The theory of evolution is one of the best-known scientific theories around. Try to make it through a day without using or hearing the word "evolution" and you'll see just how widespread this theory is.

Evolution is fascinating because it attempts to answer one of the most basic human questions: Where did life, and human beings, come from? The theory of evolution proposes that life and humans arose through a natural process. A very large number of people do not believe this, which is something that keeps evolution in the news.

In this edition of HowStuffWorks, we will explore the theory of evolution and how it works. We will also examine several important areas that show holes in the current theory -- places where scientific research will be working in the coming years in order to complete the theory. The holes are considered by many to be proof that the theory of evolution should be overthrown. As a result, quite a bit of controversy has surrounded evolution ever since it was first proposed.

Let's start off by taking a look at the basic principles of the theory of evolution, look at some examples and then examine the holes.

The Basic Process of Evolution
The basic theory of evolution is surprisingly simple. It has three essential parts:

• It is possible for the DNA of an organism to occasionally change, or mutate. A mutation changes the DNA of an organism in a way that affects its offspring, either immediately or several generations down the line.

• The change brought about by a mutation is either beneficial, harmful or neutral. If the change is harmful, then it is unlikely that the offspring will survive to reproduce, so the mutation dies out and goes nowhere. If the change is beneficial, then it is likely that the offspring will do better than other offspring and so will reproduce more. Through reproduction, the beneficial mutation spreads. The process of culling bad mutations and spreading good mutations is called natural selection.

• As mutations occur and spread over long periods of time, they cause new species to form. Over the course of many millions of years, the processes of mutation and natural selection have created every species of life that we see in the world today, from the simplest bacteria to humans and everything in between.

Billions of years ago, according to the theory of evolution, chemicals randomly organized themselves into a self-replicating molecule. This spark of life was the seed of every living thing we see today (as well as those we no longer see, like dinosaurs). That simplest life form, through the processes of mutation and natural selection, has been shaped into every living species on the planet.

In the book "The Dragons of Eden," Carl Sagan summarized the theory of evolution in this way:

Accidentally useful mutations provide the working material for biological evolution -- as, for example, a mutation for melanin in certain moths, which changes their color from white to black. Such moths commonly rest on English birch trees, where their white coloration provides protective camouflage. Under these conditions, the melanin mutation is not an advantage -- the dark moths are starkly visible and are eaten by birds; the mutation is selected against. But when the Industrial Revolution began to cover the birch bark with soot, the situation was reversed, and only moths with the melanin mutation survived. Then the mutation was selected for, and, in time, almost all of the moths are dark, passing this inheritable change on to future generations. There are still occasional reverse mutations eliminating the melanin adaptation, which would be useful for the moths were English industrial pollution to be controlled. Note that in all this interaction between mutation and natural selection, no moth is making a conscious effort to adapt to a changed environment. The process is random and statistical.

Can such a simple theory explain all of life as we know it today? Let's start by understanding how life works and then look at some examples.

How Life Works: DNA and Enzymes
Evolution can be seen in its purest form in the daily evolution of bacteria. If you have read How Cells Work, then you are familiar with the inner workings of the E. coli bacteria and can skip this section. Here's a quick summary to highlight the most important points in How Cells Work:

• A bacterium is a small, single-celled organism. In the case of E. coli, the bacteria are about one-hundredth the size of a typical human cell. You can think of the bacteria as a cell wall (think of the cell wall as a tiny plastic bag) filled with various proteins, enzymes and other molecules, plus a long strand of DNA, all floating in water.

• The DNA strand in E. coli contains about 4 million base pairs, and these base pairs are organized into about 1,000 genes. A gene is simply a template for a protein, and often these proteins are enzymes.

• An enzyme is a protein that speeds up a particular chemical reaction. For example, one of the 1,000 enzymes in an E. coli's DNA might know how to break a maltose molecule (a simple sugar) into its two glucose molecules. That is all that that particular enzyme can do, but that action is important when an E. coli is eating maltose. Once the maltose is broken into glucose, other enzymes act on the glucose molecules to turn them into energy for the cell to use.

• To make an enzyme that it needs, the chemical mechanisms inside an E. coli cell make a copy of a gene from the DNA strand and use this template to form the enzyme. The E. coli might have thousands of copies of some enzymes floating around inside it, and only a few copies of others. The collection of 1,000 or so different types of enzymes floating in the cell makes all of the cell's chemistry possible. This chemistry makes the cell "alive" -- it allows the E. coli to sense food, move around, eat and reproduce. See How Cells Work for more details.

