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There are quite a few points that are worth discussing in that file, Joe. I find orphan genes particularly interesting and would love the chance to work on some and try to pin down some of the mechanisms of their emergence. But to the HIV point, I see how you've arrived at your numbers but I have a problem with using these observed mutations as a proxy for HIV evolution overall and even moreso for extrapolation to other organisms' ability to evolve. My understanding of your problem is that if HIV, a rapidly evolving RNA virus, can undergo such a massive degree of sequence evolution without evolving new functions (presumably it's explored a huge amount of protein structure space but none have granted novel functions), how is it that we've done it over and over again, that is, evolved novel proteins, with our tiny population size and slow mutation rate. Is that right?

The fact is, we have no idea how much novelty was invented during the past 25 years of HIV evolution, we only know how much was invented and kept in the population as a result of its ability to improve the virus's ability to infect humans. HIV is pretty flippin awesome at infecting humans as it is, so any novel protein structures would have to be doing something really neat to outcompete the rest. If we were talking about a very dynamic environment, then these new guys may have had a leg up, but since we know that natural selection shapes allele frequencies in response to environmental conditions, and we're interested in the past 25 years of viral replication in human hosts, we really shouldn't be expecting all that much fixed novelty.
If you're interested in RNA virus evolution, I'd suggest this book by Eddie Holmes (the author of that HIV evolution review paper you linked): http://www.amazon.com/Evolution-Emergence-Viruses-Oxford-Ecology/dp/0199211132
It's fantastic.

I want to stop you here to make it clear I agree with almost half of what you've written. Specifically:

1. Your example of evolution in butterfly wings
   
2. High genetic diversity is beneficial so long as the diverse alleles aren't deleterious. Inbreeding in small populations leads to extinction.
   
   Now for the parts I disagree with.
   
   > The problem for you is that the very definition of "deleterious" with regard to fitness is that it is selected against via natural selection.
   
   What you're not understanding is that if the rate is too high, as it is in reptiles, birds, and mammals, deleterious mutations arrive faster than selection can remove them. From a paper last year, "mutations must be kept at a very low level to maintain genome integrity and yet must be frequent enough to support evolutionary change."
   
   And you can calculate what rate is too high. According to High genomic deleterious mutation rates in hominids, (Nature, 1999)
   
   
3. "It has been estimated that there are as many as 100 new mutations in the genome of each individual human. If even a small fraction of these mutations are deleterious and removed by selection, it is difficult to explain how human populations could have survived. If the effects of mutations act in a multiplicative manner, the proportion of individuals that become selectively eliminated from the population (proportion of `genetic deaths') is 1-e^-U, where U is the deleterious mutation rate per diploid, so a high rate of deleterious mutation (U>>1) is paradoxical in a species with a low reproductive rate."
   
   They worry about a deleterious rate of U much greater than 1 as being prohibitively high and we're talking about it being 6-20+, since we now know the functional genome is much larger than we thought it was in 1999. Taking their Poisson probability distribution and using U=6, that means 1-e^-6 = 99.752% of the population will have to be selected away each generation for two lucky enough to have no deleterious mutations to survive and maintain constant population size. That would require on average about 806 offspring per female--impossible for most mammals, birds, and reptiles.
   
   > If a thousand tiny deleterious mutations that are almost inconsequential occur and ONE of them being existent in the population provides the phenotype needed to survive a major environmental change then ALL of them were justified and the mechanism that lead to such a large rate of detrimental mutations was itself beneficial.
   
   This still decreases the size of the functional genome. Those thousand deleterious mutations are replacing specific code with random noise. Supposing they have little effect on fitness because they aren't needed under most of the common selective pressures (likely), if evolution reduces in this manner that does not explain how they could have arisen in the first place.
   
   I feel like I need to cite some papers here so you know I'm not just blowing smoke.
   
