Saturday, May 30, 2009

Dissection of the will

An experiment separates the threads of consciousness and action

One of the deepest sources of supernaturalism is the mystery of consciousness- the sense that our soul/spirit is so unmaterial, shiny, and pure that it could not possibly be sullied with evolutionary origins, messy neurological mechanisms, and eventual death. There is an undeniable and to some an unbridgeable tension between this remarkable experience and its rather obvious dependence on our brains.

One expression of this tension is the doctrine of "free will", which has two senses. One theological dilemma is, if god is so good and powerful, why are we not His obedient automata? Because He gave us free will, with which to be bad and yet also with which to worship Him, if we are smart, because he likes to be freely loved, not slavishly obeyed. Related to this theodicy is the second sense of free will- that our inmost soul yet still partakes somehow in the divine to the extent that it is immaterial, has a smidgen of moral knowledge (often ignored), and is eternal, even if, looking backward, it has its origin in a mysterious and divine implantation process concomitant with sperm and egg intromission.

At any rate, we feel free in our actions, while at the very same time physics tells us that no action happens without causes- causes that would obviate the felt authorship of our actions. The answer in scientific terms is to posit an "illusion of free will", where our actions, when not obvious responses to conscious exigencies, are caused by unconscious promptings which simultaneously arise in consciousness as 1: the idea which "pops" into one's head to move one's arm, and 2: the action itself, activated in parallel. In this scheme, our actions all have causes, just not always causes we are aware of. And the sense of authorship is a fiction conjured simultaneously as the actual causes activate planning and action.

The motor areas of the brain are known to form a crescent across the top midline from ear to ear, where past experiments have generated a "homunculus", or map of body parts moved by stimulating brain locations in this region. A completely separate sensory homunculus maps bodily sensations to brain locations, and is not involved in this work.

A group in France experimented on seven patients getting brain surgery for other reasons, stimulating the surfaces of their brains to figure out how actions arise and how they are perceived. Stimulation in the areas shaded purple below, which are in the motor area, caused body parts to move, but without any cognition that the person had caused the action, that they had wanted to cause the action, or indeed that the action had taken place at all.

Conversely, stimulation in the areas shaded yellow and orange below (the volitional field) caused patients to experience urges to begin an action, and at higher levels of stimulation, even the sensation they had carried out an action, though none had actually taken place. One patient, stimulated with 5 mA at site a in the figure, said "I felt a desire to lick my lips", while at 8 mA at the same location was quoted "I moved my mouth and talked, what did I say?" (Doubtless these quotes are translations from the French!) No action took place, however, and electrical EMG recording of the corresponding muscles gave no trace of any activity, confirming that the feeling the patients had was not connected to their bodies.

Locations of experimental stimulation, in the motor area (purple) and volitional area (orange, yellow), also called Broca areas 39 and 40. The SMA lies slightly forward of the motor area.

Of these two fields, the motor field is easier to understand. The output end of the process could be followed down the spinal chord and even to the muscles with electrical stimulation, creating actions authored by the experimenter rather than by the patient, who would have no sense of volition. The paper mentions that lesions in this area of the brain are sometimes associated with "patients who obstinately claim that they can move their paralyzed limbs." This paralysis is not physical but due to a disconnect between volition, which is intact, and motor execution, which is not. Additionally, the paralysis is not apparent to the patient, indicating that, as the paper hypothesizes, perception of action is more dependent on the internal sense of volition, which assumes as a matter of course that an action has taken place as planned, than on feedback from the body, surprisingly enough.

Tracking down the sense of will and authorship is more interesting. A consistent model is that a normal action engages a more extensive network of brain activity, of which only tiny portions were activated in these experiments. One terminus of a consciously or unconsciously generated action is the motor areas that actually control their fulfillment (purple), but another terminus elsewhere (yellow, orange) creates the consciousness first of wanting to do the action, and if intense enough, of having performed it. This second area may later integrate sensory feedback to enhance the sense of authorship and allow learning, but based on these experiments, this feedback is not critical to a sense of authorship, matching the conclusion of Wegner. The volitional area maps closely to the mid-brain regions that were pointed out in a recent blog to be the best guess for those responsible for consciousness.

There is another area adjacent to the motor field, called the supplemental motor area (SMA), where others have done experiments of this type. Here, electrical stimulation generates both what is sensed as an urge to perform an action contrary to one's will, and also, at higher currents, the action itself. The key distinction is that here, the urge is recognized to be contrary to the patient's will (as happens in various tic and involuntary movement syndromes), while stimulating the volitional area creates such will directly, without generating the action. The SMA may be a preparatory area for motor action, placed after the unconscious originating signal has separated between paths to the motor area and to the volition/will/feedback area, but still having partial input to non-volitional consciousness.

