SARS E!

How does this virus assemble and get out of the cell? The key proteins are named S, M, N, and E.

True to their tiny size, viruses typically have short genomes and short names for their genes, which are relatively few. Coronaviruses generally have two halves to their genomes- a big polyprotein that gets translated right away from the genome RNA, and encodes key proteins, some of which interfere with host functions, and others of which include its own replicase, and proteases that cleave itself into those pieces. The other half of the genome is expressed later, into the proteins that make up the baby virions- the envelope and nucleocapsid, along with a slew of smaller proteins that have other, and sometimes still unknown, functions.

Once all this has gotten going, the virions have to assemble and escape from the cell- a complicated and interesting process, not completely understood, though blowing up the cell through inflammation, apoptosis, and general tissue destruction certainly helps. Genomic viral RNAs, as they are made in the cell cytoplasm by the viral replicase, get bound by the N protein, which is the viral protein that binds and packages the genome, and also has binding sites for the M protein, which organizes the outside envelope. N has other roles in controlling host processes, but this is its major function. These N+genome RNA complexes (which are regarded as the nucleocapsid) find their M partners sticking out of the endoplasmic reticulum (ER, or actually a post-ER compartment called ERGIC) that is the major site in cells of protein synthesis of membrane proteins and secreted proteins. Binding promotes budding of the genome complex into the ER, forming a nascent virion, now inside the ERGIC.

Final portion of the SARS life cycle. Virion proteins are made by ribosomes (green) from gene-sized portions of the viral genome, at lower left. The nucleocapsid protein (yellow) gathers up the replicated RNA genomes into packages, and then docks onto the membranes of the ERGIC, or endoplasmic reticulum-golgi intermediate membrane compartment, specifically on the M proteins (red) exposed there, that have been translated into the endoplasmic reticulum and formed homogenous rafts. Then all that is left is to follow the endocytic pathway out of the cell, or wait for the cell to blow up by other means. In actual virions, there are many more M proteins than S proteins, and extremely few E proteins.

The M protein has in the mean-time been synthesized in vast amounts and has several important properties, being the main protein that constitutes and drives formation of the viral envelope. It is an integral membrane protein, and associates with itself, in a particular array that prefigures the complete virion and excludes non-viral membrane proteins. M protein also, in these rafts of itself, makes space for the S protein- the surface spike which gives the virus its name (corona) and which binds to the next target cell- in someone else's lung tissue. And it binds to the N protein, so that the virus envelope engulfs the packaged genome as it docks from the cytoplasm.

E protein from original SARS. That is it! Red denotes hydrophobic amino acids, blue hydrophilic, and stars the charged amino acids.

That leaves the E protein.. what is it doing? It is a tiny (76 amino acid) membrane protein, important, though not essential, for viable viruses. Indeed it is so important that viruses with this gene experimentally removed, while able to limp along at low levels, quickly evolve a new one from scratch. But it is present in virions only in very small amounts. Its structure indicates one transmembrane domain, but predictions have been ambiguous- some methods predict two, some only one. This may suggest that this protein truly has somewhat ambiguous membrane localization, which might suggest a key function in the budding process, encouraging the last, critical transition from membrane invagination to true, fully enclosed virion.

You might not need many E proteins to do this, just a small ring around the final lip of the M-protein led vesicle. E binds to M protein, and the two of them alone are sufficient to make virion-like particles in experimental cells. N protein is not needed at all, nor a genome! Yet E is thought to also be able to bind to S, helping anchor it in the viral envelope. E can also bind to itself in complexes form membrane pores, one of whose effects is to promote inflammation and apoptosis, i.e. cell death. As if that weren't enough, E protein also contains a regulatory domain (PBM) that can bind hundreds of cellular proteins to regulate cell function, particularly dysregulating cell-cell junctions to form multi-cellular synctia that allow viral spread to neighboring cells, while impeding immune responses. A lot to do for such a small protein!

