Which Came First, Sex or Death?

Bodies to do the dirty work: on the origin of germ cells, somatic cells, and bodies.

Imagine you are a termite colony. The vast majority of termites can not reproduce- they are disposable workers for the good of the whole, while the alates, or winged reproductive caste, are set aside to reproduce new colonies. Your body works the same way ... virtually all its cells are on a one-way trip to death, with only the germ cells, and a vanishingly small proportion of those, giving rise to descendents in a bid for immortality.

Once upon a time, all cells were immortal. That is to say, they had no intrinsic lifespan, and could live as well as reproduce endlessly. Why give that up? A recent paper discusses the ins and outs of germ-somatic cell and tissue separation which happened early in multicellular animal evolution.

There are several theories about why this division of labor would take place. One is simple practicality- that not all cells are in a position to reproduce. Would you like your bone cells to send out new embryos to form babies? Such a democratic system would be a big mess, though plants approach it with their capacity to generate reproductive structures from any active meristem. And anyhow, every cell shares the same genome, so it shouldn't make that much difference which one in a body makes the germ cells, right?

Other theories focus on what a germ tissue can be optimized for, such as going through relatively few rounds of replication, thus minimizing mutation, or being fed by other cells, so that they do not have to do their own metabolism, which is mutagenic, again reducing the rate of mutation. While female germ cells often adhere to the former theory, male germ cells tend not to, being produced in vast profusion, requiring high rates of replication. The authors of a recent paper focus on the latter hypothesis, called the "dirty work" hypothesis; that bodies are devised to do all the dirty work of life, while the germ cells are protected from dangers of many sorts, especially from metabolic damage.

Metabolism is a messy process, spewing free radicals and other damaging chemicals about the cell. Both the production of carbohydrates using solar energy to split water molecules, and the process of using carbohydrates by splitting oxygen and returning CO2 to the air are very high-energy processes, as one can see any time something burns. Metabolic enzymology controls them, but at some point, free radicals have to be made, high-energy electrons need to be shot from one place to another, and there is no perfectly safe way to do this. The mitochondrion is an attempt to keep the danger contained in a membrane-enclosed space, but that is not completely effective either.

The paper is computational one, modelling various ecological strategies connected with this hypothesis.

"We tested the dirty work hypothesis using digital evolution, an approach where digital cells are self-replicating computer programs that evolve in an open-ended fashion and are theoretically capable of performing any computational function. For this study, we consider a world of 400 multicellular organisms (“multicells”) that compete for space, where the rate of reproduction of each multicell depends on the number and rate of computational functions being executed by constituent cells."

Basically, if you impose a mutagenic cost of doing the basic processes of life- gathering food, digesting it, metabolizing it, etc., then it stands to reason that if germ cells are spared these risks in a multicellular colony or organism, they will be able to spread their genomes with less mutagenic risk to future generations. Of course, some mutations are needed. A minimal level is required for adaptation and evolution, and some organisms even ramp up their rates of mutation when under stress, in a somewhat desperate bid for success. But on the whole, evolution has put vast resources and endless optimization into the project of high-fidelity reproduction, because as any Darwinian knows, most mutations are harmful.

So it should not be surprising that multicellular organisms rapidly took advantage of this opportunity to increase fidelity by segregating germ cells away from everything else, and building bodies to do all the so-called dirty work, including sex and thinking- which is, incidentally, very metabolically expensive.

Segregation of germ and non-germ cells, in a virtual evolution program, plotted on the X-axis, vs bands of mutagenicity going downwards from  zero (top) to high levels (bottom). 

The experimenters set various levels of mutagenicity to their virtual life tasks, and found that at intermediate levels, their virtual life forms would segregate non-reproductive cells into a soma with pretty much complete probability. At very low mutagenisis levels, there was no advantage to such segregation, and it did not evolve. At very high levels of mutagenicity, specialization of some cells (i.e. the body) to deal with mutagenic activities was essentially lethal, so such environments were avoided entirely rather than adapted to. Their simulations are clever, if very schematic. But they get the simple point across, that the origin of divided somatic / germ bodies is easily understood as a natural consequence of multicellular evolution.

So what about sex? Many bacteria have some form of sex, exchanging bits of their DNA, despite being single-celled and having only one genome to play with. Therefore sex developed long before death did, in the sense of the programmed death of a somatic body after reproduction, as is common among all animals and plants. No cell lives forever, but those that reproduce by binary division have no clear point of death. In contrast, our bodies, specialized for the complex operations of getting a living in a hostile world up to the point when a new generation can be created and nurtured out of the germ cells, have a very definite, genetically programmed (if only by default) endpoint. The way life spans vary between species of animals, but much less within them, suggests strongly that life span is not an accident, but is part of the developmental program, making way for the new generation on an optimized schedule, for evolutionary, and even cultural, rejuvenation.

As one might imagine, these ideas are related to the selfish gene hypothesis, put forth by George Williams and popularized by Richard Dawkins. Which is that bodies are the robotic (and disposable) entities devised by genes for their propagation. That is a strongly skewed perspective, however, making of the gene an almost conscious, greedy, self-sufficient, anthropomorphised totem, which is more than a little fanciful. Rather, organisms are complex communities with delegated and divided functions, one of which is to keep safe the genetic code that the whole community relies on for high-fidelity propagation. Even if the body and its mind can be viewed as disposable cat's paws for that code, they are the only part of the community that can be cognitively selfish; the gene is just a large molecule.

"The same information-work tradeoff may also have motivated a switch from RNA to DNA as the molecule of heredity. According to the RNA world hypothesis, RNA initially served as both a carrier of genetic material and a catalyst for metabolic work. However, RNA instability may have motivated a shift to DNA genomes and catalytic proteins. This is a type of molecular division of labor, ensuring both high fidelity transmission of hereditary information and the execution of critical chemical work."

• Reagan, evangelicals, and the Klan.
• Enlightenment? Not so fast!
• Just how powerful is their god, anyhow?
• Real climate action would cost only 0.2% of GDP. This is very significant news.
• Kids these days ... can not deal with the 70's.
• Sustainable economics- why GDP is not the right measure, or the right worry.
• Secrecy, corruption and fraud in private equity companies. We are shocked!
• "Yet another example of lazy, both-sides-do-it journalism."
• Otters playing the organ? What next?
• Whose side is Mary Jo White on? Shame on the SEC, as usual.
• Why incompetent men dominate in management ... we are suckers for narcissism and overconfidence.
• "Bank of America runs its business through more than 300 offshore tax-haven subsidiaries. It reported $17.2 billion in accumulated offshore profits in 2012. It would owe $4.3 billion in US taxes if these funds were brought back to the US."

The Naked One: Jainism

The sramana movements of ancient India- Buddhism, Yoga, and Jainism.

What is the best religion? One's own, doubtless. But supposing that you had to choose a different one or had none to start with, which ones do the best job of promoting human flourishing and peace, in some general and long-term sense? Most of the prime candidates (i.e. the least blood-soaked, the most philosophical) come from the East. Which is sort of a bitter pill for a Westerner to swallow. But perhaps our tendency to crazy religion bred its opposite as well- the desire to throw its chains off entirely. Be that as it may, it seems fairly obvious that peacefulness and calm are particular specialties of Eastern practices like Taoism, Confucianism, and Buddhism. And the philosophical cores of some of these are even non-theistic, which is remarkable in a culturally durable religion, considering the popularity of gods in all times. Indeed, theistic elements have crept back into most of these religions, sometimes floridly so, as has polytheism in the West.

The Axial age was a time of great religious innovation, when history starts in earnest across multiple cultures, and religious thought and doubt is first extensively recorded. Greece transitioned from Homer to Pericles, Persia adopted Zoroastrianism, China brought forth Confucious and Lao Tzu, and Buddhism was born in India, along with the Upanishads. It was perhaps humanity's first brush with broad cosmopolitanism, which brought new questions and perspectives. A new focus on the individual and the pursuit of spirituality for its own sake rather than as a quid-pro-quo for some harsh and demanding god made room for true philosophy and philosophically driven life styles. Perhaps the most peaceful of all these movements were the Jains of India, also first recorded during this time.

