Saturday, January 30, 2016

Where do Morals Come From?

Objective, or subjective? And why are we having this argument?

What is good? What does it mean for something to be good? When you judge something to be good, do you look it up in a book? Many philosophers and especially theologians insist that what is good is not a personal judgement, or subjective, but is an objective state: a fact. Whether we properly recognize such facts is the main problem of humanity, thus they strain to train children in systems of "proper" objective morality.

It seems fair to say that most philosophers have promoted an objective view of morality, from Plato onwards. Religion has a great deal to do with this, as it posits an invisible world from which these objective facts flow, despite their unobservable and apparently non-objective nature. It also posits, in some versions, law-givers such as gods who are the identifiable source of objective good, whose commands we have but to follow to be and do good.

So a great deal of one's view of morality is going to depend on one's view of religion, and the plausibility of supernatural realms which somehow undergird reality and influence us, or at least the occasional prophet and teacher. One can also mention the social virtues of objective theories of morality, for if the ethical system is given and immutable, then the social system derived from it is likewise well-founded, and revolution becomes unthinkable.

On the other hand, the decline of religion and the rise of evolutionary theory to explain life and our own formation leads to drastically different theories of morality. It becomes a genetic/psychological mechanism for group sociality. And what we think of as its (our) flaws do not come from the interference of Satan, or insufficient attention to revealed scripture, but rather from a diversity of strategies that are cleanly and clearly modelled by game theory. Cheating may at first be rewarded, but then punished by policing, in order to attain a stable cooperating society with low, but inescapable, levels of defection and badness.

But even given an evolutionary theory, are morals subjective or objective? It is an interesting question. Optimal game theory strategies are not a matter of subjective choice- they just are, like mathematics (whether you regard mathematics as objective discovered systems or not). On the other hand, our personal judgements of value, while often agreeing with the findings of game theory, (hiring police, regulating vices, rewarding virtues), never originate there. They originate in our feelings about what is good, and what would be good for us in the future.

Prohibition is a classic example, when the US experimented with total abolition of alcohol. Alcohol was causing, and still causes, great harm, personally and societally. Yet it has positive moral and hedonistic functions as well, which turned out to be so strong that a vast criminal & popular underground developed to evade its prohibition. While unintended consequences destroyed Prohibition, the original policy (and moral stance) was born out of a great deal of pain, and the reasonable judgement that overall, we would be better off as a dry country. (Muslim countries are putatively dry today, for instance- for better or worse.) Would that the harms from global warming were as immediately apparent. The lesson is that morals are at base utilitarian, with respect to our perceived/estimated future happiness.

And game theory, while documenting strategies that evolution has time and again put into practice in our moral (or amoral) natures, does not say anything about what these strategies are actually aiming for. What is good to aim at comes, evolutionarily, from the axiomatic conditions & purposes of life: survival, flourishing, reproduction. That is why things that make us happy are so carefully engineered to also be good for us or for making more of us. The system has gone a little awry in our altered industrial & hypersocial environment, but the fact that there are 9 billion humans, swarming all over the earth, is testament to its success, at least in Darwinian terms, if not in moral terms. We are continually challenged to relearn and retrain ourselves, morally and otherwise, to accommodate this new world.

So does that mean that the evolutionary axioms are objectively good, and that our moral natures boil down to the "objective" goals of greed and power? Well, a funny thing happened along the way to biological complexity, which is that morality became intrinsically complicated, including quite a bit of cooperation, empathy, and other positive elements that allow societies to arise from individuals. Our moral natures are also implanted as intuitions and instincts, and whatever the underlying axioms might be, these natures function autonomously. That is our resource to judge and teach what is good, not a theoretical axiom of evolution, however explanatory that is in retrospect. Thus if we feel like adopting a foster child, in flagrant contravention of Darwinian selfishness, that is what we will do and judge good into the bargain.

This fundamental aspect of our moral instincts- the intuitive atoms of morality, as it were- means that whatever their origins, their expression is, to us, subjective. Moral judgement is not read from a book, or from the stars, but from our hearts. This applies to the objectivist argument as well. For when do people do (and think right) what others tell them, what game theory tells them, or what scripture tells them? Pretty much never. Divine command theory has never worked. While god may judge us in some morbid fantasy of the afterlife, we judge god the rest of the time, and the judgement has not always been positive (see the Book of Job). Scriptures, parents, and other cultural influences have their role, but it is to shape our instincts so that we become better judges, not to supplant them.

