Volcano Snails

iron molluscs of the inky abyss

Volcano snails are smallish (0.5-5 cm) snails that have been found in several hydrothermal vent fields almost three kilometres deep in the Indian Ocean. Hydrothermal vents, sometimes called "black smokers", spew water laden with toxic metal salts out of the sea floor at temperatures of up to 750 C. The only reason they don't boil is because the pressure from the enormous depth prevents it.

To delicate surface-dwelling creatures like us, hydrothermal vent fields look like a reasonable approximation of some Medieval fantasy of hell. To volcano snails, they look like home.

One has to wonder how they got there. Did they evolve from some other mollusc that accidentally fell into the ocean deep and then somehow survived to breed? Or are they remnants of a long-lost Earth, when black smokers were common in the warm, shallow seas, and whole ecosystems thrived which are now reduced to a handful of species trapped on these abyssal islands? The evolutionary history of these deep sea communities is still an active area of research, and their story is complicated because they have to live without sunlight.

Everything in the upper reaches of the oceans depends ultimately on the sun for sustenance: photosynthetic algae, especially diatoms, use this energy to make simple carbohydrates, and get eaten by everything else. Some of them die and fall to the deep ocean floor, which sustains a sparse ecosystem of abyssal life.

Hydrothermal vents present a different kind of opportunity for life, because their rich chemistry is a source of energy. Chemo-synthesis, not photo-synthesis, is what sustains them. The existence of life in these chemically-driven communities implies the possibility of complex ecosystems in other regions of eternal darkness, including the ice-covered oceans of Jupiter's moon Europa, and Enceladus around Saturn.

Chemosynthetic micro-organisms (mostly bacteria) have a problem, though: they need to float in the water column to get a continuous supply of new chemicals. But if they do that, they'll drift away from the vent field and die. If instead they stick to rocks, they'll be exposed and get eaten.

This creates "selective pressure", which isn't literally anything pushing or pressing individuals to behave a particular way, but is a tendency to reward certain behaviours or capacities after the fact with a higher rate of reproduction for the individuals who exhibit them.

In this case, an individual snail that can accommodate chemosynthetic bacteria in its tissues is more likely to reproduce successfully than one that can't, because the snail can live off the bacteria. Individual bacteria that can grow within the snail's tissue get a stable home and plentiful water supply. Over generations of natural selection, this has resulted in the modern population of volcano snails, which has no source of food except the chemosynthetic bacteria growing within their enlarged oesophageal gland. The bacteria reduce hydrogen sulphide to extract energy, which results in the snails eliminating small pellets of sulphur from their gut, which for a snail would be a problem if they hadn't followed a literally twisted evolutionary path.

Evolutionary history can be seen through the mirror of modern taxonomy: different genera of the same class evolved from the same original species, and different classes of the same phylum did the same, but even further back in time. Some species travel a long way from their common root, others hardly at all: a lot of Americans came all the way from Europe, but most Europeans stayed home. This is why there are still people in Europe even though there are also people from Europe in America.

Snails belong to the class of gastropods, which includes things like slugs, which don't have shells, and whatever organism they both evolved from, it likely didn't have a shell either. So we need to think about the problems faced by a single-shelled organism in the course of its evolution, particularly: how does it defecate if its ass is covered by a shell?

The answer turns out to be: streptoneury, or "twisting", which is an evolutionary process by which internal organs re-arrange themselves over generations so that the anus and genital opening migrate up one side toward the front of the animal. The alternative to twisting would have been "folding", in which the organism bent double, but curiously this doesn't seem to ever happen. Evolution is an incremental, elaborative, process that allows organisms to migrate between stable forms by passing generation-by-generation through intermediate stages, but only some intermediate forms are viable. Presumably folded organisms suffered some disadvantages that their twisted cousins avoided.

Streptoneury is common in shelled gastropods, but the volcano snail's shell is something out of the ordinary: the inner layer is calcium carbonate, the same as most mollusc shells. Outside of that is the periostracum, which is a protective protein coating, also commonplace. The unique feature is the outer layer of iron sulphide. The sides of the foot are also scaled with iron sulphide "teeth", which likely help protect it from the crab-eat-snail world it lives in. The volcano snail is the only animal in the world that incorporates iron into its skeleton.

