Journey to the Center of the Ribosome

And to the origin of the ribosome as well.

The ribosome is a relic. It is slow and inefficient, and therefore needed and made in huge amounts in all cells. It is absurdly large, with some of the most highly conserved sequences in all of life and dozens of later additions, ingloriously pasted on the outside. While those later additions are all proteins, its catalytic core is made of RNA, explaining both its age and its slowness. For it is a relic of the RNA world, and itself marks the beginning of the mechanism of protein synthesis that would provide the catalytic capacity to transcend that world. But the ribosome itself would never be superceded, only jury-rigged and augmented. While other molecules like lipids and metabolites are also crucial to biogenesis, this early phase is called the RNA world because RNA is widely thought to be the main catalytic and informational molecule.

Schematic of the ribosome, showing decoding on the small subunit, and peptide synthesis on the large subunit (top). Sausage-like tRNAs are shown lining up preparatory step (RF, also called the A site), the transferring step (P), and the exit step (E). The peptidyl transferase core is made of RNA, so all key aspects of this machine are run by RNA.

So where did the ribosome begin? Its core function is to line up an RNA message that carries the genetic code, to which other RNAs dock, by sequence recognition. These special (transfer RNAs, or tRNAs) have amino acids stuck on their other ends, which then likewise line up and get linked together, forming the nascent protein. It is pretty clear that, while the genetic code now has three nucleotides per unit (codon), enabling 64 possibilities and in fact coding for 20 amino acids, it began with only two, offering 16 possible amino acids. About half of current amino acids are now coded by "degenerate" codons, where the last letter doesn't make any difference- all four (say, GGU, GGC, GGA, GGG, for glycine) code for the same amino acid. 

A more detailed structure of the ribosome, with RNA shown in thin orange helixes, and proteins shown in teal and green ribbons. The tRNAs are shown in gray (E), orange (P) and purple (A).

From a great deal of other work, it has been shown to be possible (though whether likely, or inevitable, is another matter) for RNAs to assemble in pre-biotic chemical conditions, and to laboriously operate on each other with catalytic effect, both in polymerization and degradation. Indeed, our mRNA splicing apparatus remains, like the ribosome, based on an RNA catalytic core. And this work suggests that RNAs of some length, like maybe under 100 nucleotides (nt) are plausible, while longer ones would be less plausible. There is some debate about whether in later epochs, the RNA world could have hosted very long RNAs, thereby making up in length and complexity what it generally lacked in conformational precision and chemical versatility. So the question arises- how much is really needed to get to the protein synthesis stage of biogenesis? How might several RNAs have come together to collaborate in this dance of protein synthesis, and what were the minimal requirements? 

The pseudo-dimeric core of the peptidyl transferase center, pulled out of the larger ribosome structure. This tiny structure is what the current workers attempted to use to simulate very early forms of protein synthesis.

The site within the ribosome where the single amino acids are linked together (polymerized) is called the peptidyl transferase center. Given properly tRNA-linked acyl-amino acids, it takes only proper steric encouragement, not extra inputs of energy such as ATP, to create the peptide bond. It turns out that the peptidyl transferase center of the ribosome can be thought of as a dimer of two ~ 60 nt long RNAs. Structures of that center show this as the extremely conserved, somewhat kinked helical dimer within all current ribosomes. But can such tiny RNAs do the job? Or do they absolutely require the kind of superstructure in which they are currently embedded? 

A recent paper shows that they can do the job by themselves, if very inefficiently.

"The actual reaction occurs within a semi-symmetrical molecular pocket that hosts the A- and P-tRNAs, situated within the peptidyl transferase center (PTC), which provides the sites for the two CCA-tRNA ends. This semi-symmetrical entity provides the framework for optimal positioning of the ribosomal substrates in a favored stereochemistry for peptide bond formation and it confines the void required for the motions associated with protein elongation. The amazingly high conservation of this semi-symmetrical site structure, which seems to be preserved throughout the entire living kingdom, indicates that it is resistant to evolution. Hence, suggesting that it could have existed as a self-folded active entity in the pre-biotic world. Therefore, called by us the protoribosome, i. e. the ancestor of the contemporary ribosome."

