About ianmillerblog

I am a semi-retired professional scientist who has taken up writing futuristic thrillers, which are being published by myself as ebooks on Amazon and Smashwords, and a number of other sites. The intention is to publish a sequence, each of which is stand-alone, but when taken together there is a further story through combining the backgrounds. This blog will be largely about my views on science in fiction, and about the future, including what we should be doing about it, but in my opinion, are not. In the science area, I have been working on products from marine algae, and on biofuels. I also have an interest in scientific theory, which is usually alternative to what others think. This work is also being published as ebooks under the series "Elements of Theory".

Warp Drives

“Warp drives” originated in the science fiction shows “Star Trek” in the 1960s, but in 1994, the Mexican Miguel Alcubierre published a paper arguing that under certain conditions exceeding light speed was not forbidden by Einstein’s General Relativity. Alcubierre reached his solution by assuming it was possible, then working backwards to see what was required while rejecting those awkward points that arose. The concept is that the ship sits in a bubble, and spacetime in front of the ship is contracted, while that behind the ship is expanded. In terms of geometry, that means the distance to your destination has got smaller, while the distance from where you started gets longer, i.e. you moved relative to the starting point and the destination. One of the oddities of being in such a bubble is you would not sense you are moving. There would be no accelerating forces because technically you are not moving; it is the space around you that is moving. Captain Kirk on the enterprise is not squashed to a film by the acceleration! Since then there have been a number of proposals. General relativity is a gold mine for academics wanting to publish papers because it is so difficult mathematically.

There is one small drawback to these proposals: you need negative energy. Now we run into definitions, and before you point out the gravitational field has negative energy it is generated by positive mass, and it contracts the distance between you and target, i.e. you fall towards it. If you like, that can be at the front of your drive. The real problem is at the other end – you need the repulsive field that sends you further from where you started, and if you think gravitationally, the opposite field, presumably generated from negative mass.

One objection often heard to negative energy is if quantum field theory were correct, the vacuum would collapse to negative energy, which would lead to the Universe collapsing on itself. My view is, not necessarily. The negative potential energy of the gravitational field causes mass to collapse onto itself, and while we do get black holes in accord with this, the Universe is actually expanding. Since quantum field theory assumes a vacuum energy density, calculations of the relativistic gravitational field arising from this are in error by ten multiplied by itself 120 times, so just maybe it is not a good guideline here. It predicts the Universe has long since collapsed, but here we are.

The only repulsive stuff we think might be there is dark energy, but we have no idea how to lay hands on it, let alone package it, or even if it exists. However, all may not be lost. I recently saw an article in Physics World that stated that a physicist, Erik Lentz, had claimed there was no need for negative energy. The concept is that energy could be capable of arranging the structure of space-time as a soliton. (A soliton is a wave packet that travels more like a bubble, it does not disperse or spread out, but otherwise behaves like a wave.) There is a minor problem. You may have heard that the biggest problem with rockets is the mass of fuel they have to carry before you get started. Well, don’t book a space flight yet. As Lentz has calculated it, a 100 m radius spacecraft would require the energy equivalent to hundreds of times the mass of Jupiter.

There will be other problems. It is one thing to have opposite energy densities on different sides of your bubble. You still have to convert those to motion and go exactly in the direction you wish. If you cannot steer as you go, or worse, you don’t even know for sure exactly where you are and the target is, is there a point? Finally, in my science fiction novels I have steered away from warp drives. The only times my characters went interstellar distances I limited myself to a little under light speed. Some say that lacks imagination, but stop and think. You set out to do something, but suppose where you are going will have aged 300 years before you get there. Come back, and your then associates have been dead for 600 years. That raises some very awkward problems that make a story different from the usual “space westerns”.

Seaweed and Climate Change

A happy and prosperous New Year to you all. The Great New Zealand Summer Vacation is coming to an end, so I have made an attempt at returning to normality. I hope all is well with you all.

Last year a paper in Nature Communications (https://doi.org/10.1038/s41467-021-22837-2) caught my eye for two reasons. First, it was so littered with similar abbreviations I found it difficult to follow. The second was that they seemed to conclude the idea of growing seaweed to absorb carbon dioxide would not work, but  they seemed to refuse to consider any option by which it might work. We know that much of seaweed biomass arises from photo-fixing CO2, as does biomass from all other plants. So there are problems. There were also problems ten thousand years ago for our ancestors in Anatolia or in the so-called fertile crescent wanting to grow some of those slightly bulky grass seeds for food. They addressed those problems and got to work. It might have been slow, but soon they had the start of a wheat industry.

