Regulatory Dynamism in Evolution

While the proteins stay mostly the same, the management evolves much faster.

When looking at evolution in the genetic code, we tend to focus on the most conserved elements which can take us the farthest back in time. Essential proteins like metabolic enzymes that we recognizably share with bacteria, or the translational apparatus of ribosomal RNA and related proteins, shared in all life forms. But to look at more rapid and recent evolutionary processes, one has to look at other parts of the genome which churn a lot faster and can be, incidentally, far more difficult to discern.

General illustration of regulation of gene transcription; DNA is the black/green line, the yellow lozenges are histones, and protein regulator binding sites are red. Various regulators bind near and far upstream of the gene, (whose start site of transcription is shown by the arrow, bottom right), all conspiring to promote or retard formation, placement, and activation of the initiation complex of proteins (blue) that includes the RNA polymerase.

The DNA sites that direct transcription tend to be such fast-changing genetic elements. They are short, often redundant, degenerate (able to accommodate various errors) and modular, meaning that they can occur in various positions and orientations with respect to their target gene and still work. Their shortness means that they can be born by mutational accident, and also that they are hard to recognize by text-comparison methods.

Human-mouse comparison of three protein regulators, (GATA, MAX, cMyc), and a brief stretch of DNA they bind to (red and blue). The blue MAX site in the middle was born in the primate lineage, while the others are recognizably conserved. From the top, the general coordinates of the genomic region, over this gene, EPB41, which encodes a protein that provides special flexibility to erythrocyte blood cells. Then various annotated features (colored bars) looking for regulator binding sites, then graphs of the physical binding data for each regulator (colored graphs).

They are also enormously important for evolution and biology in general. There are many hundreds of gene regulating proteins encoded by the genome, each of which bind to some DNA site, typically 6 to 16 base pairs long. These protein+site complexes constitute the first line of gene regulation, and, though virtually every possible aspect of biology can be bent to regulatory uses, typically the most sensitive and influential mechanism of gene regulation.

"... there are an estimated ~1700–1900 TFs [transcription factors, or regulators] in the human genome."

A recent paper discussed a new-ish method to study the phylogeny of such sites. The first step is to use a modern technology to find such sites, physically purifying such individual regulatory proteins while they are still bound to DNA in a cell, and later sequencing the underlying DNA snippets. This allows, for a single regulatory protein, all its target sites in a genome to be mapped (at least the sites being used under the condition used to grow the cells for the experiment, in this case erythroblast cell lines). The researchers did this (or actually got data from others) for several different transcriptional regulators in human and mouse cells.

 Then they used sequence comparison methods to deduce the history of these sites in the lengthy time of divergence between the two lineages, over the sequenced genomes of baboon, chimpanzee, rat, squirrel, tarsier, and other species. They used not only sequence conservation of the sites, but larger-scale studies of how the genomes relate to each other, called synteny analysis. This depends on large regions of diverged genomes being, at least on a patchwork basis, descended from each other, even if some of the sequences they contain are not so recognizable. Over time, various accidents in recombination and replication cause genomes to slowly re-arrange relative to their ancestors.

Synteny comparisons of human and chimpanzee (top) and human and mouse (bottom). The colors from one genome's chromosomes are projected / sprinkled as they correspond to the other genome. The Y chromosome tends to have a lot of junk or unrecognizable sequence.

The finding of this paper that is of general interest is: "Notably, between ~58–79% of all human TFBSs [transcription factor binding sites] had inferred origins after the human-mouse split." This is far more rapid change than one would see in encoded proteins, of which about 80% are recognizably shared between mice and humans. It follows that the regulation system, which controls where, when, and how much genes are expressed, is far more variable through evolution, than are the products of those genes. This makes sense when we see the slight variations over human populations and among closely related species that tend to concern relative sizes of bodies and parts, slightly more or less some some feature, coloration, etc. It fits very well with the typically gradualist nature of evolution, operating on thousands of genes and hundreds of thousands, if not millions, of their regulatory sites all in parallel over populations and time.

"For all six factors analyzed, the majority of human TFBSs [transcription factor bound sites] bound in vivo were originally absent in human-mouse common ancestor, which is consistent with previous cross-species comparisons noting substantial divergence in ChIP-seq protein-binding events across the two species and similar comparisons presented here, and is also comparable to detailed analyses conducted in Drosophila using alternative approaches" 

"Genes located nearest to hominid-specific binding sites were more frequently enriched for neural and sensory-related functions, and were in many cases involved in neurological pathways (Table S2). CTCF, MYC, and SOX2 target gene sets were all enriched for GO categories involved in sensory perception, while GATA1, MYC, ETS1, and MAX were enriched for neural development and differentiation categories."

• Terrorists win ... in the US.
• And in Afghanistan.
• Annals of feudalism: the no-compete "agreement".
• A jobs shortage, not a skills shortage.
• The next financial crisis may come sooner than we think, at least to poor people.
• In praise of helicopter money.
• The shame of "rocket scientists" who work in finance / fraud.
• This week in WSJ: "... the Obama economy ..." The definition of chutzpa and hypocrisy is to cause an economic catastrophe, then do everything in one's ability to stifle effective action against it, then blame the other party for the result.

Thought Experiments in an Equal Pay World

Imagine ... what if everyone could get a job, and every job paid exactly the same? 

The labor market is highly problematic. It doesn't value people or work fairly, rewards destructive behavior (pollution, lawyering, lobbying, finance), and fails to reward socially constructive work (teaching, nursing, mothering, cleaning, farming). It tends to reinforce social hierarchies that have roots in patriarchy and class, perpetuating patterns that have questionable social value. Salary decisions are typically quite distant from business considerations, as CEOs have amply demonstrated, (both on their own behalf and over their minimum wage minions), depending more on the social and power relations of the parties involved.

There are also the persistent issues of gender and race inequality in hiring and pay- conditions that were supposed to have been solved by now, but which rear their heads again and again because of biases in the social system, if not in humanity itself. There is also the appallingly low pay provided by some of our biggest companies and industries (Walmart and farm labor come to mind) that rely on taxpayers to keep their shoddily paid employees fed, clothed, and housed. One way to solve all these problems would be to stipulate that all jobs pay the same wage. That average pay is currently about $44,322 per year, full time, in the US.

And if one is interested in addressing economic and social inequality in a comprehensive way, all the (progressive) solutions on the taxation side are trying to capture a horse after it has left the barn. The power that employers have now to pay rock-bottom wages to workers while paying themselves like kings means that they will likely have the means to make up for any tax increases. One solution is to insure that the labor market favors workers consistently, making jobs available to all, and using plenty of fiscal spending in times of slack private investment. But that simply works within the system, a system that is run, via our political and financial elites, by the incumbent powers of class and wealth, from which labor friendly policy is as likely to come as pennies from heaven.

