Saturday, November 26, 2016

Sleep Brain Waves Are Not Only Slow, But Circular

Memories are delicate physical structures in the brain, and get cleaned up / thrown out / enhanced during sleep- but how?

The mysteries of sleep are slowly becoming unraveled, and not a minute too soon, since we are both depriving ourselves of sleep as never before, and using such deprivation as an instrument of torture. Sleep seems essential for refreshing the brain in multiple ways- tidying in both physical and logical respects. A "glymphatic" system that operates at night, when the cellular volume of the brain shrinks slightly, to physically drive cleaning fluid through the brain to clear out garbage, has been one remarkable finding. Sleep is also when memory "consolidation" happens, which means reinforcing the more important ones, re-distributing or copying them from the hippocampus to the cortex, and deleting less important ones. Then there is dreaming, that link to the deep unconscious which sleep facilitates, with perhaps higher psychological functions.

A well-known feature of sleep is its brain waves, which are especially strong and slow. They appear to function as part of the memory consolidation system, but really, we know very little about them. There are two types of significant sleep waves- the sleep spindles that happen in stage 2 sleep, and the very slow delta waves that happen in the deepest level, stage 3.

A recent paper looked at the geometric pattern of the spindle waves, using epileptic patients who have had their skulls opened extensively for investigation, and allowed the researchers to apply a large field of electrodes to one hemisphere for this tangential study. It finds that instead of the whole brain pulsating with simultaneous spikes and troughs, there is a moving, circular pattern of activation, progressing from the lower temporal cortex, to the parietal cortex, on to the frontal cortex, and back to the start. This makes sense causally, in that there are always conduction delays from one place to another, so it is difficult to imagine one pacemaker (in this case the thalamus) running simultaneous electrical oscillations all over the brain.

Example of sleep spindle propagation. A shows one spindle sequence and the electrode locations, B shows the time course, and D shows averaged vector directions of propagation over all subject and readings, notably in a temporal -> parietal -> frontal direction.

The interesting thing is that this paper argues that this pattern also makes sense functionally, in that it helps consolidate connections between distant points much better than simultaneous activation would. I find their case hard to understand as well as doubtful, but it revolves around the timing issues of long-term potentiation (LTP) and depression (LTD) among neurons.

Spike timing-dependent plasticity is the name for a broad theory of how neuronal connections are managed. If two neurons are connected to each other in the usual fashion, with dendrites from A exciting the axonal network of B, the relative timing of firing of A and B has great influence on whether their connection (synapse) is strengthened for future events, or weakened. If A fires ~10 ms (milliseconds) before B, then the synapse is strengthened. This makes obvious functional sense, implying that A *caused or helped cause B to fire, a successful event that would presumably be good to enshrine in a more permanent connection. Conversely, if A fires anywhere from 10 to 50 ms after B fires, then the logic is reversed, and the physical effect is also reversed: the synaptic connection is made weaker.

Proposed theory, whereby synchronized spindles (top) would result in troughs falling on the evoked action potentials of the original targets (EPSP), causing depression / weakening of all connections. But in B, which resembles the actual state of affairs, successive spindles, when hitting the target neurons, would be at peak value, (assuming that targets of the original neurons and the spindle wave are traveling in the same direction), and thus foster strengthening of all connections.

Given that the sleep spindle waves happen at ~11-15 Hz, or about 80 ms intervals, the authors argue that if they just propagated point to point from the thalamic pacemaker out to points in the cortex, they would arrive at various times, but their effect on secondary targets- the targets of the immediately driven cells, whose firing is delayed by, say, 20 ms- would be to cause chronic long-term depression of those target connections, since the next spindle peak falls roughly into the zone of LTD.

On the other hand, if the spindle waves propagate in a wave-front fashion through the cortex, then (B in figure) the target cells would be hit more or less simultaneously by the evoked firing from the A cells excited by the spindle wave, and then the spindle wave itself as it progressed to hit them as it moved through the cortex.

The researchers go on to find, beyond from the rotational progress of the sleep spindles, that these 11-15 Hz waves entrain gamma waves as well, and they imply that over 2.5 hours of sleep which they observed in one subject, these gamma waves strengthened in a way that supports their hypothesis that the sleep spindles are progressively reinforcing neural connections, including memories.