So, what was the problem? The paper considered the Sargasso Sea as an example of massive seaweed growth. One of the first objections the paper presented was that the old seaweed fronds get coated with life forms such as bryozoans that have calcium carbonate coatings. They then state that by making this solid lime (Ca++ + CO3 -> CaCO3, a solid) it releases CO2 by reducing seawater alkalinity. The assertion was from a reference, and no evidence was supplied that it is true in the Sargasso. What this does is to deflect the obvious: for each molecule of lime formed, a molecule of CO2 was removed from the environment, not added to it as seemingly claimed. Associated with this is the statement that the lime shields the fronds from sunlight and hence reduces photosynthesis. Can we do anything about this? We could try harvesting the old fronds and keep growing new ones. Further, just as our ancestors found that by careful management they could improve the grain size (wild wheat is not very impressive) we could “weed” to improve the quality of the stock.

I don’t get the next criticism. While calcification on seaweed was bad because it liberated CO2 (so they say) they then go on to say that growing seaweed reduces the phytoplankton, and then the calcification of that gets reduced, which liberates more CO2. Here we have increased calcification and decreased calcification both increase CO2. Really?

Another criticism is that the seaweeds let out other dissolved carbon, which is not particulate carbon. That is true, but so what? The dissolved sugars are not acidic. Microalgae will gobble them up, but again, so what?

The next criticism is if we manage to reduce the CO2 levels in the ocean, we cannot calculate what is going on, and the atmosphere may not be able to replenish the levels for a up to a hundred years. Given the turbulence during storms I find this hard to believe, but if it is true, again, so what? We are busy saving the ocean food chains. Ocean acidification is on the verge of wiping out all shellfish that rely on forming aragonite for their shells. Reducing that acidity should be a good thing.

They then criticise the proposal because growing forests on land reduces the albedo, and by making the land darker, makes the locality warmer. They then say the Sargasso floating seaweed increases the albedo of that part of the ocean, and hence reflects more light back to space, which reduces heat generation. Surely this is good? But wait. They then point out that other proposals have seaweed growing in deep water and this won’t happen. In other words, some aspect of some completely different proposal is a reason not to proceed with this one. Then they conclude by saying they need more money to get more detailed information. I agree more detailed information would be helpful, but they should acknowledge possible solutions to their problems. Thus ocean fertilization and harvesting mature seaweed could change their conclusions completely. I suspect the problem is they want to measure things, possibly remotely, but they do not want to actually do things, which involves a lot more effort, specifically on location. But for me, the real annoyance is that everyone by now knows that global warming is a problem. Growing seaweed might help solve that problem. We need to know whether it will contribute to a solution or merely transfer the problem. They may not have the answers, but they at least should identify the questions that need answers.

Climate Change and Political inertness

Since the season of goodwill and general cheerfulness is approaching, it seems wrong to present even more bad news for this rather dismal year, yet we cannot hide from it, The problem was presented in Nature ( https://doi.org/10.1038/d41586-021-03758-y  and relates to the Thwaites glacier. This glacier flows off the Antarctic continent into the Southern ocean. The glacier is 120 kilometers wide and about two thirds of this flows into the Southern Ocean, but one third runs into its eastern ice shelf. Here, the flow grinds to a halt because the ice out at sea hits an underwater mountain that is about 40 kilometres offshore. The Mountain is stopping the ice from flowing.

Unfortunately, thanks to the warmer water flowing underneath, that part of the glacier is becoming unstuck from the mountain, and this is causing cracking and fracturing across parts of the ice shelf. The fractures are propagating through the ice at several kilometres per year, and are heading towards thinner ice, which may lead to the whole lot shattering. To add to the problem there is tidal flexing as the glacier starts to separate from the rock and the “up and down” movement with the tides causes the glacier to flex further upstream, including where it is over land. Because of this flexing, warm water from the Southern Ocean could make its way beneath the glacier more easily.

Current estimates are that this mass of ice over the water could shatter within five years, which would release an huge mass of icebergs into the Southern Ocean, and the whole glacier could start flowing much faster into the sea. That means sea level rise. Currently the Thwaites already loses around fifty billion tonnes of ice each year and causes 4% of global sea level rise. If this eastern ice shelf collapses, ice would flow three times faster into the sea. If the glacier were to collapse completely sea levels would rise 65 centimetres. The glacier itself is moving towards the sea at about a mile each year. This is a fairly fast moving glacier.

