Whatever Happened to Bangladesh?

Saudi funding sows a whirlwind of extremist Islam.

Bangladesh had a difficult birth, with war and something close to genocide. The irony is that the killers and rapists were Islamic co-religionists from West Pakistan, now called Pakistan. Bangladesh was saved by the Hindus of India, who drove Pakistan out of a country about which it cared evidently less than nothing. Yet Islam and Islamism survived, and seems to have come to the fore vs the other main cultural thread, which is Bengali culture.

Bangladesh has been in the news recently for the murders of four outspoken atheists, particularly the brutality and impunity with which they were carried out. Why? Why has the virus of Islamism found a home so far from the core Arab areas whose extremism we take for granted? Money seems to be the short answer. Money that funds innumerable mosques, madrassas, and a variety of terrorist groups. The private madrassa system in Bangladesh has grown enormously over the recent decades, now rivalling the state educational system, which has been forced to offer its own madrassas of a hybrid nature that combine modern and Islamic education.

The private madrassas couldn't exist without large infusions of money, (donations), since they are typically free to students. The government spends about 50 million a year on its own system of madrassas, which should give an idea of the money involved. A large amount for a poor country, but very little for a country like Saudi Arabia, whose petro-wealth makes supporting ultra-conservative Islamism all over the world relatively easy, both by way of state policy, and by private donations. Charity is a very important duty in Islam, and is prone to chauvanistic and political interpretation, funding jihadist groups, proselytizing, and fundamentalist educational activities.

There are two important native institutions of Islamism in South East Asia. One is the Deobandi school or movement, and the other is the Jamaat -e-Islami political party. Deobandis are more conservative than the mainstream Barelvi Muslims, who preserve local and mystic Islamic traditions. The Deobandis are more by-the-book, holding to the Hanafi school mostly, and putting importance on following some major tradition. This contrasts with the evern more extreme movements like the Salafists, who renouce all the traditions after the first three generations and thus base their interpretations on the Koran and Hadiths, without regard to current scholarship, mainstream schools, or famous Islamic universities.

So there are more or less Calvinist schools at work here, from the culturally traditional Barelevis, who are nonetheless quite divisive in their own right, having supported the Pakistan movement and countless instances of anti-Hindu violence, to the Islamically traditional Deobandis, to the Islamically fundamantalist Salafis and Wahhabis. Of the latter, if they had wanted to recapture the Islamic golden age, the roughly 500 years from 800 to 1250, with its cosmopolitanism and scholarship, that would be a worthwhile enterprise. But trying to recapture the days of the first generations, with their incessant bigotry and warfare, in the current age, is naturally a recipe for global disaster.

The Jamaat -e-Islami is analogous to the Muslim Brotherhood, (or the Christian Fellowship, for that matter), in working assiduously to propagandize for a religio-political fundamentalism and to place its acolytes in powerful positions. It has an interesting distain for nationalism, viewing the modernizing movements of Nasser and others in the mid-20th century Islamic world as distractions from the world-wide revolution that would bring Islam to the head of affairs globally. It was outlawed for its violence in supporting West Pakistan at independence, but was later legalized by an Islamic dictator and now is a minor party with outsized power in the parliamentary system of Bangladesh.

The extent of funding flowing from the Gulf states to Islamist enterprises in Bangladesh is very hard to judge, as it goes under many routes and guises. There are several billions in remittences from individual Bangladeshis working in the Gulf states, (and subject there to Islamist propaganda, naturally), perhaps a billion in direct foreign aid, extensive business relationships including the curious and secretive practices of Islamic banking, and unknown billions in private charity. This is not to mention the Haj and its associated opportunities for propaganda. One example: "The Saudi Arabia-based al-Haramain Islamic Foundation, banned internationally by United Nations Security Council Committee 1267, has come under suspicion, along with other charities from the Middle East, for financing terrorism in Bangladesh."

All this is working against the indigenous, orthogonal culture of Bengal, which is Buddhist/Hindu as well as Islamic, literary, and rather non-violent. A recent podcast about Rabindranath Tagore tells some of the story. But Bangladesh was and remains torn between its Bengali and Islamic identities. The Islamic union with Pakistan certainly went sour, (as do all relationships with Pakistan, apparently), yet with the Gulf states putting their thumbs on the scale for decades, we end up with continuing schizophrenia, culture war, Islamic fundamentalism, and violence.

Will Islamism burn itself out anytime soon? It seems to be powered, not by its own logic or success (see the problems ISIS has in governing anyone in a popular manner), but as a bitter reaction to the long-term decline of Islamic culture, set against colonialism and continuing cultural dominance of the West. A reaction to modernity; to Muslim powerlessness in the modern worlds of technology, cultural soft power, military power, scholarship, creative arts, feminism, gay rights, political theory, ... the list could go on. There is a great deal to be bitter about. In Bangladesh, the majority remains moderate, democratic, and peaceful. Why outsiders like the Saudis and Pakistanis would want to stir up hatred is, as usual, not clear except on a psychoanalytic plane. As usual, a belief system seeks to bolster its tenuous believability by making as many people adhere to it as possible, by fair means or foul, since success is itself a form of truth in the Darwinian world of culture and ideas.

• Another review of Islamism in Bangladesh, if a bit right wing. 
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The Humble and Nether Origins of New York

The story of New Amsterdam is surprisingly well-documented. And a little sad.

A delightful, if a little fusty, book from 1978 "A Sweet and Alien Land", tells the story of Dutch colonization of what we now call New York State, beginning with the purchase of Manhattan from the local Indians in 1626, and outward to Long Island and upstate up to Albany. There is a surprising amount of documentation available, thanks to the scrupulous record keeping of the Dutch, including the cost of Manhattan itself, a steal if there ever was one. But the most interesting facet of the story is the subtext of human density and the role it plays in conflict. Whoever has more people wins the land, a process that may someday come back to haunt us.

The land was only sweet because it was underpeopled, (from a European perspective), partly through the technological backwardness of the resident native americans, partly from their decimation by exotic diseases. Nevertheless, like other colonists up and down the new world, the Dutch had a very difficult time getting a foothold and making their old-world methods work in the new. Maize was one technology they had to learn, for example. It didn't help that the Dutch colony was not really about colonization at all, but about "harvesting" the local beaver skins. it was founded by the Dutch West India Company, the ill-starred sibling of the Dutch East India Company, expressly and solely to make enormous profits from trade in the skins, which were brought down the Hudson River from the interior by Native Americans.