Jainism, Buddhism, Yoga, as well as the Ajivika and atheistic Carvaka movements, were part of a broad reaction to Brahmanic Hinduism, called the Sramana movements (from sram, or making effort, such as the various austerities that typify its practices, maybe at an asram). Its wellsprings may go back to before the Aryan invasion that generated the Brahmanic / Vedic system, but at any rate, it constituted a sort of dramatic reformation / alternative to the dominant system. It renounced caste entirely, refused to recognize the higher status of the Brahmins or their sacrificial rituals, and set up what one might term a merit-based system of spiritual attainment, typically characterized by austerities like celibacy, begging for sustenance, minimal clothing, lack of possessions ... the opportunities are endless. It also generated the idea of life as a problematic cycle of suffering, karma and rebirth, with the goal of release from rebirth.

Jina, 11th century, unspecified, Gujarat.

The origins of Jainism are rather obscure, but the story is that there were twenty-four Jinas, who are the Jains of highest merit, having achieved liberation (from rebirth, from ignorance, etc.) through their meditative and mortifying efforts. They are typically portrayed in utterly peaceful sitting or standing meditation, clothed or naked according either of two Jain branches (Svetambara and Digambara, respectively). The last Jina, Mahavira (540-468 BCE), is most historically attested, and was a contemporary of Siddhartha Gautama. He was not the Jain founder, however, so the religion had a long and hazy history prior, of which he was a reformer and proselytizer. Indeed, Siddhartha Gautama seems to have a student of the Jains in his formative period, prior to breaking with all the strenuous penance and founding his own philosophical school / religion. Which may indeed just have been a variant of Jainism at the time. Yoga is similarly an ascetic strain of non-Brahmanic practices, even more inwardly focussed than Jainism.

The first of the twenty four Jinas, Rishaba, is of particular iconographic interest, as he is the only one with long flowing hair, which Jain monks pluck out when joining, and keep short generally. But Rishaba tends to get the aboriginal / Rastafari treatment, which to me is a striking tie to the deep history of humanity.

Jina Rishaba in standing meditation, ~3rd century, Bihar.

The philosophical focus of Jains is on a sober life and strict morality towards all living beings. The jewels are non-harming, asceticism, and non-absolutism. They theorize that bad actions (even inadvertant ones) harm the person in a physical way, accumulating karma-icules which are tiny bits of physical matter that stick to one's soul, bind one to the cycle of rebirth, and induce spiritual blindness. Their aversion to harming all life forms extends to complete vegetarianism for all practitioners, lay and monk, and even an avoidance of root crops whose harvesting (at least traditionally) involved more disruption of the ground & animals than other crops. One couldn't imagine a stronger repudiation of the classic Vedic rituals of animal sacrifice.

One wonders what Jains make of modern microbiology, not to mention their entrapment in a modern world where any participation in normal life implicates one in vast slaughter and mass extinction. They rate self-starvation to death a highly meritorious act, which goes somewhat against the human flourishing part of my criteria above, even while general abstemiousness and consciousness of ecological harm is in the long run a very positive ethic. One can tell that these philosophies had a revolutionary effects on Indian history & philosophy, for example on Mahatma Gandhi.

Jains originated in the Kshatriya caste, of warriors and administrators, one step below the Brahmins. Being a warrior is obviously not consistent with their philosophy, and Jains have gravitated toward commerce, where they have been very successful. Through history, they also have benefitted from strong alliances with some rulers, who often had political and cultural conflicts with the Brahmanic system. They have built extensive temple complexes at sites reputed to be where various Jinas attained enlightenment, and which serve as pilgrimage sites for all Jains.

Example of a pilgrimage site painting, which is displayed once a year for lay Jains who may not have a chance to go on an actual pilgrimage, and can attain some merit by viewing this portrayal of the site, full of pilgrims. No date or origin given. The location is Shatrunjaya, in Gujarat.

Their doctrine of non-absolutism deserves special comment, as it is a very mature philosophical approach completely unlike the bombastic Ja-way-or-the-highway approach one finds in typical, and especially Western, religions. It proclaims un-certainty. That any truth is provisional and different from different perspectives. Some truths may be partial rather than universal. For example, the Buddhist proposition that change-is-the-only-eternal, and the contrasting permanence of the Brahman in Hinduism each have some merits, depending on what one is talking about, from the Indian / Jain perspective. And that is surely an appropriate way to deal constructively with complex ideas with a great deal of imaginative content. It also leads to a distinct lack of a missionary impulse, one reason why Jainism remains small in number (maybe ~5 million adherents).

Over time, as is natural, Jains have made up stories about their Jina's pre-existing divinity and virgin births from which they arrived to the acclamation of various Hindu gods, etc. and so forth. It is par for the course, and has led to some remarkable art. But the basic philosophy is far less complicated, and well-versed practitioners do not expect anyone to listen to their devotions and prayers- they are understood to be meditational acts of self-improvement, not transactions with beings occupying the void. The Jinas have disappeared completely.

Many religions, indeed all social systems, harness guilt to promote good behavior, conformity, and a stable hierarchy. Jainism does take this aspect to extremes, though in light of our current planetary woes, it does so in a relatively constructive way, in a program of reducing its adherent's footprint of social violence and ecological harm. It easily ranks as the outstanding religion, if one must have one, for the present and future.

Jina, ~900, unspecified, from Karnataka or Tamilnadu.

• Same as it ever was... Chesterton was "disappointed" with the atheists of his day! "They are doubtful in their very doubts. Their criticism has taken on a curious tone; as of a random and illiterate heckling. ... Their suggestions are more vapid and vacant than the most insipid curate in a three-act farce... Their whole atmosphere is the atmosphere of a reaction: sulks, perversity, petty criticism. They still live in the shadow of the faith and have lost the light of the faith."
• Honor among traders- why some cultures don't get capitalism.
• Keynes was right about the 1980's, but who was paying attention?
• " ... people who lost their jobs in 2009, when unemployment peaked at 10 percent, had a 30 percent chance of ending up long-term unemployed."
• Sometimes, government does things better.
• Guess who worships the almighty dollar ... yes, the jihaddis.
• Peak fish: global fisheries peaked back in 1988.
• News flash: pesticides kill insects.
• Corporate felony means no one goes to jail, or even loses a job, or any pay.
• A little background on the Kochs. And present-day practice.
• The minimum wage is a human rights issue.
• Even France works harder than the US, thanks to better policy.
• DeLong on Piketty and the PikettyWorld.
• This week in the WSJ: 

"A March Gallup poll finding that most Americans worry about climate change "a little" or "not at all" is consistent with other surveys showing that the issue is not even close to being a top priority for U.S. voters." ... But when 67% want wealth in the US more equally distributed, then the majority is perhaps not always right after all.

The Science of Magic

A review of James Frazer's classic of anthropology and religion, The Golden Bough.

While the Golden Bough has come in for a great deal of criticism over the ninety years since it was published, it remains as a highly readable and innovative analysis of religion, magic, and superstition. Frazer hangs the book (an abridgement of a nine-volume monster) on the question of an obscure ritual of antique Italy, where a sacred grove of oak trees has a resident "king", the king of the grove of Nemi. This king is supposedly subject to replacement by any challenger who breaks a golden bough from the sacred tree, and defeats the king in battle. Frazer ranges (700 pages) over space and time to assemble an explication of this ritual, based on the sacred-ness of the oak to the old Celts, the especial sacredness of the mistletoe that grows on the oak, the impersonation of the god of the oak and mistletoe by the king, and the need of the community to have this king/avatar in a healthy and fertile state (i.e. killed while in good health) for its perpetually renewed fertility and happiness.

