Saturday, September 29, 2012

Ecological overshoot and extinction debt

We have wiped out plenty of other animals. Ourselves as well?

With all the discussion of the Federal debt, another far more momentous debt is being ignored- the debts we are building up in the biosphere. Two papers discuss aspects of these debts, one about how to account for extinctions that have not happened yet, but which we have baked into the cake, and the other a general perspective on how badly we are living beyond our means overall.

Extinctions are extremely saddening to a biologist. They mark a loss of riches, of wealth, which is very unlikely to be made up. We are in the middle of one of the most severe extinction episodes in the history of life, entirely brought about by us. It will take tens of millions of years after our passing for earth to re-cover itself with new versions of the ecological complexity that humans have so greedily and thoughtlessly eradicated. That is, if we ever manage to give the biosphere any breathing space at all.

How bad is it? The paper on extinction debts, which focuses on the Amazon, notes that 80% of extinctions due to historical (past) habitat loss have yet to occur. This is because extinction takes some time to play out. When we are down to the last whimpering dodo bird, or carrier pigeon, or woodpecker, or condor, we are at the end of long process of habitat destruction, eradication, and ecological simplification.

Even if we care, it takes heroic efforts to keep such species on life support- efforts which often fail because there just isn't enough habitat left anywhere, or a lack of other conditions. The condor of Calfornia remains in doubtful condition because of continual destruction by electric wires and lead ammunition, among other problems, meaning that its status is by no means assured. And with the extremely small population sizes possible after even this effort, the long-term genetic prospects of such species remain quite bleak. Other vultures are in even worse condition.

No, the way to save species is to actually save habitat, on large scales and protected conditions that preserve the compelete ecosystems on which those species depend. Here is their estimate of extinctions in the Amazon, under business as usual conditions, only among vertebrate species:

Turning to humans, how bad is it for us? Even if we deny any moral or aesthetic interest in the preservation of other species, we are a species too, and we have been generating a debt of our own, eating ourselves out of house and home. The other paper (from 2002) catalogs humanity's consumption of various biosphere services, and concludes that we are using more (1.2 fold more at the time) earths than we currently occupy, suggesting that in the business-as-usual future, we will not only see our growth slowed, but will see a sharp reduction in living standards and/or population levels, due to the ecological overshoot we are currently committing. As with extinction debts, the full cost of over-consumption can take time to show up, with a population crash the typical result.

Our living standards have already been going down for some time. My run-of-the-mill house is made of extremely dense timber that would be virtually unobtainable today. Typical construction timber is no longer old-growth, but plantation-grown pine and fir that resemble balsa wood more than oak. Fish are smaller and scarcer, with many stocks utterly fished out. Peak oil is here, and price pressures are starting, ever so slowly, to change US living habits.

The researchers looked at our gross areas of environmental impact- farming, livestock raising, timber cutting, fishing, land use for habitation and industry, and CO2 emission. We use 0.28 earths for farming, 0.15 earths for timber harvesting, and 0.61 earths for our unsustainable CO2 emission. We use 0.18 earths for the other categories, totalling to well over one earth overall- numbers that have surely grown as Asian economies have developed pell mell.

Now, this computation is a bit fanciful, mostly a way to talk about the unsustainability of our current practices. Economics would claim that we can smoothly substitute or innovate our way out of any critical shortages. But the end of a fish stock is really an end. Our living standard goes down with every loss of this kind, both in market/consumption terms, and also in aesthetic terms. It goes down as well in unexpected ways as ecosystems that serve us become simplified, for instance as the oceans turn into seas of jellies and garbage, rather than the fabulously rich seas our ancestors enjoyed. It was a garden of Eden, indeed!

It is hard to forecast the future. We know for sure that we are already beyond the sustainable capacity of the planet, and are going way beyond it in the business-as-usual scenario. The issues extend far beyond land use, atmospheric pollution and biosphere degradation to water use, the availability of obscure minerals like lithium and helium, radioactive and other forms of toxic waste, ocean acidification, an epidemic of exotic species invasions, ... the list of overuse is endless.

As animals, we are programmed to reproduce as much as possible. The typical limits to biological reproduction have been disease, competition, and starvation. Humanity has made wonderful strides in escaping each of these limits by technological and social progress. It has truly been an astonishing and world-shaking accomplishment. But if our consciousness and organizational solutions do not rise to the next level of engagement with our long-term sustainability constraints, we will not only be poorer in the future in countless small ways, but may face another dark age, as we play out a massive ecological boom and bust cycle.

  • Morsi tells us to correct the Palestinian situation, and he is right. (CSPAN)
  • Group is spelled g*o*d. Mormon groupishness, cont.
  • Muhammed = god as well. Islam seems essentially bi-deistic, as Christianity is tri-deistic or more.
  • China: model for union-busting Republicans.
  • Germany's export prowess rests mostly on underpaying its workers, and the surplus is wasted on loans to other countries.
  • Speaking of which, European internal trade imbalances continue apace. Nothing real is being done.

