The Treacherous Invisibility of Sociality

We are dealing with phantasms, which makes drawing a line among them difficult.

It is easy to take potshots at science for its blinkered focus on the measurable and the concrete. How many people have pulled out the famous Shakespeare line about the many more things, poor Horatio, than are dreamt of in your philosophy? How many times does the newest research in social sciences tell us what anyone with common sense already knows? However, on the other side, the quest by softer sciences, like economics and ecology, to man up and drown themselves in math in order to satisfy their envy of the "hard" sciences. There are clearly conflicting emotions on the matter, which occasionally boil over into Trumpism and general anti-elitism.

But understanding by way of careful observation, useful simplification / reduction / schematization is what all scholarship and learning is about. One can't get around learning about something in detail if one wants to master it, either operationally or intellectually. The scientific method was revolutionary development, not only for science per se, but for philosophy and specifically for psychology. It expresses a skepticism of knowledge gained by theoretical, authoritarian, and armchair means, untethered from whatever the object purports to be, whether physics or biblical texts or history. Just as we suspect statements made by our current president when based on nothing, likewise we should suspect other claims lacking evidence of a rigorous, empirical kind.

But there is a deep problem, which is that our most important issues and forms of knowledge are social, not measurable and concrete. While science struggles to grasp social patterns and knowledge from its particular perspective- and not yet terribly successfully- those patterns are at the same time experienced richly in everyday life by everyone and portrayed with great variety and complexity in the arts. It is the core of drama- who knows what, who likes whom, and can I see through layers of deceit.  All of this is invisible in the conventional sense. It may be encoded somewhere in our brains, but the proper level of analysis is clearly not that of the neuron. As scientists, we are left with questionnaires, polls, and, generally, utter blindness when it comes to this most important apparatus of our lives.

Hard to read?

What hides, and what exposes, the social matrix? Language is the premier medium, of course, going far beyond the pheromones, grunts, dancing, and grooming of other animals. Blushing, facial expression, and eye direction, are a few more biological examples of other ways we externalize our social feelings. Yet there is great value in hiding feelings as well, whether out of politeness or deceit. Indirection, subtlety, puns, jokes, allegories, metaphors, a single look. The cues, even when present, are devilishly hard to read, which prompts theories about how sociality drove gains in human intelligence. So even on the social level, let alone the scientific level, it is hard to know what is going on beneath the surface, where sociality truly resides.

An inference of sociality, constructed in typical mid-20th century fashion.

The result of all this is that we are very enthusiastic inferrers and theorists. Conspiracy theories, truthers, birthers are some of the more extreme manifestations, but we all have to do a lot of reading between the lines just to survive as social beings. What is a soap opera but the carefully and gleefully managed reveal of social facts that are not, in timely fashion, apparent to the participants? Some people are more skilled at all this reading and inferring than others are. Extroverts enthusiastically wade into this murky unknown, while introverts regard it as hostile territory, and tend temperamentally to populate the scientific ranks, struggling to find certainty in an uncertain and largely invisible world.

What becomes treacherous about all this is the over-enthusiastic inference of things that are not there. On the social plane this can be over-sensitivity to slights and oversights. But it can also be religion- the natural inference of sociality to inanimate phenomena. Animism seems the most natural human condition, anthropomorphizing everything around us from insects to mountains, and putting ourselves into subtle social relations with it all. The rise of patriarchy seems to have prompted a massive shift from animistic patheism to father-centric monotheism. The theological object is no more real, however, for being consolidated and blown up out of all proportion. It is still an over-enthusiastic inference of sociality / personhood put on the void. Smarter theists have given up trying to explain particular aspects of reality via crackpot theology, such as electricity or evolution. Yet "everything" is still somehow fostered, created, or underpinned by this phantasm, much as prostate health is "supported" by the latest herbal supplement or hemeopathic nostrum.

What's the harm? On the social plane, over-inference leads to a lot of drama, but is quite finely tuned and bounded by actual, empirical, interactions (though our politically partisan echo chambers breake this model). It is how we evolved to deal with each other. On the philosophical plane, it has been disastrous, giving us centuries of bad ideas, intolerant theologies, and mis-directed energies. Think of all the monks and nuns praying away in their cloisters to non-existent deities for undeserving patrons. And today we are still living in a world at war over religious differences, all based on imaginary inferences created out of the template of our social assumptions and desires.

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• Finance wins, not workers.

Round and Round We Go, Making ATP

The mechanism of the proton energy pump that lies deep within, and gives us ATP.

One of the more elegant and dynamic structures in biology is that of the ATP synthase, which lies at the heart of the mitochondrion's conversion of its proton / electromotive gradient into ATP. This large enzyme is not static, but functions like a carousel, whirling around as it lets in groups of H+ ions. Naturally, it has been heavily studied to learn the secrets of why such motion is necessary, and how it works, in detail.

Basic view of ATP synthetase components. The lower complex (a,b,c, epsilon,) is  often called Fo, and is embedded in the membrane bilayer, which otherwise keeps H+ protons out. Top is the internal side (of the bacterium or mitochondrion) and bottom is the outside, where H+ has been pumped by the processes of oxidative phosphorylation. The c subunits comprise the spinning rotor, causing the gamma subunit, which reaches up into the F1 (alpha, beta), to crank the non-spinning F1 proteins through a series of shape changes that prompt them to synthesize ATP.

The primary product of mitochondiral respiration, which burns our food in a controlled way using oxygen, is a transmembrane proton gradient, which is a mechanism that mitochondria inherited from their free-living bacterial ancestors. While it may seem odd that pumping protons out of the cell into the vast outside is a way to efficiently store energy, it was the original battery technology, a charged state that can later be used by many other processes, like transporters that couple the energy-releasing import of H+ with the energy-using import of K+, (a symporter), or with the energy-using export of Na+ (and antiporter). Yes, life is all about chemistry!

ATP quickly became an important chemical currency for life, but only small amounts can be made directly from breaking up food molecules like glucose by glycolysis. Much more can be made by carefully tuning the respiratory chain to export protons (or import electrons) during the stepwise transformations of glucose to smaller molecules, and then later using that electrical / proton gradient for other needs such as making ATP.

