Warning / Disclaimer: this is going to be a VERY long post, and there will not be a TL;DR version at the end of it. Nowhere in this am I going to claim that there is no God, and that he/she/it did not take a hand in getting the ball rolling. Your dogmatic views are all safe and secure.

All of this information can be found elsewhere on the internet, all I have done is gathered it here in one place, and corrected some small errors.

With that said here we go!

Everything is an adaptation

We tend to assume that all characteristics of plants and animals are adaptations that have arisen through natural selection. Many are neither adaptations nor the result of selection at all.

Why do so many of us plunk ourselves down in front of the TV with a microwave meal after a tiring day? Because it's convenient? Or because TV meals are "the natural consequence of hundreds of thousands of years of human evolution"?

Stop laughing. You've probably made similar assumptions. For just about every aspect of our bodies and behavior, it's easy to invent evolutionary "Just So" stories to explain how they came to be that way. We tend to assume that everything has a purpose, but often we are wrong.

Take male nipples. Male mammals clearly don't need them: they have them because females do and because it doesn't cost much to grow a nipple. So there has been no pressure for the sexes to evolve separate developmental pathways and "switch off" nipple growth in males. Some people claim the female orgasm exists for the same reason as male nipples, though this is a far more controversial idea.

Then there's our sense of smell. Do you find the scent of roses overwhelming or do you struggle to detect it? Can you detect the distinctive odor that most people's urine acquires after eating asparagus? People vary greatly when it comes to smell, largely due to chance mutations in the genes that code for the smell receptors rather than for adaptive reasons.

Yet other features are the result of selection, but not for the trait in question. For instance, the short stature of pygmies could be a side effect of selection for early childbearing in populations where mortality is high, rather than an adaptation in itself.

Multi-skilled genes

Another reason why apparent adaptations can be side effects of selection for other traits is that genes can have different roles at different times of development or in different parts of the body. So selection for one variant can have all sorts of seemingly unrelated effects. Male homosexuality might be linked to gene variants that increase fertility in females, for instance.

A non-adaptive or detrimental gene variant can also spread rapidly through a population if it is on the same DNA strand as a highly beneficial variant. This is one reason why sex matters: when bits of DNA are swapped between chromosomes during sexual reproduction, good and bad variants can be split up.

Other features of plants and animals, such as the wings of ostriches, may once have been adaptations but are no longer needed for their original purpose. Such "vestigial traits" can persist because they are neutral, because they have taken on another function or because there hasn't been enough evolution to eliminate them even though they have become disadvantageous. Take the appendix. There are plenty of claims that it has this or that function but the evidence is clear: you are more likely to survive without an appendix than with one.

So why hasn't it disappeared? Because evolution is a numbers game. The worldwide human population was tiny until a few thousand years ago, and people have few children with long periods between each generation. That means fewer chances for evolution to throw up mutations that would reduce the size of the appendix or eliminate it altogether - and fewer chances for those mutations to spread through populations by natural selection. Another possibility is that we are stuck in an evolutionary Catch-22 where, as the appendix shrinks, appendicitis becomes more likely, favoring its retention.

Wisdom teeth are another vestigial remnant. A smaller, weaker jaw allowed our ancestors to grow larger brains, but left less room for molars. Yet many of us still grow teeth for which there is no room, with potentially fatal consequences. One possible reason why wisdom teeth persist is that they usually appear after people reach reproductive age, meaning selection against them is weak.

For all these reasons and more, we need to be skeptical of headline-grabbing claims about evolutionary explanations for different behaviors. Evolutionary psychology in particular is notorious for attempting to explain every aspect of behavior, from gardening to rape, as an adaptation that arose when our ancestors lived on the African savanna.

Needless to say, without solid evidence, claims about how, for instance, TV dinners "evolved" should be taken with a large pinch of salt.

Natural selection is the only means of evolution

Much change is due to random genetic drift rather than positive selection. It could be called the survival of the luckiest.

Take a look in the mirror. The face you see is rather different to that of a Neanderthal. Why? The unflattering answer could be for no other reason than random genetic drift. With features that can vary somewhat in form without greatly affecting function, such as the shape of the skull, chance might play a bigger role in their evolution than natural selection.

The DNA in all organisms is under constant attack from highly reactive chemicals and radiation, and errors are often made when it is copied. As a result, there are at least 100 new mutations in each human embryo, possibly far more. Some are harmful and are likely to be eliminated by natural selection - by death of the embryo, for instance. Most make no difference to our bodies, because most of our DNA is useless junk anyway. A few cause minor changes that are neither particularly harmful nor beneficial.

You might think that largely neutral mutations would remain restricted to a few individuals. In fact, while the vast majority of neutral mutations die out, a few spread throughout a population and thus become "fixed". It is pure chance - some just happen to be passed on to more and more individuals in each generation.

Although the likelihood of any neutral mutation spreading by chance is tiny, the enormous number of mutations in each generation makes genetic drift a significant force. It's a little like a lottery: the chance of winning is minuscule but because millions buy a ticket every week there is usually a winner.

As a result, most changes in the DNA of complex organisms over time are due to drift rather than selection, which is why biologists focus on sequences that are similar, or conserved, when they compare genomes. Natural selection will preserve sequences with vital functions, but the rest of the genome will change because of drift.

Drifting through bottlenecks

Genetic drift can even counteract natural selection. Many slightly beneficial mutations can be lost by chance, while mildly deleterious ones can spread and become fixed in a population. The smaller a population, the greater the role of genetic drift.

Population bottlenecks can have the same effect. Imagine an island where most mice are plain but a few have stripes. If a volcanic eruption wipes out all of the plain mice, the island will be repopulated by striped mice. It's a case of survival not of the fittest, but of the luckiest.

Random genetic drift has certainly played a big role in human evolution. Human populations were tiny until around 10,000 years ago, and went through a major bottleneck around 2 million years ago. Other bottlenecks occurred when a few individuals migrated out of Africa around 60,000 years ago and colonized other regions.

There is no doubt that most of the genetic differences between humans and other apes - and between different human populations - are due to genetic drift. However, most of these mutations are in the nine-tenths of our genome that is junk, so they make no difference. The interesting question is which mutations affecting our bodies or behavior have spread because of drift rather than selection, but this is far from clear.

Natural selection leads to ever greater complexity

In fact, natural selection often leads to ever greater simplicity. And, in many cases, complexity may initially arise when selection is weak or absent.

If you don't use it, you tend to lose it. Evolution often takes away rather than adding. For instance, cave fish lose their eyes, while parasites like tapeworms lose their guts.

Such simplification might be much more widespread than realized. Some apparently primitive creatures are turning out to be the descendants of more complex creatures rather than their ancestors. For instance, it appears the ancestor of brainless starfish and sea urchins had a brain.

Nevertheless, there is no doubt that evolution has produced more complex life-forms over the past four billion years. The tough question is: why? It is usually simply assumed to be the result of natural selection, but recently a few biologists studying our own bizarre and bloated genomes have challenged this idea.

Rather than being driven by selection, they propose that complexity initially arises when selection is weak or absent. How could this be? Suppose an animal has a gene that carries out two different functions. If mutation results in some offspring getting two copies of this gene, these offspring won't be any fitter as a result. In fact, they might be slightly less fit due to a double dose of the gene. In a large population where the selective pressure is strong, such mutations are likely to be eliminated. In smaller populations, where selective pressure is much weaker, these mutations could spread as a result of random genetic drift (see Natural selection is the only means of evolution) despite being slightly disadvantageous.

The more widely the duplicated genes spread in a population, the faster they will acquire mutations. A mutation in one copy might destroy its ability to carry out the first of the original gene's two functions. Then the other copy might lose the ability to perform the second of the two functions. As before, these mutations won't make the animals any fitter - such animals would still look and behave exactly the same - so they will not be selected for, but they could nevertheless spread by genetic drift.

Use your mutations

In this way, a species can go from having one gene with two functions to two genes that each carry out one function. This increase in complexity occurs not because of selection but despite it.

Once the genome is more complex, however, further mutations can make a creature's body or behavior more complex. For instance, having two separate genes means each can be switched on or off at different time or in different tissues. As soon as any beneficial mutations arise, natural selection will favor its spread.

If this picture is correct, it means that there are opposing forces at the heart of evolution. Complex structures and behavior such as eyes and language are undoubtedly the product of natural selection. But when selection is strong - as in large populations - it blocks the random genomic changes that throw up this greater complexity in the first place.

