Christians Have All The Morals

Review of "Terrorism and Civilization", by Shadia Drury

Some weeks ago, I discussed, somewhat tongue-in-cheek, how atheists have no morals. This time we turn the other cheek to consider Christian morals in some detail. Shadia Drury published a response to the 9/11 attacks in the form of a frontal assault on religious morality and Christian morality in particular, a book that should have risen to the top of the Atheist cannon, but didn't, perhaps due to her obscurity, her gender, and the book's high price.

Her case is relentless as it is remorseful, about the opportunities lost in the West due to the twisted, irrational and inhumane doctrines that originate from the New Testament. At least the Old Testament god was understandable, if a little hot-tempered. The New one is positively terroristic. Nor does Jesus (assuming for the monent that he was a real person and that the scriptures about him are at least partly true) get off in this thorough indictment, for he brings us this new system which features carelessness about this world and its people, thought crime, eschetological selfishness, orignal sin, and eternal damnation.

Hell is, of course, one focus. Jews didn't have hell, really. That was Jesus's invention, though obviously stolen from the Zoroastrians. His doctrine is that mere belief in him is the main thing.. everything else is secondary, in any practical, moral, and eschatological sense. However, many are called and few are chosen, which is to say that even if you fulfill his need for faith, you could still end up in hell, which is painted in the most fiery colors, as endless suffering and eternal. This is pure psychological terror, obviously, and was stunningly effective against the other religions of the day, which were all more reasonable.

Jesus also introduced thought crime, since belief in him was the main criterion of salvation. He also deemed immoral thoughts as bad as immoral actions. Adultury in one's mind as bad as in the flesh, etc. So where was one to go for relief from such a regime? There is nowhere to hide. Many serious believers have been agonized by this, for example John Bunyan in Pilgrim's Progress, a despairing work full of terrors and sin.

The reason for the horrors of Bunyan's epic travellogue are that humans, in Jesus's system, are fallen and evil. They are sinners who have no right to salvation, who are saved (if at all) by grace granted in return for slavish faith. Drury makes the acute observation that Freud, that ostensible iconoclast and atheist, follows the Christian system in virtually every psychological particular, from the innate sinfulnes of man (the id), and the need for terror (repression) to keep the inner beast under control, to the therapeutic salve of confession (the couch, in place of the booth).

Nietzsche too comes in for a drubbing, in an even more profound way. The Christian morality is one of blind obedience, of faith in the unbelievable, and terrorism inner and outer. All for our own good, naturally. If one fails to reframe the basic parameters of this model of humanity, then revolt against this edifice of lies might take an ugly turn, to immorality and perverse delight in reversing every dictum of the reigning moral order, so as to return to one's "true" nature, which though sinful, is at least honest and alive. Thus the bathos about Dionysus and the amoral Übermensch.

This accepts a frame that is far from true, however. Humans are many bad things, but they are not fundamentally bad beings. We are basically good beings with complex and often conflicting needs and ideals. We are pro-social. We love and seek love in return. We are fiercely moral. Drury points out that it is our civilization and our highest ideals that are what is in some ways most dangerous about us- our ability to organize huge groups, spout ideological rhetoric about utopian ideals, not to mention creating modern technology, for warfare and totalitarianism on unimaginable scales. It is the beast within that required nurturing, and our better natures that required the most advanced instruments of repression, when one thinks of the rankest horrors of the twentieth century.

So it is time to relax. The work of civilizing ourselves remains great, and constant cultivation is certainly desirable. But it does not require terrors of religion, nor theories about how damnable we are. Nor should we leap to the other Rousseau-ian end of spectrum, where everything natural, native, and naive is all that is good. As the religiously and ideologically burned-out countries of Europe are showing, there is peace, prosperity, happiness, and not least, highly sensistive morality, in a post-Christian, moderate, and humane culture.

• Kansas is just fine ... steal from the poor, give to the rich is a winning, sustainable strategy, especially considering how damnable we are.
• The Devil and Mr. Scalia. At least one justice is a fossilized relic, and has either lost his marbles, or enjoys trolling interviewers.
• Over 100 jihadist training camps, thousands of trainees ... this is not a fringe phenomenon.
• California's sclerotic housing mess. Incumbent owners always win when new housing / zoning is killed. Especially with prop 13.
• Grexit is coming.
• Whom we feel for... white police edition.
• Another 1%. Or is it the same one?
• Enriching the 1% makes everyone poorer.

