Jews Demand Signs and Greeks Look for Wisdom, but We Preach Christ Crucified

Review of God of the Mind, by Rob Haskell

This blog had its start in a religious discussion, pitting a Christian perspective against an atheist one. That discussion never ended because these viewpoints inevitably talk past each other, based as they are on fundamentally different epistemologies and axioms. Is truth facts, or is it a person? Does it have a capital "T", or a little "t"? Does reality come first, or does faith? With this election, this conflict, usually politely ignorable at the cultural sidelines, has come front and center, as half the country has transferred a Christian style of reasoning to politics, with catastrophic consequences.

I very much wish I had had this book by Rob Haskell back in the day. It lays out in a concise and thorough way all (well, let's say many of) the philosophical and psychological deficiencies of god-belief. It is hands-down the best discussion I have ever read on the subject- well-written, with humor and incisive insight. For example, he provides the bible quote that I have used to title this post, in a discussion of Christianity's approach to reason and intellect. While reams of theology support Christianity with reasons, at the end of the day, any honest theologian and Christian thinker will say that reason doesn't get you there. Faith needs to come first. Only then does all else follow. And this "all" is laced with superstition, suspension of normal rules of evidence, submission to authority, and a need to convert the whole world to the same system of belief. It is, implicitly, a preference for unity and power over truth. No wonder they were marks for the charismatic authority of Donald Trump.

One of the most disturbing aspects of the whole debate is the moralism that creeps into what is ostensibly a reasoned discussion of viewpoints and philosophy. If one does not accept god, Christians have been taught to believe that there is a reason. Not a logical reason, but a moral reason. Depravity is a word that comes up. Lack of belief betrays a moral failure, because god is the foundation of all moral law (those twelve commandments!). Those outside the fold merely want their false freedom to enjoy debauchery and crime, without the nagging conscience, which is apparently implanted not by god at birth, (let alone by evolution, or by moral reasoning), but by regular sermons, loudly professed faith, and bible reading. A bible, we might note, that is full of militarism, sexual abuse, deceit, and political authoritarianism. The whole proposition is absurd, from the ground up, unless, of course, you are of the religious tribe, in which case it has an irresistible logic and allure.

No wonder Christians feel good, right, and justified. And feel a birthright to rule over all, to claim that the US is (or should be) a Christian nation. One where resistance to its moral imperatives would, at last, be futile.

But here we are, getting off track! Rob Haskell is a former protestant missionary and minister, graduate of Regent College, and came to his new positions through deep personal engagement and turmoil. He knows intimately of which he speaks. An interesting aspect of his book is that he is almost more focused on psychology than on philosophy. For it is psychology that drives religious conversion, drives people to prostrate themselves before the void, and drives a faith that calls itself truth. Without the indoctrination by families, for example, no religion would amount to much- certainly not Christianity. And indoctrination of the young is obviously a highly irrational process, combining the most powerful psychological forces known- peer pressure, parental pressure, authority, tradition, community, repetition, fancy costumes. Who could resist? And yet Christians have no problem claiming that the result of all this is belief in truth, with a capital T. 

Haskell recounts an educational experience he had inviting Mormon missionaries to an extended discussion of why he should take up Mormonism. They tout the book of Mormon, which Haskell knows very well is a absurd fabric of early nineteenth century prejudices and speculations. They tout the archeological work a few believers have undertaken to prove their scripture, which is highly dubious, to say the least. But at last, when reason fails and argument slackens, Haskell is urged to pray. Pray hard enough, and the light is sure to shine. And for Mormons, brought up with all the pressures and templates ready-made for their belief, such prayer is very likely to work, activating the archetypes and feelings conducive to agreement with their culture. Will the story or the prayer work for others? Rarely, but occasionally it does strike a nerve, especially in the psychologically vulnerable. Haskell recognizes, uncomfortably, that while the stories are different, the psychological methods used by the Mormons and by him as a missionary are eerily similar.

"This points back to what I've already described, namely that in evangelical thinking, and possibly in all religious thinking, the acceptance of certain crucial and non-negotiable ideas comes first. Then, after that acceptance comes the search for evidence that supports it. But that evidence always gets the short end of the stick. Evidence is great when it affirms the things that are accepted by faith. But here isn't a lot of interest in evangelical circles in evidence itself, or in thinking clearly about evidence. And when the evidence falls short, the believer goes back to where it all started: not evidence but faith. So, it's really a matter of wanting to have your cake and eat it too. There's a built-in permission to be sloppy. 'We like evidence!' says the evangelical, 'so long as it proves our point. but when the evidence brings up difficult questions, we reserve the right to toss it out and appeal to faith.' ... How can you have a serious conversation with someone who thinks like this? It's like talking with your teenager."

Rationalization and confirmation bias are fundamental aspects of human psychology. Science has developed an organized and reasonably effective way to address it, but other institutions have not, notably the echo chambers of current news and social media. We do it all the time, (I am certainly doing it here), and it is no wonder that Christians do it too. The problem is the lack of humility, where Christians revel in their fantastical story, impugn anyone so dense (if not evil) as to not get it, and twist the very vocabulary of epistemology in order to declare that "Truth" comes, not out of reality, but precisely out of unreality- a faith that is required to believe in things unseen and tales thrice-told.

• And he writes a blog, too.
• Example of typical religious condescension, by J D Vance's mentor, James Orr.
• The Discovery Institute will try anything...
• Then there is the no true Scotsman defense.
• The Supreme Court lowers itself still further.
• What makes a human brain?
• We continue speeding ever faster to disaster.
• Poisonous propaganda + AI = our future.

Damned if You do, Damned if You Don't

The Cherokee trail of tears, and the Palestinian conundrum.

History is a long and sad tale of conflict, interspersed with better times when people can put their animosities aside. Just as economics deals in scarcity and its various solutions, history likewise turns on our inevitable drive towards overpopulation, with resulting scarcity and conflict. Occasionally, special technological, spiritual, organizational achievements- or catastrophes- may allow periods of free population growth with its attendant bouyant mood of generosity. But more commonly, groups of people covet each other's resources and plot ways to get them. This was one of the lessons of Malthus and Darwin, who addressed the deeper causes of what we see as historical events.

The "New World" provided Europeans with an unprecedented release for their excess populations, especially the malcontented, the desperate, and the ambitious. They rhapsodized about the "virgin" lands that lay open, generally dismissing the numerous and well-organized natives present all over these lands, as "savages", occupying a lower technological and theological level of existence. There were plenty of rationalizations put forth, like Christianizing the natives, or "civilizing" them. But the hypocrisy of these formulations becomes clear when you consider the fate of the Cherokees, one of the "five civilized tribes". 

By the early 1800's, a couple of centuries of contact had already gone under the bridge, (as narrated by Pekka Hämäläinen in "Indigenous continent"), and native Americans were all integrated to various degrees in trading networks that brought them European goods like guns, pots, knives, and novel practices like horse riding. The Cherokees, occupying the lower Appalachians and piedmont between what is now Georgia and Alabama, were more integrated than most, adopting European farming, living, schooling, and governing practices. They even owned African American slaves, and wrote themselves a US-modeled constitution in 1827, in the script devised the scholar Sequoya.

Did this "progress" toward assimilation with the European culture help them? Far from! Their excellence in farming, literacy, and government raised fears of competition in the white colonists, and the Georgia state government lobbied relentlessly for their removal. Andrew Jackson finally obliged. He pressured the Cherokees to re-open their status as a settled nation, devised a removal treaty with a minority party, and then sent all the Cherokees in the region (about 16,000) off on the Trail of Tears, to the barren lands of Oklahoma. These Cherokees lost roughly a quarter of their population along the way, in a brutal winter. Compare this with the partition of India, where about twelve percent of the refugees are thought to have perished, out of roughly 16 million total.