What remains is to explain why moral objectivity is so attractive and so common, including among philosophers. Firstly, it is simply operationally advantageous to decare that your judgements are not just an opinion, but objectively correct and factual. Talk about a successful power-play! States, upper classes, and religions have been playing this card from time immemorial, to great success. Nothing creates genocide quite as rapidly as a full-throated propaganda campaign about how execrable, subhuman, and depraved the target group is, given as fact. Or how divinely favored, deserving, and unquestionably righteous the perpetrating group is. The more objective the framing of each of these judgements is, the more powerful.

Secondly, like our cognitive illusion of a disembodied soul, we likewise have a moral illusion of being right for objective reasons. Our apparatus of feeling right about something, like a technical solution or math problem, extends to the rightness of moral judgements. Killing is simply wrong, right? Who could possibly doubt this? Yet what happens when killing becomes the highest calling and honor in a military situation? How objective was that after all? We then come up with caveats and legalistic rules / rationalizations that make great sense from an intuitive and utilitarian perspective. But we are simply exploring our feelings, not mapping an objective territory. Something that could be said about religion generally.

  • Calculations of cooperation & morality.
  • Democracy is fragile, is perishable, conflicts with capitalism, and needs help. Great talk by Yanis Varoufakis.
  • How about making corporations pay taxes in the form of stock?
  • Corporations as net savers ... a disaster for the future.
  • Wall Street OK with Hillary, not so much with Bernie.
  • The Taliban is still "negotiating".
  • On idealism. FOX news hammered away at its ideals for years and decades, and it moved the needle on the whole political system. Sanders is FOX for the other side- agenda for the 99%.
  • Screwing workers = "economic gains".
  • Apotheosis of Republican "small government" in Flint ... if it was not already clear during Katrina.
  • Zombie policy at the Fed.
  • Tax cuts are Keynesian policy, done regressively and inefficiently.
  • Fossil fuels were a unique economic multiplier of growth and living standards.
  • Megafaunal overkill hypothesis gets more support.
  • Bernie and (lack of) religion.
  • This week in the WSJ: Peggy Noonan finally sort of gets Bernie. But can't bring herself to say the word... Occupy, which is when the 99% realized the game was rigged.

Saturday, January 23, 2016

Where do Genes Come From?

How did DNA odds and ends become new genes in the human lineage?

Every new genome is like a jigsaw puzzle made from extremely modern, sometimes unrecognizable, art. Fitting the physical pieces together, out of millions of short DNA sequencing reads, is the relatively straightforward task and is done entirely by computers these days. Identifying genes encoded from that DNA, however, is a bit more difficult. This can be done partly by computers by looking for conserved sequences similar to genes or other genomic features known in other species. Yet there are always a bunch of left-over pieces- sequences, and possibly genes, that are novel in each species. A significant problem is finding such genes, which have no reliable structural signature, and may only become apparent with intensive functional studies based on what they do.

How do such genes arise from nothing, which is to say from the large amount of junk DNA lying about in the genome? Most genes arise by duplication and specialization, like the profusion of hundreds of olfactory receptor genes. But not all. A recent paper trolled through several mammalian genomes to look at the process of entirely new gene creation. The question is- how does random DNA get turned into a useful, transcribed, and translated gene?

The transcribed part is not so difficult, actually, since it has been found that most of the genome of any eukaryote is typically transcribed at a low rate. Not only genes, but all sorts of junk and useless DNA are transcribed into  messages that are quickly discarded. Apparently, the cost of low-level promiscuous RNA production is less that that of tightening down the controls to restrict transcription only to bona fide, gold-plated genes. And such noise may be an important evolutionary resource as well.

The authors gathered up lots of this transcribed RNA, sequenced it in bulk, and filtered for a minimum length (300 nt), from human, chimpanzee, and macaque, and mouse tissues. Running all this through a computer which condensed duplicate reads and compiled the distinct RNAs, they came up with about 100,000 candidate transcripts from about 35,000 candidate coding regions per species, substantially higher than the roughly 22,000 genes known to exist. They note that the noisy excess they find accounts for about 2% of transcriptional production, vs RNA production from known genes, so the extra transcription is low level, and pretty low cost. True gene regulation causes much higher rates of transcription, at least where and when expression is really needed.