Plowing Through a Fork

DNA polymerase and DNA helicase help each other out at the replication fork.

While DNA may not have been the first molecule at the origin of life, it now forms the heart of our replicative and molecular existence, its iconic and elegant stairway storing the digital data that has taken over the world as our wonderful biosphere. Its replication is a complicated process, but has to be done rapidly, since for one of our cells to divide, three billion bases need to be gotten through. A recent paper discussed how that happens, for the DNA polymerase itself can not open up the parental DNA strand fast enough through its own locomotion. It needs a DNA helicase to help unwind the oncoming DNA, whose strands are not only glued together by their basepairs, but can be festooned with histones and all sorts of other bound proteins that need to be cleared away.

In this cartoon of DNA replication, (going right to left), the synthesis of the leading strand (top) is so undramatic that its DNA polymerase is left out altogether. But note that a helicase rides at the fork where DNA melts. In this system (from E. coli), DNA polymerase III (pink) is the major polymerase that carries out leading strand and the major part of lagging strand synthesis, while DNA polymerase I is a fill-in enzyme that fills in gaps that are left at the end of every run of DNA polymerase III. The last step on the lagging strand is sealing by DNA ligase of the DNA polymerase I run, which goes right up to the next unit of lagging strand, made previously. Unlike in the diagram, there would be no nucleotides missing when/where this ligase acts. An RNA primer for the lagging strand polymerase III synthesis is shown in green.

To digress slightly, one of the most critical complications in DNA replication is that of the lagging strand. DNA comes in two strands, but all polymerases operate only in one direction (5' to 3'). So replicating the leading strand, which runs 5' to 3', is a piece of cake, even if it requires a helicase for assistance. The other strand is called the lagging strand, and has to be made piecemeal, with the polymerase running "backward" from the replication fork, primed each time by a special RNA-synthesizing priming polymerase. So this process is intrinsically assymetrical and messy.

Anyhow, the researchers use the classic model system of polymerase and helicase from the T7 phage, which infects E. coli bacteria and comes with its own (encoded) stripped-down and efficient DNA replication machinery, for late stages of infection when it needs to pump out full viral genomes at high speed. It is known that the helicase is essential. The polymerase by itself can work, but only slowly, and is particularly retarded by GC-rich regions, the GC nucleotide pair having three hydrogen bonds compared to the AT pair's two bonds. The question for these researchers was.. how closely do the helicase and polymerase work? Are they distant partners, or cheek-by-jowl?

One could imagine that the helicase could proceed some distance ahead of the polymerase. But it is also known that the helicase doesn't work that quickly by itself either. The helicase looks like a lifesaver ring that forms around a single strand of DNA, and consumes dTTP as an energy source to tug on it, pulling it away from the duplex fork which the helicase is trying to melt. Neither activity alone explains the total high rate of DNA replication, suggesting that they work closely to help each other along. The current work put them through their paces either apart or together, and controlled by various concentrations of their inputs, dTTP in the case of the helicase, or all four deoxy-nucleotides in the case of the polymerase.

On a single strand of DNA where it doesn't need to do any helicase-ing, the T7 helicase moves along at a nice 65 nucleotides (nt)/second pace. Likewise, the polymerase, when given plenty of nucleotides and single stranded DNA, chuggs along at 200 nt/second. The final rate of the complex on duplex DNA is about 200 nt/second also, so what needs to be explained is how the polymerase regains that rate when facing duplex DNA and perhaps non-ideal concentrations of reactants, plus other obstacles. For the helicase, how and why does it go faster when yoked to the polymerase than it does on clear single-stranded DNA on its own?

Performance of DNA polymerase alone, on GC-rich DNA. It is slowed down substantially, but much less when given an excess of its substrates, the deoxynuceotide triphosphates (dNTPs).

Key computed parameters of the polymerase alone. With higher GC content in the DNA, the polymerase maximum rate (k-cat) doesn't slow down much, but its responsiveness to substrate concentration( Km) rises substantially.

One way to manipulate the system is to present the enzymes with double-stranded GC-rich DNA in comparison to AT-rich DNA, and ask what other ingredients, such as more nucleotides, do to their speed. The comparison is rather subtle, and depends on decomposing the reaction into two components, a measure of the first part of the reaction, enzyme + nucleotide binding (Km), and a measure of the second part- how fast the enzyme is at maximum if it has plenty of inputs (kcat). As shown in the first graph, the DNA polymerase is significantly slowed down by GC-rich DNA duplex. But that effect is substantially alleviated by high concentrations of nucleotides, indicating that the polymerase has problems opening the duplex DNA for lack of enough new nucleotides to stuff into the template position as the fork sporadically melts. The polymerase is not good at holding on to temporarily melted nucleotides.

