Xi Jinping Thought on Socialism with Chinese Characteristics for a New Era

China girds for defense against infiltration by Western ideas. And Wang Huning leads the way.

The current Chinese Communist Party congress prompts us to take stock of where we are in our relations with China and where China is going. The major theme is of course conservativism. Xi Jinping remains at the helm, and may stay there for several cycles to come. The party remains uniquely in control, using all elements of new and old technologies to "guide" Chinese culture and maintain power. And increasingly is trying to shape the international environment to abet its internal controls and maybe spread its system abroad.

It is worth recounting the fourteen points of Xi Jinping thought in detail, as stated on the Wiki page:

• Ensuring Communist Party of China leadership over all forms of work in China.
• The Communist Party of China should take a people-centric approach for the public interest.
• The continuation of "comprehensive deepening of reforms".
• Adopting new science-based ideas for "innovative, coordinated, green, open and shared development".
• Following "socialism with Chinese characteristics" with "people as the masters of the country".
• Governing China with the Rule of Law.
• "Practice socialist core values", including Marxism-Leninism and socialism with Chinese characteristics.
• "Improving people's livelihood and well-being is the primary goal of development".
• Coexist well with nature with "energy conservation and environmental protection" policies and "contribute to global ecological safety".
• Strengthen the national security of China.
• The Communist Party of China should have "absolute leadership over" China's People's Liberation Army.
• Promoting the one country, two systems system for Hong Kong and Macau with a future of "complete national reunification" and to follow the One-China principle and 1992 Consensus for Taiwan.
• Establish a common destiny between the Chinese people and other peoples around the world with a "peaceful international environment".
• Improve party discipline in the Communist Party of China.

The casual reader will note that Communist party dominance and retention of control is the subject of roughly four or five of these points, depending on interpretation. One can sense that control is absolutely the central obsession and fear of party. And no wonder- there are plenty of structural and historical reasons.

China has had a tumultuous history from earliest recorded times, cycling between centralization and dissolution and civil war. The golden periods were always ones of stability, while the worst were times of anarchy, banditry, decline. Then there were the colonial humiliations, from the opium wars to Japanese occupation. Whether one adds in the disastrous legacy of Marxism- which also came from the West- into the mix, is a matter of taste. As noted above, the current CCP still gives lip service to Marxism-Leninism (though pointedly not to Maoism!).

In the more current era, the West promotes free trade, human rights, and democracy as a way to contest the power and ideology of the CCP. Each have their ulterior aspects, certainly in relation to China. Human rights and democracy are obviously direct attacks on the very core values of the CCP. Free trade might seem like a no-brainer and objectively desirable. But in reality, it cements the advantages of highly developed countries, since less developed countries can never gain an advantage in high technology if their only advantage is low labor cost and poor education & other infrastructure. Therefore, China has had to protect itself from the onslaught of the West, economically, politically, and socially.

This is the basic theme of the CCP ideology, driven particularly by Wang Huning, a social scientist. academic, and now politbureau member and close advisor of Xi Jinping. Huning has been a close advisor to the last three leaders of China, and evidently a major architect of their signature mottos, "The Three Represents", "The Chinese Dream", and now "Xi Jinping thought ...". He is a close student of the US, and appears generally to be the "vision guy" for the Chinese leadership. (Maybe even the brains behind the operation, if one wants to be hyperbolic.) While Huning in his earliest writings advocated for the democratic development of China, in line with general development of a modern, mature state, and with models such as Japan, that has all been deferred and subsumed under the more immediate needs of the party. His public writing ceased after he joined the central government. 

The biggest and most traumatic historical shock guiding the CCP today was undoubtedly the collapse of the Soviet Union. (As it guides Putin as well.) Before everyone's eyes, the siren song of the West, of capitalism, and of "freedom" (particularly the freedom to be nationalist) captured the populace, and destroyed the Soviet state from within, resulting in a gangster Russia that has only painfully re-established its strength and order, turning back into an authoritarian (and nationalist) state and a colleague of China on the anti-Western world stage. 

The Chinese Communist Party avoided all that through its merciless grip on power. It never let its eye stray from the ball, or softened it heart towards its dissidents and malcontents. It patiently experimented with a mixed capitalist / one party rule system, which has turned out (so far) to be highly successful. It availed itself of all available technology and capitalist methods from the West to develop its economy at a pell-mell rate, learning especially from its fellow-tigers, Singapore, Taiwan, Japan, Hong Kong, and South Korea. However, it continues to (rightly) fear the siren songs of freedom, democracy, etc. as core threats. It conveniently uses psychological projection to blame the West for all these attractive ideas, which in truth are not exclusively Western at all, but are dreams that Chinese people have as well. (See Hong Kong, see Singapore, see Taiwan) So the ideology and the propaganda follows the age-old script of justifying a bloated, intrusive, and often very cruel state by casting the blame for dissent on outsiders.

