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.

Links

Due to the press of business, only links this week.

Tom Tomorrow surveys our moment.

• Good grids have powerful effects on price stability and renewable production.
• Were Trump voters and militants fooled, or complicit?
• The US can do more than lies. We can do truth.
• In memoriam and tribute.

Tooth Development and Redevelopment

Wouldn't it be nice to regrow teeth? Sharks do.

Imagine for a minute if instead of fillings, crowns, veneers, posts, bridges, and all the other advanced technologies of dental restoration, a tooth could be removed, and an injection prompt the growth of a complete replacement tooth. That would be amazing, right? Other animals, such as sharks and fish, regrow teeth all the time. But we only get two sets- our milk teeth and mature teeth. While mature mammalian teeth are incredibly tough and generally last a lifetime, modern agriculture and other conditions have thrown a wrench into human dental health, which modern dentistry has only partially restored. As evolution proceeded into the mammalian line, tooth development became increasingly restricted and specialized, so that the generic teeth that sharks spit out throughout their lives have become tailored for various needs across the mouth, firmly anchored into the jaw bone, and precisely shaped to fit against each other. But the price for this high-level feature set seems to be that we have lost the ability to replace them.

So researchers are studying tooth development in other animals- wondering how similar they are to human development, and whether some of their tricks can be atavistically re-stimulated in our own tissues. While the second goal remains a long way off, the first has been productively pursued, with teeth forming a model system of complex tissue development. A recent paper (with review) looked at similarities between molecular details of shark and mammalian tooth development.

Teeth are the result of an interaction between epithelial tissues and mesenchymal tissues- two of the three fundamental tissues of early embryogenesis. Patches of epithelium form dental arches around the two halves of the future mouth. Spots around these arches expand into dental placodes, which grow into buds, and as they interact continuously with the inner mesenchyme, form enamel knots. The epithelial cells of the knot then eventually start producing enamel as they pull away from interface, while the mesenchymal cells produce dentin and then the pulp and other bone-anchoring tissues of the inner tooth and root as they pull away in the opposite direction. 

Embryonic tooth development, which depends heavily on the communication between epithelial tissue (white) and mesenchymal tissue (pink). An epithelial "enamel knot" (PEK/ SEK) develops at the future cusp(s), where enamel will be laid down by the epithelial cells, and dentin by the mesenchymal cells. Below are some of the molecules known to orchestrate the activities of all these cells. Some of these molecules are extracellular signals (BMP, FGF, WNT), while others are cell-internal components of the signaling systems (LEF, PAX, MSX).

Naturally, all this doesn't happen by magic, but by a symphony of gene expression and molecular signals going back and forth. These signals are used in various combinations in many developmental processes, but given the cell types located here, due to the prior location-based patterning of the embryo in larger coordinate schemes, and the particular combination of signals, they orchestrate tooth development. Over evolution, these signals have been diverse in the highest degree across mammals, creating teeth of all sorts of conformations and functions, from whale baleen to elephant tusks. The question these researchers posed was whether sharks use the same mechanisms to make their teeth, which across that phylum are also highly diverse in form, including complicated cusp patterns. Indeed, sharks even develop teeth on their skin- miniature teeth called denticles.

Shark skin is festooned with tiny teeth, or denticles.

These authors show detailed patterns of expression of a variety of the known gene-encoded components of tooth development, in a shark. For example, WNT11(C)  is expressed right at the future cusp, also known as the enamel knot, an organizing center for tooth development. Dental epithelium (de) and dental mesenchyme (dm) are indicated. Cell nuclei are stained with DAPI, in gray. Dotted lines indicate the dental lamina composed of he dental epithelium, and large arrows indicate the presumptive enamel knot, which prefigures the cusp of the tooth and future enamel deposition.

The answer- yes indeed. For instance, sharks use the WNT pathway (panel C) and associated proteins (panels A, B, D) in the same places as mammals do, to determine the enamel knot, cusp formation, and the rest. The researchers use some chemical enhancers and inhibitors of WNT signaling to demonstrate relatively mild effects, with the inhibitor reducing tooth size and development, and the enhancer causing bigger teeth, occasionally with additional cusps. While a few differences were seen, overall, tooth development in sharks and mammals is quite similar in molecular detail. 