Performance of helicase alone on GC-rich templates. The rate is hugely slowed down no matter what the dTTP (energy substrate) concentration.

Unlike the polymerase, the kinetics of the helicase are changed by difficult-to-open GC content mostly in the k-cat, or maximum rate, with little or negative effect in the Km or substrate (dTTP) sensitivity.

Conversely, the helicase has another problem. No matter how much nucleotide (more precisely, deoxy-nucleotide triphosphate), you give it, it maxes out at pretty slow rates on GC-rich DNA. This suggests that it just isn't a terribly good helicase by itself, but if given a push...

Rate of the combined enzymes on 50% GC template is quite fast. The nucleotide concentration for the polymerase (dVTPs, which stands for a mix of dATP, dGTP, dCTP, while the dTTP is provided for the helicase) is kept extremely low. But the combined system makes a much higher rate (~70 nt/second) than the polymerase alone did at the minuscule concentration of 5 micromolar dNTPs (I estimate perhaps 10 nt/second from the graph above). This is reflected in the combined Km for nucleotides in the combined case (top, in red) vs the polymerase alone case (bottom, red).

The reason for all this is structural, that the helicase is better at grabbing on to the single strand coming out of the fork, but doesn't have much oomph behind it to plow forward continuously. The polymerase, in contrast, has a good engine, but doesn't grab onto the incoming single strand DNA well, letting it slip back into the duplex with high frequency. The complementary relationship makes sense, since you really do not want the helicase travelling off by itself unwinding the cell's DNA, but rather want it coupled to where it is really needed- right ahead of the DNA polymerase, as a kind of cow-catcher and rail splitter.

The red nucleotide pictured is fluorescent, and its melting changes the fluorescence signal as measured on the Y-axis of the graphs. Melting in the absence of any dNTP substrate is only substantial when both helicase and polymerase are present.

Lastly, with some more intricate fluorescence assays, (on which this whole work is based), the authors look at the two or three nucleotides of the fork itself, and which of them are grabbed by the two enzymes in single-stranded form. This is done without giving them any nucleotide triphosphates as energy source or substrate, so it is looking at initial binding. Polymerase or helicase alone bind to the fork, but are pretty ineffective at melting any of the first three nucleotides of the duplex (darker bars). But the two enzymes together melt them quite well (light blue bars). So it is not just the engine of the polymerase behind, but a physically cooperative binding mechanism at the fork that gets the DNA melted in advance of replication.

The authors come up with a highly schematic vision of what this might look like, with some wildly stretched DNA going into the helicase- the green rung of the non-template (right) strand. The helicase then hangs on tightly to each nucleotide that it captures, as the polymerase is busy doing its thing of synthesizing the new DNA strand.

Model of the polymerase (beige) and helicase (pink) collaborating at the replication fork.

• ISIS deploys foreigners to kill themselves. Clever! 
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• Employers pay only what they can get away with. "The minuscule gains that households have made have largely come because women have increasingly entered the workforce—meaning families are working longer hours, as they run faster and faster to stay in place." ... "Median incomes for male workers now in their thirties are about 12 percent lower than the income was for their fathers’ generation at the same age."
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• Ethical grifters.. er drifters .. in finance.
• Greek drama: "What that means is that the involvement of European governments has not helped Greece at all. ... The additional money provided by the European authorities has been used to pay off Greece’s creditors ..." Default & grexit should have been the first resort, not the last.
• MMT making dramatic inroads into the policy central plexus.
• Dawkins, Hunt, completely bonkers.
• Thanks, Warriors, for a golden moment.
• Economic graph of the week. We are far from full employment.

Sociomolecularbiology

Society affects gene expression and development, and genes contribute to social traits and behavior.

Is it any news that we are biological beings? That all aspects of our being, from toenails to theology, are biologically based? That was the premise of sociobiology, the science of the behavior and evolution of social organisms. Of which we are one. Unfortunately, the smell of eugenics was still too strong in the political atmosphere to allow thinking about how our genes affect our behavior, so that splash by E.O. Wilson died down and the science went on by other names.

