For centuries, one of the best arguments in support of divine creation has been the Argument from Design, which generally consists of the statement: Thing X is too complicated and too perfect to just exist by happenstance, so it must have been designed, and designed things require a designer, so an intelligent agent must have designed life. This argument has a long history, and its best-known proponent was eighteenth-century theologian William Paley, who formulated it as a comparison between the plausible origins of a stone and those of watch. According to Paley, a watch is obviously much too intricate to have existed forever, or to have simply sprung into existence naturally; a watch requires a watchmaker. Living beings, which are much more complex than watches, must also be designed; therefore God must have designed us.
This argument, in one form or another, is still implicitly (and often explicitly) accepted by the general public - polls suggest that 45% of Americans believe what is essentially a Biblical account of creation, and another 39% subscribe to some form of theistic or guided evolution (American Atheists).
When presented empirically, the argument typically says something like: "The human eye (bat's echolocation, walking stick's mimicry, beetle's defense mechanism, bird's flight capability, etc.) is far too perfectly designed to have evolved. It had to work perfectly the first time!" Unfortunately for the proponents of this argument, it misses a large number of very important facts about biological design and evolutionary theory.
Take the human eye, for example. It is structured in such a way that the light-sensitive photocells are effectively backwards, with their nerves pointing outward toward the light source and their photoreceptors pointing inward. Why would a sensible designer do something like this? Any modern engineer would be appalled at this inefficiency in so crucial a system. Moreover, octopus eyes are structured in much the same way, but their photocells point forwards. Why would an intelligent designer have given the octopus properly designed eyes, but given humans - supposedly his crowning achievement - poorly designed ones?
The presence of homologous structures is a similar problem. Homologous structures are body parts with similar arrangements derived from a common ancestor but used for different functions. The human arm, the horse's forelimb, the whale's flipper, and the dog's front paw are all homologous structures which make use of the same basic bones and muscles. Why would an infinitely powerful designer choose to repeat the same design over and over in his creations? Why, in his infinite wisdom, could he not use a radically different design for each of his supposedly independent creations?
Vestigial organs - a phenomenon recognized as part of evolution since Darwin's time - also present the design theory with a great difficulty. No human engineer would intentionally equip humans with an appendix, which serves no function other than to sometimes put its body's life in danger by becoming infected and occasionally rupturing. Similarly, human embryos possess a yolk sac, but it is not filled with yolk, since the embryo's nourishment is provided by the mother. It is nothing but a throwback to an earlier biological era. Was the intelligent designer especially fond of appendices and yolk sacs?
Any designer of life on our planet must have been quite incompetent - a point that has been made repeatedly in the past. Over 99% of all species that ever existed are now extinct, giving the hypothetical designer an extremely high failure rate. Even within existing species, thousands of animals die every day, most because they were insufficiently adapted to their environment. Is this the hallmark of an intelligent designer?
Finally, how does anyone know for sure that something couldn't have evolved through gradual refinement over time? This is one of those empirical claims that just can't be proved beyond the shadow of a doubt - for any thing X, there very well might be a possible series of intermediates that could have led to thing X's evolution. It might be difficult, or extremely unlikely, but it simply can't be proven that it is impossible.
Aside from the sketch of problems with the Argument from Design presented here, traditional Christian theology gets in even worse trouble when confronted with biological reality. An omniscient, omnipotent, omnibenevolent God seems quite incompatible with basic facts of biology, including extinction, carnivorous species, genetic diseases, etc. Why would an omnibenevolent being design certain wasps to lay their eggs in the live body of a caterpillar to provision the wasp larvae with a ready store of food? Why are cats, dogs, and many other mammals 100% carnivorous?
It is becoming increasingly evident that the Argument from Design just does not stand up to critical scrutiny. A designer is extremely difficult to impute based on biological evidence, and an omniscient, omnipotent, omnibenevolent one seems close to impossible. The usual dodge - arguing that the designer's ways are mysterious - effectively insulates the whole theory from disproof...or reasoned questioning.
There exists a wealth of data from a variety of fields supporting the evolution of all extant species from one common ancestor. Paleontology reveals an extensive fossil record showing the organisms of the past and their relationship to those that exist today. Molecular biology reveals that all species use the same genetic code, and evolutionary relationships can be traced through mutations in that code. Geology shows us that the earth is approximately 4.5 billion years old, providing ample time for modern complex organisms to evolve. Multiple lines of evidence all converge on a single inescapable conclusion: evolution by natural selection.
There are some that argue this conclusion detracts from the awe and wonder inspired by the natural world. For those that study evolution in depth, the sheer ingeniousness of many of its solutions are themselves a source of awe and wonder - but it is the awe and wonder of reasoned understanding, and the delight of an active mind at work unraveling the mysteries of nature.