This idea might even explain why evolution appears to speed up after environmental catastrophes such as asteroid impacts. Such events would slash the population size of species that survive, weakening selection and increasing the chances of greater genomic complexity arising through non-adaptive processes, paving the way for greater physical or behavioral complexity to arise through adaptive processes.

Evolution produces perfectly adapted creatures

You don't have to be perfectly adapted to survive, you just have to be as well adapted as your competitors. The apparent perfection of plants and animals may be more a reflection of our poor imaginations than of reality.

It's a theme repeated endlessly in wildlife documentaries. Again and again we are told how perfectly animals are adapted to their environment. It is, however, seldom true.

Take the UK's red squirrel. It appeared perfectly well adapted to its environment. Until the grey squirrel arrived, that is, and proved itself rather better adapted to broadleaf forests thanks, in part, to its ability to digest acorns.

There are many reasons why evolution does not produce "designs" that are as good as they could be. Natural selection's only criterion is that something works, not that it works as well as it might. Botched jobs are common, in fact. The classic example is the panda's thumb, which it uses to grasp bamboo. "The panda's true thumb is committed to another role. So the panda must... settle for an enlarged wrist bone and a somewhat clumsy, but quite workable, solution," wrote Stephen Jay Gould in 1978.

As this example shows, evolution is far more likely to reshape existing structures than to throw up novel ones. The lobed fins of early fish have turned into structures as diverse as wings, fins, hoofs and hands. We have five fingers because our amphibian ancestors had five digits, not because five is necessarily the optimal number of fingers for the human hand.

Many groups simply never evolve features that might have made them even more successful. Sharks lack the gas bladder that allows bony fish to control their buoyancy precisely, for example, and instead have to rely on swimming, buoyant fatty livers and, occasionally, a gulp of air. Similarly, mammals' two-way lungs are far less efficient than birds' one-way lungs. And sometimes creatures evolve features that actually reduce their overall fitness rather than increase it, such as the peacock's tail (see Evolution always increases fitness).

Use it or lose it

Continual mutation also means that if you don't use it, you lose it. For instance, many primates cannot make vitamin C, because of a gene mutation. This mutation makes no difference to animals that get plenty of vitamin C in their diet. However, when the environment changes, such loss of function can make a big difference, as one primate discovered on long sea voyages.

Evolution's lack of foresight can produce inherently flawed designs. The vertebrate eye - with its back-to-front wiring and blind spot where the wiring goes through the retina - is one example. Later adaptations have compensated for these problems to a large extent but once natural selection fixes upon a flawed, but workable, design, a species' descendants are usually stuck with it.

An organism's fitness is also relative to its environment, which is usually changing. There is a constant arms race going on between predator and prey, parasite and host. Many species have to evolve continuously just to maintain their current level of relative fitness, let alone get fitter. As the Red Queen says in Through the Looking Glass: "It takes all the running you can do, to keep in the same place."

Evolution's peak?

Humans are not running fast enough. Evolving through natural selection is about time and numbers. The number of new mutations that appear, and the number of chances that natural selection has to eliminate the harmful and favor the beneficial ones, depends on the size of a population, the number of offspring each individual has and on the number of generations, among other things.

We might like to think of ourselves as the most "highly evolved" species but, in terms of how many rounds of mutation and selection we've undergone, we are one of the least evolved species.

Around 10 billion new viral particles can be produced every day in the body of a person infected with HIV. By contrast, the total human population on Earth was no more than a few million until a few thousand years ago.

Furthermore, in a decade bacteria can produce 200,000 generations -- about the number of generations of humans there have been since our lineage split from that of chimpanzees. So it's hardly surprising that in less than a human lifespan we've seen the evolution of new diseases such as HIV and numerous antibiotic-resistant bacteria.

Although human evolution has sped up in the past 10,000 years, we are changing our environment faster still. As a result, instead of becoming better adapted we are actually becoming less well adapted to the world we are creating. Think of the huge range of modern afflictions, from obesity and allergies to short-sightedness and drug addiction, we suffer from. Viruses and bacteria might approach perfection, but we humans are at best a very rough first draft.

Evolution promotes the survival of species

In fact, evolution sometimes results in individuals or populations becoming less fit and may occasionally even lead to extinction.

The phrase "survival of fittest" is widely misunderstood (see 'Survival of the fittest' justifies everyone for themselves). Many wrongly assume it means that evolution always increases the chances of a species surviving.

There are several ways in which evolution can reduce the overall fitness of individuals or of populations. For starters, natural selection can take place at different levels - genes, individuals, groups - and what promotes the survival of a gene does not necessarily increase the fitness of the individuals carrying it, or of groups of these individuals.

For example, parasitic DNA elements, or transposons, can spread through a population even though they make their host organisms less fit. Transposons are one cause of genetic diseases such as hemophilia.

Similarly, selfish individuals may thrive at the expense of altruistic individuals in a group - making them the "fittest" - even though they make the group as a whole less competitive. Such cheaters can have disastrous consequences.

In 1932, J. B. S. Haldane suggested this could even lead to the extinction of populations - a phenomenon called evolutionary suicide. Models and some experimental evidence suggest he was right.

For instance, when nutrients run low, individual myxobacteria (slime bacteria) may come together to form a fruiting body to produce spores. Lab studies have shown that cheating myxobacteria that only produce spores and never help form the non-spore producing parts of the fruiting body can drive populations to extinction.

Genes capable of driving populations to extinction might have a practical use, however. Biologists are exploring the possibility of releasing engineered parasitic DNA into populations of malaria-carrying mosquitoes.

There is concern that something similar could happen accidentally. Fish that have been genetically modified to produce a growth hormone grow faster and larger, mature earlier and produce more eggs. But they are less likely to survive in the wild than unmodified fish. According to the Trojan gene hypothesis, a gene variant that produces such characteristics could spread rapidly through a wild population despite reducing individual fitness, and eventually drive the population to extinction.

Another way in which evolution can reduce a species' chances of survival is through the accumulation of detrimental mutations. Mutations provide the vital raw material for natural selection, so if the mutation rate is too low a population will not be able to evolve fast enough to keep up with environmental changes.

If, on the other hand, a population's mutation rate is too high, detrimental mutations may accumulate faster than natural selection can eliminate them. Eventually, the number of mutations can exceed the "error catastrophe threshold", again leading to the extinction of a population.

In theory, any species with a very small population could accumulate deleterious mutations faster than it can eliminate them. The problem is especially severe for asexual organisms such as the Amazon molly - an effect known as Muller's ratchet.

It is far less of a problem for sexually reproducing species because the exchange of genetic material between chromosomes can separate good and bad mutations. Some unlucky offspring get saddled with lots of nasty mutations and die out, while the lucky ones get hardly any.

In theory, a mutation catastrophe can also occur as a result of linkage. This refers to gene variants that are inherited together because they sit next to each other on a chromosome. Suppose a mutation that greatly increases the mutation rate somehow ends up next to a new mutation that greatly increases fitness. The immediate fitness benefits of the beneficial mutation will initially mask the deleterious effects of the "mutator" mutation, meaning both mutations will rapidly sweep through a population, ultimately with disastrous consequences.

A few doctors hope to exploit mutation accumulation to treat diseases. Certain viruses such as HIV are already close to the error catastrophe threshold. Drugs that increase the mutation rate of the viruses still further might push them over the threshold and drive a population of viruses inside a person's body to extinction.

Finally, it has long been recognized that the competition between members of the same species to reproduce - sexual selection - can favor traits that reduce a species' overall fitness. Male peacocks with the biggest and brightest tails might get the females' attention, but lugging around a heavy, conspicuous tail reduces their chances of survival.

Studies of threatened bird species suggest that sexual selection can indeed drive populations to extinction. Some biologists go so far as to blame sexual selection for the conspicuous consumption that threatens humanity's future.

According to the handicap principle, features such as peacocks' tails evolve precisely because they are disadvantageous. Consider an individual who is trying to signal to females how fit and strong he is. If the signal is easy to make, weaker males can easily cheat by making the same signal. But if making the signal is costly - such as growing a large, clumsy tail or giving away food - there's no way to cheat.

Proving that any of these phenomena have ever led to extinctions in the wild is far from easy, because any species to which this has happened are, of course, no longer around to study. The indirect evidence is growing ever stronger, though.

It doesn't matter if people do not understand evolution

At an individual level, it might not matter much. However, any modern society which bases major decisions on superstition rather than reality is heading for disaster

So your brother or mother is a creationist. Let them believe what they want, you might think. After all, it makes family get-togethers a lot easier and no difference to anyone else.