The scale-like "teeth" on the snail's foot are called sclerites, and give the snail its proper name: scaly-footed gastropod. It's the only living species with this feature, although similar scales are evident in many fossils from the Cambrian era. Before the Cambrian, lack of oxygen in the atmosphere and oceans restricted multi-cellular life to a few sesile, coral-like organisms, but about 540 million years ago some critical threshold was crossed and the "Cambrian explosion" saw a proliferation of novel, motile, forms over the following fifty million years, including the ancestors to all modern phyla, from molluscs to mammals.

So the volcano snail gives us a glimpse into the distant past, and the origins of complex, multi-cellular life on Earth, while at the same time suggesting what we might find in the dark oceans whose currents flow around the ice-moons within our solar system, and perhaps too beneath the surface on the ice-bound worlds that circle other stars.

Twenty Nine Proteins to Disrupt the World

games that covid plays

The covid genome is a hundred thousand times smaller than the human genome and encodes a measly twenty-nine proteins, compared to something closer to a million in humans.

Despite this, covid has created a pretty significant inconvenience... to its great misfortune. If there's one thing a species doesn't want is for humanity to get annoyed with it: we have a tendency to wipe out species we like, much less ones we don't.

Furthermore, we're going to learn a vast amount in the process of wiping out covid, because how viruses work is an instruction manual for what is required to operate the levers of the machinery of life.

Of the twenty-nine proteins covid makes, just four are "structural": two make up the outer membrane of the virus, another forms the armature its single strand of RNA is wound around, and the final one makes up the infective spike it uses to enter our cells. Most of the others are involved in getting the virus to replicate properly in the cell, and a handful of "accessory proteins" seem to be responsible for avoiding the host's immune response. For example, in its pre-infective state the virus is coated with chains of simple sugars that hide it from the immune system, and it is likely the accessory proteins have something to do with this.

A majority of the other non-structural proteins are created in an interesting way: rather than produce them individually, they are generated in two huge "poly-proteins" that are then cleaved into smaller bits by a protease (pronounced PRO-tee-aze, not pro-tease, which, uh, sounds like a different kind of biology entirely…) This protease enzyme is also encoded by the viral genome. Things with an "-ase" ending in biology tend to be destructive, so a prote-ase literally means "protein-breaker".

It used to be thought that the genome was a simple one-to-one template for proteins, and we'd have as many genes as there were proteins. Instead it turns out that processes like this, where there is "post-translational modification" of a gene product, is more common than not. As well as cleavage, post-translational modification can include changing the way a protein is folded. In other cases it involves sticking smaller proteins together.

Building things up out of simpler units is one of the most basic tricks that evolution has. Maybe there were at one time organisms that took a "holistic" approach to biochemistry where complex proteins weren't built out of simpler peptides that were built out of even simpler amino acids, but instead every biologically active molecule was its own thing, with no obvious internal boundaries between repeated units of the same kind.

Maybe we'll even encounter life-systems based on such a scheme when we explore other worlds around other stars. Such a biology would make organisms highly resistant to parasites and pathogens and even predators: covid and other viruses can infect us because we all share the same basic building blocks and the same genetic machinery. In a holistic ecosystem organisms could eat each other for the energy content of their carbohydrates, but would have to make all their own proteins from scratch. Parasitism would be impossible, which would make evolution radically different.

Unfortunately, we don't live in that world, so a lousy twenty-nine proteins is enough machinery to wreak havoc on our cells.

Once assembled, any protein or enzyme operates by a mix of geometry and chemistry: for one protein to bind to another, they have to have complementary chemically active sites in with mirrored geometries. Think of the active sites as being on the tips of your fingers, with left and right complementing each other chemically. If you hold both hands with the fingers making the same pattern, you can bring them together so that each tip touches its mate on the other hand. Success! You have created a bound protein! But if you hold them in different patterns, they don't mate, at least not fully, and whatever chemistry was supposed to happen, mostly doesn't.

In the case of covid (technically SARS-CoV-2), the spike protein has a component (called S1) that complements the active sites on the ACE2 protein that is part of the outer membrane of many cells, particularly in the lungs, intestine, heart, and kidneys. ACE2 is an important component of the system that regulates blood pressure (if you have high blood pressure you may be familiar with "ACE inhibitors", which help reduce it.)

One of the basic problems for viruses is that active sites on proteins tend to be, well, active, and since a good part of the virus life cycle involves floating around in the world there is a significant risk their active sites might end up binding with random junk in the environment, which would inactivate them. To avoid this, covid protects the active site on the spike protein by keeping it folded out of sight until it is needed. The folded spike protein is held in position by two hydrocarbon strands that have to be cleaved, and which are cleaved by human proteases. This ensures the active site doesn't become active until it's in the presence of a host.

