The End of Evolution By Means of Natural Selection

From the tree of life we know that histones and DNA methylases had to evolve at some point before epigenetics could happen in the eukaryote branch. Again, looking at the tree of life we know that chloroplasts and mitochondria had to evolve during eukaryote evolution. All of the evidence indicates that these structures are derived from the host cell engulfing another cell. Evolution through RM+NS resulted in a relationship that benefitted both the intracellular parasite and the host. We can find the same relationships between macroscopic species as well such as flowering plants and their pollinators, ants and aphids, etc. Evolution favors changes that benefit two different species at once. We have all of the different factors that influence how DNA is changed and how the environment shapes the genome of a species from one generation to the next. This can and does include neutral drift and a few examples of non-random mutations. What we don't observe is supernatural deities causing changes in DNA or culling a species based on a genotype. I think you have things a bit backwards. We have observations that the theory must incorporate.To use an analogy, it is often said that water always flows downhill. This is true, with a few exceptions. For example, in a siphon water can flow uphill for a short stretch. Does this violate the theory that water always flows downhill? If you want to be a stickler, yes it does. However, the general theory works in almost all situations and the exceptions have known explanations.

When the weather man states that the wind is blowing in a specific direction do you take this to mean that an intelligent force is directing it? Do you take this to mean that wind has a goal that it is blowing towards?Also, of the things you mention above none are natural selection.When we say that natural selection is undirected we mean that natural selection does not have a specific goal in mind and then shapes creatures towards that goal. This is why we see more than one type of wing, more than one type of eye, etc. There are many solutions to a problem, and natural selection finds these solutions blindly. Natural selection does not see structure. It sees fitness. Natural selection is equally blind when it comes to DNA sequence. Of course, all of the organisms through time that lacked the will to survive left no offspring so it is kind of expected, is it not?Also, if this will to survive is directed then why do we have so many different species with so many different adaptations? What makes you think that RM and NS are not fully understood? Things can be tough to understand for very specific adaptations, but the overall mechanisms are very well understood IMHO. Also, interspecies communication and cooperation is a very active field in microbiology as it relates to such areas as oral and gastrointestinal biofilms. I don't think this at all. We observe what bacteria do and don't do, and then draw conclusions from that. What else are we supposed to do?