Thus the ATP synthetase was born, but it was not born in a vacuum. Rather it seems to have been derived from prior structures that used protons to drive flagellar rotation. The tails of bacteria do not wave side to side, but rather rotate, which, given their particular semi-rigid structure, can drive bacteria forward. At the flagellar base is a rotating motor which lets in H+ ions as its energy source. This structure was evidently married with what seems to have originally been a DNA helicase- a donut-shaped ATP-using enzyme that travels along DNA, prying open the double-helix. Such enzymes are necessary during DNA replication and meiosis, of which at least replication was an ancient process. The ATP-using character of this helicase was reversed to be ATP-generating in its new setting, which is biochemically easier than it seems. Indeed, the whole ATP synthetase can still today run in reverse to use up ATP when needed.

More detailed representation of the ATP synthetase. The plasma membrane is in yellow, inside the cell (or mitochondrion) is above, and outside is below. The outside has a higher concentration of tiny water triads, which represent H3O+, or H2O plus a proton. They dock to the blue transmembrane portion (Fo) of the enzyme, as shown in green and red at the key interface. The protons are handed off to coordinate with portions of the protein in highly regulated fasion. Above, ADP comes into the synthetase part of the enzyme (F1), gets a phosphate group added (yellow and red) to become ATP. 

Two videos of this process are linked above. #2 is accompanied by a great submersible soundtrack, and shows greater detail for the ATP synthesis mechanism. And a video from the paper discussed has even higher detail, showing particularly the extensive structural reshaping that goes on within the F1 subunits that are making ATP. That mechanism could be the subject of another post.

The mechanical details are that H+ is let in only at the interface of the rotating (blue) and stationary (red) parts of the Fo membrane portion of the enzyme. It is allowed in to bind only at one site per segment (green dots), which then rotate around and eventually come back to another part of the stationary part where the H+ is finally let out via a different channel, into the cell. This specific directionality of binding and release is a sort of ratchet which lets the chemical energy in the H+ gradient drive rotational motion.

This energy is then coupled to the second element, the top (F1) complex, where the six red/pink ATP synthase subunits surround the blue shaft which comes up from the rotating Fo component. While those subunits are held stably by the orange stator element at the outside, the blue shaft is like a washing machine rotor that wrenches around, distorting each of the ATP synthase subunits in turn in ways that induce them to carry out the reaction of adding a phosphate group to ADP to form ATP.

A recent paper describes new structural and mutational studies on this enzyme complex, to look for some further mechanistic details. It used primarily cryo-electron micoscopy, which is sufficient to resolve shapes of helices in proteins, though not detailed atomic locations. Yet one can combine this with mutations, prior X-ray structural studies, selective inhibitors, and other modeling to make some interesting inferences. The key one which these authors make is that there is a critical arginine (R) amino acid in the (a) subunit, or the static red part of Fo above (orange in the diagram below), which seems to be the key to H+ conveyance. This amino acid tends to be positively charged, so it would readily bind with an aspartic acids coming along as part of the (c) subunits, popping off their bound hydrogens. It is also genetically essential, as mutations are lethal.

The proposal is that this arginine is specially exposed to the internal side of the membrane, via a channel, (curved arrow leading upward to the cytoplasm in the diagram below), and also positioned such that it can latch onto aspartic acids the blue (c) subunits after rotation. These aspartic acids (D) are carrying the protons that came in via the complementary channel from below (outside) before they started their trip around the carousel. All that time, the membrane has protected those protons from displacement by other chemicals, such as water, other proteins and amino acids, etc.

Image of the proton-conducting interface within the Fo subunit of the ATP synthase. The static (a) subunit is portrayed in orange at rear, while the passing set of c subunits (there are ten of them) are going by in front as a pink band, though dimmed for clarity. The c subunits are progressing from right to left, with hydrogens coordinated on the key aspartate (D) residue #61 on each (c) subunit of the rotating set. As they pass, they are captured by the arginine (R) residue on the static A subunit and released in the only direction possible, up the chute into the cell. Immediately thereafter, the c subunit band passes to another channel where protons can load up again from the external solution.

Those protons are portrayed above by the band containing "c D61", indicating an aspartic acid (D) on a (c) subunit's 61st coded position, whose proton could be displaced by the arginine on the other (a) subunit as it is going by. The gray band of (c) subunits is travelling towards the left, so the idea is that aspartic acid-coordinated protons coming in from the right hit the blue arginine first, where the aspartate and arginine, with their different and complementary charges, bind directly and immediately, releasing the coordinated H+ which then shoots right up the channel to the cytoplasm. At the very next position, protons come in from the outside (periplasm) to bind to the just-vacated D61 spot on the (c) subunit. It is an elegant and very spare, atomic and electrochemical ratchet.

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• A losing war against tribalism and corruption.
• Religion and war- the deep connection.
• We have lost a decade of normal economic growth.
• Born in the USA.
• A trade policy that works.
• Corporations are exiting the public sphere. Why not regulate private companies as well?

Welcome to the New Class System

Yes, there is a class system in America, and it organizes our politics.

Communists have spent 150 years trying to convince us that economic status determines class in modern societies. But most people wouldn't have it- neither the diagnosis, nor the prescription of a dictatorship of the proletariat. We are far more complicated than this reduction to the most basic dimension of existence. We have other identities and values that confer status. Who is classier- Barack Obama, or Donald Trump, who is worth many times more?

This seems to inform our recent election, explaining the attraction Trump held on such a large section of the electorate. A section that has felt scorned by the meritocratic elite that has sprung up over the last couple of generations. The bicoastal, college-educated, Whole Foods shoppers who have taken over the Democratic party, the levers of government, and the media. They are the politically correct libtards who have climbed up the class ladder via its new mechanism of ivy league education, rather than old money or blue blood.

People of the heartland have dutifully sent their children off to college, only to see them indoctrinated into the liberal cosmopolitan ethos and turn their backs as they headed off to the coasts. And what has happened? Working class people have been oppressed by the economic system run by this new elite, which is itself under the thumb of the modern corporation, when it is not a unionized cog of a sclerotic public sector.