The next step was to try to identify new, novel genes within this mess of noise. This involved discarding anything previously recognized as a gene, or related to genes in other species, by comparison to various sequence databases. This whittled the collection down to 634 in humans specifically, and 2,714 genes in humans, chimpanzees, or both (not shared with macaque or mouse). These are genes that seem to be regularly transcribed, at some length, but have not been previously recognized or annotated and are unique to their respective species. That is quite a lot, actually, for a few million years of evolution. What are they and where have they come from?

The researchers work quite hard to check whether these genes are expressed into proteins, and find evidence, for the human species, that only 21 seem to be translated. That does not mean that the others are not, but is a disappointing rate. They also find evidence for natural selection, in that the mutation rate these putative genes (though only the few that were validated above as being translated to protein) is lower than for junk DNA, indicating that it has adopted some kind of usefulness.

One theory for the origin of such novel genes is that they may come from existing gene regulatory regions that fire in both directions. Firing bidirectionally is quite common, but typically, only the downstream (sense) direction is conserved and useful, (i.e. the conserved gene), while the upstream sequences vary quickly through evolution and do not encode genes or anything else useful. In this study, they did not find any enrichment for close opposite-strand positioning of their de novo genes with existing genes, so concluded that conversion of such divergent transcripts to something useful was not a common mechanism of gene creation.

Occurrence of selected regulatory protein binding sites upstream of the putative genes. TSS denotes the transcription start site, and negative coordinates count the bases upstream on the X axis. Each regulator is noted at right, with a different color. While elevated, the frequencies hardly crack 1%, so again, this evidence suggests that only a small proportion of the collection of putative genes are actually regulated by these proteins.

What they did find was that certain DNA-binding protein regulator sites came up quite frequently upstream of the novel genes. These sites were for CREB, JUN, RFX, and M1/M2(TFIIB), rather common regulators. They also show that these sites are new just as the genes are, being typically absent from the same regions in the macaque genome, compared to the novel gene regions in chimpanzee and human. This leads to the theory that the random generation of such very short binding sites might have been the spark that originated these genes from unprepossessing DNA, after which they became more highly transcribed and attracted other regulator sites, some kind of function based on possible protein translation, and so forth into the Darwinian light.

Binding sites of the respective regulatory proteins, in logos format. This format indicates by the letter size how essential and selective a particular base is at that position of the protein binding site.
 
Unfortunately, none of their genes or proteins are more definitively assigned a function, and they dejectedly point out that the gene complements of organisms and lineages tend to be relatively stable, with lots of conserved genes, so that these novel (and putative) genes are rarely brought up to important/essential function, but rather keep being refreshed in a treadmill of molecular birth and death.

  • Another paper on the translation of promiscuous transcripts.
  • We need to fix the drug industry, with more public research, fewer patent protections, more negotiation.
  • Theories of low growth.
  • Median income in the US peaked back in 2000.
  • Are we responsible for Egypt?
  • Pakistan is a terrorist state.
  • What good did Hillary do in foreign policy? "In the case of Clinton there hasn’t been a major foreign policy decision in the Middle East she pushed for that didn’t end up being a disaster both at home and the countries she advocated meddling in."
  • Does realism mean that Hillary concedes all ideals in advance, or does idealism offer nothing but false hope because Republicans will never move? Which side is more astute?
  • David Bowie has a bit of fun, miming other singers.
  • Themes in evolution and economics.
  • Annals of stuttering while black ...

Saturday, January 16, 2016

Once Upon a Time, There Was (Not) a Ribosome ...

A new paper traces the history of the ribosome to its deepest origins.

The ribosome is one of the most precious relics we have. Not gilded or nicely framed, or even visible to the naked eye, but it shows, in its tiny structure, a past not a few hundred or thousand years ago as do our cultural relics, or many millions of years as do fossil skeletal relics, but a past over four billion years ago, around the very origin of life on Earth. While roughly three hundred quintillion quadrillion ribosomes exist in the biosphere, visualizing even one and understanding its workings has taken decades. 

Image of a complete ribosome structure. The large subunit RNA is in grey, the small subunit in turquise. Proteins stuck on the outside are purple and deep blue respectively, the 5S accessory RNA is towards the top in deep purple, and one tRNA is visible in the middle in orange. Note how exceedingly convoluted the RNA is.