Ingredient 1: the mini-rRNA sequence and presumed base-pairing.

Ingredient 2: the mini-tRNA sequence and base-pairing.

The hard part was showing that this is true, which is what two groups have done, one in Japan, one in Israel. They have demonstrated slight amounts of protein synthesis using these tiny RNA molecules, in addition to other RNAs standing in for the code and the tRNAs. This was extremely difficult to do, grinding through the careers of several graduate students and post-docs. The ingredients are as follows: one putative / mini ribosomal RNA of about 71 nt, which forms the dimer of the putative peptide transferase core, and a putative transfer RNA of about 35 nt, which was pre-supplied with an attached amino acid (alanine). Given only those two inputs, they found in the reaction products the dipeptide alanyl-alanine, indicating that one step of synthesis had occurred. The template was a tag of GGU that had been added to the mini-ribosomal RNA, to match the ACCA tail of the mini-tRNA. 

So this is a highly unnatural setting, without a true template, and with pre-charged mini-tRNA molecules, and with just-detectable efficacy. But the principle is significant- not only can RNA of relatively simple sorts that we can envision occurring in the RNA world synthesize, cleave, and alter other RNAs, but they can also get to the nascent stage of protein synthesis, one of the bigger hurdles on the way to life as we know it.

• Korean women are on strike.
• A contrary view of Ukraine.
• Comments on the Jones act.

The Eye is the Window to the Brain

Alpha oscillations of the brain prefigure the saccades by which our eyes move as we read.

Reading is a complicated activity. We scan symbols on a page, focusing on some in turn, while scanning along for the next one. Data goes to the brain not in full images, but in the complex coding of differences from moment to moment. Simultaneously, various levels of processing in the brain decode the dark and light spots, the letter forms, the word chunks, the phrases, and on up to the ideas being conveyed.

While our brain is not rigidly clocked like a computer, (where each step of computation happens in sync with the master clock), it does have dynamic oscillations at several different frequencies and ranging over variable regions and coalitions of neurons that organize its processing. And the eye is really a part of that same central nervous system- an outpost that conveys so much sensitive information, both in and out.

We take in visual scenes by jerks, or saccades, using our peripheral vision to orient generally and detect noteworthy portions, then bringing our high-acuity fovea to focus on them. The eye moves about four times per second, a span that is used to process the current scene and to plan where to shift next. Alpha oscillations (about 10 per second) in the brain, which are inhibitory, are known to (anti-) correlate with motor control of the saccade period. The processing of the visual sensory system resets its oscillations with each shift in scene, so is keyed to saccades in a receiving sense. Since vision only happens in the rest/focal periods between saccades, it is helpful, conceptually, to coordinate the two processes so that the visual processing system is maximally receptive (via its oscillatory phase) at the same time that the eye comes to rest after a saccade and sends it a new scene. Conversely, the visual sensory system would presumably tell the motor system when it was done processing the last unit, to gate a shift to the next scene.

A recent paper extended this work to ask how brain oscillations relate to the specific visual task of reading, including texts that are more or less difficult to comprehend. They used the non-invasive method of magnetic encephalography to visualize electrical activity within the brains of people reading. The duration of saccades were very uniform, (and short), while the times spent paused on each focal point (word) varied slightly with how difficult the word was to parse. It is worth noting that no evidence supports the lexical processing of words out of the peripheral vision- this only happens from foveal/focused images.

Subjects spent more time focused on rare/difficult words than on easy words, during a free reading exercise (C). On the other hand, the duration of saccades to such words was unchanged (D).