Or does it? Imagine if Mike Huckabee ends up as vice-president of the US - a mere heart attack away from the top job. Would you feel comfortable if the world's biggest superpower was run by a man who rejects evolution, thanks to the support of tens of millions of people who also refuse to accept the truth?

It is dangerous when leaders prefer dogma to biological reality: Stalin's support for the pseudoscience of Lysenko was a disaster for Soviet agriculture.

Evolving problems

The success of western civilization is based on science and technology, on understanding and manipulating the world. Its continued success depends on this, perhaps now more than ever.

Any leader who thinks evolution is a matter of belief is arguably unfit for office. How can someone who dismisses the staggering amount of evidence for evolution assembled by researchers in myriad fields possibly evaluate more subtle scientific evidence for, say, climate change?

What's more, evolution is directly relevant to many policy decisions. Infectious diseases from tuberculosis to wheat rust are making a comeback as they evolve resistance to our defenses. Antibiotic-resistant superbugs like MRSA are a growing problem. A deadly virus such as H5N1 bird flu or Ebola might evolve the ability to spread from human to human at any time, leading to a devastating pandemic. It is not possible to grasp how serious these threats are and plan for them unless you understand the power of evolution.

There are many more subtle areas where understanding evolution matters too. For instance, fishing policies that allow fishermen to keep only large fish are actually leading to the evolution of smaller fish. The tremendous changes we are making to the environment are altering many species, from rats becoming resistant to poisons to urban birds changing their songs to counter noise pollution.

There is our future, too. Modern biology is on the brink of giving us previously unimaginable power over the human body, from reshaping embryos to rewriting the genetic code and delaying the effects of ageing. Societies' views on if and how these powers should be used will inevitably be shaped by people's understanding of their evolutionary origins. Things look rather different depending whether you think we are a perfect, finished product or crude early prototypes thrown up by a desperately cruel process from whose clutches we now have to break free.

This is not to say that evolutionary theory tells us how to run societies (see Survival of the fittest justifies everyone for themselves) or make ethical decisions (see Accepting evolution undermines morality). It doesn't. It is a descriptive science, not a prescriptive one. It does, however, help us to make informed decisions.

'Survival of the fittest' justifies 'everyone for themselves'

The "fittest" can be the most loving and selfless, not the most aggressive and violent. In any case, what happens in nature does not justify people behaving in the same way

The phrase "survival of the fittest", which was coined not by Darwin but by the philosopher Herbert Spencer, is widely misunderstood.

For starters, there is a lot more to evolution by natural selection than just the survival of the fittest. There must also be a population of replicating entities and variations between them that affect fitness - variation that must be heritable. By itself, survival of the fittest is a dead end. Business people are especially guilty of confusing survival of the fittest with evolution.

What's more, although the phrase conjures up an image of a violent struggle for survival, in reality the word "fittest" seldom means the strongest or the most aggressive. On the contrary, it can mean anything from the best camouflaged or the most fecund to the cleverest or the most cooperative. Forget Rambo, think Einstein or Gandhi.

What we see in the wild is not every animal for itself. Cooperation is an incredibly successful survival strategy. Indeed it has been the basis of all the most dramatic steps in the history of life. Complex cells evolved from cooperating simple cells. Multicellular organisms are made up of cooperating complex cells. Super organisms such as bee or ant colonies consist of cooperating individuals.

Suicidal cells

When cooperation breaks down, the results can be disastrous. When cells in our bodies turn rogue, for instance, the result is cancer. So elaborate mechanisms have evolved to maintain cooperation and suppress selfishness, such as cellular "surveillance" programs that trigger cell suicide if they start to turn cancerous.

Looked at from this point of view, the concept of the survival of the fittest could be used to justify socialism rather than laissez-faire capitalism. Then again, the success of social insects could be used to argue for totalitarianism. Which illustrates another point: it is nonsense to appeal to the "survival of the fittest" to justify any economic or political ideology, especially on the basis that it is "natural".

Is cannibalism fine because polar bears do it? Is killing your brother or sister fine because nestlings of many bird species do it? Is murdering your children fine because mice sometimes eat their own pups? Is pedophilia fine because bonobo adults have sex with juveniles?

Powerful grip

Just about every kind of behavior that most of us regard as "unnatural" turns out to be perfectly natural in some nook or cranny of the animal kingdom. No one can plausibly argue that this justifies humans behaving in the same way.

Yet even though such examples expose the utter absurdity of appealing to what is "natural" to judge right from wrong - the naturalistic fallacy - we seem to have a strange blind spot when it comes to evolution. Survival of the fittest has been claimed to justify all kinds of things, from free markets to eugenics. Such notions still have a powerful grip in some circles.

However, natural selection is simply a description of what happens in the living world. It does not tell us how we should behave.

Evolution is limitlessly creative

It might seem like there is no end to nature's inventiveness but there are some features that could probably never evolve, at least on Earth

It often seems that nature invented pretty much everything that can be invented long before humans arrived on the scene - including the wheel, kind of. There is a salamander living in the Californian mountains that coils itself up and rolls downhill when threatened, for example. The pearl moth caterpillar goes one better and can roll itself along a flat surface for four or five revolutions to escape predators.

Nevertheless, there are structures that would clearly be useful but have never evolved. Zebras with built-in machine guns would rarely be bothered by lions, some point out. So why can evolution invent some things but not others?

This is an extremely difficult issue to tackle: how can we study something that has not happened? One way to approach it is to start with a question used by those who deny evolution and believe that many of nature's inventions, such as the eye or the bacterial flagellum, are simply too complex to have evolved. What use is half a wing, they ask? (see Half a wing is no use)

Very useful, it turns out. The wings of insects might have evolved from flapping gills that were originally used for rowing on the surface of water. This is an example of exaptation - structures and behaviors that evolved for one purpose but take on a wholly new one, while remaining useful at every intermediate stage.

Come in, over

Turn this argument around, however, and it suggests that some features cannot evolve because a half-way stage really would be of no use. For example, two-way radio might be useful for many different animals, for making silent alarm calls or locating other members of your species. So why hasn't it evolved? The recent invention of Nano scale radio receivers suggests it is not physically impossible.

The answer might be that half a radio really is useless. Detecting natural radio waves - from lightning, for instance - would not tell animals anything useful about their environment. That means there will be no selection for mutations that allow organisms to detect radio waves. Conversely, without any means of detecting radio waves, emitting them would serve no useful purpose. Radar might not be able to evolve for similar reasons.

The contrast with visible light could hardly be greater. It is clear that simply detecting the presence or absence of light would be advantageous in many environments, that even a blurry picture is better than nothing at all, and so on right up to hawk-eyed sharpness.

Seaweed skies

Emitting visible light can be helpful too, even for creatures that cannot detect it themselves. For the bioluminescent phytoplankton that light up ocean waves, for instance, it is a way of summoning predators that eat the phytoplankton's enemies. A similar argument applies to sound: it is not hard to see how forms of echolocation evolved independently in groups such as bats, cave swiftlets and whales.

One might also wonder why plants that float in the sky like balloons have never evolved. The idea does not seem too far-fetched at first glance: many seaweeds have floats called pneumatocysts, filled with oxygen or carbon dioxide. Other algae can produce hydrogen. So fill a large, thin pneumatocyst with hydrogen and perhaps a seaweed could fly. Flying plants would beat water and land plants to the light, giving them a big advantage, so why aren't our skies filled with living green balloons?

Perhaps partly because large pneumatocysts with extremely thin membranes would be far more vulnerable to predators and damage from waves, so an intermediate stage could never evolve. What's more, algae produce hydrogen only when there's a lack of sulphur in the water, and in any case the molecules of hydrogen gas are so tiny that they would leak out of any pneumatocysts. Half a hydrogen balloon doesn't look very good for anything, at least on our planet. Even evolution has its limits.

Natural selection cannot explain homosexuality

There are numerous evolutionary mechanisms that might explain homosexual behavior, which is common in many species of animals.

"Simple reasoning shows that evolution cannot explain homosexuality - how would a homosexuality gene get selected for?" "Why have the genetic traits predisposing to homosexuality not been eliminated long ago?"

Such arguments are surprisingly common - and completely wrong.

Homosexual behavior has been observed in hundreds of species, from bison to penguins. It is still not clear to what extent homosexuality in humans or other animals is genetic (rather than, say, due to hormonal extremes during embryonic development), but there are many mechanisms that could explain why gene variants linked to homosexuality are maintained in a population.

