Saturday, August 26, 2017

Mass Transit is Pleasant Travel

Let me count the ways.. I love mass transit.

Love to drive? Some people do. But do you love to drive in LA? The pleasure of driving goes down dramatically in congested conditions, where what was once a carefree sail down the freeway turns into a white-knuckled fight for free space, slowing to a frustrating crawl through a baking, exhaust-filled parking lot. Then there is the fear of accident and injury. Every day, the radio traffic report provides bland "injuryaccident" reports from the metro area. Driving has turned into a nightmare.

The US has not built significant infrastructure, particularly roads, for decades, and it shows in worsening traffic conditions. In parallel, housing prices go up, thanks to an unwillingness to zone for growth in housing as well as in traffic. Yet our population still goes up, despite the sclerosis in public policy. What can be done?

Entering BART trains is easy...

Some urban areas have an answer to the car, and it is mass transit, either by train or bus. The New York subway system ridership has gone up steadily, and is now at 5.7 million per day. The Bay area subway system, BART, has also experienced strong gains, to half a million riders per day. All this despite the growth of ride-share services which, while they may relieve the user of the task of driving, do nothing to resolve the uncertainty and unpleasantness of congestion on the roads.

I have recently switched to transit for a long cross-Bay Area trip, and it has been a revelation. Gone is the road rage and isolation, replaced by abundant people-watching and the ability to just look out the window, or rest (or work). The occasional stress of making a properly-timed bus or train is significantly less than the constant stress of preventing death or collision in a car. Granted, the seats are rarely very comfortable, and not everyone is friendly, or even sane. But on the whole, it is an easy call, especially since the direct costs are almost precisely the same, even before amortizing the cost of the car itself, not to mention those to the planet.

  • Is Afghanistan a satrapy?
  • Afghanistan: rural areas are important, Pakistan is still bad.
  • Pakistan: "Who, us?"
  • Science- broken, or not so bad? And do different fields have different standards and forms of corruption?
  • Our media maelstrom.
  • This just in: insecticides kill insects.
  • Bullies and jerks.. why?
  • Workers will still get the shaft.
  • Russia is still there.
  • How far will denialism go?
  • Environmental graph of the week: California electricity grid during the eclipse. Overall peak demand is about 40,000 Megawatts, so solar generation provides roughly one quarter of peak demand in the state.
The California Electric grid, 08/212017, 5 PM (top), compared to the day before (bottom).

Saturday, August 19, 2017

School of Hate

13 Reasons and the dark side of high school.

Why all the hate? Hate has elected a president, and is his tireless message over the twitter-waves. Hate is loose in the Muslim world, in a campaign to instill fear in its enemies. We seem to be prone to it, and can be consumed by it, unawares.

I have been enjoying a Netflix series, thirteen reasons why, which incidentally was partly shot in my city. The titular reasons are ones for suicide, of the main character Hanna. And they are recounted by her in tapes being played after the fact, as the series progresses, by her best friend, Clay. Generally, the production is not very innovative, but the flashbacks and dream sequences are done with great care and style.

Its topic is how horrible high school is in America. Leaders of Britain may be formed on the playing fields of Eton, but American leaders are formed in the hallways and locker rooms of our public high schools. Which are not a pretty sight. The series is a very frank, if lavishly dramatized, look at how teens jockey for power and status, mostly by running down and terrorizing their schoolmates.

Most obvious are the jocks. Having bought into the official / corporate / archetypal system of status through athletics, they are children of privilege, loved by the administration, confident that even if they are not liked, they will be popular anyhow- that is just the way the social system works. They don't come off well in this show, giving in to every amoral whim from booze to bullying to social media meanness, thoughtless when they are not being mean.

From there, we go on to other dramatic dilemmas, of closeted gay students, stalking photographer, catty ex-girl friends, and so forth, salted by a variety of subplots among the adults, like the big-box "Walplex" taking over the town and the school administration covering its ass from Hanna's parents' lawsuit. Hanna was evidently failed, if not terrorized, by a fair proportion of the student body among others. I have not gotten to the end, but she will clearly have plenty of reasons when we get there.