   
4. "If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10 , an average individual carries ~ 100 lethal equivalents." He concludes with, "Because the stochastic mutation load paradox appears real, it requires a resolution.", Kondrashov, why have we not died 100 times over, J theor Biol, 1995
   
5. "The aging process shows, indeed that statements one frequently hears, to the effect that the Darwinian theory is as obvious as the Earth going round the Sun, are either expressions of almost incredible naivete or they re deceptions. ... with such widespread evidence of senescence in the world around us, it still seems amazing that so many people think it "obvious" that the biological system as a whole should be headed in the opposite direction. ... The best natural selection can do, subject to a specific environment, is hold the deleterious mutations in check. When the environment is not fixed there is slow genetic erosion, however, which natural selection cannot prevent. ... natural selection cannot turn back deleterious mutations if they are small, and over a long time a large number of small disadvantages escalate into a serious handicap. This long term inability of natural selection to preserve the integrity of genetic material sets a limit to its useful life..." Hoyle, Mathematics of Evolution, 1999
   
6. "Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern. ... Intensified natural selection only marginally slows the accumulation of deleterious mutations.", Using computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load, Intl. Conf. Computational Science, 2007
   
   The third paper is from John Sanford, a Cornell geneticist whose invention of the gene gun led to most of the world's GM crops. He converted from atheism to creationism partly because of this problem. Mendel's Accountant, the free/open source program his team wrote for the simulation, is peer reviewed and used/cited by other researchers. You can try it yourself and reproduce their results.
   
   Minor points
   
   > HOWEVER, that allele will never achieve a majority share of the population
   
   It doesn't have to and it's unlikely the deleterious alleles will. Everyone deteriorates in their own way.
   
   > Are you saying that all mutations to such sections of the genome are necessarily detrimental?
   
   Almost all within these regions of high functional specificity are either detrimental or neutral. In flies: "among all 91 genes, the expected average proportion of deleterious amino acid polymorphisms in samples is 0.70 ± 0.06. These results again support the widely held belief that most amino acid polymorphisms are deleterious". Also, "30–50% of single amino acid mutations [within protein coding regions] are strongly deleterious, 50–70% are neutral or slightly deleterious and 0.01–1% are beneficial.". So about 70% are deleterious, 30% neutral, and a very small percentage are beneficial.
   
   > Are you assuming that these functions cannot ever change in any way without critically damaging the organism?
   
   If common descent is true, to be conserved between species over tens of millions of years means that there weren't any selective pressures that came up during that time where they were beneficial. Critical damage--no. Most are likely only very slightly damaging.
   
   > Eliminating? Why are you always assuming loss of material?
   
   I don't mean removed. I mean a sequence with high specificity required for its function (such as protein folding, a binding site, a stop codon, etc.) being replaced with random noise.

>but every now and then you get a truly beneficial one that does create information.

I'm not arguing there are no beneficial mutations. I'm arguing that the experiments thus showcased did not show an increase in information. Its just scrambled, or deleted. Less information, less variety, less and less options. And the really naughty part about this is the bait and switch - I asked for an increase in information experiment, and I get an article that fallaciously references the Lenski.

>probably reads more than he'd like..

I would suggest this book because he might like to follow his philosophies to their frightful conclusions.

>"evolution is just a theory" makes most of the "arguments not to use"

I didn't ever say this! Please read my statements before shoving words into my mouth. So do you know that there is a difference between science, and a scientific theory? Did you know that speciation has a root word, 'species', that BrunnerPB admittedly agrees that its a non-scientific word? So then, would you explain to me why I have to accept a word as a scientific definition when its root words and concepts are not? A word like 'speciation' is packed full of evolutionary precepts wont be simply slid into usage without challenge.

>Our side isn't even considered a theory, after all.

Am I in crazyland? Do you even know what a theory is? And who are you sourcing in with this statement? Creation theory is alive and viable, defensible, and in my opinion, enjoys much stronger evidence and arguments than the assumptions of evolutionary theory. Might I suggest a book for you sir - In Six Days: Why Fifty Scientists Choose to Believe in Creation. Its not blind faith that has convinced me in special creation - its evidence.

*edit: formating

Yes, the nerosurgeon that it happened to wrote a book in which he details the brain wave activity being monitored.