Tag: free radicals

Fingerprinting an exoplanet

Life, death, and multiple Gaias

Keith S. Taber

NASA might be said to be engaged in looking for other Gaias beyond our Gaia, as Dr Milam explained to another Gaia.

This post is somewhat poignant as something I heard on a radio podcast reminded me how science has recently lost one of its great characters, as well as an example of that most rare thing in today's science – the independent scientist.

Inside Science episode "Deep Space and the Deep Sea – 40 years of the International Whaling Moratorium", presented, perhaps especially aptly, by Gaia Vince

I was listening to the BBC's Inside Science pod-cast episode 'Deep Space and the Deep Sea – 40 years of the International Whaling Moratorium' where the presenter – somewhat ironically, in view of the connection I was making, Gaia Vince – was talking to Dr Stefanie Milam of Nasa's Goddard Space Flight Centre about how the recently launched James Webb Space Telescope could help scientists look for signs of life on other planets.

From: https://jwst.nasa.gov/content/meetTheTeam/people/milam.html

Dr Milam explained that

"spectra…give us all the information that we really need to understand a given environment. And that's one of the amazing parts about the James Webb space telescope. So, what we have access to with the wavelengths that the James Webb space telescope actually operates at, is that we have the fingerprint pattern of given molecules, things like water, carbon monoxide, carbon dioxide, all these things that we find in our own atmosphere, and so by using the infrared wavelengths we can look for these key ingredients in atmospheres around other planets or even, actually, objects in our own solar system, and that tells us a little bit about what is going on as far as the dynamics of that planet, whether or not its has got geological activity, or maybe even something as crazy as biology."

Dr Stefanie Milam, interviewed for 'Inside Science'
"Webb has captured the first clear evidence of carbon dioxide (CO2) in the atmosphere of a planet outside of our solar system!" (Hot Gas Giant Exoplanet WASP-39 b Transit Light Curve, NIRSpec Bright Object Time-Series Spectroscopy.)
Image: NASA, ESA, CSA, and L. Hustak (STScI). Released under 2.0 Generic (CC BY 2.0) License – Some rights reserved by James Webb Space Telescope
Do molecules have fingerprints

Fingerprints have long been used in forensic work to identify criminals (and sometimes their victims) because our fingerprints are pretty unique. Even 'identical' twins do not have identical fingerprints (thought I suspect that fact rather undermines some crime fiction plots). But, to have fingerprints one surely has to have fingers. A palm print requires a palm, and a footprint, a foot. So, can molecules, not known for their manual dexterity, have fingerprints?

Well, it is not exactly by coincidence (as the James Webb space telescope has had a lot of media attention) that I very recently posted here, in the context of new observations of the early Universe, that

"Spectroscopic analysis allows us to compare the pattern of redshifted spectral lines due to the presence of elements absorbing or emitting radiation, with the position of those lines as they are found without any shift. Each element has its own pattern of lines – providing a metaphorical fingerprint.

from: A hundred percent conclusive science. Estimation and certainty in Maisie's galaxy

In chemistry, elements and compounds have unique patterns of energy transitions which can be identified through spectroscopy. So, we have 'metaphorical fingerprints'. To describe a spectrum as a chemical substance's (or entity's, such as an ion's) fingerprint is to use a metaphor. It is not actually a fingerprint – there are no fingers to leave prints – but this figure of speech gets across an idea though an implicit comparison with something already familiar. *1 That is, it is a way of making the unfamiliar familiar (which might be seen as a description of teaching!)

Dead metaphors

But perhaps this has become a 'dead metaphor' so that now chemicals do have fingerprints? One of the main ways that language develops is by words changing their meanings over time as metaphors become so commonly used they case to be metaphorical.

For example, I understand the term electrical charge is a dead metaphor. When electrical charge was first being explored and was still unfamiliar, the term 'charge' was adopted by comparison with the charging of a canon or the charge of shot used in a shotgun. The shot charge refers to the weight of shot included in a cartridge. Today, most people would not know that, whilst being very familiar with the idea of electrical charge. But when the term electrical charge was first used most people knew about charging guns.