You can see that, in any living cell, DNA helps create enzymes, and enzymes create the chemical reactions that are "life."

Sexual Reproduction
Bacteria reproduce asexually. This means that, when a bacteria cell splits, both halves of the split are identical -- they contain exactly the same DNA. The offspring is a clone of the parent.

As explained in How Human Reproduction Works, higher organisms like plants, insects and animals reproduce sexually, and this process makes the actions of evolution more interesting. Sexual reproduction can create a tremendous amount of variation within a species. For example, if two parents have multiple children, all of the children can be remarkably different. Two brothers can have different hair color, different heights, different blood types and so on. Here's why that happens:

• Instead of a long loop of DNA like a bacterium, cells of plants and animals have chromosomes that hold the DNA strands. Humans have 23 pairs of chromosomes, for a total of 46 chromosomes. Fruit flies have five pairs. Dogs have 39 pairs, and some plants have as many as 100.

  The human chromosomes hold the DNA of the human genome. Each parent contributes 23 chromosomes.

• Chromosomes come in pairs. Each chromosome is a tightly packed strand of DNA. There are two strands of DNA joined together at the centromere to form an X-shaped structure. One strand comes from the mother and one from the father.
• Because there are two strands of DNA, it means that animals have two copies of every gene, rather than one copy as in an E. coli cell.

  Photo courtesy U.S. DOE, Human Genome Project

• When a female creates an egg or a male creates a sperm, the two strands of DNA must combine into a single strand. The sperm and egg from the mother and father each contribute one copy of each chromosome. They meet to give the new child two copies of each gene.
• To form the single strand in the sperm or egg, one or the other copy of each gene is randomly chosen. One or the other gene from the pair of genes in each chromosome gets passed on to the child.

A gene is nothing but a template for creating an enzyme. This means that, in any plant or animal, there are actually two templates for every enzyme. In some cases, the two templates are the same (homozygous), but in many cases the two templates are different (heterozygous).

Here is a well-known example from pea plants that helps understand how pairs of genes can interact. Peas can be tall or short. The difference comes, according to Carol Deppe in the book "Breed your own Vegetable Varieties":

...in the synthesis of a plant hormone called gibberellin. The "tall" version of the gene is normally the form that is found in the wild. The "short" version, in many cases, has a less active form of one of the enzymes involved in the synthesis of the hormone, so the plants are shorter. We refer to two genes as alleles of each other when they are inherited as alternatives to each other. In molecular terms, alleles are different forms of the same gene. There can be more than two alleles of a gene in a population of organisms. But any given organism has only two alleles at the most. Shorter plants usually cannot compete with the taller forms in the wild. A short mutant in a patch of tall plants would be shaded out. That problem isn't relevant when a human plants a patch or field with nothing but short plants. And short plants may be earlier than tall ones, or less subject to lodging (falling over) in the rain or wind. They also may have a higher proportion of grain to the rest of the plant. So shorter plants can be advantageous as cultivated crops. Specific mutations or alleles are not good or bad in and of themselves, but only within a certain context. An allele that promotes better growth in hot weather may promote inferior growth in cold weather, for example.

One thing to notice in Deppe's quote is that a mutation in a single gene may have no effect on an organism, or its offspring, or its offspring's offspring. For example, imagine an animal that has two identical copies of a gene in one allele. A mutation changes one of the two genes in a harmful way. Assume that a child receives this mutant gene from the father. The mother contributes a normal gene, so it may have no effect on the child (as in the case of the "short" pea gene). The mutant gene might persist through many generations and never be noticed until, at some point, both parents of a child contribute a copy of the mutant gene. At that point, taking the example from Deppe's quote, you might get a short pea plant because the plant does not form the normal amount of gibberellin.

Another thing to notice is that many different forms of a gene can be floating around in a species. The combination of all of the versions of all of the genes in a species is called the gene pool of the species. The gene pool increases when a mutation changes a gene and the mutation survives. The gene pool decreases when a gene dies out.

One of the simplest examples of evolution can be witnessed in an E. coli cell. To get a better grip on the process, we'll take a look at what happens in this cell.

The Simplest Example of Evolution
The process of evolution acts on an E. coli cell by creating a mutation in the DNA. It is not uncommon for the DNA strand in an E. coli bacterium to get corrupted. An X-ray, a cosmic ray or a stray chemical reaction can change or damage the DNA strand. In most cases, a particular E. coli cell with mutated DNA will either die, fix the damage in the strand or fail to reproduce. In other words, most mutations go nowhere. But every so often, a mutation will actually survive and the cell will reproduce.