But Frazer's more important program is far less prone to criticism, surely appropriate, about the validity of his specific and quite fanciful speculations and associations, with regard to oaks, death by trial, fecundidty of crops, and all the rest. That program is to show in very general terms that magic is the science of the primitive conditions, and religion a somewhat more chaotic, though equally logic-driven, intermediary between the two. It revolves around a few key premises, on which are built, with inexorable logic, the myriad rituals and superstitions of humanity. Human history becomes a very continuous, more or less desperate, and highly affecting, effort to make sense of our bewildering surroundings and hard fate.

"In magic man depends on his own strength to meet the difficulties and dangers that beset him on every side. He believes in a certain established order of nature on which he can surely count, and which he can manipulate for his own ends. When he discovers his mistake, when he recognizes sadly that both the order of nature which he had assumed and the control which he haad believed himself to exercise over it were purely imaginary, he ceases to rely on his own intelligence and his own unaided efforts, and throws himself humbly on the mercy of certain great invisible beings behind the veil of nature, to whom he now ascribes all those far-reaching powers which he once arrogated to himself. Thus in acuter minds magic is gradually superceded by religion, which explains the succession of natural phenomena as regulated by the will, the passion, or the caprice of spiritual being like man in kind, though vastly superior to him in power."

Unfortunately ...

"Small minds can not grasp great ideas; to their narrow comprehension, their purblind vision, nothing seems really great and important but themselves. Such minds hardly rise into religion at all. They are, indeed, drilled by their betters into an outward comformity with its precepts and a verbal profession of its tenets; but at heart they cling to their old magical superstitions, which may be discountenanced as forbidden, but cannot be eradicated by religion, so long as they have their roots deep down in the mental framework and constitution of the great majority of mankind."

Naturally, the conception that the wheels of nature are entirely without personality, remorse or recourse, is extremely foreign, and remains foreign to human nature. Yet when the more careful investigations of modern science point in that direction, religion inevitably (if reluctantly, and noisily) trails off towards ever more impotent and indiscernible deities, falls by the wayside, and becomes a species of psychotherapy rather than an unassailable, holistic system of explanation for the social, moral, physical, and invisible worlds.

Ironically, as Frazer puts it, the scientific world-view is closer to the primitive magic than it is to the intermediate stage of religion. Magic assumes a relatively law-ful system of invisible nature, where supernatural beings and arcane rules, though plentiful, are also easily compelled by ritualistic formulae. For example, step in a crack, and break your mother's back. Or break a mirror, and get seven year's bad luck. On a more positive note, wearing the costume of an animal will make that animal more available, and less reluctant to be killed. Just because none of the magic works doesn't mean that logical thought based on lawful premises isn't taking place. The propositions of religion, however, are typically far less certain. Gods can not be so easily compelled, so the idea of cause and effect recedes into the background, from which it can take a very long time for scientific thought to proceed to the next stage of existential theory.

"The fatal flaw of magic lies not in its general assumption of a sequence of events determined by law, but in its total misconception of the nature of the particular laws which govern that sequence. If we analyze the various cases of sumpathetic magic which have been passed in review in the preceeding pages, and which may be taken as fair samples of the bulk, we shall find, as I have already indicated, that they are all mistaken applications of one or other of two great fundamental laws of thought, namely, the association of ideas by similarity and the association of ideas by contiguity in space or time. A mistaken association of similar ideas produces homeopathic or imitative magic: a mistaken association of contiguous ideas produces contagious magic. The principles of association are excellent in themselves, and indeed absolutely essential to the working of the human mind. Legitimately applied they yield science; illegitimately applied they yield magic, the bastard sister of science. It is therefore a truism, almost a tautology, to say that all magic is necessarily false and barren; for were it ever to become true and fruitful, it would no longer be magic but science. From the earliest times man has been engaged in a search for general rules whereby to turn the order of natural phenomena to his own advantage, and in the long search he has scraped together a great hoard of such maxims, some of the golden and some of them mere dross."

For example, the idea of contamination by contiguity is surely very close to the truth of the germ theory of disease, so it counts as a dim harbinger of a true scientific theory, however much abused. And even imitative magic, if one counts it under the banner of the placebo effect and related social influences which we learn increasingly have strong effects on health, has its place in the history of proto-scientific ideas.

But what seems to me even more basic than these two principles which Frazer returns to time and again is the power of thought itself. What seems to run through the core of magical thinking is not just the rituals of imitation and purification that make up its outward preoccupations, but the conviction that our thoughts themselves are enormously powerful, and are listened to with great attentiveness by one's adversaries and boon-givers, from the lowly animist placation of vegetable spirits to prayers sent to highest theological riddle. Just as a baby assumes that its intensely thought will, accompanied by a good bit of crying, will, indeed must, gain a response, adults habitually assume that they inhabit a world that is always paying attention. To them.

We seem naturally to assume that the whole world thinks as we do, and indeed with even greater clairvoyant responsiveness. Magic generally involves an effort of thought, by individuals or a whole community. When the hunt is danced in the costumes of the prey, no one thinks that the deer are lurking in the shadows watching and awarding points for artistry. No, the thought-waves are assumed to radiate through the magical channels, to make known the intense desire of the tribe, and bend the prey or its superintendent deities to the people's will.

Likewise with voodoo, with sympathetic medicine, and all sorts of magical thinking. The critical component is not the stage prop, but the intense thought and will brought to bear in a ceremonial ritual, combined with a healthy dose of optimism. Why would anyone think this works? One reason is that our natural milieu is social. We are even more social than we think we are. Our brains seem to have evolved principally out of social competition, and we hang desperately on our social status, which is indeed a matter of life and death. The second reason is that our principal mortal adversaries are conscious agents, whether other people (such as in war) or wild animals for whom we are (were) prey. So naturally we evolved to think of our most significant interactions with the world in social terms, with some thinking entity on the other side, just waiting to do us in, or help us out.

But even those two reasons don't fully suffice, since however close we are to someone, they still do not read our minds to such an extent. No, the fundmamental reason has to be simple narcissism & immaturity. That if we wish for something hard enough, the cosmos is sure to listen and heed. However wonderful Neil DeGrasse Tyson's vast and orderly Cosmos is, it can't hold a candle to that cosmos.

Surely, we didn't have much else to go on in primitive times. So making ourselves feel a bit more powerful by way of intense thought concentration couldn't have done much harm, and might have done a great deal of good, by way of vivid visualization of intended results. However little effect it may have had on its intended targets, it had very significant, and probably quite beneficial effects on us.

And that is one reason to bring magical thinking back, at least a little. Medicine is an example of science gone a little overboard, with patients pinioned in a sterile, inhumane, unsupportive environment. This environment used to betoken a priestly class of innovative healers, with white lab coats and all, but by now it is just a harried and unwelcoming factory. The enormous success of alternative medicine, herbalife, and all the rest is a testament to the failure of the regular medical system to truly care for its subjects. A rapprochement would not to allow bad medicine, like homeopathy and noxious herbs, in the door, but would encourage ritual, arts, community interaction, and supportive psychological practice to permeate the medical establishment at all levels, putting people, not diseases, back into the focus of medico-community care.

The basic point is, insofar as ritual, hope, and narcissism are conducive to comfort and social ease, we may need more of them, even while keeping magic well away from the philosophical and scholarly pursuits that drive our rigorous knowledge of reality forward.

"Thus the old magical theory of the seasons was displaced, or rather supplemented, by a religious theory. For although men now attributed the annual cycle of change primarily to corresponding changes in their deities, they still thought that by performing certain magical rites they could aid the god who was the principle of life, in his struggle with the opposing principle of death.
...
And as they now explained the fluctuations of growth and decay, of reproduction and dissolution, by the marriage, the death, and the rebirth or revivial of the gods, their religious or rather magical dramas turned in great measure on these themes. They set forth the fruitful union of the powers of fertility, the sad death of one at least of the divine partners, and his joyful resurrection. Thus a religious theory was blended with a magical practice. The combination is familiar in history. Indeed, few religions have ever succeeded in wholly extricating themselves from the old trammels of magic. The inconsistency of acting on two opposite principles, however it may vex the soul of the philosopher, rarely troubles the common man; indeed, he is seldom even aware of it. His affair is to act, not to analyze the motives of his action. If mankind had always been logical and wise, history would not be a long chronicle of folly and crime."