So, initially, electrical 'charge' was a metaphor to refer to the amount of 'electricity' – which made use of a familiar comparison. Now it is a dead metaphor, and 'electrical charge' is now considered a technical tern in its own right.

Another example might be electron spin: electrons do not spin in the familiar sense, but really do (now) have spin as the term has been extended to apply to quanticles with inherent angular momentum by analogy with more familiar macroscopic objects that have angular momentum when they are physically rotating. So, we might say that when the term was first used, it was a metaphor, but no longer. (That is, physicists have expanded the range of convenience of the term spin.)

Perhaps, similarly, fingerprint is now so commonly used to mean a unique identifier in a wide range of contexts, that it should no longer be considered a metaphor. I am not sure if that is so, yet, but perhaps it will be in, say, a century's time – and the term will be broadly used without people even noticing that many things have acquired fingerprints without having fingers. (A spectrum will then actually be a chemical substance's or entity's fingerprint.) After all, many words we now commonly use contain fossils of their origins without us noticing. That is, metaphorical fossils, of course. *2

James Lovelock, R.I.P.

The reason I found this news item somewhat poignant was that I was listening to it just a matter of weeks after the death (at age 103) of the scientist Jim Lovelock. *3 Lovelock invented the device which was able to demonstrate the ubiquity of chlorofluorocarbons (CFCs) in the atmosphere. These substances were very commonly used as refrigerants and aerosol propellants as they were very stable, and being un-reactive (so non-toxic) were considered safe.

But this very stability allowed them to remain in and spread through the atmosphere for a very long time until they were broken down in the stratosphere by ultraviolet radiation to give radicals that reacted with the ozone that is so protective of living organisms. Free radical reactions can occur as chain reactions as when a radical interacts with a molecule it leads to a new molecule, plus a new radical which can often take part in a further interaction with another molecule: so, each CFC molecule could lead to the destruction of many ozone molecules. CFCs have now been banned for most purposes to protect the ozone 'layer', and so us.

Life is chemistry out of balance

But another of Lovelock's achievements came when working for NASA to develop means to search for life elsewhere in the universe. As part of the Mariner missions, NASA wanted Lovelock to design apparatus that could be sent to other worlds and search for life (and I think he did help do that), but Lovelock pointed out that one could tell if a planet had life by a spectroscopic analysis.

Any alien species analysing light passing through earth's atmosphere would see its composition was far from chemical equilibrium due to the ongoing activity of its biota. (If life were to cease on earth today, the oxygen content of the atmosphere would very quickly fall from 21% to virtually none at all as oxygen reacts with rocks and other materials.) If the composition of an atmosphere seemed to be in chemical equilibrium, then it was unlikely there was life. However, if there were high concentrations of gases that should react together or with the surface, then something, likely life, must be actively maintaining that combination of gases in the atmosphere.

"Living systems maintain themselves in a state of relatively low entropy at the expense of their nonliving environments. We may assume that this general property is common to all life in the solar system. On this assumption, evidence of a large chemical free energy gradient between surface matter and the atmosphere in contact with it is evidence of life. Furthermore, any planetary biota which interacts with its atmosphere will drive that atmosphere to a state of disequilibrium which, if recognized, would also constitute direct evidence of life, provided the extent of the disequilibrium is significantly greater than abiological processes would permit. It is shown that the existence of life on Earth can be inferred from knowledge of the major and trace components of the atmosphere, even in the absence of any knowledge of the nature or extent of the dominant life forms. Knowledge of the composition of the Martian atmosphere may similarly reveal the presence of life there."

Dian R. Hitchcock and James E. Lovelock – from Lovelock's website (originally published in Icarus: International Journal of the Solar System in 1967)

The story was that NASA did not really want to be told they did not need to send missions with spacecraft to other words such as Mars to look for life, rather that they only had to point a telescope and analyse the spectrum of radiation. Ironically, perhaps, then, that is exactly what they are now doing with planets around other star systems where it is not feasible (not now, perhaps not ever) to send missions.