So, what do we do about it. In this case it is probably impossible to do much. There is no way to stop a glacier moving. The only possible thing to do to stop the sea level rise would be to somehow engineer more snow to fall further inland to Antarctica. Fifty billion tonnes of snow each year would cancel out the sea level rise, but we all know that is not about to happen any time soon. But not to worry. Senator Manchin does not believe in climate change as a hazard, and he will torpedo President Biden’s efforts to get the US to do something. This Senator wants to burn more coal, and this one man will torpedo everyone else’s limited efforts. So is the Senator right? No. We might not be able to stop the Thwaites, but there are worse problems downstream we can still stop if we act before they become activated. Of course, he is not alone. Australia is selling more coal, China is building more coal-foired power stations, Germany has turned of nuclear to burn lignite. A cartoon in our paper had it: the Devil was reading about our activities and he said, “Aw, no fun. They’re not even pretending to try now.”

The nature of the problem is what we call hysteresis. If you have an equilibrium, such as when there is no change of temperature in an object over time, this arises because the heat loss equals the heat input. Now, suppose you increase the heat input a little. Now we are out of equilibrium, but since the heat loss depends on the temperature what you expect is the temperature will rise to reach the equilibrium position corresponding to where the heat loss now equals the heat input. Unfortunately, it doesn’t quite work like that. Suppose I have a lump of iron, and I increase the amount of heat going into it. The surface may well get warmer, but heat then starts flowing into the inside of the object. It takes time before the object reaches the new temperature. With something like ice, it is worse. The ice will warm, but once it gets to its melting point the increased heat flowing in starts to melt the ice. The ice stays at the same temperature. If we increase the heat flow inwards there is no change, other than the ice melts faster. Then, when it has all melted, suddenly the temperature starts to increase quickly.

To some extent, that is what has happened on our planet. Our greenhouse effect has been slowing the heat loss to space, and since the heat input remains the same, effectively the system is absorbing more heat. However, to start with all that happened was the surface of the oceans warmed up and some ice melted. So we ignored the problem because we observed no change in temperature, and poured more heat in. All that did was warm more water and melt more ice. The problem then is that we have now reached the point where the increase in heat that we are pouring into the Earth is starting to reach the point where the effects that absorbed heat without altering our temperature too much have now reached the end of their capacity. We are now going to make major changes to the planet, and we cannot stop them because the forces are already in place to generate far more heat.

Another characteristic of hysteresis is you cannot reverse what you have done simply by stopping increasing the heat input. Because the ice is melting because the water is above its freezing point, if we stopped adding heat now and stopped all greenhouse emissions, the oceans are still warm and the melting continues. However, there are thresholds. One calculation (Nature 585 (2020) p 538) indicated that for every degree of global temperature rise up to 2 degrees above pre-industrial levels will lead to 1.3 metres of sea-level rise. Between 2 – 6 degrees of warming it doubles to 2.4 metres per degree, and between 6 – 9 degrees, we get an extra 10 meters per degree. Further, the nature of hysteresis is that this is irreversible. If we want to turn it around we have to reduce global temperatures to one degree below what they were in 1850.

With that dismal thought, I wish you all a very Merry Christmas and all the best for 2022. This will be my last post for the year, and as usual I shall resume in mid-January. Finally, there are still my ebooks on the Smashwords sale.

Ebook Discounts at Smashwords

From December 17 – January 1, my ebooks at Smashwords will be significantly discounted. The fictional ebooks, which are thrillers and, similar to Andy Weir, with real science in the background, 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.


‘Bot War:  A technothriller set about 8 years later, a more concerted series of terrorist attacks made by stolen drones lead to partial governance breaking down.

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.


Spoliation. A thriller set about asteroid mining, where some of the miners mysteriously disappear. Then someone tries tο weaponise a large asteroid. A story of greed, corruption and honour, combining science and visionary speculation that goes from the high frontier to outback Australia.


There is also the non-fictional “Biofuels”. This gives an overview of the issues involved in biofuels having an impact on climate change. Given that electric vehicles, over their lifetime probably have an environmental impact equivalent to or greater than the combustion motor, given that we might want to continue to fly, and given that the carbon from a combustion exhaust offers no increase in atmospheric carbon levels if it came from biofuel, you might be interested to see what potential this has. The author was involved in research on this intermittently (i.e. when there was a crisis and funding was available) for over thirty years. https://www.smashwords.com/books/view/454344

What Happens Inside Ice Giants?

