Portents of Overpopulation

The many ways we can tell humans have overrun the planet.

I was reading a slight book on the history of my county, built around photos from our local historical society. What struck me was how bucolic it used to be, more agrarian and slow paced, yet at the same time socially vibrant. A scarcity of people makes everyone more positive about meeting and being with other people. Now the region is much more built-up, with more amenities, but less open space and seemingly less social mixing. All this got me thinking about the social indices of overpopulation.

There are many ways to evaluate human overpopulation. Famine and starvation is perhaps the simplest, a specter that was thought to be imminent in the 1970's, with "The Population Bomb". Lately we have become aware of more subtle problems that the planet has due to our numbers, like pervasive plastic pollution, deranged nitrogen and other chemical cycles, and climate heating. There has been a constant descent down ladders of resource quality, from the mastodons that were hunted out thousands of years ago, then fisheries destroyed, then ranges overgrazed, to the point that we are making hamburgers out of peas and soy beans now. Minerals follow the same course, as we go farther afield to exploit poorer ores of the critical elements like copper, aluminum, rare earth elements, helium, etc. 

Sustainability is not just a word or a woke mantra. It is a specter that hangs over our future. Will humans be able to exist at our current technological level in a few hundred years? A thousand? Ten thousand? There is no way that will be possible with our current practices. So those practices unquestionably have to change. 

But apart from the resource constraints that overpopulation presents, I have been struck by the sociological factors that point in the same direction, and are spontaneous responses to what is evident in the environment. In my community and the state of California, there is a vocal debate about housing. Localities have settled into a comfortable stasis, where no new housing is zoned for, existing housing values go up, and existing residents are happy. But the population of the state continues to go up, housing becomes increasingly unaffordable, and the homeless lie all over the streets and parks. There seems to be a psychological state where most current residents see the current situation as sufficiently dense- they are not interested in more growth, (We don't want to become LA!). They instinctively sense that we have collectively reached some kind of limit, given our technological setting and psychology.

Declining birth rates across the developed world point in the same direction. Perhaps the expense of raising a child into the current lifestyle is too high, but there may be something more basic going on. Likewise the broad acceptance of gay / LGBTQ lives, where previously the emphasis was on "natural" and fertile growth of the human population, without any consciousness of limits. People seem less social, less likely to go out from their cocoons and streaming pods. Political divisiveness may also be traceable to this sociological turning point, since if growth is off the table, the pie is static, and political and economic competition is increasingly zero-sum instead of collective and growth-oriented. Public works fall into this trap as well, with public agencies increasingly sclerotic, unable to plow through conflicting entrenched interests, and unable to grow, or even maintain, our infrastructure. One could invoke a general anti-immigrant sentiment as another sign, although anti-immigrant campaigns have featured periodically throughout US history, usually mixed, as now, with racial selectivity and animus.

Imaginatively, dystopias seem to rule over the science fiction universe, as Hollywood seems to take for granted a grim future of some kind, whether inflicted by aliens or AI, or by ourselves. Heroes may fight against it, but we do not seem to get many happy endings. The future just looks too bleak, if one is looking far enough ahead. It is hard to generate the optimism we once had, given the failure of the technological deliverances of the twentieth century (fossil fuels, nuclear power, fusion power) to provide a truly sustainable future. Everyone can sense, at an intuitive level, that we are stuck, and may not get a technological fix to get us out of this jam. Solar power is great, but it is not yet clear that the triumvirate of wind, solar, and batteries are truly enough to feed our need for power, let alone the growing appetites of the not-yet-fully developed world. And if it is? Human populations will doubtless grow to the point that those technologies become untenable in turn, with a hat-tip to Thomas Malthus. 

We should be proud of the many great things that this period of prosperity has allowed us to accomplish. But we should grieve, as well, for the costs incurred- the vast environmental degradation which at the current pace is accelerating and compounding through many forms. Humans are not going to go extinct from these self-induced crises, but we will have to face up to the absolute necessity of sustainability over the long term, or else "the environment" will do so for us, by reducing our populations to more sustainable levels.

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LPS: Bacterial Shield and Weapon

Some special properties of the super-antigen lipopolysaccharide.

Bacteria don't have it easy in their tiny Brownian world. While we have evolved large size and cleverness, they have evolved miracles of chemistry and miniaturization. One of the key classifications of bacteria is between Gram positive and negative, which refers to the Gram stain. This chemical stains the peptidoglycan layer of all bacteria, which is their "cell wall", wrapped around the cell membrane and providing structural support against osmotic pressure. For many bacteria, a heavy layer of peptidoglycan is all they have on the outside, and they stain strongly with the Gram stain. But other bacteria, like the paradigmatic E. coli, stain weakly, because they have a thin layer of peptidoglycan, outside of which is another membrane, the outer membrane (OM, whereas the inner membrane is abbreviated IM).

Structure of the core of LPS, not showing the further "poly" saccharide tails that would go upwards, hitched to the red sugars. At bottom are the lipid tails that form a strong membrane barrier. These, plus the blue sugar core, form the lipid-A structure that is highly antigenic.

This outer membrane doesn't do much osmotic regulation or active nutrient trafficking, but it does face the outside world, and for that, Gram-negative bacteria have developed a peculiar membrane component called lipopolysaccharide, or LPS for short. The outer membrane is assymetric, with normal phospholipids used for the inner leaflet, and LPS used for the outside leaflet. Maintaining such assymetry is not easy, requiring special "flippases" that know which side is which and continually send the right lipid type to its correct side. LPS is totally different from other membrane lipids, using a two-sugar core to hang six lipid tails (a structure called lipid-A), which is then decorated with chains of additional sugars (the polysaccharide part) going off in the other direction, towards the outside world.

