From Whence Came SARS-C-V-2?

Some of you may have heard rumours that SARS-CoV-2 arrived for us via bats. Now I know that a lot of people think it came from a research lab in Wuhan, but my guess is bats, and recent research into bats gives food for thought. They have a weird immune system, and they can tolerate all sorts of viruses. Accordingly, there are a number of research centres sprouting up around the world. Both China and the US have announced specific funding pots into research into bats and viruses. However, according to Nature (vol 615, pp576 – 580) one of the better advanced such studies is housed in Singapore. There, they captured 19 specimens of cave nectar bats and from them have bred a small colony that now has 140 members. Apparently this is quite an achievement because in general bats are very difficult to breed in captivity. The bats enjoy freshly chopped melon, papaya and mango, powdered milk, and, er, nectar. Which I suppose they would, given their name. There are apparently 1,450 species of bat in the world, but very few have been bred. So far, the successes include these cave nectar bats, Jamaican fruit bats, Egyptian fruit bats, and “big brown bats”. Nobody so far has managed to breed a horseshoe bat. (How did it get that name?) Why is this important? Because horseshoe bats are known to host an exceptional diversity of coronaviruses.

Subsequent research into bats is difficult. Actually catching them is difficult and there are safety challenges, given that such bats may well give you a disease you do not want. Then, once you have bats, it appears bat cells are extremely difficult to propagate. All the genetic toolkits used for mice and human cells are not available. There are  very few monoclonal antibodies that are used to tag immune cells. For a long time there was no high-quality genome, which means researchers still do not have a clear picture of the basic architecture of the bat immune system.

It is not just coronaviruses that are of interest. Some species also host viruses as deadly as rabies, Ebola and Marburg. (Collecting such bats would be problematical.) The question then is, how come bats can host the viruses without showing signs of infection? It seems that one of their attributes is they maintain high levels of interferons, which raise the alarm and set off the means of quashing viral replication. They also have proteins that interfere with viral replication and prevent viruses from leaving cells  if they get in. Their cells are equipped with an efficient system of disposing of damaged cell components. Finally, when pathogens do intrude, they do not overreact with an outsized inflammatory response, which is often more dangerous to humans than the actual damage done by the virus. However, this has another effect. Instead of expending all the effort to get rid of all the virus, the bat tolerates a low level and creates an adaptive response that clicks into action if it encounters further pathogen.

Thus a couple of horseshoe bats were captured in a cave in Spain, and from the body parts (after bats died) pluripotent stem cells were obtained and sequenced RNA expressed from these and found an abundance of sections that were essentially viral fragments, many being from coronaviruses. The bat cells appeared to suck up viral information “like a sponge”. It is not clear what this means but it would seem to indicate that the bat is continuously polishing up its immune system, generating and maintaining the equivalent of a low level of multiple vaccines all the time. Thus, from the viral point of view, bats are the ideal propagating medium. Once infected, they can spread the infection for an indefinite time.

Where this will go is anyone’s guess. Apparently in the US a start-up has raised $100 million in venture capital funding, so some think there is a future in bats. On the other hand, a bat that can carry around Marburg without showing adverse signs is not a species I would want to get too close to.

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Ebook Discount: A Face on Cydonia

From March 23 – 30, A Face on Cydonia,  the first in a series, will be discounted to 99c/99p on Amazon. On a TV program from Mars early in the 22nd century a battered butte on the Cydonia Mensae morphed into the classical face and winked. By 2129, following growing pressure suggesting a cover-up, Grigori Timoshenko forms an expedition to settle this “face” for once and for all. He recruits Fiona Bolton, a world expert in sonic viewing; Sharon Galloway, the developer of an AI digging device for a major corporation; also, Nathan Gill, a Martian settler. He has Jonathon Munro forced on him. Galloway hates Munro while Bolton hates corporates, so in a party with hidden agendas and with members hating each other, the gloss of visiting another planet soon wears thin. A story of corruption, greed, murder, the maverick, the nature of Mars, and with the problem of why would an alien race be interested in such a disparate party. Book 1 of the First Contact trilogy.