Its convoluted RNA is both the contemporary site of protein synthesis in all cells, and a record of an extremely obscure past that preceeds many other key events in the history of cellular, or even pre-cellular, life, like the use of DNA for information storage, and the use of RNA as a temporary copy for that information. But how to read this record? That is a contentious question, which recent papers battle over. 

Frame from an animation that illustrates the structure and activity of the ribosome.
An animation from the ribosome wiki page illustrates its basic activities and structure. First, L-shaped tRNAs (dark blue, held by some helper enzymes in light blue) arrive at the cleft between the large subunit (green) and the small subunit (yellow), each bearing their single amino acid. Only the tRNA that matches the mRNA (black) codon held by the small ribosomal subunit gets to stay and lend its cargo to a growing protein chain, which emerges through a lengthy tunnel upwards and out the back of the large subunit. Eventually, since we are in this case making a secreted or membrane-bound protein, the emerging protein chain is captured by an adaptor which sends the whole ribosome over to the endoplasmic reticulum, (wavy black membrane molecules), where it docks to a channel that allows the new protein to be extruded right through the membrane as the rest of it is synthesized.

The main paper (by group A) provides a fascinating story of the origin of the ribosome, from the ground up, using a couple of structural rationales that allow them to deduce which portions of RNA structure come before or after others. The first rule is that existing RNA helices do not get disrupted by later additions. New additions tend to pop out orthogonally, as shown below, into new helices that are attached to the precursor, but don't disrupt its structure. Due to this phenomenon, the linear sequence of a ribosomal RNA is quite difficult to map onto to its three dimensional structure. Researchers tend to make startingly intricate diagrams to do so.

Growth of one small segment of ribosomal RNA, from bacteria (E. coli and P. furiosus) to eukaryotes (S. cerevisiae and H. sapiens). In blue is shown the bacterial core structure, to which in archaeal bacteria is added the green extension. Eukaryotes then added the orange and red extensions. Note how the extensions do not alter the preceding structures, but tack on either by lengthening existing helices or popping out orthogonally.

The second rule concerns interactions that later RNA segments can have with prior ones, the A-minor stabilization effect. While the RNA double helix is relatively stable, it can be further anchored by supportive hydrogen bonds from another base that swings into the minor groove from another helix. Examples are shown below:

One type of interaction where an adenosine from another helix (yellow) nestles close to a pre-existing duplex (blue), interacting with it by hydrogen bonds at several points and increasing the overall structural stability. This is one way to make something stable out of a lot of spaghetti-like RNA.

A more complex example of A-minor interactions that come from helix H-86 (yellow, green, brown) into the minor groove of helix H-75 (teal, grey). Note how some of the A bases (brown) are swung our of their own duplex to provide this interaction. Their partner bases have presumably found other interactions in the larger structure.

These rules make it conceivable to track one's way backward through the current enormous and complicated structure to its earlier precursors. The method can also be validated with a comparison between the eukaryotic and bacterial ribosomal RNAs, which clearly have an ancestral relationship that is reflected in just such structural expansions and new interactions, as shown above.

Another group (B) of researchers begs to differ, however, and published a disparaging paper about how these techniques are subjective and error-prone. This group appears to use more traditional phylogenetic methods, such as sequence comparisons, plus some kind of energy minimization, but claims that even using group A's stated methods, they would come to different conclusions. In particular, the crucial difference is whether the peptidyl transfer center (PTC), which is where protein synthesis from amino acids is actually carried out, was the first bit of the ribosome to exist (group A), or whether another part was primordial, a part that helps the ribosome rock between one tRNA and the next, an essential part of overall mechanism.

While I am no expert and have not delved into the details of each model, I would tentatively side with group A in this spat, and it is a very significant one. Their model of the ribsome beginning as a non-specific protein synthesizer makes sense in many ways. Their methods also make a more sense than sequence or structural stability methods used by group B that are fine for short-range phylogenetic work, but are notoriously off the mark when it comes to deep phylogenies, especially for RNA. group B also has tendecy to self-cite to a fault. On the other hand, whatever method one chooses, group B is right that it is quite a stretch, and perhaps ultimately subjective, how one gets to the very start of the process- the first few helices of RNA that began as the nucleus of the large ribosomal subunit. While an origin at the PTC is a very sensible proposal, even given the structural methods it is hardly incontestable.