A small part of the annals of ethnic cleansing, US edition. Needless to say, the "Indian territory" ended up a lot smaller than originally promised.

 

Georgia was thus ethnically cleansed, and does not seem to experience a great deal of regret about it. The logic of power is quite simple- the winner gets the land and spoils. The loser is lucky to not be killed. That the Europeans were significantly more powerful than their native antagonists doesn't change the logic, though it might appeal to our empathy and nostalgia in retrospect. The Cherokees and other Native Americans might have been accepted into US society. They might have been given one or two states for their sovereign governments, as the Mormons managed. There were a lot of possibilities that might have made us a more interesting and diverse nation. But at the same time, most Native Americans participated fully in the politics of power, terrorizing each other, making slaves of each other, and killing each other. They were not innocents. So the fact that they came up against a stronger power was hardly a novelty, though in this case that power was blundering and cruel, shared very few of their cultural coordinates, and was highly hypocritical about its own.

All this comes to mind when viewing the Israeli-Palestinian conflict. Israel won the major Middle East wars that so dramatically emasculated the Palestinians, first in the civil war that left Jordan and Egypt in charge of the Palestinian areas, then in the 1967 war that left all these areas in Israeli hands. But what to do with them? On founding, Israel was a liberal, New Testament kind of country, with humanist values and lefty kibbutzim. The then-recent Holocaust also caused a bit of hesitance when it came to either killing or exiling the losing Palestinians. Indeed, given that its neighbors Jordan and Egypt lost these wars, it would have made some sense at that time to deport all the Palestinians, of which there were about one to two million. But rather than do that, or make a firm border, Israel immediately started encroaching into Palestinian territory with security areas and "settlements", and has set up an ever more elaborate, though selectively porous and self-serving, security and boundary system.

Both sides have a schizophrenic reaction to the other. On the Palestinian side, the psychology of losing has meant quietism and acquiescence by some, but resentment and militantcy by others. Both lead to a spiral of worse treatment, the weakness of the former inviting abuse, and the desperate depredations of the latter inciting revenge, "security" measures, and tighter occupation. The provocations by each side are unendurable, and thus the situation deteriorates. Yet, in the end, Israel has all the power and the responsibility to come up with a long term solution. Over the decades, Israel has morphed from its founding ethos into something much more conservative and Old Testament, less beholden to the humanisitic ideals of the post-WW2 period. The wanton killing, starvation, and collective punishment of Gaza makes visible this moral breakdown.

The Palestinians can't win either way, either through Hamas's implacable hatred and impotent attacks, nor through the acquiescence of the Palestinian National Authority, which, in thanks for its good behavior, has received the creeping expansion of Israeli "settlements" on its land. These now take up, according to a detailed map, about 1/3 to 1/2 of the land of the West Bank. Overall, the options are: 1) to expel the Palestinians outright, which appears to be, for Gaza at least, where Israeli policy is heading, (made more ironic by the realization by historians that the Biblical Exodus never actually took place), or 2) to continue to muddle along in a torturous occupation with creeping dispossession, or 3) to grant Palestine some kind of autonomy and statehood. Assimilation, (4), long dreamt of by some, seems impossible for a state that is fundamentally an ethnic (or theological) state, and whose whole raison d'etre is ethnic separation, not to even mention the preferences of the Palestinians. Though perhaps assimiliation without voting rights, in sort of semi-slavery or apartheid, is something the Israelies would be attracted to? Perhaps insignia will need to be worn by all Palestinians, sewn to their clothing?

Map of the West Bank of the Jordan, color coded by Palestinian marginal control in brown, and settler/Israeli control in red.

What should happen? Indigenous Americans were infected, decimated, hunted down, translocated, re-educated, and confined to a small and very remote system of reservations. Hopefully we have have progressed a little since then, as a largely European civilization, which is putatively shared by Israel. Thus the only way forward, as is recognized by everyone outside Israel, is the two-state solution, including a re-organization of the Palestinian territories into a final, clearly demarked, and contiguous state. Israel's current political system will never get there. But we can help the process along in a few ways.

First, it is disappointing to see our current administration shipping arms to Israel at a furious pace, only to see them used to kill thousands of innocent, if highly resentful, civilians. Israel has plenty of its own money to buy whatever it needs elsewhere. We need to put some limitations on our military and other aid relationships, to motivate change. (Though that raises the question of Israel's increasingly cozy relationship with Russia). Second, we should recognize Palestine as a state, and bring forward its integration into the international system. This will not resolve its borders or myriad security and territory issues viz Israel, but it would helpfully motivate things in that direction. Israel has constantly cried wolf about the lack of a credible partner to negotiate with, but that is irrelevant. Israel is perfectly capable of building the walls it needs to keep Palestinians at bay. But then it wants pliant workers as well, and a peaceful neighbor, security viz Jordan and Egypt, territorial encroachments, and many other things that are either destructive, or need to be negotiated. 

By far the most constructive thing that could be done is to freeze and re-organize the Jewish settlements and other periphernalia that have metastasized all over the West Bank. There is no future without a decent and fair solution in territory, which is the third big thing we need to press- our own detailed territorial plan for Palestine. For one thing, Israel could easily vacate the whole corridor / valley facing Jordan. That would give a consolidated Palestine a working border with a country that is now peaceful, quite well run, and friendly to both sides. There are countless possible maps. We just need to decide on one that is reasonably fair and force it on both sides, which are each, still after all these years, apparently unwilling to imagine a true peace. This means principally forcing it on Israel, which has been the dominant and recalcitrant party the entire time.

The Cherokees are now one of the largest indigenous populations in the US, at roughly a quarter million, with their own territory of about seven thousand square miles in Oklahoma. They have internal and partial sovereignty, which means that they deal with their own affairs on a somewhat independent basis, but otherwise are largely subject to most laws of the enclosing governments. The Cherokees could easily have been assimilated into the US. Only racism stood in the way, in a mindset that had long descended into a blind and adversarial disregard of all native Americans as "others", (the irony!), competitive with and less than, the newly arrived immigrants. We could have done much better, and one would like to think that, a hundred or a hundred and fifty years on, we would have.

In the end, the West (read as European civilization, as developed out of the ashes of World War 2) is either for or against wars of aggression, ethnic cleansing, apartheid, and human rights. Israel has won its wars, but never faced up to its responsibilities to the conquered Palestinians, and has tried to have it both ways, to be viewed by the world as a modern, enlightened state, even as it occupies and slowly strangles the people it defeated decades ago. 

• Slovenly strategic thinking. But really, visionless long-term politics.
• One Gazan speaks.
• Settler colonialism.
• Who's the victim?
• Shades of Scientology ... the murky networks of the deep evangelical state.
• In California, solar still makes sense.

Empty Skepticism at the Discovery Institute

What makes a hypothesis scientific, vs a just-so story, or a religious fixation?

"Intelligent" design has fallen on hard times, after a series of court cases determined that it was, after all, a religious idea and could not be foisted on unsuspecting schoolchildren, at least in state schools and under state curricula. But the very fact of religious motivation leads to its persistence in the face of derision, evidence, and apathy. The Discovery Institute, (which, paranthetically, does not make any discoveries), remains the vanguard of intelligent design, promoting "skepticism", god, alternative evolutionary theories, and, due to the paucity of ways to attack evolution, tangential right-wingery such as anti-vaccine agitation. By far their most interesting author is Günter Bechly, who delves into the paleontological record to heap scorn on other paleontologists and thereby make room for the unmentioned alternative hypothesis ... which is god.

