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ance, of human design, thought, wisdom, and intelligence…. By this argument a posteriori, and by this argument alone, do we perceive at once the existence of a Deity, and his similarity to human mind and intelligence (Dialogues Concerning Natural Religion).

The link between adaptation, biological complexity, and omnipotent design was apparent not only to philosophers and theologians. As phrased in the 1600s by the Christian scholar and scientist John Ray:

You may hear illiterate persons of the lowest Rank of the Commonality affirming, that they need no Proof of the being of God, for that every Pile of Grass, or Ear of Corn, sufficiently proves that…. To tell them that it made it self, or sprung up by chance, would be as ridiculous as to tell the greatest Philosopher so (The Wisdom of God Manifested in the Works of Creation).

When Darwin boarded the HMS Beagle in 1831, he had no inkling that his voyage of discovery would eventually lead him to a revolutionary concept: that a purely natural process—natural selection—can yield biological outcomes that otherwise seem to have the earmarks of intelligent craftsmanship. Natural selection is an inevitable process of nature whenever organisms show heritable variation in their capacity to survive and reproduce in particular environments, but the operation has no more consciousness or intelligence than do natural physical forces such as gravity or weather. Thus, Darwin’s key legacy is not the mere demonstration that evolution occurs (several of Darwin’s predecessors were aware that species evolve), but rather the stunning revelation that a natural rather than a supernatural directive agent can orchestrate the evolutionary emergence of biological adaptations.

Nevertheless, 150 years after Darwin the challenge of understanding nature’s complexity remains in many regards in its infancy. Only recently has science developed the necessary laboratory tools for delving deep within the molecular structure and function of genes that underlie particular complex adaptations (such as the eye, or the body plans of vertebrate animals). Only recently has it become possible to conduct genomic analyses in ways that permit the discovery of heretofore unspecified structural and regulatory genes that contribute to the molecular assembly of complex organismal phenotypes. Only recently have phylogenetic methods progressed to the point where the histories of complex phenotypes can be reliably elucidated. Scientific progress is occurring on many related fronts as well. For example, recent developments in evolutionary genetic theory (such as formal network analysis) have opened exciting new avenues for exploring the geneses and maintenance of biological complexity at the levels of genetic and metabolic pathways.

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