The bottom line is that the sense of authorship is conjured in an area of the brain that doesn't actually cause the action, but is a post-processing epiphenomenon. This sense is essential to learning, to a coherent sense of self, and to moral responsibility, but it is not causally essential. Given that the causes of action are often "reflex", or "spontaneous", or otherwise unconscious, it would require impossible circular logic to have our sense of authorship be mechanistically equivalent to actual authorship.

Incidental links
  • Philosophy bites podcast does neuroscience- the senses, blindsight, mirror neurons, alienation, anarchic hand, bodily coherence, etc.
  • New Yorker profiles neuroscientist Vilayanur Ramachandran, who deals with paralysis and other neurological oddities.
  • Science mag review of above paper.
  • Feminist atheist activist ... Taslima Nasreen
  • Supernaturalism explained, and podcast.

Saturday, May 23, 2009

Peak food

Our food supply floats on an ocean of petroleum, whose peak is now.

Peak oil has become part of the common parlance: the time when global production of oil reaches an all-time peak, followed by inexorable decline. Whether that peak is now or a few years away, rising demand will outstrip supply and dramatically increase prices as soon as the economic system gets back to normal. An analysis of the oil price spikes of 2008 indicates that while some of the rise was due to speculation in a classic bubble, most was due to real supply-demand dynamics, (reflecting low demand elasticity), which will re-assert themselves soon enough.

The price spikes in oil encouraged the diversion of food (corn) to fuel (ethanol) in the US. This contributed to a spike in food prices around the world which caused quite a few political problems. Another connection between fuel and food is that modern agriculture is heavily fuel-intensive, using (in the case of corn) about 140 gallons of (fossil) fuel per acre. To put this in perspective, that is enough to drive a 25 mpg car from coast to coast in the US. One estimate puts fuels used in agriculture at three calories for every food calorie consumed, amounting in the US to ten percent of fuel use. Rising fuel scarcity and cost will increase costs of fertilizer, machinery, processing, and ultimately, food. Poor countries will be most susceptible, especially when the green revolution, which is strongly fossil fuel-based, meets high fuel prices in competition with wealthier users.

Food systems also face other limitations such as amounts of arable land and water. A great deal of irrigation water is pumped from aquifers that are rapidly depleting, and in some cases from fossil aquifers that will never be replenished. Climate change derived from the fossil fuels already consumed is altering the availability of arable land, reducing areas in the tropics where higher heat can cause outright desertification or make some crops impossible to grow, and re-scheduling major agricultural rivers that are fed by glaciers. At the same time, climate change may expand arable areas in northerly locations like Siberia. Erosion and desertification are reducing arable land all over the world, since the current monoculture practices, however conservatively practiced, draw down soil resources instead of building them up.

Another critical element is population. All of nature follows the biological imperative of over-reproduction, spending all immediately available resources on the next generation, which is in turn left to gather what resources it can from the environment. In our case, we have found ways to borrow spectacular amounts of resources from our surroundings that will never be there to support future generations. This certainly applies to fossil fuels, but also to other minerals and to ecological services from the oceans, air, forests, and soils that are being depleted with little thought for the long term. Over the last few centuries we have gotten used to exponential growth in population, which even with the rosiest possible assumptions is unsustainable.

One could conclude that our "developed" way of life is an elaborate ponzi scheme- a lonely peak in earth's human population history, never to be repeated and foretelling harsh conditions on the declining side. Will such harsh conditions be required to restrict human population? Sadly, one has to say that the answer seems to be yes. There is little evidence that human societies are sufficiently conscious of truly long-term sustainability issues to be able to tear themselves away from our well-programmed biological imperatives. Certainly the Pope has no compunction urging continued fertility even in the poorest and most ecologically devastated precincts of his flock. It is only the modern development (and female empowerment) process that values quality over quantity in human reproduction, but at the same time it is the very process that eats us out of house and home in other ways.

Can technology make up the shortfall in resources, especially in energy, as well as mitigate the fallout of ecological devastation? That is not yet clear. Economists tend to be perennial optimists, assuming that, given the right incentives, our rich technological culture will create replacement commodities, in this case literally out of thin air. But just how extreme will those incentives have to get? Will they degrade our ability to live in developed ways? Will they prompt wars for food, water, and fuel? If the green revolution that has been so dependent on leveraging fossil fuels stalls, will poor countries face demographic catastrophe?

Right now the most daunting challenge will be resisting the temptation to double-down on this grand ponzi scheme, mortgaging yet more future resources and biosphere health by fleeing to even dirtier and climate-killing fossil fuels such as tar-sands, oil shales, and coal. That is the ultimate collective question- whether we can rise above what looks in bare economic terms to be an almost inexorable tragedy of the commons by collectively safeguarding earth's environment for those (perhaps fewer) humans and other inhabitants who succeed us.

