Book Binding

Life's Instruction Book is physically very different from a man-made instruction book, like a bicycle assembly manual. The differences give it a set of properties that are also very different from a bicycle manual. (The information in Life's Instruction Book is also very differently organized than that in a bicycle manual.)

A bicycle instruction book consists of a number of pages, bound together (probably by staples) and placed in a cover of sturdy material for protection. The instructions themselves are printed on the pages in ink.

DNA chains Life's Instruction Book is made of DNA. A DNA molecule is like a pair of origami paper chains, running side by side. Each link in the chain represents a different "letter" of an instruction. Rather than the letters being printed on the links, though, the links have different shapes to record the letters. Each of these letter-links is called a base. There aren't very many kinds of letters in Life's instruction book. Where most human languages have twenty or more letters, the language Life's Instruction Book is written in has just four. The four letters are A, C, G, and, T. These letters are short for the chemical names of the bases: adenosine, cytosine, guanine, and thymine.

DNA links The four bases come in two pairs, A-T and C-G. In the Instruction Book, the pairs are always found together, one letter in one of the chains, and one in the other. So, if there's a G in one chain, the base across from it in the other chain must be a C. The same is true for A and T. Since the bases must pair with each other, they are called complements. For example, since C must pair with G, C is called G's complement. Each of the bases in a pair clings to its complement, due to its shape. The linking between the bases holds the pair of chains together. The two chains neatly wrap around each other; this is the well-known DNA double helix. For additional strength, the DNA double helix is wound around structural proteins called histones.

The clinging of the pairs of bases allows a worker to repair the Instruction Book. Should a link be damaged or even entirely knocked out of the Book, a repair worker can look at the base in the other chain to figure out what the missing base must be. This is an important part of how Life prevents its Instructions from being changed (mutated).

In real life, complementary bases are held together by their chemical properties as well as their shapes. Curious readers should take a look at the textbooks mentioned in the bibliography for the details.


DNA wrapped around a histone
Any change to an organism's Instruction Book, whether big or small, good or bad, is called a mutation. Anything that can cause a mutation is a mutagen. We'll describe the types of mutations and their effects while talking about reproduction. We'll look at some mutagens at the same time, and a few more by themselves.

An Instruction is always entirely written from letters on one of the chains of the Instruction Book. This chain is called the coding chain, because it encodes a gene. There's usually no Instruction on the other chain, which is called the non-coding or complementary chain. Some bacteria and viruses do manage to carefully overlap Instructions on both chains, but this is unknown in multi-cellular life.

If you want to read about mutations now, start with Smudging the Book and Is Change Good?.
Promoters and other notes Life needs to control its Instructions are written on the bases of the Book's chains as well. Most of these are found just before the Instruction they regulate, but some are after it or even within the Instruction. A few are even far away from their Instruction.

So how many bases do Instruction Books hold? Bacterial Instruction Books are pretty short: they contain a few million bases. Since the typical Instruction is a few thousand bases long, their Instruction Books contain a few thousand Instructions. Eukaryotes have much bigger Instruction Books. The smallest have tens of millions of bases; the largest have hundreds of billions. There doesn't seem to be much sense to why some eukaryotes have Instruction Books so much larger than others. Humans' Instruction Books are in the middle of the range, with about five billion bases. Sharks' and frogs' Instruction Books are about the same size. On the other hand, both the largest and smallest Instruction Books are found in the plant kingdom.

Does this huge size range mean that some eukaryotes have thousands of times more Instructions than others? No, it turns out that the situation is more complicated.

In many organisms, Life's Instruction Book isn't packed with Instructions. While the Books used by bacteria contain almost nothing but Instructions and their promoters, the Instructions in the Books used by multicellular living things make up only a few percent of their letters. There are usually huge gaps between Instructions that are many times the length of a typical Instruction. These gaps are filled with a variety of things. Some of the space is filled with Instructions whose promoters have mutated to become so weak that they are therefore no longer used. These unused Instructions are called psuedogenes. Other gaps contain information needed to make copies of the Book. Still other gaps are filled with old retro-viruses that infected the Book long ago. The bulk of the space in most multi-cellular Life's instruction books (including humans') is simply filled with gibberish that doesn't seem to do anything.

Not only are eukaryotes' Instruction Books filled with junk, their individual Instructions are as well. Most eukaryotic Instructions are made up of parts that will produce a worker (called exons) and parts that won't (introns). While this complicates the process of making workers, it provides eukaryotes with the ability to swap different exons between Instructions to produce new kinds of workers. We'll describe the details and effects of exon shuffling under sexual reproduction.
The physical arrangement of Life's Instruction Book differs between bacteria and higher organisms as well. In bacteria, the ends of the DNA double helix are simply joined together to form a loop. Some bacteria contain parts of their Instruction books on smaller loops, called plasmids. This is something like a real instruction book having supplements for special cases, like a bicycle manual having a supplement for attaching optional features, such as headlights.

Eukaryotes split up their Instruction Books further. Their Books are so large (comparatively) that they're split up into a number of separate pieces called chromosomes. These pieces of the Book are somewhat like the volumes of an encyclopedia: while each one contains a large number of Instructions, the sum total of the information is scattered around among all of them. Unlike plasmids, which bacteria can generally live without, a eukaryote requires all of its chromosomes to live and reproduce. (In real life, there are a few rare cases in which a eukaryote can live without a full set of chromosomes.)

Eukaryotes do one other funny thing: each of their factories keeps two copies of its Instruction Book. The two copies are nearly the same, and the chromosomes that make up each copy are kept together in pairs. Having two copies of their Instruction Books allows eukaryotes to preserve their Instructions in the face of genetic change. Where do the two copies come from? Like all living things, eukaryotes get them from their parents. The advantages and complexities of having two copies arise from sexual reproduction.

Having now taken a detailed look at how the Instruction Book is put together, let's now take a similarly close look at how workers are made.

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
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