Peak Carbon?

Are we at peak oil, perhaps even peak burning? Thanks to Donald Trump, renewables are looking better than ever.

It turns out that using the oil weapon opens people's eyes to the alternatives. The Saudis have recognized for a long time that stability in oil pricing and supply was the way to keep the world addicted. But in the current wars, Russia has used the natural gas weapon, and Iran has used the oil weapon. Now the addicts realize what a thin needle it is that brings them the fossil fix. After two months of closure on the Strait of Hormuz, the economic responses around the world have been surprisingly muted. While Paul Krugman rang the alarm of $200/barrel oil, prices have stabilized around $110 or so. It turns out that demand is more elastic than anticipated, at least it has been while supplies are still in transit. However, as physical shortages begin to hit, prices may rise again.

As a matter of strategy, the US administration is clearly flailing, unwilling to recognize a loss, and callous about the worldwide harms being imposed by its fruitless dithering. Is a blockade of Iran going to break its government? That is highly unlikely. They have been through much worse, such as during their war with Iraq. Trump's attacks and insults have rallied the population, entirely contrary to the administration's intention, but entirely foreseeably. Iran's sensitivity to economic pain is much lower than ours. And, as the administration was already doing on an ongoing basis prior to its war, it continues to make enemies of the US around the world, more so with each passing day that shipping in the Persian Gulf is stalled.

Paul Krugman bemoaned the "demand destruction" that continued shortages and high prices would cause, which may lead to economic slowdowns, perhaps recession. However I welcome it. It represents conservation of this precious resource, and, one might say, more realistic pricing that brings in, at least to a small degree, the widespread harms of fossil fuels. When one adds volatility and geostrategic dependencies, on top of the gross environmental harms, and what is now an economic disadvantage of fossil fuels when compared with renewable energy, the solution is clear, if not easy. The transition to renewable energy is going to accelerate.

Trend of world-wide carbon emissions.

Currently, the world is at the cusp of still-rising carbon emissions. This means that, even after all the climate conferences, and the reports, the activism, and the technological development, humanity as a whole is still burning more fossil carbon every year than the year before, and thus increasing the CO2 concentration in the atmosphere ever faster, and driving the climate crisis to ever-accelerating harms and disasters. Is it possible that this strategic-economic crisis, brought on by the blundering of a demented US administration- one that has done all in its power to deny climate change and scuttle the energy transition- will finally turn the tide? Could we be at peak carbon? And if so, will the downslope of emissions be faster than the upslope, in this slow-motion catastrophe? One can see that the US is already past peak carbon, and the state of California stands at 75% of the peak carbon emissions, which happened back in 2004. The upslope has been driven by highly uneven, and gradual, technological development and increased population. The downslope will be driven by the much more globally integrated rise of renewable technologies, so it has a chance of happening at a faster pace, despite the challenges of transitioning difficult economic sectors like trucking and aviation.

With the economic tailwinds of cheaper energy storage technologies, coupled with other advances in geothermal, solar, and wind power collection, the transition is inevitable. But public policy can make it faster or slower. The Biden administration worked towards the future, while the current administration works against it. Outside the US, China is enabling both its own transition and those of all other countries by leading extremely efficient solar and storage manufacturing. Those economics are going to eliminate new coal plant construction, and eventually use of all fossil fuels. China now sells more EV than fossil-based automobiles. While it has a prodigious fleet of coal-burning power plants, and is still building new ones, the overall level of coal power generation has leveled off, as it closes plants close to reduce pollution in sensitive urban areas.

While ironies abound, the important part of the story is that the biosphere is baking and needs help as fast as possible. If that help comes through the narcissism of small-minded tyrants, so be it. 

• Caesar, King, tomato, tomahto.
• Coding is toast.
• Renewable energy has beaten methane in the US electricity generation.
• Krugman chimes in.

The History and Future of a Single Mutation

The CCR5delta32 confers resistance to HIV. Where did it come from?

We are edging into an age of precision medicine, where the causes of our maladies will be known in molecular detail, allowing treatments that address them at the root. Given the parlous state of medicine today, in the midst of financial breakdown and a continued mediocre level of basic diagnosis, it is hard to believe this is a corner we can turn. But vaccines have long been in this category, of addressing the precise pathogenic causes of disease, and oncology is fitfully getting there, given advances in DNA sequencing and in treatments based on specific mutations.

HIV is also a beneficiary of this approach, since the discovery of its pathogen led directly to a variety of effective (if not yet permanent) treatments. A researcher in China created gene-edited humans with a specific mutation that will render them resistant to HIV. The mutation he chose for this work is called CCR5delta32, and it does not naturally exist in Chinese populations. 

But it does exist in European populations, at a roughly 10% rate in single copy. When present in two copies, it provides complete immunity to HIV, while if present in one copy, it slows infection substantially. A recent paper rooted through the available ancient and present genomes to figure out where this mutation came from. 

CCR5 is a cell surface receptor for cytokines 3, 4, and 5. These are all pro-inflammatory cytokines, and they interact with multiple receptors. Here, as in so many other respects, the immune system is riven with redundancy, so that it can grapple with as many contingencies as possible. Cytokines are signaling molecules for the immune system, which is an unusual organ, being dispersed all over the body with numerous cell types all patrolling around, and communicating with each other by long- and short-range chemical messages. It turns out that the major form of HIV uses the CCR5 protein to get into our immune cells, explaining why CCR5delta32, which is totally non-functional, has such a dramatic effect on HIV susceptibility. 

While people carrying CCR5delta32 are generally fine, this defect does confer a variety of subtle changes to their susceptibility to other infectious diseases and cancers. That explains why this mutation has settled at its low level in the European populations, probably balancing the occasional benefit against a specifically CCR5-seeking pathogen against its natural functions that form the basis of its existence in the first place as a part of immune system that is conserved in all mammals. The Chinese gene-editing researcher came under withering criticism not only for breaching the generally agreed moratorium on human germline gene editing, but also because the net effect of this mutation is, on the whole, negative, raising risks of numerous diseases, despite its beneficial effect on HIV. 

The authors run several models and populations in an attempt to time the origin of the CCR5delta32 mutation, and portray its positive selection over the ensuing millenia.  CHG- Caucasus hunter-gatherer; EHG- Eastern hunter-gatherer; WHG- Western hunter-gatherer; ANA- Anatolian Neolithic ancestry. The bottom axis is time, and the Y axis is the frequency of the mutation in these populations. "Modern DAF" refers to the inclusion of the data set of current (not ancient) population frequencies, (top), which the authors claim leads to continued rates of selection (last 2,000 years) that are artifactual.

So where did it come from? The new authors gather up a large variety of population samples from around the world, and from ancient humans, back to about ten thousand years ago. They find the first instance of the mutation in one sample at 5.8 thousand years ago. After that, its frequency rises dramatically, up to about two thousand years ago, when it levels off. They conclude that this mutation originated about seven to nine thousand years ago, in the steppes of Eastern Europe / Western Asia, and was under strong positive selection at first, spreading to the current frequency of about 10% of the population / alleles. All occurrences on other continents can be accounted by the spread from this source.

