You said that you said that "DNA is responsible for the creation of a protein based on the order of the nucleotides." Then you said that only "1.5% of our genome is responsible for the formation of protiens." What exactly do the rest of the 98.5% do? Also, what exactly do you define evolution as, as in the progression of species (ape, ape/man, man), adaptation of species (like the nylon eating bacteria), or the whole Big Bang/primordial ooze/man rises from the sea story?
The other 98.5% of our DNA are responsible for turning on and off various genes
(link). This is still a very small amount of the genome. Most of it just doesn't do anything and is complete nonsense. But, some of that nonsense can tell us about our evolutionary past. For example, we (along with every other great ape) have the genetic remnants of the gene that allows for the synthesis of vitamin C
(link). In that massive amount of non-coding DNA endogenous retroviruses (ERVs) have been found
(link). When a retrovirus (virus without DNA) it inserts its RNA into the nucleus, uses the cell's own mechanisms to copy it into the DNA (via reverse transcription) and now the host cell will make new viruses.
This diagram shows the mechanism
(link):
Since genetic replication isn't perfect, it is possible for the gene to mutate. This destroys the gene and makes it complete garbage and is an ERV. Now, when a retorvirus infects a somatic cell, it's pretty meaningless and dies with the individual. But, when a germ cell (sperm or ova) is infected by an ERV the dead gene can be passed on to a new generation. The presence of the same ERV can tell us which organisms have common ancestry. Now, before you say that two organisms could be infected by the same virus, there's a bit more I have to add. The insertion point is completely random. And from my previous post I showed that there are ~3,000,000,000 bases in the human genome. That is ~3,000,000,000 possible locations for the virus to insert its gene. And there have been several ERVs that are shared between humans and other apes. This can be used to make ancestral trees, like one below
(link):
If you're interested, this video does a good job explaining ERVs:
http://www.youtube.com/watch?v=TUxLR9hdorI
And I define evolution like any biologist. It is the change of allele frequencies over successive generations that leads to descent with modification. One of the consequences is that all life has common ancestry, but evolutionary theory says nothing about how life came to be. That is abiogenesis.
Regarding the list of beneficial mutations, I still believe that these mutations are limited. At the end of time, dogs will still be dogs and cats will still be cats unless some crazy guy decides to try to make some sort of chimera.
Give me the mechanism that limits genetic change. I already gave you the mechanisms that change genomes and how it can bring about a huge amount of variation. By the way, evolutionary theory does state that "dogs will still be dogs and cats will still be cats," but it goes a bit further. Eukaryotes will still be eukaryotes (we are eukaryotes, so are bdelloid rotifers), animals will still be animals (we are animals, so are jellyfish), chordates will still be chordates (we are chordates, so are frogs), mammals will still be mammals (we are mammals, so are cows), primates will still be primates (we are primates, so are lemurs), apes will still be apes (we are apes, so are gorillas), and hominids will still be hominids (we are hominids, so were neanderthals). That is why evolution is descent with modification, anything new will still fall into previous classifications. Animals appeared
610 million years ago
(link) and have only grown to be more varied since then, but all descents are still animals and will always be animals.
I did some of the reading on speciation and still found that whatever mutations and adaptations occured, they still remained the same basic organism as in a population of flies has yet to be seen to evolve into a population of birds. This still leaves the question of the origin of life which has yet to be explained by evolution (all life, not just terrestrial life).
Wrong field, you want abiogenesis for that, if you want to discuss abiogenesis feel free to start a new topic. And flies will never evolve into birds, see above for why.