I find this work very hard to take seriously, though it comes from a very serious lab. If the neural network is 3-dimensional and extensive across the cortex, there is no way to predict the transmission time (estimated above at 20 ms) from one neuron to the next. Nor does the orientation of each particular sub-network necessarily have anything to do with the circular rotation scheme seen in the electrical recordings. That geometric data is much more easily explained as a mechanistic consequence, even side-effect, of not being able to activate all areas of the brain at the same time. Lastly, the idea that sleep spindles, or any process, indiscriminately strengthen all neural connections seems unhelpful, since the point of the "consolidation" process is both to discard old and minor memories / connections as well as to enhance more significant ones.

Graphs of spindle wave phase, taken 5.6 minutes apart in one subject. This suggests to the authors that coherence is progressively enhanced through the stage 2 sleep process, presumable due to positive neural connections being strengthened. Related videos and data are at the publication site.

At the same time, I do not have a counter-theory about how these waves accomplish their function, which certainly is connected with memory management. (Please comment if you have greater insight into these processes or this paper!) So we have a great deal to learn. It is a fascinating area of research, trying to build a unified theory of how the anatomical connections in the brain, and the electrical functions including oscillations of various periods, function to make our minds function, and refresh.

Saturday, November 19, 2016

Fighting the Civil War, Over And Over Again

Reflections on the election.

There- we have had our election, and the rednecks (and orange haired) won. Why the bitterness? Why the perpetual lack of understanding of what the other side values and thinks? Why the deep differences of values in the first place? Coalitions may have always been fluid in the US, but the divides between North and South, and between rural and urban, have been relatively durable. There are differences of interest, of upbringing, of tone, and education reflected in this geographic segregation. It is a typical path for any promising young person to leave the country, go to college, and make a new life in the urban, elite centers, forsaking and perhaps even repudiating the culture she or he sprang from.

On top of that rural/urban, or heartland/bicoastal split is the North-South split, which is more cultural in origin: the culture of slavery, to be specific. The many poisons of slavery- its devaluing of humans and casual terrorism, its terror of disruption of a hierarchical social order, its lazy economics of privilege and stasis, its pathetic, patriarchal, and false romances of militarism, chivalry, and the lost cause, seeped so deeply that we continue to fight the Civil War, over and over and over again.

Many cultures have drawn durable victimization narratives from traumatic loss, such as the Muslim Shia's defeat in the battle of Karbala in 680, or the Serb defeat in the battle of Kosovo in 1389, or the Jewish episodes of slavery in Egypt, exile in Babylonia, and final loss of Jerusalem. Such narratives tend to be pathetic, racist, romantic, unrealistic, and for all those reasons, highly effective.

It is evident that politics is conducted in narratives, not policy. Hillary may have had her 23 point plans, and they surely would have served Trump's voters better than Trump's own policies, which as far as we can tell, consist of giving lots of money to rich people like himself, (no wonder he isn't taking the salary!). But the media decided that the email controversy was a better hook with which to explore her personal narratives of secretiveness and control. How they squared this with a bemused attitude towards Donald Trump, who was actually in court for fraud, among a countless other number of obvious scandals, is hard to understand. The media clearly did not understand the nature of Trump's methods or message. This, after two decades of FOX news.

In the absence of narratives on the scale of world wars, which did so much to unify the country in the 20th century, the US political system is structured in a particularly bad way for a politics of emotional narratives. Our two-party, winner-take all system amplifies very small differences into momentous swings in power, focuses campaigns on only a few swing states and small populations, and sets the two parties as a duopoly that excludes new ideas / narratives and rheifies a binary tribal split in the electorate.

So, the perpetually disgruntled South makes a reliable partner in the modern Republican party for the CEO and financial class, united only in their fear of progress- social or regulatory, respectively- towards a modern state that would foster a fairer, more equitable nation by ameliorating the ravages and inequities of the free market, and the inherited social and economic disabilities that keep the class and racial structure so entrenched.

Barack Obama almost sank his first presidential campaign when he was recorded as saying that the rural folks cling to their guns and religion. It was a classic gaffe- as impolitic as it was true. The divide is real. Is the distain deserved? As a liberal atheist in favor of gun control, my natural inclination is yes, it is deserved. This election proves it yet again, that a tasteless, racist, and shallow blowhard could propose a set of policies almost totally at odds with the interests of his voters, not to mention the country and the world, yet win on narratives of hate and revanchism.

