Write like an Egyptian

I've read an excellent book on Egyptian history and theological development by Jan Assmann, a German Egyptologist. The book is a bit more convoluted than I had hoped, but herewith is an outstanding excerpt that provides insight into the book, into the mind of Egypt, and into human nature generally.

Selected parts of an Egyptian hymn of the daily ritual, dating to the middle kingdom, ~2040-1650 BC:

The king

worships the sun god in the early morning

upon his emergence when he "opens his orb,"

when he flies up to heaven as scarab

he enters the mouth,

he emerges from the thighs,

at his birth in the eastern sky

His father Osiris raises him up,

the arms [of the air gods] Hu and Hauhet receive him.

He sets himself down in the morning bark.

The king knows

this mysterious speech that the "eastern souls" speak,

when they make jubilant music for the sun god

at his ascent, his appearance on the horizon

and when they open for him the wings

of the gates of the eastern horizon

so that he can voyage forth on the ways of the heavens in his boat.

He knows their aspect and their incarnations,

their mansion in God's-Land.

He knows their locations,

when the sun god goes forth at the beginning of his journey.

He knows that speech uttered by the crews

when they pull the bark of the orb of the horizon

He knows the birth of Re

and his transformation in the flood.

He knows that secret gate through which the great god came forth,

he knows him who is in the morning bark,

and the great image in the night bark.

He knows his landing places on the horizon

and your steering equipment in the heavenly goddess.

...

Re has set up the king

on the earth of the living for ever and ever

to speak justice to the people, to satisfy the gods,

for the generation of ma'at [good/justice], for the destruction of isfet [bad/chaos].

He gives the divine offerings to the gods,

and mortuary offerings to the transfigured.

The name of the king

is in heaven like [that of] Re.

He lives in joy

like Re-Horakhty.

The dignitaries rejoice when they see him.

The subjects give him ovations

in his role of the child.

...

Assmann comments:

This text enumerates everything the king must know for the worship of the sun god in the morning: the nature of the cosmic process, its various stages, its scenic and constellational arrangements, and its salvational meaning as rebirth; he knows the deities involved, their actions, their speech, the circumstances of their lives; and he knows the spatial framework of the process- heavenly gates, barks, landing places, steering equipment. The king must know all this precisely in order to be able to intervene effectively in the cosmic process with his worshipful speech. His fears are less that one day the sun might no longer rise than that the salvational meaning of the process might be lost or forfeited. The king, then, performs an officium memoriae. He must summon all his mnemonic power to keep this salvational knowledge present. The world thus maintained is a world of meaning, of language, of knowledge, of relations and reflections, an anthropomorphic reading of the universe with a correspondingly cosmomorphic image of human order. The hourly ritual bans cosmic chaos, and with it the chaos in man himself.

pp210-211, The mind of Egypt., 1996/2002

• An Assmann festschrift
• The scarab

Green comments in passing

Cap and trade

I'm deeply disappointed over the casual brushoff that congressional Democrats have given the greenhouse gas cap-and-trade (C&T) portion of the Obama budget.

The government desperately needs ongoing revenue sources to ameliorate future debt, fuel prices are low enough to make an increment for C&T relatively painless, and the rate of climate change is accelerating, so it is the perfect time to bring this system online. It looks worrisomely like the congress is hopelessly in the pocket of industrial interests, even on the Democratic side.

Ideally, instead of C&T, a straight carbon tax would be instituted, which would be transparent, easy to apply, and would rise over time to reduce emissions as needed. The C&T system is more complex to administer, and prone to corruption and mis-pricing, as has been seen in Europe. The amount of emissions have to be ascertained somehow, which, short of simply taxing fuel, is difficult to measure.

Some would surely say that the economic recession already decreases emissions, thus making the whole project of reducing emissions less urgent. Nothing could be more irresponsible. The last decade has been lost in policy terms. Temperature rise is gathering steam, and the lag in the system means that substantial further temperature rise will still take place in the next decades were our emissions to halt immediately.

In addition to the physical lag, there is also a political lag, where our leadership will only slowly translate into action in other countries, just as our lack of leadership and action over the last decade has provided the excuse for others, especially in the developing world, to match our do-nothing policy.

It is high, high time to ask for the small sacrifice that will get us going in the right direction of stewardship of this precious and delicate planet.

• Oil is still getting short, despite the downturn, so purely in peak oil terms, we need to plan ahead.

And what's up with Paul Krugman?

Paul Krugman has emerged as the prime critic of the administration's newest plan to set up a market in toxic assets. His articles and interviews have been a bit vague, but I think what he is saying is that the program conjures buyers (with federal sweeteners), but will not create sellers. The government's example shows an asset face value $100 being bought at $86 by new investors. If that was all we had to worry about, we wouldn't be in a crisis. No, banks are carrying assets worth $5, $0, or even deeply negative values, thanks to "sophisticated" financial filleting, and they are petrified at having to sell them or honestly value them on their balance sheets.

Thus the danger is that the most toxic assets will stay right where they are- hidden in the vaults of zombie banks who will continue to lurk in the economic shadows, waiting desperately for the general economic upturn that will magically re-value those assets to something rather than nothing. That is why the other half of the strategy- the stress-testing and recapitalization [ed- strike recapitalization, how about orderly bankruptcy of insolvent banks?] of problem banks- is equally important. Most commentators seem to think that this stress-testing is merely window dressing, since Geithner is a Republican at heart, has little money to play with right now, and little immediate prospect of getting more. Hopefully not, is all I can say.

• For a more conspiratorial and pessimistic take on this, read Glen Greenwald.

Balancing economic morals

Thoughts about our continual navigation between the extremes of socialism and capitalism

The further we get into our current economic mess, the clearer its connections to psychology and morality become. Trust is the coin of the realm, and if trust breaks down, nothing can paper it over. With respect to this week's storm over the AIG bonuses, is the trust represented by written contracts sacrosanct, however corruptly arrived at, or is the more important trust that among citizens- that they treat each other fairly and take a measure of responsibility for their actions?

Taking a longer view, a persistent tension exists between idealistic economic morals, represented by family-related concepts, communitarianism, socialism, communism, and realistic, competitive economic morals, represented by Darwinian competition and capitalism. We are experiencing a deep shift from several decades celebrating the second (with the active support of religious conservatives, who so readily jettisoned communitarianism they supposedly valued) to the first, via the ascendence of Democrats, and the realization that we had gone too far towards free (and chaotic) markets.

On the one hand, communitarian values accord with a great deal of human nature, since we can be peaceful, loving, and caring to the point of altruism. We want to be loved, not only for what we do, but for simply being. Christianity claims to stand for love, even of enemies, whatever its actual history records. (Check this for a fascinating look at the business of morals.) The communist ideal spoke most definitively to this ideal in economic terms, saying that we could indeed have our cake and eat it too- give freely according to our capacity and get according to our needs. No wonder communist regimes were atheistic- they were poaching on the same utopian turf as Christianity.

As we know, such idealism is insufficient to run a real economy, and the alternate morality of competition, realism, and capitalism has carried the day. This also accords with human nature (not to mention game theory more generally), since we are competitive at the same time as we are loving, and no amount of ideology can wish that nature away. Even if 90% of humans were totally altruistic, the other 10% could mess things up royally in an idealistic economy. Beyond our internally divided natures, the structure of society also conspires to promote competitive morals, since there is always inequality of talent and resources, leading to inequality of returns, whose owners will, by nature, usually be in favor of further inequality.

The rich have the money to make more money by the magic of capitalism, and they also have the resources to play the political system to best advantage. Historically, they have, as a rule, authored the political system outright, in the forms of oligarchies, kingships, and so forth. Our own enlightened system, for all its ideals, was authored by the most well-to-do specimens of the age, and reflected that dominance in many ways (such as the perpetuation of slavery). Thus by both economic and political means, capitalism inexorably creates economic inequality by a rich-getting-richer and the poor-getting-poorer ratchet effect, just as biology observes that organisms inherit and achieve inquality in their struggle for existence and propagation.

