mm-Hmmm ...

The critical elements of conversation that somehow didn't make it into the "language". A review of How We Talk, by N. J. Enfield.

Written language is a record of elision. The first written languages were hardly more than accounting symbols, and many early forms of writing lacked basic things like vowels and punctuation. The written forms are a shorthand, for those practiced in the art of spoken language to fill in the blanks, and they still hide a great deal today. For example, the same letter, such as "a" can stand for several vowel sounds, as in ate, art, ahh, am, awe. Another rich part of the language left on the editing room floor are completely unrecorded (except by authors of dialog looking for unusual verisimilitude) sounds, like um, ah, huh, mm-hmmm and the like. N. J. Enfield makes the case that, far from being uncouth interjections, these are critical parts of the language, indeed, part of an elaborate "conversation machine" which is one behavior that distinguishes humans from other animals.

Arabic, a language commonly written without vowels.

When we are in conversation, time is of the essence. We expect attentiveness and quick responses. It is a relationship with moral aspects- with obligations on each side. The speaker should repeat things when asked, not take up too much of the floor, provide clear endings to turns. Enfield describes a very disciplined timing system, where, at least in Japan, responses begin before the first speaker has stopped. Other cultures vary, but everyone responds within half a second. Otherwise, something is discernably wrong. One thing this schedule indicates is that there is a sing-song pattern within the speaker's production that signals the ending of a speaking turn well before it happens. The other is that there is an serious obligation to respond. Not doing so will draw a followup or even rebuke from the speaker. Waiting more time to respond is itself a signal, that the response is not what is desired.. perhaps a "no". It can also be softened by an "uh" or "er" kind of filler that again signals that the responder is 1. having some difficulty processing, and 2. paving the way for a negative response.

Likewise, "mm-Hmm" is a fully functional and honorable part of the language- the real one used in conversation. It is the encouraging sign that the listener is holding up her part of the bargain, paying attention to the speaker continuously. Failing to provide such signs leads the speaker to miss a necessary interaction, and interject.. "Are you listening?".

Finally, Enfield deals with "Huh?", a mechanism listeners use to seek repair of speech that was unclear or unexpected. When a response runs late, it may switch to "Huh?", in a bid to say that processing is incapable of making sense of what the speaker said, please repeat or clarify. But at the same time, if something of the original speech can be salvaged, listeners are much more likely to ask for specific missing information, like "Who?", or "where was that?" or the like. This again shows the moral engine at work, with each participant working as hard as they can to minimize the load on the other, and move the conversation forward in timely fashion.

Huh is also a human universal, one that Enfield supposes came about by functional, convergent evolution, due to its great ease of expression. When we are in a relaxed, listening state, this is the sound we can most easily throw out with a simple breath ... to tell the speaker that something went off track, and needs to be repeated. It is, aside from clearly onomatopoeic expressions, the only truly universal word among humans.

A conversation without words.

It is a more slender book than it seems, devoted to little more than the expressions "uh", "mmm-Hmmm", and "Huh?". Yet it is very interesting to regard conversation from this perspective as a cooperation machine, much more complex than those of other species, even those who are quite vocal, like birds and other apes. But it still leaves huge amounts of our face-to-face conversational engine in the unconscious shadows. For we talk with our hands, faces, and whole bodies as well. Even with clothes. And even more interesting is the nature of music in relation to all this. It is in speech and in our related vocal intimacies and performances that music first happens. Think of a story narration- it involves not only poetry of language, but richly modulated vocal performance that draws listeners along and, among much else, signals beginnings, climaxes, endings, sadness and happiness. This seems to be the language of tone that humans have lately transposed into the free-er realms of instrumental music and other music genres. Analyzing that language remains something of an uncharted frontier.

• Machines can do it too.
• Varieties of technoreligion.
• Monopoly is a thing.
• Appalling display of religious fundamentalism: The US ambassador to Israel refers to old testament and 3,000 year old rights of Israel. If other 3,000 year old land claims were to be honored, the US would be in substantial peril!
• In praise of Jimmy Carter.
• Collapse or innovation.. can we outrun the Malthusian treadmill?
• Truth and Rex Tillerson.
• Sunlight makes us feel better.
• We still have a public sector pension crisis.
• Economic graph of the week. Worker quit rates are slowly rising. Will that affect pay?

The Biology of Fluoride

Fluoride has no biological functions, other than the need to get rid of it.

Fluorine is the smallest and most reactive halogen, a relative of chlorine, bromine, and iodine. Chloride is ubiquitous in salts and in the ionic milieu of our bodies, and iodine has found a central role in metabolism in virtually all species. Even bromine has various biological roles, though mostly in microorganisms. Fluorine, however, has found no role at all, despite being relatively common- more abundant in rocks than chlorine, let alone bromine or iodine. Its only part to play is as a noxious ion to get rid of. And all organisms have ways to get rid of it, via both active and passive trasporters. More on that below.

Humans, in their wisdom, however, have found some remarkable uses for fluorine. Modern chemistry uses it a great deal, to make very tough chemicals like Teflon, Lipitor, and Lexapro. Virtually nothing displaces fluorine from carbon bonds, so its compounds, while very useful, also end up as rather persistent waste products. More interesting, however, is our practice of ingesting fluoride (the ionic form of fluorine) in small amounts for oral health. This has been a subject of tremendous controversy and conspiracy theorizing for decades. But the benefits couldn't be more clear- teeth are much tougher from trace topical exposure to fluorine, which works its way into the crystal structure of enamel.

However, ingesting fluoride is another matter. It is reputed to cause kidney problems at higher concentrations, but there is very little epidemiology to support claims that these risks start at low concentrations.. anywhere near the levels used in drinking water supplementation. Similar to observations of bone deformities and tooth fluorosis, the syndrome of too much fluoride common in geologic regions with excess fluoride, there would have been observations of rampant kidney or other disorders. But that doesn't seem to be the case, other than very sketchy reports. At any rate, the therapeutic dose of fluoride put in water supplies is about 30 micromolar, while the newest regulations in the US establish a conservative cap of about 100 micromolar, in light of the lack of any use for higher concentrations, and the occasional problems from higher natural exposure, top which the artificial amount adds.

So we can't do much with fluorine, biologically speaking. Indeed it is generally toxic, messing with the phosphate chemistry that is central to all life. How do we get rid of it? There are three mechanisms, overall. In animals, our kidneys take care of it, using clever ion transport to excrete excess fluoride. (Recall that the first step of the kidney's work is to remove all the small solutes from blood plasma, and then later to selectively bring back the important things we want, like sugar, some salts, lactate, water, etc. The remainder that is not actively re-absorbed includes such oddities as fluoride.)