That work has found, among other things, many connections between our psychology and our physiology. It should be no surprise that we are profoundly affected, to the point of suicide and other forms of death, by information that first arrives to our brains. Our immune systems are sensitive to social state, as are digestion, mood, activity, etc. Hypertension is one of many long-term consequences of stress, for example. This close relationship leads to to idea that we might be able to judge happiness by objective measures, rather than exclusively by self-report. And that would open up new vistas in morality, particularly morality vis-a-vis other species.

But it goes the other way as well, as our social capacities are based on biology. Psychological traits of great complexity can run in families, and scientists are only starting to gain glimpses of genetic alterations that cause such traits and their variation. The very ability to be flexible, to learn and adapt, is itself obviously of genetic origin. The question, typically, is how much people differ in significant social traits and how much we should care about that. We pride ourselves on meritocratic systems of education, business, and government that weed, select, and reward those who are gifted, who also align with and master the social system. But are we just rewarding something that the persons themselves had little to do with, just as criminals typically have little responsibility for their genetic or social deprivations, or actors for their looks? We may be, but reward we must, as a sociological necessity, if we want societies to benefit from good rather than bad talents.

Is it also an evolutionary necessity? Should those who succeed in the existing social system be rewarded with more reproduction? Typically we do not and should not have sufficient confidence in the universality or durability of our social system to make that case in its most brutal, eugenic sense. However, we should not be blind to the genetic underpinnings of social success and all its consequences. For example, the trend toward intellectual atheism that is so fervently touted in other areas of this blog fights a rate-dependent battle against the higher reproductive success as well as intellectual insularity of religious populations. What is the deconversion rate compared to the biological and ideological reproduction rate? Is religiosity a positive trait for humans? How much to we care about our evolutionary trajectory, a path we are on whether we are conscious of it or not?

Anyhow, as an example of the genetic implications of sociality, a recent paper described a gross increase in genetic complexity that accompanied the social evolution of bees. They found a measurable correlation between social complexity and gene regulatory complexity, which is a step in addressing the question of the interrelation of genes and behavior, in general.

Bees come in many social levels, from solitary to "eusocial", a term the E. O. Wilson made up to describe animals that are not  just polite and social as we and many other animals are, but behave as super-organisms, with genetically determined castes with division of labor, and restriction of reproduction to a small subset of those castes. The members of such a collective have no independent existence, die when the hive dies, and are seen by evolution as a group that has group-level traits that are extensively selected for.

Phylogenetic tree of the species considered. Solitary bees are marked in blue, simple sociality in green, more advanced sociality in yellow, and full-blown eusociality on red. 

The researchers basically lined up lot of genomes, from various levels of social organization among the bees, and looked especially at promoter regions, where the primary control over gene expression happens. They found a striking increase in complexity, which is to say number of binding sites for regulatory proteins, all over the genomes of the more social species. Indeed there was a 10-to-1 bias of genes that gained promoter binding sites over those that lost sites in the more social species. This is a dramatic effect, and makes sense in terms of the "mode-switches" required on a genetic level to create castes with separate developmental and behavioral traits out of one ancestral species.

Bias found among orthologous bee genes (that is, the same between each species) between those that gained promoter regulatory sites in more social species (blue) and those that lost them (red). The X axis is not genes, but the individual regulatory proteins whose DNA-binding sites were identified.

They also found, interestingly, that the particular genes involved in these increases were not the same in different social insect lineages. They took different genetic / evolutionary routes to eusociality in detail, even though they ended up with similar properties. So this is a kind of convergent evolution that shows that group selection and the sociality it selects for did not just arise multiple times in life's history out of some kind of molecular happenstance, but is an optimal ecological solution that attracts quite a bit of selection, as we can tell by the dominance of social species, both in the insect world and in our own.

Overlap among the various social lineages of which genes showed rapid, positive evolutionary selection. The result is that there is very little overlap, indicating that there are many ways to skin the social cat.

• Termites, same story is pending.
• Sociological reflections on WD Hamilton.
• Review of Churchland, on the brain and morality.
• More on body-mind interconnections.
• What the Y chromosome says about out of Africa models.
• Do voters understand economics, from today's ideological, corporate media?
• Global warming doesn't mean more plants, it means more desert.
• Breaking up big SDI banks would be "un-American".
• Notes on currency manipulation.
• Notes on division of labor, and why technology is probably more important to the organizational structure.
• NIH talk on depression- current research status and promising developments.

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.

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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.

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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.

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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.

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