Due to the press of other business, only links this week:
Are angiosperms 135 million years old, or 275 million years old?
We live among a hodgepodge of plants from different evolutionary epochs, with flowering plants being the most recent, (including the even more recently evolved grasses), alongside the more ancient conifers, cycads, ferns, mosses, and lichens. All have a place in diverse ecosystems, but what is their true history? This has been difficult to establish in more than broad outlines, due, as usual, to the patchy nature of the fossil record, and the difficulties of aligning it with what we now have as the molecular record. Angiosperms have been a particular sore spot, ever since Darwin, who recognized that the sudden appearance and radiation of flowering plants, roughly 130 million years ago, was a problem for evolutionary theory.
A paper from a few years back offered a carefully aligned molecular and fossil analysis of angiosperms, coming to the conclusion that they actually originated ~275 million years ago (MYA), and must have persisted in some cryptic fashion through the ensuing 150 MY before making a splash in the fossil record. How is this kind of analysis done? First, the best early fossils are tabulated, with secure dating and clear characteristics that include them among angiosperms. The most ancient example is a sample of pollen, from roughly 125 million years, which looks strongly like it came from angiosperms. These fossils are also assigned to plant lineages, so that their appearance can inform the branching points of the phylogenetic diagram, whether that diagram is based purely on these fossils and their morphology, or based on molecular data.
Then a set of gene sequences is collected, which are conserved between all the surveyed species, and aligned so that their changes can be fed into a program that counts all the differences. It was clear through this work that some lineages changed faster than other ones (the faster ones are marked with blue flares towards the right. Since the sampled species are all ones that exist now (time 0), being able to provide DNA, and since the branch points are in any case shared between the lineages that descend from them(at their origination points), faster change / evolution in one lineage vs another will be readily apparent, and the researchers just have to make up some rules to judge where to come down in time assignments when faced with such discrepancies. The more serious problem is that such different speeds can totally derange this kind of analysis, making a faster-changing lineage seem much older than it is. So pinpointing the branch points between lineages is extremely important to pin down such hard-to gauge branch lengths.
Biologically, it is now well known that lineages vary substantially (up to ten fold, less so in longer lineages and time spans) in their speed of molecular change.. molecular evolution is not a clock. Faster change tends to happen when populations are small, and when big evolutionary transitions have happened. For example, plants, and specifically angiosperms, have gone through whole-genome duplications that represent major evolutionary watersheds. These duplications supplied raw material for countless diversifications and specializations of genes, with especially rapid change in molecular sequences either released from previous selective constraints, or subject to new ones via new roles.
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| Integrated phylogenetic diagram of the evolution of angiosperms, marking key fossils that inform branch point timing (lettered blue circles), and ranges of possible branch points derived from the molecular alignments (red circles). At bottom is time, in millions of years before present. |
What can explain the big gap in estimated angiosperm origins? There are three basic hypotheses. First is that the molecular data is correct, which implies that there is an extremely long (150 million years) history of cryptic angiosperms that have not (yet) been detected in the fossil record. There are smatterings of findings in the literature that suggest that such fossils may be (or may have been) found, but I don't think these have been widely accepted yet (especially when they come from highly questionable sources).
The second hypothesis is that something about the very early evolution of angiosperms (like the very early evolution of eukaryotes, and the very early diversification of macroscopic animals) was accelerated in molecular terms, (as discussed above in terms of differing rates between lineages), rendering the apparent molecular phylogeny much longer than the real one. That includes the prodigious radiation of the many lineages in the diagram above, all before the first fossil is found.
The third hypothesis, much beloved of creationists, is that god did it. A mystery like this is ripe for invoking the solution to all mysteries, which is it does not need to be explained in the normal mechanistic terms of the natural world, but rather can be chalked up to the author of all things, god. While this hypothesis, at least for believers, solves this one nagging mystery, it brings on a few others. Why does the rest of biology through this vast lineage still follow the plodding path of gradual (if uneven) development? Why jump in to create this mystery when so many other lineages in the fossil record do not present similar mysteries? Why did god insist upon, (presumably for the ultimate appearance of us as humans), the whole four billion year process of life's plodding development, when the whole thing could have been authored at once and at the start? What amazing societies we could have developed with a four billion year head start!
