Atomic Butterflies

Red AdmiralWhen I first moved to my current house some 20-years ago, my next-door neighbour had a buddleia growing in their garden which overhung part of my driveway. In the summer, the shrub was a resting spot for a multitude of red admiral butterflies, which exploded into a swarm if I got too close. Sadly, that buddleia was a casualty of renovation work a few years ago but even if the shrub had survived, I suspect the butterfly swarm might still be a thing of the past. Every year the UK organises the big butterfly count where over 100,000 members of the public score the number and species of butterflies in a particular area over a given time. This year they reported the lowest average number of butterflies since recording began in 2010.

The red admiral is a migratory butterfly, happy to inhabit that buddleia in the summer but then heads south for the winter. If conservationists are to identify the causes of the falling population, then they need to understand the red admiral’s migratory behaviour, and that’s not such an easy thing to do. The traditional approach is to capture butterflies, place labels on their wings before releasing them back into the wild, then record the labels as butterflies turn up in other geographic locations. This is a hit and miss method because information on migration routes rely on butterfly labels turning up in the expected location. Moreover, insect migration, known as migration phenology, can be deceptively complex, sometimes involving journeys of thousands of kilometres over more than one generation. Wing labelling therefore provides a snapshot in time, rather than overall and longer-term migration phenology data. Instead of relying on wing labels, recently scientists have turned to isotope analysis to attain more nuanced migration phenology data.

I have mentioned isotopes in previous blog posts, and they are essentially different versions of the same chemical element, distinguished only by the atomic mass. Hydrogen, for example, has an atomic mass of one because its nucleus has one proton. An isotope of hydrogen called deuterium on the other had has an atomic mass of two, because its nucleus has one proton and one neutron. Scientists distinguish isotopes by given the total number of protons and neutrons as a prefixed superscript to the elemental symbol. Hydrogen is 1H and deuterium is 2H for example. All the chemical elements have a range of isotopes. For instance, the most common isotopes of oxygen are 16O, 17O and 18O (all oxygen atoms have 8 protons, 16O all has 8 neutrons, 17O has 9 neutrons and 18O has10 neutrons). The relative combinations of isotopes in molecules depends upon their surrounding physical conditions. The relative amounts of hydrogen and oxygen isotopes in water, for example, reflect the conditions of evaporation from oceans and precipitation as rain. Pour a glass of water from your tap and the blend of 1H216O, 1H217O, 1H218O, 2H216O, 2H217O and 2H218O depends upon where on planet Earth your tap resides. 

Butterflies incorporate hydrogen isotopes into wing keratin, which is a fibrous protein found in hair (and butterfly wings). Once formed, keratin is stable, locking in the isotopic pattern. The 2H to 1H isotope ratios vary according to rainfall and local temperatures and so can be used as regional markers. To compare isotopes in butterfly wings to specific regions requires data on geographical isotope patterns. This is achieved through painstaking sample collection and analysis over wide landscapes, to build what’s called an isoscape.

Traditionally considered to have regular migration patterns, red admirals go to northern Europe in the spring where they reproduce with the next generation heading south for the winter. Although hydrogen isotope analysis confirmed this general concept, it also revealed complexities not previously realised. Analysis of 2H showed red admirals migrate from the south probably as far away as north African locations in the spring, but in August they originated further from the north in what are two distinct migration patterns. In spring, butterflies migrating from the south carried eggs but we find no eggs in August on butterflies coming from the north. Differences in 2H patterns measured in central Europe in spring compared to winter, are consistent with the butterflies reproducing in the Mediterranean during winter. In contrast to the migratory patterns of spring and winter, in autumn 2H isotope patterns indicated butterflies are of a more local origin. Surprisingly, they may be two populations of red admiral because the 2H isotope patterns in those from western Europe rarely correspond with those of north-eastern Europe migrating in the autumn. Based upon isotopic patterns therefore, the migration phenology of the red admiral is far more complex than first realised.

The reason why some butterflies seem to be on the decline remains obscure, but the red admiral is not alone in this respect. In North America, monarch butterflies that overwinter in the Oyamel forests of Mexico have suffered an 80% decline and the possibility of extinction looms. Phenology studies on monarchs, prior to 1997, was carried out using traditional wing labelling techniques but despite hundreds of thousands of butterflies being tagged, they only ever found 125 in Mexico. In 1998 a Canadian research group turned to using isotopes of hydrogen and carbon to trace the origins of monarch butterflies. They measured 2H and 13C in the wings of monarchs captured in Mexico and compared the isotope abundances to isoscapes across North America. Data for 2H reflected local rainfall and 13C data correlated to milkweed, the principle food source for monarch caterpillars. They determined that around half of the monarchs that overwintered in Mexico originated from the Midwest corn and soybean belt of the United States, Nebraska, Kansas and Texas on the western edge and the coastline to the east. Once these butterflies migrated to the Oyamel forests they bred and the next generation returned to its origins in the Midwest. Some conservationists believe that pesticides and genetically modified crops are responsible for the butterfly decline but others point to limiting factors on the migratory routes (now there’s a better understanding of those routes). Either explanation is possible but isotope analysis turned up another possible explanation.

