Posts Tagged ‘fiction’

The brewer’s yoke, the domestication of microbes

// July 15th, 2012 // Comments Off on The brewer’s yoke, the domestication of microbes // Recent Research

Something happened when I was spliced, something wrong. Some random event in my chromosomes, I suppose it was. In any event, I wound up lacking. My sister took all the toxin genes, and I was left with nothing.

It’s a scary world out there for a fungus without a toxin. How would I strike fear into the hearts of all animals who dared to eat the plants I was eating? How, without my precious aflatoxin to attack the liver, causing acute sickness or eventual cancer?

Quite simply, I’m surprised I lasted as long as I did before they found me.

Indeed, I’m not sure how they did find me. I had a pretty good disguise, growing colonies of blue along the endless islands of white rice grains, just like my toxic cousins always had. Safe from munching animals by my don’t-eat-me mimicry, the promise of sickness is the discoloured rice.

For some reason, these sake brewers saw past it all. I thought I was a goner when they lifted me up from the wild and plonked me into a house of wood.

Then I saw the food.

A. oryzae in heaven. Image by Forrest O.

It’s hard for mould like me to see, lacking in the eye department, but I knew it was there. An endless carpet of steamed rice. With my filamentous fronds I could touch it. Drill down into it and grow cottony soft, sprout fruiting bodies on the surface and spread on and on.

Call me legion, for we are many. Better yet, call me qū meí jūn in Pinwin, kōji-kin in Japanese, nulook-gyun in Korean or the grandiose Aspergillus oryzae in scientific circles. Back then, some 2000 years ago, I didn’t know who I was, or that I would one day be the National Fungus of Japan.

That’s when the changes happened.

I didn’t notice at first, I don’t know that there was ever a master plan. It felt… natural. Human hands, bristling with microbes and pitted with pores, dropped me into heaven. And when I had eaten the heaven for a time, they picked me up and dropped me once more into fresh heaven.

Incomprehensible! These hands must have spent hours polishing the rice to remove all the husks, then steamed it to perfection, cooled it so I didn’t burn my filaments, then spread it out – just for me! It was like being a king! King Kōji-kin!

I'm a national icon, and pretty cute too. Image by Ryoku Kasinn

As they fed me and I ate, we gradually adapted to please one another. Heaven grew ever more heavenly, until the temperature and humidity was just so.

For my part, I started growing much faster, hell, I had brilliant conditions for it and not a doubt in the world that I could grow as fast as I pleased. Fearlessly fast.

Over generations, they selected only the best for their purposes, which at that stage I knew nothing about. They selected the sons and daughters (hell, we’re all of one gender here) that could best turn rice starch to sugar. They also preferred fungi of least colour, but most smell and flavour. Each generation, the best of me would be plucked and propagated.

Turning starch to sugar is a tricky thing. I suppose the point of starch is to tie up the sugar molecules into a big, complex network so the plant can use them later. For me, kōji-kin I secrete the amylase enzymes, biological machine that chops starch into pieces of sweet. From a couple of recently-licked hands, I’ve learned humans make the same enzyme in their saliva. My amylases, however, not only make glucose, but a few other sugars that produce a wonderful flavour.

But why, pray tell? Have you worked it out yet?

Winemakers use yeast to turn the natural sugars in grapes into alcohol. Beer brewers must malt their barley, partially growing the seed to convert starch to sugar, to ferment it with yeast into alcohol.

And I, the humble fungus, plucked from the wild a millennia ago for a deficit in character. My non-toxic self excels, above all other moulds, in turning rice starch into sugars.

From the beds of heaven, me and my alchemical rice is transferred to the fermenting tank. Mixed with yeast, water and more rice, then left to stew in our own juices for a month.

This mash is pressed and filtered, and the sweet, alcoholic liquid that pours forth is bottled as sake.

Not to ring my own bell filaments, but I make soy sauce and miso too. That’s a whole meal – appetizer, main, and a drink.

Domesticated A oryzae (left) and wild A flavus (right). Image by John Gibbons, Vanderbilt University

These days I hardly recognise myself! So much of me has changed by growing with the sake brewers. Though I still share some 95% of my genome with my wild and toxic cousin A. flavus (and you, human reader, share 99% of yours with a chimpanzee), I am given all I could ever want to eat and praised world-over for my skill in sake making. While A. flavus, the wild thing, is targeted daily for a war against fungi with resistant crops and competitive yeasts.

What must the wolf think of the dog? Or the auroch of the cow? Well, to their accusations I say this: We may change our genes and appearance for protection and care, but, in doing so, we also mould the humans who cooperate with us. Through their attentions and skills, they, too, are domesticated.

This story was inspired by this recent research by Vanderbilt University into the domestication of microbes. “Although people don’t often think about it, we haven’t only domesticated animals and plants, but we have also domesticated dozens of different microbes.” – Assistant Professor of Biological Sciences Antonis Rokas in the press release. You can find more information on brewing sake here, and a beautiful description of koji pampering by interns at a sake house in Japan who blogged their experiences.