In the author's main finding, alpha oscillations were correlated as the person shifted from word to word, pausing to view each one. These oscillations tracked the pausing more closely when shifting towards more difficult words, rather than to simple words. And these peaks of phase locking happened anatomically in the Brodmann area 7, which is a motor area that mediates between the visual system and motor control of the eye. Presumably this results from communication from the visual processing area to the visual motor area, just next door. They also found that the phase locking was strongest for the start of saccades, not their end, when the scene comes back into focus. This may simply be a timing issue, since there are lags at all points in the visual processing system, and since the saccade duration is relatively fixed, this interval may be appropriate to keep the motor and sensory areas in effective synchronization.

Alpha oscillation locks to some degree with initiation of saccades, and does so more strongly when heading to difficult words, rather than to easy words. Figure B shows the difference in alpha power between the easy and difficult word target. How can this be? 

So while higher frequency (gamma) oscillations participate in sensory processing of vision, this lower alpha frequency is dominant in the area that controls eye movement, in keeping with muscle control mechanisms more generally. But it does raise the question of why they found a signal (phase locking for the initiation of a saccade) for the difficulty of the upcoming word, before it was actually lexically processed. The peripheral visual system is evidently making some rough guess, perhaps by size or some other property, of the difficulty of words, prior to fully decoding them, and it will be interesting to learn where this analysis is done.

• New uses for AI in medicare advantage.
• Some problems with environmental review.
• No-compete "agreements" are no such thing, and worthless anyhow.
• We wanna be free.

An Origin Story for Spider Venom

Phylogenetic analysis shows that the major component of spider venom derives from one ancient ancestor.

One reason why biologists are so fully committed to the Darwinian account of natural selection and evolution is that it keeps explaining and organizing what we see. Despite the almost incredible diversity and complexity of life, every close look keeps confirming what Darwin sensed and outlined so long ago. In the modern era, biology has gone through the "Modern Synthesis", bringing genetics, molecular biology, and evolutionary theory into alignment with mutually supporting data and theories. For example, it was Linus Pauling and colleagues (after they lost the race to determine the structure of DNA) who proposed that the composition of proteins (hemoglobin, in their case) could be used to estimate evolutionary relationships, both among those molecules, and among their host species.

Naturally, these methods have become vastly more powerful, to the point that most phylogenetic analyses of the relationship between species (including the definition of what species are, vs subspecies, hybrids, etc.) are led these days by DNA analysis, which provides the richest possible trove of differentiating characters- a vast spectrum from universally conserved to highly (and forensically) varying. And, naturally, it also constitutes a record of the mutational steps that make up the evolutionary process. The correlation of such analyses with other traditionally used diagnostic characters, and with the paleontological record, is a huge area of productive science, which leads, again and again, to new revelations about life's history.

One sample structure of a DRP- the disulfide rich protein that makes up most of spider venoms.

 The disulfide bond (between two cysteines) is shown in red. There is usually another disulfide helping to hold the two halves of the molecule together as well. The rest of the molecule is (evolutionarily, and structurally) free to change shape and character, in order to carry out its neuron-channel blocking or other toxic function.

One small example was published recently, in a study of spider venoms. Spiders arose, from current estimates, about 375 million years ago, and comprise the second most prevalent form of animal life, second only to their cousins, the insects. They generally have a hunting lifestyle, using venom to immobilize their prey, after capture and before digestion. These venoms are highly complex brews that can have over a hundred distinct molecules, including potassium, acids, tissue- and membrane-digesting enzymes, nucleosides, pore-forming peptides, and neurotoxins. At over three-fourths of the venom, the protein-based neurotoxins are the most interesting and best studied of the venom components, and a spider typically deploys dozens of types in its venom. They are also called cysteine-rich peptides or disulfide-rich peptides (DRPs) due to their composition. The fact that spiders tend to each have a large variety of these DRPs in their collection argues that a lot of gene duplication and diversification has occured.

A general phylogenetic tree of spiders (left). On the right are the signal peptides of a variety of venoms from some of these species. The identity of many of these signal sequences, which are not present in the final active protein, is a sign that these venom genes were recently duplicated.

