Nominee for Most Amazing Protein: RAD51

On the repair and resurrection of DNA, which gets a lot of help from a family of proteins including RAD51, DMC1, and RecA.

Proteins do all sorts of amazing things, from composing pores that can select a single kind of ion- even just a proton- to allow across a membrane, to massive polymerizing enzymes that synthesize other proteins, DNA, and RNA. There is really no end to it. But one of the most amazing, even incredible, things that happens in a cell is the hunt for DNA homology. Even over a genome of billions of base pairs, it is possible for one DNA segment to find the single other DNA segment that matches it. This hunt is executed for several reasons. One is to line up the homologous chromosomes at meiosis, and carry out the genetic cross-overs between them (when they are lined up precisely) that help scramble our genetic lineages for optimal mix-and-matching during reproduction. Another is for DNA repair, which is best done with a good copy for reference, especially when a full double-strand break has happened. Just this week, a fascinating article showed that memories in our brains depend in some weird way on DNA breaks occurring in neurons, some of which then use the homologous repair process, including homology search, to patch things up.

The protein that facilitates this DNA homology search is deeply conserved in evolution. It is called RecA in bacteria, radA and radB in archaea, and the RAD51 family in eukaryotes. Naturally, the eukaryotic family is most closely related to the archaeal versions (RAD51 and DMC1 evolving from radA, and a series of other, and poorly understood family members, from radB). In this post, I will mostly just call them all RAD51, unless I am referring to DMC1 specifically. The name comes from genetic screens for radiation-sensitive mutants in human and other eukaryotes, since RAD51 plays a crucial role in DNA repair, as noted above. RAD51 is not a huge protein, but it is an ATPase. It binds to itself, forming linear filaments with ATP at the junction points between units. It binds to a single strand of DNA, which is going to be what does the hunting. And it binds, in a complicated way, to another double-stranded DNA, which it helps to open briefly to allow its quality as a target to be evaluated. 

This diagram describes the repair of double strand breaks (DSB) in DNA. First the ends are covered with a bunch of proteins that signal far and wide that something terrible has happened- the cell cycle has to stop.. fire engines need to be called. One of these proteins is RPA, which simply binds all over single-stranded DNA and protects it. Then the RAD51 protein comes in, displaces RPA, and begins the homology search process. The second DNA shown, in dark black, doesn't just happen, but is hunted for high and low throughout the nucleus to find the exact homolog of the broken end. When that exact match is found, the repair process can proceed, with continued DNA synthesis through the lesion, and resolution of the newly repaired double strands, either to copy up the homolog version, or exchange versions (GC, for gene conversion). 

This diagram shows how the notorious (when mutated) oncogene BRCA2 (in green) works. It binds RAD51 (in blue) and brings it, chain-gang style, to the breakpoints of DNA damage to speed up and specify repair.

There have been several structural studies by this point that clarify how RAD51 does its thing. ATP is simply required to form filaments on single-stranded DNA. When a match has been found and RAD51 is no longer needed, ATP is cleaved, and RAD51 falls off, back to reserve status. The magic starts with how RAD51 binds the single stranded DNA. One RAD51 binds for every ~3 bases in the DNA, and the it binds the phosphate backbone, so that the bases are nicely exposed in front, and all stretched out, ready to hunt for matching DNA.

A series of RAD51 molecules (in this case, RecA from bacteria) bound sequentially to single-stranded DNA (red). Note the ATP homolog chemicals in yellow, positioned between each protein unit. One can see that the DNA is stretched out a bit and the bases point outwards.

A closeup view of one of the RAD51 units from above, showing how the bases of the DNA (yellow) are splayed out into the medium, ready to find their partners. They are arranged in orientations similar to how they sit in normal (B-form) DNA, further enhancing their ability to find partners.

The second, and more mysterious part of the operation is how RAD51 scans double-stranded DNA throughout the genome. It has binding sites for double-stranded DNA, away from the single-stranded DNA, and then it also has a little finger that splits open the double-stranded DNA, encouraging separation and allowing one strand to face up to the single stranded DNA that is held firmly by the RAD51 polymer. The transient search happens in eight-base increments, with tighter capture of the double-strand DNA happening when nine bases are matched, and committment to recombination or repair happening when a match of fifteen bases is found.  

These structures show an intermediate where a double-stranded DNA (ends in teal and lavender, and separated DNA segments in green and red) has been captured, making a twelve base match with the stable single-stranded DNA (brown). Note how the double-stranded DNA ends are held by outside portions of the RAD51 protein. Closeup on the right shows the dangling, non-paired DNA strand in red, and the newly matched duplex DNA with green-brown colored base interactions.

These structures can only give a hint of what is going on, since the whole process relies so clearly on the brownian motion that allows super-rapid diffusion of the stablized single-strand DNA+RAD51 over the genome, which it scans efficiently in one-dimensional fashion, despite all the chromatin and other proteins parked all over the place. And while the structures provide insight into how the process happens, it remains incredible that this search can happen, on what is clearly a quite reliable basis, day and day out, as our genomes get hit by whatever the environment throws at us.

"Unfortunately, most RAD51 and RAD51 paralog point mutations that have been clinically identified are classified as variants of unknown significance (VUSs). Future studies to reclassify these RAD51 gene family VUSs as pathogenic or benign are desperately needed, as many of these genes are now included on hereditary breast and ovarian cancer screening panels. Reclassification of HR-deficient VUSs would enable these patients to benefit from therapies that specifically target HR deficiency, as do poly(ADP)-ribose polymerase (PARP) inhibitors in BRCA1/2-deficient cells."

Lastly, one paper made the point that clinicians need better understanding of the various mutations that can affect RAD51 itself. Genetic testing now is able to find all of our mutations, but we don't always know what each mutation is capable of doing. Thus deeper studies of RAD51 will have beneficial effects on clinical diagnosis, when particular mutations can be assigned as disease-causing, thus justifying specific therapies that would otherwise not be attempted.

• Let's make taxes public.
• A plea for less sugar.

Renewable Power in Africa

Prospects for growth in electricity access and in clean energy.

Africa is an enormous continent, notoriously larger than China, the US, and Europe combined. Its population is also large- as large as that of India, at about 1.4 billion people. This population is growing rapidly, while its social and economic systems are developing more slowly. But as we know, the main ingredient of an advanced economy is power, which as traditionally been drawn from fossil fuels. Advanced economies are in the painful and reluctant process of transitioning away from fossil fuels. We can do a lot to help Africa to leapfrog this history by front-loading renewable energy.

There was a recent paper about the hydropower prospects in Africa. It notes that there are many projects on the drawing board, with many undammed rivers on the continent. But as we have learned in the US, the implications of river damming are quite destructive and wide-spread. For example fish ladders simply do not work- not at the scale needed to keep fish populations (and fisheries) healthy. Then there are problems of siltation, water temperature, erratic flows, and population displacement. There is a movement in the US to remove dams wherever possible, to free ecosystems back to a functional state. 

