Category Archives: science

Monkeypox 4: SitRep

My latest update on the background to the monkeypox scare.

UK Situation

  1. As of the time of writing the UK has identified 71 cases. [4]
  2. The vast majority of identified cases are isolating at home and do not require hospital admission. [1]
  3. The closest contacts of confirmed cases are being offered the smallpox vaccine. This is the so-called “ring vaccination”. [1]
  4. These closest contacts – anyone who has had direct or household contact with a confirmed case – are being told to isolate for 21 days (ie. the longest incubation period). [1,2]
  5. The same high-risk contacts are advised to avoid immunosuppressed people, pregnant women and children under 12, as these groups are more vulnerable to serious infections. [1]
  6. Contacts are being asked to provide their details for contact tracing. [2]
  7. Sexual Health Clinics are still open for business, but are reported to be doing telephone triage. [4]

Global Situation

  1. More than 131 confirmed cases are being investigated in 15 countries. [4]
  2. More than half the cases are in Spain and Portugal. [1]
  3. The WHO says the outbreak is “containable” and is providing advice to countries on how to tackle the situation. [4]
  4. There seems to be some scaremongering (emanating from the NHS?) that you can be infected by eating meat. [5] Frankly, in my view, this is nonsense. Yes, in theory it may be possible to catch monkeypox from eating undercooked meat from an infected animal – which almost certainly means bushmeat. The chances of a food animal getting monkeypox and getting into the human food chain has to be vanishingly small.

Epidemiology

  1. Genetic analysis of three monkeypox viruses from the outbreak have found it closely matches the virus that spread from Nigeria in 2018 and 2019. [1]
  2. Monkeypox is less transmissible than SARS-CoV-2; the original Wuhan strain had an R0 of about 2.5. Monkeypox has had R0 under 1 in past outbreaks. [3]
  3. A high fraction of SARS-CoV-2 transmission, maybe half(?), comes from people who aren’t showing symptoms at the time; whereas monkeypox transmission before symptom onset seems to be relatively rare, if it happens at all. [3]
  4. The fact that very little if any monkeypox transmission occurs without symptoms means that if people start isolating once they begin to feel sick, they should be able to prevent almost all onward transmission. [3]
  5. Moreover monkeypox spreads slowly (symptom onset is 5-21 days from infection) compared with Covid (symptom onset 1-4 days). [4]
  6. This long incubation time gives contact tracers more time to identify contacts and set up ring vaccination. [3]
  7. Putting that all together suggests that cases are unlikely to rapidly increase and get out of control. [3]
  8. Studies suggest that a Belgian man contracted the virus on a recent trip to Portugal. [1]
  9. The pattern of the outbreak suggests the virus is spreading primarily through sexual networks. [1]
  10. Super-spreader events may have boosted the outbreak since it arrived in Europe. [1] This could be around the rave scene in Spain; a Gay Pride event in the Canary Islands is apparently being investigated. [6]
  11. Cases are being found which have no identified contact with west Africa. [2]
  12. Scientists have a big challenge as they currently do not know how many unreported cases there are; they’re currently seeing only the tip of the iceberg. [2]

References

[1] https://www.theguardian.com/world/2022/may/22/monkeypox-uk-health-security-agency-to-announce-more-cases
[2] https://www.bbc.co.uk/news/uk-61546480
[3] https://threadreaderapp.com/thread/1528450298901155841.html
[4] https://www.bbc.co.uk/news/health-61570562
[5] https://www.thisislocallondon.co.uk/news/national/uk-today/20159989.monkeypox-nhs-issues-warning-anyone-eats-meat-uk-cases-rise/
[6] https://www.thisislocallondon.co.uk/news/national/uk-today/20160206.monkeypox-outbreak-sex-raves-spain-belgium-may-blame/

Monkeypox 3: Viral Replication

Following up on my earlier comment about monkeypox being a DNA virus and different to SARS-Cov-2 (which is an RNA virus), I figured a bit more (very low tech) explanation may help. First off some very simple explanations. (Don’t worry if you don’t know what any of these things are; just think of them as “stuff” or “method”.)

Virus. A pseudo-cell basically composed of some minimal amount of genetic code (DNA or RNA) encapsulated in a lipid (ie. fatty) membrane. It is unable to reproduce on it’s own and has to hijack the machinery of a host cell to make more copies of itself.