• Luhrmann on god: the imaginal dialog.
• Epilepsy and god ... a tangled history!
• What happens when truth loses to mythos and shameless egoism.
• A history of Social Security "reform". Remember that about 1.5% of every 401K goes into the pockets of the financial industry, year in and year out, with no risk, while participants are lucky to break even.
• The man who saved Wall Street, and let Main Street rot.
• Are unions the answer to inequality and excess corporate power?
• The GDP we devote to climate care will not be "lost".
• Dysfunctional culture, dysfunctional religion.
• The Phillips curve is dead. The inflation-unemployment environment is more dynamic.
• Summers on Piketty.
• Bruenig on Summers.
• Economics needs some help. "I sincerely doubt that methodology is discussed little because mainstream macroeconomists think it is unproblematic. I am quite confident that it is discussed little, because the methodology of mainstream economics is indefensible."
• WSJ Quote of the week, a neat bit of circular logic on climate heating, er, global warmism:

"This columnist is probably as unqualified as Marcus or Lapidos to evaluate the scientific merits of global warmism. But because we distrust climate scientists, we're with Rubio in being inclined to think it's a bill of goods. The trouble for global-warmist journalists like Marcus and Lapidos is that an appeal to the authority of a distrusted source undermines rather than strengthens one's argument."

Watching the Watchers

Signs and theories of consciousness; review of Consciousness in the Brain, by Stanislas Dehaene.

We love it, can't do without it, and wouldn't be without it. We worship it, and warp it with drugs and crazy religion. But what is it? Consciousness is rather hard to describe. Stanislas Dehaene does an excellent job, however, in a status report on what is known about the physical correlates of consciousness, showing that consciousness can indeed be studied and conforms to the "workspace" theory elegantly elaborated by Bernard Baars almost 30 years ago.

Most of what our brain does is unconscious. When we lay eyes on something, imagery just happens. We have no introspective knowledge of the enormous processing that goes into rendering a visual scene. It was only with the invention of computers and the pursuit of artificial intelligence (and of modern animation with its farms of rendering computers) that its scale could be properly appreciated. The refined end-product just pops into consciousness, making it seem oh so easy. What is important to realize, however, is that vast and various processes are taking place in the background, all the time, whether we attend to them or not. Writing in 1988, Bernard Baars paints it as follows:

"A fourth popular metaphor may be called the "search light" or Theater Hypothesis. This idea is sometimes called "the screen of consciousness." An early version may be found in Plato's classic Allegory of the Cave. Plato compared ordinary perception to the plight of bound prisoners in a cave, who can see only the cave wall with the shadows projected on it of people moving about in front of a fire. The people projecting the shadows are themselves invisible; they cannot be seen directly. We humans, according to Plato, are like those prisoners -- we only see the shadows of reality. Modern versions of the Theater Hypothesis may be found in Lindsay & Norman, Jung, Crick, -- and throughout this book. It has been beautifully articulated by the French historian and philosopher Hyppolite Taine (1828-1893): "One can therefore compare the mind of a man to a theatre of indefinite depth whose apron is very narrow but whose stage becomes larger away from the apron. On this lighted apron there is room for one actor only. He enters, gestures for a moment, and leaves; another arrives, then another, and so on ... Among the scenery and on the far-off stage or even before the lights of the apron, unknown evolutions take place incessantly among this crowd of actors of every kind, to furnish the stars who pass before our eyes one by one, as in a magic lantern." Taine managed to combine several significant features in his theater image. First, he includes the observation that we are conscious of only one "thing" at a time, as if different mental contents drive each other from consciousness. Second, he incorporates the Tip-of-the-Iceberg Hypothesis, the idea that at any moment much more is going on than we can know. And third, his metaphor includes the rather ominous feeling that unknown events going on behind the scenes are in control of whatever happens on our subjective stage (cf. Chapters 4 and 5)."

 ...

"Thus consciousness involves a kind of a filter -- not an input filter, but a distribution filter. The nervous system seems to work like a society equipped with a television broadcasting station. The station takes in information from all the wire services, from foreign newspapers, radio, and from its own correspondents. It will analyze all this information quite completely, but does not broadcast it to the society as a whole. Therefore all the various resources of the society cannot be focused on all the incoming information, but just on whatever is broadcast through the television station. From inside the society it seems as if external information is totally filtered out, although in fact it was analyzed quite thoroughly by automatic systems. Consciousness thus gives access to internal unconscious resources."

Putting it in my own words, what is the point of consciousness? It seems to be the caboose on the train of thought, seeing things well after they occur, getting highly summarized and schematized reports, whether of perceptions, or even of actions we are doing. The key function seems to be its role of integration, memory, and broadcast. Subliminal (unconscious) data that don't get into consciousness seem to die forthwith. The parallel processing capacity of the brain seems to send the vast majority of what it does into the circular file, never to enter memory, never to be weighed and considered, never to be transformed into language, the coin of much internal thinking as well as social community and extended consciousness. Consciousness seems be the narrow, single-lane road that imposes a top-level, purpose-driven time-sequencing on our brain, so that the most important thing at any given time can be attended to in isolation and with all needed resources, from the large variety available.

The core of the book reports from Dehaene's own work, which uses the visual system to demonstrate a dramatic phase transition between unconscious and conscious mental events. His group, and many others, use a rapidly presented image, which is quickly followed by some other "masking" image, which is is a noisy kind of background that doesn't trip the same kind of consciousness (i.e. subjective recognition) that the discrete test image, of, say, a face, presents. The subject reports whether the first image was seen or not, and can be subjected to various brain imaging tests, bias tests, etc. Typically, if the first image was presented for 60 milliseconds before being superceded by something else, it is consciously perceived and reported. If it is presented for less than 40 milliseconds, subjects never report it, if it is subsequently masked. But brain scans, and other subtle responses, indicate that their visual systems did process that brief image to an extensive degree. It just didn't make it into consciousness.

Experimental method. Top shows locations of surface EEG electrodes. Bottom shows the image presentation sequence, with consciousness-tripping words shown briefly between neutral "masking" symbols. 29 milliseconds is typically too brief to register consciously, if replaced with a subsequent masking image.

When an image does make it into consciousness, the researchers see a diagnostic EEG wave from a high-density array of electrodes on the subject's head, a strong "P3" wave of electrical voltage over the parietal lobe about 300 to 500 milliseconds after the stimulus. This is proposed as a signature of consciousness, which can be studied, manipulated with TMS, and even used diagnostically to evaluate patients in comas or other vegetative states for "locked-in" consciousness. It tracks with high fidelity the subjective state of the observer, rather than their objective inputs. Likewise, when epilepsy patients getting electrodes provide access directly to their brains, the same things are observed at the cellular level. Individual cells can be recorded, generally in the frontal areas, that only fire when, say, a picture of Bill Clinton is subjectively observed, and not when it is presented and ignored, or not recognized. There is much more to be said on the topic, but it is clear that we have some very definite, if rough, physical correlates of consciousness in hand.

From his most recent paper, Dehaene reports more of the same, using EEG electrodes all over the subject's head, which produce event-related potentials, and, after computation, event-related spectral perturbations. Phase coherence also gains significantly when the perceived word comes into consciousness. In the figure below, the beta-band brain waves are tracked, about 400 ms after image presentation, and the Granger correlation presented between discrete brain areas. An enormous leap in activity and coherence happens in the experimental condition, on right.

Point-to-point Granger correlation of beta brain waves, compared between masked (left) and unmasked (right) procedures, of which the latter is subjectively conscious, and shows here dramatically increased phase coherence.