A recent post discussed the twists and turns of ichthyosaur evolution. Or should we say biological change through time, with unknown causes? Ichthyosaurs flourished from about 250 million years ago (mya) to 100 mya, with the last representatives dated to 90 mya. They were the reptile analogs of whales and dophins, functioning as apex predators in the ocean. They were done in by various climate crises well-prior to the cometary impact that ended the Cretaceous and the reign of dinosaurs in general.

Bechly raises two significant points. First is the uncertain origins of Ichthyosaurs. As is typical with dramatic evolutionary transitions like that from land to water in whales, the time line is compressed, since there are a lot of adaptations that are desirable for the new environment that might have been partially pre-figured, but get fleshed out extensively with the new ecological role and lifestyle. Selection is presumably intense and transitional fossils are hard to find. This was true for whales, though beautiful transitional fossils have been found more recently. And apparently this is true for the Ichthyosaurs as well, where none have been found, yet. There is added drama stemming from the time of origin, which is right after the Permian exinction, perhaps the greatest known extinction event in the history of the biosphere. Radiations after significant extinction events tend to be rapid, with few transitional fossils, for the same reason of new niches opening and selection operating rapidly.

Ichthyosaur

Bechly and colleagues frequently make hay out of gaps in the fossil record, arguing that something (we decline to be more specific!) else needs to be invoked to explain such lack of evidence. It is a classic god of the gaps argument. But since the fossils are never out of sequence, and we are always looking at millions of years of time going by with even the slimmest layers of rock, this is hardly a compelling argument. One thing that we learned from Darwin's finches, and the whole argument around punctuated equilibrium, is that evolution is typically slow because selection is typically not directional but conservative. But when selection is directional, evolution by natural selection can be startlingly fast. This is an argument made very explicitly by Darwin through his lengthy discussions of domestic species, whose changes are, in geological terms, instant. 

But Bechly makes an additional interesting argument- that a specific hypothesis made about ichthyosaurs is a just-so story, a sort of hypothesis that evolutionary biologists are very prone to make. Quite a few fossils have been found of ichthyosaurs giving birth, and many of them find that the baby comes out not only live (not as an egg, as is usual with reptiles), but tail-first. Thus some scientists have made the argument that each are adaptations to aquatic birth, allowing the baby to be fully borne before starting to breathe. Yet Bechly cites a more recent scientific review of the fossil record that observes that tail-first birth is far from universal, and does not follow any particular phylogenetic pattern, suggesting that it is far from necessary for aquatic birth, and thus is unlikely to be, to any significant extent, an adaptation. 

Ha! Just another story of scientists making up fairy tales and passing them off as "science" and "evolutionary hypotheses", right?  

"Evolutionary biology again and again proves to be an enterprise in imaginative story-telling rather than hard science. But when intelligent design theorists question the Darwinist paradigm based on empirical data and a rational inference to the best explanation, they are accused of being science deniers. Which science?" ... "And we will not let Darwinists get away with a dishonest appeal to the progress of science when they simply rewrite their stories every time conflicting evidence can no longer be denied."

Well, that certainly is a damning indictment. Trial and sentencing to follow! But let's think a little more about what makes an explanation and a hypothesis, on the scientific, that is to say, empirical, level. Hypotheses are always speculative. That is the whole point. They try to connect observations with some rational or empirically supported underlying mechanism / process to account for (that is, explain) what is observed. Thus the idea that aquatic birth presents a problem for mammals who have to breathe represents a reasonable subject for an hypothesis. Whether headfirst or tailfirst, the baby needs to get to the surface post haste, as soon as its breathing reflex kicks in. While the direction of birth doesn't seem to the uninitiated (and now, apparently to experts with further data at hand) to make much difference, thinking it does is a reasonable hypothesis, based on obvious geometric arguments and biological assumptions, that it is possible that the breathing reflex is tied to emergence of the head during birth, in which case coming out tailfirst might delay slightly the time it takes between needing to breathe and being able to breathe. 

This argument combines a lot of known factors- the geometry of birth, the necessity of breathing, the phenomenon of the breathing reflex initiating in all mammals very soon after birth, by mechanisms that doubtless are not entirely known, but at the same time clearly the subject of evolutionary tuning. And also the paleontological record. Good or bad, the hypothesis is based on empirical data. What characterizes science is that it follows a disciplined road from one empirically supported milestone to the next, using hypotheses about underlying mechanisms, whether visible or not, which abide by all the known/empirical mechanisms. Magic is only allowed if you know what is going on behind the curtain. Unknown mechanisms can be invoked, but then immediately become subjects of further investigation, not of protective adulation and blind worship.

In contrast, the intelligent design hypothesis, implicit here but clear enough, is singularly lacking in any data at all. It is not founded on anything other than the sentiment that what has clearly happened over the long course of the fossil record operates by unknown mechanisms, by god operating pervasively to carry out the entire program of biological evolution, not by natural selection (a visible and documented natural process) but by something else, which its proponents have never been able to demonstrate in the least degree, on short time scales or long. Faith does not, on its own, warrant novel empirical mechanisms, and nor does skeptical disbelief warrant them. Nor does one poor, but properly founded, hypothesis that is later superceded by more careful analysis of the data impugn the process of science generally or the style of evolutionary thinking specifically.

Imagine, for example, if our justice system operated at this intellectual level. When investigating crimes, police could say that, if the causes were not immediately obvious, an unnamed intelligent designer was responsible, and leave it there. No cold cases, no presumption of usual natural causality, no dogged pursuit of "the truth" by telegenic detectives. Faith alone would furnish the knowledge that the author of all has (inscrutibly) rendered "his" judgement. It would surely be a convenient out for an over-burdened and under-educated police force!

Evolution by natural selection requires a huge amount of extrapolation from what we know about short time scales and existing biology to the billions of years of life that preceeded us. On the other hand, intelligent design requires extrapolation from nothing at all- from the incredibly persistent belief in god, religion, and the rest of the theological ball of wax not one element of which has ever been pinned down to an empirical fact. Believers take the opposite view solely because religious propaganda has ceaselessly drilled the idea that god is real and "omnipotent" and all-good, and whatever else wonderful, as a matter of faith. With this kind of training, then yes, "intelligent" design makes all kinds of sense. Otherwise not. Charles Darwin's original hypothesis was so brilliant because it drew on known facts and mechanisms to account (with suitable imagination and extrapolation) for the heretofore mysterious history of biology, with its painfully slow yet inexorable evolution from one species to another, one epoch to another. Denying that one has that imagination is a statement about one's intelligence, no matter how it was designed.

• Only god can give us virulent viruses.
• The priest who knew it so well, long ago.
• A wonderful Native American Film- Dance me outside.
• With a wonderful soundtrack, including NDN Kars.
• We need to come clean on Taiwan.
• Appeasers, cranks, and fascist wannabes.
• Vaccines for poor people are not profitable.
• California is dumbing down math, and that will not help any demographic.

Everything is Alive, but the Gods are all Dead

Barbara Ehrenreich's memoir and theological ruminations in "Living with a Wild God".

