For centuries, many theists have attempted to deduce the existence of a supernatural creator and sustainer of the universe from the visible features of the natural world. One common way they do this is by selectively pointing to instances in nature of beauty and complexity as revealed by the exploration and study of natural objects, which include examples of carefully-balanced regularity and order. The “argument from design” states that such beauty, complexity and order could not possibly have come about by material processes alone. Something more is needed, namely a supernatural Designer or Creator.
In the early nineteenth century, the Anglican theologian and philosopher William Paley (1743-1805) famously presented this argument in his 1802 book Natural Theology. Offering up a teleological defense of divine causation of nature on the terrestrial scale, Paley’s book begins with the now-famous “Watchmaker Analogy.” The structure of the analogy, in Paley’s own words, is as follows:
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 . . . But suppose I had found a watch upon the ground, and it should be enquired 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 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; that, if the several parts had been differently shaped from what they are, of a different size from what they are, or placed after any other manner, or in any other order, than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use, that is now served by it. 
Paley’s Watchmaker Analogy can be more succinctly represented by way of a simple syllogism:
- The complex inner workings of a watch necessitate an intelligent designer for the watch.
- If the complicated watch requires a designer, the far greater complexity of x (a particular organ or organism, the structure of the solar system, life itself, the entire universe, etc.) also necessitates a designer.
Paley’s reader is invited to imagine him walking through a completely natural locale (forests, deserts, and remote beaches have been used in modern retellings of the analogy), and coming across a lone watch on the ground. The analogy suggests that this watch obviously cannot be an artifact of the surrounding nature, that it must have been designed by an intelligent agent.
Throughout the rest of his book, Paley extrapolates this analogy to every instance of organized complexity in the natural world, and in so doing based his case on fundamentally flawed logic. The reason the nature-hiker is able to apprehend that the watch in the heath is not an artifact of nature in the first place is because nature can easily be distinguished from design. We are cognitively-developed enough to recognize that which has been made by an intelligent agent for what it is, and we can also discern what is purely natural and not designed by anyone. But if Paley’s argument is true, we should not be able to tell the difference between design and non-design! The most important failure in Paley’s argument is that it lacks an objective frame of reference from which one can compare design to non-design. The only reliable indicators of genuine design derive from experience, and Paley failed to provide a means of distinguishing design from non-design that is independent of those indicators.
Another major weakness in Paley’s argument is that it turns on an over-extended metaphor and conflates analogy with reality. Nearly a quarter century before the publication of Paley’s book, the Enlightenment philosopher David Hume made this observation the basis of his objection to earlier versions of the Argument from Design that were sounded by theologians in his time. In Hume’s great book Dialogues Concerning Natural Religion, published posthumously in 1779, three fictional characters vigorously debate the question of whether mind or matter is the constitutive principle underlying the order observed in nature. Cleanthes defends the Design Argument, maintaining that the “curious adapting of means to ends, throughout all nature, resembles exactly, though it much exceeds, the productions of human contrivance; of human designs, thought, wisdom, and intelligence.”  This resemblance of natural to artificial effects leads Cleanthes to infer the existence of an ultimate “Author of Nature” who possesses an intelligent mind similar to that of human engineers. This argument is demolished by Philo, Hume’s skeptical character in the Dialogues and his mouthpiece:
Thought, design, intelligence, such as we discover in men and other animals, is no more than one of the springs and principles of the universe, as well as heat or cold, attraction or repulsion, and a hundred others which fall under daily observation. . . . 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 anything 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? . . . 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? 
While metaphors and analogies are often useful for effectively communicating hard-to-grasp concepts to people, they can never be the foundation of any strong logical argument. A runaway metaphor cannot be stopped. When anything and everything can be applied to it, all semblance of logic goes out the window. This problem brings us back to the objection posed earlier regarding the argument’s lack of an objective frame of reference. What would a thing not designed by God look like, and how would this non-designed thing operate? I have posed this question to several theists who have recycled Paley’s argument and they have never been able to provide a straightforward answer.