The researchers even went on to deploy a computer model of tooth development that incorporates twenty six gene and cellular parameters, which had been developed for mammals. They could use it to model the development of shark teeth quite well, and also model their manipulations of the WNT pathway to come out with realistic results. But they did not indicate that the overall differences in detail between mouse and shark tooth development were recapitulated faithfully by these model alterations. So it is unlikely that strict correspondence of all the network functions could be achieved, even though the overall system works similarly.

The authors offer a general comparison of mouse and shark tooth development, centered around the dental epithelium, with mesenchyme in gray. Most genes are the same (that is, orthologous) and expressed in the same places, especially including an enamel knot organizing center. For mouse, a WNT analog is not indicated, but does exist and is an important class of signal.

These authors did not, additionally, touch on the question of why tooth production stops in mammals, and is continuous in sharks. That is probably determined at an earlier point in the tissue identity program. Another paper indicated that a few of the epithelial stem cells that drive tooth development remain about in our mouths through adulthood. Indeed, these cells cause rare cancers (ameloblastoma). It is these cells that might be harnessed, if they could be prodded to multiply and re-enter their developmental program, to create new teeth.

• Boring, condescending, disposable, and modern architecture is hurting us.
• Maybe attacking Russia is what is needed here.

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.

Visualizing Profilin

Profilin as a part of the musculo-skeletal system that motors our cells around. But how can we tell?

Our cells have structural elements called the cytoskeleton. The term is a misnomer, since the cytoskeleton comprises the muscles of the cell as well as its rigid supports. There are three types of rigid element- actin filaments, intermediate filaments, and microtubules. Intermediate filaments are the stable, relatively inert part of the equation, making up structures like keratins that shape our skin, hair, and nails. Actin and microtubules, however are highly dynamic and contribute to amoeboid motion, developmental cell motions, neural extensions, and all kinds of other shape changes cells perform. Microtubules are bigger and stiffer, (25 nm diameter, hundreds of times stiffer than actin filaments), and participate in big, discrete processes like separating the chromosomes at division, and forming the core of cilia that wave from the outside of the cell. 

Actin (6 nm diameter) is more pervasive all over the cell, and is what provides the main motive force of ameboid motions and cell shape change. Indeed, our muscles are mostly composed of great quantities of actin along with interdigitated filaments of its corresponding motor protein (myosin) in orderly, almost crystalline, arrays. Both myosin and actin create motion in two ways- by their own polymerization / depolymerization, and also by way of motors that can move along their lengths.

Images of cells showing fluorescence labeling of skeletal components. Microtubules are shown in green, and DNA in blue. Panel C shows a neuronal growth cone with actin labeled in red. Note how microtubules and actin cooperate, with actin in the lead, pushing out the cell edges by force of its own polymerization. Panel A shows resting cells, with the microtubule organizing center in red. E shows a yeast cell with microtubules spanning its length. G shows a dividing cell at M phase, where microtubules organize the separation of chromosomes, after the microtubule organizing center has itself first divided into two.

A recent paper discussed new tools in the quest to visualize profilin, one of the many accessory proteins involved in managing the cytoskeleton. The most basic role of profilin is to bind to monomers of actin helping them recharge (that is, exchange their ADP for a new ATP). There is a lot of profilin in the cell, and it mostly sits around complexed with actin, preventing it from spontaneously polymerizing. But then if a signal comes in, profilin has binding sites for formin proteins, which tend to be the main instigators of cell shape change and actin polymerization, and can orchestrate the handoff of actin from profilin to growing actin filaments.

The overall actin cycle. Actin monomers are constantly coming on and off of filaments. ATP-charged actin is held in reserve in complex with profilin (dark shapes). Then formins or other accessory proteins can encourage addition to a filament, at one end, called the barbed end. While in filaments, actin gradually hydrolyzes its ATP, forming ADP. Actin with ADP is prone to dissociation, which may be encouraged or discouraged by various other accessory proteins. The resulting actin monomers are then re-bound by profilin and the cycle begins again.