Even in Darwinian terms, however, systems are not all one or the other- cooperation coexists with competition. The greatest strides in evolution (the union of cells to form eukaryotes, and the collaboration of cells to form multicellular organisms) were instances of cooperation in a sea of brutal competition. The question for us is how to balance idealism and realism, using the conscious levers of politics to ameliorate the natural workings of capitalism.

From the early history of Rome through the French revolution and on to today, societies grapple with this problem, trying to stave off chaos and revolt in reponse to gross inequality either through more effective oppression by those who have (Sparta, Soviet Russia), or by creating egalitarian processes to counteract the ratchet effect of competitive economics, hoping to buy off, co-opt, or even truly integrate the have-nots and have-less's.

The legitimacy of the political system hangs in the balance too, since while some inequality is inevitable, and quite a bit can be sanctioned by religious fiat, traditions of nobility, and the like, it seems ultimately impossible for humans to see bitter economic hardship and opulent luxury side by side without coming to the conclusion that something needs to change, often radically. We are too idealistic for that, as are, incidentally, monkeys as well.

In pre-history, intensely competitive tribes and city-states didn't bother with even the rhetoric of egalitarianism, killing each other to gain land, goods, and trade. The rich killed the poor. In antiquity, richer cultures developed the innovation of enslaving the poor- an advance, considering the alternative. This was the accepted reality of Greece and Rome.

But it was an unstable system, since after a few generations, slaves captured from far-away battles became full participants in the culture, with claims of native citizens, in practice if not in name. A novel egalitarian ethic was certainly one attraction of the nascent Christian movement in Imperial Rome, though in the beginning it attracted the upper crust and especially women, not slaves themselves, and Christianity ended up being quite compatible with slavery in the early US and elsewhere. In the middle ages slavery was transformed into feudal serfdom, as the Roman state broke down, centralization was lost, and new economic conditions gave a modicum of power to the lower classes, especially after bouts of the plague.

Skipping ahead to the French revolution, again the economic system was a shambles of vast inequality, and the new breath of enlightenment, given vibrant reality by the American experiment, rudely pulled away the veil of false consciousness- of the superiority of the nobility, of the inerrancy of the clergy, of the divinity of the King. The peasantry was fed up and ready to take its place at the table which it had laid. Thereafter, European societies fitfully moved towards increasingly egalitarian economic systems, exemplified by the Scandanavian countries of today. The process has been a political one of regulating and counter-acting the natural workings of the capitalist system to soften its Darwinian destructiveness and spread its wealth, while preserving its intrinsically productive aspects.

Where are we in the US on this scale? We have had our own brushes with slavery, serfdom, and peasantry in a dizzyingly dynamic and condensed history. While there are plenty of rags-to-riches stories of those who have parlayed their labor and smarts into wealth, our system remains classic in its tendency to reward capital and connections, and to tax labor and consumption. This process led to the huge inequities of the gilded age, which were then addressed by the legislated expedients of anti-trust, trade unionism, the estate tax, and the progressive income tax.

It is a commonplace that we are in another guilded age, after each of the above expedients were weakened in the last decades of Republican dominance, resulting in huge and growing disparities of wealth. Once again in industry after industry, winners and the well-connected get paid huge amounts. Miniscule differences in capability are remorselessly amplified by a bidding war into dizzying highs and lows of pay. Losers get paid less and less, as a perennial excess of low-skilled labor competes for lower wages, helpfully globalized to evade domestic social and political accommodations. Those in the middle make do on two salaries where one would have sufficed a generation ago, because that is exactly what the labor market will bear. Those who have been entrusted with the money of others have been particularly flagrant in rewarding themselves, under the philosophy that they needed to "share" the wealth in order to be properly "motivated". Yet the motivation of others farther down the ladder of connections and capital is left to the bare exigencies of survival in an atomized labor market.

At any rate, one can see a pendulum swinging back and forth, between natural capitalist differentiation and popular indignation and revolt, adjusted by the technical possibilities of each epoch. Now that a new administration proposes to raise the progressivity of the tax code in an effort to mitigate wealth disparity, the media, at the behest of its owners, cry "class war", uttering their worst fear and taking belated refuge behind the state that they had worked so hard to degrade and defang. But it is not war that the majority want, but a re-balancing of the system. It is simply another step on the long road to the golden mean of a morally defensible (in idealistic terms) as well as practical society with optimal prosperity. (Prosperity itself being a moral good, leading to cosmopolitanism and peace, while poverty leads to more desperate competition, violence, chaos.)

In the end, each extreme, either of idealistic utopianism or of pitiless capitalism, is catastrophic in both moral and practical terms. Ancient Rome died essentially of unfettered crony capitalism, where the rich garnered vast resources on huge estates, and used their political power to relieve themselves of taxation. The result, once new resources stopped flowing in from foreign conquests, was decay of the economic system which had become top-heavy and corrupt. We see this today when our own guilded ages become so top-heavy that the economy shrinks because all the riches at the top can not make up for the far larger lower class virtually unable to participate in economic activity.

The golden mean of moderated, regulated capitalism/socialism keeps the creative energies of humanity flowing, both in the form of competition between people and firms, and in the form of cooperative creativity that rests on freedom to innovate and fail without personally disastrous consequences. Universal health care makes us free in important ways, just as low taxation makes us free in different ways.

Incidental link:

• My favorite correspondent reaches a new low of sputtering hatred.
• A closely related economics article at salon.
• And yet another related review of Karl Marx, by Hitchens
• Cringely calls the bailouts immoral, later on.

---

To decrease contemporary corporate cronyism, a few suggestions for revised corporate governance:

1) Prohibit any corporate director from serving on more than one board. This job is important enough to be done well. Bringing more talent into this system is important- into the upper echelons of corporations generally. Being on a board should be a serious job, not a chummy spa trip.

2) Prohibit executives from serving on a board of their own or of other companies. They already have a job. That should be what they are doing and focusing on. Serving on another board automatically compromises their responsibilities to their own company. As for their own company's board, this is even more important. The company's board needs to be distinct from its management, so that they actually check each other, rather than scratch each other's backs.

The special case of a founder being involved in a company would present them with the choice of being an executive or a board member. For private (non-public) companies, something more lenient could be arranged, such as allowing large shareholders (owning 10% or more shares, perhaps) to be on the board, whether they are executives or not.

3) The board organizes and runs annual meetings and shareholder voting, including the election of new board members and the review of executive performance. They should have their own small staff or be able to outsource details of this task so that the executives of the company can, again, focus on running the business of the company, not the business of the board. Conversely, the management would have a voice at the annual meeting and elsewhere to say whether the board had run off the rails (or to resign if needed), but they would never be the same as the board.

4) Stock options should be given on a 5-year plan. They can not be redeemed until five years from grant date, and then would be redeemed at the mean price of the ensuing year, not the spot price at time of redemption (to be organized by an escrow system of automated selling). This means that redemption decisions need to be made a year in advance. Companies would publicize all requests for year-out redemption by executives, sharing key information with the public, including size of options and when they decide to sell. The bottom line is that managers, if incentivized with stock, should be tied to it similarly with long-term stockholders, rather than day-trading against them. Large bonuses and other forms of non-salary pay should be treated similarly, paid only after some time has passed to make clear whether past performance actually merited it.

Hallucinations

A little more of the plumbing underlying hallucinations comes to light.

One fascinating sub-field of molecular biology, particularly pharmacology, is the hunt for things called "orphan receptor ligands". Receptors are proteins at the cell surface that recognize hormones, neurotransmitters, inflammatory molecules, and other signaling molecules, and then alert their cell about that message. They are the eyes and ears of the cell, and humans have over 800 of one family of them, the GPCR receptors, including ~350 olfactory receptors that sit in nasal membranes a detect aromatic chemicals. This family mediates many important messages in the body, and more to the point, constitutes the single largest class of drug targets, since interfering with such specialized signaling systems is an effective way to influence a cell's functions. Getting drugs to these receptors is also easy, since they sit right on the surface of the cell, pointing outwards. In contrast, getting drugs inside cells can be quite difficult.