Uranus and Neptune are a bit weird, although in fairness that may be because we don’t really know much about them. Our information is restricted to what we can see in telescopes (not a lot) and the Voyager fly-bys, which, of course, also devoted a lot of attention to the Moons, since a lot of effort was devoted to images. The planets are rather large featureless balls of gas and cloud and you can only do so much on a “zoom-past”. One of the odd things is the magnetic fields. On Earth, the magnetic field axis corresponds with the axis of rotation, more or less, but not so much there. Earth’s magnetic field is believed to be due to a molten iron core, but that could not occur there. That probably needs explaining. The iron in the dust that is accreted to form planets is a fine powder; the particles are in the micron size. The Earth’s core arises because the iron formed lumps, melted, and flowed to the core because it is denser. In my ebook “Planetary Formation and Biogenesis” I argue that the iron actually formed lumps in the accretion disk. While the star was accreting, the region around where Earth is reached something like 1600 degrees C, above the melting point of iron, so it formed globs. We see the residues of that in the iron-cored meteorites that sometimes fall to Earth. However, Mars does not appear to have an iron core. Within that model, the explanation is simple. While on Earth the large lumps of iron flowed towards the centre, on Mars, since the disk temperature falls off with distance from the star, at 1.5 AU the large lumps did not form. As a consequence, the fine iron particles could not move through the highly viscous silicates, and instead reacted with water and oxidised, or, if you prefer, rusted.

If the lumps that formed for Earth could not form at Mars because it was too far away from the star, the situation was worse for Uranus. As with Mars, the iron would be accreted as a fine dust and as the ice giants started to warm up from gravitational collapse, the iron, once it got to about 500 degrees Centigrade, would rapidly react with the water and oxidise to form iron oxides and hydrogen. Why did that not happen in the accretion disk? Maybe it did, and maybe at Mars it was always accreted as iron oxides, but by the time it got to where Earth is, there would be at least ten thousand times more hydrogen than iron, and hot hydrogen reduces iron oxide to iron. Anyway, Uranus and Neptune will not have an iron core, so what could generate the magnetic fields? Basically, you need moving electric charge. The planets are moving (rotating) so where does the charge come from?

The answer recently proposed is superionic ice. You will think that ice melts at 0 degrees Centigrade, and yes, it does, but only at atmospheric pressure. Increase the pressure and it melts at a lower temperature, which is how you make snowballs. But ice is weird. You may think ice is ice, but that is not exactly correct. There appear to be about twenty ices possible from water, although there are controversial aspects because high pressure work is very difficult and while you get information, it is not always clear about what it refers to. You may think that irrespective of that, ice will be liquid at the centre of these planets because it will be too hot for a solid. Maybe.

In a recent publication (Nature Physics, 17, 1233-1238 November 2021) authors studied ice in a diamond anvil cell at pressures up to 150 GPa (which is about 1.5 million times greater than our atmospheric pressure) and about 6,500 degrees K (near enough to Centigrade at this temperature). They interpret their observations as there being superionic ice there. The use of “about” is because there will be uncertainty due to the laser heating, and the relatively short times up there. (Recall diamond will also melt.)

A superionic ice is proposed wherein because of the pressure, the hydrogen nuclei can move about the lattice of oxygen atoms, and they are the cause of the electrical conduction. These conditions are what are expected deep in the interior but not at the centre of these two planets. There will presumably be zones where there is an equilibrium between the ice and liquid, and convection of the liquid coupled with the rotation will generate the movement of charge necessary to make the magnetism. At least, that is one theory. It may or may not be correct.

Your Water Came from Where?

One interesting question when considering why Earth has life is from where did we get our water? This is important because essentially it is the difference between Earth and Venus. Both are rocky planets of about the same size. They each have similar amounts of carbon dioxide, with Venus having about 50% more than Earth, and four times the amount of nitrogen, but Venus is extremely short of water. If we are interested in knowing about whether there is life on other planets elsewhere in the cosmos, we need to know about this water issue. The reason Venus is hell and Earth is not is not that Venus is closer to the Sun (although that would make Venus warmer than Earth) but rather it has no water. What happened on Earth is that the water dissolved the CO2 to make carbonic acid, which in turn weathered rocks to make the huge deposits of lime, dolomite, etc that we have on the planet, and to make the bicarbonates in the sea.