Virions lacking E, made with only M, are abnormally shaped, and ones made with mutant E proteins have novel, still abnormal, shapes. This leads to the idea that M forms flat sheets, and E helps the viral envelope curve, as it must to form the spherical virion. As mentioned above, it is also quite possible that E helps with the ultimate encirclement of the virion, the final membrane-fusing stage of budding that is actually rather tricky to accomplish and requires specialized machinery in the cell and in most membrane-envelope viruses. So there remains quite a bit to learn about the machinery of this virus, for all we know so far. And we are naturally even more curious about more practical matters, like whether all this can help create a vaccine, how exactly it spreads, whether it provides immunity after infection and for how long, and how much each of our protective measures, like masks, gloves, washing, disinfecting, etc., really help.

• Social networks, evolution, the friendship paradox, and epidemic modeling.
• Coronaviruses remain viable for over an hour in aerosol, and for many hours on hard surfaces. So they spread everywhere, mask or no mask.

Birth of a Gene

Where do genes come from? Well, lots of them rise right out of the muck- the junk of the genome, according to one paper.

Can genes arise out of nothing? The intellegent design folks spent a lot of sweat and pseudo-math showing that that was absolutely impossible. But here we are anyhow. They got their physics and math wrong. New genes arise all the time, mostly from pre-existing genes, by duplication events which are rampant, given the capacity of biological systems to replicate their constituent molecules. The human genome carries vast fleets of genes whose origin is duplication over evolutionary time - hundreds of zinc finger transcription factors, hundreds of odorant receptors, not to mention tens of thousands of duplicated transposons and viral remnants. And yet, can genes arise from nothing at all?

A recent paper says that yes, many functional genes have come from completely non-functional DNA, rather than pre-existing genes. While not the same as assembling a gene from the primordial soup, an event that remains difficult to reconstruct while singular in its global impact, this claim does suggest that the long-term plasticity of our genomes and of biological functions is even higher than many biologists appreciate. These researchers use synteny as their touchstone- the tendency of genes to stay in the same place on chromosomes through time, to conclude that most genes that lack homologs in other species did not arise by duplication, but by the conversion of some junk DNA to a functional state.

Syntenic relations of some of the human chromosomes, with those of chimpanzee. Lines indicate concordant / homologous positions. Note several massive inversions, and a few smaller segments that have jumped from one location to another. But on the whole, our genomes are highly similar in gross structure.

Humans and chimpanzees have strongly syntenic chromosomes, since we are so closely related. Most chromosomes line up precisely, with a few dramatic inversions (places where a portion of a chromosome in one lineage flipped orientation by recombination), and a few gaps and migrations of segments to new locations. This means that it is easy to trace which gene is ancestrally related to which gene in the other species. But not just genes, all nearby portions of the DNA are similarly lineally related, even if they are not well-conserved, as the cores of genes typically are. The researchers used human, fly, and yeast lineage tracing, benefiting from the large numbers of genomes that have now been sequenced from closely related species. This allowed them to determine the origin of novel genes lacking homologs among other species, but situated between normal, and normally homologous, genes. Either that novel gene arose in place, from the materials available, or else it came from elsewhere as a duplication or gene conversion event, with recognizable antecedents.

At a gene with no recognizable homolog (green), synteny helps to tell us that its origin was from a pre-existing gene, not from junk DNA.

Given all that information, one can then ask- did this gene decay from some known gene that is homologous to others among many species, and if so, how long did that decay take? At this point we need to define gene similarity. Typically software programs can give quantitative answers to how similar two protein sequences are, or two nucleotide sequences. But there is a twilight zone where similarity is so low that it can not be computationally recognized- like a game of telephone after too many transfers. But that does not mean that the two sequences are not lineally related, or even that they don't have the same function. There are many examples of protein pairs with no discernable sequence similarity, but very similar structures and functions. So evolution can go places our computers can not quite follow, though that may change once we solve the protein folding problem.

The authors portray the estimated time to gene degradation for orphan genes they studied, based on their presumed ancestors identified by synteny analysis. A very long time, in any case, but even longer for humans. my = millions of years. and the Y axis is proportion of the genome, going up to 10%.