"More than 300 hydropower plants, corresponding to an additional 100-GW power capacity, are under consideration across the continent."

The article made the basic point that, given the state of other renewable power sources, and the prospect of lower water levels and droughts due to climate change, that roughly half of the planned hydropower projects they know of are economically inviable, even putting aside environmental considerations. 

This leads to the question of what to do instead? Maybe the answer is microgrids. In the developed world, it is increasingly common for people to take control of their own electricity production through the use of solar power. But at a single house level, power inputs and consumption are both erratic and require a lot of storage capacity to furnish a reliable system. The typical system is highly reliant on the larger grid to manage this intermittency. Microgrids occupy a middle range between grid-scale power, which is subject to problems of centralized political and social development, and the individual house, where the expense of managing fully independent electrical supply is highest.

The current grid in Africa, colored for >66 kV (dark blue) and the rest light blue. Note the patchy regional distribution, with lots of underserved areas. The US has a much denser grid. 

A map that suggests likely locations for smaller microgrids in Africa.

These maps note that there are many underserved areas in Africa- some concentrated urban areas, and a great spread of rural areas. Electrification is well-advanced in South Africa and the heart of West Africa. But there are many rural areas that would be better served by microgrids of various scales. Microgrids can be altered over time and integrated into larger systems. Their production and storage capacities are both beneficial for larger grid stability and scalability. Africa is, naturally, positioned ideally for solar power, and the Sahara is a natural location for massive power installations, to serve both Europe, the Middle East, and Africa.

A proposal to run a super-grid around much of Africa, to harness supplies from the Sahara, among other sources.

One of the main characteristics of renewable power is that it has high up-front costs. The fuel is free, and clean. But the mechanisms to capture and store it are expensive. Thus if we want to encourage a more rapid transition to sustainable power systems in Africa, we would help pay for the up front costs, sharing capital investment in the interests of everyone, both here and there. Africa is currently a big exporter of oil and gas. As other regions transition away from those fuels, it is imperative that this production not be redirected and propped up by further Western investment, but rather replaced with better energy sources.

• Advanced nuclear power is not going to cut it.
• The heat pump song.
• Treason, again.
• On silence and isolation.
• Housing prices should not always go up.
• Medicare disadvantage.

Ideologies of Work

Review of Elizabeth Anderson: "Hijacked: How neoliberalism turned the work ethic against workers, and how workers can take it back."

We live by the sweat of our brow, though work. At least that has been the story after we were thrown out of the garden of Eden, where we had previously foraged without effort. By the time of Puritans, work had been re-valued as being next to godliness, in what became known as the Puritan work ethic. Elizabeth Anderson takes this as her point of departure in a fascinating historical study of the winding (and mostly descending) road that attitudes toward work took down the centuries, in the perennial battle between workers and parasites who have found ways to avoid sweating, yet eat just the same ... or better.

Anderson trots through all the classical economists and philosophers, down to John Stuart Mill and Marx, showing two main threads of thought. First is the progressive thread, in which the Puritans can (curiously) be classed, as can Adam Smith. They value work as both a cultural and meaningful activity, not just a means of sustenance. They think everyone should work, and criticize anyone, high or low, who shirks this responsibility. Genteel landowners who spend their time hunting rather than improving their estates are just as culpable as drunkards and other able-bodied peasants who fail to do their share. Learning and innovation are highly valued, as not just ameliorating the lot of those making improvements, but at the same time raising the wealth of, and standard of living for, all.

In contrast is the conservative thread. Anderson herself describes it trenchantly:

"From the conservative perspective, however, poverty reflected an individual's failure to filfill the demands of the work ethic. Society is at fault solely in establishing institutions that violate natural law in promoting vice through provisions such as the Poor Law. Conservatives agreed that the Poor Law must therefore be abolished or radically reformed. If poverty is caused by the vice of the poor, the remedy for poverty must be to force the poor to practice virtue, to live up to the demands of the work ethic. Conservatives differed somewhat on which virtue was most necessary for the poor to practice. Priestly focused on frugality, Bentham on industry, Malthus on chastity, Paley on contentment (understood as the opposite of covetous envy of the rich). Thus, Priestly hoped to convert poor workers into virtuous bourgeios citizens through a legally mandated individual savings plan. Bentham favored a workfare system that turned the working poor into imprisoned debt peons of capitalist entrepreneurs. Malthus advocated leaving the poor to starvation, disease and destitution, but offered them the hope that they could rescue themselves by postponing marriage and children. Burke and Wately agreed with Malthus, but attempted to put a liberal-tory paternalist veneer on their view. ...

"The moral accounting that assigns responsibilities to individuals without regard- and even in inverse proportion- to the means they have to fulfill them remains a touchstone of conservative thought to the present day. ...

"The ideology of the conservative work ethic is distinguished by a harsh orientation toward ordinary workers and the poor, and an indulgent one toward the 'industrious' rich- those who occupy themselves with making money, either through work or investment of their assets, regardless of whether their activities actually contribute to social welfare. in practice, this orientation tends to slide into indulgence toward the rich, whether or not they are industrious even in this morally attenuated sense. ...

"Here lies a central contradiction of the conservative work ethic. All the conservatives claimed that the key to overcoming poverty was to make the poor bourgeois in attitude. All they needed to do was adopt the work ethic, or be forced to adopt it, along with the spirit of competitive emulation, the desire to better others in the race for riches and ensure that one's children not fall beneath the standard of living in which they were raised. Poverty was proof that they hadn't adopted bourgeois virtues and aspirations. This presupposed that the poor suffered from no deficit in opportunities. The path to prosperity was open; the poor were simply failing to take it. Yet we have seen that, Priestly partially excepted, conservative policies knowingly reduced the opportunities of the poor to acquire or retain property, work for themselves, or escape precarity."

My major critique of Anderson's analysis is that putting all this conflict and history into the frame of the work ethic is inappropriate and gives the work ethic far more weight than it merits. Firstly, everyone thinks of themselves as working. The most sedentary rentier doubtless thinks of his or her choosing among investments as of critical importance to the health and future of the nation. Even his or her shopping choices express taste and support a "better" sort of business, in that way performing work towards a better community. The English royals probably see themselves as doing essential cultural work, in their choice of hats and their preservation of cherished traditions. Parenting, community associations, and political agitation can all, to an expansive mind, be construed as "work". And indeed some of our greater artistic and other accomplisments come from the labors of wealthy people who were entirely self-directed rather than grubbily employed. All this implies that a work ethic can be accommodated in all sorts of ways if markets are not going to be the standard, as they hardly can be in any philosophical or moral system of a work ethic. This makes work ethics rather subjective and flexible, as Anderson implicitly demonstrates through the centuries.