Imagine, for example, a bunch of identical E. coli cells that are living in a petri dish. With plenty of food and the right temperature, they can double every 20 minutes. That is, each E. coli cell can duplicate its DNA strand and split into two new cells in 20 minutes.

Now, imagine that someone pours an antibiotic into the petri dish. Many antibiotics kill bacteria by gumming up one of the enzymes that the bacteria needs to live. For example, one common antibiotic gums up the enzyme process that builds the cell wall. Without the ability to add to the cell wall, the bacteria cannot reproduce, and eventually they die.

When the antibiotic enters the dish, all of the bacteria should die. But imagine that, among the many millions of bacteria living in the dish, one of them acquires a mutation that makes its cell-wall-building enzyme different from the norm. Because of the difference, the antibiotic molecule does not attach properly to the enzyme, and therefore does not affect it. That one E. coli cell will survive, and since all of its neighbors are dead, it can reproduce and take over the petri dish. There is now a strain of E. coli that is immune to that particular antibiotic.

In this example, you can see evolution at work. A random DNA mutation created an E. coli cell that is unique. The cell is unaffected by the antibiotic that kills all of its neighbors. This unique cell, in the environment of that petri dish, is able to survive.

E. coli are about as simple as living organisms can get, and because they reproduce so rapidly you can actually see evolution's effects on a normal time scale. In the past several decades, many different types of bacteria have become immune to antibiotics. In a similar way, insects become immune to insecticides because they breed so quickly. For example, DDT-resistant mosquitoes evolved from normal mosquitoes.

In most cases, evolution is a much slower process.

The Speed of Mutations
As mentioned in the previous section, many things can cause a DNA mutation, including:

• X-rays
• Cosmic rays
• Nuclear radiation
• Random chemical reactions in the cell

Large organisms such as human beings average about one mutation per ten gametes [a gamete is a sex cell, either sperm or egg] -- that is, there is a 10 percent chance that any given sperm or egg cell produced will have a new and inheritable change in the genetic instructions that make up the next generation. These mutations occur at random and are almost uniformly harmful -- it is rare that a precision machine is improved by a random change in the instructions for making it.

According to "Molecular Biology of the Cell":

Only about one nucleotide pair in a thousand is randomly changed every 200,000 years. Even so, in a population of 10,000 individuals, every possible nucleotide substitution will have been "tried out" on about 50 occasions in the course of a million years, which is a short span of time in relation to the evolution of species. Much of the variation created in this way will be disadvantageous to the organism and will be selected against in the population. When a rare variant sequence is advantageous, however, it will be rapidly propagated by natural selection. Consequently, it can be expected that in any given species the functions of most genes will have been optimized by random point mutation and selection.

According to the book "Evolution," by Ruth Moore, it is possible to speed up mutations with radiation:

So Muller put hundreds of fruit flies in gelatin capsules and bombarded them with X-rays. The irradiated flies were then bred to untreated ones. In 10 days thousands of their offspring were buzzing around their banana-mash feed, and Muller was looking upon an unprecedented outburst of man-made mutations. There were flies with bulging eyes, flat eyes, purple, yellow and brown eyes. Some had curly bristles, some no bristles...

Mutations fuel the process of evolution by providing new genes in the gene pool of a species.

Then, natural selection takes over.

Natural Selection
As you saw in the previous section, mutations are a random and constant process. As mutations occur, natural selection decides which mutations will live on and which ones will die out. If the mutation is harmful, the mutated organism has a much decreased chance of surviving and reproducing. If the mutation is beneficial, the mutated organism survives to reproduce, and the mutation gets passed on to its offspring. In this way, natural selection guides the evolutionary process to incorporate only the good mutations into the species, and expunge the bad mutations.

The book "Extinct Humans," by Ian Tattersall and Jeffrey Schwartz, puts it this way:

...in every generation, many more individuals are produced than ever survive to maturity and to reproduce themselves. Those that succeed -- the "fittest" -- carry heritable features that not only promote their own survival but are also passed along preferentially to their offspring. In this view, natural selection is no more than the sum of all those factors that act to promote the reproductive success of some individuals (and its lack in others). Add the dimension of time, and over the generations natural selection will act to change the complexion of each evolving lineage, as advantageous variations become common in the population at the expense of those less advantageous.

Let's look at an example of natural selection from How Whales Work.

