A Crime Against Humanity

Climate protection is the moral issue of our time.

One Christmas book that came my way was "Facing Climate Change", by Jeffrey Kiehl. It is a Jung-meets-the-climate-problem book. Evidently we should all hug a tree and get in touch with our Selves. It is, in short, preaching to the choir, and that in the gentlest possible way.

While the problem is principally psychological, the climate problem will take more aggressive thought and action to solve. At the same time, it is soluble. A recent New Yorker article focused on negative carbon- ways to remove CO2 from the atmosphere, which is what we need to have any hope of keeping biospheric catastrophe at bay. It will take country-sized infrastructures and improved technologies to solve, but is solvable. Given the collective will to solve it, there are plenty of policy and technical tools at our disposal.

The main problem is neither technical nor depth-psychological. It is moral, and reminds me of slavery in the US, and the resulting Civil War. Both sides knew it was wrong, and both sides benefitted from it economically. One side had the moral fiber to stand up and say that slavery was wrong, so wrong that it needed to, at least, be confined to the South, and ideally, abolished as an institution. The abolitionists were viewed as extremists and whackos at the time, unrealistic, weak, and sentimental. The other side prevaricated, rationalized, and ultimately fought tooth and nail to keep that system of incredible rapacity, greed, and injustice intact.

We are all implicated in climate change. We all know it is real, even if CO2 is invisible and its consequences relatively nebuous and distant. Denial, among the denialists, is but a stage of grief, for the greedy and wasteful freedoms we all grew up with and would like so much to maintain. The current Trumpian moment is one last hiatus from reason and responsibility, the dead end of an old and immoral regime. The US limped on for decades through the slavery crisis, reaching compromise after compromise, in hopes of saving a divided nation from the bloodbath that came. We have so far limped through two and a half decades, more or less, from the time when global warming was widely recognized, with analogous, if less heated, controversies, denial, and compromises.

Temperatures, decade by decade, and getting hotter.

Thankfully, addressing climate change will not require a war. Those poor nations most affected by it are far more likely to yearn to join the polluters than they are to start a war agaist them. In the US of the eighteenth century, the slaves likewise did not revolt in any successful way- the issue was not pressed by its victims, but by morally engaged onlookers- the abolitionists. Those economic interests most entwined with fossil fuels, at least in the US, are not politically independent, and while their corrupt influence is enormous, they are not unreachable by democratic governance.

What we need is a clear moral statement about the matter, in the vein of Uncle Tom's Cabin. That novel cast a new, brutal light slavery as it had never been lit before- as morally depraved and unsupportable by any civilized person. Climate change is a crime against the biosphere and against future generations of humanity, of vast proportions. We are slowly destroying whole ecosystems and ways of life, and robbing our children, en masse and comprehensively, of a healthy biosphere.

Al Gore started the process with his "Inconvenient Truth". It established the problem as undeniable, and moved many people with its moral urgency. But evidently we need more- a more compelling statement of the impossibility of being a moral person while denying climate heating or leaving it to someone else to solve. Most Americans agree, generally, but not with the urgency that leads to voting or action, and those who are most powerful seem to be most irresponsible on this front. Thus we are very close to a tipping point, and defining the issue with greater moral clarity could push us towards action.

Polar bears can help, but images and anecdotes are not enough.. there has to be a stronger comprehensive narrative around the issue.

With slavery, the logical end point was clear, even though it was also highly unpopular- the full enfranchisement and integration of African Americans into American society. With climate change, arbitrary lines have been drawn, but need to be periodically re-drawn as we spew our way through CO2 concentration limits and temperature thresholds. Two degrees? Or two and a half? This is one more way that this problem is devilishly easy to ignore and evade. The accords that have been reached so far, in Kyoto and Paris, have fallen far short of what is needed, and the only way to change that is through moral suasion- making it morally impossible to do otherwise than what is responsible to our future selves and progeny.

• Regulations? We don't need no stinkin regulations.

Pterosaurs

Yes, they really did fly- the amazing world of pterosaurs.