Incidental links:
  • Black sun takes a rosier view of the technological possibilities
  • While others are more alarmist
  • Liberals have their own angle on the taking-to-the-hills movement
  • Easter Island offers a classic cautionary tale
  • More data on peak oil
  • And in completely other news, corruption continues apace

Saturday, May 16, 2009


On the moral and historical bequests of Christianity

A correspondent is carrying on a long campaign of polemic about how great the Christian tradition is, how it is still holding up our moral universe, and how we are going to end up in heck when it dies. Putting aside the question of whether the historical origin of moral ideas is relevant to their continued utility and propagation, and also putting aside the question of how our culture ever swallowed the tribal propaganda of "Christianity=goodness", the simple question is: would we have gotten to the rights-granting, cosmopolitan, quasi-egalitarian, humanistic western culture of today faster or slower had it not been for Christianity?

The question is one of alternative histories. What was Christianity really responsible for? What would have happened in its absence? While it is easy to point to the high-lights and low-lights of Christian history, it is much more difficult to do more than speculate about what would have happened in its absence. In scientific terms, with a single sample and no controls, how can the historian draw any conclusions?

Economists also have a term for this problem- "opportunity cost". These are the costs of all options and opportunities foregone when one makes a choice to invest money one way. If I put my money into a savings account, I forego the opportunity of investing it in the next big stock ... or the next big ponzi scheme. Only in hindsight do such opportunity costs become even partly clear, to our pleasure or regret, though of course we never know the half of what would really have been possible. But in the larger swaths of history, such alternatives are neigh-well incalculable. We do not know how a western culture bereft of monotheisms might have fared. We know how things were going in the classical world, but then Constantine, Justinian, and Muhammed arrived.

Christians typically point to the bad aspects of antiquity- slavery, infanticide, and brutal entertainments. Non-Christians can point to many bad aspects of the age that followed- economic collapse (whether due to religious naval-gazing and un-realism or to other issues of cultural decline coincident with Christianity), intolerance and persecution, the evaporation of serious philosophy, sciences, etc.

Ironically enough, the learning of pre-Christian antiquity was revered by all sides right up into the enlightenment and beyond, though understood rather differently by humanists and by the theists influenced by Augustinian and Thomist re-readings of classical works. Edward Gibbon certainly took a very sour view of Christianity, blaming it for sapping the ancient vitality of Rome and leaving it in ruins. And slavery was hardly foreign to more recent Christian cultures such as the American South. Each side has plenty of ammunition, but can the causality of any of this be nailed down? Can we conclude anything about what would have happened in the absence of Christianity? Was it bad or good?

Speaking rigorously, I don't think we can. We have no time machines and no alternative universes for experimentation. Relative to scientific experiment, history is both endlessly complex and unrepeatable, not to mention recorded with bias the minute anyone puts pen to paper. Thus it is likewise impossible to say based on historical arguments whether losing Christianity in the present age will be good or bad either. Nevertheless, I am happy enough to paint my own picture of the situation, calling out what historical scholarship there is and emphasizing the progress that had taken place in the ancient world, with Hellenism being a strong progressive influence as Rome softened in its various cruelties as time went on.

Perhaps the most pointed question is- did the ancients have any concept of human rights, and was this concept ascendant or not in the pre-Christian age? That may be the most likely wedge into the door of alternative history, indicating whether antiquity was on a path to modernism which Christianity nipped in the bud, delaying for over a millenium, or on the other hand whether Christianity revolutionized the moral order of the ancient world in a way that laid the foundations, as nothing else could have, of the goodness of our current system.

The modern history of formal human rights traces a complex enough path, from the Magna Carta to the American and French revolutions, and on to World War 2 and its aftermath. But there are plenty of ancient antecedents as well. It is fair to say that every culture, insofar as it differentiates itself from the state of nature, has ideas about personal rights and moral status that, while rarely giving equal status to all, accord some kind of status and thus right to each person, be she at the lowliest level of untouchability in traditional India.

The Greek and Roman worlds had highly developed philosophies of morals and ethics- which the early church held in substantial reverence, insofar as they could be reconciled with its own systems. Plutarch's ethics have been appreciated up to the present time, including his advocacy of humane treatment of slaves and animals, as have those of Plato and Aristotle, though none (other than the Stoics, in a spiritual sense) speak of universal egalitarianism. Several cultures of the ancient world had complex written forms of law, including Hammurabi's code (1750 BCE) and its descendents in Babylonia, and Rome, with its baroque constitution and primary division between plebians and aristocrats/senators dating to the 300's BCE. So while the Magna Carta is a touchstone of Anglophone jurisprudence and rights, it is far from the first word on the matter.

Slavery in the ancient world was a substantially different affair from what it was in the American South, with substantial mobility between the status of free, slave, recently liberated, and back to fully free. Large influxes of slaves arrived with military capture, and their fate was various- a practical death sentence when sent to the mines or sea galleys, less harsh in agricultural work, crafts, industry, or domestic service. Slaves were employed in all sorts of work, skilled and unskilled, with very few lines of work deemed exclusive either to slaves or to nonslaves. Slaves of the imperial household could become very high-ranking administrators throughout the empire. (The Bible's story of Joseph in Egypt makes the same point at an earlier time.)