It is very heartening to see the field of consciousness studies take off and make concrete findings, even to the point of saving locked-in patients from gruesome fates. But I was expecting another chapter in the book, where Dehaene would explain how consciousness actually works! Some parts of his model are not problematic. There seem to be many processes, from all the senses, from our memory, and elsewhere, that all get computed and prepared for conscious presentation. There is a continual competition for getting onto that "stage" by way of complicated salience calculations, always weighing the importance of each stream of input. I experience this one-at-a-time limitation all the time when I try to read something at the same time I listen to a podcast or a phone meeting.. it simply can't be done. I can attend to only one language-related task at a time, period.

And, reading a bit between the lines, it is also quite reasonable to posit that our ability to think about something, such as keeping an image in mind, involves recurrent loops of data going between the executive areas (frontal and parietal) to the input module involved, such as the visual areas. It is reasonably well-understood that the lower-level processing areas get very active connections back from the frontal areas both for attention focussing, and for re-generating their inputs for continued keeping-in-mind. Thus the information is not just tranferred from A to B, and deposited. Rather, the content is always re-presented by the originating system, though it can then be remembered, dissected mentally, rotated, expressd in language, etc. This implies a strong neural activity signature in the source areas of sensation as well as frontal areas of the brain when consciousness is active, which is indeed seen, as global connectivity and correlated waves/ firing, vs fragmented, localized patterns of activition under anaesthesia. It also implies some kind of code or lingua franca going back and forth that we really have very little idea of at this point.

I would go farther to propose that autism may be a defect in this one-at-a-time system, where the subject is inundated with excess stimulation, and perhaps unregulated stimulation. In cases where some particularly ornate unconscious calculation is mistakenly injected directly, rather than summarized as is usual, one may see the savant syndromes that are so amazing and correlated with autism. (I'll note that Dehaene posits a simlar theory for schizophrenia, as a fragmented consciousness, with insufficient filtering of images, voices, etc.) To extend the study of consciousness to a serious explanation of its defects and syndromes would be extremely rewarding.

I also agree with Dehaene when he dismisses the philosophical "free will" problems of agency for a putative artificial consciousness with a page or two of rather sharp argument. On the other hand, he waves away the so-called "hard" problem of consciousness with a paragraph of his faith that it will be dissolved in further data. But it is worth grappling with more explicitly. How exactly does a stab of pain affect us subjectively when a robot would not be so affected, as it is not conscious? How do we differ from machines, or if we don't, how can machines be made conscious?

Both Dehaene and Baars have a conviction that if the phenomenon of consciousness is described in ever more detail, at some point an understanding of this issue will naturally emerge. That may be so, but it would be highly beneficial if some theoretical insight could be developed beforehand. That is the position, incidentally, of Giulio Tononi and colleagues, whose recent paper offers a blizzard of obscure theorization about information density and consciousness, which I can't begin to interpret. They offer one interesting observation, however:

"Under special circumstances, such as after split brain surgery, the main complex may split into two main complexes, both having high ΦMax. There is solid evidence that in such cases consciousness itself splits in two individual consciousnesses that are unaware of each other."

Unfortunately, neither approach seems to have really pulled into the station yet, so we can only continue to make up metaphors for what is going on, based on ever more detailed observations of the phenomenon. I would propose something like an engine turning over, based on a basic awake + conscious cortical-thalamic loop of activity, which then pulls in (with brain wave synchrony) perceptual and other loops reverberating to all the other parts of the brain whose processing is available. Dehaene does offer one vision, speaking of the workspace model of consciousness:

"The entire machine is only partially affected by external inputs. Autonomy is its motto. It generates its own goals, thanks to spontaneous activity, and these patterns in turn shape the rest of the brain's activity in a top-down manner. They induce other areas to retrieve long-term memories, genrate a mental image, and transform it according to linguistic or logical rules. A constant flux of neuronal activation circulates within the internal workspace, carefully sifting through millions of parallel processors. Each coherent result moves us one step forward in a mental algorithm thta never stops- the flux of conscious thought. Simulating such a massively parallel statistical machine, based on realistic neuronal principles, would be fascinating...."

But how is that going to work, and are there current systems that provide a kernel for such a dream? I think there are, in the form of the UNIX operating system. It runs countless parallel or near-parallel processes, with its capability of sending jobs to multiple processors and splitting processor time in very fine slices among many users and sub-processes. It can even share results between processes, though they have to be carefully structured. What is needed is a separate computer of a substantially different stucture that interacts with such a unix-type machine, picking off its most significant results to a single constantly running thread of very general rumination on its own conditions, and the most significant happenings internally and externally. It would transmute this into language when possible, internally, if not to external listeners.

Now, one has to realize that all of our mental experiences are the firings of neurons. This is equally true for the plainest visual scene as for the sharpest bite of pain or sweetest apple. Nothing is direct. Yet it feels like there is a watcher inside- a soul, or homunculus, which is the "real" perceiver and target of all the complex data processing. From all we now know, this can not possibly be true. And it would make little sense anyhow, since that homunculus would have to have some mechanism of its own to feel qualia, plus mechanisms to communicate out and back to the rest of the brain system which we know with certainty does at least part of the data processing.

No, the perceiver is part of the system itself, somehow, transmuting all those qualia from electrical buzz into poetry. This is the hard problem- how some portion of the brain system, i.e. consciousness, is the perceiver while most of the rest of our brain and body goes about its business in the dark. And this perceiver is also a powerful director of other activities and agent, interacting with the unconscious systems, getting data, setting alarms, applying focus and attention, getting inundated with streams while trying desperately, during meditation, to get nothing at all.

One gets the distinct sense that is one of the brain's great illusions, like making a pain in the toe feel like it really is in the toe, not in the brain. Or like re-setting time so that we don't notice the ~400 milliseconds it takes for any perception to come into consciousness. Indeed, consciousness is the master illusion, enabling all the others. But how does the magic work? It remains a work in progress.

• "We find that completely closing the HS to fishing would simultaneously give rise to large gains in fisheries profit (>100%), fisheries yields (>30%), and fish stock conservation (>150%)"
• Even more lame than the creationists hating on Cosmos: the recent film God's not dead, about a totally realistic philosophy class.
• But sectarian prayer.. now OK in government, for those grievously oppressed Christians.
• Speaking of oppressed, some billboards.
• That is some kind of god they've got...
• Pakistan, as usual, is a threat to the entire world.
• Which computer languages are hot, which not?
• Yes, Virginia, there really is junk DNA.
• "Not a single U.S. airport is among the top 100 airports in the world."
• Is Obama for real on climate heating? I hope so.
• Stanford divests from coal.
• New England is being set up for an Enron-tastrophe.
•  Some technical notes on savings gluts. And stagnation.
• Martin Wolf is turning against capitalism. Maybe the shareholders are not the be-all and end-all. Who really bears the risk of corporate idiocy? The employees do, in very large part. "All those who have stakes in the company that they are unable to hedge bear risks. The most obvious such risk-bearers are employees with firm-specific skills. Human capital is perhaps the least diversifiable and insurable of all our valuable assets. Among all forms of human capital, the least hedgeable are firm-specific skills."
• A little honesty on the right: The plutocrats are in charge, and thank god!
• Quote of the week, from Answers in Genesis:

"This episode of “Cosmos” offers a lot of beautiful graphics and special effects, but in the end it should be lumped with fairy tales like Tinker Bell or Shrek. Yet Bible-believing creation scientists who are willing to look at the world through the history provided in God’s Word without the prejudice and blind ignorance can “read” in earth’s geology a true and exciting account of our history. And biblical truth is a much better account than fiction."

Fixing the NCAA

How can college sports be fair to players?

March madness is now well past, but the bittersweet taste lingers, of seeing so many starry-eyed young strivers bossed around by extremely well-paid coaches and staffs, funded by enormous television contracts, paid for by our eyeballs and cable bills. It is really a plantation system.