However a more serious problem with Anderson's analysis is that it leaves out the ethic of power. Her presentation laments the sad misuse that the work ethic has been subjected to over the years, (by conservatives), without focusing on the reason why, which is that a whole other ethic was at work, in opposition to the work ethic. And that is the power ethic, which values domination of others and abhors work as commonly understood. Or, at best, it construes the organization of society for the benefit of a leisured upper crust as work of momentous, even civilizational, significance. Nietzsche had a field day calling us to recognize and embrace the power ethic, and not hide it under sweeter-smelling mores like the Christian or work ethics.

Anderson does helpfully discuss in passing the feudal background to the Puritan work ethic, where the Norman grandees and their progeny parcelled out the land among themselves, spent their time warring against each other (in England or in France), and lived high off the labors of their serfs/peasants. No thought was given to improvement, efficiency, or better ways to organize the system. Conservatism meant that nothing (god-willing) would change, ever. Even so, the work of politics, of war, and of religious ideology was never done, and the wealthy could easily see themselves as crucial to the maintenance of a finely-balanced cultural and economic system.

Anderson also notes that the original rationale of the gentry, if one must put it in an economic frame, was that they were responsible for military support of the king and country, and thus needed to have large estates with enough surplus in people, livestock, horses, and food to field small armies. When this rationale disappeared with the ascendence of parliament and general (at least internal) peace, they became pure rentiers, and uncomfortably subject to the critique of the Puritan work ethic, which they naturally countered with one of their own devising. And that was essentially a restatement of the power ethic, that the rich can do as they please and the poor should be driven as sheep to work for the rich. And particularly that wealth is a signifier of virtue, implying application of the work ethic, (maybe among one's forebears, and perhaps more by plunder than sweat, but ... ), or transcending it via some other virtues of nobility or class. 

But in Locke and Adam Smith's day, as today, the sharpest and most vexing point of the work ethic is not the role of the rich, but that of the poor. By this time, enclosure of lands was erasing the original version of the job guarantee- that is, access to common lands- and driving peasants to work for wages, either for landowners or industrialists. How to solve extreme poverty, which was an ever more severe corollary of capitalism and inequality? Is it acceptable to have homeless people sleeping on the streets? Should they be given work? money? social services? education? Do the poor need to be driven to work by desperation and starvation? Or is the lash of work not needed at all, and lack of wealth the only problem? Malthus was doggedly pessimistic, positing that population growth will always eat up any gains in efficiency or innovation. Thus it requires the predatory power of the gentry to enable society to accumulate anything in the way of capital or cultural goods, by squelching the poor in sufficient misery that they will not over-reproduce.

The progressive view of work and the poor took a much more sanguine view. And here one can note that much of this discussion revolves around "natural" laws. Is the population law of Malthus true? Or is the natural communitarian tendency of humans also a natural law, leading to mutual help, spontaneous community formation, and self-regulation? Are some people "naturally" superior to others? Is a hierarchical and domineering social system "natural" and necessary? Adam Smith, in Anderson's reading, took a consistently pro-worker attitude, inveighing against oppressive practices of employers, collusion of capital, and cruel goverment policies. Smith had faith that, given a fair deal and decent education, all workers would strive to the best of their abilities to better their own condition, work diligently, and thereby benefit the community as well as themselves.

For the story of Eden is fundamentally wrong. Humans have always worked, and indeed valued work. Looking outside the window at a squirrel trying to get into the bird feeder ... is to see someone working with enthusiasm and diligence. That is our natural state. The only problem was that, as human civilization progressed, power relations, and then even more- industrialization- generated work that was not only cruel and oppressive, but meaningless. The worker, forced to work for others instead of him- or herself, and routinized into a factory cog, became fully alienated from it. How to get workers to do it, nevertheless? Obviously, having a work ethic is not a full solution, unless it is of a particularly astringent and dogmatic (or tyrannical) sort. Thus the dilemma of capitalist economies. For all their trumpeting of the "natural laws" of competition and "freedom" for employers to exploit and workers to be fired, capitalism violates our true natures in fundamental ways.

So the question should be, as Anderson eventually alludes to, do we have a life ethic that includes work, rather than just a work ethic? She states plainly that the most important product of the whole economic system is ... people. Their reproduction, raising, education, and flourishing. It is not consumption products that should be the measure of economic policy, but human happiness. And a major form of human happiness is doing meaningful work, including the domestic work of the family. The world of Star Trek is even alluded to in Anderson's last chapter- one where no one works for subsistance, but rather, people work for fulfillment. And they do so with zeal.

Anderson sees great potential in the more progressive forms of the work ethic, and in the social democratic political systems that implemented them after World War 2. She argues that this is the true legacy of Marxism (and of Thomas Paine, interestingly enough) and expresses the most durable compromise between market and capital-driven corporate structures and a restored work ethic. Some amount of worker participation in corporate governance, for instance, is a fundamental reform that would, in the US, make corporations more responsive to their cultural stakeholders, and work more meaningful to workers. Tighter regulation is needed throughout the private economy to make work more humane for the very low-paid, giving workers better pay and more autonomy- real freedom. More public goods, such as free education to university levels, and better provision for the poor, especially in the form of a job guarantee, would make life bearable for many more people. For my part, inheritance seems a key area where the ethics of the dignified work and equal opportunity run up against completely unjust and artificial barriers. In America, no one should be born rich, and everyone should grow and express themselves by finding a place in the world of work.

• Annals of capitalist control.
• Corporations and the royal we.
• More equal societies are better societies.
• The Stepford wife.
• The Supreme Court is dangerously wrong.

Getting Cancer Cells to Shoot Themselves

New chemicals that make novel linkages among cellular components can be powerful drugs.

One theme that has become common in molecular biology over the years is the prevalence of proteins whose only job is to bring other proteins together. Many proteins lack any of the usual jazzy functions, like catalytic enzyme, or ion channel, or signaling kinase, but just serve as "conveners", bringing other proteins together. Typically they are regulated in some way, by phosphorylation, expression, or localization, and some of these proteins serve as key "scaffolds" for the activation of some process, like G-protein activation, or cell cycle control, or cell growth. 

Well, the drug industry has caught on, and is starting to think about chemicals that can do similar things, resulting in occasionally powerful results. Conventional drug design has aimed to bind to whatever protein is responsible for some ill, and inhibit it. Such as an oncogene, or an over-active component of the immune system. This has led to many great drugs, but has significant limitations. The chemical has to bind not just anywhere on the target, but at the particular spot (the active site) that is its business end, where its action happens. And it has to bind really well, since binding and inhibiting only half the target proteins in a cell (or the body) will typically only have a modest effect. These requirements are quite stringent and result in many protein targets being deemed difficult to drug, or "undruggable".

A paradigm for a new kind of chemical drug, which links two functions, is the PROTAC class, which combines binding with a target on one end, with another end that binds to the cell's protein destruction machinery, thereby not just inhibiting the target, but destroying it. A new paper describes an even more nuclear option along this line of drug development, linking an oncogene with a second part that activates the cellular suicide machinery. One can imagine that this approach can have far more dramatic effects.