In 2018, 2H and 13C isotope analysis on captured monarchs in south Florida showed there were two populations, one resident to Florida and the other migratory. Not all monarchs are migratory therefore, and it seemed Darwinian evolution was at work because the resident population had a smaller wing size. The migratory population mostly originated from the Midwest and the Texas-Oklahoma border, which correlates to the origins of the Mexican population. This raises the intriguing possibility monarchs are not so much on the decline but perhaps relocating away from Mexico and towards Florida. Given the complexity of red admiral migration so elegantly revealed by isotopic analysis, I’d like to think perhaps those butterflies which once rested on the buddleia overhanging my garden have just moved on to more suitable locations as our climate warms. Without evidence perhaps this is wishful thinking but I’m sure the answer is hidden somewhere within the isotopes.

Death by Liquorice

A blog post for the non-expert

Liquorice
The media is reporting a 54-year-old construction worker from Massachusetts has died of liquorice poisoning. Not for the first time when dealing with such issues, the press reports are so similar that they were likely all cloned from the original source, a paper in the New England Journal of Medicine. I thought, therefore, a blog post for the non-expert might put the toxicology of liquorice into perspective.

They make liquorice from the root of the flowering plant Glycyrrhiza glabra, largely native to western Asia. Media reports will tell you a substance called glycyrrhizic acid contained within the root, is responsible for its toxicity. This is correct, to a point. I blogged on the terpene pathway in plants before, pointing out the biochemical connection between turpentine and rubber, and even cannabidiol.  Glycyrrhizic acid is yet another byproduct of this pathway, but in this case it also has two sugar molecules attached. Glycyrrhizic acid itself is not particularly toxic because the sugars inhibit its absorption through the gastrointestinal tract. Bacteria in the digestive system however, remove the sugars to make glycyrrhetinic acid, which is absorbed into the bloodstream and that’s where the trouble starts.

There’s an enzyme with the somewhat complicated name of 11-β-hydroxysteroid dehydrogenase, but those nice biochemists have shortened it to 11β-HSD which is less of a mouthful. 11β-HSD converts a sterol called cortisone into cortisol, which, amongst other things, affects how the kidneys regulate sodium and potassium transport. Messing around with the body’s sodium and potassium levels can lead to a variety of problems. In fact there’s a disease called Cushing’s syndrome, where too much cortisol in the bloodstream leads to a decrease in potassium and a condition known as hypokalemia. Glycyrrhetinic acid is a sterol-like compound* which 11β-HSD mistakes for cortisone, throwing a metaphorical spanner in the biochemical works. This leads to excretion of potassium and sodium retention and in turn causes cardiac arrhythmias and renal failure, which is what seems to have happened to the Massachusetts construction worker. 

Some quarters of the press seem amused there’s such a thing as liquorice poisoning, but we should remember the victim had family and friends who might not see it as a joke. I suspect some will call for a liquorice ban, and warnings have been around for some yearsParacelcus. In truth it’s not as simple as that because it’s not only sold widely as a confection, we use glycyrrhetinic acid and its related compounds in a range of foods as a natural sweetener and also in some cosmetics from lipstick to suntan lotion. Some believe liquorice has curative properties for anything from cancer to being an anti-viral –  claims which I believe we should all take with a pinch of salt. The trouble is that anything is toxic if taken in sufficient amounts. This was realised back in the 15th century by a German-Swiss physician, alchemist, astrologer and occultist with the horrendous name of Philippus Aureolus Theophrastus Bombastus von Hohenheim. Perhaps even in his own time, his name may have been a bit of a mouth-full, because he was just known as Paracelsus. Amongst a lot of mumbo-jumbo of his age, he got at least one thing right. He famously said, “what is it that is not poison? All things are poison and nothing is without poison. It is the dose only that makes a thing not a poison.” Over time this became abbreviated to, “the dose makes the poison.”  Anything taken in excess can be toxic, even the most benign of substances, like water for example. Water intoxication, or hyperhydration, is rare but there are occasional cases. In 2007 for example, a Californian woman died after taking part in a water-drinking contest where she drank up to 4 L in an hour. At the other end of the scale, all vegetables contain tiny amounts of more potent toxins. Potatoes, for example, have substances related to glycoalkaloid poisons found in deadly nightshade called solanines. You might believe celery is the most beguine ingredient in a healthy salad but it has a carcinogenic chemical known as psoralen. Cabbage, broccoli and cauliflower all contain a group of chemicals called glucosinolates, which can impair thyroid function. Your body is more than capable of coping with these small of potentially toxic substances in your everyday diet. In fact we have evolved some exquisite detoxification biochemistry to do so with no need for so called detox diets. Talking of detox, grapefruit, so popular with that fad, contains furanocoumarins that inhibit certain enzymes otherwise involved in everyday natural elimination of toxins from the body – biochemical irony!

The Massachusetts construction worker supposedly ate a bag and a half of liquorice a day – that’s around 400-500 grammes. In 2004 a Yorkshire woman in the UK, suffered serious muscle failure requiring hospitalisation after eating less than half that amount of liquorice per day. So the lesson is, everything in moderation and remember Paracelsus, anything in large enough doses can kill you. Now where did I put those Bassetts Liquorice Allsorts?

 

  • – to be more precise it’s a triterpenoid but I’m not getting into that level of detail

Serial killers are no joke

IMG_2276For those of you reading this in the UK, you may have seen the three-part drama on ITV called Des, which followed the serial killing career of Dennis Nilsen. An horrific and macabre story and yet somehow frighteningly captivating. As scary as serial killers are, they represent a minuscule proportion of the population and so the chances of ever coming into contact with one are equally minuscule. Once however, I got disturbingly close.