The resentment, while fueled by economics, is experienced far more viscerally as cultural, as condescension towards "fly-over" country, the South, Texas, religion, State's rights, and any place not "progressive". Obama's gaffe about people clinging to guns and religion was far more damaging than any policy statement. Was it condescending? Yes. Was it true? Of course. Well, the clingers saw their revenge in Donald Trump, a man clearly of their own class, despite his totally different background (New York!). His very classlessness was a marker of a certain class, and his rude comments about the non-whites, his mafioso bling, his religion as thin as a KKK sheet, were all signs of the right class, one that would take power in a new Jacksonian revolution.

Andrew Jackson- true populist, not fake populist.

But a funny thing happened on the way to this supposed populist revolution. It turns out that the Republican coalition, which Trump exemplifies so well, is made up of two classes, not just one. The resentful social clingers are just one part of it. The populous part, but hardly the most powerful. The other part is money. Pure, unadulterated greed. The 1%, and the 0.001% particularly, are the true soul of the conservative movement and Republican party, buying its elections and ordering up its policies. The new administration now has a plutocrat in every henhouse, whose clear goals are to destroy the walls that the government, in its liberal incarnation, has put up against their greed and predation.

These, finally, are the people who exemplify the communist maxim about class being determined by the ownership of the means of production. Despite having all they could wish for, they are defined by their desire to have more. Trump himself lives for the competitive zeal of destroying others, via deals, insults, and bullying. He is also dynastically inclined, grooming his offspring to inherit the empire. Being insecure in their wealth, they also feed endless propaganda about how great they are, how appropriate it is to put the most "successful" people in charge of all affairs, how success in business, or inheritance, betokens public virtue rather than its opposite.

So the test of the new regime, telling us whom it really serves, is coming when they let their money speak, via the budget and tax policies. Will inheritance taxes be eliminated? Who gets the most from the tax cuts? Why destroy the consumer financial protection agency? We know the answers already, and it does not accord in the least with a populist program. Trump has been meeting assiduously with CEOs to ask them what policies they would like, how workers should be treated, and taxes reduced. What can possibly be populist about the outcome? How thoroughly can they entrench a new system, where democracy is fully neutered, in favor of plutocracy?

So, once again, the clingers, true to their social concept of class, are being sold down the river by their comrades in the GOP, whose interests lie precisely in keeping them downtrodden, while throwing an occasional bit of social red meat in their direction, plus plenty of propaganda via the house organs.

In the end, we have three classes in the US, pulling in quite different directions. The downtrodden middle and lower classes, the cosmopolitan liberal middle, and the plutocratic top end. As Hillary Clinton found out, democracy alone isn't enough in the face of an antiquated constitution, shameless opponents, and buckets of money. How the Republican coalition continues to hold in the face of its stark contradictions has long been, and remains, a mystery, especially from the vantage point of California, where that contradiction has doomed it to obscurity. But clearly the social class consciousness of the Republican base is far stronger elsewhere, and can be traded on with what seems like impunity.

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• Oh, those out-of-touch technocrats.
• Feelings of white victimhood ... of all things.
• Piracy on Australia: when free markets don't work. "If you decrease your output by half but as a consequence increase your price by a factor of ten, you’re better off decreasing your output."
• Other precedents for Trump.
• Making America great, with BS.
• And lies.
• Swamp draining? More like swamp-a-lago.
• Someone must and will lead on climate change.
• Stiglitz on Trump.
• Black on Arrow: Crime still pays, and economics is not rational.
• Win for inequality- let's repeal fuel efficiency standards!
• Whence Macedonia?
• China rising.
• Everyone deserves a union.
• Wealth distribution is a policy issue, not a technology issue.

Memories ... In the Corners of My Mind

Where Do Memories Go? Where Do They Stay? How do we get them back?

There has been some debate about where memories end up in our brains, whether in the hippocampus exclusively or distributed through much of the neocortex. The spectacular case of HM, who could not form new memories after his entire hippocampus was removed, (plus some other nearby structures), indicated that older memories were still accessible from elsewhere, while all new memories are formed and reside at least temporarily in the hippocampus. However some types of memories do not appear to get re-distributed from the hippocampus. HM was missing quite a bit of explicit (also called declarative) memory from prior to his surgery, for instance, including everything in the prior year, and decreasing amounts going backwards for eleven more years. Other types of memory, such a short-term, working, implicit, motor, and procedural memories remained functional, however, for new formation as well as retrieval.

It is known that sleep plays an important role in the "consolidation" and redistribution of explicit memories within the hippocampus and from there to the cortex. During sleep, significant memories are replayed, which strengthens their encoding and allows their replication to more stable storage in the cortex. Ironically, sleep prevents forgetting. The redistribution process can take months to years, accounting for the deficits experienced by HM. On the other hand, sleep impairs, while new novel experiences enhance, the consolidation of some memories within the hippocampus, probably by enhancing the salience of the entire sequence of experiences. Current work indicates that memories get to the cortex quite quickly, with a "parallel process" between both areas strengthening them over time.

A recent study looked at this memory consolidation process, and asked what happens to conflicting memories- which might prompt over-writing of an initial memory with a later, corrected one. Yes, this was another study done with rats and mazes, testing their ability to retain memories of locations over various time periods, and over intervening activities, such as sleep, after the target location was changed. The rats learned the locations of both targets quite quickly, and returned to those locations preferentially in future trials, a week later, no matter where the actual target was.

If the rats where allowed to sleep between the switched training sessions, they lost the first memory more than if they had been deprived of sleep and exposed to further novel events between training sessions. This led to a conclusion that the hippocampal encoding (but not the cortical) is enhanced by activity and novelty, rather than sleep. The next step in the experiment was to alter the memory type by allowing the rats to explore the training area extensively for a few days prior to the training. This allowed them to gain a fuller context for the experiences to come, context that is believed to be stored not only in the hippocampus, but also in the cortex, being part of the consolidated and distributed memory system. After this protocol, rats allowed to sleep significantly out-remembered the sleep deprived rats when tested, and performed particularly well if the experimenters threw in a cruel trial a day after training, where no target was present in the maze at all.

