The sun that we circle outputs light at a wide range of wavelengths, but has a peak at light coloured yellow-green. Our eyes are most sensitive to light waves that are yellow-green.
Our bodies cannot create vitamin C; without it, we fall apart in about two months. Fortunately, that vitamin is in some of the food we eat, in enough quantities to save us from a slow, painful death.
We come equipped with a staggeringly complex defence system, that can detect and tag potential invaders for immediate removal. It has many layers, ranging from white blood cells that roam the body to the simple act of raising our body’s temperature, which inhibits some common attackers while boosting the effectiveness of some other immune components.
All three of these are clear evidence of design. But how can such complicated systems arise from simple molecules and proteins? Does this not point to the “guiding hand” of a higher deity?
Cranes and Skyhooks
Like so many proofs, this one dates back to the Greeks. I’m going to pin this one on Socrates; his mouthpieces Plato and Xenophon claims that he claimed that the way human eyelids protected human eyes was no accident. It was very much designed by a grand designer.
Does it not strike you then that he who made man from the beginning did for some useful end furnish him with his several senses–giving him eyes to behold the visible word, and ears to catch the intonations of sound? Or again, what good would there be in odours if nostrils had not been bestowed upon us? what perception of sweet things and pungent, and of all the pleasures of the palate, had not a tongue been fashioned in us as an interpreter of the same? And besides all this, do you not think this looks like a matter of foresight, this closing of the delicate orbs of sight with eyelids as with folding doors, which, when there is need to use them for any purpose, can be thrown wide open and firmly closed again in sleep? and, that even the winds of heaven may not visit them too roughly, this planting of the eyelashes as a protecting screen? this coping of the region above the eyes with cornice-work of eyebrow so that no drop of sweat fall from the head and injure them? again this readiness of the ear to catch all sounds and yet not to be surcharged? this capacity of the front teeth of all animals to cut and of the “grinders” to receive the food and reduce it to pulp? the position of the mouth again, close to the eyes and nostrils as a portal of ingress for all the creature’s supplies? and lastly, seeing that matter passing out of the body is unpleasant, this hindward direction of the passages, and their removal to a distance from the avenues of sense? I ask you, when you see all these things constructed with such show of foresight can you doubt whether they are products of chance or intelligence?
(“The Memorabilia,” Xenophon, Book I.4, translated by H. G. Dakyns)
And that settled it for about two thousand years. There was no other way to explain biological design, so most people declared religion the winner by default. The most famous example comes to us via William Paley.
In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for any thing I knew to the contrary, it had lain there for ever: nor would it perhaps be very easy to show the absurdity of this answer. But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer which I had before given, that, for any thing I knew, the watch might have always been there. Yet why should not this answer serve for the watch as well as for the stone? why is it not as admissible in the second case, as in the first? For this reason, and for no other, viz. that, when we come to inspect the watch, we perceive (what we could not discover in the stone) that its several parts are framed and put together for a purpose, e. g. that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day; […] This mechanism being observed (it requires indeed an examination of the instrument, and perhaps some previous knowledge of the subject, to perceive and understand it; but being once, as we have said, observed and understood), the inference, we think, is inevitable, that the watch must have had a maker: that there must have existed, at some time, and at some place or other, an artificer or artificers who formed it for the purpose which we find it actually to answer; who comprehended its construction, and designed its use.
(“Natural Theology, or Evidences of the Existence and Attributes of the Deity collected from the Appearances of Nature,” William Paley. 1802.)
You can probably guess the rest; Paley points to evidence of design in nature, and argues that there must have been a designer for it all, and again we wind up invoking a god.
Right off the bat, we stumble across some fishy logic. Suppose you have no idea how the planets formed around the sun. Does this mean you have to accept my theory as truth, that they were all deposited there by a giant space clam? Of course not. A theory that doesn’t explain the data or is riddled with internal inconsistences can be safely discarded, even if it’s the only game in town. It’s not enough to say “God did it,” you have to describe how God did it. How did God put most marsupial mammals in Australia, and not elsewhere? How did he keep placentals away, even though they could comfortably live there?How did the long-dead remains of marsupials get to Antarctica, given the hostile climate and huge ocean walling that continent off? If it can’t explain data like that, we’ll be forced to look for an alternative to the God theory instead of blindly accepting it.
The publication of “De Humani Corporis Fabrica,” by Andreas Vesalius, was the first of many hints that there was another challenger out there. Scientists began looking at human beings and other animals in some detail, instead of parroting the claims of long-dead Greeks, and discovered odd bits that didn’t make sense. Why, for instance, do we have a disabled third eyelid? You’d think an intelligent designer would either have given us a functional one, or none at all. Why are some people unable to see colour, and why is it far more common in men then women? The “clean” design of the ancient Greeks was dissolving into a “complex” design, which seemed eager to stir in a few contradictions and poor choices too.
David Hume is the first philosopher I can find that argued against a supernatural designer. In his “Dialogues Concerning Natural Religion,” published in 1779, the character Cleathes invokes the Design proof. His foil, Philo, slowly begins to dismantle it.
But can a conclusion, with any propriety, be transferred from parts to the whole? Does not the great disproportion bar all comparison and inference? From observing the growth of a hair, can we learn any thing concerning the generation of a man? Would the manner of a leaf’s blowing, even though perfectly known, afford us any instruction concerning the vegetation of a tree?
