Vietnam: the Good Fight

Maybe not wise or practical, but morally, Vietnam was justified, especially in hindsight.

It was culturally traumatic, and militarily disastrous. It was a collossal mistake and soure of bitterness for decades. The Vietnam war remains a touchstone of shame and division in the US; a toxic and momentous legacy in Vietnam itself. I saw the first several episodes of Ken Burns's treatment of how we got into that war, and found it very interesting, historically. The documentary's tone was drenched with sadness and tragedy. But it also let some significant facts leak in.

The problem was that the government of South Vietnam was a mess. It was essentially a successor state to the French colonial regime, while the government of the North was the successor of the successful independence fight, led by the communists / Viet Minh. The North capitalized on its credibility with effective PR, and before you know it, the South was overrun with Viet Cong and related insurgents, sympathisers, and agents, especially in the rural areas. And all seem to agree that Ho Chi Minh would have won the re-unification elections that were never held. But the North was not all it seemed. It was also a brutal communist state- a predator state. According to Wikipedia:

"The Socialist Republic of Vietnam, along with China, Cuba, and Laos, is one of the world's four remaining one-party socialist states officially espousing communism. Its current state constitution, 2013 Constitution, asserts the central role of the Communist Party of Vietnam in all organs of politics and society."

This, two decades after the fall of the Soviet Union, and four and a half since the end of the American War (Vietnam War). This is a durable system! While Vietnam has lately followed China's lead in adopting limited capitalism, we should not imagine that it is a free or prosperous country. It remains very much in the totalitarian camp.

At the time, the US had just been through a similar war, in Korea, another tough slog defending the South from a blitzkrieg by the North. In that case, the US and the South were successful, and now South Korea has transformed into a happy, rich country, exporting K-Pop off an assembly line that seems to have no limit. Meanwhile, North Korea has remained stable in its way- stably dictatorial and desperately poor.

These are the conditions that the US was consciously defending South Vietnam from, and we were very right to do so. Unfortunately, the French had so thoroughly loused things up, between their import of Catholicism, their moral blindness in denying the Vietnamese what they had themselves had just fought World War 2 to regain, their futile war in Vietnam, and their organization of the South under Emperor Bao Dai and Prime minister Ngo Diem, that propping up the South proved impossible. The US did not want to replicate the colonialism of the French, just to keep the South out of the communist hands. But as it turned out, we would have had to do so and run the whole country, indeed on a rather brutal basis, if we really had wanted to save the situation. The problem was never military, but political- the people of the South were so mistreated by their government that their will to fight, in the myriad ways one has to fight in a civil and a guerrilla war, had dropped to zero.

So I think we should recognize that the US was doing a noble and proper thing in this war. Leaving the South defenseless, or cutting and running after we had gotten involved, would have been expedient, but not morally good. However, in hindsight, those would have been the wisest policies, saving everyone a great deal of death and waste. But that is a different point, both from the moral perspective, and given that hindsight comes too late. We can grant that many people, not least of whom were John Kennedy and Lyndon Johnson, recognized to some degree the bad, almost futile situation they were getting into. But while we can doubt their wisdom in not following their own analyses with greater discipline and political courage, their moral purposes were not bad ones.

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Measuring Genetic Fitness

Yes, it is a thing, and is quantitative. But it can be hard to measure, especially when genetic epistasis enters the picture.

Biological fitness is often thought about in nebulous terms, as unquantifiable, even taboo. But in genetics, it has a specific and quantifiable meaning- the likelihood of a gene, organism, or other unit of study to make it into the next generation. For example, an antibiotic resistance gene may have very high fitness in a bacterial population under antibiotic pressure, and also confer high fitness on its host organism as a whole. In those terms, fitness is measurable and quantifiable, especially for tiny laboratory organisms which reproduce quickly, have relateively few genes, and are easy to measure and manipulate. But it can be very difficult to evaluate elsewhere, and not just because organisms like us reproduce slowly and have lots of genes.

