Bacteria Form Communities Too

Moral issues among the tiniest life forms.

Sometimes it takes a village, even for bacteria. Famous for being mindless, pitiless, evolutionarily-honed automatons, it turns out that bacteria have need of community and have ways to detect and signal that a community is ready for action. Not only that, they have ways to punish cheaters who do not pull their weight for the collective, tiny as it might be.

A recent computational biology paper developed game theory models based on bacterial dynamics to explore what signals are needed for group cooperation and how they evolve. Suppose that some bacteria face a food source (say a piece of wood) that requires acidic pH to digest. One bacterium isn't going to make much headway by itself. But if a thousand gather and crank out some protons in unison, they could make themselves a feast. Then what if one of them decides to loaf around, eating its fill but not producing any acid to help digestion?

This presents a series of problems. First, each bacterium needs to be able to tell whether there are enough colleagues about to make a collective / individual effort worthwhile. Second, it needs to know whether such a decision is shared by the others, so that they act in unison. And third, of course, they need to devise some way to punish or mitigate cheating and loafing.

Incidentally, these authors refer routinely to a personified "Nature", as in "We shall assume that Nature may choose between two different states ...". This is somewhat off-putting, and doubtless a consequence of being computationally oriented, making them wish to make it clear when they are speaking of natural cases, versus in silico, modelled cases. This should, however, not create any presumption of a theology of some shadowy entity behind the curtain or pan-consciousness, etc.

The authors simulated basic game theory conditions where individuals either signal or do not signal, with varying costs, and either cooperate or do not, responding or not responding to the majority signal around them. The idea was to vary the costs and benefits, and introduce mutants that employ other strategies, to ask what conditions lead to stable conditions, especially those resembling the world we actually see, where cooperation is, among bacteria, reasonably common.

In fairness, they asked themselves quite limited questions, focussing on whether signalling systems routinely evolve under conditions where cooperation is beneficial. Obviously, the answer to this is going to be yes, under any state where the conditions vary and are not adverse, requiring cooperation, all the time. The strategies they entertained were brutally simple- either signal or don't, and either cooperate or don't. So there was little subtlety.

Bright / beige areas show where most of the simulated populations reside under various conditions, while practicing the cooperative, signalling responsive strategy. The Y axis is cost of signalling. Very high costs (as a proportion of the benefit gained) do inhibit signalling, but this is biologically not very realistic. The various graphs then show: 1. selection pressure for the cooperative benefit, which strongly stablizes cooperation, as well as signaling  2. As the cost of cooperation rises, populations are OK with higher signalling costs, given a relatively high selective constraint for cooperation, (gamma 𝛾 is set at 5). 3. If the rate of bad conditions rises to high levels, it makes no sense to signal that fact, really, and populations cooperate, either without signaling at all (i.e. all the time) or in response to a lack of signal.

One further problem is that the authors have given themselves the simplification that only one mutant form can exist at a time, either invading and taking over the whole population, or dying out before the next mutant strategy comes onto the scene. That means that a shirker strategy of benefitting from the cooperation of others may briefly invade a more cooperative population, but can never realistically take over the population when the benefits of cooperation (i.e. selective pressure for cooperation) are set high.

Thus the main question that we would realistically have about cooperative strategies, which is about the stable rate of shirking in otherwise cooperative populations, and the evolution of counter-strategies of detection and punishment, never come up in this analysis.

Thankfully, there is other work in the field that has established punishment strategies, though not yet any active surveillance and detection strategies, which might be beyond bacteria's cognitive capacity. In one example, the human pathogen Pseudomonal aeruginosa secretes small amount of cyanide, which the cooperators are resistent to, but the cheaters are not.

Small as they are, bacteria face basic dilemmas of survival and group action. They have the glimmerings of moral needs and one can readily see how increased capabilities led to increasingly complex behaviors of evasion, deception, and group control that we express in our moral systems.

• Another paper on the collective propensities of bacteria.
• Some notes on the origin of the Origin.
• Hello, eco-pod.
• Some questions are lies. Many of them, actually.
• MMT at the BOE.
• Obscene spending by the rich. But honestly, the real problem is that they don't spend enough.
• Workers need more power. Freedom for companies does not equal free markets.
• The case for vacation.
• A private company committing fraud? We are shocked!
• Fiscal policy would have been very effective. Paying people more would likewise be very effective.
• All you can really fault the Fed, in policy terms, is for not pushing for more fiscal policy. This paper also makes the important point that higher unemployment equals higher inequality.
• Organized crime is dead.. long live finance.
• Bill Mitchell on the full employment period and policies, vs our feudal age.
• Walmart hires according to pure managerial and business merit, reinforcing the idea that CEOs deserve extraordinary pay and power on a marginal utility & productivity basis.

Mesmeric Maleness in The Bostonians

What was Henry James thinking in his novel about women's suffrage?

Henry James lived in the closet, a Victorian "bachelor" transplanted from the US to Britain. I don't know much about either him or his work, but was somewhat mystified by his novel, The Bostonians. This review is spoilers all the way down, so quit now if you don't want to know the plot.

It is a triangle at heart, with one vertex named Olive Chancellor, a rich, young Boston woman dedicated heart and soul to the liberation of all women. James's prose is wonderfully evocative in the first half of the book, describing her joyless, earnest, spinster life, and particularly her hatred of men- individually, corporately, comprehensively. Her long-lost cousin Basil Ransom forms another vertex. He is not from Boston, but rather from a South that is still prostrate after being crushed by the Civil War, and setting up shop in New York as a lawyer, to very little success. He is apparently handsome and well-spoken, indeed well-mannered, but given to the most retrograde opinions, especially when it comes to women. When he comes to Boston for the first meeting of their lives, he meets the last vertex of the plot, the lovely Verena Terrant.

Verena is slightly younger than Olive, pretty, and the daughter of relatively low-class parents of whom the father is a mesmeric healer. He has passed his gift in some degree to his daughter, who is a captivating public speaker and is introduced to both Olive and Basil at a public meeting of the local women's movement sponsored by a friend of Olive's, and speaks briefly about women's rights and oppression. Verena is instantly recognized as a sensation, and Olive spends the first half of the book taking her under her wing as a protoge, to speak all the things she herself is not talented enough to say, at least in public.

The second half of the book describes an excruciating compaign by Basil, who has been equally captivated, though in an entirely different way, to win Verena's heart and shut her mouth. He jokes and mocks in a light-hearted way, but when they finally have a serious discussion, Verena is shocked and repulsed by his antediluvian attitudes. Verena is consistently portrayed as exceedingly bright and quick-witted, ready with sharp, though never bad-tempered, repartee.