As one can imagine, the supply dwindled from overkill, and never came up to the company's expectations. So the colony was left with little investment, few defenses, and mediocre personnel. Its strong suits were its prime central position on the coast, outstanding harbor, and easy-going culture, compared to the fanatics up in Boston. The population was roughly 270 by 1640, and 4,000 by 1664. In the absence of completing claims early on, the Dutch expanded their network of outposts from Connecticut down to Delaware, but the outlying sites were doomed from lack of personnel and from encroachment, not by Indians, but by other Europeans, particularly disenchanted New Englanders who took over the Connecticut area, and then Long Island.

The book proceeds through the gory details of successive governorships, which  will leave aside, except to note that it was an excruciating position to occupy, faced with rude, obstreperous colonists, and months travel from one's putative overseers in Holland. and from there he was ruled by two bodies- the West India Company, and the Dutch government proper. Neither of which appreciated the great difficulties of the new colony, and provided as little guidance as they did resources.

The English had as little foresight in their settlement of the new world, it being a dumping ground for religious dissenters (New England) or for deluded economic opportunists (Jamestown and the South). But for them, the settlement took precedence over the economic plunder, and the people came. When enough had populated New England in the later 1600's, they cast their eyes southward upon the weak settlement in New Amsterdam. A few political machinations later, particularly in England where the king's brother York was eager for a feather in his cap, and they presented an overwhelming show of force and defeated governor Peter Stuyvesant on September 5, 1664, with very little firing or bloodshed.

Who should own the land? Those who currently possess it, or those who can most densely populate it and put it to its most productive economic (and martial) use? Or those who have the firepower to take it? As soon as Europeans took over land in the new world, they set up systems of property deeds and law that completely contravened their original mode of acquisition, which was by swindling, terror, killing, and stealing. Europeans continually overwhelmed and "opened" up lands during American settlement on the basis of both higher density and stronger force. If density and productivity is the rule, we may eventually be on the short end of such a competition from Asia. Even Mexico, at 64 people per square kilometer, has about twice the population density of the US.

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Seeing Speech in the Brain

An fMRI study of brain dynamics during speech production.

fMRI is now a standard method to look at brain activity, though its resolution in both time and space are poor. It only detects changes in blood volume, which is an indirect, if regular, response to neuronal activity. Additionally, the (living) brain is always on, churning away at its own fantasies and unconscious levels, so the differences between resting and active states can be quite hard to detect, especially at this gross level of resolution.

A recent study took a stab at detecting speech production in the brain by fMRI, analyzing the data by correlation between regions. They broke up the brain into 212 regions, and measured the mutual correlation between each of them under separate tasks given to 14 subjects. The first task was the resting state, when the subject's eyes were closed and they were told to have no specific thoughts. Not the greatest method, from my experience of meditation, actually(!) The other two tasks were 1. they were asked to make simple eeee and iiii vowel sounds, and 2. they were asked to repeat simple but complete English sentences. The respective brain correlation networks are shown below.

Correlation maps among the best-correlated nodes selected from a total of 212 nodes (brain volumes) of fMRI activity in an average of 14 subjects. Nodes are colored "hotter" the more connected they are to others, and the lines between them are colored "hotter" depending on the strength of correlation. The A images show the complete map. The B, C, D, and E graphs are sub-selections of the data by "hotness" of the nodes, with the most connected (red) in the B maps, etc.

While the complexity of these images resists interpretation, they show several notable things. First is the overall lower connectivity in the resting state, which is dominated by green-level correlations. There are only about 3 "hot" nodes, as shown in the B sub-graph, in red. In contrast, during speaking of either syllables or sentences, far more nodes (15, and 11, respectively) are highly connected, and the overall graph is heavily weighted towards higher connectivity. The identity of the "hot" nodes is difficult to pin down in functional terms, but they seem to be dominated by premotor and motor cortex regions, noted as 6 and 4 in the graphs.

Secondly, while the syllable graphs have even higher connectivity in some respects than the sentence graphs, they show much less involvement of the frontal cortex, which is entirely absent in the orange and green-level correlation graphs, compared to the sentence speech case. This makes, on the face of it, complete sense, and supports the idea that we are seeing aspects of speech processing going on through this method. The emphasis in the syllable case is on the motor processing, while the full sentence case adds in executive complexity as well as some cerebellar fine sequencing control. That the resting state shows some frontal cortex activity and connection also stands to reason, if one assumes that uttering plain syllables leads to utter boredom, while letting the mind run free with "no thoughts" is likely to lead, frequently, to some relatively complex thoughts.

Did they find anything interesting? Long lists of brain areas with slight differences were offered, but seem to deserve much deeper (future) analysis to come up with anything approaching a theory of how speech production circuitry might look and work in a comprehensive way. This is really only a first peek at the issue, using crude imaging and advanced analysis methods.

The researchers try to further differentiate the brain states by an analysis of their modularity. The claim is that the speech producing brain seems to have tighter and more intensively local activity than the resting state, whose weaker correlations seem more widely and loosely spread. The speaking brain also generates more active modules, such as one reaching into the cerebellum. Unfortunately, despite some extremely snazzy graphics, I found the data impossible to interpret, and not, on the face of it, compelling, though reasonable enough. It is going to take a great deal more work, and perhaps better technology, to map the speech circuitry in a useful way. Without much better spatial and especially temporal resolution, one can't capture such dynamic and nano-scale activities.

An example quote points to possible functions underlying what was imaged. But the differentiation from the resting state was not very strong, since it showed plenty of connections / correlations as well, just slightly weaker.

"The SPN [speech production network] core sensorimotor hub network established connections with the brain regions responsible for sound perception and encoding (auditory cortex), phonological and semantic processing (parietal cortex), lexical decisions and narrative comprehension (middle/posterior cingulate cortex), motor planning and temporal processing of auditory stimuli (insula), control of learned voice production and suppression of unintended responses (basal ganglia), and modulation of vocal motor timing and sequence processing (cerebellum)."

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Spock and the Next Myth

From monomyth to polymyth. Double-header reviews of "The Origins of the World's Mythologies", by E.J. Michael Witzel, and "I am Spock", by Leonard Nimoy. 