Fitness as a concept typically applies to deviations such as mutations, or sub-populations or sub-species, against a background of normal (i.e. wild-type) gene / whole population. It a measure of difference from the norm. The wild-type organism would have a fitness of 1, and a mutant with, say, a fatal developmental defect, has a fitness of 0. For a population, the collection of all fitness values is called the fitness landscape, the average being 1, but the deviations being very significant, as we know from our own populations. The population having some complex landscape of more and less fit individuals evolves through time with more fit genotypes gaining population share, and less fit genotypes (by definition) declining. One of the major functions of sexual reproduction is to continually re-arrange the fitness landscape to a more diverse and dispersed state by mixing and recombining genotypes, so that much of the deleterious mutational load of the population ends up segregated to low-fitness craters in the landscape, and is disposed of efficiently. But the same token, beneficial alleles can be more rapidly combined to reach fitness peaks.

A notional fitness landscape, from low (blue) to high (red). Populations with sex/recombination (a, right) have a much faster path to fitness peaks within this landscape. Note also that this is a very additive landscape, without epistatic or other complex genetic effects.

When considering the fitness value of individual genes and their combinations, the starting assumption is that they will be additive. That is, the quantitative fitness value for, say, an altered hemoglobin that allows survival at higher altitude will be independent of, and additive with, the fitness value for being able to consume yak milk in adulthood, via changes in lactase enzyme expression. But the fitness of one gene often affects that of others, an interaction that geneticists call epistasis. If I have a genetic propensity for alcoholism, and also a genetic propensity to liver failure, the combination, while conceptually and mechanistically independent, may end up far more lethal than either one would be alone. One extreme form of epistasis is synthetic lethality, where two mutations that are individually tolerated turn lethal when they occur together. Since everything in organismal biology is to some degree connected with everything else, epistasis is very common, and thus fitness values or, similarly, disease prognostic effects that we might be interested to determine for various allele variants, (i.e. mutations), as seen increasingly in the diagnostic clinical setting for humans, can be very tricky to estimate.

A recent paper advanced the measurement of fitness in complex genetic situations and from practical forms of data. It is naturally difficult to measure fitness across whole genomes and populations. Typically, an observation is made of relative fitness for an isolated gene/allele, where one mutation outcompetes another, in a shared genetic background (using model organisms). This ranking or rank-order style of data is far more accessible and thus more common than are detailed calculations of absolute fitness. This is true for single genes, and even more true for complex combinations that may exhibit epistasis. Yet the rank-ordering of fitness for alleles, genotypes, organisms, or other entities remains a very rich source of information, which the authors exploit to find novel epistatic effects.

Epistasis = ( w00+w11) - (w01+w10), where fitness is "w", and the genotypes are 00 (wild type), 11(double mutant) and 01, 10 (each single mutant). Epistasis, i.e. the deviation from additivity, can be positive or negative, and is quantitative to the extent that the fitness values they are based on are quantitative. The figure below gives a very simple example that indicates epistasis between two loci on the basis of very minimal fitness data.

Depiction of two known rank-order fitness relationships, and a conclusion of epistasis from such minimal / partial data. Arrows point towards higher fitness, and show ranks, in a rock-paper-scissors kind of sequence. Highest fitness is at the top, and least is at the bottom. We can already see that something is not additive, as one of the single mutants is more fit than the double mutant, while the other single mutant is more fit than the wild-type. If all effects were additive, the advantageous 01 mutation would not make the 11 double mutant less fit than the 10 single mutant.

Taking this to more loci and complex relations, the authors venture into Dyck numbers, graph isomorphism, Walsh coefficients, and other obscure methods to organize these rank analyses, and come out with computationally easy ways to analyze all this for any number of loci, to help geneticists make sense of what patchy / partial data they may have at hand.

Antibiotic resistance shows clear epistasis. Among four mutations relevant to antibiotic resistance in the TEM-class of bacterial antibiotic resistance gene, (a beta lactamase common in hospitals, in E. Coli, H. influenzae, and N. gonorrhoeae), having all mutations (TEM-50) is most resistant and thus most fit, but surprisingly, no single mutation (TEM-84,-19, -17, -33) confers better resistance than having none at all. But honestly, one didn't need a computer to figure this out.