But other organisms that live directly in the soup, i.e. microorganisms, all need to take specific and active measures on the cellular level against fluoride. An important point in this chemistry is that fluoride has a significant acid-base preference. HF forms at relatively high pH (pKa of 3.4, much higher than HCl, which stays ionic to pH 1 and below, an oddity of fluoride's chemistry), which means that in moderately acidic environments, external HF can easily form and diffuse into cells as an uncharged entity, and there, under more neutral conditions, dissociate and be trapped as F- ions. This leads to chronic over-loading of cells with F-, (up to 30X over external levels), which can be remedied by a protein channel (second mechanism) that lets these ions back out passively, while not letting out other ions such as the closely related chloride. The third mechanism, exclusively used by bacteria, is active antiport, (H+/F-), using the stored energy of the proton gradient (high outside, low inside) to drive F- excretion.

 

Structure of two copies of E. coli-derived Fluc, a passive fluoride channel/exporter. The proteins are blue and yellow, respectively, the membrane represented by black lines, and the fluoride ions are modeled as gray or red balls. Given the symmetry of the proteins and their passive role, the orientation (up/down) makes no difference. The channel is formed at the interfaces between the two proteins.

A recent paper described the simple passive transporters that are ubiquitously used for fluoride export in microbes. They are odd in that it takes two proteins to form a functional transporter. The channel through which the F- ion passes is on the surface between the two proteins, in a symmetric structure that forms two channels (above). In eukayotic microbes like yeast cells, two such genes have become fused to form one gene encoding a protein that retains dimeric symmetry, but one of whose channels has become non-functional / vestigial.

A close-up view of one of the channels, showing some of the key individual amino acids that coordinate / bind to the fluoride ion as it travels along. This close physical and electrostatic coordination insures that nothing that is not fluorine can get through. Notably, part of the job is done by uncharged phenylalanine residues, (blue and orange ring structures), which are usually regarded as hydrophobic, but have a slight face/edge polarization that can be exploited by strong ions

The channel is, understandably, very tight, with intensive coordination all along the way, particularly with uncharged phenylalanines which provide an unusual side-ways polar coordination that is proposed to make the channel particularly specific to F-, vs Cl-. And it is very selective- over 10,000-fold selective for F- vs Cl-. Replacing these phenylalanines with the hydrophobic amino acid isoleucine reduces F- transport to negligible levels. It would have been interesting to ask what a less bulky and less hydrophobic replacement like glycine or threonine does to the channel's activity, perhaps making it significantly less selective, while still functional.

• Unfit to serve on a sewer board, cont. Climate, shimate.
• Desperate US military and allies have lost ground.
• Antitrust should not be just about consumers.
• Property is monopoly.
• Tourism makes up 8% of carbon emissions.
• Lowdown on money laundering.
• Driving remains dangerous.
• Some non-profits are not so non-profitable.

Green Power

California's open political structure opens the opportunity for the Green party to create a revolution.

A recent op-ed in the local paper by a Republican party official complained about California's open primary system. This system runs primaries and general elections without regard to party affiliation. The top two finishers in the primary run against each other in the general election. In California, this has resulted in many state-wide races being contested between two Democrats. The Republican party no longer has a lock on one position on the general election ballot as they used to, and this naturally rankles. The editorialist complained pathetically about lack of diversity (of all things!), and how the choice between two Democrats was so limited. It was whining at its most exquisite.

California has frequently been in the political vanguard, whether in tax revolts or in progressive climate change policy. The 60s were headquartered here. California has put redistricting on a non-partisan basis. The open primary system has been a dramatic success, giving the best two candidates a hearing before the voters in the general election, and reducing partisanship and cronyism in the state. One side benefit is that voters can register with a minor party without the penalty of being locked out of the key primary races, which are no longer parochial, but open to all. This new political landscape (which was the beneficent and ironic gift of Arnold Schwartzenegger) could lead to another progressive advance, in the form of a revitalized Green party.

Trends in party affiliation in California. Greens come in at 0.62%- currently negligible.

The Democratic regime in California has not been a bad thing on the whole. Under Jerry Brown, who operates as a centrist, the drama surrounding budget battles and other fringe issues has been sharply reduced. Except for the pension crisis, the state has been quite well run, if inefficient. Advances in climate change regulation, marajuana legalization, gun control, and formal resistance to the Trump administration are generally appreciated. Trump is reviled. Education and infrastructure funding remain dreadful. There is little stomach in the state for a return of Republicans as the opposition, (they are now legislatively locked out of veto power), which would bring back endless bickering and corrupt dealing. There is, however, room for less corporatism and more progressivism, which is what a stronger Green party could provide.

The Green party currently is not much healthier than the Republican party, unfortunately. In California, it fields a grand total of 60 office holders, none of which are statewide. Its web sites and organization seem moribund. Due to the two-party structure at the national level, it is unthinkable to support it in presidential races, where it would be a spoiler to benefit Republicans. But with open primaries in California, the party could cultivate a state-wide program and candidates, while vowing to back the Democratic party (or whichever party is more aligned with Green objectives) in races that are significantly contested by Republicans, which is to say, effectively support the left. That would provide a solid platform for activism within the state, building the movement and the party.

Each non-presidential race would have to be carefully evaluated for whether the participation of a Green candidate would raise the chances of Republican / Conservative victory significantly. In primaries, this is likely be a negligible risk as things stand. At least one Democrat will always win in non-rural districts. For the general election, if a Green candidate is not running, Greens would support the Democratic candidate, or whichever one most agreed with the Green agenda. This would make for a sort of mature, parliamentary-style politics, where coalitions are assembled in response to conditions.

Oddly, however, the Green party is officially against the open primary system, mistakenly thinking that the loss of a coveted (though pointless) automatic spot on the general election ballot outweighs the decisive gain of flexibility for their voters and sympathizers in the primary election. They want something still better, like proportional representation, logic that to me seems maybe nice in theory, but self-defeating and irrelevant in practice. Worse, the national Green party is a disaster, indeed a toxic blight on the left, pushing its presidential candidate in the teeth of all logic and experience. That is no way to succeed.

The Republican editorialist bemoaned the lack of competing perspectives and arguments in California politics. But the voters have decisively rejected the Republican program of meanness, business cronyism, labor expoitation, environmental degradation, and xenophobia, which has only become more extreme and blatant on the national level. Maybe the discussion that voters in the state really want is one between Democrats and those who want progress to go even faster- toward single payer health care, faster de-carbonization of the economy, more effective business (and internet) regulation, and more balanced housing and transportation growth, among many other issues. The climate is shifting.