The long, strange trip that LPS takes to its destination. Synthesis starts on the inner leaflet of the inner membrane, at the cytoplasm of the bacterial cell. The lipid-A core is then flipped over to the outer leaflet, where extra sugar units are added, sometimes in great profusion. Then a train of proteins (Lpt-A,B,C,D,E,D) extract the enormous LPS molecule out of the inner membrane, ferry it through the periplasm, through the peptidoglycan layer, and through to the outer leaflet of the outer membrane.

A recent paper provided the structural explanation behind one transporter, LptDE, from Neisseria gonerrhoeae. This is the protein that receives LPS from a its synthesis inside the cell, after prior transport through the inner membrane and inter-membrane space (including the peptidoglycan layer), and places LPS on the outer leaflet of the outer membrane. It is an enormous barrel, with a dynamic crack in its side where LPS can squeeze out, to the right location. It is a structure that explains neatly how directionality can be imposed on this transport, which is driven by ATP hydrolysis (by LtpB) at the inner membrane, that loads a sequence of transporters sending LPS outward.

Some structures of LptD (teal or red), and LPS (teal, lower) with LptE (yellow), an accessory protein that loads LPS into LptD. This structure is on the outer leaflet of the outer membrane, and releases LPS (bottom center) through its "lateral gate" into the right position to join other LPS molecules on the outer leaflet.

LPS shields Gram-negative bacteria from outside attack, particularly from antibiotics and antimicrobial peptides. These are molecules made by all sorts of organisms, from other bacteria to ourselves. The peptides typically insert themselves into bacterial membranes, assemble into pores, and kill the cell. LPS is resistant to this kind of attack, due to its different structure from normal phospholipids that have only two lipid tails each. Additionally, the large, charged sugar decorations outside fend off large hydrophobic compounds. LPS can be (and is) altered in many additional ways by chemical modifications, changes to the sugar decorations, extra lipid attachments, etc. to fend off newly evolved attacks. Thus LPS is the result of a slow motion arms race, and differs in its detailed composition between different species of bacteria. One way that LPS can be further modified is with extra hydrophobic groups such as lipids, to allow the bacteria to clump together into biofilms. These are increasingly understood as a key mode of pathogenesis that allow bacteria to both physically stick around in very dangerous places (such as catheters), and also form a further protective shield against attack, such as by antibiotics or whatever else their host throws at them.

In any case, the lipid-A core has been staunchly retained through evolution and forms a super-antigen that organisms such as ourselves have evolved to sense at incredibly low levels. We encode a small protein, called LY96 (or MD-2), that binds the lipid-A portion of LPS very specifically at infinitesimal concentrations, complexes with cell surface receptor TLR4, and sets off alarm bells through the immune system. Indeed, this chemical was originally called "endotoxin", because cholera bacteria, even after being killed, caused an enormous and toxic immune response- a response that was later, through painstaking purification and testing, isolated to the lipid-A molecule.

LPS (in red) as it is bound and recognized by human protein MD-2 (LY96) and its complex partner TLR4. TLR4 is one of our key immune system alarm bells, detecting LPS at picomolar levels. 

LPS is the kind of antigen that is usually great to detect with high sensitivity- we don't even notice that our immune system has found, moved in, and resoved all sorts of minor infections. But if bacteria gain a foothold in the body and pump out a lot of this antigen, the result can be overwhelmingly different- cytokine storm, septic shock, and death. Rats and mice, for instance, have a fraction of our sensitivity to LPS, sparing them from systemic breakdown from common exposures brought on by their rather more gritty lifestyles.

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E. O. Wilson, Atheist

Notes on the controversies of E. O. Wilson.

E. O. Wilson was one of our leading biologists and intellectuals, combining a scholarly career of love for the natural world (particularly ants) with a cultural voice of concern about what we as a species are doing to it. He was also a dedicated atheist, perched in his ivory tower at Harvard and tilting at various professional and cultural windmills. I feature below a long quote from one of his several magnum opuses, Sociobiology (1975). This was putatively a textbook by which he wanted to establish a new field within biology- the study of social structures and evolution. This was a time when molecular biology was ascendent, in his department and in biology broadly, and he wanted to push back and assert that truly important and relevant science was waiting to be done at higher levels of biology, indeed the highest level- that of whole societies. It is a vast tome, where he attempted to synthesize everything known in the field. But it met with significant resistance across the board, even though most of its propositions are now taken as a matter of course ... that our social instincts and structures are heavily biological, and have evolved just as our physical features have.

Remembrance of Climates Past

As the climate heats up, we are heading back in time, very rapidly.

Climate change is the challenge of our times and of our planet. However attractive it is to not care, to ignore it, to hide in traditional ways of thinking, to let inertia have its way, inexorable change getting worse by the year. The American way of life can not go on, and will not go on as before. This year has been a remarkable demonstration of the range of catastrophe, from melting Arctic villages to Pacific Northwest heat waves, California wildfires, record draught on the Colorado river, hurricanes running out of letters, and catastrophic floods in Europe. Migration crises around the world point to another implication- that as the global South becomes unlivable, increasing hordes of people will be knocking on the borders of the Northern countries, who have authored the mess.