These researchers synthesize and demonstrate a chemical that binds on one end the oncogene BCL6, mutations of which can cause B cell lymphoma. This gene is a transcription repressor, and orchestrates the development of particular immunologic T cells called T follicular helper cells. One of its roles is to prevent the suicide of these cells when an antigen is present, which is when the cells are most needed. If over-expressed in cancer, these cells think they really need to protect the body and proliferate wildly.

The other end of this chemical, called TCIP1, binds to BRD4, which is another transcription regulator, but this one activates the cell suicide genes, instead of turning them off. Both ends of this molecule were based on previously known structures. The innovation was solely in linking them together. I should say parenthetically that BRD4 is itself recognized as an oncogene, as it can promote cell growth and prevent cell suicide in many settings. So it has ambivalent roles, (inviting a lot of vague writing), and it is somewhat curious that these researchers focused on BRD4 as an apoptosis driver.

"TCIP1 kills diffuse large B cell lymphoma cell lines, including chemotherapy-resistant, TP53-mutant lines, at EC50 of 1–10 nM in 72 h" 

Here EC50 means the effective concentration where the effect is 50% of maximal. This value of 1.3 nano molar is a very low concentration for a drug, meaning it is highly effective. TP53 is another cancer-driving mutation, common in treatment-resistant cancers. The drug has a characteristic and curious dosage behavior, as its effect decreases at higher concentrations. This is because each individual end of the molecule starts to bind and saturate targets independently, reducing the rate of linkage between the two target proteins, and thus the intended effect.

Chemical structure of TCIP1. The left side binds to BRD4, a regulator of cell suicide, while the right side binds to BCL6, an oncogene.

The authors did numerous controls with related chemicals, and tracked genes that were targeted by the novel chemical, all to show that the dramatic effects they were seeing were specifically caused by the linkage of the two chemical functions. Indeed, BCL6 represses its own transcription in the natural course of affairs, and the new drug reverses this behavior as well, inducing more of its own synthesis, which now potentiates the drug's lethal effect. While the authors did not show effectiveness in animals, they did show that TCIP1 is not toxic in mice. Neither did they show that TCIP1 is orally available, but administered it by injection. But even by this mode, it would, if effective, be a very exciting therapy. Not surprisingly, the authors report a long series of biotech industry ties (rooted at Stanford) and indicate that this technology is under license for drug development.

This approach is highly promising, and a significant advance in the field. It should allow increased flexibility in targeting all kinds of proteins that may or not cause disease, but are specific to or over-expressed in disease states, in order to address those diseases. It will allow increased flexibility in targeting apoptosis (cell suicide) pathways through numerous entry points, to have the same ultimate (and highly effective) therapeutic endpoint. It allows drugs to work at low concentrations, not needing to fully occupy or inhibit their targets. Many possible areas of therapy can be envisioned, but one is aging. By targeting and killing senescent cells, which are notorious for promoting aging, significant increases in lifespan and health are conceivable. 

• Biden is doing an excellent job.
• Annals of mental decline.
• Maybe it is an anti-addiction drug.
• One gene that really did the trick.
• A winning issue.
• It is hard to say yet whether nuclear power is a climate solution, or an expensive distraction.

Ions: A Family Saga

The human genome encodes hundreds of proteins that ferry ions across membranes. How did they get here? How do they work?

As macroscopic beings, we generally think we are composed of tissues like bones, skin, hair, organs. But this modest apparent complexity sits atop a much greater and deeper molecular diversity- of molecules encoded from our genes, and of the chemistry of life. Management of cellular biochemistry requires strict and dynamic control of all its constituents- the many ions and myriad organic molecules that we rely on for energy, defense, and growth. One avenue is careful control across the cellular membrane, setting up persistent differences between inside and outside that define the living cell- one may say life itself. Typical cells have higher levels of potassium inside, and higher levels of sodium and chloride outside, for example. Calcium, for another example, is used commonly for signaling, and is kept at low concentrations in the cytoplasm, while being concentrated in some organelles (such as the sarcoplasmic reticulum in muscle cells) and outside. 

All this is done by a fleet of ion channels, pumps, and other solute carriers, encoded in the genome. We have genes for about 1,555 molecule transporters. Out of a genome of about 20,000 genes, this represents a huge concentration(!) of resources. One family alone, the solute carrier (SLC) family, has 440 members. Many of these are passive channels, which just let their selected cargo through. But many are also co-transporters, which harness the transport of one ion with that of another which may have an actively pumped gradient across the membrane and thus provide an indirect energy source for transfer of the first ion. The SLC family includes channels for glucose, amino acids, neurotransmitters, chloride, cotransport (or anti-transport) of sodium with glucose, calcium, neurotransmitters, hydrogen, and phosphate. Also, metals like zinc, iron, copper, magnesium, molybdate, nucleotides, steroids, drugs/toxins, cholesterol, bile, folate, fatty acids, peptides, sulfate, carbonate, and many others. 

It is clear that these proteins did not just appear out of nowhere. The "intelligent" design people recognize that much, that complex structures, which these are, must have some antecedent process of origination- some explanation, in short. Biologists call the SLC proteins a family because they share clear sequence similarity, which derives, by evolutionary theory, and by the observed diversification of genes and the organisms encoding them over time, from duplication and diversification. This, sadly, is where the "intelligent" design proponents part ways in logic, maintaining perhaps the most pathetic (and pedantic) bit of hooey ever devised by the dogmatic believer: "specified information", which apparently forbids the replication of information.

However, information replicates all the time, thanks to copious inputs of energy from the sun, and the advent of life, which can transform energy into profusions of reproduced/replicated organisms, including replication of all their constituent parts. For our purposes, one side effect of all this replication is error, which can cause unintended replication/duplication of individual genes, which can then diverge in function to provide the species with new vistas of, in this case, ionic regulation. In yeast cells, there are maybe a hundred SLC genes, and fewer in bacteria. So it is apparent that the road to where we are has been a very long one, taking billions of years. Gene duplication is a rare event, and each new birth a painful, experimental project. But a family with so many members shows the fecundity of life, and the critical (that is, naturally selected) importance of these transporters in their diverse roles throughout the body.

A few of the relatives in the SLC26A family, given in one-letter protein sequence from small sections of the much larger protein, around the core ion binding site. You can see that they are, in this alignment, very similar, clearly being in the same family. You can also see that SLC26A9 has "V" in a position in alpha helix 10, which in all other members is a quite basic amino acid like lysine ("K") or arginine ("R"). The authors argue that this difference is one key to the functional differences between it and SLC26A6.

