I apologize for taking this long to get back to you.  Blogging and online debates have fallen to the bottom of my totem pole of priorities recently (which is probably a more positive than negative development).

Nevertheless, I wanted to inform you that I've looked at those links that you shared.  They have prompted me to start doing a little research here and there.  I am not a trained scientist, so their technical language is pretty difficult to follow as well, but I figured I could try to at least get the gist of them. 

Just a couple wrap-up points from me:
With regard to the philosopher/theologian argument, you understood my position correctly.  However, I admit that I do not share your willingness to allow the biologist/scientist to waver too far from his field of inquiry into such non-scientific fields as ethics, epistemology, legal systems, etc.  While I do admit the biologist can provide insights into these fields, I remain completely convinced that he cannot explain the ultimate meaning, the fundamental principles, and the background epistemology necessary to do properly establish himself as an authority in these fields.  The Bahnsen/Stein debate is particularly enlightening on this point.  I remain convinced that the philosophers and theologians must establish the presuppositional framework, the epistemology, and metaphysical outlook in order to justify the use of the scientific method.  The scientific method cannot justify itself since it relies on empiricism.  That's why Dawkins is wrong to say that non-scientific things should be subjected to empiricism for proof…empiricism is not meant to prove non-scientific things.  Empiricism is not and cannot be a final standard for proof for anything outside of material existence, including itself.  

Anyway, I also just wanted to remind you of the purpose of why I joined this discussion: there are very intelligent and qualified scientists/biologists and non-scientists who do not accept evolution or have significant doubts as to its validity.  In fact, a friend of mine just shared a link on his facebook page the other day to this list of scientists who are skeptical of evolutionary explanations in science: http://www.dissentfromdarwin.org/.  I hope, if anything, that point has been made clear in my posts and that I've proven that evolutionary theory is not as widely accepted in science as the postulate that the earth is round (just for the fun of it, I tried looking up scientists who doubt that the earth is round and I couldn't find any). 

Thanks for taking the time to engage in this discussion!  I have appreciated the back-and-forth. 

I'd like to add a small point.  Often these arguments from an ID/creationist/theist perspective land back on familiar points, i.e. "I can accept microevolution, but not macroevolution" and "Scientists are narrow-minded when they disregard supernatural explanations".  What really becomes a sticking point for me is this:  do you accept the scientific method?  Do you accept that knowledge can be gained by the process of posing a hypothesis and testing that hypothesis?
 
If you take an antihistamine to treat your pollen allergies, if you know that your plane will lift off the ground, and if you put sunflower seeds instead of ham in your birdfeeder, then you obviously do accept that the scientific method generates knowledge that can be used and trusted to be true. Why then does the scientific method, whereby we have come to understand everything else about our world, lose merit when it comes to evolution, human nature, the origins of life, and even the origins of the universe?  If the scientific method is powerful enough to move us from a da Vinci drawing of paper wings to a shuttle rocketing into space, then why is it not powerful enough to generate knowledge about biodiversity? 
Evolutionary biologists, cosmologists, and astrophysicists use the same scientific method used by dairy scientists to bring you the best milk and pharmaceutical companies to make the best beta blockers.  The theories that we have about the origins of biodiversity are the best theories and taken to be true because, and only because, they have undergone the same rigorous scientific method that is used by every other field and every other scientist seeking some sliver of knowledge. 

In my opinion–and in the opinions of many other scientists–every claim made about the origins of the universe and life on Earth is potentially testable under the scientific method.  So far, every scientific test has pointed to a natural explanation and not a supernatural one, and until the reverse is true, there is no reason to ever posit a supernatural explanation for natural phenomena.

You bring up some interesting points. Keeping in line with our numbering system, here would be my replies:

1 and 4. I do think that it's possible to debate whether 1+1=2, but I have no interest in doing so and nor do you, it seems, as we both generally accept this to be the case. But I mentioned it originally only to point out that things we understand to be universally true can be called into question. When I think about this point, I think of whether hypothetical intelligent aliens would have some understanding of those fundamental constants you alluded to, or indeed numbers/counting/binary/other concepts humans consider to be absolutely true. So let's throw this point out as irrelevant, as it seems we are in agreement.