Once it binds with ACE2, another part of the spike protein comes into play and fuses the viral membrane with the cell membrane, creating an opening that allows the viral RNA to pass into the interior of the cell and start its unpleasant work.

The details of how the viral RNA reprograms the cell to make copies of the virus are still being worked out, but the amount of research money and intellectual focus being thrown at this problem is such that progress is being made very rapidly.

The viral genome and the twenty-nine proteins it's responsible for creating are becoming a laboratory to understand important aspects of cellular function, pointing the way toward what works and what doesn't.

Between mRNA vaccine research and work on the virus itself, we're on the threshold of a new and powerful understanding of the most basic mechanisms of life.


Sources:

Early report on spike protein mapping: https://www.livescience.com/coronavirus-spike-protein-structure.html

Useful high-level breakdown on various covid proteins and their actions: https://cen.acs.org/biological-chemistry/infectious-disease/know-novel-coronaviruss-29-proteins/98/web/2020/04

Lots of detail on covid spike protein structure and behaviour: https://www.nature.com/articles/s41594-020-0468-7

Excellent technical review of covid infection process with attention to potential drug targets: https://www.nature.com/articles/s41401-020-0485-4

Practical Warp Drives?

springs, radio waves, and faster-than-light travel

To understand warp drives and why they might really exist, it helps to understand one of the most general phenomena in physics, which is how circumstances beyond our control are often where insights into the universe begin.

Our various physical laws tell us that if we create these circumstances then this motion will result. But the laws don't tell us how to create those circumstances, or even if we can create them.

The simplest case of this is Newton's second law, F=m*a: the acceleration multiplied by the object's mass is equal to the force acting on it. So for any given force we can figure out the acceleration, and once we know the acceleration we can integrate it to find the velocity and position. The force itself is often a function of velocity and position, which makes the math tricky--we end up having to solve things called second order differential equations, often with brute computational force--but the principle remains simple.

In a lot of cases, the force is directly proportional to an object's displacement from some equilibrium position, which results in something called simple harmonic motion. But in other cases it's vastly more complicated: we can easily find materials in nature that have force laws we don't know how to reproduce.

For example, duplicating the complex springiness of cartilage in human joints using synthetic materials is beyond us. Our equations tell us "if you can make a material with this sort of springiness, it will result in a joint motion like that", but we're on our own when it comes to figuring out how to create the material. Newton is no help at all.

We ran into the same problem with Maxwell's electromagnetic equations back when Queen Victoria was in the middle of her long reign. This set of four equations says if we wiggle a charged particle back and forth in just the right way it should generate waves in the electromagnetic field. It took the German physicist Heinrich Hertz twenty years to figure out how to do the wiggling appropriately--oscillating currents in specially-shaped wires called "antenna"--and produce what we now call "radio waves".

Newton and Maxwell are the "simple" cases. Einstein's equations--which describe gravity--consist of sixteen inter-related second-order differential equations, and it's fair to say that after a century of progress we are still figuring out how to wrap our heads around them.

In each of these cases there is a "source term"--forces for Newton, electric charge for Maxwell, and mass or energy for Einstein--and the equations tell us "arrange a source term like this, and motion like that will follow."

Recent work has found a couple of source terms that appear to allow "warp drives": solutions to Einstein's equations that would let us to travel faster than light by stretching space around an object to create a wave it can ride like a surfer.

The first of these ideas was entirely theoretical. In the early '90s Mexican physicist Miguel Alcubierre found an arrangement of "negative energy" that produced a solution to Einstein's equations containing a "bubble" of space-time that could move at any velocity. Because the inside was effectively hidden from the rest of the universe, an object in the bubble could move with it, even faster than light.

This was exciting, but had two problems. The first is that no one knows how to create "negative energy", or even what it means... if anything. Our mathematical descriptions of reality often describe more reality than we actually have.

For example, we routinely throw away "negative time" solutions to wave equations because we never see waves going backward in time. This is the difference between physics and mathematics.

Sticking a negative sign in front of the source term in Einstein's equations tells us what would happen if we lived in a universe where negative energy was a meaningful thing, but it doesn't tell us if we're actually living in that universe. And if we are, it doesn't tell us how to create or control negative energy, which sounds hard, especially as it turns out Alcubierre's configuration requires converting just about the whole universe into "negative energy" to work. Although a few people have found tricks that might bring that down by a lot, it's still on a scale where we'd have to be able to gather up whole galaxies of negative energy, which sounds like the kind of thing you'd need to have a warp drive to do.

