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Longenecker's complaint of bias is a red herring. It's probably overstated; the atheists I know or read (and I know and read a lot of them) don't seem to have any special bias or prejudice against Catholics. I myself was baptized a Catholic, and I didn't have any particular antipathy towards religious people until I started talking to them about religion about 12 or 13 years ago. But even if he were absolutely correct, so what? The rational person does not eliminate bias before rationally examining a position, she eliminates bias by rationally examining a position. Indeed, a rational person holds the view that her intuitions are suspect, and she looks carefully to disprove them. Rational argument stands up on its own; finding prior bias does not affect the intrinsic merit of the arguments at all. Longenecker's assertion of bias is therefore irrelevant; let him examine the arguments.
In Misunderstanding God: Where Atheists Go Wrong in Opposing Christianity Joe Heschmeyer explores only two of his "four questions" in any depth: scientism and the definition of God. Indeed, the idea that atheists believe that "religion is invariably violent" is nonsensical on its face, and the focus on biblical literalism is, as I'll discuss below, primarily political. But even on these two points, Heschmeyer, whom Longnecker relies on, fails to make a substantive case against atheists.
The philosophical debate about "scientism" is not only complicated, it is obfuscated to a degree that emerges from philosophers arguing with theologians, two professions that seem to consider obfuscation to be their primary product, can sum up. So let me sum up. In its most broad sense, "science" just means "knowing," so "science is the only way of knowing" is a tautology. In a more restricted sense, "science" means a particular methodology, the Scientific Method, broadly conceived. Broadly conceived (i.e. the simplest theoretical system to explain observed phenomena), "science" encompasses experimental science, historical investigation, the legal process, as well as our prosaic, day-to-day knowledge about the world. The philosophical charge against scientism usually rests on an equivocation fallacy between the broad sense of relation to observation and the narrow sense of one particular set of techniques to relate statements to experiments (usually double-blind clinical experiments), a fallacy that Heschmeyer indulges at length.
According to Heschmeyer, "Since the claim that all truth must be scientifically provable is not itself scientifically provable, it’s self-refuting (by the claim’s own standard, it renders itself false)." But Heschmeyer is rehashing Logical Positivism, a philosophical position abandoned almost a century ago. The modern epistemology of science starts not with Logical Positivism but with Popper's falsificationism. According to Popper, a statement that is not disprovable by observation is not a statement about the world. Accordingly, because the statement, "The Scientific Method (broadly conceived) provides knowledge," is not disprovable by observation, it is not a statement about the world. It is a metaphysical statement. Popper, and most modern philosophers, do not condemn metaphysics; we want to clearly separate metaphysics, statements about how we investigate the world, from statements about the world itself. Much philosophical work has been done since Popper, of course; for example, philosophers generally consider the theory instead of the statement to be the testable unit, and we have completely rewritten Popper's deficient ideas about probabilism. We have more sophisticated problems today, but the obvious philosophical problems that Heschmeyer discusses were solved long ago.
Perhaps unintentionally, Heschmeyer is perpetrating a Kansas City Shuffle: he wants to distract us with the claim that atheists reject history as "unscientific" to draw attention away from his claim that there is good historical evidence for the existence of God. But regardless of the scientific status of historical investigation, Heschmeyer's naive confidence in the historical evidence is misguided. Whether the historical evidence supports the actuality of an event that even appeared to be a resurrection is in considerable doubt. The scholarly record is extensive, from both atheist and theist historians, and opinion, both of atheists and theists, is divided.
*As opposed to anthropological/sociological sense of history as the construction of narratives to establish the traditional legitimacy of cultural elements.
Indeed, Heschmeyer double-fakes us, because in the sense of history as the determination of what really happened in the past*, history cannot even address, much less "prove," the existence of God. After going on at length about the support provided by the historical evidence, Heschmeyer waffles on whether evidence is even applicable:
One of the best indicators of this confusion is the repeated demand for “evidence” of God’s existence, by which my interlocutors typically mean some kind of scientifically verifiable trace of this elusive and most likely mythological being. My attempts to tell them that the Creator of the entire universe cannot be, by definition, an object within the universe are met, usually, with complete incomprehension.But it's not just a matter of finding "traces"; Heschmeyer's conception of God is not falsifiable: the existence of God is a purely metaphysical issue, not a matter of scientific knowledge.
Evaluating metaphysics is much trickier than evaluating scientific concepts: what standards do we use? The establishment of standards is itself a metaphysical concept. Heschmeyer tells us that religious people "understand religion to be objectively true, as true as '3 x 3 = 9'"; it is not like "having a favorite color: that is, a subjective claim, and a matter of mere personal preference." But what does Heschmeyer mean by "objectively true"? Is having an opinion about what is objectively true substantively different from just having an opinion? These are complicated metaphysical questions that (perhaps fortunately) neither Heschmeyer nor Longnecker explore.
Neither Heschmeyer nor Longnecker answer two crucial questions. How do they know "[their] religion to be objectively true, as true as '3 x 3 = 9'"? And what might they mean by knowing itself? They reject falsificationism, fair enough. But what do they offer in its place? They construct an idea that cannot be proven wrong by any conceivable observation, and then they demand belief because it cannot be proven wrong. All the while rejecting the infinity of alternative unfalsifiable beliefs because... well, just because.
But the philosophical "struggle" is completely beside the point. First, philosophy (with few exceptions) and theology (without exception) are completely useless endeavors. It need not be so, but professional academic philosophers have turned the field into nothing more than an academic circle-jerk, and the money we spend on philosophical academia can be justified only in that it keeps philosophers and theologians from getting in the way of grown-ups who have work to do. More importantly, the philosophical battle for theism was lost more than two thousand years ago with Epicurus and Socrates. The entire philosophical and theological struggle since then has been to hide this utter philosophical defeat. (Which may be one reason philosophy has constructed itself into irrelevance.)
The fundamental struggle is not philosophical, it's political. Religions assert political power, authority and privilege. They claim a private, superior position to tell us what is good and bad. They claim an historically enormous and presently substantial portion of our wealth and labor. In extremis, they claim the right to ignore democratic law and the authority of the state to protect members of religious institutions who break those laws. No atheist cares that people such as Heschmeyer and Longnecker want to engage in philosophical twiddle-twaddle in the privacy of their own homes and churches. We do, however, care that they want to rule us. I don't believe that the hierarchy of the Catholic Church wants to rape our children, but they do want — indeed they must have, if they are truly to be rulers — the right to rape our children; it is incoherent that the rulers should ever, under any circumstances, be answerable to the ruled.
We reject that rule. Utterly. Completely. As long as they seek to rule, we will oppose them. We will oppose them with philosophy. We will oppose them with argument. We will oppose them with mockery and ridicule. And, when necessary, we will oppose them with the legitimate authority of the civil, democratic state.