In the late 1980s I worked for a Manchester-based company that made scientific analytical instruments called mass spectrometers. Crude versions of these instruments were first developed by Francis Aston as part of the effort to decipher the internal workings of the atom in the early 1900s. Over the years which followed, mass spectrometers evolved into probably the most important analytical instrument of modern science. Put simply, mass spectrometers are molecule weighing machines. They smash molecules into fragments by bombarding them with charged atoms or electrons, then separate the fragments according to their molecular mass in electromagnetic fields. My job title was “Applications Chemist” which essentially entailed traveling the world helping develop analytical methods for the company’s customers (it also meant a lot of sales support, but we’ll move on from those memories as quickly as possible). On one occasion, they dispatched me to a forensic laboratory in Sacramento, California.

These were the days before satellite navigation and I got lost several times on my drive from San Fransisco to my Sacramento destination. I eventually arrived at the crime lab with some relief and several hours late. There, before a burley security guard allowed me to enter the building, I had to surrender my passport and sign some legal documents detailing long-term prison sentences which would be imposed if I didn’t adhere to the rules. My host – whose name I sadly cannot remember – explained that they were trying to develop an analytical method to detect drugs in hair. This was nothing particularly new and I had worked on something similar previously. An innocuous request did not prepare me for what was about to come. In the laboratory were a series of little plastic bags containing dark brown – perhaps reddish – matted hair samples. My host allowed me to pick one up, and I commented the hair didn’t look particularly fresh. I was then told the story of their origin.

At first sight Dorothea Puente looked like a sweet grandmother, unassuming with round spectacles and snow-like hair. She had however, earned the nickname of “Death House Landlady.” She murdered at least six elderly boarders, some with mental disabilities, the bodies of whom she disposed around her property. The nature of the murders was a little sketchy but she seemed to have drugged her victims with a tranquilliser called flurazepam. My objective was to help the forensic scientists analyse hair samples obtained from exhumed victims to see if we could detect the drug.

It took around two weeks on two separate trips before we had the beginnings of an analytical method. At her trial it was stated the drug was found in all her victims, but whether this resulted from the analytical method I helped develop or not, I don’t know. Even though I worked on the periphery however, it’s an experience I’m unlikely to forget. I was several stages removed from the murder investigation but to be faced with samples of her murder victims – pieces of hair that once grew on the heads of human beings before being slaughtered by a deranged old lady, was disturbing enough to disrupt my sleep for weeks. There are, of course, those who get much closer to serial killers than I ever did and I honestly don’t know how they cope coming face to face with the homicidal lunatic fringe of our species. Leading the case against Dennis Nilsen, was Detective Chief Inspector Peter Jay who became a chain smoker and left the police force two years after the investigation closed. The impact of serial killers it seems, go far beyond those who they kill.

Cannabis tyres

PlantI started my post-graduate scientific career as a plant biochemist (phytochemist to be more precise). Once talking to a geologist about how fascinating plants are, he replied, “plants just get in the way of the rocks,” and so I guess your interests very much depend on your viewpoint. I moved up the career evolutionary  tree from plants to clinical pharmacology, and clinical pharmacologists had one prospect in common with geologists, they also thought plants were boring. Clinical pharmacologists and geologists are both wrong.

The Flemish chemist and physiologist Jan Baptist van Helmont (1580-1644) showed his dedication to phytochemistry when he weighed a growing tree and the soil in its pot every day for five years. The tree gained weight, but the soil remained unchanged and so he concluded the increase in weight must have come from water perculating up through the roots. We know today Van Helmont was only half right. Imagine a lonely carbon atom in a molecule of carbon dioxide, minding its own business, just quietly causing climate change, when it wanders into a leaf. There photosynthesis, powered by the energy of sunlight, captures carbon from atmospheric carbon dioxide, splits water drawn up through the roots, and joins the molecular fragments together to make a substance called 3-phosphoglycerate. And from this molecule, it makes all the stuff of plants. This is itself amazing, because those vegetables you had with your dinner, that tea or coffee you just drank and the cotton vest you’re wearing, contains carbon that, a short time ago, was floating around in the air.

Proving my interests reflect my viewpoint, my early efforts with phytochemistry focused on substances called terpenes, and these still hold a fascination for me to this day. Carbon in terpenes, like all carbon in plants, ultimately came from carbon dioxide, but it’s their journey forward that interests me most. As its name implies, turpentine (or turps) used as a solvent and paint-thinner comes from plant terpenes, but that same phytochemical pathway branches out in many directions. From the same terpene origins, comes the fragrance of plants from lavender (linalool) to oranges and lemons (limonene) and pine disinfectant (pinene). Condense a few more terpenes together and you get plant sterols. Some margarines, for example, are rich in β-sitosterol, a plant sterol with cholesterol-lowering properties. Keep going, joining up more terpenes and you end up with rubber, which oozes out of tapped rubber trees as latex. Take a side branch of terpene phytochemistry starting with geraniol, which gives geraniums their aroma, and you finish up following a more notorious route to cannabidiol. All these substances are towns and villages along the same photochemical road, where you can stop and sample, or carry on to the next destination.

So next time you watch that TV traffic cop show, where boy racers have burned rubber and provided a positive test for cannabis, remember as they put the cuffs on the miscreants, the rubber in the tyres and the weed they smoked have an unseen phytochemical connection. Now tell me that’s boring – I dare you.

Ammonium nitrate: a Jekyll and Hyde chemical

Please donate to the appeal if you can, as hospitals are reporting they are unable to treat further casualties as hundreds of beds immediately filled up following the blast.