It turns out that everyone is a seeker. Somewhere there must be something or someone to tell us the meaning of life- something we don't have to manufacture with our own hands, but rather can go into a store and buy. Atheists are just as much seekers as anyone else, only they never find anything worth buying. The late writer Barbara Ehrenreich was such an atheist, as well as a remarkable writer and intellectual who wrote a memoir of her formation. Unusually and fruitfully, it focuses on those intense early and teen years when we are reaching out with both hands to seize the world- a world that is maddeningly just beyond our grasp, full of secrets and codes it takes a lifetime and more to understand. Religion is the ultimate hidden secret, the greatest mystery which has been solved in countless ways, each of them conflicting and confounding.

Ehrenreich's tale is more memoir than theology, taking us on a tour through a dysfunctional childhood with alcoholic parents and tough love. A story of growth, striking out into the world, and sad coming-to-terms with the parents who each die tragically. But it also turns on a pattern of mystical experiences that she keeps having, throughout her adult life, which she ultimately diagnoses as dissociative states where she zones out and has a sort of psychedelic communion with the world.

"Something peeled off the visible world, taking with it all meaning, inference, association, labels, and words. I was looking at a tree, and if anyone had asked, that's what I would have said I was doing, but the word "tree" was gone, along with all the notions of tree-ness that had accumulated in the last dozen years or so since I had acquired language. Was it a place that was suddenly revealed to me? Or was it a substance- the indivisible, elemental material out of which the entire known and agreed-upon world arises as a fantastic elaboration? I don't know, because this substance, this residue, was stolidly, imperturbably mute. The interesting thing, some might say alarming, was that when you take away all the human attributions- the words, the names of species, the wisps of remembered tree-related poetry, the fables of photosynthesis and capillary action- that when you take all this this away, there is still something left."

This is not very hard to understand as a neurological phenomenon of some kind of transient disconnection of just the kind of brain areas she mentions- those that do all the labeling, name-calling, and boxing-in. In schizophrenia, it runs to the pathological, but in Ehrenreich's case, she does not regard it as pathological at all, as it is always quite brief. But obviously, the emotional impact and weirdness of the experience- that is something else altogether, and something that humans have been inducing with drugs, and puzzling over, forever. 

Source

As a memoir, the book is very engaging. As a theological quest, however, it doesn't work as well, because the mystical experience is, as noted above, resolutely meaningless. It neither compels Ehrenreich to take up Christianity, as after a Pauline conversion, nor any other faith or belief system. It offers a peek behind the curtain, but, stripped of meaning as this view is, Ehrenreich is perhaps too skeptical or bereft of imagination to give it another, whether of her own or one available from the conventional array of sects and religions. So while the experiences are doubtless mystical, one can not call them religious, let alone god-given, because Ehrenreich hasn't interpreted them that away. This hearkens back to the writings of William James, who declined to assign general significance to mystical experiences, while freely admitting their momentous and convincing nature to those who experienced them.

Only in one brief section (which had clearly been originally destined for an entirely different book) does she offer a more interesting and insightful analysis. There, Ehrenreich notes that the history of religion can be understood as a progressive bloodbath of deicide. At first, everything is alive and sacred, to an animist mind. Every leaf and grain of sand holds wonders. Every stream and cloud is divine. This is probably our natural state, which a great deal of culture has been required to stamp out of us. Next is a hunting kind of religion, where deities are concentrated in the economic objects (and social patterns) of the tribe- the prey animals, the great plants that are eaten, and perhaps the more striking natural phenomena and powerful beasts. But by the time of paganism, the pantheon is cut down still more and tamed into a domestic household, with its soap-opera dramas and an increasingly tight focus on the major gods- the head of the family, as it were. 

Monotheism comes next, doing away with all the dedicated gods of the ocean, of medicine, of amor and war, etc., cutting the cast down to one. One, which is inflated to absurd proportions with all-goodness, all-power, all-knowledge, etc. A final and terrifying authoritarianism, probably patterned on the primitive royal state. This is the phase when the natural world is left in the lurch, as an undeified and unprotected zone where human economic greed can run rampant, safe in the belief that the one god is focused entirely on man's doings, whether for good or for ill, not on that of any other creature or feature of the natural world. A phase when even animals, who are so patently conscious, can, through the narcissism of primitive science and egoistic religion, be deemed mere mechanisms without feeling. This process doesn't even touch on the intercultural deicide committed by colonialism and conquest.

This in turn invites the last deicide- that by rational people who toss aside this now-cartoonish super-god, and return to a simpler reverence for the world as we naturally respond to it, without carting in a lot of social power-and-drama baggage. It is the cultural phase we are in right now, but the transition is painfully slow, uneven, and drawn-out. For Ehrenreich, there are plenty of signs- in the non-linear chemical phenomena of her undergraduate research, in the liveliness of quantum physics even into the non-empty vacuum, in the animals who populate our world and are perhaps the alien consciousnesses that we should be seeking in place of the hunt through outer space, and in our natural delight in, and dreams about, nature at large. So she ends the book as atheist as ever, but hinting that perhaps the liveliness of the universe around us holds some message that we are not the only thinking and sentient beings.

"Ah, you say, this is all in your mind. And you are right to be skeptical; I expect no less. It is in my mind, which I have acknowledged from the beginning is a less than perfect instrument. but this is what appears to be the purpose of my mind, and no doubt yours as well, its designed function beyond all the mundane calculations: to condense all the chaos and mystery of the world into a palpable Other or Others, not necessarily because we love it, and certainly not out of any intention to "worship" it. But because ultimately we may have no choice in the matter. I have the impression, growing out of the experiences chronicled here, that it may be seeking us out." 

Thus the book ends, and I find it a rather poor ending. It feels ripped from an X-Files episode, highly suggestive and playing into all the Deepak and similar mystical tropes of cosmic consciousness. That is, if this passage really means much at all. Anyhow, the rest of the trip is well worth it, and it is appropriate to return to the issue of the mystical experience, which is here handled with such judicious care and restraint. Where imagination could have run rampant, the cooly scientific view (Ehrenreich had a doctorate in biology) is that the experiences she had, while fascinating and possibly book-proposal-worthy, did not force a religious interpretation. This is radically unlike the treatment of such matters in countless other hands, needless to say. Perhaps our normal consciousness should not be automatically valued less than more rare and esoteric states, just because it is common, or because it is even-tempered.

• God would like us to use "they".
• If you are interested in early Christianity, Gnosticism is a good place to start.
• Green is still an uphill battle.

A Gene is Born

Yes, genes do develop out of nothing.

The "intelligent" design movement has long made a fetish of information. As science has found, life relies on encoded information for its genetic inheritance and the reliable expression of its physical manifestations. The ID proposition is, quite simply, that all this information could not have developed out of a mindless process, but only through "design" by a conscious being. Evidently, Darwinian natural selection still sticks on some people's craw. Michael Behe even developed a pseudo-mathematical theory about how, yes, genes could be copied mindlessly, but new genes could never be conjured out of nothing, due to ... information.

My understanding of information science equates information to loss of entropy, and expresses a minimal cost of the energy needed to create, compute or transmit information- that is, the Shannon limits. A quite different concept comes from physics, in the form of information conservation in places like black holes. This form of information is really the implicit information of the wave functions and states of physical matter, not anything encoded or transmitted in the sense of biology or communication. Physical state information may be indestructable (and un-create-able) on this principle, but coded information is an entirely different matter.

In a parody of scientific discussion, intelligent design proponents are hosted by the once-respectable Hoover Institution for a discussion about, well, god.

So the fecundity that life shows in creating new genes out of existing genes, (duplications), and even making whole-chromosome or whole-genome duplications, has long been a problem for creationists. Energetically, it is easy to explain as a mere side-effect of having plenty of energy to work with, combined with error-prone methods of replication. But creationistically, god must come into play somewhere, right? Perhaps it comes into play in the creation of really new genes, like those that arise from nothing, such as at the origin of life?