As for the relativity and the earth being round, I wouldn't go so far as to bin "the earth is round" with "1+1=2". The theory that the earth is round, like the theory of evolution, is something that could be readily falsified; both can be measured and observed. Both have accumulated large masses of data that have failed to falsify them. That was the reason I suggested it as a more suitable analogy, and I still think that to be the case.

2 and 3. I did intentionally narrow the scope of my statement to "well-regarded biologists". I think that a physicist who hasn't extensively studied evolution (i.e. gotten a degree in evolutionary biology or genetics) is no more qualified than the Pope or the auto mechanic to speak authoritatively on the matter.

Your argument seems to be that there are theologians and philosophers who are very well-versed in evolutionary theory and still reject it, and in that sense you have given me some homework, which I appreciate. The degree on the wall is not necessary, I'll grant you, but it goes a long way in confirming that someone has rigorously rather than cursorily investigated a topic.

The same argument goes both ways, I guess. I agree that there is a limit to the scope of expertise of well-regarded biologists (who don't have Pope degrees on their walls, if you'll forgive the irreverance). On the other hand, as someone who studies the evolution of social organisms, I see how evolutionary biology speaks to the formation and stability of morality and punishment systems (ethics). I don't think that these subjects are out of the jurisdiction of evolutionary biologists.
As for Dawkins's arguments against spirituality, he largely argues that hypotheses of the divinity of Jesus or the existence of a Creator are not immune to empiricism, and he argues for their nonexistence from a probabilistic standpoint. But this particular point I don't think is relavent to the debate at hand.

5. Let us go ahead and define evolution as it is frequently defined in my field- merely as a change in the frequency of alleles (versions of genes, such as the yellow pea color allele versus the green pea color allele) in a population over time.
A consequence of evolution thus defined is divergence of these populations over time, which can ultimately lead to speciation.

I also would like to direct your and the other readers' attention to a subtle but frequently-misunderstood point: humans did not evolve from the extant apes- they share a common ancestor with each other (a proto-human/proto-ape, if you will).
As for the birds, certain lineages of dinosaurs were indeed their ancestors.

Based on what you've said, it seems like you accept what is largely understood as microevolution (evolution on a population scale over relatively short periods of time- as in things like antibiotic resistance). You refer to this as "adaptation".
You don't accept macroevolution (which focuses on larger spatio-temporal scales during which things like speciation occur).
This being the case, I have some homework of my own for you- a few examples of instances of populations which have begun to speciate on smaller time scales that have been observable over a single human lifetime (the top two are pretty technical, but the take home messages should be pretty clear) :

https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=1E34N_j_iiI9SbllzDnN02QIrV7Z0sdJv2JAAKXQJxfBMIE2mMQfYzNRafmzW&hl=en_UShttp://en.wikipedia.org/wiki/Polyploidy” rel=”nofollow”>http://www.jstor.org/sici?sici=0003-0147(198806)131:6%3C911:SVDSOH%3E2.0.CO;2-Y&

https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=1E34N_j_iiI9SbllzDnN02QIrV7Z0sdJv2JAAKXQJxfBMIE2mMQfYzNRafmzW&hl=en_UShttp://en.wikipedia.org/wiki/Polyploidy” rel=”nofollow”>https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=1E34N_j_iiI9SbllzDnN02QIrV7Z0sdJv2JAAKXQJxfBMIE2mMQfYzNRafmzW&hl=en_US

https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=1E34N_j_iiI9SbllzDnN02QIrV7Z0sdJv2JAAKXQJxfBMIE2mMQfYzNRafmzW&hl=en_UShttp://en.wikipedia.org/wiki/Polyploidy” rel=”nofollow”>http://en.wikipedia.org/wiki/Polyploidy
http://www.pnas.org/content/108/24/9733.full

Hope this debate is a fruitful exercise for you, too… I should warn you that it will frequently take me some time to generate responses. This blog, while tons of fun, is not my top priority for the time being.