Putting aside this conflict, the proposal from group A, which should be regarded as educated speculation, is an elegant model of ribosomal and translational origins. As shown above in the animation, the two ribosomal subunits work together but do very different things. The small subunit holds into the mRNA message, and thus the three-base codon end of each tRNA (technically, the anti-codon loop) which reads the message. The large subunit holds onto the other end of each tRNA, which is charged with an amino acid, catalyzes its polymerization into a growing protein chain, and conducts that chain out through a tunnel that keeps it from gumming up and folding prematurely. Each time translation completes, the two halves of the ribosome separate, indicating their functional and historical independence.

Thus the earliest stages of the proposed scheme have the large and small subunit evolving entirely independently. The primoridal large subunit's peptide transfer center is proposed to have been making uncoded, unspecific mini-proteins or peptides, possibly in a bid to create a cell surface, food storage, or some other function, even waste disposal. It goes without saying that all this assumes the existence of a pre-cellular RNA world, where RNAs have been functioning as enzymes and inheritance units, and perhaps other necessities, for some time. The proto-small subunit is in the simple business of binding to other RNAs, which is not an unlikely scenario.

The second step of the model is the key phase where the various partners come together. A nascent tRNA helix that had been carrying amino acids to the proto-large subunit for non-specific polymerization gains a helical extension that lets it mediate over to the proto-small subunit carrying short coding RNAs. Whether there were exchangeable, readable RNAs (what are now mRNAs) is doubtful at first, but just the ability to make a consistent protein product based on any code available, even the small subunit's own structural RNA, might have been an advantage. While this was happening, the exit tunnel from the peptide transfer center was also lengthening and tightening as the large subunit evolved, preventing fouling of the apparatus by newly made peptides.

Lastly, the small subunit adopted the switchable code mechanism, which made it a generic partner in the protein synthesis, presenting mRNA produced elsewhere. What the virtue of this might have been in an RNA world, without DNA, is a bit hard to understand, but assuming that such RNAs were specially marked, and not just anything floating around, this might have usefully expanded the protein repertoire. Then we are off in normal evoutionary directions, stabilizing the structure with added RNA and proteins, adding a multitude of factors that check-point the process with respect to starting and completing full protein chains, adding energy, allowing docking to membranes, increasing efficiency and fidelity, generating more mRNAs of ever greater complexity, installing DNA as the repository of mRNA codes, etc.

Interested readers are urged to read the original paper, which goes into much more detail about these steps and the various strucures involved. While speculative, this study opens very interesting vistas on the origin of life, on which the ribosome is such a valuable, if cryptic, window.


  • We are killing the golden pollinators.
  • High-end physics may have reached the end of the line.
  • Virtual reality to the rescue.
  • Corporations lie about climate change, and fund other liars.
  • A tiny bit of thanks to anti-trust enforcement.
  • Macro policy is empirically too tight.
  • Yes, the Fed made a mistake. "Given that, the US Federal Reserve’s decision to tighten monetary policy looks like an important blunder."
  • Stiglitz on the last year in global trade & policy.
  • Republicans on poverty- absurdist postmodernism.
  • Republicans blame others for their own terrible economic policy.
  • How the class war gets waged and won, Martin Feldstein edition.
  • A diagnosis of narcissism.
  • Deconstructing Rubio.
  • Kids for Trump, with Ameritude: warning, painful video.
  • Krugman on inequality.
  • A basic discussion of investment economics, savings, the zero bound, stagnation, and public spending.
  • Indeed, the drop in oil investment is causing a macro slowdown, even though the savings in oil prices should be causing prosperity and growth. "U.S. capital investment—which never really recovered from the housing bust—has been hit particularly hard by cutbacks in oil-field capital expenditures. That took 44 basis points off real U.S. output in the first quarter of 2015, 88 basis points in the second, and 33 basis points in the third."
  • And with oil prices cratered, there is no better or more important time for a carbon tax.
  • Time to let go of the Saudis. But does that just open the door for others to make the Middle East even worse?

Saturday, January 9, 2016

Concentrated Evil

The Litvinenko case, the polonium trail, and Putin's Russia.

A decade ago, a grisly case right out of the cold war erupted in Britain, when former KGB/FSB officer Alexander Litvinenko was poisoned and killed. On the day of his death, almost a month after the poisoning, it was finally established that he was poisoned with polonium, one of the more obscure radionuclides known to man, and one only manufactured by man, indeed manufactured only in Russia.

