his source is a custom version of the Bible for Warren's fundamentalists. The real translation is " The LORD, whose name is Jealous, is a jealous God", which lies among a discussion of how the Israelites should storm and desecrate the shrines of other religions.

Likewise, Warren cites "What pleases the LORD more: burnt offerings and sacrifices, or obedience to his voice? It is better to obey than to sacrifice." 1 Samuel 15:22. The language here is accurate, but this is no invitation to tea and scones, or to a Saddleback encounter group. The obedience demanded in this passage is genocide against the Amalek. One wonders whether this is a god that Warren's parishoners have any knowledge of or desire to get to know. The fact is that the Bible is a cobbled-together melange of historical and poetic texts, riven with inconsistencies, cross-purposes, and moral evil. To believe that one can take it literally, as Warren does, (most hilariously with the Noah story), is intellectually dishonest and incoherent.

And that is the fundamental lesson, in this age of fake news. The internet was hardly the first method of purveying falsehoods. Historians such as Homer and Herodotus never let truth get in the way of a good story, and standards were no higher among the many ancient story tellers and scribes who contributed to the Bible. They all had agendas, as does Rick Warren. Their narratives often begin in fact, and then veer into myth and fantasy, as most evident in the book of Revelations. The whole Jesus story is so full of archtypes and "purpose-driven" fables that it is impossible at this point to separate anything out that might have had to do with an actual person.

No, the Bible is an amazing cultural document, from our brutish and benighted, yet hopeful, forebears. It documents substantial moral and intellectual progress on its pages, in its transition towards a more or less pacifist dispensation (though whether that was by choice, or by Roman force is another matter). We have continued that progress in the modern age by, ironically, leaving its fervid fantasies behind and basing our intellectual life on the firmer foundations of empiricism and humanistic empathy. Fundmentalists work double-time to "prove" that their literal views of God and the Bible are true, but they are doomed to failure. That general intellectual failure is seen both in their amazingly corrupt bargain with Donald Trump and the revanchist Republicans, and in the declining numbers of parishoners in the pews. The decline of religion has been far slower than many had imagined, given that its intellectual foundations have been defunct for centuries, but is ever so slowly coming to pass, however purposeful its pastors.

• Vae victis.
• If the net won't be neutral, why not go to a dark net?
• Saunas may be better than SSRIs.
• Could Ismail Khan solve Afghanistan?
• It hardly needs repeating, whom the tax plan really benefits.
• Medicare is on the chopping block.
• America is in crisis.
• A history of redistribution.
• Online ads for online content ... is not working.