LncRNA: Goblins From the Genomic Junkyard

One more addition to the zoo of functional RNAs.

A major theme over the last couple of decades of molecular biology is the previously unanticipated occurrence of many sorts of small and not so small RNAs that do not code for proteins. In addition to buttressing the general proposition that RNA came early in the history of life and retains many roles beyond being merely the conveying medium of code from DNA to protein, these novel RNAs illuminate some of the complexity that went missing when the human genome came in at under 20,000 protein coding genes.

The current rough accounting of human genetic elements. While we have only 19,954 protein coding genes, we have a lot of other material, including almost as many pseudogenes, (dead copies of protein-coding genes), and even more RNA genes that do not code for proteins. The count of mRNA transcripts is high because splicing of a protein-coding gene is frequently variable and can generate numerous distinct mRNA messages from one gene. Similarly, the start and stop points of transcription can be variable for both mRNA and lncRNA genes.

RNAs perform many functions, such as the catalytic core of the ribosome, the amino-acid complementary-coding role of tRNAs, the catalytic core of the mRNA splicing apparatus, guides to edit and modify ribosomal RNAs, and miRNAs that repress expression of target genes. LncRNA stands for long non-coding RNAs, which were discovered by global analyses of RNA expression. Long transcripts were found that did not have protein coding frames, did not clearly derive from degraded pseudogenes (degraded copies of protein coding genes), and which occasionally still had significant conservation and thus evident selective constraint and function.

Another piece of background is that these expression analyses have found, as the technology advanced in sensitivity and comprehensiveness, that most of our genome is transcribed to RNA. Not only do we have a large amount of junk DNA, like transposons, repetitive elements, pseudogenes, intron and regulatory filler, etc., representing at least 90% of the genome, but most of this DNA is also transcribed at a low level. We have quality control mechanisms that dispose of most of this RNA, but there have been partisans of another perspective, particularly among those who first found all this transcription, that these transcription units are "functional", and thus should not be dismissed as "junk".

Eugene Koonin is not of that persuasion. His recent review of this field, and of lncRNAs in particular, with Alexander Palazzo, generates an extremely interesting model of why most of this is junk, and how such junk RNA can occasionally gain function. Some lncRNAs are important, typically helping nearby genes stay on. One of the most significant lncRNAs, however, represses its nearby genes, and is central to the process of X inactivation. XIST is 17,000 nucleotides long- very long for a non-coding RNA- and binds to dozens of proteins including chromatin remodeling enzymes and X-chromosome scaffold proteins, all in a byzantine process that shuts down the extra X chromosome that females have. This prevents the genes of that chromosome, which encompass many functions, not just sex-specific ones, from being expressed two-fold higher in females than in males.

How to make sense of all this? How can there be many thousands of lncRNAs, but only a few with function, and those functions rather miscellenous, typically local, and centered on transcriptional regulation? The tale begins with one of the many quality control features of the transcription apparatus. When a gene is transcribed, the polymerase as it goes by deposits chromatin marks (on the local histones) that prevent other transcription complexes from initiating within the gene. This prevents extra initiation events that would produce truncated proteins, which can sometimes be very harmful, lacking key regulatory domains. So the theory posits that much of the stray transcription of junk DNA through the rest of the genome, especially in the form of long lncRNAs, has a similarly repressive effect, reducing local initiation within those "gene" bounds. This might be particularly helpful to prevent interference with regulatory events happening in those regions, controlling transcription through the region rather than allowing it to happen sporadically all over.

As a first step, it is innocent enough, and not likely to have strong selection constraints, typically of a low level, and perhaps eventually responsive to some regulatory events, depending on the needs of the nearby coding gene. Nor would the lncRNA that is made have any function at all. It would be junk very literally, would not get spliced, or exported out of the nucleus, and probably get degraded promptly. Its sequence is under no particular selection, and would drift in neutral fashion. The second step then happens if this RNA were to gain some kind of function, such as binding some regulatory protein. There are many RNA and DNA binding proteins in the cell, so this is not difficult. Xist binds to over 80 different proteins. These proteins then might have local effects, as long as the lncRNA remains attached to its own transcription complex during its own synthesis. Such effects might be activating the nearby gene, loosening or tightening nearby chromatin. Given the (arbitrarily large) size of the lncRNA, and the typically small size of nucleic acid binding determinants that proteins recognize, there is little limit to how many such interactions could be accumulated over time, always subject to selection that likely centers around fine-tuning of effects on nearby genes. Indeed, this regulation could allow the relaxation or loss of more proximal regulators, making the lncRNA increasingly essential. After enough interactions accumulate, the lncRNA may remain tethered to local landmarks, and its activity persist after its synthesis ends, prompting selection against its degradation.

In this way, increasingly elaborate mechanisms can be built up, out of very modest selective effects, combined with a lot of drift and exploration of neutral mutational space. This theory provides a rationale for what we are seeing in the lncRNA landscape- a huge number with little to no ascertainable function, but a few that have grown into significant regulators of their local or extended chromatin landscape. It also informs the mechanism by which they function, not as some new exciting mechanism of action by a discrete RNA species, as was found with miRNAs, for instance, but rather an agglomeration of adventitious interactions that will be different in each case, and highly variable in effect.

"Indeed, although complexity in biology is generally regarded as evidence of “fine tuning” or “sophistication,” large biological conglomerates might be better interpreted as the consequences of runaway bureaucracy—as biological parallels of nonsensically complex Rube Goldberg machines that are over-engineered to perform a single task"

 

• Best president for Blacks?
• Do reason and truth drive us?
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• Charles Turner.
• Life in the lab.

Rise and Fall of the US

What happened to our 20th century solidarity?

A recent issue of The New Republic carried an article by its publisher that discussed Robert Putnam's diagnosis of the decline of American civic community and solidarity. In the generational arcs of US history, we have had high solidarity, and consequent productive and progressive political eras, only a few times- the colonial era, the Republican interlude while the South had seceded, the progressive era around the turn of the 20th century, and the post-WW2 boom. Perhaps much of the 20th century could be classified that way, up to the 1970s. At any rate, we are obviously not in such an era now. We are, in contrast, floundering in an era of incredible political and social divisiveness, of unproductive public institutions, and of social atomization.

"Just as Putman and Garrett identify an upswing, they also trace a decline beginning in the 1970s. For this, too, they offer an explanation that departs from the standard historical narrative, suggesting that it was not Ronald Reagan who brought the long period of liberal rule to an abrupt halt, but rather the baby boomer of the 1960s who, turning from the communitarian idealism of the early part of the decade toward a more self-oriented direction, set off a chain reaction that ended up blowing the whole Progressive-liberal order to smithereens."

But the article does not really articulate what happened, other than to cite the many dramas of that time, and propose that the US had a bit of a "nervous breakdown", in a transition from a conformist 50's, through the wide-open and tumultuous 60's, to the me-centered 70's. Perhaps this dates me, but I did live through some of those times, and I think can offer a more specific analysis. I'd suggest that the principal elements of the downturn arose from fundamental violations of trust by the state. The US had conducted WW2 with great moral and logistical authority. The grunts always grumbled, and there were plenty of fiascos along the way, but overall, there was a consensus that the elites and people in charge knew what they were doing. They not just won the war, but fostered unprecedented prosperity in its wake. 