Science and Society

An interesting question is to what extent should a person’s loyalties lie towards society? Suppose you own a business in a mall, and you happen to know that right now business is going well and lots of electronic transactions are going into your account. You are making money hand over fist, but by some means you learn there is a bomb somewhere in the mall,  but you are reasonably confident that nobody in your premises will be seriously injured when it goes off . Do you immediately clear the mall, or do you keep quiet for a while and let the money keep flowing? You might think the answer to that is obvious, but is it?

Now let us shift the problem down the chain of responsibility. An employee of the business believes there is a gas leak down the other end of the mall. Again, the business he works for will be safe, but he suspects that if he stops the flow of money he may well be fired. What does he do? Now, let us shift the imminence. You have some engineering knowledge and you are employed by the owner of the Christchurch TV building after the first earthquake, and you notice some of the floors are not level. You look up the architectural plans and you see the floors are debatably not properly anchored to the walls. Do you blow the whistle and get everyone out, at the risk of being fired, or let things stay, on the basis the building is safe enough now, and it withstood a serious earthquake? Finally, in each case, you are the owner, and a worker brings the information to you. What do you do?

With your answers to those questions safely established, now consider that according to Chemistry World (Feb. 2023) in 1977 the scientists at Exxon Mobil had completed some extremely capable climate modelling and had reached conclusions similar to what few other reached until the start of the new millennium. A study of Exxon-Mobil’s internal reports clearly showed the effects of mankind’s burning of fossil fuels, and these could be easily separated from natural effects. ExxonMobil kept insisting the science was too uncertain to know when, or if, human-caused global warming might be measurable. The ExxonMobil scientists predicted 2000 +/- 5 years. They just made it -the IPCC declared it was measurable in 1995.  Thus armed with excellent scientific evidence, the Chief Executives Raymond and Tillerson insisted there was a  “high degree of uncertainty” in climate models. Tillerson was CEO from 2006 to 2017 when the evidence was in that the predictions were accurate and if anything under-estimated the adverse effects. Further, ExxonMobil had a long history of funding  third parties to make misleading claims on climate change. Armed with that experience, Tillerson  subsequently became Secretary of State under Donald Trump. Had ExxonMobil spent such funds on promoting research to find the answers to the problems with climate change, we would be much better off. Interestingly, ExxonMobil’s defence regarding the misleading statements is that free speech is protected under the Constitution. Of course, “free speech” that is demonstrably wrong that is made to gain money is also known as fraud, and that is less well protected.

What particularly annoys me is that part of the solution may lie with biofuels. After cyclone Gabrielle, a huge amount of forestry waste was washed down into rivers and has become a major problem. That could be turned into liquid fuel as could the organic fraction of municipal waste by hydrothermal liquefaction. It is possible to do this in a variety of ways, I have done it in the lab, there has previously been a demonstration plant proposed to be built in the US, but was abandoned after the price of oil slumped. And we know the Bergius process converted lignite to liquid fuels, with Germany making over a million tonnes this way through 1944, despite plant being bombed. ExxonMobil had the internal skills to address the engineering issues and could have made this a possible option now. It would not solve everything, but it would have used their experience to provide a partial solution.

Switching slightly, some readers may recall my fascination with aluminium/chorine batteries. The reason is that aluminium is easily available, and in principle offers a large capacity because while one atom of lithium provides work from one electron, aluminium has three. I suggested fuel cells based on the chemistry in my e-novel Red Gold because aluminium and chlorine would be readily available on Mars. Now, a novel battery has been claimed (Angew. Chem. Int. Ed. 2023, 62, e202216797) with a phenoxazine cathode (no cobalt!). A gram is claimed to have a capacity of 133 mAh at 0.2A, and has run for 50,000 cycles with no loss. If these can be manufactured with such performance, general reasonably priced electric vehicles become a possibility.