Let's start with some easy issues first. How would currently high-paying professions be staffed if they were not paid differentially? Such work as financial engineering, dentistry, or medicine. Or CEO, lobbyist, sports star, political consultant, movie actor? The current system is, frankly, obscene in this regard. Would NBA teams not be able to field players if they did not paid them like kings? Probably, and one might get players who actually want to play, and they would be selected just as stringently, because the ancillary benefits of fame, status, and pleasure would remain, and the limited number of teams (and audiences) would remain likewise. More obscure fields like oil drilling, sales and marketing, dental hygienist, etc. might be more difficult to fill. But are they really paid that well? Typically not. It would probably just take some modest interest and training to attract people who otherwise might end up as farm workers or janitors, with less pleasant work conditions.

Similarly, the challenge and personal rewards of professions like medicine would remain and attract perhaps an even better class of trainees than they do now. Professions such as finance whose mind-numbing and pointless nature is now relieved only by their high pay might indeed contract, and frankly that would be a very good thing. So we would enter a world where students study what they are interested in, and enter professions that suit them, which select them on every basis of training and qualification as now, but without the lure of unusual monetary reward or penalty.

How about the low-wage work on which so much of the economy depends? Firstly, easily half of this work is completely useless. Unlivable wages allow many employers to hire far more people than needed, (fast food, retail; imagine being a walmart greeter), flood markets with low-margin franchises, and avoid efficiencies and mechanization. Labor shortages commonly spur efficiency gains. Secondly, a great deal of effort otherwise spent fighting against and dealing with unions might be saved by an equal pay regime. But in the end, paying people decently should come ahead of the consumer's ability to command the cheapest goods and services.

Entrepreneurialism is a somewhat more ticklish problem. How should we encourage business formation, innovation, family businesses, investment, and all the other energies of the free enterprise system if greed is no longer the central motivator? I think a general answer to that is to separate corporate and personal income on a stringent basis. If one wants to start a company that does great things, fine. One can grow it to globe-straddling size, but one can not pay oneself more than any other employee. That goes for bonuses, shares, etc.. all the remuneration that is now fair game would be strictly controlled, via the tax reporting system, and perhaps other enforcement, to one simple salary.

This relates to the problem of how investment would take place. Personal savings from such a system would probably be modest, and insufficient for the capital needs of the economy. People would generally be more dependent on (and willing to pay for) government programs to manage life-cycle savings, catastrophic contingencies, education, etc. I think one way to deal with the investment issue would be to allow special corporations (one might even call them "banks"!) and corporate entities like non-profits and educational institutions to have investment holding roles. Thus there would be a large ecosystem of investors and investments that do not significantly touch /affect personal income, but run large-scale investments in private enterprises due to the good judgement and personal values of the people involved. If the managers were unsuccessful, they might be demoted from their C-suites to street sweeping, but their personal income & sustenance would not be affected. One's social standing (and values) would be a much stronger aspect of motivation than greed, as would the personal satisfactions of the work one does. This would perhaps hearken back to the conditions in Antiquity, (occasionally, at least), when leading people and families competed to contribute to the state, not to leach from it, due to an intense sense of honor and reputation.

How about parenting? A fair system would pay for child care, whether done by parents or outside caregivers. So perhaps a parent could be paid through the first five years of a child's life if the parent decided to stay home, ideally at a full salary. This would make the decision to work or stay home shaped by personal preferences, such as career goals, rather than about finances. The same would go for care-giving to elderly parents and relatives, subject to some kind of certification that it is a full time occupation.

Perhaps the most difficult aspect of such a system is the impetus towards a black market, to under-the-table payments, gold-plated executive suites that pay in helicopter rides, escort services, etc. In our political system, with all the principles and deterrents against corruption, corruption remains rampant, indeed functionally legalized. Similar pressures would be inevitable in a tightly controlled equal pay system. Communist systems routinely elevated powerful people into great effective wealth, whatever their nominal salary. The best I could propose is again a strict separation between corporate and personal books, with transparency and strict regulation of what goes where. The current system of business tax deductibility, for example, requires extensive itemization and reporting, all to create an appalling drain on the public coffers, for the benefit of those need no such benefit. In the end, we organize society to limit some freedoms, (killing, fraud, theft), so that other and better freedoms may flourish. And perhaps the freedom to pauperize / feudalize your fellow citizens might not be as valuable as the freedom to have a decent and equitable life.

And how would this universal pay be set? It would be a broad economic policy exercise that fits closely with MMT (macro)economics. The tuning could be quite simple- if inflation threatened, pay would not be raised, while recession or deflation would be easily solved by raising the standard salary. Ultimately, its level and its value would be set by overall GDP and productivity, but the government, as the creator (and destroyer) of the currency, could easily make more or less of it and spend it in the form of salaries or other projects to fine-tune through any economic variation. Variations that, naturally, would be rare if not unheard of in this proposed society.

It is a thought experiment to imagine a system less besotted by greed, class, and injustice, more valuing of human e-qualities. One has to doubt its feasibility, but I believe it is a relevant ideal, or perhaps counter-ideal, for our time.

• Worship of money and those with it, cont.
• The middle class is kaput.. how did this happen in a democracy?
• Gates on Piketty. 
• "One side insists that the only important question is whether the truth-claims of religion are actually true; the other side says that question doesn’t even matter, and then wonders what “truth” is, anyway. It’s the overly literal-minded versus the hopelessly vague."
• More on austerity.
• Could we bring extinct animals back? But without habitat or stable climate, what would be the point?
• Reality, as usual, has a liberal bias.
• Meltdown in Iraq- the final chapter of Bushistic incompetence.
• Bolivia- a happy case study of good governance and fiscal policy ... and throwing out the IMF.
• On the impunity of finance.
• Annals of feudalism ... Conoco bullies its employees.
• The US deficit is low ... too low, as deflationary concerns drive the markets, and especially the specter of Europe melting down.
• Sleep is really, really good for your brain.
• Death might not quite as bad as imagined, either.
• Insanity and religion ... not always either / or.
• ISIS propaganda image of the week. Move along ... nothing Freudian here.

Organizer Without a Brain: the Centrosome

The microtubule organizing center of eukaryotic cells, which guides mitosis and nucleates cilia.

One of the more immediate wonders of biology is the division of cells and the organized march of chromsomes that accompanies it, girdled by a beautiful web of microtubules. These microtubules all emanate from something called the microtubule organizing center (MTOC), or centrosome, which is itself strictly duplicated during cell division. It all looks so alive. Yet the process is one of molecules each doing their little thing in blind fashion to make a greater and very dynamic whole.

In this image of a large eukaryotic cell, DNA is stained blue, microtubules are stained green, and the centrosome is stained red / orange. At some point during the mitotic process, the kinetochores (possibly the pink/lavender spots) would line up strictly along the midline between the two centrosomes.

Centrosomes are special to eukaryotes- there is no trace of them in bacteria. They also have no DNA or other sign of being descended from some symbiotic or other bacterial forebear, unlike the mitochondrion or chloroplast, perhaps even the peroxisome. (Though some researchers find they contain a few special RNAs and argue for an endosymbiotic origin on that basis.) Yet they are quite complex organelles, based on the same tubulin that composes the microtubules of the cell generally, but with hundreds of other proteins added in. They organize not only the microtubule asters that drive mitosis, but also form the basal bodies of cilia- the flaggella of eukaryotic cells, again composed of microtubules. These cilia in turn have important, though only recently-discovered roles in mechanisensory and chemical signaling.

