Overseas

“I think that if you go overseas with a superficial attitude, intending to come back home in a year, you won’t get much out of the experience. Particularly if you’re young, you should go with the intention of completely immersing yourself, ready to spend the rest of your life there. You should be determined not to come home until you’ve achieved one goal you’ve set for yourself overseas. “
Tahira Satoshi

I found this quote in literally a plain text file in my Dropbox. Tahira is a high-ranking executive in the pharma company I used to work at before I came to South Africa. I can no longer remember what the context was – probably some big internal company meeting, but obviously I transcribed it because I thought it was wonderful advice and I still do.

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Redang

Everything in monochrome. Black sea, sand white in the moonlight, black trees. Ribbons of grey cloud. The black upward arc of an old boat beached long ago.

Flying foxes – huge bats – passing over the face of the moon. Their nightly commute for sweet fruit dangling from trees untouched by human hands.

The dinosaurian scrape, scrape of a turtle dragging herself up the beach. The length of a medium dog, but she weighs as much as a big man. So much weight. You and your partner glance at each other. No rush. She will take her time.

Far down the beach, a ruby star bobs. Another pair of volunteers are bustling around their turtle with a clipboard: when did she start to dig, when to lay, how many eggs, when did she close up. Buried treasures.

The ransom, the debt. Chagar Hutang, Redang.

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A Journal of the Plague Year

Link to my review on Goodreads (same text as below).

The book, free on Gutenberg.org.

This was pretty entertaining reading in the grip of a pandemic. Just to be clear, Defoe himself was a small kid at the time of the Great Plague of London. This first-person account may be based on the journals of his uncle Henry Foe.
Three hundred and fifty-five years seems like a very long time ago. But the ideas and experiences in this book seem surprisingly contemporary, not just because of our circumstances. You can see why historians already call this time the “Early MODERN Era.” He keeps quoting bits of the weekly bills of mortality just like how we’re all pasting screenshots of the latest case numbers on social media.
Despite acknowledging that he is a layman, the narrator has a lot of insights based on observation about disease control. He criticises the shutting up of houses with sick and healthy household members together. This conflates isolation of the sick with quarantine, which properly applies to exposed but healthy people. The narrator notes that rich men who owned 2 houses and were able to send the sick family member away before the authorities shut up their house were often able to save the rest of the family. Chinese epidemiologists who studied the Wuhan outbreak came to the same conclusion – lockdown only slowed the spread, what stopped it was centralised quarantine.
Another epidemiological concept that’s been confirmed in modern studies is a “second wave” when people think it’s over and relax their precautions and rush back to urban centres.
There is also a heartwrenching conversation with a poor boatman who makes a living selling groceries to ship owners or merchants who are living aboard their ships to keep away from the city. Meanwhile he can’t go near his family because his wife and one of his children have the plague, and the child is probably dying. He has to keep himself healthy because they will starve otherwise. It reminded me of the plight of Uber drivers and workers in the “gig economy” or older informal economies who are struggling to make a living right now.
Not all is grim; there is also an entertaining account of two poor men who decide to leave the city, end up meeting up with a small group of other vagrants, and somehow end up convincing villagers that they are an entire gang of armed bandits.
By the way if you are not from London I highly recommend having Google Maps at hand while reading this.

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BSL3 birdwatching

There are two large black-and-white corvids in South Africa, the pied crow and the white-necked raven. The reason I know this is because I had an argument with my partner’s friend who’s an older South African guy. He took us for a drive and we saw a big black and white bird flying in the distance and I said that looks too big to be a crow and the beak is really heavy, I think it’s a raven. He said no, it’s a pied crow, I used to have one as a pet.

Some months later I happened to find a bird book and lo and behold South Africa does have a raven that is also black and white and it does indeed have that scary looking beak which is much thicker than the crow’s.

Anyway last Friday I was working in the Biosafety Level 3 lab at the top of our tower. This time of year the pied crows like to come and hang out on the sunshades that are installed outside the building’s windows. Then I noticed there was A RAVEN sitting right next to a crow! A chance to take a photo of both of them together! But being that I don’t bring personal belongings into BSL3, the only normal camera in the room (besides the confocal microscope) was the laptop that we use for taking labnotes. By the time I had unplugged it and pointed it out the window, the raven had flown away.

