My second reason for doubt is the very mechanism evolution uses to function- random mutation- which as many biologists acknowledge is usually, if not always, harmful.
Evolution also involves natural selection. It is a two step process where random mutation produces variation within the population and natural selection reduces the number of deleterious mutations while increasing the number of beneficial mutations.
However, if evolution is still occuring to this day, how come there are no transitional forms in existense today IE. fish with half formed limbs and such.
Your question can take on many meanings, so you may need to clarify exactly what you are looking for.
Do you mean to ask why we don't see transitional features that carried over from past evolutionary events? If so, then your question is easily answered. Let's use mammals and reptiles as an example. From the fossil record we know that modern mammals evolved from ancient reptiles. This means that modern reptiles and modern mammals share a common ancestor. Both lineages branched off at this point, and each lineage continued to evolve. In the mammal lineage, many of the branches died off. However, there is one mammalian lineage where these transitional features have been preserved: the monotremes. The most famous species of monotreme is the platypus. In this species we see a very primitive lactation system, a body temperature much cooler than other mammals, and leathery eggs like those laid by modern reptiles. As you can imagine, not all transitional features are going to be preserved in a lineage over time.
There are two things to keep in mind:
1. All lineages evolve. Reptiles did not stop evolving after mammals branched off. The same goes for all of the mammalian lineages that branched off after they evolved from reptiles.
2. Extinction happens. Lineages where transitional features can still be seen are at risk for extinction, as much as any other lineage. One of the reasons we do not see preserved transitional features is that those lineages went extinct.