But how can we see all this? Making proteins fluorescent has been now for decades the amazingly effective way to vizualize them. And one can do that either live, or dead. For the latter, the cell is chemically embalmed and permeabilized, then treated with antibodies that bind to the protein(s) of interest. Then a second set of antibodies are applied that bind to the first set, and are labeled with some fluorescent tag, and voila- images of where your protein of interest is, or was. But much more compelling is to see all this in living, working, and moving cells. To do that, the protein of interest is mutated to add an intrinsically fluorescent tag, such as green fluorescent protein. But profilin is so small, and so packed with critical binding sites, that there is little room for a fluorescent tag protein that is, in fact, almost twice as large as profilin itself. 

What to do? These researchers attached a little tail to one end of the protein, off which they then added their tag, in this case a protein called mApple, chosen for its nice red fluorescence spectrum that doesn't interfere with the other greens and blues typically used in these experiments. The paper is mostly then a laborious verification that this new form of profilin fully functions in cells as the wild type does, engages in all the same interactions, (as far as known), and thus consitutes a wonderful new tool for the field.

An atomic structure of profilin bound to actin. Profilin is a very small protein with many important interactions. That makes altering it very tricky. How to create a fluorescent form, or squeeze in some other tag? Profilin binds to actin, to microtubules, to formins and other proteins with PLP (poly-proline) domains, and to phosphoinositide 4,5-bisphosphate (PIP2), which is not even shown here.

It turns out that profilin binds to microtubules as well as to actin. And so do formins. As shown above in the image of a neural growth cone, though the composition of actin and microtubules and their size and other characteristics are very different, they cooperate extensively, thus must have mechanisms of crosstalk. Not much is known, unfortunately, about how this works- while a good bit is known individually how each of the actin and microtubule systems work, how they work together is poorly understood. But one thing these researchers show is that profilin, along with its abundance all over the cell, is also concentrated at the microtubule organizing center. Indeed, some mutations that cause the disease ALS occur right in these regions of profilin that bind microtubules. So something important is going on, and hopefully this new tool will speed work towards greater understanding of how the cytoskeletons operate.

Profilin imaged in a live cell, with other tagged molecules. At left, profilin occurs all over the cell in its role as actin buffer and storage partner. But note a couple of dots on each side. Next is shown the same cell labeled on alpha tubulin, the major component of microtubules. Next is show DNA, which is condensed, as this cell is undergoing division. Last is shown the merged images, with DNA in blue, tubulin in green, and profilin in red/orange. The dots turn out to be the microtubule organizing centers that run the spindle which is orchestrating chromosome segregation.

• Keep 'em high.. a way to smooth gas price volatility, and fight climate change.
• And we need a carbon tax for comprehensive decarbonization.
• Liberals tied in knots by homelessness.
• All public school systems are at risk.
• Someone has been watching a little too much Grit TV.
• Cry me a river- about a shortage of post-docs.

Balancing Selection

Human signatures of balancing selection, one form and source of genomic variation.

We generally think of selection as an inexorable force towards greater fitness, eliminating mutations and less fit forms in favor of those more successful. But there is a lot else going on. For one thing, much mutation is meaningless, or "neutral". For another, our lives and traits are so complicated that interactions can lead to hilly adaptive landscapes where many successful solutions exist, rather than just one best solution. One form of adaptive and genetic complexity is balancing selection, which happens when two alleles (i.e. mutants or variants) of one gene have distinct roles in the whole organism or ecological setting, each significant, and thus each is maintained over time. 

A quick example is color in moths. Dark colors work well as camouflage in dirty urban environments, while lighter colors work better in the countryside. Since both conditions exist, and moths move around between them, both color schemes are selected for, resulting in a population that is persistently mixed for this trait. Indeed, the capacity of predators to learn these colors may also lead to an automatic advantage for the less frequent color, another form of balancing selection. Heterozygotes may also have an intrinsic advantage, as is so clearly the case for the sickle cell mutation in hemoglobin, against malaria. These are all classic examples. But to bring it home, a society has only so much capacity for people like Donald Trump. Insofar as sociopathy is genetic, there will necessarily be a frequency-dependent limit, where this trait (and other antisocial traits) may be highly successful at (extremely) low frequency, but terminally destructive at high frequencies.