All this turned around in the late 60's. I am also reading a history of the CIA, by Tim Weiner, "Legacy of Ashes". This is a deeply biased book, focusing on every failure of the CIA, pronouncing it as an institution utterly and irredeemably incompetent. What is noticeable, however, is that the CIA's successes are generally far more costly than its failures. The coups it sponsored in Iran and Guatemala, et al. came back to haunt us down to the present day. Eisenhower founded this pandora's box of disastrous meddling, (i.e. covert action) and Kennedy accelerated its use. One of its signature accomplishments was the slow process of getting us enmeshed in the Vietnam war. This was the single most influential disaster that discredited the US government to its own citizens. While in principle, we were doing a great thing- saving South Vietnam from communism and totalitarianism- in practice, we had no idea what we were doing, did not understand the nature of the civil war, or the impossible corruption of our allied government, and conducted the war in a fog of lies and delusions. The daily body counts were a visceral expression of revulsion against the state.

But this kind of incompetence became a pattern in major events like Watergate, inflation, the oil crisis, and the Iran hostage crisis. Each one showed that our leaders did not know what they were doing- the best and brightest turned out unequal to the crises we faced. A succession of presidents fell victim to fundamental breaches of trust with the country. Inflation, for example, made us feel helpless- that the money itself was being eaten away by processes that were virtually occult in their mystery and darkness. Gerald Ford urged a kind of vodoo economics- that perhaps a public relations campaign urging personal savings and voluntary spending reductions could heal "the economy". But the solidarity he was counting on was evaporating, and the rationale was transparently absurd and unequal to the crisis, which had been brought on by the oil shock and by profligate government spending and interest policy through the Vietnam era. It would not be until the advent of Paul Volcker that we would get a public servant with the courage and intellect to slay this beast, through an extremely costly campaign of squelching private investment.

So it was not Ronald Reagan who started the process of me-ism over patriotic solidarity. He was only expressing the sad consequence of a long series of failures and breaches of faith when he claimed that government is not the solution, government is the problem. So what was the alternative? The other major institutions of common action were and remain the corporation, and this era saw the valorization of capitalism as the system that works. It had the Darwinian structure and motivations that enforced effectiveness, even excellence. It was the environment that unleashed entrepreneurial freedom, then harnessed it for the common good. We know now that all this was vastly oversold, and ignored all the reasons why we have states to start with. But the pendulum had swung decisively from the public sphere to the private.

An unfortunate consequence of such a swing is that the party and ideology of privatization has little interest in fostering effective governance. So the competence of the state erodes further with time, becoming increasingly unable to do basic functions, and becoming corrupt as private interests gain relative power. Our current administration, were it not in power, would be a parody of self-serving corruption and incompetence. It is the pinacle of the Reagan revolution, and it is degrading, day by day, our ability to govern ourselves. This seems to be why these generational shifts take so long to correct. It is not only that we need to recognize the hole we have fallen into on an intellectual and scholarly level, but that enough voters (and enough extra to overcome the entrenched powers of capital in propaganda, lobbying, campaign finance, and other forms of corruption) have to have felt this in their bones to give an alternative ideology a chance to retake charge of the state and rebuild its capacity for effective action. 

• Where are the vaccines? What are the vaccines?
• Not everyone likes Barrett.
• Make the Apocalypse great again.

Vision Bubbles up into Perception

Visual stimuli cause progressive activation of processing stages in the brain, and also slower recurrent, rebounding activation, tied to decision-making.

Perception is our constant companion, but at the same time a deep mystery. How are simple, if massively parallel, sensory inputs assembled into cognition? What is doing the perceiving? Where is the theater of the mind? Modern neuroscience is steadily chipping away at these questions, whether one deems them "hard", unscientific, or theological. The brain is a very physical, if inaccessible, place, forming both the questions and the answers.

A recent paper made use of MEG, magnetoencephalography of electrical events in the brain, to track decision-making as a stepwise process and make some conclusions about its nature, based on neural network modeling and analogies. The researchers used a simple ambiguous decision task, presenting subjects with images of numbers and letters, with variations in between. This setup had several virtues. First is that letters and numbers are recognized, at a high level, in different regions of the brain. So even before the subjects got to the button pressing response stage, the researchers could tell that they had cognitively categorized and perceived one or the other. Second, the possibility of ambiguity put a premium on categorization, and the more ambiguous the presented image, the longer that decision would take, which would then hypothetically be reflected in what could be observed here within the brain.

The test presented. An image was given, and the subject had to judge whether it was a number, a letter, and what number/letter it was.

The researchers used MRI solely to obtain the structures of the subject's brains, on which they could map the dynamic MEG data. MEG is intrinsically much faster in time scale than, say, fMRI, allowing this work to see millisecond scale events. They segmented the observed stages of processing by some kind of statistical method into 1- position and visibility of the stimulus; 2- what  number or letter it is; 3- whether it is a number or a letter; 4- how uncertain these decisions are; 5- the motor action to press the button responding with all these subjective reports. In the author's words, "We estimated, at each time sample separately, the ability of an l2-regularized regression to predict, from all MEG sensors, the five stimulus features of interest." These steps / features naturally happen at different times, perception being necessarily a stepwise process, with the scene being processed at first without bias in a highly parallel way, before features are picked out, categorized, and brought to consciousness, in a progressively less parallel and more diffuse process.

Activation series in time. The authors categorized brain activity by the kind of processing done, based on how it was responding, and mapped these over time. First (A, bottom) comes the basic visual scene processing, followed by higher abstractions of visual perception. Finally (A, top) is activation in the motor area corresponding to pressing a response button. C and D show more detail on the timing of the various processes.

It is hard to tell how self-fulfilling these analyses are, since the researchers knew what they were looking for, binned the data to find it, and then obtained estimates for when & where these binned processes happened. But assuming that all that is valid, they came up with striking figures of cognitive progression, shown above. The initial visual processing signal is very strong and localized, which is understandable first because the early parts of the visual system (located in the rear of the brain) are well understood, and second because those early steps take in the whole scene and are massively parallelized, thus generating a great deal of activity and signal in these kinds of analysis. This processing is also linear with respect to the ambiguous nature of the image, rather than sigmoidal or categorical, which is how higher processing levels behave. That is because at this level, the processing components are just mindlessly dealing with their pixel or other micro-feature of the scene, regardless of its larger meaning. The authors state that 120 milliseconds is on average where the rough location (left or right of the screen) is decided by this low level of the visual system, for instance. By 500 milliseconds (ms), this activity has ceased, the basic visual analysis having been done, and processing having progressed to higher levels. The perception of what the letter is, (225 ms) and whether it is a letter or number (370 ms) happens roughly around the same time, and varies substantially, presumably due to the varying abiguities of what was presented.

At around 600 ms, the processing of just how uncertain the image is seems to peak, a sort of meta-process evaluating what has gone on at lower levels. And finally, the processing directing the motor event of pressing the button to specify what the subject has decided about the item identity or category (just a binary choice of left or right index finger) comes in on average also around 600 ms. Obviously, there is a great deal going on that these categorizations and bins do not capture- the MEG data, though fast, are very crude with respect to location, so only the broadest distinctions can be attempted.

