Sorry, it took me a little while to go through the Boyko paper. It's super statistics heavy. What I'm reading from there is that 27.3–29.0% of mutations are neutral, 30-42% are moderately deleterious, all the rest are highly deleterious or lethal. The statistics indicate that 10-20% of mutations have been fixed by positive selection (again assuming a common ancestor with chimpanzees). Deleterious, as you mentioned, specifically means harmful to reproduction. So in this context, diseases like Huntinginton's, hemophilia, familial ALS, sickle cell, Lynch syndrome would be considered "neutral". These statistics are mostly derived from Americans of African decent, as the clustered rate of mutation in Americans of European decent was too high to model well.
The Jonsson paper had a similar average rate of mutation of order 10^-8 per base pair as the other paper we looked at, which translates to about 3 per generation.
So what I don't understand, and maybe you can help me, is that in the extreme case of 20% of mutations being avoided by positive selection, there's still 7% of mutations with potentially horrific consequences. This is already excluding the over 70% of mutations that decrease reproductive fitness. What evolutionary pressure is there to keep "neutral" genetic diseases from accumulating in a population over time? How can "beneficial" mutations outweigh this burden? Mathematically, it seems to me that macro evolution is impossible. Am I missing something?
First, I want to thank you for having this discussion with me. I've been wanting to discuss these ideas with someone for some time.
As to the referenced article, a couple of points stand out to me:
The first paper cited by Nachman and Crowell compares pseudogenes between humans and chimpanzees assuming that one evolved from the other over a known period of time. Rejecting the assumption that humans did not evolve from chimps would render this sort of evaluation inaccurate.
The last sentence of the first point, that harmful mutations do not survive long, is not supported by any literature on the page, and I believe it to be wishful thinking. There are many examples of human genetic diseases that do not decrease the reproductive capacity of those carrying them, which to me would imply, again without literature support, that those mutations would accumulate over time in a population.
I would also disagree with the 5th point, where any beneficial mutation disproves young earth creationism. Young earth creationists must believe in a much higher rate of so-called micro evolution, since all the variation we see on earth must have taken place in the last 6 thousand years or less.
"The impenitent sometimes excuse themselves by saying of professed Christians, "I am as good as they are. They are no more self-denying, sober, or circumspect and their conduct then I am. They love pleasure and self-indulgence as well as I do." Thus they make the faults of others an excuse for their own neglect of duty. But the sins and defects of others do not excuse anyone; for the Lord has not given us an erring human pattern. The spotless Son of God has been given as our example, and those who complain of the wrong course of professed Christians are the ones who should show better lives and nobler examples. If they have so high a conception of what a Christian should be, is not their own sin so much the greater? They know what is right, and yet refuse to do it."
I understand that the sun gives low entropy energy to earth, and pockets of entropy can decrease as long as the whole system increases. However, my room exists on earth, so I still think it is an adequate analogy.
More seriously, I would like to see a mathematical treatment of the probability of biologically detrimental mutations vs. beneficial or neutral mutations.
As I said, personal experience. I'm not sure how I was insulting anyone else's beliefs. That's literally why I believe in intelligent design: I believe that evolution is mathematically impossible.
I believe in intelligent design because the theory of evolution boils down to: if you left your room messy for 1 billion years, when you came back it would be the Taj Mahal.
The real fundamental root cause of my belief in God comes from personal experiences.
The idea of a god dying for ants