A recent paper showed structures for two SLC family members, which each transport chloride ion, but differ in that one exchanges chloride for bicarbonate, while the other allows chloride through without a matched exchange (though see here). SLC26A9 is expressed in the gut and lung, and apparently helps manage fluid levels by allowing chloride permeability. It is of interest to those with cystic fibrosis, because the gene responsible for that disorder, CFTR, is another transporter, (of the ABC family), and plays a major role doing a similar thing in the same places- exchanging chloride and bicarbonate, which helps manage the pH and fluidity of our mucus in the lung and other organs. SLC26A9, having a related role and location, might be able to fill some of the gap if drugs could be found to increase its expression or activity.

SLC26A6 is expressed in the kidney, pancreas, and gut, and in addition to exchanging bicarbonate for chloride, can also exchange oxalate, which prevents kidney stones. Very little, really, is known about how all these ion transporters are expressed and regulated, what differentiates them, how they relate to each other, and what prompted their divergence through evolution. We are really just in the identification and gross characterization stage. The new paper focuses on the structural mechanisms that differentiate these two particular SLC family members.

Structure of two SLC transporters, each dimeric, and superimposed. The upper parts are set in the membrane, with the lower parts in the cytoplasm. The upper parts combine two domains for each monomer, the "core" and "gate" domains. The channel for the anion threads within the center of each upper part, between these two domains. Note how structurally similar the two family members are, one in green+gray, the other in red+blue.

Schemes of how SLC26A6 works. The gate domain (purple) is stable, while the core domain (green) rocks to provide access from the ion binding site to either outside or inside the cell.

Like any proper ion channel, SLC26A6 sits in the membrane and provides a place for its ion to transiently bind (for careful selection of the right kind of ion) and then to go through. There is a central binding site that is lined specially with a few semi-positively charged amino acids like asparagine (N), glutamine (Q) and arginine (R), which provide an attactive electronic environment for anions like Cl-. The authors describe a probable mechanism of action, (above), whereby the core domain rocks up and down to allow the ion to pass through, after being very sensitively bound and verified. This rocking is not driven by ATP or other outside power, but just by brownian motion, as gated by the ion binding and unbinding steps.

Drilling a little closer into the target ion binding site of SLC26A6. On right is shown Cl- in green, center, with a few of the amino acids that coordinate its specific, but transient, binding in the core domain pocket. 

They draw contrasts between these very closely related channels, in that the binding pocket is deeper and narrower in SLC26A9, allowing the smaller Cl- to bind while not allowing HCO3- to bind as well. There are also numerous differences in the structure of the core protein around the channel that they argue allow coupling of HCO3- transport (to Cl- transport in the other direction) in SLC26A6, while SLC26A9 is uncoupled. One presumes that the form of the ion site can be subtly altered at each end of the rocking motion, so that the preferred ion is bound at each end of the cycle.

While all this work is splitting fine hairs, these are hairs presented to us by evolution. It is evolution that duplicated the precursors to these genes, then retained them while each, over time, developed its fine-tuned differences, including different activities and distinct tissue expression. Indeed, the fully competent, bicarbonate exchanging, SLC26A6 is far more widely expressed, suggesting that SLC26A9 has a more specialized role in the body. To reiterate a point made many times before- having the whole human genome sequenced, or even having atomic structures of all of its encoded proteins, is merely the beginning to understanding what these molecular machines do, and how our bodies really work.

• A cult.
• The deep roots of fascism in the American Right.
• We are at a horrifying inflection point in foreign policy.
• Instead of subsidizing oil and gas, the industry should be charged for damages.
• Are we ready for first contact?

MRGA

Make Russia Great Again: Conservative, white, Christian, low levels of immigration, despotic ... what's not to love about Russia?

It would be unbelievable if it weren't true. The Republican party, which conducted the Red Scare of the 50's, and stood up for democracy, political conservatism, apple pie, patriotism, and militarism around the world, now stands for something quite different. A combination of hatreds- for Democrats, for immigrants, and, seemingly, for personal freedom- seems to have sent the Trumpy ecosystem into a very weird place, where Russia is good, autocracy is strength, and American democracy is weakness. What are real patriots to do?

Republicans in congress sure look like they are selling out Ukraine. After linking aid to southern border fixes, they realized that the fixes were going to be politically beneficial to Democrats, as would the Ukraine aid, so both were scuttled. The newest proposal appears to cut Ukraine aid, and not accept the Senate bill, but that is also stalled. We are, at best, in for a long negotiation, all furthering the interests of making Russia great again. And Trump himself was not shy about putting it all in words, declaring Putin's invasion of Ukraine "smart", and inviting invasion of more NATO countries.

This policy is, in essence, throwing away the whole post-war order and rationale for American power, stretching across our innumerable alliances from Europe to Japan. It is unimaginable to any serious student of American power and the last hundred years. But here we are, serving the interests of our enemies in the most blatant ways. Russia, needless to say, is not our friend. Could have been our friend, in the post-Cold War period, but Russia ended up under the thumb of Putin, whose hatred of the West appears foundational to his political success, and even more, to his KGB heart. 

What is the deeper thread behind this craziness? I think it goes back to the culture war. Republicans have decisively lost the overall culture war in America. Gay marriage is here to stay, diversity is mainstream, and even abortion is, after the overturning of Roe, a huge loser for Republicans. They are souring on America in a fundamental way, and looking elsewhere for inspiration. Like Nazi Germany, Hungary, and Russia. At least that is the way it looks and the way they, and especially Trump, talk. And with enough money and propaganda behind them, Republicans can to some extent buck the math and the good will of contemporary American democracy. The question is- how far? The last presidential election was razor-thin, but still, not a great indication that this strategy is going to be broadly popular, and recent elections have shown even worse results. 

In addition to straining to help Russia, this movement is doing anything but making America great again. Our friendships around the world are in tatters, with everyone nervously eyeing the next election. Republicans stand firmly behind making a sociopathic dolt president, for a second time. And their Supreme Court is authoring a new epoch of medieval jurisprudence. This is how empires crumble, when powerful factions decide that their hold on power is more important than the law, more important than petty democracy, more important than peace and stability, more important than truth, and that a little insurrection or civil war might not be such a bad way to force their views down everyone else's throats. When backed by oodles of money, shamelessness, and a relentless propaganda bullhorn, it is, needless to say, highly combustible.

• When people feel powerless.
• Oh, those innocent days.
• Platitude.
• Want to die in the arms of a corporation?
• Hunter Biden Hunter Biden Hunter Biden.
• Plastic is trash.
• Economic effects of the war in Russia.

A New Form of Life is Discovered

An extremely short RNA is infectious and prevalent in the human microbiome.

While the last century might be called the DNA century, at least for molecular biology, the current century might be called that of RNA. A blizzard of new RNA types and potentials have been discovered in the normal eukaryotic milieu, including miRNA, eRNA, lincRNA. An RNA virus caused a pandemic, which was remedied by an RNA vaccine. Nobel prizes have been handed out in these fields, and we are also increasingly aware that RNA lies at the origin of life itself, as the first genetic and catalytic mechanism.