The centrosome and its component centrioles. The micrograph cross section shows parts of each centriole from one centrosome.

The centrosome is composed of two centrioles, one of which is the mother, and the other the daugher. At each cell cycle, they split apart and each grows another daughter centriole to reconstitute a full centrosome. Each centriole resembles a microtubule, which is a tube of nine paired tubulin tubules, but has an extra set of tubules, so nine triple tubules of tubulin. At the base of each centriole is something called a "cartwheel", which is made up mostly of a non-tubulin protein (Sas6) that forms a nine-fold symmetric ring that nucleates growth of the centriole, which in turn nucleates growth of the microtubule.

Detailed structure of microtubules (top) and the centriole (bottom). Note the two pairs of tubules in the microtubule, but triplets in the centriole, or basal body. The third tubule appears to template or make space for the dynein arms, which are the motors that allow cilia, for instance, to wave and move.

Models of the molecular structure of the "Cartwheel" protein complex, which  (d) templates and nucleates the centriole structure. Microtubules (purple) fit to the outside spokes of the cartwheel (blue). In the electron micrograph (e), three cartwheel stacks can be seen at the bottom, at the base of the centriole, and higher up, with lower electron density, the microtubule.

"Studies using human cells have revealed a mechanism that regulates cartwheel assembly through controlling the amount of SAS-6 in the cell. SAS-6 starts to accumulate at the end of the G1 phase and decreases in anaphase through proteasomal degradation mediated by APC/CCdh1 [19]. When the SAS-6 level is artificially increased by overexpression of non-degradable SAS-6, excess procentrioles are formed on the mother centriole."

Another electron micrograph of the centrosomes and their microtubule junctions.

The main component of all these structures is tubulin, the building block of all microtubules, which, along with actin, make up the cellular cytoskeleton of eukaryotes. Actin is smaller and free to form more flexible structures, (as well as being used to form the structural scaffold of muscle action), while microtubules make bigger structures (in cellular terms) like that which spans the whole cell for division, making cilia / flagella, and conducting cargoes along the enormous distances of nerve cell axons. Not all eukaryotes have centrosomes, (notably plants and yeast don't), but all have some form of microtubule nucleating center, (MTOC), of sometimes more modest construction. While microtubules are made of alpha and beta tubulin, the centrioles have a third form, gamma tubulin, which only exists at the nucleating base, not in the bulk structure.

Diagram of nucleation from a cartwheel (red) to a centriole (blue).

Unfortunately, less is known about how all this works dynamically than about its structural components. A recent paper covered two key proteins (Cnn and DSpd-2, in fruit flies) that seem to be all that are required to turn a bare centriole into a busy MTOC with hundreds of other proteins in a nimbus around it (the pericentriolar material). These key proteins are controlled by phosphorylation which is a common element of the cell cycle, and when turned on, come into the most interior precincts of the centrosome/centriole, and then migrate slowly outwards, with new molecules arriving at the center as long as the cell is in the requisite state.

"Mimicking phosphorylation allows the PReM domain [part of Cnn] to multimerize in vitro and Cnn to spontaneously assemble into cytosolic scaffolds in vivo that can organize MTs. Conversely, ablating phosphorylation does not interfere with Cnn recruitment to centrioles, but inhibits Cnn scaffold assembly. We speculate that, like Cnn, DSpd-2 can assemble into a scaffold and that this assembly is regulated in vivo so that it only occurs around mother centrioles."

At the other end, a good deal more is known about how microtubules attach to the kinetochores (structures at the center of chromosomes -at DNA centromeres- that anchor them to the mitotic spindle). This is not really in the scope of the post, but again, phosphorylation of key proteins is the theme, as is regulated assembly and disassembly of the microtubule itself. Disassembly right where it abuts the kinetochore causes shortening, thus tightening of the whole spindle, as long as the kinetochore has properly captured microtubules on/from both sides, i.e. both centrosomes, which is another complicated and phosphorylation-regulated process.

Example of a model for microtubule dynamics during one part of mitosis, with microtubules in purple,  (and unconnected microtubules in yellow, cell edge in gray), the centrosome in pink dots, and relevant motor proteins in green and salmon. The point is that, if relevant motors and attachment functions are regulated and happen at the right times, the system can accomplish complex tasks.

It is worthwhile to note that while the replication of the centrosome and its component centrioles is strictly regulated with the cell cycle, the same core system is used to create the basal bodies of cilia, and can create organizing centers from scratch. It does not require a pre-existing centrosome (unlike mitochondria, chloroplasts, and cells, which always come from pre-existing respective cells or cell-ish organelles). Sometimes, the basal body is the same as the centrosome; when cell division is done it migrates to the membrane. But many cells have multiple cilia, and each one has a newly created basal body at its base, whipped up without the complicated replication process. So it appears that replication is more a regulated restriction of MTOC creation than it is a necessary precondition of MTOC birth.

The science of the microtubule nucleation systems is still underway, but the direction is clear, as in any other area of molecular biology that has been laid bare to date. Molecules of some complexity, equipped with various means of regulation, such as regulated transcription and synthesis, outright destruction, interaction with various partners, or covalent modification like phosphorylation, neddylation, methylation, palmitoylation, GPI-anchoring, etc., can find their places and times of action in chemically explicable ways within a cell that is a vast, if microscopic, machine.

• A relevant review of centrosomes, and a second, and a third.
• Motors on the microtubules.
• Freedom & security flows from law, not from the barrel of a gun.
• But paranoia is patriotism and apple pie.
• Economics can say a few things about recent events.
• To save Lehman or not?
• Poor, poor, AIG.
• Quackonomic vocabulary.
• Inequality and the freezing of upward mobility, in Venice.
• Government by the corrupt, for the corrupt.
• Startups not all they are cracked up to be.
• The European economy is disastrous across the board.
• Krugman on the crisis.
• Requiem for the incandescent light bulb, though for its corrupt business practices, who knows?

Environmentalism is anti-American

Book Review of the biography of Rachel Carson, "On a farther shore".

Are we part of nature, or above it? Did god give it to us for our domination, or did we wriggle from its bosom to the condition of (bare) consciousness and power that threatens to undo the patient work of millions of years of evolution? Thousands of years ago, we had already killed off all our immediate ancestors in the hominid line and countless other species of megafauna. Now we have taken over most of the arable land of earth, comandeered much of the fresh water, polluted the rest of it, as well as the oceans, killed off many more species, doubled the concentration of CO2 in the atmosphere and the fixed nitrogen in the biosphere, and are facing ocean acidification and dramatic climate heating as an irreversible future fate.

But two generations ago humanity (and that would be the US) created the most immediately alarming and noxious dangers of all- nuclear weapons with their attendent radioactivity, and a fusilade of biocides and other poisons emerging from the postwar chemical industry- pesticides, herbicides, plastics, drugs, "food" additives, cleaners, etc. After a cavalier start to the era, when Las Vegas visitors turned out with their sunglasses to watch nuclear tests, the far-reaching dangers came increasingly to public consciousness, resulting in the above-ground nuclear test ban treaty of 1963, and the establishment of the EPA in 1970 and banning of DDT in 1972.

