@raisemeup
It looks like you may have a hard time understanding speciation. If you take any type of evolution class in college you will learn speciation can occur through multiple mechanisms (geographic barriers, physical barriers, time barriers). However, you first need know what a species is. There is not an agreement for what a species is. However, most will agree that different species do not reproduce, if they reproduce they do not produce viable offspring, or the offspring themselves are not able to produce viable offspring. For example, a donkey and a horse can mate to produce a mule. However, mules are not fertile. Therefore, donkeys and horses are separate species. Now, with bacteria it is a little different. They do not have intercourse. So, species are determined by genetic differences, particularly in 16S rRNA. Now, even this gets a bit complicated because many different species of bacteria can still exchange genes through what is called horizontal gene transfer. Here are some experiments previously performed that deal with speciation.
http://www.darwinwasright.org/observations_speciation.html
Don't worry, there are many more I can find as well if you need them. The last article you posted was a joke. First, the article was clearly from a biased website (with sections for intelligent design and "faith and science". If you show me an article that was published in a reviewed scientific journal I will be a little more impressed. Second, what is posted in the article is mostly true and depicts nothing wrong with Lenski's experiment. It just has a small paragraph at the end that criticizes Lenski for no reason. raisemeup-"Lenski's experiment do nothing but break, degrade or tweak pre-existing genes and add no information necessary to create new machinery." Of course, the odds and statistics show that this is the way it typically happens. For example, it was evolutionary advantageous for Vitamin C genes to be mutated. Why? because most primates come from the tropics where there is a lot of fruit with Vit C. Producing extra proteins to produce vit C would have wasted the organism's energy. Therefore, those who still produced vit C died out. Now, as for new genes, they are also produced be tweaking pre-existing genes. Evidence shows most genes were duplicated first and then tweaked this is how new genes typically form. This is why it is possible to study how different genes are related to each other and when they formed. Our genomes also expand by transposons and viruses. Did you know 8% of the human genome was inserted by viruses? Any "misinterpretation of facts" that you mentioned is typically by people who don't know enough about science and biology. If you are going to critique a scientific theory which has been tested for over a hundred years then you at least need to know enough about the subject.
Now, as for fact and theories, all of evolution is composed of theories. All of science is theory. Scientist never talk about facts (or they shouldn't). However, you also need to know what a theory is. All theories have been tested (people have attempted to falsify them). This process of experimenting and testing for theories instead of just excepting them is what makes science so useful. Now, some theories are stronger than others. This is just something you need to be aware of. For example, science might say there is a theory that the earth revolves around the sun. Of course, this may be wrong. The earth could be surrounded by a bubble that creates an optical illusion. However, based on all the data gathered and what people have seen, there is very, very, very strong evidence that the earth revolves around the sun. This is the same with all of science. This is also the same with evolution. Here is an article I showed earlier
http://news.harvard.edu/gazette/story/2014/02/evolution-in-real-time/
I could probably find his work in a published scientific journal. However, the Harvard gazette will probably do. Now, almost all of evolution has been highly tested. This includes test by crazy bible fanatics in the 1800s who would probably risk there lives to disprove Darwin's theory of evolution. Did it happen? Did even one of them succeed? No. This is because the data humans have gathered and the tests they have performed showed them this this is the way stuff works (or it at least appears this is the way it works (bubble illusion earth)). If there was data that truly went against evolution and tipped the evidence scale then it would be published in a scientific journal and it would be a huge deal because many bible people would care about it. You need to understand that science doesn't care about the opinions of people and it doesn't care about how people "Think" the world works. Science just cares about how the world actually works (or at least what evidence shows about how the world works).
Einstein: "God does not play dice"
Bohr: "Don't tell god what to do"