Publish and Perish, part 17: Cracking the Code

[Context: read the previous part or start at the beginning. TW: bad amateur fiction!]

By the standards of Conley College, Room 111 of Joplin Hall, with 125 seats, was a very large lecture room. Gerald always enjoyed standing at the podium there; it made him feel important.

Before calling the class to order, he projected a screenshot of an online news headline onto the room’s giant screen: “Scientists Crack the Code of Another Primate Genome!”

“OK, everybody, let’s get started,” Gerald said. “I hope you all had a good weekend…”

One of his feistier front-row students cut in. “How was your weekend, Dr. Cutler?”

Gerald liked it when students displayed some mild curiosity about his life.

“Well, Mitch, if you must know, I had a fabulous time grading your quizzes,” he said. “They aren’t quite done yet, so I’ll return them on Wednesday, but they looked pretty good overall. However, several of you astonished me with your highly original hypotheses about the function of the endoplasmic reticulum.” He decided to go for an unplanned punchline. “I kept reading these answers and going, ‘er…. that was rough!’”

As a few students cackled or groaned at his joke, Gerald shifted gears. “OK, OK, enough ribosome humor for now,” he said as if quieting a boisterous comedy-club crowd. He pointed to the headline on the screen. “This headline popped up in the news last week. What do you think it means? Anyone?”

A few hands went up. Gerald called on someone in the back whose name he did not yet know.

“I’m guessing that another genome was just sequenced,” she said.

“All right. Do others have similar ideas? Raise your hand if so.” More hands shot up.

“OK. Good. I agree. Now consider this: is sequencing a genome the same thing as cracking a code?”

Mitch, the how-was-your-weekend guy, shot back, “Well, the headline writer seemed to think so.”

Gerald smiled. “Fair enough,” he said. “But did this journalist — who might have a degree in, you know, English, or one of those subjects — did the journalist get it right, in your opinion? Turn to your neighbor and discuss. You have two minutes.”

They seem animated this morning, Gerald thought as he observed the conversations. Sure enough, the first student to report out had an interesting take: “A sequence of letters, in and of itself, is not a code. A code involves mapping one domain to another domain: this means that, or this goes with that.”

Another student countered, “But if it’s a code that we haven’t solved yet, it’s still a code, right?”

Gerald tried to keep things going. “Good question!” he said. “However, my specific question here is not whether a code exists, but whether a code has been quote-unquote cracked. So, does the sequencing of a genome represent the cracking of a code? Or is the genome sequence just more data to which the same old code applies?”

“The same old code?” repeated Jori, another front-row eager beaver. “You mean like the table of the 64 mRNA codons?”

“Yes, very good,” said Gerald. “The table we went over last week, as originally derived by Nirenberg and Khorana and Holley. You all remember that, right?”

There were a couple of nods and a lot of blank faces. In an instant Gerald had managed to drain the room of 90% of its energy.

“Come on, people… That was like five days ago…. Marshall Nirenberg? The cell-free translation of poly-uracil?”

“Sorry … Poly-what-a-sill?” called a voice from the back, followed by titters of laughter.

Gerald sighed. “OK, this is important. Let’s do a bit of review,” he said.

And then, to his own surprise, he found himself beatboxing: “Bum, chhh, buh-dum-bum, chht. Bum, chhh, buh-dum-bum, chht.”

As the first couple rows started to clap along, Gerald switched to rhythmic chanting: “Nirenberg — he cracked the code! Nirenberg — he cracked the code! Following Crick and Watson’s road, Nirenberg — he cracked the code!”

More words came to him, and he sent them out into the room with inexplicable confidence: “Breaking open cells of E. coli, he took their ribosomes, that’s no lie! Poly-U in, phenylalanine out! It was Nobel stuff without a doubt!”

Even in his trance, Gerald sensed that it was time to wrap things up. “Nirenberg — he cracked the code! Nirenberg — he cracked the code! One codon down, sixty-three to go! Nirenberg — he cracked the code!”

A moment of stunned silence was followed by what sounded to Gerald like raucous applause. He wondered: What have I done?

Mitch broke in once again. “That was, um, pretty weird, Dr. Cutler. Is Nirenberg your scientific hero or something?” He said this in a pleasant voice, as if gently teasing.

“Well, think about it,” said Gerald. “This guy literally discovered the code upon which all life is based! You could not ask for a better, cooler scientific legacy than that, in my opinion. The rest of us have a lot of catching up to do.”

He tried to smile, then quickly abandoned the depressing comparison of himself to Nirenberg.

[Update: the story continues with part 18.]