Covid Rings a Bell

How Covid causes such intense inflammatory reactions, via Toll receptors.

Those who have gotten a Covid vaccine might have an appreciation of our adaptive immune system. This comprises the B and T cells that learn about detailed features on pathogens that invade us, and then form, through an amazing feat of genetic reprogramming, novel proteins (such as antibodies) that can precisely zero in on those pathogens and call in lethal powers such as killer cells, phagocytes, neutrophils, etc. But there is another part, called the innate immune system, which is not adaptive, is evolutionarily older, and plays key roles in our day-to-day defense as well as in the beginning phases of the adaptive response. For how, after all, are pathogens recognized in the first place so that the adaptive response can even get started?

The innate immune system has many layers and actors, being very ancient. But one of its themes is that it recognizes "patterns", rather than the ultra-specific "epitopes" that the adaptive immune system gears itself up against. These patterns come in a two general forms, called pathogen-associated molecular patterns (PAMPs), which as the name implies come from outside, and damage-associated molecular patterns (DAMPs), which are typically cellular debris of various kinds that give notice that an injury has occurred. (There are also MAMPs and XAMPs for microbial and xenobiotic patterns, respectively.) PAMPs can include bacterial cell wall components like lipopolysaccharides and peptidoglycans, flagellin, fungal chitin, and a variety of nucleic acids such as double-stranded RNA characteristic of viruses, single stranded RNA, and DNA without special host markings.

What detects these patterns? Well, there are cell surface receptors for that, called the Toll-like receptors, or TLRs. Toll is a fly gene that was originally found to play important roles in development, (in German, it means "fantastic"), helping (together with its developmental ligand, Spätzle) embryos figure out their up/down, or dorsal/ventral polarity, and express the appropriate cell types to those locations. It was later found that fly adults use Toll for a totally different purpose- the activation of their innate immune systems, even though what pathogens it recognizes in that setting is still not known. All animals have TLRs, and plants have related systems, so this kind of thing is very ancient. Humans have at least 13 TLRs, so several bases are covered, making it difficult for a pathogen to completely escape this method of relatively crude detection.

The TLRs mediate immune responses against four general types of molecular patterns comprising damage/danger-associated molecular patterns (DAMPs), microbial/microbe-associated molecular patterns (MAMPs), pathogen-associated molecular patterns (PAMPs), and xenobiotic-associated molecular patterns (XAMPs). They do this by directly binding them. For instance, long double-stranded RNA, which is a common viral component, is detected by human TLR3. The TLR proteins form little hooks facing out from the cell. It takes two of them to fully bind one of the pattern molecules they detect, and when such a pair of TLRs forms, then their internal domains dimerize and set off a cascade of signaling inside the cell that serves as a danger alert. In this case, the antiviral program of interferon production, among many other genes, is activated. 

A structural model of a pair of TLR receptors, binding in this case a double stranded RNA. One TLR is blue, the other purple. One RNA strand is green, the other red. Binding the pathogenic pattern molecule drives dimerization of the receptor, which then causes its cell-internal domains to pair up and drive an activating signaling cascade.

Among the genes activated are signaling molecules called cytokines that alert and attract cells of the adaptive immune system ( T-cells and antigen presenting cells). Further genes are activated that process and present pieces of the pathogen pieces to those adaptive immunce cells. So the innate immune system, which has many other components, is a critical stage of our defensive system, both in its own right and as an initiator of the adaptive system.

This gets us back to Covid, where the SARS CoV2 virus causes extraordinary immune system activation in some people, a condition that is far worse than the original infection. A recent paper (review) suggested that the spike protein- the very same protein that is the first to dock to our respiratory epithelial cells, and the one that all the vaccines are made against, also binds in combinations of TLR2, TLR1, and TLR6. They do not show direct binding, but show that the spike protein by itself generates high TLR activity, and that this activity is composed of dimers of either TLR2+TLR6 or TLR2+TLR1. These receptors are known for the following activities:

• TLR2: Binds glycolipids from bacteria and also zymosan from fungi.
• TLR1: Binds lipopeptides, components of bacterial cell walls.
• TLR6: Binds diacyl lipopeptides, components of bacterial cell walls.