Does this mean that HIV was prevalent long, long before the current pandemic? Hardly. The authors can not say anything about it, but one theory would be that some other disease had a similar profile. It certainly was not the Black Death, as the authors show that this mutation had no change in frequency over that gruesome pandemic. Another hypothesis is that general reduction in inflammatory response might be beneficial in some settings, as has been found for Covid-19, though here again, this mutation does not have any known positive or negative net effect on Covid-19 susceptibility or course. 

It is amazing that we have enough sequences of ancient DNA to be able to reconstruct this kind of thing- to be able to trace where and when some influential mutation occurred, and how it traveled and spread. It is a tour-de-force of bio-archeological reconstruction.

• When you escape reality, and morality.
• Some environmental benefits are flowing from the current war.
• We may be at peak oil, courtesy of the US.

The Death of Boredom and the Future of Politics

Can politics work without a civic sphere?

How can we have a loneliness epidemic when we are connected like never before? It is a problem that perplexed Robert Putnam in "Bowling Alone". He put it mostly down to TV, internet, and the growth of passive and isolated forms of entertainment generally. When you read between the lines of history of any time before about one hundred years ago, you realize that people were, before the modern age, bored out of their minds. Who plays cards? Who puts on operas, or runs numbers, or goes bowling? Who needs an Easter pageant, or a three-to-four-hour baseball game? Only people with nothing better to do. If you wanted music, you had to make it. If you wanted conversation, you had to share it. Human society was built on simple quid pro quos- social rewards and resolution of boredom and isolation for personal participation.

But that deal has broken down dramatically in the modern age. We have a thousand channels, talk radio, recorded music. With AI, we are getting personal chatbots and bespoke romantasy partners. Sports have slid tectonically from participation to spectation. Boredom is a thing of the past, though if you do want to play cards, plenty of computers are willing to take a hand.

An interesting article in the New Republic knit this together very nicely with the problems we are having in politics. In the US, political engagement is increasingly shallow, leaving the field to extremists who can still call up foot soldiers to storm the ramparts. What happened to the Occupy movement? For all its inherent logic and flash organization, it fizzled into nothing because it gave little thought to its own institutionalization (indeed, was allergic to organization) and durable engagement, all the while railing against the overwhelming organization and deep pockets of the entrenched systems of capitalism. The Left is notoriously inable to herd itself into an effective, organized force. While capitalism is naturally organized and institutionalized by virtue of naked self-interest and corporate structures, civic groups grow out of far more disparate, and evanescent, motivations. Unions have been an attempt to organize around a countervailing, while still self-interested logic, which inherently limits their reach and coherence. The true civic sphere, however, is threadbare.

Political parties have similarly shallow roots. In California, the governor's race has 61 candidates, and little control by the party establishment, particularly by the Democratic establishment that supposedly runs the state. Like other non-profits, parties ask little of their adherents, other than possibly a monetary contribution, and wouldn't dream of holding truly social events that could deepen civic engagement. Expectations of civic engagement have hit rock bottom, mostly because people have tuned out across the civic spectrum. The testimonial dinner is a relic. The ice cream social is unheard of. Service organizations like Rotary and Elks are fossils, unions are on life support. Events and organizations that previously kept people entertained and involved in a civic way are scarce. These traditions both trained people for common action, and led to the kind of networking and contact that fed political consciousness and activity. They also helped to vet people directly for office holding (see the recent Swalwell case). 

Bernie Sanders can draw a crowd, but do those crowds go out, organize, and persist?

Republicans have found a partial solution to these problems by ginning up endless outrage through their propaganda outlets, predominantly talk radio and hate TV. While motivating, the results have, naturally, been intellectually disastrous and have us teetering on the edge of fascism. Democrats, as the more level-headed and progressive temperament, have not used the same tools effectively, and shouldn't. What should they do? Well, the field for civic engagement is pretty wide open. For example, one could imagine a tax on political advertisements, say 10%, which is collected by the government / FEC, and sent to counties or municipalities for civic engagement purposes, either election-related or not. This would create a fund for local talks, events, civic education, and the like that would, in theory, complement the advertising that is increasingly vacuous and meretricious. 

Another approach is direct action, where Democrats could use some of their energy and resources to build civic engagement, outside of straight campaigns. Just as the Republicans have harnessed ancillary issues like abortion and tax cuts that energized specific segments of their base, Democrats have to be a bit more canny about asking for more engagement and offering more involvement. Climate change is a great example, where a wide spectrum of individual action (trash pickups, solar panel installation, water quality testing) could be integrated into civic engagement that builds party alignment and ultimately, institutional strength. All great religions know that the more you ask, the more you get, and the deeper the commitment of followers. Additionally, the left already has a bewildering array of non-profits, whose efforts would ideally be more closely integrated with the Democratic umbrella to generate more organizational power- synergy or leverage, in business-speak.

On the other hand, how could civic disengagement be accommodated rather than fought? One approach might be to enhance the vetting and exposure of candidates by having nominating conventions at the local level. Even though California has an open primary, and thus does not grant each party automatic spots on each ticket, the parties should not shy away from selecting, testing, and promoting candidates. This should not be a central commitee operation hidden in the dark, the province of interested apparatchiks, but open forums that promote philosophies as well as people.

We are in a tough position, trying to keep politics alive in a world where its underpinnings- of civic engagement, communal organization and leadership, and simple conviviality- are fading in a deluge of individualized enjoyments. Political parties are at the forefront of this change, and need to think very deeply about how to keep themselves relevant and effective.

• Tax reform
• Is power based on insults?
• Everybody has deterrence these days.
• Who is being served here?
• Patient, heal thyself.
• Norway is going electric.

Pumping Calcium

An ornate ion pump manages rapid outflow of calcium.

In the beginning, the egg cell experienced a wave of calcium release, triggered by union with a sperm cell. This blocked other sperm from entering, and prepared the egg to become a zygote and embark on embryogenesis. It is but one example of the pervasive role of calcium signaling among animals. Another is the muscle activation cycle, which relies on calcium release from the specialized sarcoplasmic reticulum (in response to a nerve activation) to get the cell as a whole contracting. Generally, calcium is kept very low in the cytoplasm, and high in the endoplasmic reticulum and outside the cell. Thus, channels gated by electrical activation or other signals can cause rapid cytoplasmic calcium spikes and signal widely within a cell. 