National Geographic recently had a beautiful spread on pterosaurs- those ungainly creatures that nobody thought could fly, until, apparently, we realized they really did fly. Indeed, they ruled the skies for over 160 million years- far longer than birds have. They operated a good deal like bats, with wings of membrane spread between modified fingers, which also stretched back to their legs. But a crucial difference is that, unlike bats, pterosaurs used only a modified fifth finger to carry the outside of the wing. The other fingers made up a strong hand about mid-wing that could be used for walking and lifting off. Thus pterosaurs were much better walkers than bats, and could also lift off from a standstill more effectively.

Reconstruction of the largest known pterosaur, Quetzalcoatlus, as tall as a giraffe, from the late Cretaceous.

What remains astonishing is how much apparent weight these animals carried, especially in front. The largest known pterosaur, Quetzalcoatlus, weighed about 440 pounds and had an enormous head. The head may have been quite thin, but, with neck, takes up roughly half its length. All pterosaurs tended to have large heads, and frequently added remarkable crests or horns, as if snubbing their beaks at aerodynamics. But looks are deceiving, since, like the toucan's bill, pterosaur crests and bones are hollow, very thin (1 mm), and thus were very light. The classic Pteranodon, with a crest almost as long as its enormous bill, is estimated to have weighed only 25 pounds, easily carried by a wingspan of 25 feet. Whether they could have carried off the hapless Zara Young is another matter.

Beautiful specimen of Rhamphorhynchus, from the Jurassic, with impressions of wing and tail membranes.

What is almost as compelling as the fossils of pterosaur bones are fossilized trackways, which show them in action. Over thirty walking tracks have been found, and one paper even describes what the authors interpret as a landing track. Typical pterosaur walking tracks show the heavier hind feet on the inside, and the wing/hands much more lightly on the outside. At each stride, the rear feet pull up roughly parallel to where the wing/hands have just left (b, in the figure). In these novel tracks, which begin abruptly, there are only hind feet for two strides, before the wing/hands appear. Secondly, the first hind feet tracks have elongated claw marks. Thirdly, the first two or three hind foot track sets are parallel and show a very short stride, different from typical walking gaits, of which the rest of this track is an example. These characteristics all lead to the idea that this pterosaur was landing, and hopped a couple of times with both feet before transitioning to a walking gait.

150 million year-old tracks from France. Top is an interpretation of the middle tracks, as evidence of landing. Below is a typical walking sequence and interpretation from the same location / source. The scale bar at bottom is 10 cm, so this pterosaur was relatively small.

This is not new work, dating from 2009, but the message is still a little hard to wrap one's head around- that tens of millions of years went by with these incredible creatures carrying on the battle for survival, with great success, and high style as well.

Nyctosaurus gracilis, reconstructed, from the late Cretaceous.

• A dumber nation- Thanks, Scott Pruitt!
• Xmas notes on another flying life form.

Structure of the Polytene Chromosome

Fly researchers have had a special microscope on their genetic subject for a century. Now we know why.

The DNA of our cells is enormous, and at the same time it is microscopic. Our 3 billion basepair genome is six feet long. Yet each of our cells contains a copy that is exquisitely wrapped up and so difficult to observe that it took X-ray crystallography and decades of experiment and inference to divine its true nature. Fruit fly researchers had a significant head start, however, with their recognition that a few fly cells make a form of their genome that can be observed with relative ease.

A "squash" of Drosophila polytene chromosomes. The upper left inset shows condensed normal mitotic chromosomes for comparison- they are very small. What do the bands signify?

Polytene chromosomes are made by larval insects in their salivary glands, apparently for the purpose of amplification of gene expression. Rather than develop ways to super-express the salivary protein products they need so much of from the usual single DNA copy, these cells re-duplicate their DNA many times, (about 1000-fold), while keeping it joined in a sort of synaptic alignment, which would normally only be apparent during cell division. They can then express selected genes to high levels with less regulatory effort. These "on" genes are apparent as puffs in the chromosomes when they are prepared with special stains and visualized under a regular microscope.

