So your an Athiest

[TheRocketSurgeon]

Sorry I took so long to reply... the moment I wrote that I'm not busy, the phone calls started. *sigh*

I'm gonna do this piecemeal, since we're getting into a lot of sub-discussion...

1. Changing one word to another is making different information, but not new. In order for evolution (molecules to man) to work, you need to actually increase the number of nucleotides, and point mutations don't do that (accept again the frameshift, which I still believe to always disrupt the protein's function). I understand that point mutations aren't always harmful, but every time I try to find examples of beneficial mutations I get something like Sickle Cell Anemia, which decreases the hemoglobin's function in normal conditions. Do you know of any beneficial mutations?

That "different information" IS new information, if it's a combination that hasn't been seen before, or seen before in that organism.

What are "normal conditions"? I know what you think you mean by it, but life evolves in a changing environment, and one which frequently adds new threats (invasive species, new diseases, climate change, etc) to which the creature must adapt. Sickle Cell allows for survival in a particular environment. However, you are correct that it is a poor example-- it's a simple example, but not necessarily the best one. You might look into the CCR5+ mutation which allows HIV patients to resist the virus by altering one of their glycoproteins on the surface of the cell so the virus can't "latch on" and invade the CD4 cells. You might look into the mutation "accident", ~5 million years ago, that led to the rise of human intelligence:

http://www.scienceagogo.com/news/2007040..._sys.shtml

2. We have already covered transposable elements in class, and I'm still not seeing how it is a creative process. It seems to again just be altering existing information. No new nucleotides are being added (unless its a retrotransposon) Your sentence example leads to an inferior sentence after the phrase gets inserted. I have trouble accepting that random nucleotide changes could lead to a sequence for a transposable element, when the odds of getting nucleotides in a functional order seem to be unlikely unless they offer immediate selective advantages (which I don't think the transposons would). Don't you think that the transposons could be seen as a design to allow antibiotic resistance to be transferred among bacteria to keep bacterial populations from being wiped out? This seems like what you would expect from a design given the important ecological role that microbial life plays.

Can you understand that ALL of these things we're discussing happen EACH time an organism reproduces, and that it occurs throughout the population? Any new mutation, even if it's just a rearranging of what's already there, adds new information to the gene pool. If you keep thinking of genetics as an individual thing rather than looking at the gene pool overall, you're going to have a hard time passing that class. Evolution often happens by combination... say, a duplication followed by a frame shift followed by a couple of point mutations, etc, and not always in the same individual, because these genes are being passed down to each generation. It is the accumulation of the changes that may suddenly do something that alters the function in a novel way, but which confers an advantage that lets the individual have more offspring, contributing more of the new gene to the population. THAT is actually what evolution is, a change over time in the gene pool, including sub-pools splitting off to form a new "direction" in the evolutionary line... a split in a branch on the tree of life. You seem to be confusing two different questions: one is "how does new DNA attach to a genome to create more places for evolution to operate upon" and the other is "how does the genome change over time to produce novel phenotypes"?

3. I just worry that changing the wording of a sentence is never going to improve the information content of that sentence.

Sure it can. Perhaps a slightly more-efficient protein, perhaps one that triggers other systems in the endocrine system that allow you to run faster than others (like Lance Armstrong's oversized heart, which allowed him to win even before he started juicing... those steroids he used were just altering what his genes already said for his system to produce, artificially, but the process can occur naturally if the genome says to do so), or one that makes you resistant to a disease that wipes out 90% of the rest of your tribe, and so on and so on.

To use a literary example, "Frankly my dear, I don't give a darn" was what the movie studios wanted Gable to say in Gone with the Wind. It's only one transposition (or shift) and one point mutation away from the version the author insisted upon, "Frankly my dear, I don't give a damn", but the difference is night and day. This is even more true in DNA, where a single change can result in an entirely different amino acid, which makes a different protein chain, which folds a bit differently, and may do radically different things.

4. If the duplicate genes can be regulated, then does that mean that the promoter and promoter proximal elements  of the gene are also duplicated during the event? Also I think there might be something to the idea of irreducible complexity, because if you have a protein being "played" with by evolution, then it is only going to settle into its role as part of the molecular machine if, when by doing so,  the cell has an improved chance of survival. The cell would not have an improved chance of survival unless the new protein actually had a useful function. The protein changing from one intermediate form over time would have to have a constant use to the cell to not be selected against, right?

Not necessarily. It might "tax" a cell/organism to have genes that effectively do nothing, or which nearly-duplicate another process, but as I've already pointed out... we all have them. Life is not always 100% efficient (I'd say never). Natural Selection only operates against a gene when it confers a selective disadvantage, in terms of reproducing. If it doesn't interfere with the organism's ability to make babies (which can also make babies), but also doesn't help, then it is neutral.

When you say "being 'played' with by evolution", you have the entire concept wrong (with all due respect). Evolution doesn't do anything. It's simply something we observe, after-the-fact. The only thing actually happening is the biochemistry of reproducing DNA. The genes don't even care what the other genes do, unless it impacts their little part of the overall machinery, as you call it. There's no goal to evolution. It is blind and random, except as the environment and breeding challenges impact the Natural Selection process (which is entirely separate from the "adding new information" question).

In short, it works like this. Two primary things expand the diversity of the genome in a gene pool: Mutations and Recombination. Two primary things reduce it: Natural Selection and Genetic Drift.

That's it. That's really all there is to it. The genome becomes more varied, and NS trims it back into a shape that is favored by the environment because some make more babies than others. Easy-peasy. Everything else I'm hearing from you sounds like psychological projection of our own concepts onto chemicals that couldn't care less what we think they are doing, or that we think someone had to make those chemicals combine just THIS way or THAT way.

Not reality.