The ancestors of whales lived on land -- there is evidence of the evolution of the whale from life on land to life in the sea (read How Whales Work for details), but how and why did this happen? The "why" is commonly attributed to the abundance of food in the sea. Basically, whales went where the food was. The "how" is a bit more perplexing: Whales are mammals, like humans are, and like humans, they lived and walked on solid ground, breathing air into their lungs. How did whales become sea creatures? One aspect of this evolution, according to Tom Harris, author of How Whales Work, is explained as follows:

To make this transition, whales had to overcome a number of obstacles. First of all, they had to contend with reduced access to breathable air. This led to a number of remarkable adaptations. The whale's "nose" moved from the face to the top of the head. This blowhole makes it easy for whales to breathe in air without fully surfacing. Instead, a whale swims near the surface, arches its body so its back briefly emerges and then flexes its tail, propelling it quickly to lower depths.

Photo courtesy Sea World Orlando

Odd as it seems that the whale's "nose" actually changed positions, the theory of evolution explains this phenomenon as a long process that occurs over perhaps millions of years:

• Random mutation resulted in at least one whale whose genetic information placed its "nose" farther back on its head.
• The whales with this mutation were more suited to the sea environment (where the food was) than "normal" whales, so they thrived and reproduced, passing on this genetic mutation to their offspring: Natural selection "chose" this trait as favorable.
• In successive generations, further mutations placed the nose farther back on the head because the whales with this mutation were more likely to reproduce and pass on their altered DNA. Eventually, the whale's nose reached the position we see today.

Natural selection selects those genetic mutations that make the organism most suited to its environment and therefore more likely to survive and reproduce. In this way, animals of the same species who end up in different environments can evolve in completely different ways.

Creating a New Species
Imagine that you take a group of Saint Bernards and put them on one island, and on another island you put a group of Chihuahuas. Saint Bernards and Chihuahuas are both members of the species "dog" right now -- a Saint Bernard can mate with a Chihuahua (probably through artificial insemination) and create normal puppies. They will be odd-looking puppies, but normal puppies nonetheless.

Given enough time, it is possible to see how speciation -- the development of a new species through evolution -- could occur among the Saint Bernards and the Chihuahuas on their respective islands. What would happen is that the Saint Bernard gene pool would acquire random mutations shared by all of the Saint Bernards on the island (through interbreeding), and the Chihuahuas would acquire a completely different set of random mutations shared by all of the Chihuahuas on their island. These two gene pools would eventually become incompatible with one another, to the point where the two breeds could no longer interbreed. At that point, you have two distinct species.

Because of the huge size difference between a Saint Bernard and a Chihuahua, it would be possible to put both types of dogs on the same island and have the exact same process occur. The Saint Bernards would naturally breed with only the Saint Bernards and the Chihuahuas would naturally breed with only the Chihuahuas, so speciation would still occur.

If you put two groups of Chihuahuas on two separate islands, the process would also occur. The two groups of Chihuahuas would accumulate different collections of mutations in their gene pools and eventually become different species that could not interbreed.

The theory of evolution proposes that the process that might create a separate Chihuahua-type species and Saint Bernard-type species is the same process that has created all of the species we see today. When a species gets split into two (or more) distinct subsets, for example by a mountain range, an ocean or a size difference, the subsets pick up different mutations, create different gene pools and eventually form distinct species.

Is this truly how all of the different species we see today have formed? Most people agree that bacteria evolve in small ways (microevolution), but there is some controversy around the idea of speciation (macroevolution). Let's take a look at where the controversy comes from.

Holes in the Theory
The theory of evolution is just that -- a theory. According to "The American Heritage Dictionary," a theory is:

A set of statements or principles devised to explain a group of facts or phenomena, especially one that has been repeatedly tested or is widely accepted and can be used to make predictions about natural phenomena.

Evolution is a set of principles that tries to explain how life, in all its various forms, appeared on Earth. The theory of evolution succeeds in explaining why we see bacteria and mosquitoes becoming resistant to antibiotics and insecticides. It also successfully predicted, for example, that X-ray exposure would lead to thousands of mutations in fruit flies.

Many theories are works in progress, and evolution is one of them. There are several big questions that the theory of evolution cannot answer right now. This is not unusual. Newtonian physics worked really well for hundreds of years, and it still works well today for many types of problems. However, it does not explain lots of things that were eventually answered by Einstein and his theories of relativity. People create new theories and modify existing ones to explain the unexplained.