A common assumption is that homosexuality means not having children, but this is not necessarily true, especially in cultures other than our own. Until it became acceptable for same-sex couples to live together in western countries, many homosexual people had partners of the opposite sex. In some traditional societies, various forms of non-exclusive homosexuality were common.

Reasons why

Among animals, homosexual behavior is usually non-exclusive. For instance, in some populations of Japanese macaques, females prefer female sexual partners to male ones but still mate with males - they are bisexual, in other words.

It has also been suggested that homosexuality boosts individuals' reproductive success, albeit indirectly. For instance, same-sex partners might have a better chance of rising to the top of social hierarchies and getting access to the opposite sex. In some gull species, homosexual partnerships might be a response to a shortage of males - rather than have no offspring at all, some female pairs raise offspring together after mating with a male from a normal male-female pair.

Another possibility is that homosexuality evolves and persists because it benefits groups or relatives, rather than individuals. In bonobos, homosexual behavior might have benefits at a group level by promoting social cohesion. One study in Samoa found gay men devote more time to their nieces and nephews, suggesting it might be an example of kin selection (promoting your own genes in the bodies of others).

For your health

Or perhaps homosexuality is neutral, neither reducing nor boosting overall fitness. Attempts to find an adaptive explanation for homosexual behavior in macaques have failed, leading to suggestions that they do it purely for pleasure.

Even if homosexuality does reduce reproductive success, as most people assume, there are plenty of possible reasons why it is so common. For instance, gene variants that cause homosexual behavior might have other, beneficial effects such as boosting fertility in women, as one recent study suggests, just as the gene variant for sickle-cell anemia is maintained because it reduces the severity of malaria. Homosexuality could also be a result of females preferring males with certain tendencies - sexual selection can favor traits that reduce overall fitness, such as the peacock's tail (see Evolution always increases fitness).

Given that, until recently, homosexual behavior in animals was ignored or even denied, it's hardly surprising that we cannot yet say for sure which of these explanations is correct. It could well turn out that different explanations are true in different species.

Creationism is a coherent alternative to evolution

The only thing that creationists agree on is that they don't like evolution. Even Genesis gives two contradictory accounts of creation

If someone tells you that creationism provides a better explanation for life on Earth than the theory of evolution, ask them which version of creationism.

Among creationists, there is an extraordinary range of beliefs about how life came to be. A few creationists accept that evolution produced the great diversity of life on Earth - apart from humans. Others think all life evolved but that the process was guided by a supernatural being.

Other creationists accept that evolution can lead to minor changes (microevolution) but deny that lots of little changes can result in new species or even new groups of organisms (macroevolution). Some think a deity created the very first life but then left it to evolve by itself.

Then there's the vexed issue of timing. "Young Earth Creationists" regard the Genesis account as "inerrant" despite its contradictions (see Evolution is wrong because the Bible is inerrant), and claim the planet was created about 6000 years ago. "Old Earth Creationists" meanwhile accept the hundreds of lines of evidence suggesting otherwise.

God, amok

This schism is just the beginning. Some don't dispute the earth's apparent age but believe it is an illusion (the omphalos hypothesis, which some summarize as "God faked it"). Yet others claim that the planet itself is billions of years old but that life on it was created only recently.

Creationists do at least all believe in a creator. But who is it: God, Allah, Yahweh, Brahma, Zeus, Olorun, aliens or a giant hermaphrodite?

Those who have studied our planet and the life on it, however, have come to very clear conclusions: the Earth is around 4 billion years old and all the life on it gradually evolved from much simpler forms. There is no evidence of any kind of outside intervention, and no need to invoke it to explain what is known. Yes, there are many debates among biologists, geologists and cosmologists over the finer details, but these will be resolved sooner or later by new discoveries or experiments. Reality is the ultimate arbiter.

By contrast, there is no way to resolve the often vast differences between the numerous forms of creationism. Anyone can come up with their own version of creationism (and many do). How do you convince the followers of the Flying Spaghetti Monster, for instance, that his noodle is not the real creator?

The theory is wrong because the Bible is 'inerrant'

This argument is undermined by the hundreds of errors and inaccuracies and contradictions found in Bible. It is anything but "inerrant".

A few creationists are honest enough to admit that the evidence supporting the theory of evolution is irrelevant as far as they are concerned: as it contradicts the "Word of God", it simply has to be wrong.

Some Christians regard the text of the Bible as literally true or, to use their term, as "inerrant". If people reject evolution on this basis, it is only fair to ask whether this belief stands up.

Whichever translation of the Bible you look at it is not hard to find errors. The texts are full of internal contradictions as well as historical and scientific inaccuracies.

There are so many examples it is hard to know where to start. Take its cosmology: according to the Bible, the earth is flat and immovable, the moon emits its own light, the sky is solid and the stars can be shaken from the sky by earthquakes.

Its mathematics is also poor. How many sons do you count: "The sons of Shemaiah: Huttush, Igal, Bariah, Neriah, and Shaphat, six" (I Chronicles 3:22). Such errors are common. The value of pi is given as 3, even though many other cultures had already worked it out with greater precision.

Bible biology

Its biology is no better. The Bible claims that rabbits chew the cud, that the pattern of goats' coats can be changed by what their parents look at while copulating, that only dead seeds can germinate and that ostriches are careless parents.

Fundamentalists try to explain away some of these examples in the light of what we now know: pi is approximately three, they point out, while rabbits eat their own droppings, which is a bit like chewing the cud. But such explanations essentially admit that the Bible is not the ultimate source of of reliable truths about the world.

In other words, if you want to know anything from how rabbits digest their food or how to breed goats to the value of pi or whether the sun orbits the earth or vice versa, you have to turn to science and mathematics, not the Bible. If that's the case, then surely the same is true of how life on Earth came about?

So how reliable is the Bible chapter that relates to evolution? Let's leave aside the long-standing evidence that Earth is older than 6000 years and that there was no world-wide flood, and look at what else Genesis says.

Genesis 1 gives the order of creation as plants, animals, man and woman. Genesis 2 gives it as man, plants, animals and woman. Genesis 1:3-5 says light was created on the first day, Genesis 1:14-19 says the sun was created on the fourth. Genesis 7:2 says Noah took seven pairs of each beast, Genesis 7:8-15 says one pair.

The list goes on. The fruit of the tree of knowledge is said to kill within a day of being eaten, yet Adam and Eve don't die after eating it. Genesis says there were giants (Nephilim) before the flood and that the flood annihilated all creatures other than those on the ark, but Numbers says there were giants after the flood.

Sorting it out

Attempts to resolve these contradictions are almost as old as the Bible itself. Those who regard the Bible as inerrant tie themselves in knots trying to explain them away (hands up who believes that T. rex was once a peaceful vegetarian?), or even take it upon themselves to rewrite the Bible to expunge them.

However, there are far too many errors, inaccuracies and contradictions to dismiss them all. The only rational and reasonable conclusion is that the Bible is not inerrant.

Don't believe me? Good, that's the spirit. Question everything. Go look up all these examples for yourself and make up your own mind.

Accepting evolution undermines morality

Actually people in more secular countries appear to behave more morally. And even if this claim was true, that would not alter the facts or justify their suppression.

"Darwinism claims that living beings have evolved as a result of coincidences and by means of a struggle for life. This evil morality advises people to be egoistical, self-seeking, cruel and oppressive."

Such views are not uncommon. The unspoken implication is either that "Darwinism" (see Biologists are Darwinists) is wrong because it leads to immorality, or that this knowledge should be suppressed even though it is true. Both are nonsense. Even if it were true that accepting the theory of evolution undermined people's sense of morality, it is not a reason to doubt the reality of evolution. This is equivalent to arguing that atomic theory must be wrong because a nuclear war would be catastrophic.

It is also simply not true that evolution undermines morality. Certainly there are examples of people appealing to evolutionary ideas to justify behavior some would regard as immoral, although the best example one creationist could find was a song called The Bad Touch by the Bloodhound Gang, with its chorus: "You and me baby ain't nothin' but mammals. So let's do it like they do on the Discovery Channel."

On the other hand, one could draw up an extremely long list of examples of people appealing to religion to justify immoral behavior, from slavery and racism to suicide bombings and genocide. This kind of exercise proves little, though.