The human genome project identified the genes encoding all these receptors, (which occur only in eukaryotes), but could not tell us what they do. Evolutionarily, they all arose as accidental copies of an ancestral version, forming a family with conserved sequences and structures. But our interest is all in their differences- what distinct signalling molecule (or ligand) each one binds, and what that signal means to the cell. Currently about half of all human non-olfactory GPCR receptors have known ligands, and the rest are called "orphan" receptors, since their partners in signalling ("ligands") are unknown. Thus the search for orphan receptor ligands, especially by drug companies, who stand to benefit enormously from new ways to twiddle with our biology. Recent successes have found receptors for the appetite hormone orexin, the circadian hormone melatonin, adrenaline, nociceptin, and many others.

Recent papers in Science nail down some new data about two erstwhile orphan GPCR receptors in the brain- one, the receptor for the hallucinogen DMT, and the other, active in the development of Alzheimer's disease. The second study does not identify the ligand for its orphan receptor (GPR3), rather, it demonstrates that it is expressed in areas of the brain typically affected in Alzheimer's, that its overexpression stimulates excess amyloid peptide production, the hallmark of Alzheimer's, and that deletion of the gene both eliminates amyloid peptide production and reliably prevents the disease in mice that otherwise develop it. Finding the ligand of this receptor will be even more interesting now that its importance is so clearly laid out.

Perhaps more interesting, however, is the first article reporting that another orphan GPCR (sigma-1) turns out to be the receptor for the hallucinogen DMT. Several hallucinogens have already had their receptors characterized. Marijuana binds to a sub-family of GPCRs called the cannabinoid receptors, which also bind the endo-cannabinoids which have physiological roles in, as one would expect, mood, learning, pain, and general cognition. LSD binds to a variety of dopamine and serotonin GPCR receptors, of which a serotonin receptor appears to be the key mediator of action.

Little is known about the sigma-1 receptor, other than that it might influence functions as diverse as schizophrenia, cell death, immune suppression, and sterol metabolism. It is known to be a receptor for the antipsychotic haloperidol as well as cocaine, but (before this work) not for any endogenous ligand. Yet mice with this gene knocked out appear fine- viable and fertile. The one assay that this article reports for DMT action is hypermobility, where mice placed in an open space move twice as much when under the influence. This effect was completely abrogated when the gene for the sigma-1 receptor was deleted, indicating that at least some of what the mice experience during their bout of exogenous DMT is due to the action of this GPCR receptor.

It is, however, quite frustrating to not know more about what the mice are experiencing- are they hallucinating? Do they have spiritual experiences on DMT? Does loss of this receptor make their lives dull? With this new knowledge, however, drugs can be devised to specifically (and reversibly) activate and de-activate this receptor, which should eventually lead to better (non-recreational) experiments in humans.

Thus one more receptor has found an endogenous ligand, and one more hallucinogen has found its binding partner in the brain. DMT is the key ingredient of one of the most potent hallucinogens- the ayahuasca mixture from South America, and is closely related to the active chemical in psilocybin mushrooms. It is quickly metabolized and non-addictive, and seeing increased use in Europe and the US. Not much is known about DMT's role or action in the brain, since it is a minor and very transient metabolite. However one article indicates that at lower doses, it might function as a relaxant:

"In these studies, administration of a non-hallucinogenic dose of DMT (0.05 mg/kg) produced a relaxed and comfortable mental state in many subjects. We propose that the main effect of endogenous DMT may resemble low-dose, non-hallucinogenic DMT administration, providing a homeostatic response to alleviate, rather than promote, psychotic symptoms."

"At intravenous doses of 0.2 and 0.4 mg/kg, there was a “nearly instantaneous onset of visual hallucinatory phenomena, bodily dissociation, and extreme shifts in mood, which totally replaced subject’s previously ongoing mental experiences.”"

"At low levels, DMT may be an endogenous anxiolytic, whereas higher, “unnatural” levels (such as those associated with psychedelic/hallucinogenic activity) produce extreme shifts in consciousness."

The near-death experience may then be a final spasm of DMT production, passing from the calming amounts that relieve anxiety and pain to the prodigious amounts that induce hallucinations.

This receptor-ligand system is extremely complex and far from understood- the many roles of the sigma-1 receptor and those of DMT indicate that hallucination is probably a side-effect rather than the central point of their function. Indeed, why do hallucinations happen at all? We live in what might be termed a finely tuned hallucination all the time, with one's brain constantly spinning scenarios, images, and ideas, more or less tethered to reality. Dreaming is even more clearly a matter of ongoing hallucination. One of the most important recent themes of neurobiology is that cognition is a creative process, where our inner structures and activities play a leading role in shaping perceptions, focusing attention, and filtering emotions. Perception is as much a top-down process as it is a bottom-up process driven by the sensors of the eyes, ears, etc.

The tuning by which consciousness is created and kept on an even keel requires complex timing adjustments, keeping various inputs in register and adjusting perceptual time for our state of attention, whether bored, focused, or doodling. The same goes for conscious contents, such as daydreams, perceptions, ideas, emotions. It all seems a terrible mess, since a huge amount of unconscious material needs to get in, and yet not overwhelm the thread of consciousness.

Clearly, natural selection would promote accuracy of perception and focus on critical tasks in the outside world, such as when time slows down dramatically during dramatic events, and our minds become oddly clear. But the need to accommodate many other contents and situations necessitates major and ongoing adjustments, which may be what DMT and other chemicals may be doing at a gross level, tweeking normal consciousness in ways that cause what we call hallucinations when pumped to extremes.

One last question is why people routinely take hallucinatory experiences to have great spiritual significance. Many practices tread this path, such as meditation, fasting, ecstatic prayer, and Sufi whirling, not to mention peyote, ayahusca, and the Delphic visions of ancient Greece. Muhammed is thought to have had a form of epilepsy that is associated with intense visions, and the desert sojourn of Jesus laid the foundation of all his later preaching.

Naive views of spirituality assume that there are other planes of existence or reality where spirits reside, in accordance with our dreams, fairy tales, and native intuition- the supernatural, of which we get glimmers through this smoky glass of psychedelia. But there has to be more. Hallucinations are not just perceptual voyages through uncharted ethereal realms, but also affective experiences of great power, notoriously subject to the emotional tenor of the setting (causing good or bad "trips" on LSD). This is the forte of the shaman, who sets the parameters of such activities with great care. A single extraordinary emotional experience can motivate a lifetime of dedication, so it should not surprise that drugs that send the mind to its emotional and conceptual boundaries might leave unshakeable imprints.

Being real

What happens when, in the search for who you are, something shocking happens, like being the wrong sex?

Life is a quest to satisfy the conditions of our being. We need sustenance, love, esteem, knowledge. We need to express ourselves, and we need to negotiate a role in life or persona that is acceptable both to society and to our inner selves, and through that persona make and pursue our dreams. Each person has a unique nature, and, taking a Darwinian view, each nature conceived and brought to fruition exists to test itself against the world on a hero's quest, and find some measure of success. And then to make way for the next generation- a new jumble of the genetic kaleidoscope, composed piece-meal of the successes of the past.

We can take most of our identity for granted- buy it off the rack, as it were. From earliest childhood we are molded to various standards of civilized behavior, each found by our forebears to be consistent with their natures, and thus surely consistent with ours as well. The standard roles available are wide-ranging enough- child, adult, man, woman, worker, scholar, reprobate, adventurer, mother, pillar of society, etc. Somewhere in there we are supposed to embody our dream which expresses who we are, and find a way to enjoy life.

In the story books, the quest to find out who one is often leads to unexpected but usually pleasant discoveries. Cinderella finds that she is destined for nobility, by way of her shoe size. Harry Potter finds that he is a wizard, after suffering through an intolerably bourgeois childhood. Adolescence is all about finding something wonderful and strange within- an unexpected power, prone to misuse and misunderstanding. The journey to finding out how one can fit into society and be happy at the same time is a matter of finding, in part, who one is and how that being fits into the many known categories of human variation, whether accountant, model, coach, organizer, nurse, sportsman, etc.

