The Power of Prophecy

What makes prophecy such a compelling narrative device in fantasy and myth, and a psychological fixation?

Humans have been obsessed, from the beginning, with the future. As the only animal conscious of the future, its inscrutibility quickly became a frustrating obsession. One wikipedia page lists 372 forms of divination. Some of the earliest far Eastern writing we have is from divination using bones with wishes or questions written on them. How natural is it, then, to imagine that there is someone on the other end to tell us the answers, or some people gifted intrinsically or through some divine possession or shamanic training to foretell the future? My newspaper still publishes the daily horoscope, a sadly watered-down echo of these most fervent longings to peer into the unknowable.

It has been a fixation in drama, from Oedipus to Harry Potter. The Greeks went to Delphi and received dramatically cryptic answers, which could be famously misinterpreted. Oedipus fell into this trap, fulfilling precisely what he had strained every nerve to prevent. When used in fiction, prophecies are relentlessly fulfilled, since otherwise, why bring them up? Like for the more generic foreshadowing technique, the magic only works when the portents are true, and the characters, while twisting every which way to evade or fulfill them, find in the end that fate has spoken with one voice out of the timeless dimension.

The Harry Potter series makes generous use of prophecy, both in its main plot lines, where Harry is marked in advance in various ways for his extraordinary fate, including the special symbol tattooed on his face, and in one particular episode, where the characters fight it out in a hall of phophetic orbs, climax of the fifth book. The bible, of course would hardly be the book it is without a flood of prophecies. The new testament was in large part composed around the supposed fulfillment of various prophecies made in the old, with some squeezing and patching required. The king of the Jews who came to save the world  bears hardly any resemblence to what the old prophets were expecting! Yet, mysteriously and gloriously, the fulfillment came about in the least expected way, etc... Then the New Testament closes with another round of even more feverish prophecies, in the form of revelations where the mundane world will finally receive its just deserts and be swept away in favor of a new and perfect dispensation.

Stonehenge, in part an astronomical prediction machine.

Obviously, it is empowering to feel even a little in control of fate, a little gifted with insight into the future. Why else are countless people betting on sporting events? Why else make such a fetish of astronomy and the prediction of what can minimally be predicted- the steady progress of the days and seasons? It is endlessly maddening to know that the future is coming, but know so little about it. But the tide has turned a bit over the last few centuries as a new mode of thought came to the fore- science. The successful analysis and prediction of Halley's comet showed on a poplular level the power of Newton's system and its ability to predict the future. Now we can predict the weather with startling accuracy, at least a week or so in advance, and can likewise predict the climate decades into the future, somewhat to our horror. Yet there is so much that still eludes prediction. Even in the physical world, earthquakes remain a frustrating challenge, apparently fundamentally unpredictable. And despite the "end of history", human affairs remain not just unpredictable, but irrational, as our current political regime so amply demonstrates.

In its humbler incarnations, prophecy is merely evidence of intelligence- a keen imagination or intuition that is able to discern where things are going sooner than the next person. This is where sports betting and stock picking get their acolytes. But beyond that it is clearly a fictional device- one that we love in its fateful foreshadowings and tragic struggles, but one that has never risen above that level to divine inspiration, reading the mind of god. Naturally, that is because such a thing does not exist. We are trapped within the plodding arrow of time, as we are under the spatial light-speed limit, as we are under our own mastery of fate, such as it is, having no other to turn to.

• Like we need more billionaires running things, and preaching about the national debt.
• Wealth is the problem, far more than income.
• And we have the candidates to solve it.
• George Will does something good.
• Protect your and your country's health- leave facebook.
• Treason and corruption, continued.
• Income tax rates have no effect on economic growth.
• But what do economists know, anyway?

Frankenplant

40% more efficient plants? Done!

What is the most common protein in the biosphere? It occurs in plants, right? Right- it is RuBisCO, the enzyme that fixes carbon dioxide from the atmosphere, is the workhorse of agriculture, and hero of the fight against global warming, should we choose to grow more plants instead of burning them down. Its full name is ribulose-1,5-bisphosphate carboxylase-oxygenase, meaning that its substrate is a five carbon sugar (ribulose) that has two phosphates attached, and the enzyme attaches a carboxyl group from CO2, but can also attach an oxygen instead (the oxygenase part). And therein lies the problem. RuBisCO is phenomenally inefficient (maybe ten reactions per second) and error-prone (using oxygen [O2] instead of CO2 roughly a quarter of the time), which is why it is made in such prodigious quantities, amounting to half the protein complement of leaves.

Plant researchers have been casting about for a long time for ways to make this core reaction more efficient. But have had no success. Indeed, an interesting paper came out a few years ago arguing that as far as this enzyme is concerned, the shape and chemical similarity between CO2 and O2 are so close that RuBisCO is perfectly optimized, exchanging speed for what specificity is possible given its substrates. It varies quite a bit in this tradeoff, depending on the specific environment, arguing that the optimization is quite dynamic over evolutionary time. One of the few innovative solutions that plants have developed is not a tweek to the enzyme, but a physiological compartment present in C4 plants (like corn), which concentrates CO2 and excludes O2, thus resolving the competitive constraint for some of their chloroplasts. Their RuBisCO enzymes are adapted to have a slightly more relaxed attitude- slightly less specific for CO2, while also almost 2-fold faster, gaining an significant advantage.

The error pathway, fixing oxygen instead of CO2, is called photorespiration, since it uses up oxygen like regular respiration, but now in a completely wasteful way. The product is phospho-glycolate instead of 3-phospho-glycerate, and the glycolate is both inhibitory to photosynthesis and difficult to dispose of. It is typically exported from the chloroplast, and bounced around between the peroxisome and mitochondrion in its way to being turned into the amino acid glycine, all at the cost of roughly twelve ATP. It is hard to believe that this waste goes on day in and day out across the biosphere, but it seems to be the case. One might note that this yet another case of the steep price of success, since RuBisCO evolved in a high CO2 environment. It was the success of the photosynthetic process that covered the earth with green and filled the atmosphere with what was to all existing life forms a poison- oxygen.

Now, a team of researchers have engineered a way around this conundrum, at least reducing the cost of glycolate recycling, if not resolving the fundamental problems of RuBisCO. They describe the import of a set of genes from other species- one from pumpkin, one from the alga Chlamydomonas, and five from the bacterium E. coli, plus a genetic suppressor of glycolate export from the chloroplast, all resulting in a far less costly recycling system for the waste product glycolate.

