Death and Resurrection ... Of a Gene

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

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

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

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

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

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

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

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

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

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

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

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

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• Update on the cerebellum.
• Cuba and capitalism, of a sort.

Dreaming Our Way Out of Capitalism

Review of "Understanding Capitalism", by Richard Wolff.

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

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

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

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

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

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

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

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

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

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

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

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

Just Whose Foreign Policy Is This?

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

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

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

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

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

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

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

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

• Or perhaps other influences were at work.

How 5S rRNA Gets Into the Ribosome

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

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

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

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

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

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

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

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