One of the more interesting scientific papers has just appeared in Nature Astronomy (https://doi.org/10.1038/s41550-021-01487-w) although the reason I find it interesting may not meet with the approval of the authors. What the authors did was to examine a grain of the dust retrieved from the asteroid Itokawa by the Japanese Space agency and “found it had water on its surface”. Note it had not evaporated after millions of years in a vacuum. The water is produced, so they say, by space weathering. What happens is that the sun sends out bursts of solar wind which contains high velocity protons. Space dust is made of silicates, which involve silica bound to four oxygen atoms in a tetrahedron, and each oxygen atom is bound to something else. Suppose, for sake of argument, the something else is a magnesium atom. A high energy hydrogen nucleus (a proton) strikes it and makes SiOH and, say Mg+, with the Mg ion and the silicon atom remaining bound to whatever else they were bound to. It is fairly standard chemistry that 2SiOH → SiOSi plus H2O, so we have made water. Maybe, because the difference between SiOH on a microscopic sample of dust and dust plus water is rather small, except, of course, Si-OH is chemically bound to and is part of the rock, and rock does not evaporate. However, the alleged “clincher”: the ratio of deuterium to hydrogen on this dust grain was the same as Earth’s water.

Earth’s water has about 5 times more deuterium than solar hydrogen, Venus about a hundred times. The enhancement arises because if anything is to break the bond in H-O-D, the hydrogen is slightly more probable to go because the deuterium has a slightly stronger bond to the oxygen. Also, being slightly heavier, H-O-D is slightly less likely to get to the top of the atmosphere.

So, a light bulb moment: Earth’s water came from space dust. They calculate that this would produce twenty litres of water for every cubic meter of rock. This dust is wet! If that dust rained down on Earth it would deliver a lot of water. The authors suggest about half the water here came that way, while the rest came from carbonaceous chondrites, which have the same D/H ratio.

So, notice anything? There are two problems when forming a theory. First, the theory should account for everything of relevance. In practice this might be a little much, but there should be no obvious problems. Second, the theory should have no obvious inconsistencies. First, let us look at the “everything”. If the dust rained down on the Earth, why did not the same amount rain down on Venus? There is a slight weakness in this argument because if it did, maybe the water was largely destroyed by the sunlight. If that happened a high D/H ratio would result, and that is found on Venus. However, if you accept that, why did Earth’s water not also have its D/H ratio increased? The simplest explanation would be that it did, but not to extent of Venus because Earth had more water to dilute it. Why did the dust not rain down on the Moon? If the answer is the dust had been blown away by the time the Moon was formed, that makes sense, except now we are asking the water to be delivered at the time of accretion, and the evidence on Mars was that water was not there until about 500 million years later. If it arrived before the disk dust was lost, then the strongest supply of water would come closest to the star, and by the time we got to Earth, it would be screened by inner dust. Venus would be the wettest and it isn’t.

Now the inconsistencies. The strongest flux of solar wind at this distance would be what bombards the Moon, and while the dust was only here for a few million years, the Moon has been there for 4.5 billion years. Plenty of time to get wet. Except it has not. The surface of the dust on the Moon shows this reaction, and there are signs of water on the Moon, especially in the more polar regions, and the average Moon rock has got some water. But the problem is these solar winds only hit the surface. Thus the top layer or so of atoms might react, but nothing inside that layer. We can see those SiOH bonds with infrared spectroscopy, but the Moon, while it has some such molecules, it cannot be described as wet. My view is this is another one of those publications where people have got carried away, more intent on getting a paper that gets cited for their CV than actually stopping and thinking about a problem.

Quantum weirdness, or not?

How can you test something without touching it with anything, even a single photon? Here is one of the weirder aspects of quantum mechanics. First, we need a tool, and we use the Mach-Zehnder interferometer, which is illustrated as follows:

There is a source that sends individual photons to a beam splitter (BS1), which divides the beam into two sub-beams, each of which proceed to a mirror that redirects them to meet at another beam splitter (BS2). The path lengths of the two sub-beams are exactly the same (in practice a little adjustment may be needed to get this to work). Each sub-beam (say R and T for reflectance and transmitted at BS1) is reflected once by a mirror. When reflected, they sustain a phase shift of π, and R sustains such a phase shift at BS1. At BS2, the waves going to D1 both have had two reflections, so both have had a phase shift of 2π and they interfere constructively, therefore D1 registers the photon arrival. However, it is a little more complicated at D2. The original beams T and R that would head towards D2 have a net phase difference of π within the beam splitter, so they destructively interfere and the original beam R continues in the direction of net constructive interference hence only detector D1 registers. Now, suppose we send through one photon. At BS1, it seems the wave goes both ways but the photon, which acts as a particle, can only go one way. You get exactly the same result because it does not matter which way the photon goes; the wave goes both ways but the phase shift means only D1 registers.