The reduction of nuclear radiation has been enormously successful, with negligible impact from current uses. The Chernobyl and Fukushima nuclear disasters have been the sole, and very large, blots on a very good record of radiation control (negligible amounts were released in the Three Mile Island disaster). Whether we want to use more nuclear power or not for the sake of climate change is a reasonable question.

Our record on control of biocides and other environmentally harmful chemicals, on the other hand, is far less impressive. Their use is less individually dramatic than that of nuclear technology, but their scale is mind-boggling. Every home and garden center hosts a biocide department that reeks to high heaven. DDT may have been banned, but an endless supply of other biocides have been concocted that are applied over the best land to kill all insects on it. The holocaust is ongoing.

"In 2006 and 2007, the world used approximately 5.2 billion pounds of pesticides"

Rachel Carson played a large role in our budding environmental awareness, both in her early work in books like "The Sea Around Us" that celebrated the beauty and interest of the natural environment, and in her last prophetic work on the dangers of the new pesticides, "Silent Spring". This biography is a worthy testament to her drive and talent which formed out of very unlikely materials (being a self-made professional woman in the 1950's) an earth-shaking message.

Indeed she could even be regarded as a significant religious leader, inspiring love for the world, and issuing prophetic warnings about its mistreatment at the hands of humanity, due in part to a lack of spiritual awareness, or misdirection. Humans have an innate religious sensibility about nature, and all the old religions treat it with reverence. The Celts had their sacred groves, worship of trees, and custom of bringing holly and mistletoe to their dwellings at the winter solstice. Unfortunately, the monotheisms, with their worship of a blown-up self-image, put nature into the shade as something to be dominated, something lost anyhow (Eden), even dirty and unclean. The unholy mix with post-war technologies allowed the dream to become a reality ... to "purify" the world of insects, vermin, disease, and all kinds of uncleanliness.

Obviously there is a great deal of good in cleanliness. But we learn that even our own health benefits from some amount of infection and dirt, lest our immune system idly turn its attention on our own tissues by mistake. Which is not to mention the wider ecological benefits of moderation and species diversity, and particularly in less wanton destruction of insects and other unheralded organisms that may not be the "stars" of our nature shows.

While we have banned the most noxious chemicals, (thalidomide, DDT, aldrin, lead arsinate, etc.), our systems and policies are simply not up to the task of protecting ourselves or the environment in a more comprehensive way. They are not precautionary, but rather wait for some dramatic harm to come to light before starting studies and investigations that take forever. The neonicotinoid insecticides are still being applied by the ton, despite their clear harm to bees (not to mention to all other insects).

Why? Principally, it is the agricultural and chemical interests, and their conservative allies, that fight chemical control policies every step of the way. There was once a time, when the EPA was founded, when conservatives were true to their name and cared about conservation, not only of their power, but of the environment as well. Those times are long gone, as the interests of the 1% diverge increasingly from those of the rest of society, indeed of humanity in general. Their loud patriotism tells us that government is bad, taxes always too high, scientists are all lying, and corporations always tell the truth. The worship of self has turned from a projected image of god to the even worse god of Mammon.

"It had only taken a few short centuries to move from a time when we gazed out at the ocean and wondered what was over the horizon. Now, she said, "our whole earth has become only another shore from which we look out across the dark ocean of space, uncertain what we shall find when we sail out among the stars." Based on the experience of her own generation- which had brought the world to such a dangerous crossroads- Carson said it was now time for the inheritors of earth and it many difficulties to finally prove human mastery not of nature, but of itself. "Your generation," she said, "must come to terms with the environment."

• Wildlife is in dramatic decline.
• Bees are in especially dramatic decline ... collapse.
• Fly less to fight climate change.
• On the psychology of evil, corruption, ideology, contradiction, hypocrisy, and other forms of humanity.
• In the new economy, nice guys finish last.
• Cute kids ... these days.
• The recent US military campaign has little immediate effect. ISIS keeps gaining ground, and "One estimate puts the number of overall desertions for the Iraqi Army at over 90,000."
• How and why the Fed shores up the global dollar system.
• But banks run the Fed, so of course ... the Fed serves Goldman.
• Goldman, Lehman, Enron.
• AIG as a money-laundering bailout. "Alternatively, maybe Mr. Geithner simply felt that Goldman and the like had a more legitimate claim to billions of dollars in funds than the taxpayers who were footing the bill."
• Bonanza gets one in against the bankers (Episode 284, The Trackers)
• Pray our way, or the highway.
• To screw workers, employers talk out of both sides of their mouths.
• This week in the WSJ, annals of irony: "But does anybody in the government feel it is necessary to be truthful about anything anymore?"   
• Economic graph of the week.. just how dramatically our economy has changed over the last 60 years. We've already had a class war, and we lost.

Prosecutors Gone Wild

Truth is the first casualty of bureaucracy. Review of "Licensed to Lie".

Sidney Powell is a defense lawyer and erstwhile prosecutor who got tangled up in defending one of the Enron cases, launching an unwelcome odyssey into prosecutorial malfeasance. Her book is an excoriation of the prosecutors, Justice department, courts, and justice system as a whole as it took shape under the Bush Administration and continues under Obama. She summarizes everything in a final chapter that helpfully names names in bold type.

The case was the "Barge" trial, which accused a set of Merrill Lynch functionaries of colluding with Andrew Fastow to conduct a sham transaction whereby Enron "sold" a set of electric generating plants (on barges in Nigeria) to Merrill Lynch so that Enron could book a sale, while actually guaranteeing that Enron would buy the Barges back in a matter of months. The point was to help Enron temporarily cook its books and goose income. In the whole spectrum of Eron cases, and certainly in terms of harms alleged, this one was quite minor.

The defense disputed the entire case, and maintained that the transactions were actual sales, and that no one in Merrill Lynch did anything wrong. Powell's particular client, whom she picked up at the appellate level, was James Brown. His testomony was consistent on this and related points, both in grand jury testimony and at trial ... that his understanding was that the transaction was legal, if inadvisable.

Unfortunately, the defense was not allowed to use all of Brown's testimony, or much testimony from elsewhere, because the prosecution played keep-away with the evidence in the case, intimidated relevant witnesses, and pursuaded the court to adopt bizarre legal theories, jury selection processes, and jury instructions. Prosecutions generally have a duty to give the defense any exculpatory or even relevant information, called the "Brady" materials. Since the government typically runs the investigation, the prosecution is the party with all the evidence. Defendants do not have the resources or the powers to do as much investigating. This natural assymetry is supposedly resolved by the "Brady" rule. But of course, prosecutions are sorely tempted, and have every motivation, to hide such material if they find it inconvenient to their case. As they would.

It is a fundamental issue of whether the legal system exists to find truth, or whether it exists to win prosecutions. In the Enron cases, the government was under extreme political pressure to win, and to put some scapegoats in jail. The public, and especially the public in Houston where all the trials were held, was in no mood to split legal hairs about procedure. They wanted blood. Powell's tale is remarkably engaging, even gripping, for a narrative about US appellate processes that in this case dragged on for almost a decade. Her client served one year in jail, railroaded in by prosecutorial shennanigans that are, frankly, breathtaking.