  • Economic production and class structure, in flux.
  • Crocker on past policy.. harsh on Bush, soft on Pakistan.
  • MMT godfather Godley described the current crisis in 1992: "If a country or region has no power to devalue, and if it is not the beneficiary of a system of fiscal equalisation, then there is nothing to stop it suffering a process of cumulative and terminal decline leading, in the end, to emigration as the only alternative to poverty or starvation."

Saturday, September 22, 2012

Switching channels: Attention in the brain!

Selective visual attention in the brain is connected through the pulvinar area in the thalamus.

For most of us, a primary experience of consciousness is vision, and more specifically selective control of our visual experience. Our eyes take in far more than we can "process" at any time, so it is essential to limit this stream, at the same time that it empowers our sense of sovereignty, even if our attention is pulled by external events and easily manipulated by conjurers, film directors, and advertisers.

Visual pathways, early stages. Signals coming from the retina are channeled through the LGN to the visual cortex at the back of the brain. They percolate up through the V1 to V8 areas and branch into upper (dorsal) and lower (ventral) streams to other areas of the brain.
Vision flows in complicated pathways in the brain, from the eyes though a central waystation (geniculate nuclei in the thalamus) to the visual cortex at the very back of the brain for processing into ever more abstract and meaningful representations, during or after which it forks into two streams. The upper (dorsal stream) coming into the parietal cortex forms most of our unconscious visual awareness of motion and location, directing motor control, while the lower (ventral stream) heads back to the thalamus and into the temporal cortex, and seems to provide identification (what) information, (interconnected with memory), and emotional salience information. It seems to be the more consciously available pathway.

Of course we want to focus on the most emotionally salient information. And we want to notice aspects of both streams at the same time, for unified perception. A recent paper describes pathbreaking techniques in identifying and recording key routes of the visual pathway in macaques, and finds that an area in the thalamus may serve as an orchestrator of visual attention.

What is attention? In neuroscience, it is increasingly recognized as synchronized neural firing among distributed brain regions, binding together various processed aspects of a particular scene. While consciousness per se remains unresolved, attention has been the focus of great, er, attention. Most perceptual pathways appear to have feedback pathways going back from higher abstract thinking levels into their primary processing systems which can either shut off or call forth activity that is synchronized with the calling regions. In the visual system, there is the added problem of synchronization between the two streams.

Location of the pulvinar relative to the rest of the visual pathways.  This image depicts some of the visual pathway, but not the key connections studied in this paper.

That is where the current work comes in. The pulvinar area of the thalamus is sort of a transgressive part of the brain, sending connections to many higher cortical levels rather than residing within linear tracts of visual or other forms of processing. Indeed, most of the cortex maps to various and overlapping regions of the small and central pulvinar nuclei. And lesions in the pulvinar cause attention deficits. A decade ago, the pulvinar nuclei of the thalamus were proposed to play a role in this synchronization and binding for visual attention specifically:
"The scheme requires that multiple groups of neurons, distributed within and across separate areas, be capable of attaining synchronous firing by means of re-entrant circuitry (Tononi et al. 1992). It is by facilitating this process that the pulvinar could play a coordinating role in cortico-cortical communication." 
"Ultimately, the synchronized neural assembly is proposed to mediate the perceptual binding of different object features (von der Malsburg & Schneider 1986; Tononi et al. 1992; Eckhorn 1994; Singer & Gray 1995). If the pulvinar is a key element of the assembly, damage to the pulvinar should have a noticeable effect on feature binding. There is already some preliminary evidence in favour of this prediction, documenting one patient’s report of illusory conjunctions of colour and letter form (i.e. ‘misbinding’) in the visual hemifield contralateral to a pulvinar lesion (Ward et al. 2002)." -From Shipp, 2003

So the current researchers carefully mapped the connections they were interested in, between the ventral stream of the visual pathway (occipital V4 to the temporal-occipital border area, called TEO) and the pulvinar area of the thalamus. Using amazing MRI/DTI imaging, they could do this individually for each monkey they experimented on, finding precisely where the nerve projections from the two cortical areas overlap in the pulvinar (a method called tractography). That is where they stuck their electrodes, taking electrophysiology to a new level of long-range circuit specificity. They had electrodes both in the overlap area in the pulvinar and in the originating locations in the V4 and TEO cortical  areas, tracking precisely connected signals over long distances in a living (more or less!) brain.
Mapped connections between relevant areas, in schematic terms. Red arrows are forward processing (feed forward, FF), going with the flow of visual information, while green arrows are feedback signals (FB). The numbers refer to the cortical layer being targeted, and the greek symbols refer to the frequency band of the nerve firing. TEO refers to the temporal/occipital boundary region which is part of late-stage visual processing. The experiments were oriented to detecting the alpha-band signals going from the pulvinar back into V4 and the TEO, and telling whether they have coordinating effects.