So it is mystifying in the extreme that James engineers the plot to have Verena fall hopelessly in love with Basil, especially when there was another suitor much better suited, so to speak- rich, handsome, sympatico, supportive, and a wonderful pianist to boot! Olive had previously extracted a promise from Verena that she would never marry, so as to keep the sisterhood unsullied, but this is a promise that one knows immediately is as doomed as it is inappropriate, since Verena is cut from far more colorful cloth than Olive.

Nevertheless, James requires that Verena's brain falls out of her head to have us believe the ending, where Basil scoops her up from the spectacular proscenium where Olive has arranged to have Verena give the feminist manifesto to the assembled throngs of Boston's high society. Basil whisks her away to a married life- full, as James promises at the end, of tears. James makes out Basil as some kind of enchanting reptile:

Verena writes to Basil from her Cape Cod cottage, where he had invited himself in unannounced and proceeded to court Verena for several weeks:

"In the course of the day Ransom received a note of five lines from Verena, the purport of which was to tell him that he must not expect to see her again for the present; she wished to be very quiet and think things over. She added the recommendation that he should leave the neighborhood for three or four days; there were plenty of strange old places to see in that part of the country. Ransom meditated deeply on this missive, and perceived that he should be guilty of very bad taste in not immediately absenting himself. He knew that to Olive Chancellor's vision his conduct already wore that stain, and it was useless, therefore, for him to consider how he could displease her either less or more. But he wished to convey to Verena the impression that he would do anything in the wide world to gratify her except give her up, and as he packed his valise he had in idea that he was both behaving beautifully and showing the finest diplomatic sense. To go away proved to himself how secure he felt, what a conviction he had that however she might turn and twist in his grasp he held her fast. the emotion she had expressed as he stood there before poor Miss Birdseye was only one of her instinctive contortions; he had taken due note of that- said to himself that a good many more would probably occur before she would be quiet. A woman that listens is lost, as the old proverb says ..."

The Bostonians was not well-received in its day, nor since, I think, and no wonder. Here is the novelist, however skilled in his language, making marionettes of his characters instead of following their development based on their given, or even plausible, natures. George Eliot and Leo Tolstoy come to mind as authors who were far more organic in their creations and their willingness to properly mould their characters and then follow them, come hell or high water, to more believeable, as well as artistically deep and edifying, conclusions.

Then there are the sexual issues involved. Olive is commonly understood to be a lesbian, but I would disagree. Hatred of men is not by any means confined to lesbians, or characteristic of them. Olive is consumed by her ideas, and by do-good-ism, and while I may have missed something, there is no overt note of lesbianism in the book. The closest one comes is in the final scenes when Olive loses Verena in a cataclysm of public and private humiliation. Which is all understandable enough on the terms given, without making the additional inference of sexual involvement between the two, in any form whatsoever.

On the other hand, Basil's magnetism is wholly unaccountable. He is repulsive equally to Verena, to Olive, and to the reader. The courtship is posed as a brutal contest of will, which Basil wins, apparently due to being male, confident, and conservative, with no high opinion of women. Verena, on the other hand, tends to have a submissive character, first to her parents, who are lightly sketched in the book, and then to Olive. Her fall for Basil might be taken as a sort of opposites attract kind of story, or as a defect in her character whose double edge cuts Olive so grievously. Even so, given Verena's high consciousness, her conquest seems in the end an insult to women in general, which hopefully was not James's aim.

James communicates none of his own ideas on the suffrage question directly, treating each side with cruel derision, including Basil's. He makes of another character, Olive's sister Mrs. Luna, an eye-fluttering, female wile-throwing ogre. But he also presents the feminists as dedicated and effective in a public, political sense, which belies Basil's conviction that they have no place in public. He dreams of having the public's ear for his own views, and exhults when one of his articles is accepted by a obscure crank magazine, while Verena and Olive actually do have the public's ear and are busy organizing a lengthy campaign for empowerment. One which took a century and more to come to pass, but which James of all people should have appreciated somewhat better than he shows here.

• Fix education by making better teachers, not by flogging them.
• Libraries remain critical institutions.
• Attention, Pluto, we are getting closer!
• "This gene, HLA-B, is the most variable in the entire human genome, with thousands of known forms in existence."
• Krugman on the coming Grexit: what if Germany is the last one holding Euros?
• Bill Mitchell on the Grexit.
• Bernie deserves a little more love.
• Which side is Hillary on these days?
• Smarter presidents do smarter things.
• One more place where "free" markets don't work- electric utilities.
• Occupy, indecisiveness, consensus, and theology. We need more structure.
• Bailout risk ... indicates more regulation is needed.
• On the brazen impunity of banks. And again..
• Economic quote of the week, by Brad DeLong: "... the aggregate economic costs to America of local NIMBYism now appear to me to be much larger than I would have thought reasonable decade ago: we are no longer a country in which people can afford to move to places where they will be more productive and more highly paid because high-productivity places refuse to upgrade their residential density."

Atheists Have No Morals

A "truth" one comes up against all the time. And what are morals, anyhow?

You hear it all the time, as an atheist. "How can you be moral if you don't believe in anything?" Or some variation, perhaps citing Nietzsche in more sophisticated versions. It is an earnest enough question, given the life-long indoctrination that religions practice, and the dependence- intellectual, social, and moral- they foster.

In large part it is a tribal badge, this conviction that we are the good ones and the others are not good. Without even looking into the particulars of a community's moral code, one can assume that they view theirs as good, and those of outsiders as deficient if not evil. Even the mob has its code of honor. Religious community membership commonly functions as a social signal of trustworthiness, of goodness, good intentions, and proper upbringing. It was not long ago that everyone had to be a member of a local church, or the national church, or was shunned. The Muslim world exemplifies this tendency, currently.

In that it does not differ much from nationalism, or membership in any other club, masonic order, Elks lodge, etc. But religions claim much more. The typical religion not only forms a social club, but to validate its existence and inflate its importance, claims to know mysteries of which the lay bumpkin is ignorant- the nature of the cosmos, the ultimate reality, and the desires of god. It offers cosmic as well as personal transcendence, and offers an objective moral order. This is the rock on which believers lay their bigotry, that they have answers to moral questions which for the atheist have no answers, leading presumably to despair at best, murder at worst.

This moral order has been under continuous renovation from time immemorial, but that doesn't keep theologians from claiming that it is objective and absolute, thus giving them the power to conflate what supposedly is (what god wants) into what you should do. God said X, therefore you must do X. Only, so much scripture has piled up in the mean time, so full of conflicts and ambiguity that there is simply no way to a clear interpretation. On the one hand, this means that all fundamentalisms are doomed to be just as subjective and self-serving as the modernist / deviationist interpreters, and on the other hand, it means that the devout need the services of some interpreter, to render fatwas out of the thicket of their so-called objective text.