On the flip side, there have to be pumps that keep the cytoplasmic concentration low, and a recent paper elucidates the structure of one such pump that is remarkably fast, while also closely regulated. It is an impressive machine. PMCA2 is an ATP-using calcium pump that sits in the plasma membrane and carries out what is called the Post-Albers cycle. This is a flip-switch mechanism for pumping ions, where ATP drives conformational switches alternately exposing ion binding sites to each side of the membrane. When the pore is open to the cytoplasm, there is no competition from higher concentrations outside, so the active site can bind one internal calcium, given a high-affinity site. Then, after the conformational switch, the pore is exposed to the outside, and at the same time the site is reconfigured to be lower-affinity, releasing the calcium ion into a high concentration environment. Neurons especially use calcium signaling extensively to operate synapses and regulate growth and development. Their rapid and frequent signaling requires a pump that has especially high capacity. PMCA2 operates at a maximal rate of several thousands of Ca2+ ions pumped per second.

Cartoon of the Post-Albers cycle, which is shared by a large family of active ATP-using pumps that transfer ions against their chemical concentration gradient. M is the main transmembrane domain of the pump, where the ions traverse the membrane. The N, P, and A domains are regulatory, especially binding and cleaving ATP  at an interface between the N, P, and A domain. The cycle links power steps (1,2) with conformational changes that carefully gate the pumping process.

And that is not all. Since calcium has a charge of 2+ and this pump does not intend to alter charge across the membrane, the pump simultaneously has binding sites for counter-ions (generally two OH-) that are transferred in the opposite direction from the calcium. Not only that, but every pump of this kind requires regulation of various kinds. PMAC2 is activated by phosphatidyl inositol 4,5 bisphosphate (PIP2), which is another important signaling molecule generated by specific PI kinases in response to activation of G-protein coupled receptors or protein kinase C, which may respond to external signals. In very general terms, these tend to be pro-growth or stress-induced pathways. These regulatory processes can tune the overall rate of recovery from rapid Ca2+ signaling events, by adjusting the level and activity of pumps like PMAC2. 

ATP binds at the N/P/A domain interface, and its hydrolysis (and loss of ADP) generates extensive shape changes, including into the transmembrane M domain. At the very bottom, the calcium ion is shown in green, bound inside the M domain pumping channel. The motions here are subtle, but enough to dramatically reshape the calcium channel.

The authors, using various substrate variants and other tricks, were able to develop structures of PMAC2 in several steps of the pumping cycle, using cryo-electron microscopy. The ATPase site in the N domain (red) is far from the channel that conducts the calcium ion (brown, far bottom). They show extensive shape changes from binding or losing the ATP molecule, though they mostly concern the intracellular domains (red, blue, yellow). The effects on the transmembrane pore domain are rather subtle, shown on right. The authors claim that, compared to other pumps of this large family, the structural changes are significantly less, suggesting that evolution for speed has caused the mechanism to become more efficient, with less wasted motion per conduction event, at least in the channel region itself.

Relation of the PIP2 binding domain (orange/red stick figures) to the calcium core binding site. PIP2 appears to be essential for rapid pump operation. At bottom is shown some schematics of the gating provided by PIP2 in bound and unbound states, especially via the D873 side chain (negatively charged aspartic acid).

They also find that the activating molecule PIP2 is neatly parked right next to the main calcium binding and conduction region, and is more or less essential for enzyme activity. In the graph above (e), they show that several single mutations made in the calcium binding high affinity site, for example switching the negatively charged D873 for the positively charged K (lysine), kills ion pumping activity. Mutation of the PIP2 binding pocket (KKQ->TLL, around position 347) likewise kills enzyme activity.

Relation of the counter-ion channel (red dots) with the calcium channel. Both are essential parts of the mechanism. Closeups with the coordinating protein side chains shown on the right.

The whole mechanism is alluded to in the last figure, where the central calcium binding site is shown, with the general direction of calcium pumping. The counter-ion transport area is shown nearby as a flurry of red dots (standing for water molecules, which at this scale are interchangeable with OH ions). Specific single mutations in either area, either changing negatively charged E412 to positively charged lysine at the calcium binding pocket, or changing polar S877 in the water/hydroxy binding area to the bulky and hydrophobic F (phenylalanine), each kill pumping activity (graph). 

While it would be ideal to have a more dynamic representation of what is going on, the new structures give tremendous detail, including the associated ATP, PIP2, calcium, and water molecules. The mutations also nail down several functional points. Obviously a rather intricate and well-oiled machine that keeps its bit of cellular calcium homeostasis on an even keel. It is hard to believe that the sum of thousands of machines like this one is life, but the deeper we look the more true that appears to be.

• Gullibility-maxxing.
• There is a serious bifurcation in Catholic thought.
• Reality has a well-known liberal bias.
• Well, that didn't work out so great.
• Is the internet going to collapse?

Not Every Transcript is Golden

 Reflections on junk DNA, and junk transcripts.

Some time ago, a large project in molecular biology determined that most regions of the genome are transcribed. The authors and most observers took this to mean that most regions are functional, quite in contrast to the reigning theory up to that point, that our genomes host a smattering of genes floating in a sea of "junk" DNA. That theory was based on the now-ancient observations of reannealing curves for bulk DNA from humans and other species which found that most of our DNA re-anneals very quickly, due to the fact that it is repetitive. Most of our genomes (60%) are taken up with LINE repeats, SINE repeats, old retro-transposons, stray duplications, and other repetitive material that, at a first glance, seems like junk. There has been a battle ever since, between proponents of junk DNA and those who see function around every corner. As we learn more about the genome, many more functions have indeed come to light, like distant enhancers and regulatory RNAs of many flavors. But overall, there still seems to be a lot of junk. 

A recent paper took an oblique shot at this field, looking at the profusion of alternative gene transcripts, which can number into the hundreds for a single gene. (This was also reviewed.) These are generally called isoforms, and arise due to variable ways one gene's RNA products can be initiated, terminated, and spliced. So not only are most regions of the genome transcribed in some form, actively transcribed regions can be transcribed and processed in myriad ways to lead to different RNA products. Here again, there has been an analogous argument, about whether every such isoform has a function, or whether isoforms might arise from more or less sporadic processes, often as unintended and non-functional sparks coming out of the machinery. The importance of isoforms is very well documented in many cases, so the possibility of function, sometimes highly conserved, is not in question. Only the importance of every last variation in combinatorial collections of isoforms that can number into the hundreds.

Here is an image from the first page (of about six pages) of RNA transcripts coming off the notorious BRCA1 gene, which is intensely studied for its role in breast cancer. Each line is a distinct mRNA transcript. Each darker bar is an exon, which are separated by introns. The darker colored exons are in the protein coding region, while the lighter exons signify the untranslated upstream and downstream ends. I count about 315 transcripts described for this genetic locus. The idea that each of these has some evolutionarily constrained and important function is, on the face of it, absurd.

