A fun and lightweight 10-minute (very basic, but highly-accessible) primer into the mechanisms by which new viruses appear to emerge via spillover infection and viral evolution. I was pleased by the accuracy of the animations including efforts to show relative scale of microorganisms and the (correct) illustration of RNA as the genetic material of a coronavirus (many illustrators draw all viruses as carrying a double-stranded DNA payload).
An increasing number of people are reportedly suffering from an allergy to the meat and other products of nonhuman mammals, reports Mosaic Science this week, and we’re increasingly confident that the cause is a sensitivity to alpha-gal (Galactose-alpha-1,3-galactose), a carbohydrate produced in the bodies of virtually all mammals except for us and our cousin apes, monkeys, and simians (and one of the reasons you can’t transplant tissue from pigs to humans, for example).
The interesting thing is that the most-common cause of alpha-gal sensitivity appears to be the bite of one of a small number of species of tick. The most-likely hypothesis seems to be that being bitten by such a tick after it’s bitten e.g. deer or cattle may introduce that species’ alpha-gal directly to your bloodstream. This exposure triggers an immune response through all future exposure, even if it’s is more minor, e.g. consuming milk products or even skin contact with an animal.
That’s nuts, isn’t it? The Mosaic Science article describes the reaction of Tami McGraw, whose symptoms began in 2010:
[She] asked her doctor to order a little-known blood test that would show if her immune system was reacting to a component of mammal meat. The test result was so strongly positive, her doctor called her at home to tell her to step away from the stove.
That should have been the end of her problems. Instead it launched her on an odyssey of discovering just how much mammal material is present in everyday life. One time, she took capsules of liquid painkiller and woke up in the middle of the night, itching and covered in hives provoked by the drug’s gelatine covering.
When she bought an unfamiliar lip balm, the lanolin in it made her mouth peel and blister. She planned to spend an afternoon gardening, spreading fertiliser and planting flowers, but passed out on the grass and had to be revived with an EpiPen. She had reacted to manure and bone meal that were enrichments in bagged compost she had bought.
Of course, this isn’t the only nor even the most-unusual (or most-severe) animal-induced allergy-to-a-different-animal we’re aware of. The hilariously-named but terribly-dangerous Pork-Cat syndrome is caused, though we’re not sure how, by exposure to cats and results in a severe allergy to pork. But what makes alpha-gal sensitivity really interesting is that it’s increasing in frequency at quite a dramatic rate. The culprit? Climate change. Probably.
It’s impossible to talk to physicians encountering alpha-gal cases without hearing that something has changed to make the tick that transmits it more common – even though they don’t know what that something might be.
“Climate change is likely playing a role in the northward expansion,” Ostfeld adds, but acknowledges that we don’t know what else could also be contributing.
Meat Me Half-Way
To take a minor diversion: another article I saw this week was the BBC‘s one on the climate footprint of the food you eat.
A little dated, perhaps: I’m sure that nobody needs to be told nowadays that one of the biggest things a Westerner can do to reduce their personal carbon footprint (after from breeding less or not at all, which I maintain is the biggest, or avoiding air travel, which Statto argues for) is to reduce or refrain from consumption of meat (especially pork and beef) and dairy products.
Indeed, environmental impact was the biggest factor in my vegetarianism (now weekday-vegetarianism) for the last eight years, and it’s an outlook that I’ve seen continue to grow in others over the same period.
Seeing these two stories side-by-side in my RSS reader put the Gaia hypothesis in my mind.
If you’re not familiar with the Gaia hypothesis, the basic idea is this: by some mechanism, the Earth and all of the life on it act in synergy to maintain homeostasis. Organisms not only co-evolve with one another but also with the planet itself, affecting their environment in a way that in turn affects their future evolution in a perpetual symbiotic relationship of life and its habitat.
Its advocates point to negative feedback loops in nature such as plankton blooms affecting the weather in ways that inhibit plankton blooms and to simplistic theoretical models like the Daisyworld Simulation (cute video). A minority of its proponents go a step further and describe the Earth’s changes teleologically, implying a conscious Earth with an intention to protect its ecosystems (yes, these hypotheses were born out of the late 1960s, why do you ask?). Regardless, the essence is the same: life’s effect on its environment affects the environment’s hospitality to life, and vice-versa.