The system in some ways resembled the early US colonial system of indenture as much as the more radical system of negro slavery. Slaves were often trained in advanced technical arts/crafts and treated as income-producting investments. Slaves could be and often were freed, and while they then still lacked some rights, their children became full Roman citizens, completing the cycle of mobility. Free persons could be sold into slavery for debt or children by their parents, but this became rarer with time as society became less comfortable with slavery, and by far the main source was conquest, so that when the Roman empire ceased to expand, the population of slaves gradually declined as well. Another general trend was the common subjection of all to the state, which became more onerous in taxation as time went on, to some extent levelling the status of free and slave, ultimately arriving at the common position of feudal tennancy for each.

The cultural trend was towards increased rights for slaves, and while slavery continued to be accepted throughout antiquity, by Christian and pagan alike, it is not hard to imagine that had other systems of thought and economics prevailed, especially if the ancient economy hadn't taken a nosedive, slavery might have been abolished long before it actually was in the West.

My primary source is a book by William Westerman (1955) "The slave systems of Greek and Roman antiquity", from which (by way of Google books) I offer a series of quotes below. Another source is Rodney Stark's "The rise of Christianity", where he estimates the overall numbers of Christians in the period (based on a 40% growth rate from an estimated 1000 adherents circa 30 CE), from which we can conclude that before about 300 CE, they would have had no general influence in society. By 200 CE, the population of Christians in the empire was by this estimate roughly as high as the number of Hindus, Buddhists, or Muslims in the US currently- visible in some settings, but more exotic than influential.
  • 50 0.0023%
  • 100 0.0126% (7,530 in the entire empire)
  • 150 0.07%
  • 200 0.36%
  • 250 1.9%
  • 300 10.5%
  • 350 57%

"It is generally conceded that the condition of the slaves of Italy and the public attitude toward them, as compared with that which had existed previously in Italy and Sicily, had undergone a marked change during the first two centuries of the Empire [roughly 30 BCE to 170 CE] in the direction of an increased humanity in respect to them. At this time the philosopher Apollonius of Tyana [3 BCE to 97 CE] states that everyone except barbarians accepts the fact that slavery is degrading, and that only barbarians will heedlessly sell their children into slavery. This indicates that the society of the time had reached the humanitarian realization that, in the institution of slavery, damage other than that of purely material kind was inflicted upon a human being by the simple fact of his enslavement. This movement may be connected with the growth of the prerogatives gained by the servi publici throughout Italy and in the Roman and Latin colonies of the West: it was probably abetted by the honorable position attained by the slaves and freedmen of the imperial household through their efficient services in the administration of the Empire."

"One may respect Seneca as an early and bold exponent of this general change in feeling regarding slavery which was so characteristic of the early Empire. But the sources our of which this transformation arose in the acceptance of slaves lay deeper than the teachings of the Roman Stoicism of Seneca. Chronological reasons regarding the spread of Christianity, and the acceptance of the institution of slavery by the new religion, make it apparent, also, that the new attitude did not spring from Christian doctrine. This does not mean, however, that Christian teaching did no contribute, within the limits of its own communities, to the feeling or equality between slave and free labor which appeared in the early Empire."

As late as 410, well after the triumph of Christianity in the Empire, slaves were still about:

"It is, nevertheless, not to be denied that a fairly large group of Gothic, German, and Hunnish were to be found in Italy who must be classified as legally enslaved persons, subject to transfer by sale and lacking recognized legal personality. This become clear from the terms dictated in A. D. 410 by Alaric, the Visigothic chieftain, to ensure his withdrawal from Rome. This lay in the demand that all the barbarians held as slaves in Rome must be turned over to him if he were to leave the city. This stipulation would have no meaning if these captives were men free to move and so to join the forces of Alaric."

Conversely, Constantine participated in the reduction of free labor to virtual slave status:

"The reduction of free agrarian workers to a state of actual bondage is officially recorded in a mandate of Constantine I issues A. D. 332. It provided that the coloni who might flee or might plan to flee from their overlords must be returned to them and be shackled in irons- 'so that they might fulfill, under the compulsion of a merited condemnation to servitude, the obligations which befitted them as free men.'"

.. "The bestowal upon the landowners, by the enactment of Constantine I in A. D. 332, of the right of punishing their coloni as they might punish their own slaves is clear."

.. " the coloni later come to be referred to as 'slaves of the land itself to which they were born.' This change in terminology expresses realistically the degree of the descent toward enslavement which the coloni had undergone."