Myths are essential. They organize our world with purposeful, dramatic meaning, and situate us in a cosmos that is otherwise utterly mystifying and inhuman. All cultures have them, and the weakness of a cultural myth, such as that of late Rome, indicates lack of confidence and can lead to general malaise and decline. Where are we on this spectrum? It is hard to say, but the bulldozing confidence of Indian extermination, manifest destiny, and saving-the-world-through-democracy seems to have slacked off in recent decades. We have settled the frontiers, won the cold war, and possess an unwieldy world-wide empire which is as ungrateful as it is costly.

Our myths / ideologies of progress and unlimited human potential are met at every turn with stark limits, whether in the form of stunningly regressive religious ideologies from the world of Islam, which have fired the imaginations of millions in revolt against our neocolonial domination, or in the form of CO2, which tells us that our profligate ways can not continue without turning Earth into a wasteland. What next?

Before we get to that, it is good to ask what has led to this point: the history of human myths. Eminent scholar Michael Witzel has written a tome on the subject, a vast attempt to put human myths world-wide into a system of lineal evolutionary relationships that go back 50,000, even 100,00 years, to the origins of modern humans, more or less. Quixotic? Quite. Turgid? Totally. In fact, this is a poorly written book that is chaotically disorganized, repetitive, and keeps putting the cart of theory ahead of the horse of evidence. The theory, basically, is that there are common threads of myth (a remote high god, a golden age in the past, and a flood that punished humanity) that traces back lineally to the beginnings of modern human consciousness. This collection of themes was substantially elaborated in all descendent cultures, and especially so in a subset of northern cultures that covered the Indoeuropean, East Asian, and North American regions, to a full story line from creation to apocalyptic destruction, which we know so well in the Bible and other sources.

The theory is obviously full of holes and exceptions at every turn, and I ended up siding with the much-disparaged Jungian counter-view that stories like these are more or less spontaneous and heavily anthropomorphic emanations from human psychology, uniting universal questions with archetypal answers. The completeness of one's story line may have more to do with the local cognitive and organizational gestalt than with thousands of years of lineal descent, notwithstanding the sometimes remarkable durability and accuracy of oral traditions.

It is interesting to note that the putatively more primitive (what Witzel names Gondwana) mythical themes seem more relevant to human meaning, as they tend to be more animistic, very landscape-focused, ancestor-focused, and transactional. The other lineage in Witzel's system (the Laurasian) is more hierarchical, filled with generations of gods, complex and colorful relations between them, plus the stories of Prometheus and original sin, but posits few interactions between contemporary humans and the cosmos. It seems, frankly, more concerned with supporting a temporal hierarchy of king and nobility than with filling the world at large with personally significant meaning.

At any rate, however ancient these myths are, they no longer function for most people in the developed world (putting aside for the moment the continuing social hold of organized religions on billions of people, who may not consciously realize or participate in the ancient and absurd nature of the implicit cosmologies, the fictional heros, or the drama of human sacrifice in the chalice, etc). Our modern cosmos is definitely not that of the scriptures, and nor is our spiritual or moral universe. Through the enlightenment, all this was gradually discarded in favor of true stories, and in return we gained the immense confidence that such revolutionary factuality bestowed, having, in essence, escaped from Plato's cave- from the murk of fantastical fictions into the sunshine of reality, and the immense technological powers that this reality turned out to harbor.

Does all that mean that myth is now dispensible? Not at all. While we have dispensed with the various fairy tales received as myth through the ages, (which, in fairness, many cultures, like the far northern Inuit, treat in very playful fashion rather than the reified & doomed earnestness common among the reigning monotheisms), the function of myth goes well beyond a factual reporting of our past. That origin story has been replaced with a new, and durable reality. What we have subsisted on, ideologically, since the enlightenment, has been the myth / ideology of progress, because the reality we discovered was even more magical than the classical myths had foretold. The elegance and vastness of the real cosmos, from the tiniest particle to the big bang, is more astonishing. And the utility of fossil carbon, nuclear power, electricity, silicon circuits, and the countless other secrets that have been revealed have multiplied our powers, not to mention our populations, many, many times over.

Yet where is the meaning? If all our powers merely serve to satisfy greed, which turns out to be bottomless, what have we gained? Prosperity does seem to have some positive moral effects, making people more secure, less violent, and more capable of caring for others (up to a point). But if one looks closely at traditional cultures, one sees great and deep happiness there as well. It is not at all clear that our hugely wasteful, hive-like societies are optimal on ethical, social, or spiritual levels.

I think we are seeking a new myth, or myths. The last time there was such ferment and seeking was the axial age, which capped an epoch of great human progress to give us our current, if relic, organized religions. What will the current age provide? It remains very difficult to say, since one key property of a myth / ideology is that it is fictive. It is a construction that provides confidence and meaning without recourse to facts, though at the same time, it is hopefully not antagonistic to the appreciation of true stories about reality. Patriotism is a common example. Everyone can be patriotic and love their country, yet every country is not better than every other one.

One one level, we are bombarded with what might be called micro-myths, from books, movies and TV shows. Most are mere stories, not rising to the level of comprehensive narrative about our past, relations with the world, and most importantly, our future. The products out of Hollywood are becoming ever more simple and formulaic, with their comic book characters. Which might make them increasingly mythical, if they weren't so dedicated to only one facet of the cultural myth: the hero tale, reminiscent of works like the Ramayana.

A much-loved example of a more complete myth is that of Star Trek. The recent death of Leonard Nimoy provided an occasion to watch some eposodes and read his (second) autobiography, "I am Spock". Which is a wonderful book, filled with warmth and insight. Nimoy not only portrayed Spock in the original series and the string of films, but directed two of the films, had a wide-ranging career in other acting and directing roles, and made countless appearances, among other more or less successful projects.

He speaks with great nostalgia and appreciation of the role. While Nimoy is surely more than just Spock, Spock is in turn far, far more than Nimoy was, created, or bargained for. Star Trek, and its science officer particularly, created a modern myth of continued human progress, with high ethics and integrity, intrinsic diversity, and (weekly) adventure devoted to searching through that complex reality that surrounds us, bringing peace and reason in equal measure. (Was Spock a Christ-like alien being brought to the Federation via his human mother to redeem mankind through logic? The mind reels!)

It spoke volumes to its own time, and just as strongly to ours. Exploration doesn't have to happen in the outer world of aliens and M-class planets. It can be questions of basic science or forays into the inner worlds psychology, conducted scientifically or artistically. And it includes a dedication to solving the big problems with everything we can muster, particularly reason and logic: climate change, social justice, economic prosperity. The metaphor is quite general, and we can all be in on the adventure.