New pathways (red, blue) inserted into tobacco plants, plus inhibition of the glycolate transporter PLGG1. Some of the wild-type pathway for diposing of glycolate is sketched out on the right.

Firstly, glycolate export was suppressed by expressing a tiny RNA that uses the miRNA system to target and repress the gene (PLGG1) encoding the main glycolate transporter. Secondly, the researchers imported a whole metabolic system from E. coli (red part at top of diagram) that efficiently processes glycolate to glycerate, which, with a phosphorylation (one ATP) can be taken right up by the RuBisCO cycle. Lastly, they backstopped the bacterial enzymes with another pair that oxidize glycolate to glyoxylate (glycolate oxidase), and then (malate synthetase) combine two of them into malate, a normal intermediate in cellular metabolism. This was all done in tobacco plants, which, sadly, are one of the leading systems for molecular biology in plants.

Wild-type plant is on the far left, and a sample plant with all the engineered bells and whistles (AP3) is on the far right, showing noticeably more robust growth.

Combining all these technologies, they come up with plants that show biomass productivitiy 40% higher than the parent plants, as well as reducing plant stress under high light conditions. After 3 billion years of plant evolution, this is a shocking and impressive accomplishment, and can be extended to all sorts of C3 plants, like wheat and other grains (that is, non-C4 plants). Due to the number of genes involved, unintentional spread to other plants, such as weeds, is unlikely. But given the urgency of our CO2 waste problem, one wonders whether we might welcome such escapes into the wild.

• Some notes on Sweden.
• MMT is coming into the mainstream, despite kicking and screaming.
• Complete regulatory capture of the consumer financial protection bureau. Now protecting predatory lenders.
• For some countries, history is circular.
• The tribulations of absolute pitch.

Ice Cream is True

Many philosophers seem to think that what we like and want may also be true. Critique of "On Truth", by Simon Blackburn

Hardly any academic field is subject to such divergent opinions as philosophy. While most people ignore philosophy and especially what philosophers say, with complete indifference, if not mockery, philosophers see themselves as grappling with the most enormous questions that lie at the very heart of our society and humanity. They are the ones asking the deepest questions of what is good, what is true, what is meaning, and what is being. Why, oh why are they marooned in ivory towers writing tedious monographs that no one reads or cares about? Specialization is particularly pernicious in this field, transforming what might be a pleasant conversational raconteur and dorm room bullshitter into an academic mired in most arcane and pointless hairsplitting, in emulation of fields of actual research, employed solely because university students must, after all, have philosophy courses.

Still, hope springs eternal that the mental firepower so evident in the written work of these fields could come down off the mountain and briefly enlighten the masses about what is true. Such is the project of Simon Blackburn, eminent atheist philosopher retired from Cambridge and other institutions. His book is modeled on that great work of Harry Frankfurt, On Bullshit. Bullshit happens when the speaker doesn't care about truth at all, whether for it (truth) , or against it (lying). Our current president puts out a lot of bullshit, but mostly he is a pathological liar with a genius for coming up with the most mendacious and divisive lie in any situation. That is why speaking with Muller was deemed by everyone around him to be a "perjury trap". Going further, the new politics we inhabit seems to have left rational discourse behind. The right decries political correctness, which cruelly enforces reason and decency. The solution is to create an emotional discourse full of tribal identifiers but otherwise senseless, making of our politics a simple blue/green contest, ending up, ironically enough, in identity politics.

Blackburn also takes some political shots, which, since he is British, aim mostly at the egregious lying prevalent in the pro-Brexit campaign. But the book is largely a survey / critique of philosophical attitudes towards truth. The starting point, naturally, is the correspondence theory of truth. While called a theory, is it more a definition- that truth consists of mental models that correspond with reality. Heliocentrism is more true than geocentrism, Thucidides is more true than Herodotus, NPR news is more true than FOX news. Blackburn takes those outré philosophers (postmodernists particularly) to task for disputing such basic conceptions.

"At the end of the twentieth century the intellectual fashion known as postmodernism took an ironical stance towards science, regarding it in an anthropological spirit as simply the ideology of a particular tribe of self-selecting people calling themselves physicists, chemists, engineers, and biologists. The standpoint seemed to many to be a sophisticated response to science's claims to authority. It was tough-minded and knowing, and its proponents could flatter themselves as having seen through and exploded spurious claims to authority, as relativists and skeptics typically do. It was all very exciting- until one saw the same sophisticates using iPhones and GPS devices, relying detergents and paints and aeroplanes, vaccinating their children, and doing all the other things that the progress of science has enabled us to do. And then its glamour disappears, and instead it looks more than a little bonkers."

But there have been other, less dismissive approaches to defining truth- the coherence theory and pragmatism. Both take a step back from the correspondence definition, in light of our practical difficulties in knowing when we have gotten to that glorious state of correspondence. Coherence substitutes an agreement among authorities, such as a convergence among physicists of the late 1800's that everything of importance had already been found, and it was only left to work out the details. Global warming supplies another example- if 99% of relevant experts assign it to human causes, then perhaps it is, for all practical purposes, true. Pragmatism takes a similarly indirect approach relying on practical effects for validation of a truth. If planes fly, then much of the aeronautical theory underlying them is likely, again, to be true. I think it is useful to class coherence and pragamatism as methods of ascertaining or approximating truth, not as definitions. The point of truth remains getting us in sync with reality. If we were gods, then no pragmatism or coherence among authorities of lines of evidence would be needed- we would just know what the truth is, but it would still be a matter of correspondence between reality and our sovereign mind.

From there, things really start going downhill. Blackburn makes a diversion into deflationism, which claims that the correspondence theory is not so much a theory as a tautology, therefore meaningless. The problem here is a reliance on absurd linguistics. The word truth is generally not needed in truth claims, like "grass is green", as opposed to "the thought that grass is green corresponds with the facts", or "it is true that grass is green". It should be obvious that in the first phrase, the word "is" does a lot of work, setting out the truth claim quite clearly. It is hardly meaningless, or not a truth claim, thus it is little surprise that adding extra "truthy" qualifiers hardly add anything.

