Perl is...

...the duct tape of the internet.

~Hassan Schroeder, first web-master of Sun.

Transcription as Compilation

It occurred to me the other day that a useful metaphor for making proteins is, not a factory as current thinkiing goes, but rather, that of compiling a computer program from its source code. Treating transcription, the making of protein from its DNA sequence, as a parser seems to be a more natural end-point to the idea that is a computer code.

Like any science, molecular biology is driven by metaphors. The most popular method has been the factory metaphor. DNA is understood to be a DNA serves as a blue-print of the cell. A rough-n-ready copy of the blue-print is made in the form of RNA, which is read by machinery of the ribosome to make a protein. This forms the infamous central dogma of molecular biology: DNA -> RNA -> Protein

blueprint-factory metaphor has reigned supreme. In this method, we think of proteins as little machines, and we marvel at the Rube Goldberg machines that seem to inhabit the cell no matter where we look.


Traditionally, transcription inside the cell is seen as a manufacturing process. The

But recently, cracks have started to appear in this edifice. Now that researchers are beginning to glean the intricate machinery that regulates the DNA, the language of networks have started filter down into the literature. Filaments of interactions, where proteins that are made from the DNA blueprint, then itself binds back onto the DNA, producing a convulted linkages of cause-and-effect that is impossible to separate back into the clean stark lines of the central dogma.
What is a compiler? A compiler is a computer program that turns text written in one language (C++) into machine code that can be read by a computer. But reading a Joel Spolsky article, I came across the idea that translation from one language into another is also compilation. The example given was the first C++ compiler. Bjorne Stroustroup originally wrote the object-oriented extension to C as a pre-processor command. But the idea was that you would write the C++ program, as designed by Bjorne, and then the pre-compiler would turn that into C, then a C compiler would turn that into machine code, ready to run on your machine's microchip. Joel pointed out that this pre-compilation step is actually compilation. There was just as much work in translating C++ to C as there was in translating C to machine code.

And then I saw the analogy. What if DNA was C++, RNA was C and proteins was machine code? Yes, the hard and dirty work inside the cell was done by the protein code, representing the deep dark actions of the biochemistry, and of course, DNA was the C++. The analogy stretches even further when you think about compiler macros that are often embedded in C++ source files that depend on important information about the enviroment that the program is compiled in. This would make the compiler the ribosome.

So what does this analogy gain us? Well for starters, we can steal some ideas from compilers and apply it transcription. For instance, one common goal in language designers is boot-strapping. A computer language is essentially embedded in the compiler, a binary program that translates a computer program, as expressed in the text C++ file, into machine language. Boot-strapping means that a particular computer language is sophisticated enough to encode everything needed to write the compiler in that language. In C, we write the C compiler in C itself. With an existing C compiler, we should be able to compile the source code the compiler and output a functional binary of the compiler (this need not be identical to the existing compiler). In designing new versions of a C compiler, one must first use an older version of the compiler, to generate the binary of the new version of the compiler. But the moment of truth is when we use the new version of the compiler to generate itself in itself using its own source code.

So a test of a DNA, RNA, ribosome, protein is the ability to bootstrap. We use the ribosome to read the RNA that includes the ribosome component proteins, to make the new proteins, which are assembled into a new ribosome. There even examples of the old versions running around. For instance, mutant experiments often fold RNA from a latter eukaryotic orgnaism into the cell of a prokaryote. And the prokaryote will happily make (or compile) the visitor RNA, if the RNA makes it all the way through the cellular protective layer.

A strategy for all political stripes...

An apt summary of Republican political strategy:

....voice or no voice, the people can always be brought to the bidding of the leaders. That is easy. All you have to do is tell them that they are being attacked and denounce the pacifists for lack of patriotism and exposing the country to danger. It works the same way in any country.

~Hermann Goering, 1946.

source: made in a statement to G. M. Gilbert, a pyschologist who intervied Goering in prison during the Nuremberg war-crimes tribunal (Nuremberg Diary, Gilbert, 1961, Signet NY).

Diving into the ocean shore for the very first time...

Most of the stories about the Israeli pull-out of the Gaza strip seem to be derogatory of the Palestinians, except for this poignant story [need subscription] in the San Jose Mercury Times:

Palestinian teenagers Mahmoud Barbakh and Mohammed Jaroun grew up just a few minutes from the Mediterranean, but had never been to the beach.

On Monday, they waded into the waves with their jeans rolled up, then abandoned all caution and threw themselves into the surf.

"It was the sweetest thing in the whole world," said 15-year-old Mahmoud.

Candide on Katrina

Jon Stewart is the Voltaire of the early 21st century. He and his talented band of writers/editors/directors sum up, in a brilliantly edited montage, everything that is sickening about the Bush Administration's response to Katrina. And they are never less than absolutely funny about it. (source: onegoodmove.org/1gm/1gmarchive/002364.html).

[click on picture to play video]

Mini-sex

I was at this dinner-party, and as the topic of conversation wandered to sex, one women blurted out, "I lost my virginity to mini-sex."

Mini-sex? What the hell was that? Was it sex amongst midgets? I had to find out.

So I asked, "What, ah, is mini-sex?"

"Oh you don't know? Well, mini-sex is when it's five thrusts or less." Apparently, not very satisfying for a woman.

So boys, just try to hold it out for the sixth, and you won't be shamed and laughed-about behind your back.

Runaway email

Two secretaries in a Sydney law firm got sacked, after a flamewar started over a missing ham sandwich.

Ms Nugent writes a group email, "Yesterday I put my lunch in the fridge on level 19 which included a packet of ham, some cheese slices and two slices of bread which was going to be for my lunch today. Overnight it has gone missing and as I have no spare money to buy another lunch today, I would appreciate being reimbursed for it."

Melinda Bird replies that Ms Nugent had probably left her lunch on a different floor.

Ms Nugent taunts Ms Bird for being blonde.

Ms Bird responds, "Being a brunette doesn't mean you're smart, though."

Ms Nugent e-mails co-worker: "Let's not get personal, Miss Can't-Keep-A-Boyfriend."

Flame-war escalates.

Email exchange is forwarded to other colleagues at the firm (Allens Arthur Robinson).

Email is then forwarded to other offices in Sydney, including Westpac, Deloitte, Macquarie Bank, and JP Morgan. As one on-looker remarks, "This is magic. You can't script this sort of thing."

Ms. Bird and Ms. Nugent are fired.

Update: Groin's Grab has the complete exchange, with pictures.