Is the distain from the other side deserved- that the US has become a feckless, feminized country of politically correct pansies? Are the elites incompetent? Yes, that has its truth as well. Just looking at the state of public management, where public employees get over-generous pay and pensions, as though the last forty years had never happened, yet accomplish so little, which is apparent as sclerotic breakdowns of public institutions and infrastructure, and the impossibility (or astronomical expense) of building anything new. It is an easy, perhaps lazy critique, but our infrastructure is symptomatic of a nation whose public policy is not keeping up with public needs, or an optimistic, future- and growth-oriented outlook.

All of which does not justify this step into a political abyss, however. Does progress in reason-, law- and process-based public policy necessarily end up in gridlock, as an excess of process and attention to every possible stakeholder, including corrupt interests and non-human species, extends decision times to infinity? No, it is the political gridlock that is far more damaging, since where there is a coherent will, there is a way. With the (white) South firmly in its pocket due to a hermetic social and media atmosphere, and supporting regressive policies in general, the Republican party has now spent decades as the party of shameless, regressive, and especially, destructive politics. It is an inheritance from Newt Gingrich, and from Roger Ailes at FOX. The refusal to consider Obama's last Supreme Court nominee was the epitome of partisan depravity. The Bengazi investigations were a witch hunt in the purest sense, and have now at long last paid their final dividend.

It is worth noting that during and after the Civil War, the Republican party (what a different party, then!) led a surge of progressive public policy, from land grant colleges and banking to railroads. The nation was suddenly unshackled from the political weight of the South, and though the necessities of war had their dramatic effects, the philosophy of the Republican (prior Whig) party were also an important ingredient. One wonders what might have happened had the South succeeded in its secession. We might have become a spectrum of Americas from the progressive and industrial Canada and Union nations to the more feudalistic Confederacy and Mexican nations.

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Saturday, November 12, 2016

The Lineage History of India

India is a complex mixture of humanity, but genetics can tease out the main themes.

Humans have been migrating all over the place for thousands of years, yet there are still distinct geographic differences in human phenotypes, and now visible with molecular technology, genotypes. This allows us to look back in time to infer large migrations that happened long before the historical periods, like late and post-Roman times where many migrations in and around Europe are documented, if scantily.

Out of Africa. A process that started about 70,000 years ago.

India is a particularly interesting subject for this kind of analysis, because it has been a crossroads for tens of thousands of years, first for the migration out of Africa that led to the peopling of Australia, and then other influxes from all directions, most recently from the north, with the Indo-Europeans and then the Arab invasion. Secondly, India has also had an unusual degree of stasis since these migrations, embodied in its caste system, which may have frozen some of these genetic signals in static communities.

A recent paper continues a body of work that looks at these issues, and concludes that there are four different population signatures detectable in the mainland Indian population, and that the caste system has been in genetic terms a relatively recent development- in the last thousand years or so.

They sample hundreds of thousands of variable genetic markers (snps) from 367 people of 18 recognized ethnic groups of India. This data is put through a traditional statistical analysis of related-ness to come up with 69 sub-populations, and four principal components: those differences in the data that most efficiently explain the most differentiation into the least number of large groups. The main graph is below:

The green elipse identifies Indo-European populations, such as Brahmins from Gujarat and West Bengal, Khatri, and Maratha. The red elipse identifies Dravidian-speaking tribal populations. The turquise elipse identifies South-East Asian-influenced populations, such as Korwa, Birhor and Gond which are a Dravidian mixture. Lastly, the blue elipse identifies Tibeto-Burman originating populations such as Jamatia, Tripuri, and Manipuri, living in the northeast.