Gaia and Gaia

But Lovelock became best known for his development and championing of the Gaia theory. According to Gaia (the theory, not the journalist), the development of life on earth has shaped the environment (and not just exploited pre-existing niches) and developed as a huge integrated and interacting system (the biota, but also the seas, the atmosphere, freshwater, the soil,…) such that large scale changes in one part of the system have knock-on effect elsewhere. *4

So, Gaia can be understood not as the whole earth as a planet, or just the biota as the collective life in terms of organisms, but rather as the dynamic system of life of earth and the environment it interacts with. In a sense (and it is important to see this is meant as an analogy, a thinking tool) Gaia is like some supra-organism. Just as snail has a shell that it has produced for its self, Gaia has shaped the biosphere where the biota lives. *4

The system has built in feedback cycles to protect it from perturbations (not by chance, or due to some mysterious power, but due to natural selection) but if it is subject to a large enough input it would shift to a new (and perhaps very different) equilibrium state. *5 This certainly happened when oxygen releasing organisms evolved: the earth today is inhospitable to the organisms that lived here before that event (some survived to leave descendants, but only in places away from the high oxygen concentrations, such as in lower lays of mud beneath the sea), and most organisms alive today would die very quickly in the previous conditions.

It would be nice to think that Gaia, the science journalist that is, was named after the Gaia theory – but Lovelock only started publishing about his Gaia hypothesis about the time that Gaia was born.*6 So, probably not. Gaia is a traditional girl's name, and was the name of the Greek goddess who personified the earth (which is why the name was adopted by Lovelock).

Still, it was poignant to hear a NASA scientist referring to the current value of a method first pointed out by Lovelock when advising NASA in the 1970s and informed by his early thinking about the Gaia hypothesis. NASA might be said to now be engaged in looking for other Gaias on worlds outside our own solar system, as Dr Milam explained to – another – Gaia here on earth.

Notes:

*1 It is an implicit comparison, because the listener/reader is left to appreciate that it is meant as a figure of speech: unlike in a simile ('a spectrum is like a fingerprint') where the comparison is made explicit .

*2 For some years I had a pager (common before mobile phones) – a small electronic device which could receive a text message, so that my wife could contact me in an emergency if I was out visiting schools by phoning a message to be conveyed by a radio signal. If I had been asked why it was called a pager, I would have assumed that each message of text was considered to comprise a 'page'.

However, a few weeks ago I watched an old 'screwball comedy' being shown on television: 'My favourite wife' (or 'My favorite [sic] wife' in US release).

(On the very day that Cary Grant remarries after having his first wife, long missing after being lost at sea, declared legally dead, wife number one reappears having been rescued from a desert island. That this is a very unlikely scenario was played upon when the film was remade in colour, as 'Move Over Darling', with Doris Day and James Garner. The returned first wife, pretending to be a nurse, asks the new wife if she is not afraid the original wife would reappear, as happened in that movie; eliciting the response: 'Movies. When do movies ever reflect real life?')

Some of the action takes place in the honeymoon hotel where groom has disappeared from the suite (these are wealthy people!) having been tracked down by his first wife. The new wife asks the hotel to page him – and this is how that worked with pre-electronic technology:

Paging Mr Arden: Still from 'My Favorite Wife'

*3 So, although I knew Lovelock had died (July 26th), he was still alive at the time of the original broadcast (July 14th). In part, my tardiness comes from the publicly funded BBC's decisions to no longer make available downloads of some of its programmes for iPods and similar devices immediately after broadcast. (This downgrading of the BBC's service to the public seems to be to persuade people to use its own streaming service.)

*4 The Gaia theory developed by Lovelock and Lyn Margulis includes ideas that were discussed by Vladimir Vernadsky almost a century ago. Although Vernadsky's work was well known in scientific circles in the Soviet Union, it did not become known to scientists in Western Europe till much later. Vernadsky used the term 'biosphere' to refer to those 'layers' of the earth (lower atmosphere to outer crust) where life existed.

*5 A perturbation such as as extensive deforestation perhaps, or certainly increasing the atmospheric concentrations of 'greenhouse' gases beyond a certain point.

*6 Described as a hypothesis originally, it has been extensibility developed and would seem to now qualify as a theory (a "consistent, comprehensive, coherent and extensively evidenced explanation of aspects of the natural world") today.