Natural Hydrogen

Smoking is a hazard to life, but there was an exceptional demonstration in Mali in 1987. According to an article in Science (vol 379, 631) since most of Mali needs water, some people were digging a well. They got down to 108 meters, but no water, so they gave up. Then, to their surprise, a wind started coming from the hole. How could that be. Someone stuck his head over the hole to look, and he was smoking. The wind exploded in his face. The well then caught fire, and continued burning with a colourless flame, with no soot. What they had discovered was a deposit of hydrogen. At first, this was regarded as an oddity, but according to the journal Science there is now more interest in “natural hydrogen”. As for the Malian hole, a local team installed an engine designed to burn hydrogen and hooked it up to a 300 kW generator. For the first time, the local village had electricity. The suggestion now is that hydrogen deposits may be more common than generally thought.  So why has it taken this long to find them? Mainly because the hydrogen does not originate from natural gas, so it is not found in the same places. Indeed, it is found in the very places that natural gas and oil are not found. The Malian gas was an accident; they were looking for water.

So where does it come from? Interestingly enough, the way it is made was a critical component of how I argued that the precursors to life originated. In my opinion, the planet originally accreted its water attached to rock, most of it to aluminosilicates, which later under heat and pressure lost their water and were extruded to the surface as granite. The reason Earth has far more granite than any other rocky planet is that it formed at a distance from the star where the accretion disk temperatures allowed aluminosilicates to phase separate early in the disk, and subsequently attract water and act as a cement to help form Earth. (Indeed, so far Earth is the only planet with significant amounts of granite, although I expect there will be some on the Venusian highlands. Granite floats on basalt, which is why we have continents.) The question then is, what happened to the water? Obviously, some was emitted and now comprises our oceans and fresh-water reserves, but was all of it? Was some retained deeper down? There is one estimate, in the Handbook of Chemistry and Physics, that suggests there is just as much down there as up here.

Suppose there is, and suppose it is deep enough to be hot. Near the surface, basaltic rock, which comprises olivines and pyroxenes, has its iron content as ferrous. Thus an olivine has the formula {Fe,Mg} SiO4. The brackets mean it can have any combination of them, and additionally, any other divalent element, so that the valence of the bracketed part sums to four. Pyroxenes have the formula {Fe,Mg}SiO3, where the valencies of the bracketed part sum to two. (Ferrous and magnesium both have a valency of 2.). However, there are two routes such rock can make hydrogen. The first is that water, ferrous, and heat make ferric and hydrogen. So water on much basaltic rock will make hydrogen if the pressure and the heat are high enough. The second is that given enough pressure, olivine at least converts three ferrous ions to two ferric plus one iron atom. That iron atom will react with hot water to make ferric oxide and hydrogen. The silicate mantle makes up over 80% of Earth’s volume, so there is no shortage of basaltic-type rock. The question then is, is the water there? It almost certainly was, once. There is a further point. If there is a source of carbon there, including carbonates, the hydrogen makes methane.

One of the further interesting things about the Mali “hole” is that flows so far have not depleted. Oil involves millions of years for the conversion; hydrogen is made in seconds as long as the water can meet fresh ferrous or metallic iron. What we don’t know is whether it accumulates in large volumes. It is one thing to make hydrogen and provide power for a small village; it is a totally different matter to make a serious change to the nature of our economy.

Hydrogen is not without its problems. One is storage, another is the question of pipelines. However, there is a large part of the economy that is unsuitable for electricity as a source of power. These include large vehicles, aeroplanes, and places where high temperature under reducing conditions is needed. An example is steel-making. Carbon is needed to reduce iron oxide to iron, but hydrogen works just as well. Further, currently a lot of hydrogen is made today, but in making it we emit 900 million tonne of CO2. If we tried to make that with electricity, we need a 1000 terrawatt of new “green” power generators. Getting it from the ground would be very attractive, except, of course, the hydrogen may not be anywhere near the demand. There are a number of seeps throughout the world, but most are too feeble even to consider, although again, they may conceal far deeper down. One problem with hydrogen is the small size of the molecule means it leaks. That makes it hard to transport, but it also makes it hard to accumulate naturally. Overall it is difficult to assess whether this is an answer to anything, or merely a curiosity.