That's a big TV screen.

The CCP has also been highly effective in many areas. It obviously keeps tabs on everyone with not just surveillance, but with social surveys and party members at the grass roots, and even allows limited local protests, so that it has a feeling for what the people want, despite a lack of formal democracy. It has engineered a miracle of infrastructure, trains, and housing. Indeed, there is an overhang of construction that it is slowly winding down, in the current real estate crunch. It has protected its population comprehensively from Covid, surely saving millions of lives, even as it imposes stark, and likely not sustainable, costs. It has recognized the dangers of bitcoin and shut down the cryptocurrencies in comprehensive fashion- something we might learn from. And it is leading the way in solar manufacturing and installation, even while its use of coal remains catastrophic. It continually identifies and fights corruption in its own ranks, recognizing that a one-party state is an invitation to rot and sclerosis.

But the fundamental conundrum remains- how to justify and strengthen a one-party state in the midst of the rising well-being, education and sophistication of its own population. The other tigers, including even Singapore, all began with strongly authoritarian systems that each evolved, in parallel with their economic development, into more or less free democracies today. While one can sympathize with the CCP's desire to avoid the chaos of the Soviet Union's demise, the now more cogent and relevant models of political evolution in the local region are far more positive stories, which the CCP seems to pointedly, and lamentably, ignore. 

Indeed, China appears to be heading in a different direction, a bit more like that of North Korea. Their wolf warrior diplomacy is given to vitriolic statements and bullying, now showcased over Taiwan. Their internal propaganda is increasingly nationalistic and strident, following the Xi Jinping thought's guidelines of shaping the cultural values of China to be more cohesive and disciplined. (Covid hasn't helped, either.) It is increasingly intolerant of diversity, as shown against minority ethnic groups, which are being wiped out in systematic terms. For example, the government offers generous subsidies to minority members who marry Han ethnic partners, and drives the same policy by locking up large numbers of Uyghur men for re-education. China's ideological leaders are groping for CCP-friendly "values" that can effectively block what they view as foreign viruses, but which are, in point of fact, endogenous and natural to the human condition.

Under Xi and Wang Hunting, the party is still searching for those elusive "socialist core values" that are uniquely Chinese, not Western, not from the backward (and somewhat feudal) countryside, and supportive of the Communist party. But all they have come up with are greed/capitalism, nationalism, an obsession with stability, and a new personality cult. 

While I can not foretell the future, this does not seem like a good way to go. In foreign policy, one can measure success by how friendly the neighboring countries are- in this case to China, and to the US. There are areas of the world where very peaceful relations exist, such as across the EU, and between the US and its neighbors. That does not seem to be the case in the South China Sea. The constant drumbeat of threats and bullying by China, against Taiwan in particular, but others as well, various territorial disputes, and a enormous military building spree have put everyone very much on edge, and not on friendly terms. This is a fundamental problem for China, and for the rest of us if they bull their way into a world war.

Domestically, it is quite possible for the repressive system to continue indefinitely, given its continuing determination and often very intelligent management, always on guard against the heresies of freedom and goodwill. But that would be giving up an important future path. The Chinese culture would have greater growth prospects, and greater beneficial consequences at home and abroad, if it opened up and tolerated greater pluralism. Its economic dynamism is up till now built on foreign technology, and its ability to innovate and operate truly in the vanguard of world development depends on some significant degree of political and social dynamism as well, not on Big-Brotherism. 

So I see a future where inevitably, the CCP will have to experiment with grass-roots democracy in order to resolve its fundamental value and motivation conflicts as growth slows and China becomes a wealthier country. These will be frought and dangerous experiments. But in time, there is a chance that they will lead to the same kinds of opening that other Asian countries have experienced so successfully, with the gradual development of another party, and a more humane and less paranoid culture. Conversely, insistence on repression tends to spiral into a need for additional repression, with corresponding chances for a dramatic crackup that might produce another one of the grand cycles of Chinese history.

• Another review, focusing on Xi Jinping.
• On the dangers of private schools.
• Critique of the Nobel prize in economics.
• Religion and the nuttery.

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.

• Some communities rode out the hurricane just fine.
• Loretta Lynn, RIP.
• Eye care- another frontier in predation.
• Christians can't deal with disagreement, claim oppression.
• If you need to delve further into sociopathic narcissism ...
• Essential background on Ukraine.

For the Love of Money

The social magic of wealth ... and Trump's travel down the wealth / status escalator.