How much damage can a couple of molecules do?

Just how dangerous is Novichok?

Keith S. Taber

"We are only talking about molecules here…

There might be a couple of molecules left in the Salisbury area. . ."

Expert interviewed on national news

The subject of chemical weapons is not to be taken lightly, and is currently in the news in relation to the Russian invasion of Ukraine, and the concern that the limited progress made by the Russian invaders may lead to the use of chemical or biological weapons to supplement the deadly enough effects of projectiles and explosives.

Organophosphorus nerve agents (OPNA) were used in Syria in 2013 (Pita, & Domingo, 2014), and the Russians have used such nerve agents in illicit activities – as in the case of the poisoning of Sergey Skripal and his daughter Yulia in Salisbury. Skripal had been a Russian military intelligence officer who had acted for the British (i.e., as a double agent), and was convicted of treason – but later came to the UK in a prisoner swap and settled in Salisbury (renown among Russian secret agents for its cathedral). 1

Salisbury, England – a town that featured in the news when it was the site of a Russian 'hit' on a former spy (Image by falco from Pixabay )

These substances are very nasty,

OPNAs are odorless and colorless [and] act by blocking the binding site of acetylcholinesterase, inhibiting the breakdown of acetylcholine… The resulting buildup of acetylcholine leads to the inhibition of neural communication to muscles and glands and can lead to increased saliva and tear production, diarrhea, vomiting, muscle tremors, confusion, paralysis and even death

Kammer, et al., 2019, p.119

So, a substance that occurs normally in cells, but is kept in check by an enzyme that breaks it down, starts to accumulate because the enzyme is inactivated when molecules of the toxin bind with the enzyme molecules stopping them binding with acetylcholine molecules. Enzymes are protein based molecules which rely for their activity on complex shapes (as discussed in 'How is a well-planned curriculum like a protein?' .)

Acetylcholine is a neurotransmitter. It allows signals to pass across synapses. It is important then that acetylcholine concentrations are controlled for nerves to function (Image source: Wikipedia).

Acetylcholinesterase is a protein based enzyme that has an active site (red) that can bind and break up acetylcholine molecules (which takes about 80 microseconds per molecule). The neurotransmitter molecule is broken down into two precursors that are then available to be synthesised back into acetylcholine when appropriate. 2

Toxins (e.g., green, blue) that bind to the enzyme's active site block it from breaking down acetylcholine.

(Image source: RCSB Protein Data Bank)

A need to clear up after the release of chemical agents

The effects of these agents can be horrific – but, so of course, can the effects of 'conventional' weapons on those subjected to aggression. One reason that chemical and biological weapons are banned from use in war is their uncontrollable nature – once an agent is released in an environment it may remain active for some time – and so hurt or kill civilians or even personnel from the side using those weapons if they move into the attacked areas. The gases used in the 1912-1918 'world' war, were sometimes blown back towards those using them when the wind changed direction.

Image by Eugen Visan from Pixabay 

This is why, when small amounts of nerve agents were used in the U.K. by covert Russian agents to attack their targets, there was so much care put into tracing and decontaminating any residues in the environment. This is a specialised task, and it is right that the public are warned to keep clear of areas of suspected contamination. Very small quantities of some agents can be very harmful – depending upon what we mean by such relative terms as 'small'. Indeed, two police officers sent to the scene of the crime became ill. But what does 'very small quantities' mean in terms of molecules?

A recent posting discussed the plot of a Blakes7 television show episode where a weapon capable of destroying whole planets incorporated eight neutrons as a core component. This seemed ridiculous: how much damage can eight neutrons do?

But, I also pointed out that, sadly, not all those who watched this programme would find such a claim as comical as I did. Presumably, the train of thought suggested by the plot was that a weapon based on eight neutrons is a lot more scary than a single neutron design, and neutrons are found in super-dense neutron stars (which would instantly crush anyone getting too near), so they are clearly very dangerous entities!