In answering the open questions that still remain unsolved, the theory of evolution will either become complete or it will be replaced by a new theory that better explains the phenomena we see in nature. That is how the scientific process works.

Here are three common questions that are asked about the current theory of evolution:

• How does evolution add information to a genome to create progressively more complicated organisms?
• How is evolution able to bring about drastic changes so quickly?
• How could the first living cell arise spontaneously to get evolution started?

Question 1: How Does Evolution Add Information?
The theory of evolution explains how strands of DNA change. An X-ray, cosmic ray, chemical reaction or similar mechanism can modify a base pair in the DNA strand to create a mutation, and this modification can lead to the creation of a new protein or enzyme.

The theory of evolution further proposes that billions of these mutations created all of the life forms we see today. An initial self-replicating molecule spontaneously formed. It evolved into single-cell organisms. These evolved into multi-cell organisms, which evolved into vertebrates like fish, and so on. In the process, DNA structures evolved from the asexual single-strand format found in bacteria today into the dual-strand chromosomal format found in all higher life forms. The number of chromosomes also proliferated. For example, fruit flies have five chromosomes, mice have 20, humans have 23 and dogs have 39.

Evolution's mutation mechanism does not explain how growth of a genome is possible. How can point mutations create new chromosomes or lengthen a strand of DNA? It is interesting to note that, in all of the selective breeding in dogs, there has been no change to the basic dog genome. All breeds of dog can still mate with one another. People have not seen any increase in dog's DNA, but have simply selected different genes from the existing dog gene pool to create the different breeds.

One line of research in this area focuses on transposons, or transposable elements, also referred to as "jumping genes." A transposon is a gene that is able to move or copy itself from one chromosome to another. The book "Molecular Biology of the Cell" puts it this way:

Transposable elements have also contributed to genome diversity in another way. When two transposable elements that are recognized by the same site-specific recombination enzyme (transposase) integrate into neighboring chromosomal sites, the DNA between them can become subject to transposition by the transposase. Because this provides a particularly effective pathway for the duplication and movement of exons (exon shuffling), these elements can help create new genes.

Another area of research involves polyploidy. Through the process of polyploidy, the total number of chromosomes can double, or a single chromosome can duplicate itself. This process is fairly common in plants, and explains why some plants can have as many as 100 chromosomes.

The amount of research in this area is truly remarkable and is teaching scientists amazing things about DNA. The following links give you a taste of that research, and are interesting if you would like to learn more about these topics:

• Maize as a model for evolution
• Using Jumping Genes to Elucidate Gene Function
• Speciation by Polyploidy
• Genomes Online Database
• Genome Evolution Search Engine Query
• Studies in Probabilistic Sequence Alignment and Evolution

Question 2: How Can Evolution Be So Quick?
Imagine that you create a very large cage and put a group of mice into it. You let the mice live and breed in this cage freely, without disturbance. If you were to come back after five years and look into this cage, you would find mice. Five years of breeding would cause no change in the mice in that cage -- they would not evolve in any noticeable way. You could leave the cage alone for a hundred years and look in again and what you would find in the cage is mice. After several hundred years, you would look into the cage and find not 15 new species, but mice.

The point is that evolution in general is an extremely slow process. When two mice breed, the offspring is a mouse. When that offspring breeds, its offspring is a mouse. When that offspring breeds... And the process continues. Point mutations do not change this fact in any significant way over the short haul.

Carl Sagan, in "The Dragons of Eden," put it this way:

The time scale for evolutionary or genetic change is very long. A characteristic period for the emergence of one advanced species from another is perhaps a hundred thousand years; and very often the difference in behavior between closely related species -- say, lions and tigers -- does not seem very great. An example of recent evolution of organ systems in humans is our toes. The big toe plays an important function in balance while walking; the other toes have much less obvious utility. They are clearly evolved from fingerlike appendages for grasping and swinging, like those of arboreal apes and monkeys. This evolution constitutes a respecialization -- the adaptation of an organ system originally evolved for one function to another and quite different function -- which required about ten million years to emerge.

The fact that it takes evolution 100,000 or 10 million years to make relatively minor changes in existing structures shows just how slow evolution really is. The creation of a new species is time consuming.

On the other hand, we know that evolution can move extremely quickly to create a new species. One example of the speed of evolution involves the progress mammals have made. You have probably heard that, about 65 million years ago, all of the dinosaurs died out quite suddenly. One theory for this massive extinction is an asteroid strike. For dinosaurs, the day of the asteroid strike was a bad one, but for mammals it was a good day. The disappearance of the dinosaurs cleared the playing field of most predators. Mammals began to thrive and differentiate.