It is clear, therefore, that some hypotheses create more problems than they solve. Inviting scientists to consider and comment on harebrained hypotheses is not going to end well. The solution to this problem is going to be some combination of the first two hypotheses, of rapid molecular evolution at the start of a major radiation, and some as-yet missing material in the fossil record. Innovative organisms are very likely to be rare, though whole cryptic lineages surviving for many tens of millions of years is hard to posit without more evidence. Yet it is also a given that fossils will necessarily appear after the actual events of lineage branching, thus will always post-date the calculated molecular branching point.
Translation efficiency has some weird rules, and a tortured history.
One would think we know everything there is to know about the workhorse of bacterial molecular biology, Escherichia coli. And that would be especially true for its technological applications, like the expression of engineered genes, which is at the very heart of molecular biology and much of biotechnology. Getting genes you put into E. coli expressed at high levels is critical for making drugs, and for making enough for structural and biochemical studies. For decades, the wisdom of the field was to design introduced genes using the codon adaptation index (CAI). This is a measurement of the three-letter codes (codons of the genetic code) that are used in highly expressed genes. They tend to correspond to tRNAs that are more abundant in the cell. So, for example, the amino acid leucine is encoded by six different codons, any of which can be chosen at intended leucine positions in the intended protein. In E. coli, CTG is over ten times more frequently used than CTA, however. Thus, even though they code for the same amino acid, one is more common, perhaps because its cognate tRNA is more common and more easily used during translation. This is basically a diffusion-based argument, that translation will be easier if the tRNA that carries the next amino acid is easier to find.
A recent paper provides a remarkable review of this field. For one thing, it turns out that use of the CAI has virtually no effect on translation efficiency. Whether using rare or common codons, translation is equally efficient for introduced genes. Needless to say, this is quite surprising. It seems as though the role of common vs uncommon tRNAs/codons is more to manage the health of the cell by relieving bottlenecks to translation in a global sense and managing the free pool of ribosomes, rather than regulating the efficiency of translation of any particular mRNA message. tRNAs are highly abundant generally, so there are significant savings possible by managing their levels judiciously, and reducing investment in some versus others.
So what does affect the efficiency of translation? Some messages are better translated than others, after all. The authors point to a completely different mechanism, which is the melting stability of the first ten codons of the mRNA message. RNA can form hairpin and other secondary structures / shapes, and this can apparently strongly affect the ability of ribosomes to find initiation sites. While eukaryotic ribosomes scan in from the 5 prime cap of the mRNA, bacterial ribosomes bind directly to a sequence slightly upstream of the initiating AUG codon. And this can be inhibited by mRNAs that are not neatly ironed out, but knotted up in hairpins and loops.
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| Ratio of occurrence of nucleosides in the third codon position of the first ten codons of high versus low expressing genes in E. coli. This was not run on native E. coli genes, but on a large panel of transgenes engineered from outside. The strong bias towards A at this position in high expressing genes shows a preference for initiating sequences to have weak secondary structure, allowing better ribosome access. |
Use of A-rich sequences around the ribosomal initiation sites and the first ten codons, then, dramatically increases the translation efficiency, (via the initiation efficiency) of introduced genes, and provide a much more robust method to control their expression. But then the authors make another observation, which is that the bacteria themselves do not seem to use this mechanism for their own genes. In a massive analysis of data from other labs, (below), there is actually a negative correlation between the quality of the initiation region (X- axis) and the abundance of the respective protein (Y- axis). Again, quite a surprising result, which the authors can only speculate about.
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| There is negative correlation between the initiation codon quality (X- axis), as shown above, and the native E. coli gene expression level (Y- axis). So these cells are not optimizing their translation at all in accordance with the findings above. |
The picture that they paint is that highly expressed genes in E. coli benefit from consistent, smooth translation. This depends less on maximal initiation speed than on the holistic picture of translation. The CAI optimal codons (called translationally optimal in this paper, or TO) tend to be poor at initiation, but have good codon-anticodon pairing and thus low A content. So there are conflicting pressures at work, in basic chemical terms, where different codons are intrinsically good for initiation, and complementary ones for elongation. The obvious solution is to use the initiation-optimal codons for the first ten codons, and translationally optimal codons the rest of the way. But that is not what is found either. The authors claim that, for native proteins, lower levels of initiation are actually beneficial for smoother protein production with less noise from time to time and cell to cell.