Rational morality

A better way of assessing the effects of embracing evolution is to compare countries with different levels of acceptance. Countries where higher numbers of people accept evolution have lower rates of murders, sexually transmitted diseases, teenage pregnancies and so on. In fact, more secular societies are healthier in almost every regard, one 2005 study concluded. [link to globalhealth.washington.edu]

This kind of crude correlation does not prove accepting evolution actually promotes moral behavior, nor that religion promotes immoral behavior. Indeed, other studies suggest the issue is far more complex. But it does prove accepting evolution does not immediately lead to the breakdown of society, as some creationists claim.

Those who dismiss evolution as immoral often assume that religion is crucial to morality. As in: "People who believe in evolution have no basis for a moral code, other than the preeminent concern to pass on one's genetic inheritance."

In fact, there is growing evidence that we have an innate moral sense - that morality is something that evolved, in other words. This may seem surprising to those for whom the phrase "survival of the fittest" conjures up images of lions ripping each other to shreds and stags clashing antlers. But "the fittest" can mean the cleverest, the sneakiest, the best camouflaged, the least aggressive, the most attractive - or the least selfish.

Natural selection can favor altruism and fair play in certain circumstances. Behaviors such as loyalty to kin, intolerance of theft and punishment of cheats - the roots of morality - can be seen in many of our primate cousins.

Evolutionary theory leads to racism and genocide

Darwin's ideas have been invoked as justification for all sorts of policies, including some very unpleasant ones. But evolutionary theory is a descriptive science. It cannot tell us what is right and wrong.

Rather than attack evolution directly, some try to tar it by association. The claim is often made that the theory of evolution leads inevitably to eugenics and to atrocities like those perpetrated by Hitler. These claims are irrelevant to the reality of evolution and are also largely untrue.

Let's start with Darwin himself, who is often accused of being a racist and a eugenicist. Yet Darwin went very much against the ideas of his time by dismissing some of the perceived differences between races. For instance: "...this fact can only be accounted for by the various races having similar inventive or mental powers."

The following passage is often quoted by those who accuse him of supporting eugenics: "It is surprising how soon a want of care, or care wrongly directed, leads to the degeneration of a domestic race; but excepting in the case of man himself, hardly any one is so ignorant as to allow his worst animals to breed."

The next few paragraphs are often left out: "...If we were to intentionally neglect the weak and the helpless, it could only be for a contingent benefit, with overwhelming present evil. Hence we must bear without complaining the undoubtedly bad effects of the weak surviving and propagating their kind..."

Eugenical Christians

There is no doubt that some of those who supported eugenics cited Darwin's theory of evolution as inspiration or justification, but then evolution has been invoked to support all kinds of notions and schemes, from communism to capitalism.

Biology tells us what is, not what ought to be. It is descriptive, not prescriptive or normative. It can inform our decisions by telling us what the likely outcome of different actions will be, but not which of these outcomes are ethical or desirable.

In retrospect, it is clear that many of the eugenic policies implemented in the early 20th century were based as much if not more on racial and social prejudices than on any understanding of genetics and evolution. Some may have used evolutionary theory as an excuse, but that does not make it the cause.

What's more, many of the most enthusiastic promoters of the eugenics movement in the US, which led to policies such as compulsory sterilization, were evangelical Christians. As Mary Teats explained in her book The Way of God in Marriage: "The great and rapidly increasing army of idiots, insane, imbeciles, blind, deaf-mutes, epileptics, paralytics, the murderers, thieves, drunkards and moral perverts are very poor material with which to 'subdue the world', and usher in the glad day when 'all shall know the Lord'."

As for the Holocaust, the murder of able-bodied and able-minded people solely on the basis of their religion can hardly be called eugenics. It is incredible to blame Darwin while overlooking the role of Christianity in fostering anti-Semitism over the centuries.

In 1543, for instance, Martin Luther wrote a booklet called On the Jews and Their Lies calling, among other things, for Jews to be expelled or forced to do manual labor, and their synagogues and schools burned. The booklet was displayed at Nazi rallies. And this is how Hitler described his motivations in Mein Kampf, in which there is no mention of Darwin or the theory of evolution: "Hence today I believe that I am acting in accordance with the will of the Almighty Creator: by defending myself against the Jew, I am fighting for the work of the Lord."

Religion and evolution are incompatible

There are various ways in which the known facts about evolution can be reconciled with theistic religions. Some of these ways might be illogical and irrational, but they are no more illogical and irrational than other aspects of religions.

The biologist Stephen Jay Gould argued that there is no conflict between science and religion: "Science tries to document the factual character of the natural world, and to develop theories that coordinate and explain those facts. Religion, on the other hand, operates in the equally important, but utterly different, realm of human purposes, meanings, and values."

This line is popular with those who wish to avoid confrontation. Most people, however, see both science and religion as making factual claims about the natural world, and no scientific facts are harder to reconcile with religious claims than those of evolution. Almost all the major religions are divided on the issue, with some sects, priests or scholars accepting it as reality and others rejecting it.

Needless to say, evolution is incompatible with a literal interpretation of the creation myths that form part of many religious texts, such as Genesis (see Evolution is wrong because the Bible is inerrant). Of the major religions, only Buddhism escapes this fundamental conflict: its founder is said to have refused to answer questions about the origin of life.

God steps in

Polls suggest many people in western countries who believe in a supernatural being accept that evolution happened but believe its course was somehow influenced by that being.

In the absence of a time machine that would allow us to observe every step in the evolution of humans, the possibility that some deity or alien intervened in the process cannot be ruled out.

However, this "god of the gaps" argument is the logical equivalent of standing on a beach pointing to missing sections in a trail of footprints and claiming the creator must have flown between the gaps - even as incoming waves create more gaps in the trail, and even as the ordinary-looking person who made the footprints can be seen walking along in the distance.

Even without that time machine, we are starting to identify many of the mutations that made us human, such as ones related to learning, speech and brain size, and there is nothing supernatural about them. As more and more genomes are sequenced, and more fossils unearthed, we will be able to fill in ever more of the details.

In the beginning

What about a being who set evolution in motion but didn't interfere in the process? This is how the geneticist Francis Collins sees it: "At the moment of the creation of the universe, God could also have activated evolution, with full knowledge of how it would turn out." Others take this further, suggesting that while the universe was designed to ensure some kind of intelligent life evolved, the results of evolution were not entirely predestined.

The "deity who set evolution in motion but didn't interfere" interpretation avoids any conflict with the established facts of evolution, but it also raises some tricky questions. For instance, why would a caring deity choose to "create" through such a cruel process? If animals don't have "souls", at what point did early humans acquire them?

Finally, some people regard "God" not as a conscious being who stands outside the universe and intervenes in it, but more as the divine present in all things. In this view, God is nature. Such pantheistic ideas have been suggested by adherents of all the major religions over the ages.

So are religion and evolution incompatible? It depends who's judging. The idea that many religious people find most satisfactory - that a deity intervened in and directed the evolutionary process - cannot be disproved but is not supported by any evidence. The interpretations that are most compatible with what we know - that God did not intervene in evolution after creating the universe, or God is nature - are ones that many believers find unpalatable.

Of course, some biologists such as Richard Dawkins and PZ Myers are well known for dismissing all theistic religions. However, the question of whether religion and evolution are compatible is not the same as the bigger question of whether any theistic religion is compatible with reason and rationality.

Half a wing is no use

Just as objects designed for one purpose can be used for another, so genes, structures and behaviors that evolve for one purpose become adapted to do another.

Ever used a newspaper to light fires or mop up spills? Stood on a chair to reach something? Or swatted flies with a rolled-up copy of New Scientist? Just as objects designed for a specific purpose can be co-opted for something quite different, so features that evolved to do one task can be used for another - and often are.

But what use is half a wing? It's a question that those who doubt evolution first asked more than a century ago. When it comes to insects, rowing and skimming could be the answer. Stonefly nymphs have flapping gills for extracting oxygen from water. When standing on the water's surface, early insects could have used these gills for getting oxygen and propulsion rowing simultaneously. Some stoneflies still stand on the surface and "row" across water using their wings.

Over time, flapping could have replaced rowing as the main means of propulsion, allowing insects to skim across the water's surface: low levels of friction on this scale mean proto-wings would not have had to generate much air flow to be useful for skimming.

As these proto-wings became more efficient and specialized, early insects may have taken further steps towards flying. While some skimming insects keep all six legs on the water's surface, faster skimmers keep just four legs or two legs on the water. This surface-skimming hypothesis concerning the evolution of insect flight shows how flapping gills could gradually have turned into wings while remained useful at every stage.

From T-rex to sparrow

What about the wings of birds? In some dinosaurs, the scales covering their bodies evolved into hair-like feathers, most likely to insulate warm-blooded bodies or help keep eggs warm.

