history, links, medical, natural history, science

Monthly Links

Our monthly collection of links to items you may have missed. It’s the usual miscellaneous collection.

Science, Technology, Natural World

That big explosive volcano in Tonga is still surprisngly intact although the caldera looks to be a huge hole.

On the curiosity of organ pipes apparently violating a rule of sound.

And now for something completely different, for which I see many new applications … Apparently female mice release banana-scented urine when pregnant to deter males. [£££]

You all know by now that wasps are one of my favourite subjects. Here are two articles from Seirian Sumner, who’s book on wasps Endless Forms is out this week. First a piece in the Observer Magazine, and then her take on five facts about the gruesomeness of solitary wasps. [Prof. Seirian Sumner is the academic who runs the Big Wasp Survey which I’ve contributed to over the last several years.]

Back to more mundane(?) animals, researchers have been looking at the domestication of the horse. [LONG READ]

Jackdaws are democratic and use noise to make decisions.

Health, Medicine

Medicine in particular, and all of us in general, need to reassess and update our knowledge and the history of the female body.

Having said which, here’s a piece on how sex affects our immune systems and our brains.

Sexuality

The UK’s Office for National Statistics has found that for the first time ever over 10% of young women identify as “lesbian, gay, bisexual or other”.

Social Sciences, Business, Law

On the issues around making conscious software, why we should an why we shouldn’t. [£££]

Art, Literature, Language, Music

Historian and mythographer Marina Warner visits the British Museum’s exhibition Feminine Power: The Divine to the Demonic, which explores the volcanic power of goddess cults.

History, Archaeology, Anthropology

New research on human coprolites reveals parasite eggs which suggest the builders of Stonehenge ate undercooked offal.

Workers at Osuna in southern Spain have uncovered an important, and hitherto unknown, Phoenician necropolis.

The Romans used silphium for just about everything: perfume, medicine, aphrodisiac and condiment. But in trying to cultivate it and increase yields they killed it.

Researchers have managed to successfully sequence the genome of a Pompeii victim. Turns out he was “Italian”!

Melting ice on an alpine pass in Norway has revealed a 1500-year-old shoe amongst many other artefacts.

The Amazon appears to be full of lost pre-Columbian settlements and urban sprawl.

A short item on Ragged Schools, and especially the one for girls in Hastings.

Modern purple dyes were invented in London in the 1850s and initially manufactured close to where I now live.

Two short articles on the eccentricity that is Winchelsea Beach in Sussex.

IanVisits goes to look at the de Haviland Aircraft Museum on the edge of North London.

Lifestyle, Personal Development, Beliefs

Now here’s a real first world problem if ever there was one … should we embrace a cashless society? But one thing the author overlooks is that in a cashless society everything becomes electronic – which is fine until there’s a computer or power outage (accidental or sabotage).

Our favourite zen master, Brad Warner, is another one with a new book coming out.

And finally … they’re generally hated, but we should really like them: stinging nettles. Eat them, make fabric from them, or just let them be to grow butterflies.

medical

Monkeypox 5. Two Important Articles

I’m not going to provide another round-up of news on monkeypox; I’ll do that when there is some useful news.

However there are two important articles in the last couple of days which I want to draw attention to.

How to tell if your rash is monkeypox? See this from the BBC: Got a new rash? Monkeypox or something else?

Secondly many experts are saying that monkeypox is actually not what we should be worrying about; there are far more dangerous diseases waiting to pounce. See: Monkeypox isn’t the disease we should be worried about.

medical, 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/

medical, science

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.

medical

Monkeypox 2. More Background

Here’s some more background on Monkeypox, following my item from Friday.

Let’s be very clear, right up front … We are not witnessing another Covid, and we’re not days away from lockdowns to contain the spread of monkeypox. However, this is an unusual and unprecedented monkeypox outbreak which has taken scientists who specialise in the disease by surprise – and that’s always a concern. [4]

Spread & Behaviour

  1. Monkeypox is so rare that that most doctors will never see a case in their lifetimes. [2]
  2. Monkeypox is not known to spread easily between people, although cases emerging in several countries at once, and signs of transmission in the community is striking. [1,2]
  3. However the UKHSA saying the risk to the population “remains low”. [1]
  4. The US Centers for Disease Control (CDC) states: “Human-to-human transmission is thought to occur primarily through large respiratory droplets. Respiratory droplets generally cannot travel more than a few feet, so prolonged face-to-face contact is required.” [1]
  5. The virus doesn’t usually spread easily between people as it requires prolonged close contact. [3]
  6. Its R value is generally less than 1, so outbreaks naturally peter out. [3]
  7. Monkeypox can also spread through close contact or by contact with clothing, towels or bedding used by an infected person. [1,3]
  8. It isn’t regarded as a sexually transmitted infection, but it can be passed on during sex via skin-to-skin contact. (This should not be surprising!) [1]
  9. It’s not clear why gay and bisexual men are disproportionately affected. Are sexual behaviours making it easier to spread, or is this just coincidence? After all this is, in general, a community that is more aware of sexual health and getting checked out. [4]
  10. So the latest cases raise many questions and the scientists don’t really have the sense yet of what’s driving this, especially as there’s no travel link that’s identified that links the cases. [2]
  11. So the scientists are very much in response mode: trying to identify cases and trace potential contacts. And because many of the cases don’t join up scientists are aware they’re seeing only the tip of the iceberg. [2,4]