A common enough misconception

This type of thinking reflects a common learning difficulty. Quanticles such as atoms, atomic nuclei, neutrons and the like are tiny. Not tiny like specs of dust or grains of salt, but tiny on a scale where specs of dust and grains of salt themselves seem gigantic. The scales involves in considering electronic charge (i.e., 10-19C) or neutron mass (10-27 kg) can reasonably be said to be unimaginatively small – no one can readily visualise the shift in scale going from the familiar scale of objects we normally experience as small (e.g., salt grains), to the scale of individual molecules or subatomic particles.

People therefore commonly form alternative conceptions of these types of entities (atoms, electrons, etc.) being too small to see, but yet not being so far beyond reach. It perhaps does not help that it is sometimes said that atoms can now be 'seen' with the most powerful microscopes. The instruments concerned are microscopes only by analogy with familiar optical microscopes, and they produce images, but these are more like computer simulations than magnified images seen through the light microscope. 3

It is this type of difficulty which allows scriptwriters to refer to eight neutrons as being of some significance without expecting the audience to simply laugh at the suggestion (even if some of us do).

An expert opinion

Although television viewers might have trouble grasping the insignificance of a handful of neutrons (or atoms or molecules), one would expect experts to be very clear about the vast difference in scale between us (people for example) and them (nanoscopic entities of the molecular realm). Yet experts may sometimes be stretched beyond their expertise without themselves apparently being aware of this – as when a highly qualified and experienced medical expert agreed with an attorney that the brain sends out signals to the body faster than the speed of light. If a scientific expert in a high profile murder trial can confidently make statements that are scientifically ridiculous then this underlines just how challenging some key scientific ideas are.

For any of us, knowing what we do not know, recognising when we are moving outside out of areas where we have a good understanding, is challenging. Part of the reason that student alternative conceptions are so relevant to science learning is that a person's misunderstanding can seem subjectively to be just as well supported, sensible, coherent and reasonable as a correct understanding. Where a teacher themself has an alternative conception (which sometimes happens, of course) they can teach this with as much enthusiasm and confidence as anything they understand canonically. Expertise always has limitations.

A chemical weapons expert

I therefore should not have been as surprised as I was when I heard a news broadcast featuring an expert who was considered to know about chemical weapons refer to the potential danger of "a couple of molecules". This was in relation to the poisoning by Russian agents of the Salisbury residents,

"During an interview on a BBC Radio 4 news programme (July 5th, 2018), Hamish de Bretton-Gordon, who brands himself as one of the world's leading chemical weapons experts, warned listeners that there may be risks to the public due to residue from the original incident in the area. Whilst that may have been the case, his suggestion that "we are only talking about molecules here. . .There might be a couple of molecules left in the Salisbury area. . ." seemed to suggest that even someone presented to the public as a chemistry expert might completely fail to appreciate the submicroscopic scale of individual molecules in relation to the macroscopic scale of a human being."

Taber, 2019, p.130
Chemical weapons expert ≠ chemistry expert

Now Colonel de Bretton-Gordon is a visiting fellow at  Magdalene College Cambridge, and the College website describes him as "a world-leading expert in Chemical and Biological weapons". I am sure he is, and I would not seek to underplay the importance of decontamination after the use of such agents; but if someone who has such expertise would assume that a couple of molecules of any substance posed a realistic threat to a human being with its something like 30 000 000 000 000 cells, each containing something like 40 000 000 molecules of protein (to just refer to one class of cellular components), then it just underlines how difficult it is to appreciate the gulf in scale between molecules and men.

Regarding samples of nerve agents, they may be deadly even in small quantities, but that still means a lot of molecules.

Novichok cocktails

The attacks in Salisbury (from which the intended victims recovered, but another person died in nearby Amesbury apparently having come into contact with material assumed to have been discarded by the criminals), were reported to have used 'Novichok', a label given to group of compounds.

"Based on analyses carried out by the British "Defence Science and Technology Laboratory" in Porton Down it was concluded that the Skripals were poisoned by a nerve agent of the so-called Novichok group. Novichok … is the name of a group of nerve agents developed and produced by Russia in the last stage of the Cold War."

Carlsen, 2019, p.1

Testing of toxins is often based on the LD50 – which means finding the dose that has an even chance of being lethal. This is not an actual amount, as clearly the amount of material that is needed to kill a large adult will be more than that to kill a small child, but the amount of the toxin needed per unit mass of victim. Although no doubt these chemicals have been directly tested on some poor test specimens of non-consenting small mammals, such information is not in the public domain.