Clay in class

But why is hate so easy? Is hate fun? Is it natural? Yes on both counts. Fascists know well that crowds and hate are a potent, even easy, combination. But it is also one of the most primitive, selfish, and useless emotions. Children hate quite easily, and have grievances that erupt into towering emotion. Growing up means putting a lid on them, so that we can work with all sorts of people, and work effectively without getting side-tracked by emotional baggage. We have created a emotional petri dish for teens by concentrating them in schools, with lots of leisure time, and little serious work. No wonder that the devil finds them such easy prey. Which is to say, their childish emotions, not quite under control or under moral direction. That we elected such an immature person as president speaks to a larger failure of our educational system- that it has failed to advance not just one, but far, far too many US citizens to an emotionally healthy and insightful adulthood.

All religious traditions have technologies of controlling hate, even if they then channel it to their own ends. Buddhists take the most uncompromising approach, decyring all such emotions as false, and engaging in lengthy love-inflected meditation to expunge such thinking. Yet Buddhists have had their wars and hate speach all the same- pacifists have a problem when faced with adversaries more willing to hate than to love. Christians have an ethic of love, yet hatred of Jews (how ironic!) flourished for centuries all the same. Muslims have the Sufi branch, their relatively pacifist brethren. But on the whole, Muslims have a simple and straighforward relation to hate- a deeply tribal approach where infidels are hated, and believers are loved. Except when they are of other sects, in which case they are hated anyhow. The Middle East is about to blow up again, along the Saudi Arabia - Iran axis of hate. So religions are a useful source of ideas and methods of human cultivation, but by no means the or a general answer to moral teaching.

Is it good that American school students go through an education in bullying, hate, and power politics? Most make it through OK, and many find highly positive environments where they find support and direction towards a happy adulthood. Does sobering, even terrorizing, interaction with the dark side build maturity, as it does in fairy tales and dreams? Perhaps so, but the costs are enormous, since many children do not make it out whole and unscathed. Simply put, children do not make a mature society when left to themselves. The under-adulted structure of public schools leaves quite a bit to be desired, in that it does not sufficiently occupy or guide young people.

Saturday, August 12, 2017

Genocide, Lebensraum, and the American Dream

Overpopulation is the normal condition, with intermissions after genocide.

As a recent article pointed out, the American Dream has undergone some changes. Where in the Depression, it was an idea of human decency, equal opportunity, and basic living standards for all, it has more recently become more focused on a prosperity gospel, with owning a house as the centerpiece of "making it". This presents great problems, since our society has become so sclerotic and unequal that defining our civic values by such inflated metrics leaves a very large and increasingly restive population behind. One hears echos of "Let them eat cake".

Long before either epoch, however, the American Dream was one thing- free land. Land for the desperate paupers of Europe, land for anyone willing to work, land for the taking and "proving". Rich, beautiful, verdant, and virgin land. With occasional interludes for gold rushes where the free-for-the-taking wealth was underground rather than on the surface. It was a Dream built on the genocide and dispossession of the previous occupants of all this land- the Native Americans. While most of that work was done silently by European diseases, the nascent colonial states were not shy about cleaning up the loose ends, with a manifest destiny of taking ownership of all useful lands of any kind across the continent, leaving the native peoples, when they were not killed directly or by mistreatment, in reservations on the most miserable land available.

Why, then, were we so exercised about the policy of the Nazis in the next century to spread eastward, over the great prairies of central Europe, in search of "Lebensraum"? Was it that those prairies were already occupied? Or was it that they were occupied by people significantly more similar to ourselves, not susceptible to the European diseases, and aready farming, and ready to complain in comprehensible languages? That of course is a bit unfair, since the Nazis authored a much wider range of mayhem, through Europe and world-wide, than just their push to the East. But it is worth re-evaluating our national epic and mythology in this light, since it brings out fundamental forces that recur through history, and promise rocky times ahead.