Now, suppose we block one of the paths? Now there is no interference at BS2 so both D1 and D2 register equally. That means we can detect an obstruction on the path R even if no photon goes along it.

Now, here is the weird conclusion proposed by Elitzer and Vaidman [Foundations of Physics 23, 987, (1992)]. Suppose you have a large supply of bombs, but you think some may be duds. You attach a sensor to each bomb wherein if one photon hits it, it explodes. (It would be desirable to have a high energy laser as a source, otherwise you will be working in the dark setting this up.) At first sight all you have to do is shine light on said bombs, but at the end all you will have are duds, the good ones having blown up. But suppose we put it in the arm of such an interferometer so that it blocks the photon. Half the time a photon will strike it and it will explode if it is good, but consider the other half. When the photon gets to the second beam splitter, the photon has a 50% chance of going to either D1 or D2. If it goes to D1 we know nothing, but if it goes to D2 we know the photon went to the bomb. If the bomb was any good it exploded, so if it did not explode we know it was a dud. So if the bomb is good, the probability is ¼ that we shall learn without destroying it, ½ that we destroy it, and ¼ that we don’t know. In this case we send a second photon and continue until we get a hit at D2, then stop. The probability that we can detect the bomb without sensing it with anything now ends up at 1/3. So we end up keeping 1/3 of our bombs and locate all the duds.

Of course, this is a theoretical prediction. As far as I know, nobody has ever tested bombs, or anything else for that matter, this way. In standard quantum mechanics this is just plain weird. Of course, if you accept the pilot wave approach of de Broglie or Bohm, or for that matter my guidance wave version, where there is actually a physical wave other than the wave being a calculating aid, it is rather straightforward. Can you separate these versions? Oddly enough, yes, if reports are correct. If you have a version of this with an electron, the end result is that any single electron has a 50% chance of firing each detector. Of course, one electron fires only one detector. What does this mean? The beam splitter (which is a bit different for particles) will send the electron either way with a 50% probability, but the wave appears to always follow the particle and is not split. Why would that happen? The mathematics of my guidance wave require the wave to be regenerated continuously. For light, this happens from the wave itself, from Maxwell’s theory of light being an oscillation of electromagnetic waves. The oscillation of the electric field causes the next magnetic oscillation, and vice versa. But an electron does not have this option, and the wave has to be tolerably localised in space around the particle.

Thus if the electron version of this Mach Zehnder interferometer does do what the reference I say claims it did (unfortunately, it did not cite a reference) then this odd behaviour of electrons shows that the wave function for particles at least cannot be non-local (or the beam splitter did not work. There is always an alternative conclusion to any single observation.)

Where did a Nervous System Come From?

Ever wondered how a nervous system evolved, and how we evolved to get around to thinking? If you do think about it, at first sight it is not obvious how it evolved; what caused it? The point about evolution is that it progresses in tiny steps, so what could possibly be a step towards a nervous system? It has to be something really simple that a minor change from the first simple organism that feeds and reproduces, BUT it has to do something that gives it an advantage, so the question comes down to what could that be?

The first thing to note is that there would be little point in a single-cell creature developing such a system. The point of a nervous system is to coordinate the activities of different parts of the whole, but a single cell is sufficiently small that coordination is unnecessary. Notwithstanding that, there may be an advantage for a single cell to sense whether there are nutrients nearby. The first such cells would simply absorb, but if it could sense when there were nutrients or not, it would have a better way of knowing whether to reproduce. That could arise initially with nothing more than having two activities. Microalgae show such an extremely primitive sensing. If a microalga has a good supply of nitrogen, it makes nucleic acid as fast as it  can, together with some protein, and these are just what it needs to reproduce. If it is nitrogen starved, it cannot turn off its photosynthesis mechanism so it takes CO2 from the air and makes lipids. It just swells up with fat! If it cannot get nitrogen nutrients for a prolonged time, it bloats and dies.

According to Musser et al. 2021 (Science 374: 717 – 723) a clue to how the nervous system evolved comes from sponges. Sponges are an animal clade that lack neurons, muscles or a gut, so they are rather simple. They have canals for filter feeding and waste removal and they have cilia that drive water flow. Yet despite this simple structure, they perform whole-body contractions that can expel debris, and while they have no integrated signalling functions, nevertheless they have genetic material usually found in nerves and muscles. Apparently sponges can use an intricate cell communication system to regulate their feeding and potentially eliminate invading bacteria. They do not have neurons, but they have genes that encode proteins to help transmit chemical signals, which could be regarded as an initial move towards a nervous system.

