Maradona and a Biochemist

I start this blog post with, “I don’t want to sound bitter but…” and then I’ll go on to probably do just that. The media is full of tributes to Diego Maradona; some call him a genius, some a deeply flawed legend. Screenshot 2020-11-30 at 11.23.29For me personally, he was a cocaine addict connected to the Mafia who had a talent for kicking a football – when he wasn’t cheating. Does that sound bitter? Well, actually it’s not Maradona specifically I have a problem with but more the celebrity-culture which worships its heroes no matter how damaged their persona becomes.

Some years ago I had the great privilege of meeting Fred Sanger. Who, you might ask? Fred Sanger was a British biochemist and one of only three people to receive two Nobel Prizes in Science; one in 1958 for his work on proteins and another in 1980 for the way DNA stores its code in a sequence of bases. Both proteins and the genetic base-code sequence have appeared repeatedly on this blog in respect to the battle against Covid-19. Sanger was one of the great pioneers of biochemistry, whose groundwork has already led to the saving and betterment of countless lives, and will undoubtedly continue to do so for many years to come. There is an institute in Cambridge named after him, the Wellcome Sanger Institute where the Nobel Laurette, John Sulston did so much on the Human Genome Project. The Wellcome Sanger Institute continues its work in Fred Sanger’s name to this day, including sequencing viral genetic codes.

Just before I met Fred Sanger at a ceremony in London in the mid 1990s, I visited the National Portrait Gallery and discovered a painting of the scientist by Paula MacArthur. I mentioned this to him and he wasn’t keen on it because he thought the way his eyes were painted made him look like a stereotypical mad scientist.  Judge for yourself, if you think we was right. 

He died in 2013. There were obituaries in some newspapers and BBC Radio-4 did a piece on him in the Last Word. But compare the outpouring of hero worship adorned on a household name because he was a cocaine addicted footballer and someone who saved the lives of thousands, if not millions and few have ever heard of. I admit I’m biased but I’m left with a feeling that much of humankind has its priorities rather confused.

Pfizer-BioNTech are making a mRNA vaccine, but what is that?

Covid-19 blog for the non-expert

Screenshot 2020-11-12 at 14.27.24The Pfizer-BioNTech vaccine for Covid-19 is all over the media. What hasn’t been in the headlines so much, is that this is a mRNA vaccine and if successful, it’ll be the first of its type. Some say they will not take it because it’s “rushed” but this misses the point that we are not making vaccines in the same way we did even a few years ago, and in fact mRNA vaccines have been in development for over three decades.

But what is a mRNA vaccine and why are they so important? In this blog post I try to explain.

The general principle behind a vaccine is that it contains something called an antigen – a piece of the target pathogen (or something resembling the pathogen) that the body recognises as being foreign. The antigen is such that it’s able to trigger an immune response, but without causing the disease itself. In a way, it fools the immune system an infection has occurred, thus sounding the bugle for attack. The attack in the case of the immune system is to produce antibodies that latch onto the antigen acting as beacons to white blood cells (called T-cells) which come along and destroy the pathogen. Key to vaccination is the fact that the immune system bares a grudge even bigger than in a Mafia war. The immune system, like the Corleone family, “goes to the mattresses” and patiently waits. If the antigen, this time in the form of the genuine pathogen, should reappear, then the immune system comes out of hiding and attacks before the disease has had a chance to fire a shot.

To understand how a mRNA vaccine brings the immune system into play against a pathogen, we first need a little biochemistry. As I’m sure you know, DNA contains a code in the form of base-pairs which our biochemistry translates into proteins. There is however, an intermediate step whereby the code in DNA is first translated and carried to the protein-making mechanisms within cells by messenger-RNA (mRNA). This is happening inside the cells of your body all the time, making new protein from enzymes to muscle to haemoglobin. A mRNA vaccine works on the principle that part of the viral DNA (or RNA in the case of SARS-CoV-2) is translated to mRNA in the laboratory. Following modification, this mRNA gets placed into a lipid nanoparticle. Before any Bill Gates conspiracy theorists get too excited, the lipid nanoparticle isn’t a microchip, it’s simply a lipid (fat) particle about a billionth of a meter in diameter (hence “nano”) that helps the mRNA cross biological membranes to enter cells. Once in the cell, the protein-making machinery translates mRNA into the viral antigen. In many ways, this is similar to what the virus does when it takes over a cell to make more copies of itself – biotherapeutic irony perhaps. Once the viral antigen is present, then the immune system triggers in the same way I’ve described above. It sounds simple, but there are complexities. The viral antigen, made from mRNA, is part of the spike protein on SARS-CoV-2, which latches onto the human cell to gain entry. It’s important to select mRNA for an appropriate part of the spike protein because the cunning virus coats much of it in sugar molecules to hide it from antibodies. Biochemistry is never that straightforward.