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Beirut explosionThe explosion which rocked Beirut’s Port was almost certainly caused by inappropriate storage of 2,750 tons of ammonium nitrate. But what is ammonium nitrate and why is it dangerous and yet used so widely?

Often called the elements of life, carbon, hydrogen, oxygen, sulphur and nitrogen, combine in the most stupendously complex ways, to make proteins, and with the absence of sulphur, DNA, which controls the biochemistry of all species on Earth. Photosynthesis captures elemental carbon, hydrogen and oxygen to make the stuff of plants, which then journey through the animal kingdom from insects to elephants, and even you and me. Nitrogen is a little different because some plants draw it up through their roots and others fix the element from out of the atmosphere. Either way, nitrogen is essential to plant growth, which is why the nitrogen fertiliser market is worth around $55 billion per year. Plant nitrogen sources come in two types, ammonia and nitrate. Ammonia (NH4) is the chemically reduced form of nitrogen, and nitrate is the oxidised form, NO3. Ammonium nitrate NH4NO3, therefore, has both the oxidised and reduced forms of nitrogen in the same molecule, which is why it’s so popular as a fertiliser. But containing both the oxidised and reduced forms also makes it a very odd compound, one which according to some interpretations of its chemistry, should not exist. Put this ghost-like chemical existence together with the fact that nitrogen is omnipresent in explosives and you get some idea of why I’ve called it a Jekyll and Hyde chemical.

Chemical bonds within certain nitrogen based compounds can release large amounts of energy with explosive capacity. Take, nitroglycerine, trinitrotoluene (TNT) and nitroamine in C4 as just three well-known examples. Ammonium nitrate is not in the same explosive category, but those high energy nitrogen bonds are nevertheless present. Sitting on a pivot between its reduced and oxidised forms, ammonium nitrate decomposes to nitrous oxide gas (NO2) and water when it gets hot, then as the temperature increases in turns to nitrogen, oxygen and water. These reactions are exothermic, in that they release heat and under right (or wrong) conditions, a chain reaction runs away releasing the gases with explosive power. The principle gas, nitrogen dioxide, is what caused the brown plume after the Beirut explosion, a characteristic telling chemists ammonium nitrate was involved even before it was announced.

Providing ammonium nitrate is stored and handled correctly, it presents little risk, evidenced by the fact farmers all over the world safely hold stocks as fertiliser. Do it wrong however, and you can get into big trouble. In 1921 in Oppau, Germany, a store of around 4.5 kilotons of ammonium nitrate set hard after it became wet. Workman, tired of using pickaxes to break it up, turned to dynamite. The resulting explosion killed an estimated 700 people and obliterated the town. Other ammonium nitrate explosions across the world have killed several thousand people over the years and in every case, the ultimate cause was poor handling or storage of the chemical.

Chemists can make ammonium nitrate intentionally explosive by mixing it with diesel fuel. It’s used as an industrial explosive known as ANFO (Ammonium Nitrate Fuel Oil) in mining and quarrying, but it also became a readily accessible favourite of the IRA in the 1970s and 1990s. Timothy McVeigh and Terry Nichols used the same mixture in the Oklahoma bombing of 1995.

If you’ve eaten any bread recently, it’s a good bet the nitrogen in the wheat came from ammonium nitrate. But if food production is the Dr Jekyll side of that chemical, its explosive potential is the Mr Hyde, be it deliberate terrorism, or chemical incompetence.

What is interferon and is it effective against Covid-19?

A blog post for the non-expert

Our best hope against Covid-19 is an effective vaccine, and efforts in that direction are galloping along like no other time in history. There are so many vaccines being investigated, it’s hard to keep up with the numbers, but at the time of writing there appear to be well over 100, with around 40 in active clinical trials. Despite a lot of dangerous nonsense circulating the internet that Bill Gates wants to control our DNA through microchips implanted via vaccines, in reality they are without doubt the most successful weapon in humankind’s fight against infectious disease. The adage that vaccines “prime the immune system against infection” hides an incredible biochemical complexity, that’s truly mind-blowing. If you want a simplistic, but more accurate description of what a vaccine does, I’d describe them as “interjecting into the body’s biochemistry to up-regulate the immune system against an infecting organism”. More accurate perhaps, but, I’ll grant, less catchy.

It’s undoubtedly true, Covid-19 is likely to remain as disruptive and destructive as ever, until one, or more, of those vaccines comes through. In the meantime however, scientists are also investigating drug-based approaches to alleviate symptoms and save the lives of those infected. Now and again one of these drugs, such as dexamethasone hits the headlines but there’s one reported recently, albeit behind the headlines, which, like a vaccine, interjects into the complexity of the immune system to exert its therapeutic effect – and that’s interferon.

As ever, we have to be cautious of the claims because so far we only have a press release (I blogged on science by press release previously) but interferon is currently used to treat, for example, viral infections in asthma patients and so does have an established track record. There are two sides to understanding the effectiveness of any drug, the mechanism by which it works, and to what extent it improves patient recovery. Let’s look at the mechanism first. 