• Change your party registration right now!
• We are choking on zoning.
• CO2 is not only rising, but rising faster than ever.

Concept as a Shadow of Percept

Binding and grounding- How does our brain organize concepts, properties, and relations?

Evolutionarily, brains developed to interact with the outside world, developing out of senses to orient the organism for food and defense. The basic senses came first, and then the ever more complex networks / computations to deduce what their signals mean and ultimately to build an entire world model, against which to evaluate changes in perception. While perception is now heavily influenced by such mental models, it did not begin there.

This history informs the question of where concepts reside in the brain. The wetness of water is something we feel, and our conception of it is naturally tied to our perception / sensation of it. Our language makes unending use of metaphors that extend this concrete perception-based ontology to the highest abstractions. If someone is a dirty scoundrel, they are only metaphorically dirty, and the visual and tactile aspects of dirtiness are evoked to enrich and clarify the abstraction. While one might imagine that, like computers, our brains store this conceptual data of definitions, categories, properties, etc. just about anywhere, whether in a distributed holographic engram or in dedicated storage areas, the fact is that data storage is localized, such that lesions in various parts of the brain can disrupt recall of specific classes of skills, properties, facts, faces, experiences, etc.

It is also apparent that much of this storage is coincident with our perceptual apparatus (and motor and emotional apparatus). Thus, a brain scan of someone asked to think about and apple and how it differs from a grape will light up areas in the later visual system where incoming perceptions of apples and grapes are decoded into the shape, color, size, etc., which we understand as being their respective properties. Perhaps olfactory and tactile areas come into play as well. Likewise, thinking about a guitar might generate activity in the motor planning areas, providing concepts about playing one. So, analogous to a spotlight of attention, we also have back-casting mini-spotlights of classification and conceptualization that connect "higher" areas in the frontal cortex (which are perhaps asking the questions) to motor, emotional, and perceptual areas, allowing the system to encode complex conceptual schemes once only, where they are first established, in the grounded areas such as in perceptual processing. Once there, they can serve both the immediate perceptual needs of classification, and the evidently related needs of rendering the same classes as concepts.

"Not only is object property information distributed across different locations, but also, these locations are highly predictable on the basis of our knowledge of the spatial organization of the perceptual, action, and affective processing systems. Conceptual information is not spread across the cortex in a seemingly random, arbitrary fashion, but rather follows a systematic plan."

This is the subject of a review, and of a recent paper which attempts to show that it is white matter tracts that constitute the property recognizing units of the brain, not the grey matter targets of their communication. They call this model "representation by connection", and their case is not well made. Yet the overall topic is extremely interesing, so here goes. The fact that this characteristic distribution of property storage in the peripheral systems exists is not in dispute. What is still uncertain is how it is all knit together and what, exactly, is being communicated back and forth. And, of course, what out of these ingredients constitutes the resulting gestalt of consciousness.

The new paper tries to make a big distinction between grey matter (the dense cellular areas of the brain) and white matter (the tracts of myelinated connecting axons, which have recently been so beautifully traced by DTI MRI. They collected 80 people who have suffered lesions in various localized areas of the brain, due to strokes, hemorrhage, or trauma, and correlate their deficits in object property recall / naming, which are specific and diverse, with separately derived maps of white matter tracts, and semantic / notional distance between the same concepts, as provided by a sampling of normal college students. The latter was taken in several dimensions, including properties of color, manipulability, motion, phonological, shape, usage, and others, but only set up a conceptual space field- it was not explicitly correlated with brain anatomy.

"Distributed GM (grey matter) regions that represent different attribute dimensions (e.g., shape, color, manner of interaction) of the same object are connected by WM (white matter). The WM linking pattern itself would then contain multiple dimensions of information in these GM regions and, importantly, additional information about the manner of mapping among various attributes. The incorporation of these elements has been argued to be necessary for the “higher-order” semantic similarity relationships, which are not explained by attribute-specific spaces, to emerge."

The authors developed anatomical maps of normal white matter tracts, and then developed a map of semantic correlations given the defects in the brain damaged patients, over-laying their cognitive defects, on the same object classification tasks as above, over their individual brain defect regions. The question was then, once the semantic defects were anatomically mapped, are their relative positions correlated with the mapping in conceptual space done by normal volunteers? One would naturally expect that yes, cognition of similar objects (scissors, knives) would happen in spatially close areas of the brain. This was indeed found. What it means, however, especially for the author's theory, is extremely hard to say. It is especially hard as the paper is not well written, (the group is from China), leaving their core ideas rather murky.

"In conclusion, using a structural-property-pattern-based RSA (representational similarity analysis) approach, we found that the WM (white matter) structures mainly connecting occipital/middle temporal regions and anterior temporal regions represent fine-grained higher-order semantic information. Such semantic relatedness effects were not attributable to modality-specific attributes (shape, manipula- tion, color, and motion) or to the representation contents of the cortical regions that they connected and were above and beyond the broad categorical distinctions. By connecting multiple modality-specific attributes, higher-order semantic space can be formed through patterns of these connections."

Example of one finding. Two brain areas of gray matter in the left hemisphere (red, superior temporal gyrus; and green, the calcarine sulcus) are linked by a mapped white matter tract. The graph shows a significant r-value for the correlation between the neural similarity (map of white matter lesions by properties reported to be defective) and the author's custom mapping of semantic similarity.

They do claim explicitly that the corresponding gray matter maps from the brain-damaged patients did not correlate as well with the semantic space patterns as did the white matter maps. But this is not so surprising, as gray matter regions (which could be imagined as the CPUs of the brain) are all connected via the white matter (the networking cables). So for a process that depends on the collation of numerous pieces of information, (the concept property units harvested from each percept / action planning/ emotion region), it would be natural to expect that cutting the cables might be a cleaner way to cause particular property type deficits. That doesn't mean, however, that it is the cables that are conscious, or that are doing the most important processing.

So I think, aside from the operational issues, which look rather daunting in this paper and whose resulting correlation maps are only marginally compelling, there are serious theoretical issues that indicate that while this field is ripe for advancement, this does not seem to be the paper to get us there.

A much more through and positive review than this one.

• Bernie does what no one else will- the employment guarantee.
• Techies are building a dystopia built on surveillance, invasion of privacy.
• Egypt remains a mess, without economic prospects and with overpopulation.
• What is going so wrong in Mexico? We don't even know who is corrupt any more.
• Lack of competition is pervasive.
• Unfit to serve on a sewer board, II.
• Nature -and- nurture.