I have been reading the archly sarcastic "The Theory of the Leisure Class", by Thorstein Veblen. It introduced the concept of "conspicuous consumption" by way of arguing that social class is marked by work, specifically by the total lack of work that occupies the upper, or leisure class, and more and more mundane forms of work as one sinks down the social scale. This is a natural consequence of what he calls our predatory lifestyle, which, at least in times of yore, reserved to men, especially those of the upper class, the heroic roles of hunter and warrior, contrasted with the roles of women, who were assigned all non-heroic forms of work, i.e. drudgery. This developed over time into a pervasive horror of menial work and a scramble to evince whatever evidence one can of being above it, such as wearing clean, uncomfortable and fashionable clothes, doing useless things like charity drives, golf, and bridge. And having one's wife do the same, to show how financially successful one is.

Veblen changed our culture even as he satarized and skewered it, launching a million disgruntled teenage rebellions, cynical movies, songs, and other analyses. But his rules can not be broken. Hollywood still showcases the rich, and silicon valley, for all its putative nerdiness, is just another venue for social signaling by way of useless toys, displays of leisure (at work, no less, with the omnipresent foosball and other games), and ever more subtle fashion statements.

Conversely, the poor are disparaged, if not hated. We step over homeless people, holding our noses. The Dalit of India are perhaps the clearest expression of this instinct. But our whole economic system is structured in this way, paying the hardest and most menial jobs the worst, while paying some of the most social destructive professions, like corporate law, the best, and placing them by attire, titles, and other means, high on the social hierarchy.

As Reagan said, nothing succeeds like success. We are fascinated, indeed mesmerized, by wealth. It seems perfectly reasonable to give wealthy areas of town better public services. It seems perfectly reasonable to have wealthy people own all our sports teams, run all our companies, and run for most political offices. We are after all Darwinian through and through. But what if a person's wealth comes from their parents? Does the status still rub off? Should it? Or what if it came from criminal activities? Russia is run by a cabal of oligarchs, more or less- is their status high or low?

All this used to make more sense, in small groups where reputations were built over a lifetime of toil in support of the family, group, and tribe. Worth was assessed by personal interaction, not by the proxy of money. And this status was difficult to bequeath to others. The fairy tale generally has the prince proving himself through arduous tasks, to validate the genetic and social inheritance that the rest of the world may or may not be aware of. 

But with the advent of money, and even more so with the advent of inherited nobility and kingship, status became transferable, inheritable, and generally untethered from the values it supposedly exemplifies. Indeed, in our society it is well-known that wealth correlates with a decline in ethical and social values. Who exemplifies this most clearly? Obviously our former president, whose entire public persona is based on wealth. It was evidently inherited, and he parlayed it into publicity, notariety, scandal, and then the presidency. He was adulated, first by tabloids and TV, which loved brashness (and wealth), then by Republican voters, who appear to love cruelty, mean-ness, low taste and intellect, ... and wealth. 

But now the tide is slowly turning, as Trump's many perfidies and illegal practices catch up with him. It is leaking out, despite every effort of half the media, that he may not be as wealthy as he fraudulently portrayed. And with that, the artificial status conferred by being "a successful businessman" is deflating, and his national profile is withering. One might say that he is taking an downward ride on the escalator of social status that is in our society conferred largely by wealth.

All that is shiny ... mines coal.

Being aware of this social instinct is naturally the first step to addressing it. A century ago and more, the communists and socialists provided a thoroughgoing critique of the plutocratic class as being not worthy of social adulation, as the Carnegies and Horatio Algers of the world would have it. But once in power, the ensuing communist governments covered themselves in the ignominy of personality cults that facilitated (and still do in some cases) even worse political tyrannies and economic disasters. 

The succeeding model of "managed capitalism" is not quite as catastrophic and has rehabilitated the rich in their societies, but one wouldn't want to live there either. So we have to make do with the liberal state and its frustratingly modest regulatory powers, aiming to make the wealthy do virtuous things instead of destructive things. Bitcoin is but one example of a waste of societal (and ecological) resources, which engenders social adulation of the riches to be mined, but should instead be regulated out of existence. Taking back the media is a critical step. We need to reel back the legal equation of money with speech and political power that has spread corruption, and tirelessly tooted its own ideology of status and celebrity through wealth.

• California police could use some supervision too.
• Marin- a cruel gerontocracy?

Why Did we Have a Civil War?

It is still a hard one to figure out.

One of the dividends of winning the Cold War was internal division. With no outside enemies or competing ideologies, we were left to become irritated with each other, Newt Gingrich leading the way. It is a general feature of humanity that we are competitive and find points of irritation with each other if there are no supervening projects or conflicts to bind us together. One would think large projects like climate change might be such an overwhelming common challenge and project, but no, it doesn't seem have the immediacy and social drama we need. Thinking and caring deeply about the biosphere is a specialized affair. 