To get some perspective on the change, we can look backwards into the geological record to see where we are going, and how fast. Earth has had a very diverse climatic history, from its beginning in a Venus-like cloud of high CO2 and no oxygen, to "snowball earth" freezes, to torrid warm periods extending to the poles. Over the last few billion years, earth's climate has had a fundamentally, if slowly, self-correcting mechanism based on CO2 production and consumption. CO2, needless to say at this point, is the main variable in our atmosphere's tendency to retain or give up solar heat. Volcanoes liberate CO2 from geologic and organic buried carbon. Organic carbon can also be liberated by fires and decomposition of organic carbon, including exposed coal, methane, and oil deposits. On the other hand, the biosphere fixes and buries carbon, and on an even more vast scale the weathering of exposed rocks drives the formation of carbonate minerals that lock up atmospheric CO2. When conditions are warm, weathering of rocks accelerates, as can organic fixation and burial, drawing down CO2. When conditions are cold, ice sheets cover the land and inhibit both organic fixation and rock weathering, allowing CO2 to build up in the atmosphere.

These cycles mean that over a scale of millions of years, earth does not get caught irretrievably (as Venus has) in an inhospitable climate. Instead, our recent ice ages ebbed and flowed, back and forth as the CO2 balance in the atmosphere responded fitfully to geologic conditions. The dramatic snowball periods, which occurred just before the Cambrian period, came to an end even though the earth-wide snow cover dramatically reduced solar absorbance. But it also reduced weathering and organic fixation of CO2, so eventually, CO2 built up to the very high levels needed to overcome the snowball effect and the climate snapped back to very warm conditions.

A key point in all of this is that climate change over earth's history has been driven geologically, and thus has been slow. Slowness has critical effects in allowing the biosphere to adapt. The typical driver is a new spate of volcanic eruptions, which release lots of CO2. This takes thousands of years to happen, so while this can be fast in geologic terms (a prime example is the Paleocene-Eocene thermal maximum, which took maybe 20,000 years to drive the climate from very warm to quite torrid, roughly 55 million years ago). However, the homeostatic mechanisms kicked in, and this torrid phase only lasted  a couple of hundred thousand years. Another example has been the slow uplift of the Tibetan plateau, which exposed a great deal of rock to weathering, thus drawing down atmospheric CO2. This is thought to have driven the cooler temperatures and glaciations of the last few million years.

A notorious exception is the K-T boundary extinction, where an asteroid hit the earth and changed the climate overnight. And life suffered correspondingly, with all the dinosaurs wiped out. (Well, all except for birds). Whatever was not pre-adapted somehow for this instant crisis failed to make it through. The stress this put on the biosphere is obvious, catastrophic, took many millions of years to recover from, and changed the trajectory of evolution dramatically.

An extremely rich graph of the last 70 million years of earth's climate, from a recent benchmark paper. Temperatures are shown on top right, while the isotopic findings that undergird them are shown on top left (temperature proxy based on oxygen isotopes) and bottom left (carbon concentration proxy based on carbon isotopes). The overall trend is correlation between the two, with CO2 the primary driver of higher temperature, and subject to swings for various geologic and biological reasons. Temperature is also affected secondarily by orbital mechanics and other factors. Even the Eocene high temperatures were driven by CO2, though the correlation is not so clear here.

What does all this mean for our current trajectory? The graph above helpfully supplies the current IPCC scenarios of temperature change, under stringent, medium, and business as usual scenarios. The temperature today (green) is already equivalent to conditions of about five million years ago. So in time machine terms, we have travelled, in the span of a century, five million years of climate history, to before the recent ice ages. We are already beyond the stringent scenario, obviously, so the only possible futures we have to look forward to are the medium and no-action scenarios, which, within the next fifty to one hundred years, will put us, in time machine terms, fourteen and forty million years into the past, respectively. And what of the century after that? CO2 stays in the atmosphere for many thousands of years, so not only do we have to reduce emissions now, we will have to remove those that have already happened. Climate stewardship will be humanity's job whether we like it or not.

The biosphere can not cope with this rate of change. While we often think in narcissistic terms of how humans will suffer, we are the lucky ones, being the most adaptable creatures ever devised by evolution. Our problems are nothing compared to the rest of the biosphere. The ability of animals to migrate or shift their ranges is highly strained by the availability of the rest of their essential networks, mostly based on plants at the base of the ecological network. And plants are not going to have the ability to migrate at these speeds and generate new ecosytems in more northerly areas. To us, the speed of climate change is slow, barely discernible on a lifetime scale. But in earth history terms, it is blindingly fast, just a blip over an asteroid impact, and far faster than normal ecosystem dynamics, let alone evolution, can cope with. Uncounted species are falling by the wayside, victims of another great extinction in earth history in this, the anthropocene geological epoch.

Time machines are exciting tropes of science fiction, allowing amazing journeys and byzantine plot twists. But usually, the outcome is not good, since changing the time line has unpredictable and sometimes catastrophic effects. Typically, a ruse is employed to extricate the heroes from the twisted plot, and everyone sighs with relief at the end when the normal time line is restored. Our climate path is not heading for such a happy ending. We are gambling, now consciously and willfully, with not only our own civilizational existence, but with the progressive and rapid degradation of the entire biosphere, on this warp-speed trip into the geological past.

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Transmission of SARS-CoV2

Reflections on viral spread.