So where do they come from? Sequences of the peptides themselves are of limited assistance, being small, (averaging ~60 amino acids), and under extensive selection to diversify. But they are processed from larger proteins (pro-proteins) and genes that show better conservation, providing the present authors more material for their evolutionary studies. The figure above, for example, shows, on the far right, the signal peptides from families of these DRP genes from single species. Signal peptides are the small leading section of a translated protein that directs it to be secreted rather than being kept inside the cell. Right after the protein is processed to the right place, this signal is clipped off and thus is not part of the mature venom protein. These signal peptides tend to be far more conserved than the mature venom protein, despite that fact that they have little to do- just send the protein to the right place, which can be accomplished by all sorts of sequences. But this is a sign that the venoms are under positive evolutionary pressure- to be more effective, to extend the range of possible victims, and to overcome whatever resistance the victims might evolve against them. 

Indeed, these authors show specifically that strong positive selection is at work, which is one more insight that molecular data can provide. (First, by comparing the rates of protein-coding positions that are neutral via the genetic code (synonymous) vs those that make the protein sequence change (non-synonymous), and second by the pattern and tempo of evolution of venom sequences compared with the mass of neutral sequences of the species.

"Given their significant sequence divergence since their deep-rooted evolutionary origin, the entire protein-coding gene, including the signal and propeptide regions, has accumulated significant differences. Consistent with this hypothesis, the majority of positively selected sites (~96%) identified in spider venom DRP toxins (all sites in Araneomorphae, and all but two sites in Mygalomorphae) were restricted to the mature peptide region, whereas the signal and propeptide regions harboured a minor proportion of these sites (1% and 3%, respectively)."

 

Phylogenetic tree (left), connecting up venom genes from across the spider phylogeny. On right, some of the venom sequences are shown just by their cysteine (C) locations, which form the basic structural scaffold of these proteins (top figure).

The more general phyogenetic analysis from all their sequences tells these authors that all the venom DRP genes, from all spider species, came from one origin. One easy way to see this is in the image above on the right, where just the cysteine scaffold of these proteins from around the phylogeny are lined up, showing that this scaffold is very highly conserved, regardless of the rest of the sequence. This finding (which confirms prior work) is surprising, since venoms of other animals, like snakes, tend to incorporate a motley bunch of active enzymes and components, sourced from a variety of ancestral sources. So to see spiders sticking so tenaciously to this fundamental structure and template for the major component of their venom is impressive- clearly it is a very effective molecule. The authors point out the cone snails, another notorious venom-maker, originated much more recently, (about 45 million years ago), and shows the same pattern of using one ancestral form to evolve a diversified blizzard of venom components, which have been of significant interest to medical science.

• Example: a spider swings a bolas to snare a moth.

New World Order, or Old World Order?

As we gaze into the future, are we looking at a new Cold War?

The international landscape is taking on a tone of deja vu these days, as we return to Kremlinology and proxy wars. It feels like a new Cold war is upon us. The familiar lineup of Russia and China, with various other formerly communist states, are aligned against "the West" writ large: the US with core European countries, plus also those European post-Soviet states that turned in revulsion against their former captor. Only Belarus was left behind as a pawn of Russia. Iran is perhaps the one large country that was previously part of the US coalition and has decisively switched to the other side, though several countries like Turkey, Indonesia, and Pakistan are non-aligned or hostile.

But the familiar names and grudges belie vast changes in the landscape. The principal shift is that the Soviet economic system, and the communist economic systems more widely, is no longer the albatross it once was. Virtually every country has ditched communism (or, more precisely, top-down planning), discovered capitalism, and put it to work resolving fundamental economic problems and built modern economies, more or less. North Korea may be the only exception, (and perhaps Cuba), showing its entreprenurial spirit in the sphere of international crime, but otherwise hewing doggedly to a fully planned economy. China is foremost in this new authoritarian movement, having mastered a hybrid system of one-party politics and multi-party economics. This new model, (perhaps pioneered ultimately by Singapore), is a far more concerning and long-term threat than communism ever was. Straight communism was brutally impractical, and demanded correspondingly brutal methods of implementation. As it turned out, it was only attractive to the most extreme authoritarians, such as Lenin, Stalin, Mao, and Ho Chi Minh, and their starry-eyed believers. 