"A distinct tendency to lessen the old Roman Republican harshness in the treatment of slaves had already become evidence in special enactments of the first two centuries of the Empire. Generally these took the form of legislation designated to better specific external conditions of enslavement practice which obviously needed to be changed. The continuation into the post-Diocletian period of legislation of this type may be regarded both as an indication and as a result of the drying up of the older sources of slave supply."

"So long as the Christian communities were unconcerned about the underlying justice and injustice of enslavement as a part of the labor system it was impossible for Christian doctrine to conceive the idea of its abandonment, much less formulate a plan to that end. A contradiction was thus established, which continued for many centuries, between Christian acceptance of slavery and its tenet of the equality of all in the sight of God. Anti-Christian writers had been conscious of that paradox between Christian ownership of slaves and their tenet of equality of all who accepted Jesus as the Anointed One."

"An unexpressed feeling of malaise about the institution of slavery was neither new to Christianity in antiquity nor peculiarly the result of its teachings. In the history of the system of slave labor, from the time of the earliest written records of man's experience with it, a certain discomfort about it can be detected in the applied or suggested restrictions which were imposed upon its operation."

"In the formulation of the Christian attitude toward slavery the discussion of it by the Apostle Paul was the determining factor. Fundamentally, Paul's view of the institution did not diverge widely from that of the early and middle Stoic teaching. For those converted to the belief in Christ, free or slave status was not a matter of consequence."

"To Saint Augustine, also, the explanation of the system of slavery in the world at large, presumably including enslavement of Christians to fellow Christians, lay in the fact that it existed by the decision of God as punishment for original sin. In God there is no injustice. Therefore the slave system is justified since God nows how to assign different punishments according to the deserts of the wicked."

"The canons of the Council of Elvira are now customarily dated to A. D. 306. At this meeting it was provided that freedmen whose patrons were of the laity should not be appointed to positions in the clergy. This is a retrogressive movement, presumably in protection of the property interests of slave-owners, whether they be Christians or non-Christians. The same type of decision, in this case respecting the admission of slaves into the monastic life, was taken by the council of Chalcedon held in 451. At that meeting it was provided that slaves should not be accepted by the monasteries except with the express consent of their owners. Anyone concerned in an evasion of this canon was threatened with excommunication."

"There is another facet of the problem which must also be evaluated. If Christian thought was, from its origin in the teaching of Jesus, invested with ideas so incompatible with slavery that it must in the end break the long hold upon human societies which the system had held, why was this inevitable consequence delayed for eighteen centuries after the brief mission of the Nazarene?"

On the slave trade ...

"The food supplied the slaves was probably neither good nor too abundant. We hear no such complaint about it in the ancient literature- which may not mean much. Despite the comparison, favorable as it may be to antiquity in this one respect, [the hardships of slave trafficking being worse in the modern age], one still misses in the Christian literature some note of protest against the trade in slaves or against those who participated in it. For in the pagan literature, both that in Greek and that in Latin, the slave trader stood in low esteem."

And Westermann concludes:

"The failure of Christianity over the succession of the centuries to bring the inner opposition of its ideal into an open conflict with the stark realism of slavery must be acknowledged and faced. It can only be explained in terms of time-conditioning and of difference of environment.
The lines on which he [Alfred North Whitehead] has sketched the moral bases of the antislavery feeling are, nevertheless, boldly and correctly drawn. He ascribes its beginnings to Plato's evaluation of the supreme importance of the human soul and carries it through the long period of the influence of Christian thought in developing it.
'In the Middle Ages institutional Christianity became an instrument of conservatism instead of an instrument of progress.' It was the convergence of the effects of different ideas- those of Christianity, the humanitarianism of the eighteenth century, and finally the idea of democracy- which eventually brought about the abolishing of human enslavement. It was the necessity of the development of these ideas, and the long wait for their convergence until the time arrived when the material conditions were favorable to it, which best explains the failure of the anti-slavery feeling for so many centuries to culminate in abolition."

As a side-light on our current upheaval, slavery could be seen as a primitive form of bankrupcy law, with insolvent debtors first, in historical sequence, becoming slaves, then feudal tenants, then imprisoned paupers, and finally now, liberated entrepreneurs, trailed only by the faintest whiff of their latest bankruptcy.

Anyhow, the conclusion I would draw from all this is that Christianity was by no means the essential ingredient in the rise of human rights, liberality, and egalitarianism in the West. What would have happened in its absence is unknown, but many threads of antiquity were already trending in the direction of amelioration and humane treatment, which are the typical precursors to abolition.

Saturday, May 9, 2009

The spiritual atheist

Does spirituality have anything to do with the supernatural?

Julian Baggini recently wrote that he overheard a traveller claiming "I don't believe in God, but I'm a spiritual person". I'd guess that this person was saying that she does not believe in supernatural entities (let alone in beseeching them for benefits), but nevertheless experiences spiritual emotions (which is to say, love) and believes in the human spirit- the mental and social existence by which we develop personal meaning and express love for the world we find ourselves in and the people who populate it.