No, our divisive dramas are much more trivial. But in the US there is a pattern, and that is the role of the South as a political / cultural block. It is reminiscent of the process leading up to our first Civil War, where a morally progressive North irritated and alienated a traditional and depraved South. Not that both sections of the country were not fully complicit in slavery, dispossession of the native peoples, and other forms of oppression. It was a matter of degree. But at some point of cultural and moral advancement, it becomes untenable to express our greed and competitiveness in terms of slavery. Slavery requires, as Harriet Beecher Stowe illustrated, a comprehensive deadening of moral sensibility, even while one's senses of honor, greed, religion, not to mention social propriety, may remain fastidious. Dedication to social competition rather than social justice is the order of the region. 

I have been listening to a lengthy podcast narrating the events of the Civil War, which is particularly strong on the introductory phase, explaining various proximate and deep causes of the conflict. What strikes me again and again is the contingency of the whole thing. And its nobility, in a way. The North could easily have washed its hands of the whole conflict, and let the South secede and go its own way. That is what the South was counting on, and many foreign countries, and many (Democrats) in the North as well. As the Union was battered in battle after battle, the mood in the North came perilously close to letting go. 

It took two converging arguments to hold the Northern coalition together- union and abolition. Each one was somewhat abstract and each one alone would probably not have been sufficient to force a war. Abolition was a minority position all the way through the war, and evidently afterwards as the South slid back into de facto slavery. Yet it fired a key segment of the Northern population with great fervor, to take an active interest in what the South was doing, and force an end to slavery rather than let it continue in an independent breakaway nation. There were religious arguments, and arguments of simple humanity, but why young men from Maine should kill those in Virginia about it was not entirely obvious.

The case for union was even more abstract. The union of the states was ostensibly a voluntary affair, and while no mechanism was offered to secede, no formal bar to secession was enshrined in the constitution either. The logic of union was that a nation made up of voluntary associations that could crumble at will was no sound nation at all, and not the kind of country that the prosperous, growing, Manifest Destiny United States was supposed to become. Lincoln labored long and hard to articulate this argument, in his debates and other speeches, including eventually the Gettysburg Address. 

But I think it remains difficult to grasp, even in retrospect. The Southern states felt understandably snookered into a constitutional deal that did not explicitly say it was a one-way trap, but turned out to be one, depending on the (military) willingness of the North to keep them in chains, as it were. The Northern states had many commercial, cultural, and other reasons to regard the South as an indissoluble part of the nation, (most Founders were Southern, for one thing), but fighting a war over it? That was a lot to ask, especially when the result would be at best the forced subservience of half the states and population- what kind of union is that? On the other side, the South didn't fully realize that once you start a war, positions harden and emotions heighten, such that the North felt increasingly bound to see it through to the bitter end. A bit like Ukraine today.

Which feeling was stronger, that of Southerners for preservation of their independence, prerogatives, and economic basis, that of Northerners in their revulsion over the retrograde moral environment of slavery? Or that of Northerners over the preservation of the unique constitutional / democratic experiment as a precious, indissoluble inheritance? The motivations of the South were clear enough, however base. But the motivations of the North, while understandable, seem insufficient to fully justify an extremely bloody war (not that they imagined that extremity at the outset). Thus I see the Northern policy as in some degree idealistic and noble, going far beyond the minimum needed to keep its business going and people happy. 

The North could never have kept the union together and abolished slavery without a war. Some in the North were more abolitionist than pro-Union, and some more pro-Union. Despite the manifest breakdown in North-South relations and the various ante-bellum compromises that kept the union together, keeping those factions aligned was very difficult, before the war, during the war, and through the endless aftermath of reconstruction, Jim Crow, and the Civil Rights movement, and now Southern Republicanism (of all things!) and Trumpism. 

Was the outcome beneficial, in any historical sense? It is very difficult to know how the counterfactual would have turned out. The South might have become a vast banana republic, incorporating Cuba and other territories to its own south. The North would doubtless have continued its ascent to be an industrial collusus and leader of the next century. They might well have remained at peace, despite many points of competition and contention, and traded so that the North would have retained effective access key raw materials from the South. Slavery would have continued, and it is very hard to tell for how long and in what form.

This is where the diplomatically inclined would jump in to say.. it would have been better to negotiate a deal and avoid war. There is always a deal out there that is better than war, which is an ultimate failure and disaster. Compromise after compromise had been made before the war, and shattered by increasingly divergent views on states rights, voting rights, and human rights. If every party had clairvoyance about the future course of events, they might have seen a better way. But we are not clairvoyant, and war is a way to change the conditions of the future rather than to split differences. Wars are certainly the last resort, but remain the final way to decide fundamental existential and power issues, and to change the basis of the future. That is the simple fact of the matter, in a world that is fundamentally competitive. In the words of Vegetius, "Let him who desires peace prepare for war".