The point was then to test whether the pulvinar leads the synchronization of visual signals going between the cortical areas, as though it generates attention based either on rapid perceptions in lower areas of the visual pathway (say, suddenly seeing a snake/stick), or on signals from executive areas that exert voluntary attention control.

The task the macaques were set was to follow a spot on a video screen and rapidly report whether the subsequent shape at that spot was one of two possibilities, for a juice reward. In the experimental cases, the spot was engineered to happen in what the researchers knew was the receptive field (RF) for the neurons they had previously mapped and stuck with electrodes. So the question was whether the monkey's rapt attention (verified with infrared gaze tracking) raised the level of synchrony among the areas being recorded, and whether the pulvinar played a leading role in setting that synchrony.

The authors present data showing that these visually connected pulvinar neurons fire more when the monkey is paying attention to their receptive fields. They also find that the frequency of this firing is maximal in the alpha band around 10 Hz. Firing during attention was also closely correlated between the points they connected anatomically- the pulvinar and the V4 and temporal-occipital cortices. And finally, they use a relative timing method (Granger causality) to argue that, when the monkey was attending to the receptive field of the recorded neurons, and was in the attending period between presentation of the cue-spot and presentation of the puzzle shapes, neuron firing in the pulvinar significantly led the correlated firing in each cortical area it was tied to, not the reverse.

Inferred causality (i.e. prior in time and closely correlated in activity) of neural firing, between the tested areas of the visual system in macaque. Significant signals and causality in the alpha frequency band (10 Hz) are only seen going from the pulvinar (PUL) to the cortical visual processing areas V4 and TEO which are sequential in the usual sequence of visual feature processing. This supports the theory that the pulvinar drives attention-related synchronicity across the the visual processing system.

So one can ask where the regulatory decision of the pulvinar arises from. One hypothesis is that we have an immaterial soul that directs these things. Just kidding! As mentioned above, our attention may be involuntarily drawn by features of the scene (some visual pathways connect to the amygdala), or by a higher voluntary decision. In either case, the model would be that once a receptive field was decided on, the pulvinar helps pull the perceptual scene together by coordinating the firing of much or all of the visual pathway for that receptive field, and perhaps coordinating it as well with higher levels that receive that information.

Model (from Shipp, 2004) for attention in the visual system. The pulvinar (VP) receives signals and returns feedback from all areas of the linear/parallel visual feature processing pathway, governing which features or receptive fields are synchronized and thus attended to. The pulvinar receives input to drive its selection of what to attend to from both high level (prefrontal and parietal and frontal eye fields; PEF, FEF) and from low-level areas (the superior colliculus, SC and amygdala, not shown.

The alpha frequency band seems central to vision: "Evidence suggests that the rhythmic excitability of alpha oscillations gates visual events, with the phase of the alpha oscillations being critical for the transmission of visual information."

And, since consciousness seems more closely tied with the gamma band of higher frequency oscillations, the current authors add: "Because low-frequency oscillations modulate higher-frequency oscillations, we tested whether attention increased cross-frequency coupling between alpha and gamma oscillations within V4 and TEO. To measure cross-frequency coupling, we calculated the synchronization index between cortical alpha oscillations and the gamma power envelope. Across the population, there was a significantly greater synchronization index for V4 and TEO during the delay period, when attention was directed to the RF location rather than outside the RF (sign tests, P < 0.05; fig. S3, A and B), suggesting that alpha oscillations contributed to the attention effect on gamma frequencies."

So there you have it.. a few steps towards a physical theory to flesh out the "spotlight of attention" theory that has been an important subject of recent cognitive psychology and neurobiology, not to mention armchair philosophy.

  • Another review of this paper.
  • A living death at Guantanamo.
  • The Republican brand is not doing so well.
  • Corruption in Washington.. why do we even bother to pay attention? But Sarbanes is proposing a small donor voucher system.
  • Rick Perry: Satan is at fault.
  • Labor day- a day to honor the 1%.
  • Pakistan bans YouTube. Then declares national holiday of hate.
  • Afghanistan.. just like Vietnam, with an even more corrupt state.
  • A primer on money as debt.
  • MERS can't foreclose, because it doesn't hold real titles.
  • The US universal (rural) phone subsidy system is a corrupt, antique mess.
  • Economics quote of the week, by David Ricardo via Mark Thoma, to the effect that some kind of redistribution or remediation might be in order in a capitalist economy that destroys its demand for labor by way of efficiencies, machinery, and off-shoring:
"... the same cause which may increase the net revenue of the country, may at the same time render the population redundant, and deteriorate the condition of the labourer. "

Saturday, September 15, 2012

Please don't use the word "epigenetic"

A pet peeve, and a review of E. O. Wilson's "Social Conquest of Earth".

Of all current authors, I am probably most sympatico with E. O. Wilson, biologist and proselytist for the preservation of biological diversity. Wilson has many axes to grind, and sharpens several of them in his most recent book, on the social conquest of Earth. One is his atheism. As do many thinking people, he sees religion as a vestige- a culturally rich, but philosophically impoverished expression of our group nature in complex psychological projection. So it is slightly ironic that another of his targets is the pope of atheism, Richard Dawkins, foremost exponent of the "selfish gene" model that dismisses any possibility of group selection operating in evolution.