The likely starting point for mRNA vaccines appears to be 1989 when a San Diego biotech company called Viral Inc published the first paper*. In the early days, it was all done in test tubes (in vitro) or with animal models and the first human trials took place in the early 2000s. Despite some efforts, a successful mRNA vaccine has eluded researchers up until now, and so if the Pfizer-BioNTech vaccine is successful, it will be first in its class. Of course, no therapy is entirely risk free and some side effects have been reported over the years, but I’ll leave this to another time, if the vaccine gets approval. I should add however, that in respect to the current Covid-19 clinical trials with over 43,000 participants, the vaccine does look very safe.  The other issue with this type of vaccine, which the media has widely publicised, is the need for storage at -70℃ because of the inherently unstable nature of mRNA. That, however, is a logistical question and so I’ll not tackle that one here. Personally, I would say there’s some benefit in a more gradual roll-out, if for nothing else to allay the fears of some of the public on its safety. (However, -70℃ storage does cause problems in the developing world).

If this does turn out to be the first mRNA vaccine the implications are indeed profound. This is what’s known in the biotech industry jargon as a platform technology. As time goes on and we acquire more experience, then its perfectly possible a mRNA vaccine could be made within a few months to combat future pandemics – which will surely come sooner or later (let’s hope later). In fact, it’s not necessary to even isolate the virus in order to make the vaccine, it can be done from just knowing the sequence of the genetic code, which is routine these days. In the case of SARS-COV-2, the disease (Covid-19) was first reported in December 2019, and by February 2020 the 26,000 – 32,000 RNA code sequence went round the world via the internet. The rate limiting step therefore, will likely not be the vaccine itself but the safety tests and clinical trials.

And finally a note of extra optimism. If Pfizer-BioNTech stalls then other vaccines are coming through apace and I suspect announcements will appear soon. Some of these will be other mRNA vaccines and others will be vector types. And, as some have asked, would I take it? You bet – I’d be first in line if I could be.

We have likened the pandemic to wartime and in many ways that analogy holds true, because it’s times of the greatest threat to humankind that we seem to make our most profound advances.

* R.W. Malone, P.L. Felgner, I.M. Verma, Proc. Natl. Acad. Sci. U.S.A., 86 (1989), pp. 6077-6081. 

90% effective Covid-19 vaccine

The headlines are jubilant with “Covid-19” vaccine 90% effective. As one of those skeptical scientists, I’m in a difficult position because I don’t want to dampen any hope, but at the same time it’s worth questioning the headline to see what’s really behind it.

The announcement was from Pfizer and BioNTech, and the media are pretty much echoing the contents of their press statement. I’ve blogged previously on science by press statement, rather than relying on peer reviewed literature and so this should should be the first warning bell. 

Many might assume that 90% effective means that on average in a population of 100 people, 10 will get full blown Covid-19 and 90 will be symptomless and not be carriers. This is however, a simplistic interpretation because effectiveness can be calculated based upon (1) ability to prevent infection (2) ability to prevent the disease, although individuals are still infected, and (3) ability to prevent serious disease. There is also the issue of how effective a vaccine reduces the infection rate to others, generally known as herd immunity. (This is, incidentally, the genuine type of herd immunity associated with vaccines, not the idea that we go out and get the disease, which has pretty much now been debunked).

The Pfizer-BioNTech vaccine is of the messenger-RNA type, which if effective, will be the first of its type. Although the science is sound, this class of vaccine does not have a track record, as yet. Looking any deeper at present is difficult without the full peer reviewed publication and all we have to go on is a press release. I’ll nevertheless, end by saying a vaccine even with a low rate of effectiveness could make a huge difference, and so we should very optimistic. Nevertheless, let’s temper the optimism with a little realism and wait and see how things develop. 

New Covid-19 tests

A Covid-19 blog post for the non-expert

Screenshot 2020-11-04 at 11.34.43We’ve been hearing how the UK government wants to return to normal life under its £100bn Operation Moonshot Covid-19 testing programme. Headlines such as those in the Daily Mail have proclaimed “Prospect’ of 10-minute ‘rapid turnaround’ Covid tests” but others including the BMJ are not so sure. I thought, therefore, the time was right to look at the emerging Covid-19 tests Operation Moonshot is pinning its hopes on, and see how they work. 

In a previous blog post I looked at two Covid-19 test techniques, one which detected the presence of the virus itself and another which looked for the presence of an antibody to the virus in a blood sample. Scientists don’t hang around during a pandemic and two new tests are coming into play, known as the Lateral Flow Test (LFT) and Loop-Mediated Isothermal Amplification, or a LAMP. In this post, I will look at what LFT and LAMP are, how they work, and what are their advantages and potential shortcomings.

Some media reports have given confusing accounts of these new tests, probably because they are based on existing technology and the technical terms describing them are very similar. In an attempt to avoid confusion here, I will first provide definitions of the four most important technical terms.

Antigen – this is what’s being tested. With Covid-19 the antigen is a protein on the SARS-CoV-2 virus.