There’s an attractive symmetry to it, isn’t there, in light of the growth in alpha-gal allergies? Like:
- Yesterday – agriculture, particularly intensive farming of mammals, causes climate change.
- Today – climate change causes ticks to spread more-widely and bite more humans.
- Tomorrow – tick bites cause humans to consume less products farmed from mammals?
That’s not to say that I buy it, mind. The Gaia hypothesis has a number of problems, and – almost as bad – it encourages a complacent “it’ll all be okay, the Earth will fix itself” mindset to climate change (which, even if it’s true, doesn’t bode well for the humans residing on it).
But it was a fun parallel to land in my news reader this morning, so I thought I’d share it with you. And, by proxy, make you just a little bit warier of ticks than you might have been already. /shudders/
Fantastic lightweight introduction to bacteriophages and how they can potentially be our next best weapon against infection as we approach the post-antibiotic age. Plus an interesting look at the history and the discovery of bacteriophages!
So, I’ve not been well lately. And because a few days lying on my back with insufficient mental stimulation is a quick route to insanity for me, I’ve been trying to spend my most-conscious moment doing things that keep my brain ticking over. And that’s how I ended up calculating pi.
Pi (or π) is, of course, the ratio of the circumference of a circle to its diameter, for every circle. You’ll probably have learned it in school as 3.14, 3.142, or 3.14159, unless you were one of those creepy kids who tried to memorise a lot more digits. Over the years, we’ve been able to calculate it to increasing precision, and although there’s no practical or theoretical reason that we need to know it beyond the 32 digits worked out by Ludolph van Ceulen in the 16th Century, it’s still a fascinating topic that attracts research and debate.
Most of the computer-based systems we use today are hard to explain, but there’s a really fun computer-based experimental method that can be used to estimate the value of pi that I’m going to share with you. As I’ve been stuck in bed (and often asleep) for the last few days, I’ve not been able to do much productive work, but I have found myself able to implement an example of how to calculate pi. Recovery like a nerd, am I right?
Remember in school, when you’ll have learned that the formula to describe a circle (of radius 1) on a cartesian coordinate system is x2 + y2 = 1? Well you can work this backwards, too: if you have a point on a grid, (x,y), then you can tell whether it’s inside or outside that circle. If x2 + y2 < 1, it’s inside, and if x2 + y2 > 1, it’s outside. Meanwhile, the difference between the area of a circle and the area of a square that exactly contains it is π/4.
Take those two facts together and you can develop an experimental way to determine pi, called a Monte Carlo method. Take a circle of radius 1 inside a square that exactly contains it. Then randomly choose points within the square. Statistically speaking, these random points have a π/4 chance of occuring within the circle (rather than outside it). So if we take the number of points that lie within the circle, divide that by the total number of points, and then multiply by 4, we should get something that approaches the value of pi. You could even do it by hand!
Oh, and it’s all completely open-source, so you’re welcome to take it and do with it what you wish. Turn off the graphical output to make it run faster, and see if you can get an accurate approximation to 5 digits of pi! Or slow it down so you can see how the appearance of each and every point affects the calculation. Or adapt it into a teaching tool and show your maths students one way that pi can be derived experimentally. It’s all yours: have fun.
And I’ll update you on my health at some other point.
So yeah: that’s not entirely pleasant. A couple of days ago I was diagnosed with what was supposed to be a minor bladder infection and given antibiotics. Then yesterday I became feverish and collapsed. And now I’m in hospital.
But on the upside, they’ve spent all night pumping me full of some kind of intravaenous antibiotic that must be made from like unicorn spunk and leprechaun tears or something because it’s frankly magical: feeling so much better today than yesterday.
Just wanted to say hi. Hi, all!
I’m pretty sure that an outside observer, given the advance knowledge of this blog post, could easily tell when I’m in the process of getting over an illness just by the food I eat. I’m pretty sure that I have a particular ‘tell’ in the foods I look for when I’m on the cusp of recovering from a cold, like now: or, I suppose, on those rare occasions that I’ll have drunk enough to be suffering from a hangover.