So although Alcubierre demonstrated an extremely intriguing loophole in the "nothing goes faster than light" restriction we think we're living with, his work didn't spark any sudden rush in technological development.

But the thing about intriguing loopholes is they lead other people to wonder if there might be more of them.

New work by Edmund Lentz in Germany has removed that negative energy constraint, and shown how to construct a configuration of positive energy that will allow macroscopic objects move at arbitrary velocities by warping space-time around them.

The amount of energy involved is still huge--something like 1/10th the mass of the sun converted into energy in the form of multiple plasma lenses around a volume that's 100 m across and 1 m thick--like the "saucer section" of Star Trek's Enterprise, but squashed really flat--but there may be tricks to bring it down to something closer to what is achievable, and there may even be natural circumstances where similar conditions prevail, in the hot, diffuse plasmas that surround highly magnetized neutron stars. These wouldn't have the right configuration to travel at warp speed, but they could be (distant) laboratories to allow us to study such effects even if we can't yet create them in the laboratory.

Lentz's work has only recently been published, and there may be holes in his argument or insurmountable practical difficulties, but it opens up a promising new frontier for investigation, and suggests that practical interstellar travel might be far closer than anyone dared dream.

The Geomagnetic Field

where it comes from, where it's going (Siberia, apparently)

Most of us remember that the terrestrial magnetic field has something to do with swirling currents of conducting, iron-rich fluid in the Earth's core, but after that it gets pretty vague. It turns out we aren't alone in this: while computer models are inching closer to something that will generate a realistic field, they still aren't quite there yet.

When they do get there, though, it will make the magnetic field and its variations a powerful probe of the "interior geography" at the base of the Earth's mantle, where enormous structures influence the circulation in the outer core.

The curious thing about the Earth's field is that it exists at all, because when you think about it, swirling a conducting fluid doesn't do anything much. Put some salt water in a glass and whoosh is around and no sparks fly, compasses are not deflected. If you're like me, the only thing that really happens is the floor gets wet.

Why would a circulating, conducting fluid in the Earth's core be different? For one, scale matters a lot: phenomena that are undetectable at a scale of a few centimetres can become dominant over the Earths' radius of 6800 km. But there's more to the story.

The Earth has four major layers due to how temperature and pressure increase with depth. Low levels of radioactive material--mostly uranium and thorium--are present throughout the Earth, and the heat they give off raises the temperature to almost 6000 C at the centre (sorry, Jules Verne fans!). At the same time, pressure increases with depth, which increases the melting point of rock. Competition between these two effects results in the layering we observe, with solid crust, plastic mantle, liquid outer core, and solid inner core.

The crust is the cold outer layer, fifteen to twenty kilometres thick, which floats on top of the next layer down: the mantle. In the mantle, rock is hot enough to flow slowly, but isn't really a liquid. It has a lot of structure, much of which we are still learning about, from half-melted remnants of long-subducted continents to lobes that influence everything from volcanoes to the position of the magnetic poles.

Beneath the mantle lies the outer core, which is iron-rich, electrically conductive, liquid rock, and below that the pressure is high enough to create the solid inner core, despite the 6000 C temperature. The inner core is almost all iron, but it's too hot to hold much of a magnetic field: the Earth's field instead is due to the convective flow of the outer core, but how this "dynamo" works is not immediately obvious. As our experiment with swirling salt water shows, moving a conducting fluid does not automatically generate a magnetic field.

But... moving a conducting fluid in a magnetic field does generate an electric current. This is how electric generators work: we move a conducting loop in a magnetic field and the electric field that is induced causes a current to flow around the loop. The thing about electric currents, though, is that they cause magnetic fields, so if there is a magnetic field with a conducting fluid moving in it, there will be a secondary magnetic field created by the current generated in the conductor by the primary magnetic field... and it turns out there are self-sustaining geometries where the secondary magnetic field created by this process is capable of regenerating itself, at which point the field that got it all started no longer matters.

Without a continual influx of energy from the core's heat, the field would die away in about twenty thousand years, which gives a sense of how much power is going into this. When I swirl a glass of water and then stop, the swirling dies away in seconds, not hundreds of centuries.

In a sense, then, the magnetic field of the Earth is its own cause: once it exists, it's capable of sustaining itself so long as there's heat from the core to drive it. But where did it come from in the first place?