The authors took an interesting evolutionary approach, reasoning that species with larger population sizes experience more stringent purifying selection, and thus should (in theory) show tighter control over stray genomic products such as isoforms, if most transcript isoforms are neutral (or even deleterious) accidents, rather than intentional and functional forms. Thankfully, animals come in a wide range of population sizes, from insects to crocodiles and primates; very large to very small. While population size is hard to calculate, several convenient proxies are known, like lifespan, body size, etc. When they totted everything up, they saw clear correlations between these proxies and the number of alternative RNA products per gene- also termed transcript diversity. They sliced up the data by organ where the RNA was expressed, and by the source of the RNA variation- either different initiation, different termination, different splicing. In all cases the trend was the same. In species with larger population sizes, the diversity of transcripts was lower, agreeing with their hypothesis that when greater selecive force is available, the slop from the transcription and transcript processing machinery declines.

The authors draw correlations between alternative splicing (AI) diversity in an organism's cells and its population size. 

The authors additionally note that there is a similar relationship between alternative splice site usage and expression level of a gene. That is, the higher the gene expression, the less likely that minor splice sites are used, indicating that here again, higher selective pressure helps to clear out non-functional off-products of the transcription apparatus.

The correlations found here are only that- correlations. While significant, they are not terribly strong, let alone stark. So it is evident that our gene expression machinery has a lot of play in it, and this falls on a spectrum from deleterious to critically functional. It is, after all, machinery, not divine. It is also grist for evolution itself- it is useful to have some slop so that there is always some diversity in the gearing to accommodate new selective pressures. But the idea that just because a distinct transcript exists, it is biologically functional, or that, similarly, because a genomic region is transcribed, it is a "gene" rather than junk DNA.. that does not hold water. Every nucleotide in the genome has its own unique selective constraints, and for many of them, that constraint is zero.

• The world order, and our position in it, is crumbling.
• Whence Hungary?
• Another AI tax, as if gobbling up power wasn't bad enough.
• Mindless.

Death and Resurrection ... Of a Gene

The SLAMF9 gene became non-functional in the human lineage, and then later was re-activated. Why?

Biology is amazingly intricate, but it is often also needlessly complex- evidence for the haphazard, if eventually pointed, mechanisms of the evolutionary process. We will take up the discussion of "junk" DNA again next week, but molecular biology is full of redundant and excessive processes, which should certainly be mystifying from a "design" perspective. At the frontier of natural selection are neutral and near-neutral genetic elements, which change over time due to chance, lacking selection pressure towards conservation. Pseudogenes (of which we have about 20,000- almost as many as functional genes) are one form of neutral element. They are typically remnants of functional genes that have been duplicated and inactivated by mutation. They are a lively area of genome annotation because it is hard to be sure that they are really dead. Despite what looks like an inactivating mutation, they typically still produce RNA transcripts, and may produce partial or alternative proteins as well. The literature is full of experiments finding products and activities from genes annotated elsewhere as pseudogenes. And what looks like a pseudogene from one sample might just be an allele, the same gene being whole and active in other people.

So, it is hard to know what any particular genetic region is doing without a lot of evolutionary, functional, and even population analysis. A recent paper looked deeply at one gene- a gene that seems to have flipped back and forth between functional and non-functional states in the human lineage. It is a rare example of a gene coming back from what is usually a one-way trip into mutational oblivion, once its function- and thus selective pressure for conservation- have disappeared.

SLAMF9 is one of a family (signaling lymphocyte activation molecule family) of surface receptors that occur in many cells of the immune system, help activate responses in these cells, and also recognize some viruses and bacteria. They bind to each other and to other components of the immune system, creating complex signaling networks. Genes involved in our immune systems are commonly subject to rapid evolution, the arms race against our many pathogens being relentless. Sometimes that takes the form of gene inactivation, if a particular receptor, for instance, has been turned against us by a pathogen that uses it for binding and cell entry. 

This week's authors were facing a conundrum. They were studying SLAMF9, and found the mouse version easy to clone and express in the lab. But the human version ... that was another story, frustratingly impossible to express in usable amounts. When they looked at the protein sequence, they were in for a big surprise:

At the front end of SLAMF9, there is very strong conservation across mammals... except when it comes to humans! The signal peptide is what directs this protein to be inserted into the plasma membrane, and is cleaved off the mature protein. In red is highlighted the region starkly different in humans, which naturally affects (not in a good way) the signal cleavage process. "a" and "b" point to important domains of the cytoplasmic side of the final protein, which are just barely preserved/conserved in the human form.

This alignment among various mammalian versions (orthologs) of SLAMF9 shows that they are all pretty much the same... except for the human version. All the way from mouse to chimpanzee nothing has changed at the front end of this protein. That is amazing in itself, showing very strong conservation. But then after our lineage split from chimpanzees, something weird. A small segment at the front of this protein is totally different. This area is important because it carries the cleavage site of the signal sequence. The signal sequence directs the protein to be sent to the membrane (as this is a trans-membrane receptor), and this cleavage site is bad, explaining why the author's attempt to express this protein went so poorly. It might be enough for modest expression in the natural setting, but not enough for their investigations.

At the DNA level, it is clear that what happened to the protein was a double frame shift in translation, out of frame at the front, then recovered frame at the second mutation. The mutations must have been independent events, but the order of their occurrence is not known. The first intron trails off to the left, while the coding sequence tails off to the right.

When they looked at the DNA sequence, the reason for this change in the protein sequence became clearer. There was a frame shift, with only small changes in the DNA sequence that led to the bigger change in the protein sequence. On the left, there is a shift in the splice site at the end of the first intron (splice acceptor). This shifts the mRNA product by four bases (vs the start site of translation), creating a frame shift in translation, as portrayed in the amino acid codes given. On the right, there is a one nucleotide deletion, causing another frame shift that brings the translation back into the normal frame. 

They sampled all the available archeological samples from the human lineage- Neanderthals and Denisovans, and each were the same as the current human sequence. So, whatever happened did so between the split from chimpanzees and the advent of these available homo species. And what happened were two distinct events- the second frame shift and the first frame shift are independent genetic mutations. 

Which happened first? That is uncertain, but the authors show that the right-most frame shift (called g.621delT) did not influence the change in the splice site. The splice site change was caused by a series of about six mutations within the first intron, (not shown), which shifted the pattern of mRNA self-hybridization that helps direct splice site selection. So it is likely that the splice site change happened first, essentially killing the gene. And then the downstream frameshift happened later on to rescue it in a partial, not very well-expressed way. However, either mutation could have happened first to functionally kill off this gene, and then further mutation(s) to recover its function. In any case, both events happened within this roughly six-million-year time span that generated our immediate lineage, becoming firmly fixed as the only version of this gene now in our collective genome.

What might cause these events? It all goes back to the function of SLAMF9. As shown above, it is very highly conserved. But, being part of the immune system and the interface we show to pathogens, it is also on the front line of the bio-warfare arms race. As humans started ranging far beyond their original habitats, they doubtless encountered many new pathogens. It seems likely that killing off this gene might have resolved one such fight, at least for a little while, perhaps by removing a pathogen entry point. But later on, it became beneficial to recover it, which is to say that new mutations that restored its function even a little bit were evidently selected for, and spread in the population. There was a race at this point between the accumulation of more (now neutral) mutations that would have permanently inactivated this gene, and the advent of that one special mutation that could save it. The overall conservation of SLAMF9 argues that saving it must have conferred significant benefits.