None of this is very surprising, given the clear ethnic diversity and the local neighborhood of India. More interesting are their reflections of the stability of these groups. There is very low mixture, though the sampling was modest, with an average of 20 people per ethnic group and 5 per inferred sub-population. The hypothesis, drawn from literary and historical sources, is that there was originally substantial mixing between the North and South Indian populations, but that this ceased with the gradual establishment of the caste system. The researchers use haplotypes to track how much mixture there has been, and how long it has been going on, or been in abeyance. (Though there are other views.)
"We estimated that all upper-caste populations, except MPB from Northeast India, started to practice endogamy about 70 generations ago. The length distributions of the AAA blocks and the ASI blocks within any one of these populations (GBR, WBR, IYR) were very similar. The most parsimonious explanation of this is that the practice of gene flow between ancestries in India came to an abrupt end about 1,575 y ago (assuming 22.5 y to a generation). This time estimate belongs to the latter half of the period when the Gupta emperors ruled large tracts of India (Gupta Empire, 319–550 CE)."

Thus the golden age of India, which happened during this time, seems to correspond with a hardening of the social order. What effect the latter had on the former, or the decline of the former, is perhaps food for thought.

Saturday, November 5, 2016

Time is a Great Mystery, But the Self is an Even Greater One

What is time? And can a physics professor harness it for spiritual speculation? A review of Richard Muller's book about the nature of time, entitled "Now".

We are all critics and all cranks. Some just get a wider audience. Richard Muller, distinguished professor of physics at Berkeley, recounts a good deal of his pathbreaking research in his latest book, as well as roles in founding and inspiring the work of others, some of which / whom went on to win Nobel prizes. Along the way, he provides a high level and very pleasant introduction to the highlights of twentieth century physics. But he can't seem to resist going down some very personal tangents as well, like free will, Richard Dawkins, and a profession of faith.

His views on time are obviously the theme of the book, and the tease as well. He keeps the meat of the matter till the last few pages. To put it most simply, he dismisses the common idea that the progression of time in the universe is connected to the increase of entropy that is expressed in the second law of thermodynamics. Instead, he proposes that time, having been created with the advent of the big bang, as was space itself, represents the continual expansion of that four-dimensional construct that is our universe. Thus we all exist in a "now" that is the bleeding edge of cosmic 4-D expansion, just as space itself is continually expanding. Looking outward at anything, however close or far, is always looking back in time into areas of the universe that have already happened. And just as there is no center or edge to the expansion of space, there is also no edge to the progression of time- all points in space progress through "now", leaving aside the relativistic oddities of some "nows" getting slowed down by relative spatial or gravitational acceleration.

I find this idea very attractive. It is far more sensible than the entropy idea, and probably the best thing going, until we gain a deeper understanding of the mysteries of cosmic origins, the structure of space, and of quantum physics in particular. The latter still resists both unification with other aspects of physics and, frankly, common sense. Yet this edge-of-the-big-bang is far from a theory- it is just a hunch, with minimal predictions, the main one of which is that time might be accelerating along with the accelerating expansion of the universe, if space and time happen to be linked in that way.

However, when it comes to amateur philosophy, the book makes a good deal less sense. Muller spends an effective few chapters on the limits of science and philosophical physicalism- the great deal that we don't know, and perhaps can't know. The nature of the origin of the big bang, given that it originated both the time and space that we are familiar with, is surely one. The various mysteries of quantum physics are others. But some of his other suggested limits edge into very questionable territory.

Combined with other known limits, like the indeterminacy of quantum mechanics, and Gödel's theorems of incompleteness, we end up with large areas of reality that are essentially unknowable, at least in a scientific sense. One of these is the future. Because of quantum indeterminacy, as well as chaos theory, physics turns out to not be deterministic as the classical physicists had believed since the time of Newton. This provides, in Muller's eyes, openings for things like qualia, free will and souls.

There is a long discussion of the "what it is like to see red" question, featuring Mary, who is raised in a grey world but knows didactically everything there is to know about color vision. When she first sees color as a mature adult, does she learn anything new? Muller's answer is yes, and he takes that as an intrinsic limit on human knowledge.

The whole qualia question, which is what the "seeing red" exercise is about, seems to me to say much less than Muller and others think. He believes that it points to something beyond our physical constitution that characterizes us- a soul. For the same reason, he claims that he would not want to be transported à la Star Trek, for even if his physical body were reconstituted down to the smallest detail, he might not end up being "himself". Again, a non-material soul lies at the bottom of this, which he explicitly claims, even though he is doubtful whether it survives death:
"When I see blue, do you see blue? That is not a scientific question. Does that make it invalid? This issue is related to the difference between the brain and the mind. Is there something beyond the brain, something behind the circuitry, something more than the physical, mechanical set of atoms, something that can not only see, but knows what a color looks like? I can't prove to you that such knowledge exists. I can only attempt to pursuade you."