This is a brief update based on studies of SARS-CoV2 transmission over the course of the pandemic. They mostly nail down features that we already know, and offer a comparison with influenza, which has interesting differences in its transmission. One observation is that influenza has been eradicated to an astonishing degree by our efforts to prevent SARS-CoV2 transmission, a testament not only to the lower transmissibility of influenza, but also to the regular round of death and illness that we have been putting up with for millennia without much complaint.

After all the hand-wringing about hand-washing, we gradually learned that this new virus is almost exclusively passed by aerosols through the air, with limited range in space and time. Also that, despite the infinitesimal size of the virus, that face masks of many kinds are effective in knocking down both emission and reception of viral innocula by several-fold. This is doubtless because both the viruses with their lipid coats, and the moist aerosols they reside in, are quite sticky, prone to capture by even rough cloth filters with channels many times the size of a viral particle. The notorious superspreader events are characterized by 

• indoors, close physical proximity to others
• limited air circulation
• an infected person, typically asymptomatic, engaging in
• vocal activity, like singing or loud talking
• with no mask

Scale drawing of surgical mask fibers, against viral and aerosol particle sizes.

Meditation is not conducive to transmission, nor do most infected people transmit their infection. Superspreaders seem to have a very high viral load in key areas of their vocal or respiratory tracts that leads to abundant aerosol emissions with high viral counts. For recipients, it takes numerous viruses to establish an infection- something like 300 for influenza, and something similar for SARS-CoV2. This is a live virus count, not counting inactive viruses, which are always part of the produced and transmitted population of particles. The reason is probably due to our various innate clearance mechanisms, both physical and molecular, meaning that only one virus may get through to successfully infect someone, out of a population of thousands that that person breathed in. 

SARS-CoV2 transmission vs influenza. SARS-CoV2 seems to survive longer in air, leading to more infections in enclosed spaces. Being outdoors subjects the aerosols to getting blown away, and to purifying UV light. This graph does not show it, but SARS-CoV2 also differs in having high viral loads prior to symptom onset, or sometimes without any symptoms, making isolation and contact tracing very difficult.

Additionally, infection by one or few viruses may present a speed problem, where they can not grow an infection fast enough relative to the ability of the immune system to respond and put out small fires. Only if the inoculum immediately generates a large conflagration (think Molotov cocktail) is the fire department overwhelmed, at least for a few days. This leads in turn to the fascinating prospect of mass inoculation with small doses of the virus. Understandably, this is not a popular idea, with its similarity to playing roulette. It resembles the old-fashioned method of small pox inoculation, which used to be done with small doses of actual small pox, not cow pox as was later introduced by Jenner. 

But it may be a significant explanation behind the enormous conundrum of the low impact of Covid-19 on tropical and low-income countries. These countries (India, Central America, Nigeria) show quite high seropositive rates, indicating wide-spread infection. But their death rates and hospitalization rates are very low, and they have escaped this pandemic with relative ease. While reporting issues and pre-existing immune exposure are possible explanations, so is a possible warmer outdoor culture with lower innocula and lower-severity infections. An interesting aspect of inoculum size is that it can have far-reaching consequences, with lower-level infections leading to smaller viral counts in the aerosols emitted, thereby causing smaller, less-severe infections in the next recipients.

The study of viral transmission and infectivity could have profound effects on how we deal with this and similar diseases, and one has to say that it has been frustrating that our knowledge of it remains haphazard, and has been so slow in coming, with such mediocre experiments, false starts and poor messaging.

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Eating the Wild Things

Despite humanity's long tradition of eating wildlife, it is high time to rethink it as a practice. 

The coronavirus outbreak certainly gives one pause, and time to think about what we are doing to the biosphere and to ourselves. It also makes one wonder about the wisdom of killing and eating wildlife. I have been reading a book about a different disaster, the struggles of the crew of the ship Essex, back in 1820. This Nantucket-based factory ship was hunting whales in the middle of the Pacific when, in an ironic, yet all too-rare turn of events, a huge male sperm whale rammed and sank the mother ship as the smaller whaleboats were out killing its relatives. Months of drama, extremity, and cannibalism ensue, (for the humans), after which a fraction of the crew survive to tell the tale. It seems to us now bizarre, and beyond wasteful, that street lights in Nantucket were lit with whale oil, and that people would sail all over the world's oceans just to kill whales for the oil in their heads and blubber. Humans have an instinct for survival, and for the most concentrated source of various goods, and, whether under the colors of capitalism or simple greed, think little of externalizing costs, no matter how brutal and far-reaching, whether eating each other, "fishing out" some rich source of food, causing extinctions, or setting Charles island of the Galapagos ablaze in an inferno (another episode that occurs in this ill-starred history). One must be "hard" in this business of living, after all.

Well, we can do better. Now, two centuries on, we are still abusing the biosphere. Some ways are new, (climate change, plastics, insecticides), but others are old, such as over-fishing. Factory ships are still plying the great oceans of the world, vacuuming up wild animals so that we can eat them. And not just do they derange whole ecosystems and litter the oceans with their waste, but they also kill a lot of innocent bystanders, euphemistically called "bycatch"- sea turtles, albatrosses, dolphins, whales, etc. Albatross populations are in steady decline, from very low levels and heading towards extinction, for one main reason, which is the fishing industry.

This simply has to stop. It is a tragedy of the commons, on a collossal scale, all for the atavistic desire to eat wild animals. Human overpopulation, coupled with technology, means that no wild animals stand a chance in an unregulated environment- not in Africa, not in Brazil, and not in the international oceans. We are killing them by a thousand cuts, but do we also have to eat them, as the final indignity and form of waste?