There are proposals to pay college students, but I would like to go in a different direction. It is appropriate to pay student athletes in the coin of education, if they are really getting an education. So the first and most obvious reform has to be to award full, four-year, no-strings scholarships. Right now, scholarships are renewable, per year, or even less. This makes getting one the same as working for one boss- the coach, as the student can be fired at will for non-performance, sent packing from the school as well as the team. Are academic scholarships awarded on such a cold-blooded, mercenary basis, replicating the worst aspects of our at-will employment system? No, and nor should athletic scholarships. If the institution values the student, they should pay the full freight and allow that student the basic personal and academic freedom to do what they want with all the opportunities of higher education.

But I would add just one more thing, which is that salaries (which is to say, total pay) at all non-profit institutions (such as colleges, whether public or private), should be capped at something like ten times the minimum wage. It is truly revolting to see star college coaches feted as the second coming, building empires that overshadow the rest of their institutions, and being paid in grandiose terms, all on the backs of young athletes they so shamelessly exploit. Any non-profit is supposed to have a public purpose and an ethic of service, which is antithetical to the blowout contracts and naked greed so much on display. Will all the good coaches go to the NBA? Good riddance! May they join the Clippers.

This kind of rule would have beneficial effects in many areas. In our local area, we were once saddled with a predatory hospital chain that extracted money, gave mediocre service, and paid its executives like princes, and was, you guessed it, a non-profit. CEO-scale pay is a sign of a profit mind-set and purpose, not a non-profit mind-set. Such a rule might also light a fire under the effort to increase the minimum wage, which has few powerful natural advocates otherwise.

Indeed it is high time for a new model of work and pay, where the primary motivation of work is the work itself. Running a company, school, or non-profit organization has far more meaningful rewards than the money involved, so the idea that pay should be set exclusively by some market mechanism using the fig leaf of marginal productivity to cover essentially random factors of luck, access, career choice, negotiating prowess, and inborn talent, is both counter-productive, and morally repugnant. Sure, reward people for greater effort and effectiveness, but within a reasonable band that doesn't bankrupt our communal institutions and more importantly, doesn't turn everyone involved into avatars of greed. Human worth is a far more complicated proposition.

Lastly, what to do about the media ecosystem, which vacuums up money whether the students and coaches get paid alot or not? The NCAA, under this system, would naturally be a non-profit subject to the same salary caps as its member schools. So the money would be negotiated as usual, but would all go to the general accounts of the schools participating. Not to their athletic departments, not to their coaches. If they want to run big programs and enjoy sports, let them do so in light of their wider institutional responsibilities. The whole college sports machine needs to be toned down a little, and the focus taken from the rabid onlookers and spectacle (i.e. madness, to put it in technical terms) to the young people who should, after all, be getting an education, first and foremost.

• Would lying about atheism be moral?
• A lengthy riff on programming. Which is all bad.
• Creationists are still about, still nuts.
• Wealth must be destroyed, to save the planet.
• Iraq is falling apart. A template for Afghanistan?
• Correlation between money spent on guards and inequality.
• Financial crime is no longer reported as crime, let alone prosecuted as crime. As long as money is flowing upwards in the class hierarchy.
• This week in the WSJ: "Insider trading not only does no harm, it can have significant social and economic benefits including a more accurate pricing of stocks."
• The Fannie/Freddie replacement plan doesn't sound very good.
• Another response to Piketty- socialize wealth.
• Peter van Buren on Piketty.

Primitive Prozac: Religion as Anxiolytic Therapy

Or- I'd rather have a frontal theophany than a bottle in front of me.

"Religious suffering is, at one and the same time, the expression of real suffering and a protest against real suffering. Religion is the sigh of the oppressed creature, the heart of a heartless world, and the soul of soulless conditions. It is the opium of the people. The abolition of religion as the illusory happiness of the people is the demand for their real happiness. To call on them to give up their illusions about their condition is to call on them to give up a condition that requires illusions." -Karl Marx

Marx, unfortunately, lived before modern neuropharmacology. But whether the blunderbuss of opium, (or alcohol), or the scalpel of prozac, we are clearly in need of something to get us through the night, and self-medicate in all cultures and all times. Religion seems to be one such universal method of relieving anxiety, and comes up for a chapter in Jared Diamond's book, The World Until Yesterday, titled "What electric eels tell us about the evolution of Religion". To boil it down brutally, Diamond, wearing his sober sociologist's hat, tabulates seven functions of religion, dialed to various levels among different religions, cultures, and times:

• Supernatural explanation
• Defusing anxiety through ritual
• Providing comfort about pains and death
• Standardized organization
• Preaching political obedience
• Moral codes of behavior towards strangers
• Justification of wars

What I realized in reading this is that most of these points, and probably the most significant ones, can be collected under the head of antianxiety medication, individual and collective. We are a very anxious species. Our great intelligence and ability to model past, future, and social structures, etc. has also granted us an expanded, indeed infinite, ability to worry and fret. Squirrels seem anxious too, so this is not a new phenomenon. Chimpanzees soothe each other mostly via grooming, something we seem to have given up in favor of language and social interaction, of which religion is perhaps the most powerful form. Part of our transition from prey to predator species may have been finding some way to calm down, which in our case became, in part, religious practice, rather than the more biological alterations that allow other top predators, like lions and raptors, to seem so calm and unruffled.

Not knowing something makes us anxious, to the point that we habitually make up stories to fill the gap. There seems to be some kind of law against telling a child "I don't know" in response to all those natural, and pressing, questions. So we make up stories. This can be the fount of the greatest art- a project of self-expression and self-understanding, in the guise of an origin story, story of a constellation, of a deity, etc. But still, it betrays an odd kind of anxiety about gaps in our knowledge- an anxiety that has led us to science as well.

Other people make us anxious, not knowing what is in their minds, especially their intentions toward us. Disease makes us anxious, especially back when next to nothing was know about it. Death makes us extremely anxious, being the end of all we hold dear, and typically involving unspeakable suffering besides. We are existentially anxious, about what it all means, where it all came from, who is in charge, what our life is worth. Similarly, the future makes us anxious. It is a big unknown. Historically, many people didn't even take the sun rising again for granted, but developed elaborate rituals and theologies to help that process along.

All these sources of anxiety can be addressed through religion. It explains the unknown, at least sufficiently to allay naive anxieties about cosmic origins, natural surroundings, biology, and disease. Perhaps it assures us about a destination after death, and furnishes a father figure who provides both ultimate justice and meaning to life. It also relieves an enormous amount of social anxiety, providing us with a "gang" to hang with, with some hierarchical structure and rules of interaction, which relieve the anxiety of social chaos. The meaning that religion provides allays at once our social, existential, and intellectual anxieties. Indeed, Diamond's last point about justifying wars can be framed in a similar way. What keeps us typically from making war is prudence and anxiety about the future, about losing, and about the personal price paid by some, even if the group wins. Religion can wipe away each of those anxities by painting a glorious picture of the cause, the boons to be gained, and glory falling especially to those who die in such a cause.

This is hardly a new observation, but seems insufficiently appreciated by those trapped in the is-religion-true (nor not) debate. Not being remotely true hardly makes it useless or pointless.

For instance, from book on religions of antiquity:

"During the process of acculturation from childhood, this heritage is transmitted to all members of a community who absorb is, and are thus enabled to sidestep the burdensome intellectual challenge of developing a personal or private explanation of the order of the real and its counterpart in the imaginaire. Myths constitute the vehicle of transmission of this collective account, which undergoes adjustment corresponding to changes in the objective conditions of the historico-social formation in which they are elaborated. It this becomes a cultural mediator of great importance, offering a shifting form of explanation that allows members of the community to face, without excessive anxiety, a reality that might otherwise appear chaotic and uncontrollable." - Jaime Alvar Ezquerra, in "Romanizing Oriental Gods: Myth, Salvation, and Ethics in the Cults of Cybele, Isis, and Mithras" 2008.