Do we today have the capacity to conceive of and adhere to such esoteric and high principles as actuated the North in the last civil war? Our recent president tried to stage a coup, and we can hardly bestir ourselves to care about it. The Supreme Court is impersonating the Taney court, finding that our constitution does not, in fact, protect elementary human rights, such as privacy. We are facing climatic catastrophe that is leading to mass migration, war, and challenges to our fundamental basis of existence, (farming, and addiction to fossil fuels), not to mention imperiling the biosphere at large. And we can hardly bestir ourselves to care about it. Again, half the country, centered in the South, feels morally condescended to and responds with spite and revanchism. Again, the rich fight with every tool to keep things the same and shut our eyes to the dangers ahead. 

While the political dramas of today will likely pass away without taking to arms, despite the militant recklessness of the Southern end of the political spectrum, it is hard to be as optimistic about our other challenges. When the US looks ahead today, it sees change, constraint, and decline. It is a hard future to face, and many quail from doing so, (whatever their vacuous and delusory slogans). But face it we must, lest it turn from a challenge into a rout.

• The polycrisis of capitalism.
• Krugman on pessimism and division.
• Such a deal!
• Either a carbon tax or a crypto tax.
• We have not even hit peak oil yet.
• The war we really don't need. Not that I generally agree with Chris Hedges.

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.

• Meanwhile, a Christian court makes us a Christian nation, like it or not.
•  Length of Covid infection and viral shedding is unaffected by strain or vaccination status.

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.

• Fisheries are killing far more than fish.
• Grooming on youtube.
• Wolves really touch a nerve.

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.
• Yes, chimpanzees can talk.
• The rich are getting serious about destroying democracy.
• 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.

A Road of Grass- Migrations Along the Asian Steppe

Genomics data confirms that the Avars were of East Asian origin before taking over the Carpathian basin.

Historians have gradually accorded increasing respect to the various Central Asian groups that swept in and terrorized Europe for a millenium, including in turn the Scythians, Huns, Avars, Mongols, and Turks. The Mongols particularly created a golden age of commerce across the Silk Road, which Marco Polo traveled to such great adventure. This history is both extremely dynamic, and poorly documented, as these nomadic cultures left little behind, especially writing. Their roots range from Iran and the Indo-Europeans to the Mongolian and Tungusic regions. A putative "Altaic" language group extends from Hungary all the way to Korea and Japan, though it is a disparate group arising more from interchange and borrowing than from a single origin- testament to the frequent traffic along the steppes.

To settled cultures, both in Europe and in China, these nomads were terrors, living on their horses, infinitely mobile, and possessing powerful weapons like their composite bows. The continual succession of these cultures (unlike, say, the long stability of ancient Egypt) also indicates that they fought constantly among themselves, in true Darwinian fashion. Success revolved around not only technical innovation and a martial culture, but also social abilities to forge groups large and cohesive enough to control vast regions, despite the tendency of warriors to fight ... with each other.

The Avars were one of this succession, historically known as invaders of the Carpathian Basin who set up a brief empire (~570 to 790 CE) after defeating Goths who had in turn succeded the Huns, who had replaced the Romans of Pannonia. At their height, the Avars ruled from Turkey to Austria, but were within two hundred years defeated by the Franks, who were soon followed by the Magyars, who finally stayed to found what is now Hungary. One can see that the Balkans, which lie in this region and towards the Adriatic, have had a tumultuous history. The Avars had reputedly come from the far East, after the nascent Turks defeated the Hunnic / Rouran center, of which the Avars were supposedly a successor, offshoot, or client group. Historians have been divided, though, since there is little evidence of far Eastern influences in the Carpathian archeology, and competing accounts put their origin more Westerly, around the Urals or Caspian basin. 

"The Rourans were defeated by the Turks, who had been their subjects, in 552–555. Their empire fell apart and, according to the contemporary Chinese sources, the core Rouran population was brutally massacred. Some of the Rourans fled to China and soon disappeared from sources. Another group of the Rourans is commonly thought to have migrated westwards and become the Avars of European history"

But a recent paper (largely authored by Hungarians) has settled the matter. They sequenced DNA from numerous burials dated through the Avar era, and compared them to a variety of samples from across the steppes. They find that indeed, the earliest and richest graves of the Avar era have almost exclusively far East Asian DNA markers, from what is now roughly Mongolia, while later remains show increasing admixture with the local Western Europeans. 