Interferon is a protein, and since I’ve blogged on the complexity of proteins before, I’ll not repeat it here. There are three types of interferon, alpha (α), beta (β) and gamma (ɣ), but the one of interest here is β-interferon. It comprises 166 amino acids along with attached sugars (see image). In the immune army, interferon belongs to the signal corps. As virusesInterferon attack, cells release interferon sounding a warning bell to other cells that a virus is on the rampage. Cells receiving the message switch on genes to up-regulate antigen presentation, which essentially means they present the immune system with something to attack. Antibodies are then made against the antigen, which place flags on the viral particles for an army of white cells to attack and destroy. All well and good, but some viruses have evolved ways to block interferons, like jamming the signal corp’s radios so they can’t communicate. The virus causing dengue fever, for example, is well known for this assault on interferon and there’s evidence SARS-CoV-2 can do something similar. Introducing additional β-interferon directly into the lungs through a nebuliser, so the hypothesis goes, restores the balance and the signals can get through once more.

The theory appears sound, but how effective is β-interferon against Covid-19 in practice? Evidence to date comes from a single study of 101 patients randomised between those receiving β-interferon (code named SNG001) and those receiving a placebo. The study was conducted by Synairgen plc who reported patients receiving β-interferon were, on average, released from hospital 3-days earlier than those on a placebo. Recovery over 28-days was almost four-times higher with β-interferon although it had little effect on the death-rate. The key findings are in the company’s press release.

Media emphasis has been on Covid-19 death rates but the virus also causes much suffering and leaves some survivors with significant medical problems. Until an effective vaccine does come along, drugs such as β-interferon and aforementioned dexamethasone, which at first sight may seem to have limited efficacy, nevertheless have a potentially important role in the fight against the most severe symptoms. There are also other drug regimens emerging, such as administration of multiple therapies. One recent study looked at combining β-interferon with ritonavir and ribavirin, for example. 

As cells receive interferon’s viral distress call, it can induce flu-like symptoms, which on top of those of Covid-19 is certainly problematic. But small steps are welcome during a pandemic and it nevertheless gives reason for optimism.

Covid-19 was genetically-engineered

A Covid-19 blog post for the non-expert

Germ warfareThe story that Covid-19 is a genetically-engineered virus from a Wuhan laboratory has gone viral across the internet (dated pun intended). President Trump implied it, and the Daily Express ran a 10th March headline, “Coronavirus may have been genetically engineered for the efficient spreading in the human population, a bombshell new study has claimed.” The article was withdrawn soon after.

The title of this post is deliberately provocative, and it may attract conspiracy theorists, so I’ll say up front, there is no evidence whatsoever SARS-CoV-2, the causative virus for Covid-19, was genetically engineered in China, or anywhere else. Instead, everything points towards completely natural origins which Charles Darwin would recognise (and probably say, “I told you so”). If you’re not a conspiracy theorist and you want to know why I’m confident this is the case, read on.

Everyone has heard of Covid-19 (caused by SARS-CoV-2),  Middle East Acute Respiratory Syndrome (caused by MERS-CoV) and Severe Respirator Syndrome (caused by SARS-CoV). These are well known because the infection spread across multiple countries but there have been four other, less infective and therefore less well known outbreaks, HKU1, NL63, OC43 and 229E. In all seven cases, the coronavirus jumped from an animal species into human. How do we know this? It goes back to the genetic code and Darwinian evolution.

The molecular structure of DNA comprises bases called purines and pyrimidines pointingDNA inwards from a double helical backbone of phosphate and deoxyribose sugar. There are two purines called adenine and guanine and two pyrimidines called thymine and cytosine. The DNA molecule is constructed somewhat like a child’s magnetic building kit, where north and south poles of magnets stick together to make a cube or a pyramid, or other similar shape. The child soon discovers that although north and south poles stick together, north-north or south-south poles repel. They can’t build their pyramid from magnets joined with like-poles, no matter how hard they try. Like north and south poles of magnets, bases of DNA can only join pyrimidine to purine, never pyrimidine to pyrimidine or purine to purine. In fact, they are more specific than that, because adenine (A) always bonds to thymine (T) and guanine (G) always bonds to cytosine (C). The sequence of A-T and G-C in DNA forms the genetic code, and is collectively known as the genome. It encodes for all the processes of life that makes everything from viruses to you and me. (There are some great animations on DNA and its function here).

How does a sequence of A-T and G-C go to make the complexity of all life? The DNA helix unwinds and makes ribonucleic acid (RNA) from the A, T, G, C template. RNA is like DNA except it has ribose instead of deoxyribose, and instead of thymine it has another base called uracil. Putting aside the complexities of the three types of RNA (messenger – mRNA, transfer – tRNA and ribosomal – rRNA) the molecule translates the A,T, G,C code into a series of amino acids. Each amino acid is coded by a sequence of 3 bases, GGT, for example, codes for the amino acid, glycine. By joining together long strings of amino acids, we make proteins and proteins control all the biochemistry of life. To quote from a previous blog post:

“Proteins are hugely complex molecules made from strings of up to 20 distinct types of amino acids. Some proteins contain hundreds or even thousands of individual amino acids; the muscular protein, titin has 30,000 of them. The long strings of amino acids fold like tangled pieces of string but unlike string, the tangles are very precise. Proteins have molecular grooves and pockets where specific biochemical reactions take place. The grooves and pockets are analogous to spanners and wrenches in a biochemical tool kit, each fitting a particular sized nut or bolt in building the machinery of life.”

Coronaviruses take a shortcut that leaves out DNA, and goes directly to RNA, but it’s still the sequence of bases which codes for viral existence. It takes over the genetic machinery of mammalian cells, mostly human lung cells in the case of SARS-CoV-2, to make viral proteins, which builds lots of new viruses. The human cells are destroyed in the process, giving us the symptoms of Covid-19. If you wanted to engineer a coronavirus pandemic, then you would have to start with its RNA and it’s the same genetic sequence that tells us SARS-CoV-2 was made by mother nature herself.