From there, the discussion descends into aesthetics, morality, and religion. Blackburn seems to have a hard time making sense of these fields, virtually giving up critique, and laying out lots of philosophical history and attitudes, which end up putting quite a bit of value on truth talk in these fields. For example, if we all agree that killing babies is bad, then it is true that killing babies is bad. Or, if ice cream is good, then it is true as well. There is a lengthy discussion of the formation of tastes, such that experts with deep knowledge of some art form can educate others to have more refined tastes, which all seems to form an argument for the truth of the tastes and the authority of the experts.

"But if we have been careful and imaginative and profited from the best opinion of others in the common pursuit, we can be reasonably confident that we have done justice to the topic [of some case of artistic evaluation]. We can advance our opinions, which also means we can judge them, perhaps provisionally and in cognisance of our own fallibility, as true."

But here I have to differ fundamentally. Philosophy deals with what is true and what is good. These are not the same things. Just because everyone agrees on something being good ... does not make it true. The criterion is radically different, being our judgement of goodness for human existence, whether for us personally, or for larger social structures such as our family, country or global society. Even if that judgement is putatively objective, such as population growth in response to "good"  policies or virtues, the value of that criterion remains subjective, as it is we who value population growth and flourishing, not perhaps the other animals who may die as a result. So one might claim it to be true that something is good, given expert justification or widespread agreement, but calling things true because they are good, or very good, in some aesthetic, moral, or other subjective sense, is bad philosophy as well as bad language. Whether Blackburn really intends this claim is unclear due to the murky nature of the discussion, unfortunately. At any rate, it is the age-old gambit of religions, to cast what they wish and like as truth. For philosophy to confusedly retain this atavism in its approach to morality and other goods would be deeply mistaken.

• Lawyers and truth.
• Facebook is evil.

UBI: Creeping Communism or Libertarian Liberation?

Review of "Give People Money", advocating for Universal Basic Income, by Annie Lowrey. Subititled "How a universal basic income would end poverty, revolutionize work, and remake the world".

This is a good book if one wants to read a litany of complaints about late capitalism- inequality, crummy work, appalling poverty in the midst of plenty, gender inequality and unpaid work, misdirected foreign aid. One might indeed say that never have so many reasons been adduced for a policy with which they are so tenuously connected. To put the argument briefly, if we were to give everyone in the US a monthly income of, say, $1,000, no questions asked, it would by definition end poverty, set an effective minimum wage of roughly $6.25 (full time), and cost about $3.8 trillion, roughly doubling the federal budget.

What are the various problems that the UBI is thought to address? First is of course poverty. While $6.25 is even below the current minimum wage, it is enough for a bare existence. Lowrey cites several experiments in poor third world countries that show that this kind of income is generally put to good use- much better use than aid that comes in the form of second-hand clothes, bed nets, shoes, or any of the other myriad do-good schemes that first world donors cook up. But there is a crucial difference- these experiments are conducted among a functional population generally at par for their society, whose only problem is that they, as are everyone else around them, poor, relative to more developed economies, whose goods and technologies are available for a price.

The poverty-stricken in the US are, by contrast and almost definition, dysfunctional, with health problems, drug problems, intellectual problems, and other issues that money alone is unlikely to fix, and may well make worse. San Francisco has had, for example, a long-term program to switch from money to in-kind and supportive care. If the problem is merely lack of money, then yes, cash assistance is an ideal solution. But UBI is, for this problem, a nuclear bomb, spewing money to everyone regardless of need, and possibly to the detriment of those in the most need of more structured help. There are better policies, as there are for virtually every problem that UBI putatively addresses.

Day laborers wait for work. Would UBI help?

Another problem dwelt on in the book is crummy jobs and inequality in its many dimensions, from a slipping middle class to persistent gender and racial discrimination and lack of wealth accumulation. Needless to say, the pittance represented by UBI is going to address none of these issues. The best that might be said is that it gives something, which is more than nothing, to those out of the workforce who are caring for children, the elderly, on a love-instead-of-money basis. And since the poor are disproportionately female and minority, they would also benefit the most from UBI, at least in subjective / relative terms. But again, it is a pittance, and since everyone gets the UBI, it does a poor job addressing inequality, particularly if its funding comes from a regressive source like a carbon tax, though better if it comes from an income or financial transaction tax. It does not even raise the minimum wage, given its extremely low level.

The more convincing, and libertarian, argument for a UBI is its simplicity and possible role in replacing other poverty programs. Aid like food stamps, housing assistance, and work training are all rather paternalistic and ridden with absurd paperwork, dehumanizing conditions, and arcane regulations. While some of these burdens come from simple bureaucratic evolution, most come from intentional policy built up to discourage people from becoming poor by penalizing and controlling them in various ways, resulting usually from right-wing and Southern racist politics. Replacing much of this with cash is very attractive, even if much of the new income will be wasted or if its amount fails to cover actual needs like housing in expensive areas. However, as mentioned above, many of the poor are dysfunctional, and got to where they are due precisely to their inability to handle money. To make cash assistance work, the responsible sheep would need to be separated from the goats who will end up on the street even with a UBI. This would inevitably bring back the caseworkers, rules, and other periphernalia of the welfare state.

The next level of the libertarian argument is that robots are going to take all our jobs, to which UBI is a solution. It pains me to have to say this, but this makes little sense. First, automation has been with us since the invention of the spear. Lowrey herself quotes Bill Gates: "What the world wants is to take this opportunity to make all the goods and services we have today, and free up labor let us do a better job of reaching out to the elderly, having smaller class sizes, helping kids with special needs. You know, all of those are things where human empathy and understanding are still very, very unique. And we still deal with an immense shortage of people to help out there." Clumsily put, but you get the idea- taking care of each other is the core of what we as people want to do, and should be doing. Making widgets is only one baroque byway on the true path of our life's work. Lowrey closes by mentioning the Star Trek economy- where no one needs money, all fundamantal needs are fulfilled, yet there are still jobs and ambition- a competition for status directly, not via the accumulation of money, but through the medium of work and service.

