Gödel, Escher, Bach An Eternal Golden Braid by Douglas R. Hofstadter

given, but there is no complementary base where the enzyme is bound at

that instant, then the enzyme just detaches itself from the strand, and its job

is done.

It should be mentioned that when a "cut" instruction is encountered,

this pertains to both strands (if there are two); however, "delete" pertains

only to the strand on which the enzyme is working. If Copy mode is on,

then the "insert" command pertains to both strands-the base itself into the

strand the enzyme is working on, and its complement into the other strand.

If Copy mode is off, then the "insert" command pertains only to the one

strand, so a blank space must be inserted into the complementary strand.

And, whenever Copy mode i~ on, "move" and "search" commands

require that one manufacture complementary bases to all bases which the

sliding enzyme touches. Incidentally, Copy mode is always off when an

enzyme starts to work. If Copy mode is off, and the command "Shut off

copy mode" is encountered, nothing happens. Likewise, if Copy mode is

already on, and the command "Turn copy mode on" is encountered, then

nothing happens.

Amino Acids

There are fifteen types of command, listed below:

cut cut strand(s)

del delete a base from strand

SWI switch enzyme to other strand

mvr move one unit to the right

mvl move one unit to the left

cop turn on Copy mode

off turn off Copy mode

Ina insert A to the right of this unit

InC insert C to the right of this unit

Ing insert G to the right of this unit

int insert T to the right of this unit

rpy search for the nearest pyrimidine to the right

rpu search for the nearest purine to the right

Ipy search for the nearest pyrimidine to the left

I pu search for the nearest purine to the left

Each one has a three-letter abbreviation. We shall refer to the three-letter

abbreviations of commands as amino acids. Thus, every enzyme is made up of a

sequence of amino acids. Let us write down an arbitrary enzyme:

rpu - inc -cop - mvr - mvl - swi - Ipu -int

and an arbitrary strand:

TAGATCCAGTCCATCGA

(^508) Self-Ref and Self-Rep