So it is not really objective after all, and one empathetic judge or practitioner can do more for her flock than gaggle of rule-divining theologians. But wait, isn't the mere proposition of an objective moral order worth something, and better than the utter nihilism of atheism? Isn't the dedication to seeking moral truths, however far we are from discerning or attaining them, one key point of religious engagement and a noble quest that separates us from the brutish, thoughtless, care-less atheists? And even if the moral order is ambiguous, isn't the promise of a deity who sees all and judges all a prod to good behavior?

Well, those are fascinating questions. If one doesn't really know what is good in a reliable, clear way, however, it hardly seems helpful to have an eye of Sauron watching our every move, or the promise of eternal suffering if we take a wrong step. Theologians themselves are all over the map on the reality of hell and the nature of posthumous justice. The Catholic church recently excused babies from their stay in purgatory, after centuries of selling indulgences and demanding pennance of endless varieties from its adherents to get their loved ones out of it. The fact of the matter is that we behave as if our conscience is our final judge, whatever our theological commitments. It is our conscience that is the field of moral battle, whether it is cultivated by a program of guilt and self-hatred, one of compassion and calm introspection, or one of empathy with other living beings of all kinds including humans.

More interesting is the question of the quest for moral laws. Our legal systems are always straining to make their apparatus and judgements seem as objective as possible. Guilty! Innocent! The lure of certainty seems to be a strong feature of human nature, and this illusion is surely of practical benefit to our systems of communal judgement. A cautionary example can be seen in the sorry state of our Supreme Court, which has, though its nakedly ideological bickering and party-line decisions, ceded any claim, even illusory, to objective, above-the-fray judgement.

So each religious tradition toils on, seeking that final, absolute moral object that will tell its children to go to bed on time and to turn off their cell phones. And the kicker is that they phrase this as finding out "what god wants", as if unloading all the ethical work to someone else elevates our moral nature. As you can probably tell, I regard this as quixotic at best, for our morals are very much ours, and are fundamentally subjective and biological. Had we no empathy for our fellow creatures, all would be lost, whatever the absolute moral code. Conversely, the person who cares for others and expands her sympathies to the largest possible extent has no need of theological commandments.

So seeking for objective morals is a fool's errand. But that doesn't mean that there is no room for serious moral inquiry, particularly that premised on things that are real, like the existence, needs, and desires of others and our many levels of individual and communal interest. It is complicated enough without invoking unseen phantasms.

Which brings us back to the atheist. Once one understands that there is no moral high ground for those who pound on bibles or cart about granite slabs inscribed with the ten commandments, and that communities will typically grant themselves moral superiority whatever the content of their codes and practices, (one is reminded of the extensive forgiveness the Catholic church lavished on its wayward priests), one is left on a much more even playing field.

Religious people are often perplexed by the apparent uprightness of atheists. They seem to be smart, well-behaved, oddly capable of putting up a good front and not getting into trouble. What could be going on? Statistics of course reinforce that impression. Atheists are indeed better-behaved than religious people, staying married longer, murdering less, having fewer abortions, committing less crime, etc. Truly, a conundrum.

It almost seems as though attentiveness to reality, not only in the form of science, evolution, and similar nerd-ish fixations which lead many atheists to their philosophy, but in the forms of civic affairs, politics, history, and psychology- attentiveness in short, to other people- might form a sounder moral education than indoctrination in some crazy story about master beings, resurrections, perfect scriptures, and eternal life. The humanist viewpoint (which is the general atheist position) may not have the plotline and passion of dramatic religions, but that may be a point in its favor. While religions often foster the best in humanity, they frequently seem to go astray, whether due to inattention in the face of the distracting, even overwhelming, story they carry, or directly from some part or interpretation of that story that gives official license to violate the most basic elements of human morality. The Israel-Palestine conundrum comes to mind.

When pressed, a religious person may offer that, sure, given the culture we have inherited, most atheists still manage to do alright, but this comes from the solid grounding that Christianity has given the West (insert culture and religion of choice here). At some point, if religion continues to decline and our cultures lose this moral anchor, there is no telling what might happen. Even those idyllic quasi-socialist countries of Scandinavia that are the most secular in the world still have state churches and their rich moral patrimony.

This gets the correlation all wrong, however. It is the most religious countries that are the most backward, and the least that are socially more just, with lower crime, incarceration, etc. If religion were having all these salutary effects, why aren't the most religious countries the happiest, and the least most ridden with crime and immorality? But we see the exact opposite. It is almost as though religion is a counter-reality coping mechanism that is most attractive in countries mired in poverty and corruption, if not causing poverty and corruption. And that it seems to be unnecessary in effectively atheist countries like Luxembourg, Norway, and Denmark, either personally to help people survive adverse conditions, or communally to foster good behavior.

Additionally, one should realize that in the West, Christianity had over a millenium of free reign during the Dark and Medieval Ages. Much good was done, but I think on balance, the moral tenor of the West has increased considerably since that time, in the wake of the Enlightenment. It was the Enlightnment that generated secular concepts like fundamental human equality, human rights, democratic government, rationalism in public policy as well as scientific investigation, and much more. As ideals, they owe quite a bit to the preceeding religious conceptions, but were remade on a secular basis that made them far more effective, as it was the church itself that was a significant source of oppression, corruption, and obscurantism. We have gone to far greater moral heights in the modern age than were ever achieved previously, even while we grapple with enormous problems of scientific & political success. There were several horrible atheist movements and governments in the 20th century, which must be noted, but which have thankfully each been substantially reformed if not eliminated. Each could be seen as a religious movement of an idealistic, fanatical sort, at least in sociological, if not theological, terms.

Lastly, what of personal spirituality? Even if religions make people no more moral, empirically, than other philosophies, and even if they are factually false, and even if theology is a parody of scholarship, isn't the personal resonance with our surroundings, deep questioning, and quest for some kind of transcendence a significant feature of humanity, and of human morality?

I would actually agree with that, with some caveats, since the atheist is, in reality, just as spiritual as the religious person. The problem is whether one indulges this innate impulse with inferred pseudoscience and systems of social control based on hosts of invisible beings. The wonders of nature remain wonderous whether one chalks them up to deities or not. Religion is an *example of humans yearning for understanding and meaning, but is far from the apotheosis or sole source of meaning, let alone legibility for understanding the world. It is healthy for people to share their spiritual questions, insights, and commitments with each other, which is why not just religions, but academies, libraries and universities were invented. Here is where love- for spirituality is really the love of life and the world around us- is exercised as the freedom to be interested in and draw meaning from ... other people, phenomena of nature, arts and self-expression, and the best thinking that humanity has to offer.