Within a matter of months, Martin Sixsmith produced the definitive account of this case (at least until the Russian government files are opened) in his book, The Litvinenko File. An interesting aspect of the case is the question whether the killers knew the nature of their poison. One has to conclude that they didn't, as they left trails all over the place. Polonium had been used before, in Russia, and, Sixsmith surmises, on Litvinenko in London a few weeks previously, though at an insufficient dose.

In some respects it is the perfect poison, killing slowly and remorselessly, with no antidote or treatment. It is colorless, odorless, and generally undetectable, even by airport security equipment tesing for radiation, which responds to beta and gamma rays. Polonium only produces alpha particles, which have the distinction of being immensely powerful, but also very heavy. They rip up a person's cells, but do not travel far, either in liquid or in air. Yet once Scotland Yard knew what to look for, it was child's play to trace the killer's trail in all its complexity and carelessness, through numerous hotels, restaurants, airplanes, and offices.

Primer on forms of radioactivity. The alpha particle is large, very energetic, and bumps into things readily, so it can't go very far but does a lot of damage.

The killers were former KGB/FSB agents, on very friendly terms with Litvinenko. Indeed, he never suspected them and the ruse to meet with him revolved around various business dealings they had together to gather business intelligence on Russian firms, seemingly the leading industry of Russian ex-agents.

But people do not leave so easily from the FSB. Its hold is both operational (terror-ational, one might say) and sentimental. Like the Marines, or any other high-intensity and high-stakes brotherhood, it forms very strong psychological, tribal bonds. Even when, as the FSB, it is infected by business interests, gangsterism, and rampant corruption. Litvinenko had truly burned his bridges, however. He found himself in London a hunted exile and turncoat, tarred far and wide by the Kremlin and his old associates as a traitor, his image used as target practice on the FSB shooting range. Nothing rankles quite like hearing someone tell you the truth about yourself.

His fall happened in two steps. First, Litvinenko had been asked by his FSB boss to knock off the leading oligarch of the day, Boris Berezovsky, the power behind the throne of Boris Yeltsin. The rationale for this may have been competing business interests, and/or disagreement with Beresovsky's dovish stance on the Chechen insurgency, or something else. In any case, it was an unwritten, verbal order. Litvinenko was shocked, and did a couple months of his own due diligence (so to speak) to see where this order came from and how the cards would fall if he carried it out. He decided to refuse, and not only that, went to Berezovsky to tell him about it. Not only that, but the two then hatched a press conference to tell the world about it, with the ostensible aim of pressuring Vladamir Putin, whom Berezovsky had just installed as head of the FSB, to root out these presumably rogue elements. As Berezovsky owned the leading national TV channel, the coverage was generous, to say the least.

But were they rogue elements? Here we get to the ever more concentrated precincts of evil. While Berezovsky was no shrinking violet, had mob connections of this own, and had knocked off his share of rivals in his climb to wealth & power, he was a progressive force in the Kremlin, tamping down the Chechen disaster, fighting corruption, and trying to bring the government into the modern era, at least in the telling of this book, which relies heavily on Berezovsky's own testimony. He thought Putin was sympatico, but it quickly became apparent that the press conference did not have its intended effect. Instead it made Putin and everyone under him livid with rage. Where Putin has taken Russia since that time, one can see for oneself. It is a despotic system with extensive media and political censorship. Dissidents, such as Anna Politkovskaya, get shot in uninvestigated, not to mention unsolved, murders. Putin has taken his bullying to global dimensions now with Ukraine and Syria, attempting to export his vision of despotic state terror- the "strong leadership" that seems to be such a turn-on to our own Donald Trump and other elements of the Republican right.

To make a long story short, Berezovsky continues to look on the bright side, recommends Putin to be Yeltsin's successor, and is promply destroyed by Putin, eventually finding a very comfortable exile and political asylum in London (if occasionally punctuated by assassination plots). Litvinenko is jailed several times by the FSB and put through various courts, one of which is less kangaroo-like than the others, and eventually flees the country with great difficulty. The FSB has turned the handful of colleagues who had joined him at the press conference, but can't quite turn Litvinenko himself- whether due to his romantic heroism and integrity, or his estimation that he would be sacrificed anyway, is not quite clear. Litvinenko continues to be Berezovky's flunky in London, and both continue a campaign of vilification and propaganda against Vladimir Putin. More in a long line of Russian dissidents and agitators operating in Western Europe, starting with Lenin himself. One particularly irritating truth Litvinenko turned up was that the FSB was responsible for the Moscow apartment bombings which killed 307 civilians and which they quickly pinned on the Chechens, leading directly to Putin's election and the renewed and vicious Chechen war.