We're not totally sure, but the most likely source of the original magnetic field is the sun. Sun-like stars typically go through an early phase where they have very strong magnetic fields, many thousands of times greater than the modern value. This would be more than enough to get the geomagnetic dynamo going on Earth, and once going, it would sustain itself. So the Earth's magnetic field is quite probably the self-sustaining remnant of the primordial solar magnetic field.

Once it gets started the field strength is determined by the internal dynamics, not the primordial field. Computer models of those internal dynamics have yet to match the observed field using realistic parameters, though, so there there is more going on than we yet understand.

When we do finally figure it all out, there is a chance that we can use such modelling as a kind of "computational telescope" pointed at the Earth's core, especially the underside of the mantle. The magnetic field isn't a simple dipole, but has global variations (as well as local anomalies due to magnetic ore deposits), and it changes with time in both strength and direction. Irregularities can form in the convective currents, and these result in everything from the field's deviation from a perfect dipole, to the north pole’s recent wandering toward Siberia, to periodic short-term "excursions" of a few centuries, to longer-term reversals that last tens of thousands of years and are typically spaced by a few hundred thousand years or more.

Since these non-uniformities and fluctuations are in part a result of the structure of the underside of the mantle, a detailed understanding of the Earth's field may allow us to map that surface, because its shape will be an input into our computer models. That will allow us to generate a topography of hidden mountains and canyons that deflect the currents of stone, thousands of kilometres beneath our feet, that no human eye will ever see.

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[Thanks for subscribing! This is the VERY FIRST “World of Wonders”, and next week we’re going to jump from beneath the Earth to beyond the sky, possibly via warp drive! I’m happy to take questions and any feedback on what people would like to see more (or less) of. As well as the comment section (if you’re a substack member) this e-mail address is set up so you can respond to it and I’ll get the message! —TJ]

Introducing World of Wonders

Joyous essays on knowledge and reality

I’m TJ Radcliffe and this is World of Wonders, a newsletter of popular science in (I hope) the tradition of Asimov and Sagan. My focus is on clear accounts of observations, experiments and ideas in the sciences, from archeology to zoology, with an emphasis both on what we know, and how we know what we know. The current publication schedule is weekly, on Fridays.

Knowledge requires that we manage uncertainty, not seek an impossible and uninteresting certainty. I’m a free-wheeling Bayesian, dedicated to updating my beliefs about what is most plausible in the face of new evidence.

We live in a world where there is a constant flood of new knowledge and an even greater sea of speculation. New results and theories are often reported without enough context for people outside the field to understand, or given a sensational twist. My aim is to describe the context—including the history where it matters—and explain the significance and possible implications of some discovery, with special attention to how likely it is to be wrong. I’m not focused on new discoveries, and will write about long-term problems or old knowledge that I think is unusual or interesting. I take requests!

My perspective is that of a working scientist who has been involved in research in a diversity of fields, with a heavy emphasis on simulation, numerical methods, and hands-on experimental technique. Like most experimentalists, I have a healthy scepticism with regard to theory, and think there is some wisdom in the aphorism that “theorists have never had any trouble explaining the results of experimentalists, even when those results later prove to be incorrect.”

I am a Canadian, and have a PhD in physics from Queen’s University in Kingston, Ontario. Academically, I’ve worked at Caltech, the University of Mantioba, and Queen’s, and am one of the 1380 physicists who were awarded the 2016 Breakthrough Prize in Fundamental Physics, in my case for playing a small part in the Sudbury Neutrino Observatory collaboration in the 1990s. My last academic appointment was as an adjunct in Pathology and Molecular Medicine at Queen’s: I’ve spent a good deal of my career working in various areas of medicine, including genetics (mostly cancer) and computer-assisted/image-guided surgery systems. I’ve also founded and run a successful scientific consulting company, and been a manager and executive at various corporations, both startups and established enterprises. From 1995 to 2020 I was a licensed professional engineer (mechanical/engineering physics) in Ontario and (latterly) British Columbia.

My interests and expertise are eclectic, and I am profoundly committed to Enlightenment principles of free and open inquiry into objective reality, with a goal of producing uncertain knowledge that will mostly not stand the test of time.

Finally: I’m a poet, and find it stimulating to write under tight constraints. For that reason, and to keep my work focused and entertaining for you, the reader, I’ve decided to restrict myself to precisely 1000 words for each topic I write on (except for this intro note and similar administrivia) as counted by a simple algorithm. A thousand words makes for something long enough to be interesting and short enough to respect your time. I provide sources—everything from Wikipedia to the original research publications when they are available—for anyone who wants to dig deeper.

If you’re interested in understanding more clearly what we know and how we know it, this is the place for you!

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