DNA. This is the chemical code which holds all our genes. It is composed of the “double helix” of two strands of DNA twined round each other – think of two intertwined springs. In order for the cell machinery to read the text of the DNA the two strands have to be zipped apart and then afterwards zipped back together. Think of this as a whole jumbled box of knitting patterns

RNA. This is essentially a short piece of code created from a piece of a single strand of DNA; it typically provides the instructions for making a single protein. Think of it as a single knitting pattern, extracted from that box of patterns.

Transcription is the process of unzipping the DNA and copying it to make the RNA; this happens only in the cell nucleus (the strong box which holds the DNA). As in all copying, errors can creep in. So the machinery in the cell nucleus contains a proofreading function which finds the errors and discards the overwhelming majority of them.

There are essentially two types of virus, characterised by how they store their genetic information: DNA viruses and RNA viruses.

DNA viruses (for example, monkeypox) have to insert their genetic code, held as DNA, into the cell nucleus, as that’s the only place where it can be transcribed into RNA. So transcription errors are booted out by the proofreading function and mutation happens very rarely.

RNA viruses (for example, SARS-Cov-2 and flu) don’t have DNA; their genetic code is held as RNA. RNA doesn’t use the cell nucleus for transcription and hence can’t take advantage of the proofreading function. So transcription errors don’t get weeded out and mutations happen very frequently.

The process of using RNA as a blueprint to make proteins etc. is called translation.

And that is an incredibly simplified description of the processes. The details are hideously complex, so hideously complex one can quite see why some people find it hard to believe this has arisen through evolution.


Here’s an equally very simplified diagram (what I drew) of the processes.

Very basic cell process and how it’s used by viruses
Click the image for a larger view

So that hopefully shows why Covid-19 is dangerous, why we need a new flu vaccine every year, and why we hopefully don’t need to be too worried about monkeypox.

Monthly Links

So here’s this month’s selection of links to items you missed the first time and will wish you hadn’t. And of course it’s the usual mixed bag, starting with the hard stuff.


Science, Technology, Natural World

Researchers think they’ve worked out the origin date for the ancient Antikythera mechanism – although they don’t all agree. I find this whole artefact just mind-boggling.

Antikythera Mechanism

A different set of researchers think they’ve uncovered the fossil remains of a dinosaur and some other creatures killed and entombed on the actual day the Yacatan asteroid hit 66m years ago.

First humans and animals, then trees, and now it seems mushrooms talk to each other.


Health, Medicine

Derek Lowe, our favourite pharmaceutical chemist, looks at why phenylephrine is useless as a decongestant.

Vagina Obscura, a new book by Rachel Gross, reviews the biology of female organs, including the vagina, uterus and ovaries, and how scientists are filling in the gaps in knowledge.

Maybe sometime, maybe soon, medicine will be able to “fix” menstruation.

Here’s a young lady with a very rare and disturbing visual condition.


Sexuality

If you fancy a trip to Italy you have until 15 January next year to see the current exhibition of Pompeii’s sex scenes and erotica.


Environment

It seems that peregrine falcons have have made my local (Ealing) hospital their base – well the appalling building has to be good for something!

Giant Orchid (Himantoglossum robertianum)

Meanwhile in Oxfordshire, Giant Orchids (Himantoglossum robertianum) have been found growing wild for the first time in the UK.

It’s being reported that new government rules will provide extra protection for adders and slowworms; which will be good if it happens.


History, Archaeology, Anthropology

A farmer in Gaza has uncovered a 4,500-year-old statue of Canaanite goddess.

Archaeologists at Uruk in Iraq have unearthed, and are trying to recover, an ancient Sumerian riverboat.

Meanwhile in the Assam region of India archaeologists have found more than a few ancient and mysterious giant stone jars.

Still in the ancient world, the grave has been found of an ancient Peruvian who was buried with tools for cranial surgery.

Nearer to home, and to our time, Dr Eleanor Janega, of Going Medieval, looks at the old moneymaking trick of selling indulgences.

Eleanor Janega also writes about a favourite saint: St Sebastian.

In 1580 there was an earthquake, with an epicentre in the Dover Straits, which damaged London’s (Old) St Paul’s Cathedral; needless to say this spawned a flurry of pamphlets – the Facebook of their day.

And almost right up to date, IanVisits looks at a new exhibition about the history of the UK’s postcodes.


London

On another track, IanVisits takes a look behind the scenes at the huge upgrade project nearing completion at London’s Bank Underground station.


Lifestyle, Personal Development, Beliefs

Dungeness (Image: IanVisits)

Oh no! Not again! Yet another item from IanVisits! This time he takes a day trip to Hythe and Dungeness – to explore both and also ride on the Romney, Hythe & Dymchurch Railway.


Shock, Horror, Humour, Wow!

And finally for this month Tom Lamont in the Guardian takes a look at a day in the life of (almost) every vending machine in the world. [LONG READ]



April Quiz Answers

OK, so here are the answers to this month’s quiz questions. All should be able to be easily verified online.

April Quiz Questions: Physical Science

  1. How much water is there on Earth per human being? Roughly 175 trillion litres ± 15%
  2. What was the name of the first, Russian, man-made satellite? Sputnik I
  3. How many internal reflections of light take place in the formation of a primary rainbow? Two
  4. Roughly how long does it take for the sun’s light to reach Earth? Eight minutes
  5. Which Russian chemist published the first widely recognised Periodic Table? Dmitri Mendeleev

Answers were correct when questions were compiled in late 2021.

April Quiz Questions

This year we’re beginning each month with five pub quiz style questions, with a different subject each month. They’re not difficult, but it is unlikely everyone will know all the answers, so hopefully you’ll learn something new, as well as have a bit of fun.

April Quiz Questions: Physical Science

  1. How much water is there on Earth per human being?
  2. What was the name of the first, Russian, man-made satellite?
  3. How many internal reflections of light take place in the formation of a primary rainbow?
  4. Roughly how long does it take for the sun’s light to reach Earth?
  5. Which Russian chemist published the first widely recognised Periodic Table?

Answers will be posted in 3 weeks time.

You May Have Missed …

Here’s this month’s selection of links to items you may have missed.


Science, Technology, Natural World

Would you like to fly round the moon? If so, then NASA are giving away free flights for your name on their upcoming Artemis I mission.

Image NASA. Click for larger view.

Cosmologist Katie Mack talks about spotting and combating physics falsehoods online.

Researchers have found the huge and mysterious Hiawatha crater in Greenland to be 58 million years old.

Zoologist Lucy Cooke is waging war on Darwin’s prevailing view of the dominance of males and their benefit from promiscuity. Two articles, the first from the Guardian, the second from New Scientist [£££].

Palaeontologists have described a ten-limbed ancestor of modern octopuses, and named it after Joe Biden.

The largest ever family tree of humanity reveals our species’ history, where we originated and how we spread across the world. [£££]

The Eden Project in Cornwall have succeeded in getting their nutmeg tree to fruit for the first time since planting in 2001.

Image Eden Project

There’s a new drive to produce the red dye cochineal industrially without having to squash thousands of insects.


Health, Medicine

Here’s an interesting article about the work to identify which flu strains to put in this year’s vaccine – and some of the people who spend their lives trying to spot the emerging strains. [LONG READ]

And now another pair of articles, this time looking at the long-term, but haphazard, effect of Epstein-Barr virus, which is responsible for glandular fever. Again the first is from the Guardian, and the second from The Atlantic. [LONG READS]


Environment

One American academic has demonstrated that by just redesigning both homes and industrial processes it is possible to use almost no external power – and overall it is the cheapest solution! And yes, he has actually done it, and lives in the house.

An iconoclastic letter in New Scientist suggesting that as we’ve paved over much of our world we would do well to rip it up and plant trees instead. [£££]


History, Archaeology, Anthropology

1700 years ago a Roman boat sank in shallow waters just off Mallorca on the Spanish coast. Archaeologists are now retrieving the amazingly well preserved cargo.

In what shouldn’t be a surprise the teams restoring Notre Dame in Paris have found early tombs and a lead sarcophagus under the cathedral’s floor.

Medievalist Dr Eleanor Janega goes looking at non-written communication in Norwich.

And here’s Eleanor Janega again, this time looking at medieval attitudes to semen and female sexuality.

Despite our misogynistic view, there were female composers in the Renaissance. Now more of the ground-breaking work of Maddalena Casulana has been pieced together and performed.

Now not quite up to date … An expedition has found the surprisingly intact wreck of Ernest Shackleton’s ship Endurance off coast of Antarctica.

Image Falklands Maritime Heritage Trust/NatGeo

London

IanVisits takes an opportunity for a look inside London’s Ukrainian Cathedral.

IanVisits has also managed a sneak preview of London’s new Elizabeth line railway (aka. Crossrail).


Lifestyle, Personal Development, Beliefs

Comedian David Baddiel talks about his life-long love of cats. [LONG READ]

Meanwhile a forensic pathologist wishes that a legacy of Covid lockdown is that we change the way we talk about death.

Japan may also need a new narrative as their so-called “killing stone” has split in two, releasing superstition and allegedly a nine-tailed fox. In two stories there’s the usual media-hyped look in the Guardian; however the Japanese think the media have the story wrong as Hiroko Yoda writes on Twitter.

And finally one of the great British train journeys which is high on my bucket list … the longest journey on a single train from Aberdeen to Penzance. I actually want to do Thurso/Wick to Penzance, with Kyle of Lochalsh, Fort William and Mallaig thrown in. I’m not holding my breath in the hope of ever doing it.



Monthly Links

Here are my monthly links to items you may have missed, but didn’t know you didn’t want to.


Science, Technology, Natural World

Despite extensive studies, scientists still can’t agree on Chernobyl’s impact on wildlife. [LONG READ]

Try putting your ear to the ground … scientists are discovering that life in the soil is unexpectedly noisy. [LONG READ]

So can melting permafrost release ancient pathogenic microbes? [£££££]

It seems that magpies care! They’ve outwitted scientists by helping each other remove tracking devices.

But an even bigger problem … Do birds have language, at least in a way we would recognise? [LONG READ]

Finally in this section … a very short piece on the curiosities that are Britain’s pipefish.


Health, Medicine

A very worrying look at how the GP’s job has changed in the last 30 years. [LONG READ]

Researchers are discovering that bones are a lot more than bits of scaffolding.

How does what you eat affect your sleep, and vice versa?

What happens when depression collides with the menopause and perimenopause? [LONG READ]

Oh dear! Apparently everything we thought we knew about posture is wrong. [LONG READ] [£££££]

At last some good news … Apparently dark chocolate (at least in moderation) is good for your health, and for the microbiome.


Sexuality

So here’s a relationship therapist on how to have better sex.


Environment

Cranes were reintroduced to Britain in the late 1970s, and now they’ve had their best year for 400 years.


History, Archaeology, Anthropology

A fossil of a large pterosaur has been found on the Isle of Skye.

Recent research is suggesting that the meteor which killed off the dinosaurs fell to Earth in the Spring.

Palaeontologists are coming to the conclusion that the extinction of the Neanderthals was not caused by the brutal domination of Homo sapiens.

Remains of woolly mammoth, and some other Ice Age remains have been found in Devon.

Some important prehistoric chalk sculptures, thought to be childhood artefacts, have been uncovered in Yorkshire.

Trousers are one of those wonders of civilisation in that their construction is not overtly simple or logical. So it’s astonishing that the oldest known “pants” seem to have originated in Asia, and a pair is survived around 3000 years. And the weaving is absolutely amazing.

Back at home, Museum of London archaeologists have found an 8m Roman mosaic floor in Southwark, just south of the Thames.

Here’s our favourite Medieval Historian on the power and influence of women in medieval times. [LONG READ]

Still with the medieval, researchers have found what appears to be the earliest known account of ball lightning in England, dating from 1195.


London

Just one London item this month … the Museum of London will close this December for 4 years, while it moves to its new home in the old Smithfield Market.


Lifestyle, Personal Development, Beliefs

And finally in this issue … British Naturism has, again, pointed out that it is not illegal to go naked in your back garden, and that it is not a matter for the police.


Monthly Links

Here be my monthly collection of links you may have missed …


Science, Technology, Natural World

Herman Hollerith’s Tabulating Machine was built for the 1890 US census, and led to the first data processing company (which was to become IBM).

So just why did cat-like animals disappear from North America for 6 million years? [£££]

The curious ways of the fishing cats are being revealed by scientists.

