This bone topic caught my interest so I did some reading. Lots to learn about adaptations. This research paper was a challenge to read but with a dictionary I got through it. Penguins are an interesting species that 'fly' underwater in the same conceptual way that submarines do.
I finally had a minute to take a look at this. You are right, the technical jargon was way above my head and I'm sure the author's IQ is about 50 points higher than mine.
I think this paragraph from the introduction sums up the standard evolutionary position pretty well:
"George Gaylord Simpson proposed a three-stage theory of penguin evolution: an initial volant stage; a stage during which small-bodied early penguins were capable of both aerial flight and wing-propelled diving; and a final flightless wing-propelled diving stage (Simpson,
1946). Placing the acquisition of key morphological adaptations within the context of this three-stage model is key to understanding broad-scale patterns in the evolutionary history of penguins.
Unfortunately, no fossil ‘proto-penguins’ from the first two stages have been recognized. Nonetheless, penguins have an extensive fossil record from the final flightless stage that, together with comparisons to extant penguins and outgroup taxa, can provide insight into the pattern of acquisition of the many derived features that these birds employ in underwater wing-propelled diving."
Basically, because of preconceived notions, they "know" there must have been three stages to penguin evolution. Unfortunately, the first two stages are not supported (yet) by the fossil record. So, let the fanciful conjecture ensue by looking at outgroup taxa that are not penguins or related to penguins. This is 100% speculative.
With such a vast and diverse assortment of fossils, folks can line up animals with similar traits in various forms of complexity to make the record say whatever they want it to, but the fact remains that this doesn't mean one came from the other. I could line up a unicycle, a bicycle, a motorcycle, a motor trike, a compact car, a midsize truck, a nice medium-duty chipper truck, and finally, a forestry bucket truck with a 60' boom and try to tell you that this is the evolutionary history of a bucket truck. Look at the gradual increase in the number and size of the wheels. Look at the gradual increase in engine size over the years. And, look at that amazing boom that arose over the eons from natural selection! No one would buy that, would they?! The fact is, each vehicle was designed for a specific reason and serves a specific purpose. Each vehicle is fully formed. No where is there a motor trike dragging a half-developed fourth wheel behind it. The wheel would have to be fully formed from the start to increase the vehicle's ability to survive. A gimp wheel (or wing, or leg, or eye, or reproductive organ for that matter) would weed the specimen out. How many mutations would have to occur at the same time to form an arm or leg? Hundreds? Thousands? I don't know, but I do know the number is beyond astronomical, especially considering there are no known beneficial mutations. Mutations are a loss of information. We are devolving if anything. This is the second law of thermodynamics (the law of increased entropy) at play. Systems move from orderly to disorderly if left on their own. Mutations are building up in the human genome. We see this readily with an increase in genetic disorders and disabilities.