Rhetorically, it is no contest. Dawkins is the better writer. But substantively I go with Wilson, whose main point seems to be to gloat that he was right during his sociobiology crusade of the 70's to say that our social instincts are patterned by evolution- a point that is, frankly, old hat by now. Secondarily, he argues that, that human nature, the conflicted expression of those various instincts, is better explained by group selection than by kin selection. Indeed, towards the end of his life, fellow Harvard theorist Stephen J. Gould was reluctantly also groping in the direction of group selection, in even more inarticulate ways and despite his vitriolic personal battle against Wilson over sociobiology.

As Wilson makes clear, while the nucleotide may be the unit of inheritance, it is not the target of selection. Targets of selection are any unit of life that experiences failure or success in the grand race of life. If my heart fails, there may be any number of genes at fault, but my entire organism, with all my genes including the defective ones, go with it down the drain. Likewise, if the group I live in is cohesive enough to share ideas, learn new technologies, and exterminate other groups, then all our genes, including any and all that led to this success, also succeed. Indeed, groups can gain far more than the cost of cooperation, (i.e. it is not a zero sum game), regardless of who is related to whom within the group, suggesting that group selection can be quite strong.

In the long run, as recombination and sexual reassortment happen, the genes contributing most significantly to targeted traits are specifically affected in their frequency, which is also put down to natural selection, in reductionist shorthand. But it is always the phenotype that the the world sees and reacts to that is the direct target of natural selection, and this phenotype can be complex and expressed at the group level.

Specifically, Wilson dismisses the kin selection model that he had long followed, and that Dawkins popularized and sets so much store by. In brief, kin selection posits that our altruism, as generated by evolution, extends only so far as our genetic relationships, such that parents care for their children 50% as much as for themselves, and for their nephews only 25%, for their cousins 12.5%, and so forth. One can understand its seductiveness to those trying to find systematic formulas underlying the messy process of evolution.

One problem is that genetic relationship is actually far more difficult to measure than such a pat genealogical method would have it. We are 99% identical to chimpanzees, after all. So our true relatedness to other humans is really a graded and complex function, dependent on tribal history and much else. We seek marriage with tribe-external partners after all, which doesn't fit the kinship model at all.

For example, if one has ten children, one can hardly (rationally) run 50% chances of sacrificing one's life for each one. And indeed, if all were lost in some catastrophe, one might have the opportunity of having yet more children, so the theoretical math of kin-based sacrifice makes very little sense on its numerical face, even before one gets to the putative dedication of uncles, aunts, and more distant relations.

Unfortunately, Wilson can hardly tear himself away from his ants, termites, and other insects, in making these points, and somewhat weak comparisons to human societies. And this is a shame, because- as much as I also love them, and as much as they serve as a technical model for social evolution- in the large sweep of life on Earth, the social insects are not the revolutionary force Wilson makes them out to be, and focusing on them misses a much more important story. It is a problem Wilson shares with Ernst Mayr, another stable-mate at Harvard and fellow don of 20th century evolutionary theory- a resolute focus on macroscopic life.

To me, the prime transitions in the history of life are five: First, the origin of life itself, second, the origin of photosynthesis, third, the origin of the eukaryotic cell, which is the platform for all advanced life, fourth, the generation of multicellular organisms from eukaryotic cells, and fifth, the origin of humans, who have so dramatically surpassed all that went before and are terraforming the biosphere to god-knows what condition, before dreaming of doing the same to other ill-starred planets.

Now, the first two of these transitions were biochemical innovations. But the others were social in nature, which is why Wilson's book misses out so dramatically on a more interesting story when drawing comparisons to humanity. The eukaryotic cell is the fusion of at least two very different bacterial cell types into a shocking new entity. Whether voluntary or coerced, it was a matter of intense cooperation between what is now the mitochondrion that supplies oxidative energy, and what is now the nuclear genome and its complex organellar apparatus, which supplies the command and control, and which ballooned up to enormous proportions compared to any bacterial cell. Eukaryotic cells took the path of sloppy complexity rather than typical bacterial streamlining, and this made all the difference in the long run. Later, chloroplasts were added to the mix to come up with the plant cell, which has clothed the earth in green, and helped fill the atmosphere with oxygen.

The advent of multicellular organisms is even more clearly a case of social cooperation and group selection overcoming individualism to create a phenomenally powerful new kind of life. We are collections are cells that each have a full genome, yet think nothing of killing themselves for the good of the whole. Our cells are far more dedicated to the collective than the most robotic ant, and have formed structures that surpass any ant colony in complexity.. i.e. the brain, or come to think of it, an ant colony. [Late addition- Melvyn Bragg reviews the cell.]