Those dinosaurs with feathers on their limbs might then have started to exploit the aerodynamic properties offered by feathers, perhaps gliding between trees or running faster along the ground. Fossils show a gradual transition from downy, hair-like feathers into the rigid flight feathers that form the key part of birds' wings.

Another idea that is gaining favor is that flapping forelimbs helped the ancestors of birds to run up steep slopes or climb trees - a technique many birds still employ today.

Without a time machine it is difficult to prove exactly what early birds or insects used "half a wing" for. But it is now clear that half a wing can have all sorts of uses. Indeed, there are numerous examples of physical structures and behaviors that evolved for one purpose acquiring another one, a process called exaptation.

Reuse recycle

Evo-devo - evolutionary developmental biology - is even starting to identify the precise mutations that underlie such changes. For instance, the forelimbs of the ancestor of bats turned into wings partly thanks to a change in a gene called BMP2 that made its "fingers" far longer than normal.

The webbing between the extra long digits that makes up the bat wing is a reappearance of a long-lost feature: as embryos, all tetrapods initially develop webbed digits, a hangover from our fish ancestors. Normally, this webbing kills itself off at an early stage, but in bats this cell suicide is blocked.

Repurposing a structure does not have to involve the loss of the original structure. Reptilian jaw bones turned into mammalian ear bones, without the loss of the jaw. The neural circuitry that allows us to make fine limb movements may have been adapted to produce speech as well.

In fact, almost every feature of complex organisms can be seen as a variation on a theme. Switching off one gene in fruit flies, for instance, can turn their antennae into legs.

On the shoulders of fish

Sometimes just one aspect of a feature can be co-opted for another use. The first hard mineralized structures to evolve in our ancestors were the teeth of early fishes known as conodonts. Once the ability to form hard hydroxyapatite had evolved, it could be exploited elsewhere in the body and may have been the basis of the bony skeletons of all vertebrates.

As these examples show, there are all kinds of routes by which structures and behaviors that evolved for one purpose can contribute to new structures and abilities. Just because it is not immediately obvious how something as complex as a bacterial flagellum evolved (see The bacterial flagellum is irreducibly complex) does not prove it did not evolve.

An even more interesting question than what half a wing is good for is whether some features cannot evolve because half of them really would be useless. Such thought experiments might not prove anything but they can be fun (see Evolution is limitlessly creative).

Evolution is not predictive

It might not be possible to predict exactly what life will look like in a billion years but what counts are the predictions that can be made

Cosmologists make precise predictions about what will happen to the universe in 20 billion years' time. Biologists struggle to predict how a few bacteria in a dish might evolve over 20 hours. Some claim that this lack of precise predictive power means evolution is not scientific.

However, what matters in science is not how much you can predict on the basis of a theory or how precise those predictions are, but whether the predictions you can make turn out to be right. Meteorologists don't reject chaos theory because it tells them it is impossible to predict the weather 100% accurately - on the contrary, they accept it because weather follows the broad patterns predicted by chaos theory.

The difficulty in predicting the course of evolution arises partly because organisms are free to evolve in quite different directions. The descendants of a single species of ape living in Africa around 6 million years ago, for instance, ended up taking rather different paths; those that eventually led to gorillas, chimpanzees and humans. Such splits in populations might stem from tiny initial variations.

The evolutionary paths these apes took might also have been influenced by changes in the climate. As this shows, the history of life on this planet has been partly shaped by chance events. If an asteroid hadn't wiped out the dinosaurs, the first intelligent life form might have been very different, if indeed human-like intelligence had evolved at all. If we could wind the clock back 4 billion years and let life evolve all over again, its course might be very different.

Old age planet

Nevertheless, although evolution's predictive power might appear limited, the theory can be and is used to make predictions at all sorts of levels. Darwin realized that the Earth must be very old for there to have been enough time for all the life on it to evolve. It has turned out to be even older than he thought.

He also predicted that transitional fossils would be discovered, and millions (trillions if you count microfossils) have been. Researchers have even been able to predict the age and kind of rocks in which certain transitional fossils should occur, as with the half-fish, half-amphibian Tiktaalik.

Or take the famous peppered moth, which evolved black coloration to adapt to pollution-stained trees during industrialization in Britain. Remove the pollution and the light strain should once again predominate, which is just what is happening.

Bugged by bugs

Perhaps the most striking prediction in biology was made in 1975 by entomologist Richard Alexander. After studying the evolution of eusocial insects such as termites, he predicted that some burrowing rodents in the tropics might have evolved the same eusocial system - as later proved to be the case with the naked mole-rat.

Evolutionary theory can and increasingly is being put to more practical use. For instance, if you genetically engineer crops to produce a pesticide, it is clear that resistant insect strains are likely to evolve. What is less obvious is that you can slow this process by growing regular plants alongside the GM ones, as was predicted and has turned out to be the case.

Many researchers developing treatments for infectious diseases now try to consider how resistance could evolve and find ways to prevent it, for instance by giving certain drugs in combination. This slows the evolution of resistance because pathogens have to acquire several mutations to survive the treatment.

Most predictions relate to very specific aspects of evolutionary theory. If a eusocial mammal like the naked mole-rat had not been found, for instance, it would have proved only that Alexander's ideas about the evolution of eusocial behavior were probably wrong, not that there is anything wrong with the wider theory. However, some broad predictions - including the age of Earth, the existence of transitional fossils and the common origin of life - are crucial tests of the basic theory (see Evolution cannot be disproved).

Evolution cannot be disproved

There are all sorts of findings and experiments that could have falsified evolution. In the century-and-a-half since Darwin published his theory, not one has.

To count as science, hypotheses and theories should make predictions that might turn out to be wrong. In other words, it should be possible to falsify these ideas. Some claim this is not true of evolution, but this is simply because we find it hard to imagine how different life might have been if it had not evolved.

When asked what would disprove evolution, the biologist J. B. S. Haldane reportedly growled: "Fossil rabbits in the Precambrian". What he meant is that the progression over time seen in the millions of fossils unearthed around the world is exactly what evolutionary theory predicts.

Unicellular organisms, for example, appear before multicellular ones. Jawless fish precede jawed fish. Lunged fish precede amphibians. Amphibians precede reptiles. Reptiles with scales precede mammals and birds with modified scales (fur and feathers). Apes precede humans. All it would take is one or two exceptions to seriously challenge the theory.

Fraudulent claims

Clearly if the first fossil amphibians were older than the first fossil fish, it would show that amphibians could not have evolved from fish. No such exceptions have ever been found anywhere. There have been a few claims to this effect, of course, but even most creationists admit that these claims are fraudulent.

Rabbits with feathers could also disprove evolution. There are animals with a mixture of mammalian and reptilian features, such as echidnas, and there are fossils with a mixture of bird and reptilian features, such as the toothy archaeopteryx. However, no animals have a mixture of mammalian and bird features.

This is just what would be expected if birds and mammals evolved from separate groups of reptiles. There is no reason why an "intelligent designer" would not have mixed up features, such as creating mammals with feathers and efficient bird-like lungs, or furry, breast-feeding ostriches.

Furthermore, if all organisms were created to fulfill particular roles, they might be unable to evolve. Instead countless experiments, both planned and unplanned, show that organisms of all kinds evolve and adapt to changing conditions, providing the changes are not too abrupt. The breeding of plants and animals, or artificial selection, has produced an incredible range of forms in just a few thousand years, such as turning wolves into Chihuahuas and great danes. In the laboratory, researchers have been able to produce bacteria, plants and animals with all kinds of novel characteristics. They have even produced entirely new species .

In the wild, too, there are numerous examples of evolution in action. Many viruses and bacteria have changed dramatically in the space of a human lifetime, from HIV adapting to humans to H5N1 bird flu. Several fish species are becoming smaller, thanks to the selection pressure exerted by humans catching all the large fish. Weeds like Crepis sancta are adapting to cities by changing their seeds.

Deep time

If Earth was very young, that would also be a problem for evolution, because evolution by natural selection requires vast stretches of time - "deep time" - as Darwin realized. Some thought evolution had been falsified in the 19th century, when physicist Lord Kelvin calculated that the Earth was just 30 million years old. That's far younger than Darwin's 300-million-year estimate, which Darwin based on how long it would have taken to erode a rock formation called the Weald in the UK. But both were wrong. Several lines of evidence, including lead isotopes, show that Earth is far older than even Darwin imagined: about 4 billion years.