Heroes, Superheroes, and Saviors

What do we see in the hero myth? With apologies to Joseph Campbell.

I was watching the TV version of Dune, which, while much better than the movie, hardly matches the book. Seeing it again made it painfully clear how this story, so gripping to my younger self, is a formulaic hero tale, just as Harry Potter would be for the next generation, Frodo Baggins was for the one before, and Arthur, Beowulf, Jesus, Buddha, Rama, and Odysseus have been since antiquity. What do we see in them, and why are they so riveting?

Obviously, these tales speak to the meaning of life, in a direct and comprehensive way. Though mostly for males- Heroes and their students are, as a rule, male. They go on adventures, lead others, resolve mysteries, and ultimately solve communal problems. What they achieve is status, renown, and perhaps the hand of the princess, who is the typical hero of the female archetypal tale (though see also Dorothy, Alice, Mulan, et al.).

These qualities have relatively little to do with one's purely individual path through life, judged by, say, happiness, or one's success in earning a living, attending to the humdrum affairs of personal life, comfort, and family. Rather, it is a wider social role and service that is the point, and fame is the coin of this realm. The hero slays monsters that have terrified the people and despoiled their crops. Or he retrieves the chalice that gives everlasting life and salvation. Or he uses a mysterious force to lead a rebel alliance against the totalitarian galactic empire.

Horses? This quest needs no horses!

Hero tales are formative for those in formation- the maturing child, who instinctively yearns to accomplish something significant, which is the path to status in the collective, and thus to relative power and reproductive success. But what defines success and significance? It is necessarily the collective that must define what is important, via its bards who recite its problems both perennial and topical, provide the grist of heroic adventure and conflict, and award fame for their successful conclusion. Whether it is raging beasts in the countryside, Orwellian tyranny, taunting goddesses, or a world-wide conspiracy of death-eaters, the threat is not individual, but collective, and thus the hero serves the collective, something "greater than himself", as many people express their seeking behavior. Success of any kind is attractive, but to be truly compelling, success needs to resolve big problems and be valued by others. (Though in fairness, the hero may toil in obscurity and only be recognized in retrospect, perhaps long after his death, to have solved the momentous problem. Such a tale may have additional romance, and happen in reality all too often, but is not typically what a reader wishes to emulate for her or his own life path.)

One characteristic element of the standard hero tale is the reckoning with the father. Luke Skywalker finally meets his maker in a climactic scene. Jesus naturally has mixed emotions about his father, whoever that might be, who has left him up on the cross. The father represents the existing system, which has formed the hero, but which also perpetuates all the problems that he exists to solve. The father must be transcended for the tale to conclude successfully. Paul Atreides has spiritual and temporal powers far beyond his father's, and succeeds where the father had failed. More interestingly, Jesus, while always respectful of the father and putatively acting in his service, ends up totally upending the father's theology and bringing a new dispensation, whether that was "in reality" his intention or not.

Sometimes the goal of a quest is so abstract and theologically attenuated as to be absurd. Maybe the quest was the important thing after all.

More complicated is the role of the special gift. Harry Potter has the mark of the lightning flash, and special powers of leadership and magic. All the Marvel heros have some special power. Heroes are typically born of noble houses, though they may be unrecognized or abused for some of the story. What is the function of all this apparatus? Isn't the point of the hero tale to inspire normal boys to seek glory for themselves from/for their collective? Why start with abnormal heroes? The quest needs to be done in a noble way, morally upright. But that hardly requires a particular form of birth.

I think much of this has to do with the inner quest, which is another aspect of the hero tale. In order to seek outer glory, the hero needs first an inner quest, to find the confidence, knowledge, and personal resources to do extraordinary things. Jesus grappled with satan in the desert, while Paul Atreides grapples with sandworms in the desert (always an epic setting; Lawrence of Arabia grappled there with a recalcitrant, but noble, Arab culture). Each person has some special gifts and skills, and an important aspect of life, particularly adolescence, is to find what those might be. The ability to be clairvoyant, or to accumulate The Force are symbolic of momentous discoveries about the self which happen during growth to adulthood. While few of us will find nirvanna, or that we are the son of god, nevertheless whatever we do find will be the key to our ability to differentiate ourselves from the crowd, while earning its respect. Each person follows this archetypal path, and it is typically a difficult and uncertain one, thus the universal interest it evokes.

The noble house and lineage aspect seems more atavistic. One of the hero's special gifts / typical traits (which is key to the story's cultural and pedagogical significance) is to be naturally noble in deportment, morals, and martial prowess. Given our instinctive racism and appreciation for inheritance of traits, it is then natural to make this occur by having the hero some secret child of the king, or an acknowledged child who breaks out of the mold and takes a different path (Buddha). Or who comes both from a noble family and from the planet Krypton. Surely we could come up with a more modern way to handle this! Even the Black Panther is of noble birth. Tolkein gets points on this score for his low-class heroes in the Lord of the Rings.

But there is also a superstitious element. Luck is one thing the hero needs to have on his side, and this has traditionally been bound up with cosmic forces and mysteries, instinctively (and animistically) personified. Special forms of communication with these forces, or at least encouraging signs from them, would by this primitive instinct, be essential to success. One can take this in more rational way, however, to indicate a certain humility and appreciation before the complex and often inscrutable real forces that form our basis of operations, including the social forces that may not be ready for the hero's revolutionary work and need to be brought along by way of their primitive beliefs, whatever their nature and value.

Maybe a little self-flagellation would help?

It is particularly pathetic when a hero is so venerated and his boons are so attractive that his devotees make a fetish or even religion of him, employing a priesthood to retail third-hand boons of a studiously invisible nature. Generally, the emulation of nobility, and inner quests modeled on that of the hero, are not a bad thing. But the whole point of the tale was to find and develop one's own self and one's own resources- one's unique gifts and path in life- rather than to adopt another's wholesale, or worse yet, to fantasize about fictional powers and benefits that can be cadged via supplication and abasement. That would be to fundamentally misunderstand the point of the hero archetype, going so far as to reverse it as an engine for the most unheroic behavior. Thankfully, such overblown renditions have been relatively rare over the recent centuries (though Scientology, and before that, Mormonism, stand as significant and unfortunate counter-examples). Yet overall, absurd hero-religions, mostly stemming from more distant epochs, remain all too common.