This is somewhat odd, since a pathogen would normally try to avoid triggering these sorts of receptors and responses. And a virus would particularly have little business activating a series of bacterial-specific TLR receptors. Covid may yet evolve towards evasion rather than activation, as it evolves to become endemic in humans and trade virulence for transmissibility. But for now, it is a here-and-gone kind of pathogen which seems to value immune activation and the associated respiratory expectoration that goes along with it. The authors also suggest that this activation may be a diversionary tactic, setting off the anti-bacterial alarms, and thus quieting the antiviral alarms, which the virus has more reason to fear. SARS CoV-2 is a wily antagonist, apparently purposefully activating some front-line immune defenses and landing many victims in a form of immune system over-activation called the cytokine storm.

• What is the value of money and labor over time?
• How about using big box stores for something useful?
• Climate change has nothing to do with us- Supreme Court.
• Afghanistan suddenly is overpopulated with regard to its new governing and technological environment.
• Crypto- not a lot of there there, aside from all the environmental destruction.
• Greenwashing.

Some Theological Aspects of Modern Economics

Economics remains in a difficult intersection between science and humanities, with distinctly political and ideological conflicts.

We seem to be in a passion play about inflation right now. It is skyrocketing, or zooming, etc. It is a huge crisis. But, since it is measured year-over-year, maybe it is just a simple bounce from the depths of the pandemic when demand and prices, especially for gasoline, were negligible, and some businesses shut down. Now demand is back, but some sectors of the economy are having a hard time meeting demand, especially for workers, so prices are going up, by modest amounts. Some stories say that "inflation is never temporary". Others say the structural dislocations will pass and things will get back to normal. One can tell the ideology quite clearly from the story line. Conservatives have double motives to paint it a crisis, to disparage the current president (tax cuts had nothing whatsoever to do with this!), to support the preservation of capital and capitalists, and to generally box in policy makers from spending money on truly momentous objectives, like addressing climate change.

Why is this such a drama? Why isn't economics more of a science? In real sciences, you do not see competing schools of thought, such as the Chicago and the Keynesian schools of economics, the New Keynsians and the Modern Monetary Theorists, which last for decades and never seem to resolve their warfare. Maybe that is because real sciences don't study anything important. But more likely, real sciences have methods to efficiently describe and resolve their differences- with reference to reality- that economists do not seem to have. For in the macroeconomics realm, there is not a lot of experimentation that one can do. It is a field more like history, from which scholars and observers tend to draw the lessons they want to draw, not the ones that would serve them best. Or theology, whose subject is wholly illusory, such that its practitioners are not really in the business of studying anything observable at all, (or even discernible!), but in social management- how to build ideologies and propagandize with effective rhetoric, how to build churches, how to sermonize, whom to target in their weaker moments, what and whom to value, which social hierarchy to support, and how to do so.

Economics is far from illusory, and plenty of economists do the truly scientific work of describing the economy as it is, giving us the grist of statistics from which the theorists can spin their opinions. It is at the policy and macro level where things get theological, where moral and ideological commitments outweigh technocratic sense. For economics at the policy level is fundamentally Darwinian- how one wants to split the pie depends on who you think is worthy- morally and operationally. Economics is not intrisically democratic- far from. There are some who are worth more to the system, depending on one's standpoint. The Ricardians (with the Chicago school carrying on its supply-side banner) deemed production and producers the only important parts of the mechanism. Demand would take care of itself as long as producers were given maximum latitude to conduct business and trade as they wished. As the ideological cycle turned, entrepreneurs were once again the vanguard and watchword in the eighties and nineties. 