An example of one test of a rat trained the week before. The training runs were, first target top left, followed by sleep, and second, target at bottom right, followed by distraction and sleep deprivation. The rat clearly remembered the second training much better. This was true even if the training regimens were reversed, and the one followed by sleep occurred second.

Lastly, the researchers studied molecular markers in their subject's brains, to see where cell and synapse growth was taking place in response to all these exciting events. For all conditions, the brains showed a great deal of neural activity and synaptic consolidation, i.e. expression of genes like cFos and Zif-268, right after training. However five hours later, things were a little different. Expression in the hippocampus was significantly down among animals who had gotten some sleep, but up if they were sleep deprived.

Conversely, marker expression in the cortex was the reverse- up in rats who had slept, down in those continually kept awake with more play and other novelties. This was particularly interesting since sleep alone drove a significant decline in cortical expression of these genes in control animals. That such brief training events can have effects on such gross brain areas through subsequent sleep, for hours and days, may argue more for the traumatic nature of the training, (done in water mazes, where the rats are desperately searching for a hidden platform), than normal learning in, say, a school environment.

Nevertheless, this kind of work shows what is going on in the field of memory research, as we try to figure out why, where, and how memories are distributed in the brain, which ones are kept, which ones erased, how they are schematized and compressed, and how they are retrieved again and altered during that retrieval. In this case, the researchers make the claim that their procedures have dissected a difference between cortical memory formation, which is enhanced by sleep and inhibited by intervening learning and activity, versus hippocampal memory formation, which experiences the reverse.

They did not have much to say in the end about conflicting memory formation, since the rats seemed to deal with this aspect just fine, (though less well after sleep). They remembered both maze solutions, even if one had been superceded by another for a few training runs. But the relational nature of cortical memory, which seems to grasp memories better if they are situated in a known matrix of prior experience, is interesting. And the speed of this cortical memory consolidation is also interesting- a matter of days, not the weeks or months that has been the model in the wake of HM.

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• Sanity is getting the upper hand, and the nuts won't have it.
• What the Islamic & Persian world did for math.

Truth is the First Casualty of Fascism

Is he a clown, or a fascist? Depends on who believes him, and who follows him.

We are in new territory, in American politics. Never before has such a vile know-nothing bully been elected as president. George Washington is surely spinning in his grave. But other countries have been here before- Italy perhaps foremost, with its experiences of Benito Mussolini and Silvio Berlusconi. Each was thought to be a clown, at least originally. The dark side of political clown-ishness, however, is fascism.

The signs are everywhere, from the campaign, to the inaugural address, to the flurry of hate unleashed in the first weeks in office. The pillars of fascism are an authoritarian mind-set, use of hate as the most powerful political emotion, scapegoats to focus hate on, lying, systematic hatred and denigration of the press, dedication to business interests, militarism, and use of extra-legal means and general destruction of institutions and due process in favor of direct use of, and displays of, power. And then more lying.

The President's inaugural address and festivities exemplified all these trends. There was national renewal and rebuilding the country, as though it was not already built. There was "American carnage". Really? Crime hardly our biggest problem. It was a play for power, to justify extreme measures and authoritarian approaches. God was invoked constantly, not only by the blessers and benedicters, but by the President himself, as though he had a theological leg to stand on. "We will be protected by God", "... the same almighty creator". There was the cheap nationalism. "America first, America first!", and "a total allegiance to the United States of America".

There were fawning claims of putting power back in the hands of the people in several places in the speech. Which makes the ensuing flurry of executive orders seem rather odd, since they exemplify the power of one, not of the many. Even in representative terms, he represents a minority of those who voted. But no matter. The narcissistic identification of the leader with the whole is another facet of authoritarianism. And of narcissism.

The order banning Muslim and refugee immigration was further evidence, among many other orders and tantrums. The claim was that this would make us safer, evidently in light of the carnage that such immigrants were causing on US streets. Scapegoating and the lying are, as usual, inextricably linked. The authoritarian has to have enemies and can not have enough of them in reality, at least ones who are easy to hate. Thus Hitler and the Jews, or Mussolini and the pacifists and communists. We will have to watch the ratchet of hate and scapegoating very carefully. Now it is Muslims and Mexicans. Next is the press, whom the President calls garbage, and the worst people on earth- when he isn't sucking up to them, that is. Who will be next? The civil servants? The Democratic states unwilling to join immigrant roundups? The lawyers of the ACLU? The scientists? The logic of bullying is that anyone who is not clearly cowed is a threat and must be hounded into submission, or else the bully does not feel secure.

Bulldozing through institutions was another part of the immigration order, now being so thoroughly picked apart in the courts. Fascism is impatient with process and legal forms. The scapegoats must be eliminated immediately, and the leader must show his virile power to crush all opposition, with scathing tweets, if not with his armed followers or suborned organs of the law. It is ironic, though not surprising, that he has landed in the wrong end of federal court mere days after pledging so faithlessly to protect and defend the constitution.

But truth is the most serious casualty of this process, and ingredient in the many facets of fascism. All politics involves lying and coloring the facts to some degree. But most politics takes place in a zone of acceptable shadings of the truth, through a normal discourse of free media filtration and critique. This President has been notoriously immune to fact-checking through his campaign, and keeps tweeting lies. His enablers and advisors seem to be selected for their pusillanimity in accepting such alternative facts. The internet has brought us an unmediated liar as president, whose voters loved that he was not a normal politician. Little did they realize that this means he lies more rather than less!

The danger of Muslims in the US- lies. The carnage in the "inner city"- much less than a decade ago. The bad deals with Mexico, China, Iran- lies. The crowd size at the inauguration- lies. Voter fraud, and the idea that the actual popular vote favored the President- lies. Each lie is engineered to set up an false enemy or normalize an appalling view or policy. Each lie is engineered to augment the President's power, needing immediate executive action to fix. Who buys it? Well, the poll numbers have been dropping by the day, so this round of lying does not seem very effective.

The destruction of truth in our political discourse owes relatively little to the President and his appalling acolytes, however, but much more to the larger ecosystem of the right, particularly FOX news. They have been building startingly false and destructive narratives for decades, which curiously support the corporations and the rich while denigrating the government- the one entity that can stand in the way of the rich gathering the rest of our economy into its greedy fingers.