Additionally, lower initiation rates preserve free ribosome levels globally, another important goal for the cell, via evolutionary selection. The authors find, for instance, a correlation between low variability of initiation (low noise) and low initiation rate. This is a bit mystifying, since ribosomes should always be present in excess, and it is not immediately apparent why holdups to translation initiation would lend themselves to more even initiation. Perhaps the search process by which ribosomes find free mRNAs is inefficient, so that those with slower initiation sequences have a constant backlog of incoming, bound and poised ribosomes, while after they get past the initiation region, those ribosomes progress rapidly and rejoin the free pool. That would be one way of setting up a smooth production process, suitable for essential protein products, that is relatively insensitive to the free ribosome concentration and other variations in the cell.
Technologists trying to express some drug-associated protein in bacteria don't care about smoothness and noise, but just want to maximize production while not killing the cell (or before killing the cell). So all these subtle considerations that go into the evolution of the native gene complement of E. coli and its high or low expression levels don't apply. But for researchers trying to predict the expression level of a given natural gene, it is maddening, since it seems currently impossible to predict the expression level (via translation) of a gene from its sequence. It is one more case where modeling of what is going on inside cells is surprisingly difficult, even for a system we had thought we understood, in one of the simplest and most well-studied bacteria. As researchers never tire of saying ... more research is needed.
Voltage sensitive domains can make switches out of ion channels, antiporters, and other enzymes.
The heart of modern electronics is the transistor. It is a valve or switch, using a small electrical signal to control the flow of other electrical signals. We have learned that the simple logic this mechanism enables can be elaborated into hugely complex, even putatively intelligent, computers, databases, applications, and other paraphernalia of modernity. The same mechanism has a very long history in biology, quite apart from its use in neurons and brains, since membranes are typically charged, well-poised to be sensitive to changes in charge for all sorts of signaling.
The voltage sensitive domain (VSD) in proteins is an ancient (going back to archaea) bundle of four alpha helices that were first found attached to voltage-sensitive ion channels, including sodium, potassium, and calcium channels. But later it became fascinatingly apparent that it can control other protein activities as well. A recent paper discussed the mechanism and structure of a sodium/hydrogen antiporter with a role in sperm navigation, which uses a VSD to control its signaling. But there are also voltage-sensitive phosphatases, and other kinds of effectors hooked up to VSD domains.
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| Schematic of a basic VSD, with helix 4 in pink, moving against the other three helices colored teal. Imagine a membrane going horizontally over these embedded proteins. When voltage across the local membrane changes, (hyperpolarized or de-polarized), helix 4 can plunge by one helical repeat unit in either direction, up or down. |
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| The helices of numerous proteins that have a VSD domain (in red) are drawn out, showing the diversity of how this domain is used. |
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| A schematic of the logic of this pathway, and of the SLC9C1 anti-porter. At top, the transport mechanism is crudely illustrated as a rocking motion that ensures that only one H+ is exchanged for one Na+ for each cycle of transport. The transport is driven thermodynamically by the higher concentration of Na+ outside. |
But these researchers weren't interested in what the sperm were thinking, but rather how this widely used protein domain became hitched to this unusual protein and how it works there, turning on a sodium/hydrogen antiporter rather than the usual ion channel. They estimate that the #4 helix of the VSD moves by 10 angstroms, or 1 nm, upon voltage activation, which is a substantial movement, roughly equivalent to the width of these helices. In their final model, this movement significantly reshapes the intracellular domain of the transporter, which in turn releases its hold on the transporter's throat, allowing it to move cyclically as it needs to exchange hydrogen ions for sodium ions. This protein is known to bind and activate an adenylyl cyclase, which produces cAMP, which is one key next actor in the signaling cascade. This activation may be physically direct, or it may be through the local change in pH- that part is as yet unknown. cAMP also, incidentally, binds to and turns up the activity of this transporter, providing a bit of positive feedback.
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| Model of the SLC9C1 protein, with the VSD in teal and a predicted activation mechanism illustrated (only the third panel is activated/open). Upon voltage activation, the very long helix 4 dips down and changes orientation, dramatically opening the intracellular portion of the transporter (purple and orange portion). This in turn lets go of the bottom of the actual transporter portion of the protein (gray), allowing alkalinization of the cytoplasm to go forth. At the bottom sides, in brown, is the cAMP binding domain, which lowers the voltage threshold for activation. |
Realism, idealism, and false realism in the Ukraine war.