Coronaviruses jump from one species to another, making them so called zoonotic viruses, but this isn’t that uncommon. In fact perhaps three quarters of all viruses are zoonotic, or at least transmitted through a vector, such as mosquitoes. SARS-CoV-2 most probably started out in horseshoe bats, based on a 96% identical RNA sequence to the RaTG13 virus endemic in that species. There is also a related RNA sequence in SARS-CoV-2 implicating the scaly anteater, called a pangolin, as an intermediary species before infecting humans. The origins of SARS-CoV-2 are written right there in its genetic code but we have to be careful because there’s much we don’t know about viruses carried by the thousands of mammalian species across the world. We do know that the vast majority of species-hops, result in a cul-de-sac for the virus and it’s only extremely rarely that a virus jumps into humans and then is able to transmit human to human. It seems however, a mutation in RaTG13 to SARS-CoV-2 is one of those rare cases.

But what about the 4% difference in RNA between RaTG13 and SARS-CoV-2, where did that come from? The genome of RaTG13 changed for the same reason the genome alters in any organism. Random changes as imperfections in the RNA→protein process arise as mutations. Some mutations are fatal and the organism dies, and some give it a small advantage so it perpetuates through the generations. Once a chance mutation in RaTG13 RNA gave it the advantage of human to human transmission – it then thrived giving us Covid-19. This random mutation, followed by biological selection is what defines Darwinian evolution. It’s happening all the time, it’s just we don’t see it until there’s a pandemic.

Not all parts of any genome are equally susceptible to mutation and one notable region of the SARS-CoV-2 RNA is particularly prone to variation. This is the region which codes for the so-called spike protein that recognises a receptor on the mammalian cell enabling it to enter that cell and infect it. It’s this variable region of RNA in coronaviruses generally that gives them their nasty species-hopping talent. From analysis of the RNA sequence, all seven coronavirus outbreaks likely originated from other mammalian species through variations in RNA coding for spike proteins. By looking at the RNA sequence in this variable region we know, both MERS-CoV and SARS-CoV, like SARS-CoV-2, most likely originated in bats, while the milder HKU1 coronavirus originated in mice and OC43 likely came from cattle. Scientists have identified precise changes in RaTG13 RNA and the corresponding amino acid sequence alterations in the spike protein which transformed it to SARS-CoV-2, enabling it to latch onto a human cell-surface protein called ACE leading to infection (I blogged about ACE previously). From the rate of coronavirus mutation, we can estimate this mutation probably occurred sometime in the last 40 to 70-years. There’s nothing unusual in the way RaTG13 mutated to SARS-CoV-2 and, indeed, it’s exactly what you would expect it to do, given the right opportunity as humankind expands into previously uninhabited ecosystems.

Worryingly, the mutation which gave us SARS-CoV-2 does not optimise the spike protein’s infectivity and so Covid-19 is actually a milder disease than nature might have given us. Even more worryingly, a variant was recently identified where another change in the variable spike protein region has increased SARS-CoV-2’s potency. The trouble is, a single error in copying the virus’s 30,000 base pairs in the RNA code can result in replacement of one amino acid in the protein for another, thereby changing the protein’s functionality. Where GGT codes for glycine, for example, just one changed base to GCT now codes for the amino acid alanine.

The problem with all conspiracy theories, be it genetically engineered SARS-CoV-2, or fake moon landings, they use a simple lie to hide the complex truth. As soon as you get below the surface, conspiracy theories lack detail and rely instead on the idea of vast networks of people, all somehow holding on to the dastardly secret. Like all the world’s virologists and molecular geneticists conspiring to keep genetically engineered SARS-CoV-2 from the unknowing public. And the fact I’ve just explained the natural process by which SARS-CoV-2 arose, just makes me part of the conspiracy. I’d like to explain more, but I’m scheduled to attend an illuminati meeting in Atlantis, so I’ll see you next time.

Murder and Atoms

Richard Hill and fellow hikers were walking in the Yorkshire Dales, about an hour’s drive from where I live, when they stopped to take a photograph. He stood by a stream near to the Sell Gill Holes caves in Pen-y-ghent but didn’t notice, just behind him, was the face-down body of a half-naked woman. They were two kilometres from the nearest road and the body had likely been dumped on higher ground one to two weeks earlier, before being washed down by torrential rain over the previous 24-hours.  It was the decomposing body of a 25-35 year old woman wearing green Marks and Spencer jeans, socks and a wedding ring. This was back in 2002 and an E-fit picture and police enquiries made at that time turned up nothing. Oddly, no one meeting her description had been reported missing anywhere in the country.

Locals affectionately called her the Lady of the Hills, they gave her a funeral and buried her in the village cemetery. The case went cold, until the new forensic technique of stable isotope analysis arrived on the scene. 

The chemical elements listed in the periodic table are defined by the number of protons in their nucleus, one for hydrogen, two for helium, and so on until the 92 protons of uranium. Although atoms of any given element always have the same number of protons, they can have different numbers of another sub-atomic particle, the neutron. All hydrogen atoms for example, have one proton but one in 6,250 also has a single neutron and about one hydrogen atom in a quintillion has two neutrons. This subclass of elements, defined by the number of neutrons, are called isotopes. Those hydrogen atoms with one proton are an isotope of hydrogen called protium. Those atoms with one proton and one neutron are an isotope of hydrogen called deuterium. Those atoms with one proton and two neutrons are an isotope of hydrogen called tritium. And as the atom packs in more neutrons, so its mass increases, protium with a mass of one, deuterium with a mass of two and tritium with a mass of three. Chemists identify which isotope is which from its atomic mass, including it as a superscripted prefix to the elemental symbol, such as, 1H for protium, 2H for deuterium and 3H for tritium. The periodic table, that we are all familiar with, lists only the elements themselves but behind each of the elemental boxes is a plethora of isotopes.