The one thing we can't do is travel to other star systems. The warp drive that the show is based on physically impossible, so the myth remains firmly fictional in that critical respect. Whether there are dramatic and intelligent beings in other star systems may also remain unknown. In theory, there must be many other civilizations around the galaxy, let alone the universe. But detecting them seems only remotely plausible, and interacting with them, frankly impossible. Still, using some modest artistic license to reveal human ideals and possibilities is a far cry from the monotheistic myths which not only posit, but demand, belief in a vast conspiracy & hierarchy of spirits and other supernatural phenomena as clearly dredged from our psychological makeup as they are scientifically unbelievable.

This is a bridge that we crossed, intellectually, with the enlightenment. Gone are the days when everyone had to believe the same thing, and draw meaning from the same wholly crazy story. Because no myth fully answers each person's questions and perspective. The answer is that we live and will continue to live in a world of many myths, a polymythic culture, and should be quite wary of a single myth returning to dominate. America is particularly diverse, which is reflected in a wildly divergent zoo of cultural myths, from the die-hard son of the Confederacy to the roccoco sexuality of of hip-hop. Start Trek is only one myth of a great variety, one that resonates with many, with positive humanism at its core.

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Consciousness and Unconsciousness Are Different

Further work on the mechanics of consciousness.

Of all the scientific problems, consciousness is among the most interesting. It is the study of ourselves, of our most intimate nature, whose very proximity makes investigation problematic, not to say perilous. Its intrinsic structure misdirects us from its physical basis, and it has thus been the subject of millennia of fruitless, indeed unsound and narcissistic, speculation. Not that there is any significant evidence that goes against the basic reductionist model that it all happens in our brains, but how it happens ... that remains largely unknown, due to the rather bizarre technology involved, which is miniaturized, rapidly dynamic, very wet, and case-hardened, in addition to being ethically protected from willful damage.

A recent paper took another step towards teasing out the dynamic differences between conscious and unconscious processing using EEG and MEG, that is, electrical and magnetic recordings from the scalps of human subjects while they are looking at various visual tests. Visual spots were very briefly presented, to register at the very limits of visual perception. Then the subjects were asked both whether they consciously saw the spot, and in either case, where they thought it was.

An interesting wrinkle in this work is that even if the subjects didn't consciously see the spot, their guesses were much more accurate than chance. This is because of the well-known phenomenon of blind-sight, by which we still process our visual perception to very high levels of analysis whether it enters consciousness or not. So the researchers ended up with three classes of brain state from their subjects- consciously perceived images, unconsciously perceived and correctly placed images, and unconsciously perceived but not correctly placed images. The last set is assumed to the most basic level of unconscious perception, which is interrupted before higher levels of visual analysis or transmission between the visual system and the conscious guessing system.

A technical advantage of this method is that in virtually all respects, the conscious, correctly guessed case is the same as the unconscious, correctly guessed case. The visual system found the object, and the guessing system was told where it was. Only the consciousness system is left in the dark, as it were, which these researchers try to exploit to find its electrical traces.

Real location plotted against reported location. Subjects perform far above chance, (on diagonal), whether they consciously think they saw the visual feature or not. A line was presented in one of  eight radial locations, as indicated on right.

They spend the paper trying to differentiate these brain states by their EEG and MEG scanning methods, and find that they can detect slight differences. Indeed, they try to predict the visual spot location purely from the brain signals, independent of the subject's report, and find that they can do a pretty good job, as shown below. This was done by machine learning methods, where the various trials, with known results, are fed into a computer program, which picks out whatever salient parts of the signals might be informative. This learned pattern can then be deployed on unknown data, resulting in novel predictions, as they present.

Programmatic classifiers perform better than chance in predicting the visual location, even in cases (unseen, incorrectly reported) where the subject had no idea where the visual feature was, either consciously or unconsciously. The classifiers also follow the internal processing of perception in the brain over time, which all happens pretty much within a second.

The researchers also show that even when unconscious, and even when wrongly reported by the subject, the brain data can pick up the correct visual location quite a bit of the time, and it is encoded out to quite late times, to about 0.6 seconds. This indicates that just because a percept is unconscious doesn't mean that it is much more brief or transient than a conscious one.

At this point they deepened their decoding of the brain signals, looking at the differences between the conscious + correct guess versus the unconsciousn + correct guess trials. What they found supported the consensus interpretation that consciousness is an added event on top of all the unconscious processing that goes forth pretty much the same way in each case.

Further classifier developed to detect the difference between conscious and unconscious perception. Those trained on conscious data (dark line) see extra processing when given conscious data, while the reverse is not true.. those trained on unconscious data (gray line) fail to see anything different when exposed to conscious data.

"These analyses indicate that seen–correct trials contained the same decodable stimulus information as unseen–correct trials, plus additional information unique to conscious trials."

Great, so where are these differentiating signals coming from? When they tried to deconstruct the programmed decoding by location, they found that they could roughly locate the signals in the superior frontal and parietal lobes. But this was a pretty weak effect. The consciousness part of the signal was difficult to localize, and probably happens in wide-spread fashion.

Two examples of localized classifiers. The superior frontal (bottom) sees (slightly) different processing in the conscious data, while the rostral medial frontal location (top) sees nothing different at all. Localization was relatively weak, overall.

Finally, the researchers tried another analysis on their data, looking whether their classifiers that were so successful above in modelling the subject's perception could be time-shifted. The graphs above track the gradual development, peaking, and decay of the visual perception, all in under one second. Could the classifier that works at 300 milliseconds also work at 500 milliseconds? If so, that would imply that the pattern of activity in the brain was similar, rather than moving about dynamically from one processing center and type to another.

Rough model of the researcher's inferences about processing steps consistent with time-shifting the classifiers over conscious (left) vs unconscious (right) data. They suggest that the conscious data points to successive and different processing steps not present in the unconscious case.

They found that, roughly speaking, their data supported a dramatic distinction between the two tested cases of consciously seen versus unconsciously seen and corrected located. Up to about 300 milliseconds, both were the same, characterized by a succession of visual processing steps where the classifiers for each time slice were useless for other time slices. Thereafter, for the next 500 milliseconds, the time-range of their models went up dramatically, but significantly less so for the conscious case than the unconscious case. This suggested to them the next model, where consciousness involves a series of further processing steps that are not just a long-term reverberation of the perception set up at 400 milliseconds (right side), but additional processes that look different in the EEG / MEG signals and require different classifiers to be picked up in data analysis (yellow, black, and blue curves on the left). These are not as tight as the earlier lock-step series of gestalts, but are detectably different.

