The years thing seems to make everything probable, because we have basically 600 MM years of evolution from something simple to everything today, and that's a lot of time. But it is not infinite. When we look at what evolution actually accomplishes in 10k generations, it is basically a handful of point mutations, frameshifts, and transpositions. Consider humans have 50MM new functioning nucleotides developed over 6 million years from our 'common ape' ancestor: where are the new unique functioning nucleotides (say, 1000) in the various human haplogroups? Evolution in humans seems to have stopped. Dawkins has said given enough time 'anything' can happen. True, but in finite time a lot less happens.
They've been looking at E. coli for 64000k+ generations. That's where we should see something, and instead all we get is turning a gene that is sometimes on, to always on (citT), via a mutation that put it near a different promoter gene. That's kinda cool, and I admit there's some evolution, but it seems to have limits.
But, thanks for the respectful tone. I think it's important to remember that people who disagree with you can be neither stupid or disingenuous (there's a flaw in the Milgrom-Stokey no-trade theorem, and I think it's related to the 'Fact-Free Learning' paper of Aragones et al.)
Of the millions of proteins on the planet it is unremarkable most exist elsewhere, just as it's likely most parts in a car can be found in other machines. Further, these aren't identical proteins, merely 'homologous' ones, where there's a stretch of, say, a 70% match over 40% of the protein, so that makes this finding not surprising (lug nut in engine A like fastener in engine B). A Type 3 Secretory System has about 1/3 of the proteins in a flagellum (depends which T3SS, which flagellum), but to get from one to the other needs probably ten thousand new nucleotides in a specific constellation, and nothing close to that kind of change has been observed in the lab w/ fruit flies or E. coli. So, it's possible, but still improbable, like turning one of my programs into another via random change and selection, there are many similarities in all my programs, but it just would take too long. Possible is not probable, and unlike cosmological improbabilities, there's no anthropic principle to save this. Pointing out homologs still leaves the problem of tranversing a highly spiked fitness landscape, but if this is ever demonstrated on say, a new protein complex in E. coli, I'd say, you win (but more complex than moving a gene closer to a promoter region as in the citT).
I'm a big Eliezer fan, and like reading this blog on occasion. I consider myself rational, Dunning-Kruger effect notwithstanding (ie, I'm too dumb or biased to know I'm not dumb or biased, trapped!). In any case, I think the above is pretty good, but I would stress the ID portion of my paper, which is in the PDF not the post, is that the evolutionary mechanism as observed empirically scales O(2^n), not O(n), generally, where n is the number of mutations needed to create a new function. Someday we may see evolution that scales, at which point I will change my mind, but thus far, I think Behe is correct in his 'edge of evolution' argument (eg, certain things, like anti-freeze in fish, are evolutionarily possible, others, like creating a flagellum, are not). As per the Christianity part, the emphasis on the will over reason gives a sustainable, evolutionarily stable 'why' to habits of character and thought that are salubrious, stoicism with real inspiration. Christianity also is the foundation for individualism and bourgeois morality that has generated flourishing societies, so, it works personally and for society.
My younger self disagreed with my current self, so I can empathize and respect those why find my reasoning unconvincing, but I don't think it's useful in figuring things out to simply attribute my belief to bias or insecurity.
Ever notice sci-fi/fantasy books written by young people have not just little humor, but absolutely zero humor (eg, Divergent, Eragon)?
Allele variation that generates different heights or melanin within various races, point mutations like sickle cell, the mutations that generate lactose tolerance in adults, or that affect our ability to process alcohol, are micro-evolution. They do not extrapolate to new tissues and proteins that define different species. I accept that polar bears descended from a brown bear, that the short-limb, heat-conserving body of an Eskimo was the result of the standard evolutionary scenario. I have no reason to doubt the Earth existed for billions of years.
Humans have hundreds of orphan genes unique among mammals. To say this is just an extension of micro-evolution relies on the possibility it could happen, but you need 50MM new nucleotides that work to arise within 500k generations. Genetic drift could generate that many mutations, but the chance these would be functional assumes proteins are extremely promiscuous. When you look at what it takes to make a functioning protein within the state-space of all amino acid sequences, and how proteins work in concert with promoter genes, RNA editing, and connecting to other proteins, the probability this happened via mutation and selection is like a monkey typing a couple pages of Shakespeare: possible, but not probable.
This all argues for a Creator, who could be an alien, or an adolescent Sim City programmer in a different dimension, or a really smart and powerful guy that looks like Charlton Heston. The argument for a Christian God relies on issues outside of argument by design