Schematic selective landscapes. Sometimes selection just optimizes an existing trait by intensifying it (1), or moving it along trait space to a new optimum (2). But other times, multiple forms (i.e. variants, or mutations) of a given locus each have some useful / beneficial characteristic, and may be selected either discretely for particular effects (3), or generally for their diversity (4).

One laborious method to find such sites of balancing selection in a genome is to compare it to genomes of other species. If the same variants exist in each species over long periods of divergence, that argues that such conserved sites of diversity are maintained by balancing selection. Studies of humans and chimpanzees have found some such sites, but not many. But these methods are known to be very conservative, missing out on what is likely to be most cases.

A recent paper offered a slighly more sensitive way to find signs of balancing selection in the human genome, and found quite a lot of them. (Some background here.) It is based, as many investigations of selection are, on a special property of protein-coding genes, due to the degeneracy of the genetic code, that some mutations are "synonymous" and lead to no change in the coded protein, and others are "non-synonymous" and do change the protein. The latter would be assumed to be visible to selection, and sometimes give significant signals of conservation (i.e. low rates of change between species and populations, and few variations maintained in a population). This embedded signal/control pairing of information helps to insulate against many problems in analysis, and can tell us pretty directly how severe selection is on such sites. 

It is worth adding that each basepair in the human genome has its own selective constraints. One position may code for the active site of some enzyme and be extremely well conserved, while the next may be a "synonymous" that has very few or no selective constraints, and another lies in junk DNA that doesn't code for anything or regulate anything, is effectively neutral, and can be changed with no effect. The system is in this sense massively parallel, and able to experience evolution individually at each site concurrently. On the other hand, selection on one site affects the frequencies at nearby sites, since selective "sweeps" through that area of the genome drag the nearby regions of DNA (and whatever variants they may harbor) along, whether positively if the site is increasing in frequency, or negatively if it is deleterious and causing death of its bearers. The reach of this "linkage" effect depends on the recombination frequency, which is relatively low, leading the moderate stability (and linkage) of relatively large "haplotypes" in our genomes.

At any rate, as the methods for detecting selection improve, more selection is detected, which is the lesson of this paper. These authors claim that while their method still significantly under-estimates balancing selection, they find evidnce for the existence of hundreds of sites in humans, when comparing genomes between different geographic regions of the world. A couple hundred of these sites are in the MHC regions- the immunological areas of the genome that code for antibodies and related proteins. These are well-known to be hotspots both for diversity and for the ongoing selective arms race vs pathogens (as we have recently experienced vs Covid). Seeing a lot of balancing selection there makes complete sense, naturally. 

The authors note that their focus on coding regions of the genome, and other technical limitations such as the need to find these sites through population comparisons, argues strongly that their estimate is a severe undercount. Thus one can assume that there will be at least several thousand sites of balanced selection in humans. This is quite apart from the many more sites of ongoing unidirectional selection, mostly purifying against problem mutations, but also towards positive characteristics. An accounting that is only starting to get going, over the vast amounts of variation we harbor. So we live in a dynamic world, inside and out.

• Green fuel for airplanes... really?
• Barr is not the good guy here.
• Free speech- not entirely free.
• Court to workers: drop dead.
• Islam and the megadrought.
• Is crypto this cycle's subprime black hole?

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.

Cracking the Kinome Code

Attempts to figure out what causes phosphorylation events in our cells.

Continuing with biological codes, this week's topic is protein phosphorylation sites. Phosphate groups are negatively charged, so they have dramatic electrical field as well as steric effects when attached to a protein. Though many other forms of protein modification are known, phosphorylation is an extremely common route of biological regulation in cells- a way to supplement binding, complex formation, and allosteric interactions between proteins for regulatory purposes. The human genome is estimated to encode 518 protein kinases- that is, proteins that phosphorylate other proteins. Because each one can have hundreds of substrates or targets, this is a lot, gives rise to complex networks of reguation, and is called the "kinome", in analogy with the genome, microbiome, proteome, etc. Kinases are roughly divided between those that target tyrosines (Y) in substrate proteins, and those that target the chemically similar serine and threonine (S/T).