This is transcendence with discipline, making of ourselves better beings, morally as well as intellectually. The idea of getting on the good side of an invisible being, or counting on another life better than this one, if such theories are not well-founded, seems a little cheap in comparison to humble dedication to slow betterment in & of this life.

• Annals of religious BS. Being personally related to god prevents drug abuse: "We have multiple ways of knowing: we have intuition, we have rigorous logic, we have investigation. We need to use them all. They’re all important, valid forms of perception."
• Annals of really serious religious BS.
• Some people call it mystery, others call it BS.
• Annals of denial: rise of the "nones" = culling of those "pretend Christians".
• Atheism is on the rise in the Middle East.
• Keeping tabs on Syria. And Iraq.
• On being wrong, and being really, really wrong.
• Virtually any existing condition is "Pareto optimal".
• Climate action is needed immediately.
• Happiness is an institutional, social issue.
• Banks are too big, and we can make them smaller.
• What is the problem with Keynes? Just imagine if government worked consistently against economic feudalism instead of for it.
• Were the founding fathers Keynesians?
• Finally, a church I can relate to.

Death of a Species

Callous indifference and business-as-usual greed dooms the delta, and the delta smelt.

As ecological icons go, the delta smelt isn't much. A small silver fish, like a zillion others. But it lives in the way of dredgers, bulldozers, farmers, shippers, and a thirsty multitude. It was put on the endangered species list in 1993, and has kept right on dwindling, until in the most recent count, a single smelt was found. One.

The San Joaquin / Sacramento / San Francisco Bay delta used to be a very large estuary of marshes, reeds, rivers, and islands that gradually fed the great rivers of the Sierras into the Bay and thence through the Golden Gate the Pacific ocean. Fresh water met briny in constant tidal and rain-fed flows. Smelt were obviously not the only beneficiary of this rich ecosystem, but countless shellfish, mammals such as beavers, insects by the billion, and birds by the million. The delta was a major stop on the Pacific flyway for migrating birds. And it was the conduit for several species of now-endangered salmon.

Comparison of the delta as it was, and as it is now. Virtually all its marshland and most of its complex river habitat is gone.

Despite the popular image of California as a state of nature and natural wonders, it has been pillaged in the name of greed from the beginning. The Spanish mission system started the ball rolling by enslaving and decimating the native peoples. Then the gold rush led to thorough destruction and pollution of the rivers, while working its way upwards into the hardrock mines of the Sierra. Next was agriculture, which in California became a rapacious and short-sighted industry, well-illustrated in the now-obscure novel by Frank Norris, The Octopus. Then it was onwards to a thorough re-plumbing of the state by the water lords of Southern California. The latest incarnation of this get-rich quick ethic was the dot-com bubble, by which Silicon Valley took investors all over the world to the cleaners.

The little smelt and all the natural riches it stands for had little chance, of course, when there was free, fertile land to be had by diking, draining, and dredging. A state which had some inclination to protect the spectacular, yet conveniently remote and barren, high Sierras, had no appreciation for the ecological values of wilderness in the bottomlands, even for flood control, which is increasingly difficult as so much of the "reclaimed" land is under sea level, protected by primitive, flimsy dikes. With the extended drought and the vast rerouting of fresh water, the delta has begun to flow backwards, introducing salt as well. But the state, being owned by its commercial interests, leaves public and ecological policy to die a quiet death, along with the smelt.

The planetary climate and biosphere face similar forces of corruption, greed, inertia, and neglect, which will just as soon see it die with a whimper than plan in a public and morally forward thinking spirit for future generations of all species.

• Notes on our friends the Saudis.
• Secularization hypothesis finds new support.
• Further notes from the religion of peace.
• The odd history of US fundamentalism.
• Bruce Bartlett just can't take the corruption any more.
• Even if corruption is quite natural.
• Notes on real estate redlining.
• Economics is not yet a science.
• Silence on fiscal policy is dereliction by central banks.
• Bill Mitchell on the Australian budget process. A cartoon.
• Aetna raises its minimum wage: "The pay raise and benefit program for low-wage workers will cost Aetna only $26 million, while the CEO alone made $15.6 million last year, though most of it in stock options."
• Some problems with TPP.
• Class and money beats performance.
• Essay on the new frontiers of brain science, and its changing nature.
• 110 year old infrastructure for trains? We can do better.
• Two banks find a judge with a spine, after they lied to convince Fannie and Freddie to go subprime.
• Economic graph of the week: Stiglitz on inequality.

The Imperialism of Universal Values

We shouldn't pretend that everyone shares our values.

Values are not universal. It is simple as that. The imputation of our values, even the most rationally derived and well-meaning, to others does not mean they are shared by them. We can claim that there is a basic human nature that intrinsically shares some values. But even then, others may have different priorities, so that even if they share many individual values, they might rank them differently, preventing us from claiming any basic set as absolute or universal. Indeed,  ideologies are notoriously powerful in re-arranging our values, to the point of valuing death over life.

The brief interlude of enthusiasm for universal rights, in the wake of World War 2, might seem to belie this philososphy. But really, it was more of an exercise in victor's justice and idealism, as well as cultural imperialism, than it was a free response of all countries around the world to the new concepts of inalienable human rights. Half the signatories to the declaration of human rights were, after all, totalitarian countries of various stripes. And it came under immediate protest from Islamic countries.

This informs the debates about Muslim responses to Charlie Hebdo, other cartoon provocations, and the West in general. Others may simply not rank free speech as highly as religious belief and cultural tradition. We in the West have a hard-won rationale to prefer our ranking, religion being a font of sensitivities and claims to power that, given precedence, tend to grow endlessly, gobbling up all other rights and ideologies. But the Muslim world has its centuries-long experience as well, which can't simply be disregarded and overrun for the sake of what we call progress. Even if we ideally could take a poll of each affected Muslim to truly, democratically, figure out what they want, as opposed to what their various mouthpieces, governments, and leaders want, that presupposes the validity of democracy, which itself is a contested value.

The same issue extends to the treatment of women. The current Western dispensation towards liberation and equality is extremely novel, even in the West, so whatever its moral virtues in our eyes, and even those of Muslim women if that be the case, it can't claim any intrinsic universality.

This is all to say that the attacks by Muslims on offensive authors and artists can not be addressed by lecturing them or the Muslim world on the sanctity of free speech, human rights, and obvious morality. There may be an argument to make from within the Muslim tradition. The Quran expresses occasional mildness towards unbelievers, instructing to treat them fairly and ignore them otherwise. Unfortunately, such arguments stand little chance against the major themes of the Quran, which pours hatred and scorn on unbelievers and apostates on most other pages.

