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A common debating tactic, and a successful one in the eyes of many, is to say that whenever religion and science have a dispute about some question of fact, religion always loses.  The implication is that religion should never make any factual claims, and it is even implied that religion has no contact with reality. Supporting evidence for this claim is said to include the physics of Galileo, the geology of Hutton and Lyell, the biology of Darwin, and the psychology of Freud and others. Religion, especially supernatural religion, has always lost in the past, and it will always lose in the future. We should either abandon it or at least adopt a liberal version that makes no testable claims.
There are several problems with the above scenario. First, strictly speaking, the disputes were not really between science and religion; there were scientists on the “religion” side, and theologians on the “science” side. It would be more proper to make the claim that the argument was between naturalistic and supernaturalistic philosophies.
If so, the Galileo affair does not really belong with the other examples. The Galileo affair resulted from the reaction of the Catholic Church, which had just been rocked by the Protestant Reformation, to the cosmology of Copernicus. The only issues which might impact the conflict between naturalistic and supernaturalistic philosophy were whether incidental details in the Bible were to be treated as ontologically (really) accurate, or merely phenomenologically (only describing appearances) accurate, and the authority of the Catholic Church. As far as I know, it does not even involve the authority of the Pope speaking ex cathedra, as I know of no such pronouncement of the Pope on the Galileo affair.
It could be (and has been) argued that the other “advances” listed above were not really advances. Certainly a creationist will not find them very persuasive. But there is a more basic flaw in the argument. Specifically, there are important counterexamples to the argument. Religion does not always lose.
We need to rephrase the above statement to give it more empirical content, because we can never be completely certain that science has a particular theory. Even if a theory appears to be well ahead of another, it is always possible that more evidence will tip the scales in favor of the currently out-of-favor theory. Thus a believer in naturalism could always claim that in a given subject where a supernaturalist explanation fits best with the known facts, more facts will tip the scales. Just wait a while; your supernatural explanation will turn out to be wrong or unnecessary. Of course, a supernaturalist could argue in a similar manner. And both statements are basically faith statements. The only evidence we can have for them is that the same process has occurred in other areas of knowledge in the past.
So we will rephrase the proposition more carefully. Scientific and historical hypotheses arising from and/or compatible with supernaturalistic philosophy sometimes have considerably more empirical support than hypotheses arising from and/or compatible with naturalistic philosophy. Perhaps more importantly, this support has, in some cases increased with time.
In the domain of history, one counterexample to the “religion always loses” argument is the reliability of the chronology of the books of Kings and Chronicles in the Bible. For a long time, skeptics believed a “Biblical” chronology did not exist, and that what confused pieces of chronology did exist were totally incompatible with the “real”, secular chronology. After Thiele,  the chronology of Kings and Chronicles was (and is) seen not only as coherent, but able to serve as a corrective to secular chronology.  A Biblical approach has won, or at least has shown itself to be much better at explaining the data. Religion did not lose in this case, and it appears unlikely to lose in the future here.
Another counterexample is the book of Daniel, where skeptics originally confidently stated that Belshazzar never existed, that the chronology was hopelessly confused, and that since the entire book was fiction, there was no point in looking for the characters in history. With time, that view of history has been forced to change. Belshazzar not only existed, but also turned out to be the crown prince (also king in Hebrew parlance), able only to offer the third rulership in the kingdom. The chronology of Nebuchadnezzar taking captives from Jerusalem turns out to have been precisely correct. Perhaps most interesting, the names of Daniel  and his three friends  have been found in Babylonian documents. This does not mean that every statement in the book of Daniel has been confirmed. The identity of Darius the Mede is still in doubt (although we have not eliminated all candidates). But the case for the historicity of Daniel is clearly better than it was in the past. Religion is winning here.
These cases are from history. Can the same be said of science? If one is a Seventh-day Adventist, it can. For over a century, Adventists defended, on the basis of what they believed to be inspiration, the view that tobacco was an insidious but deadly poison. At the time this view was not shared by the scientific community, but over the last 50 years the evidence has become overwhelming that the hypothesis originally associated with religion was correct. Religion did not lose here. The same comments, although not quite as vigorously, can be made about vegetarianism.