The researchers show that this time to gene decay is much faster in flies and yeast than it is in humans. What takes 200 million years in yeast or 400 million years in flies (10% of lineage-ancestral, syntenic genes decayed to unrecognizeable similarity) takes an extrapolated 2 billion years in human genes. This may be due to the vastly different generation times of these species, considering that meiosis may be the most likely time for genome rearrangements.

An example (MNE1) of a large protein coding gene (in single letter code) that has essentially no recognizable sequence similarity, but still has synteny and functional homology with its relative (here, from S. ceverisiae to K. Lactis, both yeasts).

The next question was- how many of the novel genes across the genome came from that decay process of pre-existing genes, and which did not, rather (by default) coming from de novo origination out of the local DNA segment? It is a complicated question, a function of how one calculates similarity, and models synteny across related species. Do lineages where the matching syntenic DNA disappeared rather than decayed count towards the de novo origin hypothesis, or do they count as similar DNA that supports the decayed gene hypothesis? Since one partner in the homology pair is absent, the analysis depends on having enough other lineages fully sequenced to figure out what happened in detail. The authors' conclusion is that, on the whole, only one-third of novel genes arose from decay processes, and the rest arose de novo. That is a stunning conclusion, and sort of buried in the paper, which focuses on the decay processes that are easier to analyze, and comprise all the figures.

Unfortuntely, their logic breaks down when it comes to this conclusion. Yes, genes degrade to various degrees over time when they fail to see strong selection for function. That is given. But their key assumption is that their derived rate of gene decay at syntenic positions (let us say X) can be extrapolated over the entire genome. They thus claim that since, from separate analysis, Y is the number of genes in the entire genome that are novel (or orphan, lacking recognizable relatives), that Y - X is then the proportion that did not degrade from pre-existing genes, but rather arose denovo from other non-gene genetic elements. From this, they offer an estimate of roughly Y = 3*X, leaving 2/3 of Y coming from somewhere else, presumably de novo formation. The problem is that degradation of a gene at a syntenic position is a special case, compared to the also quite frequent duplication of genes and other sequences to distant locations which is another source of pseudogenes and ultimately of gene degradation and novel or orphan sequences. The mutation rates that apply to these cases are likely to be different, because the syntenic case never involves gene duplication, at least not in the recent past, by definition. Duplication is far more likely to lead to an immediate loss of function and selection than is degradation in a syntenic location.

So I do not think we can conclude what this paper (and an accompanying review) claim. They have not demonstrated at all the de novo origin of novel genes, but only suggested such origins from highly questionable negative evidence. Nevertheless, the topic is an interesting one, and someone is likely to study it with more care than was done here. Many tiny open reading frames and other stray genetic proto-elements litter our genomes, and other studies have shown that practically all of them are expressed at some level, at least as RNA, if not as proteins. So the question remains- whether and at what rate any of them gain an actual selected function, rising to the level of a gene of significance to the organism.

• I wonder what a psychopathic clown melt-down looks like.
• Never waste a chance to be utterly corrupt.
• Making America number 1 ... in disorganized health care and coronavirus deaths.
• Government operates mostly in an economy of blame, not of wealth or effectiveness.

We Live in Each Other's Heads

Family, faith, abuse, and gaslighting- review of "Educated", by Tara Westover.

Memoir can be a powerful form, combining truth with the most personal urgency. Westover's coming of age saga tells of a prepper childhood spent far away from any school or doctor, in an isolated Mormon family in Idaho- a patriarchy of one. It was also idylic, with a mountain to themselves, horses, seven children, and the freedom roam and explore. The children, though not taught formally, were also free to roam intellectually, if they could do so on their own. The trajectory of Tara's childhood appears distinctly downhill, however, as she matures from carefree child to a girl who needs to be squeezed into the appointed role of a Mormon woman, wife, mother. The story revolves most strongly around the social pressures that she gradually comes to realize are choking her- love that curdles into control, so that time-honored roles are fulfilled, and life can go on as always.