Symptoms

  1. The incubation period between infection and symptoms is long, ranging from five to 21 days. [3]
  2. The first symptoms of monkeypox include fever, headache, muscle aches, backache, swollen lymph nodes, chills and exhaustion. [1]
  3. A rash can also develop, typically on the face first and then on other parts of the body, mainly hands, feet and genitals. The rash can initially look like chickenpox, before forming scabs. [1]
  4. Swollen lymph nodes are a defining feature found in monkeypox but not so common in chickenpox. Currently there are very few kids with monkeypox but the UK is seeing a big surge in chickenpox. So sick kids are more likely to have chickenpox, but be vigilant. [5]
  5. The pictures of large blisters and scabs in the media are an unusual presentation and thought to be more common with the more serious Congo strain of the virus. Most presentation is with small pustules and lesions which are no more than 5mm in size. (Pictures in the references.) [5]

Different Strains

  1. There are two main types of monkeypox: the Congo strain and the West African strain. Only the West African strain has been identified in the UK. [1]
  2. The death rate from the Congo strain is thought to be 1 in 10, whereas it is only 1 in 100 for the West Africa strain.
    These are likely to be upper estimates as it is unknown how many (mild) cases go unreported. [1]
  3. It is unknown at this time if the current outbreak is due to a new strain of monkeypox. The sequencing work now being carried out should tell us. [1]
  4. Very early genetic analysis suggests the current cases are very closely related to forms of the virus seen in 2018 and 2019. It is too early to be sure, but for now there is no evidence this is a new mutant variant at play. [4]

Treatments

  1. The antiviral drug tecovirimat is approved in Europe for treating monkeypox, smallpox and cowpox; and approved in the US for smallpox. [1]
  2. The Jynneos vaccine is approved in the US and Europe for preventing monkeypox and smallpox in people aged over 18.
  3. In addition, those who are old enough to have been vaccinated against smallpox as babies should have some protection. Routine smallpox vaccination ended in the UK in 1971 and in the US in 1972. [1]

Pandemic?

  1. Monkeypox isn’t COVID. They’re very different diseases caused by different viruses with markedly different properties. COVID was completely unfamiliar when it first appeared, but monkeypox is a known quantity, and experts on the virus actually exist. [3]
  2. While researchers aren’t completely ruling out a pandemic, they don’t think it is at all likely. [1]
  3. Experts stress that monkeypox is very different from coronavirus. Monkeypox is a DNA virus so it does not mutate as rapidly as Covid or flu. [4]
  4. They’re also saying it’s important not to put this on the same level as a novel coronavirus. [1]
  5. Nevertheless monkeypox is a test of the lessons that the world has (or hasn’t) learned from COVID. [3]
  6. The US, at least, is in a better position with monkeypox than with Covid. They had not planned for a coronavirus pandemic, but they have spent decades thinking about how to handle smallpox bioterrorism. [3]
  7. The UKHSA are saying the risk to the UK population amid the ongoing outbreak “remains low”. [1]

Finally … Be vigilant. If you’re at all concerned phone 111 (in UK) or your doctor. But if you think you might have monkeypox DON’T just turn up at a doctor’s surgery (or sexual health clinic, or hospital); phone ahead so they know you’re coming and can prepare appropriate PPE and protective measures. [5]

References

[1] https://www.newscientist.com/article/2321212-could-monkeypox-become-a-pandemic-heres-everything-you-need-to-know/
[2] https://www.washingtonpost.com/health/2022/05/18/monkeypox-faq/
[3] https://www.bbc.co.uk/news/health-61524508
[5] Meaghan Kall of UKHSA on Twitter; https://twitter.com/kallmemeg/status/1528044499288657920

food+drink

Culinary Adventures #85: Peach & Apple Tart

Here’s another simple concoction.

This Peach and Apple Tart is so simple I’m not even going to write a full recipe.

First off, see what you have in the cupboard. As well as a block of puff pastry we had some frozen cooking apple and a big jar of peaches in brandy. But you could use almost any fruit (or roast(?) veg if you want a savoury version).

By now you know how to make a pastry case and blind bake it. If not, see this BBC Food video; it works for shortcrust and puff pastry. I prefer to use bought puff pastry – as I did in this case – but I will make shortcrust (see here). I don’t worry about my results looking as pristine as in the video – this is neither a restaurant nor a competition!

When I’d got my blind-baked pastry case, I put a layer of apple in the bottom and topped it with the peach halves. There was some of the light syrup left from the peaches, so I drizzled a couple of teaspoons of this on the apple in the gaps between the peaches. I finished off with a few fragments of walnut and glazed the edges of the pastry with some more of the syrup.

This was then baked for about 30 minutes, covered with foil for the last 15 minutes to stop the pastry over browning. When removed from the oven I immediately glazed the peaches and pastry again with the syrup, and left it too cool before removing from the tin.

Straight from the oven, having been glazed.
OK, it isn’t pretty, but we’re not in a competition.

Had I had any I would have used either glacé cherries or candied peel instead of the walnuts. But the idea here is to use what you happen to have – and if necessary be able to rustle something up quickly.

amusements, beliefs

May Quiz Answers

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

May Quiz Questions: Mythology & Religion

  1. In Greek mythology who or what guards the gates of the Underworld? Cerberus, a three-headed dog
  2. Theravada and Mahayana are branches of which major world religion? Buddhism
  3. Which group of traditionalist Christians of Swiss German Anabaptist origins was founded by Jakob Ammann? The Amish
  4. According to Norse legend, what animals pulled Thor’s chariot across the sky? Two goats
  5. What three words begin the Book of Genesis? In the beginning

Answers were correct when questions were compiled in late 2021.

medical

Monkeypox

OK guys, so here’s another (not quite new) zoonotic disease for us to get our heads round and which piques my forensic nature: Monkeypox.

As of writing there are now 20 cases reported in the UK [1], with over 100 across mainland Europe [5] – where there seems to be a hotspot in Spain – and cases in the US, Canada and Australia. It is being suggested [2] that a number of cases will be being missed due to a similarity with chickenpox.

Monkeypox is a viral disease which is thought to be carried mostly by rodents and is prevalent in remote central and western areas Africa. Cases outside Africa are almost always associated with travel to that continent. That makes the current outbreak in the UK and beyond especially interesting. Although the first reported UK case in early May was in someone recently returned from west Africa, many of the more recent cases apparently do not have an obvious connection to African travel. Perhaps even more interesting is that a significant number of the UK cases are in men who have sex with men (MSM).

The virus is not transmitted in the same way as Covid or flu, but through close bodily contact with an infected person; it can enter the body through broken skin, the airways, eyes, nose or mouth [3]. However it has not previously been described as a sexually transmitted infection – although sex tends to involve close bodily contact! Spread is also possible from infected animals (eg. monkeys, rodents) or from virus-contaminated objects (eg. bedding and clothing).

Unfortunately the initial symptoms are very much like most viral illnesses: fever, headaches, swollen glands, back pain, aching muscles and a general listlessness. Only later does the rash develop; it often begins on the face, and then spreads to other parts of the body, most commonly the palms of the hands and soles of the feet. The rash, which can be extremely itchy, goes through several stages before forming a scab, which later falls off. Although there is no treatment for monkeypox, and no specific vaccine, most cases resolve within 2-3 weeks.

As the name implies, monkeypox is an Orthopoxvirus very closely related to smallpox (also cowpox). The smallpox vaccine is reportedly highly effective protection [3], so anyone who has been vaccinated against smallpox should have some protecton. Have you been vaccinated against smallpox? Smallpox vaccination was compulsory in the UK between 1853 and 1971 [4] so many people over 50 will have been vaccinated, although apparently compliance was falling before the vaccination requirement was removed.

Should we be worried? Current advice is NO. The risk to the public at large is thought to be very low especially as the virus does not spread easily. But then we originally thought that about Covid-19. So no, don’t panic or be alarmed; but do remain alert and if in any doubt about symptoms talk to your GP.

References
[1] https://www.bbc.co.uk/news/health-61506562
[2] https://www.thisislocallondon.co.uk/news/national/uk-today/20154025.monkeypox-cases-uk-double-20/
[3] https://www.bbc.co.uk/news/health-45665821
[4] https://www.ncbi.nlm.nih.gov/books/NBK545998/
[5] https://www.independent.co.uk/news/health/monkeypox-virus-infection-case-symptoms-live-uk-b2083515.html

food+drink

Culinary Adventures #84: Superior Cheese Scones

Here’s another experiment from last weekend. And one which turned out as brilliantly as I had hoped.