So perhaps the better argument is simply one of cultural self-preservation. We have a right to our values, whatever they are, and while it would be ideal to convince others of their goodness and rationality, that is far from a guaranteed course. Perhaps these defenses of free speech and rights of journalists are really directed to the choir, to buttress the values we already share, in the face of a terroristic challenge. Which is in fact straightforward cultural warfare, seeking to displace our values with others, and tactically to turn our virtues of openness against us.

The hijab is a particularly effective and notable aspect of this cultural war, being fought in Europe for the most part, the frontier between Middle East and West. While migrants are desperately seeking the safety and economic refuge of Europe, many of those already there seek to carve out cultural islands separate from the larger society, (though often perforce, being discriminated against), and sometimes, to hear what is going on in European mosques, against the larger society. The hijab is a public reminder and marker of this social segregation and power, showing a separate sub-society in the midst of the larger one, even while it relies paradoxically on the freedom the larger society makes possible. It is a message that may be read in various ways, but one way is surely as a rebuke to the dominant values, as many other religious movements have expressed through European history, incidentally.

How do these values relate? If the rebuke being offered were of a constructive nature, as nuns and monks have embodied for centuries, (at least if one takes a charitable perspective!), complete with distinctive clothing, it would not raise much ire. But the offered value system seems, at least to the West, highly distasteful, based as it is in the bigotry of the Quran and the bitter patriarchy, dysfunction, and closed-mindedness of modern Islam. For they have their imperialistic, universal values as well.

It just remains for us to reject those values, without assuming that those who are trying to displace them actually, paradoxically, believe in them. And to protect ourselves physically and socially from their proponents. What makes it tricky is that the Muslim community in this instance is not monolithic, like some army of Mongols at the gates. Many seek to assimilate, the vast majority are peaceful and appalled by their own coreligionists. So it becomes a policing issue of detecting insurgents within the gates; something that, while surely corrosive to our assumptions and traditions of openness, is hardly unprecedented in the history of the West, going back through the Cold War to the history of Venice, which in its heyday had particularly effective intelligence services.

• Prospects for the Middle East ... look poor.
• Afghans aren't the only corrupt ones in Afghanistan.
• Dennett on religion & the future.
• Religion and science are not in conflict at all. Hmmm.
• Scientology was already a criminal organization back in 1973.
• Ford Doolittle, on the stupidity of nature.
• Will management be the last employees?
• Reich on the TPP. Corporations want to run our countries ... more than they do already.
• Krugman: Jobs, pay, and stability are the issue in Baltimore.
• Krugman: Redistribution really works.
• Krugman: Thinking would also work, if more people did it.
• State's rights aren't always the top priority in Nuttistan.
• Supreme court lays another egg. Corruption is OK for other people.
• Economic efficiency has virtually nothing to do with today's inequality. Power and ideology are the issues.
• Bill Mitchell on money and banks, pt 1, pt 2.
• Economic graph of the week, from the IMF. Our finance industry is negative, not positive.

Do Neurons Use GPS?

No, neurons and their axons use chemical guidance signs to find out where they should be going, in huge migrations though development.

The brain and nervous system don't just happen by way of cell division during development. They are products of enormous migrations from points of cellular birth, which are generally at the edges of the nascent structure, such as the ventricles of the brain. And getting the cells to the right place is only half the story, as neurons then send their axons all over the place as well, to create those amazing connections that run our bodies and minds. Neurons that enter our feet typically have their cell bodies at the base of the spinal chord and send axons along a tortuous path that of course ends up going about three feet in adults. It is astounding.

Some of our neurons are very long, and for most neurons, their axons as well as cell bodies migrate substantial distances during development.

Obviously, the mechanisms behind these movements are going to complex. One example is in the brain, where new neurons travel out to the various layers they are destined to inhabit via a scaffold of guide cells, the radial glia. Even when such physical structure helps out, the primary mechanism is a sort of pheromone system, like what ants use when making trails, but a good deal more involved. A recent paper describes the chemical signals that guide neural axons of the mouse through a critical crossing at the midline of the spinal chord.

These axons are called "commissural axons", since they cross the bilateral joining point, or commissure between the two sides of the body. In the brain, the corpus collosum is a large bundle of such axons.

"For example, commissural axons are initially repelled by bone morphogenic proteins (BMPs) in the dorsal half of the spinal cord. They are then attracted by gradients of Netrin-1, Sonic hedgehog (Shh) and vascular endothelial growth factor (VEGF) towards the floor plate."

The floor plate (bottom) secretes two molecules, Shh and Netrin, in wild-type mammals. If either one is mutated and absent, neurons that normally use gradients formed by those molecules to know where they are going do not find their way as reliably.

"While it is known that both Shh and Netrin-1 form gradients, it is not clear how steep the gradients are in vivo and how this steepness influences axon pathfinding in gradients formed by single or multiple guidance cues. Although theoretical chemotaxis modeling has suggested that two overlapping attractive concentration gradients could increase the probability of a cell making a correct decision about the gradient direction, this prediction has not been tested experimentally."

The "pass" from one side of the spinal chord to the other, at the early embryonic times when this axon extension process takes place, is called the floor plate of the neural tube. It is the site of expression of at least two guidance molecules, the proteins Shh and Netrin. These are secreted and form a gradient that is sensed by receptor proteins on the axons, specifically by their pseudopod-like front end called the growth cone. One trick is that once axons find their way to the floor plate, they need to reverse their response pattern so that they grow away from it instead of towards it. This repulsion from the floor place is known to be mediated by another molecule, Slit.

But that is not the topic of the current paper, which simply makes the observation that for the attraction phase of axon growth, two signals is better than one. This has been presaged by mutant studies where the mutation of each individual gradient attractant, Shh and Netrin, causes worse axon guidance, but not a complete breakdown of commissure formation as happens when both are deleted (see figure above).

Neural growth cones seen in the process of deciding where to go. Gradients are indicated by the black triangles at sides, as set up in the lab. "A" presents a schematic of a growth cone showing asymmetry of the protein signaling kinase SFK, which accumulates internally on the more highly stimulated side, reflecting part of the cell's mechanism for detecting the outside guidance molecule signaling gradient. SFK responds to both Netrin and Shh.

The researchers take this all in vitro, reproducing the gradients with microfluidic cells, and asking how their cultured neurons move in response. They find that, as expected, gradients that are shallow as they are in the embronic setting where the axons spend most of their time are not very good at guidance for each molecule individually.