A "puff" of opened and expressing DNA is visible at upper left. The three panels are 1: staining with a general fluorescent DNA dye (green) along with a specific red dye targeted to a gene of interest (red; see arrows- this was a DNA-primer-based detection, so quite direct). 2- the customary orcein / Giemsa stain for visible light microscopy. 3- a light filter specific for the fluorescent red dye in the first panel bring out its locations.

The great Red Book of Drosophila genetics offers a comprehensive mapping of genes with respect to the "cytology" of these polytene chromosomes. The figure above was prepared by modern molecular biology reagents, which makes locating a gene of interest easy. But before all that, genetic mapping was done by tracking visual changes in the polytene chromosomes and mutations that befell gross genetic loci and had phenotypic consequences, such as re-arrangements of DNA that cut a gene in half. Decades of such work, correlated with more standard genetic mapping by recombination, resulted in a dense roadmap of genetic markers distributed along the characteristic banded pattern of the Drosophila polytene chromosomes.

But why were the polytene chromosomes banded in the first place? What were these landmarks that everyone relied upon? A recent paper re-opens this issue and links the interband zones (the lighter areas in both the green-stained and the orcein-stained preparations above) to the specific molecule function of transcriptional insulation. "Bands" are richer in DNA, while the interbands have less DNA. What do they have instead? Evidently proteins, of a particular sort.

Genes are packed pretty tightly in the DNA of our genomes, and are regulated by sites in the DNA that are typically nearby and upstream with respect to the direction of transcription. But "nearby" could mean tens of thousands of basepairs away. Thus it has been found that a great deal of looping goes on to bring such distant regulatory sites close to the gene start site where they have their effect. This naturally raises the question of why such regulatory sites don't just loop over to some other gene distant on the chromosome, or even on a different chromosome. In the tight confines of the nucleus, such things are doubtless quite possible.

Enter the "insulator". These appear to be special proteins that bind DNA situated between gene regions, keeping the regulatory apparati of each functionally distinct. The authors of this work reviewed the field and then carried out new crosslinking experiments that track genome-wide which DNA segments are close to others, or to specific proteins. That means that they essentially "froze" the 3-D structure of the DNA relationships with a chemical that promiscuously crosslinks any DNA or proteins close to each other. They then cut and joined those proximate DNA segments to each other with ligase, and sequenced the junctions at large scale to determine all the junction points.

The fact is that polytene chromosomes are sort of blown-up representations of normal DNA in the nucleus, which is normally not just randomly jumbled about, but is arranged in loci and loops organized around gene regions. That means that this kind of experiment, which was conducted on early Drosophila embryo cells, and not on the salivary cells that generate polytene chromosomes, is looking at the native looping and regional structure in normal cells, at least at that particular developmental stage, which will have its unique pattern of genes turned on and off.

They found it was easy to discern topological structure in these nuclei, just as others have before. Specific regions of DNA are in close contact, while others are not. It is not a random jumble. More importantly, there are a set of about 5,000 zones that had high local interaction, but less interaction with others- they termed these topologically associated domains (TADs). The boundaries between these correlate with other work finding high accessibility to DNase, and finding proteins bound that are called insulators. Yet other work on the polytene chromosomes found that they exhibit about 5000-6000 visible bands, the borders of which are again highly accessible to DNase, and the sites of insulator protein binding.

The hallmark of insulator proteins is that when DNA sites for their binding are engineered between enhancers and the gene they typically regulate, they tend to cut that communication. The mechanism behind this is not clear yet. It could be because looping is a progressive process, starting locally and scanning out to the nearest gene, in a kind of sewing machine model.

In any case, the authors draw on all this work to put the pieces together, and claim that polytene banding, as detected by DNA and other stains, show this structure at the visible level, with topological gene units housed in the dark bands, and the light units housing intergeneic segments, with insulators in between. Since Drosophila has almost 16,000 genes, this indicates that many of these topological units house multiple genes, an example of which is the homeobox complex, where complex and coordinated regulation extends over several nearby genes.