Take this lunchtime, for example. I’ve been off work for the last couple of days, laid low by what seems to be the very same cold that I was sure I’d dodged when everybody else got it, last month (I blame Annabel, the contagious little beast, who’s particularly keen on shoving her hands into people’s mouths). Today I’m back on my feet, but working from home: I skipped breakfast, but by lunchtime I felt able to face some food, and quickly determined what it was that I really wanted:
Egg & Cheese Wafflestack
Serves: 1 unwell-but-recovering person
Preparation: 15 minutes
Difficulty: if you can’t make this, get the hell out of the kitchen
4 × frozen potato waffles. I’m using Birds Eye ones, but honestly, who can tell the difference?
~ 30g mature cheddar cheese, grated or thinly sliced, brought to room temperature so it melts quickly
2 × eggs
A little vegetable oil
Tomato ketchup (alternatively, brown sauce works well)
Grill the waffles in accordance with the instructions. Meanwhile, fry the two eggs (“sunny side up”: keep the yolk fluid). Assemble in stacks, with each stack consisting of cheese sandwiched between two waffles, topped with an egg and the ketchup. Serve immediately. Eat as quickly as you dare.
So now I’m sitting here eating the taste of delicious recovery, generating 4096-bit strong probable prime numbers (like you do), and reading the feedback on a browser plugin I released recently. And every part of that is a huge improvement upon lying ill in bed.
This is the first in a series of four blog posts which ought to have been published during January 2013, but ran late because I didn’t want to publish any of them before the first one.
2012 was one of the hardest years of my life.
It was a year of unceasing disasters and difficulties: every time some tragedy had befallen me, my friends, or family, some additional calamity was lined-up to follow in its wake. In an environment like this, even the not-quite-so-sad things – like the death of Puddles, our family dog, in May – were magnified, and the ongoing challenges of the year – like the neverending difficulties with my dad’s estate – became overwhelming.
The sudden and unexpected death of my dad while training for his Arctic trek, was clearly the event which had the most-significant impact on me. I’ve written about the experience at length, both here on my blog and elsewhere (for example, I made a self-post to Reddit on the day after the accident, urging readers to “call somebody you love today”).
In the week of his death, my sister Becky was suffering from an awful toothache which was stopping her from eating, sleeping, or generally functioning at all (I tried to help her out by offering some oil of cloves (which functions as a dental contact anesthetic), but she must have misunderstood my instruction about applying it to the tooth without swallowing it, because she spent most of that evening throwing up (seriously: don’t ever swallow clove oil).
Little did she know, worse was yet to come: when she finally went to the dentist, he botched her operation, leaving her with a jaw infection. The infection spread, causing septicæmia of her face and neck and requiring that she was hospitalised. On the day of our dad’s funeral, she needed to insist that the “stop gap” surgery that she was given was done under local, rather than general, anasthetic, so that she could make it – albeit in a wheelchair and unable to talk – to the funeral.
Five weeks later, my dad finally reached the North Pole, his ashes carried by another member of his team. At about the same time, Ruth‘s grandmother passed away, swamping the already-emotional Earthlings with yet another sad period. That same month, my friend S****** suffered a serious injury, a traumatic and distressing experience in the middle of a long and difficult period of her life, and an event which caused significant ripples in the lives of her circle of friends.
Shortly afterwards, Paul moved out from Earth, in a situation that was anticipated (we’d said when we first moved in together that it would be only for a couple of years, while we all found our feet in Oxford and decided on what we’d be doing next, as far as our living situations were concerned), but still felt occasionally hostile: when Paul left town six months later, his last blog post stated that Oxford could “get lost”, and that he’d “hated hated 90% of the time” he’d lived here. Despite reassurances to the contrary, it was sometimes hard – especially in such a difficult year – to think that this message wasn’t directed at Oxford so much as at his friends there.
As the summer came to an end, my workload on my various courses increased dramatically, stretching into my so-called “free time”: this, coupled with delays resulting from all of the illness, injury, and death that had happened already, threw back the release date of Milestone: Jethrik, the latest update to Three Rings. Coupled with the stress of the 10th Birthday Party Conference – which thankfully JTA handled most of – even the rare periods during which nobody was ill or dying were filled with sleepless nights and anxiety. And of course as soon as all of the preparation was out of the way and the conference was done, there were still plenty of long days ahead, catching up on everything that had been temporarily put on the back burner.