But suppose there's a problem- suppose that who we seem to be is violently at odds with who we are? The most determined roles in society are gender roles, encoded in our natures via an entire chromosome, and thus necessarily accomodated in all the aspects of society that reflect how most people have in the past expressed their gendered natures- separate fashions for men and women, legal structures for marriage, roles from military participation to prison incarceration. Crossing this boundary is almost inconceivable, but that is the fate of the person who is transgender.

Several stories have appeared in the last year describing the transgender experience, extremely affecting in a Kafka-esque conviction of being born in the wrong body. While homosexuality is relatively common, and by some biological theories is a side-effect of selection for high levels of cross-gender orientation in the other sex (but see here as well), transgender conditions are less common- a biological error not just in the orientation of sexual desire, but in the deeper property of gender identity as a whole.

• Autobiographical story, from Salon
• Radio segment, partly autobiographical
• Atlantic story of affected younger children

Transgender conditions raise a host of philosophical problems. How can gender be a property of the brain? Scientists used to think of the brain as a blank slate, to the point that whichever gender a child was raised as would stick for life, with no further problems. One story recounts the horrifying case of a boy whose circumcision was botched, who was raised as a girl, proceeded to total revolt against his gender assignment, and ended up committing suicide. Clearly gender is not a blank slate, but is as much encoded in the brain as in the genitals. Some girls (and boys) want to wear tiaras and dresses, some can't stand them. Clearly there is some kind of sex-dependent mental programming that is tightly tied to the physical programming, but which in rare occasions is uncoupled or switched. In this case the physical programming is useless, even repugnant, showing as clearly as possible that the brain is the dominant organ of sexuality.

Why is a disconnect between one's feelings and one's received role so repugnant? Why not accept how one is treated, and use that to one's advantage? Why all the discomfort with being the wrong gender? Not being afflicted, I can not be certain, but if society has over the millennia tailored suitable gender roles, then one's day is going to be filled with countless irritations and discomforts if one is transgender. Whether it is wanting to wear dresses, or to nurture a doll, or to not play with trucks, or to be attracted to men, one's desires are going to be thwarted time and time again. They are part and parcel of who one is, both inside and outside.

Are there some desires that are beyond the pale? So disruptive to society that it has a right to force individuals to put a lid on their own desires? Certainly, but not in this area. Temperamental conservatives tend to differ, but if no criminal harm is being done, the individual need to express and embody one's particular blend of gender proclivities should be sovereign. Society's gender roles can withstand the assault of deviance, since those roles are in the first place nothing but the negotiated average of gendered desires in the past. Indeed, the opening of many different approaches to gender expression is a breath of fresh air to the common tendency of societies to get sclerotic in their adherence to tradition. Not to mention that people who are at home with themselves make much better parents than those who are acting a lie.

Could transgender tell us something about spirituality? There is an intriguing, and I think informative, parallel between the inner experiences involved in "knowing" that god exists, and "knowing" that one is the wrong sex. Both are intuitions that are not spelled out, but are "deep" feelings about the nature of reality- one's personal reality that is extremely difficult to express to others, but at the same time must be expressed, because it is not just a dry observation, but an earthshaking revelation of identity and meaning. The conversion experience, as related by William James and Francis Collins, among many others, is notoriously personal and impervious to reason.

de Maistre and Radical chic

Theists daydream about crushing modernity, in favor of "Radical Orthodoxy".

One of Isaiah Berlin's finest works (see the side-links) was his essay about the intellectual outlook of Joseph de Maistre, the staunchly conservative Catholic Savoyard who lived through the French Revolution and wrote whitheringly against it, against modernity, against rationality, and against all points un-Catholic.

His great insight was about the dark side of human nature- how people want to be in chains, want to sin and be forgiven, want to sacrifice their lives on the altar of authority, and thus need and want to be led by their betters, or indeed by anyone with plausible authority. He saw clearly the acidic nature of rationality and atheism, which would wash away the veneration of throne and altar as divine manifestations, imperturbable and unanswerable, which best undergirds such patriarchal, hierarchical systems. He despised the French revolution, yet was fascinated by power, legitimate and illigitimate. One can see clear affinities with Machiavelli, even as de Maistre hewed devotedly to the Roman Catholic church (see fideism). He knew that to see through the contingency of such institutions and theistic rationalizations was to destroy everything- to destabilize the delicate threads of society, with no assurance that anything at all, or at any rate anything worthwhile, was ready to replace them.

Echos of de Maistre's philosophy, which was highly influential in its time, especially in reactionary Russia and restoration France, continue down to our day, through Fascism, opposition to Vatican II, Opus Dei, and most recently, in a curious phenomenon that calls itself "Radical Orthodoxy" (RO). Not coherent enough or palatable enough to be a philosphy, RO calls itself a "sensibility", and seeks the usual conservative dream of universal subservience to clergy and church- of stability promised by verities imbibed unthinkingly and enforced ruthlessly. A medieval world where being outside the church is literally unthinkable, and atheism but a rumor from far away and long ago.

de Maistre's views were a powerful antidote to the enlightenment faith in human rationality, which did indeed have an excessively sangine view of our (or at least revolutionary Frenchmen's) ability to reshape society to the ideals of Liberté, Egalité, Fraternité, instead authoring a rather sanguinary episode that was saved (depending on one's view of him) only by the Machiavellian hand of Napoleon and his even more sanguinary excesses abroad (admittedly, in response to the relentless aggression of the horrified theo/auto-cratic enemies of the French revolution).

Optimism or pessimism about the human condition- that is the question. In the end, even de Maistre knew he was waging at best a holding operation, since the progress of the sciences and rational thought was so demonstrable and invigorating to so many, despite the missteps along the way. It was left to the next century for the full excesses of each extreme to be made explicit in the death-grapple between Germany, with its romantic religion of Volk und Blut, and the Stalinist dictatorship of the proletariat. Each partook in some measure of both extremes, claiming rationalist sanction by way of various pseudosciences (race studies and eugenics on the one hand, and historical determinism on the other, among many others), while also feeding deeply on romantic irrationalist attitudes, including leader-cults and nationalism, to create updated terror-states.

Thankfully, other political systems have cast a less harsh light on the possibilities of reason in the guidance of human affairs, but the modern age remains deeply discomfiting to those who are not at home in the ultimately self-determined and meaningless nihilism of fully realized modernism. This nexus of self-made meaning, rampant liberty, and penetrating skepticism offend those who seek timeless truth and structure in their inner and outer lives, however illusory.

Thus Radical Orthodoxy, a minor theological revolt from the Anglican church that sidles up to Rome, (indeed holding a recent conference right by the Vatican, with the howlingly misleading title "The Grandeur of Reason"), and offers patently irrationalist mystical maunderings to communicate its "sensibility". A sensibility which offers a critique without criticism- a cry of protest against modernism without rational content, as far as I can tell (or Mr. J. Irwin either, who was there). Which seems, at base, to wish its way back into the early middle ages, when life was good for the clergy, everyone knew their place, and none of the doubts introduced by the Renaissance had yet reared their head, let alone the utterly corrosive skepticism of modernity. Indeed, they have something of a bone to pick with the eleventh century pre-scholastic Duns Scotus, [ed. note- a correspondent points out below that Scotus was 13th-14th century, and taught at the height of scholasticism] and his excessive use of reason! No community will be conceivable outside the church, and while the church will be perfectly humble and humanistic, somehow nothing could be done or authorized without its sanction.

What is the Grandeur of reason, in their eyes? Well to quote Irwin, "What brings this reductionism to pass, it is claimed by both [pope] Benedict and Radical Orthodoxy, is the ‘self-imposed limitation of reason to the empirically falsifiable’." The grandeur of reason turns out to be its extension and broadening into faith- thus giving blind faith the name "reason" just because, well, reason has a nice ring to it in this modern age, doesn't it? Apparently the outright proclamation of faith, pure and simple, is unappetizing for theologians who call themselves "thinkers", so their answer is to slap the sticker of reason on whatever they happen to hold as faith, and hope no one notices.