Summary of experiments, showing both axon migration (the cell bodies are dots, and the axons lines) and SFK kinase orientation within growth cones, all responding to the combination of two shallow signaling gradients more reliably than to either alone.

They also show that within the guided growth cone, a key protein (kinase) that transmits the Netrin and Ssh signals from outside to inside itself adopts a biased concentration gradient, matching what is detected outside. Aside from validating the other findings, this provides some rationale for large sized of growth cones, which by spreading out physically can detect relatively shallow gradients of their signalling molecules.

It is not a momentous paper, but a small step on the way to learning how the nervous system develops ... from one cell to the most complicated machine in the universe.

• This week in Nuttistan: "ISIS also imposed gun control immediately upon takeover of the terrain under its control.  Totalitarians fear weapons as the only threat to their supremacy.  Do not ever allow yours to be confiscated. The next step is enslavement and death."
• Who are you calling "we"?! Just because someone discovered the Higgs doesn't mean that everyone is a smartypants.
• A godsend for the godless.
• A corrupt God vs the New Deal.
• Big data needs big rules and regulation.
• We have a lot to answer for in Cambodia.
• Grexit is neigh, and neigh-well unavoidable.
• Going to college? Caveat emptor.
• The blue line isn't so thin. And is increasingly corrupt.
• Remember the Dominican Republic?
• Climate change talk is like religion? Just what does the GOP think is wrong with religion?
• Oh ... ISIS deals with some more so-called apostates.

Radio 1: Consciousness as a Streaming Information Service

The benchmark of modern theories of consciousness, by Bernard Baars, 1986: "A cognitive theory of consciousness."

One of the more contentious and mysterious areas in science is consciousness. Its existence was long denied by behaviorist psychology, yet long-standing schools of (idealistic) philosophy have held that it is the only thing that exists at all- that all else is an illusion, or at least subsidiary to the great reality which is consciousness. The universe itself is conscious!

Well, that is absurd, but it indicates the trickiness of a subject that attempts to explain our ability to think about subjects. One quickly gets into philosophical, if not logical, thickets. But it is pretty clear that inanimate matter doesn't think, while we and our fellow animals have, after billions of years of painful evolution, graded abilities to think about things, including ourselves, which arise from that organ behind our eyes ... the brain.

The study of consciousness is now a hot academic field, but that happened only in the last couple of decades, after the long hiatus of behaviorism. Bernard Baars's book from 1986 is a watershed in the field, presenting a functional theory of consciousness which has little to say about its physiological basis, but has profound things to say about its phenomenology, internal logic, and purpose. Its model (consciousness as global workspace) remains the basis for current work in the field.

In some respects, consciousness is extremely small, not to mention slow. We can barely attend to one thing at a time and remember maybe five to seven things in short term memory. Anything we do consciously must be done at a snail's pace, and only once learned becomes faster as it also becomes automatized, and sinks into the unconscious. The unconscious is, in contrast, endlessly vast, taking care of physiological functions all over the body, analyzing speech as we hear it, translating our thoughts into speech as we speak it, and on and on. It is a parallel, not serial, fleet of processors, some of which are very fast. Any action we take is made up wholly of unconscious mechanisms. All we are conscious of is maybe the goal of reaching for a cup, (or typing a letter on a keyboard), and all the calculation and activations in between are taken care of, like magic. A practiced typist won't even think about reaching for individual letters anymore, but will fluently type by the word, or more.

Yet consciousness does one thing that none of these other, learned, unconscious processes do, which is broadcast information extremely widely over a vast population of other (unconscious) processors. When reading some text- consciously, and only consciously- it is judged by a variety of processes that operate outside of immediate consciousness. Is the syntax correct? Is the style fashionable? Is the content interesting? Is the spelling correct? Is the meaning connected to the last sentence? The fact that these issues and many others can only be analyzed when one is "paying attention" has great meaning for the nature and role of consciousness.

I used to think that consciousness was the caboose on the train of thought. The classic experiments of Libet showed that for any action, even so-called voluntary action, electrodes can pick up activating signals well before one is conscious of a choice being made. And it is obvious with the slowness and high-level nature of consciousness that anything that enters it has gone through a great deal of prior processing at other levels of the system. But that doesn't mean that consciousness is only a spectator. No other process provides the integrating, broad reach across virtually every process in the brain, at a high level. Bringing something into consciousness means testing it for coherence at many levels, from spelling to consonance with our model of the world and hierarchy of goals.

Thus consciousness is an active function, specially tasked with broadcasting novel data far and wide over the multifarious pool of unconscious processes, which can each in turn comment on what they see. Is an object moving in the distance? Such an event exites special visual processors and calls to attention what may have not been there before. Conscious attention then allows us to consult our full cognitive battery of memory, world model, goals, etc. to decide what that object might be, in relation to our needs.

This leads to Baars to consider the stream of consciousness phenomenon. Why is it so tenuous and fluid? The fact is that we are virtually unable to attend to unchanging stimuli. Even loud noises, if repeated endlessly, fade out of awareness. The hedonistic treadmill is notorious for habituating us to any pleasure or good forture we may experience, which is soon taken for granted and cast aside in a search for the *next great thing. Consciousness concerns itself with information, in the formal computational sense. Whenever some activity starts to pall or become routine, it fades from consciousness. When learning new skills, this is a good thing, as sufficient repetition causes the whole process to go automatic and unconscious, like touch typing. Good or bad, the phenomenon seems to be universal as well as clearly adaptive. We are constantly on the hunt for novelty and information. Whatever is been-there-done-that is relegated to the dustbin of memory, or obliviousness.

It should also be obvious at this point why conciousness is so narrow and singular. If some data is supposed to be broadcast and commented on by many, indeed all available, other processes for integrated evaluation of an ambiguous or novel situation, there can only be one such item at a time. Consciousness is a radio station we listen to one story at a time. It is, and must be, a serial processor. Baars marvels at the then-trendy studies in biofeedback, which demonstrated that with enough training, virtually every part of the body and mind can be manipulated consciously. Individual muscles can be trained, blood pressure changed, etc. This phenomenon is coming into clinical use for various prosthetic appliances, which can be controlled by all sorts of muscles or thought patterns that wouldn't at first glance be candidates for actuators of voluntary action.