If we want to save the biosphere from utter impoverishment, humanity needs a change of heart- an ethic for keeping the wild biosphere wild, rather than running it like so much farmland, or so much "resource" to be pillaged, whether "sustainably" or not. Obviously, eating meat at all is a fraught issue- ethically, and environmentally. But surely we can agree that wild animals, and wild ecosystems, deserve a break? Conversely, where we have so screwed up ecosystems by eliminating natural predators or introducing invasive species, we may have to kill (and yes, perhaps eat) wild animals in systematic fashion, to bring back a functional balance. Go to town on feral hogs, boa constrictors, Asian carp, etc. (But try to do so without poisoning yourselves and the evironment with lead.) The point is that we are stewards of this Earth now, like it or not, and ensuing generations over the next hundreds and thousands of years deserve an Earth with a functioning biosphere, with some semblance of its original richness.

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Mother of us All- the Eukaryotic Ancestor

A new archaeon looks very much like an early transitional form between archaea and eukaryotes.

Even more than the invention of photosynthesis or the transition to multicellularity, the transition from bacteria to eukaryotes was perhaps the most dramatic and momentous evolutionary event after the origination of life. Bacteria are everywhere, and still dominate the biosphere in many respects with an unparalleled range of biochemistries. But they have severely limited prospects, being so streamlined in their genetic and sexual practices that they seem unable to escape their single-celled, remorselessly competitive fate.

Eukaryotes are known to have originated in the fusion of at least two different bacteria-like microorganisms, one perhaps an amoeba-like hunter, the other the bacterium that became our mitochondrion. Plus another that in plants became the chloroplast. There are several theories about the details, of which several propose metabolic symbiosis- that the original exchange between the mitochondrial progenitor and its host was actually not amoeboid engulfment, but quite gradual and voluntary, uniting a methanogenic partner that used small organic compounds and hydrogen as its inputs- making methane- with a methanotrophic host that produced various organic compounds from methane plus CO2 without complaint.

But once joined, eukaryotes did so much more, generating countless innovations in cell organization, sex, genetic control, organelle subspecialization, membrane management, cytoskeletal structure, among others, that it is hard to believe this event ever happened, and difficult to reconstruct its steps. In this regard, it is similar to the origination of life, where several obstacles (enclosure of a cell with selective transport, replicative mechanism, and metabolic power, perhaps among others as yet unappreciated) all had to be surmounted in some fashion before something that we would call life existed- a process that remains a topic of wide-ranging speculation.

But the starting point for eukaryotes seems to have been an archaeon- a member of the third major kingdom of life discovered only in the 1970's, which are unicellular like bacteria, but have many distinct molecular and genetic mechanisms that are more closely related to eukaryotes than to bacteria. These seem to be our nuclear ancestors, with a lot of bacterial genetic material added later on, either from the early mitochondrial symbiont, or from other transfers, which enriched their biochemical range. The big questions are- what caused the unification of these two life forms, and why did it result in such an extensive profusion of other innovative traits? A recent paper (review) is devoted to the first question to some degree, discovering a new archaeal species that is the closest yet to such a transitional form.

"We confirmed the presence of 80 eukaryotic signature proteins, which are also observed in related Asgard archaea."

To do this, they cultivated deep marine sediments from around Japan in an oxygen-free bioreactor, feeding methane (plus a bunch of antibiotics, to kill off any bacteria) in order to cultivate organisms that are notoriously hard to cultivate. They were looking for anaerobic archaea that die in oxygen, and live off of methane, which they get typically from partner bacteria. The hydrogen that the former (methanotrophs) produce from methane is toxic in large amounts, so having a partner to use it and give methane in return is a partnership made in heaven. Those partners (at first, methanogens) eat hydrogen and CO2, or other small organic molecules and produce methane. The new methanotroph is not just picky about conditions it will grow in, but extremely slow-growing, doubling in the best of conditions in about 20 days. These are not E. coli! Indeed, the whole project took a decade.

The idea to culture such obscure and obdurate organisms comes from two sources. First were existing hypotheses about how eukaryotes got started, in the form of metabolic collaborations described above, between disparate micro-organisms, centering on the use and exchange of methane and hydrogen, in addition to electrons and other compounds. Second were surveys of marine sediments and many other habitats for raw DNA, which has been sequenced in vast amounts. Such DNA is obviously a messy mixture, but given enough patience and computer power, one can re-assemble many interesting distinct genomes out of it, and some transition-like genomes have been glimpsed in this way. But what could be the corresponding organism? That was the question.

The author's phylogenetic tree across all kingdoms, using ribosomal proteins, highlighting the new organism's (red) position as sister group between archaea and eukaryotes. Note how relatively deep the divergence (X-axis) is between bacteria at the bottoms, and all other life forms.

One key analysis was to put this new organism into a phylogenetic tree, using the incredibly well-conserved sequences of the ribosomal proteins. The diagram above shows that the new organism, dubbed MK-D1, sits right at the threshold of the eukaryotic group, just as one would expect for an ancestor. It constitutes, to date and in molecular terms, the closest organism to eukaryotes that is not one itself. The diagram also shows, yet again, the vast molecular gulf between bacteria (at the very bottom) and archaea, which occupy most of the middle. While eukaryotes (top) are clearly a sister group of archaea, it is the divide between archaea and bacteria that is the most profound within the whole biosphere.

