Anthem-" Surely in all the years of the study of genetics, a mutation has been generated in the lab and passed on. Where are all these new species of bacteria, fruit flies, rats, etc.?" ...
Fruit flies can be bred to have unique traits (red eyes, short wings) but they are still fruit flies because despite a single new trait they can still breed with other fruit flies (the definition of species). New traits will pass on to new generations (a real genetic change), but a new species only results when enough traits are changed to prevent interbreeding between population. The fruit fliy populations you point to are unique and changed genetically, but it will take more change (no obstacle but time) to create a new species.
Unless you believe Daschunds and hairless cats and dairy cattle roamed the plains with saber tooth tigers, you can see the effect human selective breeding pressures (survival benefit for some) can have over a short period. Human desire for smaller, cuter, and more productive domestic animals translated to a survival benefit for animals with certain genes... Applied repeatedly selective pressure on genepools have shifted the feral wolf, bobcat and oxen into the animals we see today. When lifestyles and traits keep the domestic animals from breeding with their wild counterparts a new species is said to have formed. The process of evolution in the wild is similar, only preference is for more practical traits.
The sickle-cell trait is a commonly used example of an adaptive mutation. SickleCell trait is most common in Africa, where it provides some survival advantage against malaria. The downside (sickle cell disease) is outweighed in africa by the benefit, as malaria is prevalent there... hence the gene is spread through the population. Dark skin (protective against the sun) also developed as a trait in populations in the sun belt. These are small genetic changes offering a survival advantage in a certain area in response to an environmental challenge (In sun poor, malaria free areas sickle cell is selected against and fairer skin is selected for.. possibly to allow vitamin D conversion by the sun). These are examples of single mutations which have spread among different human population due to their survival benefits. New species are a matter of degree, and not defined until interbreeding is not possible between to populations. Still, specific examples of evolution in process are everywhere.
Anthem" It takes considerably more than one individual with a mutation for the mutation to persist. Again, it has never been demonstrated. " " All you have to do is cite some examples where a mutation persisted and was an advantage to the organism" Those examples are everywhere... on the microbiology level MRSA is a Staph species subtype that has become resistant to almost all antibiotics except Vancomycin. The resistance in this population is caried on genes selected for by previous generations of bacteria being killed off, leaving only the MRSA subpopulation. With increasing exposure to vancomycin Vancomycin resistant strains are NOW being seen : (. Regarding humans selection of genes promoting dark skin and sickle-cell trait in africa are examples of benificial mutations occuring and spreading through a population due to survival advantage (selection pressure).
Regarding "one example of a beneficial mutation occuring and persisting (being heritable)" I would say that such mutations occur all the time if you accept genetic variety as the definition of benificial mutations (as mutations are random... selective pressures determine if they are benificial and propagated through the species). Most desired traits (height, strength, wings that would allow me to fly) are polygenic and change only by degree, while other desired traits are subtle, making detrimental changes (very high cholesterol) easier to detect, while beneficial spontaneous mutations (lower cholesterol) remain harder to detect except through population studies. Nevertheless, heritable, dramatic and beneficial changes (for certain environments) do occur. Examples 1) Human Hirsuitism (the werewolf gene), a single mutation resulting in a warm coat of hair... good for surviving oil depletion
http://www.accessexcellence.org/WN/SUA05/wolfman.html 2) Mutation of the 5AR2 gene prevents prostate cancer and hair loss (male pattern baldness) and is heritable, discovered in a 3rd world village noted to have no baldness : ). 3) Polydactyly (multiple fingers) is another Autosomal dominant trait that can pop up in families unexpectadly and be passed down (I find extra fingers benificial, but benificial is subjective). Anyway, isolated mutations obviously occur (thats why they count fingers at a baby's birth : ) and are sometimes benificial (though that is a subjective word).
edit: Not to NOW (oops)