5. Beneficial mutations are often the correcting of mistakes, right? As one guy put it, it's like punching somebody with a dislocated arm in the shoulder and accidentally putting his arm back in the socket.
Yes I would agree with that. The fact that after all of this time it is still possible to make an improvement to the function of an enzyme etc. is a result of the fact that changes are making it ever so slightly less efficient at broadly the same rate.
What do you mean here by "an arbitrary line can be drawn"? And you didn't even mention about their ability to interbreed. Are you telling me they are just going by comparisons of the DNA now and if they are significantly different enough from each other they call them a new species? If so, that's ridiculous - and dishonest. (Not you, them.)
As far as I know the positioning of the species boundaries is arbitrary by necessity. If I am a different species from my distant ancestor then I could not bread with them. But in order for me to exist, interbreeding must broadly have been possible for all of the intervening time period. It is unlikely that a change will happen that is so dramatic that a parent could not breed with their own child (yuck - I know sorry). But the drift might mean that my great to the power n grandfather could not breed with my great to the power n grand daughter. So where do you draw the species differention line? Is it on me? Cause I could definitely have breed with either my father or son (yuck again)!
When you are looking across between different genetic lines derived from the same parent it is slightly easier. Humans cant breed with monkeys. (although they must have transitional ancestors that could interbreed.
Your conclusion is sound and I follow all the steps. But it doesn't seem like any real evolution took place. No inability to interbreed. No new organs or body parts. To go from an amoeba to a man you have to get instructions to created a lot of parts that didn't previously exist. Some researchers say that at the currently observed mutation rate there simply has not been enough time even in 4.6 billion years to do that.
Sorry to be grim again but children are born with extra limbs etc. It can come out of small changes very rarely. I guess the obvious example of organ generation is making an eye. If you have cells, you can make them light sensitive with very small changes to their code (we do this with bacteria sometimes), if this change happened in an organism rather than a cell then you would have the start of an eye. So if you are imagining the construction of a whole new sense organ in one go then it is indeed fantastically unlikely. If you are looking for the even that leads to light sensing then it is quite common.
From a light sensing cell to an eye is just a process of time.
I think I would agree that the probability of randomly inserting a whole eye in one go into a code that contained no such thing is certainly so small that it would not even have happened once in 4.6 billion years. But the process can take a shorter, easier and certainly quicker route by summing up billions of small changes (at 1 a year if necessary) and still make it in that time frame with oddles to spare.
As a final thought on speed....the rate of mutations is wildly different between different types of organisms and even the same organism in different environments. It would be a mistake to extrapolate the rate of mutation seen in the lab now to the rate present back in the mists of time....