But it could be countered that these supernaturalist positions were sectarian, and in any case did not deal a major blow to naturalism. Are there any cases more directly relevant to the creation-evolution controversy?
It turns out there are. The first example is in cosmology. The question at issue was whether the universe extended backwards in time indefinitely or if there was a finite limit to the age of the universe. The former was strongly favored by most scientists, often with an explicit anti-supernatural bias expressed as the reason for their preference.  This bias formed a major part of the objection to Big Bang cosmology. If the universe had a beginning, it at least suggested that it might require a Creator. The desire to protect an eternal universe was so great that in attempting to do so, Einstein made what he later called his “greatest mistake”, introducing a cosmological constant into the equation for the universe to keep it roughly static. However, the weight of evidence now is solidly behind the concept that the universe did have a beginning. Religion is not losing here.
Another example is the existence of vestigial organs. Vestigial organs have been used as an argument against design, and therefore against a designer, since Darwin. In the classical exposition, Wiedersheim  listed over 150 structures that he considered vestigial. He was careful to note that some of them, such as the thyroid and adrenal glands, probably had some function, in which case they might not be truly vestigial, and that this could be the case with other organs. But some of his followers were not so cautious, and it was not uncommon for such organs as the thymus, the pituitary, and the appendix to be written off as completely useless. This lack of caution was necessary if vestigial organs were to be used against believers in design, because if there was some function that could be attributed to them, then their existence in a designed organism would not count as evidence against a designer.  However, this lack of caution was ill-advised, as further investigation has found a reasonable function for all these structures, destroying, sometimes dramatically, the argument against design. It could be argued that in this case anti-supernaturalist prejudice actually was detrimental to science, tending to cause scientists not to investigate possible functions for a structure because the prejudice was that it had no function.
It could be further argued that anti-supernatural prejudice actually killed people. Although the spleen was not on Wiedersheim’s list, when I went to medical school it was commonly written off as a practically useless organ that we would be better off not having, as it tended to bleed when it got injured. Its only use was to show that humans and dogs, for example (where it stores blood for autotransfusion in case of bleeding), shared a common ancestor. As a result, when it did get injured, it was commonly removed, without any attempt to preserve its function. It was only later that it became apparent that not having a spleen predisposed one to overwhelming pneumococcal infections. Surgical practice today is to preserve splenic function whenever possible, either by repairing the spleen, or failing that, by leaving small bits in the abdomen and hoping that they attach themselves.
History repeated itself with the “junk DNA” controversy. When DNA was discovered, many evolutionists predicted that there were vast quantities of totally useless DNA in the genome of various organisms including humans. As noted by Standish,  they were perhaps ignoring evolutionary theory in their anti-supernaturalist bias. But the point remains that supernaturalists generally made a better prediction about the extent of “junk DNA”, and that in this case an anti-supernaturalist bias actually hindered research (the reverse of what is usually claimed).
This brings up an important point. One of the reasons “science” (naturalism) claims not to lose is that it incorporates findings which were originally thought to favor “religion” (supernaturalism). Thus the temporality of the universe, and some other ideas such as the harmfulness of tobacco, are simply incorporated into the naturalistic model, and the modern believer in naturalism often may not be aware of the religious overtones to the previous controversies. The topic is viewed as simply another example of the steady advance of science.
The same could have been true for religion. For example, most theologians have incorporated a heliocentric view of the solar system into their theology. But the believers in naturalism will not let them forget that at one time the majority of Christians (not all; note Philip Melancthon) disagreed with the heliocentric theory, and the Catholic Church disagreed strongly enough that it forced Galileo to recant and banned his books, an action it has been forced to repudiate. The Church was in error here. But if one can hold modern Christianity accountable for the mistakes of the majority of its predecessors, one can also hold naturalism accountable for the mistakes of the majority of its predecessors.