1.Extremely certain.  Beyond the fact that 2+2 must equal 4, there are essential mathematical patterns and values that are embedded into the fabric of the universe's structure.  Although I admit I haven't read any of his works, consider Martin Rees's argument (based on his study of astrophysics) that there are six numerical values embedded into the universe that, if changed by the slightest fraction, would cause an end to the universe's existence. Consider also the intricately complex patterns that are the result of constants found in nature that offer both artistic and architectural inspiration, such as the Golden Mean, pi, etc.  Beyond that, there are mathematical principles that, if an engineer or architect were to violate, bridges would collapse, computer systems fail, etc.  So, although admittedly not all aspects of mathematical study are definitive and proven as universally applicable, there obviously has to be a certain level at which there are universal mathematical values/principles that are essential for not only existence, but also the ability to know and reason.

2. It's interesting that you both shifted and narrowed the scope of my original claim from "qualified scientists" to "well-regarded biologists."  Nevertheless, I'll provide you with a couple names to consider, but I will also emphasize that there is a wide variety of scientists across many disciplines that either significantly doubt or outright reject evolutionary theory. 

As far as biology goes, Dr. Dean Kenyon (Ph.D. from Stanford University) once wrote a book called "Biochemical Predestination," which he thought at the time provided an explanation for the origin of life from a evolutionary biological perspective (using a study of virus production/reproduction).  After a time of reading resources from non-evolutionary scientists and a personal study of DNA, he came to conclude that his original arguments were flawed and he now teaches creationism at San Fransisco State University (with the support of the university due to their commitment to academic freedom). 

Although not strictly a biologist, Dr. Ben Carson is a world-renowned neurosurgeon who rejects evolution.  He has made groundbreaking advances in his field and is widely respected for his efforts as a scientist and medical expert.

If you want a list of qualified scientists who are academically trained ranging from across practically all fields of scientific inquiry who also reject evolution, then here's a few links.  I've clicked on some of the bios and I've seen Ph.D.'s from Harvard, Oregon State University, UCLA, University of Illinois, etc.  You can certainly disagree with them, but there's no way you can argue that they are lack credentials and are not qualified. 

http://www.christiananswers.net/creation/people/
http://www.answersingenesis.org/home/area/bios/

Note:, these are generally creationist scientists, not just ID scientists.  If one were to include the list of ID scientists, then there would be many more. 

3. Another scope shift on your part.  I did not say theologians and philosophers try to reject evolution based on the scientific merits of it.  Rather, they have attacked evolutionary philosophy and the resulting naturalistic philosophies which are connected to evolutionary assumptions. Included in this is the instance when the scientist tries to go outside of his area of expertise, such as Richard Dawkins or Gordan Stein, to try to argue philosophical, ethical, and spiritual realties when their study as biologists gives them no legitimate methodology for doing so.  There are many philosophers and theologians who are ready to demonstrate that such an approach is inadequate, irrational, and educationally irresponsible.  They have done so in a highly intelligent and compelling way…look up for example, Dr. John Lennox's response to Steven Hawking's claim that there is no God, or look up Dr. Greg Bahnsen debate with Gordan Stein.  Beyond this, they can demonstrate how the philosophical realities of evolutionary assumptions are absurd, relying on those who reject evolution out of their scientific expertise to handle the debate on the scientific forefront.  Such philosophers and theologians do not hold opinions about evolution akin to those held by an auto mechanic or chef (again, false analogy). 

4. I unfortunately can't accept the theory of relativity because I have no expertise with regard to it.  I would presume too much of myself to know how to debate it.  I wouldn't accept the "world is round theory" because that just as certain as mathematics.  Equating evolution to either math or "world is round" is granting evolutionary assumptions too much ground when it has not necessarily deserved it. 

5. For the purposes of this discussion, I am using evolution only in the sense that we are discussing the evolution from one type of  species into another, i.e. a bird to a dinosaur, an ape to a human, etc, over the course of millions/billions of years.  I am not discussing adaptation, which everyone from evolutionists to creationists accept.  I admit this is a hastily constructed and rather crudely stated definition, so feel free to improvise as you see fit.