Randman, I think that your problem is a basic lack of knowledge about the basic theory. It is compounded by a large helping of Dunning-Kruger and by the fact that you already decided where the truth was and care not a bit for the truth.
So, it is going to be a waste of my time but I will go back to some basics. For the proverbial lurker's sake:
As said, new genes are sometime produced by evolution, mostly, it is caused by gene duplication followed by genetic drift so you ends up with two progressively divergent copies of the same gene.
Some genes can be passed along and modified for a long back, their origin arching back to a distant homologue providing very different function. A while ago, I mentioned the long distant origin of the hemoglobin molecule, dating back to a time before even there was oxygen enough to breath...
The article you mentioned is the same thing. Some genes that our evolution have co-opted as part of our neural system actually have their origin into a surprisingly distant past. That's really cool, but not something that is unknown from us, and certainly not something that would put the theory of evolution in debate...
You also seem not to understand the notion of convergent evolution.
As you know, mutations produce various copies of the genes, and natural selection increase the prevalence of the better adapted ones.
For example, an organism that leaves in a dark environment, will tend to get darker so that to be less visible to predators. Ok?
So, what about two organisms living in the same dark environment? Well, the same selective pressure will apply to both of them and they will tend to both get darker.
Similar pressure, similar solutions.
Now, if you have similar ecological niches, putting similar selective pressures to two organisms, the theory of evolution actually predicts that these organisms should evolve similar solutions.
And yet, these solutions will only superficially similar. The wings of a bat may look like that of a bird, similar pressures, but these solutions, the shape of a wing, are achieved in very different ways.
Similarly, the marsupial and placental mouse may share similarities, due to a somewhat similar ecological niche, but they also have significant differences.
Even more, if you look at their genes you will see that the placental mouse is still very much a placental mammal and that the marsupial one is very much a marsupial.
Different clay but modelled similarly because put into a similar mold.
You also don't seem to have a very clear idea of the timing of evolutionary time.
You give the example of corals as being a very simple and primitive organism, for example, but, in reality, they arrived quite late.
Sure, they are very old but they are still 'only' Cambrian. That is 500 millions years old. Life already was
3.5 billions years old by that time. This organism was already very complex.
As for
Schweitzer's discovery; you have, once again, misunderstood what was going on.
Yes she did report some protein, but certainly not whole cells as you are saying, nothing to suggest a level of freshness anywhere similar to the one you describe. Indeed, she herself mentioned that she did not consider her findings as supportive of young earth creationism... Furthermore, it must be mentioned that her lab's practice of secrecy have been made replicating her findings difficult and that they have been criticized for it. Also, there have been suggestions that their equipment might have been contaminated by Ostrich samples they were previously working with. Right now, it is difficult to know for sure but one thing is certain, this discovery should be taken with a grain of salt...