The quality of the hero story plays an important role in its society, of which it is a gauge and exemplar. Just think of the pervasive influence of Homer's epics, or of Christianity. It defines not only the archetypal problems to be faced, but the standard of morality / nobility the aspiring hero must have to engage in its quest / solution. Star Wars cast the enemy as a Stalinist totalitarianism, while Buddhism cast the enemy as Maya and attachment to outer and fleeting things. While moral good and bad are perennial problems of the human condition, other aspects can change. The balance between inner and outer quests is a key indicator of a tale's maturity and spiritual content. Our current tales seem to center on the Marvel universe, of which I know very little. But it seems generally dedicated to extravagant violence and justice, with a somewhat infantile/regressive tone, overall. There is limited inner focus. They seem on the level of the Bond franchise, but without the understatement or style. It was extremely disturbing when, after 9/11, there was a rash of corner-cutting hero tales that supported the use of torture.

John Cleese strikes a heroic pose.

At this time when the actual culture is run by those fitting an antihero archetype, (technically, the heel), and the planet truly in peril, it is even more imperative that the stories that form our hero mythology and guide our questing youth be well-constructed, compelling, positive, and timely in their selection and portrayal of problems. Vietnam was a watershed in this regard, sending us from the morally simple comforts of the old Westerns and Hollywood classics, into self-lacerating work like Apocalypse Now and The Deer Hunter, and most recently, Game of Thrones. This depressing trajectory reflects changes in American culture, which has become more complicated and self-doubting, (perhaps mature), even mean. Realistic? That is hardly the point of the hero tale, frankly. Many recent film-makers have tried their hand at the saving-the-planet story, surely the one we need most of all, (from Avatar to Independence Day), but none seem to have become canonical. Someone needs to do a better job painting the deep challenges of the day for tomorrow's heroes.

• Unfit to serve on a sewer board. But then, who helped elect him?
• In praise of curated data. Sort of the opposite of Twitter, Facebook, and the other new news, but not cheap to do.
• New tech, same as the old tech.
• Liberals sometimes can't help drinking the right-wing economic koolaid.

Feelings, Nothing More Than Feelings ...

Charles De Gaulle and the greatness of France. Review of his war memoirs.

Fin de siècle France was a mess. After a century of social and political enervation, France was not the powerful country she was over most of Western history. Proust is a fair barometer, obsessed by the distant glories of the noble houses, but met in the present with their dissipated exemplar, Baron de Charlus. World War 1 was billed by some as a romantic rite of purification by blood, but turned out to be throughly ruinous and horrible, leaving the France even more adrift and traumatized, despite having "won".

Naturally, France then failed to face up to the rapidly developing threat from the East, and crumpled igominiously once the Germans came, entering into the quasi-occupation / collaboration that was Vichy. Who was appalled by this? Everyone, even the Germans. And especially Charles de Gaulle, a government minister and military figure who had argued over the prior decade for military mechanization and mobilization, to supplement the static Maginot line. He was incensed that the government chose to surrender and enter into collaboration, instead of spiriting off what and who they could to France's extensive overseas possessions and continuing the war from there (while leaving the French continental population to whatever administration the Germans saw fit to impose).

Seeing no one else stepping up to that task, he took it on himself, powered by the radio broadcasting resources of the BBC. He stands as one of the great statesmen of the century, single-handedly organizing the Free French resistance against what turned out to be the millenarian and cataclysmic Hitlerian regime, leading the French state during the very delicate and difficult post-war period, and also re-organizing the French state (the Fifth Republic) along new lines, within which it still exists today.

At the liberation.

Vain? Yes. Monomanical? Absolutely. A selective memoirist? Yes. A born politician? Evidently. De Gaulle was obsessed with the greatness of France, a phrase that comes up time and again in his memoir. He most potent weapon was the word "No". When Britain wanted to get some payback for all its assiduous help, by, say, acquiring some of the French possessions in the Middle East like Lebanon and Syria, De Gaulle said no, and fought them off. De Gaulle faught tooth and nail for every colonial backwater, and later on for every inch of German territory he could wrest out of the Allies. This "No" rose out of the power De Gaulle developed as head of the French people, nurturing their feelings of pride, and victimization, and hope, through the long years of occupation, and the slow process of liberation.

The most interesting aspect of the book is the careful (if self-adulatory) accounting De Gaulle constantly keeps of how his listeners are feeling- how the spiritual bond between him and troops being reviewed, or crowds hearing his speaches, or the French community at large, is developing. It is feelings which are the object of propaganda, the sinews of civic community, and the foundation of national power. These feelings start off rather tenatively, but via the radio broadcasts, and through slow persistence on the ground, first setting up shop in England, then Brazzaville (then part of the French empire, wrested from Vichy), then Algiers, and finally Paris, De Gaulle gains the hearts of the French, and enters into uncontested administration of post-war France. De Gaulle also carefully took charge of the internal French resistance, by supplying arms, other logistics, and leadership.

A sample quote: De Gaulle, installed back in Paris, receives a communication from Marshal Pétain, earlier the titular head of the Vichy regime, now on his way to imprisonment in Germany, to the effect that Petain would like to negotiate with De Gaulle about the transfer of formal powers of administration in France, i.e. his own surrender, in order to prevent civil unrest.

"But what reply could I make to this communication? In such matters, sentiment could not stand in the face of the rights of the state. The Marshal referred to civil war. If by that he meant the violent confrontation of two factions of the French people, the hypothesis was quite out of the question. For among those who had been his partisans, no one, now, rose up against my power. There was not, on liberated soil, one department, one city, one commune, one official, one soldier, not even one individual who professed to oppose De Gaulle our of loyalty to Pétain. As for reprisals, if certain factions of the resistance might commit retaliatory actions against the people who had persecuted them in collaboration with the enemy,  it devolved upon the public authority to oppose itself to such actions, while insuring the action of justice. In this matter, no compromise was conceivable."

It is an object lesson for our time, in making a nation great again. Firstly, De Gaulle writes very well, in style that is admired in France, and also communicates his clarity of intellect, even in translation. Secondly, he generates increasingly representative advisory councils as he goes along, always taking the temperature of the major threads of French resistance (including the communists whom he loathes). Instead of tearing down state structures, he continually builds up new ones, in preparation for effective administration of ever larger populations and areas. Thirdly, he is never a poodle for foreign powers, standing up for French interests at every point, even when there is no France to stand up for. And fourth, his mind is always on the big picture. There are no scandals in this book, only high policy and monomaniacal focus on the objectives of a healthy France, Europe, and world.

He sees that in order to conduct the resistance from colonial territories, he will have to promise their independence, at least in principle. But getting from there presents enormous problems, especially when the British push Arab and Islamist agitation. De Gaulle ended up being the one to wind up the bitter Algerian war, (1962), selling out the various pied noir (settlers, in current parlance) to grant Algerian independence. When the US dreamt up the United Nations, De Gaulle viewed it with suspicion (and, in view of the ill-fated League of Nations, with some distain), even as he successfully got a seat on the security council. While this council may seem an absurd anachronism today, its original aim was rather evidently to serve as an anti-German league, consisting of all the Allied powers from WW2, particularly those surrounding Germany.