What gets access to consciousness? Again, unconscious processes lead the way. A big driver is our internal hierarchy of goals, one of the major unconscious functions that interacts with conciousness. Do we want a sandwich? A walk? A newspaper? Money? Survival? Life is complicated that way, as needs come up all the time at all levels. When a super-high level goal comes under fire, we are rivetted. Earthshaking experiences change conciousness itself, by re-arranging the unconscious contexts that underly it- it is not the earth that shakes, at least most of the time. Hallucinogens like LSD can have this kind of deep, long-lasting effect. On the other hand, if information comes along that violates a high-level model of reality particularly egregiously, we may also block it out rather than take on the problem of breaking down our painstakingly developed models of reality, (contexts, in Baars's teminology). Thus we fight cognitive dissonance to save them by rationalization, confirmation bias, denial, etc. Bears makes a point of the coherence that conscious contents must have to be useful, which rests on the cooperation of the many unconscious processes / contexts that join to create conscious contents. If these sub-processes conflict rather than cooperate, the result may not be conscious novelty, but rather indecision at lower levels and lack of consciousness on that topic.

Dreams naturally arrive on this train of thought as well, though Baars leaves that topic as an exercise for the reader. Baars does note that consciousness is heavily visual, with much less vivid access to abstractions than to scenes in front of our eyes. He speculates that this may indicate the evolutionary history of consciousness began in straight sensation, and only later attracted goal evaluation, retrospection, planning, inner speech, and all the other aspects that so enrich consciousness for us. During sleep we are released from the immediate layers of the goal system, so one might hypothesize that the consciousness apparatus turns towards free experimentation, using imagery to explore the deeper levels of our unconscious contexts- the goal, memory and prediction systems, which are susceptible to many complexities and internal contradictions. Dramatic role-playing, which is such staple of waking entertainment as a way into the mysteries of the human condition, are here personally staged for our continuing development.

Indeed, the theater is a leading metaphor for consciousness itself:

One can compare the mind of a man to a theater of indefinite depth whose apron is very narrow but whose stage becomes larger away from the apron. On this lighted apron [i.e. front of the stage] 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 ... . 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.
-Hyppolite Taine, 1871

Lastly, one must wonder at how this is instantiated physically. The fact, and it does seem to be a fact, that consciousness involves wide broadcast of its narrow content, with far-flung systems both understanding what they are receiving and sending back ongoing commentary, requires a lingua franca of the mind. One aspect of this is clearly the gamma oscillation, which co-occurs with attentive consciousness and fits the model of something that unites broad but temporary coalitions of brain areas. But what is the code? What is the wave carrying? Is mere coordinated activation from one specialized area to another enough to form useful communication? That is hard to believe, but as yet, our tools are too narrow, or too crude in time or space resolution to figure out what this code might be.

Baars speculates that all goals and abstractions seem to have fleeting imagery in consciousness, again harkening back to the perceptual bias of consciousness. Our use of metaphor in language is naturally tied up with this phenomenon. Thus it may be imagery that is in some functional sense the lingua franca of the system, thought that still does not say how so many parts of the brain could recognize this language, especially the many humble parts that really do not seem to deal in imagery at all, like syntax checking, posture, "aha"- type solution verification, etc. Perhaps imagery forms a high-level language of aspirations, fears, planning, etc., without being needed for low level processes. This would tie in with the Jungian conception of the unconscious, with its core of archetypal images, our experience of them in dreams, and our need to develop and express them in art.

• Cognitive nature and nurture in Scrabble.
• But is the presidential campaign "news" enough to enter consciousness?
• People do have their own facts.
• On anger, and its cheap dismissal.
• Myths of the mythically-minded.
• A big key to poverty- violence, lawlessness, corruption.
• Like in Qatar.
• Best case scenario from the WSJ: wages are awful, peaked in 1972.
• The labor market won't do it alone ... we need better policy towards redistribution.
• Do we need "low cost, low wage" economies anywhere in the US? Where public assistance makes up the difference? No is the short answer.
• IBM luvs Louisiana.
• Reason prevails, barely, in Comcast merger.
• Props to the Hubble.
• Neonicotinoids even worse than thought.
• Islam: "But it also brought together peoples who’d never had a common worldview, or shared humanity, before." And.. "And there can be no freedom if we are stuck believing in people, like Hirsi Ali and her ilk." ... who had to move to the US due to Islamist threats on her life. The author is scattershot in his apologetics, but well-intentioned.
• Please don't use bar graphs for complex data.
• A little mesmerizing cymbalon.

The WSJ agrees- wages have been stagnant for a very long time in the US, clearly not related to productivity growth.

Evolution Sweeps Away Diversity

Natural selection carries off a large portion of neutral genetic diversity in large populations.

One would expect that large populations accumulate much more genetic diversity than small ones, over time. But if you watch those nature shows about herds of wildebeest roving over the Serengeti, it is very hard to see that variation. They behave as one, and look highly similar. Indeed, contrary to naive theory, larger populations tend not to have proportionately more genetic diversity than small ones. Why? The classical equilibrium law of population genetics assumes that larger populations naturally would have more variation, proportional to the number of members and the lengths of their various separate lineages. To balance this out, it also takes longer for any single new mutation to spread through such a population, so the ultimate rate of fixation of new mutations is no faster in large populations that it is in small ones.

"Under the assumptions of the neutral model of molecular evolution, the amount of variation present in a population should be directly proportional to the size of the population. However, this prediction does not tally with real-life observations: levels of genetic diversity are found to be substantially more uniform, even among species with widely differing population sizes, than expected."

But empirically, this expected high level of variation has not been true, even for neutral (unselected) alleles. This difference between theory and reality has been termed a paradox, and a recent paper (review) recounts the arguments above, showing that it is natural selection which constantly clears off accumulated variation, including completely neutral alleles that have no selective effect at all. This paper is not the first to address this whole paradox theoretically, but is the first to give an definitive quantitative solution.

"We show that genomic signature of natural selection is pervasive across most species, and that the amount of linked neutral variation removed by selection correlates with proxies for population size. We propose that pervasive natural selection constrains neutral diversity and provides an explanation for why neutral diversity does not scale as expected with population size."

Comparison of two species, one with large population size (fruit fly, A) and one with very small population size (Przwalski's horse, B). The gray dots are estimates drawn from 500k basepair windows across each genome of the local recombination rate (X axis), which can vary a great deal along chromosomes, and the local level of mutation and variation (Y axis). In a completely neutral theory, these measures should not correlate with each other (red line). The model developed in the paper is shown in the blue lines, where in a large population with lots of selection going on, regions with relatively low recombination show dramatically less variation, consistent with the rare selected mutation in those areas (whether positively or negatively selected) carrying a large number of neutral alleles with them, either to fixation (positive selection) or to their demise.

The issue is one of linkage. Imagine a long chromosome, with lots of genes and mutations. If one of those mutations is bad, then all the other mutations near it will be carried along with the bad one into oblivion, even if they did no harm themselves. The degree of linkage is a matter of the local recombination rate. Some areas of our genome recombine much faster than other areas, and thus allow more fine (selective) separation between nearby mutations, as they end up in different gametes and individuals due to the recombination that happens during meiosis.