"All of the early-Avar-period individuals (DTI_early_elite), except for an infant and a burial with typical characteristics of the Transtisza group, form a tight cluster with a high level of ANA (ancient North East Asian) ancestry. They are located between present-day Mongolic- (e.g., Buryats and Khamnigans) and Tungusic/Nivkh-speaking populations (e.g., Negidals, Nanai, Ulchi, and Nivkhs) together with the only available ancient genome from the Rouran-period Mongolia."

"The remaining 9 late-Avar-period individuals show minor (<40%) to almost negligible (<5%) admixture with ANA-related sources, while the major ancestry component can be approximated by one of the preceding local groups for most of the individuals"

In discussions of these eras, hundreds of years can go by rather quickly. Still, the mobility and dynamism of these peoples is astonishing. Rome had already experienced the knock-on effects of tribes such as the Scythians driving other peoples westward before them. And the Indo-European invasions were something similar, farther back in the mists of time. Such migrations and conquests kept on happening, thanks to the love these people had for their horses, the endless flatness of the landscape, and the rich pickings available among settled cultures around their periphery.

The Steppe region marked in brown. Sites of burial remains that were sequenced are marked, extending clear across Asia, allowing the authors to classify particularly early and high-status burials in the Carpathian basin (left-most) as most related to a far eastern origin.

Today, Russia (whose lengthy period under Mongol rule strongly shaped its culture) has resumed the mortal competition for empire among the flatlands of Central Asia and Eastern Europe. While we can marvel at the relentless valor of Huns and Avars, seeing such ruthlessness up close in our own time isn't abstract history, it is thoroughly appalling.

• The sleeze just keeps getting worse.
• The Webb telescope is working great.
• Making ebikes easy.
• Is the Bible age-appropriate reading material?
• Another reason for inflation.
• Six minutes hate ... and lies.

Love Beauty Truth

Book review of "Finding your Feet after Fundamentalism", By Darrell Lackey. With apologies to the other book.

An old friend has published a book. We had an epistolary relationship, fretting about creationism, intelligent design, and related topics back when those were livelier issues than today (and it directly inspired the birth of this blog). He was on his way out of Christian fundamentalism, and into something more liberal, even post-modern. His new book is a somewhat autobiographical account of the problems of fundamentalism, and of leaving fundamentalism as one's tradition. Naturally, evangelism dies hard, and takes this new form of broadcasting the good news of a more moderate and decent Christianity.

The book hits hardest on the issue of Donald Trump. No scandal has so thoroughly demonstrated the ultimate hypocrisy of fundamentalism than its allegiance to Trump. The transaction has given religious conservatives control of the Supreme Court, (though perhaps that owed more to Mitch McConnell), but in return, they showed their support for the most morally vile and incompetent person ever to hold the job. Lackey relates how he was fully in the FOX news orbit in the 90's, happily imbibing its bile. But then something snapped, and by the time of the Trump election, he had fully left fundamentalism and its communities behind. Living in California might have something to do with it, since liberalism, at least of a lip-service sort, is the dominant way of life here. Something that Republicans have learned the hard way. 

Yet the interesting part is how strenuously Lackey hews to Christianity, proclaiming that liberal versions are not gateway drugs to atheism. Quite the contrary- close attention to the actual New Testament provides ample justification for things like supporting marginalized communities, helping the poor, afflicting the rich, and viewing one's enemies as possibly reasonable human beings, if not friends in the making. He mentions how false it is for evangelicals to be so eager to spread the good word, but at the same time so deaf to the words of others that actual relationship is impossible- an evangelism of a closed-off community. 

For what are the fundamental values? Lackey cites love and beauty. Love is clear enough, (and damning enough regarding the FOX- driven culture of conservative Christianity), but the role of beauty needs a little more explaining. Religious thinkers have spared no effort in extolling the beauty of the world, but in the current world, serious artists are rarely Christian, let alone make Christian art. Why is that? Perhaps it is just intellectual fashion, but perhaps there is a deeper problem, that art, at least in our epoch, is adventurous and probing, seeking to interrogate narratives and power structures rather than celebrate them. Perhaps it is a problem of overpopulation, or of democracy, or of living in late imperial times, or of modernism. But whatever the framework, contemporary Christian communities have become the opposite of all this- anti-intellectual, tone-deaf, and art-hostile (not to mention power-mad). It must be exasperating to someone with even the least appreciation for finer things and for art that is "interesting".

Jean-Michel Basquiat- too messy for insensitive temperaments.

