Have you actually read it? What makes you think I haven’t looked into it? In fact your article just proves my point. It lists four hypotheses, ie just-so stories, each of which slavishly following the model of random mutation and natural selection. Not only does this not prove a theory, but even on their own terms they are highly problematic. For example to quote your own article:

Although the evidence in favor of this model is scientifically plausible, the evidence against it is substantial. For instance, a cursorial flight model would be energetically less favorable when compared to the alternative hypotheses. In order to achieve liftoff, Archaeopteryx would have to run faster than modern birds by a factor of three, due to its weight. Furthermore, the mass of Archaeopteryx versus the distance needed for minimum velocity to obtain liftoff speed is proportional, therefore, as mass increases, the energy required for takeoff increases. Other research has shown that the physics involved in cursorial flight would not make this a likely answer to the origin of avian flight. Once flight speed is obtained and Archaeopteryx is in the air, drag would cause the velocity to instantaneously decrease; balance could not be maintained due to this immediate reduction in velocity. Hence, Archaeopteryx would have a very short and ineffective flight. In contrast to Ostrom's theory regarding flight as a hunting mechanism, physics again does not support this model. In order to effectively trap insects with the wings, Archaeopteryx would require a mechanism such as holes in the wings to reduce air resistance. Without this mechanism, the cost/benefit ratio would not be feasible.

But consider even if the just-so stories were somewhat believable. What exactly does it prove? Isn’t it simply digging the heels in and doubling down on the original framework being the only one?

It seems Planck’s Principle is true for evolutionary biology like it has been for many other fields: https://en.wikipedia.org/wiki/Planck%27s_principle

The style of this comment is exactly the sort of religious attack-dog attitude I often encounter on this topic. Very low on substance, high on bluster. When the evidence or argument is not on the side of your dogma, is best defense is a good offense, eh?

This kind of passive-aggressive comment is oozing self-assuredness while clearly having never delved into the material, nor ever read the thing they linked to. It’s almost as if they have just googled it briefly, found a wikipedia article, and said “you are totally mistaken! See, just a minute of googling will have shown how deluded you are, you unbeliever / heterodox person / whatever.”

Except your article doesn’t do what you hope it does, and most of the substance of your comment is an adhominem swipe at whoever dared question the premises. You’re hoping there’s something in the article you barely read, to answer the major issue, without bothering to delve into it yourself. Or perhaps the person will be embarrassed enough by your bluster, to stop questioning. Either way, a win for the dogma.

Imagine in any other area of life (eg solving a murder) if you always drew the target around an arrow (eg assuming that murders are always done by men) and then in every tough case came up with a million plausible but problematic just-so stories that always follow the model. What would it prove? Rather, the fact that the you keep concocting problematic stories in itself may reveal a major bias towards your underlying hypothesis, which makes you less objective as a scientist (or detective, or whatever in other areas of life).

Read this essay by Karl Popper, called Science as Falsification, it’s not very long: https://staff.washington.edu/lynnhank/Popper-1.pdf

It was during the summer of 1919 that I began to feel more and more dissatisfied with these three theories—the Marxist theory of history, psycho-analysis, and individual psychology; and I began to feel dubious about their claims to scientific status. My problem perhaps first took the simple form, ‘What is wrong with Marxism, psycho-analysis, and individual psychology? Why are they so different from physical theories, from Newton’s theory, and especially from the theory of relativity?’

To make this contrast clear I should explain that few of us at the time would have said that we believed in the truth of Einstein’s theory of gravitation. This shows that it was not my doubting the truth of those other three theories which bothered me, but something else. Yet neither was it that I merely felt mathematical physics to be more exact than the sociological or psychological type of theory. Thus what worried me was neither the problem of truth, at that stage at least, nor the problem of exactness or measurability. It was rather that I felt that these other three theories, though posing as sciences, had in fact more in common with primitive myths than with science; that they resembled astrology rather than astronomy.

I found that those of my friends who were admirers of Marx, Freud, and Adler, were impressed by a number of points common to these theories, and especially by their apparent explanatory power. These theories appeared to be able to explain practically everything that happened within the fields to which they referred. The study of any of them seemed to have the effect of an intellectual conversion or revelation, opening your eyes to a new truth hidden from those not yet initiated. Once your eyes were thus opened you saw confirming instances everywhere: the world was full of verifications of the theory. Whatever happened always confirmed it. Thus its truth appeared manifest; and unbelievers were clearly people who did not want to see the manifest truth; who refused to see it, either because it was against their class interest, or because of their repressions which were still ‘un-analysed’ and crying aloud for treatment.

The most characteristic element in this situation seemed to me the incessant stream of confirmations, of observations which ‘verified’ the theories in question; and this point was constantly emphasized by their adherents. A Marxist could not open a newspaper without finding on every page confirming evidence for his interpretation of history; not only in the news, but also in its presentation—which revealed the class bias of the paper—and especially of course in what the paper did not say. The Freudian analysts emphasized that their theories were constantly verified by their ‘clinical observations’. As for Adler, I was much impressed by a personal experience. Once, in 1919, I reported to him a case which to me did not seem particularly Adlerian, but which he found no difficulty in analysing in terms of his theory of inferiority feelings, although he had not even seen the child. Slightly shocked, I asked him how he could be so sure. ‘Because of my thousandfold experience,’ he replied; whereupon I could not help saying: ‘And with this new case, I suppose, your experience has become thousand-and-one-fold.

That is what just-so stories are for adherents of neo-Darwinianism!