The word spirit is widely used in secular ways- team spirit, human spirit, high spirits. This is a sign that the language already makes room for what we all sense- that what we see before us is the core meaning, and that the common assumption that this "spirit" has a supernatural component or origin is an added hypothesis, not the core meaning. If we, given the evidence of contemporary biology, neurobiology and psychology, conclude that there is no such thing as an afterlife, a Cartesian soul, angels, or holy ghosts, then animal and human spirits remain as a practical matter, even if supernatural spirits are a dead letter.

This accords with the various spiritual movements that have found a home here in California, from EST to the summer of love, to burning man, most of which have little to do with supernaturalism, or if they do, of a very tempered sort.

Jesus was right that man does not live by bread alone, but wrong in his physics- that an invisible being shrouded in inscrutible writings tells us how to live or needs our prayer, that Jesus was the son of god, that believers live everlastingly after death and nonbelievers are damned forever to hell, etc. These were all metaphorical issues at best, if not self-serving propaganda, and to take them literally was and remains an error. The ancient Egyptians located the soul and its capacity for communal responsibility and gratefulness to creation in the heart, carefully embalming hearts of the deceased for eternity while scooping out and discarding their brains. That scientific error had no effect, of course, on their capacity to exercise their spiritual emotions. As Barak Obama says, his mother was intensely spiritual, without believing in god, spirits, or anything of the sort.

Thus, whether believing in supernatural spirits or not, spirituality labels our capacity to express enjoyment in connecting with others, in experiencing love for our surroundings, and even in listening to new-age music and meditating. The deeper forms of this enjoyment tend to fall on the instinctive axes of purity and sacredness, which form our responses to dirt vs cleanliness, bodily functions vs abstraction, courseness vs nobility, mundane versus unusual events (rainbows, waterfalls, thunderstorms .. beauty of all kinds). In this way we keep our ideals in sight and subjectively transcend the mundane day-to-day of the human condition. Whether there is some other reality to escape to is a separate, scientific question whose answer appears strongly negative. At any rate, it is the inspiration of these feelings and this quest that is critical, with usually positive results.

Indeed spirituality could be described as a form of love, focused on entirely intangible objects in the case of religion, complete with attendant blindness, infatuation, and jealousy, such as we see expressed by the lovers of Allah in the Middle East. The terminology of religion is drenched with such romantic displacement, referencing the heavenly father, the love he has for us, the marriage of nuns with Jesus, his everlasting mercy, our desperation and desolation were he to desert us, hatred for those who fail to appreciate the same love we do, etc. and so on. However, infatuations with invisible beings are liable to misuse by those entrusted to interpret the desires of the love-object, as well as being over-amplified by particularly imaginative devotees. Thus keeping this kind of love directed to real objects, such as visible people and surroundings, is psychologically healthier than the alternative, forming a grounded spirituality rather than a religion whether dogmatic or mystical.

Another way to approach the cognitive origins of spirituality is through the work of psychologist Carl Jung. Jung's focus was on the unconscious, which runs our lives, is deeply mysterious, is (as far as we are concerned) omniscient and omnipotent, is the source of our energies, and generates fantasies and dreamscapes that recapitulate time and again the basic forces of human nature. The unconscious is central to understanding ourselves and our meaning in life, and is the subject of endless symbolic representations in religion and myth ... of the center, yin and yang, the inner core, the foundation stone, the cross, the mandala, etc.

Myths of the hero's quest usually symbolize this inner core of the self as an object of great power, often hidden in a cave, a body of water, or an underworld, such as the pearl of great price, the grail, the ring, or the magic sword, which when found may make the hero whole, healed, or help her save the world. It is really the image of god within, though its valence may occasionally be dark and demonic instead. It is what religions commonly term the soul, whose supposed supernatural properties symbolize the unfathomable ground of personal existence which, because it encompasses our existence, also generates the existence of the entire world on our behalf, in a manner of speaking.

It appears to be natural to flip what is internal, deep, and personal into the most cosmic conceivable entity ... the supernatural god that is everything, inheres in everything, knows everything. While polytheistic gods represent only parts of our psychological selves, whether anger, love, dedication, selfishness, creativity, etc., monotheism amplifies the entire subconscious foundation (the inner cosmos, one might say) into a correspondingly lofty and over-inflated projection. Thus it is that believers are so "deeply" attached to belief- not because it makes rational sense or models the external world, but because it represents the most important and personal element of existence, with which they are in continual communion, from which they receive counsel, and with which they seek a closer relationship.

How else to explain such things as the phantasmagoria of the book of Revelation? These are in no way visions of reality whether past or future, but expressions of extreme inner turmoil and pain- of the powerlessness and humiliation of an oppressed sect, salved by a fantasy of world domination by the righteous in a hopefully imminent future. Similar dynamics lie behind the hidden twelfth Imam of Shia Islam and other millennial and salvational ideas, clear up to Communism and its mythical classless, stateless society.