When it comes to inflation, similarly vast ideological forces are at work. The progressive Kenyesian policy environment of the 1960's was eroded, then eviscerated by Milton Friedman's and the Chicago school's general neo-Ricardian attacks during the 1970's, in our period of stagflation. It was genuinely destructive to experience inflation at relatively high levels, and the solution ended up being deep recessions ultimately authored by Jimmy Carter via his appointment of Paul Volker. The power of workers to bid for higher pay and inflation-protected pay was destroyed by de-unionization, outsourcing and off-shoring. Those forces largely remain today, suggesting that the current inflation blip will be transitory. 

Inflation is measured in consumer prices, so it largely reflects low-end wages that are spent most readily, rather than the stock market or other places where the rich invest. As long as wages are kept down, then inflation will be kept down as well. The big question is how the economy splits the pie- between wages at the low and middle levels, versus returns on capital / wealth and executive pay. This balance has been heavily out of kilter over the last few decades. This may have been great for keeping inflation down, but has obviously had highly corrosive effects on much else, from the opioid epidemic, to our great dependence on China for goods and supply chains, and our political breakdowns. So economics is not just about the economy, but about a great deal more- who we value and what vision we have for the future.

Keynes in his magnum opus had some wry comments on this phenomenon, in 1936:

"The completeness of the Ricardian victory is something of a curiosity and a mystery. It must have been due to a complex of suitabilities in the doctrine to the environment into which it was projected. That it reached conclusions quite different from what the ordinary uninstructed person would expect, added, I suppose, to its intellectual prestige. That its teaching, translated into practice, was austere and often unpalatable, lent it virtue. That it was adapted to carry a vast and consistent logical superstructure, gave it beauty. That it could explain much social injustice and apparent cruelty as an inevitable incident to the scheme of progress, and the attempt to change such things as likely on the whole to do more harm than good, commanded it to authority. That it afforded a measure of justification to the free activities of the individual capitalist attracted to it the support of the dominant social force behind authority."- John Maynard Keynes, The General Theory of Employment, Interest, and Money

• Resisting the lies is harder than you think.
• Sustainability is the big issue, and our politics are too small to address it.
• Democracy is hanging by a thread.
• And each side seems to think it is saving democracy, apparently. Though only one side does so undemocratically.
• Of course.. Republicans dedicated to state destruction will support crypto.

Choices, Choices

Hippocampal maps happen in many modes and dimensions. How do they relate to conscious navigation?

How do our brains work? A question that was once mystical is now tantalizingly concrete. Neurobiology is, thanks to the sacrifices of countless rats, mice, and undergraduate research subjects, slowly bringing to light mechanisms by which thoughts flit about the brain. The parallel processing of vision, progressively through the layers of the visual cortex, was one milestone. Another has been work in the hippocampus, which is essential for memory formation as well as mapping and navigation. Several kinds of cells have been found there (or in associated brain areas) which fire when the animal is in a certain place, or crosses a subjective navigational grid boundary, or points its head in a certain direction. 

A recent paper reviewed recent findings about how such navigation signals are bound together and interact with the prefrontal cortex during decision making. One is that locations are encoded in a peculiar way, within the brain wave known as the theta oscillation. These run at about 4 to 12 cycles per second, and as an animal moves or thinks, place cells corresponding to locations behind play at the trough of the cycle, while locations progressively closer, and then in front of the animal play correspondingly higher on the wave. So the conscious path that the animal is contemplating is replayed on a sort of continuous loop in highly time-compressed fashion. And this happens not only while the animal is on the path, but at other times as well, if it is dreaming about its day, or is resting and thinking about its future options.

"For hippocampal place cells to code for both past and future trajectories while the animal navigates through an environment, the hippocampus needs to integrate multiple sensory inputs and self-generated cues by the animal’s movement for both retrospective and prospective coding."