• "A single long-haul flight per year over the past decade leads to about $25k ($6,000–77,000) in future damages by 2100."
• These people run our lives?
• Update on the cerebellum.
• Cuba and capitalism, of a sort.

Dreaming Our Way Out of Capitalism

Review of "Understanding Capitalism", by Richard Wolff.

When I picked up this book, I thought it was going to be a sober analysis of capitalism, by a real economist. But what I was met with was something quite different- a Marxist screed with the most flaccid intellectual grounding, disingenuous and dishonest by turns. Wolff apparently has been paid to teach economics at liberal institutions, but this book is evidence that they have little idea what they are buying. 

Not that I am unsympathetic. Capitalism is a highly problematic system. But it hardly helps to make statements like: "Given China's huge influence on poverty measures, one could claim that reduced global poverty in recent decades results from an economic system that insists that it is not capitalist, but socialist." Note the squirrely way this is phrased, not defining the economic system, but noting only the wholly outdated self-description. China is one of the most capitalist countries in the world right now, having harnessed naked capitalism (and a lot of stolen IP) to raise its industries and living standard dramatically. 

Or how about this, in a discussion of why the idea that capitalism is highly innovative is a myth: "Yet the USSR, for example, exhibited much small business formation on its collective farms, in its service sector, and in its black markets, all replete with competition and innovations." If black markets are evidence of the innovative capacity of socialist economies, then the US is surely headed for Marxism forthwith.

It is almost funny how poorly this book is argued, and how formulaic its critiques and nostrums. But it provides a jumping-off point for a discussion that is a bit more grounded. Wolff casually describes capitalism as just another system, like feudalism and mercantilism, having its day and sure to pass on to some other, better system. He ends up promoting worker-owned cooperatives that are democratically run, where every action is voted on. Needless to say, such ideas have not, and will not, go anywhere. They are simply not practical. For we are, at base, dealing with human nature and the imperatives of existence. 

The state of nature (in larger societies) is organized crime- the strong rule the weak, and call themselves noble. Workers are managed by aristocrats (and priests), who make a fetish of not doing any work themselves. The feudal system was an attempt to give some order to this system of relations, by raising the serfs from mere slavery, and mandating some notional reciprocal duties. Capitalism, as even Marx appreciated, was an enormous advance over feudalism, putting the workers and businesses both on firmer legal footing, with a (labor) market intermediating between them. Labor markets have all sorts of problems and biases, but with advances in regulation and labor agitation, it has become for most people a relatively civilized way to exchange labor for money. 

Is capitalism still unfair? Yes, grossly so. But let's look two of its most basic injustices. First is that it takes money to make money. If one is born rich, one can be a capitalist and not work a day on one's life. Capitalism puts a high value on using that money to take risks and create businesses. But most rich people are content to buy bonds and sit on their money. What kind of capitalism is that? On the other hand, there is a large industry of venture capital that exists to lure money from the pockets of dentists and other rich people, promising high returns from risky ventures. This is the kind of essential engine that classical capitalism envisions- a tireless hunt for new business opportunities and technologies that will, in the end, make the economy more efficient and raise the standard of living. 

Wolff offers a telling example of capricious unfairness in management, where a business brings in a machine that replaces half of its workers, who are fired. He decries the loss of jobs, and suggests that the machine be used instead to fund continuing pay for all the workers. But just in the section before, he had decried the much-vaunted efficiency of capitalism as a myth. It does not sound like a myth here, where more work is done by fewer workers, and those fired workers are then freed to go off into other (presumably) productive forms of work.

Maybe China does a better job using state capitalism to deploy large amounts of capital. Maybe the USSR did a reasonable job, for a couple of decades, in deploying capital to build its heavy industry and arm for World War 2. And maybe free capital markets tend to vacillate between over-enthusiasm and credit contraction. But over the long term, it is clear that relatively free capital markets (with lots of government regulation!) do a good job of finding innovative business prospects and driving efficiency increases over the whole economy. So ... we should definitely think about taxing wealth, and finding ways to make the rich use their money in socially beneficial ways. But the idea that voters, or the state, can do a better job of general capital deployment is not realistic.

A second gross unfairness is management and surplus production. Why are workers still treated like slaves, told what to do, and then underpaid? Sadly, the fact is that management is a difficult job too. We had a worker-run bakery down the street in our city, and it only lasted a few years, because of the inherent problems of not having someone in charge of a business organization. The leading methods of worker-owned corporation now are oriented to giving workers ownership (like the Publix supermarket chain), but not management roles. Workers are on the board, but they do not run the day-to-day operations, because there simply has got to be decisiveness, accountability, and responsibility up the chain of a productive organization. Whether these roles have to be paid a lot more is open to question. But they do have to exist. Even in socialism, political commissars were part of management.

It is worth noting here that while management and unemployment are the disciplining factors for workers, competition is the disciplining mechanism for capitalists (in addition to government regulation). Without competition across the gamut, for labor, for markets, and for inputs, capitalists can abuse their workers and their customers. That is why a renewed focus on antitrust enforcement is an essential part of any progressive program of state oversight over the capitalist system.

As the example of black markets shows, market capitalism is a natural way of organizing human activities and satisfying our desires. But capitalism has plenty of problems. Capital and credit markets can not be left to their own devices. Glaring market failures, like in medicine, show that whole sectors of the economy have no business being capitalist businesses. Capitalism is an engine for turning "externalities", like minerals, air, and creativity, into money, heedless of destructive effects. So capitalism needs heavy regulation and continual reform to tame it into something that provides us with a civilized life. But at its core, it merely expresses our desires, needs, and ambitions, and that core engine needs to be preserved as well.

• When your Tesla crashes, it's your fault.
• Cheap e-vehicles are all the rage.. scooters, bikes, trikes.

Just Whose Foreign Policy Is This?

Our foreign policy appears to be led by people whom Trump gets weak in the knees for. Does that serve US or world interests?

US foreign policy serves not only US interests. We share an interest in the peaceful, prosperous, and sustainable future of the whole world, and as the leading nation, have an outsize role in its development. That is why Barack Obama got a Nobel peace prize, and why Donald Trump will not. As with most bullies, Trump puts on a show of strength and enjoys humiliating the weak. But there is also a curious weakness. He also loves humiliating himself at the feet of bigger and tougher bullies, for reasons that I frankly do not understand. 