The authors go on to press a further observation, which is that the higher level processing is relatively slow, and processing devoted to these separate aspects of the perceptual event takes longer and trails off slower than one might expect. Comparing all this to what is known from artificial neural networks, they conclude that it could not possibly be consistent with strictly feed-forward processing, where one level simply does its thing and communicates results up to the next level. Rather, the conclusion, in line with a great deal of other work and theorization, is that recurrent processing, making representations that are stable for some time some of these levels, is required to explain what is going on. 

This is hardly pathbreaking, but this paper is notable for the clarity with which the processing sequence, from visual stimulus to motor response, is detected and presented. While working in very broad brushstrokes regarding details of the scene and of its perception, it lays out a clear program for what comes next- filling in the details to track the byways of our thoughts as we attend consciously to a red flower. This tracking extends not only the motor event of a response, but also to whatever constitutes consciousness. This paper did not breathe the word "conscious" or "consciousness" at all, yet a video is provided of the various activations in sequence showed substantial prefrontal activity in the 450 ms range after image presentation, constituting a sixth category in their scheme that deserves a bit more attention, so to speak.

• A high-level talk about how blood supply in the brain responds to neural activity.
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• On the appalling ineffectiveness of the flu vaccine. It makes one wonder why we are waiting for the phase III trials of the coronavirus vaccines.
• US to Taliban: "Please?"
• A day at the Full Circle Ranch.

Coronavirus M protein

Why is SARS-CoV2 such a protean virion?

Some viruses have a crystaline structure- a capsid that is absolutely uniform, dictated by the proteins that make it up in orderly arrays. The classic T4 bacteriophage is like that, and one of its features is that it stuffs its DNA contents into the capsid under extremely high pressure (20 atmospheres). That allows those contents to shoot out later with great force, into its victim- a bacterium with a strong cell wall. Coronaviruses and related influenza viruses are not like that at all. Their RNA contents are loosely collected, and the capsid assembled in cellular membranes, ending up with a variable, almost floppy, shape. The way into the next target cell is not via a physical power-injection system, but much more gently, by using one of the eukaryotic cell's several mechanisms for endocytosis to slip inside, and then veer off from the fate of being digested like food, and instead set up shop inside its own custom-made system of vesicles. 

The coronavirus surface (envelope) is composed of only a few proteins- the spike (S) protein that sticks out and attaches to, and initiates fusion with, target cells; the envelope (E) protein, which is a minor helper towards the virus's final shape; and the membrane (M) protein, which makes up most of the envelope. E is not essential, and S is not essential at all for virus formation, but M is quite essential. It gathers in huge amounts at internal membranes (called ERGIC) in rafts in preparation for virus assembly. Meanwhile the N protein has bound to special sequences on the genomic RNA, forming a sort of chromosome. The genomic RNA also has a particular tail that can bind directly to M protein. It is M that really orchestrates the whole assembly process, binding to the genomic RNA, to N, to E, and to S proteins, not to mention membrane lipids.

Schematic of the coronavirus envelope structure. The spike (S) protein in light gray sticks outwards. The nucleocapsid (N) protein in dark gray organizes the strands of genomic RNA. The envelope (E) protein in yellow occurs occasionally to impose curviture on the envelope, encouraging it to adopt a spherical shape. And the membrane (M) protein in black forms the bulk of the envelope, binding to and organizing all the other components. These authors find that occasional M proteins (red) lack inward projections. 

Incidentally, a recent paper came out about influenza M protein, which plays a very similar role, except that influenza virions are even more variable, forming into both spheres and filaments. These authors were able to generate remarkable images of the influenza M protein forming into very regular filament arrays, seen in cross-section, below. 

Filaments of M1 protein from influenza virus, see in cross-section, with a littering of half-helices lying about. The core of these filaments would be filled with infectious genomic RNA. Scale bar is 1000 nm.

So- why so unstructured? First, the viral envelope is developed from cellular membranes, and the final virus envelope still has some amount of lipids from those membranes. These tend to be quite fluid, limiting the structural regularity that can be achieved. Also, since there is no need for pressurized injection to the target, there is no need to obsess about the virus container as a totally defined, rigid body. It is apparent, from the micrographs below, that virion volumes can vary substantially, at least two-fold, suggesting that sometimes two genomes can get packed into one virion, or even more. Where is the harm in that? Given some spread by aerosols, twice the virus dose is perhaps a reasonable tradeoff for a slightly bigger and less spread-able virion container.

Is M a target for the immune system or for vaccines? No, no one seems to care about it, since it is the S protein that is most exposed on the surface and the key for attaching to and infecting new cells. Yet all parts of the virus life cycle are interesting, and it is certainly possible that small molecule drugs directed against M could be highly disruptive, to virus assembly if not to already- formed virions. Drug targets or not, these proteins play a humble structural role, knitting together virions so that they can go out into the hostile world on a puff of air and survive a few hours, enough to enter new hosts incautious enough to be gabbing in enclosed spaces.

A comparison of virions grown without S protein (top) or with S protein (bottom). Nor is N protein required for virion formation, really. It is M that organizes everything. These experiments use another coronavirus, mouse hepatitis virus (MHV).

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• Snowflakes on the Supreme Court can not deal with freedom.

Eugenics, the Catholic way

Woe betide any tampering with God's nature! However, destroying it with overpopulation is OK.

The current Supreme Court battle puts a spotlight on Catholicism in law and ethics. With the impending justice, six of the nine will be Catholic. The more rightward Catholic justices are coming from a culture that has some peculiar views on itself, on key ethical issues, and on the future of the world. First is its self-righteousness. Fundamentalist Catholics like Antonin Scalia and Attorney General Barr are confident that they come to government service steeped in the most exacting and time-honored moral code- that of the church which has been in existence going on two thousand years. It is a church that has weathered millennia of political turmoil and tectonic shifts of philosophy. But does all that history make it right? Does durability imply anything other than a canny grasp of human psychology, both in keeping its parishioners in the fold, and in keeping the wheels of its authoritarian structures turning? I don't think so. Far better moral systems have been imagined and enacted, and the Church has, time after time, grudgingly taken them up, typically a century after the rest of society. Today, a Catholic woman is nominated to the Supreme Court. Maybe in a hundred years, a female cardinal? 

But what is particularly galling is the prating about the sacredness of life. William Barr has restarted federal executions, to add to all his other lying and subversions of justice, giving one a curious impression of this "culture of life". What is obviously a simple policy of patriarchal power is dressed up in gilded rhetoric of concern for "life", which, maddeningly, is swallowed as gospel by the women who are its victims. For opposition to contraception and abortion are foremost attacks on the agency and full personhood of women, who are demoted to vessels for male procreation. But the Catholic church's policy is not just patriarchy of a demeaning and sexist kind, it also constitutes a eugenic policy. Ron Turcotte, one of the great horse jockeys, born in a family of twelve children in French Catholic New Brunswick, recalled in his autobiography that the priest would make the rounds of local families and berate every woman who did not have babies in diapers. The Catholic imperative is to fill up the world with Catholics, no matter the suffering of women, families, or communities. The entire biosphere groans under vast overpopulation. And what is the answer of the Catholic church? More Catholics, more oppression, more mental straightjackets. Care for creation apparently does not extend to continence on the part of men, basic personal rights or autonomy on the part of women, or to creation in general.

Just another day at the Supreme Court.