One of these Nobel prize winners recently undertook a hunt for small RNAs that might be lurking in the human microbiome- the soup of bacteria, fungi, and all the combined products that cover our surfaces, inside and out. What they found was astonishing- an RNA of merely 1164 nucleotides, which folds up into a rigid, linear rod, which they call "obelisks". This is not a product of the host genome, nor of any other known organism, but is rather some kind of extremely minimal pathogen that, like a transposon or self-splicing intron, is entirely nucleic-acid based. And the more they hunted, the more they found, ultimately finding thousands of obelisk-like entities hidden in the many databases of the world drawn from various environmental and microbiome samples. There is some precedent for this kind of structure, in the form of hepatitis D. This "viroid" of only 1682 nucleotides is a parasite of hepatitis B virus, depending on that virus for key replication functions. While normal viruses (like hepatitis B) encode many key functions of their own, like envelope proteins, genome packaging proteins, and replication enzymes, viroids tend to not encode anything, though hepatitis D does encode one antigenic protein, which exacerbates hepatitis B infections.

The obelisk RNA viroid-like species appear to encode one or two proteins, and possibly a ribozyme as well. The functions of all these are as yet unknown, but necessarily the RNAs rely entirely some host cell (currently unknown) functions to do their thing, such as the RNA polymerase to create copies of itself. Unknown also is whether they are dependent on other viruses, or only on cells for their propagation. Being just discovered, the researchers can do a great deal of bioinformatics, such as predicting the structure of the encoded protein, and the structure of the RNA genome. But key biology, like how they interact with host cells, what functions the host provides, and how they replicate, not to mention possible pathogenic consequences, remain unknown.

The highly self-complementary structure of one obelisk RNA sequence, leading to its identification and naming. In green is one reading frame, which codes for the main protein, of unknown function.

The curious thing about these new obelisk viroid-like RNAs is that, while common in human microbiomes, both oral and gut-derived, they are found only in 5-10% of them, not in all samples. This sort of suggests that they may account for some of the variability traceable to microbiomes, such as autoimmune issues, chronic ailments, nutritional variations, even effects on mood, etc.

Once a lot of databases were searched, obelisk RNAs turn up everywhere, even in some bacteria.

This work was done entirely in silico. Not a single wet-lab experiment was performed. It is a testament to the power of having alot of genomes at our disposal, and of modern computational firepower. This lab just had the idea that novel small viroid-like RNAs might exhibit certain types of (circular, self-complementary) structure, which led to this discovery of a novel form of "life". Are these RNAs alive? Certainly not. They are mere molecules and parasites that feed off, and transport themselves between, more fully functional cells. But they are part of the tapestry of life, which itself is wholly molecular, with many amazing emergent properties. Whether these obelisks turn out to have any medical or ecological significance, they are one more example of the lengths (and shorts) to which Darwinian selection has gone in the struggle for existence. 

• Want to become a rabbi?
• Hey, what happened to reading?
• Is hell other people?

How the Supreme Court Should Rule in the Colorado Ballot Case

There is one path forward that can salvage the court's standing.

The US Supreme Court is sinking to unusual depths of corruption and illegitimacy. Bush v. Gore was a step down in its ability to manage the rules of our political and legal system, where it made a hasty and, it claimed, one-time-only carve-out for its favored candidate, leading to almost a decade of tragically bad policy and poor government. Then came Citizens United, another step downward, opening firehoses of secret money from the wealthy, using the fig leaf of "free speech" to cover the corruption of politics with money. Then came the overturning of Roe, deeming women unworthy of rights that are far more basic and intimate than those enumerated in the Bill of Rights. And most recently have come the drumbeat of reports of corruption among the right-wing justices, who appear to regard themselves as too dignified to abide by the laws and norms they hold others to.

Now it is faced with a case that tests the very core of the court's abitlity to do its job. What does the constitution mean? Does the fourteenth amendment mean what it says, and if so, should it be enforced? A great deal of commentary suggests, probably correctly, that this court is desperately looking for a way out of this legal conundrum that allows it to do nothing and avoid overturning any apple carts. That would not, however, be a wise course. 

To recap, the Colorado case was brought by voters who sought to bar Donald Trump from the Colorado primary and general election ballots, due to his participation in the insurrection of January 6, 2021. The fourteenth amendment to the federal constitution bars such participants from federal and state offices. The Colorado Supreme Court ultimately agreed, sending the case to the US Supreme Court. The congressional report on the January 6 events makes the record of those events quite clear. It uses the word "insurrection" several times, as do many of its sources, and it is crystal clear about the participation by and culpability of Donald Trump in those events. 

The question is really about how the Constitutional provision should be brought into execution, being worded without a lot of explicit legal structure. One thing it does say is that congress can relieve its prohibition in individual cases by two-thirds votes of each house. But it leaves unsaid who should adjudicate the question of fitness for office, as is also the case for the more basic qualifications such as age and citizenship. Trump had previously, and ironically, dabbled in these same legal waters by casting doubt on the citizenship of Barack Obama. But since no one with half a brain took him seriously, the issue never entered the legal sphere.

Well, the worst course would be to let the clear language of the constitution lay inert and find some technicality by which to do nothing. What I would suggest instead is that the court recognize that there needs to be a national adjudicating power to decide this question in the case of candidates for national office (and indeed for any office whose qualifications are mentioned in the constitution). And that power should be itself, the US Supreme Court. The court might invite the legislative branch to provide more regular methods of fact-finding, (or even a clarifying amendment to the constitution), but given the constitutional clear intent, history, and logic, (not to mention the general Article III clauses putting all questions arising from the constitution in its hands), the court should take upon itself the power to say that the buck stops at its door. And naturally, in consequence, that Trump merits disqualification, on the facts of the January 6 events as found by the lower courts, and on his position as an officer, indeed the paramount officer, of the United States.

This solution would neatly take over from the states the responsibility of saying that any national candidate meets or does not meet the various qualifications set forth in the constitution. Such cases could begin in state courts, as this one did, but would need to go to the US Supreme Court for final decision. This solution would hold Trump to account for his actions, a principle that Republicans have, at least  traditionally, cherished. This solution would also go some way to removing the stain of the Bush v Gore decision, and establish a new and clear element of constitutional jurisprudence, in setting forth who adjudicates the qualifications of national political candidates. In fact, this function can be tied to the practice of having the chief justice of the United States administer the oath of office to the incoming president. It would be proper for the court to be the institution that decides on the basic fitness tests, and thus who in general may take the oath, while the people decide the political outcome of the election, among fit candidates.

I am no legal scholar, but the merits of this solution seem pretty clear. On an earlier occasion, the court summarily took on the task of determining the constitutionality of laws. This role was not explicitly set out in the text, but was a logical consequence of the structure that the constitution set up. Here likewise, the logic of the constitution indicates strongly that the final word on the fitness of candidates for national office must rest with, not the voters, not the states, and not the legislative or, heaven forbid, the executive branch, but with the federal judicial branch, of which the US Supreme Court is the head.