When I was first appointed executor of my dad’s estate, I said to myself that I could have the whole thing wrapped-up and resolved within six months… eight on the outside. But as things dragged on – it took almost six months until the investigation was finished and the coroner’s report filed, so we could get a death certificate, for example – they just got more and more bogged-down. Problems with my dad’s will made it harder than expected to get started (for example, I’m the executor and a beneficiary of the will, yet nowhere on it am I directly mentioned by name, address, or relationship… which means that I’ve had to prove that I am the person mentioned in the will every single time I present it, and that’s not always easy!), and further administrative hiccups have slowed down the process every step of the way.
You know what would have made the whole thing easier? A bacon sandwich. And black pudding for breakfast. And a nice big bit of freshly-battered cod. And some roast chicken. I found that 2012 was a harder year than 2011 in which to be a vegetarian. I guess that a nice steak would have taken the edge off: a little bit of a luxury, and some escapism. Instead, I probably drank a lot more than I ought to have. Perhaps we should encourage recovering alcoholic, when things are tough, to hit the sausage instead of the bottle.
Becky’s health problems weren’t done for the year, after she started getting incredibly intense and painful headaches. At first, I was worried that she was lined-up for a similar diagnosis to mine, of the other year (luckily, I’ve been symptom-free for a year and a quarter now, although medical science is at a loss to explain why), but as I heard more about her symptoms, I became convinced that this wasn’t the case. In any case, she found herself back in the operating room, for the second serious bit of surgery of the year (the operation was a success, thankfully).
I had my own surgery, of course, when I had a vasectomy; something I’d been planning for some time. That actually went quite well, at least as far as can be ascertained at this point (part three of that series of posts will be coming soon), but it allows me to segue into the topic of reproduction…
Because while I’d been waiting to get snipped, Ruth and JTA had managed to conceive. We found this out right as we were running around sorting out the Three Rings Conference, and Ruth took to calling the fœtus “Jethrik”, after the Three Rings milestone. I was even more delighted still when I heard that the expected birth date would be 24th July: Samaritans‘ Annual Awareness Day (“24/7”).
As potential prospective parents, they did everything right. Ruth stuck strictly to a perfectly balanced diet for her stage of pregnancy; they told only a minimum of people, because – as everybody knows – the first trimester’s the riskiest period. I remember when Ruth told her grandfather (who had become very unwell towards the end of 2012 and died early this year: another sad family tragedy) about the pregnancy, that it was only after careful consideration – balancing how nice it would be for him to know that the next generation of his family was on the way before his death – that she went ahead and did so. And as the end of the first trimester, and the end of the year, approached, I genuinely believed that the string of bad luck that had been 2012 was over.
But it wasn’t to be. Just as soon as we were looking forward to New Year, and planning to not so much “see in 2013” as to “kick out 2012”, Ruth had a little bleeding. Swiftly followed by abdominal cramps. She spent most of New Year’s Eve at the hospital, where they’d determined that she’d suffered a miscarriage, probably a few weeks earlier.
Ruth’s written about it. JTA’s written about it, too. And I’d recommend they read their account rather than mine: they’ve both written more, and better, about the subject than I could. But I shan’t pretend that it wasn’t hard: in truth, it was heartbreaking. At the times that I could persuade myself that my grief was “acceptable” (and that I shouldn’t be, say, looking after Ruth), I cried a lot. For me, “Jethrik” represented a happy ending to a miserable year: some good news at last for the people I was closest to. Perhaps, then, I attached too much importance to it, but it seemed inconceivable to me – no pun intended – that for all of the effort they’d put in, that things wouldn’t just go perfectly. For me, it was all connected: Ruth wasn’t pregnant by me, but I still found myself wishing that my dad could have lived to have seen it, and when the pregnancy went wrong, it made me realise how much I’d been pinning on it.
I don’t have a positive pick-me-up line to put here. But it feels like I should.
And so there we were, at the tail of 2012: the year that began awfully, ended awfully, and was pretty awful in the middle. I can’t say there weren’t good bits, but they were somewhat drowned out by all of the shit that happened. Fuck off, 2012.
Here’s to 2013.
Edit, 16th March 2013: By Becky’s request, removed an unflattering photo of her and some of the ickier details of her health problems this year.
Edit, 11th July 2016: At her request, my friend S******‘s personal details have been obfuscated in this post so that they are no longer readily available to search engines.