Jialat.

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Tuberculosis research for dummies

This is a work in progress article to form an easily understandable starting point for biologists new to TB research. I’m publishing it in incomplete form mainly as a to-do list for myself. The goal is to link to a FEW comprehensive reviews and landmark historical papers because the number of reviews out there is really overwhelming.

This is not for laypersons seeking basic information about TB as a disease, you can easily find that elsewhere.

Anatomy of the bug

In vitro growth characteristics

  • Classical growth media
  • What is the meaning of Rough vs Smooth colonies
  • Approximate doubling times of lab strains
  • Why do we grow it in broth with surfactant, and what are the circumstances where yo shouldn’t
  • What is OADC
  • Decontaminating clinical isolates for culture
  • How is MGIT used in research besides clinical diagnostics
  • Antibiotic resistance genes that can be used for reporter or expression plasmids
  • Transformation of Mtb with plasmids

Genetics

  • Mycobrowser: database of genes for Mtb H37Rv and a bunch of other reference species/strains
  • The “Rv” numbering system, where does it come from?
  • RD1 and what genes are in it (therefore, which antigens would you NOT expect to see adaptive responses to from BCG-vaccinated-only individuals)
  • What antigens are in PPD
  • What antigens are in Quantiferon

Other differences between Mtb and M.bovis versus non-tuberculous mycobacteria (NTMs)

Common lab strains and where they came from

  • H37Rv vs H47Ra
  • CDC1551
  • Erdman
  • Strains of BCG
  • Strains of smeg

History for nerds

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Life Sciences in the Apocalypse

Thought experiment no.1: If you were trapped at work during the zombie apocalypse, how long could you survive on lab reagents?

  • drink tissue culture medium like soup. Add BSA (bovine serum albumin), or Western blot blocking reagent (skim milk), or FBS (foetal bovine serum) for added protein and flavour
  • make jelly with agar, agarose, and gelatin flavoured with sucrose
  • drink carboxymethyl cellulose as a source of fibre so you don’t get constipated
  • unfortunately you would be very short of lipid foods in the average TC lab, hopefully drinking FBS and human serum if you have it would provide sufficient for health
  • if you have any biotinylated antibodies you could drink them as a source of vitamin B7 but the quantity will probably not last long- eat mice, washed down with molecular biology ethanol

Thought experiment no.2: The zombie apocalypse has burnt itself out and you are the sole living biologist among the few survivors. You ate all the nontoxic stuff in your lab. How do you restart life sciences diagnostics and biomanufacturing in your house?

  • steal an old fashioned pressure cooker to use as an autoclave (cannot Instant Pot, no electricity)
  • get a stupid cat that knows how to catch mice but not kill them quickly so you can start a mouse breeding programme
  • build a shed with a tall chimney that catches the wind for doing biohazard work in unidirectional air flow so you don’t die
  • culture bacteria on food grade agar-agar and sterilised potato
  • (you cannot use food grade agar to run DNA gels because it’s too wavy – trust me I have tried this because I wanted to know why molecular biology grade agarose is so expensive)
  • try to find some cows and bulls that haven’t been eaten by zombies so you can get foetal bovine serum. Of course this part will take many years until the herd is big enough to harvest sustainably, therefore, you won’t be able to do mammalian tissue culture for a long time
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The Transformer

(As with many other dreams, this takes place in a large building, which is the labyrinth that contains everything in the world.)

I was in a room with white plastic tables and MDF bookshelves, perhaps a meeting room in a library or goverment office. There were several cages filled with shredded paper on some of the shelves and tables, holding baby mammals of various species. I opened one of the cages containing a very small puppy with ginger fur, but young as it was, it attacked me.

“Don’t touch the animals,” warned one of the government officers waiting around with me. “You don’t know what can happen if they bite you.” The bite of a puppy with milk teeth? I wondered.