 "The high level of decoding observed on seen trials, over a long time window of ∼270–800 ms, combined with a low level of off-diagonal temporal generalization beyond a fixed horizon of ∼160 ms, implies that a conscious location is successively encoded by a series of about four distinct stages, each terminating relatively sharply after a processing duration of ∼160 ms. Conversely, the lower decoding level and longer endurance observed for unconsciously perceived stimuli indicate that they do not enter into the same processing chain."

One has to conclude that these are mere hints of what is going on, though more accessible hints, via EEG, than those gained so painfully by fMRI and more invasive techniques. What these inferred extra processing steps are, where they take place, and how they relate to each other and to our subjective mind states, all remain shrouded in mystery, but more importantly, remain for future investigation.

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Reading the Genetic Tea Leaves

How a cancer drug diagnostic / prognostic panel works.

Molecular medicine is coming, slowly, but surely. Drug companies have been forced to lead the way, because drugs are molecules, affect other molecules in our bodies, and can't be understood without learning about the molecular workings of the body.

Cancer has been a leading focus for this approach, because of its thousands of molecular manifestations which can cross the traditional organ boundaries, and its protean mechanism of molecular progression, accumulating mutations in many genes before turning dangerous. And because of its maddening self-on-self method of attack. One of the most significant cancer-related genes is TP53, which is mutated in about half of all cancers, and which in most of the rest is mis-regulated by way of other mutations. It encodes a protein (p53) that plays a central role in activating DNA repair processes in response to damage and general stress, in halting the cell replication cycle, and even in activating cellular suicide when repair is impossible. Getting rid of this protein is naturally a key step to keeping a wayward cell alive and allowing it to accumulate even more mutations.

This is one reason why, in addition to sequencing our normal genomes as part of regular medicine in the near future, our tumors and other sampled tissues will also be sequenced and analyzed to find accidental mutations that may be causing disease. For instance, over 100 tumors are known to afflict the skin, causing all sorts of lesions, each with a different set of causal mutations.

A recent paper from the drug company Novartis concerns a drug it has developed for p53, and particularly its interaction with another protein, HDM2, which turns it off. This drug interferes physically with the binding of these two proteins, thereby leaving p53 more active, and allowing it to kill its host cell in case it is cancerous, via the suicidal processes of apoptosis. But all this can only work if p53 has not been mutationally deactivated in that cancer.

So the researchers looked for a reliable way to test patients for p53 activity, and came up with the work of this paper, which is a collection of other genes whose activity, when on, says that p53 is active and thus "druggable". The test is not to sample DNA, but RNA from the tissue, asking about the transcription and thus activity of these selected indicator genes. From the p53 gene itself, RNA may be quite abundant, but if it has some tiny mutation that kills the activity of the encoded protein, then it is functionally dead. It is thus more effective to test the activity of genes that are "downstream" from it, in circuit terms, to find out whether p53 is working or not. Since one big function of p53, which binds DNA, is to turn other genes on.

The panel consists of 13 genes, developed using cell lines that were carefully selected for their response (or lack of response) to this new drug which inhibits the p53-repressor interaction. These were filtered down from 10,000 or more genes that were tested at the outset, as being the most informative. Each of them are targets of p53 transcriptional activation, which makes them obviously downstream in a circuitry sense.

List of genes used in the diagnostic/prognostic test for p53 function, comprising other genes that p53 activates.

None of these genes are dramatically regulated in the drug treatment case, only about a couple fold change in RNA levels in most cases. But the technology is now sensitive enough to detect such small changes reliably. About a third of the genes in the panel are directly annotated to function in apoptosis, which, in addition to informing on the status of the cellular p53 protein, also informs on the status of the key pathway by which this drug works- the cell suicide pathway.

So there it is, a prognostic test that amounts to something like a thermometer to tell how the patient is doing, but in molecular terms, about a specific molecular pathway, that then indicates the use of specific molecular counter-therapies.

• Incidentally, another set of cancer mutations are so knarly, they kill each other off.
• Piketty on Merkel: A colossal and cruel mistake is happening. And incidentally, Germany reneged on colossal amounts of debt back in the day, repeatedly.
• Dreadful US policy in Bosnia, and the distinction between massacre and genocide.
• Ephemerality in the arts ... what streaming gets us, and then doesn't get us.
• Finance naturally lends itself to crime, of huge proportions.
• Toles on the GOP clown circus:

Crime, Punishment, and Unemployment

The penal and the anti-labor policy attitudes are closely connected. A July 4 meditation.

I follow MMT economics, which has a great deal to say about our attitude towards employment and unemployment. This attitude has hardened dramatically over recent decades, from a supportive responsibility of government in the wake of the Great Depression and the unifying experience of World War II, down to the Romney credo of "I like to fire people", though he might think twice when "corporations are people too, my friend".

An analogous shift has taken place in our attitude towards criminals and crime, from making an effort to punish in proportional ways and rehabilitate, down to the current lock 'em up and let 'em rot attitude, sweeping up whole demographic communities in its wake.

We have migrated from a consciousness of social complexity and social duties of the collective, towards a starky individualistic sink-or-swim ethic that made of the losers or victims of various social pathologies scapegoats to be ostracized and made even more miserable. We have gone from a temporary suspension of the class war back into its most fetid trenches, as the rich, running their own political party and Ministry of Truth, emit an endless stream of NewsSpeak pertaining to an ideology of blaming the poor for being poor, and idolizing the rich for being hard working exemplars of the American way, richly deserving of every penny they have and in no way beneficiaries of societal inequalities and happenstance.

Now, promotion of striving and hard work is great. But the extent to which we have lost sight of common responsibilities and the role of luck in everyone's lives, and made unpersons of the unemployed (and the incarcerated) has been astonishing. The political system was barely able to muster the empathy to pass the first stimulus bill, and only after it was larded up with plenty of non-stimulative tax cuts for the rich and generous aid to banks. Now the system is completely inert, dedicated to the proposition that helping the unemployed is the absolute last item on the list, behind fixing our national debt in 2040 and cutting lower middle class supports like Medicare, Social Security, and public education.