Antibody – is a protein associated with the immune system which locks on to an antigen such one on the SARS-CoV-2 virus. Since the virus has many proteins, the body will raise a range of different antibodies, each sticking onto its own viral antigen.

Monoclonal antibody – this is an antibody made in the laboratory that targets one specific antigen. All the antibody molecules are clones of one another, with essentially the same molecular structure, which is where “monoclonal” gets its name.

RNA – Ribonucleic acid is the genetic material inside SARS-CoV-2. (Some viruses have DNA and others, such as SARS-CoV-2, have RNA). SARS-CoV-2 RNA comprises a chain of around 30,000 nucleic acids (known as bases) which codes for viral proteins.

The current gold standard test for Covid-19 is the Polymerase Chain Reaction, or PCR test (see previous blog post). In a nutshell, the method replicates SARS-CoV-2 RNA many times over, generating enough material for it to be reliably detected. PCR is used routinely in molecular biology and once we know the code-sequence of the genetic material, scientists can usually generate a PCR test within a few weeks. Running a PCR test however, is not straightforward and requires laboratory conditions and skilled analysts. In particular, PCR has multiple heating and cooling cycles to promote the required chemical reactions, and the reagents, being relatively complex, demand continuous preparation. Loop-Mediated Isothermal Amplification (LAMP) is still a PCR method, but operates at a single temperature (60-65 ºC – hence “isothermal”) and does not require the same fresh reagents. These, and other modifications, reduces the time to carry out a LAMP test to as little as 15-minutes, or an hour in the case of Covid-19.  The test also has the potential to be run on a bench-top type device rather than requiring sophisticated laboratory conditions. While LAMP sounds like a great leap forward, it’s nevertheless a recent development in Covid-19 testing and so we have to remain cautious to its reliability. It no doubt has great potential but the traditional PCR will remain the gold standard, at least for the time being.

While LAMP detects viral RNA, LFT detects viral protein. It does this using monoclonal antibodies, which is probably the source of confusion between LFT and an “antibody test”. So to be clear, there is a test which looks for the presence of an antibody to SARS-CoV-2 in blood that shows if you’ve contracted the disease sometime in the recent past. LFT does not do this, it detects the presence of the virus itself.  LFT technology has been around for some time and it’s used in home pregnancy testing kits. LFT is divided into two types known as sandwich and competitive. In the sandwich type, lines appear showing a positive test, in the competitive type the absence of lines indicate a positive test. The LFT for Covid-19 is the sandwich variety. The device comprises a flat plastic plate (see image), with a well at one end and a panel where lines appear if the test is positive. A sample from the nose or throat is placed into the well, where it migrates along the plate by capillary action. It reaches a line of monoclonal antibodies (made to recognise a specific SARS-CoV-2 antigen) which are attached onto a tiny particle, typically made of gold or carbon (the antibody-particle complex is known as a conjugate). We classify the particles as nanoparticles because they are about a billionth of a meter in diameter.  The conjugate, along with the bound SARS-CoV-2 antigen, continues to migrate along the plate by capillary action until it reaches another line of monoclonal antibodies. These monoclonal antibodies don’t recognise the SARS-CoV-2 antigen however, but the monoclonal antibody conjugate. (You can see where things get confusing because the antibody conjugate is now essentially an antigen to the second monoclonal antibody). As the conjugate binds to the second line of monoclonal antibodies, they hold the particles upwards forming a visible coloured band – that is a positive test. Depending upon the test, there may be more than one line indicating a positive test and an indicator line showing the device is working correctly.

LFTs are tricky things to develop, which is why it’s taken until now for them to appear. Appropriate monoclonal antibody production is not straightforward and even variables such as capillary flow-rate within the device can affect reliability. The first LFTs have however, passed their assessment and should be available soon. They have the advantage that the test is complete in about 10-15 minutes and do not need a sophisticated laboratory to carry them out. Don’t get too excited however, because the announcement by the Prime Minister may have been a little over optimistic, in that it still requires some expertise and you are unlikely to be able to do them at home. LFTs have a higher rate of false positives than RNA-based methods and so a positive result may necessitate confirmation via PCR or LAMP. Nevertheless, with appropriate training LFTs should have a major impact on test and trace.

For both LAMP and LFT the one huge advantage is not so much the tests themselves, rather than the impact on logistics. The biggest problem we’ve had in the UK has been getting test results back within an appropriate time frame, which sparked arguments over government statistics on testing capacity versus actual tests returned. Both LAMP and LFT however, have the potential of testing while-U-wait. And of course, tests continue to evolve and perhaps the next big step might be a simple saliva test.

And I will leave this post with some optimism flavoured with realism. Despite politicians saying no one could have predicted Covid-19, in truth it was inevitable sooner or later.  Equally so, is the occurrence of another pandemic sometime in the future. I hope that the words of Friedrich Hegal don’t come true, “we learn from history that we do not learn from history” and we retain Covid-19 testing capability ready to rapidly adapt to a new virus. Fingers crossed.

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

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.


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.