The Ukraine war has been a disaster. That much is certain. But who caused it, and could it have been averted with better policy from us? And what would the costs of such a policy have been? There is a large school of foreign policy "realists" (exemplified by John Mearsheimer) who think that Russia was driven to this war by the inexorable encroachment of NATO towards the Russian borders. Thus we are at fault, just as much as Russia, which is actually dropping bombs on Ukraine and cutting a blood-soaked swath through its eastern and southern regions. The imperialism of Russia over its neighbors is perfectly understandable, realistic, and OK. By this argument, Russia has been crystal clear that offering Ukraine the distant prospect of NATO membership, as we did in 2008, was a declaration of war (by us!). Russia has tried to negotiate in good faith all through this time, and kept working for peace, even as it could see its interests eroded, and the necessity of war increasing. Till at last, it was forced by our policy to take over Crimea, and ultimately, in the face of increasing infiltration by Western interests in Ukraine, launch the full scale war we see today.
While this is one perspective on the level of grand strategy and traditional balance of power views, it leaves out one of the actors in the drama, and is a curious way to apportion blame for manifest evil. The actor it leaves out is Ukraine, which might want to have some say in its own destiny. And the evil is the way in which this realist school casually consigns countries to "spheres of influence", fated to be sat upon by their neighboring bullies. Perhaps world history is one long story of bullies fighting it out over riches and territory. But does it have to be? It does not, and therein lies the difference between war and peace, blame and praise.
Realists point to America's own empire, perhaps most explicitly outlined in the Monroe Doctrine. This statement by John Quincy Adams claimed the entire Western Hemisphere to be a special zone where European meddling was unwelcome, and defended by the nascent power of the United States. This was largely aspirational at the time, and European imperialist powers continued meddling in the hemisphere nevertheless, even invading the US itself in the war of 1812. And of course, the Monroe doctrine was not intended to set up a US empire at all, but was rather an anti-imperialist document, promoting the self-determination of the countries of South and Central America. We have since certainly done our share of meddling, taking several large portions of Mexico for our own territory, corrupting various Central American countries in commercial and anti-communist quasi-empires. But on the other hand, for the most part we have had friendly and peaceful relations, even (the shambolic Bay of Pigs invasion aside) keeping our hands off of Soviet-allied Cuba.
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| Evolution of the Russian empire, over the centuries. Whether the areas under Russian occupation ever wanted to be there, or now wish to stay there, remains a live question. |
It is clear that our view of empire is not, currently, a traditional one. We have lots of friends, lots of allies, and lots of power, of soft and hard kinds. But we have not set up a barrier of involuntary client states against regional threats. NATO is emblematic as a voluntary alliance. It was and remains a collective (if US-dominated) alliance of countries trying to deter a third world war. Such a war was first contemplated to arise from the European antagonists who had just fought the two preceding wars - Germany, France, and the UK. But as they rebuilt their societies on both an economic and moral basis, it quickly became clear that the real threat was going to come from the new Soviet Empire, which had quickly swallowed up all of Eastern Europe.
Each of these Eastern European countries had their dreams of freedom crushed in the wake of Germany's defeat, and each was correspondingly eager to leave the Soviet Empire when the cold war, at long last, came to an end. Vladimir Putin blames Mikhail Gorbachev for loosening the reins and thoughtlessly letting the empire crumble. The current Russian state celebrates its greatest holidays around the high water mark of another leader, more the Putin's taste- Joseph Stalin, when Russian power was at its (relative) peak. Putin's idea of power is expressed in his relation with Belarus- a thoroughly cowed and pliant frontier, from which Russian conveniently launched a large portion of its invasion of Ukraine. It is typical of this curdled and "realist" perspective that the wishes of the people involved count for nothing. Their aspirations and well-being are irrelevant, the imperial state and its power are what matter.
As an aside, Michael Kimmage has recently written a book-length analysis of Ukraine. It is a quite balanced history of the whole run-up to the war, laying out the moves, thoughtless or not, taken by both sides. Here, one gets a sense that Putin was sensing weakness in the West, in the wake of our Iraqi and Afghan debacles. But where this book really shines is in its epilogue, which is a pean to the power of history itself.
