Reading the Book

How do living things give workers their Instructions? Life's Instruction Book is passive; it needs something to read it. It turns out that all living things have special workers -- we'll call them "dispatchers" for now -- whose job it is to read the Instruction Book and give workers their jobs. Well, almost: the dispatchers actually make the workers to carry out their jobs. For each Instruction, the dispatchers make one kind of worker. If a living thing has a hundred different kinds of workers, it must have a hundred Instructions in its Instruction Book. Real organisms have lots of different kinds of workers. E. coli, a bacterium that lives in the human gut, has about 4,400 kinds of workers. People have about 100,000 kinds.

This answer begs another question: how do the dispatchers know when a worker is needed or not? Some kinds of work need to be done all the time, some kinds need to be done when specific conditions are met, still others can be done except when certain things are happening. How do the dispatchers know which is which?

a promoter Life's Instruction Book has some special features about it that allow the dispatchers to decide which workers to make. The Instruction Book contains a note in the margin by each Instruction that marks the Instruction's beginning. These notes (called promoters) tell a kind of dispatcher called a transcription factor where to bring other dispatchers to make workers to carry out the Instruction. (The other dispatchers needed to make a worker are RNA polymerases and ribosomes. The RNA polymerase copies the Instruction into a message for a ribosome. Ribosomes read the messages to make workers that carry out the instruction. Details of how the dispatchers work -- and the reasons for their mysterious names -- are given in Making Workers.)

Promoters are not all equally good at attracting the attention of a transcription factor as it reads the Instruction Book. Those that almost always get noticed are called strong promoters, those that often get overlooked are called weak promoters. The different strengths of promoters provide living things some control over how many workers to make to carry out an Instruction. Strong promoters are noticed by almost every transcription factor that passes by them, so many workers are made for those Instructions. Few workers are made for Instructions with weak promoters.

Changing the numbers of workers that carry out an Instruction still doesn't quite control which work gets done when. That's the job of two other kinds of dispatchers, activators and repressors.

an activator Activators try to attract more transcription factors' attention to promoters for work that needs to be done. Most of them work by pointing out those promoters to the transcription factors by pointing and waving, but some seem to go further by leading the transcription factors over to the Instructions they want them to copy. To make matters more complicated, not all of the activators are equally good at getting the attention of the transcription factors; some can shout louder than others. Transcription factors tend to spend more of their time making workers for Instructions with noisy activators.

a repressor Repressors prevent unneeded Instructions from being carried out. Most of them work by covering up the promoters of Instructions, so that the transcription factors don't see them. Some also (or instead) cover up the Instruction itself, so that the transcription factors can't copy them. Some very aggressive repressors try to push activators or transcription factors away from the promoters they're looking for. Like promoters and activators, repressors vary in how well they turn off Instructions.

a repressor covering up a promoter
The interplay among promoters, activators, and repressors is complex and constantly changing. As living things' needs change, they make different kinds of activators and repressors to turn Instructions on and off. Occasionally, living things make different kinds of transcription factors -- which are not all alike in the kinds of notes they read -- to respond to big changes in Life's needs. All of these changes result in the ribosomes getting changing Instructions about what kinds of workers to make. It's even possible that some ribosomes are being told to make activators to turn an Instruction on at the same time as others are making repressors to turn it off. The activators and repressors then have to fight it out to see if the Instruction gets carried out. This isn't as bad as it sounds, since the Instructions for these contradictions are found in the Book itself; this is how the Instruction Book tells life how to live. In fact, most of the Instructions in Life's Big Instruction Book deal with telling the dispatchers which other Instructions to follow. So, at any given time, there are thousands (in some living things, tens of thousands) of kinds of workers crowded around the Book trying to tell the ribosomes what to do next. Fortunately, the ribosomes are a patient bunch.

There's one last dangling thread to tie off: how do the activators and repressors know when to attract attention? The Instruction that made them lets them sense a certain thing; it says says something like, "If you step in water on the floor, run over to the Book, stand by promoter #3148 and make lots of noise." Some activators and repressors don't sense things directly, but instead react to being handed notes by other workers that can. For example, let's say that there's a worker whose job it is to detect fires outside the factory. Rather than have him run to the Book when he sees a fire, his Instruction tells him to print up lots of notes that say "There's a fire outside!" and pass them around the factory. When the activators for fire-fighting Instructions get these notes, they run back to the Book and try to get the dispatchers to make the fire company. At the same time, repressors getting these notes try to shut down production of flammable substances. In this way, one worker can signal many activators and repressors to do a complex job. The process of passing messages from few workers to many workers is called a cascade.

Part One: Reading the Book
Introduction
Everything I needed to know, I learned from...
Reading the Book
Getting Organized
Workers, Tools, and Materials
How workers are organized
Seeing the Unseen
Book Binding
The Anatomy of a Worker
Making Workers
Seeing the Unseen -- Double Vision

Part Two: Copying the Book

Part Three: Improving the Book

Table of Contents
Questions? Comments or Suggestions? Copyright Notice