But this is probably not what libertarians have in mind. Their idea is more that the eggheads and Hank Reardons of Silicon Valley can keep on working their interesting, highly paid jobs, and not worry about stepping over homeless people, or being responsible employers in the new app-disintermediated gig economy, or facing the pitchforks of a vast and growing proletariat, all by feeding them crumbs of UBI. It is hardly an attractive future. On the other hand, one can view UBI as the first phase of future communism, where everyone shares in a basic level of decency, regardless of contribution. The UBI might be programmed to increase with time, in proportion to economic productivity or technological displacement. I can not regard this as an attractive future either, really, given the fundmantal importance of work in our personal and communal lives, and the impossibility of seeing an end to work, or having some principle to tell us what the best level of UBI should really be. Having ever-growing numbers of parasites living off the fat of the robots is reminiscent of ancient Rome, where maybe one fifth of the city population was on the dole, supported by the vast resources of the empire and armies of slaves. While this system was durable, lasting over five centuries, it does not look to me like one worthy of emulation.

Lastly, there are the children. Lowrey does not go into in detail since its ramifications may be so perverse, but supposing that UBI is granted from birth, the accumulation of children would likewise accumulate a sizeable income. Such an excessively pro-child policy would encourage more children among those most poor and most dependent on UBI, a social and plantery disaster.

---

What is an alternative to all this? A job guarantee has many positive characteristics, which I have mentioned previously.

• It gives money to those in need, not to everyone.
• It provides a decent standard of living, not a pittance, perhaps $25,000 per year, plus benefits.
• It automatically sets a substantial floor for wages, working conditions, and benefits for the private economy.
• It is automatically and strongly counter-cyclical, increasing when the private economy goes into recession.
• It naturally replaces much of the current poverty infrastructure.
• It provides services, insofar as the job holders are doing something productive.
• One could imagine a central job board, used internally by government projects and prospective employees, but also by private employers to make better offers to those employed in the program.

I would envision the job guarantee system as offering a full range of government-run work, from NASA engineering to street sweeping. Employees could be fired at will, demoted from better jobs to worse jobs, (or promoted), as their talents, behavior, and willingness to move merit. If they crash out of the simplest jobs, like litter pickup and invasive plant clearing, they could be offered a basic income for no work (at the UBI level of $12,000 per year- plus health insurance, which would be universal anyway). The conditions would be that they stay out of jail, off the streets, and out of drug and mental facilities. If they crash out of that, they would be faced with more paternalistic options of case worker intervention, food vouchers, group home living, having their finances handled by a trustee, etc. At this level, work requirements would not exist anymore, or lifetime caps, etc.

One of the most positive aspects of communism was its guarantee of work. The work may not have been efficient, but it gave everyone a place in society, and a paycheck, and benefits. It is one of the few aspects of communism worth emulating, if it can be made to work alongside a higher-paying, innovative, and well-regulated private economy.

Combining a job guarantee, cash benefits, and more controlled programs, a spectrum of appropriate options would be available at all levels of society to lift everyone out of poverty, to intervene where needed, to provide maximal freedom, and to use public money efficiently. Whether job guarantee holders actually accomplish anything is secondary- the major benefits occur regardless. Yet as noted above, there is a great, indeed infinite need, for work. For example, child care up to school age, and elder care (given some certification of disability and need for care) could qualify for one job guarantee position, regardless of the status of other people in the household. This would help families cope with services that are so important to society at large.

• Bitcoin is absurd and wasteful.
• Could gerrymandering get even worse?
• Fixing refrigeration is the top climate change solution.
• Reich on paying the rich to "fund" the government. (Which is quite unnecessary.)
• A recession is on the way.
• Collusion.
• The real crisis is climate change. And a fascist president.

Not a crisis

Not a crisis

To Re-engineer a Bacterium

Computational modeling of E. coli regulatory circuitry suggests that some bloat has crept in over the years.

Are we at the point of redesigning life? So far, studies of biology have relied on observation, and on mutations, generally for the worse. We have also tinkered around the edges by introducing new modular functions to some species, most notoriously pesticide and herbicide resistance in crop plants, and antibiotic resistance in bacteria. But what about redesigning whole organisms? A paper from a few years back (2012) took a stab at redesigning the genome of the model bacterium, E. coli, for simplicity. The quest was pretty elementary- ask whether the genes of the organism could be re-organized to function as well as the wild-type genome, but in fewer operons, with simpler regulation. Operons are sets of protein-coding genes lined up like a multi-car train, all induced transcriptionally by one promoter at the upstream end. The more similar functions one can stuff into one operon, the simpler the overall regulatory system can be. On the other hand, the joined genes are harnessed together in mRNA/transcription terms, so any regulatory flexibility that might be useful at that level is lost.

A schematic operon, with a promoter and other regulatory sites, which drive transcription of a set of coding genes, which are transcribed into one mRNA message, which is then translated into a series of distinct proteins. What is gained from chaining many related genes into one operon?

It was, admittedly, a rather academic exercise, with limited criteria for "normal function" of the genome: that its genome should produce all the products of the wild-type organism under ~100 different environmenal conditions. And it was all computational, done by iterative, computer-based evolution but never translated into a lab test of actual organisms (though synthesizing a bacterial genome based on this data is probably quite practical at this point). What they did have was a set of differential equations expressing key regulatory activities of a normal cell, concerning its metabolism, environmental inducers, transcriptional regulators, and genome targets. This is not a full cell simulation, leaving out protein translational controls, degradation, cellular structure and other modes of regulation, but still covers a lot of territory.

Process of computational refinement of the target genome, making random variations, then assaying for modularity and transcriptional output, and then iterating again, many times. Top graph shows regulatory modularity, which increased almost monotonously due to the design of the genome manipulations. Bottom graph is the (computed/simulated) similarity of the transcriptional output vs the original genome, which takes a big hit at first, before climbing back to the original state.

They performed thousands of computerized steps of shuffling regulatory sites and genes around the imaginary genome, testing the result each time for its similarity to the wild-type case in terms of output, and for its modularity/simplicity. As one can see in the graph above, (bottom), the output was quite unlike the standard (wild-type) for a long time during this simulation, before regaining an approximation of the wild-type pattern later on. Clearly the first order of business was simplification, with accuracy of output secondary. The final results are impressive, given the limitations, reducing the total number of operon clusters to about 1/4 of the original.

Example loci from the work. After genome re-organization, several operons have many more genes (black arrows, text notes).