"Although we have applied our method here only to fitness, any other continuous phenotype of interest can be analyzed in exactly the same manner. The fitness landscape w is then replaced by a more general genotype-to-phenotype map. For example, rather than using it as a fitness proxy, one may be concerned about the drug resistance phenotype itself and its genetic architecture."

We will soon have our complete genomes at hand as a normal part of our medical record. This will uncover an ever-growing list of deviations and oddities, whose significance will be the subject of many decades of study. The work above is just one of many kinds of methods that will be attempting to make sense of our genetic variations, with the goal of peering into our medical and inter-generational futures.

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Theory of the Predator Class

A review of Thorstein Veblen's "The Theory of the Leisure Class."

The Occupy movement seems so long ago. The most durable movement to come out of the 2008 economic crash seems, in retrospect, to be the Trumpian revisionists- the Tea Party / Santelli Republicans who alchemized a total breakdown of financial markets and lack of proper regulation into a movement to hobble government even more, and increase inequality over its already breathtaking levels.

The fight between the predators and the prey, however, is perennial, from our most ancient records of Greek cities, between the oligarchs and the demos. The last century saw the most vociferous and ideological movement against inequality and aristocracy, in the form of communism. Sadly, that turned out almost as badly as the royalist/aristocratic/capitalist propaganda portrayed- an appalling recreation of status-ridden tyrannies, with the added insult of thorough-going inversions of truth, in the name of a worker's paradise.

But before all that, in 1899 Thorstein Veblen published a classic critique of the aristocratic system and its capitalist derivatives, whose leaders he called the "leisure class". It laid the foundations of institutional economics, was a scathing re-analysis of the class and economic system of the time, and prefigured many later developments, such as feminism and our continued inability to distribute our enormous wealth equitably with the consequence that the vast majority remain highly dependent on jobs and salary for sustenance, living more or less hand to mouth. Unfortunately, his writing is quite pedantic. But it is also archly sarcastic, so much so that it becomes a sort of a comic masterpiece. Here he describes the role of religion and its various officers and adherents as an example of economic (not to mention intellectual) waste sponsored by the aristocratic elements of society:

"While belief is by no means confined to the leisure class, that class to-day comprises a disproportionately large number of believers in the occult sciences of all kinds and shades. By those whose habits of thought are not shaped by contact with modern industry, the knowledge of the unknowable is still felt to be the ultimate, if not the only true knowledge."

The leisure class is in Veblen's system the predators of society, lineally decended from the owners, kings, chiefs, and nobles of yore. They live by the work of others. Their need to show status is not reflected in useful activities or service to the collective, but in waste- the waste of time, of money and especially of other people's time, which all goes to show their power and position. Their servants are dressed just so, their wives do not labor and conduct futile charitable activites. Their religions are devoted to a supernatural leisure class which lives even more wastefully than they do, intermediated and officered by an utterly useless class of theologians and priests. Their scholarly institutions are likewise based on theological origins, study useless things, (Veblen's time period was the late 1800's), and adopt finely graded and conservative ceremonies of punctilious status, all to show the capacity of the sponsoring and attending aristocrats to waste prodigious amounts of time and resources.

The sad part of all this is that the aristocratic class leads the society in a ladder of wasteful emulation. Like the British royal family, or its more modish incarnation in the James Bond character, the class with little to do but waste its time forms the inescapably rivetting spectacle and model of the ideal life, and thus what the lower classes should aspire to. Naturally, this is abbetted by native greed and ambition, for all aspire to be not just like the leisure class, but part of it. This leads to endless consumption and living beyond one's means, ironically sabotaging the very goal of gaining the wealth required to gain entry. In this way, the upper classes unconsciously collaborate with the middle and especially lower classes in a conservatism that perpetuates an invidious system.