The current war on Iran is not really in the US interest. Iran had already been boxed in by last year's attacks, which had supposedly obliterated any nuclear ambition. It is Israel that, in the person of Bibi Netanyahu, has been beating the drum about attacking Iran for several decades. It is Netanyahu who has been whispering in Trump's ear about how easy all this would be, including how the Iranian government would crumple under sustained assault. But I am sure our own intelligence knew better- that the Islamic state of Iran is a tough customer, having lived through the original takeover and US hostage crisis, then the brutal war with Iraq. It has legions of loyal IRGC and Basij all over the country. 

Unlike Netanyahu's view of things focused on its tactical defense, the US interest is in the long-term positive evolution of Iran, not in its tactical weakening. The bombing campaign is not only not going to break the government, but will make it stronger vs its people internally. The two likely paths it will lead to are, (at best) a civil war breaking out among the current actors in power, if they are not happy with the new supreme leader and the defense the Islamic leadership takes in this war. Or second, and more likely, the continued involution and isolation of the Iranian government, heading towards a North Korean model in a culture of suffering and perpetual resistance. And also, incidentally, the acquisition of a nuclear bomb at any cost. The idea that the powerless masses will somehow march their way into power during a bombing campaign is ridiculous.

So it is obvious that Trump was sweet-talked into this war, with no request from congress, no clamor from the American people, and no precipitating threat abroad, by none other than Netanyahu. And he was not smart enough to realize that he would not have a way out that serves US interests. Now oil prices are up, stocks are down, and those economic interests who really have the president's ear are going to be urging surrender after what, strategically speaking, has been a futile and immiserating affair. 

Even worse has been our policy towards Russia and Ukraine. It is evident that Trump loves to talk with Vladimir Putin, and Putin knows how to manipulate Trump. Just this week, the US dropped sanctions on Russian oil, in a bid to clean up its catastrophe in the Persian Gulf. Not seize Russian oil and sell it into world markets to benefit Ukraine, not block shipments of Russia's shadow fleet, but outright dropping sanctions. It is unbelievable, in any world where US interests drive US policy.

The Ukraine fight would have benefited from more decisiveness from the start, obviously. At least the Biden administration was rhetorically consistent, on the side of Ukraine, its position in Europe, and supporting our European allies. Our strategic interest is firstly in keeping Europe free of military conflict (as we keep the North American region). And secondly in containing Russia, in its new guise of anti-NATO imperialist revanchist power. Now all these aims are subordinated to getting a bad real-estate deal in Eastern Ukraine, and giving Russia what it wants. 

All through the second Trump administration, the US has been following Russian desires, reducing our support for Ukraine to nothing, berating Volodimir Zelensky in person, and bad-mouthing our European allies and alliance structures. How is all this in the US interest, when our core power stems from leadership of a community of like-minded and like-valued allies that have particularly and especially foresworn making Europe a battlefield? It is making the US weaker by the day. All due to the mental weakness of Donald Trump.

• Or perhaps other influences were at work.

How 5S rRNA Gets Into the Ribosome

For a minor component, it gets a lot of molecular love.

As mentioned several times in this space, the ribosome, which synthesizes proteins according to mRNA instructions, is an extremely ancient and complicated machine. Its core, including the catalytic site, is RNA. This marks it as a hold-over from the RNA world, as the thing that made proteins, (probably tiny proteins at first), before proteins had become a thing. But boy has there been a lot of duct-taping since then. In humans, there are four ribosomal RNAs, eighty proteins pasted on the outside, and hundreds of other proteins or RNAs involved in assembling the ribosome, not to mention dozens of initiation factors and other regulators that help during translation.

A recent paper discussed the maturation of 5S ribosomal RNA, which is the smallest rRNA, and one whose function is more peripheral than the large central 16S and 23S rRNAs. It is present in all life forms, though ribosomes inside mitochondria do without it. Its processing is an interesting case study of the complexity that has accumulated over the eons. Exactly what the 5S rRNA does remains a bit unclear, though it clearly contributes to the dynamics of the large ribosomal subunit, and occupies the "central protuberance". One group ligated it into the large subunit 23S rRNA, showing that translation still worked quite well with the 5S portion stably tacked into the structure. But then they also found that these ribosomes fell with high frequency into an unproductive locked state, suggesting that the independent nature of the 5S rRNA plays an important role in the dynamics of the ribosome. 

At any rate, the assembly of 5S into the rest of the structure is a story in itself. There are multiple steps involved, some involving ATP-using helicases. As it comes off the gene, 5S rRNA is bound by two proteins- the TFIIIA regulatory factor that activates its transcription, and also La protein (aka La antigen), which is a storage protein, named after systemic lupus, for which it is one immune target. To be incorportated into ribosomes, the RNA is next bound by a complex of Rpl5 and Rpl11, which will remain with the 5S RNA and become part of the eventual ribosome. Next come Rpf2 and Rrs1, which are two assembly facilitators that bind as a complex. Then comes Rsa4, which is similarly an assembly protein that helps the whole mess bind to the proper place on the (immature) large ribosomal subunit. Lastly, Rea1 (called MDN1 in humans) is an ATP-driven RNA helicase that wrenches the whole 5S-containing protuberance into its final and quite different position. 

The authors provide a scheme for the stepwise processing and assembly of 5S rRNA into the ribosome, involving numerous assembly factors, ribosomal proteins, and a helicase. 

It is quite an amazing story of progressive assembly, all to attach an element of the ribosome that is hardly central, but is rather a relatively late accretion on the machinery. Nevertheless, it evidently deserves specialized attention for correct placement. 

A less schematic view of various steps heading toward ribosomal assembly. 5S rRNA is in teal, and the helicase Rea1 is in dark gold, mounted like a wrench at the top of the (late) structure.

• We are strangling Ukraine. Why?
• Building more housing reduces housing shortages.

Bad Faith

"Skepticism" about vaccines, or about evolution... isn't skepticism at all.

This was going to be a post about the Ediacaran epoch, which is a fascinating time, spanning the hundred million years before the Cambrian, when animals began to appear in the fossil record. First tentatively, as sessile sheets of tissue, then later as beautiful motile segmented discs (below), and later still as something a bit more aggressively shaped. All this is yet another (as though more were needed) justification of the overall scheme of evolution developed by Charles Darwin, who knew about what in his time was already a distinct and puzzling lack of animal fossils below the Cambrian strata. If one seeks data in good faith, and while pursuing a well-reasoned hypothesis, one is bound to find something interesting! Incidentally, David Attenborough and the BBC gave an excellent treatment of this era.

The beautiful, and slightly motile, Dickinsonia, from the mid-Ediacaran, about 560 million years ago.

Yet there are some who don't see things that way. Over at the Discovery institute, they don't discover anything, but they do write blogs taking potshots at science. No fossil is enough, no explanation is acceptable. There is always a question left to answer, a gap that has not been filled, wherein God can be squeezed. It is the essence of bad faith, arguing not from reason and evidence, but from a pre-existing truth that must be defended at all costs, particularly against an inveterate enemy which ignores them so assiduously. An enemy who publishes, and publishes, and for whom the God hypothesis is not even worth mentioning in the quest to explain how things happen. Who regards them and their arguments as beneath contempt.