These researchers describe a new piece of the story, that alternate theta cycles can encode different paths. That is, as the wave repeats, the first cycle may encode one future path out of a T-maze, while the next may encode another path out of the same maze, and then repeating back to A, B, etc. It is evident that the animal is trying to decide what to do, and its hippocampus (with associated regions) is helpfully providing mappings of the options. Not only that, but the connecting brain areas heading towards the prefrontal cortex (the nucleus reuniens, entorhinal cortex, and parahippocampal gyrus) separate these path representations into different cell streams, (still on the theta oscillation), and progressively filter one out. Ultimately, the prefrontal cortex represents only one path ... the one that the rat actually chooses to go down. The regions are connected in both directions, so there is clearly top-down as well as bottom-up processing going on. The conclusion is that in general, the hippocampus and allied areas provide relatively unbiased mapping services, while the cortex does the decision making about where to go, and while it may receive.

    "This alternation between left and right begins as early as 25 cm prior to the choice point and will continue until the animal makes its turn"

A rat considers its options. Theta waves are portrayed, as they appear in different anatomical locations in the brain. Hippocampal place cells, on the bottom right, give a mapping of the relevant path repeatedly encoded across single theta wave cycles. One path is encoded in one cycle, the other in the next. Further anatomical locations (heading left) separate the maps into different channels / cells, from which the prefrontal cortex finally selects only the one it intends to actually use.

The hippocampus is not just for visual navigation, however. It is now known to map many other senses in spatial terms, like sounds, smells. It also maps the flow of time in cognitive space, such as in memories, quite apart from spatial mapping. It seems to be a general facility to create cognitive maps of the world, given whatever the animal has experienced and is interested in, at any scale, and in many modalities. The theta wave embedding gives a structure that is highly compressed, and repeated, so that it is available to higher processing levels for review, re-enactment, dreaming, and modification for future planning. 

Thus using the trusty maze test on rats and mice, neuroscientists are slowly, and very painfully, getting to the point of deciphering how certain kinds of thoughts happen in the brain- where they are assembled, how their components combine, and how they relate to behavior. How they divide between conscious and unconscious processes naturally awaits more insight into what this dividing line really consists of.

• Biochar!
• More about the coup attempt.
• Yes, there was electoral fraud.
• The more you know about fossil fuels, the worse it gets.
• Graph of the week. Our local sanitation district finds over a thousand omicron genomes per milliliter of intake, which seems astonishing.

Desperately Seeking Calcium

How cells regulate internal calcium levels.

Now that we are getting a crash course in molecular biology and evolution courtesy of the pandemic, many will be familiar with the intricate and dynamic activities of some proteins. The SARS spike protein doesn't just dock at a particular receptor on our pulmonary epithelial surfaces, but goes through a gymnastic routine to facilitate membrane fusion as well. Many other proteins have dynamic behaviors as well- something that was not fully appreciated back when structural biology was in its infancy and knowing anything about the structure of a protein or DNA or RNA required it to be locked into crystaline form for X-ray diffraction studies.

Another example came up recently, involving calcium regulation within cells. Calcium is a hugely important ion and regulator, central to core signaling cascades in all eukaryotic cells- to neuronal function, and to muscle activation, among many other roles. Our blood levels of calcium are tightly regulated, (to within a 20% range), mostly by way of an axis of parathyroid hormone between the parathyroid gland and the kidney, with additional effects from factors such as vitamin D, calcitonin, and estrogen. So our cells can rely on having a constant level of calcium on the outside. How do they maintain their levels internally?

One way is to have a large store socked away, as we have in bones for the body generally. Within cells, the endoplasmic reticulum (ER) turns out to have far higher concentrations of calcium than the rest of the cytosol, up to 10,000 fold. In muscle cells, the ER gets a special name- as the sarcoplasmic reticulum. Many calcium regulatory events rely on calcium being released briefly from the ER, having some effect, and then gradually getting pumped back in. But what if the ER is short of calcium? That would be a crisis!  