Example: The Evolution of Mammals
65 million years ago, mammals were much simpler than they are today. A representative mammal of the time was the species Didelphodon, a smallish, four-legged creature similar to today's opossum.

In 65 million years, according to the theory of evolution, every mammal that we see today (over 4,000 species) evolved from small, four-legged creatures like Didelphodon. Through random mutations and natural selection, evolution has produced mammals of striking diversity from that humble starting point:

• Humans
• Dogs
• Moles
• Bats
• Whales
• Elephants
• Giraffes
• Panda bears
• Horses

Let's take Carl Sagan's statement that "A characteristic period for the emergence of one advanced species from another is perhaps a hundred thousand years, and very often the difference in behavior between closely related species -- say, lions and tigers -- does not seem very great." In 65 million years, there are only 650 periods of 100,000 years -- that's 650 "ticks" of the evolutionary clock.

Imagine trying to start with an opossum and get to an elephant in 650 increments or less, even if every increment were perfect. An elephant's brain is hundreds of times bigger than an opossum's, containing hundreds of times more neurons, all perfectly wired. An elephant's trunk is a perfectly formed prehensile appendage containing 150,000 muscle elements (reference). Starting with a snout like that of an opossum, evolution used random mutations to design the elephant's snout in only 650 ticks. Imagine trying to get from an opossum to a brown bat in 650 increments. Or from an opossum to a whale. Whales have no pelvis, have flukes, have very weird skulls (especially the sperm whale), have blow holes up top, have temperature control that allows them to swim in arctic waters and they consume salt water rather than fresh. It is difficult for many people to imagine that sort of speed given the current theory.

Example: The Evolution of the Human Brain
Here is another example of the speed problem. Current fossil evidence indicates that modern humans evolved from a species called Homo erectus. Homo erectus appeared about 2 million years ago. Looking at the skull of Homo erectus, we know that its brain size was on the order of 800 or 900 cubic centimeters (CCs).

Modern human brain size averages about 1,500 CCs or so. In other words, in about 2 million years, evolution roughly doubled the size of the Homo erectus brain to create the human brain that we have today. Our brains contain approximately 100 billion neurons today, so in 2 million years, evolution added 50 billion neurons to the Homo erectus brain (while at the same time redesigning the skull to accommodate all of those neurons and redesigning the female pelvis to let the larger skull through during birth, etc.).

Let's assume that Homo erectus was able to reproduce every 10 years. That means that, in 2 million years, there were 200,000 generations of Homo erectus possible. There are four possible explanations for where the 50 billion new neurons came from in 200,000 generations:

• Every generation, 250,000 new neurons were added to the Homo erectus brain (250,000 * 200,000 = 50 billion).
• Every 100,000 years, 2.5 billion new neurons were added to the Homo erectus brain (2,500,000,000 * 20 = 50 billion).
• Perhaps 500,000 years ago, there was a spurt of 20 or so closely-spaced generations that added 2.5 billion neurons per generation.
• One day, spontaneously, 50 billion new neurons were added to the Homo erectus brain to create the Homo sapiens brain.

One line of current research is looking at the effect of very small changes in DNA patterns during embryonic development. Any new animal, be it a mouse or a human, starts life as a single cell. That cell differentiates and develops into the complete animal. A tremendous amount of signaling happens between cells during the development process to ensure that everything ends up in the right place. Tiny changes in these signaling processes can have very large effects on the resulting animal. This is how the human genome, with at most 60,000 or so genes, is able to specify the creation of a human body containing trillions of cells, billions of carefully wired neurons and hundreds of different cell types all brilliantly sculpted into organs as diverse as the heart and the eyes. The book "Molecular Biology of the Cell" puts it this way:

Humans, as a genus distinct from the great apes, have existed for only a few million years. Each human gene has therefore had the chance to accumulate relatively few nucleotide changes since our inception, and most of these have been eliminated by natural selection. A comparison of humans and monkeys, for example, shows that their cytochrome-c molecules differ in about 1 percent and their hemoglobins in about 4 percent of their amino acid positions. Clearly, a great deal of our genetic heritage must have been formed long before Homo sapiens appeared, during the evolution of mammals (which started about 300 million years ago) and even earlier. Because the proteins of mammals as different as whales and humans are very similar, the evolutionary changes that have produced such striking morphological differences must involve relatively few changes in molecules from which we are made. Instead, it is thought that the morphological differences arise from differences in the temporal and spatial pattern of gene expression during embryonic development, which then determine the size, shape and other characteristics of the adult.

