The developing front in this battle is "Intelligent Design", which asserts that the universe, and especially the biological organisms in it, could not have come about by chance.  Rather it must have been created by some process of intelligent design (although the word "God" is scrupulously avoided).  In part it is the latest incarnation of "Creation [pseudo] Science", but it is has also attracted a few scientific agnostics.  The primary strategy is to question how complexity could have evolved from small incremental changes.  In many cases this has been done fairly and cogently, and (again in my own personal opinion) points have been made which deserve serious consideration from professional evolutionary biologists. In fact scientists have raised very similar questions themselves (the evolution of flight and sex) and have been chewing on them for decades.

However it is just plain silly to say that unresolved questions about how Evolution occurred are evidence that it didn't occur at all. Opponents of Evolution are fond of saying it is a "secular religion", and based on the behavior of some biologists, they are not entirely wrong. On the other hand, one of the strongest arguments that Evolution is a science, and not a religion, is precisely the fact that there are questions. If Evolution were truly a religion, there would be only received wisdom, dogma and absolute TRUTH. The insistence that God can be used as the default explanation for every ignorant gap in human knowledge is a philosophical debate of long standing, and even has a name ("God in the gaps"). Unfortunately the result is theologically unsatifying. As Science answers more and more questions, God is ignominously squeezed out of one gap after another.

Potentially, an even more contentious point is that if we insist on using logic and rationality  to deduce the existence of "Intelligent Design" - and thus the implied existence of an "Intelligent Designer then -  if we are intellectually honest - we cannot avoid continuing the rational approach to its logical conclusion; that the nature of the design tells us about the nature of the Designer. This idea goes all the way back to Roger Bacon in the 13th century who believed that the philosophical reason for science "consists in this, that through the knowledge of his creature, the Creator be known".

The problem is that an attempt to use rationality, logic and science to prove the existence of a Creator or Designer sometimes turns up answers which are unpalatable.  Over 125 years ago Francis Galton (a cousin of Charles Darwin) used mathematical statistics to test the hypothesis of God.  Using the methods of science, Galton found that the hypothesis of God's existence must be rejected.  The standard answer to this, accepted by mainstream scientists and theologians, has come to be that belief in a higher being is a matter of faith, and that God, unlike nature, is inaccessible to the rational and experimental methods of science. Rebelling against this philosophical accord, "Intelligent Design" now makes a fresh attempt to prove the hypothesis of a supernatural designer through science.  Its advent must necessarily rake up all of the old conundrums.  In addition, it poses new ones - especially from the perspective of Genomics. When the anatomy and physiology of individual organisms is examined, the design is usually pedestrian and derivative.  Now that we can examine the architecture of the genome, the implications for "Intelligent Design" are even worse.

When we look at the genome, the design is no longer merely uninspired;  now - if we even think of it as design at all -  it is incompetent, slovenly and negligent. Many mistakes (pseudogenes) have been made and then left lying around.  Rough drafts are  cobbled together from bits and pieces of previously created elements (exons), but then the extra pieces (introns)  are not even removed and the joints neatly finished.  Instead a Rube Goldberg system of splicing is thrown in to make the whole rickety contraption work.  The workplace itself is rife with negligence.  The product has been attacked and parasitized (transposons and retroposons).  Some of the parasites are not even killed, but when they have been, the dead bodies (LINES and SINES) are not cleaned up;  they are left lying around to rot, and the damage they caused is not repaired.

If logic and rationality lead us to the deduction of "Intelligent Design" then they also lead us to some unflattering deductions about the nature of the designer.  When this is realized by the public at large, I suspect that the response will be outraged accusations of blasphemy and atheism.  However, this would be intellectually dishonest!  Science cannot be brought into the arena of religion to one-sidedly support the assertions of Faith, while political and polemical attacks are made on any contrary results. The advocates of "Intelligent Desing" should consider that this approach, if honestly pursued, could be devastating for traditional religious belief. 

There is little question (in my opinion) that the advocates of "Intelligent Design" have squarely identified some of the weaknesses of evolutionary theory. Evolutionary biologists should be expected to address these problems honestly. However, at this point in time "Intelligent Design" has little claim to scientific legitimacy, and it is well on its way to degenerating into the fraudulence and political posturing of "Creation [[pseudo] Science".