Wilson's distaste for the molecular is also apparent in his breezy genetics, which brings me to the word "epigenetic".  This word has two different meanings, each of which are covered by other and better words. It is so extensively butchered in the lay press that I think the best we can do for it is to retire it completely.

The original meaning of epigenetic is any mechanism of generational inheritance that does not follow usual (Mendelian) mechanisms dependent on DNA sequence. A prime example is the little war that goes on in the embryo/fetus between the paternal and the maternal genomes. The DNA sequences of the genomes are not the problem. Rather, selected areas of DNA are marked in each gamete with additional chemical alterations that selectively cause some genes from the male genome to be expressed more or less, and vice versa in the female genome. The fight is for maternal resources, which the male genome wants to extract maximally (growing big fetuses) and the maternal genome wants to conserve for other children and the mother's health (smaller and less needy fetuses). Several genes that have roles in fetal and especially placental development are known to be competitively imprinted, with the allele from each parent either on or off in early development. This phenomenon is more precisely known as genomic imprinting.

The other meaning of epigenetic is cited by Wilson himself, in the midst of a truly atrocious piece of genetics: "If you are genetically prone to mesothelioma and you work in a building leaking asbestos dust, you are more likely that you co-workers to develop the disease. If you are genetically alcoholism-prone and socialize with heavy drinkers, you are more likely than your genetically less-prone friends to become addicted. The epigenetic rules of behavior that affect culture, and have arisen by natural selection, act the same way but have the opposite effect. They are the norm, and strong deviations from them are likely to be scrubbed out by either cultural evolution or genetic evolution, or both. Seen in this light, both genetic rules of gene-culture coevolution and disease susceptibility are consistent with the broad definition of 'epigentic' used by the U.S. National Institutes of Health as 'changes in the regulation of gene activity and expression that are not dependent on gene sequence', including both heritable changes in gene activity and expression (in the progeny of cells or individuals) and also stable, long-term alterations in the transcriptional potential of a cell taht are not necessarily heritable.'"

All I can gather is that Wilson simply means to say that the penetrance of various traits and disease susceptibilities is not 100%, due to our biological complexity. Again, Wilson is not molecularly inclined, which is unfortunate. But this second definition itself is a big mess. It is far more broad than the one given above, applying grossly to all biological development. Why do liver cells give rise to other liver cells? Epigenetics! Apparently all programs of cell differentiation that lock in a cell type and maintain that cell type in progeny cells is epigenetics. Or even changes in gene activity that are not heritable, but only "long term". No wonder people are confused. This should all simply be called biological development and differentiation.

Needless to say, the popular press doesn't know what to do with this term either. It is often presented as some fundamental challenge to Darwinian evolution, as though natural selection was now "facing a challenge" from "new findings" in epigenetics. As outlined for the first definition, genomic imprinting can indeed mess with Mendelian models of inheritance. But this is in no way a challenge to natural selection, and indeed remains completely dependent on gene sequences, just in a more indirect way than usual paradigm.

Suppose for instance, that a parent's or grandparent's experience of famine predisposes children to lower diabetes and cardiovascular disease risk. The mechanism behind this might be altered methylation of a few gametic genes, (conferred by an environmental effect on regulation of these methylase genes, combined with pre-existing target preferences among disease-affecting genes), which is carried through to one or two subsequent generations to alter gene expression and produce this phenotypic effect.

Such methylation patterns don't happen by magic, but by enzymes in turn regulated by other processes, such as an environmental effect of starvation. So the inheritance pattern might resemble the Lamarkian model in some superficial way, but ultimately, the source lies in the genes, their products, and their interaction with the environment. Whether the trait is in any way affected by natural selection over the long term, or is just a random effect in a complex system, there are genetics going on here, just not typical Mendelian genetics.

Anyhow, confusion is rampant, and partly due to the extraordinarily broad and ambiguous meanings of "epigenetic" as a word. So I would suggest that it not be used at all, and other more precise descriptions provided, without all the freight of novelty and mystery that "epigenetic" tends to bring in its wake. Incidentally, "emergence" has a similarly bad influence in the popular media, being little more than a signpost for "extremely complicated, so don't even ask".

Getting back to Wilson's book, the beginning and end seemed to me the strongest parts, where he speaks directly to his concerns and hopes for mankind. Religion falls clearly into the group selection theory, as one of our strongest psychological peculiarities and social glues. Just ask Mitt Romney and his fellow Mormons. Indeed, it has been doing a bit too good of a job, as you can see in the Middle East among many other places & times, rationalizing inhumanity in the name of the group.

When discussing religion with a believer, typically the last argument, after all the pseudo-science and reason have been left behind, is- how can you be moral without religion? This is a clear expression of the core religious value- of promoting the group values (what we commonly regard as "good" morals) over individual selfishness independence, disobedience, and skepticism. It is a serious social conundrum, but antiquated organized religions are hardly the best way to resolve it. With our increasingly planetary society and planetary problems, it is high time to tone down such groupishness and follow a different model, such as the secular Scandinavians do, to a more broadly responsible and conscious form of society.