The family eventually splits into two halves- three children who escape into the larger world, get educations, live independently, and are forced, because the family can love only those who are obedient, to break ties. And the four children who not just stay behind, but work for the family business. Tara has the most spectacular escape, getting a PhD in history at Cambridge, and using her scholarly skills to write this book which lays so much bare. She also learns a lot of philosophy ... and is no longer a Mormon.

Oh, how things have changed- the Oprah interview.

But it took a lot of agony, and some therapy, to get there. The core of the book is really about physical and mental battles with the male patriarchs- the father, Gene, and the brother, Shawn. The father is one of those cranky autodidacts who figure everything out for themselves, and then insist they are right (even writing blogs about it!) and speaking on God's behalf. He runs a junk yard, salvaging copper, iron, and other materials from junked cars in the most unsafe ways, getting various family members injured in the process. Finally, he manages to get himself half-incinerated by taking a blowtorch to unemptied gasoline tank, and, while surviving by the grace of his wife's diligent care, is hobbled for life. More striking, however is his prediction that the Y2K crisis will bring on the Days of Abomination. He is convinced that the end-times are near, society will break down, and they, on their mountain will happily be both safe and vindicated. Lectures on these themes go on endlessly. But as he and Tara watch TV that millennium night, nothing happens, and she sees him visibly diminish, brought down by a cruel reality.

The father provides the baseline fundamentalism and ultimate leadership in the family dynamic. But Shawn brings the muscle. His relationship with Tara has mostly been very close and positive. But it is also clear that he is a psychopath, and Tara's maturation brings out a dark, controlling and vindictive side. He makes a practice of calling her a whore for any transgression of the patriarchal code, then nigger if she has gotten dirty in the junk yard, then abusing her in cruel and physical ways. Afterwards, he says it was all in good fun, and she can just tell him to stop any time, right? We now call this gaslighting, though no one had a name for it back then. For a teen age girl, it was shameful, degrading, and confusing. And it is fully backed up by the family, since the father doesn't see anything wrong with a bit of horseplay and role enforcement, and the mother- well, the mother can not cross the father.

Years on, after some degree of consciousness raising, Tara has the temerity to call Shawn on his behavior. The father goes on an extensive campaign to close the family ranks, and finally comes to Tara to give he the climactic choice of the book- accept his priestly blessing, which is to say accede to the patriarchal hierarchy and squelch her own memories and growing self, or else be ostracized. Westover has told this story in excruciating detail in order to make sense of this moment, to show how powerful social control can be, capable of turning people against themselves and against their very knowledge of reality.

Why? The evolutionary argument is reasonably clear- people, living in social systems, need to have some shared understandings of each other and reality. These understandings are tied up with power and who gets to run these systems- whose interests are served. And it is historically clear that those who are disagreeable enough to buck the established narrative very often end up dead- burned at the stake, forced to drink the hemlock, run out of town, ostracized. The line between justice in some necessary civic sense, and totalitarian measures against deviance, impiety, and disobedience is not a clear one. It is a modern innovation to separate the state from religious conceptions of the social order, now leaving each religious community to police its own congregants with other tools. But over the long arc of human history and pre-history, these were closely intertwined, indeed indivisible. Being trapped in one's family and tribe meant getting along with its reality, whatever that might be.

Tara is almost crushed by the choice, and the dissonance of being loved by people who increasingly seem both untethered from reality, and intensely controlling of their communal version of it. She goes through years of depression and doubt, torn to the core between loyalty to family, and loyalty to what she is shaping as her new self, fostered on intellectual adventures that go unimaginably beyond what her former (and alternate) self could have achieved. Is it worth it? That is the frequent problem of waking up from a religion (or a family) - that one has to lose its comforts and support in order to understand it more fully and overcome its glaring limitations.

• You don't have to be smart to run a cult.
• Thanks, Tea Party.
• Stupidity is generally not the answer.
• How many times does this president need to be impeached?
• Bill Mitchell on the job guarantee, and on bandwagons.
• How's your sky?
• Some more nice piano.

How do we Get Out of Here?

It is hard to tell just yet how the coronavirus lockdown will end. Some scenarios.