The self-applied moniker of "Radical" is not RO's only claim to chic, for they are self-avowedly postmodernist as well. Whatever claims to deconstruct modernism and reach beyond the horrors of penetrating rational thought is their friend, and postmodernism is certainly that, since in most understandings it attacks the very capability of humans to understand anything, as per Lyotard, Derrida, and Foucault, to the point that their own writings demonstrate what they set out to prove. It is a fellow obscurantism with which the RO theists feel very much at home. All the same, they appear blind to how postmodernism is even more thoroughly critical of the "logocentrism" and other universal narratives that RO wishes to shelter from thought than it is of the residual certainties of modernism.

For that is the point of RO, isn't it? To proclaim, propagate, and enforce an orthodoxy (kerygmatically, as they would say) without skepticism, quarter or second thought. That is why they yearningly look up to the Catholic church, which stands as such a monolith of unappealable, unapologetic, infallible orthodoxy in a sea of doubt and skepticism, even as it quietly steers its ship with the times, claiming to be best friends with the Muslims and Jews after all, casting off limbo with a press release, settling pederasty case after case as quietly as it can, and otherwise reluctantly trimming its course to the critiques of enlightened reason and morality. And the ruby slippers, dresses, and hats- out of this world!

de Maistre would be deeply pleased by the continued appeal of ultra-conservative thought. His battle goes on and on, one golden age replaced by another in the rear-view mirror, and those who have authority based on nothing other than superstition and tradition deathly afraid that the winds of reason will lift up their skirts and blow them away.

Incidental links:

• Mullahs and the postmodernists.
• Fascinating and revolting tale of a postmodernist taking it to the limit.
• The Sokal hoax, uncovering postmodern pretensions and obscurantism.
• A theist puzzles over RO.
• A correspondent provides an excellent primer on RO.

The meaning of charisma

It is curious how religion propagates through charismatic personalities. What does that say about its truth?

The charismatic personality is something mysterious and powerful. People such as Bernie Madoff, Robert Schuller, Joan of Arc, Steve Jobs, Jesus of Nazareth, and Barak Obama project an aura of complete conviction and meaning that leads to great social power. When everyone yearns for meaning, those who seem to have it figured out and wrapped up with a bow, yours for only $99.99, are the purveyors of the ultimate product.

This came to mind while reading that the televangalism empire of Robert Schuller is falling apart amid his attempt to grant, and then revoke, succession to his son, also named Robert Schuller. Do scientists and engineers spread their "truths" by such fragile and nepotistic means, dependent on the salesmanship of motivational speaking and the intimacies of televised rhetoric? Apparently not.

Personal meaning is the currency of charisma, and speech its medium. Obama electrified the nation with his "journey" which said implicitly that we collectively might not be bad people, but good people. We might not be torturers, bigots, and killers, but a generation that heals and transcends the divides of race, terror, and culture. What that meant for each of us was powerful, and resonated increasingly the more we learned of his capacity to be the change through his own moral composure and competence.

Very well- the political system has granted us the means to re-imagine and redefine our social meanings. It is religion, however, that traffics in even more ultimate meanings, purporting to situate us in narratives of cosmic importance, artfully contrived out of the many myths and imaginings of our ancestors, refined into a supremely addictive product that, once ingested and believed, appears to be virtually impossible to kick.

Whether it is the story that we are loved unconditionally and utterly by an invisible god, (though if we do not believe we will burn in hell forever), or the story that we are on the side of good with our god Ahura Mazda in an eternal fight against evil, as proclaimed by Zarathustra, each religious construct exists to situate us as meaningful, valuable beings in what is otherwise an intrinsically meaningless universe.

What is different about these narratives, each full of meaning, yet so different in their premises and plausibility? Must personal meaning come from narratives involving supernatural beings, or can it also derive from reality-based narratives? That is the existential question, and the answer is that reality-based meanings are always relational and relative. They are situated in our historical, social and intellectual worlds, which are fluid and changing as new issues, new goals, and new forms of consciousness arise. They can never be absolute.

Religion offers absolute meaning staked on completely exterior references. That is why the supernatural is such a fixture of the religious experience. It offers a separate geography for the safe-keeping of ideals, dreams, and wishes, completely unsullied and unaccountable to the here and now. That is also why religious leaders claim their truths and guidance to be unchanging (even infallible!), even as they work tirelessly to keep up with social trends, or else give up the ghost to others that do.

The artists of religion are its charismatic preachers and especially prophets, who offer themselves as mediums of divine inspiration and fulfillment, conduits to a more perfect world. But of course that ideal world is not separate or absolute, but is entirely a matter of imagination, and some of its imagineers are more in tune with the times and persuasive than others. The competition between such imaginative visions is called theology, except when it degenerates into actual warfare, in which case it is called Jihad, or Crusade, or the thirty-years war, etc.

A similar phenomenon takes place these days on the "motivational" speaking circuit, where luminaries of rhetorical skill and celebrity draw audiences searching for meaning and fulfillment, though this time it is, as a rule, meaning in their work, and fulfillment in the form of money. The economic system relies on many jobs that are extremely hard to construe in any deeply meaningful way, yet people need to find meaning to keep their sanity. Thus the need for motivational speaking, which reframes the work of capitalism as life fulfillment, as Olympic-caliber competition, or as military valor. Inspiration comes in a kaleidoscope of heroic forms.

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These threads all come together in the work of the Reverend Dr. Creflo A. Dollar, whose Christian ministry (and "Change Experience" revivals) promise earthly prosperity and eternal happiness, all for a low contribution, since, as his scriptural motto goes: "Give, and it shall be given unto you".

Most divines naturally look down their noses at this crass mixture of the sacred and the prosperous, as if real human meaning could never be found in this world, but only in the next. In this position they may be less personally fraudulent than the Reverend Dollar, but they are still selling what has to be termed a big lie. Indeed, Christians often will argue that they recognize that their Christ story is, on the face of it, so preposterous and absurd that they would be the last to believe it, were it not that it really did happen and really is true. (Unlike all those other religions!)

Anyhow, the common denominator in these insprirational interactions is the imaginative construction and infusion of meaning into human existence- an existence that has little meaning on its own, and thus cries out for assistance, whether high or low. Assistence comes from those who have the gift to convey their own certitude and faith so well that they can sweep others up into what has been called in Steve Jobs's case, a "Reality distortion field". That was the job of the shaman, as it is of the priest and pastor today. Humans are very suggestible- a property that is essential to our sense of meaning and continuing social existence, but which is also prone to misuse by advertisers, con men, politicians, et al., when not studiously counterbalanced with skepticism.

In government, this essential skepticism has been installed by means of constitutions, separations of power, checks and balances, and party competition, so that suggestibility and mania can be slowed down by some degree of automatic critique and review.

It was the wisdom of the enlightenment to agitate for a similar check on religious zeal: the policy of dissociating it from the state. Given that religions come in all intensities and sizes, and do not necessarily have internal checks and balances, their effect on the society in general needs to be limited lest, as is so common historically, they unite with the state and its instruments of coercion to carry their zeal to all, whether voluntarily receptive or not (see Constantine, et al.).

This separation protects the society at large from religious extremes, but does little to protect those caught in the clutches of religious movements from their own suggestibility. Whether the cult is small (Scientology, CUT) or large (Christianity), human suggestibility and its allied capacities of total belief and commitment can lead to tremendous grief (as well as to tremendous happiness).

And that in the end is the meaning of charisma. Like scientific knowledge, it is a tool that can be used for good or ill. But it is in some ways far more powerful than knowledge alone, since it puts that knowledge to active use. It can unite and carry people into common projects that uplift, give meaning and improve the world, but its generated meanings can just as well be profoundly destructive, as the extreme movements of the twentieth century (Nazi-ism, Boshevism, Mao-ism) make so clear. The charismatic leader can only express and channel what his listeners are prone to hear- what is current or nascent in the zeitgeist. Thus we as individuals have a reciprocal duty to cultivate the better angels of our natures, both in our routine debates and in our responses to extraordinary leadership.

Each of us individually has a duty to recognize our susceptibility to charismatic suggestion and to bring skepticism to bear. But more deeply, we have to recognize that our own skepticism and reason is insufficient in the face of our biases, so we need to seek humility and continually listen to and face honestly what critics have to say. And we should lead our lives, defining our own meaning, rather than following the dictates of others, living or dead.