It is all so ironic, since, conceptually speaking, the society needs as much labor as possible. There are elderly to take care of, parks to clean, solar panels to install.. the list is endless. Just because the private sector can't manage to employ everyone does not by any means imply that everyone can't be employed usefully or can't be paid decently.

It is doubly ironic since work is by now a very artificial concept. We are far past the state of needing everyone's hands on the plow to grow our food and outfit our caves. The modern economy has endless roles for everyone to make each other's lives better, and one highly significant way to do that is simply to employ those who would like to be employed. Indeed, if we make labor easy to sell, that stabilizes society by reducing the need for crime. Crime would become a luxury instead of a necessity.

But the rich have, though their political party, made abundantly clear where they stand in all this. They rather keep labor down and ill-paid rather than build the country's infrastrucure.  They rather enforce their ideology of private capitalism over the public good, with a job market exclusively at the beck and call of private employers. They rather keep inflation low than foster economic growth. They rather keep and expand their marginal advantages in a declining system rather than tend to our common institutions and future collective prospects. It is appalling.

• Human sacrifices demanded by the priests of plutocracy.
• Same story in Britain.
• Reich on the costs of imprisonment.

Christians Have All The Morals

Review of "Terrorism and Civilization", by Shadia Drury

Some weeks ago, I discussed, somewhat tongue-in-cheek, how atheists have no morals. This time we turn the other cheek to consider Christian morals in some detail. Shadia Drury published a response to the 9/11 attacks in the form of a frontal assault on religious morality and Christian morality in particular, a book that should have risen to the top of the Atheist cannon, but didn't, perhaps due to her obscurity, her gender, and the book's high price.

Her case is relentless as it is remorseful, about the opportunities lost in the West due to the twisted, irrational and inhumane doctrines that originate from the New Testament. At least the Old Testament god was understandable, if a little hot-tempered. The New one is positively terroristic. Nor does Jesus (assuming for the monent that he was a real person and that the scriptures about him are at least partly true) get off in this thorough indictment, for he brings us this new system which features carelessness about this world and its people, thought crime, eschetological selfishness, orignal sin, and eternal damnation.

Hell is, of course, one focus. Jews didn't have hell, really. That was Jesus's invention, though obviously stolen from the Zoroastrians. His doctrine is that mere belief in him is the main thing.. everything else is secondary, in any practical, moral, and eschatological sense. However, many are called and few are chosen, which is to say that even if you fulfill his need for faith, you could still end up in hell, which is painted in the most fiery colors, as endless suffering and eternal. This is pure psychological terror, obviously, and was stunningly effective against the other religions of the day, which were all more reasonable.

Jesus also introduced thought crime, since belief in him was the main criterion of salvation. He also deemed immoral thoughts as bad as immoral actions. Adultury in one's mind as bad as in the flesh, etc. So where was one to go for relief from such a regime? There is nowhere to hide. Many serious believers have been agonized by this, for example John Bunyan in Pilgrim's Progress, a despairing work full of terrors and sin.

The reason for the horrors of Bunyan's epic travellogue are that humans, in Jesus's system, are fallen and evil. They are sinners who have no right to salvation, who are saved (if at all) by grace granted in return for slavish faith. Drury makes the acute observation that Freud, that ostensible iconoclast and atheist, follows the Christian system in virtually every psychological particular, from the innate sinfulnes of man (the id), and the need for terror (repression) to keep the inner beast under control, to the therapeutic salve of confession (the couch, in place of the booth).

Nietzsche too comes in for a drubbing, in an even more profound way. The Christian morality is one of blind obedience, of faith in the unbelievable, and terrorism inner and outer. All for our own good, naturally. If one fails to reframe the basic parameters of this model of humanity, then revolt against this edifice of lies might take an ugly turn, to immorality and perverse delight in reversing every dictum of the reigning moral order, so as to return to one's "true" nature, which though sinful, is at least honest and alive. Thus the bathos about Dionysus and the amoral Übermensch.

This accepts a frame that is far from true, however. Humans are many bad things, but they are not fundamentally bad beings. We are basically good beings with complex and often conflicting needs and ideals. We are pro-social. We love and seek love in return. We are fiercely moral. Drury points out that it is our civilization and our highest ideals that are what is in some ways most dangerous about us- our ability to organize huge groups, spout ideological rhetoric about utopian ideals, not to mention creating modern technology, for warfare and totalitarianism on unimaginable scales. It is the beast within that required nurturing, and our better natures that required the most advanced instruments of repression, when one thinks of the rankest horrors of the twentieth century.

So it is time to relax. The work of civilizing ourselves remains great, and constant cultivation is certainly desirable. But it does not require terrors of religion, nor theories about how damnable we are. Nor should we leap to the other Rousseau-ian end of spectrum, where everything natural, native, and naive is all that is good. As the religiously and ideologically burned-out countries of Europe are showing, there is peace, prosperity, happiness, and not least, highly sensistive morality, in a post-Christian, moderate, and humane culture.

• Kansas is just fine ... steal from the poor, give to the rich is a winning, sustainable strategy, especially considering how damnable we are.
• The Devil and Mr. Scalia. At least one justice is a fossilized relic, and has either lost his marbles, or enjoys trolling interviewers.
• Over 100 jihadist training camps, thousands of trainees ... this is not a fringe phenomenon.
• California's sclerotic housing mess. Incumbent owners always win when new housing / zoning is killed. Especially with prop 13.
• Grexit is coming.
• Whom we feel for... white police edition.
• Another 1%. Or is it the same one?
• Enriching the 1% makes everyone poorer.

Plowing Through a Fork

DNA polymerase and DNA helicase help each other out at the replication fork.

While DNA may not have been the first molecule at the origin of life, it now forms the heart of our replicative and molecular existence, its iconic and elegant stairway storing the digital data that has taken over the world as our wonderful biosphere. Its replication is a complicated process, but has to be done rapidly, since for one of our cells to divide, three billion bases need to be gotten through. A recent paper discussed how that happens, for the DNA polymerase itself can not open up the parental DNA strand fast enough through its own locomotion. It needs a DNA helicase to help unwind the oncoming DNA, whose strands are not only glued together by their basepairs, but can be festooned with histones and all sorts of other bound proteins that need to be cleared away.