There are many more twists to the plot, but that is the essence. Britain refused to render Berezovsky or Litvinenko extradited to Russia for their supposed crimes, and in return, after the murder and investigation, Russia refused to render the two killers to Britain either. Sixsmith does not surmise that Putin was directly responsible for ordering the killing, or even the official FSB, but rather that an atmosphere of permissiveness and impunity, combined with livid hatred and an implicit desire to do something sure to please the bosses, including Putin, resulted in this dangerous and cruel plot. The murderers were not current FSB officers, but very much part of the larger FSB family.

What is particularly appalling about all this is the lying and attitude towards decency and truth that is endemic to this story, to Russian culture generally, and to the KGB/FSB most centrally of all. When the case blew up, the Russians put out fanciful theory after extravagant lie. A private business deal blew up. Killed by Berezovsky. Killed by British intelligence. Litvinenko killed himself. The idea that anyone might be interested in the truth seems, to them, a joke. ["Russia Today's editors wrote that Epstein said there was "no substantial evidence against Lugovoy"] Putin tried various ploys to blame others and made nacissistic jokes about it being done on purpose by some Western element or agency to embarrass him at a high-profile summit. Putin and his cronies- at home, in the Ukraine, in Syria, and elsewhere- continue to wage information warfare, treating their people as sheep to be bludgeoned by propaganda, in a macho demonstration of who can screw with whom. But what can you expect from someone whose first toast when elected to the presidency was to ... Comrade Stalin?



Extra note. The chemistry of polonium 210 is interesting, as gleaned from a paper cited on the Wiki site. US scientists at the Hanford complex (now the most toxic superfund site in the US) published its method of production. Bismuth 209 metal is placed into a reactor, bombarding it with neutrons. This produces polonium atoms, which are removed by melting the bismuth and extracting (mixing) it with immiscible sodium hydroxide at 500 degrees C. Virtually all of the new polonium goes into the hydroxide liquid phase, after which the bismuth can be re-solidified and put right back into the reactor. On the one hand, it is a very elegant procedure, chemically. But obviously it is also susceptible to extremely dangerous accidents.



  • Russia is still lawless.
  • Which is apparently no deterrent for the Orthodox church to get in bed with the state again.
  • Marilynne Robinson on religion, fear, more fear. And why bad religion wins.
  • Why is any religion still about?
  • Religion is being peddled to unsuspecting children. As usual.
  • Fact, schmact. How postmodern Christianity saves us from polarization, distinctions, facts, reason, etc.
  • The changing and growing shape of hatred in the Middle East.
  • Can joyful tidying go too far? "To discard the stuff we’ve acquired is to murder the version of ourselves we envision using it."
  • China's cruel status quo policy on North Korea- keep them barefoot, so they don't turn in to South Korea.
  • Yanis Varoufakis on the European situation.
  • Real guns are OK. Fake guns, not so much.
  • What it is like to own a gun in Australia.

Saturday, January 2, 2016

Where do Thoughts Come Together?

Brain anatomy and the binding problem- some scanning attempts to localize concept integration.

Our minds can range incredibly widely, from shopping to integrated circuits, from sewing to theology. More specifically, our knowledge and memory spans vast scales and topics, as a typical video of micro to macro universe scales shows. How can we handle all this? How and where is it stored, and how it is put together again?

In philosophy this is, part, called the binding problem, which asks how features of perception and conception are put together into the larger concept of, say, a rose. Neuroscience has taken a low-key path of labelling our thought and memory patterns as "schemas", which are sort of cartoons of thought, shaping what new things we can fit into our minds and learn, which may be encoded into memories as engrams. Schemas are the structures which can be added together for larger conceptions, or drilled into and ramified to create new distinctions and greater detail. Operationally, schemas allow someone to learn something quickly instead of slowly, largely circumventing the hippocampus as a way-station for memory consolidation / storage. This is all reviewed in a fine paper from 2012.