These new organisms are unexpectedly small- tiny, indeed. They are not the huge phagocytic amoeba that have often been imagined engulfing hapless bacterial partners about to be taken hostage. No, the methanogenic partners that are co-cultured by these researchers are far larger, by roughly ten-fold. But the new methanotroph has some interesting behaviors, such as putting out extensive cell projections and curious vesicles. It also has, as expected, a variety of genes that characterize eukaryotes, such as actin, profilin, Ras, G-beta like protein, TPR motifs, Zinc finger and HTH proteins, core transcription proteins like TFIIB, SMC, Ankyrin motifs, histones, SNARE-like proteins, signal recognition factor.

Micrographs of the new organism, MK-D1. Left is a high-magnification electron micrograph showing membrane vesicles budding off the main cell. Scale, 200 nm. Right is a scanning electron micrograph of two or three cells with dramatic projections emerging, plus some previously budded vesicles lying about. Scale, 1 micron.

Of course, this organism exists now, a couple billion years after its imagined ancestor occured in a lineage that we speculate was related to one that led to eukaryotes. So it is a stretch to make this diagnosis of a transitional form. Except that relict forms seem to litter the biosphere, such as the stromatolites that still crop up in Australia, and the vast hordes of bacteria and archaea that remain the metabolic engines of the biosphere, in perpetual competition, yet also largely frozen in their lifestyles and roles.

When free oxygen was introduced into the biosphere by nascent photosynthesis, starting roughly two and a half billion years ago, the putative methane-exchanging organisms all needed extra partners to detoxify it, for instance bacteria which oxidize (using O2) organic compounds to CO2. This, finally, was the motivating force for the partnership with the true mitochondrion, which performs the same service today, providing enormous amounts of energy along the way. The transition from the loose partnership cultured by the current researchers to the one that truly gave rise to eukaryotes is a bit murky under their class of hypotheses, but there are other hypotheses that make a more direct job of it.

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How do we Get Out of Here?

It is hard to tell just yet how the coronavirus lockdown will end. Some scenarios.

With the US having frittered away its early opportunity to contain incoming travel and the spread of SARS-CoV-2, we lost containment and now have an endemic pandemic. Nor are our health authorities pursuing definitive contact tracing and quarantine of all cases/contacts- some regions of the country are even well beyond this possibility. Time lines for the lockdown are being progressively extended, without a clear end-game in sight. Where will it end?

The China Solution
China has done draconian quarantines and close tracking, contact tracing, and isolation. And they have stamped out the epidemic, other than a tickle of cases, supposedly mostly coming from abroad. How ironic, but also impressive. They have used institutions and norms of close social control, sometimes rather blunt and indiscriminate, to get the upper hand over this contagion. The prospects for us doing the same are dim. Neither our public officials nor population have the stomach for it. Thus this is not a realistic scenario as an endgame for the US pandemic.

Slow burn
No, we take a more relaxed approach, hoping that the pandemic will magically recede. But that is unlikely to happen, given the vast reservoir of uninfected people, and the virus's high infectivity. So far, the US has ~300,000 cases, and ~8,000 deaths. Assuming that the reported case rate is one-tenth of actual cases, there might be three million people who have been exposed and recovered, out of a population of over 300 million. Exposing everyone would thus result in roughly a million deaths. This will happen no matter how good our social isolation is, or how long it lasts, because the minute anyone pokes their head out, they will be exposed. Without comprehensive tracking and isolation of cases/contacts, our laissez-faire approach leads to a slow burn (also termed flattening the curve) where our hospitals might be able to keep up with the extended crisis, but we still take an enormous hit in illness and death.

Exposure testing
One supplement to the slow burn scenario is the addition of exposure testing, for antigens to SARS-CoV-2. If these tests were broadly offered, like at grocery stores and by home delivery, we could at least recognize a large population that is immune and thus can move freely, (perhaps wearing a scarlet letter!), helping to re-establish economic and other essential activities. This is like having some amount of herd immunity, without waiting for the entire population to have been exposed. But it would not significantly curtail the slow burn, since we are still unwilling to keep everyone else out of circulation in a comprehensive fashion.

County quarantine
Some areas of the country are doing much better than others, and could set up local clean zones and boundaries. Once cases were reduced to a small trickle, the health departments could do what they failed to do at the outset, which is to block and test at all borders, and comprehensively trace contacts and enforce isolation internally. Given the large and necessary traffic of deliveries of goods, especially food, this is quite unlikely to happen, and would represent a sort of breakdown of our political society. But the behavior of the Federal administration, giving a "you're on your own" message to states and localities, does make this scenario more likely. It also ends up being a sort of slow burn, since any locality can not forever keep up such isolation. It would have to continue until the advent of a final solution- a vaccine or treatment.

Vaccine or treatment
This is the magic solution everyone is waiting for. The antivax movement isn't looking so good at this moment,when everyone's attention is focused on virology, epidemiology, and public health. Candidate vaccines are easy to dream up- any protein from the virus could be expressed in some heterologous system (like in E. coli cells or yeast cells) in massive amounts, and injected into people to generate immune responses. But effective vaccines are another story. Coronaviruses and other respiratory viruses tend not to generate strong and durable immune responses. That means that their ingredients just are not that immunogenic- they have devious ways to hide from immune surveillance, for one thing. Indeed, we still do not have good vaccines (or treatments) against the common cold. So a good vaccine will need to use all the tricks of the trade, such as multiple protein pieces, both invariant and variable, and immune-stimulating adjuvants/additives, to make an effective vaccine. It may take a year, but it may also take several years.