As Thomas Malthus observed, the natural state of any population of organisms, including humans, is overpopulation. Remissions of this state can happen by predation or catastrophe. Genocides, devastating wars, plagues, droughts, and the like can provide brief respite from this normal, cramped condition. The discovery of the Americas by Europeans was one such event, (as it had been for the Clovis people and their predecessors as well), providing an escape valve, given a total lack of compunction about stealing the lands of others. Another such event has been the technological development of the West, especially our use of fossil fuels, which have magnified our powers and particularly our farming capabilities, with new fertilizers and machinery. This has meant that through the last roughly 300 years, we (especially in North America) have faced a substantially relaxed Malthusian constraint compared to most human cultures. I recently read the biography of the famous jocky Ron Turcotte, who narrates his childhood in New Brunswick thus:
"We have four kids. A big family now is six. Back then, when we were growing up, families of twelve or thirteen were common. One family had twenty-three. We had a very strict priest. if you didn't have kids, you weren't doing what God put you on earth for." ... "The priest would come in, and if there wasn't one baby in diapers, one in the womans' arms, and one in the oven, he'd say the couple was not doing its Christian duty."

So here we are, at a state of dramatic overpopulation, using the lands, air, and minerals of earth far, far beyond her ability to sustain us, using fossil fuels which can never be replaced and which are heating the climate and destroying the biosphere. In the US, we are coming to a state of culture and class war that is a sign of stasis/crisis. The pie is not growing bigger. Overpopulation generally means, culturally, that there is an excess of workers relative to productive capacity, which gives power to capital and those who already have power. It is the kind of situation that leads to inequality, castes, feudalism, and sclerosis.

There are no more frontiers, and we are already living far beyond earth's carrying capacity. By the natural processes of selfish greed, our home is turning into a dump. For example, we are not, in all honesty, close to resolving our carbon dependence, among many other limitations- emissions are rising, not falling, let alone reversing damage already done. In the US, our population is rising relentlessly, yet we have not built significant roads for decades, or even maintained the ones we have. For various reasons of self-interest and cultural drift, we are collectively unwilling even to face up to the population we have, let alone make room for more, were that even desirable. So until we resolve our long-term sustainability issues, we should focus on population reduction, ideally with a universal one-child policy.

While the American Dream has narrowed to one of personal greed, we are at a point when we can and need to think globally, for the long term. The dream should be one of sustainability, over hundreds and thousands of years, given the momentous consequences of our current technologies and lifestyle. Giving in to rampant population growth, however natural it may be, dooms us to an ever more impoverished country and planet. It would be a tragedy, alongside the related tragedies of denying the very reality of climate change, and weakening our scientific and social consciousness of its future course and consequences.

Sunday, August 6, 2017

An Egg Asks: Which Way is Up?

One of the prototypical morphogens, bicoid, tells fly eggs what's head and what's tail.

Translating the digital instructions of the genome into an actual body is the complicated work of development. It is obvious that the instructions are not explicit or specific, mapping out where every organ, cell, and molecule is supposed to go. Rather, the code provides ingredients and rough guides to channel development in favorable directions, relying heavily on implicit, default processes to fill in the details.

One way to amplify a digital code is to use a morphogen- a substance with an analog character, whose concentation varies with location and can give many of those locations different instructions. Morphogens are used extensively in body and brain development, and one of the first to be found genetically was bicoid, one of the proteins responsible for telling Drosophila eggs which end is anterior, and which posterior. The name comes from bicoid mutants, which end up with two tails (bi-caudal) and no head- naturally a fatal condition.

Effects of a complete bicoid deficiency.