Well, needless to say, they were all in for Trump. If one likes to argue in bad faith, why not vote for the master? The new administration doesn't seem to have much stomach for the Darwinian evolution culture war of decades past (though there are three years to go.. who knows!?). But they have been doing their best to destroy science in the US and put China in the lead for good. Whether it is climate science, medical science, space science, it is all being gutted. Diplomats and other experts? Who needs them? We have discarded our allies, and our best friends are now Victor Orban, Vladimir Putin, Muhammad bin Salman, and Bibi Netanyahu. Fairness and legality at the Justice Department? Who needs that? The theme is kicking intelligent, moral people in the teeth, to bring in a callous, greedy and corrupt new dispensation for the US. One of the more alarming and consequential elements of this campaign has been against vaccines. All the real scientists were thrown off the advisory panels, replaced with vaccine "skeptics". 

We in the US have a long history with vaccines. The revolutionary war featured solicitations for soldiers already vaccinated against (or recovered from) smallpox, the most frightening scourge of the army's camps. Later on, Washington approved mass vaccination for the army. Vaccination in that day (variolation) was no easy matter. It involved introducing someone else's smallpox into an opened vein, and taking all the risks of infection. It was lethal 1-2% of the time, but those were better odds than the 25% death rate from normally contracted small pox. These people knew how to assess risks, and took the vaccination risk to forestall the greater risk. Then there was the polio vaccine, in the 1950's, that wiped out another scourge. One would think that getting a vaccine made in record time that promptly resolved the Covid pandemic and saved millions of lives would have been greeted with a bit more appreciation. But no, it was all too easy to take that science for granted, and adopt bad faith arguments against that and other vaccines.

Today's vaccines still carry risk, though minuscule compared to variolation. The odds are incredibly good. It takes no brains at all to judge vaccines worthwhile. But we have "skeptics". Why do we have them? For the same reason that we have Donald Trump, or have believers in religion. Humans are gullible and seek easy truths over hard ones. It is easy to feel squeamish about getting an injection. It is easy to believe that a con man with enormous self-confidence and wealth has some degree of competence. And it is easy to believe that we as humans are special with some special someone running the universe who cares about our fate. Those are the easy truths, archetypally ingrained, apparently. It takes higher intellectual standards and discipline to look at reality and accept that many easy truths are not true at all. 

For all their religious faith, (and indeed because of it), the religious people who pervade the current administration, Supreme Court, and culture war strongholds routinely argue in bad faith. They are pre-selected for their ability to believe stupid and wrong things. They are not sincere in looking for evidence, or making logical arguments. They put forth laughable legal arguments. They hardly even bother to explain why the "endangerment finding" on CO2 is wrong on the merits. They care about loyalty ahead of competence. And do not even understand what might be systematically wrong about raging corruption. When faith (in their charismatic leader, or their warped religious convictions) comes first, intellect takes a back seat. That is the fundamental rule of this new dispensation in the US, and it will be damaging us for a very long time.

• Clowns in high places.
• History repeats, the second time as farce.
• An AI winter?
• To touch, or not to touch, in curling.
• The rich just keep getting richer.
• For three justices, the law has no meaning whatsoever.

We Have Rocks in Our Heads ... And Everywhere Else, Too

On the evolution and role of iron-sulfur complexes.

Some of the more persuasive ideas about the origin of life have it beginning in the rocks of hydrothermal vents. Here was a place with plenty of energy, interesting chemistry, and proto-cellular structures available to host it. Some kind of metabolism would by this theory have come first, followed by other critical elements like membranes and RNA coding/catalysis. This early earth lacked oxygen, so iron was easily available, not prone to oxidation as now. Thus life at this early time used many minerals in its metabolic processes, as they were available for free. Now, on today's earth, they are not so free, and we have complex processes to acquire and manage them. One of the major minerals we use is the iron-sulfur complex, (similar to pyrite), which comes in a variety of forms and is used by innumerable enzymes in our cells. 

The more common iron-sulfur complexes, with sulfur in yellow, iron in orange.

The principle virtue of the iron-sulfur complex is its redox flexibility. With the relatively electronically "soft" sulfur, iron forms semi-covalent-style bonds, while being able to absorb or give up an electron safely, without destroying nearby chemicals as iron alone typically does. Depending on the structure and liganding, the voltage potential of such complexes can be tuned all over the (reduction potential) map, from -600 to +400 mV. Many other cofactors and metals are used in redox reactions, but iron-sulfur is the most common by far.

Reduction potentials (ability to take up an electron, given an electrical push) of various iron-sulfur complexes.

Researchers had assumed that, given the abundance of these elements, iron-sulfur complexes were essentially freely acquired until the great oxidation event, about two to three billion years ago, when free oxygen started rising and free iron (and sulfur) disappeared, salted away into vast geological deposits. Life faced a dilemma- how to reliably construct minerals that were now getting scarce. The most common solution was a three enzyme system in mitochondria that 1) strips a sulfur from the amino acid cysteine, a convenient source inside cells, 2) scaffolds the construction of the iron-sulfur complex, with iron coming from carrier proteins such as frataxin, and 3) employs several carrier proteins to transfer the resulting complexes to enzymes that need them. 

But a recent paper described work that alters this story, finding archaeal microbes that live anaerobically and make do with only the second of these enzymes. A deep phylogenetic analysis shows that the (#2) assembly/scaffold enzymes are the core of this process, and have existed since the last common ancestor of all life. So they are incredibly ancient, and it turns out to that iron-sulfur complexes can not just be gobbled up from the environment, at least not by any reasonably advanced life form. Rather, these complexes need to be built and managed under the care of an enzyme.

The presented structures of the dimer of SmsB (orange) and SmsC (blue) that dimerize again to make up a full iron-sulfur scaffolding and production enzyme in the archaean Methanocaldococcus jannaschii. Note the reaction scheme where ATP comes in and evicts the iron-sulfur cluster. On right is shown how ATP fits into the structure, and how it nudges the iron-sulfur binding area (blue vs green tracing).

A recent paper from this group extended their analysis to the structure of the assembly/scaffold enzyme. They find that, though it is a symmetrical dimer of a complex of two proteins, it only deals with one iron-sulfur complex at at time. It also binds and cleaves ATP. But ATP seems to have more of an inhibitory role than one that stimulates assembly directly. The authors suggest that high levels of ATP signal that less iron-sulfur complex is needed to sustain the core electron transport chains of metabolism, making this ATP inhibition an allosteric feedback control mechanism in these archaeal cells. I might add, however, that ATP binding may well also have a role in extricating the assembled iron-sulfur cluster from the enzyme, as that complex is quite well coordinated, and could use a push to pop out into the waiting arms of target enzymes.