  • Jesus carries an M16.
  • And you can call him up for whatever you might want. No, really.
  • Speaking of phone calls, why does the joint Chief genuflect to a nutbar?
  • Mitt's close relation to his group, and distant relation to his own brain: "In Salt Lake, they told me it was okay to take that [pro-choice] position in a liberal state." ... "With any bishop who excommunicates a woman, I will not question his reasoning. I will support the bishop."
  • Utter corruption in the business arbitration biz.
  • The beginnings of our current cycle of plutocratic capture of the political system, in the Nixon administration.
  • Yes, Obama is an introvert- and that is a good thing. Lincoln was too.
  • The chief rabbi, refracted though Peter Hearty, on how science is rubbish.
  • Financial right-wingery rampant in Europe too.
  • Money supply experts agree with MMT.
  • US economic growth will not get better.
  • Sister Rosetta Tharpe- smokin' blues guitarist and vocalist, 1960.

Saturday, September 8, 2012

Tribe and country: Mitt's frame for America

The one hive or the many in existential competition- how do we want to live?

I listened with fascination to several speeches of the Republican convention. It is remarkable, really, in this age of video, facebook, powerpoint, writing, printing, and many other so-called revolutions in communication that the speech remains the coin of our political realm, just as it was in ancient times and beyond (with apologies to the political attack ad, surely an up-and-coming form of political communication). Even when every single word out of a politician's mouth is a lie, speech at length remains the unparalleled window into the person, a connection desired by both the speaker and the listener.

In the lengthy runup to Mitt Romney's speech, an elderly couple from his congregation (stake) spoke about how kind and thoughtful Mitt was as their pastor when their eleven-year old son was hospitalized, and then died, of cancer. Among much else, they mentioned that their son wished to be buried in his Boy Scout uniform. This got me thinking about the role of groups in Mormon life, and in America.

Romney himself, while gauzy with platitudes, offered a program of reducing the federal government while somehow supporting small businesses, reducing the deficit, cutting lots of taxes, and creating twelve million jobs. For all the opportunism, flip-flopping, lying, and numbers that don't add up, I think he is honest about his views about the federal role. He was characteristically stingy with praise for the government he seeks to lead, mentioning Neil Armstrong, the Statue of Liberty, and the raid on Osama bin Laden. On the other hand, he and everyone else at the convention focused ceaselessly on small business, family and faith:
"The strength and power and goodness of America has always been based on the strength and power and goodness of our communities, our families, and our faiths."
Sure, it is the purest distillation of platitude, but there is something more- a vision of what groups count in America and how they should relate. On the one hand, there is Romney's experience in a minority faith and in a ruthlessly competitive business environment. And on the other, there is the technocratic approach of Federal and other levels of government to create public goods and restrict internal competition on a rational, conscious basis, partly out of moral fairness, partly to reduce violent and other unnecessary conflict, but also partly to increase the overall efficiency of our business and other communities.

As a missionary in France, he participated personally in the great Darwinian struggle that is religion in America- to show one's faith, serve one's faith, and grow one's faith, planting flags all over the world. His service to his bereaved parishioners was one of countless expressions of his dedication to his faith and to no other. The couple's son imbibed this love of the group like mother's milk; the Mormons use scouting assiduously to train their young in this regard.

Likewise, in business, Romney participated in brutal tribal struggles, first to manage and advise businesses for competitive growth, and later to identify targets for asset-stripping and debt loading. He has not shied from winning through hostile maneuvers, destroying companies, buying off managements against shareholder interests, convincing banks to give unsustainable loans, environmental pollution, and many other methods that in any larger perspective would be counted as "sins". But in the service of his group and himself, much leeway is allowed.

The picture one gets is of a man dedicated to group competition in the rawest way. I am not such a group-oriented person, so I find this all a bit hard to understand. But Romney's frame seems to be of a light federal government presiding over a ruthlessly competitive landscape, and may the cleverest and hardest businessman win, may the most hive-like religion win, and may the devil take the hindmost. If one does not have a functional group allegiance, his prescription would be to get one. In his experience, the Mormons have a full social service system, and would probably have their own sharia-like legal system, were that possible. He already pays taxes/tithes to his religion/hive, so one can understand why paying another set of taxes to provide frequently similiar social services to others outside his faith would stick in his craw.

He sees the sub-groups and tribes in America as the proper frame of competition and ultimate improvement. Out of the crucible of inter-group competition comes success, and the Republicans worship nothing like competitive success. The convention featured successful people, real or imagined, who harped again and again on the need to not punish success, and reveled in their financial and reproductive success. Their main slogan petulantly and ceaselessly repeated their conviction that they and they alone had built their own successes.. no help needed from no educational system, public services, legal apparatus, federales, or the like.