Prevalence of government types, world-wide. There has been a noticeable regression over the last decade or two.

But the new model is much more widely applicable and attractive. Even we in the US had a narrow escape during the last administration, and half the country remains in thrall to its lure. If power is one's goal, autocracy, or "managed democracy", is far more attractive than a truly competitive democracy. While in the 20th century many authoritarian states transitioned to democracy, this century has shown a different trend, as countries like Hungary, India, Venezuela, and Russia head away from more or less functional democracy. 

The Ukraine war has obviously broken all this open, manifesting Vladimir Putin's seething resentment that yet one more former Soviet "Republic" and Imperial satrapy resisted all his efforts at corruption and cooptation, and through force of popular will dared to aligned itself with the West. Every country has to choose a position, and those positions were recently enunciated in the recent UN assembly vote against the aggressor. China has exposed itself as fatally hypocritical to its former mantras of non-interference, peaceful coexistence, and national self-determination. Support of its fellow authoritarian, in war that so closely mirrors the one it contemplates against Taiwan, takes precedence over any lip-service to principle or peace. The Western coalition of democracies fell naturally into line as well, in reaction to the horror that was unfolding, which everyone thought the experiences of the last century would have made impossible. Not so! The new authoritarian model has an ancillary and deeply related property, which is revived imperialist ambitions, just as it did back in World War 2, and earlier.

An interesting question is where India lands in this new alignment. It would seem a pretty simple proposition for India to condem the appalling and cruel invasion (couched in the clearest imperial and anti-democratic ambitions). India itself has been nibbled at by the bellicose ambitions of both Pakistan and China. But no. India abstained from the UN vote, along with China. India is propping up Russia by buying its discounted oil, and is otherwise mum, hearking back to its non-aligned status during the cold war. This is not helpful, as the world's largest country by population, and largest putative democracy. But India itself has been heading into an authoritarian, in its case Hindutva, direction, and clearly is torn regarding its allegiances, whether to true democracy, or to managed democracy, and its long-time quasi-friend, Russia. While it doubtless seeks to avoid the looming world where it ends up on the opposite side from an alliance between China, Russia, and possibly Pakistan and Iran, (which also abstained), that world is coming regardless. India flirted with alliance with the US over the last two decades, but this recent stance would seem to doom that relationship, or make it a non-reciprocal one. That India's stand is unprincipled goes without saying. Whether it will be tactically effective is another matter. Unlike smaller countries, India does not rely on rules in the international arena, but rather on power. Failure to support others in the face of unjustified and brutal invasion and spiteful bombardment of civilians saps international solidarity, impairs India's international reputation, and weakens its own future claims to sympathy when the wolf is at its own door. But its relationship with Russia may be valuable enough to repay those costs.

It should be obvious that, as a collective action problem, the way to avoid war is for all other countries to band together to forstall, condemn, reverse, and punish belligerent invasions like that started by Russia. Allowing Russia to get away with a half-a-loaf negotiated takeover would only invite future attempts by it or other aggressors. Punishment, when concentrated on the perpetrators, (not necessarily their national and captive populations), is critical to deterrence.