Beauty has deep Christian connotations. The world is god-made, good, and thus beautiful, as indeed we all feel it to be. But life is also messy, competitive, and dark. Death and suffering are part of it as well. If we refuse to own those aspects of the world, and of ourselves, we become blinded to the true nature of things, and expose ourselves to unintended and invisible expressions of the dark side, as we see in the deep hypocrisy on the subject of Trump, on sexual morals, and countless other areas within fundamentalism / evangelicalism. Lackey ticks off a lengthy list of subjects where conservative Christians have become blind to the obvious teachings of Jesus while fixated on relatively minor cultural flashpoints and red meat- symptoms of a general moral blindness borne of, arguably, flaccid aesthetic and intellectual habits.

So I would like to offer another value, which is truth. As a scientist, it is a natural place for me to start, but I think it is both illuminating of, and interrelated with, the other virtues above. What modern artists seek is to express truths about the human condition, not just ring out positive affirmations and hallelujas. Truths about suffering as well as truths about beauty. What scientists seek to do is to find how this world we find ourselves in works, from the cosmos down to the gluon. And they do so because they find it beautiful, and, like addicts, would like to unlock more of that beauty. Beauty inspires love, and love ... can only survive on truth, not lies. So I think these values live in a reinforcing cycle.

All that implies that there is another step to take for someone who has left fundamentalism. That is, to re-evaluate Christianity as a whole. While the achievement of decency (and better taste) by the renunciation of FOX and its religious satellite communities is an enormous step, indeed a momentous one for the preservation of our country's sanity, grappling seriously with the value of truth would suggest an extra leg to the trip. Not to put too fine a point on it, but Christianity as a whole is a questionable proposition, philosophically. As a narrative and moral system, it clearly has positive as well as negative potentials. But as a "truth"- with its miracles, resurrections, triune deity, and salvation at the end of the line, (whether for the elect, the saved, the good, or for all)- well, it is impossible to take seriously without heavy doses of tradition and indoctrination.

For his part, Lackey has headed in another direction, into the Eastern Orthodox church, finding a place that richly satisfies the fundamentalist urge to return to one of the most traditional and historically continuous churches in existence, and also one that does not tie itself into intellectual knots about literal truth, living biblically, and the like. Orthodoxy accepts mystery, and cherishes its ancient rites and structures as sufficient theology. It is not modernist, or goaded by the enlightenment to make a rational system of something that so obviously resists reason. 

For there is a fine line between lies, illusions, and truths. As anyone who is married will understand (or a citizen of a country, or part of a corporation, or part of any social structure), truth is not the only or necessarily best virtue. A bit of illusion and constructive understanding can make a world of difference. Narrative, ideology, framing, etc. are essential social glues, and even glues of internal psychology. So, given that illusions are integral, the work to identity them, bring them into consciousness, and make positive choices about them is what matters, especially when it comes to social leadership. Do we choose narratives that are reasonably honest, and look forward with hope and love, or ones that go down the easy road of demonization and projection? And what role should the most traditional narratives in existence- those of the ancient religions- have in guiding us?

• Beautiful? You be the judge.
• Kasparov on freedom and evil.
• Kids should be able to navigate neighborhoods.
• Lies and disinformation are a public health crisis.
• More variants are always coming along.
• We are not doing enough against climate heating.

A Brief History of DNA Sequencing

Technical revolutions that got us to modern DNA sequencing.

DNA is an incredibly elegant molecule- that much was apparent as soon as its structure came out. It is structurally tough, and its principles of information storage and replication are easy to understand. It is one instance where evolution came with, not a messy hack, but brilliant simplicity, which remains universal over all the life that we know. While its modeled structure was immediately informative, it didn't help to figure out its most important property- its sequence. Methods to sequence DNA have gone through an interesting evolution of their own. First were rather brutal chemical methods which preferentially cut DNA at certain nucleotides. Combined with the hot new methods of labeling the DNA with radioactive P32, and of separating DNA fragments by size by electically pushing them (electrophoresing) through a jello-like gel, this could give a few base pairs of information.

A set of Maxam-Gilbert reactions, with the DNA labeled with 32P and exposed to X-ray film after being separated by size by electrophoresis through a gel. Smallest are on the bottom, biggest fragments on on the top. Each of the four reactions cleaves at certain bases, as noted at the top. The intepretation of the sequence is on the right. PvuII is a bacterial enzyme that cleaves DNA, and this (palindromic) sequence noted at the bottom is the site where it does so.

Next came the revolution led by Fred Sanger, who harnessed a natural enzyme that polymerizes DNA in order to sequence it. By providing it with a mixture of natural nucleotides and defective ones that terminate the extension process, he could easily develop far bigger assortments of DNAs of various lengths (that is, reads) as well as much higher accuracy of base calling. The chemistry of the Maxam-Gilbert chemical process was quite poor in base discrimination. This polymerase method also eventually used a different isotope to trace the synthesized DNAs, S35, which is less powerful than P32 and gave sharper signals on film, which was how the DNA fragments were visualized after laid out and ordered by size, by electrophoresis.

