So, the first assumption the theory of natural selection makes is that new organisms are coming into existence all the time as a natural process? While there is certainly evidence that variations do in fact occur in organisms, I would not necessarily say these variations are NEW. For example, you probably do not look exactly like your mother or father, however your great, great, great, great, great, grandchild still has a chance of looking exactly like your father or mother or even you. So what's happening here? It would appear that the variations being observed by natural selection are simply the mixing of traits and genes that already have and do exist in our genome. It works the same with dog breading. You want a fast dog with no tail? Take a tailless Boston terrier and bread it with the fast Grey hound. Obviously their is some trial and error here, figuring out dominant and recessive genes but still. Regardless, the Chromosomes will trade out, and with time and experimentation you will have your fast dog with no tail. Bare in mind that, though the observed genetic combination in this situation may itself be new, at least in the same way the doughnut breakfast sandwich is new, the geneses themselves however, have gone unchanged. The components for the doughnut and the breakfast sandwich have only been mixed. (not too sure about this metaphor)
For the theory of natural selection to work, it needs new genes, but those new genes need to come from somewhere. Neo Darwinism argues that Mutations could produce the new genetic sequencing required to create the variation needed. However since the founding of Darwinism, Science has yet to cataloged a single mutations of this nature. Never once has a mutation ever been recorded to increase the amount of genetic information present in an organisms gene pool. This has even been admitted and acknowledged by leading scientists like Richard Dawkins, who, to this day, still advocate natural selection as truth, despite being unable to produce any examples or evidence for this theory.
The second assumption survival of the fittest makes is that the better equipped organism always survives, ignoring the fact that luck plays a huge factor in an organisms survivability. Yes the bigger stronger organism may have a greater number of opportunities to succeed in its current environment, however it should be noted that environments change all the time. Additionally the weaker smaller organism might just survive because his competition was killed off by a volcanic eruption or because a cliff gave way underneath him.
The third assumption is that when an organisms genes are removed from the gene pool by extinction or death that it is a good thing. However as a result of that unique organisms death, its entire respective genepool has now lost the ability to regain all of that organisms potentially beneficial traits forever. Furthermore, this is a loss of genetic information not the gaining of it. Of course you may say that those traits were no longer necessary for the organisms survival at the time and yes you would be right. However lets say that the creatures environment reverts back or changes again to were the now extinct organism would have been better suited? The supposed better organism would then suddenly be less equipped to survive in its environment because the genes which it now needs to survive are gone forever. They are extinct. An example of this occurs when a bacteria becomes resistant to antibiotics. Its rare when it happens but ultimately the reason for the resistance has actually been traced to a mutation. What's more, as rare and remarkable as this mutation is, the change it causes does admittedly increase that organisms chances of survival when confronted with antibiotics. But what happens to the organism once the antibiotics are removed? Typically the mutation has come at the cost of altering a protein or system that is important for the normal functioning of the bacteria. As such the mutation which once improved that organisms chances of survival, in a live or die situation, has now crippled it and limited its ability to survive, or at least compared to its un-mutated siblings.
The forth big assumption is that 99% of all species are now extinct. This one is more of a technicality because it depends entirely on how you classify a species. I personally prefer to classify organisms by their biblical kinds, which means that if an organism is capable of reproduction then it is the same species. That being said, take a look at the entire canis genus(K9 animals foxes wolves dogs). Since they can all reproduce they are all technically the same species. That means foxes dogs, wolves, and coyotes are all the same animal. Which means if wolves were to die out, I would not count it as the extinction of the wolf species, but rather just the permanent removal of the wolves genes from the canis genepool. No less tragic yes but still. Honestly I would even go as far as to make the argument that, since the dawn of creation, their has never once been a new species. All of the variations we see in creation today can simply be attributed to the random mixing of genes that have always been present in the current genomes, MINUS the many we have lost as a result of specialization and extinction. As such I find it a little unlikely that 99% of all species are gone, because if you think about it, the bulk of them are all still technically here. They are broken disfigured shadows of what they used to be, many missing entire chunks of their genetic code but most are technically still here. The saber tooth tiger is gone but the cats are still here, yes they will never again have those terrifying jaws again, but that was simply one gene in their much larger genepool.
If you think about it, in a interesting twist my own theory is still technically a type of evolution. After all I am arguing that in the beginning God Created two of every creature: Man, Dog, and cat, and that that all of the different varieties of cat, from the lion to the sabretooth tiger, to common house cat, all had one single pair of ancestors. The main difference however between my theory and the secular theory is that I believe in an evolutionary forest rather than a single evolutionary tree. Furthermore I believe that the original cat must have been one very frightening creature to behold indeed.