In other words, there just are not that many differences in the DNA of a human and a whale, yet humans and whales look totally different. Small collections of DNA mutations can have a very big effect on the final result.

Right now, the signaling mechanisms that wire up the 100 billion cells in the human brain are something of a mystery. How can the mere 60,000 genes in the human genome tell 100 billion neurons how to precisely wire themselves in the human brain? No one right now has a clear understanding of how so few genes can meticulously wire so many neurons. In a developing fetus in the womb, DNA is correctly creating and wiring up millions of cells per minute. Given that DNA does wire up a working human brain every time a baby is born, it may be the case that DNA has special properties that make evolution work more efficiently. As the mechanisms become better understood, the effects of DNA mutations during development will become better understood as well.

Question 3: Where Did the First Living Cell Come From?
In order for the principles of mutation and natural selection in the theory of evolution to work, there have to be living things for them to work on. Life must exist before it can to start diversifying. Life had to come from somewhere, and the theory of evolution proposes that it arose spontaneously out of the inert chemicals of planet Earth perhaps 4 billion years ago.

Could life arise spontaneously? If you read How Cells Work, you can see that even a primitive cell like an E. coli bacteria -- one of the simplest life forms in existence today -- is amazingly complex. Following the E. coli model, a cell would have to contain at an absolute minimum:

• A cell wall of some sort to contain the cell
• A genetic blueprint for the cell (in the form of DNA)
• An enzyme capable of copying information out of the genetic blueprint to manufacture new proteins and enzymes
• An enzyme capable of manufacturing new enzymes, along with all of the building blocks for those enzymes
• An enzyme that can build cell walls
• An enzyme able to copy the genetic material in preparation for cell splitting (reproduction)
• An enzyme or enzymes able to take care of all of the other operations of splitting one cell into two to implement reproduction (For example, something has to get the second copy of the genetic material separated from the first, and then the cell wall has to split and seal over in the two new cells.)
• Enzymes able to manufacture energy molecules to power all of the previously mentioned enzymes

Obviously, the E. coli cell itself is the product of billions of years of evolution, so it is complex and intricate -- much more complex than the first living cells. Even so, the first living cells had to possess:

• A cell wall
• The ability to maintain and expand the cell wall (grow)
• The ability to process "food" (other molecules floating outside the cell) to create energy
• The ability to split itself to reproduce

• Perhaps the original energy molecule was very different from the mechanism found in living cells today, and the energy molecules happened to be abundant and free-floating in the environment. Therefore, the original cell would not have had to manufacture them.
• Perhaps the chemical composition of the Earth was conducive to the spontaneous production of protein chains, so the oceans were filled with unimaginable numbers of random chains and enzymes.
• Perhaps the first cell walls were naturally forming lipid spheres, and these spheres randomly entrapped different combinations of chemicals.
• Perhaps the first genetic blueprint was something other than DNA.

• Spontaneous creation - Random chemical processes created the first living cell.
• Supernatural creation - God or some other supernatural power created the first living cell.

And it doesn't really matter if aliens or meteorites brought the first living cell to earth, because the aliens would have come into existence through either spontaneous creation or supernatural creation at some point -- something had to create the first alien cells.

Most likely, it will be many years before research can completely answer any of the three questions mentioned here. Given that DNA was not discovered until the 1950s, the research on this complicated molecule is still in its infancy, and we have much to learn.

The Future of Evolution
One exciting thing about the theory of evolution is that we can see its effects both today and in the past. For example, the book "Evolution" mentions this:

The earliest known reptiles are so amphibian-like that their assignment to one category or the other is largely a matter of opinion. In this area of life, however, there was no missing link; all the gradations from amphibian to reptile exist with a clarity seldom equaled in paleontology.

In other words, there is plenty of evidence, past and present, for some sort of evolutionary process. We see it in bacteria and insects today, and we see it in the fossil record through the development of millions of species over millions of years.

After thinking about questions like the three mentioned in the previous sections, different people come to different conclusions. In the future, there are three possible scenarios for the theory of evolution:

• Scientists will come to a complete understanding of DNA and show how mutations and natural selection explain every part of the development of life on this planet.
• Scientists will develop a new theory that answers the questions posed above to almost everyone's satisfaction, and it will replace the theory of evolution that we have today.
• Scientists will observe a completely new phenomenon that accounts for the diversity of life that we see today. For example, many people believe in creationism. In this theory, God or some other supernatural power intervenes to create all of the life that we see around us. The fossil record indicates that hundreds of millions of new species have been created over hundreds of millions of years -- Species creation is an intense and constant process with an extremely long history. If scientists were to observe the creation process occurring the next time a major new species comes into existence, they could document it and understand how it works.