Indeed, being based on state secrets, there is limited public data on Novichok and related agents. Carlsen (2019) estimates the LD50 for oral administration of 9 compounds in the Novichok group and some closely related agents to vary between 0.1 to 96.16 mg/kg.

Carlsen suggest the most toxic of these compounds is one known as VX. VX was actually first developed by British Scientists, although almost equivalent nerve agents were later developed elsewhere, including Russia.

'Chemical structures of V-agents.'
(Figure 2 from Nepovimova & Kuca, 2018 – subject to http://creativecommons.org/licenses/BY-NC-ND/4.0/)
n.b. This figure shows more than a couple of molecules of nerve agent – so might this be a lethal dose?

Carlsen then argues that the actual compounds in Novachok are probably less toxic than XV, which might explain…

"…why did the Skripals not die following expose to such high potent agents; just compare to the killing of Kim Jong-nam on February 13, 2017 in Kuala Lumpur International Airport, where he was attacked by the highly toxic VX, and died shortly after."

Carlsen, 2019, p1

So, for the most sensitive agent, known as XV (LD50 c. 0.1 mg/kg), a person of 50 kg mass would it is estimated have a 50% chance of being killed by an oral dose of 0.1 x 50 mg. That is 5 mg or 0.005 g by mouth. A single drop of water is said to have a volume of about 0.05 ml, and so a mass of about 0.05 g. So, a tenth of a drop of this toxin can kill. That is a very small amount. So, if as little as 0.005 g of a nerve agent will potentially kill you then that is clearly a very toxic substance.

The molecular structure of XV is given in the figure above taken from Nepovimova and Kuca (2018). These three structures shown appear to be isomeric – that is the three molecules are structural isomers. They would have the same empirical formula (and the same molecular mass).

Chemical shorthand

This type of structural formula is often used for complex organic molecules as it is easy for experts to read. It is one of many special types of representation used in chemistry. It is based on the assumption that most organic compounds can be understood as if substituted hydrocarbons. (They may or may not be derived that way – this is jut a formalism used as a thinking tool.) Hydrocarbons comprise chains of carbon atomic cores bonded to each other, and with their other valencies 'satisfied' by being bonded to hydrogen atomic cores. These compounds can easily be represented by lines where each line shows the bond between two carbon atomic cores. The hydrogen centres are not shown at all, but are implicit in the figure (they must be there to 'satisfy' the rules of valency – i.e., carbon centres in a stable structures nearly always have four bonds ).

Anything other than carbon and hydrogen is shown with elemental symbols, and in most organic compounds these other atomic centres take up on a minority of positions in the structure. So, for compounds, such as the 'VX' compounds, these kinds of structural representations are a kind of hybrid, with some atomic centres shown by their elemental symbols – but others having to be inferred.

From the point of view of the novice learner, this form of abstract representation is challenging as carbon and hydrogen centres need to be actively read into the structure (whereas an expert has learnt to do this automatically). But for the expert this type of representation is useful as complex organic molecules can contain hundreds or thousands of atomic centres (e.g., the acetylcholinesterase molecule, as represented above) and structural formulae that show all the atomic centres with elemental symbols would get very crowded.

So, below I have annotated the first version of XV:

The VX compound seems to have a molecular mass of 267

This makes the figure much more busy, but helps me count up the numbers of different types of atomic centres present and therefore work out the molecular mass – which, if I had not made a mistake, is 267. I am working here with the nearest whole numbers, so not being very precise, but this is good enough for my present purposes. That means that the molecule has a mass of 267 atomic mass units, and so (by one of the most powerful 'tricks' in chemistry) a mole of this compound, the actual substance, would have a mass of 267g.