Darwin also proposed that all life has descended from a common ancestor. This idea, originally based on studies of anatomy and development, is being confirmed by genome sequencing. All life on Earth has turned out to work in essentially the same way: organisms store and translate information using the same code, with only a few minor variations between the most primitive organisms. Huge chunks of this information are identical or differ only slightly even between species that appear very different. Some key developmental genes in the fly can be replaced by the mouse versions without any ill effect, for instance.

No foresight

Had life been designed, though, even organisms that look similar could have turned out to have very different inner workings, just as an LCD screen has a quite different mechanism to a plasma screen. Human designers are already creating a range of new life forms whose molecular underpinnings will be very different from those of existing life forms.

Some argue that it would have made sense for a "designer" to make all species variations on the same theme, but wouldn't this apply only to a designer with limited resources or imagination? An all-powerful creator could have made a world in which every single species was entirely unique and unrelated to any other.

You also might expect the work of a creator to be easy for us to spot evidence for, just as Craig Venter has "signed" the synthetic bacterial genome he created. Instead, the bodies and genomes of complex creatures reveal a total lack of any intelligence or foresight.

Most of our DNA for instance, consists of millions of defunct copies of parasitic DNA. Our bodies are riddled with obvious "design" flaws, from the blind spot in the eye to the bizarre meandering path of our vagus nerve. Furthermore, the high rate of mutations in humans make it inevitable that some people will be born with awful genetic diseases such as cystic fibrosis or Huntington's. The inescapable conclusion is that if indeed life were designed, the designer was lazy and incompetent at best, or cruel at worst.

Evolution is just so unlikely

By weeding out harmful mutations and assembling beneficial ones, natural selection acts like an "improbability drive" that can, given enough time, produce results that appear utterly impossible at first glance

In a recent TV special shown in the UK, called The System, a mother with big debts was persuaded to borrow even more money to bet on a horse race. Having been sent correct predictions of six previous races, she believed illusionist Derren Brown really had come up with a foolproof system for predicting the outcome of races.

In fact, the producers of the show started by sending different predictions to nearly 8000 people. After each race, those sent predictions that turned out to be wrong were eliminated and another set of varying predictions sent to the remaining participants. What appears utterly extraordinary at first - sending someone correct predictions of the winners of six races - seems very ordinary as soon as you understand that thousands of people got wrong predictions.

Confronted by the marvels of the living world, many people jump to the same conclusion to the woman in the program: they cannot be the result of chance alone. But what we don't see are all the failures: the countless numbers of creatures that died in the egg or in the womb, or hatched or were born with terrible defects, or fell victim to predators or disease because of some weakness.

In the wild, most individuals die long before they get a chance to reproduce. The living organisms on Earth are the result not just of six rounds of selection, as in the TV programmed, but of trillions. This, not chance, is the crucial factor in evolution.

Three steps to evolution

To understand evolution, you need to appreciate three things. Firstly, that quadrillion-to-one chances actually happen all the time. Secondly that, while mutation is random, which mutations survive often is not. And thirdly, given enough time, the accumulation of one beneficial mutation after another can produce amazingly complex systems. Natural selection can be seen as a kind of improbability drive that - given enough time - makes the apparently impossible extremely likely.

If you pick even the simplest creatures alive today and calculate the odds of getting their genome by randomly shuffling DNA sequences, you'll find they are pretty astronomical. Even matching the sequence of the simplest virus is stupendously unlikely.

Does this prove evolution is impossible? Try this: get a pack of cards, shuffle it well and spread it out so you can see the sequence. Now try to generate the same sequence by shuffling another pack.

Done it yet? The universe might end before you succeed. If shuffles are truly random, the chance of generating any particular sequence of 52 cards is 1 followed by 68 zeroes - and yet such an incredibly unlikely event happens each time any pack is shuffled.

Shifting genes

In all living creatures, the "pack of cards" is constantly being shuffled. Damage to DNA or mistakes in replicating it generate random mutations, ranging from changes in single "letters" to duplications or deletions of huge chunks of DNA. The vast majority will be either harmful or neutral - only a few will be beneficial. But as the card example shows, even if all beneficial mutations are highly unlikely, this doesn't mean they cannot happen.

In fact, the odds of a beneficial mutation occurring are higher than you might think. One recent study of the E. coli gut bacterium puts the rate as high as 1 beneficial mutation for every 10,000 new bacteria.

That might not sound like much but populations of many simple organisms can number in the trillions, with new generations appearing every hour or less. Do the sums.

What really matters, though, is what happens after mutations appear. That's when natural selection kicks in. Each new organism's life is essentially a rigorous testing process. Those with a harmful mutation will tend to die out, while those with a beneficial mutation that gives them a competitive edge will thrive and produce more descendants. This means that beneficial mutations will become more common in a population, while harmful mutations disappear.

This process happens over and over again. If individuals with one beneficial mutation thrive and multiply, eventually another beneficial mutation will occur in one of them. Over time individuals with both beneficial mutations will come to dominate a population, making it likely for yet another beneficial mutation to appear in one of them...

Benefits of sex

What's more, in species that can swap genetic material, for instance by reproducing sexually, beneficial mutations that occur in separate individuals can be combined in their descendants. In this way, natural selection can create the astonishing organisms we see around us, the result of countless trillions of beneficial mutations slowly assembled over billions of years (see Mutations can only destroy information).

It's true that how the process got underway in the first place is still something of a mystery. We won't begin to know just how likely or unlikely the origin of life was until someone manages to get life to evolve from scratch in the lab or discovers life that originated independently, perhaps on another planet. What is clear, however, is that as soon as the first primitive entities capable of replicating themselves emerged, further evolution was inevitable.

And the more evolution there is, the faster it may become. In fact, evolution might produce "evolvability". For instance, as organisms evolve systems that can cope with a wide range of environmental conditions, further evolution might become more feasible - an idea backed by recent experiments showing evolution can be speeded by varying the environment.

Such ideas remain controversial. What is indisputable is that while the end results of evolution might appear utterly impossible, once you understand the way in which natural selection can collect and distil the results of chance events, there's nothing impossible about it at all.

Mutations can only destroy information

Biologists are uncovering thousands of examples of how mutations lead to new traits and even new species. This claim not only flies in the face of the evidence, it is also a logical impossibility.

Most people lose the ability to digest milk by their teens. A few thousand years ago, however, after the domestication of cattle, several groups of people in Europe and Africa independently acquired mutations that allow them to continue digesting milk into adulthood. Genetic studies show there has been very strong selection for these mutations, so they were clearly very beneficial.

Most biologists would see this as a gain in information: a change in environment (the availability of cow's milk as food) is reflected by a genetic mutation that lets people exploit that change (gaining the ability to digest milk as an adult). Creationists, however, dismiss this as a malfunction, as the loss of the ability to switch off the production of the milk-digesting enzyme after childhood.

Rather than get bogged down trying to define what information is, let's just look at a few other discoveries made by biologists in recent years. For instance, it has been shown a simple change in gene activity in sea squirts can turn their one-chambered heart into a working two-chambered one. Surely this counts as increasing information?

TRIMming the genome

Some monkeys have a mutation in a protein called TRIM5 that results in a piece of another, defunct protein being tacked onto TRIM5. The result is a hybrid protein called TRIM5-CypA, which can protect cells from infection with retroviruses such as HIV. Here, a single mutation has resulted in a new protein with a new and potentially vital function. New protein, new function, new information.

Although such an event might seem highly unlikely, it turns out that the TRIM5-CypA protein has evolved independently in two separate groups of monkeys. In general, though, the evolution of a new gene usually involves far more than one mutation. The most common way for a new gene to evolve is for an existing gene to be duplicated. Once there are two or more copies, each can evolve in separate directions.

The duplication of genes or even entire genomes is turning out to be ubiquitous. Without a duplication of the entire genome in the ancestor of modern-day brewer's yeast, for instance, there would be no wine or beer. It is becoming clear that every one of us has extra copies of some genes, a phenomenon called copy number variation.

The evolution of more complex body plans appears to have been at least partly a result of repeated duplications of the Hox genes that play a fundamental role in embryonic development. Biologists are slowly working out how successive mutations turned a pair of protoHox genes in the simple ancestors of jellyfish and anemones into the 39 Hox genes of more complex mammals.

Newly minted

Can mutation really lead to the evolution of new species?