The chemistry and reactivity of isotopes of the same element are almost identical, prompting their discoverer, Frederick Soddy, to say “put colloquially, their atoms have identical outsides but different insides.” The neutron does have some effect on the behaviour of the isotope and they separate out slightly under the right conditions. Take a spoonful of water from the Arctic or Mid-Pacific ocean and the isotopes of oxygen and hydrogen will be slightly different. Water with lighter isotopes is the first to evaporate, leaving behind seas enriched with heavier isotopes in warmer climes. Pour a glass of water from your tap and the blend of 1H216O, 1H217O, 1H218O, 2H216O, 2H217O and 2H218O depends upon where on planet Earth your tap resides. Similar effects can be seen with all the isotopes to differing degrees, and as those isotopes are taken up into the body, they leave an atomic trail of breadcrumbs as to where you’ve been. Isotopes incorporated in tooth enamel is locked in for life and so reveal where you were raised as a child. Isotopes in hair reflect more recent travels.

The forensic scientist and author of a 2010 book on forensic isotope analysis, Wolfram Meir-Augenstein of Robert Gordon University in Aberdeen, arranged to have hair, teeth and bone from the Lady of the Hills analysed for isotopes of carbon (13C), oxygen (18O), hydrogen (2H) and nitrogen (15N). Those in her hair matched proportions found in North Lancashire or South Cumbria and given the rate of hair growth she must have lived close to those areas in the time immediately leading up to her death. Isotopes in teeth and bone however, indicated she was from Thailand. Was she a so called Thai bride? 

Enquiries in Thailand eventually identified her as Lamduan Armitage new Seekanya, who had married in Thailand and then moved to Portsmouth, Rugby and then to Preston in Lancashire consistent with isotope analysis of her hair. DNA comparisons with family members in Thailand confirmed her identity last year.

As with so many other cold cases, her killer has not been identified. Police have said her husband, who lives in Western Kanchanabur, Thailand, is not a suspect but the Thai Examiner expressed frustration with the investigation. The British Newspaper The Sun, is campaigning to bring the culprit, whoever that may be, to justice. 

Isotopes can only go so far but without them it’s unlikely the women buried in the Yorkshire Dales would have ever been identified. And that has to count for a lot. I hope this blog post becomes out of date quickly, and this cold case can indeed be closed.

Education through adversity

A different sort of pandemic blog post, and a rather personal one.

There are problems reopening schools, universities are going virtual and post-graduates are struggling to complete. Education is having a hard time, and many students are rightly concerned about the impact this will have on their careers. If I was in this situation, I’d be worried as well – but I want to tell my personal story because it might offer a glimmer of encouragement, at least I sincerely hope so.

I come from a very working class background. Although not so uncommon for the time, I was raised in a house without a bathroom and with an outside toilet. The bath, as it was, was in the kitchen and filled from the sole hot water tap in the house only on a Sunday night. This might sound like the start of a “Four Yorkshireman Sketch” but I tell you this because it wasn’t just the material things of life that were in short supply but an attitude to life more generally. Seen as something for other people, education was “not for the likes of us” and the only book in my home was a Bible. I failed my eleven-plus and went to a terrible secondary modern school in South East London where the highlight of the curriculum was football. My family made me leave school at sixteen with a few CSEs,* whereupon I became an apprentice plumber at the now long-gone gasworks on the Old Kent Road. It was on the number-53 bus journey to and from work, where I read my first book, the Kraken Wakes, by John Wyndham. Something inside me made me curious and, determined to get an education, I took every opportunity I could. Oddly, my lucky break was being made redundant and I ended up getting a job at the gas-appliance testing laboratory, also on the Old Kent Road. Scientist there were all too happy to show me how to calculate the efficiency of gas-appliances, which I could soon do for myself, giving me a step up in the world. One of my unofficial teachers wore leg braces because of childhood polio. That puts the times into perspective.

I went to night school to get qualifications for University but it’s a tough route and since that time I have nothing but admiration for those who choose a part-time education. I was doing well until one Saturday morning the motorbike I was riding collided with a delivery van. Smashed up very badly, I was lucky to survive. In and out of hospital for nearly three-years, somehow I kept the education going and eventually found myself an undergraduate at the ripe old age of twenty six. When I graduated, then married with one child, I managed to ignore my mother who constantly berating me to “get a proper job”, and I embarked on a PhD. This opened doors completely invisible to me in those early days. The journey took me to three adjunct professorships, some amazing experiences and, sadly, osteoarthritis from the motorcycle accident. Even so, my journey hasn’t ended and I’m still learning new things. Having been bitten by the bug of curiosity, I can never be cured of an insatiable desire for knowledge. It will stay with me until I am no more.

I’m recounting this mini-autobiography because although I’m sure there will be many students despairing for their future, if you are determined, if you have a drive for education, if that curiosity is overwhelming, you will make it in the end. It might take longer, it might be harder, but you’ll look back and be proud of an achievement through adversity. Take it from someone who’s been there, and if I can do it, believe me anyone can. Stick with it and it’ll be worth it, I promise.