So these researchers took a census of multiple genomes from many different species, (63 billion sequencing reads in all), measuring local recombination rates and mutation rates. They found that the bigger the species' population, the more clearly the prediction of correlation between the two measures came out in the data. Thus fruit flies, with a vast natural population, have roughly two-thirds the genetic diversity one would naively expect. The rest seems to have ended up shot down, innocent victims standing a little too close to more deleterious mutations.

In smaller populations, selection is just as fierce, but the level of neutral genetic diversity isn't expected to be as large in the first place, so loss by random drift plays a stronger role than loss as a byproduct of selection.

Humans are an good example. Now we are a huge population, but in genetic terms, we are practically clones compared to most other species. This is mostly because we were a very small population not long ago, and have only reached seven billion in an evolutionary eyeblink. So we have the genetics of a small population. But even in small populations, selection will have this diversity reducing effect, at a lower level. The intense selective evolution we went through over the millions of years prior not only kept populations small, but spread attractive and advantageous features through the population, at the expense of some of the other variation that was lying about.

In a way, this is an explanation for why species remain coherent entities through time. Their genetic diversity doesn't just grow endlessly into genetic chaos, but stays centered, in some abstract sense. Recombination and mating keep the genetic elements of the population continually mixing in a cloud of closely related forms, but it is selection that trims the outliers, both neutral and deleterious, keeping the cloud coherent, even as it also moves the entire cloud in new directions over the evolutionary landscape.

• The progress of inequality. (with graphs). Did supply-side mean 1%-side?
• Some sharp words for those new atheists.
• But people will believe anything. In for a penny, in for a pound with Scientology.
• A hopeful sign towards a more equitable world.
• Theology remains utterly absurd.
• Keynes on inequality, interest, the lower bound, and demand.
• Pay what you wish: the IRS is now toothless.
• "Redistribution", or justice?

RNA, RNA Everywhere

The enhancers that drive transcription are themselves transcribed, in a regulatory process.

The last decade or two have not only brought a genomic revolution in molecular biology, but also remarkable discoveries in RNA, finding micro RNAs, conserved long non-coding RNAs, piRNAs, siRNAs, snoRNAs, and now eRNAs, for enhancer RNA. Even though most of the genome is junk and remains junk, 80% of it is transcribed, so the cell turns out to be a flurry of all sorts of incredibly diverse RNAs beyond the classic molecular biology trinity, which is: mRNA to carry the gene sequence from the DNA, tRNAs that serve as the plug-in adapters between triplets on those mRNA messages and the amino acids they will become in the protein, and the rRNA that forms the body and catalytic core of the ribosome, operating the converyor belt that brings together the first two RNAs to synthesize proteins.

In retrospect, we perhaps should not have been so surprised, since RNA has been there from the most ancient period of life, and the messiness of biology tends to elaborate complexity, using any wrinkle or handle as a regulatory process. But for a couple of decades we were blinded by the preponderant relative mass (and, to be fair, importance) of the RNA trinity in the cell, and only recently have we had the technical means to find the great diversity lurking beneath.

A recent review catalogues the findings and hypotheses about the newest member of this tribe, eRNA, in detail. In eukaryotes, especially as they become more complicated, genes are driven by quite elaborate collections of "enhancers", which are DNA segments typically far upstream, by thousands to hundreds of thousands of base pairs, that bear a cluster of DNA binding sites where regulatory proteins bind, which either turn that gene off or on. One gene may have many separate enhancers, each typically devoted to one phase of development and/or one location in the body where it drives the activity of its target gene.

Schematic of gene control, showing an enhancer (LCR) that has several colored regulatory proteins bound to it. At the same time that it loops through space to contact its target (ßmaj gene), it is also transcribed to short RNAs (red) by RNA polymerase (P). The small discs all over the place are histones (H), which are modified with various colored methyl and acetyl groups in another regulatory process.

Enhancers can do this because they form loops from their distant sites, to contact the start point of their target gene, at what is called the promoter (pictured above as a bold elbow+arrow, when active). This arrangement means that it hardly makes much difference how far away the enhancer is- the proteins it binds can ignore the many kilobases, sometimes hundreds of kilobases, of linear distance in the DNA between themselves and the target gene's start site. But it also means that there needs to be some way to "insulate" one gene and its gaggle of far-off enhancers from those of other genes, which one wouldn't want crossing over into each other's territory and turning each other on. That is a story for another time.

The new and quite paradoxical finding is that enhancers are themselves transcribed, and that these resulting eRNAs are not just accidental junk, but play a significant role in the operation of the enhancer and the regulation of its target gene. As pictured above, (in red), eRNAs come streaming off the enhancer long before the target gene gets turned on. And if those eRNAs are degraded by an experimenter's intervention, typically (and ironically) by programming siRNAs against them, then the target gene turns on much less than otherwise. So it is not just the act of enhancer transcription that is important, though that is thought to have some regulatory effects as well, but the products themselves, at least in some cases.

eRNAs are thought to interact with another level of regulation, which operates through the histones which typically package all eukaryotic DNA. Any protein that binds to a specific site needs to get through this packaging, which can happen in some cases by detecting the DNA on the outside of the histone, or by waiting for a stochastic loosening of the histone from the DNA. But after the pioneer proteins find their sites, they can attract other regulators that specifically modify lysines (K) on the histone with methyl and ethyl groups, neutralizing their charge and lowering their binding affinity to the negatively charged DNA. This process "opens" up the chromatin for other regulatory proteins to bind. The specific lysines that are modified on histones constitute a complex code that marks areas in chromatin for various stages of transcriptional and other activity. The eRNAs have yielded mixed behavior in this pathway, sometimes being required for histone modification at target genes, though not typically at the enhancer region.

Much is still unknown about these eRNAs- how general their occurrence is, how they work, what these little RNAs are doing in the enhancer-promoter complex, and what drives their own transcription. It is like wheels turning within wheels, within wheels- where does the gene activation process ultimately begin?

• Bonus reference on eRNA.
• The NCAA competition is wonderful, but its organization and inequality are not. This should be nationalized.
• Like lots of other things.
• Bibi has a screw loose.
• Yes, religion doesn't make any (rational) sense. And, yes, theological institutions are a farce, educationally.
• In case you were clueless about the NBC saga.
• Pilots are another abused class of worker. No wonder one gets depressed.
• Austerity correlates with recovery ... negatively.
• Open carry? Not at the NRA convention.
• People are instinctively socialist, and fair. Image from the talk, on inquality: