We are not inferring design to account for a black box, but to account for an open box.
Despite some remaining puzzles, there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.
Thus it seemed to Haeckel that such simple life could easily be produced from inanimate material.
As can be seen even by this limited number of examples proteins carry out amazingly diverse functions.
In many biological structures proteins are simply components of larger molecular machines.
Many people, including many important and well-respected scientists, just don’t want there to be anything beyond nature. They don’t want a supernatural being to affect nature.
As the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met skyrockets toward the maximum that science allows.
We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.
In order to say that some function is understood, every relevant step in the process must be elucidated.
The basic structure of proteins is quite simple: they are formed by hooking together in a chain discrete subunits called amino acids.
Skin is made in large measure of a protein called collagen.
Throughout history there have been many other examples, similar to that of Haeckel, Huxley and the cell, where a key piece of a particular scientific puzzle was beyond the understanding of the age.
The theory of undirected evolution is already dead, but the work of science continues.
Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on.
It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection.
It is a shock to us in the twentieth century to discover, from observations science has made, that the fundamental mechanisms of life cannot be ascribed to natural selection, and therefore were designed. But we must deal with our shock as best we can and go on.
It was only about sixty years ago that the expansion of the universe was first observed.
In the abstract, it might be tempting to imagine that irreducible complexity simply requires multiple simultaneous mutations – that evolution might be far chancier than we thought, but still possible. Such an appeal to brute luck can never be refuted... Luck is metaphysical speculation; scientific explanations invoke causes.
The conclusion of intelligent design flows naturally from the data itself – not from sacred books or sectarian beliefs. Inferring that biochemical systems were designed by an intelligent agent is a humdrum process that requires no new principles of logic or science. It comes simply from the hard work that biochemistry has done over the past forty years, combined with consideration of the way in which we reach conclusions of design every day.
If nutritionists can’t easily determine how one dietary factor affects human health, evolutionary biologists can’t tell what affected the survival of long dead animals.