Carbon dating radioactive decay is only useful if the decay occurs at a constant rate- anything that alters that rate (such as a natural disaster) will alter the estimated age (most likely increasing its estimated age).
First of all, radioactive decay is like clockwork...even better because it always occurs at a constant rate. Tic, toc, tic, toc, tic, toc....we even have a mathematical formula that measures the halflife of these things. They're actually quite dependable. You take a sample and compare how much of the radioactive element you have to the product which results as it releases alpha, beta, or gamma particles.
A natural disaster could scramble up the debris, I suppose...but it's hardly feasible to say that every place on earth has been hit by a natural disaster. Even if that was the case and rocks do appear older you do realize we're talking in the hundreds of millions, even billions of years and that we give a +/- a few million years in either direction. There's no way we'd be so off the mark that we'd mistake a 6,000 year old rock for a 500 million year old one.
These elaborate hypotheses were created to try to describe the impossible from an evolutionary standpoint: the origin of life from non-life.
No, the hydrogenosome hypothesis concerns the formation of the eukaryotic organism from the previously existing eubacteria and archea. Basically an archea takes a hydrogen producing eubacteria into itself in order to benefit from it's hydrogen production...as such it becomes a chimera, a new organism formed from two others. That led to the present day mitochondria and choloroplasts we see in animals and plants today.
That's called endosymbiosis, by the way. If you want proof of it, then I got it. 
In 1966, microbiologist Kwang Jeon was studying single-celled organisms called amoebae, when his amoebae communities were struck by an unexpected plague: a bacterial infection. Literally thousands of the tiny invaders — named x-bacteria by Jeon — squeezed inside each amoeba cell, causing the cell to become dangerously sick. Only a few amoebae survived the epidemic.
However, several months later, the few surviving amoebae and their descendents seemed to be unexpectedly healthy. Had the amoebae finally managed to fight off the x-bacterial infection? Jeon and his colleagues were surprised to find that the answer was no — the x-bacteria were still thriving inside their amoebae hosts, but they no longer made the amoebae sick. There were more surprises when Jeon used antibiotics to kill the bacteria inside an amoeba — the host amoeba also died! The amoebae could no longer live without their former attackers. Jeon discovered that this was because the bacteria make a protein that the amoebae need to survive. The nature of the relationship between the two species had changed entirely: from attack and defense to cooperation.
http://evolution.berkeley.edu/evolibrary/article/0_0_0/endosymbiosis_01 Science. :HOT:
Now...as to how life began. That's an interesting question that's still up in the air. Either way, that's how eukaryotes were formed and that experiment proves the concept. Off the scientific record, I'm willing to consider creation at this point. There are 4 basic traits that all cells share- plasma membrane, DNA(or RNA), ribosomes, and ATP synthase...and you're right, it would be quite difficult to get all of those together at the same time. So that's where I would consider the idea of creation. You get past this point and everything works out according to these hypotheses. A spontaneous creation of everything we see today is just not feasible to me with all the evidence to the contrary. Maybe not molecules to man, but I can certainly see microbes to man rather easily.
Wings on flightless bird DO have a function.
For penguins, yes, they act as flippers...ostriches use them as a mating display, I'll even give you that. Emus, cassowaries, kiwis, and rheas have no use for their wings...none whatsoever. Snakes have leg bones, they have no use...sometimes they even manifest as little spurs which don't do anything. Whales have leg bones too, but they aren't used for anything. You skipped over the appendix, as well. That's useless...aside from getting infected. If they have important functions(or any function at all), then they're not vestigial.
Here's a top 10 list...although it seemed to be acting weird for me. If all you get are pictures, scroll to the very bottom for the text that goes along with them. http://www.livescience.com/animals/top10_vestigial_organs.html
Name one REAL beneficial mutation (and don't say antibiotic resistance or sickle cell anemia). It's impossible to name one because none exist.
Antibiotic, disease and pesticide resistance are fantastic examples of mutation. I'm not sure why you want me to exclude them. The organism mutates and survives the attacks on it by these chemicals. The flu mutates every single year...that's why we have different shots every year.
This site has a bit about mutations: http://www.talkorigins.org/indexcc/CB/CB101.html and some references and links to other stuff if you want to check it out.
Common ancestor" as Evolutionary Scientists use it (refering to species being interrelated)- NOT a kid who looks like his parents.
I know what you mean...I was using that as a short term example. Descendents will always possess traits of their predecessors. From parent to offspring...now extrapolate that over time and chances are very high that there will be some common traits, usually in very basic morphology at least in some small way. Although genetics has really taken over when proving relationships these days, kudos to Carl Woese.
Whew...that's all for tonight, gotta get my shuteye.
~Zoo
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