These are images of all proteins from rat neurons, spread out on a 2-dimensional gel, one dimension (vertical) by weight, and the other dimension (horizontal) by isoelectric point. At top, the experiment is stained for overall protein. At bottom, it is labeled for all the phosphotyrosines that exist. That is, all proteins that have been, under these conditions, phosphorylated by the minority of kinases that are tyrosine-targeting. There is clearly a lot going on.

The typical sequence of events is that some upstream signal, such as binding a hormone at the cell membrane, will turn on a kinase, which then phosphorylates a target protein. This will cause the target protein to interact with new partners, perhaps to be degraded, perhaps to be transported to the nucleus, or perhaps to phosphorylate yet other targets in an amplifying cascade of regulatory events. While not as fast as neuronal action, this regulation is typically much faster than the typical gene expression route, where a signal activates transcription of some gene, which is transcribed to mRNA, which is spliced and processed, and eventually translated to make the target proteins. Thus regulation by phosphorylation is critical for all sorts of rapid biological responses, like metabolic tuning and hormonal actions. 

One key problem in the field is mapping exactly what each kinase does, and what kinase is responsible for each phosphorylated target site. Massively parallel methods are now able to identify all the phosphorylated proteins in a cell (after killing it, naturally). But knowing what process and individual kinase was responsible for each of those events... we are much farther away from mastering that level of knowledge.

Similarly to the transcription regulator problem a couple of weeks ago, the sites that kinases act at are characterized by motifs that can be illustrated by a diagram of colored probabilities (below). In this case, the kinase (AKT, one of the most influential in the cell), is a serine/threonine targeting enzyme, so the center of its site must have one of those two amino acids. Then there are a couple of argenines (R) at the minus 3/4/5 positions, a hydrophobic amino acid at +1, and otherwise there are few restrictions. 

A probabilistic view of the AKT kinase target sequence, where this serine/threonine kinase attaches phosphate groups on other proteins that it regulates.

Like in the transcription regulator case, the targeting code is pretty loose and degenerate. That drives researchers to probabalistic methods to wring as much mapping as they can out of current data, which was the topic of a recent paper. The title is "Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data". But "accurate" is a relative word. The graph below of recall and precision, which are standard terms of art in probability, using reserved portions of the data to test data accuracy, show a maximum of ~65% and 70%, respectively. That means that about 65% of true values are successfully collected from the underlying data, and 70% of the data collected is actually true. That may be best of class, but one wouldn't want to stake one's life, or even one's drug development program, on it.

Measures of accuracy of various methods of guessing what kinase is responsible for a given phosphorylated target site. Precision and recall are developed vs reserved (non-training) test data. The current author's method is IV-KAPhE in yellow.

This researcher set up an extensive pipeline to add together numerous sources of information. First is PhosphoSite, a database of kinase target sites and other interactions gathered both by hand from the literature and from private mass-scale data sources. Then he added co-expression data, which can hint that a kinase and target are present in the same cell, and thus candidates for interaction. Then came semantic data from general gene classifications, which can hint that a kinase and target work in the same process, and thus again likely to act in concert. A few additional databases, and he could, in classic Bayesian fashion, assemble a new resource that outperforms any of the individual ones in predicting what kinase is responsible for any given phosphoprotein that one has dug up in some mass-spec experiment. All that said, the method only covers kinases about which something is known, which currently runs to 349 kinases, well short of the total number mentioned above. So both in coverage and accuracy, we have a great deal to learn.

• Silence is golden, and healthy.
• Please throw out your halogen lamps.
• Watch Lucy pull the football away again.
• Allerdings, a lesson in German.

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.

What Binds to DNA?

Large scale studies of what binds to DNA over whole genomes.