A recent paper discussed genes in humans that have over our recent evolutionary history arisen from essentially nothing. It drew on prior work in yeast that elegantly laid out a spectrum or life cycle of genes, from birth to death. It turns out that there is an active literature on the birth of genes, which shows that, just like duplication processes, it is entirely natural for genes to develop out of humble, junky precursors. And no information theory needs to be wheeled in to show that this is possible.

Yeast provides the tools to study novel genes in some detail, with rich genetics and lots of sequenced relatives, near and far. Here is portrayed a general life cycle of a gene, from birth out of non-gene DNA sequences (left) into the key step of translation, and on to a subject of normal natural selection ("Exposed") for some function. But if that function decays or is replaced, the gene may also die, by mutation, becoming a pseudogene, and eventually just some more genomic junk.

The death of genes is quite well understood. The databases are full of "pseudogenes" that are very similar to active genes, but are disabled for some reason, such as a truncation somewhere or loss of reading frame due to a point mutation or splicing mutation. Their annotation status is dynamic, as they are sometimes later found to be active after all, under obscure conditions or to some low level. Our genomes are also full of transposons and retroviruses that have died in this fashion, by mutation.

Duplications are also well-understood, some of which have over evolutionary time given rise to huge families of related proteins, such as kinases, odorant receptors, or zinc-finger transcription factors. But the hunt for genes that have developed out of non-gene materials is a relatively new area, due to its technical difficulty. Genome annotators were originally content to pay attention to genes that coded for a hundred amino acids or more, and ignore everything else. That became untenable when a huge variety of non-coding RNAs came on the scene. Also, occasional cases of very small genes that encoded proteins came up from work that found them by their functional effects.

As genome annotation progressed, it became apparent that, while a huge proportion of genes are conserved between species, (or members of families of related proteins), other genes had no relatives at all, and would never provide information by this highly convenient route of computer analysis. They are orphans, and must have either been so heavily mutated since divergence that their relationships have become unrecognizable, or have arisen recently (that is, since their evolutionary divergence from related species that are used for sequence comparison) from novel sources that provide no clue about their function. Finer analysis of ever more closely related species is often informative in these cases.

The recent paper on human novel genes makes the finer point that splicing and export from the nucleus constitute the major threshold between junk genes and "real" genes. Once an RNA gets out of the nucleus, any reading frame it may have will be translated and exposed to selection. So the acquisition of splicing signals is a key step, in their argument, to get a randomly expressed bit of RNA over the threshold.

A recent paper provided a remarkable example of novel gene origination. It uncovered a series of 74 human genes that are not shared with macaque, (which they took as their reference), have a clear path of origin from non-coding precursors, and some of which have significant biological effects on human development. They point to a gradual process whereby promiscuous transcription from the genome gave rise by chance to RNAs that acquired splice sites, which piped them into the nuclear export machinery and out to the cytoplasm. Once there, they could be translated, over whatever small coding region they might possess, after which selection could operate on their small protein products. A few appear to have gained enough function to encourage expansion of the coding region, resulting in growth of the gene and entrenchment as part of the developmental program.

Brain "organoids" grown from genetically manipulated human stem cells. On left is the control, in middle is where ENSG00000205704 was deleted, and on the right is where ENSG00000205704 is over-expressed. The result is very striking, as an evolutionarily momentous effect of a tiny and novel gene.

One gene, "ENSG00000205704" is shown as an example. Where in macaque, the genomic region corresponding to this gene encodes at best a non-coding RNA that is not exported from the nucleus, in humans it encodes a spliced and exported mRNA that encodes a protein of 107 amino acids. In humans it is also highly expressed in the brain, and when the researchers deleted it in embryonic stem cells and used those cells to grow "organoids", or clumps of brain-like tissue, the growth was significantly reduced by the knockout, and increased by the over-expression of this gene. What this gene does is completely unknown. Its sequence, not being related to anything else in human or other species, gives no clue. But it is a classic example of gene that arose from nothing to have what looks like a significant effect on human evolution. Does that somehow violate physics or math? Nothing could be farther from the truth.

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Hand-Waving to God

A decade on, the Discovery Institute is still cranking out skepticism, diversion, and obfuscation.

A post a couple of weeks ago mentioned that the Discovery Institute offered a knowledgeable critique of the lineages of the Ediacaran fauna. They have raised their scientific game significantly, and so I wanted to review what they are doing these days, focusing on two of their most recent papers. The Discovery Institute has a lineage of its own, from creationism. It has adapted to the derision that entailed, by retreating to "intelligent design", which is creationism without naming the creators, nailing down the schedule of creation, or providing any detail of how and from where creation operates. Their review of the Ediacaran fauna raised some highly skeptical points about whether these organisms were animals or not. Particularly, they suggested that cholesterol is not really restricted to animals, so the chemical traces of cholesterol that were so clearly found in the Dickinsonia fossil layers might not really mean that these were animals- they might also be unusual protists of gigantic size, or odd plant forms, etc. While the critique is not unreasonable, it does not alter the balance of the evidence which does indeed point to an animal affinity. These fauna are so primitive and distant that it is fair to say that we can not be sure, and particularly we can not be sure that they had any direct ancestral relationship to any later organisms of the ensuing Cambrian period, when recognizable animals emerged.

Fair enough. But what of their larger point? The Discovery Institute is trying to make the point, I believe, about the sudden-ness of early Cambrian evolution of animals, and thus its implausibility under conventional evolutionary theory. But we are traversing tens of millions of years through these intervals, which is a long time, even in evolutionary terms. Secondly, the Ediacaran period, though now represented by several exquisite fossil beds, spanned a hundred million years and is still far from completely characterized paleontologically, even supposing that early true animals would have fossilized, rather than being infinitesimal and very soft-bodied. So the Cambrian biota could easily have predecessors in the Ediacaran that have or have not yet been observed- it is as yet not easy to say. But what we can not claim is the negative, that no predecessors existed before some time X- say the 540 MYA point at the base of the Cambrian. So the implication that the Discovery Institute is attempting to suggest has very little merit, particularly since everything that they themselves cite about the molecular and paleontological sequence is so clearly progressive and in proper time sequence, in complete accord with the overall theory of evolution.

For we should always keep in mind that an intelligent designer has a free hand, and can make all of life in a day (or in six, if absolutely needed). The fact that this designer works in the shadows of slightly altered mutation rates, or in a few million years rather than twenty million, and never puts fossils out of sequence in the sedimentary record, is an acknowledgement that this designer is a bit dull, and bears a strong resemblence to evolution by natural selection. To put it in psychological terms, the institute is in the "negotiation" stage of grief- over the death of god.

Science Fiction as Theology

Let's look higher than the clouds. Let's look to the stars.

I have always been rather dismissive of theology- the study of something that doesn't exist. But if one takes it in a larger sense of a culture of scripture, story telling, morals, and social construction, then sure, it makes more sense. But then so do alot of other stories. I have been enjoying the Foundation series via streaming, which is at best "inspired" by the original books, yet takes its premises reasonably seriously and grows a complex and interesting set of story lines to what by the end of the first season is a positive and promising conclusion. I would ding it for excessive adherence to Star Wars-style action and simplistic morality, compared with the more cerebral original, but that is only to be expected these days.