So when I hear "distinguished" lawyers, scholars and ethicists from Catholic institutions pontificate about the evils of genetic engineering, stem cell research, or use of embryos in research, (not to mention abortion or assisted suicide, among many other topics) I can not take them seriously as intellectuals- as anything other than mouthpieces of an antiquated system of oppressive, and now catastrophic, archetypes of political and social power. It is one thing to be a scholar of an artistic tradition full of glorious human expression and yearning quests for deeper connection with whatever power animates the world. But with the loss of humanism, then Protestantism, Catholicism retreated into an intellectual fortress of defense, nostalgia, and counter-reformation. The Federalist societies, the constitutional textualists, the Opus Dei fundamentalists... this ecosystem that has funded and nurtured a conservative assault on US legal institutions, apparently heavily Catholic, all are backward time machines fixated on dead controversies and traditional, frankly eugenic, policies of world domination. 

Nominee Barrett's textualism, following Scalia, seems to endanger the last century or two of constitutional interpretation. Whatever is not explicitly enumerated in the text is not, by this view, in the federal government's power. This could include women, (other than the 19th amendment; notably, the word "he" is used repetitively to refer to the president, representatives and other officers), federal regulatory authority in countless areas such as labor, antitrust, and finance, and the very meanings of concepts like cruel and unusual punishment, militias, privacy, due process, "needful rules", and "general welfare". The constitution and statutes are frequently vague, precisely so that society can construct its meanings according to the spirit of the document, not a cramped view of its letter, or a psychoanalytic plumbing of its mental conditions of origination.

Nor is Catholicism alone in this backwardness and revanchism. Islam shares its authoritarian, righteous, patriarchal, misogynistic, domineering mentality, even while lacking a pope. It goes the Catholics one better by approving of polygamy, another eugenic gambit. Consequently, Islam has even higher birth rates than Catholicism, immiserating its populations, stoking misplaced resentment, and imperiling the biosphere. However, Muslims in the US are not at this time constructing legal pipelines into US federal judgeships or dominating the Supreme Court, so their similarities in this regard are of global, but not federal, concern.

• Yes, religion is an issue here.
• Extended video of Barrett expressing her views, as also linked above.
• Abortion was perfectly fine in colonial America.
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• Donald's hair is charged to the taxpayer. Also, Ivanka.
• Maybe the whole business deduction system should be scrapped.
• What happens if ACA dies?
• State of our politics- getting people to not vote.

Science Says ...

What are facts, and how can we respect them?

The recent and prevalent locution of "science says ..." is grating to everyone- scientists, civilians, red, and blue. We get the shorthand meaning, but it has unpleasant, domineering overtones. Yet, sadly, something needs to be said, if facts can not make themselves heard. The "science says ..." mantra means that not only is something a fact, but it is widely, perhaps unanimously, recognized as a fact by experts who know where such facts come from and what they mean. Lately this usage has been in flood due to the pandemic, a way for data-driven people to criticize their more negligent neighbors.

The problem is that facts are not always totally clear or secure. So we have to fall back on arguments from authority, to support what we believe are important actions, based on other values. Masks were originally denigrated - by scientists! - as not very useful for protection against viruses that were small enough to easily pass right through typical cloth. But as more data came in, it became clear - to scientists - that even partial filtering and simple dispersion of infectious aerosols was quite helpful, not only for others facing a possible asymptomatic carrier of SARS-COV2, but to mask wearers themselves, by reducing the infecting dose. This is especially true in a setting with decent ventillation. Evidence piled up from epidemiological studies as well as mechanistic studies of mask wearing, that even lax masking is better than none. Now a shorthand for all that is "science says...". 

But the evidence is hardly 100%. Small studies and suggestive trends in disease data from well and poorly-masked populations make for important public health recommendations, but not quite facts. More detail and mechanism will be helpful, including the relative amounts of virus capture and dispersion by masks, and the role of the infectious dose in the severity of disease- the race that is run between viral replication and immune defense. Few people are themselves directly conversant with all this work, which means that most have to appeal to the authority of those that are. But then any blogger can claim to be an authority, and declaim a different set of conclusions and thus facts. 

We seem to have mostly settled down about these facts, tentative as they are, when it comes to the coronavirus, even though actually respecting them and changing habits comes hard to some. But climate change has been a different matter, being so economically important and implicated in everyone's current way of life. One's conservatism is directly related to resistance to changing one's way of life, which necessarily implies denying and disbelieving the once-subtle, now overwhelming evidence that "science says" assigns blame for accelerating climate change to us and our production of heat-trapping gasses.

Facts? What facts?

This is where the "science says ..." mantra becomes politically fraught and adversarial. If reality is knocking on your door and telling you to repent, confess your sins, and change your ways, experience tells us that is has to knock extremely hard. Addicts tend to change only after they have hit rock bottom, and see death in the eye. Listening to a bunch of pointy-heads and libtards go on about the biosphere, arctic ice, and obscure species is just not compelling. Quite the opposite- it is often taken as offensive and completely out of touch with a fossil fuel addict's immediate struggles and attachment to basic habits and ways of being.

And who cares about facts anyhow? Not the modern Republican party, not our president. Whether "science says" those facts or their own eyes behold them, the social facts of political control in grossly unfair setting of US power structures, and continuing support from the morally unmoored rich and their corporations, are far more significant than any global risks that all will bear with increasing pain over the coming decades. The social facts of the right wing media's blizzard of propaganda are likewise shaping a totally different world, in both values and truths and facts, than what scientists are perceiving. The mantra of "science says" then comes to mean a set of values rather than just facts, that we should perhaps attend to non-human species and ecosystems instead of worrying about a war on Christmas; that expertise is more valuable than con-jobbery and lying propaganda; that worrying about the vastly excessive human population on Earth might be more important than saving every fertilized egg for the patriarchy. For science is a value system, both in its methods and its objects. It is largely and generously funded by society, but naturally has its own agenda, which seems far-sighted and logical enough to its practitioners, but is, in the end, a set of values, which themselves will be judged by society as worthy of propagation, or not.

• An example of how the science has to be parsed pretty carefully, by expert observers. Masks, planes, and time.
• Our degraded country.
• That tired Taliban, ready to take over all of Afghanistan.
• Medicare advantage, or disadvantage?
• Are we great again, or what?
• Climate action and inaction.. still highly insufficient.

An American Economic History, Through Farming

From plantations to free soil, and back to plantations.

Today, farming is a small part of our economy. But it remains existentially important, and politically and culturally significant far beyond its share of GDP. The family farm evokes the heartland, the honest toiler, the communal and salt-of-the-earth values of rural life. The United States was founded on the promise of land- ever more land taken from Native Americans for ever more white people to till. Land was the original job guarantee. Anyone disgruntled with their current condition could go West. Some created vast plantations or ranches, while most founded family farms. When some of the last arable land on the frontier became available in Oklahoma, it resulted in the notorious land rush of 1889, typified by "Sooners" who jumped the gun into this so-called unassigned territory. A generation or two on, they authored the dust bowl by their enthusiasm and negligence.

The late 1800's were a pivotal period. The frontier was closing, industrialization was changing the workforce and mechanizing farming. It was perhaps the high point of the family farm, as so movingly portrayed in its perils, pride, and community, in the film version of The Wizard of Oz. One underappreciated cause and purpose of the Civil War was to preserve free soil and free labor as the guiding principle in new territories and states. The plantation system of labor was the alternative, just as firmly rooted in American soil as the small family farm, and just as greedy for new frontiers. Plantations were the original corporate agriculture, driving an army of employees (i.e. slaves) over vast acreages of market-crop monocultures, typically cotton, tobacco, and, in the Carribean, sugar cane.