An example is given above. The arc operon is turned on in anerobic (low oxygen) conditions, and encodes factors that repress aerobic loci, such as those involved in oxidative phosphorylation- the use of oxygen to generate ATP efficiently. In the rewired cell, this promoter encodes not one, but 11 other genes as well, probably gaining time and parallel control for a lot of other functions that could benefit from coordinate regulation. But what is galS doing there? This is a key regulator that turns on galactose import, a function completely unconnected with anaerobic conditions. This is one instance (which the authors bring up themselves) where, due to the limited selective pressure these experimenters put on their models, they came up with an intuitively poor result. But overall, they document that, as expected, the functions of genes now coalesced into single operons are overwhelmingly similar as well.

This work, while abstract, and unlikely to have resulted in a bacterium as fit in the wild as its founding strain, is a very small example of computational cell and molecular modeling which has, like artificial intelligence, been the next big thing in biology for decades, but is becoming more powerful and may actually contribute something to biology and medicine in the coming decades.

• An analogous simplification experiment in yeast cells.
• A good diet is lots of activity.
• The Fed is wrong.
• It is hard for a fool not to look foolish.
• How European banks (and the Euro) fostered the financial crisis: “Six European banks were pumping out “private label MBS” from their “US … affiliates””.
• Libraries are civic institutions full of wonder.
• Just how dead is the Republican party?

Solar Power is Not as Easy as it Looks

Adding the first increment to the grid is far easier than adding the last, if we want to decarbonize electricity. Review of "Taming the Sun", by Varun Sivaram

Global warming is no longer a future problem, but a now problem, and getting rapidly worse. We need a total societal focus on extricating ourselves from fossil fuels. Putting aside the brain-dead / know-nothing ideology of the current administration, the world is broadly, if grudgingly, onboard with this program. What is lacking are the political will and technical means to get there. California now gets 29% of its electricity (including imports from other states) from renewables, of which 10% is photovoltaic (PV) solar power. The grid operator shows a pleasing daily graph of solar power taking over one-third of electricity demand around mid-day.

A typical day on California's power grid. at mid-day, and fair portion of the state's power comes from solar power (teal). But come sundown, many other plants need to ramp up to provide for peak demand.

 
Varun Sivaram's book is an earnest, somewhat repetitious though well-written and detailed look at why this picture is misleading, and what it will really take to go the rest of the way to decarbonization. Solar power has very bad characteristics for electrical grid power- the grid operator has no control over when it comes in, (it is not dispatchable), and it all tends to come in at the same time of day. While this time (mid-day) is typically one of heavy usage, it is not the peak of usage, which comes during the transition to cooking and evening activities, from 5 to 7 PM. This means that not only does the rest of the grid have to work around solar's intermittency, but the rest of the grid has to constitute a full fleet of power plants for peak needs- solar will not reduce the need for either baseline or peak power capacity.

This is extremely disappointing, and means that adding the first 10% of solar to the grid is relatively easy, but adding more becomes increasingly difficult, and offloads rising expenses to other parts of the system. We do not have the technical means to economically address these issues yet. Solutions come in two basic forms- energy storage, or alternative modes of non-CO2 emitting generation.

Storage technologies by current capacity and capability. Pumping water uphill into reservoirs is the only existing method of storing power in grid-scale amounts over long periods.

Storage is easy to understand. If we could only bottle all that solar electricity somehow, all would be well. Even if we can't save summer power for winter, but save it only for a few days, we could build enough solar generation capacity (at the current cheap and falling prices) to cover our needs at the lowest production time of year, and throw away the excess the rest of the year. This assumes that, over a suitably large geographic area, there will not be so much extended cloud cover that this could not be reasonably planned. But such storage technology simply does not exist yet. The diagram above mentions some of the major candidates. The best known are chemical batteries, like lithium ion. This is how off-grid and home backup systems manage the intermittency of solar power. But these are expensive, which is why it is cheaper to buy power from the local utility than to go off-grid, and also cheaper to build a grid-tied solar system than go off-grid. The most mature grid-scale storage technology is hydropower- pumping water back uphill into a reservoir. This is obviously not available in most places where storage is needed.

Where various storage technologies are in development.

Other methods like flywheels, raising and lowering rocks, etc. are all on the drawing board, but not yet in practical deployment at grid scale, or even demonstrated to be economic at that scale. Making fuels like hydrogen or hydrocarbons from solar energy is another prospect for storage, but again are not currently economical. Hydrogen has been touted as the all-around fuel of the future for many uses, but is so difficult to handle that, again, it is far from currently practical. Getting there will take money and effort. 2050 is when we need the power sector substantially decarbonized, world-wide (if not sooner!). It sounds far off, but it is only about 30 years- a very short time in power technology terms. The scale needed is also gargantuan, so we need these solutions to get off the drawing board as soon as possible- there is no time to waste.

The alternative methods of no-carbon generation are currently wind and nuclear, with CO2 storage (sequestration) from fossil fuel plants as a further option. Carbon sequestration is not a new technology, and is something that would be directly motivated by a carbon tax, though it is also phenomenally wasteful (as are many of our more adventurous methods of producing fossil fuels, like tar sands)- a fair fraction of the energy produced goes right back into compressing and pumping the CO2 back underground. Wind is also getting to be a mature technology, and shares with solar the problem of intermittency, so is not a solution for dispatchable or baseline power. Sivaram does note at length, however, that a helpful technology for both solar and wind is long-distance DC transmission, which would allow rich sources, like the plains states, or the Sahara, to be connected to heavy users.

The dream of the next generation of nuclear power, which has not been demonstrated at grid scale.

That leaves nuclear power as an important element in future power systems. Generation IV nuclear power promises cleaner, proliferation-proof, more efficient, and more sustainable nuclear power. China has several programs in development, as does the US. Again, as with all the other necessary technologies for a fully sustainable grid, these are not mature technologies, and need a great deal of research and development to come to fruition. I will not even delve into fusion power, which is not demonstrated terrestrially in principle, let alone development.

The point of all this, as made at some length by Sivaram, is that the key to getting to a decarbonized future (for electricity, the easiest energy sector to deal with) lies not simply in scaling up the PV present into a glorious future. Rather, it lies in further intensive research and development of a variety of complementary technologies. The next question naturally is: will the private sector get us there, even if there were a carbon tax? The answer is- unlikely. The Silicon Valley model of venture capital is not well-suited to the energy sector, where innovation comes in small increments, the regulatory weather is heavy, and the scale in time and capital to money-making deployment is huge. There needs to be continued, and vastly expanded, government direction of the research, along with much other public policy, to address this crisis.