The mayor arrived at last. He had once been the mayor of New York City but had been sacked from office. Somehow he had found the labyrinth and taken it over. He had an entourage of two or three other men in suits, including a dark-haired, good-looking young one.

One of the officers who had been waiting with me stood up at the front of the room and began speaking. She said that they had (developed? Been given?) a machine that could temporarily transform any mammal into any other species of mammal. What this meant for the city was that it could make huge sums of money by setting up a Contract Research Organisation. But unlike other animal CROs that did toxicology and efficacy studies in rabbits, mice, and dogs, this new CRO could produce data from living human bodies. But since the humans were really just rabbits, mice, and dogs, it would enable them to do incredible experiments that could never be performed on real humans.

She invited the mayor to view a live demonstration of the transformer. One of the other officers took the cage with the ginger puppy, as well as another containing two hooded lab rats. We headed to the main lift lobby and took a lift down, down so the way to one of the lowest floors in the basement. To my surprise, the lobby doors opened on a small theatre with red velvet curtains framing its stage.

A closed booth with a desk and a laptop next to it stood on the stage. To the right of the stage was a pile of empty cages, smelling of various things. One of the officers from the first room mounted the stairs to the left of the stage and headed towards the computer and booth with the puppy. I didn’t see what happened to it, because the mayor’s young assistant suddenly seemed to be in distress.

He held his hands in front of him, bent sharply at the wrist with the fingers together, stiff and straight. He tried to sidle away from the group, but it was impossible not to notice him. As he shook his head, his ears grew large, triangular and floppy, and he grunted repeatedly. The mayor grimaced in disgust. The two other suits, without any other command, stepped up behind the younger man and drew long knives from their jackets. They swung together.

I ran without waiting for the blades to fall. There was a wet thwack and a crack together, the sound I have heard hundreds of times in butcher shops. Shouting. I ran out and through the corridors, around the back of the theatre to where I knew from my years-long inhabitation of the labyrinth that the cargo lifts should be, hoping that the VIPs and bureaucrats would not. Some surprised workers were loading empty plastic crates of the kind live chickens are transported in. I shoved them aside rudely and dived in. I punched the button for the forty-ninth floor over and over, praying for the door to close quickly.

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Hotel level

I had a dream that my sisters and I were hunting for something precious through a labyrinth of hotel rooms. (It’s always a labyrinth.) We kept getting killed. But every time we respawned, the traces of how far we had gotten before were still there. A set of lockpicks tossed in a corner. Muddy footprints at a junction.
In the last room I remember before waking up, my sisters were cornered on a sofa by a man who was threatening them with a lethal weapon. I was standing off to one side, so I could see that on the wall behind the sofa one of us had scrawled “escape route: ARSON”. And on the side table within reach of their hands, an oil lamp, lit…

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Pegang anjing

I just remembered the weirdest damn thing from my primary school days. A stray dog had puppies at the side of the sports field and I spent a bunch of spare time in class making these elaborate disposable mittens out of exercise book paper and gum, because the school toilet didn’t have soap to wash hands and it was the only way I could think of to be able to pick up the puppies and still be able to touch my lunch box and play with my Muslim friends afterwards.

(My parents had drilled it into us that we had to wash our hands with soap after touching animals before eating and it never occurred to me to take that any way other than literally. As an adult owning an indoor cat an dog both on my bed as I write this, I have relaxed a little on that rule…)

I was like 8 or 9 years old, max. (Because it was in Taiping, and I can timestamp my entire life by location because I’ve never lived anywhere longer than four years.) At that age already got biosafety/must wear PPE mentality. No wonder I work in infectious diseases now.

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Achivey

This morning I was chatting with a physician from a Francophone country who’s volunteering at a charity clinic while waiting to pass her exams to practice in South Africa. I asked her what health problems she commonly sees among the clients.
“Scabies, allergic rhinitis, achivey…”
“What’s achivey? I haven’t heard of it before.”
“It’s a virus, it can be sexually transmitted, it cause AIDS.”
“Ohhhhhhhh that’s how you pronounce “H”, “I”, “V” in French!”
😂😂😂😂

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