An alternative, and perhaps more likely, solution, is for this court to state all the principles above, but then hold that in its judgement, Donald Trump is fit for office after all. Maybe it will deem the insurrection just a little insurrection, and not the kind of big insurrection that would turn a jurist's head (despite the over thousand charges filed, and hundreds of federal convictions so far). Or maybe it will deem Trump insufficiently involved in the insurrection to merit disqualification. What it can not do is deem him not an officer of the federal government- that would be beyond belief. The pusilanimous, partisan sophistry of this alternative would not go over well, needless to say. Many would ask whether Clarence Thomas, himself virtually a participant in the insurrection at one remove, should have recused himself. Minds would be blown, but few would be surprised, since for this court, expectations could hardly be lower. Going against its partisan grain would, on the other hand, be a signal and heartening achievement.

This second approach would at least resolve the legal questions, but at the cost of further erosion of the court's legitimacy, given that the events of January 6 are so well documented, and the constitutional peril that Trump poses so obvious. For the whole point of having a Supreme Court which takes on tough issues and plugs logical holes in our constitution is that it also takes some care to plug them well, and preserve our democracy in the process.

• What happens when the Supreme Court gives in to politics?
• One state, one system.
• A solar energy insurrection in Puerto Rico.
• Democratic inequality is related to wealth inequality.
• More on the court case- ballots vs office holding.

Spiritual Resources for the Religiously Abstemious

Nones are now a plurality in the US. What are we supposed to do?

The Pew research institute recently came out with polling that shows a significantly changed religious landscape in the US. Over the last couple of decades, while the religious right has been climbing the greasy pole of political power, gaining seats on the Supreme Court, and agitating for a return to patriarchy, their pews have been emptying. The religiously unaffiliated, or "nones", comprise 28% of the US population now, almost double the level two decades ago.

One has only to see the rabid support evangelicals give their orange-haired messiah to understand what has been turning people off. Or glance over the appalling chronicle of sexual abuse unearthed in the Catholic church. Maybe the horsemen of the Atheist apocalypse have had something to do with it. Russia under Putin is strenuously demonstrating that the same system can be just as cruel with or without religion. But these patterns of gross institutional, moral, and intellectual failure, and their ensuing critiques, are hardly new. Luther made a bit of hay out of the abuses of the Catholic church, Voltaire, among many other thinkers, ridiculed the whole religious enterprise, and Hitler was a forerunner of Trump in leaning on religion, at least early in his career, despite being a rather token Christian himself (other than in the antisemitism, of course). What is new now?

A dramatic rise in numbers of people with no religious affiliation and little interest, from Pew polling.

I am not sure, frankly. Europe has certainly been leading the way, showing that declining religion is quite compatible with prosperous and humane culture. But perhaps this phenomenon is part of the general isolation and atomization of US culture, and thus not such a good thing. It used to be that a community was unthinkable without a church (or several) to serve as the central hub. Churches served to validate the good and preach to the bad. They sponsored scout troops, weddings, charitable events and dinners, and committees and therapeutic encounters of all sorts. They were socially essential, whether one believed or not. That leaders of society also led the churches knit the whole circle together, making it easy to believe that something there was indeed worth believing, whether it made sense or not.

Now, the leadership of society has moved on. We are mesmerized by technology, by entertainment, and sports, perhaps to a degree that is new. The capitalist system has found ways to provide many of the services we used to go to churches for, to network, to get psychotherapy, to gossip, and most of all, to be entertained. Community itself is less significant in the modern, suburban, cocooned world. Successful churches meet this new world by emphasizing their social offerings in a mega-church community, with a dash of charismatic, but not overly intellectually taxing, preaching. Unfortunately, megachurches regularly go through their own crises of hypocrisy and leadership, showing that the caliber of religious leaders, whatever their marketing skills, has been declining steadily.

The "nones" are more apathetic than atheistic, but either way, they are not great material for making churches or tightly knit communities. Skeptical, critical, or uninterested, they are some of the least likely social "glues". Because, frankly, it takes some gullibility and attraction to the core human archetypes and drama to make a church, and it takes a lot of positive thinking to foster a community. I would promote libraries, arts institutions, non-profits, and universities as core cultural hubs that can do some of this work, fostering a learning and empathetic culture. But we need more.

As AI takes over work of every sort, and more people have more time on their hands, we are facing a fundamental reshaping of society. One future is that a few rich people rake off all the money, and the bulk of the population descends into poverty and joblessness, unneeded in a society where capitalism has become terminally capital-intensive, with little labor required. Another future is where new forms of redistribution are developed, either by bringing true competition to bear on AI-intensive industries so that they can not take excess profits, or by thorough regulation for the public good, including basic income schemes, public goods, and other ways to spread wealth broadly. 

Such a latter system would free resources for wider use, so that a continuing middle class economy could thrive, based on exchanges that are now only luxuries, like music, personal services, teaching, sports, counseling. The destruction of the music recording industry by collusion of music labels and Spotify stands as a stark lesson in how new technology and short-sighted capitalism can damage our collective culture, and the livelihood of a profession that is perhaps the avatar of what an ideal future would look like, culturally and economically.

All this is to say that we face a future where we should, hopefully, have more resources and time, which would in principle be conducive to community formation and a life-long culture of learning, arts, and personal enrichment, without the incessant driver of work. The new AI-driven world will have opportunities for very high level work and management, but the regular hamburger flippers, baristas, cabbies, and truck drivers will be a thing of the past. This is going to put a premium on community hubs and new forms of social interaction. The "nones" are likely to favor (if not build) a wide range of such institutions, while leaving the church behind. It is a mixed prospect, really, since we will still be lacking a core institution that engages with the whole person in an archetypal, dream-like fantasy of hope and affirmation. Can opera do that work? I doubt it. Can Hollywood? I doubt that as well, at least as it applies to a local community level that weaves such attractions together with service and personal connection.

• Those very highly moral religious people.
• Molecular medicine is here.
• Why do women have far more autoimmune syndromes?
• What to do about Iran.
• "As we’ll see, good old-fashioned immortality has advantages that digital immorality cannot hope to rival." ... I am not making this up!

Evolutionary Elaboration of mRNA Splicing

An RNA helicase scoots through the spliceosome to advance the process of mRNA splicing. And some other tricks.

In our cells, virtually all mRNAs transcribed from DNA have to go through an editing process to cut out intervening junk called introns. This process is called splicing, and its evolutionary origin, later elaborations, and current mechanism are all quite interesting. Life didn't start with introns, and only eukaryotes have them as a regular feature of their genomes. They appear to have arrived with the bacterium that became our mitochondria, which come from a lineage that has (relatively few of) what are called group II self-splicing introns. These are RNA segments that behave a bit like transposons, being able to jump into DNA, and then reverse-transcribe that segment into a copy of itself in genomic DNA. 