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World of Warlords

Why does the US keep funding warlords? And then wonder why "those people" are always fighing each other? Review of Ronan Farrow's "War on Peace".

What went wrong? We have asked ourselves that after countless foreign debacles, from Vietnam to Afghanistan and Iraq. Why does every intervention turn to ashes, and every good intention end in embarrassment and hatred? Ronan Farrow, celebrity diplomat and journalist, has an answer. Though he has been through a rough family life, Farrow is a smart cookie, and after starting with an absurdly puffy profile of Richard Holbrook, the book eventually settles down into sharp vignettes of American policy and institutions gone awry, and a case for rebuilding our diplomatic capabilities. Part of the war of the title is being waged on the State Department, conducted by the military and successive presidents ending up with our absurdly anti-State current executive. But it is facile to call that a "War on Peace", as though State is our Department of Peace. It is, rather, our reserve of strategic, long-range thought and professional experience in international affairs, and arm of American power, whether advancing that power dictates peace, war, or cold war.

"There are two types of military dispute, the one settled by negotiation and the other by force. Since the first is characteristic of human beings and the second of beasts, we must have recourse to the second only if we cannot exploit the first." -  Cicero, as quoted in the book. Which is incidentally ironic, given the relentlessly bloodthirsty culture and methods of Rome.

The Pax Americana of the post-war era has served us very well, not to mention most other countries. It has been a time of dramatically improving living conditions, rising population, and governance. It has been built on overwhelming conventional power, combined with formal alliances with countless partners and soft leadership by a system both prosperous and just (more or less) which others can aspire to. The outstanding example of this is China, which in its emulation of our mode of production has lifted itself out of dire poverty over the last four decades, and done so very peacefully.

On the other hand, we have made countless blunders when trying to force conditions to our favor more actively. Iraq is a shining example. We destroyed a country only to belatedly realize we had no idea how to run it or whom to hire to do the job. Then we skidaddled prematurely, leaving behind chaos. We have stuck more persistently with Afghanistan, (up to the present moment, at least), but remain in a quagmire of epic proportions with a government that is hopelessly corrupt, filled with warlords. This is where Farrow's book starts to come into the picture. Why so many warlords? Why all the corruption, and why is the facade of democracy so thin?

Afghan president Ghani, trapped in a power structure full of warlords, armed militias, and corrupt elements.

Going back to the start of the war in 2001, we used existing forces that were already arrayed against the Taliban, namely the warlords of the Northern Alliance. Integrated with a US air campaign, they quickly swept the field. But then, in the absence of other alternatives, we kept turning to them to run things, and kept arming them and turning to them again. The CIA and the military led the way, partnering with whoever could supposedly provide the goods- that is men and power, to use our guns and intelligence. But it was always a rotten deal, buying long-term dysfunction for short-term convenience. After World War 2, would we have turned to extremist militias to run Germany and Japan, just because they were most enthusiastic to kill their enemies? Funding and arming the most extreme elements of a society is certainly the best way to get those arms used, but not always the best way to rebuild that society.

Indeed much of our foreign policy over the last few decades has consisted of arming our motley friends. Pakistan is exemplary in this regard. We have been shipping them billions of dollars of military aid since 1955. And what do we have to show for it? A country that is one of the leading state sponsors of terrorism, which is in perpetual cold war if not armed conflict with both of its neighbors India and Afghanistan, whose clear policy is to destabilize Afghanistan, and which lies to us and the world without compunction. And which has blithely acquired nuclear weapons along the way, subjecting the whole world to the spectre of extreme Islamist takeover of a cataclysmic arsenal.

It has not been a very successful policy, whatever benefits the CIA may think it has gleaned over the years. The worst part is that all this aid has strengthened the military as the leading institution of Pakistan, leading to innumerable coups, overwhelming political power even when a general is not serving as president, as well as economic and media power, to the atrophy of civic life and democracy. The best that we could do at this point is to issue a heartfelt apology to the Pakistani people that we have contributed to the militarization of their society, cut all military aid, and focus on continuing constructive dialog with everyone in the region, especially India.

Similarly, in Central and South America, we have spent far too much time and money chasing leftist mirages with right-wing funding, helping to cause the chaos that is now driving so many migrants to our borders from El Salvador, Guatamala, and Honduras. Instead of dramatic stunts of cruelty at the border, we would be much better served setting up a region-wide peace and governance process to help these countries regain stability and democratic institutions. Where is that effort? Nowhere to be seen in this administration. Farrow describes a long-term trend by which the military and the intelligence/security complex in Washington has gained power and money, versus our organs of diplomacy and long-term intelligence, which have atrophied. Nation-building became a dirty word. So now we are now dealing with a series of unbuilt nations, several of which we have unbuilt ourselves. Fear has gained over reason, much to the detriment of our domestic institutions, not to mention our approach to world affairs.

One might even say that the US has become one of the greatest terrorist regimes in the world, engaging proxy wars and armies across the globe often to rather dubious ends and resulting in vast "collateral" damage. It is our lack of expertise and inability to understand other cultures and conditions that leads to the horrors/blunders of Vietnam and Iraq. And that can not be fixed with more know-nothing "strength" from dotards, or with ever higher military budgets and military "aid" packages to anyone willing to throw their own people under the bus of American interests. We are the policeman of the world, at least for the moment. The question is whether the model we pursue is one of SWAT-style military policing, or one of community policing. The former breeds problems on both the short and long terms, while the latter solves them.

And one can note that these practices and attitudes do not stay safely abroad, far from our own culture. The militarization and warlordism of our foreign policy sees its reflection in the growing domestic mania for guns, security, walls, and the installation of a would-be warlord in the White House. While the most grievous harms of this administration may be the diminishment of our network of international relationships and influence, US society is being corroded internally as well by the pessimistic, fearful, and ignorant tenor of the security state.

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Screwy Locomotion: the Spirochete

How do spirochete bacteria move?

Getting around isn't easy. Some of our greatest technological advancements have been in locomotion. Taming, then riding, horses; railroads, automobiles, airplanes. Microorganisms have been around for a long time, and while flying may be easy for them, getting through thicker media is not, nor is steering. The classic form of bacterial motion is with an outboard motor- the flagellum. The prototypical bacterium E. coli has several flagella sprinkled around its surface. Each flagellum is slightly helical, thus forming a languid sort of propeller, which if turned along its helical axis, (at roughly 6,000 rpm), can propel the bacterium through watery media. Turning multiple flagella in this same direction (counter-clockwise) encourages them all to entangle coherently and unite into a bundle. It turns out, however, that bacteria can easily switch their motors to the opposite direction, which causes the flagella to separate, and also to flail about, (since for a left-handed helix, this is the "wrong" direction), sending the cell in random directions.