Two stories on the discovery of new to science, or rare, species. First a variety of previously undescribed plants. And secondly the hunt for the saloa an almost never seen Asian antelope.


Health, Medicine

A review of the book Recovery: The Lost Art of Convalescence by Dr Gavin Francis. It turns out that proper convalescence is a hugely key stage in getting better.

Worldwide there are a very small number of people who cannot forget anything. One young woman describes what it is like to be medical exception.


Sexuality

It turns out that female dolphins have a clitoris very much like humans, which suggests they too experience sexual pleasure.


Environment

Electric cars and the like may be the way forward, but there are huge problems with their lithium batteries, especially at the end of their lives. [LONG READ]


Art, Literature, Language

There is undoubtedly a joy in rediscovering and reclaiming long-lost words, as Susie Dent extols.

So why are ministers (and educationalists) so obsessed with teaching children to read using phonics?


History, Archaeology, Anthropology

Archaeologists have suggested that some ancient metal tubes unearthed over 100 years ago might be the oldest surviving drinking straws.

The body of Egyptian pharaoh Amenhotep I is so well preserved that after 3500 years it is still able to revel much about the man, thanks to modern scanning and that it has never been unwrapped.

The remains of a huge Roman fort, built on the orders of Emperor Caligula, has been discovered near Amsterdam.

A huge mosaic floor has been found in a Roman villa in Rutland, and was featured on the BBC’s Digging for Britain.

New research is suggesting that medieval warhorses no bigger than modern-day ponies, and not huge carthorses as we thought.


London

IanVisits discovers the unexpected history of the stone benches outside Kensington’s museums.


Lifestyle, Personal Development, Beliefs

Another of our favourite bloggers, Diamond Geezer, takes a look at the curiosities of sleep.

Meanwhile Caroline’s Miscellany discovers the old tradition of Molly dances.


Shock, Horror, Humour, Wow!

There’s sad news as the landmine-hunting hero rat Magawa has died at the age of 8 after a stellar career.

And finally something to bring joy … here’s a video of an amazing automated LEGO factory that builds miniature log cabins from cucumbers. Enjoy …


Monthly Links

So here for the last time in 2021 is my compilation of links you may have missed the first time.


Science, Technology, Natural World

The simplicity of Occam’s Razor was seen by a medieval monk. [£££]

Chemists are finally beginning to get to the bottom of marijuana’s skunky scent.

It has become recognised that plants are interconnected via a network of underground fungi, and now there’s a project trying to map that network.

Scientists investigating a restored coral reef in Indonesia have recorded many sounds (not yet tagged to specific species) to a backing of snapping shrimp.

Still with fish, the tiny Batman River Loach* (Paraschistura chrysicristinae, above), long thought extinct, has been rediscovered in SE Turkey. [* It’s named after the Batman River!]

Meanwhile back on dry land, scientists working on the Indonesian island of Sulawesi have identified 14 previously unknown species of shrew.

Between 2014 and 2018 there were many cats found dead especially around south London, and the perpetrator was long thought to be some warp-headed human. However research by the Royal Veterinary College has shown the cats died due to a variety of causes and were subsequently scavenged by foxes. This had long been suspected by some of us, despite being vilified by vigilante groups.


Art, Literature, Language

Artists have long been doing battle with the censor (in many forms) over the depiction of pubic hair and nudity, and photography is no different. [LONG READ]

Those much-loved kids TV characters The Clangers were not a anodyne as we all thought.

Here’s a video about an incredibly fragile instrument: the Glass Armonica, invented by Benjamin Franklin. [VIDEO]

Writer Alan Garner talks about books that have been important to him.

This lady makes a living folding paper: it is sculptural, absolutely incredible and way beyond origami. [VIDEO]


History, Archaeology, Anthropology

Palaeontologists have found some ancient footprints which suggest that there were at least two hominid species living alongside each other in East Africa around 3.6m years ago.

Really quite modern by comparison, a 5700-year-old tomb in the Cotswolds has revealed a surprising family history of the occupants.

Around 700 years later a start was made building Stonehenge, the subject of a 2022 exhibition at the British Museum.

There is now evidence that some while after the building of Stonehenge there was a mass migration into Britain which accounts for around half of British peoples’ genetic make-up.