Superior Cheese Scones

Superior Cheese Scones, straight out of the oven.
Note the tiny one from the ends of the pastry!

Makes about 12 small or 6 large
Prep Time: about 15 minutes
Cooking Time: about 25 minutes

Ingredients

280g Self-Raising Flour
50g Butter
150g Cheddar Cheese, grated; plus a bit extra for topping
160ml Milk
1 tsp Baking Powder (yes as well as the SR flour)
Pinch or two of Salt (not too much as the cheese is salty)
1 tbsp fresh ground Black Pepper
2 tbsp Tomato Paste
1 tbsp Garlic Paste
1 Egg, beaten (for glazing)

Method

  1. Preheat the oven to 200/fan 180/gas 5, and line a baking tray with parchment.
  2. Sieve the flour and baking powder into a mixing bowl, with the salt.
  3. Add the butter and rub in to combine to breadcrumb consistency.
  4. Add the cheese and black pepper and mix thoroughly.
  5. Add the tomato paste and garlic paste, followed by the milk a little at a time, to get a soft, pliable but not sticky dough. Go carefully with the milk as you may not need it all; or you may need a splash more.
  6. On a floured surface roll out the dough to about 1″ (2.5cm) thick.
  7. Use a pastry cutter to cut out circles and place them on the baking sheet, being sure to leave a gap between each one.
    Carefully reform any trimmings as they’ll likely make 1 or 2 more scones.
  8. Brush the scones with the egg, and top with a sprinkle of cheese.
  9. Bake for about 25 minutes, until risen and golden.
  10. Allow to cool on a wire rack (if they last that long!).

Notes

  1. When cut the scones should be light and moist; and they’ll be a golden orange colour from the tomato.
  2. Enjoy them with butter, or cheese, or … <well your choice>.
  3. We used Applewood cheese, which came through really well and gave the scones a lovely slightly smoked flavour, with a subtle background of tomato and garlic.
  4. If you double up the mixture, you’ll still only need one egg.
  5. I might try this with some olives instead of the tomato and garlic.
quotes

Monthly Quotes

This month’s selection of quotes encountered.

In every way, the notion of women’s unsuitability didn’t just happen. It was systematically and consciously created. And, of course, another way of keeping women in their place is to insist that their minds just don’t allow them to inhabit traditional male bastions.
[Prof. Stephen Reicher]

In a time of deceit, telling the truth is a revolutionary act.
[George Orwell]

The most amazing thing about the human mind is that you literally never have to stop putting things into it; you can always learn more if you want to, and there is always more to learn.
[Katie Mack]

[T]here are parts of your own body less known than the bottom of the ocean, or the surface of Mars. Most researchers I talked to blamed this dearth of knowledge on the black-box problem: the female body is considered more complex, more obscure, with much of its plumbing tucked up inside. To get inside it, we’ve needed high-tech imaging tools, tools that have only come around in recent decades. When I heard these answers, I couldn’t help thinking of what science has done in the twenty-first century: put a rover on Mars, made a three-parent baby, built an artificial sheep uterus. And we couldn’t figure out the composition of vaginal mucus?
[Rachel Gross; Vagina Obscura]

For centuries, science has been treating women as walking wombs, baby machines and incubators of new life. This narrow perspective has prevented us from asking questions and making advancements that could help all of us live longer, healthier lives. It’s time for a paradigm shift. We need to finally see the female body for what it truly is: a powerful constellation of interlocking elements, each part indivisible from the whole, that work together to support our health from cradle to grave. As we fill in the missing parts of this picture, we will undoubtedly expand our understanding of all bodies.
[Rachel Gross; https://www.theguardian.com/books/2022/may/09/the-big-idea-why-we-need-to-rewrite-the-history-of-female-bodies]

We have the most profound and bizarre psychological block against providing assistance to people in need in cash. We insist against all evidence that they will mostly waste it. In fact cash is the single most practical, efficient and effective intervention for improving lives.
[Rory Stewart]

Listen carefully to everything your children want to tell you, no matter what. If you don’t listen eagerly to the little stuff when they are little, they won’t tell you the big stuff when they are big, because to them all of it has always been big.
[Catherine M Wallace]

Life. One long panic punctuated by cups of tea.

The goddess [Kali] symbolises, we are told, evil being cut away, hypocrisy undone, abusive powers crushed. I rather hoped the necklace of severed male heads she wears might be portraits of well-known oppressors, but no, they mostly look like Salvador Dalí.
[Marina Warner; https://www.theguardian.com/culture/2022/may/16/goddesses-marina-warner-volcanic-power-of-witches-she-devils-divinities-british-museum]