But, despite winning the Civil War for free labor, and adapting to progressively greater levels of mechanization, the family farm is dying, and has been dying for decades. A recent piece in the New Yorker describes the situation in Wisconsin, which has seen a steep decline in family dairy farms, driven out of business by the inexorable efficiencies and amorality of corporate farming. Capitalism is the remorseless agent, setting up new plantations on rebooted principles of cheap labor and enormous scale. Instead of slaves, the labor is now an unending flood of poor and undocumented hispanics, ready to work for less, and under poorer conditions, than "free" labor.

Is this the kind of capitalism we want more of? Is the kind of rural America we look forward to? It is more than a little ironic that rural America voted overwhelmingly for the Republicans, who offered nostalgic nostrums while being the foremost purveyors of capitalist fundamentalism, cheap oppressed labor, and rural decline. Thus some might say, they deserve what they are reaping. But that is merely spite speaking, not policy. It is clear that government policy has had a great deal to do with this evolution of farming, from lax labor policy to trade policy and growing regulatory and bureaucratic complexities, and explicit farm support systems that support corporate farms foremost.

So, we have been divided from the outset, between a corporate, plantation model of farming, and a small-holder, family model of farming. The memorialized plantations of Mount Vernon and Monticello are fascinating examples of the former, each originally worked by an army of slaves to create in this new land a rich, even refined existence for the lords of the manor. It was Jefferson's dream that America would be overspread by small family farms, even as he himself ran a brutalizing corporate operation. It was just one more of his romantic dreams, along with a discomfort with slavery that did not extend to emancipating his own slaves. But the US did indeed make his dream real across the Midwest by eradicating slavery and accepting floods of immigrants to run their own farms and found rural communities. 

The silo-inspired Emerald City. Was it a storage and processing cooperative?

It is clear that it will take deep changes in policy to preserve family farming, and humane and ecologically sound farming. Not just cash payments to farmers, as the current administration is attempting to save its political position, but a much more thorough rethinking of how rural America should operate. We need far stiffer rules for labor and ecological practices on large farms, so that the playing field is leveled. We need better support for cooperative processors, buyers, bankers, equipment supply, transporters, and extension systems so that small farms have the long-term support they need to survive. We need to edge away from stark capitalism towards a mixed model, for instance maintaining some price supports with intelligent government planning, so that farmers are not whipsawed by lethal market forces. And making those price supports graduated against farm size, to recognize the unique value, and unique challenges, of the small farm.

• "There can be no permanent disfranchised peasantry in the United States."- from the inaugural address of James Garfield, 1881.
• The biosphere is going downhill.
• Everyone has hope.
• Toadies in the swamp.
• A lack of innovative thinking in the medical community.
• The Taliban will soon be running things.

Genetics and the Shahnameh

We have very archetypal ideas about genetics.

Reading a recent translation of the Persian Epic, the Shahnameh, I was impressed with two things, among all the formulaic focus on war and kingship. First was what it did not say, and second was its attitude, which is shared with all sorts of traditional societies, towards blood, nobility, and what we now understand as genetics. This epic, which transitions from wholly myth in the first half to quasi-history in the second, stops abruptly at the Arab conquest. Not a word is uttered past the overthrow of the last Persian pre-Islamic ruler. Not a word about Islam, not a word about the well over three hundred years of history of Persia under the Arab yoke by the time this was written circa 1000 AD. That says a lot about what the author, Abolqasem Ferdowsi, regarded as the significant boundaries of Persian history. Not that he was opposed to narrations of decline and suffering. The final era of the Sassanian Empire was one of chaos and decline, with regicides and civil war. But apparently, that history was still Persian, while the Arab epoch was something else entirely- something that Iran is still grappling with.

The epic is full of physical descriptions- kings are always tall as cypresses and brave as lions, women are always thin as cypresses, their faces like full moons and their hair musky. True kings radiate farr- glowing splendor that they show from a young age, which marks them as destined rulers. But farr can also be lost, if they turn to the dark side and loose popular support. The Chinese have a similar concept in the mandate of heaven, which, however, is not portrayed as a sort of physical charisma or halo. Children are generally assumed to take after their parents, for good or ill. The concept of the bad seed comes up in the Shahnameh, especially in the saga of Afrasyab, king of Turan and long-time antagonist of Persian kings and their champion, Rostam. Persian king Kavus has fathered a great (and handsome) champion, Sayavash. Through several plot twists, Sayavash must leave Persia and is adopted by Afrasyab, even marrying his daughter. But then the drama turns again and Afrasyab kills Sayavash. Thankfully, Sayavash had already fathered a future king of Persia, whom the Persians suspect of bad lineage, due to his descent from Afrasyab- a suspicion that they are slow to overcome.

"By the time the boy was seven years old, his lineage began to show. He fashioned a bow from a branch and strung it with gut; then he made a featherless arrow and went off to the plains to hunt. When we was ten he was a fierce fighter and confronted bears, wild boar, and wolves. ... Seeing the boy's noble stature, he dismounted and kissed his hand. Then he gazed at him, taking in the signs of kingly glory in his face."

Ancient peoples have generally taken nobility and bloodlines very seriously, for several reasons. First, obviously, is that children do take after their parents, for good and ill, just as ethnic groups similarly have some distinctive characteristics. Second is that, for practical as well as psychological reasons, people always seek good rulers and stable ruling systems, which in the aristocratic, patriarchial setting means an orderly transition from king to prince. The fairy tale (archetypal) ending is that the prince and princess take over the kingdom, and everyone lives happily ever after. Third, is that hierarchy of some sort seems to be part of our cultural DNA. Someone or group is always up, others down. Whatever the group or organization and whatever its professed principles, hierarchy re-asserts itself. Those on top want naturally to stay on top, and bequeath that position to their future replicas, i.e. their offspring. To do that they will generate all the practical advantages they can, and into the bargain foster a mythos of just distinction, based on their glorious bloodline, if not outright divine sanction from god. Thus genealogical trees, heraldry, etc.

The Shah is not like you or me...

The ruling houses of Europe over the whole post-Roman Era were infested with these archetypes and mythologies. Marrying "up" or "down" was a vast game carried out across the continent. And what has it gotten us? Prince Charles. It is obvious that something went awry in this genetic exercise of assortive mating, as it did ultimately in the tragedies of the Shahnameh as well. The behavior of royals generally fails to select for all the positive traits that are ultimately needed. Their training fails frequently as well to expose those good traits that do exist. But most of all, genetics is far more of a crapshoot than the archetypes allow. 

Children do take after their parents, but there are stringent and interesting limits. A child gets only half of each parent's genes, and those genes may be from either copy in each parent. That copy might have been totally silent- recessive vs the other dominant allele. Two brown-eyed parents can have a blue-eyed child, if they are heterozygous for eye color. Multiply this over thousands of loci, and the possibilities are endless. This is why traits of the grandparents sometimes are thought to come up unexpectedly, or novel traits entirely. The genetic mixing that takes place on the way to new life is carefully engineered to replicate, but with wide variation on the theme, such that any child is as much a child of its wider lineage and environment as of its particular parents. Genetic defects remix during this process as well, concentrating in some children, and leaving others fortunately free to realize greater potentials. The obsessive concentration of lineages that characterize royalty systems, such as was taken to an incestuous extreme in Egypt, leads to inbreeding, which means the exposure of defective alleles due to excessive homozygosity. We all have defective gene alleles, which are typically recessive, and thus get exposed only when they pair up with an equally defective partner. Thus an extreme focus on lineage and purity leads to its own destruction.