This brings us to a final point. The argument that “religion always loses” is used to avoid having to deal with some subject where supernaturalism is apparently winning at present, and where if it wins, naturalism is dead. Naturalism can survive the historicity of the numbers in Kings and Chronicles, or the toxicity of tobacco, or even (as deism) the Big Bang. Naturalism cannot survive without a naturalistic explanation for the origin of life. And yet there is not such an explanation, not even a remotely plausible one. The more we know, the worse it looks.
Naturalism implicitly recognizes this. The best evidence for this is the insistence on the monophyletic origin of life. In the face of the Cambrian explosion and different genetic codes for some organisms (e.g., Paramecium), naturalists continue to insist that all organisms on Earth share a common ancestor. If they really believed that life were that easy to start, they would simply accept the hypothesis that it started a number of different times. The fact that they insist on the monophyletic origin of life is testimony that they implicitly recognize that it is extremely difficult to get life started even once, let alone multiple times.
But believers in naturalism are absolutely committed to a naturalistic origin for life. Some idea of the strength of the commitment can be gathered from a passage in an excellent (and still accurate) book by Robert Shapiro entitled Origins: A Skeptic’s Guide to the Creation of Life on Earth.  In it he points out the flaws of the various theories, finally opting for a theory of short non-modern peptides as the least problematic. But on p 130 he displays his own viewpoint:
Some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin for life have failed unequivocally. Further, new geological evidence may indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. In such a case, some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.
So naturalism requires a defense against the obvious. And the best defense is, “We have never lost yet. You always do if you wait long enough.” In the case of the origin of life, it appears that naturalism would have lost a long time ago if its adherents had not refused to recognize the loss. The major problem with the “religion always loses” defense is that it is not true. Even in hindsight it is not true without distorting the record, and from a prospective point of view (the only point of view from which we can currently view the future), it is certainly not true. It should be recognized as what it is, a faith statement disagreeing with the apparent lessons of history. Religion does not always lose.
Paul A Giem
See, for example: (a) Yandell KE. 1986. Protestant theology and natural science in the twentieth century. In: Lindberg DC, Numbers RL, editors. God and Nature: Historical Essays on the Encounter between Christianity and Science, p 448-471. Berkeley and London: University of California Press; (b) White AD. A history of the warfare of science with theology in Christendom. 2 vols. NY: Dover Press.
Thiele E. 1983. The mysterious numbers of the Hebrew Kings. 3rd ed. Grand Rapids, MI: Zondervan Publishing House.
Strand KA. 1996. Thiele’s biblical chronology as a corrective for extrabiblical dates. Andrews University Seminary Studies 34:295-317.
Shea W. 1988. Bel(te)shazzar meets Belshazzar. Andrews University Seminary Studies 26:67-81.
Shea W. 1982. Extra-biblical texts and the convocation on the Plain of Dura. Andrews University Seminary Studies 20:29-57.
Robert Jastrow (1978. God and the astronomers. NY: W. W. Norton and Co.) notes the phenomenon. Although the supernaturalists were not always on one side, or the naturalists on the other, as noted by Helge Kragh (1999. Cosmology and controversy. Princeton, NJ: Princeton University Press, p 251-268), there was still a tendency to line up on the side most compatible with one’s evaluation of theism.
Bernard H, Bernard M, translators. 1895. The structure of man: an index to his past history. Howes GB, editor. London: MacMilllan and Co.
For an anti-supernaturalist argument to succeed, it is important for the structure under consideration to have no function. It is not enough simply for it to have minimal and easily compensated function. Otherwise, such structures as little fingers or toes could be considered unnecessary, as there are very few functions that cannot be performed equally well by humans who have lost their little fingers and toes, and yet it seems unreasonable to claim that they could not have been designed.
The attractiveness of such an argument is such that it is still not completely dead. It surfaces, for example, in: Miller KR. 1999. Finding Darwin’s God. NY: Cliff Street Books, p 100-101.
Standish TG. 2002. Rushing to judgment: functionality in noncoding or “junk” DNA. Origins 53:7-20.
Shapiro R. 1986. Origins: a skeptic’s guide to the creation of life on Earth. NY: Summit Books.