Science fiction is having a golden age, as a way to tell important, probing stories and consider alternative futures. The Star Trek franchise generally sticks with hopeful futures, which I certainly favor. Their world is post-money, post internal conflict, post-disease. But philosophically alive through contact with other civilizations. The theological implications are momentous, as we envision a culture very different from our own, and blessed with various magical means of deliverance, like transporters, replicators, and warp drives. Where the "science fiction" books of the Bible were mostly dystopian (Job, Revelation, Genesis), Science fiction in our era straddles the line, with plenty of dystopian offerings, but also hopeful ones. Whether Star Wars is hopeful might be a matter of debate, since bad guys and bad empires never seem to go away, and the position of the resistance is always impossibly dire.

White male mathematician Hari Seldon takes on the role of god, in the Foundation series. He calculates out the future of the galaxy, clairvoyantly predicting events, and then comes back from beyond the grave to keep guiding his flock through crisis after crisis.

Are Star Trek futures any more realistic than those of Revelation? Are they theologically more sound? I think yes on both counts. Revelation is a rather unhinged response to the late Jewish era in its apocalyptic relations with Rome, as it headed into exile and the diaspora. There is a welter of reworked Old Testament material and obscure references, turning into florid visions that have misled Christians for centuries. Star Trek and the other science fiction franchises, on the other hand, are a bit more restrained in their visionary quests and escatologies, and more hopeful, for abundant futures where some problems have been solved while other forms of politics and history continue to call for strong moral values. This is quite different than the bizarre and ecstatic culmination of Revelation at the end of history, in the last days.

We also get to live out the visions, on a small scale, as technology advances in the real world. Smart phones have transformed our lives, for instance, one promise kept from the early science fiction days. And our only real hope for dealing with climate change is to harness better technologies, rather than going down dystopian roads of degrowth, famine, and war. So there are real futures at stake here, not just visions of futures.

While our current physics totally bars the adventures that are portrayed in contemporary science fiction epics, their theological significance lies in their various visions of what humanity can and should do. They, as Revelation, are always keyed to their historical moment, with America ascendent and technologically advanced over other cultures. But they do not use their magical elements and story arcs to promote quiescence and slack-jawed wonder at the return of the son of god, who will make everything right and mete out judgement to all the bad people. (Or do the opposite, in the case of Job.) No, they uniformly encourage resistance against injustice, and hopeful action towards a better world, or galaxy, or universe, as the case may be.

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Death at the Starting Line- Aneuploidy and Selfish Centromeres

Mammalian reproduction is unusually wasteful, due to some interesting processes and tradeoffs.

Now that we have settled the facts that life begins at conception and abortion is murder, a minor question arises. There is a lot of murder going on in early embryogenesis, and who is responsible? Probably god. Roughly two-thirds of embryos that form are aneuploid (have an extra chromosome or lack a chromosome) and die, usually very soon. Those that continue to later stages of pregnancy cause a high rate of miscarriages-about 15% of pregnancies. A recent paper points out that these rates are unusual compared with most eukaryotes. Mammals are virtually alone in exhibiting such high wastefulness, and the author proposes an interesting explanation for it.

First, some perspective on aneupoidy. Germ cells go through a two-stage process of meiosis where their DNA is divided two ways, first by homolog pairs, (that is, the sets inherited from each parent, with some amount of crossing-over that provides random recombination), and second by individual chromosomes. In more primitive organisms (like yeast) this is an efficient, symmetrical, and not-at-all wasteful process. Any loss of genetic material would be abhorrent, as the cells are putting every molecule of their being into the four resulting spores, each of which are viable.

A standard diagram of meiosis. Note that the microtubules (yellow) engage in a gradual and competitive process of capturing centromeres of each chromosome to arrive at the final state of regular alignment, which can then be followed by even division of the genetic material and the cell.

In animals, on the other hand, meiosis of egg cells is asymmetric, yielding one ovum / egg and three polar bodies, which  have various roles in some species to assist development, but are ultimately discarded. This asymmetric division sets up a competition between chromosomes to get into the egg, rather than into a polar body. One would think that chromosomes don't have much say in the matter, but actually, cell division is a very delicate process that can be gamed by "strong" centromeres.

Centromeres are the central structures on chromosomes that form attachments to the microtubules forming the mitotic spindle. This attachment process is highly dynamic and even competitive, with microtubules testing out centromere attachment sites, and using tension ultimately as the mark of having a properly oriented chromosome with microtubules from each side of the dividing cell (i.e. each microtubule organizing center) attached to each of the centromeres, holding them steady and in tension at the midline of the cell. Well, in oocytes, this does not happen at the midline, but lopsidedly towards one pole, given that one of the product cells is going to be much larger than the others. 

In oocytes, cell division is highly asymmetric with a winner-take-all result. This opens the door to a mortal competition among chromosomes to detect which side is which and to get on the winning side. 

One of the mysteries of biology is why the centromere is a highly degenerate, and also a speedily evolving, structure. They are made up of huge regions of monotonously repeated DNA, which have been especially difficult to sequence accurately. Well, this competition to get into the next generation can go some way to explain this structure, and also why it changes rapidly, (on evolutionary time scales), as centromeric repeats expand to capture more microtubules and get into the egg, and other portions of the machinery evolve to dampen this unsociable behavior and keep everyone in line. It is a veritable arms race. 

But the funny thing is that it is only mammals that show a particularly wasteful form of this behavior, in the form of frequent aneuploidy. The competition is so brazen that some centromeres force their way into the egg when there is already another copy there, generating at best a syndrome like Down, but for all other chromosomes than #21, certain death. This seems rather self-defeating. Or does it?

The latest paper observes that mammals devote a great deal of care to their offspring, making them different from fish, amphibians, and even birds, which put most of their effort into producing the very large egg, and relatively less (though still significant amounts) into care of infants. This huge investment of resources means that causing a miscarriage or earlier termination is not a total loss at all, for the rudely trisomic extra chromosome. No, it allows resource recovery in the form of another attempt at pregnancy, typically quite soon thereafter, at which point the pushy chromosome gets another chance to form a proper egg. It is a classic case of extortion at the molecular scale. 

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Desperately Seeking Cessation of Desire

Some paradoxes, and good points, of Buddhism.

I have been reading "In the Buddha's Words", by Bhikkhu Bodhi, which is a well-organized collection / selection of translations of what we have as the core teachings of Buddhism. It comes from the Pali canon, from Sri Lanka, where Buddhism found refuge after its final destruction in India after the Arab invasions, and offers as clear an exposition of the Buddhist system as one can probably find in English. A bit like the scriptures of Christianity, the earliest canons of Buddhism originate from oral traditions only recorded a hundred or so years after Buddha's death, but as they are slightly less besotted with miraculous stories, the collection has more of a feeling of actual teaching, than of gnomic riddles and wonder stories, not to mention Odyssean mis-adventures.

Both prophets make audacious claims, one to be god, or its son, the other to have attained a perfectly enlightened state with similar implications for everlasting life (or lack of rebirth, at any rate). Each extends to his followers the tempting prospect of a similarly exalted state after death. Each teaches simple morals, each attracts followers both lay and career-ist, the latter of whom tend to be rather dense. Each launched an international sensation that bifurcated into a monastic/ascetic branch of professional clerics and a more popular branch that attained a leading role in some societies.

But Buddhism has attained a special status in the West as something a bit more advanced than the absurd theology of Christianity. A theology that could even be deemed atheist, along with a practice that focuses more relentlessly on peace and harmony than does what Christianity has become, particularly in the US. It is congenial to seekers, an exotic and edgy way to be spiritual, but not religious.