The differences between ethnicities are far less than those between families. Human lineages may have some strongly selected and differentiated traits, such as skin color, but such traits are exceedingly rare. Otherwise, our genetics are a cloud of variation that crosses all ethnic lines. Humans were a single lineage only a few hundred thousand years ago, or less, so broadly speaking, we are all the same. Indeed compared to most species, such as chimpanzees, we have much less genetic variation overall, and are virtually clones, due to the relatively recent bottlenecks of extremely low population that reduced genetic diversity. Our current population size relative to those of the other great apes certainly does not reflect conditions in the past!

Education was another ingredient in the traditional systems of nobility and aristocracy. Only the rich could afford an education, so only the upper crust were educated, thus gaining one more credential in addition to their genetic credentials, over the middle and lower classes. Such notions of aristocracy died perhaps hardest in military circles, where officers were long an aristocratic class, selected for their connections, not their ability. It was one of the great American innovations to establish a national military college to which admission was distributed liberally to deserving candidates, (at the same time as similar academy was set up in revolutionary France by Napoleon). It is obvious that the capacity for education was far more widespread than originally conceived, and we benefit today from the very active diffusion of education for everyone. Yet not all are college material. Some children are bright, some less so. Genetics and early development still count for a great deal- but good (and bad) genes can come up anywhere. That means that in the end, the American system of meritocracy, for all its defects, of which there are many, and despite its significantly unfulfilled promise to many, is a huge advance over the hidebound traditions, archetypes, and injustice, of aristocracy.

But back to genetics- what are we finally to make of genetics, eugenics, and noble bloodlines? It is clear that humans can be selectively bred, just like any other animal. Twins and twin studies make it abundantly clear that all sorts of traits- physical and mental- are gene-based and heritable, to striking extents. It is also clear that historical attempts at eugenics have not turned out well, whether through systems of nobility or more modern episodes of eugenics. The former were largely self-indulgent and self-serving ideologies designed to keep power and status among an elite, within which poor choices in mates and inbreeding consistently led to genetic doom. The latter were ideological exercises in frank racism, no more anchored in positive values, genetic or otherwise, than the aristocracies of yore. There have been occasional successful genetic experiments in human breeding, such as the Bach family, Yao Ming, and Stephen Curry, which show what can be done when one puts one's mind to it! (The Trump brood may also be cited as another, if negative, example.)

But generally, selective breeding implies a single set of values that constitute its goal. Our values, as a society, are, however, diverse in the extreme. We celebrate some people more than others at a political or social level, but have been heading in the direction, since our country's founding, of recognizing the dignity and worth of every person without exception, along with their freedom to form and express their own values. We can neither agree on a society-wide set of specific values that would shape any form of selective eugenics, nor allow individuals to go beyond the bounds of normal mate selection to plunge into cloning, genetic alterations, and the like, to inordinately expand their genetic influence on succeeding generations. All that would strike at the heart of the social project that is America- to foster individual opportunity and merit, while at the same time respecting the rights and worth of each individual- indeed, each way of life. It is likely that, given the technology, we might come to a general consensus to eradicate certain genetic diseases and syndromes. But beyond that lies a frontier of genetic engineering that the US is particularly poorly suited to cross, at least until we have made America great again, so to speak, and become another society entirely.

• Some calming piano.
•  Oh, yeah- remember the tax cut? That went to the rich.
• Some people are prepping for war.
• Maybe low-dose infection is one way to approach Covid-19.
• International fisheries are not just environmental disasters, but human rights disasters.
• The difference between being a con man and being a president.
• Some possible futures for Earth. RCP 8.5 takes us (in a matter of 80 years) to conditions last seen 40 million years ago.
• Followup quote from Frederick Douglass:

"Color prejudice is not the only prejudice against which a Republic like ours should guard. The spirit of caste is malignant and dangerous everywhere. There is the prejudice of the rich against the poor, the pride and prejudice of the idle dandy against the  hard-handed workingman. There is, worst of all, religious prejudice, a prejudice which has stained whole continents with blood. It is, in fact, a spirit infernal, against which every enlightened man should wage perpetual war."

Why Are Cells So Small?

Or, why are they one size, and not another?

One significant conundrum in biology is how cells know what size they are, and what size they are supposed to be. Bacteria are tiny, while eukaryotic cells are huge in comparison. And eukaryotic cells vary tremendously in size, from small yeast cells to peripheral nerves that span much of your body, even on to ostrich eggs. Outside of yeasts, not much is known about how these cells judge what size is right and when to divide. A recent paper proposed that the protein Rb plays an important role in setting cell size, at least for some eukaryotic cell types.

Rb is named for retinoblastoma, the form of cancer it is most directly responsible for, and is a well known gene. Many other cancers also have mutations in Rb, since it is what is called a "tumor suppressor gene". That is, it is the opposite of an oncogene. Rb interacts with hundreds of proteins in our cells, but its most important partner is transcription activator E2F1, an activator of cell cycle progression. Rb binds to and inhibits the activity of E2F1, (and a family of related proteins), halting cell division until some alteration takes place, like a regulatory phosphorylation that shuts Rb off, or an insufficient amount remaining in the cell.

The researchers took a clue from yeast, whose gene Whi5 accomplishes similar inhibition of the cell cycle as Rb, and is known to regulate the size of cells at division. So this work was not a big surprise. The interesting aspect is that Rb now has one more role, which logically integrates with its other known roles in the cell cycle. The authors used cells that over or under-express Rb to show that the copy number of Rb has a significant, if not overwhelming, effect on cell size. 

Amount of Rb correlates with the size of cell. The authors set up an inducible genetic construct to drive Rb expression, from zero to four times normal amounts.

So how do they imagine this mechanism working? Rb is a durable, stable protein, with a half-life almost twice as long (29 hours) as the cell division cycle in the conditions the experimenters used. Secondly, all Rb is pretty much in the nucleus, attached to DNA. So at cell division, roughly equal amounts necessarily partition to each daughter cell, even if their cell volumes are very different. Thereafter, each cell synthesizes Rb at a low rate, which does not keep up with cell growth, especially during the G1 phase of the cell cycle- that period prior to DNA replication and commitment to division. In fact, very little Rb is made in that period, allowing it to serve as a limiting factor through dilution as the cell grows. And when it is sufficiently dilute, it then contributes to the decision to have new cell cycle, by letting go of its repression of E2F1.

How several proteins accumulate during the cell cycle. Rb is shown in dark blue, and hardly accumulates at all in G1, the growth phase of the cell cycle before DNA replication (S phase) and division (M phase). For comparison, nuclear volume and a generic translation protein (EF1) rise monotonically with cell growth. Cdt1 is a key licensing factor for DNA replication. It accumulates during G1, and after the DNA replication origins fire, is destroyed by the end of S phase. Conversely, Geminin is a protein that binds to and represses Cdt1, preventing re-replication of DNA that has already replicated once. It accumulates during S phase and stays high until after division. After S phase, more Rb is made, partially catching up to the current cell size. 