One instance of this tension between inner and outer (projected) depths has been the contest between Gnosticism and Christian Orthodoxy, where Gnosticism (subject of a future post) tends to be mystical, concerned with personal, even occult, spiritual experience and whole-ness, tied to a conception of the divine as lying within, rather than without. The early chuch patriarchs fought long and hard against such "heresies", despite their abundant concordance with much of Jesus's teachings. And they had to fight them over again in the modern age, as first the Protestants sought personal intermediation with Jesus and the Bible, and now post-Nietsche, when the whole idea of an exterior god appears increasingly ludicrous, and new age and psychotherapeutic movements find spiritual expression once again in a quest for, or study of, the internal cosmos.

Jung described these tensions 90 years ago:
The barrage of materialistic criticism that has been directed against the physical impossibility of dogma ever since the age of enlightenment is completely beside the point. Dogma must be a physical impossibility, for it has nothing whatever to say about the physical world but is a symbol of "transcendental" or unconscious processes which, so far as psychology can understand them at all, seem to be bound up with the unavoidable development of consciousness. Belief in dogma is an equally unavoidable stop-gap which must sooner of later be replaced by adequate understanding and knowledge if our civilization is to continue. (Symbols of Transformation, 1916)

Ritual practices of mental journey such as prayer, fasting and meditation accomplish the purification and separation from mundane life that help many people pay attention to deeper sensibilities which are the wellspring of spiritual feeling. The circumambulation of the Kaaba during the hajj is an example that symbolizes a return to the center- of the universe, of the religion, of the original tribal tradition, and of the soul/self. Specially noteworthy are the hallucinogenic drugs used to attain what participants routinely cite as highly meaningful spiritual states, such as ayahuasca, peyote, and perhaps marijuana. These clearly enhance spiritual sensibilities as they alter consciousness, providing an awareness that consciousness is a dynamic construction built on a highly mysterious, even foreign, unconscious and neurochemical foundation, as they also amplify feelings of connection with what is coming through the opened doors of perception.

But there is a fine line between recognizing, even participating in, the significance of spiritual practices and symbologies, and lending them personal belief. Each person appears to have individual thresholds of suggestibility and sensibility in this all-important field of personal meaning. But the dangers of "drinking the Koolaid" should not keep atheists from appreciating the psychological powers such belief systems, or from engaging with them as metaphorical vehicles for personal expression and communal understanding.

Cognitive science is just beginning to evaluate how the most basic decisions and concepts are made, and is relatively far from analyzing how the brain creates feelings like consciousness and spiritual emotion (what Freudians tend to call "infantile regression"). Depth psychology is currently neglected because it deals with complex psychological themes that have yet to be seen in an MRI, even as they inform every movie, cartoon, and novel. This resembles, ironically, the occultation of all mental contents during the scientific behaviorism heyday of the 1950's, when technical limitations created an analogous conceptual blindness. We know that the fount of meaning and motivation, not to mention religious theology, lies inside the brain. Can atheists be comfortable experiencing and expressing spiritual emotions, even as we simultaneously analyze their origin and their misappropriation into the rationalizations of religion?

Incidental links:
  • NYT columnist Charles Blow gets it.
  • It is rather ironic that the pope, of all people, would deprecate witchcraft in Africa, when Jesus himself cast out devils in Mark 1, and the Vatican still employs an exorcist and trains them. Is there is a bit of professional jealousy here?
  • Bart Ehrman's quest for truth and reason.
  • Why do we tell stories? Our brains are social modeling machines.
  • Theology, as presented on YouTube.
  • ... or as presented on the Philosophy bites podcast.
  • A very nice professor of religion discusses meaning.
  • Psychologists are studying goodness.
  • Somewhat lighthearted philosophical discussion of reason vs religion, aiming for reconciliation, but admitting that he can't get there.
  • Daniel Dennett gives an excellent talk about cognition and religion- far better than his book, actually.
  • The cartoonist gives me a hard time!
Beauty is truth, truth beauty,—that is all Ye know on earth, and all ye need to know. -Keats

Saturday, May 2, 2009

The ribosome as ancient relic

The ribosome is a fascinating and enormous vestige of the RNA world

One little problem of biology is its ultimate origin. Darwinian biology traces back to something called the "last common ancestor" (LCA for short)- a bacterium-like species from which all life appears to have diversified, containing DNA, proteins, and a membrane. But what came before the LCA? Much of the machinery of the LCA descended from a lengthy process of prior evolution, partly chemical in nature, which is to say that heritability of traits might have been due more to replication of the individual parts of the proto-cell (e.g., by natural expansion of its membrane with like-structured compounds), than by a segregated informational molecule that encoded everything else. For membranes, this is still the case. There is no gene that "encodes the membrane", though there are now plenty of genes that encode proteins that manage membranes and synthesize their components.