Indeed, the ticket's tax proposals clearly relieve the successful of yet more taxes, making the unsuccessful pay instead. This would truly be karmic justice- an Indian caste-style system of rewarding and entrenching what looks from the outside like privilege and guanxi rather than broader concepts of fairness, a national community, or even a smoothly functioning or broadly prosperous macro-economy.

Sure, Romney has some uses for the federal government, especially in the no-holds-barred inter-group competition that is international affairs. Looking outward, the military serves the interests of our national group, even while the tree-huggers and one-worlders seek rationality and unification on that level as well. No, America is exceptional, will brook no limits to our power, and will rule the world right up until China pries the last M16 from our cold, dead, hands. Competitive in/out group tribalism informs the Republican perspective at all scales.

What follows from all this is that any regulation or redistribution that is rationally conceived on the governmental level, especially the federal level, to redress wrongs, to equalize opportunities, or soften the blows of fate, are fundamentally anathema to the Darwinian war within America among its many competing sub-groups. However glaring the need or clear the benefits from a public good, or however arbitrary and clearly remediable the workings of fate, Republicans- and Romney foremost among them- are deeply uncomfortable with any impairment of their ability to win- by fair means, or more significantly, by foul. A true competitor seeks any and all advantages, and doesn't whine about rules, fairness, or morals.

His conduct of the campaign is emblematic, changing positions with gymnastic precision, and lying through his teeth. His attitude is.. of course I am lying.. I'm trying to win an election, right? We're all adults here, and you know as well as I that I am lying. Just so long as you don't tell anyone, because as you know, I am a highly successful and socially dominant person, so my lies are OK.

It is evident that Romeny sees nothing wrong with paying a mere 13% of his income in taxes, even though each year he makes far more than he will ever need. Indeed, he has gone to heroic lengths to cheat the government out of every possible cent. And in Ryan's budget proposals which Romney applauds, he will be paying less than 1% in taxes. It is evident that Romney sees nothing wrong with screwing workers out of their benefits and jobs, as long as his company/hive wins. He can build companies and add jobs if that is what it takes to win, but if not, then that is what his competitive position demands. Nothing personal, it's only business. It is evident that Romney sees nothing wrong with voucherizing medicare and medicaid, along with cutting what remains of the social safety net, (similarly, Republicans seek weakened civil rights protections, environmental protections, and campaign finance rules), so that the groups he is part of can have a freer hand in the grand competition of making it in America.

I get it, of course. I've read Hayek. Competition is an irreplaceable tool in micro-economics and most other pursuits. Competition is a large part of how humanity got to where it is today, and how we operate. I watched the Olympics. But competition is not the whole story, either operationally in how best to run an economy from the macro perspective, historically in explaining how humanity evolved, nor morally in deciding what kind of society we want to live in. Even in efficiency terms, excess competition can be intensely negative, as shown by global financial crisis, our handsome dividend from freeing the financial industry from oversight in favor the free-form screw-anyone-you-can competition of which Mitt Romney is such a champion.

Who does the truly great things in our nation? Who does the pure research, the interstate highway building, the space exploration, the education, the civil rights enforcement, and the park preservation? Towards the end of his speech, Romney cited Steve Jobs as an iconic business innovator. Jobs would turn in his grave, but more significantly, his success was rather different from Romney's example. He cared about the product and the customer's experience more than the money. He was an artist after a sort. A hippie at heart. His success was built on countless public investments and non-competitive facets of our society, all the way from the transistor (enabled by ATT's monopoly position and essentially academic research arm), to the internet and public education. And Apple barely survived the monopolistic jihad of Microsoft, which but for the government's antitrust intervention would have snuffed Apple out completely.

What is the balance we want? We can see the stark costs of all-out intergroup competition through history and all over the world. Especially in the Middle East, Afghanistan, and the Balkans. Societies that let inter-group competition get out of control tear themselves apart into smaller societies. Societies that let successful groups win to impose continuing inequalities and exempt themselves from common duties become feudal / caste-ridden. On the other hand, societies that suppress competition excessively, like the Soviets, tend to find it emerging on other planes, like the political. We surely need some, but we need it carefully channeled, regulated, and limited. Along these lines, the Olympics are a model of highly, even painstakingly, managed competition.

I come from a Star Trek mindset where ever-greater collections of societies (the Federation of Planets!) would gather together in peaceful and beneficial coexistence, facing existential (and dramatic) threats arriving only from outside. Here on Earth, we have serious planet-wide business to attend to, what with destroying the biosphere and all. The Republican program is understandable from a primitive psychological mindset, but would take us backward by a century, if not several.

  • A nation of "takers"?
  • Class war, ad infinitum ad obliviosum.
  • Willful screw-the-poor and everyone else policy, British edition.
  • Where is the war on poverty now?
  • Whatever happened to unions?
  • Oh, this is what happened to unions.. complete victory by money/business in politics, including total corruption of one party and partial corruption of the other.
  • Obamacare rocks.
  • Energy independence is a chimera... real security means using less oil.
  • Geology and religion.. how much does one "owe" the other?
  • Religion continues to yield dividends in terror.
  • The Taliban is still there, still losing the battles and winning the war. There continues to be a fatal political, legitimacy, and power vacuum at the center- in Kabul.
  • We really need fiscal policy.
  • Political image of the week, from the super pack.

