Into the Fold · story 1
The Lantern in the Jellyfish
A kitchen question: Why is the jellyfish glowing?
Beto had a glow stick, and the glow stick had stopped.
It had been bright green at the start of the evening, the kind of green that makes your hand look like it belongs to someone else. Now it was dull and grey, and there was a split near one end where Beto had bent it too far. He sat on the edge of the Green with the stick across his knees, turning it over.
"I could take it apart," he said.
"Please don't," said Danya, who was twelve and had been sent to find him for dinner. "It's full of chemicals. And it's finished anyway. That's what they do."
"The jellyfish at the museum doesn't finish," Beto said. "It glows every time. Why?"
Danya opened his mouth to answer and found he had nothing to say. On the poster at the small museum there was a jellyfish as clear as glass, with a ring of green dots around its edge. He had read the poster twice. It said the jellyfish glowed. It did not say why.
The hammer rang once. A spark jumped off the anvil and did not go out. It waited. They followed.
Among the barrels
The Fold was crowded. That was the first thing. Everything bumped into everything: water, salt, tiny pieces of things neither of them had names for, all jostling, all the time, nothing standing still. The spark hung above them like a warm full stop.
Then they saw the barrels.
Each one was a little can made of strips, eleven of them, laid side by side and curved round into a tube. The strips were ribbons of protein chain, running up and down, up and down, held to each other along their edges. And right through the middle of each can, like a thread through a bead, ran one more piece of the same chain.
In the middle of that thread, inside each barrel, sat a small green light.
"Lanterns," said Beto.
"How do we know this is the glowing one?" said Danya. "There's loads of stuff here."
It was a fair question, and he did not get an answer from anyone, because nobody in the Fold answers questions. So he looked. The light was only in the barrels. Not in the water, not in the jostling bits. In the barrels, in the middle, every time.
"Same shape," said Beto. "Every one. Same shape, same light."
The wrong tool
Beto is the kind of person who takes things apart. He had taken apart a radio, a stapler and, once, by accident, a chair. He reached out to the nearest barrel, found the loose end of its chain, and pulled.
The barrel came undone like a jumper with a pulled thread. The strips peeled away from each other. The tube went floppy, then stringy, then it was just a long wobbly chain, bumping about like everything else.
The light went out.
Beto held the end of the chain and stared at it. All the same pieces were still there. Not one was missing. But there was no light anywhere.
"I broke it," he said.
"You unfolded it," said Danya slowly. "It's all still there. It's just not a barrel any more."
Beto let go of the chain. It drifted off among the jostling things, and the two of them stood for a while next to a barrel that was still whole and still glowing, looking at the difference.
The light was made from the chain itself, from three of its own building blocks, side by side in the middle thread. But those three only made light while the barrel was folded around them, holding them still and keeping the water off. Take the barrel away, and the same three blocks were just three blocks.
"So the shape is the lantern," said Beto. "Not the stuff. The shape."
Blue in, green out
Something else was in the jellyfish with the barrels: a different protein, rounder, with no lantern of its own. Every now and then a speck of calcium bumped into one of these and stuck, and when it did, there was a flash of blue light.
"That's the glow stick bit," said Danya. "Chemistry. Something gets used up and you get light."
The blue did not get far. Wherever one of the round proteins sat close to a barrel, the blue energy passed straight across into the barrel's middle, and what came out of the barrel was green.
Blue in. Green out. Again and again.
"It's changing the colour," said Beto. "The round one makes blue and the barrel turns it green."
Danya held his hand up into the faint bluish light that came down through the water from above. Where it fell on the barrels, they gave out a little green too.
"It takes blue light from anywhere," he said. "It doesn't care where it comes from." Then he frowned. "No. It doesn't care about anything. It's a shape. Blue goes in, green comes out. That's all."
"That's not all," said Beto. "That's brilliant."
Ink and pencil
Before they left, Danya did what he always does. He asked how anyone could be sure.
The answer was in two places. People had grown crystals of this exact protein and fired X-rays through them, and the pattern the X-rays made had shown the barrel, strip by strip. That was something measured. And a computer program called AlphaFold had also predicted the barrel just from the order of its building blocks, and had said how sure it was about every single piece.
When the Fold draws a protein, it draws the sure parts in firm ink and the unsure parts in soft pencil. For this barrel nearly everything was ink. Only a few pieces right at the very end of the chain, the last loose bit, were pencil.
"So the barrel's real," said Danya. "Measured, and predicted, and they agree."
"And the end's a bit wobbly," said Beto.
"The end's a bit wobbly," Danya agreed. "That's not wrong. That's just the end."
The spark gave a small flicker, the way a candle does when a door opens somewhere.
The spark dimmed to a warm dot and settled back on the anvil. The Green was just the Green again.
Back on the Green
The next evening Beto had a new glow stick. He bent it until it cracked, shook it, and it glowed. He did not cut it open. He held it up next to the poster of the jellyfish at the small museum and looked from one to the other.
"Yours gets used up," said Danya. "The jellyfish keeps making the blue, and the barrels keep turning it green."
"As long as the barrels stay barrels," said Beto, and put the glow stick in his pocket in one piece.
The Honest Page
Every story in the Fold mixes three kinds of thing. Here is which is which.
Seen (measured in an experiment)
- GFP's shape: an eleven-strand barrel with the light-making group held in the middle, from X-ray crystal structures (PDB 1GFL, the natural protein, and 1EMA, a one-letter variant; both 1996).
- In the crystal jelly Aequorea victoria, a second protein, aequorin, gives out blue light when calcium binds it, and GFP turns that energy into green light.
- GFP takes in violet and blue light (its two strongest peaks are near 395 and 475 nanometres) and gives out green light (near 509 nanometres).
- Unfolded GFP does not glow. The light-making group forms from three of GFP's own amino acids only after the chain has folded.
Predicted (computed by AlphaFold, with how sure it is)
- The pencil-and-ink drawing below comes from AlphaFold's prediction for GFP, residue by residue. AlphaFold is very sure about almost all of the barrel.
Imagined (made up for the story)
- Beto, Danya and the spark, and the two children shrinking small enough to stand beside a protein.
- Barrels big enough for two children to stand beside. A real GFP is about 4 nanometres tall: thousands of them would fit across the width of a hair.
- Pulling the light out by hand. Nobody can do that; it is a picture of what unfolding does.
At the table
You need: a yellow highlighter pen, a sheet of white paper, a blue LED torch, and a dark room.
Draw a thick stripe with the highlighter. Turn the lights off and shine the blue torch on the stripe. The ink takes in the blue and gives out a bright yellow-green, the same blue-in, green-out idea as the barrel. Now try a red or white light, and compare.
For the grown-up at the table
GFP was first described in the crystal jelly in the 1960s. The 2008 Nobel Prize in Chemistry went to Osamu Shimomura, Martin Chalfie and Roger Tsien "for the discovery and development of the green fluorescent protein, GFP". Biologists now attach GFP to other proteins so they can see where those proteins are inside living cells. A cracked glow stick works by chemiluminescence (a reaction that uses chemicals up); the highlighter works by fluorescence (light in, different light out), which is what GFP does. Please keep glow sticks closed: the liquid irritates skin and eyes.
See it for yourself
The Fold is one of the spark doors on the Green, the town green shared with Spark & Anvil.