The Sanger sequencing method. Note the much longer read length, and cleaner reactions, with fully distinct base specificity. dITP was used in place of dGTP to help clarify G/C-rich regions of sequence, which are hard to read due to polymerase pausing and odd behavior in gel electrophoresis. 

There have been many technological improvements and other revolutions since then, though none have won Nobel prizes. One was the use of fluorescent terminating nucleotides in place of radioactive ones. In addition to improving safety in the lab, this obviated the need to generate four different reactions and run them in separate lanes on the electrophoretic gel. Now, everything could be mixed into one reaction, with four different terminating fluorescent nucleotides in different colors. Plus, the mix of synthesized DNA products could now be run through a short bit of gel held in a machine, and a light meter could see them come off the end, in marcing order, all in an automated process. This was a very significant advance in capacity, automatability, and cost savings.

Fluorescent terminating nucleotides facilitate combined reactions and automation.

After that came the silicon chip revolution- the marriage between Silicon Valley and Biotech. Someone discovered that silicon chips made a good substrate to attach DNA, making possible large-scale matrix experiments. For instance, DNA corresponding to each gene from an organism could be placed at individual positions across such a chip, and then experiments run to hybridize those to bulk mRNA expressed from some organ or cell type. The readout would then be fluorescent signals indicating the level of expression of each gene- a huge technical advance in the field. For sequencing, something similar was attempted, laying down all possible 8 or 9-mers across such a chip, hybridizing the sample, thereby trying to figure out all the component sequences of the sample. The sequences were so short, however, that this never worked well. Assembling a complete sequence from such short snippets is nearly impossible.

What worked better was a variation of this method, where the magic of DNA synthesis was once again harnessed, together with the matrix layout. Millions of positions on a chip or other substrate have short DNA primers attached. The target DNA of interest, such as someone's genome, is chopped up and attached to matching primers, then hybridized to this substrate. Now a few amplification steps are done to copy this DNA a bunch of times, all still attached in place to the substrate. Finally, complementary strands are all melted off and the single DNA strands are put through a laborious step-by-step chemical synthesis process, similar to how artifical DNA is made to order, across the whole apparatus, with chemicals successively washed through. No polymerase is used. Each step ends with a fluorescent signal that says what the base that just got added was at that position, and a giant camera or scanner reads the plate after each pass, adding +1 to the sequence of each position. The best chemical systems of this kind can go to 150 or even 300 rounds (i.e. base pairs), which, over millions of different DNA fragments from the same source, is enough to then later re-assemble most DNA sequences, using a lot of computer power. This is currently the leading method of bulk DNA sequencing.

A single DNA molecule being sequenced by detecting its progressive transit through a tiny (i.e. nano) pore, with corresponding electrical readout of which base is being wedged through.

Unfortunately, our DNA has lots of repetitive and junky areas which read sizes of even 300 bases can not do justice to. We have thousands of derelict transposons and retroviruses, for instance, presenting impossible conundrums to programs trying to assemble a complete genome, say, out of ~200 bp pieces. This limitation of mass-sequencing technologies has led to a niche market for long-read DNA sequencing methods, the most interesting of which is nanopore sequencing. It is almost incredible that this works, but it is capable of reading the sequence of a single molecule of single stranded DNA at a rate of 500 bases per second, for reads going to millions of bases. This is done by threading the single strand through a biological (or artifical) pore just big enough to accommodate it, situated in an artifical membrane. With an electrical field set across the membrane, there are subtle fluctuations detectable as each base slips through, which are different for each of the four bases. Such is the sensitivity of modern electronics that this can be picked up reliably enough to read the single thread of DNA going through the pore, making possible hand-held devices that can perform such sequencing at reasonable cost.

All this is predicated on DNA being an extremely tough molecule, able to carry our inheritance over the decades, withstand rough chemical handling, and get stuffed through narrow passages, while keeping its composure. We thought we were done when we sequenced the human genome, but the uses of DNA sequencing keep ramifying, from forensics to diagnostics of every tumor and tissue biopsy, to wastewater surveillance of the pandemic, and on to liquid biopsies that promise to read our health and our future from a drop of blood.

• Is originalism progressive?
• Crypto is insane- a climate disaster, ponzi-ridden, crime-facilitating, sanctions-busting.
• Who lies, and who believes them? It tends to be a consistent demographic.
• The insurrection is not over.
• "The Capitalist system was never designed to satisfy societal needs."
• How do you pronounce "mayonnaise"?
• Big box and big parking lot solar? Obviously a good thing.
• Jane Fonda is onboard.