So your an Athiest

[AAA]

I don't think there are vestigial organs. Most of the time a structure with an unknown function will be labeled as a vestige by evolutionists, only to have its function discovered later. Although I would agree that the idea of vestigial organs is biologically possible, because we know that biological information degrades in function rapidly if it isn't under selective pressure (aka  fish that live in underwater caves losing their eyesight). But that fits well within the constraints of biological change that is possible still with the top-down view of biological life. Degradation of the genetic code information is demonstrable, but improving it is not.

You clearly haven't taken Invertebrate Zoology or Comparative Anatomy yet (I'm assuming you dissected the cadaver in Anatomy & Physiology), if you think that. We dissected simultaneously a shark and a cat, and looked at organs that were barely developed in one that were fully developed in the other, and ones which were fully functional in the shark which had become vestigal in the cat. The fact that both evolved from ancestors who handed down those genes, to be used in different ways as needed, is obvious. But I think that's where you're making your error-- you're seeing only the modern versions, and evolution over a very short timescale, and taking that as your only basis of comparison.

Vestigal organs do indeed exist, even if they still have a function. An example is the wing of an ostrich. Obviously, the ostrich is descended from smaller birds which still had flight capacity-- the wings still grow, but can no longer serve their primary function. Yes, they're still used for balance and for cooling, but it's not necessary that this bird have wings as part of the design, if made "from scratch" by a Designer. Kangaroos, which did not evolve from birds, manage just fine without that form of balance and cooling, for instance, as a bipedal creature. The wings are therefore vestiges (look it up) of a functional system from before, which no longer serves the purpose for which it originally evolved-- they are vestigial.

If you look at the evolution of whales, from fossils of semi-aquatic land creatures into modern whales, you can clearly see the slow vanishing of the hind legs into the vestiges that remain, now inside the body. The genes didn't "go away", they simply Naturally Selected for gene variants which were the smallest, as those proto-whales were the better swimmers.

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As for the "impossible" to develop new information in the genome, I think you're seriously stretching. If/when you take Invertebrate Zoology, you will be able to see still-existing creatures that represent each stage of the development of increasing complexity that eventually led to the notochords and to us. It's a common misconception that life is a "rising ladder", dating back to Aristotle, and that life is trying to evolve "up", with more-advanced/complex forms replacing older ones; more commonly, the new group that branches off does not replace its ancestors but becomes their cousins, and only good old-fashioned extinction determines whether or not the original group disappears... many ancient types of creature still exist in our oceans, and show a clear transition from simple life to complex, adding systems along the way, from the deuterostome system of embryonic development to digestive tracts to nephridic systems to neural nets/systems, etc.

Also, common ancestry is clearly shown in our DNA, even if you're not looking at active DNA sections (exons) which produce visible phenotypes. If you look at the ~95% of our DNA which is inactive (and thus not altered by Natural Selection pressures), yet still passed down intact to each new generation, you can clearly see "scars"/markers which indicate common heritage between us and the chimpanzees, for instance. You can do this for all nearly-related species (if too much time goes by, even the slow rate of point mutations will eventually "static" over the similar bits), comparing what the phenotypic traits tell us makes them related by inference with actual, physical and mathematical proof that they are related. DNA markers should have disproved the Theory of Evolution completely, after the Polymerase Chain Reaction came out in 1985 and rapid scanning became available in the mid-90s, but it didn't; it instead independently confirmed everything we had discovered by other means. There can be no serious question that evolution and common ancestry are facts.

Why, then, are we more intelligent than the chimpanzees, our near-cousins? Simple: we evolved a more-complex version of the gene that allows for intelligence.

http://www.livescience.com/49960-human-b...found.html

If you open your eyes and look, there are numerous examples of what you're claiming doesn't happen. It may seem unlikely, but it's an observed reality. That's why Darwin famously said that his ideas would sound incredible to people, until they went on to consider the things he had actually observed... and the observation has expanded greatly since his time, with more research and better technology. Despite the propaganda from the Intelligent Design crowd, their ideas simply hold no merit.

A classic example of ID propaganda that turns out to be unsupportable in reality can be found in the transcript of the Kitzmiller case, where Dr. Michael Behe (Darwin's Black Box author) was busted on his contentions during cross-examination, showing that his ideas were based on suppositions that cannot be backed up, and on ignoring the proofs of the very things he claimed were not possible in nature. Just because someone has a PhD next to their name doesn't mean they're practicing good science.

http://rationalwiki.org/wiki/Michael_Behe

You are right, I have never taken comparative zoology as we do not offer it at my university. Maybe in grad school.  As for your picture of the whale evolution, don't you think you could take any organisms with similar phenotypes and put them in order of similarity and lead from anything to anything else? You could portray anything you want with those examples.

You talk about the 95% of DNA that is inactive. I'm sure you're just meaning that it doesn't code for proteins, because they are finding out that virtually all DNA has active functions (mostly regulatory code). The examples of DNA mapping supporting evolution is open to debate. It sometimes fits evolutionary predictions, but it sometimes doesn't. For example I have read that the Y-Chromosome sequences for the two do not fit evolutionary predictions, as they vary a lot. The evidence conflicts, which is very frustrating. When only one side of the evidence is shown, it shuts down scientific discussion and is dangerous to our progression.

I also agree that just having a PhD doesn't make you right, but I understand their arguments, and I hope you can understand why I am conflicted and hesitant to accept Darwinian evolution as it has been taught. There are just so many chicken or the egg problems that I don't think that I can just accept it. It is our job to critique the theory and look for its flaws. If I just accept the theory based on the fact that it accounts for some of the evidence, then we may miss a better explanation for life if it comes along. I'm offended that you say the intelligent design scientists are spreading propaganda, when all great advancements of science come from questioning the accepted theory. If all people questioning the accepted theories is labeled as crazy and unscientific, then no one will question anything, and science will grind to a halt.