First, the legal theory of the prosecution was, in part, that Brown and colleagues, by supposedly arranging a sham transaction, had deprived Enron shareholders of "honest services". This was a novel, even non-sensical, doctrine, and was reversed on appeal. Secondly, the prosecution alleged that, by its theory of the case, Brown had lied to the investigators and juries, thus perjuring himself. Thirdly, they alleged that all the evidence attesting to the legal nature of the transacation was ass-covering, belied by separate verbal promises they alleged had been made by Fastow and others to Merrill.

The problem with all this was that their own evidence pointed in the opposite direction. Fastow's own interviews mentioned explicitly that he had offered only a best-efforts promise to re-market the barges to other companies (which was indeed done and did occur, and was legal). But those interviews were suppressed by the prosecution, which relied on non-direct evidence from secondary players whom it pressured to testify according to their theory by threats of indictment. Fastow had already agreed to turn state's evidence in return for a reduced sentence (10 years, reduced eventually to six years, which was shockingly minimal in light of his masterminding the entire Enron debacle. He also probably retains some of his ill-gotten gains.)

Indeed, eventually Powell and colleages obtained detailed transcripts and notes from the Brown prosecution where the prosecution (or prior investigators) had highlighted in yellow the precise exculpatory testimony that would have easily acquited Mr. Brown and belied the entire theory of the prosecution. It was thus made quite plain that the prosecution had committed (and continued to cover up) gross misuse of their powers, which had the effect of destroying several innocent people's careers. Even after this information came to light, the judge in the original case continued to unwaveringly support the prosecution, blatantly ignoring defense arguments of gross malpractice, and despite having been overturned on several crucial issues on appeal.

This would have remained a typical defense attorney cry into the void except that another case came along during the same period featuring several of the same higher level officials in the Department of Justice- the case of Senator Ted Stevens. Similar tactics were used to develop a false theory of the case, hide exculpatory testimony, and railroad his jury to conviction (I hasten to add that I have no political sympathy with Stevens or indeed author Powell, who seems a red-as-they-come Texas Republican).

The (appellate) judge in that case did what the Brown judge did not do, which was, (in addition to reversing the case), to blow the whistle on the prosecution and call for a special prosecutor to investigate the Department of Justice's prosecution. The resulting report laid bare blatant abuse of the Brady rule and other forms of malfeasance- the same pattern that Powell was experiencing in her case. Unfortunately, this report neither took the highest levels of the Justice Department into its scope, nor had an discernable effect on any Department employee. Except for one: Nicholas Marsh, a low-level prosecutor on the Stevens case committed suicide as the investigation was underway. All the others either landed in cushy private firm jobs, or were promoted to higher levels in the government. One became a White House Counsel to Obama.

There are good political reasons to incentivize certain prosecutions. The late financial meltdown was clearly undermotivated in the prosecution department- no one went to jail for clearly illegal as well as phenomenally damaging acts and practices. Whole industries riven with illegal practices have been held harmless for their actions. There may also be a lack of legal tools to perform such prosecution and render justice. For instance, none of the fines that the Department of Justice has extracted from the various banks (investigations and findings that have remained secret, thus useless in the cause of justice) came from individuals. They come from the future earnings and innocent shareholders, not from the managers who actually performed the illegal actions and destroyed their companies and / or the economy at large, and who even in all likelihood remain in their jobs. Perhaps the legal structure to hold the responsible officers to account, not to mention claw back their ill gotten gains, does not exist (yet, though the Sarbanes-Oxley laws were supposed to have resolved some of that, yet were not deployed for the financial crisis non-prosecutions)

Whatever the case, the answer is not to run an illegal prosecution against minor actors who committed no crime, in a kangaroo court. Our country is better than that. What is equally disturbing is that this continued from one administration to the next, clearly signalling a fundamental lack of accountability in the department's bureaucracy and an unwillingness by the new administration to put its mandate into action. In so many instances, the Obama administration has kept the actors, and practices, of the old intact, prosecuting whistleblowers rather than listening to them, deporting and mistreating immigrants in droves, and keeping the military-industrial-espionage complex humming. The change has been much less than promised.

Powell's money quote: "Blind judges do not render blind justice."

• A Holder retrospective.
• Hope in Afghanistan, or endless dysfunction? "A thousand beggars can live under one quilt, but two kings cannot share a kingdom."
• Not just military-industrial, but now military-industrial-espionage complex.
• Rent extraction by finance. Is what they do useful? Or is it sheer embezzlement?
• The government is losing all the revenue that goes instead into tax avoidance.
• Pat Robertson: our genocide better than your genocide.
• Right wing Christians ... reality is not a strong suit.
• Climate, schmimate- science will deal with it, right?
• Guns 'n apple pie- and don't let Gabby Giffords tell you different.
• Yes, you are dying ... and truth is the answer.
• Germany vs the Euro, cont.
• That magical number two.
• Pension funds got suckered into the hedge fund scam. And who pays? Not the retirees.
• Yes, the inflation fight is not really about inflation.
• Reality is outstripping perceptions of the new feudalism.
• One more reason the 70's were a dreadful decade- it was when economics went awry.
• The psychology of free will.
• Again, just what is an economy good for?
• "As Krugman goes on to note, the nation’s 400 richest households, who paid more than 50 percent of their income in taxes at midcentury, now fork over less than one-fifth of their income."

What is the Opposite of PTSD?

On the Arthurian and Homeric battle hymns.

I have been reading Mallory's tales of King Arthur, and wondering at the lovingly described jousting, ado-ing, dueling, damsel-saving, and battling. Why so much space devoted to minute variations of the most tedious material? Why is Sir Launcelot the main character of the romance, not King Arthur? Why such a flood of testosterone?

We have heard a great deal about PTSD, where ex-soldiers can't get scenes of trauma out of their heads. We also have just been through the anniversary of World War 1, with ongoing head-scratching about why the cosmopolitan and civilized countries of Europe let themselves descend into the depths of hell. A generation with PTSD resulted, especially in France, which supinely rolled over in the next war, unwilling to face up to the developing reality.

Mallory reminds us (as Homer did long before) that war is joyous. Men live most vividly in war, and always have. They (I am generalizing wildly on a postulated average) have evolutionary settings that care for others and engage in all the other positive morals of quotidian life, but in addition, are fixated on power, danger, honor, competition, and ultimately, war. Those who succeed through these trials come out glowing with pride, as did our greatest generation, at least many. They are feted by others, lionized, valorized and given all good things, especially social power. Not for nothing was John Kennedy's administration named "Camelot". The tellers of tales have no better material, in the culture that this process produces- the patriachy.

PTSD is the dark side of this psycho-socio-genetic legacy, especially now that chivalrous rules of engagement no longer apply, and the horrors of war come upon everyone, winner or loser. Few came out of the trenches of WW1 with glowing pride, and few again come out of our recent wars in Iraq or Afghanistan so crowned with honor and success. The US military occupies an uncomfortable tension between the mechanization, routinization, and sanitization of war, vs the need to keep its soldiers motivated and charged-up for battle.