One way-station on the path to the LCA, prior to the appearance of DNA, appears to have been a period called the RNA world. RNA (ribonucleic acid) is not as chemically stable as DNA, and is also not as physically rigid as DNA. Being chemically stable is great for DNA (by virtue of a single oxygen subtraction from RNA, thus the "deoxy"), but having chemical reactivity and flexibility is an interesting property of RNA, making it capable of catalyzing reactions as well as carrying information. Thus was born the idea that RNA embodies in one molecule two of the key parts of the original aspects of life- metabolism and heritable information, though quite inefficiently for each.

Scientists now fall over each other to create clever catalytic schemes using RNA, which can cleave other molecules and ligate RNAs, depending on its sequence and shape. A nobel prize has been awarded in this field, and quite a bit of in-vitro evolution has been done to optimize what are called "ribozymes". A quasi- self-reproducing system has recently been devised whose input is short fragments of RNA, which get ligated together by their large products, leading to amplification of the catalytic RNAs, as well as selection and diversification.

But the main evidence for the RNA world comes not from the proof-of-principle experiments, but from the many vestiges that remain in modern cells, first and foremost of which is the translation system. Translation is the process of making proteins from the genetic code- currently DNA. DNA is copied into "messenger" RNA, the mRNA is spliced (by an RNA-based "spliceosome"), capped, and transported out of the nucleus, where it docks to ribosomes which synthesize the encoded protein by reading off three-nucleotide codons.

The ribosome is a huge scaffold (~3,000 kDaltons, or about 20 times the size of an average protein) composed of RNA and proteins that holds the participants and synthesizes the protein, but it does not actually do the codon reading- that part is done by yet another RNA species, the transfer RNAs, which are small L-shaped RNAs that expose an "anti-codon" at the top of the stem of the "L" which hybridize with and "read" codons on the mRNA, and which on their other end carry a single amino acid. Once the ribosome has the right tRNA docked to the mRNA codon, it then spends a little energy to add that tRNA's amino acid to the protein chain it is synthesizing.

Schematic of the translation cycle, with tRNAs pictured in blue,
mRNA in green, and the ribosome in gray.

The key observation, proven only in the last decade, is that the core catalytic activity of polymerizing proteins is in the RNA part of the ribosome, not the protein parts. Indeed, deduced structures of the ribosome show an RNA core decorated with numerous peripheral proteins, as one would imagine if the core were the ancient site of catalytic action, which was later enhanced with various proteins that help efficiency, stability, and regulation. And this RNA is also extremely ancient and well-conserved, recognizably similar in its sequence between all organisms, no matter how distant.

So to recount, translation of proteins involves RNA at every stage- the message/template, the critical bridging function (tRNA) between information code unit and amino acid unit, and lastly the catalytic activity to put them together. I have not even mentioned the RNA catalysis involved in splicing and processing the mRNA, and the RNA core (SRP) involved in docking ribosomes to membranes when making membrane proteins, nor the incredibly ornate pathways of RNA synthesis and modification involved in making ribosomes themselves.

Detailed structure of the inner face of half of a ribosome,
showing key portions of RNA (in red) that interact with the
complementary half. Proteins are in purple.

"There is now strong evidence indicating that an RNA World did indeed exist on the early earth. The smoking gun is seen in the structure of the contemporary ribosome (Ban et al. 2000; Whimberly et al. 2000; Yusupov et al. 2001). The active site for peptide bond formation lies deep within a central core of RNA, whereas proteins decorate the outside of this RNA core and insert narrow fingers into it. No amino acid side chain comes within 18 Å of the active site (Nissen et al. 2000)." - Joyce and Orgel, The RNA world, 2005

Taking the long view, the ribosome is absurdly large and inefficient. DNA and RNA polymerases typically clock in at ~500 kDa, or a fifth the size of ribosomes. The cell spends a huge part of its mass and effort on these little machines. The E. coli cell devotes between 15% to 45% of its dry mass to ribosomes. A rational designer would base the whole mechanism on proteins, which are much better catalysts, and make it far smaller, replacing tRNAs with much smaller protein-based bridging units as well. But no. This is a classic case of sunk costs, of path-dependent development, of sclerotic infrastucture. Cells can not just redesign their most critical function- their method of translation, so we appear to have a luxuriant and wasteful remnant of what we began with- a world where efficiency might not have been the top priority, given the difficulty of making anything work reliably.

So what came before this putative RNA world? Did RNA arise out of the chemistry of early earth spontaneously (highly unlikely), or did it have precursors in the form of crystalline minerals that aided stereo-specific polymerization other organic chemicals? There are plenty of theories, and growing knowledge of the environmental and chemical conditions, which seem to have been propitious, but evidence is extremely thin, if one wishes to stick to evidence.