The Biggest Problem of Them All

From Physics World, something unexpected. The “problem” is, er, the Universe. Problems don’t come much bigger! To put this in perspective, the major theory used to describe it is Einstein’s General Relativity. There is only one problem with that theory: everything should collapse into a singular “point” and it doesn’t. To get around that problem, Einstein introduced something he called “the Cosmological Constant”, which effectively was something pulled out of thin air in an ad hoc way to at least admit the obvious problem that the Universe remained large. Worse, this steady universe could not be extrapolated to the infinite past. Somewhere along the line it had to be different from now. It was then that Georges Lemaȋtre proposed a theory that space was expanding, to which Einstein replied that his maths were correct, but his physics abominable. However, Einstein had to backtrack because Hubble showed it was expanding. (Actually, Lemaȋtre had provided evidence, but Hubble’s was better.) The idea was that all matter started from a point, and space expanded to let the energy collapse into matter. Fred Hoyle jokingly referred to this as “The Big Bang”.

All was well. Space was expanding uniformly, so the galaxies were moving away from each other uniformly, on a very large scale, but with localized variation in between. Why space was expanding was left unanswered. Thus on a very large scale, the gravitational interactions between distant galaxies was diminishing, which violates the concept of the law of conservation of energy. (Energy does not have to be conserved, though. Energy is a tricky topic in general relativity.) Hoyle was keen on a steady state universe, and while he accepted the Universe was expanding, he took the idea that if everything was moving apart, that loss of gravitational energy was made up for by the creation of new matter. This was not generally accepted, and the question of this energy imbalance remained.

There is worse. To maintain a constant expansion rate, general relativity requires a constant energy density, and how can that arise when space is expanding? The only way would seem to be that this energy density is a property of vacuum. Vacuum is, therefore, not nothing. There is nothing like an opportunity in physics to get speculation going, and “not nothing” is such an opportunity. Quantum field theory announced the vacuum is full of extraordinarily tiny harmonic oscillators, which convey a zero point energy to space. We have our energy accounted for. All was good, until it wasn’t. It was obvious to take the quantum field theory and see if it fitted with observation on galaxies. It did not. In fact the error was a factor of ten multiplied by itself 120 times (Adler, R. J., Casey, B., Jacob, O. C. 1995. Vacuum catastrophe: an elementary exposition of the cosmological constant problem. Am J. Phys 63: 620 – 626.) This was the most horrendous disagreement between calculation and observation ever.

Then came a shock: not only were the galaxies moving apart, but such motion was accelerating. This was caused, in terms of labelling, by something called dark energy. It should be noted that at this point, dark energy is merely a term that essentially is a holding term to recognize that something must be causing the acceleration. So, what is it? The good news is that whatever it is can also account for the general expansion. All we need is something that is getting bigger as the universe expands.

Now, we have a proposition, which is called “cosmological coupling”. The concept starts with the observation that the  mass of black holes at the heart of distant galaxies have been growing about ten times faster than simply accreting mass or merging with other black holes would allow. The coupling means that the growth of the black holes matched the accelerating expansion of the universe. The concept seems to be that the singularity of black holes is replaced by additional “vacuum energy”. Their coupling means that if the volume of the universe doubles, so does the mass of black holes, but the number of black holes remains constant. The logic is that “something” must give rise to the expansion of the universe, and since no other object exhibits similar behaviour, black holes must be the “something”. Is that valid? There is a problem for me with that explanation, apart from the fact that correlation does not mean causation. The evidence is the Universe took on massive expansion initially, then calmed down, and then the expansion accelerated again. During the initial expansion there would be few if any black holes. Then, suddenly, there was a massive growth of them, but that happened at a time when the universe expansion was at its slowest, then when the final acceleration started, the black holes had settled down to minimal growth. The required correlation for the hypothesis seems to be, if anything, an anti correlation.

Smashwords Ebook Discounts

Until March 11,  my ebooks at Smashwords will be significantly discounted. The fictional ebooks include”

Puppeteer:  A technothriller where governance is breaking down due to government debt, and where a terrorist attack threatens to kill tens to hundreds of millions of people and destroy billions of dollars worth of infrastructure. One man has been selected to stop the terrorist, but who selected him? Why has he been given clues nobody else has, and nobody else will believe, and what can one man do?

http://www.smashwords.com/books/view/69696

‘Bot War:  A technothriller set about 8 years later, a more concerted series of terrorist attacks. AI in weapons turns out to be a bad idea when the robots are stolen and controlled by others. And How do you fight the weapon designed that nobody an stop?