Correlation between polytene banding and cross-link contacts, in one segment of the genome. Banding is on top, and cross-link contacts are show in color. The crosses form out of topological localities with high internal contact rates, and lower external contact. At bottom is shown a gene track of the region from Flybase. Blue vertical bits are exons.

Correlation between polytene banding and cross-link contacts, in one segment of the genome. Banding is on top, and cross-link contacts are show in color. The crosses form out of topological localities with high internal contact rates, and lower external contact. At bottom is shown a gene track of the region from Flybase. Blue vertical bits are exons.

This is problably not news to the field, which is why this paper was buried in an obscure journal, but it is nice to see new methods make sense of quite old historical problems, and to recognize that we were looking at significant and functional genomic features all the time, from the first staining of these giant chromosomes in 1881.

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Native American Cleansing, Army-Style

Review of Keith Murray's "The Modocs and Their War".

It was a brief national sensation during the Grant administration, but now a forgotten episode in the ethnic cleansing of the West. A tiny band of obscure Native Americans in Northern California resisted the US army for a year, engaging over ten times their own numbers, turning whole army units into demoralized fleeing cowards. A splinter group of the Modocs, numbering about 65 fighting men, were induced to go to a reservation in Oregon around 1865, but naturally found the experience unappealing, and decided to return to their native lands. With the US distracted by the Civil War and its aftermath, they were left alone for several years, while the settlers that were encroaching on their lands threw up increasingly bitter complaints.

Lava beds at Tule lake

One feature of these native lands, around Tule lake on the border with Oregon, are lava beds with very rugged topography. While barren, these also make excellent natural fortifications. The Modoc band, with their leader Captain Jack, made thorough use of them to hold off a determined Army attack on January 16 and 17, 1873, inflicting about 50 casualties while suffering none of their own. In fact, the Modocs throughout this episode ran circles around their enemies in tactics, logistics, scouting, and intelligence. In contrast, the Army of the West was a notorious home to cast-offs and hirelings, with little motivation and very great expense. There was an actual F-Troop involved, bringing quite appropriately to mind the old TV show about Western Army incompetence and corruption.

Eventually, the Army brought in hundreds of soldiers, plus units of friendly Native Americans, and hunted the Modocs down after they had thoroughly exhausted their supplies, not to mention their shaman's spiritual powers. Four of the leaders were hanged, and the rest shipped off by train to a reservation in Oklahoma, where the Modoc nation survives, barely.

I highly recommend this book, which dates from 1959. It is painstakingly researched, clearly told, and well-, sometimes sardonically, written. Murray reflects on the failings of the US Army, when faced with highly motivated and guerrilla resistance. He reflects:

"When the student of the Indian troubles turns from men or events to generalizations, he is struck with the obvious fact that the most serious aspect of the Modoc War was that the government had clearly learned nothing from its experience. Even while Captain Jack was awaiting execution at Fort Klamath, the civil government of Oregon expressed concern over the actions of certain Nez Percés of Joseph's band living in the Wallowa Valley of northeastern Oregon" .. which then led to similar mistreatment, broken promises, incompetence, and a long and tragic war of resistance.

The portents for Vietnam are alarming here, not to mention the displacement and mistreatment of the Palestinians. But to stick to domestic affairs, the overall dynamic was one of moral turpitude and greed on a national level, which the Army was put in a hopeless position to manage and mitigate. While the (Northern) US is justly proud of its moral position in the Civil War, its position towards Native Americans was one of ethnic cleansing, not to say extermination. The press of manifest destiny and the homesteading / settler movement encroached relentlessly on Native American lands. Treaty after treaty was signed, then ignored or reneged, boxing Native Americans into smaller and smaller reservations. We may call them concentration camps. They are on the worst possible land, in the most remote corners of the nation.

Territories of the Nez Percé. Green shows original treaty lands,  while the inner orange shows what they are left with today.

