Thank you for your response. No I will take it apart.
Let me first say that I do not know you. It seems that you do not know me. (I say that because if you had done some research you could find information on the web, since I use my real name, and on this website where my views are well spelled out.) Thus nothing I say here is personal.
I don't really know how to respond. I know how the article begins... I think both of the starting points (competition vs. EO Wilson's cooperation) are not contradictory and perhaps bringing in the article was misleading.
If you know the article you cite to back up your position contradicts your position, why did you cite it? You think that both starting points are not contradictory, but Where is your EVIDENCE? The scientific method is based on evidence, not opinion.
I cited two opposing scientific views expressed by two acknowledged experts and gave my reasons for favoring one of them. You gave me an opinion based on no evidence and no reputable science as far as I can tell, and as far as you are able to document.
Both of them are really built on Darwin's actual idea of natural selection of particular traits. Some of the traits that are selected for bring about this cooperation (as many organisms rely on others in a group to survive and the survival of the group is more favorable than a particular individual). And others of the traits result from who is 'best fit' to thrive in an often changing environment (and competition in this sense is the other half of the coin-this is not competition in the sense of how we typically think where you want others to lose and only you win but with finite resources/predators/etc. certain organisms have a 'competitive edge').
This statement is manifestly untrue. Darwin, based on the population theories of Malthus, believed that struggle between individuals for scarce natural resources is the basis for natural selection. If you can prove otherwise, please do so. To be sure Darwin was mistaken, which you point out after you say he was right.
Then you say that many organism use symbiosis as their survival strategy, while others us competition, but this type of competition is not selfish. When Dawkins came up with the Selfish Gene, he was trying to be faithful to Darwin understanding of how Natural selection works, and I think he was. You are providing with no evidence that he is not. So again you are saying that natural selection is not based on the struggle for survival as Darwin and Dawkins claimed, but on symbiosis as Lynn Margulis said.
Now we know that an organism does not sit around and think of ways to out compete others or adapt to its environment, so how does this happen? Well, every offspring represents a new allele or a new possible adaption, but it is not the organism which chooses which allele will survive and flourish, but the environment or ecology determines this. Thus it is the ecology which selects. Since it is God Who created the environment and gives it form, purpose, and direction, it is God Who uses natural selection to create Nature and humans.
I still don't see how Methodological Naturalism can 'work better.' I guess my disagreement/confusion is related to 'rational' vs. 'physical.' I do not see how the fact that the physical world is 'in accordance with reason/logic' means that it is metaphysical. Obviously, if nature (and again you keep capitalizing 'nature' as if it implies some deity) was not understandable, we couldn't understand it and methodological naturalism wouldn't work.
We live in the intellectual world of "Western dualism," which means the Natural and the Metaphysical. Methodological Naturalism is part of this dualistic view, but it claims that Nature is not rational. Thus theoretically it does not work as you claim it does.
Western dualism is good because it has brought science a long way, but it is not perfect. It is now time to move beyond Western dualism or risk failure. The world does not stand still, and yet we are afraid to change because we know that change can be dangerous also. We need to be willing to move from the good to the better.
Though we wouldn't even be having this discussion as we'd both likely be dead since modern science would not have developed without a working methodological naturalism and the average life expectancy would still be in the mid to low 20s.
This is a bogus argument which places science against Christianity. Modern science grew out of Christianity, so there is no inherent conflict. If you want to use bogus arguments to justify the status quo, that is your right, but it comes with a very high price.