False as it must necessarily be, the model works just so long as most members don't question it too hard. Like the classic answer about the turtle that holds up the world... "It's turtles all the way down!" Beyond such a superficial level (which, bless them, drives theologians to such contortions), the content hardly matters at all. It is the psychological lifting of weight that is so valuable. Problems only arise when people take their myth too seriously, insisting on a truth that isn't there. A natural corollary is the rise of modern religious toleration (an echo of the polytheistic all-for-on and one-for-all model in Western antiquity). For if deep down, we realize that religions give us a therapeutic service, then the flavor doesn't make much difference, for all their various and impossible claims to truth. It is very similar to the situation of modern psychology, which has realized that talk therapy is highly beneficial, pretty much regardless of the Freudian / Jungian / Dynamic / Cognitive / etc. forms it may take. It works because it throws a lifeline of structured, social, soothing calm.

What is a modern person to do? Our intellectual insecurity has been resolved in vast degree by diligent intellectual practice, i.e. by science and other forms of disciplined inquiry. Our physical insecurities have been resolved in large measure by just government and economic prosperity (and lots of oil!) No one in today's developed world should go hungry, or be crushed under political oppression, let alone be attacked by wild animals. Prosperity has also brought great social freedom, though not solidarity or communalism. Quite the opposite- it has given us atomization and anomie.

Psychotherapy addresses, in some degree, this small facet of the anxieties that religion treats so comprehensively, not touching issues of the collective at all, for example. Prozac is an even less productive solution, relieving the physiological symptom, but not addressing either individual or collective problems, assuming that they are problems, and that social engagement in a religious-style community helps solve them. For our anxieties are not just hindrances, they have a purpose, (at normal levels), driving us to plan for the future, form protective and productive communities, learn all we can about our environment, etc.

So, social isolation, personal meaning, and death remain significant unresolved forms of anxiety for which religion remains a functional prescription, in competition with prozac and other aids. Ritual, for instance, whatever its content, provides a socially calming and organizing activity that has largely been lost to non-religious modern people. We see pieces of ritual in musical concerts, political events, newspaper reading, school attendance, business formalities, even facebook obsessing. But none is as powerful as the religious practice that whips it all together into a compelling Sunday morning multi-ritual production of cultural connection and cosmic import.

And meaning? The modern worldview, for all its anxiety-allaying efforts in other spheres, denies intrinsic meaning in this life, while denying future lives altogether. We have no more meaning than a fly that lives its day in the sun, or a grain of sand. We naturally adopt inborn meanings, through our family and social lives, and our competitive natures. And we create other meanings in profusion, high and low, including that confection of meaning called religion. Religion has been the exercise above all others that assures us of some ultimate reason for it all, and has been exceedingly difficult to replace in that respect. The only answer, in refusing all false meanings and empty faiths, is an astringently stoic / existentialist philosophy that is perhaps the single strongest characteristic of modernity.

• But others wonder whether it isn't just peer pressure and indoctrination.
• Calculus was once heretical.
• Atheists have mystical experiences too. But they interpret them skeptically.
• American atomization, anxiety, and anomie.
• Brain injury can give, as well as take away.
• Sado-monetarism, Swedish edition.
• The mortgage system is still rife with fraud and lawlessness.
• Korean ferry disaster is another story of corruption and revolving doors.
• Some successful government programs. 
• But we have not been keeping up with the highway fund / gas tax.
• Why does "freedom" not extend to all users of the internet?
• Colbert does Cliven. Plus, more on guns.
• Wolf on money: nationalize it!
• Solow on Piketty. "This is Piketty’s main point, and his new and powerful contribution to an old topic: as long as the rate of return exceeds the rate of growth, the income and wealth of the rich will grow faster than the typical income from work."
• Doutat on Piketty.
• And for remarkable disclosure (and self-disclosure)... WSJ on Piketty. After explaining how CEOs certainly don't deserve what they are paid, (what a foolish theory that would be!), but are the fortunate cronies of crony capitalism, they conclude:

"A more useful prescription, long before anyone heard of Mr. Piketty and his gloomy novelties, is the prescription promoted by boring-old Social Security reformers. They've long argued for turning Social Security into a system of real savings, via private accounts, so every American can become a capital owner and benefit from [CEO] Mr. Mulally's incentives too."

The Big Brain Domain

The mystery of protein domain DUF1220 and brain evolution.

Someday, the human genome will be an open book to us, telling us how we develop from an egg, and what is likely to go wrong along the way. But for now, we know only glimmers about it. We know all the letters of the DNA code, but frustratingly little about what they mean. An example is the fascinating story of DUF1220.

DUF stands for "domain of unknown function". DUF1220 is family of brief protein sequences, one example of which is "EKVQELYAPREVQKAEEKEVPEDSLEECAITCSNSHHPCESNQPYGNTRITFEEDQVDSTLID". This uses a code where each amino acid constituent of a protein is one letter. A slightly more sensible way to look at it is put several family members in a linup, as it were:

Alignment of 10 family members of DUF1220, with most conserved amino acids in red, and hydrophobic amino acids marked with green bars.

Each member of the domain family is in its own row, lined up with the others as best a computer can do. The well-aligned positions, with mostly the same amino acid, are in red, and less so are blue. I have added a few green markers above to show which positions are hydrophobic, carrying amino acids like F, V, I, L, A, W, Y, and the like, which tend to lie inside folded proteins like oil drops form in water. So, by my own speculation, it looks a bit like an alpha helix, with regular hydrophobic residues lying at roughly seven or so amino acid intervals, appropriate to one face of the helix lying against the interior of a protein while the rest is exposed to the outside, to water and other molecules.

One human gene is 3768 amino acids long and contains 43 iterations of the DUF1220 domain, marked in pink.

But this is very conventional. Many, many proteins take on this kind of structure. Going up a level to the genes, we see that in one gene carrying this domain, it occurs tandemly 43 times. Wow! What could be going on? Such a long protein, singing the same song, over and over again. This is common in structural types of proteins, less so in enzymatic or regulatory proteins, but who knows? An ancestor of this family seems to be involved in regulation of protein phosphorylation and activity, but very little else is known about what it might be doing in any physical way.

Up one more level, to the genome, we see that there is a family of ~23 of such genes in humans, mostly on chromosome 1, which carry various numbers of this small domain, adding up to about 277 copies in all of this domain in the genome. Why so many genes, why so many approximate copies of this domain? This kind of amplification tends to be a quick and dirty solution on the part of evolutionary processes, to get more of some beneficial gene product. Later on, once the regulation of some of these genes is optimally tuned up, extra copies can be left to die as pseudogenes and deletions.

Going up to the evolutionary level, we find that there has been a dramatic expansion of these genes and this domain over the mammalian and especially primate lineage, from none in birds, to a few in rodents, to a hundred in monkeys, to 290 copies of DUF1220 in humans:

Evolutionary history of DUF1220-containing genomes. Years before present are listed up the middle line.  Numbers of DF1220 domains are listed at right. The miscellaneous notes in the tree refer to named sub-families of DUF1220-containing genes, and a few other related issues.

There seems to be a strong correlation of duplications of this gene or segments of it with closeness to humans in the primate lineage, which would make sense if this gene, say, had something to do with generating bigger and better brains.

And that is something we do know something about, since mutations in these genes come up in a variety of disease conditions, which is to say, human phenotypes. A recent paper found that deletions in this chromosome 1 family lead to microcephaly (small head), while duplications lead to macrocephaly (big head) birth defects. Other mutations among these genes lead to autism and other mental disorders.

"... we have shown that of all the 1q21 genes examined (n 1 ⁄ 453 [subjects]), only DUF1220 sequences exhibit a significant direct correlation with brain-size phenotypes in both pathological and normal human populations. Although we provide data implicating the loss of DUF1220 copy number in 1q21-associated microcephaly, the data are also fully consistent with the view that increases in DUF1220 copy number underlie 1q21-associated macrocephaly." 

"Twelve genomic diseases have been linked to CNVs [copy number variations] in the 1q21.1- 1q21.1 region. They ... include autism, congenital heart disease, congenital anomaly of the kidney and urinary tract, epilepsy, intellectual disability, intermittent explosive disorder, macrocephaly, Mayer-Rokitansky-Küster-Hauser syndrome, microcephaly, neuroblastoma, schizophrenia, and thrombocytopenia-absent-radius syndrome." 