But how much sense does it really make? For starters, much of the Buddhist mythology and theology is simply taken from its ambient Hindu environment. The cycle of rebirth, the karma that influences one's level of rebirth, the heavens and hells, all come from the common understandings of the time, so are not very particular to Buddhism. Buddhists did away with lots of the gods, in favor of their own heros (Buddha, and the Bodhisattvas), and developed a simplified philosphy of desire, suffering, and the relief of suffering by controlling desire, optimally through advanced meditation practices. Much of this was also ambient or at least implicit, as Buddha himself began as a normal Indian ascetic, trying to purify himself of all taints and mundane aspects. For his Buddhist Sanga, he dialed things back a bit, so that the community could function as a social system, not a disconnected constellation of hermits.

Bodhisattvas floating in heaven. These are Buddhists who have attained enlightenment but not entered permanent heaven, choosing rather to have compassion on humanity in its benighted state.

As a philosophical system, it seems paradoxical to spend so much effort and desire in seeking nirvanna and the benefits of lack of desire. To sit in meditation for years on end demands enormous discipline. To submit to a life of begging and poverty takes great will and desire for whatever is promised on the other side. This is not evidence of lack of desire, much less the kind of wisdom and knowledge that would license its practitioners to advise lay people in their mundane affairs (or politicians in affairs of state). And the ethical system that Buddha promulgated was simple in the extreme- merely to be and do good, rather than being and doing bad, all staked on the age-old promise that just deserts would be coming after death.

No, Buddha was clearly a charismatic person, and his insight was social, not philosphical. Remember that he was a prince by birth and education. I would suggest that his core message was one of nobility- of idealism about the human condition. In his system, nobility is not conferred by birth, but by action. All can be noble, and all can be ignoble, regardless of wealth or birth. For the mass of society, it is control over desire that allows virtue and prosperity- i.e. nobility. Those who are addicts, whether to power, to drugs, to bitterness, to sex, or innumerable other black holes of desire or habit, are slaves, not nobles. This is incidentally what makes Buddhism so amenable to the West- it is very enlightenment-friendly kind of social philosophy.

The monks and Sanga of Buddhism were to be the shock troops of emotional discipline, burning off their normal social desires in fires of meditation and renunciation, even as they were on the hook for a whole other set of desires. Which are, in my estimation, wholly illusory in their aim, despite the various beneficial effects of meditation, in this world. They provide the inspiration and template for the society at large, modeling a form of behavioral nobility that any and all can at least appreciate, if not aspire to, and model in their own circumscribed lives and ethical concerns. I think that is the real strength of the Buddhist system. The monks may be misled in philosophical terms, but they fulfill a critical social role which governs and moderates the society at large. 

The monks provide another benefit, which is population control. One of the greatest pressures on any society is overpopulation, which immiserates the poor, empowers the rich, and can ultimately destroy its resource base. While the monastic institutions are a great burden on their societies, they also help keep them sustainable by taking in excess males who might otherwise become brigands and parents. This is particularly evident in traditional Tibet, despite the corruption of the monastic system by clan rivalries and even occasional warfare.

The fact of the matter is that desire is the staff, even essence, of life. Those who lack desire are dead, and Buddhist monks sitting in endless renunciation are enacting a sort of living death. Nevertheless, they have an important function in their societies, which is one we see replicated in the priests of Orthodox and Catholic Christianity (most of the time) and other ascetics and clerics around the world. Buddha was right that the management of desire is absolutely critical to individual and communal social life. Compare his system, however, with the philosophy of the Greeks, which arose at roughly the same (axial) time. The Greek philosophers focused on moderation in all things- another way, and I would offer, a healthier way, to state the need for discipline over the desires. They additionally fostered desires for knowledge and as complex ethical investigations, which I would posit far outstripped the efforts of the Buddhists, and gave rise, though the Greeks' continuing influence over the Roman and ensuing Christian epochs in Western Europe, to a more advanced culture, at least in philosophical, legal, and scientific terms, if not in terms of social and political peace.

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God Save the Queen

Or is it the other way around? Deities and Royalties in the archetypes.

It has been entertaining, and a little moving, to see the recent celebration put on by Britain for its queen. A love fest for a "ruler" who is nearing the end of her service- a job that has been clearly difficult, often thankless, and a bit murky. A job that has evolved interestingly over the last millenium. What used to be a truly powerful rule is now a Disney-fied sop to tradition and the enduring archetypes of social hierarchy.

For we still need social hierarchy, don't we? Communists, socialists, and anarchists have fought for centuries against it, but social hierarchy is difficult to get away from. For one thing, at least half the population has a conservative temperament that demands it. For another, hierarchies are instinctive and pervasive throughout nature as ways to organize societies, keep everyone on their toes, and to bias reproduction to the fittest members. The enlightenment brought us a new vision of human society, one based on some level of equality, with a negotiated and franchise-based meritocracy, rather than one based on nature, tooth, and claw. But we have always been skittish about true democracy. Maximalist democracies like the Occupy movement never get anywhere, because too many people have veto power, and leadership is lacking. Leadership is premised naturally on hierarchy.

Hierarchy is also highly archetypal and instinctive. Maybe these are archetypes we want to fight against, but we have them anyhow. The communists were classic cases of replacing one (presumably corrupt and antiquated) social hierarchy with another which turned out to be even more anxiously vain and vicious, for all its doublespeak about serving the masses. Just looking at higher-ranking individuals is always a pleasant and rewarding experience. That is why movies are made about the high ranking and the glamorous, more than the downtrodden. And why following the royals remains fascinating.

But that is not all! The Queen is also head of the Anglican Church, another institution that has fallen from its glory days of power. It has also suffered defections and loss of faith, amid centuries-long assaults from the enlightenment. The deity itself has gone through a long transition, from classic patriarchial king in the old testament (who killed all humanity once over for its sins), to mystic cypher in the New Testament (who demanded the death of itself in order to save the shockingly persistent sinners of humanity from its own retribution), to deistic non-entity at the height of the enlightenment, to what appears to be the current state of utter oblivion. One of the deity's major functions was to explain the nature of the world in all its wonder and weirdness, which is now quite unnecessary. We must blame ourselves for climate change, not a higher power. 

While social hierarchy remains at the core of humanity, the need for deities is less clear. As a super-king, god has always functioned as the and ultimate pinnacle of the social and political system, sponsoring all the priests, cardinals, kings, pastors, and the like down the line. But if it remains stubbornly hidden from view, has lost its most significant rationales, and only peeps out from tall tales of scripture, that does not make for a functional regent at all. While the British monarchy pursues its somewhat comical, awkward performance of unmerited superintendence of state, church, and social affairs, the artist formerly known as God has vanished into nothing at all.

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Evolution Under (Even in) Our Noses

The Covid pandemic is a classic and blazingly fast demonstration of evolution.

Evolution has been "controversial" in some precincts. While tradition told the fable of genesis, evolution told a very different story of slow yet endless change and adaptation- a mechanistic story of how humans ultimately arose. The stark contrast between these stories, touching both on the family tree we are heir to, and also on the overall point and motivation behind the process, caused a lot of cognitive dissonance, and is a template of how a fact can be drawn into the left/right, blue/red, traditional/progressive cultural vortex.

This all came to a head a couple of decades ago, when in the process of strategic retreat, anti-evolution forces latched onto some rather potent formulations, like "just a theory", and "intelligent design". These were given a lot of think tank support and right wing money, as ways to keep doubt alive in a field that scientifically had been settled and endlessly ramified for decades. To scientists, it was the height of absurdity, but necessitated wading into the cultural sphere in various ways that didn't always connect effectively with their intended audience. But eventually, the tide turned, courts recognized that religion was behind it all, and kept it out of schools. Evolution has more or less successfully receded from hot-button status.