In this cartoon of DNA replication, (going right to left), the synthesis of the leading strand (top) is so undramatic that its DNA polymerase is left out altogether. But note that a helicase rides at the fork where DNA melts. In this system (from E. coli), DNA polymerase III (pink) is the major polymerase that carries out leading strand and the major part of lagging strand synthesis, while DNA polymerase I is a fill-in enzyme that fills in gaps that are left at the end of every run of DNA polymerase III. The last step on the lagging strand is sealing by DNA ligase of the DNA polymerase I run, which goes right up to the next unit of lagging strand, made previously. Unlike in the diagram, there would be no nucleotides missing when/where this ligase acts. An RNA primer for the lagging strand polymerase III synthesis is shown in green.

To digress slightly, one of the most critical complications in DNA replication is that of the lagging strand. DNA comes in two strands, but all polymerases operate only in one direction (5' to 3'). So replicating the leading strand, which runs 5' to 3', is a piece of cake, even if it requires a helicase for assistance. The other strand is called the lagging strand, and has to be made piecemeal, with the polymerase running "backward" from the replication fork, primed each time by a special RNA-synthesizing priming polymerase. So this process is intrinsically assymetrical and messy.

Anyhow, the researchers use the classic model system of polymerase and helicase from the T7 phage, which infects E. coli bacteria and comes with its own (encoded) stripped-down and efficient DNA replication machinery, for late stages of infection when it needs to pump out full viral genomes at high speed. It is known that the helicase is essential. The polymerase by itself can work, but only slowly, and is particularly retarded by GC-rich regions, the GC nucleotide pair having three hydrogen bonds compared to the AT pair's two bonds. The question for these researchers was.. how closely do the helicase and polymerase work? Are they distant partners, or cheek-by-jowl?

One could imagine that the helicase could proceed some distance ahead of the polymerase. But it is also known that the helicase doesn't work that quickly by itself either. The helicase looks like a lifesaver ring that forms around a single strand of DNA, and consumes dTTP as an energy source to tug on it, pulling it away from the duplex fork which the helicase is trying to melt. Neither activity alone explains the total high rate of DNA replication, suggesting that they work closely to help each other along. The current work put them through their paces either apart or together, and controlled by various concentrations of their inputs, dTTP in the case of the helicase, or all four deoxy-nucleotides in the case of the polymerase.

On a single strand of DNA where it doesn't need to do any helicase-ing, the T7 helicase moves along at a nice 65 nucleotides (nt)/second pace. Likewise, the polymerase, when given plenty of nucleotides and single stranded DNA, chuggs along at 200 nt/second. The final rate of the complex on duplex DNA is about 200 nt/second also, so what needs to be explained is how the polymerase regains that rate when facing duplex DNA and perhaps non-ideal concentrations of reactants, plus other obstacles. For the helicase, how and why does it go faster when yoked to the polymerase than it does on clear single-stranded DNA on its own?

Performance of DNA polymerase alone, on GC-rich DNA. It is slowed down substantially, but much less when given an excess of its substrates, the deoxynuceotide triphosphates (dNTPs).

Key computed parameters of the polymerase alone. With higher GC content in the DNA, the polymerase maximum rate (k-cat) doesn't slow down much, but its responsiveness to substrate concentration( Km) rises substantially.

One way to manipulate the system is to present the enzymes with double-stranded GC-rich DNA in comparison to AT-rich DNA, and ask what other ingredients, such as more nucleotides, do to their speed. The comparison is rather subtle, and depends on decomposing the reaction into two components, a measure of the first part of the reaction, enzyme + nucleotide binding (Km), and a measure of the second part- how fast the enzyme is at maximum if it has plenty of inputs (kcat). As shown in the first graph, the DNA polymerase is significantly slowed down by GC-rich DNA duplex. But that effect is substantially alleviated by high concentrations of nucleotides, indicating that the polymerase has problems opening the duplex DNA for lack of enough new nucleotides to stuff into the template position as the fork sporadically melts. The polymerase is not good at holding on to temporarily melted nucleotides.

Performance of helicase alone on GC-rich templates. The rate is hugely slowed down no matter what the dTTP (energy substrate) concentration.

Unlike the polymerase, the kinetics of the helicase are changed by difficult-to-open GC content mostly in the k-cat, or maximum rate, with little or negative effect in the Km or substrate (dTTP) sensitivity.

Conversely, the helicase has another problem. No matter how much nucleotide (more precisely, deoxy-nucleotide triphosphate), you give it, it maxes out at pretty slow rates on GC-rich DNA. This suggests that it just isn't a terribly good helicase by itself, but if given a push...

Rate of the combined enzymes on 50% GC template is quite fast. The nucleotide concentration for the polymerase (dVTPs, which stands for a mix of dATP, dGTP, dCTP, while the dTTP is provided for the helicase) is kept extremely low. But the combined system makes a much higher rate (~70 nt/second) than the polymerase alone did at the minuscule concentration of 5 micromolar dNTPs (I estimate perhaps 10 nt/second from the graph above). This is reflected in the combined Km for nucleotides in the combined case (top, in red) vs the polymerase alone case (bottom, red).

The reason for all this is structural, that the helicase is better at grabbing on to the single strand coming out of the fork, but doesn't have much oomph behind it to plow forward continuously. The polymerase, in contrast, has a good engine, but doesn't grab onto the incoming single strand DNA well, letting it slip back into the duplex with high frequency. The complementary relationship makes sense, since you really do not want the helicase travelling off by itself unwinding the cell's DNA, but rather want it coupled to where it is really needed- right ahead of the DNA polymerase, as a kind of cow-catcher and rail splitter.

The red nucleotide pictured is fluorescent, and its melting changes the fluorescence signal as measured on the Y-axis of the graphs. Melting in the absence of any dNTP substrate is only substantial when both helicase and polymerase are present.

Lastly, with some more intricate fluorescence assays, (on which this whole work is based), the authors look at the two or three nucleotides of the fork itself, and which of them are grabbed by the two enzymes in single-stranded form. This is done without giving them any nucleotide triphosphates as energy source or substrate, so it is looking at initial binding. Polymerase or helicase alone bind to the fork, but are pretty ineffective at melting any of the first three nucleotides of the duplex (darker bars). But the two enzymes together melt them quite well (light blue bars). So it is not just the engine of the polymerase behind, but a physically cooperative binding mechanism at the fork that gets the DNA melted in advance of replication.