Yes. Several species of abalone shellfish have evolved due to mutations in the protein "key" on the surface of sperm that binds to a "lock" on the surface of eggs. This might appear impossible, but it turns out that some eggs are prepared to be penetrated by deviant sperm. The same thing can happen in fruit flies, and likely in many other groups too. In yeasts, the mutations that led to some new species forming have not only been identified, they have even been reversed.

The list of examples could go on and on, but consider this. Most mutations can be reversed by subsequent mutations - a DNA base can be turned from an A to a G and then back to an A again, for instance. In fact, reverse mutation or "reversion" is common. For any mutation that results in a loss of information, logically, the reverse mutation must result in its gain. So the claim that mutations destroy information but cannot create it not only defies the evidence, it also defies logic.

All biologists are Darwinists

Modern evolutionary theory is built on some - but not all - of Darwin's ideas, but has gone far beyond them.

It is often assumed that biologists eagerly embraced Darwin's theory about the origin of species when he unveiled it, and that scientists continue to accept all his ideas to this day.

In fact, various ideas about the evolution of life had been around long before Darwin came up with his theory. It was the compelling evidence that Darwin assembled in his 1859 book On the Origin of Species, however, that really convinced most biologists of the evolution of life by descent with modification from a common ancestor.

Modern biologists see Darwin's greatest contribution as the main mechanism he proposed: natural selection. During Darwin's lifetime, however, many biologists were not convinced that it could account for evolution, and the idea fell out of favor.

In the 1930s, it was revived by population biologists, who proved that natural selection is a very powerful force driving evolutionary change (but not the only one). And with the development of genetics, biologists began to discover exactly how evolution takes place. This led to a new understanding of evolution, based on discoveries in many different fields, called the modern synthesis.

Modern evolution

In many ways the modern synthesis is an extension and refinement of Darwin's ideas, but there are also some important differences. In particular, some evolution is now attributed to genetic drift.

While Darwin was right about most things, he also made a fair few mistakes. The biggest was his hypothesis of "pangenesis", described in detail in his 1868 book The Variation of Animals and Plants Under Domestication. According to this theory, beneficial characteristics acquired during the life of an organism could be passed onto offspring over the course of several generations, thanks to particles called "gemmules" shed by body cells that became concentrated in the reproductive organs.

Darwin thought this could explain, for instance, why children are born with thicker skin on the soles of their feet than elsewhere, but this idea was dismissed in the 20th century. There's a twist in this tale, though: a few biologists now think there might be ways for traits acquired during an organism's lifetime to be passed on. However, it has yet to be proved that this can happen and, even if it can, it is very much the exception rather than the norm.

Darwin's other mistakes are more trivial. For instance, in one edition of Origin of Species, Darwin enthused about "Eozoon canadense", which had been identified as a primordial microorganism by others but whose "fossils" turned out to be nothing more than mineral formations.

Darwin also thought the dog was a hybrid of several wild ancestors whereas chickens had only one ancestor. Actually, it turns out the the opposite is true. He also suggested the lung evolved from the swim bladder of fish, whereas nowadays it appears the reverse is true.

Some biologists are now calling for a revision of the modern synthesis to take into account of how new findings have changed our view of, for instance, the nature of genes, the origin of sex, epigenetic inheritance, levels of selection and speciation. Such a revision, however, would merely formally recognize what biologists have already learned in recent decades.

So what have they learned? In a sentence, that while the concept of evolution by natural selection proposed by Darwin was simple, over the Earth's 4-billion-year history it has led to incredibly complex and often unexpected consequences.

The bacterial flagellum is irreducibly complex

Actually, flagella vary widely from one species to another, and some of the components can perform useful functions by themselves. They are anything but irreducibly complex.

It is a highly complex molecular machine. Protruding from many bacteria are long spiral propellers attached to motors that drive their rotation. The only way the flagellum could have arisen, some claim, is by design.

Each flagellum is made of around 40 different protein components. The proponents of an offshoot of creationism known as intelligent design argue that a flagellum is useless without every single one of these components, so such a structure could not have emerged gradually via mutation and selection. It must have been created instead.

In reality, the term "the bacterial flagellum" is misleading. While much remains to be discovered, we now know there are thousands of different flagella in bacteria, which vary considerably in form and even function.

Different strokes

The best studied flagellum, of the E. coli bacterium, contains around 40 different kinds of proteins. Only 23 of these proteins, however, are common to all the other bacterial flagella studied so far. Either a "designer" created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up.

What's more, of these 23 proteins, it turns out that just two are unique to flagella. The others all closely resemble proteins that carry out other functions in the cell. This means that the vast majority of the components needed to make a flagellum might already have been present in bacteria before this structure appeared.

It has also been shown that some of the components that make up a typical flagellum - the motor, the machinery for extruding the "propeller" and a primitive directional control system - can perform other useful functions in the cell, such as exporting proteins.

Changing zooms

It has been proposed that the flagellum originated from a protein export system. Over time, this system might have been adapted to attach a bacterium to a surface by extruding an adhesive filament. An ion-powered pump for expelling substances from the cell might then have mutated to form the basis of a rotary motor. Rotating any asymmetrical filament would propel a cell and give it a huge advantage over non-motile bacteria even before more spiral filaments evolved.

Finally, in some bacteria flagella became linked to an existing system for directing movement in response to the environment. In E. coli, it works by changing flagella rotation from anticlockwise to clockwise and back again, causing a cell to tumble and then head off in a new direction.

Without a time machine it may never be possible to prove that this is how the flagellum evolved. However, what has been discovered so far - that flagella vary greatly and that at least some of the components and proteins of which they are made can carry out other useful functions in the cells - show that they are not "irreducibly complex".

More generally, the fact that today's biologists cannot provide a definitive account of how every single structure or organism evolved proves nothing about design versus evolution. Biology is still in its infancy, and even when our understanding of life and its history is far more complete, our ability to reconstruct what happened billions of years ago will still be limited.

Think of a stone archway: hundreds of years after the event, how do you prove how it was built? It might not be possible to prove that the builders used wooden scaffolding to support the arch when it was built, but this does not mean they levitated the stone blocks into place. In such cases Orgel's Second Rule should be kept in mind: "Evolution is cleverer than you are."

Yet more misconceptions

Here are just a few more easily refuted common misconceptions about the theory of evolution.

Evolution is just a theory

Yes it is, like Einstein's theory of special relativity. By theory, scientists mean an explanation backed by evidence. What creationists mean is that evolution is just a hypothesis, unsupported by evidence - which it is not. Evolution is a fact as well a theory.

Darwin recanted on his deathbed

If Einstein had recanted his theories on his deathbed, would the universe be any different? Scientific hypotheses stand or fall on the evidence, not on the whims of their proposers. But for the record, this myth, popular among creationists, is not true.

There are no transitional fossils

There isn't a nice way of saying this: anyone making this claim is either appallingly ignorant or an outright liar. In fact, there are far too many fossils with intermediate features to count - trillions if you include microfossils. These fossils show the transitions between major groups, from fish to amphibians, for instance, as well as from one species to another. New discoveries are continually made, from the half-fish, half-amphibian Tiktaalik to an early giraffe with a shorter neck than modern animals.

Here is a link to the wikipidea page on transitonal fossils: [link to en.wikipedia.org]

There are serious problems with the theory of evolution

Would you jump off a skyscraper on the basis that the clash between general relativity and quantum theory means there are serious problems with our theory of gravity? It makes no more sense to question the reality of evolution because scientists are still debating about some of its finer aspects than it does to question the existence of gravity for the same reason. There are still plenty of details to fill in but, as surely as dropped objects fall, life has and continues to evolve.

If we all evolved from apes, why are there still apes around in this world?

Chihuahuas, great Danes and every other type of dog were bred from wolves, but there are still wolves in the world. And what breeders do deliberately can happen naturally: when a species splits into separate populations that cannot interbreed, these populations can evolve in very different ways. The emergence of a new species does not necessarily mean the disappearance of the old one, although in fact the apes we evolved from are long extinct - chimpanzees and gorillas are our cousins, not our ancestors.

Evolution violates the second law of thermodynamics

The second law of thermodynamics states that entropy, a measure of randomness, cannot decrease in a isolated system. Our planet is not a isolated system.

Er, that's it. There are longer ways of saying the same thing if you prefer.

If you are still with me I applaud your tenacity, and welcome your discussion. The theory of evolution is constantly evolving as new evidence is uncovered, but just like the theory of gravity we KNOW that evolution happens. But if you choose dismiss evolution because it is a theory, then I invite you to dismiss gravity for the same reason, and find a very tall building to jump off from and come up with your own conclusions