One of the many rearguard arguments of anti-evolutionists was that sure, there is short-term evolution, like that of microbes or viruses, but that doesn't imply that larger organisms are they way they are due to evolution and selection. That would be simply beyond the bounds of plausibility, so we should search for explanations elsewhere. At this point they were a little gun-shy and didn't go so far in public as to say that elsewhere might be in book like the Bible. This line of argument was a little ironic, since Darwin himself hardly knew about microbes, let alone viruses, when he wrote his book. The evidence that he adduced (in some profusion) described the easily visible signs of geology, of animals and plants around the world, (including familar domestic animals), which all led to the subtle, yet vast, implications he drew about evolution by selection. 

So it has been notable that the vistas of biology that opened up since that time, in microbiology, paleontology, genetics, molecular biology, et al., have all been guided by these original insights and have in turn supported them without fail. No fossils are found out of order in the strata, no genes or organisms parachute in without antecedents, and no chicken happens without an egg. Evolution makes sense of all of biology, including our current pandemic.

But you wouldn't know it from the news coverage. New variants arise into the headlines, and we are told to "brace" for the next surge, or the next season. Well, what has happened is that the SARS-COV2 virus has adapted to us, as we have to it, and we are getting along pretty well at this point. Our adaptation to it began as a social (or antisocial!) response that was very effective in frustrating transmission. But of late, it has been more a matter of training our immune systems, which have an internal selective principle. Between rampant infections and the amazing vaccines, we have put up significant protective barriers to severe illness, though not, notably, to transmission.

But what about the virus? It has adapted in the most classic of ways, by experiencing a wide variety of mutations that address its own problems of survival. It is important to remember that this virus originated in some other species (like a bat) and was not very well adapted to humans. Bats apparently have countless viruses of this kind that don't do them much harm. Similarly, HIV originated in chimpanzee viruses that didn't do them much harm either. Viruses are not inherently interested in killing us. No, they survive and transmit best if they keep us walking around, happily breathing on other people, with maybe an occasional sneeze. The ultimate goal of every virus is to stay under the radar, not causing its host to either isolate or die. (I can note parenthetically that viruses that do not hew to this paradigm, like smallpox, are typically less able to mutate, thus less adaptable, or have some other rationale for transmission than upper respiratory spread.)

And that is clearly what has happened with SARS-COV2. Local case rates in my area are quite high, and wastewater surveilance indicates even higher prevalence. Isolation and mask mandates are history. Yet hospitalizations remain very low, with no one in the ICU right now. Something wonderful has happened. Part of it is our very high local vaccination rate, (96% of the population), but another part is that the virus has become less virulent as it has adapted to our physiology, immune systems, media environment and social practices, on its way to becoming endemic, and increasingly innocuous. All this in a couple of years of world-wide spread, after billions of infections and transmissions.

The succession (i.e. evolution) of variants detected in my county. 

The trend of local wastewater virus detection, which currently shows quite high levels, despite mild health outcomes.

So what has the virus been doing? While it has many genes and interactions with our physiology, the major focus has been on the spike protein, which is most prominent on the viral surface, is the first protein to dock to specific human proteins (the ACE2 cell surface receptor), and is the target of all the mRNA and other specific subunit vaccines. (As distinct from the killed virus vaccines that are made from whole viruses.) It is the target of 40% of the antibodies we naturally make against the whole virus, if we are infected. It is also, not surprisingly, the most heavily mutated portion of the virus, over the last couple of years of evolution. One paper counts 45 mutations in the spike protein that have risen to the level of "variants of concern" at WHO. 

"We found that most of the SARS-COV-2 genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection."

Structure of the spike protein, in its normal virus surface conformation, (B, C), and in its post-triggering extended conformation that reaches down into the target cell's membrane, and later pulls the two together. Top (in B, C) is where it binds to the ACE2 target on respiratory cells, and bottom is its anchor in the viral membrane coat (D shows it upside-down). At top (A) is the overall domain structure of the protein, in its linear form as synthesized, especially the RBD (receptor binding domain) and the two protease cleavage sites that prepare it for eventual triggering.

The spike protein is a machine, not just a blob. As shown in this video, it starts as a pyramidal blob flexibly tethered to the viral surface. Binding the ACE2 proteins in our respiratory tracts triggers a dramatic re-organization whereby this blob turns into a thin rope, which drops into the target cell. Meanwhile, the portion stuck to the virus unfolds as well and turns into threads that wind back around the newly formed rope, thereby pulling the virus and the target cell membrane together and ultimately fusing them. This is, mechanistically, how the virus gets inside our cells.

The triggering of the spike protein is a sensitive and adjustable process. In related viruses, the triggering is more difficult, and waits till the virus is engulfed in a vesicle that taken into the cell, and acidified in the normal process of lysosomal destruction / ingestion of outside materials. The acidification triggers these viral spike proteins to fire and release the virus into the cell. Triggering also requires cleavage of the spike protein with proteases that cut it at two locations. Other related viruses sometime wait for a target host protease to do the honors, but SARS-COV2 spike protein apparently is mostly cleaved during production by its originating host. This raises the stakes, since it can then more readily trigger, by accident, or once it finds proper ACE2 receptors on a target host. One theme of recent SARS-COV2 evolution is that triggering has become slightly easier, allowing the virus to infect higher up in the respiratory system. The original strains set up infections deep in the lung, but recent variants infect higher up, which lessens the systemic risks of infection to the host, promotes transmissibility, and speeds the infection and transmission process. 

The mutations G339D, N440K, L452R, S477N, T478K, and E484K in the spike region that binds to ACE2 (RBD, or receptor binding domain) promotes this interaction, raising transmissibility. (The nomenclature is that the number gives the position of the amino acid in the linear protein sequence, and the letters give the original version of the amino acid in one letter code (start) and in the mutated version (end)). Overall, mutations of the spike protein have increased the net charge on the spike protein significantly in the positive direction, which encourages binding to the negatively charged ACE2 protein. D614G is not in this region, but is nearby and seems to have similar effects, stabilizing the protein. The P681 mutation in one of the cleaved regions promotes proteolysis by the enzyme furin, thus making the virus more trigger-able. 

What are some other constraints on the spike protein? It needs to evade our vaccines and natural immunity, but has seemingly adapted to a here-and-gone infection style, though with periodic re-infection, like other colds. So any change is good for the purpose of camouflage, as long as its essential functions remain intact. The N-terminal, or front, domain of the spike protein, which is not involved directly in ACE2 binding, has experienced a series of mutations of this kind. An additional function it seems to have is to mimic a receptor for the cytokine interleukin 8, which attracts neutrophils and encourages activation of macrophages. Such mimicry may reduce this immune reaction, locally. 

In comparison to all these transmissibility-enhancing mutations, it is not clear yet where the mutations that decrease virulence are located. It is likely that they are more widely distributed, not in the gene encoding the spike protein. SARS-COV2 has a remarkable number of genes with various interactions with our immune systems, so the scope for tuning is prodigious. If all this can be accomplished in a couple of years, image what a million, or a billion, years can do for other organisms that, while they have slower reproduction cycles and more complicated networks of internal and external relations, still obey that great directive to adapt to their circumstances.

• Late link, on receptor binding vs immune evasion tradeoffs.
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• Forced arbitration is, generally, unconscionable and should be illegal.
• We could get by with fewer nuclear weapons.
• Originalism would never allow automatic or semiautomatic weapons.