A typical bacterium with multiple flagella, which will cooperate in forming a bundle when all turned in the same direction, consonant with their helicity (i.e. counter-clockwise).

These are the two steering options for most bacteria- forward or flop about. And this choice is made all the time by typical bacteria, which can sense good things in front (keep swimming forward), or sense bad things in front / good things elsewhere (flail about for a second, before resuming swimming). The flagellar base, where the motor resides, uses both ATP and the proton motive force (i.e. protons that were pumped out by cellular respiration, or the breakdown of food). The protons drive the motor, and ATP drives the construction of the flagellum, which is itself a very complicated dance of self-organization, built on the foundation of an extrusion/injection system also used by pathogenic bacteria to inject things into their targets.

Animated video describing how the flagellum and its base are constructed.

But sometimes a bacterium really needs to get somewhere badly, and is faced with viscous fluids, perhaps inside other organisms, or put out by them to defend themselves. One human defense mechanism is a DNA net thrown out by neutrophils, a type of white blood cell. Spirochetes have come up with an ingenious (by evolution, anyway!) solution- the inboard motor. This is not a motor sticking out of the bottom, but a motor fully enclosed within the cell wall of the bacterium.

Choice of directions (small forward or back arrows) that are dictated by the rotation of the flagella (blue). One set of flagella originate at the rear, and a second set originates at the front. Only if they turn in opposite directions (top two panels) does the spirochete swim coherently, either forward or back. 

How can that work? It is an interesting story. Spirochetes, as their name implies, are corkscrews in shape. In mutants lacking flagella, they instead relax to a normal bacterial rod shape. So they have flagella, but these are positioned inside the cell wall, in the periplasmic space. Indeed they form the central axis around which the corkscrew rotates, with one set of (approximately ten) flagella coming from the rear and another set from the front, each ending up around the middle. If each set rotates as hard as it can, they drive their respective ends to counter-rotate, in reaction. If the front motors (of which there are several) turn their flagella counterclockwise, as viewed from the back, they will, in reaction, drive (and bend) the nose into a clockwise orientation. If the back set of motors run clockwise, driving their flagella counterclockwise (also as seen from the back), then the rear part of the bacterium counter-rotates in clockwise fashion, and the coordinate action drives spiral bending and an overall drilling motion forward.

Video of a non-spirochete bacterium with its flagellum stick to the slide, causing the tail to wag the dog.

Video of spirochete bacteria in motion.

On the other hand, if the motors on the opposite ends of the bacterium go in the same direction, then the flagella induce opposite, instead of coordinate, counter-rotations, and the bacterium doesn't tumble randomly, as normal bacteria do, but contorts and flexes in the middle, with a similar re-orienting effect. This ability incidentally shows the remarkable toughness of these bacteria, considering the lipid bilayer nature of their key protective membranes. These bacteria can also easily reverse direction, by sending both sets of motors in reverse, operating very much like little drills. How this exquisite coordination works has not yet been worked out, however.

Reconstruction, drawn from electron microscopy, of one end of a spirochete, showing the motor orientations, the sharp hook/base of the flagellum, the membrane and cell wall structure, and one of the signaling proteins (MCP), which transmits  a sensory signal to dictate the direction of motor rotation.

One thing that is known, however, is that spirochete motors are massive- almost twice the size of E. coli motors, with special outside hooks to propagate power through the tight turn inside the periplasmic space. It is interesting that these motors can be scaled up in size, with more subunits, and more proton ports for power, as if they were just getting more cylinders in a (fossil fuel-burning) car engine.

Structure of the Borrelia flagellar motor, showing the stator (blue), which is attached to the membrane and stabilized against rotation; the rotor (yellow spokes and teal C-ring), and the gateway ATPase complex which unfolds and transmits the structural components (proteins) into the central channel from which they build the machine.

All this is in service of getting through messy, gelatinous material. The model for most of this work is the spirochete responsible for Lyme disease. The characteristic red ring seen in that infection is thought to track the progress of the spirochete outward and away from the original tick bite site, in relation to the immune system catching up via inflammation. But such viscous environments are quite common in the organic muck of the biosphere, including biofilms established by other bacteria. So the evolutionary rationale for the superpowers of spirochetes is probably quite ancient.

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Psychodrama of the Reformation

Luther's personal demons drove the split of European Christendom. A second post from "Fatal Discord", a double biography of Luther and Erasmus, by Michael Massing.

It is hard to believe, but Martin Luther was ridden with self-doubt. That is what drove him to become a monk, to confess his sins for hours a day, and to search for a way out through the scriptures and other theological writings. When he came across Augustine, he underwent a sort of conversion experience which seems to have led to a decade-long burst of energy, rebelling against the Catholic church and pouring out a prodigious flow of theses, tracts, and books on his new evangelical theology, including a full German translation of the Bible. (It is worth noting parenthetically that in these early days of printing, the pamphlets and books brought out by Luther and his adversaries were easily as intransigent, abusive, and uncivil as our current twitterverse, an atmosphere that may have had something to do with the brutal wars that ensued.)

"Now, in reading Augustine himself, Luther found nothing about free will, good works, or doing one's best. Instead, he found stern pronouncements about human wickedness, divine majesty, and undeserved grace. If Augustine was correct, the selfish urges and prideful thoughts that were continually welling up in him represented not simply his own personal failings, but ingrained features of human nature. As forbidding as Augustine's theology might seem to others, Luther took great comfort in the idea that his fate was not in his own hands."

The issue was free will. If god creates everything, rules all, and sees all time, then how much power do humans have? None, obviously. It was John Calvin who took Luther's position to its full extent, arguing for full pre-destination of everyone's fate, with a decided minority pre-destined (elected) to enter heaven, and all others going to hell. The Catholic church, despite Augustine's influence, took the more practical route of claiming some free will, such that prayer, putting money in the collection plate, feeding the poor, and even buying indulgences, would all be put on the sinner's tab when they got to the pearly gates.

Opening page of Matthew from the Luther Bible, 1534.

