Not surprising, most of the arguments Flew presents for his deistic theism run along the typical "argument from design" paradigm. He notes, for example, the gross improbability of the universe, which has led to some rather fanciful attempts by atheistical scientists to assume the existence of multiple universes (i.e., the theory of multiverse). To what extent such design-probability arguments support theism is, of course, debatable. Flew doesn't discuss, for example, the classic arguments advanced by Hume against design theology. Yet, to be fair, Flew does manage to present one argument that, if not entirely convincing, nevertheless constitutes an immense challenge to the scientific pretensions of the new atheists. This involves the perplexing question of abiogenesis:
Most studies on the origin of life are carried out by scientists who rarely attend the philosophical dimension of their findings [writes Flew]. Philosophers, on the other hand, have said little on the nature and origin of life. The philosophical question that has not been answered in origin-of-life studies is this: How can a universe of mindless matter produce beings with intrinsic ends, self-replication capabilities, and "coded chemistry"?
Paul Davies "observes that most theories of biogenesis have concentrated on the chemistry of life, but "life is more than just complex chemical reactions. The cell is also an information storing, processing and replicating system. We need to explain the origin of information, and the way in which the information processing machinery came to exist." [Davies] emphasizes the fact that the gene is nothing but a set of coded instructions with a precise recipe for manufacturing proteins. Most important, these genetic instructions are not the kind of information you find in thermodynamics and statistical mechanics; rather, they constitute semantic information. These instructions can be effective only in a molecular environment capable of interpreting the meaning in the genetic code. The origin question rises to the top at this point. "The problem of how meaningful or semantic information can emerge spontaneously from a collection of mindless molecules subject to blind and purposeless forces presents a deep conceptual challenge."
It is true that protobiologists do have theories of the evolution of the first living matter, but they are dealing with a different category of problem. They are dealing with the interaction of chemicals, whereas our questions have to do with how something can be intrinsically purpose-driven and how matter can be managed by symbol processing.
Whether this argument advances the case for theism, even of the minimal, deist sort, is open to question. But even if it doesn't advance the cause of theism, it does manage to provide a strong case against any version of militant atheism. Confronted with arguments such as this one, I cannot see how any Objectivist can continue to regard belief in God as patently irrational. Indeed, if you compare the claims of atheism with those of rational theism, it's not easy to determine which view is more rational. The rational theist argues that, because it's grossly implausible to assume that a coded chemistry could have emerged spontaneously from inorganic matter (see this article for greater explication of the point), it is not unreasonable to assume that life has its origin in some sort of intelligence or understanding that is beyond human comprehension. The atheist, on the other hand, argues that life emerges out of matter spontaneously, by "chance," as it were—that in other words, we all evolved from rocks. Is this really the more plausible view?
I'm not aware that any prominent Objectivist has said anything about abiogenesis. Perhaps it's too empirical subject for the typical orthodox Objectivist, given his unfortunate penchant for trying to determine matters of fact through logical, moral, and rhetorical constructions. Objectivists have, however, commented on deism and not with complete disfavor, either. It's not that they advocate the position; but they are not inclined to criticize it. Peikoff recognizes that it is not a religious position. Yet his view that deism is merely "the step between Christianity and outright atheism" is a bit of an exaggeration. That may have been true in the eighteenth century, but it isn't true any longer. Now the traffic tends to move in the opposite direction. Nor is it necessary to regard deism as way station between atheism and Christianity. Deism seems an entirely rational position in and of itself—perhaps the most plausible outside of agnosticism. In any case, there doesn't seem any strong reasons to object to it.
If, however, deism is not a religious doctrine (as even Peikoff admits), this raises questions as to the point of atheism, particularly of the uncompromising or militant type. What is objectionable in specific religions is not the belief in God per se, but the belief that God wants everyone to act in certain ways. If so, then the real point of issue is the morality put forth by the religious, not their belief in God. Why, then, bring up the issue of God at all?