With the publication of Charles Darwin’s groundbreaking work On the Origin of Species in 1859, Paley’s formulation of the design argument was decisively overthrown on scientific grounds, not just philosophical ones. The discovery of natural selection, the mechanism by which organisms inherit useful adaptations and change gradually over geologic time, has been repeatedly corroborated by the continued scientific study of this process in the century and a half since Darwin’s work. It has also rendered the theistic argument from design completely obsolete and unnecessary.  Darwin’s work forever revolutionized the intellectual landscape by removing the need to invoke any external Creative Agent to account for the process by which organisms came into being and acquired their present form. As Darwin wrote in the concluding chapter of Origin of Species, “What limit can be put to this power [natural selection], acting during long ages and rigidly scrutinising the whole constitution, structure, and habits of each creature, – favouring the good and rejecting the bad? I can see no limit to this power, in slowly and beautifully adapting each form to the most complex relations of life.” 
In spite of the overwhelming empirical evidence that adequately explains the appearance of design in nature without recourse to God, a gussied-up version of Paley’s faulty argument still survives today in the form of the “Intelligent Design” (ID) hypothesis advanced by theistic apologists. For example, in 1996 the biochemist and theist Michael Behe published a book titled Darwin’s Black Box: The Biochemical Challenge to Evolution. This book, which became a bestseller, is essentially a glorified version and updated restatement of Paley’s Natural Theology. In this book, Behe argues that the elusive criterion for justifiably inferring design in nature is what he calls irreducible complexity.  Throughout his book, Behe repeatedly makes statements to the effect that no natural evolutionary explanation can exist, even in principle, for the examples of complexity in living organisms that he classifies as irreducible.
Behe is not only mistaken, he is willfully ignorant. At the time he was writing his book, there existed an abundance of natural reductionist explanations in the scientific literature for the examples of complexity he cited. He could easily have found these explanations had he simply taken the time to look for them before writing his book. Behe, who is a biochemist and not an evolutionary biologist by training, was simply unaware of the scientific literature that documents numerous robust examples in nature of organic systems undergoing a series of discrete functional changes over time. If Behe was a competent researcher, he would surely have made himself aware of the fact that, six decades before, the Nobel Prize-winning evolutionary biologist Hermann Joseph Muller had already provided a plausible evolutionary mechanism for several of Behe’s so-called “irreducibly complex” systems. 
Many scientists and philosophers of science have written thorough and detailed refutations of Behe’s work, and I will not here reiterate these fine criticisms.  Instead, I will here cover the more general grounds for objecting to Behe and his fellow IDers that are based on our experience of both the natural and artificial world. By invoking complexity as a measure of design, Behe and his fellow design apologists are committing a basic category mistake. Complexity more often arises as a result of a lack of planning than as a result of intelligent deliberation, and designed things tend to be far simpler than natural things. For example, a rubber ball is, geometrically speaking, vastly simpler than a naturally-occurring rock. The reason a rubber ball is readily recognizable as a designed thing is because it exhibits regularity rather than complexity. Needlessly complex systems rarely if ever exhibit any of the characteristics of agency. As the prominent atheist biologist PZ Myers noted in a 2009 lecture, “When we build things, we don’t make them needlessly complex. We want to make them as simple and efficient as we can.” Myers nicely illustrated this point by comparing a naturally-occurring wall of driftwood on a beach with a brick wall designed and built by humans:
What we discover is that natural things are built by chance and necessity. They’re functionally unspecified. There’s nothing that says that pile of driftwood is a wall, it just functions as a wall to us. But it’s also got diverse other functions. And they all tend to be complex.
Artificial walls, on the other hand, are built with intent. They’re functionally very specific; you don’t just get a bunch of bricks and some mortar and randomly throw it around to build a wall. If you want to build a wall, you build a wall. And that makes them relatively simple. 
In addition to intentionality, functional specificity, and simplicity, we can add competence to our list of criteria that constitute true cases of design. The natural world fails this standard as well. The way evolutionary forces manifest in nature is just what we would expect if there was no external Intelligent Designer engineering objects and organisms with care. Innumerable life forms have been deemed by natural selection to be useless for reproductive success. The ruthless preying of many forms of life upon many others was excessive and unrelenting throughout hundreds of millions of years of evolutionary history and continues to be so today. Ninety percent of all living organisms that have ever lived are now extinct.