This leads to the currently most notorious lovers of honor, chivalry and blood- the islamists of IS, Al Qaeda, et al. To read the autobiography of a Taliban leader, there was no better time, nothing more vivid, than the time he spent killing infidels (or just rival factions) and bonding with his band of brothers. So it is on all sides. The question is ... not who is violent, but who is fighting for positive ends for the human community at large. Who is upholding an ideology and system that serves the general good rather than creating chaos?

The chivalric system had its good points. The Arthurian tales are filled with good knights fighting bad knights who imprison, rape, and plunder. It was a nascent form of state legitimacy, under an aristocratic oligarchy. Now we have higher standards of legitimacy, cast in terms of universal democracy and human rights. But Islam is not in the same mind-space, still fixated on patriarchy if not theocracy. Its idea of chivarly and human rights are quite different (indeed far more traditional) from those current in the West.

But is this true of the population at large, or is it only true of the extreme, the disaffected, the anti-West, and the callous rulers who use any convenient ideology to direct resentment away from themselves? That is the question that the West, and the US in particular, has been grappling with as we try to spread "democracy" in a Middle East where democracy is such a strange flower; where legitimacy flows from scripture, tradition, and turban rather than from a legalistic, post-enlightenment philosophy.

It wouldn't be a pressing issue, except that we all happen to live on the same planet. While those in the West struggle to keep the joy of war confined to the football field or the videogame, and locked within a disciplined military, elsewhere it flourishes in age-old existential terms, freed, ironically, by the chivalrous and respectful reluctance of leading powers to use the virtually infinite military violence they have at their disposal.

• Being a warrior today.
• Fanatical religiosity ... but why in the US military? (Correction)
• Better living, through plastic.
• Allied with Al Qaeda, Iran, and Hezbolla, against IS ... can it get any stranger?
• More in the annals of violent self-pity: Russia.
• Yes, it was, and still is, all Bush's fault.
• To zero carbon with a carbon tax. And for free.
• Arrested for manner of walking ... the Ferguson case and police ass-covering.
• Plato and the GO-PAC of his time.
• Bad justice, continued ... bribery and corruption are OK.
• Krugman for the Nth time.. economists failed us miserably.
• And are still failing ... the irony of Germany vs Keynes.
• The ratings agency cesspool? Still there.
• Fraud in business ... a normal condition.
• This week in the WSJ, annals of climate denial: "While the past two decades have seen progress in climate science, the field is not yet mature enough to usefully answer the difficult and important questions being asked of it." ... "Even though human influences could have serious consequences for the climate, they are physically small in relation to the climate system as a whole. For example, human additions to carbon dioxide in the atmosphere by the middle of the 21st century are expected to directly shift the atmosphere's natural greenhouse effect by only 1% to 2%."

The Origin of Life

Some papers on the earliest steps from geology to biology.

One of the great questions, second only to the origin of the universe (multiverse) and perhaps the nature of thought in the brain, is how life got started on Earth. (Leaving aside, of course, the even more daunting question of peace in the Middle East.) Of the three, the mind is well on its way to definitive solution, and the origin of the universe is rather unlikely to ever be solved, or at least there is no prospect that I can see, despite enormous advances in cosmology. The origin of life occupies a middle ground, so far off in time that certainty may be impossible, but bounded enough by our knowledge of the ambient conditions and their rich aftermath that detailed and plausible theories can be, and have been, advanced.

The papers reviewed here are not new, (dating from from 1997 and 2003), but provide background for my post two weeks ago about the divergence of Archaea and Bacteria, and constitute what I think remains the leading hypothesis for the origin of life (elaborated in more recent papers 1, 2, 3). (Other recent origin of life refs 1, 2, 3, 4, 5.) This hypothesis situates the scene of action at thermal vents at the ocean floor, where highly reduced and alkaline geological fluids percolate up into an ocean that was, at that time, far less oxidizing than today, but still, due to the prevalence of CO2, several logs more oxidizing and acidic than the geochemical fluid.

As still seen today, this fluid deposits rich chimneys of iron sulfide wherever it emerges, in a porous matrix that could host untold chemical complexity. And there are / were a full spectrum of more moderate vents, with lower temperatures and less harsh chemistries. These locations attract theorists of the origin of life because they provide a great deal of potential energy, in a form that life still uses: the electro-chemical gradient in the form of acid / base (protons) and oxidation / reduction (electrons).

They also provide the key elements (sulfur, iron, nickel, tungsten) that are needed, and the kinds of enclosed, yet semipermeable, spaces that would be needed to accumulate the compounds needed as proto-cells. So the 1997 paper by Russell and Hall delves into the kind of proto-metabolism that the energy gradients and structures at these locations might have provided. The Earth was saturated with CO2 at the time, as free oxygen had not yet been photosynthesized into existence.

But let's take a step back and ask what is needed for life. The basics are a membrane or some other compartment to keep inside and outside apart, an energy source, a metabolic system to harness that energy to create the molecules on the inside, like complex carbon molecules of our form of life, and a genetic replication system that controls the metabolism and other characters, so that they can be selected via Darwinian evolution.

Not all of these things have to happen at the same time, and the goal for figuring out how geology generates life is to locate conditions where as many of the earliest requirements are present for free in the geological environment, and deduce what had to happen at which stage thereafter. A great deal has been made of the RNA world (references 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) as a near-certainty in the progression from proto-life to the last common ancestor of all life. Our ribosome, for one thing, carries its clear signature. But this is a very late stage in the origin of life. The RNA world presupposes metabolism, a cell structure, and a replication system, even while it gives rise to a translation system that sets forth on the protein- and DNA-centric course we are on today.

So, energy is a must. Nothing can happen without it, but it can take many forms, from lighting discharges to sunlight, to chemical gradients from stable geological sources. As discussed in the previous post, chemical gradients remain the bread and butter of cellular energy, and are the most likely original form, leading to the hypothesis that undersea hydrothermal vents are an excellent candidate setting for consistent gradients of pH and redox, among other chemicals, approximating our current chemiosmotic metabolism.

Overview of Russell & Martin theory, with CO2 reduction occurring in mineral "bubbles" at the hydrothermal / oceanic interface.

Prior to biological, lipid-based membranes, such vents also supply porous rocks and somewhat sealed bubbles of rock that could serve as chambers or "cells" for pre-biotic chemistry. And lastly, they provide the actual enzymatic chemicals that remain at the core of our coupled redox metabolism- condensed iron and sulfur complexes that conduct electrons between proteins and across membranes while pumping protons in the opposite direction or reducing carbon compounds.

Example of a contemporary iron-sulfur  (Plus nickel) cluster that forms the heart of many enzymes that reduce (or oxidize) carbon compounds, in this case carbon dioxide to carbon monoxide, given water and a proton acceptor such as ferredoxin, another iron-sulfur protein.