It is difficult to run a society without rewards for good behavior, so while the Catholic church did not go the whole way to Pelagianism, it did run a middle course, rewarding (in the next world, at least!) good works, while also holding god to be super-powerful, just not all-powerful. Luther's epiphany that faith alone saves, and that good works count for nothing, solved his personal dilemma, and fueled his world-shaking rebellion. But it also left his parishoners with little incentive to do good works, or even to attend church. Luther was faced with continuing apathy through his later years in Wittenberg, reduced to berating his dwindling flock for its moral and religious laxity.

It was in the peasant's rebellion, starting about seven years after his electrifying theses, that the problems of Luther's theology really became apparent, causing self-doubt and confusion to creep back in, gradually sapping Luther's confidence, productivity, and influence. The peasant's revolt was driven by a new crop of preachers more extreme than Luther. If rebellion against the Catholic church for its worldly excesses and oppression was permissible, why not rebellion against the landowners and lords whose oppression was even worse, and whose theological support far weaker? And if all believers are priests, and all can read and interpret the bible, then why listen to the doctors of theology from Wittenberg? Luther was aghast at what he had unleashed, and turned completely around to support the nobility in this bitter and ugly fight, full of unspeakable tortures and massacres.

Luther continued to collaborate closely with the temporal authorities for the rest of his career, and the Lutheran church became a state-affiliated chuch, ridden with many of the same compromises and theological perplexities that characterize the Catholic church, and which Luther had originally thought he had escaped. The energy of the reformation would re-emerge in the Calvinists, Puritans, Methodists, Quakers, and countless other sects of which there are now many thousands. Purity is always energizing, but neither practical nor defensible in what is, in reality, a godless and complicated world. In the end, the attentive tolerance of humanism regularly turns out to be the better solution.

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The Peregrinations of Humanism

What happened to the project of Erasmus? What used to be solidly Catholic turned into atheism, aka "secular humanism".

Have there ever been non-secular humanists? Yes, virtually all were Catholic back when humanism was truly in flower, in the 1400's and 1500's. There have even been humanist popes! Humanism was a big theme of the Renaissance when Western intellectuals turned their attention to the languages and authors of antiquity with new vigor. The preceeding movement of scholasticism had built on an earlier encounter with Aristotle and Neoplatonism, which led to the founding of many universities and reached its peak in the output of Thomas Aquinas. But scholasticism was more concerned with conforming Aristotle to Catholicism and making a show of reasoned logic / dialog, (dialectic), rather than truly plumbing the depths of Aristotle's profound corpus and methods. They knew he was the intellectual giant of antiquity and far beyond their own achievements. Only with humanism was Europe ready to deal more deeply with the ancients.

This was a time when scholars started hunting in earnest for manuscripts hidden in cloister libraries, and encountered both manuscripts and scholars fleeing the now-defunct Byzantine empire. These scholars improved their Latin based on a wider familiarity with these sources, and started learning Greek and even Hebrew. Erasmus of Rotterdam was one of the greatest of these hunters and scholars, and turned his learning into (among many, many other projects) a newly corrected edition of the Bible, with Greek facing the Latin, the first time the Latin Bible had been (intentionally) revised in over a millennium. This story is told in the outstanding book, Fatal Discord- a parallel biography of Erasmus and Martin Luther.

Luther obviously runs away with the show, and the book, by fomenting a fundmental revolution in Western culture. Author Michael Massing suggests that Europe faced divergent paths, Erasmus representing the more liberal, reformist, and moderate course, which could have saved everyone a lot of trouble. Luther read Erasmus's new bible and other writings, was also inspired to learn Hebrew, and based much of his revolution on Erasmus's ideas. But Erasmus never renounced the Catholic church, and hated warfare above all other forms of waste and injustice. He was in this a humanist to the core. Luther was more of a fundamentalist, standing on Sola Scriptura- of his interpretation, naturally- come hell, high water, or martyrdom.

So what is humanism, after all? In a theological sense, it is attention to and learning from diverse aspects of the current and past world, in contrast to assuming that one's scripture contains all knowledge. If the world, humans, and human reason are all made by god, then this wider field of inquiry is not only permissible, but essential, to fully appreciate her work. On a pedagogical level, humanism became the program that Erasmus set up based on his thrilling scholarship- the learning of Latin foremost, from the great classical authors, and then Greek as well, along with rhetoric, grammar, and some logic- the Latin trivium, in short. While revolutionary in the fields of biblical studies, higher criticism, and philology generally, this program eventually fossilized into the "liberal" education in the classics that was standard through the 19th century, plaguing young minds with dead languages, long after Latin had lost its role as the universal intellectual language of Europe.

And on an ethical level, humanism is the sense that truth and scholarship must be beneficial, over their opposites, and that, in line with the rest of renaissance sensibility, human achievements and flourishing are the measure of social and theological systems. While the neoplatonists where quite consonant with the abstract, ethereal concerns of the Catholic church, other authors and ideas from antiquity were much less so, and the humanists, Erasmus as a prime example, turned into a somewhat skeptical if not critical community within the church, urging reform from the bloated, corrupt, militaristic, and intellectually lazy institution it had become.

This breakdown became evident in the confrontation with Luther. In response to his copious tracts, books, and theses detailing the problems of the church, its response was simply to assert that he was wrong, and that any opposition to the pope and tradition was inadmissible. The Catholic church failed to make a serious intellectual case, and it would take decades, if not centuries for it to do so. Book burnings were the first response, followed by the Index of banned books, which featured not only those of Luther, but those of Erasmus as well. This spelled the inevitable end of humanism in the Catholic church, since skepticism and intellectualism are incompatible with hierarchy and fealty.

Humanism had a much longer career in Protestant lands, with their greater freedom and diversity. Charles Darwin came within a hair's breadth of becoming an Anglican minister, and mostly viewed his naturalist interests in the positive light of god's work on earth. But they inevitably parted ways even here, as the mechanisms of nature gradually revealed themselves to be anything but divine. Now one hardly hears about religious humanism, as humanism has become synonymous with thorough theological skepticism and this-world ethics. What would Erasmus say? The EU has named its internal student exchange program after him, in honor of his pioneering role in promoting pan-European projects and intellectual community. He would have been appalled at the way the Protestant reformation bled Europe and led to ceaseless division. But I am sure he would still be in the intellectual, cosmopolitan vanguard, which remains humanist today.

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