It looks like we will be in this lockdown for a very long time, with reduced economic and social activity. And the more effective our social distancing, the longer we will have to stay isolated, as the flatter curve extends out in time. If we go down the China route with more draconian methods to stamp it out before it burns through the whole population, we will be in a very precarious situation until a treatment emerges, given the wide-spread, now endemic, presence of this virus world-wide if not in continuing hot spots in the US.

• For those locked in ..
• How China is controlling spread while getting back to work.

Goal: One Billion

The Earth can't take 10 billion people. 

We have environmental and cultural problems at all scales, from the local to the global. From water shortages, drought, plastic pollution, overfishing, and species extinction, to global warming, authoritarianism, social fraying, anti-immigrant fervor, and gridlocked traffic and real estate markets. There is a common thread, which is that there are way too many people. We have (at least in some places) remediated some of the worst practices we used to take for granted, like killing whales for oil, using explosives for fishing, or dumping chemical wastes into rivers and soils. But there are are few practical ways to remediate our carbon emissions, water scarcity, or need for vast farmlands. We need to take a long look in the mirror and realize that the Earth can't take it, and we are the problem- the shear number of us.

Consider the range of problems like housing costs gone wild, traffic choked to a standstill, rising education costs and competition, and political gridlock. Are these related to overpopulation as well? I think very much so. Real estate is self-explanatory. As the old saying goes, they aren't making more land. Even while plenty of land is worthless, the need for people to live near other people means that we need to live together in what have become increasingly choked megalopolises. While rich metropolises like San Francisco and London struggle with traffic congestion and decaying public services, poorer ones like Lagos, Sao Paulo, and Mumbai had few services to start with and attract ever widening circles of destitute slums.

Lagos

A deeper issue is why our political systems are breaking down as well. Public services are decaying for a reason, which is that solidarity has weakened. Half of the US electorate has checked out of communal projects of good governance, rational and positive foreign policy, and caring for others. After two centuries of extraordinary growth, first sponsored especially in the US by a marvelously depopulated New World, and then again by bounding over technological frontiers such as fossil fuels, electricity, and the green revolution, we seem to have reached a general growth plateau, (barring development of robots who will do everything for us, but burn ever more fuel in doing so), and the expansive mood has ground to a halt. One consequence is that the elites of the culture, principally the rich, no longer subscribe to an egalitarian ethic. Growth can not be relied on to lift all boats, rather it is now every class for itself. Which class wins, when money runs politics and the media, and has been turned into "free speech" by the supreme court, is obvious.

It used to be, in the "population bomb" 1970's, that we thought that famine would be the limit on population. But it turns out that, given enough fossil fuel inputs for fertilizer production, machinery, and clearing new arable land, plus a green revolution in crop breeding, food is not the limiting factor. It is a thousand other things that we are doing to the biosphere and to our societies. The tide against immigrants is clearly borne of fear, that the number of the poor who want to flee their wretched conditions is essentially limitless, and thus that prosperous countries, i.e. Europe and the US, can not offer the relatively free immigration conditions they have heretofore. The US gained vast goodwill throughout the world over the last couple of centuries by admitting countless immigrants and playing a central role in many of the technological improvements that have allowed populations to grow everywhere.

But that process seems to have reached an end point. We have picked much of the low-hanging fruit, and have come up against insurmountable barriers. Fusion power has not happened. Space colonization is completely impractical. Even electricity storage is presenting tremendous difficulties, making a large scale switch to renewable electricity virtually impossible. And the biosphere is being degraded every day. We have come up against Malthusian limits that are more subtle than famine, but need to be heeded, lest we relentlessly immiserate ourselves.

There are two general political responses to all this. The Left response is to cooperate as best we can and tighten our belts to fit in a few billion more. Open borders, save the children, conserve water and reduce electricity usage, so that all can have at least a share of whatever resources are left. The Right response is to deny that there are significant ecological limits, cast whatever limits there are in economic terms and compete to take what we can while we can, and devil take the hindmost. Neither response is very forward-looking. One can make the argument that development is the only proven way to reduce demographic growth. Therefore, we should promote development, and bring everyone up to first world standards of resource consumption, which will in turn bring birth rates down to what in Europe and Japanare less than replacement rates. But the Earth can't take that policy either. Global heating is already having dire effects. The biosphere is already decimated and impoverished.

Thus we need an even more impractical, impolitic, and direct strategy, which is to aim to dramatically reduce the human population. A rigorously enforced one-child policy over three generations would get us from the current 7+ billion people to 1 billion, which, I think, given the current technological state, is reasonably sustainable. China did an amazing thing with its one-child policy, nipping in the bud its most significant problem- that of vastly too many people for its capabilities and resources. China is now reaping the rewards of that policy, though it hardly went far enough, and China remains heavily overpopulated and rapacious as it ascends the ladder of development.

If combating climate change is a problem from hell, structurally diffuse and resistant to responsible policy, then population control is far more so. National power is to a great extent dependent on economic and population size. We have for centuries had a mania for growth, embedded in every fiber of our economic policy and national outlook. We are Malthusian to the core, and our major religions are even worse offenders, propagating the most Darwinian of reproduction policies, even while they so ironically decry Darwin's intellectual bequests. No, it is not an easy problem. But at very least, we should not fear declining birth rates as some existential catastrophe and sign of general decline. No, they should be welcomed as the least we can do, and a small part of our path to a sustainable future, for ourselves and for the biosphere that is our home.