This picture is clearly not indicative of any engineering finesse, and it takes a special kind of fanciful imagination, one that is completely divorced from external reality, to see the hand of a designer in nature. If there was a Designer external to the universe it created, this agent is clearly not as intelligent or efficient as he is made out to be by ID proponents. The human body is but one example of extremely poor design out of many hundreds that could be cited. What kind of “intelligent” designer would construct our bodies in such a way as to be susceptible to aggressive leukemia, hemophilia, sickle cell anemia, multiple sclerosis, Parkinson’s disease, Alzheimer’s disease, and all the other infirmities that have plagued humankind over the ages? Even disease-free human bodies come equipped with such masterful design features as weak knees, varicose veins, and vision that is not only gradually lost with increasing age, but that can only detect an extremely narrow slice of the electromagnetic spectrum. In a 2006 presentation for The Science Network’s annual Beyond Belief symposium, the astrophysicist and science popularizer Neil deGrasse Tyson wittily pointed out some other examples of design flaws in the human body that would get any engineer who attempted such schematics instantly fired:
You breathe, eat and drink through the same hole in your body, guaranteeing that some percentage of us will choke to death every year. Imagine if you had a separate hole for breathing and eating and talking . . . you could drink, breathe, and just talk, and you would never choke. And it’s not a hard request. Dolphins breathe and eat through different holes in their body, and that’s a mammal! Santa Clause could bring this one.
And . . . what’s this going on between our legs? It’s an entertainment complex in the middle of a sewage system. No engineer would design that at all! Ever! It’s like the wrong juxtaposition of elements. 
The Argument from Design can only be maintained from a position of subjectivity reinforced by confirmation bias and selective reasoning. The practice of science, if it is to be objective and impartial, will take note of ugliness, disorder, and inefficient physiology in nature, not just supposed instances of beauty and order. Monty Python brought some balance to the one-sidedness with which theists praise their god for all the beauty they see in nature with these lyrics from their song “All Things Dull and Ugly”:
All things dull and ugly,
All creatures short and squat,
All things rude and nasty,
The Lord God made the lot.
Each little snake that poisons,
Each little wasp that stings,
He made their brutish venom.
He made their horrid wings.
All things sick and cancerous,
All evil great and small,
All things foul and dangerous,
The Lord God made them all.
All things scabbed and ulcerous,
All pox both great and small,
Putrid, foul and gangrenous,
The Lord God made them all.
 William Paley, Natural Theology, or Evidence of the Existence and Attributes of the Deity, Collected from the Appearances of Nature (1802; reprint, New York: Oxford University Press, 2006), p. 7.
 David Hume, Dialogues Concerning Natural Religion (1779), Part II.
 Richard Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design (New York and London: W.W. Norton, 1987).
 Charles Darwin, On the Origin of Species by Means of Natural Selection (1859), Chapter XIV.
 Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: Free Press, 1996).
 H.J. Muller, “Reversibility in Evolution Considered from the Standpoint of Genetics,” Biological Reviews 14, no. 3 (July 1939): 261-80.
 Robert L. Dorit, “A Review of Darwin’s Black Box: The Biochemical Challenge to Evolution, by Michael J. Behe,” American Scientist (September-October 1997); Robert T. Pennock, Tower of Babel: The Evidence Against the New Creationism (Cambridge, MA: MIT Press, 1999), pp. 263-72; Mark Perakh, Unintelligent Design (Amherst, NY: Prometheus Books, 2003), pp. 111-140; David Ussery, “Darwin’s Transparent Box: The Biochemical Evidence for Evolution,” in Matt Young and Taner Edis, eds., Why Intelligent Design Fails: A Scientific Critique of the New Creationism (New Brunswick, NJ: Rutgers University Press, 2004).
 Neil deGrasse Tyson, “The Perimeter of Ignorance” (presentation, Beyond Belief: Science, Religion, Reason and Survival symposium, La Jolla, CA, November 5-7, 2006), https://www.youtube.com/watch?v=bcTbGsUWzuw (accessed July 12, 2015).