But, allowing that we were to take the operations of one part of nature upon another, for the foundation of our judgement concerning the origin of the whole, (which never can be admitted,) yet why select so minute, so weak, so bounded a principle, as the reason and design of animals is found to be upon this planet? What peculiar privilege has this little agitation of the brain which we call thought, that we must thus make it the model of the whole universe? Our partiality in our own favour does indeed present it on all occasions; but sound philosophy ought carefully to guard against so natural an illusion.
After pointing out this particular air gap, he invents some fanciful alternate explanations for the design of the world.
But to waive all objections drawn from this topic, I affirm, that there are other parts of the universe (besides the machines of human invention) which bear still a greater resemblance to the fabric of the world, and which, therefore, afford a better conjecture concerning the universal origin of this system. These parts are animals and vegetables. The world plainly resembles more an animal or a vegetable, than it does a watch or a knitting-loom. Its cause, therefore, it is more probable, resembles the cause of the former. The cause of the former is generation or vegetation. The cause, therefore, of the world, we may infer to be something similar or analogous to generation or vegetation. […]
The BRAHMINS assert, that the world arose from an infinite spider, who spun this whole complicated mass from his bowels, and annihilates afterwards the whole or any part of it, by absorbing it again, and resolving it into his own essence. Here is a species of cosmogony, which appears to us ridiculous; because a spider is a little contemptible animal, whose operations we are never likely to take for a model of the whole universe. But still here is a new species of analogy, even in our globe. And were there a planet wholly inhabited by spiders, (which is very possible,) this inference would there appear as natural and irrefragable as that which in our planet ascribes the origin of all things to design and intelligence, as explained by CLEANTHES. Why an orderly system may not be spun from the belly as well as from the brain, it will be difficult for him to give a satisfactory reason.
But were this world ever so perfect a production, it must still remain uncertain, whether all the excellences of the work can justly be ascribed to the workman. If we survey a ship, what an exalted idea must we form of the ingenuity of the carpenter who framed so complicated, useful, and beautiful a machine? And what surprise must we feel, when we find him a stupid mechanic, who imitated others, and copied an art, which, through a long succession of ages, after multiplied trials, mistakes, corrections, deliberations, and controversies, had been gradually improving? Many worlds might have been botched and bungled, throughout an eternity, ere this system was struck out; much labour lost, many fruitless trials made; and a slow, but continued improvement carried on during infinite ages in the art of world-making. In such subjects, who can determine, where the truth; nay, who can conjecture where the probability lies, amidst a great number of hypotheses which may be proposed, and a still greater which may be imagined?
Alas, Hume didn’t realize he was on to something; at the end of “Dialogues,” his skeptic Philo mysteriously concedes the argument to Cleathes, despite the poor replies of the latter.
The second serious alternative arrived in 1795, thanks to Erasmus Darwin,  and was then fleshed out by Jean-Baptiste Lamarck in 1809’s “Philosophie Zoologique.” Lamarck proposed that any changes made to an animal during its life were passed on to their offspring. The classic example is that a blacksmith’s son will also have the thick arms of his father. It’s almost entirely wrong,  but at least it got biologists thinking. The third edition of “On the Origin of Species,” published half a century later in 1861, lists nineteen other biologists who nearly figured out evolution for themselves, two who did come up with it (Alfred Wallace and Patrick Matthew), and one person who claimed to but probably didn’t.
Ah yes, evolution. The concept is very simple. You start with something that is capable of making copies of itself. These copies must be imperfect, at least some of the time, leading to differences from the original.  If those differences or even just the surrounding environment imposes limits on these things, then the version which copes best with those limits will be able to create more copies of itself than other variations. Repeat this many, many, many times, and the result is something that seems designed for its environment.
No really, that’s it. The process that spawned the vast diversity of life on this planet, that made creatures as wildly different as bacteria and human beings, can be comfortably laid out in a single paragraph.
It’s incredible, in that it strains credibility. How can a simple set of rules lead to such complicated results? I think I can answer that by using an even simpler example.
 Socrates spent most of his life wandering the streets, asking people annoying questions, instead of writing things down. Incredibly, this sort of behaviour kept him fed and earned him students and admirers. It’s probably for the best that he detested writing; spreading that sort of knowledge around would crash any economy.
 Paley may not have been the first to make this argument, actually. Bernard le Bovier de Fontenelle may have beaten him to the punch in 1686; refer to “The Story of Civilization: The age of Louis XIV, 1648-1715” by Will and Ariel Durant for the details.
 Ever wonder about that little pinkish thing in one corner of your eye? That’s the remains of it. The remains might still have a use, by helping to clear out grime from your eye, but it’s a shadow of what it once was.
 Every writer who mentions Charles Darwin must point out that his grandfather Erasmus nearly scooped his discovery of evolution, or pay a fine and do 42 hours of community service.
 It turns out that genes can be overridden by the environment or organism, though this doesn’t directly alter the genes themselves. These changes usually don’t pass to the next generation, but there are exceptions.
 In biology, errors are very rare, only matter in the few cells that are devoted to reproduction, and have a nasty habit of killing the organism. That last part means the mutations in the surviving animals are not completely random, in practice. Sex complicates things further by merging two plans into one, which helps spread beneficial errors more rapidly.