With the US having frittered away its early opportunity to contain incoming travel and the spread of SARS-CoV-2, we lost containment and now have an endemic pandemic. Nor are our health authorities pursuing definitive contact tracing and quarantine of all cases/contacts- some regions of the country are even well beyond this possibility. Time lines for the lockdown are being progressively extended, without a clear end-game in sight. Where will it end?

The China Solution
China has done draconian quarantines and close tracking, contact tracing, and isolation. And they have stamped out the epidemic, other than a tickle of cases, supposedly mostly coming from abroad. How ironic, but also impressive. They have used institutions and norms of close social control, sometimes rather blunt and indiscriminate, to get the upper hand over this contagion. The prospects for us doing the same are dim. Neither our public officials nor population have the stomach for it. Thus this is not a realistic scenario as an endgame for the US pandemic.

Slow burn
No, we take a more relaxed approach, hoping that the pandemic will magically recede. But that is unlikely to happen, given the vast reservoir of uninfected people, and the virus's high infectivity. So far, the US has ~300,000 cases, and ~8,000 deaths. Assuming that the reported case rate is one-tenth of actual cases, there might be three million people who have been exposed and recovered, out of a population of over 300 million. Exposing everyone would thus result in roughly a million deaths. This will happen no matter how good our social isolation is, or how long it lasts, because the minute anyone pokes their head out, they will be exposed. Without comprehensive tracking and isolation of cases/contacts, our laissez-faire approach leads to a slow burn (also termed flattening the curve) where our hospitals might be able to keep up with the extended crisis, but we still take an enormous hit in illness and death.

Exposure testing
One supplement to the slow burn scenario is the addition of exposure testing, for antigens to SARS-CoV-2. If these tests were broadly offered, like at grocery stores and by home delivery, we could at least recognize a large population that is immune and thus can move freely, (perhaps wearing a scarlet letter!), helping to re-establish economic and other essential activities. This is like having some amount of herd immunity, without waiting for the entire population to have been exposed. But it would not significantly curtail the slow burn, since we are still unwilling to keep everyone else out of circulation in a comprehensive fashion.

County quarantine
Some areas of the country are doing much better than others, and could set up local clean zones and boundaries. Once cases were reduced to a small trickle, the health departments could do what they failed to do at the outset, which is to block and test at all borders, and comprehensively trace contacts and enforce isolation internally. Given the large and necessary traffic of deliveries of goods, especially food, this is quite unlikely to happen, and would represent a sort of breakdown of our political society. But the behavior of the Federal administration, giving a "you're on your own" message to states and localities, does make this scenario more likely. It also ends up being a sort of slow burn, since any locality can not forever keep up such isolation. It would have to continue until the advent of a final solution- a vaccine or treatment.

Vaccine or treatment
This is the magic solution everyone is waiting for. The antivax movement isn't looking so good at this moment,when everyone's attention is focused on virology, epidemiology, and public health. Candidate vaccines are easy to dream up- any protein from the virus could be expressed in some heterologous system (like in E. coli cells or yeast cells) in massive amounts, and injected into people to generate immune responses. But effective vaccines are another story. Coronaviruses and other respiratory viruses tend not to generate strong and durable immune responses. That means that their ingredients just are not that immunogenic- they have devious ways to hide from immune surveillance, for one thing. Indeed, we still do not have good vaccines (or treatments) against the common cold. So a good vaccine will need to use all the tricks of the trade, such as multiple protein pieces, both invariant and variable, and immune-stimulating adjuvants/additives, to make an effective vaccine. It may take a year, but it may also take several years.

It looks like we will be in this lockdown for a very long time, with reduced economic and social activity. And the more effective our social distancing, the longer we will have to stay isolated, as the flatter curve extends out in time. If we go down the China route with more draconian methods to stamp it out before it burns through the whole population, we will be in a very precarious situation until a treatment emerges, given the wide-spread, now endemic, presence of this virus world-wide if not in continuing hot spots in the US.

• For those locked in ..
• How China is controlling spread while getting back to work.