If you mean what I think you meant by the 16th century philosophy that serves as the baseline for the consequence of the science that came after this Enlightenment period, was simply you trying to say something along the lines of: "Baseless illogical thinking was philosophically accepted as nonsensical, and something pervading all society. And since most of that sort of thinking was rooted in anti-Enlightenment proponents of religious affiliation. Finally, because we still have such high rates of people employing this way of thought, since we still have religion so commonplace in much of society, we still have to contend with such reality".
On the off chance you actually mean something different like: "Since the 16th Century, we've had philosophical thinking that tried to replace the role of God and the faith based rational of people - and is something we have to contend with in the modern day in the form of Scientism... This is because the folks who are most versed with pushing philosophy forward were classically people of theist origins (theologians), thus we have the modern day mess of science that thinks it can override philosophy, which it can't and philosophers have shown why this is the case, even with their modern decendents who aren't even theists, nonetheless demonstrate why science has to thank philosphy for pointing it in the 'right direction' that allowed it to make all the progress it has."
If it's the first, I pretty much agree, if it the latter:
I'd agree, but with some reserve. In order to understand something more mysterious, we need to devise complex rigging in order to tear it apart for observation and movement around the issue (basically as the article hints at, we require more perspectives as the more elusive an answer is). So, the complexity isn't just because we're stupid with nothing better to do, it's basically forced because solving something grand with simplicity from the offset is basically a pipe dream with any sort of understanding. The simplification occurs after the complexity is mostly understood, and then boiled back down for easy regurgitation for the rest of the population (in the same way all the engineering and math headaches involved in bringing desktop PC's to our homes and now our palms, started out as disgustingly complex talking points to even be able to discuss the notion).
Another thing is though, I don't think much of any scientific development has been much of any philosophical work, simply because science isnt' concerned with philosophical work for the most part. In the same way you being unable to quell your natural instincts like 'curiosity' or 'hunger' have nothing to do with some philosophical understanding. In fact much of scientific discovery has been forced upon us even before the existence of our species (the simple sensory systems our per-cursor species have evolved to have, and their employment, is in fact the Scientific Method being applied unwittingly and by force, without any intent on our part, or any machination directly). Much of our philosophy has to do with harmonizing/explaining the realizations we've gotten as a result of science (science here also meaning the aforementioned simple use of something like our eyes and realizing what wind is even if we only see grass moving in the distance). We don't start our lives wondering 'why' something is, simply because we have no concept of something 'being' at all in the first place. It's only after experiential events, do we then have enough baseline material to even begin to contemplate the implications of asking questions like: 'why' of something that 'is' (which is what philosophy is somewhat more concerned with). But none of us are born with the apriori philosophical mode of thinking. We first do the science (using our senses to know about our world), and then comes the philosophy to try and see 'if & how' any of our senses make 'some sense' for a lack of a better term.
EDIT: More typo corrections.
It's hard for me to reply without getting lecturish. I'll try keep it short. I wrote about this stuff a decade ago so it's hard to recall some of the details.
If we roughly split European intellectual history into three periods—before the collapse of the Roman empire, scholasticism/renaissance (by the way wholly reliant on the Middle East for preserving and transmitting the important source texts), enlightenment/global colonialism—we are in the third period. I don't think we are leaving it any time soon. As far as a central conflict goes, I also don't think we are rational people fighting irrationality or outmoded perspectives. Despite how long it's been, the main issue is still the plurality of perspectives. Our institutions certainly aren't set up for it.
Science was born from religion. The word itself is from
scientia, knowledge, which then referred to religious knowledge specifically. Knowledge of good and evil, of virtues, etc. Leibniz was the first as far as I know to come up with the term
scientia generalis, general knowledge, in the 1600s. That was an encyclopedic project to categorize existing knowledge and create a tool for new discoveries, the emphasis being that knowledge was not esoteric or limited by nature to certain subjects, that it could be easily shared and understood. This was also the same period where a lot of mechanical inventions and early automation (think windmills) appeared across Europe. A lot of math was also invented at the same time, by people (Newton, Descartes, Copernicus, Galileo, Kepler, Mersenne) who, nominally, are called either philosophers or scientists depending on the roots of the intellectual tradition of the commentary. Most current engineers and scientists know the innovations and the math, but never read the source texts, which are obviously religious even at first glance. The popular commentary by historians and public intellectuals also tends to skip over most of the way these thinkers worked out their conclusions.
If you want to define the main difference between the previous era and ours, intellectually, the shift was from searching for causes to defining interdependence. From a religious perspective, that shift in attention was from the divine to the temporary, the former tending to encompass the why of things, while the latter with how things work. Thing is, this was done consciously. There was a lot of argument about it, which led up to, for example, Laplace's System of the World being published at the end of the 1700s, which as far as I know was the first published scientific work that had no mention of God. Not because that mention didn't belong or persist silently in the background, but because it was unnecessary for the task at hand. The reasoning for the movement of the Earth relative to the other planets, their formation and destruction and so forth, was sufficiently worked out and had enough compiled observation to stand on its own. By then there was enough of a separate vocabulary which made a book like that possible. But all of that vocabulary was invented as complications or appropriations of traditional religious terms, i.e., repurposed, the same way the Christian vocabulary repurposed the vocabulary of the Greeks, Romans and Arabs. In both cases the emphasis, focus and status of terminology was shifted through laborious and complex reasoning that searched for some freer mode of expression. The language that we use now is at least partially the result of that work.
All of the emphasis on physical mechanics in the sciences fundamentally concerns the interactions of things that are in constant decay and reconstitution. Knowledge, science, in some sense, is what preserves these things beyond their transitory states. That's an eminently religious notion, and there's good historical evidence that this the perspective that led to the development of the scientific method.
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Only partially related: when "subjectivists" (I hate the word is used to designate camps) write something militant, poetic or ignorant, I tend to think of their failure being that of sh-tty subjectivism. As in, you did not examine yourself enough, you jumped to an easy conclusion. Same goes for insistent, obstinate "objectivists": you did not do enough research, you were not critical enough, you simplified and communicated poorly.