That is the theory, at least, backed by pretty good evidence. But its effect is not proportional, and not uniform among cell types. There are clearly other controls over cell size in play- this is only one. Indeed, there are a couple of siblings of Rb (in a family termed "pocket proteins") which also regulate the cell cycle, and a vast network of other controls and stimuli that impinge on it. So finding even one regulator of this kind, and finding conditions where it has strong effects on cell size, is quite significant. As for the ultimate rationale of cell size in these or other instances, Rb regulation is only a mechanism that enforces logic that has been arrived at over evolutionary time, about the practical limits and ideal proportions of cells in, in this case, the human body, in response to various situations. Smaller cells have one virtue, that they are more easily disposable- such as the countless skin and gut epithelial cells that are sacrificed daily. Our long peripheral nerves are much more difficult to replace.

Conversely, Rb has many other roles in the cell, as suggested by the vast number of its interaction partners, diagrammed below by functional classification.

Functional classification of the many proteins that interact directly with Rb. It also has about 15 phosphorylation sites that can be regulated by various kinases.

• The Fed goes all MMT, behind the scenes. No more reserve requirements, no more market-based interest manipulation.
• We are increasingly at risk of civil war.
• Guess who recommends illegal voter fraud?
• Yet another effective Chinese vaccine.
• Bob Cringely on the pandemic loan program, and other misguided incentives.
• How the virus disarms and shuts down the host cell.

Links Only

 Due the press of work and other projects, no regular post this week, only links.

• Michael Sandel on work and merit.
• The police have a long way to go.
• Utter corruption of the law, by and for fossil fuels.
• Are we having enough climate change yet?
• Road to serfdom leads through capitalism, not government.

Frederick Douglass

The autobiographies of Frederick Douglass are a milestone of US literary, political, and social history.  

To deepen my appreciation for our history and the ongoing crises, racial and otherwise, I have been enjoying the final autobiography of Frederick Douglass, of the three that he wrote. This is the longest and, for obvious reasons, most comprehensive, where he can provide details about his escape and controversial activities that had been too sensitive previously, and cover later parts of his career. It is a paragon of style, incisive analysis, and emotional impact. Not having a great deal to add myself, I give over this blog to a few selected quotes.

Douglass (then named Bailey, and in his late teens), was sent by his master to a Mr. Covey, who specialized in "breaking" unruly slaves, by supervising and working them relentlessly, and whipping them weekly. Finally, after an escape attempt, Douglass he has had enough and fights back, come what may. What comes is that Covey gives in completely, and is cowed for the rest of the year from laying a finger on Douglass.

This battle with Mr. Covey, undignified as it was and as I fear my narration of it is, was the turning point in my "life as a slave." It rekindled in my breast the smouldering embers of liberty. It brought up my Baltimore dreams and revived a sense of my own manhood. I was a changed being after that fight. I was nothing before; I was a man now. It recalled to life my crushed self-respect, and my self-confidence, and inspired me with a renewed determination to be a free man. A man without force is without the essential dignity of humanity. Human nature is so constituted, that it cannot honor a helpless man, though it can pity him, and even this it cannot do long if signs of power do not arise. p. 591 in the American library edition of the autobiographies of Frederick Douglass.

Douglass took a long tour in Britain, where he marvels at the discrimination he is not experiencing. It remains a deep statement about the work that still now remains.

I seem to have undergone a transformation. I live a new life. The warm and generous cooperation extended to me by the friends of my despised race; the prompt and liberal manner in which the press has rendered me its aid; the glorious enthusiasm with which thousands have flocked to hear the cruel wrongs of my down-trodden and long-enslaved fellow-countrymen portrayed; the deep sympathy for the slave, and the strong abhorrence of the slaveholder, everywhere evinced; the cordiality with which members and ministers of various religious bodies, and of various shades of religious opinion, have embraced me and lent me their aid; the kind hospitality constantly proffered me by persons of the highest rank in society; the spirit of freedom that seems to animate all with whom I come in contact, and the entire absence of everything that looks to me like prejudice against me, on account of the color of my skin, contrast so strongly with my long and bitter experience in the United States, that I look with wonder and amazement at the transition. In the southern part of the United States, I was a slave - thought of and spoken of as property; in the language of the law, "held, taken, reputed, and adjudged to be a chattel in the and of my owners and possessors, and their executors, administrators, and assigns, to all intents, constructions, and purposes, whatsoever". In the Northern States, a fugitive slave, liable to be hunted at any moment like a felon, and to be hurled into the terrible jaws of slavery- doomed, by an inveterate prejudice against color, to insult and outrage on every hand (Massachusetts out of the question)- denied the privileges and courtesies common to others in the use of the most humble means of conveyance- shut out from the cabins on steamboats, refused admission to respectable hotels,  caricatured, scorned, scoffed, mocked, and maltreated with impunity by any one, no matter how black his heart, so he has a white skin. But now behold the change! Eleven days and a half gone, and I have crossed three thousand miles of perilous deep. Instead of a democratic government, I am under a monarchial government. Instead of the bright blue sky of America, I am covered with the soft, gray fog of the Emerald Isle. I breathe, and lo! the chattel becomes a man. I gaze around in vain for one who will question my equal humanity, claim me as a slave, or offer me an insult. I employ a cab- I am seated beside white people- I reach the hotel- I enter the same door- I am shown the same parlor- I dine at the same table- and no one is offended. No delicate nose grows deformed in my presence. I find no difficulty here in obtaining admission into any place of worship, instruction, or amusement, on equal terms with people as white as any I ever saw in the United States. I meet nothing to remind me of my complexion. I find myself regarded and treated at every turn with the kindness and deference paid to white people. When I go to church I am met by no upturned nose and scornful lip, to tell me "We don't allow niggers in here." pp. 688-689, ibid.

 

Douglass looks at the pre-civil war politics of Southern resentment and entitlement, upon the growing spread and success of the abolition movement, which had been Douglass's work for the prior decade.

... Mr. Calhoun and other southern statesmen were more than ever alarmed at the rapid increase of anti-slavery feeling in the North, and devoted their energies more and more to the work of devising means to stay the torrents and tie up the storm. They were not ignorant of whereunto this sentiment would grow if unsubjected and unextinguished. Hence they became fierce and furious in debate, and more extravagant than ever in their demands for additional safeguards for their system of robbery and murder. Assuming that the Constitution guaranteed their rights of property in their fellow men, they held it to be in open violation of the Constitution for any American citiazen in any part of the United States to speak, write, or act against this right. But this shallow logic they plainly saw could do them no good unless they could obtain further safeguards for slavery. In order to effect this the idea of so changing the Constitution was suggested that there should be two instead of one President of the United States- one from the North and the other from the South- and that no measure should become a law without the assent of both. But this device was so utterly impracticable that it soon dropped out of sight, and it is mentioned here only to show the desperation of the slaveholders to prop up their system of barbarism against which the sentiment of the North was being directed with destructive skill and effect. They clamored for more slave States, more power in the Senate and House of Representatives, and insisted upon the suppression of free speech. At the end of two years, in 1850, when Clay and Calhoun, two of the ablest leaders the South ever had, were still in the Senate, we had an attempt at a settlement of the differences between the North and South which our legislators meant to be final. What those measures were I need not here enumerate, except to say that chief among them was the Fugitive Slave Bill, frames by James M. Mason of Virginia and supported by Daniel Webster of Massachusetts- a bill undoubtedly more designed to involve the North in complicity with slavery and deaden its moral sentiment than to procure the return of fugatives to their so-called owners. For a time this design did not altogether fail. Letters, speeches, and pamphlets literally rained down upon the people of the North, reminding them of their constitutional duty to hunt down and return to bondage any runaway slaves. In this the preachers were not much behind the press and the politicians, especially that class of preachers known as Doctors of Divinity. A long list of these came forward with their Bibles to show that neither Christ nor his holy apostles objected to returning fugatives to slavery. Now that that evil day is past, a sight of those sermons would, I doubt not, bring the red blush of shame to the cheeks of many. pp. 722-723, ibid.