The sponge that was studied has 18 distinct cell types and synaptic genes (i.e. potentially capable of transmitting a signal) were active in some of the cells that were clustered around the digestive chambers.

They then showed that some such cells send out long arms to contact the cells with hair-like protrusions that drive the water flow systems. In other words, there is something there made of protein that starts where food is digested and stretches to the cells that control the flow of water, thus either telling these cells to send more food or alternatively to clear out the debris from previous digestion. It is important to note that these connectors are not nerves and it is not a rapid communication. Nevertheless, a system that could tell when it was time to get rid of debris from the region where it digests would be an evolutionary advantage over those that could not, and would hence take a greater percentage of the food and reproduce faster. Eventually it would predominate, especially those specimens that could do it a little better than the others. Over the generations the system would gradually predominate. It should also be noted that this does not mean we evolved from a sponge. This sort of behaviour could have started many times in different families. The point is, there is a distinct advantage when developing multi-celled creatures for one end to let another end know that it would like more food, or that it is flooded with debris. Obviously, this is a long way from a nervous system. The next evolutionary step would probably be to do it faster in larger multi-celled species. However, the means of sensing food would be the first prerequisite for sending messages to help digestion; it is not just the ability to send messages, but the message must have some sensible relevance. Food (or nutrient acquisition) would be the first reason to communicate across cells. Whether this was really how a nervous system started is debatable, but at least it makes sense.

Scientific Rubbish

Just when I thought that I had probably said enough about bad science, along comes another paper in Nature, ( https://doi.org/10.1038/d41586-021-03035-y) where it was noted that hundreds of junk-science papers have been retracted from reputable journals after fraudsters manipulated the publication process. Many of these were caught in “special issues”, where in some cases the whole issue was rubbish. A special issue is often published when someone suggests that a collection of papers on a specific topic would be helpful. Thus one of those attacked was Springer-Nature’s Journal of Nanoparticle Research. A groups of what appeared to be eminent computer scientists and engineers from well-known institutions in Germany and the UK wrote to the journal’s editors suggesting a special issue about the role of nanotechnology in health care. The editorial board agreed with the proposal and created a special issue entry in its editorial management system and apparently authorised access to three group members so they could handle the manuscripts. Reliance on sloth of others always pays dividends!

It appeared that months later some members of the editorial board argued the papers were of poor quality and they investigated. However, some of the papers had already been published. The investigation revealed that the original proposers were not who they claimed to be. Now this strikes me as evidence of particular slothfulness on the part of the journals. If someone claims to be a senior person at a university, they will be listed on the University’s web page, usually with evidence to support the glowing claims. That is because if the person is any good, the University wants to take what credit it can. Now, if only I knew who these editors were, why I have a very important bridge to sell them.

Which raises the question, why do people do this? One reason suggested by the article is that the scammers offer a service to researchers who are not doing very well. For a payment, they will put the name on the paper. Oddly enough, a paper with many contributors from many places is often considered to be very good, because a lot of people will have sorted out the bad stuff. Nobody checks to see if the names really knew about the paper, so a genuine “big name” can be added. Now the researcher gets another paper from a “reputable journal” to add to their CV, which means they get help for their funding applications, or even keep their jobs. One criticism of that theory raised in the linked item was, “The papers are so obviously terrible, so why would you want them on your CV?” That reasoning is wrong because it carries an inherent assumption: those reviewing the fund application or the promotion/appointment lists actually read the papers. The CV lists a title. It may seem incomprehensible, but on its own that happens with a lot of reputable papers to those not directly involved in the field. As an example, here is the title of a paper “Single ion thermal wave packet analyzed via time- of-flight detection.” That, I must add, is a perfectly respectable paper, but how many readers would know what it was about just from the title? You would have to read the paper to know whether it is respectable, and you would need to know some physics. It would not be that difficult to write something about nanotechnology that looked vaguely respectable to those completely outside the field. All you have to do is take an existing paper and change some words, mainly nouns, but keep the verbs and important keywords.

So what should happen to stop this happening? The first question is, why are Springer and Elsevier being attacked? The answer is these are big commercial publishers, so it is money. The special issues make money without the need for particular effort. But I think the second issue is to examine why people do it? The procedures of funding research or employment must change so that the number of papers is meaningless. The third issue is that you hear that scientific papers are peer reviewed and hence have real value. What this farce shows is that peer review is a farce in many cases. But maybe that is for another time, but not next week.