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Thankfully, the President does not have the full toolchest of fascism at his command. And this goes beyond brains! He does not have enough popular support to alter the basic rules of the system. The Women's march was a very important warning shot in that respect. He does not have his own armed forces. He has only a modest grip on his own Republican party. That party is more dedicated to neutering the state than to building it up, at least in most respects. A crisis may change all these equations, but at the moment, a descent into fascism seems unlikely, despite his best efforts.

Starting with brains, it has become painfully apparent that the President's ravings are not the calculated distraction of a clever fox. Rather, they are his utmost effort at clarity and strength. There is no there there. He does not seem to have enough of a grasp of reality to manage it. Nor is the power behind the throne much more fearsome. Steven Bannon has a long history of right-wing agitation, and I studied one of his more recent films to gather an impression of his thought process: Occupy unmasked. It is an incoherent salad of clips and snark. But little sustained argument to be worried about. His actual speeches are more insidious, but they are very standard Republican pablum- the deficit is too big, the country is drowning in debt, the government needs to be cut. Nothing very novel there, just a fundamental misunderstanding of economics, an anti-worker agenda, and perhaps a note of warning to those Republicans who want to blow up the debt for tax cuts.

And the milita- the blackshirts or brownshirts, beholden to the fasicst leader- where is it? Thankfully, we have not stooped to that depth quite yet. But the way the customs and immigration service jumped to do the President's bidding, almost before the ink was dry, was highly disturbing. The order was half-baked at best, something that should have met with a bureaucratic friction and pushback for clarification, if not resistance. Likewise, the support the President has gotten from the border patrol union, to the point of incapacitating their leader, is also troubling. No one seems to be minding the values of common decency in those departments. Otherwise, the President and his acolytes are militaristic, but the military for its part sees how fake their values and rhetoric are, and will doubtless keep the crazy at arm's length. They may have disliked Obama, but that doesn't mean they want to jump from the frying pan into the fire.

How does the media environment look? Not that great, surely, but compared to something like Putin's Russia and Berlusconi's Italy, it is quite free. No amount of vitriol from the President is going to alter that, and the other institutions of government, principally the Congress, are unlikely to alter that, other than perhaps cutting public funding for the public media. Indeed the humor that has been unleashed is most cathartic and positive. The danger is mostly indirect, from a further unleashing of corporations on the public sphere, which will further pollute and damage our very notion of free speech and truth.

There have been many authoritarians, but few fascists. We can take comfort in the incompetence, small-mindedness, and stupidity of the current President to save us. But mostly, in our fellow Americans, who must draw a line. How the President was voted into office remains a conundrum, but his followership looks unlikely to grow. Quite the opposite- the poll numbers are going down; support is dwindling. The incompetence and meanness on display is offending everyone near and far. Other than base Republicans, of course. What will they do who are closer to power? Will the President's aides and advisors draw a line anywhere for decency and our long-term interests? Will the bureaucracy offer some resistance? That will only happen in concert with, and as an expression of, a general revulsion in the political system.

• The signs are clear.
• The establishment is appalled and uneasy.
• Fake olds: re-writing history. Religions have been doing it forever, of course.
• Lies as an excuse for oppression.
• Who will follow? Who will not? Especially when the crisis comes.
• Workers? Savers? Who cares?
• Cringely on H1B and L1B visas.
• Science and truth- another humdrum Democratic constituency.
• Enemies are accumulating on all sides.
• 60,000 to 100,000 visas flushed down the drain- it is shameful and culpable.
• First Things- high-end religion for Trump. And yes, racism is the left's fault.
• Trump crumples like a wet bathrobe on Taiwan.
• Afghanistan, still a quagmire.
• This what resistance looks like.

Brain: Is Size Everything?

Properties other than size also make human brains different.

There is no doubt that humans experience a unique sense of consciousness and form of cognition. While other animals like chimpanzees, dolphins, dogs, elephants, and crows are amazingly smart in general and have highly developed capabilities of their own, they don't touch our abilities for planning, remembering, focusing, and at the top of the list- language, both spoken and thought. It remains hard to characterize these differences, because we are still learning so much about the cognition of other animals, and because even with introspection, language, science, and the rest of our inquisitive armamentarium, our own mental processes remain opaque to a large degree.

However, there are clear differences, and how can they be expained? We turn out not to be the only animals with large brains. Sperm whales have brains about nine times as heavy as ours. Even some dolpins have bigger brains than we do. Monkeys typically have smaller brains than cows, despite much higher intelligence. Mice have brains that are, per body weight, almost ten times as large as ours. So size is not, by itself, the issue. There is more going on.

Biggest does not equal smartest. At least that is what we think.

On the other hand, over the last few million years, size has clearly meant something, as our brains have grown at a very rapid clip. So it appears that within a given lineage, size increases may serve as the easiest way to change cognitive capacity, and can serve as a proxy for intelligence. But it is far more hazardous to make comparisons between different lineages, since their architectures and thus capabilities may be very different. So who knows- maybe octopuses are smarter than we are, despite having smaller brains, and several of them.

But bigger is better, among our closer relatives.

For example, thanks to our particular architecture, we pack more neurons into a gram of brain than do whales, so we end up with as many or more brain cells as elephants and whales. And what is more, our brain being more compact gives those neurons a distinct advantage in speed / connectivity. There has been a good deal of work on the genetic level to look for genes and other genetic features that show accelerated evolution in the human lineage- quantitative work that can show with high confidence that some gene variation or regulatory site is novel and significant in humans. But linking that data to the human phenotype has been a challenge, as is true generally with human genetics. The best route has typically been to find other variations in the same area that lead to disease or other pathology, which can give strong clues about the overall function. Or providing mice with the human version of the gene, though the chances of seeing something informative, let alone amazing(!), by this route are rather slim.