What was the most elementary metabolism? Somehow, carbon compounds must have been reduced from the high level of CO2 and CO on early Earth to the sugars and polymers that form the basis of life, such as ATP, NAD, ribose, and the various metabolic intermediates of the Krebs cycle (which we use to break down food to CO2). The authors present a reverse Krebs cycle as the founding metabolism, where carbon compounds are built up (i.e. reduced) using electrons as well as catalytic surfaces furnished by Fe-S minerals mediating between external acid to internal alkaline conditions.

Basic energy scheme where a chemical gradient is used by iron-sulfur compounds to do enzymatic work, such as hydrogenating (reducing) CO2.

"It is the interfacing of the alkaline hot springs with the acid ocean that brings about the precipitation of an iron monosulphide (mackinawite) membrane. Electrons could have been transferred across such a membrane. Also the hydrogenating potential of the mackinawite could have been enhanced by the presence of nickel (Kouvo et al. 1963; Vaughan 1969; Morse & Arakaki 1993)." 

"Iron monosulphides such as mackinawite can contain up to 20% nickel (or cobalt and copper), probably tetrahedrally bonded between the sulphur-sulphur layers (Vaughan 1970). The FeS membrane considered here may have only adsorbed a few per cent of nickel, enough to force the cleavage of the hydrothermal hydrogen at the nickel site with the production of a transient hydride. The left-over proton would be neutralized with hydroxide in the protocytoplasm. The electrons could be transported through the membrane along the iron layer situated along (001), conducting
toward the final electron acceptor such as Fe(III) on the outside of the membrane. The atomic hydrogen could then hydrogenate the CO2 molecules bound on adjacent iron sites."

"In particular, Shock (1992, 1996) has carefully calculated the metastabilities of carboxylates, ketones and alcohols as inorganic carbonate in seawater mixes with hydrothermal solutions, with their fugacities buffered by both quartz–magnetite–fayalite (QFM) and the more oxidized pyrite–pyrrhotite–magnetite (PPM) mineral suites. The fugacity of carbon dioxide is taken as 10 bars, the presumed atmospheric pressure in the Hadean (Walker 1985; Kasting et al. 1993). ... Shock (1996) demonstrated that the possible synthesis of organic molecules between 50 and 250degC is sensitive to the fugacity of the hydrothermal solution, which must be buffered by QFM for all inorganic carbon to be converted to organic molecules. This is still a conservative choice, since 4.2 billion years ago the redox state of the mantle was probably two or three log fO2 units below that of the quartz–fayalite–magnetite buffer (Arculus & Delano 1980). Remarkably, Shock (1996) demonstrated that at temperatures below about 150degC, the longer chained polymers (dodecanoate is the longest chain considered so far) will theoretically be most represented of all the organic molecules, and that they could be generated at no energy cost."

An imagined reverse TCA or Krebs cycle, where carbon compounds are grown from humble beginnings using the free energy of the redox and pH gradients at the vent structures. What would guide the soup in any direction or to any particular compounds (including chirality) is not clear.

Given the right conditions, things might have proceeded quite rapidly ... millions of years would not be needed.

"The far-from-equilibrium conditions in which these geo- chemical processes and mechanisms operated would have been widespread for a limited period of Earth history, and would have provided ample opportunity for such a unique sequence of events leading to the minimal cell, the common ancestor of all life on this planet. Although coupled to a long-lived hydrothermal system, the actual gestation period for organic synthesis and the self-assembly of organic protocells capable of fledging and replication from within the iron monosulphide hatcheries would have to have been rapid, and may have taken weeks or months, rather than the millions of years normally assumed for the emergence of life."

The second paper takes the story onward through subsequent steps of probiotic evolution, where the metabolism becomes more ramified with phosphate (on ATP) as another energy currency, and  nascent protein and RNA enzymes develop out of the organic soup. And finally the mineral membranes are supplemented and replaced by organic ones, given some ion channels and membrane-bound enzymes to carry out metabolism. This sets the stage for escape as free-living organisms.

Cartoon of the general model of Russell and Martin, with organic pro to-metabolism generating carbon compounds which then undergo chemical evolution towards the RNA world, and eventually to organic membranes and cell walls that allow complete escape from the mineral womb at the hydrothermal vent setting.

I can hardly convey the entire theory, and at an outline level it seems reasonable. But what was the force or principle that made the carbon compounds become more complex and self-organize into an RNA world with enzymes and coding / reproduction schemes? That remains a major question (but see the collection of RNA world references cited above). Energy alone, even when channeled in some approximation of the later major microbial metabolism to a profusion of organic molecules, does not, on the face of it, direct complexity or productive competition between mineral bubbles. (The authors have a later paper that claims that conditions "forced" life to emerge, but its details are not available, and the argument seems geochemical, not biological, so it does not seem to address the competitive issue.) We can refer to the anthropic principle to say that whatever led to us must have survived somehow, but that is a far weaker theory than one that drives events based on the chemistry of the time. So I think these concepts are a strong start to a theory of the origin of life, but as yet far from the whole thing.

• Above the law- why pardoning Nixon set a bad precedent.
• Realism and Ukraine.
• "There was so much more reason for the U.S. to respond to 9/11 by invading Pakistan than there was Afghanistan."
• Who should pay for Detroit?
• "For middle-class Americans trying to save for retirement in a 401(k), bank fees take about $2 of every $5 over a lifetime of investing."
• Japan continues its curious ways of monetary sovereignty.
• The Chicago school thinks deflation is not so bad.
• MSM getting a little lefty!
• Our divided country- is speech speech, or is money speech?
• Did Apple solve payment security via biometrics?
• Quiverfull education.. a bit oxymoronic.
• Watch out: Deepak is really pissed, and has a nonphysicalist ontology on his side.
• Enron echoes "In short, Congress has consistently eroded the disincentives designed to keep corporate managers from lying to their shareholders and creditors"
• This week in the WSJ: Even someone at the Hoover institution recognizes the lack of prosecution, and the utter corruption of the financial system. "We also point out that when the Fed finally acted, it not only rescued the banks, it also bailed out their shareholders as well as the executives who had helped steer the banks and country into the crisis. In contrast, when the government rescued General Motors, it forced shareholders and bondholders to take huge financial losses and executives to be fired."

On the Truthiness of Morals

Are morals subjective or objective? A philosophical argument that really does have an answer.

It is hard to believe some of the topics that remain "live" in philosophical debate. Like the existence of free will, or the Christian trinity, or the existence of souls. Can you detect a theme here? Ideas from our religious history tend to have a very firm grip, coming as they originally did from our unconscious archetypes in the first place, no matter how little rational sense they make in a post-enlightenment intellectual world, i.e. reality. Philosophy departments the world over straddle a somewhat pernicious tension between keeping old philosophical questions alive out of honest historical study and respect for the past, versus, frankly, out of professional interest in having something to do and the safety of sticking to received perplexities, which is pretty much the opposite of what philosophy is supposed to be about.

I think the area of objective vs subjective morality is in this general position (See a lengthy discussion and series of apologetics by a proponent of moral objectivism). In theistic terms, morality is created by god, and either commanded via its prophets and scriptures, or, in more liberal versions, implanted by way of evolution to give us, if not universally moral behavior, at least close to universal discernment of what is good. The point of all this is sort of unclear, if god is all-powerful in the first place. Are we some kind of toy or weird experiment developed for its amusement?