A recent paper tried to locate where schema-tized thought gets recombined in the brain, and came up with the angular gyrus, which is a structure in the side of the brain, on the temporal-parietal border, known to function in memory, attention, and cognition. How successful they actually were in showing this is another story. They asked human volunteers to learn a very simple task- a sort of brain teaser pattern recognition task, which could give one of two results, depending on which mode or rule was applied. If one rule set was applied, the shapes seen would give one answer, and if the other was applied, another result. A day later, the subjects where shoved in a fMRI machine and tested for their recall of these rules, looking for where in their brains the activity of applying alternate frameworks or schemas to the problem happened. There were many tasks involved here:
  • viewing the screen
  • understanding the screen text that specifies which rule to apply (spatial or non-spatial)
  • interpreting the colors and locations of the imaged circles
  • deciding how to decode the problem
  • responding to the task by pressing a button with either index finger
  • providing an extra response judging the subject's own confidence, with another screen text and button press
  • having one's head in a scanner, with corresponding anxiety, boredom, discomfort, etc.

While these tasks were separated in time, it is still alot to disentangle from the whole-brain scanning which finds subtle differences of brain activity in different regions. Overall, they reported seeing activations in many brain areas. But when taking the difference between runs with different rules only, and on the second day when the subjects presumably had their schemas all set up and were tested on their recall and performance, one region stood out, the angular gyrus.
By way of introduction, they mention:
"The medial prefrontal cortex (MPFC) and hippocampus (HC), together with the parahippocampal cortex (PHC), posterior cingulate cortex (PCC), and angular gyrus (AG) have been identified as regions forming a network that is important for successful (episodic) memory retrieval."
Turning to their own results:
"To sum up, while the MPFC mainly showed increased neocortical coupling during spatial schema retrieval, the PCC was connected to an extensive network of regions during retrieval of both schema conditions. This network consistently involved MTL [medial temporal lobe], MPFC, PCC, and left AG and constitutes a set of brain regions that was previously reported to underlie successful memory retrieval."

At this point they tried to isolate the schema-specific parts of the process, making use of the ambiguous nature of their orginal testing, which had the same shapes/colors mean different things depending on the rules the subjects were taught. Thus their recall, while identical or at least very similar in the visual system, would be different wherever the rules were being applied to retrieve different learned memories. Their question was.. where do the visual processing and the rule application activations converge?

Significant difference clusters for various data comparisons. Green shows the locations of visual feature interpretation, deduced from the experimental runs where shapes were shown without further rule-based tasks. These maps were the same between the two days of experiments. Red shows the activation specific to interpreting the various rules by which the experimenters prompted subjects to interpret the same shape patterns in different ways. This activity only appeared on day two, consistent with the schema consolidation hypothesis. Blue shows the activity seen when a slightly altered set of shapes were presented on day two, with the request to interpret them by the same rules already learned. This activation is consistent with the pre-set schema being used to rapidly learn and interpret this new but similar information. The angular gyrus is where all these phenomena converge, suggesting a role in integrating them.

Answer: the angular gyrus. On the first (learning) day as well as the second (recall) day, the visual processing touched here, but the memory processing stream only activated this region on the second day, suggesting that this might be a place that specifically binds prior memories with current perceptions to yield higher-level understanding or cognition.

The angular gyrus is one of the more interesting places in the brain, associated with memory, attention, and out of body experiences. Some suggest, for instance, that it is the site where metaphors are recognized, and where concept integration takes place.
Wiki page:
"The fact that the angular gyrus is proportionately much larger in hominids than other primates, and its strategic location at the crossroads of areas specialized for processing touch, hearing and vision, leads Ramachandran to believe that it is critical both to conceptual metaphors and to cross-modal abstractions more generally. However, recent research challenges this theory."

In sum, I view the current work as somewhat sketchy. It is rather difficult to credit their extremely simple experimental protocol with isolating memory schemas specifically, or that the one-day delay created exactly the schema they thought they were looking at by brain scanning. Nevertheless, the field is in a stab-in-the-dark phase, trying to pick apart the incredibly intertwined and dynamic network of the brain, so each attempt, however flawed, is interesting and welcome.


  • Incidental citation on the posterior cingular cortex, which is also heavily involved here:
"One of the most striking physiological features of the PCC is its high rate of metabolism. In the human, cerebral blood flow and metabolic rate are ∼40% greater than average within the PCC and adjacent precuneus." 
"Therefore, the dorsal PCC is involved in detecting and responding to environmental events that may require a change in behaviour and that are not part of the current cognitive set. We envisage that dynamic interactions between the subdivisions of the PCC and other intrinsic connectivity networks are important for regulating the balance between internal and external attentional focus."
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