Related links:

• Old but good book on human herd instincts, by Wilfred Trotter.
• Topical cartoon.
• Suicide-martydom correlates more with service attendance than with religious belief.

PTSD politics

Thoughts on Palestine as a case of PTSD politics.

Trauma and victimization are profoundly and permanently damaging. Recent stories about Iraq veterans show the permanent changes that can be wrought by PTSD, analogous to the permanent brain alterations that follow tobacco, alcohol, or cocaine addiction. Our brains are plastic and impressionable, degraded by degrading conditions. People who are ground down by traumatic conditions are prone to act irrationally and harbor bottomless resentments. Conversely, those brought up in security and prosperity tend to be optimistic and open-minded. That is the underlying rationale for America's "special role" in world affairs, borne as much of our long-term prosperity and security as of our ideals and political example.

To illustrate, the post-9/11 mood on the east coast, especially in Washington, was completely out of proportion to the threat posed, either by the World Trade towers attack or the antrax attacks. The terrorists terrorized (some of) us out of our collective wits without doing very much damage in absolute terms, mostly because Americans had been coddled for decades in a placid, secure country whose major questions revolved around the levels of interest rates and consumer confidence. Our much-vaunted ideals collapsed in a heartbeat, replaced by the vengeful drum-beating of an opportunistic president.

Imagine how we would have reacted had such devastation rained down on us on a daily basis, as in the recent Gaza war, where proportionate damage would have been 83,000 dead per week in the US. Or the recent civil carnage in Iraq, where proportionate damage in the US would have been roughly 20,000 to 30,000 dead per week, every week, for six years. The mind reels at what would have happened to our society. (Compare also the current US-wide death toll of ~825 per week from car accidents and 8,300 premature deaths per week from tobacco).

With this perspective, we can appreciate the intransigence and horror of the Israeli-Palestinian relationship. Locked in enmity and mutual trauma, they hate and are hated. They seek revenge and self-respect in the face of dehumanization. The open each other's scabs, and rub salt in the wounds.

Who is at fault? Well, the problem started with the displaced trauma of European antisemitism, reaching its climax in the holocaust.* While Palestinians where largely pro-Hitler and antisemitic by long Islamic tradition, they were peripheral to the convulsive drama of Europe's Jews .. until those Jews showed up on their doorstep, looking for a home. The Zionist project long pre-dated World War two, but that was when a trickle turned into a flood, and integration of the rising tide of Jews became impossible. They wanted their own space- Lebensraum, one might say- in Palestine.

They pursued all sorts of means, fair and foul, to get it, ranging from purchases of land to terrorism of the local Arabs. Already from the start, the Palestinians had dysfunctional politics, self-defeating reponses, and some bewilderment as to why, exactly, they were supposed to give up their land because some Europeans had been evil to other Europeans. The claims of Jews to their promised land fell on deaf Palestinian ears, as did the pleadings of the British, who were nominally in charge of the territory. The whole deal just did not make any sense.

Yet with force majeure on their side, and the sympathy of the former colonial powers as well as the US and the UN, the Israeli state was born in the teeth of Arab enmity- teeth which were shortly chipped and broken on the highly westernized military know-how of the young Jewish state in the 1948, 1967, and 1973 wars, culminating in Israel's control of the entire territory of Palestine. Incidentally, as a Europeanized, Westernized outpost, Israel also fulfilled in an ironic way the dreams of the European Crusades for conversion and repossession of the so-called "holy" land.

The traditional and Biblical method of dealing with the Palestinians at this point would have been to kill the males of age and sell the rest into slavery. Unfortunately, the requisite markets for slaves no longer existed, and the Jews had raised their ethical norms in the intervening millennia. Forced exile was another option that was explored, (called, in our hygenic age, "ethnic cleansing"), but naturally, no neighbor wanted to take in the now-traumatized and bitter Palestinians, or indirectly thereby help Israel out of its enormous problem.

So Israel was faced with an existential and moral conundrum: how to deal with an embittered enemy on their doorstep, in territory under their own control, within their own ethical precepts, so recently sharpened by their own travails? The answer was to semi-officially apply a water torture of gradual land purchase and expropriation driven by the most rabidly religious settlers, (who, because they are viewed as "more Jewish" than other Israelis, are given a pass on their unethical behavior and fanaticism, not to mention the irony of being excused from military service), along with big helpings of degrading treatment and collective punishment of the Palestinians via the ensuing occupation. In return, the Palestinians mounted what resistance they could, generally small-scale terrorism and guerrilla warfare.

It is clear that Israel has fundamentally violated its own morals and those of the modern enlightened age in its treatment of the Palestinians. The Palestinians for their part have violated the same norms, though they never subscribed to them, and would never have presented any problem had their territory not been disturbed in the first place. At any rate, the problem is one for the Israelis to resolve, since it is they who have the power: the airforce, the billions in weaponry supplied by the US, the nuclear bombs. For them to claim that the Palestinians are not "partners for peace" is totally disingenuous, since the historical process they have sponsored has rendered the Palestinians justifiably aggrieved, embittered, and traumatized, not to mention powerless in all respects other than to say the one word they can manage ... "No".

It might be useful to note here that there are only two ways to win a war- one is to kill the enemy, and the other is for the enemy to give up. An enemy who refuses to give up is one you can not defeat, (see Vietnam), thus the importance of winning "hearts and minds" in the current parlance, which is far more important than realized, even now.

I had thought that the border wall against the West Bank was the beginning of a good solution, hewing the old adage that good fences make good neighbors. But unfortunately, the Israelis placed the fence not on the 1967 border which would have been the logical (and legal) place to put it, but snaking through Palestinian territory, breaking up numerous communities, all in an effort to include as many settler zones as possible, and to impair as many Palestinian communities in their vicinty as possible.

And on top of that, they still couldn't stay out of the West Bank or Gaza, continuing to build settlements on the other side of the fence, building roads restricted to Israelis, blocking Palestinian roads, patrolling, subjecting Palestinians to checkpoints, blockading trade from time to time, bombing and destroying buildings, etc., etc., etc. So the fence has been highly successful from the Israeli perspective, keeping the other side at bay and pacified in a state comparable to apartheid, as Jimmy Carter put it. But it has not been an equitable boundary upon which to build a peaceful or neighborly relationship.

That is where we are now, and the way forward is for Israel to do what is right- not to give up its own territory in the form of a "right of return" for Palestinian re-assimilation of Israel, but to fairly divide the territory using the 1967 border as a starting point, and make that division stick by getting out of the Palestinian side completely, with a relocated fence. The Palestinians will need a road corridor to communicate between the West Bank and Gaza, so negotiations could exchange land, inch-for-inch, for such a corridor in exchange for selected settlements on the Israeli border.

We can grant that the Palestinian political system is thoroughly dysfunctional, corrupt, and self-defeating. That is no reason for Israel to not do what is right- to disengage its expropriation and occupation activities and let the Palestinians take care of themselves (with reasonable means to do so, like ports of their own in Gaza, open trade, etc). Only by disengaging will either side be able to heal its particular traumas and wounds.

Additionally, the Palestinians have been egged on and used by their false friends in Iran and Syria, doing themselves precious little good, and keeping them from tending to their own interests. The only way to break these relationships is to cut the ground from under the extremists by unilaterally offering and carrying out a fair deal for the Palestinian people.

At this point, one might ask about the Gaza situation. Didn't Israel disengage there, and didn't Hamas keep sending rockets into Israel? I would offer that compared to the problems of outright occupation, the problems of occasional rockets were minor. Additionally, the disengagement was far from complete, since Israel turned around and blockaded the elected Hamas government and otherwise made life very difficult for Gaza. And the proper solution to the rocket attacks was (and remains) to reply with immediate return fire to the point of rocket origin- easily possible with basic spotting capability- rather than to wait in silence, and then indulge in a frenzy of collective punishment, intended to "send a message" or "teach a lesson" in the form of 100-to-1 killing rates ... lessons that are never learned at the point of a gun. (See a revolting piece of embedded reporting in TNR.)