It turns out that we have a sensor system for that, llinking an ER protein called STIM1, which senses levels of Ca++ in the ER with a plasma membrane channel called ORAI1, which can open to let in Ca++ from the outside. A recent paper, (review), in combination with much other past work, demonstrates how STIM1 works. The two proteins turn out to interact directly, thanks to the fact that the ER, which is a huge organelle that extends all over the cell, always has some spots that interact with the plasma membrane, called membrane contact sites. These are strucured by other proteins, so there is a set distance between the two membranes, which must never fuse together. This means that while STEM1 can get very close to ORAI1 in the plasma membrane, there will still be a gap between them. How to bridge it?

Overall model for how STIM1 works. The luminal side sticks into the ER and binds calcium (red dots). If levels are low, the protein dimerizes at the transmembrane and internal domains, causing extensive refolding of the external domains residing in the cytosol. This causes them to straighten out and span the space of the contact structure between the ER and the plasma membrane, where it activates the ORAI1 calcium channel protein by direct contact.

The STIM1 protein turns out to provide the bridge, in the form of a transformer-style mechanism that shifts it from a compact blob on the ER when calcium levels are high, to an extended rod that pokes into ORAI1, activating it, when calcium levels are low. Since it is the ER-internal level of calcium that needs to be sensed, it is the ER-internal (or luminal) portion of the STIM1 that does this sensing. It has about five calcium binding sites that, if filled, prevent its dimerization, but which if empty, promote it. Internal dimerization induces a dramatic refolding of the cytoplasmic portion of STIM1 into the active, extended rod. 

These authors were faced with a situation where the full STIM1 protein was apparently impossible to crystalize, so no full structure was available. Worse, some of the prior structural studies of fragments of STIM1 conflicted with each other. So they turned to very clever method to probe structural dimensions point by point, called fluorescence (or Förster) resonance energy transfer, (FRET). If by mutation or chemical modification one installs fluorescent molecules on a protein of interest, indeed installs two different ones, one of whose absorbtion spectrum overlaps with the emission spectrum of the other, one can measure quantitatively the distance between them.

How the FRET fluorescence method works. Different fluorophores are placed on the protein of interest, here the EFSAM luminal domain of STIM1. The absorption spectrum of one (acceptor) overlaps the emission spectrum of the other fluorophore (donor). In the first graph, the green graph shows that when the two are combined on the same molecule, emission from the acceptor goes up dramatically, due to its proximity-dependent absorbance of emissions from the donor fluorophore. The second graph shows how this protein responds to calcium, by increasing interaction (absorbance-emission intensity at 620 nm, reflecting the physical distance between the fluorescence probes) as Ca++ concentration goes down.

 

By placing fluorescence probe pairs all over the external regions of STIM1, these authors were able to definitively refute one of the prior structural models, and then outline the probable sequence of events by which STIM1 opens up into its active form. The image above ably summarizes their model, by which the ORAI1-interacting domain (CC2/CC3) is stored upside-down and inside out in the inactive conformation. It is quite a proposal, all carried out by domains which are alpha helixes hinged at strategic locations and obviously highly sensitive to slight changes in the structure, induced by the dimerization outlined above, in low calcium conditions.

Finally, they investigated a mutation which in humans causes Stormorken syndrome, a wide-ranging set of deficiencies including bleeding, dyslexia, muscle weakness, and hypocalcemia. In molecular terms it is a "gain of function" mutation. It weakens the interactions that keep STIM1 closed during high calcium conditions, so promotes its stimulation of ORAI1 and excess uptake by cells all over the body. The mutation changes argenine at position 304 in STIM1 to tryptophan, which has much different characteristics. It is genetically dominant, meaning that a single allele, combined with a wild-type allele on the other chromosome, gives the syndrome. Thus it is a powerful mutation, tweeking the sensitivity of this system just enough to screw up a lot of physiology. Deletions of this gene are not lethal, however, in part because there is also a STIM2 gene that encodes a similar function.