ResearchBlogging.orgGibbons, J. et. al. (2012). The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae Current Biology

Introducing Open Lab 2010

// March 22nd, 2011 // Comments Off on Introducing Open Lab 2010 // Science Communication

Open Lab 2010Containing the best of science writing on the web, Open Lab 2010 has been published and printed. Inside are 50 blog posts, 6 poems and a cartoon – including my very own blog post How Aqua Regia Saved Nobel Prizes from the Nazis. The book was edited by the thoughtful animal, Jason Goldman.

You can buy it as a file download or as a real, old-fashioned paperback. A known aphrodisiac, having this book on your bedside table WILL increase your attractiveness and intelligence. The cool nerdy goodness spirals out of it and is soaked up through your pores by osmosis. It’s guaranteed to be delightful for reading, displaying, or simply cuddling.

I’m beyond excited to be included in the anthology. Although I’m published online, in magazines, in newspapers, in zines, this is my first time with a real book. Strike me down with a feather, I feel like a proper writer!

May Open Lab 2010 be the first of many books with my words inside.

Buy a copy of this highly intellectually arousing book here.

Death of a hive, a science story

// February 1st, 2011 // 1 Comment » // Recent Research, Science Communication

Apis bee in honeycomb

Image by By Richard Bartz

It was late afternoon, and Aethina could smell a hive in danger.

Heavy with eggs she felt compelled to investigate. The scent wafted softly though the hot and hazy air, so faint it was barely discernible.

Driven by survival, she flew as fast as she could. Weak as the smell was it was hard to tell which direction to go. Through trial and error she travelled across small hills covered with brown grass, wilting seedlings, and huge angular mounds of dirt.

Finally she reached an ocean of bright yellow flowers heads pointed towards the sun. Interspersed between the identical tall and bristled stems were smaller flowers in purples and whites.

Like islands in the sea, these were safe havens for bees, providing a delicious variety to an otherwise blandly repetitive diet. But Aethina wasn’t hungry for nectar. The hive was close, she could smell it.

As a larva, Aethina had heard stories of her ancestors. Generations upon generations ago they had moved across an ocean too. Their land was dry like this, but filled with foreign flowers. They had travelled, said the stories, inside sweet melons.

Suddenly Aethina could see it, the hive. The smell radiated from it, a beacon of hope and danger.

She alighted and walked through the entrance.

At once the guards sprang upon her. Stinking of bee, they buzzed angrily and tried to push her outside. Her own smell must have set them off. To fend off the aggressive attack, Aethina turtled her head and legs under her hard shell. The guards could find no purchase on her smooth surface, and their suicidal stinging could not penetrate her armor.

With small steps, Aethina sneaked deeper into the hive, avoiding the cracks that riddled the tunnels. Below she could hear the cry of her kin, trapped below. As she watched, hunched under her shell, an apparently very stupid bee dripped honey down the crack, feeding her kind as though they were bee grubs.

One step at a time, slowly, slowly, Aethina forced her way though the tunnels. The attacks continued as she inched her way along, turning this way and that along the chambers.

Suddenly the attacks stopped. Poking out one antennae, and then two, she investigated her surroundings. The bees seemed to be gone, perhaps called on another mission.

There was no time to lose. Silently Aethina laid her eggs as quickly as possible, hiding them near the honey-filled pots that rose like ornamental ponds in mosaic. When they hatched, her larvae would have plenty of food nearby. It would be enough for them to molt into adulthood and find their own hives.

Unless removed by the bees, her children had a good chance of surviving. Eating, growing fat on sweet sugar and proteins, they would gradually destroy the hive. No place lasted long after becoming a Small Hive Beetle Nursery. It was only fair. After all, bees had killed her mother, and would kill her in a heartbeat.

Bees were nasty insects, particularly in this melon-founded land. There were other species of bees, natives with a barbaric tendency to catch her kind and mummify them alive. Armed with balls of sticky resin during the day, they created a lacy resin curtain every night that was impossible to get through. The old saying came back to her “Always lay near Apis, never Austroplebeia.”

For good measure, she dusted spores from her six legs. Yeast. It would consume the honey to produce more of the attractive alarm scent that guided her to the hive. Soon there would be even more beetles, and as the larva fed, the yeast would eventual turning the hive from it’s well-ordered structure into a slimy mess. It would seal the fate of this hive.

Served the bitches right, thought Aethina viciously, as she crawled into a crack to take advantage of idiot-bee hospitality.

This story is based on scientific fact. Since their accidental introduction in 2002, African Small Hive Beetles (Aethina tumida) have been decimating Australian hives of honey bees (Apis mellifera). Their larva consume the hives, while the yeast they bring in converts hives to slime. But the native bee (Austroplebeia australis) destroy the beetles with resin balls and build resin curtains.

Further reading
Stingless bees entomb beetle invaders by Anne Dolin at Aussie Bee.
Beetle and yeast team up against bees by Not Exactly Rocket Science.
Ellis, J., Hepburn, H., Ellis, A., & Elzen, P. (2003). Social encapsulation of the small hive beetle ( Aethina tumida Murray) by European honeybees ( Apis mellifera L.) Insectes Sociaux, 50 (3), 286-291 DOI: 10.1007/s00040-003-0671-7

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