• Jupiter flyby.
• Accounting for Iraq.
• What the Kochs and their ilk have wraught.
• Are the Taliban more trustworthy than Donald Trump?
• Have richer people have become more handsome?
• Bonus quote of the week, from "If We Can Keep It", by Michael Tomask.

We are in trouble. Our political culture is broken, but it is not broken for the reasons you often read that it's broken- because Washington is 'dysfunctional' or because politicians have no 'will'. No. It's broken because some people broke it. It was broken by the people who pushed the economic theory on the rest of us that has driven trillions of dollars that were once in middle-class people's pockets to the comparative few at the very top. Who refused to invest in the country anymore. Who will not even negotiate real investment. Who have been telling us for years that the market will take care of all our needs, while the market has in fact left thousands of towns and communities strafed and full of people addicted to drugs- the drugs, by the way, tht the same free market is pumping out in vastly greater quantities, and for vastly greater profits, than it did twenty years ago. And who have built up a parallel media universe in which any of these commonsense assertions are dismissed as socialist, and in which anyone who doesn't endorse the thesis of Donald Trump's greatness is denounced as un-American. 

They broke it. They broke it to gain power and to remake society in a way that was less communitarian, explicitly less equal, than the society we were building from 1945 to 1980. And- let me not forget this part- less democratic. I wrote earlier of Donald Trump's contempt for our institutions, our processes, put another way, for the democratic allocation of power. Many observers (me included, sometimes) have wondered why this didn't make Republicans recoil. The typical explanation has to do with fear of his base, but I've come to believe that the simplest explanation is the best: They didn't recoil because they're not especially bothered. They find him embarrassing at times, and they disagree with him here and there, but his demagogic approach doesn't really trouble them on the whole. They- not all of them, but certainly a critical mass of elected officials, operatives, and billionaires- no longer want to compete with and merely defeat liberalism on a level democratic playing field. They want to destroy it. This is why they do things like aggressive gerrymandering, the voter suppression laws, the attemt to change the way we elect senators, the blocking of Merrick Garland- all of which preceded Trump. They want to change the rules so they they never lose. And if destroying liberalism requires breaking the system- as it surely does- then so be it as far as they're concerned.

What Happened to the Monarchs?

Monarch butterflies are in crisis.

Flying over the Midwest, it is easy to see the impact of humans. The land is neatly tiled into monoculture farms, with hardly a wild spot in sight. Unseen is the chemical crusade that has happened over the same time period, making insects and weeds sparse on this land as well. All this has contributed to a phenomenally productive agriculture, making our food with almost factory-like consistency using a variety of high-tech machinery, chemicals, and plenty of CO2 emissions. But each of these assaults on nature has also multiplied the plight of (among many others) the Monarch butterfly, which eats weeds, is an insect, and migrates over astonishing distances in a multigenerational trek to communal wintering sites. While Eastern populations of Monarchs are in decline and in peril, the condition of the separate Western population, which circulates up the Sierra and back down the Pacific coast, is dire, headed towards extinction.

"... the Midwest lost more than 860 million milkweeds between 1999 and 2014, mostly in agricultural fields" -Entomology Today

Monarch butterflies have a curious method of migration. While birds live several years, and thus may commute several times over their lifespan, (for instance from Northern breeding grounds to Carribean or South American wintering sites), Monarch butterflies live only roughly a month. But they also migrate over long distances, either from Mexico up through the Eastern US and Midwest, or from Coastal California across Central California, to the Sierras, then North to Oregon and Washington, then back down in fall. Like birds, the Monarchs use these routes to move through optimal habitats as the Northern Hemisphere goes through its seasons. But the migration must encoded in their genes, not learned from experience or from others, since it takes several generations to make the trek, somewhat like the colonization space ships of science fiction, which would go through many generations to get to, say, Alpha Centauri.

Now a rare sight.

It also means that Monarchs rely on suitable environments (which is to say, the milkweed) every step of the way. And our technologies of weed, insect and physical habitat extermination are making enormous swathes of their routes uninhabitable, not to say lethal. The Western population is down from millions in the 1980's to 30,000 today. This is not sustainable, and likely to drop to zero unless big changes happen to render the landscape less lethal. Thankfully, there are many milkweed species, many of which can grow widely in the region, if allowed to.

But this is just a small example of the harm humans are doing to the natural world. We are a plague, and have initiated a new age in biology- the Anthropocene, complete with our own mass extinction event. While the process is well underway here in California, it is only beginning in regions like the Amazon and Africa, whose human populations are growing steadily and whose natural environments are being decimated and whose wildlife is declining, including being directly killed and eaten. Climate heating will kill off far more species, until we end up in a world of mega-cities separated by monoculture croplands and nature reserves that will be faint shadows of a vanished, and richer, world.

• A study in lying, corruption, debasement, and character.
• And going back in time, ditto.
• The mess Arthur Burns left behind.
• But is the Fed overly skittish now?
• Should we be giving foreign aid to the Targaryens?
• How about we fly less, and let the Monarchs fly more?

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.

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.

• EPI has a comprehensive solution for righting the inequality ship.
• John Dingle also has a solution.
• "Entitlements" are OK- on the importance of social insurance. Remember, the military is always insolvent, from a budgetary perspective.
• Sleazebags to the end.
• On the types of epilepsy.
• A persistent cycle of resource extraction, incumbent interests, regressive politics, and non-development. Let's not go there ourselves.
• A lesson in jazz.