This essay is eloquently written and reflects a broad knowledge of how science works and the history and philosophy of science. But it is profoundly conservative. Instead of answering "How could science be different?" the essay answers "Why should science continue to be the same?".
Of course, there are many achievements that science can claim. I'm proud to be a scientist, and proud of the community of scientists. There has never in the history of humanity been a more reliable arbiter of truth than the world community of scientists.
And yet, there are big questions that science has not answered. Some of these are not just missing pieces in the puzzle -- some of them seem to imply that we have reached dead ends. We need new foundations, new paradigms, new ways of understanding how the world works.
A few examples...
Monica Gagliano has demonstrated that plants sense sound in the environment without ears or even a nervous system. Plants learn and remember. Plants strategize and make educated guesses about the future. We associate all these activities with synapses and neural networks. Plants do these things in a fundamentally different way.
The 30-year legacy of Robert Jahn and Brenda Dunne demonstrates with 6-sigma certainty that human intention in the abstract can influence events at the quantum level. Why are there no physicists seeking to incorporate their experimental results into a new formulation of QM?
The study of life's pre-Darwinian origin has made much progress in synthesizing biochemical precursors from abiotic starting materials, and yet it is becoming clear that a self-reproducing system ("hypercycle") is elusive. This is the prerequisite for the beginning of a Darwinian process, so we can't attribute it to natural selection. We may have to face the fact that our current understanding of physics and chemistry is incompatible with life's origin.
There are dozens of labs around the world that have demonstrated cold fusion, and yet their research is excluded from mainstream publications in physics and engineering. Understanding cold fusion as a new bulk quantum phenomenon has the potential to offer solutions to most major environmental problems, and a new perspective on many-particle quantum phenomena. But the subject remains a backwater because of scientific taboos.
The Pyramids of Giza could not have been built by any technology we know today. Full stop.
There is a compelling need for new scientific paradigms. We need to re-establish the open-minded attitude that Niels Bohr epitomized when he said, "We are all agreed that your theory is crazy. The question that divides us is whether it is crazy enough to have a chance of being correct."