Are there also not intermediate examples of flight such as fish that soar and snakes and squirrels and several non-flying insects?
Doesn't the fossil record also show many, many failures, critters that had feathers but never developed the next step or critters that developed true flight but still died out or critters that were kinda in the direction of modern birds but also died out, were a deadend?
It's not even really beneficial and deleterious. What we see is "just barely good enough to get by" and "nope, didn't make the cut."
What we see if we look at living things is barely minimal design, the kid in shop class that gets the D- instead of the F. Almost nowhere do we find Good Design, Exceptional is even scarcer and Better than it has to be is almost non-existant.
To predict if a mutation would be beneficial might be more difficult, but given that an often given definition of a mutations is something like "A change in a DNA sequence", I'd like to give an example of a mutation that is highly likely to be beneficial in a certain environment: it is well known that bacteria often acquire resistance to antibiotics via horizontal gene transfer. Thus, a bacterium that has acquired an antibiotic resistance gene (which should fit the definition of a change in DNA sequence) would most likely have acquired a beneficial mutation (assuming that said antibiotic is common in it's environment and that the bacterium was not already resistant).
I agree with that but it brings in the filter, the environment.
What I am perhaps confused about it that we have had folk claim that mutations are "harmful or beneficial or neutral" and that then go on to assert that most mutaions are harmful.
That to me seems unreasonable.
As you mention there can be mutaions that are definitely harmful such as:
Since we know that certain genes are absolutely vital for survival, mutations that render these genes non-functional will by necessity be harmful (to conceive of such a mutation is easy - just delete the entire gene).
In such a case the critter dies, or is not born, or lives a short life and so that mutation simply does not get passed on.
It seems to me then that almost all the other mutations are neutral in and of themselves. If a mutation does not kill the critter or keep it from reproducing then it is neutral until it is filtered by the unique environment. The evironment then and not the mutation is what determines if that particular mutation is harmful or beneficial. Even then, there will be many mutations that are simply not critical as far as the filter is concerned, hair color, eye color, length of eye lashes, heart to the left or heart to the right, four fingers and a thumb or five fingers and a thumb.
All of those neutral mutations just get carried along, making little or no difference, just more or less sitting on the shelf, until some change in the filter, the environment might make them beneficial or harmful.