Wednesday, October 07, 2009

Science Fictional Ribosomes

small subunit of the Thermus thermophilus ribosome"What you want is to add and subtract lengths of input DNA easily, and the feedback enzyme arrangement does this. When the feedback arrangement is in place, the molecule will open itself up for transcription much more easily, and more rapidly. Your program will be transcribed onto two strings of RNA. One of the RNA strings will go to a reader - a ribosome - for translation into a protein. Initially, the first RNA will carry a simple start-up code ––

~ Blood Music
by Greg Bear, 1985
This year's Nobel Prize in Chemistry went to three scientists - Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath - for their study of the structure and function of the ribosome", the organelle assembles proteins from amino acids based on nucleic acid sequences. Since ribosomes are essential part of the cellular machinery, it's no surprise that writers who incorporate genetics and biotechnology into their fiction include it in their fiction. They even provided the name for the bioscience-based science fiction subgenre called "ribofunk".

This classic 1971 human reenactment of protein synthesis, made by the Department of Chemistry at Stanford, can give you a pretty good idea of how ribosomes work1. (Click for bigger video)
The much abbreviated version:
  • DNA sequences that encode proteins are used as a template for the transcription of messenger RNA (mRNA)
  • a ribosome attaches to the mRNA
  • protein synthesis begins at a specific sequence of three nucleotides - the AUG start codon - within the mRNA
  • a transfer RNA (tRNA) that has a sequence complementary to the start codon sequence (the anticodon) carries the amino acid methonine to the ribosome.
  • a tRNA with an anticodon complementary to the next three nucleotides in the mRNA - the next codon - also binds the ribosome, and the amino acid it carries added to the initial methionine
  • this process continues along the length of the mRNA until a stop codon is reached and the newly synthesized protein is released from the ribosome
Greg Bear's mention of ribosomes in Blood Music gets the process right. Other science fiction writers have used ribosomes much more fancifully in their stories. Take, for example, the 2003 short story "Junk DNA" by Rudy Rucker and Bruce Sterling:
"You’re about to tell me that Alan Turing anticipated the notion of DNA as a program tape that’s read by ribosomes. And I’m not gonna be surprised."

"One step further," coaxed Veruschka. "Since the human body uses one kind of ribosome, why not replace that with another? The Universal Ribosome–it reads in its program as well as its data before it begins to act. All from that good junk DNA, yes Janna? And what is junk? Your bottom drawer? My garbage can? Your capitalist attic, and my start-up garage!"

"Normal ribosomes skip right over the junk DNA," said Janna. "It’s supposed to be meaningless to the modern genome. Junk DNA is just scribbled-over things. Like the crossed-out numbers in an address book. A palimpsest. Junk DNA is the half-erased traces of the original codes–from long before humanity."
While they use lots of sciency terminology, the description of ribosome function doesn't make much sense. Of course ribosomes skip over "junk DNA" - they don't interact with DNA at all. And while some "junk DNA" may be transcribed into "junk mRNA", it appears that those sequences are degraded before they can be used to encode protein. I'm just not grokking how "junk DNA" that is primarily made up degenerate coding sequences2, could be translated into proteins that do anything more than muck up cells, even given an Universal Ribosome Turing-like machine.3

And I should say that "Junk DNA" is an entertaining story if you can gloss over the nonsensical biology details - read it for yourself for free at Asimov's Science Fiction.

I'm hoping that science fiction writers will embrace recent research exploring complex biochemistry of our cells to come up with some interesting variations on life as we know it. I just wish they would get their terms straight (of course, that's probably just me).

Oh, and if you know other SF that uses ribosomes as a plot device, mention them in the comments. I know there is an episode of Star Trek:TNG that does, but I couldn't come up with any other examples.

1. Note that the ribosomal components are not depicted to scale. They are also a bit more colorfully dressed than you find in your typical cell.

2. What most biologists call "junk DNA" is primarily made up of repetitive DNA sequences from transposable elements, not interesteringly "scribbled over" ancient genes.

3. While DNA-based Turing machines have been proposed (and even shown to work in rudimentary form), the "computations" are not performed by protein synthesis, which is the function of ribosomes I don't think that's the case, anyway. My understanding of Turing machines is a little fuzzy. Mark Chu-Carroll has posts about them here and here and here that I'm still thinking about.

My related posts:

Animation: "Animation of the small subunit of the Thermus thermophilus ribosome. RNA shown in orange, protein in blue." Taken from PDB 1FKA and animated by David S. Goodsell


Arvind Mishra said...

Up to date and timely info.But question which haunts me often is why such precise science be necessarily described in SF? Does not it scares away a general reader?

Peggy said...

I think that's a good question. Undoubtedly there are some people who don't care for SF that's heavy on the technical detail. Personally, I like both technical and non-technical SF.

However, I do feel that if the author decides to include technical detail that it be essentially correct - especially if it's the primary basis of the story. I'm not asking for grad-school level understanding - most of the terminology and concepts I'm concerned with you should be able to find in a high school biology textbook.

jim said...
This comment has been removed by a blog administrator.
Peggy said...

jim: feel free to repost your comment without the spammy links