Saturday, February 18, 2017

Memories ... In the Corners of My Mind

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

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

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

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

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

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

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

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

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


  • Plutocrats in charge of the Treasury, after a crisis they caused.
  • Another institution could be permanently damaged.
  • Treason is only if the other party does it.
  • China is the story of our time.
  • Review of Too Big to Fail.
  • We do not need to settle for depression economics.
  • Remember the EPA!
  • Sanity is getting the upper hand, and the nuts won't have it.
  • What the Islamic & Persian world did for math.

Saturday, February 11, 2017

Truth is the First Casualty of Fascism

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

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

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

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

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

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

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

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

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

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



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

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

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

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

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


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

Saturday, February 4, 2017

Brain: Is Size Everything?

Properties other than size also make human brains different.

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

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

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

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

But bigger is better, among our closer relatives.

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

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

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

Two neurons meet... The intensely spiking pyramidal neuron (red) which firs first, and the post-synaptic, receiving cell  (blue) are portrayed (C) as they were stained and micrographed in the tissue. The layers of the cortical sheet are given roman numerals. Synapses between them are numbered in D. Panel B shows an averaged stimulus -> response graph of the two cells, showing that the receiving basket cell (bc) quite frequently fires (74% of the time) when the sending cell fires, despite their very sparse synapses. The lower graph (26%) shows the other events, when pyramidal cell firing evokes only a grudging sigh in the receiving cell. In other species, this is all one would see in such single-cell stimulus / encounters. Panel A shows that the receiving cell not only fires once, but several times per upstream spike.
"Although the ratio of triggering poly- versus monosynaptic postsynaptic potentials was 0.01 in the rat and 1.73 in the human in our hands, it should be emphasized that the human patients were treated differently during anesthesia and surgery, and the excitability of human neurons might be different in the external solution also used for rat experiments."
"However, the human neocortical neurons also exhibit specializations only reported in our species. One such feature is the capacity of excitatory principal cells to elicit firing in local inhibitory interneurons with a single action potential via very strong excitatory synapses. It has been suggested that this feature has specifically evolved to enhance coordinated firing of neuronal ensembles in higher brain functions."

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


  • LSD is one hell of a drug.
  • How now, Afghanistan?
  • We are in fascist territory.
  • You knew it would be this way. Infrastructure spending turns out to be big tax cut for the rich.
  • Bully tries to offend entire world.
  • A beard of transformation.
  • A war may be brewing...
  • Not only does California have a public pension crisis, but also a pension management crisis.
  • What really happened to Lehman?
  • How did we get to this partisan hellscape?
  • But truth remains a value to some.