De Gaulle with Willy Brandt. De Gaulle was intent on building good relations with Germany, and integrating Germany into a new pan-European economic and security system.

In addition to his bitterness about Britain's greed, De Gaulle was bitter about the US as well. Roosevelt never took him seriously, and continually tried to circumvent De Gaulle in setting up occupation administrations and in conferring with the "big" allies. It is not entirely clear what the basis of this distaste was. It was putatively about De Gaulle's upstart status, as one who created his own state out of nothing, rather than sitting atop a pre-existing apparatus, not to mention a lack of democratic credentials. It was also about France's weakness- her ignominious military defeat left a sour taste, for sure. There was also France's unproductive treatment of Germany after WW1, first demanding huge reparations that prostrated and embittered Germany, then lacking the backbone to back them up or productively renegotiate them, rather allowing Hitler to thumb his nose at the Versailles regime and embark on his mad buildup to WW2. Or there may have been something else. But De Gaulle got his revenge later on, when he entangled the US in Vietnam, which was one jewel he was exceedingly reluctant to yield out of the colonial empire, especially to a bunch communists. All in all, our relations with France are a lesson on focusing on the current war and the friends you have, not the last one, or the ones you wish you had.

• "... a federal judge or magistrate judge signing off on the search warrant on the president’s lawyer after finding probable cause of criminal acts."
• Piketty on Russia. 
• Not a happy scene in Afghanistan.
• Word of the week: chromothripsis.
• A party of sociopaths?
• We need micropayments on the internet, in place of ads.

The Right Wing Mind: Lost, Revealed, or Manufactured?

A review of How The Right Lost Its Mind, by Wisconsin conservative talk show host Charles Sykes.

Oh, where are the decent Republicans? The Ronald Reagans, the Newt Gingriches, the Paul Ryans? Thus goes the lament of Charles Sykes, who writes a searching and impassioned book decrying the moral and intellectual collapse of Conservatism into right-wingnut demagoguery and authoritarianism. Like any theologian, he is not willing to go the whole distance and question the fundamental nature of American conservatism and its pieties (which he refers to as "truths" with some frequency). But he is remarkably honest about the rot that characterizes the party, even as it is ascedent politically. I recommend his work, though obviously he remains staunchly (if nicely) conservative. Being from Wisconsin, and all. He had, indeed, played a central role in denying Trump the Wisconsin primary, from his talk show perch.

There are many threads that lead from there to here, and I will break out a few of them below. The arc of his story is that the sainted William Buckley exiled the wingnuts from the Republican party, preparing it for several decades of intellectual growth and political dominance. Now they are back with a vengeance. Sykes spends most of the book describing the many ways this happened, but explaining *why it happened in any deep way is another matter altogether. One might also ask why they were there in the first place, and where did they go in the meantime?

Media: from responsible to clickbait

The fact that Trump, after all we have seen, still has a solid 35 to 40% of the population on his side indicates that America is up to its gills in wingnuts. Have they always been there? No, to a large degree, we are responsive to our social environment. People can be led. The soothing chamber of commerce environment of past Republican generations did a great deal to dampen nuttiness. Now, the spittle-drenched ravings of FOX and its analogs are doing the opposite, driving otherwise pleasant and reasonable people to embrace the very worst devils of their nature.

What is equally bad, the new media has comprehensively replaced careful, professional curation of news with a downward spiral of virality and clickbait. Facebook's business model is explicity to reward clicks. "News" that gets clicks gets paid in ad money, and wins, which means replication over the platform and from its content providers, be they basement trolls or foreign operatives. No worse information system could be designed. Facebook is sort of a machine to bring out the worst in people, mistaking titiliation for news, let alone thought. For Google search, the analysis of linking and clicking is a valuable feature, winnowing the internet down to the most significant sites. But for news, this practice has obviously disastrous consequences, given human proclivities and weaknesses. That is why news organizations came to be in the first place, over the last century.

Propaganda exhibit A. The dossier was created by one of the world's leading experts on Russia, and no significant revelation from it has been disproven. It continues to be corroborated by, and serve as the spark for Muller's and the FBI's investigation.

One example of this problem, which Sykes should have delved into, but didn't, is the villainization of Hillary Clinton. When you sit down and compare the relative merits of Trump and Clinton, in terms of experience, aptitude, scandalous behavior, poor judgement, family stench, and corruption, there is no comparison. Yet because of the totally unhinged nature of the right-wing media, which the mainstream media could not help but cover (calling it "controversial", and other normalizing locutions), the vitriolic wingnut narrative seeped into the public consciousness, to the point that "jail her" was publically acceptable as a mantra by Trump himself and his campaign.

Is conservatism authoritarian?

This leads to Sykes's most significant insight and claim, that conservatism is not the same as authoritarianism. It was the wingnuts who were and are again, authoritarian, while true conservatives do not look to a maximum leader to deliver them from political impotence, but value compromise, core values, and legal and civic norms. Here I disgree strongly. There is clearly a long and close relationship between the two. The spectre of left-authoritarianism is certainly possible. But as a rule, authoritarians are right-wing. Conservatives, as Sykes describes, work long and hard to keep this id under control, not always successfully. Law and order, xenophobia, traditionalism, religion- all these tend to be shared themes which animate both strands of the right, and of which the Trumpists are merely a more extreme manifestation. Republicans have been cultivating the "Southern Strategy" for decades, and what is more authoritarian than this concerted effort to maintain the white terror of the South?

Patriarchy is the point

Similarly, manliness, strength, and similar macho themes are very much conservative touch points, as are anti-abortion, hostility to birth control, and other measures to keep women subjugated. The Trumpist trolls are merely more open about it than their patrician forebears. We owe Sykes and his (few) colleagues in the never-Trump section of the party a great debt for their resistance, both during the campaign and ongoing. But they should not kid themselves that their cherished pieties are somehow different in policy terms than the crudities now on display in the White House.

In this respect, as in so many others, FOX has lead the way in normalizing and activating the basest instincts of the right, whether conservative or authoritarian. And now, with social media, Trump appears to have not only FOX and friends, but also legions of trolls on his side, ready to visciously attack any Republican who utters anything less than complementary. I used to think that Trump did not have his own paramilitary, so he could not get very far in subverting our establishment. But these social media forces seem to be his Brown Shirts, and have brought the rest of the Republican party to a whimpering state. Politicians who stray are subjected to relentless attacks, which for some reason they pay attention to, as though the trolls on facebook and twitter are somehow representative of the public interest. As if the thorough-going financial corruption of both parties were not bad enough!

