Any activity of Homo sapiens is intelligent. By what idea should a researcher be inspired to have the best chance for discovering the nature’s secrets?
Another reason for studying "nature" is to see what the effects thereon are of over-population of the world with humans. And then to give consideration to what remedial action might be attempted in whatever respects, to try and ameliorate the ongoing destruction (directly and indirectly) by mankind of what is on the surface of the planet. In the process of harming/upsetting "nature" (living organisms; inanimate things; climate), humanity could perhaps ultimately destroy itself, either sooner (facilitated by nuclear warfare) or later. If humans can save nature, etc., so to speak, and control their population growth, then they might in the long run save themselves.
Your conclusion: “The conclusion is that one needs to start again from scratch for these domains of science, in order to find new ways of understanding Nature.”
My answer: We started 10+ years ago (https://www.researchgate.net/publication/235351966_Generalized_hypothesis_of_the_origin_of_the_living-matter_simplest_elements_transformation_of_the_Archean_atmosphere_and_the_formation_of_methane_-_Hydrate_deposits ) “to find new ways of understanding Nature” after several-decade by no means unsuccessful work in different fields of physics and physical chemistry. In 2011, we set ourselves a task to develop on OK Theory “of the Universe development for the period from the explosion of the presolar star to origination of cellular living matter (OK is the abbreviation of the family names of the authors)” (https://www.researchgate.net/publication/235342937_Life_Origination_Hydrate_Hypothesis_LOH-Hypothesis ) and extended it later, bearing in mind the period from Beginning and including the Sun and Solar System formation and transformation, our days, and the further events in the Sun/Earth system. Moving ahead, perfecting the theory, and correcting our own errors, we formulated the Life Origination Hydrate Theory (LOH-Theory), Mitosis and Replication Hydrate Theory (MRH-Theory), Theory of appearance of monochirality of chemical substances and delay of racemization, PFO-CFO Theory of Solar System Formation and Transformation from the Beginning, and prediction of the future development of the Sun/Earth system. As you can see, we work in the context of the conclusion in your issue.
All above-listed works in their updating are available at the RG site by the address: https://www.researchgate.net/profile/Elena_Kadyshevich/contributions and in numerous discussions with my and Victor Ostrovskii’s participation at the RG site.