"However, multivariate linear regression detected a linear increase in CON1 [a sub-famliy of the genes carrying DUF1220] dosage that was progressively associated with increasing severity of each of the three primary symptoms associated with ASD [autism spectrum disorder] as measured by the ADI-R. With each additional copy of CON1, Social Diagnostic Score increased on average 0.25 points (SE 0.11 p = 0.021), Communicative Diagnostic Score increased 0.18 points (SE 0.08 p = 0.030) and Repetitive Behavior Diagnostic Score increased 0.10 points (SE = 0.05 p = 0.047)." 

"Given our recent data linking DUF1220 with neural stem cell proliferation (J. Keeney, submitted), this effect could be related to the timing and rate of neurogenesis, such that too many neurons produced too quickly may result in an overabundance of poorly connected neurons. This initial overabundance would in turn inhibit the formation of long distance projection neurons. This process, resulting from (or exacerbated by) CON1 dosage increase, could in turn lead to the excess of localized versus long-distance connectivity seen in individuals with ASD [autism spectrum disorders]."

These clues drive a great deal of interest in finding out what these genes and their encoded proteins do. They have apparently been under intense positive selection (for accumulating duplications and variants) over recent evolutionary time. And this is despite setting up a fraught situation in the genome, since repetitive sequences are more prone to rearragements and other errors, as seen in the various genetic defects located at the 1q-21 chromosomal position. They are clearly part of what makes us human, and diverse as humans.

• Doubt is still faith, if you are unwilling to change your mind.
• Australia's environmental policy... going downhill.
• But the climate can be saved, for a low, low price.
• Hits to Wikipedia can track influenza in real time.
• We are still on FIRE.
• Artificial intelligence is back, baby!
• Low taxes are not enough: Romney and friends pay no taxes at all, off-shore.
• Adam Smith was pro-Occupy.
• Wolf on Piketty: Do we really want to go back to Victorian / Dickensian capitalism?
• Polanyi: "free" markets brought and will bring disaster.
• Krugman psychoanalyzes the right. Is it too easy?
• Economics quote of the week, Brad DeLong on conservative arguments, based on maximizing overall GDP, against the minimum wage and other social controls on income, if one even grants that premise:

"The problem with this, of course, is that maximizing real income per capita does take a stand, and a very fictional stand, on interpersonal value comparisons. To maximize real income per capita is to assert that each dollar at the margin--no matter how rich is the person that goes to--has the same effect on marginal utility, has the same effect on the greatest good of the greatest number."

The Dogs of War

Review of "Savage Continent", about post-war violence in Europe.

We have, typically, a very positive view of Europe, as home (though not exclusively) to philosophy, literature, classical music, enlightened politics, science, socialist government (more or less), capitalism, human rights, the UN, and the whole package of first world development. But then there are World Wars 1 and 2. What happened? Were they some kind of aberration, or a deeper expression of our humanity? Are we finally "civilized" now, able to keep the genie in the bottle forever more?

And are Europeans, and developed countries in general, different from other peoples of the world? Obviously not. That is one of the most important messages of this book, for better or for worse. We are all human, and the systems that keep inhumanity at bay are delicate social structures, unspoken virtues of civic morality, and prodigies of carbon-fueled prosperity that are probably much less robust than we take for granted.

What happens when those structures are blown away, and armies rape and pillage their way over the land? Everyone is traumatized, and long-cultivated morals fall away. Tribal affinities, long subsumed under nationalist, or even internationalist ideologies, resurface, because the basic question is.. who is left that can I trust? Injustice begets further injustice, as those who have been violated, or live in fear and desperate straights, rationalize retaliation and pre-emption without great care as to the targets. Rumor and hatred run rampant. Those who can get away with murder and robbery, do so. We are in a dog-eat-dog setting, as social circles and controls contract dramatically, down to practically nothing.

Author Keith Lowe describes this process in the wake of World War 2, when countless scores were settled, more people were dispossessed and killed, and new wars started, all after VE day. He brings tremendous detail and narrative flair to an enormous story, spanning the continent. A recent blog post mentioned how perilous it was for Jews miraculously spared from the holocaust to return to Poland, where their homes and property had long been taken by others, and where, more significantly, German-radicalized antisemitism was alive and well.

Another example is the widespread ritual shaming of women who had slept with the enemy. A few were killed, but most were stipped and shorn for their participation in the emasculation of their own country's men and honor. Their children often had a far more difficult time, shunned both in the home country as well as in Germany, if they turned in that direction. There were vast movements of refugees, as the slave labor force of Germany was freed to return home, concentration camps emtied, and new ones were set up. Germans were kicked out of the newly West-shifted Poland, and out of Hungary and Czechoslovakia, almost 12 million in all. And even those who were not driven to move crawled out from under the rubble of war, in Germany and especially in Eastern Europe, which had been brutally overrun two or more times.

Of eleven million prisoners of war, one million died in the Soviet gulag, while 100,000 died in camps of the other occupying powers, according to Lowe. On the other hand, formal efforts to hold the perpetrators of the war accountable were virtually toothless, due partly to the continuity of fascist power structures, incensing populations across the continent, who often, particularly in Italy, took justice into their own hands.

Lowe gives particularly welcome attention to the new wars that broke out in Greece and Yugoslavia, as the new reality of an east-west cold war began to set in. In Greece, the Western allies shockingly tended to side with what had been the fascist right over the communist left, who had constituted the resistance during the war. In Yugoslavia, Tito and his communist partisans had long prioritized winning the civil war over winning against Germany, and made no bones about shooting whoever needed to be shot when it was all over. They had no time for prisoners at all.

So this is an important book, however cursorily I treat it. Right now, we are tiptoe-ing backwards into European history with Russia's "protection" of its ethnic comrades in Ukraine. Ukraine was one of the "burned-over" regions of World War 2, as if its own prior holocaust from Stalin's starvation campaign wasn't bad enough. Now Putin wants to dismember it, if he can't corrupt the whole of it into servility. Shades of German policy at Hitler's height, which brought on the previous horrors, one has to say.

But what to do? How do we respect and learn from the tragedies and mistakes of yesteryear? By starting wars more expeditiously when lines of international civility are crossed (modelled by World War 1, perhaps)? Or by foreswearing all war, until we are at the wall and must, perforce, start World War 3? Or by threading some kind of diplomatic middle way between the would-be dictators and the apathetic democracies? Putin is no Hitler, but follows the same fragile logic of bullying to power, internally and externally, with a side of external revanchism. Lowe's book does illustrate that avoiding war, even at some moral and other cost, does have enormous virtues. It also re-animates the virtues of having a decent, and powerful world government that would reign in the lawlessness of international relations.

• The nuts and bolts of the mortgage fraud machine. How Goldman got away with buying insurance against losses it itself engineered, and then got the government to pay out the policies via bankrupt AIG.
• "Eight Rich Americans Made More Than 3.6 Million Minimum Wage Workers". Why, exactly?
• Fundamentalist Biblicalism: putting head in sand.
• Wall Street- even worse landlords than regular old landlords.
• Krugman on Piketty and inequality: it's the wealth, stupid, not just the income.
• Who is running things, anyhow? "... the collective preferences of ordinary citizens had only a negligible estimated effect on policy outcomes, while the collective preferences of “economic elites” (roughly proxied by citizens at the 90th percentile of the income distribution) were 15 times as important."
• Police pay. Self-dealing doesn't just happen in board rooms.
• Economic quote of the week- Felix Salmon, reviewing Flash Boys:

"After all, the fact of the matter is that of all the various actors screwing your mom and pop out of the money in their retirement account, high-frequency traders are at the very bottom of the list. If, that is, they’re on the list at all."

• Economic graph of the week, on age-ism of the recession. Another chance for the free market to defeat the public good.

Weeks unemployed, different age groups, over recent years.