 Or is it stupidity?

Choosing to listen to the very worst that America has to offer is a sin of legislators, but they are observing, as do we all, that these propaganda and troll armies are having an effect on the electorate, influencing the easily led. This raises the question of why, in a country whose educational system was supposed to be the envy of the world, and whose people are, on the whole, the richest. What happened? Sykes certainly does not delve into that conundrum, confining himself to the mantra that as long as we stick to conservative verities of small government and high tax cuts, all with be well. But the basic fact is that human nature is to a great degree conservative, and the unthinking position is in favor of the status quo. Reform is the business of intellectuals, which some Republicans may have been, briefly, at one point. But now, dumb is their brand, and they are increasingly proud of it.

Pot calling the teacup black.

But I think there is one further hypothesis that might be considered. A recent New Yorker article mulled over the steep drop in crime over the last two decades, not only in the US, but in all developed countries. It did not come to any particular solution or explanation, other then aggressive policing policies. But I have one- lead. Our cities were drenched in lead from gasoline for decades, peaking in the 1970's before lead was banned from gasoline. Lead is known to affect cognitive development, meaning that we had demographic cohorts from that time who were likely heavily damaged by exposure to lead. While crime is a pursuit of the young, and the crime wave in the US tracks the rise and fall of lead in gasoline quite closely, politics is a more mature pursuit. Thus one can theorize that the lead-affected cohorts of the 70's peak might be the ones now responsible for the political and media system, both as voters and as participants. This would be a somewhat shocking hypothesis, yet also a hopeful one, as we are assured of a return to normalcy in a few decades, at least.

A problem of compassion

At any rate, conservatism is the unthinking choice in politics, the dedication to keeping things as they are, to stasis. While liberals express hope in the future and compassion for others, conservatives (not to mention right wingnut trolls) express fear- of others, of social innovation, of change in general, and of the state and its role in antagonizing traditional power centers like the church, the corporation, and the patriarchy. Indeed, one might paint conservatives as the faction of fear, which turns into hate on the authoritarian end of the spectrum. The mantra of small government is implicitly a mantra of big power elsewhere- of big and bullying companies, of monopoly, financialization, unemployment, and all the other ills that the modern state stands ready to remedy and regulate. Can the ideals and compassion of the left get carried away? Communism certainly proves that. But broadly speaking, the concept of a compassionate conservative is an oxymoron, and that informs both the thesis Sykes is trying to sell, and also the larger question of why this moment has brought out the Trumpist shadow.

Population pressure

One issue that seems also to get short shrift is overpopulation. The culture in the US has changed from one of hopeful frontier values with land for anyone who wanted an independent existence, to an intensely urbanized one. Most urban areas have also reached a sclerotic state of development, having "built-out" decades ago, and now find it virtually impossible to even imagine building new interstates or other substantial infrastructure that would be required to relieve (in some areas) incredible traffic problems and housing shortages. Thus we experience an increasingly zero-sum game where the 1%, instead of thinking about the future of the country and growth, are instead grabbing what they can from the system as it exists, with little thought for tomorrow, or for others. In such a frustrating environment, the appeal of rage- of blowing things up, burning it down, and starting from scratch is somewhat understandable, but only as an impulse, not a policy.

Is inequality the American way?

This hardly needs expansion in this post.

The culture war

The long-standing left-right culture war over recent decades has many fronts, and conservatives generally feel that they have lost on most of them. Abortion has been fought (so far) to a draw, outside of the reddest states where it has been exterminated in practice. The gay rights fight has be excruciatingly disasterous, however. Liberal compassion was really flying its freak flag there, and it has made the traditionalist conservatives, and their troll shadow army, outraged. The culture has moved relentlessly on, and yelling stop has had little effect in most precincts. There is one front, however, where the right has clearly won, and that is guns. This is where the most rabid partisans have occupied and expanded their ground, providing the model for scorched-earth, vitriolic, irrational, feed-the-worst-instincts propaganda. Is it fascist-inflected? Authoritarian? Or just conservative? Whatever it is, it certainly occupies the most right part of the spectrum, and it is no surprise, after its signal success in cowing legislators and advancing its agenda that this community has been taken as a model for success on the wider field of right-wing causes.

A little light relief, courtesy of Colbert.

The South

Enough said.

Ideas, shmydeas

This is perhaps the most important thread, especially in considering Sykes's work. He is tirelessly admiring of William Buckley and Paul Ryan, as substantive, thoughtful conservatives. His arc is from serious conservatism of yesteryear, and of Wisconsin, to the degraded Alt-right petulance of today. But what if the ideas were no good to start with? What if these have always been convenient and irrational fronts for serving the rich and the powerful? The Republican's attitude towards deficits has shown, as nothing else can, their shameless hypocrisy about their so-called "ideas". When Democrats are in office, deficits are disastrous and spending evil. When Republicans are in office, quite the reverse. Nor have any of the tax cuts generated Laffer-ian economic growth, merely Keynesian growth, along with deficits. The record of conservative "ideas" has been abysmal, and the new Trumpians merely recognize that this was always the case, and dispense with ideas altogether, in favor of e-motivated politics like trade bashing, immigrant-bashing, and tweeting. Then they do what they want, which is evidently to make the rich much richer, and screw everyone else, workers, the poor, the environment, the world at large.

Likewise with small government. When it comes to compassion and equality, cuts and small government are in order. But when abortion comes up, or a bloated military, the sky is the limit. No, the ideas were never more than a cover than support for patriarchy, property, and hierarchy- conservatism of the oldest kind, whether in patrician clothes, or something more swastiky. Indeed, the media issues raised above, and the lead issue, gross inequality, and all the other issues that have causal relevance for the decline of our political system, come back to a role for government itself to regulate and improve our physical and social environment. Government is our means to solve big problems, and frequently has to be big to do so.

In the end, Charles Sykes is likable and thoughtful. And his urgency in turning the Republican party back towards civility and a concern for institutions, law, and other people, is heartfelt and important. However, the idea of putting the crazies back into the closet, and reverting to the platitudes of God, Tax Cuts, and Small Government, is not viable. Sykes says so himself, urging new ideas to be developed, whose nature, however, he leaves in great obscurity. My suggestion? Join the Democratic party.