"Countries invariably conceive their foreign policies in reaction to earlier conflicts. They are led by their sense of who was wrong and who was right, of what the core problem was and what the solution to that problem was, fighting the last war until it is no longer the last war. The preoccupation with the past can be the path to wisdom, of learning from history, or it can leave countries trapped in their interpretations of the past. To investigate the origins of an ongoing war, then, is not just to chart the present moment. It is to peer, however uncertainly, into the future."
Kimmage recounts how Germany turned historical analysis on its head after World War 1 to claim that others had started it, and others were responsible for Germany's defeat, thus setting the table for a second round. Similarly, it is Putin's potted analysis of the cold war and its appalling aftermath for Russia that forms the motivation for his current war. Just like realism, this theory of the power of historical narrative serves to explain motivations and actions, and by understanding absolve the actors, to some degree, of culpabilty, making the current conflict seem inevitable. In this case, the West was doltishly uninformed and sleepwalked into an unnecessary war.
But history is not a given. It is, in places like Russia, a product of the propaganda organs, not the science organs. It is narrated with a grievence and a point in mind, and can be, in the right hands, tailored to lead to practically anything the leader wishes to happen. The idea that we should be beholden to the historical analysis of another country or its leader, and thus be on the hook for appeasing their "legitimate" demands, feelings, etc. is absurd. However much such understanding helps us analyze what other actors have in mind, it should not bind our analysis of the same history, or of the broader functioning of the international system.
Returning to the realist perspective, it recognizes the lowest common denominator in an anarchic environment- raw power. It is the mafia approach to foreign relations. Well, we have an answer to that, which is a modern perspective, modeled in a modern state that has and uses overwhelming policing power against aggressors. It is enlightenment values that have suffused Europe, providing the peace seen on the continent among the members of NATO and the EU. We have gotten so used to living amidst civilized values that a Russian invasion of Ukraine seemed unthinkable, despite a long train of preliminary invasions, explicit policy statements from Russia, and propaganda preparation. Europe should have used its power to immediately push Russia back out of Ukraine. That would have been the ideal scenario to safeguard the values that Ukraine was aspiring to, and that the West embodies.
So, what about nuclear weapons and World War 3? Russia has been rattling its nuclear saber, resorting to any threat it can to keep Ukraine weak and friendless. Needless to say, it would not be wise of Russia to use nuclear bombs in Ukraine. Whatever grievances / justification Russia has for its invasion, even internally, would collapse immediately. I think everyone recognizes that nuclear weapons exist for mutual and existential deterrence, notionally protecting Russia (in this case) from invasion by other countries. Fine. Helping Ukraine rid itself of a cruel bully, restoring its independent and original borders, is, conversely, fully justified and is the kind of aim that lends itself to a limited war. At very least at this point, we should provide Ukraine with the wherewithal for air superiority over its own territory.
Russia exemplifies old thinking from the anarchic world order. It (and China as well) want to drag the world back into that world, recreating the glory days of Stalin's empire. Or even Catherine the Great's. It is in the power of the West, as a growing collective of democratic and prosperous countries, to deny these aims, rather than appeasing them. And the expeditious and effective use of police power in Ukraine would yield dividends into the future, strengthening the collective power of the West to foster the freedom and self-determination of other nations. Could this protective concept allow movement the other way? Sure- Hungary, for instance, might want to join the Russian orbit and leave the EU. And good riddence! They would be welcome to do so. These alignments should not be determined by war, (nor, hopefully propaganda and corruption), but by national sentiment and interest.
The primitive mafia mindset is also one that afflicts certain precincts of US politics, notably the Republican presidential candidate, who can't see beyond "strength" and machismo, and seems more likely to support Putin than NATO or Ukraine. It is another case of cavalier disregard not only of decades of collective work by the West to sustain a civilized international order, but of elementary concepts of justice and self-determination. Maintaining a just peace takes steadfastness, work and sacrifice. If we do nothing, then sure, the bullies will win and the world will go right back to one where bullies have only other bullies to be afraid of. If last week's Memorial day means anything, however, it is that collective sacrifice over the long arc of US history has always served, at least in principle, more freedom and less tyranny- for others, not just ourselves.