So it was heartening that most countries were not so cynical and saw the general danger well enough to have supported the UN resolution, toothless as it was. The question overall is whether international relations progress to a new world order, or regress to an old one. Since World War 2, Europe has enjoyed substantial and deepening peace, with an especially peaceful re-integration of Germany, re-establishment of the Baltic nations, Poland, and most nations of Eastern Europe. Yugoslavia was the only region that fell into warfare, and continues in an uneasy constellation of truces, mostly enforced by the dream of joining the peaceful and prosperous European community. While the breakup of the Soviet Union was caused by, and furthered, long-standing nationalist sentiments, those sentiments were kept in check by guardrails of the "new", or liberal international order, which prizes peace and tranquility, under the policing of NATO combined arms, with those of the US at the forefront. Of course Russia had its role as well in managing the post-beakup nationalisms, for instance in Chechnya and Georgia, and it was not interested in any liberal order. But the assault on Ukraine is an entirely new line that has been crossed.

The old world order is one that foreign policy "realists" relish. The old spheres of influence, and balances of power warm the hearts of Metternichian traditionalists, savoring the way it has always been. There, guile and propaganda, selective alliances and stealth were the order of the day, throwing small countries to the dogs while the big countries do what they wish, each pursuing imperial dreams. They claim that this is just the way things are, there is no alternative, and any hopey-changey ambitions for a better international system amount to just another League of Nations or toothless UN. 

One can grant that the international scene is not, yet, bound by a legal system or effective police powers. The US has tried to be the policeman, and done a generally well-intentioned, but poor job of it. We run a vast network of military bases that has stretched over the globe, and exert soft power of many kinds. This has given room for countless small nations to pursue their dreams, subject to, but not crushed, by great power spheres and pressures. Taiwan grew into a flourishing independent democracy, Poland shook off centuries of partitions and subjugation. People power rose up in the Phillipines, in Ukraine, and in the Middle East. Africa has had a fitful time, but generally has been able to at least breathe free of explicit colonial oppression. US policy over the last few decades has been a race to establish a civil international order that is entrenched enough to survive our own demise as a superpower. Even the Iraq war was, at least in spirit, intended to break the patterns of authoritarianism that plague the Middle East, and implant a new, prosperous democracy. But bringing a new and happy dispensation on a plate of hellfire did not work out so well. Indeed, the implanted Western democracy of Israel shows more signs of aligning with the local political patterns than of changing them. 

So, change is hard, as is management of international relations in the absence of rules and police. The realists would say that other nations, both major competitors and spoilers, always line up against the powerful nation of the moment, due to natural competitiveness. But the Ukraine war should be, if any international event can be, the most glaring example of the boundary line between possible systems, and possible futures.

One can liken the old order to a city with gangs or mafia families. The gangs are always in flux, growing, shrinking, and competing. Long times may go by with relatively stable constellations, but then all hell breaks loose and the warfare is in brutal earnest. The new international order is, in contrast, more like a modern city, with representative government, laws, and a police force. Its violence confined to small-time spoilers, criminals and malcontents. Large scale warfare is unknown. Who wouldn't want the second over the first? Well, that takes solidarity- that nations do not only look out for themselves for the moment, but take a long view of the system and their long-term interests, and band together globally to make that future happen.

Perhaps the US is uniquely able to pursue this vision of international relations due to (in addition to its wealth) its makeup as a polyglot nation, its long experience with self-government at all levels, its fascination with the Western and the Police procedural as its reigning entertainment forms, and its modest remove from the European wars of imperialism and domination. We were motive forces behind both the UN and the League of Nations. Whatever the cause, the logic remains that international peace relies entirely on the collective will hold it as an ideal, and then to enforce it. This future does take some imagination, which realists seem to be lacking. But international standards have advanced significantly. Slavery used to also be just the way things were in a naturally competitive world. Poison gas used to be a standard weapon of war. We can change the landscape of international competition.

With a modicum of international solidarity and policing, the international community can put an end to imperialistic wars of aggression. And that movement starts now, in Ukraine, by beating back Russia and all the lies, cruelty, and stupid condescension that it stands for.

• History for the Ukraine conflict. Russia's policy was always predicated on keeping Ukraine down.
• Scenarios for the Ukraine conflict.
• Democracy could work better.
• Or it could work a lot better.