To me, there seems to be no reason whatsoever to propose anything beyond the physical mechanism to account for all this. We can grant that subjective experience is utterly different from didactic knowledge. That is intrinsic to beings with consciousness and experiences, and is covered by a difference of perspective. I, looking into your brain, will never have the experiences that you are having subjectively via that brain. It is like expecting someone reading the computer code behind World of Warcraft to experience gaining powers and making alliances. That supposition is a simple, but profound, category error.

Should we care about so much (subjective) knowledge and experience going up in smoke every second and every lifetime? Surely it is a tragedy, which we try to remedy by sharing subjectivity via conversation, writing, the arts, and other ways. But the fact that, being perspectivally enclosed, it is beyond science (certainly with current technologies) means neither that it is an illusion, nor that its reality is somehow "beyond the physical". Its complete dependence on the physical is clear from the biology of stroke, dementia, development, mental time delays, and innumerable other phenomena.

The wonderfulness of its construction, and its tendency to lull us into flights of subjective omnipotence or is no excuse for not taking the biology seriously. This is true even if one appreciates that physics (let alone biology) can not explain, or even represent, everything. There are many things that they can still properly explain, and many things that they put very tight boundaries on even if complete explanations are not yet available.

But there is more...
"There is a spiritual world separate from the real world.  Wave functions from the two worlds are entangled, but since the spiritual world is not amenable to physical measurement, the entanglement can't be detected. Spirit can affect physical behavior- I can choose to build or smash a teacup; I can choose to make war or seek peace- through what I call free will." 
"It is remarkable how often you run into the phrase "Science says..." to support an idea that actually has no foundation in science. It is often physicalism in disguise "Science says we have no free will." Nonsense. That statemen is inspired by physics, but it has no justification in physics. We can't predict when an atom will disintegrate, and the laws of physics, as they currently exist, say that this failure is fundamental. If we can't predict such a simple physical phenomenon, then how can we imagine that someday we will be able to show that human behavior is completely deterministic?"

The weakest aspect of the book is its numerous discussions of free will. Muller seems to have  a particularly unexamined notion of it. He cites quantum indeterminacy as providing an opening for free will, since it means that the universe is not determined. But how does randomness and indeterminate-ness help the cause? How does our ability to make choices and affect the flow of events relate to reality's constitutive randomness? An inability to predict or compute the future does not imply that our physical mechanism can not and does not make choices, including meaningful ones. For example, computers make choices all the time, and increasingly sophisticated, random-event influenced, and, to us, unintelligible ones.

If everything were determined, that would not even affect our sensation of free will. That is the Greek tragedy, where key events are pre-ordained, but still the actors feel themselves to be acting meaningfully, until the end when the hand of fate is revealed to all. Even such slim (and fictional) concessions to fate are out of the question when the future is truly unknown due to all the physical principles Muller cites.

But determined or not, it is not clear what this free will really is. In the worst-case scenario, everything is determined, and we can also predict the future- a future that we can do nothing to change, because everything up to that point as been determined as well. But how would that really feel? I think it would still feel as though we had free will, since we would have reasons for doing what we are going to do, which feel compelling, leading to exactly the actions that we are taking, predicted or not.

I think the secret is that free will is, particularly here in Muller's book, but also more generally, a code word for "soul". It is another, and even more vague, way to make claims for a non-physical entity that lies behind our most important actions and deepest feelings. The intuition is that mere mechanism can not conjure the sovereignity of choice, and is somehow separate from the all-important "I", whose immateriality and freedom are so intutively self-evident.
"Am I simply a wood chip caught in a complicated machine, bouncing around as the gears turn, confusing my rapid action with my importance?"

Why an eminent physicist feels the need to posit special, extra-scientific hypotheses around the issue of consciousness is truly unfortunate. His inability to explain the big bang does not prompt similar flights of intuition unbound, yet his lack of knowledge about biology and inability to bridge the far more modest conceptual gap between subjective consciousness and what we know scientifically (exemplified by the qualia/Mary exercise) does. It is ironic that intuition is so particularly susceptible to error and inflation when trying to analyze itself.

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