Getting back to brain function, a recent paper discussed new work in the field, particularly on the properties of neurons themselves, which might help explain some of our mental distinctiveness. This was all done on brains from recently-living humans, which are understandably hard to get and hard to work with, in a brain slice+electrodes system. One finding is that we have a unique class of "super-neurons"- cells which fire so strongly that a single one can set off responses to the next neuron and thus to larger cortical circuits. This is not seen in other species (per their claim) and is unusual because in typical brain tissue / circuits, it takes converging firings from several or many upstream cells to bump a neuron into action- which is, after all, the whole point of information integration.

The efficiency possibilities are clear. If a percept can happen from the firing of a single famous face cell, (though these are likely to be part of a neural network, rather than regimented as one cell per face), then we need fewer of them to carry memories. The cells and synapses discussed here actually target inhibitory neurons, but the logic remains the same- that if single cells can control large-scale network activities, you need fewer of them, though their tuning and activity then are of paramount importance.

Two neurons meet... The intensely spiking pyramidal neuron (red) which firs first, and the post-synaptic, receiving cell  (blue) are portrayed (C) as they were stained and micrographed in the tissue. The layers of the cortical sheet are given roman numerals. Synapses between them are numbered in D. Panel B shows an averaged stimulus -> response graph of the two cells, showing that the receiving basket cell (bc) quite frequently fires (74% of the time) when the sending cell fires, despite their very sparse synapses. The lower graph (26%) shows the other events, when pyramidal cell firing evokes only a grudging sigh in the receiving cell. In other species, this is all one would see in such single-cell stimulus / encounters. Panel A shows that the receiving cell not only fires once, but several times per upstream spike.

"Although the ratio of triggering poly- versus monosynaptic postsynaptic potentials was 0.01 in the rat and 1.73 in the human in our hands, it should be emphasized that the human patients were treated differently during anesthesia and surgery, and the excitability of human neurons might be different in the external solution also used for rat experiments."

"However, the human neocortical neurons also exhibit specializations only reported in our species. One such feature is the capacity of excitatory principal cells to elicit firing in local inhibitory interneurons with a single action potential via very strong excitatory synapses. It has been suggested that this feature has specifically evolved to enhance coordinated firing of neuronal ensembles in higher brain functions."

Additionally, learning happens very quickly among these super-neurons, so that they do not regularly overwhelm their targets. After ten minutes of stimulation, the downstream cell had already learned to ignore the stimulus. So while most processing takes place in the usual integrative network pathways to come up with usefully transformed information, there seem to be cases when directness and efficiency rose in importance, in the human lineage, and thus led to the development of these super-neurons. This kind of study adds a cell-biology level to the much-better characterized, but as yet tenuously connected phenotypic and genetic levels of differences that make humans distinctive from their ancestors and fellow-beings on the planet.

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The Challenge of Collective Action

The left habitually under-appreciates the difficulties of collective action.

Joining the recent protests against our new president, I found myself marching along in a wonderful crowd, all with common purpose and strong emotion. But what struck me was the utter innanity of the chant- Hey, Hey, Ho, Ho, etc... It was an embarrassing regression to a minimal, indeed infantile, common denominator.

Why? Why do leftist actions and protests routinely look so shambolic and fritter away their energy? Why are the high ideals not matched by high rhetoric and disciplined action? The Occupy movement added squatting to the menu of marching and chanting, but ended up in the same place- lodging a mostly inarticulate cry of protest against the System.

The same disappointments abound across the spectrum, though. The Dilbert cartoon lampoons the difficulties of corporate communication and management, among people who work together every day, yet still fail to communicate and collaborate effectively. Participating in organizations is difficult, at all levels. But that already supposes an organizational hierarchy, which is more than the deep left is willing to countenance. Can anarchists and egalitarians accomplish anything?

The System is made up of organizations of all kinds- corporations, parties, legislatures, think tanks, unions, magazines, clubs, non-profits- a wide range of institutions each with some kind of mechanism of translating personal, privately held intentions and desires into communal action. Each can get more done than a simple mob, by virtue of its mechanism- its hierarchical organization.

That is how inarticulate cries get translated into sustained action- through organization. The left creates organizations profusely, but does not typically sustain them very well. There are countless peace and justice movements, non-profits, and coalitions, which typically operate on a shoestring and have a tenuous and brief existence, due to their anti-organizational temperament.

The right is more temperamentally suited to organzation life. Hierarchy is ingrained and desirable, not an evil to be torn down. Existing organizations and orders of society are assumed to be good, not regarded skeptically, with a revolutionary glint. The corporation is a prime example of this, an organizational style that pervades our lives and politics, and is run, as a rule, by people of a right-ward temperament. Power is also understood better by those on the right, assuming as they do an organizational structure rather than a menu of nebulous ideals. The problems of gaining and using power are typically separated from those of justifying it, as hierarchy is regarded as good in itself. Thus we have the spectacle of Karl Rove rising through means that were completely immoral, but highly effective, through a succession of Republican youth groups. Thus we saw the utter nihilism of Newt Gingrich, and later Mitch McConnell, in their pursuit of power, in collaboration with a whole ecosystem of secret money, state-level gerrymandering, and media pollution.

And what is the point of all this? For the right, the preservation of hierarchy and order, of the rule by the strong over the weak, seems to be the point of whole exercise of having power. Organizational success results in successful organizations. Inquality and oppression of the powerless is part of the deal. On the other hand, for the left, the point is to make of the state a bulwark against the strong and powerful, so that inequality and injustice are reduced. But to do that, a super-powerful organization is required, i.e. the state itself, whose capture by either right or left is then the most momentous condition of society in general.

In this way, the right seeks its goals in natural fashion, while the left needs to use temperamentally unnatural and disliked methods to get to the same goal. The left thus faces an existential question- how to reconcile the dogged pursuit of power with the overall goal of taming power in society. This temperamental and philosophical problem is at the core of why democratic majorities are not enough, and why the right, despite representing in effect a very small sliver of the populace, regularly gains power.

One way to look at this is via the two-dimensional political temperament graph, plotting authoritarianism vs left-right orientation. Above, I have been conflating the two, since at least in the Anglophone world, there is high correlation of authoritarianism and right wing-ism. Indeed, one might add that the authoritarian dimension is far more momentous, historically speaking, than the left-right dimension, whatever their correlation. The diagram should look more like a vertically elongated diamond.