Biology is full of codes. There is the genetic code, but there are many others. There are protein localization codes- short sequences on many proteins that tell them where they should transported to, such as to the mitochondrion, lysozome, the exterior, or the nucleus. There are kinase codes- the positions on many proteins where modification by phosphate changes their behavior. There is a histone code, which is the set of acetylations and methylations on histone tails which have wide-ranging influence on transcription of DNA to RNA. There is a sugar code- the many glycosyl modifications of proteins displayed externally on cells, which affect how they are seen and work in that space. Lastly, there is a code of short sites on DNA where specialized proteins bind, and by which transcription and other processes are regulated. Humans have roughly 1600 loci, out of their 20,000 genes, which appear to encode such proteins, and each binds somewhere and does something in our biology. 

The important cancer-suppressing gene p53 (green), binding to DNA (orange).  To the right is a closeup, showing a few of the detailed base contacts, with dashed black lines. Proteins that bind to DNA in sequence-specific ways feel their way around by making many such shape and charge-guided physical contacts.

The study of how and where these proteins bind has a long history, with many such proteins now exceedingly well characterized, to the atomic level. But at the genomic scale, it is still something of a crapshoot to guess where and whether some DNA site binds a regulatory protein. Such proteins have rather flexible requirements, which researchers express in "motifs". These motifs are short and typically variable, or "degenerate". That is, each position in such a motif can be one of the four bases, and frequently more than one base is allowed. In the motif shown below, for the protein ZBTB33, only one G is absolutely required. The other positions are variable to some degree. Outer areas of a binding site tend to be less selective, naturally, as they are less strongly bound by the protein. Some proteins can bind to two different motifs, and some can be accessorized by partners of various kinds to bind yet other sites. Evolution is the great tinker, and in this system, interactions are frequently kept rather loose and fluid, enabling precision where needed, (partly by complexing numerous regulatory factors & binding sites with each other in large casettes), but also flexibility and adaptability elsewhere.

A representation of what DNA sequences the zinc finger protein ZBTB33 binds to. Each position along the DNA site is shown as the collection of possible bases seen in functional sites, with each shown in proportion to its frequency of occurrence. The central G is the only absolutely required base, though several others are nearly invariant.

So the question of what binds where is not an easy one to answer, just going from the sequence of the genome. Naturally, this has been the subject of recent advances in large-scale biology, enabling researchers to, for instance, identify all the binding sites of a given protein across the genome (in a given cell type and culture condition). Or alternately to identify all the "accessible" sites across a genome (and also in a given cell type and culture condition), which would be locations where chromatin is "opened" up due to the binding of whatever regulatory proteins. This latter style of experiment naturally leads to the question- what is doing all that binding?

A recent paper comes from that field, deploying the latest machine learning and convoluted neural nets to find the answer, at least on a statistical basis. They combine a series of bulk open-chromatin experiments with a database of known transcription regulator motifs to match genomic sites with plausible proteins that bind there. In usual machine learning fashion, they reserve some of the training data for testing and validation, enabling the production of ROC statistics for accuracy and for comparison with other methods, of which there are many. But what they do not do is actually test the accuracy of their data in the lab, with actual cells and proteins. That would hard for a bioinformatics lab! So their talk of "accuracy" is rather untethered from reality, though fine enough for the journal they published in, which is Public Library of Science, Computational Biology. 

All that said, this is a code that is going to be very difficult to crack, since regulatory proteins are not just highly diverse and their sites degenerate, but they are themselves regulated in many ways, by phosphorylation, sumoylation, ubiquinylation, methylation, complexing with partners, the generation of variable isoforms through transcription, and cleavage, among others. The same protein that activates transcription here may repress it there. So the "motif" is a bit of a chimera, as is its effect on gene expression. The great tinkerer has gone so far down the rabbit hole that even "Deep Mind" is going to have a hard time following it down, without further empirical advances ... such as a massive upgrades in methods to identify specific protein binding sites across the genome.

• Can steel be green?
• If Russia leaves Ukraine, the war can end very quickly. If not, then it won't.
• What happened to Finland?
• Ride hailing meets economics.
• Why doesn't CPAC go all the way to Moscow?
• Boiling point.
• Another Ukraine end game.