Thanks for the thoughtful response, Oberon.
...However, in my discussions with believers of various religions (mainly christianity, judaism, and islam, but a few others as well) I did get a few reasonable responses. For example, take the analogy of the a driver in the car. The car represents the brain, a machine designed to run. If it is damaged, the operator (the soul or driver) cannot properly use it.
Yes, that is a common metaphor, and I have already made my point about the usefulness of such metaphors in drawing conclusions. I'm not against speculation, but what does it buy us to posit the existence of this "ghost in the machine"? An observer of car behavior would ultimately discover the essential role of the driver, but no scientist (to my knowledge) has ever come up with a need to do that for human or animal behavior.
Additionally, brain activity (as far as how it equates with consciousness) is barely understood. I think that most likely what makes us who we are (the ego) is a result of a dynamic system of neural interactions in which the whole is more than the sum of its parts. Perhaps the soul is somehow interacts with or even controls/guides this neural summation. Or it's all B.S.
I do not believe that one needs to understand exactly how brains generate consciousness in order to establish that that is what they do. We can observe the effects of physical changes to the brain on consciousness, and we can associate physical changes in the brain directly with mental functions (using fMRI, for example).
True enough. However, science too has a long record of failed explanations. It is just far youner. And if one looks at certain philosophers of science (e.g. Kuhn) then the prospect of scientific understanding of this world becomes even more bleak...
I used to be a bigger fan of Kuhn's, but I now believe that paradigm shifts are less revolutionary and more incremental than he portrayed. Failure of experimentation is actually central to scientific progress. When an experiment fails, science itself is advanced. When a religious prophecy fails, that jeopardizes religious faith itself. One has to attribute it to false revelation or some other reason that preserves the integrity of doctrine.
I don't buy that completely, however. Nonetheless, the scientific method was designed and evolved from working in the lab. Control all your variables, perform the experiment, observe the result, and if you didn't prove yourself wrong, call it theory. It has done miraculous things in our world. However, it is also severely limited.
Not all science is experimental. Sometimes, it just relies on conclusions drawn from observation of nature. That is how Darwin and Wallace came to propose natural selection as the mechanism behind evolution. (That evolution was a probable cause of speciation had already become a popular idea in Darwin's time, but the selectional mechanism for it had not been discovered.)
The argument from design has not been "overturned." It is still possible for god or zeus or whatever to have guided evolution...
True. Perhaps I should have used the word "undermined" instead of "overturned".
...And perhaps this really is the last nail on the coffin. But a number of theologians and scientists today (off the top of my head Francis s. Collins or the guys who wrote "The Cosmological Anthropic Principle") look deeper inot the issue...
I'm not sure that I would call it "deeper", but it is true that the RCC has officially endorsed the idea of guided evolution. Francis Collins, a devout Catholic, may have played some role in that, but I'm just speculating. I regard this endorsement as support for my thesis, however. We haven't proven abiogenesis, so the "explanation" has shifted to the gaps that science has yet to fill.
...It is the fine-tuning of the universe itself, far more complex and intricate, and the miracle of the biological mechanisms which make life possible, and so forth (there is a great deal of literature out there both against and supporting this view, so there is really no need for me to go into great detail).
As Dawkins has pointed out, the "fine tuning" argument actually works against creationism, as it can be explained in terms of natural evolution. We find ourselves in such a finely tuned environment because we would never have evolved in any other environment. The universe is not a byproduct of the need for us to exist. We are a byproduct of the universe because of the way it turned out to be.
Playing devels advocate again: Or perhaps we are "endowed" with a sense of the spiritual, and, having given us this "gift," god sent us his only son to guide us, or sent his angel gabriel to Muhammad to spread his word, or the universal divine is made manifest in various earthly incarnations of the buddha, or whatever.
Well, I have taken pains to deny that my arguments show the impossibility of the existence of gods, but I have argued for the implausibility of such a belief on the grounds that patterns of allegedly true revelation are indistinguishable from patterns of false revelation. Besides, there are perfectly good non-religious explanations of why human beings would come to believe in gods.
Not a great argument. After all, many religions are concerned mainly with what happens after death. They might believe prayer works in one way or another, but the important thing is heaven or paradise or whatever. So the people of the right faith (and according to south park the mormons got it right) get the ultimate reward. Or maybe all those who live be certain principles do. The point is the efficacy of prayer isn't really a good measure of the likelihood of this or that religion being correct.
I strongly disagree with those who try to downplay the role of prayer in bettering their circumstances in this life. It is quite obvious that most people of faith use prayer for precisely that purpose, although they are naturally reluctant to admit a selfish motive to their devotion.
There have been cases where science is at a loss to explain documented events (e.g. various cases at the Lourdes in France)...
I know of no such cases, but I am willing to be convinced. Usually, miracles that are subjected to real scientific investigation end up debunking the religious claim--e.g. consider the famous Shroud of Turin.
More importantly, many religions don't depend on miracles at all. And for some of the major ones that do (e.g. christianity), the most important miracle occured in a time when verification and corroboration were not really available.
I believe that there are actually very few religions that are without claims of miracles. Miracles are extremely popular, you know. Science has made its reputation on achieving miraculous results by showing that miracles were not really involved in achieving them.
Absolutely. The brain is the basic hardward which allows us to be who were are (lower level control, such as the ability for babies to walk on a treadmill do primarily to spinal cord activity is pretty meaningless) is the brain. However, modern neuroscience suggests "who we are" exists somewhat apart from the individual neurons. Rather, it is a sum of neural activity greater than the individual EPSPs and so forth which allow consciousness, memory, etc. Could not the "soul" be the guiding entity in this?
I do not see how a soul would be necessary to explain "who we are", and I am not aware of any scientific work that supports such an answer to that question. Science is inherently reductionist, so we would explain a thunderstorm in terms of it natural causal constituents. However, a thunderstorm is greater than the sum of its parts, too. It is only ancient religions perhaps, that attributed souls to thunderstorms. (On the other hand, we do give names to hurricanes.)