Left/Right vs Authoritarian/Libertarian layout from politicalCompass.org. I would disagree with their placement of the main candidates, as Trump is clearly more right-wing, perhaps to an unprecedented extent in US history, as shown by his actions of just the first week of his administration. The researchers may have been hoodwinked by his various lies and poses during the campaign. Clinton, in contrast, could hardly be as rightist as shown, let alone farther right than Trump. It is an example of misreading people's characters, even by experts.

Take the Bolsheviks, as an example. Ostensibly leftist, they were also mad with lust for power, and in the end were both successful in seizing power from a rotten system, and in totally betraying their ideology to create just another version of Russian despotism. Such dedicated, organizationally competent, and doggedly power-seeking people (i.e. authoritarian) are rare on the left, since they operate against the natural temperament and ideological tendencies, which are disinterest in hierarchy and institutional power, free love, free work, free couch crashing, etc. This is the original non-profit sector. This internal, psychic opposition makes such authoritarianism particularly unstable.

Similarly, the Black Panthers only survived as long as they did thanks to some very authoritarian tendencies- hard-asses who ran the show, brandished the guns, and enforced hierarchical organization in the face of overwhelming right-wing infiltration and opposition. Relying on left-ish authoritarians to run one's organizations is clearly a recipe for disaster, however, as their temperament tends to a greater commitment to authoritarianism (i.e. power) than to leftism.

The left thus faces a deep problem. One needs leadership and hierarchy, even though few on the left are temperamentally suited to it. And one needs an ongoing diet of activities that allow groups to bond and grow their commitments and competence. The corporation, with its ongoing struggle to win the marketplace, is a good example. Churches are another, with the various personal and social goals that merge into a more or less stable institution that can occasionally be active politically as well.

The university is another, more left-aligned institution, where the society's need for knowledge and human development is channelled into maintenence of a cadre of left-leaning academics. It is typical that our universities have never taken up leadership of a larger social mission, but remain dutifully atomized in small departments, indeed individual labs and scholars, who are as distant as possible from social action. It is an example of how the temperament and interests of the left combine with subtle but influential incentive stuctures imposed from above (the competitive grant system, constant budget crises) to neuter a possible source of left social comunity and leadership.

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Cultural Trauma and Authoritarianism

What the Mongols did to the Muslim world, China, and Russia.

Russia is certainly in the news now, and what do you know, but over the holidays Santa Claus brought me Martin Sixsmith's history of Russia. It breezes all too quickly through the first millenium or so of Rus, from its semi-mythical origins in the 800's as yet another Viking outpost, like that of the Jutes, Angles, and Saxons in England, and the Normans in France, England and later in Italy and Palestine.

Sixsmith paints a picture of a reasonably cosmopolitan and open society (centered in Kiev) in the very early period, though always quarreling and lacking centralized leadership and legitimacy, as was true for most other Western regions during the middle ages (and elsewhere in human history). All that changed in 1240, when the Mongols concluded a lengthy conquest, and put Russia under a severe yoke for the following 240 years.

While there has been quite an effort in recent years to rehabilitate the Mongols, one can make the case that the rise of Western Europe over all other areas of the world in the last few hundred years is due in large part to the destruction or hobbling of its competitors by the Mongols. This applies to China, to Russia, and most profoundly, to the Muslim world.

In Russia, the Mongols exterminated entire cities and forced the remainder to pay heavy tributes, as well as a lot of bowing and scraping, to their new overlords. But contrary to Sixsmith's portrayal, the Mongol rule was not terribly heavy-handed. They ruled through the local nobility, which, while neutered, was not destroyed. The Mongols also instituted some administrative efficiencies that accelerated institutional development. Perhaps the main effect, however, was the general trauma of violation and subjugation. With no natural borders, and predatory neighbors, the Russians evidently came to the conclusion that: 1. With regard to governing style, if you can't beat them, join them (i.e. the autocratic, despotic, and extremely effective military organization of the Mongols), and 2. That autocratic central power is the only way to keep Russia whole against its many neighbors. We in the US live in such a pleasant and peaceful neighborhood (Oh, Canada!), yet still are strikingly paranoid about Communism, Islam, immigration, etc.- take your pick. Imagine if those threats were actually real!

The enormous Mongol empire, 1200's.

Sixsmith certainly draws a line between this trauma and the continuing dedication of Russia to statism and autocracy, now exemplified by Vladimir Putin's nouveau despotism. China has ended up in a very similar place, from a much longer history of dynamic centralization, but similar subjugation by the Mongols. It is easy to draw the lesson that strength is the only way to survive in such a rough neighborhood. Yet it is a conclusion a little too-easily drawn by those already in power, whose only real interest is staying in power. Both China and Russia are exemplars of the extremes of depotic rule, particularly after it was given a whole new propagandistic lease on life by a Western ideology far more amenable and convenient than liberal democracy: communism. In China, it works tolerably well at the moment, but only by being radically tamed from the heights achieved by Chairman Mao.

But the saddest trauma was suffered by the Muslim world, which was at its height when the Mongols trashed Baghdad. In the centuries since, they have not gained a continent-wide empire (excepting the conquests and splendors of Mughal period), and have fallen progressively behind Western Europe. Whether the low point was the cavalier carving up of Muslim countries by the British (and French and Russians) after the fall of the Ottoman empire, or the current Islamist insanity, the Muslim world has had an increasingly frought relationship with the rest of the world, and with Modernity.

The Muslim approach to statehood and governance has always been lacking, based as it is on Muhammed as a singular and unreplicable example. A tribal and militaristic style succeeded after Muhammed's death, in channelling the energies of the unified community to winning an enormous empire. The caliphate then kept things together loosely, with religion as the core of identity. But it was always by civil war that God decided on the winners in the battle for the next ruling family. In Europe, the Catholic church (and its monastic affiliates) provided a much more stable model of governance, via election out of an oligarchy of cardinals. Later on, the Protestant reformation prompted ever greater attention to the role of the individual, as arbiter of celestial as well as terrestrial salvation. These threads of practice and theory led, in excruciatingly slow fashion, to the secular democratic state we have today.