Bicoid mRNA is deposited by the mother in eggs in a strongly asymmetrical fashion, at their anterior poles, so they are pre-oriented. When the egg is fertilized, this mRNA starts getting translated / expressed into bicoid protein, which is the actual morphogen. This is a DNA and RNA-binding protein, and regulates the expression of other genes. Bicoid expression is inhibited in the posterior by the protein nanos, which is concentrated there. Conversely, bicoid inhibits the expression of caudal, another protein that is concentrated in the posterior and directs posterior cell fate. Bicoid regulates at least 70 other promoters/genes to activate anterior cell fates, among them the next levels of location specificity genes, the gap (hunchback, giant) and pair-rule genes (krüppel, even-skipped). The interplay of numerous positive and negative regulators of this sort, others of which take over subsequently at ever finer levels of detail, creates a relatively robust system of cell specification which allows bodies to be made consistently under a variety of temperature, nutritional, genetic, and other conditions. For details, the fly community resource is valuable, as is a reference work.

Expression of some key genes in fly embryos, bicoid at anterior (left, blue) and caudal at right (red). Evx (yellow), is a relative of even-skipped, both pair-rule genes that specify finer segmental-scale divisions in the embryo than do bicoid or caudal.

A recent paper used new methods to study the activity of bicoid in detail, turning it on and off at will. They replaced the normal version of the gene with one carrying two extra protein sequences, one of which rendered the protein conveniently fluorescent (in red), and the second of which, on exposure to light, binds to other proteins in the cell, typically turning it to an inactive state. This engineered protein provided normal bicoid function when the flies were raised in the dark, but turn on the lights, and activity dropped immediately, allowing study of exactly when it is needed, and for what. Unfortunately, this turn-off only applied to one of the protein's activities, its transcriptional activation. Its second activity, of translational repression (of caudal, among other genes) was unaffected by the light-switch protein fusion.

It had not been understood just how long during embryogenesis bicoid is needed, whether only at the start, or ongoing through many stages. What these researchers found is that bicoid is needed into surprisingly late stages, to within 10-30 minutes of gastrulation, which is very roughly the midpoint of early embryogenesis that goes from egg to hatched larva. What is bicoid doing through all these later points in time, when its fundamental job was simply to instruct the next set of location-specific genes, the gap and pair-rule genes, where to turn on- a job that is over long before gastrulation?
Impact of brief light exposure (i.e. shut-down of bicoid) on development. Note that even the briefest interruption, for 10 minutes just prior to gastrulation, causes mal-development of the anterior-most (left) head section, comparing B' and C'. "n.c." refers to nuclear division cycles, which are a standard / convenient way to time the progress of these early embryos. Proteins stained are engrailed (En), deformed (Did), sex-combs reduced (Scr), abdominal-B (Abd-B), and (not stained), ultrabithorax (Ubx).

It turns out that many genes and cell types of the anterior have evolved in the presence of bicoid, and so have come to depend on its presence. Genes farther back in the fly have to make do with lower levels of bicoid protein, are more sensitive, and need its actiavtion more briefly (such as the mid-section gap gene krüppel). But in the anterior, the large and durable amount of bicoid has fostered a dependence well beyond the early roughing-out of the segmentation pattern. For example, knirps, a gap gene with head expression, is highly sensitive to bicoid activity and plays a key role in anterior fate specification, needs bicoid activation right up till gastrulation.

Length of time bicoid is needed, with respect to position in the embryo. The colored lines depict when bicoid is required in the corresponding segment(s).

"A minimal 20 min illumination at the end of n.c. 14 abolishes the expression of the Knirps anterior domain (Kni1) capping the tip of the embryo, as well as the first Giant stripe (Gt1). "

While not terribly pathbreaking in its conclusions, this work shows progress in the level of detail being studied, enabled by remarkable technological advancements. The authors even resort to computer modelling to make sense of the complex network of regulators, only a few of which were touched on above. Fruit flies have been the leading model system of animal development for over a hundred years, and are still going strong.