Oh, yes. I do Dropbox syncing, too (this is the other good thing about org-mode: plain text files). And there might be some truth in the statement that while org-mode is excellent for a single file, things start to be less seamless when it comes to more of them... inter-file links don't seem to be that reliable, for example. Is this the reason for your One Big Org File?
For white on black, it's just (setq default-frame-alist '((background-color . "black") (foreground-color . "white"))) in your .emacs.
Actually, it's kind of typical lesswrong that I started off with a comment popularizing org-mode, but ended up changing my mind about it (well... kind of), the newest experiments include Notational Velocity (they seem to be good at the global search stuff org-mode is lacking, but not so nice indented lists locally), and also this system:
http://www.speakeasy.org/~lion/nb/book.pdf
which includes paper notebooks, maps of your thoughts and similar fancy stuff, but I haven't yet finished reading it (it's long and not exactly the most organized stuff I've ever read... but it has good ideas.)
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As some others have said, others on LW (like myself) were not always non-theists. Feel free to reach out if you'd like to discuss or need/want support. Thinking these thoughts and living as a heavily-doubting theist is extremely challenging and draining, from my experience. I was consumed during my initial questioning and ultimate de-conversion. I read and thought day and night, felt sick, alienated, lonely, etc. I wrote some posts here if you'd like to take a look:
One of the more direction-changing thoughts I had (independently and prior to finding out the concept already existed) was what John Loftus claims "The Outsider Test for Faith (OTF)." Basically, if you weren't already a subscriber to some religion, X, could you be convinced of it? Similarly, why are said miracle claims un-convincing even in the least to someone who doesn't already share your religious tradition?
I had a different twist on that. My natural inclination when researching (say, which tool to buy or which method is best) is to force myself to be agnostic to all of them and then research to see which is the most convincing. Say, googling "Milwaukee vs. Dewalt router" or "Milwaukee routers suck/are great" and "Dewalt routers suck/are great" to see what I find. I pay attention to Amazon 1-2 star reviews to look at their content. I started wondering why this shouldn't work for religion. Everyone in my religious community was suggesting that I should "have faith seeking understanding." This always struck me as "believe that you may believe more strongly." I wanted to know why the one thing that mattered the very most in the world shouldn't hold up to the same test I put my financial purchases through.
In addition, I wondered why the Bible, God's inspired book, failed to convince so many others who surely were aware of it. Assuming Christianity was true meant that other religions were false/lies/invented (by humans). Measly human minds creating stories out of thin air have been able to sway more than half the world away from God's official word?
Probably doesn't sound all that great re-writing it, but this was a pretty mind-blowing thought to me back then, and was a definite contributing factor to my ultimate deconversion. Sure, there's apologetics to counter it, but they have to work fairly hard to speculate about God's motives for not being more clear.
As others have stated outrightly or alluded to, toss in whatever apologetic ammunition you'd like and it still works pretty well. Some biblical prophecy, miracle, perfectly fitting theological aspect about Christ, etc. seem amazing to you? Why doesn't it to the nearest Muslim, Hindu, Scientologist, or Mormon? And why do things like reading golden plates from a hat or being embodied alien spirits seem so ridiculous as to not even warrant a fair shake when Christians hear them?