When crisis threw Muslims back onto their religion as the bulwark of communal identity, there was little to go on to develop state institutions. Thus states tended to revert to tribal autocracy as the model. In the Arab core of the Muslim world, this remains the rule to this day. In outlying areas, however, such as Indonesia, Pakistan, and Turkey, (possibly Egypt and Tunisia), non-religious ideologies and influences have been more powerful, such as British colonialism, and the active Westernizing secularism of Ataturk. These countries have highly authoritarian tendencies, but have so far successfully cast aside enough of their Muslim ideological baggage to make democratic systems work to some degree.

This lack of legitimate state development in the bulk of the historical Muslim world, perhaps accentuated by the trauma of Mongol destruction, is central to its current complaints. It was central to their lack of resistance to Western imperialism, to their lack of effective post-colonial governance, to lack of human development and the economic development it leads to. It was also central to our disasters in Iraq and Afghanistan, where the US dreamed of quickly implanting democracy, only to be faced by a culture utterly unprepared for it, with far more fissiparous fish to fry. If God anoints the strong to rule over the weak, by way of warfare in general and jihad in particular, what is the point of legally bound representative state institutions?

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Why Have Brain Waves?

A theory about the function of electrical brain oscillations.

The phenomenon of brain waves have been the topic of many posts here, because they are such a tempting target for brain-wide information synchronization and management. Disparate analogies such as radio broadcasting, and the clock-ing of CPU chips come to mind. Yet the phenomenon is complicated, with lots of noise and a variety of active frequencies, spanning a ten-fold range. There have been many clues about their function, such as correlation with various mental states, (attention, sleep, resting non-attention), but no coherent theory about what they do has arisen, yet.

A recent paper tries to rectify that, by dialing back the expectations of what brain waves are doing, and coming at the problem from a very basic level. Information, after all, is not being carried directly by these waves at all- they are too variable and weak for that. Information in the brain is carried by the individual cell activations, in the context of their anatomical connections, which together form patterns that dynamically model variable information states.

One problem for this system is that neuron firing needs to be sparse in order to be useful. If everyone fires at once, you have epilepsy, instead of information modeling and transfer. Inhibitory neurons help with this, dampening feedback loops and preventing runaway activation. But most phenomena that one wants to model are stable over time, or vary relatively slowly. If you are looking at a scene, little changes from one 50 millisecond frame to the next, which is why our MP3 and video compression technologies work so well. Modeling stable phenomena with sparse, randomly firing neurons leads to quite a bit of error, as shown in the author's panel b, below.

Theory for the usefulness of partial neuron synchronization for accurate data encoding. Panel b shows what happens when neurons (black slashes, for each firing) are unsynchronized, while representing a constant stimulus (signal, blue). The cumulative representation (black line) is not an optimal representation of the original signal (blue). In contrast, if the neurons still fire sparsely, but are clocked to a global rhythm, even a very rough rhythm (yellow) gives as good overall accuracy as the fully randomly firing ensemble, and shorter time intervals provide the possibility of greater accuracy (salmon, green). Panel d represents conceptually the tradeoff between random firing and synchronized firing, as measured in data reconstruction error. The optimum is somewhere in the middle.

The observation is general to all data, whether stable or not, actually. Some synchronization provides more accurate data representation over a completely random ensemble of neurons, especially if the neurons are firing sparsely enough that (as in panel a, above) none fire at exactly the same time. This is a very significant point, and by itself predicts that neuron oscillations will happen in roughly the way they are observed- widely enough to be observed and to entrain much of the neuron firing that happens, but not strongly enough to cause epileptic-like mass synchronized firing.

It turns out that that there is even more room for improvement, however. Ironically, adding a little noise can also be helpful for signal reconstruction. Since the network has to include inhibitory neurons to dampen overall feedback and also prevent simultaneous spiking of nearby neurons, they cause an additional degradation of final representation, especially since they have delays in their own response, as do the activating neurons. The problem is that despite the presence of inhibitory neurons, they can not always act fast enough to dampen spike trains, which tend to run away a bit before inhibition. Modelling this all out, the authors find that adding a bit of noise to the system helps prevent excess synchronization, with quite beneficial effects, seen in the next figure.

 "Thus, optimal coding was achieved when the balance between excitatory and inhibition was the tightest. Further, at the optimal level of noise, the spiking CV [coefficient of variation] value was near unity, implying irregular (near-poisson) single cell responses."

The population firing rate power (panel h) shows most clearly the dangers of the low or no noise regime. Adding just a little noise (blue) helps dampen runaway spike trains significantly, while also (panels e, c) improving data reconstruction accuracy. In each panel d,e,f, the stable dashed line is the orginal data to be reconstructed. CV = coefficient of variation, exc. = excitatory neurons, in. = inhibitory neurons, ram = root mean squat, an inverse measure of correlation between the original signal and the reconstructed signal. Lower numbers (error) are better.

Taken together, this work argues strongly that neural oscillations (aside from the sleep spindles and other slow-wave phenomena that have distinct maintenance purposes) have a loosely analogous role to clocking cycles in computers. They do not themselves convey any data, but facilitate better data modelling. Their strengthening during attention, motor activities, and the like would then be a sign of weak synchronization, which may be significant over large areas of the brain for assembling mental constructs, but not of anything like information broadcasting. I would take this as the leading theory, currently, of their function.

"Neural oscillations have been hypothesised to fulfill a number of different functional roles, including feature binding (Singer, 1999), gating communication between different neural assemblies (Fries, 2005; Womelsdorf et al., 2007; Akam and Kullmann, 2010), encoding feed-forward and feed-back prediction errors (Arnal et al., 2011; Arnal and Giraud, 2012; Bastos et al., 2012) and facilitating ‘phase codes’ in which information is communicated via the timing of spikes relative to the ongoing oscillation cycle (Buzsáki and Chrobak, 1995). 

Many of these theories propose new ways in which oscillations encode incoming sensory information. In contrast, in our work network oscillations do not directly code for anything, but rather, are predicted as a consequence of efficient rate coding, an idea whose origins go back more than 50 years (Barlow, 1961)."

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