"From this proposition it follows that the institution of a leisure class acts to make the lower classes conservative by withdrawing from them as much as it may of the means of sustenance, and so reducing their consumption, and consequently their available energy, to such a point as to make them incapable of the effort required for the learning and adoption of new habits of thought. The accumulation of wealth at the upper end of the pecuniary scale implies privation at the lower end of the scale."

While historically, the predator class served as the warrior class, gaining land and wealth for the group as a whole, that function is now (with any luck) in abeyance. Thus their predatory instincts are turned exclusively inward, towards engines of capitalist fleecing, of government corruption, and the like, in order to maintain wealth and status. That they would receive the free sanction of a democratic people to run roughshod over the land, as happened in 2016, may be unimaginable to contemporary intellectuals, but might not be to Veblen himself, who had a relatively pessimistic view of human nature and institutions, including its tendency towards conservatism.

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A Moronic Foreign Policy

Trump accomplishes the opposite of what he claims. But Putin would be so proud!

Is America great again? Apparently, we are getting there very fast, even faster than orginally envisioned, according to our President, who is also a very stable genius, with an extremely large button. But for some reason we are also a world-wide laughing stock, headed by a moron whose erratic spleen is vented daily on Twitter, who can't read more than a few sentences at a time, who lies compulsively, and whose wanna-be mobster management style is pathetically at odds with any trace of professionalism. His vision of greatness seems to be letting corporations and the rich (such as himself) run roughshod over everyone else. How long that will play with his base is anyone's guess. But the worst consequences of Presidential intelligence and temperament (or lack thereof) are, as usual, on foreign policy.

The US has been leader of the free world, and the industrialized world, since World War 2, and arguably since World War 1. We have been the indispensible nation, the leading economy, and the leading culture of the 20th century. We faught a drawn-out and bitter Cold War with the main ideological and geopolitical adversary, communism, which ended with the latter's complete implosion. Russia has reconstituted itself along Tzarist lines, while China has reconstituted itself along similar capitalist/authoritarian lines, but without the personality cult at the top, at least until the current president, Xi Jinping. These former communist countries have learned from each other, and from the West, to arrive at their current blend of corrupt, Orwellian one-party rule, combined with substantial personal and business freedoms. And China is growing at a clip that will make it the largest economy and leading world power in a matter of decades, if not years.

This is the current competition that we face as a governing model- one that is attractive to smaller countries like Pakistan, the Phillipines, Iran, and many others. It is a time of flux, and our leadership, while not as central as in the fight against communism, remains critical if real democracy is to supplant fake democracy. Yet our current administration is pedaling as fast as it can in the wrong direction. It is itself beholden to Russia for its existence, and the President conveys his admiration for Vladimir Putin as often as possible. It embodies precisely the same style of corrupt, authoritarian, nepotistic, and predatory tendencies as the countries we least want to emulate.

In foreign policy, this administration has been sending a lot of mixed signals. This on its face is bad foreign policy, and contributes directly to a decline in global leadership. But it is understandable, as a war plays out within the White House between the President's terrible instincts, and the obvious interests of the US as represented by his hand-picked military policy staff, by a withering State Department, and by whatever other sane people remain. So we have been making enemies on a daily basis. The President promised that he would solve the Middle East, and the Israeli-Palestinian problem. Who knew that meant giving Israel whatever it wants, and giving the finger to any notion of a peace process? The pissing match with North Korea has been both futile and contemptible. We have relinquished whatever slight claim we ever had to leadership on global warming. The sudden attack on Pakistan, while eminently understandable, was also unnecessarily bombastic. The attacks on NATO and Europe, though since reeled back by his handlers, have been very damaging to the notion that the US has anything futher to do with the future of Europe. Mexico? Don't even ask.

In sum, we are retreating from greatness on a daily basis, becoming a smaller, petulent actor on the world stage, at a time when our values are under the most subtle attack, and when competing models of governance have found new footing after the communist debacle. We seem to be rushing to join them, rather than standing for enlightened values of truth, decency, and equality.

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