Saturday, September 1, 2012

Thank god for rots!

Fungal brown and white rot species evolved in time to prevent terminal carbon burial.

Take your mind back- way back- to the carboniferous epoch. A luxurious 60 million years of high temperatures, high CO2, and high growth and burial of trees and other plant life to form the coal deposits for which it is named. Amphibians were the dominant animal, and trees the dominant plant life, having evolved bark and woody cores with the critical component lignin, a heavily crosslinked carbohydrate polymer that is incredibly tough. We certainly can't eat it, and nor can other animals.

Life was great for the trees. They had come up with a great solution to competing with their fellow plants for height and light. But it was a little too good. The carbon they sequestered into their dead hulks was impervious to decay, to the point that it was left to get buried with the ongoing geological processes, as coal. The carboniferous thus experienced a dramatic drop of atmospheric CO2, from the high levels inherited from the foregoing eras of lower plant productivity / higher recycling, never to be seen again, to some of the lowest on record towards its end, until the recent ice ages.

Geological time scale, with very rough graphs of inferred CO2 (purple) and temperature (blue). Note the dramatic drop of CO2 through the carboniferous, and its subsequent return to higher levels. Then eventually  its descends to very low levels through the recent ice ages, followed by the anthropogenic blip at the end.

Then came the rots- brown rots, which partially degrade lignin, and white rots, which chew it up completely. A recent paper describes how the earliest fossils of white rot are from ~260 million years ago, well after the close of the carboniferous (363 to 290 MYA). The researchers decided to sequence genes from a bunch of fungal rot species to determine from their molecular relationships when the true origin of this group took place. Their results indicate an origin of lignin-digesting enzymes in these fungi about 295 million years ago, consistent with a slowdown of carbon burial and the geologic resumption of net CO2 emission into the atmosphere.

How did they do that? Lignin is a heterogeneously crosslinked polymer of several short aromatic alcohols. This means that it is structurally very tough, and chemically a mess. There is no single point of attack by the usual clever catalytic enzymes that bacteria have been so successful in developing. Rather, a more blunderbuss approach is used, in the form of custom, secreted peroxidases, which harness the oxidizing power of H2O2 to blow away the lignin chemical bonds. The problem is that, if the fungus takes a too-aggressive approach to degrading the lignin, there may not be anything left to eat. Its food will have turned to ashes, (i.e. CO2), rather than a nicely slow-cooked meal of carbohydrates. Unfortunately, the details of how this is all managed are not yet known, though it is of some interest to the biofuels industry.

What is known now, through this paper, is when these key lignin peroxidases evolved, and how they diversified (to a maximum of 26 copies in one existing species of white rot. The rather complex  tree of descent is shown below, with a rough time scale at the bottom, and the key development and diversification of these lignin peroxidases (dark blue line shades). They point to node "A" as the common origin of all the current white and brown rot species, and show the copy numbers of the relevant enzymes in red throughout the tree.

Phylogenetic tree of many fungal species, focussing (top) on brown and white rot species that digest wood. 

Now, if only we could globally shut off these enzymes for a few hundred years to help us clean up the atmosphere!

  • Taibi on Mitt: pluto-hypocrite, financial mobster. Purveyor of a truly destructive form of debt. "But what most voters don't know is the way Mitt Romney actually made his fortune: by borrowing vast sums of money that other people were forced to pay back."
  • Republican unworthiness, continued. How would Romney like it if Obama started making magic underwear jokes?
  • Unworthiness, continued: A ticket of lies. I guess, if your plan is to reduce your own tax rate to 0.8%, you have to say something other than that.
  • Speaking of which, what the heck is up with Dinesh D’Souza?
  • Mitt's solution to a lack of jobs: "Or when you lost that job that paid $22.50 an hour, with benefits, you took two jobs at $9 an hour." This is a little hard to fathom, if a) Mitt was the one that screwed you out of that first job, and b) there are five applicants for every job opening.
  • Death of privacy, facebook-style.
  • Religion and spirituality keeps yielding dividends in violence.
  • Hell is not just other people, it is for other people.
  • Ideology and the creation of suffering.
  • 12-step cults.
  • Interesting proposal for stock market quantization.
  • Yes, the civil war was all about slavery.
  • Economics quote of the week, from Mark Thoma:
"When all of the misleading arguments are set aside, Romney’s economic proposal comes down to a simple tradeoff, less social insurance and other government programs for the working class, perhaps higher taxes as well, and more tax cuts for the wealthy. Perhaps that’s a tradeoff America wants to make, perhaps not – I suspect not."
  • Economics image of the week: Corporate profits (and income of the rich) are higher than ever. If they saw demand, they could invest plenty in growth & hiring. But they are saving instead.