The irony is that only a few decades after the last of the Indian wars, the country woke up, in some very small degree, to its destruction and rapine of its natural inheritance and started establishing national parks to preserve a few of the most beautiful areas. If the Native Americans had been treated with decency and fairness, with large national lands that were protected from the depredations of settlers, we would today have a much more significant system of wild areas, in addition to preserving many more Native Americans and their diverse cultures. We can only be thankful that the freed slaves were not likewise driven onto barren reservations in the West, over trails of tears.

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Truth and Enlightenment

What the Enlightenment and Modernity have wrought, and who has problems with it.

As our values of truth and honesty are slipping, it seems worthwhile to review how we got here. People generally have a tenuous relation to reality. What we see through our eyes is only its surface. We can see plants all our lives and yet have no understanding of how they work and how they came to be. Such knowledge has to come through painstaking inference into a mental model, based on clues, experiments, mutations, exceptions, and the like. Humans are champions of inference, as attested by conspiracy theories and religion- ways that our need to for theories of reality outstrips our actual knowledge, sometimes flagrantly.

Historically, there have been occasional periods when intellectuals had the prosperous and calm conditions to make progress on this front, out of the mire of preconceptions, superstitions, and traditions, and into a more measured and rational view of reality. Not that there is ever a perfectly rational view, but there are clearly more and less rational views possible. The ancient Greeks experienced one such period, founding schools of philosophy that lasted hundreds of years, and fostering the greatest scientist, teacher, and thinker of the ancient world, Aristotle. But the greatest such period was the Renaissance and subsequent Enlightenment of Western Europe, when the learning of the ancient world combined with mounting prosperity and technological development to dispell the fog of Christian theology, and made of scholarship an independent, rigorous, and institutional pursuit that continues today.

Painting is an example of this movement. The Renaissance painters learned perspective, and reveled in new powers of realistic portrayal. Realistic painting may now be old-hat, even déclassé, but after the rude iconography of the Middle Ages, it was revolutionary, reminiscent of the incredibly naturalistic statuary of Greece and Rome at their heights. Similar movements in all areas of intellectual life, including science, philology, history, politics, and social thought generally, and philosophy, brought us to modernity, where our relationship to nature is fundamentally transformed, from that of a mystified and dependent spectator, to that of a deeply understanding (if not always respectful) steward. While morals and ethics are not themselves a matter of truth and natural observation, (though they have a lot to do with integrity and honesty), the same truth-finding ethic trained on social institutions brought down, step by step, the superstitious hold of the religio-monarchical system, to the constitutional / social contract systems of today.

Francesco di Giorgio, ~1490, an idealized architectural view.

But some are not happy with this change in perspective. There were obviously losers in this process of cultural and intellectual maturation. Principally religion, which tried mightily to understand the nature of reality, while mediating our relation to it, but couldn't help putting the cart of dogma and power ahead of the horse of intellectual integrity. For honesty and truth begin in the method of getting there. True humility, not the false and preening humility of putting one's god before all other gods and considerations, is the first step to being able to even see the subtle stirrings of nature, and then to follow them out. Charles Darwin was orginally intended for the parsonage, but as he unfurled the relentless mechanism of biology, and experienced its stabs in his own life, he ended up an evident atheist, woken up to a more sober, mature, and we might say enlightened, view of our nature and situation.

Reality isn't always pretty. Facing it takes fortitude and work. Thus the astonishingly durable, if slipping, hold of religion into this, the twenty-first century. Thus also the attraction of fake news and con artists, not to mention religion. Far easier to have comfort and hope in false and familiar beliefs than to accept uncertainty and ignorance, and do the work required to resolve them, even partially. Who would have thought that, at the so-called end of history, when the US won the cold war, and spread its blend of capitalism, relative freedom, and intellectual ambition across the world, that such moral rot would set in here at home, with our plutocrats, (with the connivance of Russia, of all things!), standing at the head of an army of resentful religious traditionalists, straining every nerve to spread distrust, small-mindedness, and lies over the land?

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• What's the matter with Kansas.. will soon be the matter with the rest of us.
• ... Until the revolution.