The trick is that chemists have chosen their conversion factor between molecules and moles, the Avogadro constant of c. 6.02 x 1023, such that adding up atomic masses in a molecule gives a number that directly scales to grammes for the macroscopic quantity of choice: the mole. 5

So, if one had 267 g of this nerve agent, that would mean approximately 6.02 x 1023 molecules. Of course here we are talking about a much smaller amount – just 0.005 g (0.005/267, about 0.000 02 moles) – and so many fewer molecules. Indeed we can easily work out 0.005 g contains something like

(0.005 / 267) x 6.02 x 1o23 = 11 273 408 239 700 374 000 = 1×1019 (1 s.f.)

That is about

10 000 000 000 000 000 000 molecules

So, because of the vast gulf in scale between the amount of material we can readily see and manipulate, and the individual quanticle such as a molecule, even when we are talking about a tiny amount of material, a tenth of a drop, this still represent a very, very large number of molecules. This is something chemistry experts are very aware of, but most people (even experts in related fields) may not fully appreciate.

The calculation here is approximate, and based on various estimates and assumptions. It may typically take about 10 000 000 000 000 000 000 molecules of the most toxic Novichok-like agent to be likely to kill someone – or this estimate could be seriously wrong. Perhaps it takes a lot more, or perhaps many fewer, molecules than this.

But even if this estimate is out by several orders of magnitude and it 'only' takes a few thousand million million molecules of XV for a potential lethal dose, that can in no way be reasonably described as "a couple of molecules".

It takes very special equipment to detect individual quanticles. The human retina is in its own way very sophisticated, and comes quite close to being able to detect individual photons – but that is pretty exceptional. As a rule of thumb, when anyone tells us that a few molecules or a few atoms or a few ions or a few electrons or a few neutrons or a few gamma rays or… can produce any macroscopic effect (that we can see, feel, or notice) we should be VERY skeptical.

Work cited:
Notes:

1 Two men claiming to be the suspects whose photographs had been circulated by the British Police, and claimed by the authorities here to be Russian military intelligence officers, appeared on Russian television to explain they were tourists who had visited Salisbury sightseeing because of the Cathedral.

2 According to the RCSB Protein Data Bank website

"Acetylcholinesterase is found in the synapse between nerve cells and muscle cells. It waits patiently and springs into action soon after a signal is passed, breaking down the acetylcholine into its two component parts, acetic acid and choline."

Molecule of the month: Acetylcholinesterase

Of course, it does not 'wait patiently': that is anthropomorphism.

3 We might think it is easy to decide if we are directly observing something, or not. But perhaps not:

"If a chemist heats some white powder, and sees it turns yellow, then this seems a pretty clear example of direct observation. But what if the chemist was rightly conscious of the importance of safe working, and undertook the manipulation in a fume cupboard, observing the phenomenon through the glass screen. That would not seem to undermine our idea of direct observation – as we believe that the glass will not make any difference to what we see. Well, at least, assuming that suitable plane glass of the kind normally used in fume cupboards has been used, and not, say a decorative multicoloured glass screen more like the windows found in many churches. Assuming, also, that there is not bright sunlight passing through a window and reflecting off the glass door of the fume cupboard to obscure the chemist's view of the powder being heated. So, assuming some basic things we could reasonably expect about fume cupboards, in conjunction with favourable viewing conditions, and taking into account our knowledge of the effect of plane glass, we would likely not consider the glass screen as an impediment to something akin to direct observation.

Might we start to question an instance of direct observation if instead of looking at the phenomenon through plane glass, there was clear, colourless convex glass between the chemist and the powder being heated? This might distort the image, but should not change the colours observed. If the glass in question was in the form of spectacle lenses, without which the chemist could not readily focus on the powder, then even if – technically – the observations were mediated by an instrument, this instrument corrects for a defect of vision such that our chemist would feel that direct observation is not compromised by, but rather requires, the glasses.

If we are happy to consider the bespectacled chemist is still observing the phenomenon rather than some instrumental indication of it, then we would presumably feel much the same about an observation being made with a magnifying glass, which is basically the same technical fix as the spectacles. So, might we consider observation down a microscope as direct observation? Early microscopes were little more than magnifying glasses mounted in stands. Modern compound microscopes use more than one lens. A system of lenses (and some additional illumination, usually) reveals details not possible to the naked eye – just as the use of convex spectacles allow the longsighted chemist to focus on objects that are too close to see clearly when unaided.