Smashwords    https://www.smashwords.com/books/view/677836

Troubles. Dystopian, set about 10 years later still, the world is emerging from anarchy, and there is a scramble to control the assets. Some are just plain greedy, some think corporate efficiency should rule, some think the individual should have the right to thrive, some think democracy should prevail as long as they can rig it, while the gun is the final arbiter.

https://www.smashwords.com/books/view/174203

Ancient Egyptian Chemical Science

When did science start? To answer that, you have to ask, what is the scientific method? My answer to that is you start by observing something, and when you work out what you think made it happen, you try to use it with something else. After you have found a number of successes, you start to induce a hypothesis. Essentially, you have a set of observations, and a rule that conveys set membership. That rule is the hypothesis. You test it further, and sometimes you have success. Sometimes you find the hypothesis was wrong. The ancients, starting off from nothing, will have got it wrong more often than right.

The first example of chemistry would be when ancients found the first fire, and found that if you used it to treat meat, it was easier to eat.  Cooking was invented, and all sorts of other potential food was cooked. Sooner or later, wet clay was subjected to fire, and pottery was invented. This was not easy and it did not occur everywhere. There are a number of ancients who never learned how to make pottery. Somewhere along the line some malachite would have been in the base of a fire, and copper made. This heating of various things did a number of good things for people, and a number of not so good ones.

Once you realize you can do things, and you have an objective, you can try something, and if it works, even partially, you can subject it to a number of variations to improve your process. That is science. In ancient Egypt, one of the priorities was to find improved mummification. One of the surprises for us came from an embalming workshop in Saqqara. It was obvious that oils and resins were used, but the workshop contained a number of jars with residues in them (Nature https://doi.org/grqg2w; 2023) and the interesting thing for me is that mass-spectral analysis showed extracts from cypress and cedar trees, which are local, but there were also components from trees that grow in African rain forests, and another material that came from southern India, Sri Lanka and SE Asia. There was extensive trade even at 2000 BC, and the embalmers had obviously tried a lot of materials. The use of resins and plants with antibacterial, insecticidal and antifungal properties were used at least at 6000 BC. By the Pharaonic period, they realised that natron (sodium carbonate with some bicarbonate, chloride and sulphate) offered preservative properties. The natron was probably in solution, and the body would not have been dessicated, although dessication would follow thanks to the Egyptian hot dry air. The high pH of natron would stop any bacterial activity.

Did the ancient Egyptians gain any understanding of what they were doing. This question is more difficult to answer than it might be thought because our records are from scribes who were highly religious, which meant that so much would be recorded in terms of the Egyptian Gods, but the scribes never invented anything. They had to interpret everything in terms of religion. The problem with natron was it would bleach the skin, and the Egyptians did work out that coating the skin with resin stopped the bleaching. It is possible they worked that out because there is a papyrus (The Edwin Smith papyrus) that shows they had a rational and arguably scientific attitude to diagnosis.

The Egyptians were the first to synthesize a coloured pigment: Egyptian Blue, a calcium copper tetrasilicate, which was made by heating silica, lime and copper oxide in a flux of borate. By altering the ratio they could also make a green colour. They also made coloured pigments for makeup, including lead sulphide (black), lead carbonate (white, but also laurionite (Pb(OH)Cl) and the white powder phosgenite (Pb2Cl2CO3). These latter two had to be synthesized, and while PbS is found naturally as galena, the ore is shiny, and you will get better black with precipitation. For those who are horrified by the thought of putting lead sulphide on the skin, it is totally insoluble and could never pass through the skin.

They were also skilled at metalworking, and had a technique for soldering of gold jewellery that is of interest. They glued the objects together and put powdered malachite into the glue. When this was heated, the glue reduced the malachite to molten copper, which welded the objects together. Finally, they were good at making perfumes, and had developed techniques like distillation. They may not have had a full understanding of what they were doing, but they had a procedure by which they learned things.