Genetic code 2.0: Life gets a new operating system
In the genetic code that life has used up to now, there are 64 possible triplet combinations of the four nucleotide letters; these genetic "words" are called codons. Each codon either codes for an amino acid or tells the cell to stop making a protein chain. Now Chin's team have created 256 blank four-letter codons that can be assigned to amino acids that don't even exist yet.
To achieve this, the team had to redesign three pieces of the cellular machinery that make proteins. But they didn't stop there. The team went on to prove their new genetic code works by assigning two "unnatural" amino acids to their quadruplet codons, and incorporated them into a protein chain.
But last month there was this: Horizontal and vertical: The evolution of evolution
The essence of the genetic code is that sequences of three consecutive bases, known as codons, correspond to specific amino acids. [...] There are 64 codons in total and 20 amino acids, which means that the code has some redundancy, with multiple codons specifying the same amino acid.
This code is universal, shared by all organisms, and biologists have long known that it has remarkable properties. In the early 1960s, for example, Woese himself pointed out that one reason for the code's deep tolerance for errors was that similar codons specify either the same amino acid or two with similar chemical properties. Hence, a mutation of a single base, while changing a codon, will tend to have little effect on the properties of the protein being produced.
In 1991, geneticists David Haig and Lawrence Hurst at the University of Oxford went further, showing that the code's level of error tolerance is truly remarkable. They studied the error tolerance of an enormous number of hypothetical genetic codes, all built from the same base pairs but with codons associated randomly with amino acids. They found that the actual code is around one in a million in terms of how good it is at error mitigation. "The actual genetic code," says Goldenfeld, "stands out like a sore thumb as being the best possible."
And all of this really reminds me of this: MOS Technology 6502, Bugs and quirks:
The original 6502 and its NMOS derivatives are noted for having a variety of undocumented instructions, which vary from one chip manufacturer to the next. The 6502's instruction decoding is implemented in a hardwired logic array (similar to a programmable logic array) which is only defined for 151 of the 256 available opcodes. The remaining 105 trigger strange and hard-to-predict actions (e.g., immediately crashing the processor, performing several valid instructions at once, or simply doing nothing at all).
Eastern House Software developed the "Trap65", a device that plugged between the processor and its socket to convert (trap) unimplemented opcodes into BRK (software interrupt) instructions. Some programmers utilized this feature to extend the 6502's instruction set by providing functionality for the unimplemented opcodes with specially written software intercepted at the BRK instruction's 0xFFFE vector.
So what's the genetic equivalent of this?
Half of your toes show up in the normal place, and half wrap around and grow out the top of your head? I wonder if the genetic implementation code assumes BCD ("Decimal") mode, or if you could
and suddenly grow 16 fingers instead of ten?
I still <3 the 6502 -- old-school NMOS style, cause that's how I ROL.
That's called a "teratoma", for which I most emphatically recommend that you do not google.
The word teratoma comes from classical Greek and means roughly "monstrous tumor".
The prolonged silence you hear? That's me not clicking on the "Images" search tab.
IT'S NOT A TOMA
When my friend Terri had a baseball-sized tumor removed, she named it Terri Toma.
It's a trap!
[insert groan]
But they make such great knitting projects!
The 6502 trap technique was used later by Apple on the 68000 to implement the Macintosh Toolbox. The entry points were known as A-traps, since Apple engineers used the 0xAxxx illegal instruction vector. And then when a bunch of them went to Palm, they did the same thing in Palm OS.
These instructions are actually specified behavior of the processor. They cause an exception, and the vector can inspect the instruction in question and take appropriate action.
They're also used on the TI-89 series of calculators. A-line instructions (0xA***) are unimplimented, while F-line instructions (0xF***) are a type of branch that uses an OS routine.
Why do I know this? I'm a calculator programmer. Yeahhhhh.
That would seem to be a level above the operator of a pocket calculator.
Apparently ciliates read genetic code differently than other organisms. How exactly I don't know: maybe they use a different endianness or something.
That is one of the more interesting things I've read of late; the sort of reading that makes me want to learn more about it, thanks!
Dropping these "orthogonal ribosomes" they've made into a life form is, basically, unpossible. It's a neat hack, maybe useful for doing some in vitro synthesis with wacky amino acids, but throwing quadruplet codons into even a simple life form would be catastrophic.
And yes, I Am A Ribosome Scientist.
Yeah, that's what you want us all to think, so you can keep the mutant powers to yourself.
LOL, the only superpower I want right now is the ability to graduate. ;-)
But seriously, after reading these guys' other papers I'm pretty impressed. They used some pretty tricky bacterial genetics to evolve a parallel 30S ribosome that only recognizes and translates a specially evolved parallel mRNA, and does this without killing the cell. (In general messing with ribosomes is a great way to get non-viable.) So they can run these alongside normal operations in a cell without breaking the world. Still, these special ribosomes are one trick ponies--they ONLY work with their special mRNAs.
So I would see definite scaling issues. In a rapidly growing cell as much as 80% of the cell's energy is devoted to building new ribosomes (I think this number is from yeast, which has been tuned by humans to be an incredibly efficient biochemistry factory). Add on top of that the burden of building a separate set of specialized ribosomes that can only make your special designer protein, and you're going to get a lousy yield of designer protein I expect.
A couple years ago some researchers created a third dna base pair (beyond A-T and C-G). http://pubs.acs.org/doi/abs/10.1021/ja078223d
I hope god gets a hotfix out, I'm sick of these fucking hax.