The remaining problem will be their continuing economic relationship, which is extensive. Palestinian workers endure dehumanizing daily crossings to work in Israel, and many other critical if fraught relationships exist. No doubt Israel will be tempted to exert pressure on its neighbor in perpetuity by these means, its economy being far more vibrant and influential. It is, of course, a temptation to be resisted, since nothing good comes of such pressure, as amply documented in the relationship to date. Israel's interest on every count- demographically, economically, and strategically, is to promote the economic development of Palestine, and Israel should offer treaties to that effect.

In the same vein, it is not Israel's job or right to control the tunnels or other trade routes into Gaza. If Gazans want to import their own bombs, tanks, etc., they should be able to do so. Using such weapons is another matter, but it is ultimately deceptive as well as futile to claim disengagement from the Palestinians while controlling their most basic contacts with the outside world. Without having responsibility for themselves, Palestinians will never take responsibility vis-a-vis Israel.

At any rate, the solution lies in fairness, separation, and disengagement. The only power the Palestinians have is to say no to the Israeli offers of peace, to offer token resistance with small arms and suicide terror, or rioting and rocks when pressed to extremis. Even this power/resentment would largely dissolve if Israel unilaterally provided a fair and sustainable territorial solution as outlined above, rather than continuing to treat the Palestinians as subhuman objects of slow-motion expropriation. And how do we get Israel to do what is right? Simply by withdrawing our various forms of support if they don't. Whether Israel got to this intransigent and immoral position consciously or not, the US has the leverage to dislodge them from it. (See a Cohn piece on tough love..)

It is sad and ironic that, to realize their Zionist dream, Jews turned around and created the very ghettos, dehumanization, and hatred that they fled in Europe. It is time to recover the humanity of both sides, by giving the Palestinians what is right (with or without negotiations) and allowing both sides to begin a healing process that will take generations.

Related links:

• Podcasted discussion along the lines above, with Antony Loewenstein, heard after I wrote this.
  
• Bush secretly supplies arms to Fatah, in hopes of a coup against Hamas.
  
• Friedman makes similar points, indirectly.
  
• Cohen, on how similar rational engagement with Iran would be extremely helpful.
  
• Lengthy podcast on Israel and the fence, putatively "balanced".
• Lengthy historical treatment.
  
• Frontline segment about settlers.
• Later article on Obama's reluctance in this area.
• Later, Hitchens with an excellent piece on Israeli clerical extremism

Incidentally, an excellent review of Darwin, on this anniversary

---

* Let me note as an aside that one of the anti-semites in chief was none other than the founder of Protestantism- Martin Luther:

Martin Luther, "On the Jews and their lies", 1543

My advice, as I said earlier, is: First, that their synagogues be burned down, and that all who are able toss in sulphur and pitch; it would be good if someone could also throw in some hellfire. That would demonstrate to God our serious resolve and be evidence to all the world that it was in ignorance that we tolerated such houses, in which the Jews have reviled God, our dear Creator and Father, and his Son most shamefully up till now, but that we have now given them their due reward.

... Third, that they be forbidden on pain of death to praise God, to give thanks, to pray, and to teach publicly among us and in our country.

... Fourth, that they be forbidden to utter the name of God within our hearing.

... So let us beware. In my opinion the problem must be resolved thus: If we wish to wash our hands of the Jews' blasphemy and not share in their guilt, we have to part company with them. They must be driven from our country.

... But since they lack the power to do this publicly, they remain our daily murderers and bloodthirsty foes in their hearts. Their prayers and curses furnish evidence of that, as do the many stories which relate their torturing of children and all sorts of crimes for which they have often been burned at the stake or banished.

How to read DNA

A review of DNA sequencing technologies, from the paleolithic to the bleeding edge.

While one of the greatest discoveries of the last century, indeed of all time, was the role and structure of DNA, it did not amount to much in practical terms until methods were devised to read its code- its sequence. There has been a fascinating evolution in technologies to read DNA, and I have experienced a good share of it. Most methods are dependent on harnessing nature's own enzymes that replicate DNA in increasingly clever ways. The resulting flood of information will serve the age-old project of "know thyself".

DNA exists in almost endless lengths (bacterial genomes are typically circular, and the average human chromosome is 1.3E8 base pairs in length). So the first step in sequencing, in typical reductive fashion, is to break this linear structure into small pieces, place them into bacterial mini-genomic circles with independent replicative ability (plasmids or their relatives), and replicate/amplify them to large amounts that can be handled, sampled, sequenced, filed, bar-coded and stored.

The paleolithic method of sequencing (I've used it a few times) is based on chemistry instead of on enzymes, and is called the Maxam-Gilbert method, after its developers. First, one cuts a large batch of DNA at a specific sequence site with what is called a "restriction" enzyme- a pair of molecular scissors. Then its ends are labeled with radioactive phosphorous (P32), and one of the two ends removed with yet another restriction cut, and the remaining DNA split up into several pools, treating each pool lightly with quite hazardous chemicals that modify the DNA at certain bases (hydrazine at T and C, dimethyl sulfate at G, and formic acid at G and A). The individual units of DNA are called nucleotides, and their key parts are called bases- the A, G, C, and T of the genetic code, after their basic pH.

These chemical reactions are only roughly base-specific, and hit other bases as well, so the whole thing is woefully inefficient. The DNA is then further chemically processed to break the backbones at the modified bases, and the mixtures are eletrophoretically separated on a gel that allows fragments differing in length by a single nucleotide base to be distinguished. The radioactive label on one end ensures that only those fragments spanning from the radioactive label to the randomly cut point appear on the X-ray film that is exposed to the gel.

All the other methods to sequence DNA use the magic of DNA replication enzymes (polymerases) to read sequence, using methods devised by Fred Sanger (who is one of only three people to have received two nobel prizes in science). They do this by getting the enzyme to incorporate occasional bases with some special property- the nucleotides either stop chain elongation at random positions, allowing fragments like the ones described above to be produced directly by the polymerase, or they have other complex modifications to be described below. The enzyme does the work of reading along the DNA, and the experimenter coaxes it to tell which nucleotide base it is seeing as it goes along.

The original Sanger method used radioactive tracers such as P32 or S35 to detect the resulting DNA fragments, but advances in fluorescence technology have revolutionized this aspect of biology, as so many others (one of the latest nobel prizes went to fluorescence labeling technologies for proteins)

How do these enzymes know where to start? The DNA is continuous, but just like in a book or a chapter or a page, you have to start somewhere. And since the text in this case is A, T, G, and C with no further punctuation, the problem of knowing where you are is quite a bit more difficult than in a book. Usually a "primer" is used to start off the DNA polymerase- a short DNA fragment that can be made by pure chemistry, perhaps 20 nucleotides long, which hybridizes to its complementary sequence in the target DNA (after it has been heated up to melting temperature). If the cloning was done in clever fashion (abutting the DNA fragment to be sequenced right up to a known part of the cloning plasmid), then the same primer can be used for an entire sequenceing project.

The original human genome project used a variation of this method, where primed DNA polymerases on templates are fed a low ratio of nucleotides that have both chain terminating capacity, (di-deoxy, as opposed to DNA's single deoxy), and also have fluorescent labels (different for each of the four bases). Then the full four-label reactions with their resulting synthesized fragments are run through an extremely tiny (capillary) electrophoretic gel, at the end of which a fluorescence detector reads off the labels from the size-sorted fragments as they travel past. This is done with expensive machines, using miniaturized reactions that attain large scales of operation, taking all this work out of the hands of regular bench scientists.

A more recent technology is the 454/Illumina system (named for the companies they are offered by), which has finally dispensed altogether with the electrophoretic separation step, which has been such a painful bottleneck.

These systems lay single molecules of template on tiny islands on a glass slide (or a bead), and do an in-place PCR amplification step to park at lot of copies at that location. Then the sequencing step is performed, with A, G, C and T successively washed over all the template islands, and a luminous flash registered wherever a single step of incorporation takes place, before the next washes and next step of polymerization is performed, etc.