• Sinclair is another fair and balanced network.
• Bactra is back, however.
• After capitalism.
• The corruption is just endless.
• And it would be nice if our president weren't a Russian asset.
• If police want respect, they need to earn it.
• Ignorance of MMT would be better for everyone!

How Can Cells Divide When DNA Looks Like Spaghetti?

Topoisomerases untangle the mess, very carefully, with itty-bitty molecular scissors.

DNA is incredibly elegant as a solution to information storage and heredity. But it is also an enormous mess, with the genome of humans extending to five feet in combined length. (Imagine 9,000 miles of garden hose.) So each cell, which contains this whole amount, has a nucleus resembling an incredibly convoluted nest of spaghetti. Yet at mitosis, the chromosomes condense, separate, and neatly partition to each new cell. Some of the solution consists in how the DNA lies in the interphase cell- it is already somewhat pre-organized there. But most of the solution comes from enzymes that do not bother disentangling it- they cut the Gordian knot with enzymatic swords. Genomes were able to surmount the length problem over evolutionary time by the development of topoisomerases, which cut and religate DNA with extraordinary precision.

There are two main types of topoisomerase (named for altering topology, or the organization / twisting of DNA, without changing its energy, sequence, or composition). Topisomerase I cuts only one strand of the double-standed DNA, and can thus relieve coiling tension. Some forms can wind up the tension, using ATP. Topoisomerase II cuts both strands, and is the main enzyme that allows complete de-catenation / detangling of DNA during replication, transcription, meiosis, as well as mitosis. A recent paper looked deeply into the mechanism of this class of enzymes.

As one can imagine, the minimal requirements of a Topoisomerase II is that it hold on to both ends of the DNA it has cut, while passing through the other DNA strand which has, by virtue of general tangling, come up against it. This condition of collision needs to be detected, prior to being resolved, so that the enzyme is properly positioned. The complex also has to detect that the process has finished, and reset to the starting state, including religation of the cleaved strand of DNA. It is a tall order for a mere chemical confection to carry out, frankly.

But it turns out that enzymes can have hands, if not brains. The authors provide, on the basis of a great deal of past work as well as their own, a compelling model of how this topoisomerase performs its amazing feats.

Molecular structure of a typical topoisomerase II, composed of two copies of Top6A (green and red; second copy in gray) and two copies of Top6B (yellow, purple, and orange; second copy in gray). The G-segment DNA (~70 bp) is strung along the underside, and the T-segment DNA will shortly be accommodated in the middle, upon which the top portions clamp together. Cylinders represent alpha helices, the common secondary structure of proteins. Key domains for the activity of this protein complex are noted- the H2TH domain, which notifies Top6B that a G-segment is present- the KGRR domain, which notifies the same enzyme that a T-segment is present, and to keep the clamp closed. And lastly, the stalk/WKxY domain, which in addition to helping to bind the G-segment communicates between Top6B and Top6A that cleavage of the G-segment can happen. The G-segment will be cleaved in half at the bottom of the structure, later to be re-ligated after the T-segment has passed through. 

The enzyme (it is a tetramer made up of dimers of two separate proteins, Top6A and Top6B) forms a large hoop, with arms outstretched that will join during its action. One DNA segment, the one to be cut (the G-segment, for gate) is first bound by the underside of the hoop, centered at the middle active site which does the cutting, holding, and religation. The outstretched arms encompass the other DNA strand (the T-segment, for transit). Both top and bottom of the complex have ATPase activity, though for different purposes.

The key finding made by these authors is that the G-segment DNA is bound not only near the cleavage site (in Top 6A), but by the entire arm structure, up to a domain in Top6B that the authors call H2TH. About 70 basepairs of the G-segment DNA are bound, overall. This not only stabilizes and holds this DNA while it is being cut and the T-segment is being passed through, but it also allows the Top6B portion of the enzyme to sense the status of the whole complex, so that it can properly sequence its activities.

The KGRR feature functions to sense T-segment DNA and keep the clasp closed and ATP unhydrolyzed while the T-segment is present. The bottom graphs show ATP hydrolysis in the mutants diagrammed above, while the gel images show relaxation of the supercoiled DNA but the enzyme (moving it from the bottom to the top, left to right). ATP hydrolysis is increased to a free-wheeling state, while DNA relaxation fails to happen, in two mutant versions of the KGRR finger.

For example, the authors identify another feature near the top of Top6b, called KGRR, which is a finger that points inwards to touch the T-segment DNA. When they mutate it, they find that ATP is now freely digested in the presence of supercoiled DNA, much more actively than by the intact (wild-type) enzyme. But the enzyme is inactive ... no strand passage takes place, and supercoils are not relieved. The mutant enzyme is spinning its wheels, clasping and opening without doing anything. What this indicates is that in the normally functioning enzyme, the KGRR domain is a sensor that keeps the complex locked up till the T-segment passes out the other side, via the cleavage in the G-segment. Only then can ATP be digested by both halves of the enzyme, re-ligating the G-segment, and opening the Top6B arms to allow a new round of stress relief to take place.

Similarly, they conclude that the function of the H2TH sensor is in part to notify the Top6B part of the enzyme that a G-segment DNA is bound on the underside, allowing ATP to be bound and the clasp to close, if a T-segment also happens along. T-segments should not bind unless a G-segment is bound first. Secondly, the dramatic DNA bend adopted by the G-segment in this protein structure, especially in the locked-up conformation, draws on the supercoiling / torsional state of the DNA that is the target of action. Supercoiled DNA binds with 60-fold higher affinity than unstrained DNA.

Overall schematic of the mechanism of the enzyme- see text.

To recapitulate, the overall model is that G-segment DNA, in torsionally stressed condition, binds to the broad binding area of the underside of the enzyme. This notifies the Top6B domain that T-segment binding is acceptable. When that happens, the clasp is closed and ATP is bound, but not hydrolyzed, setting up the next step. A hinge between the two protein halves notifies Top6A that it can cut the G-segment. When that is done and the T-segment passes through, the KGRR sensor notifies the Top6B that the clasp is empty, so the ATP is hydrolyzed and the clasp releases, ready for another round.

It is an intricate molecular mouse-trap, built of ratchets and sensors of various kinds, using the jostling motion universal at this scale, plus key inputs of energy (ATP) to accomplish what on the large scale looks like an amazing feat of re-organization.

• We have a sleaze bag as president, with sleazy personal, international, business, governing, and legal ethics. Is that news?
• Why haven't we had self-driving cars for the last decade?
• Some places have fewer guns, and better policy. Some have more, and utter corruption.
• Should greed and profit be the highest societal values?
• Another introduction to MMT economics.
• Humanism.
• The new class structure, and the new left.