My Introduction to the Scientific Method – as actually practised

It is often said if you can’t explain something to a six-year-old, you don’t understand.

I am not convinced, but maybe I don’t understand. Anyway, I thought I would follow from my previous post with an account of my PhD thesis. It started dramatically. My young supervisor gave me a choice of projects but only one looked sensible. I started that, then found the answer just published. Fortunately, only month wasted, but I had no project and supervisor was off on vacation. Head of Department suggested I find myself a project, so I did. There was a great debate going on whether the electrons in cyclopropane could delocalize into other parts of a molecule. To explain, carbon forms bonds at an angle of 109.5 degrees, but the three carbons of cyclopropane have to be formally at 60 degrees. In bending them around, the electrons come closer together and the resultant electric repulsions mean the overall energy is higher. The higher energy difference is called strain energy. One theory was the strain energy could be relieved if the electrons could get out and spread themselves over more space. Against that, there was no evidence of single bonds being able to do this.

My proposal was to put a substituted benzene ring on one corner, and an amine on the other. The idea was, amines are bases and react with acid, and when they do that the electrons on the amine are trapped. If the cyclopropane ring could delocalize electrons there was one substituent I could put on the benzene ring that would have different effects on that basicity depending on whether the cyclopropane ring did delocalize electrons or not. There was a test through something called the Hammett equation. My supervisor had published on this, but this would be the first time the equation might be used to do something of significance. Someone had tried that scheme with carboxylic acids, but with an extra carbon atom they were not very responsive and there were two reports with conflicting answers. My supervisor, when he came back, was not very thrilled with this proposal, but his best alternative was to measure the rates of a sequence of reactions for which I had found a report that said the reaction did not go. So he agreed. Maybe I should have been warned. Anyway, I had some long-winded syntheses to do.

When it came to reaching the end-position, my supervisor went to North America on sabbatical, and then sequentially looking for a new position in North America, so I was on my own. The amine results did not yield the desired result because the key substituent, a nitro group, reacted with the amine very quickly. That was a complete surprise. I could make the salt, but the solution with some amine quickly discoloured. However, in a fleeting visit my supervisor made a useful suggestion: react the acids in toluene with a diazo compound. While the acids previously had been too similar in properties in water, it turned out that toluene greatly amplified the differences. The results were clear: the cyclopropane ring did not delocalize electrons.

However, all did not go well. The quantum mechanical people who had shown the extreme stability of polywater through electron delocalization turned their techniques to this problem and asserted it did. In support, they showed that the cyclopropane ring stabilized adjacent positive charge. However, if the strain energy arose through increased electron repulsion, a positive charge would reduce that. There would be extra stability with a positive charge adjacent, BUT negative charge would destabilize it. So there were two possible explanations, and a clear means of telling the difference.

Anions on a carbon atom are common in organic chemistry. All attempts at making such an anion adjacent to a cyclopropane ring failed. A single carbon atom with two hydrogen atoms, and a benzene ring attached forms a very stable anion (called a benzyl anion). A big name replaced one of the hydrogen atoms of a benzyl anion with a cyclopropane ring, and finally made something that existed, although only barely. He published a paper and stated it was stabilized by delocalization. Yes, it was, and the stabilization would have come from the benzene ring. Compared with any other benzyl anion it was remarkably unstable. But the big names had spoken.

Interestingly, there is another test from certain spectra. In what is called an n->π* transition (don’t worry if that means nothing to you) there is a change of dipole moment with the negative end becoming stronger close to a substituent. I calculated the change based on the polarization theory, and came up with almost the correct answer. The standard theory using delocalization has the spectral shift due to the substituent in the opposite direction.

My supervisor, who never spoke to me again and was not present during the thesis write-up, wrote up a paper on the amines, which was safe because it never showed anything that would annoy the masses, but he never published the data that came from his only contribution!

So, what happened? Delocalization won. A review came out that ignored every paper that disagreed with its interpretation, including my papers. Another review dismissed the unexpected spectral shift I mentioned by saying “it is unimportant”. I ended up writing an analysis to show that there were approximately 60 different sorts of observation that were not in accord with the delocalization proposition. It was rejected by review journals as “This is settled” (that it was settled wrongly was irrelevant) and “We do not publish logic analyses.” Well, no, it seems they do not, and do not care that much.

The point I am trying to make here is that while this could be regarded as not exceptionally important, if this sort of wrong behaviour happens to one person, how much happens across the board? I believe I now know why science has stopped making big advances. None of those who are established want to hear anyone question their own work. The sad part is, that is not the only example I have.