Let's assume that the theory of evolution as currently stated is the process that did bring about all of the life that we see today. One compelling question is: "What happens next?" Evolution must be at work right now. Our species, Homo sapiens, only appeared about 40,000 years ago. What does evolution have in store for human beings, and how will the change manifest itself?

• Will a child appear one day whose brain is twice as big as any normal human brain? If so, what will be the capabilities of that brain, and how will it differ from the brain seen today? Or are our brains slowly evolving right now?
• Will children appear one day who have more than 23 chromosomes? If so, what will be the effects of the new chromosomes?
• Will man learn how to control or accelerate evolution through genetic engineering? Once we completely understand different genomes, will we be able to engineer evolutionary steps that lead to new species on a much faster schedule? What would those species look like? What would we design them to do?

For lots more information on evolution and related topics, check out the links on the next page.

Lots More Information!

Related HowStuffWorks Articles

• How Cells Work
• How Cloning Works
• How Gene Pools Work
• How Human Reproduction Works
• How DNA Evidence Works
• How Nuclear Radiation Works
• How X-Rays Work
• Is there a difference between monkeys and apes?
• What is a fossil?
• Which came first, the chicken or the egg?
• How can children from the same parents look so different?

More Great Links

Sites About Evolution

• PBS: Evolution
• The Talk.Origins Archive
• The Creation/Evolution Controversy
• Amicus Curiae Brief of 72 Nobel Laureates, 17 State Academies of Science, and 7 Other Scientific Organizations, in Support of Appellees - impressive group of people endorsing evolution
• Introduction to Evolutionary Biology
• The Whale's Tale - research on whale evolution
• Mutation and Genome Evolution
• Whole Genome Homology Map: human on mouse background
• Chromosomes - nice chart comparing number of chromosomes
• Paleocene mammals of the world
• Elephant Evolution

• The True.Origin Archive
• Evolution Opponents Hold Congressional Briefing
• A Scientific Critique of Evolution
• Institute for Creation Research
• Answers in Genesis Ministries

• Maize as a model for evolution
• Speciation by Polyploidy
• Genomes Online Database
• Studies in Probabilistic Sequence Alignment and Evolution

• Introduction to the RNA World
• The RNA World: A Critique
• Did Life Begin in an RNA World?
• The Beginnings of Life on Earth
• The Probability of Abiogenesis
• From Primordial Soup to the Prebiotic Beach
• Abiogenesis: The First Frontier

• Breeding Schemes
• Pros and Cons of Inbreeding
• Diseases caused by single-factor (Mendelian) inheritance
• Basic Siberian Genetics
• Breeding Dogs for the Next Millennium
• Maine Coon Polydactyls

Books

• "Extinct Humans," by Ian Tattersall, Jeffrey Schwartz
• " The Spark of Life: Darwin and the Primeval Soup," by Christopher Wills, Jeffrey Bada
• "The Dragons of Eden: Speculations on the Evolution of Human Intelligence," by Carl Sagan
• "Defeating Darwinism by Opening Minds," by Phillip E. Johnson
• "Evolution," by Ruth Moore & Time-Life Books
• "Molecular Biology of the Cell," by Bruce Alberts, et al.
• "Walking with Dinosaurs: A Natural History," by Tim Haines
• "Dawn of Man: The Story of Human Evolution," by Robin McKie
• "Breed Your Own Vegetable Varieties," by Carol Deppe
• "The Naked Ape: A Zoologist's Study of the Human Animal," by Desmond Morris
• "The Blind Watchmaker," by Richard Dawkins
• "The Structure of Evolutionary Theory," by Stephen Jay Gould
• "At Home in the Universe: The Search for Laws of Self-Organization and Complexity," by Stuart Kauffman
• "Darwin's Black Box: The Biochemical Challenge to Evolution," by Michael J. Behe
• "The Origin of Species," by Charles Darwin
• "Darwin's Ghost: The Origin of Species Updated," by Steve Jones
• "Microcosmos: Four Billion Years of Evolution from Our Microbial Ancestors," by Lynn Margulis, et al
• "Icons of Evolution: Science or Myth?," by Jonathan Wells, Jody F. Sjogren (Illustrator)