The authors come up with a highly schematic vision of what this might look like, with some wildly stretched DNA going into the helicase- the green rung of the non-template (right) strand. The helicase then hangs on tightly to each nucleotide that it captures, as the polymerase is busy doing its thing of synthesizing the new DNA strand.

Model of the polymerase (beige) and helicase (pink) collaborating at the replication fork.

• ISIS deploys foreigners to kill themselves. Clever! 
• More guns in church is the answer, plus let's blame the victim, says NRA.
• Employers pay only what they can get away with. "The minuscule gains that households have made have largely come because women have increasingly entered the workforce—meaning families are working longer hours, as they run faster and faster to stay in place." ... "Median incomes for male workers now in their thirties are about 12 percent lower than the income was for their fathers’ generation at the same age."
• Is German labor through being squeezed?
• Cringely on IT feudalism: "H-1B has always been unnecessary."
• Pluses and minuses of Dodd-Frank.
• Just like his crony brother ... Jeb! raked in money sitting on the board of a criminal organization. One more argument, incidentally, for the completely merited pay and corresponding utility of business executives.
• Some modest suggestions on financial literacy and better retirement planning.
• Ethical grifters.. er drifters .. in finance.
• Greek drama: "What that means is that the involvement of European governments has not helped Greece at all. ... The additional money provided by the European authorities has been used to pay off Greece’s creditors ..." Default & grexit should have been the first resort, not the last.
• MMT making dramatic inroads into the policy central plexus.
• Dawkins, Hunt, completely bonkers.
• Thanks, Warriors, for a golden moment.
• Economic graph of the week. We are far from full employment.

Sociomolecularbiology

Society affects gene expression and development, and genes contribute to social traits and behavior.

Is it any news that we are biological beings? That all aspects of our being, from toenails to theology, are biologically based? That was the premise of sociobiology, the science of the behavior and evolution of social organisms. Of which we are one. Unfortunately, the smell of eugenics was still too strong in the political atmosphere to allow thinking about how our genes affect our behavior, so that splash by E.O. Wilson died down and the science went on by other names.

That work has found, among other things, many connections between our psychology and our physiology. It should be no surprise that we are profoundly affected, to the point of suicide and other forms of death, by information that first arrives to our brains. Our immune systems are sensitive to social state, as are digestion, mood, activity, etc. Hypertension is one of many long-term consequences of stress, for example. This close relationship leads to to idea that we might be able to judge happiness by objective measures, rather than exclusively by self-report. And that would open up new vistas in morality, particularly morality vis-a-vis other species.

But it goes the other way as well, as our social capacities are based on biology. Psychological traits of great complexity can run in families, and scientists are only starting to gain glimpses of genetic alterations that cause such traits and their variation. The very ability to be flexible, to learn and adapt, is itself obviously of genetic origin. The question, typically, is how much people differ in significant social traits and how much we should care about that. We pride ourselves on meritocratic systems of education, business, and government that weed, select, and reward those who are gifted, who also align with and master the social system. But are we just rewarding something that the persons themselves had little to do with, just as criminals typically have little responsibility for their genetic or social deprivations, or actors for their looks? We may be, but reward we must, as a sociological necessity, if we want societies to benefit from good rather than bad talents.

Is it also an evolutionary necessity? Should those who succeed in the existing social system be rewarded with more reproduction? Typically we do not and should not have sufficient confidence in the universality or durability of our social system to make that case in its most brutal, eugenic sense. However, we should not be blind to the genetic underpinnings of social success and all its consequences. For example, the trend toward intellectual atheism that is so fervently touted in other areas of this blog fights a rate-dependent battle against the higher reproductive success as well as intellectual insularity of religious populations. What is the deconversion rate compared to the biological and ideological reproduction rate? Is religiosity a positive trait for humans? How much to we care about our evolutionary trajectory, a path we are on whether we are conscious of it or not?

Anyhow, as an example of the genetic implications of sociality, a recent paper described a gross increase in genetic complexity that accompanied the social evolution of bees. They found a measurable correlation between social complexity and gene regulatory complexity, which is a step in addressing the question of the interrelation of genes and behavior, in general.

Bees come in many social levels, from solitary to "eusocial", a term the E. O. Wilson made up to describe animals that are not  just polite and social as we and many other animals are, but behave as super-organisms, with genetically determined castes with division of labor, and restriction of reproduction to a small subset of those castes. The members of such a collective have no independent existence, die when the hive dies, and are seen by evolution as a group that has group-level traits that are extensively selected for.

Phylogenetic tree of the species considered. Solitary bees are marked in blue, simple sociality in green, more advanced sociality in yellow, and full-blown eusociality on red. 

The researchers basically lined up lot of genomes, from various levels of social organization among the bees, and looked especially at promoter regions, where the primary control over gene expression happens. They found a striking increase in complexity, which is to say number of binding sites for regulatory proteins, all over the genomes of the more social species. Indeed there was a 10-to-1 bias of genes that gained promoter binding sites over those that lost sites in the more social species. This is a dramatic effect, and makes sense in terms of the "mode-switches" required on a genetic level to create castes with separate developmental and behavioral traits out of one ancestral species.

Bias found among orthologous bee genes (that is, the same between each species) between those that gained promoter regulatory sites in more social species (blue) and those that lost them (red). The X axis is not genes, but the individual regulatory proteins whose DNA-binding sites were identified.

They also found, interestingly, that the particular genes involved in these increases were not the same in different social insect lineages. They took different genetic / evolutionary routes to eusociality in detail, even though they ended up with similar properties. So this is a kind of convergent evolution that shows that group selection and the sociality it selects for did not just arise multiple times in life's history out of some kind of molecular happenstance, but is an optimal ecological solution that attracts quite a bit of selection, as we can tell by the dominance of social species, both in the insect world and in our own.

Overlap among the various social lineages of which genes showed rapid, positive evolutionary selection. The result is that there is very little overlap, indicating that there are many ways to skin the social cat.

• Termites, same story is pending.
• Sociological reflections on WD Hamilton.
• Review of Churchland, on the brain and morality.
• More on body-mind interconnections.
• What the Y chromosome says about out of Africa models.
• Do voters understand economics, from today's ideological, corporate media?
• Global warming doesn't mean more plants, it means more desert.
• Breaking up big SDI banks would be "un-American".
• Notes on currency manipulation.
• Notes on division of labor, and why technology is probably more important to the organizational structure.
• NIH talk on depression- current research status and promising developments.