If the chemist is looking down the microscope at crystal structures in a polished slice of mineral, then, it may become easier to distinguish the different grains present by using a Polaroid filter to selectively filter some of the light reaching the eye from the observed sample. This seems a little further from what we might normally think of as direct observation. Yet, this is surely analogous to someone putting on Polaroid sunglasses to help obtain clear vision when driving towards the setting sun, or donning Polaroid glasses to help when observing the living things at the bottom of a seaside rock pool on a sunny day when strong reflections from the surface prevent clear vision of what is beneath.

A further step might be the use of an electron microscope, where the visual image observed has been produced by processing the data from sensors collecting reflections from an electron beam impacting on the sample. Here, conceptually, we have a more obvious discontinuity although the perceptual process (certainly if the image is of some salt crystal surface) may make this seem no different to looking down a powerful optical microscope. An analogy here might be using night-vision goggles that allow someone to see objects in conditions where it would be too dark to see them directly. I have a camera my late wife bought me that is designed for catching images of wildlife and that switches in low light conditions to detecting infrared. I have a picture of a local cat that triggered an image when the camera was left set up in the garden overnight. The cat looks different from how it would appear in day-light, but I still see a cat in the image (where if the camera had taken a normal image I would not have been able to detect the cat as the image would have appeared like the proverbial picture of a 'black cat in a coal cellar'). Someone using night-vision goggles considers that they see the fox, or the escaped convict, not that they see an image produced by electronic circuits.

If we accept that we can see the cat in the photograph, and the surface details of crystal grains in the electron microscope image, then can we actually see atoms in the STM [scanning tunneling microscope] image? There is no cat in or on my image, it is just a pattern of pixels that my brain determines to represent a cat. I never saw the cat directly (I was presumably asleep) so I have no direct evidence there really was a cat if I do not accept the photograph taken using infrared sensors. I believe there are cats in the world, and have seen uninvited cats in my garden in daylight, and think the camera imaged one of them at night. So it seems reasonable I am seeing a cat in the image, and therefore I might wonder if it is reasonable to doubt that I can also see atoms in an STM image.

One could shift further from simple sensory experience. News media might give the impression that physicists have seen the Higgs boson in data collected at CERN. This might lead us to ask: did they see it with their eyes? Or through spectacles? Or using a microscope? Or with night-vision goggles? Of course, they actually used particle detectors.

Feyerabend suggests that if we look at cloud chamber photographs, we do not doubt that we have a 'direct' method of detecting elementary particles …. Perhaps, but CERN were not using something like a very large cloud chamber where they could see the trails of condensation left in the 'wake' of a passing alpha particle, and that could be photographed for posterity. The detection of the Higgs involved very sophisticated detectors, complex theory about the particle cascades a Higgs particle interaction might cause, and very complex simulations to allow for all kinds of issues relating to how the performance of the detectors might vary (for example as they age) and how a signal that might be close to random noise could be identified…. No one was looking at a detector hoping to see the telltale pattern that would clearly be left by a Higgs, and only a Higgs. In one sense, to borrow a phrase, 'there's nothing to see'. Interpreting the data considered to provide evidence of the Higgs was less like using a sophisticated microscope, and more like taking a mixture of many highly complex organic substances, and – without any attempt to separate them – running a mass spectrum, and hoping to make sense of the pattern of peaks obtained.

Taber, 2019, pp.158-160

4 That is not to suggest that one should automatically assume that one molecule of a toxin can only ever damage one protein molecule somewhere in one body cell. After all, one of the reasons that CFCs (chlorofluorocarbons, which used to be used as propellants in all kinds of spray cans for example) were so damaging to the ozone 'layer' was because they could initiate a chain reaction.

In reactions that involve free radicals, each propagation step can produce another free radical to continue the reaction. Eventually two free radicals are likely to interact to terminate the process – but that might only be after a great many cycles, and the removal of a great many ozone molecules from the stratosphere. However, even if one free radical initiated the destruction of many molecules of ozone, that would still be a very small quantity of ozone, as molecules are so tiny. The problem was of course that a vast number of CFC molecules were being released.

5 So one mole of hydrogen gas, H2, is 2g, and so forth.