Analysis of the effect of the Stormorken mutation (R304W) on the physical proximities and overall shape of the STIM1 protein. The FRET graphs track different probe pairs that were placed all over the cytosolic (folding) portion of STIM1. In these graphs, degree of FRET relative frequency shift/communication is on the X axis, while photon counts are on the Y axis. They show noticeable shifts in distances, reflected in the structural model. The mutation significantly loosens up the high-calcium folded state, inducing more Ca++  influx when it is not needed.

So, we are just full of little machines, developed and refined over the billions of years in the ongoing race to live a little better, keep things humming, and to defend ourselves against all the other machines, such as parasitic viruses.

• How the new space telescope is unfolding, and where.
• The history of another pandemic- tuberculosis.
• The importance of relationships, and trust.
• Nuttery and religion go together.
• How to plan and build a city.

Eugenics is All the Rage

Animal breeders have no qualms directing intensive systems of artificial selection.

Eugenics is defined with reference to humans, as any consideration or implementation of artificial selection. There is little doubt that it would be effective, but there is some disagreement about what an "improvement" would represent. We are not cattle to be bred to specification, but organisms with dignity and freedom- specifically freedom from meddling by others in our reproduction. Wild animals have this freedom as well, by default. But domestic animals- that is a different story. For all our "humane" societies and pampering of some, our treatment of others is distinctly undignified. And that includes their breeding. 

Across the domestic animals, from racing horses and show dogs to dairy cows and chickens, breeding these days is carried on at unprecedented intensity, with the most advanced scientific and statistical techniques. For farm animals, this has led to inbreeding and alarming malformations, such as chickens that can't walk, and cows with chronic udder infections. For dogs, the creation of fundamentally malformed breeds also leads to chronic suffering, (short snouts, short legs), as does lack of care in breeding for temperamental health.

These animals have serious problems, of a genetic nature.

Animal breeding has progressed through three major stages. First is the traditional approach, using hunches and personal judgements- using the best animals, and perhaps cross-breeding with animals from other farms to retain diversity, if any directed breeding is done at all. With a relaxed approach, this led to generally good results, establishing the great dog breeds and other livestock, where hardiness and health were always prominent values. But in pigeon, cat, dog, and other casual breeding since Victorian times, amateur breeding like this can also go rather astray. 

In modern livestock breeding, this was superseded by the use of Estimated Breeding Value, or EBV, which is a systematized way to account for the genetic, rather than phenotypic trait quality in animals, by accounting for their relatives, as far as they have been measured, and also by accounting for uncertainties around heritability and systematic and environmental effects on the trait of interest. This concept puts breeding on a far more scientific basis, with quantification of traits, and of pedigrees. One result is that the breeding value can be estimated for animals who do not even have the trait, such as male dairy cattle. Another has been that animal breeding has been even more relentlessly driven to meet commercial and consumer objectives, even ones that shift over time as tastes change.

Naturally, the EBV method has now been supplemented by DNA-based evaluations in more recent times. The ability to "see" into the genome by sequencing some or all of it, thereby establishing a landmark map based on variants distributed throughout, allows the traits (if linked to such landmarks) to be tracked in all individuals, regardless of phenotype, and even in individual gametes and fetuses. This dramatically reduces the lottery that otherwise is genetics. However, its value is significantly bounded by the fact that most interesting and desirable traits are usually not genetically simple (like, say, eye color), but are complex, influenced in very small amounts by many different loci / genes. 

This is a frontier for animal rights and humane policy development, that animals not only should be treated well, but bred well. In livestock breeding, European countries have some relatively aspirational standards and laws, the US lacks even that. The "standards" used by such organizations are the American Kennel Club are worse than nothing, as they drive breeding for looks alone, and welcome the most obscure and unhealthy breeds, regardless of grave malformations, temperamental disasters, and inbreeding. While health of the animal needs to be paramount, other issues such as the ability of animals to live without special care and infrastructure, and genetic diversity, also need to be addressed, if we are going to be serious stewards of animals in our care.

• Our inert politics.
• The sleaze never let up.