"These ancestral systems were kept in archaea whereas they went through stepwise complexification in bacteria to incorporate additional functions for higher Fe-S cluster synthesis efficiency leading to SUF, ISC and NIF." - That is, the three-component systems present in eukaryotes, which come in three types.

In the author's structure, the iron-sulfur complex, liganded by three cysteines within the SmsC protein. But note how, facing the viewer, the complex is quite exposed, ready to be taken up by some other enzyme that has a nice empty spot for it.

Additionally, these archaea, with this simple one-step iron cluster formation pathway, get their sulfur not from cysteine, but from ambient elemental sulfur. Which is possible, as they live only in anaerobic environments, such as deep sea hydrothermal vents. So they represent a primitive condition for the whole system as may have occurred in the last common ancestor of all life. This ancestor is located at the split between bacteria and archaea, so was a fully fledged and advanced cell, far beyond the earlier glimmers of abiogenesis, the iron sulfur world, and the RNA world.

• Triumph of stupidity and corruption.
• Oil fields are a mess.
• Homes are going nuts.
• But they should be getting closer.
• Gosh, there was a pedophilia ring after all.
• Who wants a concentration camp?

The Federal Reserve is an Executive Agency

On the logic of the unitary executive, and the Supreme Court.

As our system of Federal institutions melts down, one actor deserves particular blame and disgrace. That is the Supreme Court. The extreme right majority have time and again tossed consistency, precedent, and logic to the winds in order to legislate their extreme view of executive power, which unfortuitously coincides with that of the current president. They have funneled dark money into the political system, equated money with speach, refused to address the glaring problems of gerrymandering, granted the president blanket immunity, and allowed the president to eviscerate civil service protections and independent agency structures specifically constructed by the legislature. And they have often used the shadow docket to do this dirty work, not even deigning to offer explanations at all, pursuasive or not.

Now they are tying themselves into pretzels to carve out an exception for the Federal Reserve, another independent agency that the president wants under his thumb. But it isn't so easy. The Federal Reserve clearly carries out executive functions, regulating banks, and setting interest rates, mostly by cooperating with the Treasury Department in the management of government debt. Is the Fed a court? Obviously not, as their criteria for action are economic conditions, guided by a mere two parameters- the dual mandate. They flexibly respond to conditions on the ground, in order to manage the US economy and currency. That sounds like an executive function to me. Is the Fed a legislature? They do not seem to enact laws, other than under their regulatory guise. But there are countless other agencies that promulgate rules. If that were the mark of a legislative institution, the court would have had to have made a wrong turn somewhere.

No, the Fed is just as executive as any other agency, and the court can not, by special pleading, argue otherwise. Therefore, either the Fed comes under the president's malign influence, or all the other agencies that Congress in its wisdom provided with measures of independence should have those structures respected as well. 

The significance of what the court is doing here is enormous. First, in their haste to give the president anything he wants and to execute a desire, apparently burning in the breast of John Roberts since the Nixon administration, to construct an imperial presidency, the court has repeatedly authorized the counter-legislative actions of the president to eviscerate agencies such as the labor relations board, the consumer financial protection agency, FTC, AID, and many others. This constitutes the reversal of Humphrey’s Executor v. United States, which laid the groundwork of regulatory agency structures. Second, the court is now casting about for rationales to not do the same to the Federal Reserve, out of an understandable practical desire to not have the country and its economy completely melt down. 

Both threads of action lack basis, and essentially constitute exactly what the court has heretofore so bitterly complained about- legislating from the bench. But of course, when Republicans do it, it is OK. The obvious solution is for the Supreme Court to climb down from its unitary executive horse, reverse its own shadow decisions, and accept that regulatory agencies can be structured by Congress with measures of independence to preserve the public interest precisely, as now, in the face of hostile and intemperate executives. 

Across the constitutional landscape, the problem is not that the executive is too weak, it is that Congress has ceded too much of its power to the executive. Just last week, when faced with Democratic demands that homeland security be brought to heel as a civilized agency, Republican Senators floated the idea of beseeching the President for a new executive order or two. It is incredible. Through the New Deal, World War 2, and the Cold War, the executive branch grew enormously, almost beyond the capacity of Congress to conceive of, let alone oversee. Yet in the Constitution, article 1 is by far the longest, most detailed, and most extensive. Congress has the ability "To regulate Commerce with foreign Nations", "To establish an uniform Rule of Naturalization", "To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States", etc. etc. and on and on. Congress makes the rules and provides the structures within which the executive works. Indeed, "To make all Laws which shall be necessary and proper for carrying into Execution the foregoing Powers, and all other Powers vested by this Constitution." It sure seems that Congress is able, as envisioned throughout article 1, to structure executive agencies as it sees fit. 

The constitutional section on the executive branch is, in comparison, exceedingly brief, only requiring reports to congress, command of the armed forces, and the making of treaties, with the consent of Congress. He or she also gets the veto power and makes a variety of appointments, to the courts and the executive branch. That is pretty much it. All else is left to interpretation and conjecture. While the President has wide appointment powers, it is not given the he or she has equally wide dismissal powers. That would be something well within the lawmaking capacity of Congress to regulate. It is apparent from this text that Congress makes all the rules and oversees the operation of the government as a whole, in the broadest terms. Congress is the body that makes the best decisions, that are most accountable to the people, in a deliberative and careful way. Thus the most important decisions are reserved to it. It is also notable that Congress has the power to impeach officers of each of the other branches, a power none of them have over Congress. It is only the people, and Congress itself, which can remove or discipline its own members.

The need for an executive is a practical matter, for someone who is present all the time (does not adjourn for long periods), and who, by his or her nature as a single person rather than a committee, can make hasty decisions in those areas that require it. And not every area of administration, needless to say, requires such an approach. Just because the Presidency is patterned on the relations between Britain's parliament and its king (which had itself developed by that point, given the civil war, beheadings, etc. to a complex system of power sharing) does not mean that the President has infinite latitude. Far from. 

It is thus apparent from this structure and from the history from the earliest times that Congress can make institutional structures of many kinds, in its quest to do whatever is necessary and proper. The first Bank of the United States is an example of one such structure, totally divorced from the President (and perhaps overly independent, as it later turned out). Not every executive function needs the immediate attention of the President, or benefits from his or her political meddling. Sometimes the structures necessary and proper for carrying laws into execution make use of experts, or bipartisan appointees, or public-private partnerships, or tenured appointees. Right now, the Justice Department stands out as an area that particularly needs better statutory protection from the whims of the executive. The Consitution itself provides for modes of shared appointment, as when Senate approval is needed for high executive officials, or long tenure, such as for Supreme Court justices. Such methods of reining in the dangerous and highly political powers of the presidency are clearly consistent with the text, history, and spirit of the Constitution. If those methods are not working, or one does not like them, change the laws, do not unlegislate them from the bench.

• NATO is falling apart.
• Krugman has some harsh words on Warsh.
• Insults and cruelty will continue until you like me.
• Science and football helmets.