* A top-grade Certificate of Secondary Education (CSE) was equivalent to a mid-grade O-level. They were replaced in 1987 with the GCSE (General Certificate of Secondary Education).

A sober look at dexamethasone

A Covid-19 blog post for the non-expert

It stared with a 16th June 2020 press release  from the University of Oxford “Low-cost dexamethasone reduce death by up to one third in hospitalised patients with severe respiratory complications of COVID-19” – which triggered the equivalent of a media cytokine storm (pun explained shortly).

I do not want, for one moment, to dowse good news when it comes to Covid-19, but medical science is progressing during the crisis by press release and so I think it worth taking a step back to understand at the time of writing, the clinical trial is unpublished and not peer reviewed. Trawl through the media, newspapers and websites, and you’ll find pretty much a rejigging of what’s in the Oxford press release. A few newspapers, such as the Guardian, took the trouble to add some interviews but overall there was no explanation of what dexamethasone is, or what it does. So I thought I’d try to address that question in this blog post.

I once attended a lecture by Sir Martin Rees, the Astronomer Royal here in the UK, who said Astronomy was a simple subject. Many in the audience expressed surprise by this but he explained he thought real complexity was in biochemistry where there were so many interactions between molecules, membranes, cells and different tissues of the body. We might one day be able to understand the Universe’s beginnings and perhaps even how it will end, but he doubted if we would ever fully understand the multifariousness nature of biochemistry. Looking at the action of dexamethasone, I think, Martin Rees is right.

The immune system is complicated – beyond Martin Rees’s astronomy complicated. There’s probably more that scientists don’t understand about the immune system than they do. It’s evolved because there’s a whole world out there intent on killing you, one way or another, and the immune system is the ultimate defending army. A key part of the immune defence is inflammation, which is difficult to precisely define in immunological terms but in a nutshell, it’s a response against an irritant, anything from a splinter to a deadly virus, or indeed in some people, nutshells. Symptoms are erythema (redness), raised temperature, swelling and pain, which in the case of a splinter are external. Inflammation can also occur internally, such as with nut allergy for example, in which case it might become life-threatening.

Inflammation results in an increase in blood flow and an influx of a wide range immune system cells, commonly called white cells. Many of these cells were identified before their action was understood and so were named after their reaction to different stains under the microscope. And so you get, for example, basophils, neutrophils and eosinophils (eosin is a pink-red dye) as well as cells types, not named after microscopic dyes, such as mast cells, monocytes and macrophages. These cells come piling into the affray, like the proverbial Fifth Cavalry in a western movie to the sound of a bugle. Infected cells, of course, don’t have a bugle, instead they communicate with the immune system through small proteins called cytokines. There are around 80 known cytokines, including interferons, interleukins and TNF. TNF stands for tumour necrosis factor (although disregard the tumour part in the current context) and it’s one of the first cytokines produced to open surrounding capillaries to increase blood flow to allow more white cells in.

This plethora of cells and cytokines, together with other factors of the immune response such as a cascade of proteins called complement and, of course, antibodies, all react with each other making the complexity of the universe look trivial. Usually this biochemical and cellular mêlée is pretty good at seeing off infection and the inflammatory response plays an important role in that process. Don’t get the idea it’s all completely chaotic because the entire operation is controlled – or regulated in biochemistry-speak, chiefly through a structure in the cytoplasm called the “inflammasome”. Sometimes however, it all gets out of control, like a scrap between two schoolboys turning into a full scale riot. The communication proteins, the cytokines, go mad, attracting more immune cells, releasing more cytokine. It’s like the schoolboy fight going viral on social media, inviting anyone who wants a scrap from miles around. This has attained the name, cytokine storm and although it doesn’t have a precise definition, it became notorious in the 2006 clinal trial with TGN1412, which went horribly wrong. The term cytokine storm (or cytokine storm syndrome) actually originated earlier from a 1993 paper concerning adverse effects of organ transplants (1).

Now enter dexamethasone. In some cases, infection with SARS-CoV-2, the causative virus of Covid-19, sends the inflammatory response into overdrive, and that is the ultimate cause of fatality. Dexamethasone is a synthetic steroid of the type produced in the cortex (outer layer) of the adrenal gland, located just above the kidneys, and hence is called a corticosteroid. Corticosteroids find receptors in cells which initiate a chain of events involving RNA and DNA, down-regulating protein synthesis, damping down production of cytokinins and calming the inflammatory response like switching off social media in the middle of our metaphorical riot. Dexamethasone comprises a molecular skeleton common to all steroids, but with a fluorine atom added. It is a very potent anti-inflammatory drug, being around 25-times more potent than cortisol, for example. (Cortisol is more associated with the “fight-or-flight” response but it also has a role in moderating inflammation and is used as a hydrocortisone cream to treat eczema and dermatitis).

Dexamethasone is a well-establish drug used to treat a wide range of inflammatory disease including allergic responses, arthritis, lupus and some breathing disorders. In many ways it’s not surprising it helps in cases of severe SARS-CoV-2-induced inflammation and so unlike hydroxychloroquine, promoted so heavily at one point, it does seem to hold a lot of promise.

It is not however, an anti-viral, it does not inhibit infection, it is not a prophylactic, but it may save lives and for that some celebration is justified.

(1) Ferrara, J. L., Abhyankar, S. and Gilliland, D. G. (1993) Cytokine storm of graft-versus-host disease: a critical effector role for interleukin-1. Transplant. Proc. 25 1216–1217