Edit, 26th September 2016: At her request, my friend S******‘s photo was removed from this post, too.
This weekend was the worst net weekend of cinemagoing experiences that I’ve ever had. I went to the cinema twice, and both times I left dissatisfied. An earlier blog post talked about the second of the two trips: this is about the first.
You know what – 2012 has been a pretty shit year, so far. We’ve had death (my father’s), more death (my partner’s grandmother’s), illness (my sister’s horrific face infection), and injury (a friend of mine lost her leg to a train, a few weeks ago, under very tragic circumstances). We’ve had breakups (a wonderful couple I know suddenly separated) and busy-ness (a cavalcade of day-job work, Three Rings work, course work, and endless bureaucracy as executor of my dad’s will).
But it gets worse:
On Friday night, I went out with my family to watch Piranha 3DD.
This is one of those bad films that falls into the gap of mediocrity between films that are bad but watchable and films that are so bad that they wrap right around to being enjoyable again (you know, the “so bad they’re good” kind of movies). To summarise:
- Lots of nudity, all presented in 3D. If there’ll ever be anything that convinces me that 3D films are a good idea, porn will probably be it. Boobs boobs boobs.
- Fun cameos from Christopher Lloyd (Doc Brown!), David Hasselhoff, and Ving Rhames, along with enjoyable accompanying pop culture references.
- 3D films remain a pointless gimmick, still spending most of their time playing up the fact that they’re 3D (lots of long objects, like broom handles, pointing towards the camera, etc.), and still kinda blurry and headache-inducing. Plus: beams of light (e.g. from a torch) in 3D space don’t look like that. The compositor should be fired.
- The cameos mostly serve to show off exactly how unpolished the acting is of the less well-known actors.
- Plenty of less-enjoyable pop culture references: if you’re not going to do the “false leg is actually a gun” thing even remotely as well at Planet Terror, don’t even try – it’s like trying to show a good movie in the middle of your crappy movie, but not even managing to do that.
- Unlikeable, unmemorable characters who spend most of their time engaging in unremarkable teen drama bullshit. Same old sex joke repeated as many times as they think they can get away with. And then a couple of times more.
- Lackluster special effects: mangled bodies that don’t look much like bodies, vicious fish don’t look remotely like fish (and, for some reason, growl at people), and CGI that would look dated on a straight-to-video release.
So yeah: give that one a miss.
[this post has been partially damaged during a server failure on Sunday 11th July 2004, and it has been possible to recover only a part of it]
[more of this post was recovered on Friday 24 November 2017]
Here’s some stuff I found interesting this weekend:
Swedish health workers, in an effort to stem the growing cases of chlamydia among young people, have launched a ‘condom ambulance [BBC News]. If you find yourself ‘caught short’ in Sweden, just give them a bell and they’ll rush around to your house with a pack-of-three, for the equivelent cost of about £4.
Chinese researchers have used a carbon nanotube [Wikipedia] as a filament in a new, experimental light bulb [The Register]. This bulb emits more light and works at a lower threshold than tungsten at the same voltage, and was still functioning fine after being switched on and off 5000 times. The future of lighting?
And finally, researchers from Hebrew University in Israel may have found a solution to the problems associated with passwords. As it stands, ‘secure’ passwords are hard to remember, and often find themselves written down, whereas insecure ones can be cracker. Plus, for real security, passwords should be …
[this post has been partially damaged during a server failure on Sunday 11th July 2004, and it has been possible to recover only a part of it]
Feel rotten. And I’m supposed to be back at work, today. Called in sick, especially apologetically.
Had another lariam-induced mood swing yesterday, and became especially grotty to people, so went and excluded myself from them for awhile. I’ve made an appointment to see the doctor next Monday, pre-emptively: if these side-effects don’t get any better by then (I’ll be taking more of the drug today) I’ll ask about switching to one of the alternative meds. After all, as margi said, if I’m becoming intolerable in quiet company with friends, what am I likely to be like under the African sun with strangers.
And if today’s pill brings everything into line, I can cancel my appointment. Winner.
In other news, as promised, below is a picture of my beard in it’s new “Ming The Merciless” (Flash Gordon, for those of you with no film culture) configuration. And yes, I mean the 1936 one:
It’s really quite scary to look at the original Flash Gordon and realise that…