In response to the election of Abraham Lincoln, the North sought ways to avoid war ... does this attitude sound familiar?

While this humiliating reaction was going on at the North, various devices to bring about peace and reconciliation were suggested and pressed at Washington. Committees were appointed to listen to Southern grievances, and, if possible, devise means of redress for such as might be alleged. Some of these peace propositions would have been shocking to the last degree tot he moral sense of the North, had not fear for the safety of the Union overwhelmed all moral conviction. Such men as William H. Seward, Charles Francis Adams, Henry B. Anthony, Joshua R. Giddings, and others- men whose courage had been equal to all other emergencies- bent before this southern storm, and were ready to purchase peace at any price. ... Everything that could be demanded by insatiable pride and selfishness on the part of the slave-holding South, or could be surrendered by abject fear and servility on the part of the North, had able and eloquent advocates.

Happily for the cause of human freedom, and for the final unity of the American nation, the South was mad, and would listen to no concessions. It would neither accept the terms offered, nor offer others to be accepted. It had made up its mind that under a given contingency it would secede from the Union and thus dismember the Republic. pp.770-771, ibid.

 

Douglass's influence can be appreciated in small part by this piece in his honor by N. Clark Smith.

• Yes, collusion. Indeed, what on earth was Muller doing?
• The Taliban has not changed.
• We deserve even better.
• Bill Mitchell on work. Yes, somebody has to do it!
• All hail coal!
• All hail Facebook!
• Stutterers unite!
• Mourning for parts of California in flames, such as Big Basin state park.

Notes From Korea

A brief travelogue.

I've been traveling. Yes, the pandemic is the perfect time to stretch out and explore new places, virtually. "The Korean Mind" is a remarkable, and remarkably frank book about the history, culture, and mindset of Korea, built around its most significant and loaded words- so-called code words. While this unique format provides a fascinating hopscotch through Korean culture, it also gets a little repetitive, as many words cover similar territory. Duty and honor, for instance, are staples of the Korean mind-set and come up in countless guises and words.

One major theme is the extreme repression, formality, and strict hierarchy prevalent in Korean culture. Over their two thousand years of history, they have been through many vicissitudes, but retained a heavily hierarchical and duty-bound system, patterned on Chinese Confucianism. Koreans were even more inward-looking and more extremely repressed by their rulers and cultural system, at least till after the Korean War, than the Chinese or other neighbors. They were, as a whole, a true hermit kingdom for most of a millennium, like the North is still today. The author emphasizes repeatedly that the highly repressive nature of the cultural system had wide-ranging psychological effects, severely limiting circles of friendship, requiring elaborate forms of social interaction, including bribery, gift-giving, bowing and other gestures of obedience and respect, a large and mandatory set of honorifics, a curiously liberated drinking culture, and an ethic of incredible durability, hard work and survival. And integral to all this was particularly harsh treatment of women, who were (again, until very recently) on the lowest end of every conceivable hierarchy.

The author reiterates frequently that foreigners working in Korea are prone to many disasters on these accounts, since the surface placidity and formality of Koreans is part of a precise system of interactions and covers very passionate natures, ready to take offense at missteps, and even take revenge for perceived slights and disrespect. He advises an attitude of perpetual humility and the use of an experienced advisor for guidance through the minefield. Also advisable is karaoke and drinking sessions, which are standard in Korean business and life, to relax and form relationships with people otherwise held at arm's length or further. A related point is that no one "becomes" Korean. A Westerner can spend her life in Korea and marry into a Korean family, and sill not be accepted as fully Korean, or have her children accepted as fully Korean. 

Kim Hee-jung, minister of family and gender equality- a member of the enormous Kim lineage clan, and example of female power in Korea today. 

On the plus side, the release of Korea from Japanese domination after world war 2, and gradually from its own legacy of mindless authoritarianism, has in turn released huge amounts of personal and entrepreneurial energy, channelling some of that authoritarianism into corporate cultures that have taken the world by storm, and created an economic powerhouse. One aspect of Korea's cultural pride is its language, which is, as one can imagine, difficult to master in its deep cultural dimensions. This language can be written in two ways, (leaving aside Romanization as a third). One is a simplified character system called Hangul, which was devised in 1444 as a practical writing system, superseding the Chinese characters that were standard, and remained standard for centuries to come, due to the Confucianist recalcitrance of the scholar / bureaucratic class. Chinese is arduous to learn, with tens of thousands of symbols of ever-diminishing utility and frequency. Hangul has only 24 letters, so functions very much like a Western writing system, is easy to learn, and was emphasized after the liberations of the 20th century as the standard Korean writing system. Yet today, with the increasing influence of China, the study of Chinese is regaining prominence, forcing Koreans to learn three languages (Korean, Chinese, and English, and perhaps Japanese), if they want to function in international business.

The relationship of Korea with Japan is particularly interesting. Korea contributed a great deal to early Japanese culture, being more technologically and culturally advanced one to two millennia ago. Pottery is one outstanding example. Many Japanese have Korean heritage, often unacknowledged. Korea and Japan remain culturally kin. But Japan took a quite martial turn early on, becoming sort of the Vikings of the region, raiding Korea frequently. This culminated in the complete takeover of Korea in 1910, enslaving the population and trying to exterminate Korean culture. Obviously, this led to a great deal of bad blood, motivating Koreans today to beat Japan whenever they can, especially in the commercial sphere. At the same time, Koreans do a great deal of business in Japan and respect the turn that Japan has taken since the war to become a largely pacifist country.

One of the most distinctive aspects of the so-called Korean mind is an ethical stance quite distinct from what Westerners are used to- situational and highly personal ethics. The strong emphasis on correct, rule-based formality is, as natural in Confucian systems, somewhat superficial, hiding roiling emotions and resentments. Morality in this system is likewise relatively superficial, heavily oriented to save face for one's self and people with whom one has specific relationships, not staked on universal principles, truth, equality, etc. Revenge for slights is acceptable, as is complete dismissal of strangers, and lying to save face. Networking is tremendously important, through personal connections, without which a person in Korea has virtually no way to operate at all. Understandably, getting to the bottom of all this can take years of study and acculturation.

Written mostly as a guide to foreign business people, The Korean Mind is perhaps overly pessimistic about their prospects, but is tremendously enlightening for the casual reader and armchair adventurer.

• Sometimes the nuts have a point.
• How authoritarians run elections.
• From no-man to yes-man.
• The banks can now rest easy.