The ur-eukaryote seems to have had an incredibly prolific infection, which left its host genome riddled with these bits of DNA. A key point is that, in group II introns, their splicing out of a transcribed RNA message is auto-catalytic- entirely mediated by their own RNA structure. They are self-propagating parasites, which have, over time in eukaryotes, been tamed to become fertile aspects of our own gene regulation and evolution. For example, introns often fall between protein domains, allowing these relatively compact modules of protein structure to be replicated, moved, and plugged, via rare mutational events, into new settings to contribute new functions to existing or novel proteins.

A map of a group II self-splicing intron. In red are the ends of the host RNA (or DNA) which are to be either jumped into or excised out of. The rest is the structure of the intron, which carries its own catalytic ability to do these reactions. This kind of thing is what appears to have turned into our own splicing and intron/exon systems, since the core catalytic mechanisms, such as the use of lariats and branch points and RNA catalysis, are the same.

Representation of the core spliceosomal reactions in eukaryotes, which result in a free lariat form of the excised intron, and the joined exons, which go off to code for their protein. "SS" stands for splice site. The sequences in red characterize introns.

The mechanism of intron excision in our cells is, at its core, still RNA-based, even though there are now also hundreds of proteins involved in the rather massive machinery of what is now called the spliceosome. It is clear that over evolutionary time, what was originally an unwelcome and shocking invasion of proto-mitochondrial introns into the proto-nuclear host genome has been regulated, speeded up, accessorized, and integrated into our normal method of gene expression. The spliceosome is the result- a huge and dynamic complex that uses key bits descended from the original RNA catalytic components to guide and catalyze the splicing reaction.

Representation of the core splicing reactions, with the key small RNAs added in (U1, U2, U4, U5, U6). These both guide (by direct RNA-RNA hybrid formation) and perform catalysis at the two chemical bond-breaking/reforming steps.

There are three key locations seized upon by the spliceosome. First is the 5 prime splice site- the end of the coding exon and beginning of the intron, typically a "G" nucleoside at the start of the intron. Second is the branch point, an "A" near the end of the intron, which is where the chemistry of splicing begins. And third is the 3 prime splice site- the end of the intron, with another "G" nucleoside, next to the beginning of the next coding exon. While the first two sites are specifically recognized by RNA components of the spliceosome, (U1 at the 5 prime splice site and U2 at the branch site), the 3 prime splice site is simply recognized by scanning for the first "AG" downstream of the branch site.

The first reaction is to bring the branch site and the 5 prime splice site in proximity, such that the branch site A covalently invades the G at that site and displaces it, releasing the exon end and forming a loop (called a lariat, in red above) in the intronic RNA. The second reaction is to bring the 5 prime exon end over to the 3 prime exon end, and similarly prompt and invasion that links them, displacing the intron entirely.

So simple to describe, but not so easy to do. Accuracy is paramount, since the three-codon reading frame of mRNA would be destroyed by even a 1 nucleoside error in splicing. Splicing now gates the export of mRNA from the nucleus, so that only fully and accurately spliced transcripts get out to the ribosomes in the cytoplasm for translation to protein. This gating has been considered by some the very reason that the nucleus exists at all- a way to solve some of the knotty problems that arose in very early eukaryotic evolution when all these introns invaded. 

Another reaction scheme of splicing, showing the key RNA and some other proteins along the way, principally the key helicases that help drive things forward. Note where PRP2/ATP comes into the picture, just as the complex is preparing for the first catalytic step.

Be that as it may, it is clear that the originally RNA-only mechanism changed over time by accreting proteins that each decided they had something useful to add to the process. At the same time, the RNA got separated into several pieces (on independent genes) that could then be carried and precisely manipulated by these helping proteins. The spliceosome now involves five distinct small RNAs and over 200 proteins, which engage in a complex ballet of sequential steps. A special class of these proteins, the helicases, are the subject of a recent paper that provides new structural information. Helicases are proteins that can use the power of ATP to unwind DNA or RNA, or just chug along it. At least eight such proteins participate in splicing. 

Structures from a recent paper, showing how PRP2 (at bottom, in violet) chugs its way along the mRNA intron (blue) into the very heart of the spliceosome complex, partially evicting the SF3B1 protein (green), among others, and prompting many other changes. At top is shown the 19 nucleoside stretch of the mRNA that was traversed, getting close to the branch site "A" in red. 

The paper makes the interesting observation that, structurally, most of the helicases reside on the periphery of the spliceosomal complexes, while the catalytic and guiding RNA are, naturally, at the center. They use a mutant form of one of them, Aquarius, to freeze spliceosomes in a key conformation just before the branch site and 5 prime splice sites are brought together. In combination with a bunch of other structural work by others in this and other labs, they show that one dynamic event is the tracking by a second helicase, PRP2 (violet, above), that brings it from its peripheral position (b, at bottom) along the intronic mRNA (blue strand) into the core of the splicesome near the U2 RNA (c; U2 is not shown here). They show that PRP2 traverses 19 nucleosides (top, a), a rather remarkable trip that forms part of the sequence of events that brings the branch site and 5 prime splice site close to each other.

Further structures, focusing on the catalytic site and RNAs. Note how the branch site (red, "BS-A") is, after the action of the Aquarius helicase, (third panel), brought in tightly close to the 5 prime splice site (green, "5'SS) in the C, or catalytic, complex. The U2 and U6 RNAs then have an easy job of bond-exchanging catalysis.

So it turns out that these helicases appear sometimes to be used as ratchets, that start on the outside of the complex. Once activated by some prior trigger, they pull on a thread in a way that helps to overall process forward. The progression of PRP2 into the spliceosome core evicts a bunch of other proteins and activates the other helicase Aquarius. That protein is likewise positioned perpipherally but is hanging onto another thread of the intronic RNA and helps to further push the branch and 5 prime splice sites together, in a way that finally leads to the desired reaction. Note in the image above that it is the RNAs that occupy the central reaction site- the intron in blue (green), and the U6 and U2 RNAs, which catalyze this first key reaction of splicing.

RNAs are not great catalysts, so it is understandable that, as in the case of translation by the ribosome, a bunch of proteins shoehorned their way into the process (over evolutionary time) in ways that evidently made splicing more accurate and more rapid. Indeed, yeast cells get along without the Aquarius protein at all, though they otherwise have a very similar splicing apparatus, showing that the accretion of proteins on the spliceosome did not end in very early stages of eukaryotic evolution, but continued through the origin of metazoans, and may still be continuing. The added proteins did this through using their talents for precise spatial positioning, and for the use of energy (from ATP) to drive things ahead, if only by intricate conformational ballet rather than direct catalysis.

• "Ron DeSantis should be forced to carry his presidential campaign to term."
• Nones are not nuns.
• Medical errors and AI.
• The worse the better... GOP edition.
• Two minutes hate.