The virtue of this system is its extreme miniaturization and large parallelism- many different molecules can be laid down, amplified, and sequenced in one experiment. However, the read length is paltry- only about 35 (Illumina) or 300 (454) nucleotides, compared to the 800 nucleotides regularly attainable with the gel-sorting methods above.

Read length is critically important, since the next step for all these technologies is the reverse of reductionism: the re-assembly of the sequence from all the individual sequence reads, like doing a jigsaw puzzle. The reads (for a whole genome, say) are all poured into a computer program which lines up sequences that overlap, building back up to the sequence of the entire source DNA as best it can. As with jigsaw puzzles, the bigger the pieces you start with, the easier the puzzle is to solve, to an almost exponential degree.

Last, and most amazing, a recent report in Science introduces what is sure to be the next iteration- monitoring the production of a single strand of DNA on a single polymerase from a single template strand with an extremely miniaturized apparatus. Originating in the labs of Watt Webb (of which I am an exceedingly minor alumnus), and Harold Craighead at Cornell, this technique uses an odd optical property to peek into extremely tiny volumes of solution (one zeptoliter ~1E-21 liter).

It turns out that if you shine light through holes made in a conductor whose diameter are less than half the light's wavelength, the light does not get very far. If a solution is put into those holes, you can look at the fluorescent properties of the super-tiny volume right at the floor of the hole (containing in this case a DNA polymerase with template) without being distracted by the rest of the solution which may contain a high concentration of other fluorescent compounds (nucleotides). The fluorescence system looking into the bottom of the hole essentially just "sees" the occasional one or two fluorescent molecules bouncing along the bottom, or binding to the polymerase located there.

The sequencing method is then to add a solution of four different fluorescent nucleotides which contain color labels at their outer-most phosphates, which get clipped off as they are added to the growing chain. The polymerase attached to the bottom of the view-hole can use and incorporate these nucleotides with no problem, and fluorescence from the incoming nucleotide appears transiently, as it is positioned in the enzyme's active site, but before the reaction takes place that clips off the label and incorporates the rest of the nucleotide into the growing chain.

Thus the detector sees a parade of distinct fluorescence signals, one by one, as the lone polymerase does its work synthesizing a new DNA strand along the template. The tricky part is that this process happens stochastically. One incorporation event may go fast, the next slow, as diffusion of the nucleotides and even quantum effects come into play. Several incorporations of the same nucleotide may occur in succession on the template, requiring the observers to make sure they are tracking the pauses in fluorescence that occur between each step of the elongation reaction. Much of this uncertainty can be resolved technically, and also by doing a few replicates.

One advantage of this method is that read lengths are substantially increased. The researchers (who have now duly set up shop in Silicon Valley) show an experiment using a circular template with alternating G (red, below) and C (blue) halves to run off a potentially infinitely long sequencing read. They report a rate of ~3 bases incorporated per second under their conditions, with clear alternation of C and G signals, up to 4,000 nucleotides in an hour's time. This is very promising for problems in genomic sequencing like the occurrence of repetitive regions that are very difficult to piece together from short sequencing reads, and one may hope that these lengths can be extended and the polymerization times speeded up as the technique is further optimized.

All these advances mean that it will not be long before individuals can get their entire genomes sequenced at a reasonable price. The information will allow divination of the future, in the form of improved personal medical prognoses as we slowly learn more about how the genome works. And also divination of the past, since complete genomes will allow geneological analysis of unprecedented detail and depth. Our long evolutionary inheritances reside in these ~3 billion base pairs, and bringing them into the light will generate great benefits, individually and collectively.

Incidental links:

Steven Pinker on his own genome.

Very basic TED talk on genomes by Barry Schuler.

Dire warnings about privacy issues.

Chief Marin

Marin County is named after a Coast Miwok whose story is movingly told by Betty Goerke.

Not so long ago, in a galaxy not very far away, the concrete and asphalt of Marin County did not exist. Animals roamed at will, the air was pure, and the seasons passed in regular succession without the threat of expiring into the maw of global industrialization. The county was dotted with people who wove baskets of grass, gathered mussels from the bay, wove feathers into their headbands, and told abundant stories from their past, and from their imaginations.

Local anthopologist and archeologist Betty Goerke recently gathered what evidence there is about these native Americans into her book "Chief Marin: Leader, Rebel, Legend". There isn't very much, since they spoke their stories rather than blogging them, but Goerke is judicious in setting the scene and reading as much as possible from what there is. I highly recommend it.

The principle horror she describes is the California mission system. Now curiosities and museums, the missions were outposts run by Catholic priests, first from Spain (1775 to 1821), then from Mexico (1821 to 1846). The priests had final say over all matters at the mission, including command over small military detachments assigned to them. They regarded baptism as a one-way street, cajoling natives into baptisms that they hardly understood, then sending military parties out to recover any "neophytes" who dared to go home again.

Once inducted into the mission system, neophytes were treated like slaves, worked under military guard in the fields, housed in segregated "dormatories" from which there was no escape, and paid only food and clothing enough to subsist. A fascinating contrast is presented by Fort Ross, a Russian outpost slightly to the north, whose clergy made no project of enslaving the natives, nor did the military harrass them most of the time, but let them trade with and work for the fort on relatively equitable terms. "Runaways" from the Spanish to the Russian establishment were thus a constant problem. Goerke writes "Father Amorós (of the San Rafael mission) sent out a force of a few soldiers and neophytes to retrieve and harass those who had fled to Colony Ross.", and quotes the Russian Achille Schabelski, who "saw several tents of unhappy fugitives from Mission San Rafael, who, taking me for a Spaniard, fled to the mountains.". One native chief said that the Spaniards "were bad men who took his kinsmen captive and make them work like cattle in the fields".

Eventually, the Spaniards (dragged down by their theocratic tendencies) were replaced by Mexicans, who, enacting the enlightenment ideals of the time and of their own liberation, decided to release the natives with shares of the land, abundant livestock and produce from the missions. Yet corruption carried the day, and the local authorities managed to leave the native Americans with virtually nothing at all. The land they fled to was not generally recorded and deeded, with dire future consequences as Mexico gave land grants to sundry soldiers and other well-connected non-natives. While settlement was sparse this problem was not immediately apparent, but as white settlers arrived and after the Bear flag revolt revisited all the deeds in California, the die was cast for total displacement and disenfranchisement (Native Americans were not granted citizenship until 1924).

In many ways the native conditions were even worse during this time of "freedom", since the native Americans were hunted for sport and impromtu slavery by both Mexican (by General Vallejo and his relations, among many others) and white settlers. Goerke writes "In the North Bay, according to most accounts by the settlers and the military, the Indians were pursued for capture rather than murder, because the rancho owners needed men to work as laborers. ... the outcome was the same: murder, rape, and enslavement."

The role of Chief Marin in all this is rather murky. He flits in and out of the scene as a sometime pillar of the San Franscisco and San Rafael missions, sometime rebel leader harrassing the missionaries and hiding out on islands in the Bay, sometime prisoner (escaping several times), and sometime ferryman and trusted pilot about the bay. At one point in prison, he fends off a priest as follows: ".. told him with the greatest sang-froid that if the priest would not bother him while he was alive he would give his permission to make a Christian of his dead body. With this statement he dismissed this tormentor." He was respected by his adversaries, which led General Vallejo to suggest his name for the County across the Golden Gate from San Francisco. But all Goerke has to work with are baptismal, wedding, and burial records in the mission archives, and the much later histories and recollections of Vallejo and other Californios (Mexicans), after they were themselves expropriated by the inrushing horde from the east. In the end, her book is most moving in evoking the life of the Coast Miwok before, during, and after the traumas of colonization.

I'll close with one last quote from the book, from the early mission period, referring to the Russian explorer Otto von Kotzebue:

Twice a year, some of the Indians received passes that allowed them to return to their native villages for a brief period. Kotzebue observed: 'This short time is the happiest period of their existence; and I myself have seen them going home in crowds, with loud rejoicings. The sick, who can not undertake the journey, at least accompany their happy countrymen to the shore where they embark, and there sit for days together, mournfully gazing on the distant summits of the mountains which surround their homes; they often sit in this situation for several days, without taking any food, so much does the sight of their lost home affect these new Christians.'