Still in Britain, and gradually coming closer to our time, archaeologists believe they have now found physical evidence of Roman crucifixion in Cambridgeshire.

Lastly in this section, Historic England present highlights of captivating historic site listed in 2021. [LONG READ]


London

London blogger Diamond Geezer reminds us quite how big London actually is. Well it needs to be to accommodate almost 10m people!


Food, Drink

Clare Finney in the Guardian explodes some of the biggest myths about cheese.

And in a similar vein (ouch!) Alison George in New Scientist looks at how microbes create the flavours of cheese. [£££]


Lifestyle, Personal Development, Beliefs

It seems that in these plague-ridden times there’s a thriving cottage industry in dream analysis.

And finally, I leave you with the magical and restful miniature world of the terrarium.


Monthly Links

OK, so here we go with this month’s link to items you may have missed …


Science, Technology, Natural World

I don’t understand why it is that many people are afraid of spiders, because they’re much smarter than we realise.

Do you know what a wasp smells like? No, nor me. But scientists are now beginning to work it out. Oh and Vespula germanica used in tis study is one of the two common wasp specie in the UK.

While on Hymenoptera, apparently the old undisturbed woodland at Blenheim in Oxfordshire has colonies of heirs of the long lost British Honeybee. At first I found this so unlikely I had to check it wasn’t 1 April.

Researchers are now beginning to eavesdrop on embryonic/foetal animals to understand how they respond to sound. We’d known for some time that there was communication between between adults and embryos, but mostly not what it meant.


Health, Medicine

Apparently the human papillomavirus (HPV) vaccine has cut the rate of cervical cancer by around 87%.

In other research, medics are now trying to understand “immune amnesia”, where a disease (usually a virus) turns off or supresses the immune system even after recovery. Measles is especially good at this, and it could go some way to explaining why some recover especially slowly from some diseases (Covid and glandular fever come to mind). [LONG READ]


Sexuality

So here’s yet another look at ways to achieve great sex. Doesn’t it all come down to what works for you?


Environment

A new way of looking at climate change has been developed: a map showing where carbon needs to stay in nature.

As Jane Dunford in the Guardian finds out, beavers are having a significant impact on the environment where they’ve been reintroduced. Oh and just get their names!

Apparently Europe has lost almost 250 million House Sparrows in the last 40 years – that’s roughly the current UK population of sparrows every year for 40 years. Many other species are doing this badly as well, although some birds of prey are doing well.


Art, Literature, Language

The origins of “Transeurasian” languages appears to have been traced to traced to Neolithic millet farmers in NE China.


History, Archaeology, Anthropology

Glass is an everyday substance for us, but there’s still a puzzle over where it was first discovered.

As well as having high class glass, Ancient Egypt had sacred baboons although they are not indigenous to the area. Where and how were they acquired? [£££] [LONG READ]

There are a lot of large pits near Stonehenge, and it turns out they’re Neolithic and man-made, rather than natural.

Las Vegas is nothing new: the ancient Romans had a party town all their own but it is now submerged in the sea

Nearer at home Roman Britain is still producing a stream of archaeological discoveries.

The largest hoard of Anglo-Saxon gold coins to be found in England has been declared treasure at an inquest.

Meanwhile historians are revealing the secrets of the tomb of the Black Prince in Canterbury Cathedral

When an antiques dealer bought a dirty wooden bird little did he realise to has and important artefact from the marriage of Henry VIII and Anne Boleyn.

Still with the Tudors, some unsuspected, and almost pristine wall paintings have been uncovered at Calverley Old Hall in Yorkshire.

So just why is it that the Gunpowder Plot has continued to be remembered and celebrated for over 400 years?

You think we (in the UK) have a corrupt government? It has nothing on the parliaments of the 18th century. [£££]


Lifestyle, Personal Development, Beliefs

Why is body hair still a no-no, especially in the world of dance?

And now three items on modern witchcraft. First from a Scottish hedge-witch. Second on the myth of the Halloween Hag. Lastly on the witch as a modern feminist icon.

And stay right there as we’ll end on the esoteric … The sentimental celluloid fairy is essentially a product of Disney as fairies were originally rather malevolent.


Have a good Christmas everyone; the Fates permitting we’ll be back with the next edition to enliven those dreary days between Christmas and New Year.