And make no mistake, for the vast majority, religion is a its core a moral and moralistic enterprise. Scratch a theist, and you will find someone who believes that without god, all is permitted and society will fall to ruin. Indeed, the intense emotion these positions engender tell you right off the bat that something is fishy about the assertion of objective truth to morality. There are good evolutionary reasons for this nexus of groupishness and righteousness, of course, which makes it so odd that ...

Remarkably, the pull of objective morality goes far beyond the community of theists. Many philosophers, including the highly esteemed Derek Parfit, and even leading contributors to the atheist flagship magazine Free Inquiry, hold to the moral realist / objective position. Which is that morals have some kind of objective basis or "truth" value independent from our subjective pleasures and pains. This is a species of philosophical idealism, which generally believes in the reality of ideals, whether mathematical, like the ideal geometric forms, or moral, like those we feel ourselves striving for in some great communal project. Some even believe the ideals realer than the mundane reality under our feet. The connections to theism should be self-evident.

Parfit's recent work was reviewed by Peter Singer:

"Many people assume that rationality is always instrumental: reason can tell us only how to get what we want, but our basic wants and desires are beyond the scope of reasoning. Not so, Parfit argues. Just as we can grasp the truth that 1+1=2, so we can see that I have a reason to avoid suffering agony at some future time, regardless of whether I now care about, or have desires about, whether I will suffer agony at that time. We can also have reasons (though not always conclusive reasons) to prevent others from suffering agony. Such self-evident normative truths provide the basis for Parfit's defense of objectivity in ethics."

I do not see how this argument leaves the station. While there is a great role for moral reasoning in summing up our pains and pleasures to an optimized global judgement, the worm at the bottom of all this calculation remains pain and pleasure ... the very antithesis of objectivity, and the soul, if you will excuse me, of subjectivity.

This work was also reviewed by James Alexander (needs to be approached by a general internet search, not via this link):

"Parfit states the case against Political Theologians, against Nietzscheans, and against Kantian Constructivists as strongly as possible. His own position is unlike all of these in being resolutely impersonal. There is no privileged God, no privileged subject, and no intersubjective order emerging from the interaction of privileged subjects: there is, instead, an objective moral order. For Parfit this is an absolute presupposition: “If there were no such normative truths, nothing would matter, and we would have no reasons to try to decide how to live.” (Vol. II, p.619.) This view is what Parfit calls ‘Non-Metaphysical Non-Naturalist Normative Cognitivism’, or ‘Rationalism’ for short."

Excuse me, but this is nonsense. There is no need to go all axiomatic about where our reasons for "how to live" come from. They come from our inborn desires for life, liberty and the pursuit of happiness. Or however else one might like to phrase it. They are fundamentally subjective, which one can cast either as the evil and selfish dictates of the struggle for existence, or our hard-won capacity to weigh our subjective interests in communities of interdependence.

Whatever one's view, morals begin as the simple, subjective dictate to stay alive, avoid pain, and seek pleasure. (And to get exactly as much ice cream as Bobby does.) The fact that we can record the past and forecast the future, and the fact that we depend on others for virtually every facet of our existence means that our moral universe is incredibly complicated, spinning from those simple beginnings an endless negotiation about what each person might reasonably want & get in a society where others are similar moral beings with their own aims and pains. In the reigning system of democracy, we have come to a stable stand-off where the right to be a subjectively guided human is accorded to each person, with maximal freedom to pursue happiness coupled with minimal freedom to impinge on the pursuits of others. (Except for corporations, which are specially blessed immortal, amoral, and politically omnipotent persons.)

None of this needs objective morality in any respect. The idea that what we think right and best is also objectively good, while the Nazis (to take a convenient shorthand) are incontrovertable, objective evil ... well, that is simply a fantasy, though one that is incredibly seductive and occasionally quite useful. Even if every person on the planet agrees with such judgements, they remain anchored in the founding motivation that what is good for us collectively is good, and the reverse is bad- a totally self-centered and subjective criterion for morality.

Suppose, for instance, that the world community of dophins used their powers of speech to tell us something truly momentous. That they are the superior beings on Earth, and we should, (by objective morality), spend all our efforts to make the planet better for them, not for us. What would we say to that? But ... all of our philosophers say that making the world better for humans is what it is all about. One can not imagine this being very persuasive. If the dophins could drop bombs on us, would we respect them then? Or perhaps if they showed us their ability to feel pain, would we accept them as equals, let alone as superiors?

Hopefully this helps to show that not only are morals descriptively subjective, expressing how we have always generated and used them. But any normative system telling us what we should be doing is likewise inescapably based on subjective criteria as well- what we think in our wisdom, is good for us. Whether "us" is individual or collective leads to the endless dramas of our lives, in art and reality- the tension that religion labors so hard to resolve, but which remains inescapable.

The historical struggle to extend collective moral behavior to ever larger groups does not depend on any objectivity in morals, either, other than the trivial objectivity they may gain from being written in the form of stones and books. We evolved to cleave to our own group and kill the other group. So how one defines the group is of monumental moral importance. The advent of agriculture and other technologies to support ever-denser populations generated enormous societies with fluid groupings. In our age, the nation has taken pre-eminent position as the group that stands ready to demonize others, take their land, and exterminate them. While it is laudable that groups of hundreds of millions have managed to become internally peaceful, it is, hopefully, clear that the basis of such "moral" behavior is no more objective than it ever was.

• And Robots? What do we owe them?
• Word on truthiness.
• 'Nother word on the truthiness of conservative austerity.
• Mythicized history, or historicized mythology? We don't have much to go on.
• Nor did Bill O'Reilly have more to go on. "I should estimate that reporting the historical truth about Jesus falls somewhere between documenting the facts about Robin Hood and Superman."
• A few notes on Wahabism. Think of the Christians!
• It is time for a right to work. Yes, a real right to work. A real job, real pay.
• Afghans are not very clear on the concept: "Qari Bilal, the IMU leader, was freed by the Afghan government at the direction of President Hamid Karzai, Afghan officials in Kunduz have told TOLONews, which identified Bilal as "a senior al-Qaeda leader who was released from prison on two separate occasions." He leads more than 300 fighters in Kunduz province and "has masterminded numerous suicide attacks and overseen the planting of roadside bombs throughout the province."
• On the general nature and ancient origin of the ATP synthase.
• What are, or were, unions for?
• Washington Post to compete with the Washington Times.
• Finance remains the enemy, and needs to be cut down to size. Specifically, we need accountability through less debt, less tax-deductibility, more equity exposure, and long-term clawbacks of ill-gotten gains.
• Merkel, Russia, and the coming winter.
• "Despite what you may think, Americans, on average, are driving more miles every day, not fewer, filling ever more fuel tanks with ever more gasoline. U.S. oil consumption is on an upward trajectory, climbing by 400,000 barrels per day in 2013 alone."
• This week in the WSJ: climate denialism still about. "The climate-research establishment has finally admitted openly what skeptic scientists have been saying for nearly a decade: Global warming has stopped since shortly before this century began."