Saturday, July 25, 2015

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.

  • Ten feet of sea level rise? What shall we do?
  • Hilary Hahn, on her violinistic upbringing.
  • Samuelson back in the 50's: ... Fiscal policy, meaning changes in taxes and government spending, were the way to deal with the business cycle. The Bureau of the Budget could manage the economy to good effect.  He did not mention the Federal Reserve Board.
  • Krugman: "My guess is that euro exit will still prove necessary."
  • Policing in South Carolina. No cause for stop, no cause for arrest, no cause for death.
  • And what is a "lawful order"?
  • A carbon tax is needed: we can never rely on supplies becoming scarce. Or on new tech being cheaper than coal.
  • A transaction tax is finally on the table.
  • Trains are five to ten fold less carbon-emitting than planes.

Saturday, July 18, 2015

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.

  • Who should pay for recessions? The FIRE sector, obviously.
  • Pinkovskiy on Piketty. Another person seemingly fooled by the highly unusual nature of the 20th century, and the presumption of high growth as "normal".
  • Jeb! says workers just need to be screwed harder.
  • Has ISIS done what the US could not? Bring the Taliban begging?
  • GOP gearing up for WW3.
  • Lynyrd Skynyrd and all that ... the psychology of defeat and honor.
  • One fiscal union works, the other one does not.
  • A little nostalgia for early days of molecular biology.
  • Bill Mitchell: South Korea has its economic head screwed on right.

Saturday, July 11, 2015

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:

Saturday, July 4, 2015

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.