Chapter VII: The Questions Science Won’t Ask
A rule can safeguard life or outlaw judgment. From the ICU to modern science, this chapter asks what happens when systems forbid the very questions required to understand life.
Rules That Violate Function
In the ICU, I was constantly running into policies, protocols, and rules that defined what I was supposedly “allowed” to do for a patient. What I did not yet understand was that not all rules serve the same purpose. Some genuinely protect patients. Others protect institutions. It was the latter that got me every time. To everyone else, and sometimes even to me, it probably looked like I simply didn’t like rules.
What I reacted to, instinctively and viscerally, were rules that violated function.
The most absurd example I ever encountered came on my first day running an ICU at the University of Wisconsin.
I walked into a patient’s room and did what I had done thousands of times before. I checked the ventilator: synchrony, pressures, volumes. The patient was struggling. I made a few adjustments.
When I turned around, the room had gone silent.
Faces were pale. Eyes were wide. Someone finally said it.
“You’re not allowed to touch the ventilator.”
This wasn’t because I was a trainee. I was literally the new ICU director they had recruited from New York City, where I had spent a decade teaching mechanical ventilation to pulmonary and critical care specialists. I had read Martin Tobin’s Principles and Practice of Mechanical Ventilation twice. The thing was the size of two Bibles. Ventilators were my obsession.
None of that mattered.
It turned out that the ICU I had accepted leadership of had a long-standing policy: no physician, fellow, or attending, novice or expert, was permitted to adjust a ventilator unless a respiratory therapist (RT) with six weeks of mechanical ventilator training at a vocational school was physically present at the bedside.
The reason became clear almost immediately. Decades earlier, someone—likely undertrained, overtired, and working in a different era—had made a ventilator error. A patient had been harmed. The hospital had been sued. Instead of fixing training or clarifying responsibility, the institution did what institutions often do: it outlawed judgment.
From that moment forward, physicians were prohibited from directly managing the single most important machine in critical care.
The consequences, in my mind, were grotesque.
Fellows in training to become ventilator experts were functionally barred from touching ventilators. Overworked clinicians deferred adjustments because finding an RT took too long. Patients labored, desaturated, turned red, and struggled in plain view while care was delayed by rules about who was allowed to touch the machine.
I was written up for breaking that rule. On my first day. Welcome to Wisconsin.
Then, a month later, I entered the room of a severely flow-starved, cyanotic patient in distress and unconsciously did what physicians are trained to do: I changed numerous settings and rescued the patient, only to have the RT walk in afterward. Later, the email arrived.
Policy violation.
Palm to forehead. Clown world.
I was so furious that I immediately set out to change the policy, and the effort consumed months. Undoing it required innumerable committee meetings and sparked institutional trench warfare. In the end, I won, but not by reason.
Someone higher up had finally, and quietly, intervened, I suspect out of fear that I would resign if the policy remained in place (I was certainly thinking about it). At last, fellows were allowed to manage ventilators. Training improved. Patient care improved.
As a result of that experience, I never attempted to change an institutional policy again.
Rules That Outlaw Judgment
Looking back, I now see that episode as the first time I encountered a system that prohibited the very knowledge it required in order to function well. This chapter exists because, during the research for this book, I kept running into a similar kind of dysfunction.
Again and again, I found that certain texts from antiquity seemed to describe, with unsettling precision, the very material processes I was uncovering in relation to Shimanishi’s work. Yet each time I followed one of those connections further, I developed the sense that my questions were entering territory they were not supposed to enter.
I slowly discovered that what I had assumed were legitimate scientific questions were, in the modern world, more often relegated to metaphysics, philosophy, or theology.
I did not come into this book trying to “prove” anything metaphysical. In From Volcanoes to Vitality, I began with a much narrower question: why these minerals seemed to restore such striking vitality in my patients. Following that question led me first into the mechanisms of minerals in biology, then into the role of water, and from there into a broader recognition that the loss of vitality was not confined to my patients but appeared to run through modern life more generally. I expected chemistry, physiology, and perhaps even physics. I assumed the data would be messy, but that I would eventually arrive at least some partial explanations, and maybe even a few confident conclusions. I did not expect the work to lead me into questions that science seemed unable to contain.
I began to sense that the same kind of gatekeeping I had encountered in medicine was also operating more broadly in science. As I tried to understand why certain questions felt as though they were crossing a boundary, I discovered the words for the territory they were entering: teleology and design.
I learned that teleology and design had long belonged to philosophy, especially metaphysics, natural theology, and the philosophy of nature.
I also began to see a distinction between the mechanistic questions that led to the writing of FVTV and the questions that arose once I began studying texts from antiquity and Scripture. My questions had become teleological: they were asking what minerals and water were for. They also began pressing toward the question of design: whether ISAW and the Rock–Water Circuit were, in some sense, designed.
That was when I learned that modern science no longer accepts or meaningfully engages such questions, even though questions about what things are, how they are ordered, and whether their organization reflects purpose were, for most of human history, a normal part of serious thought.
When Science Banned “Why”
In the mid-nineteenth century, a conceptual framework that would later be called methodological naturalism argued that scientific inquiry should restrict itself to observable, testable, reproducible mechanisms within nature, while setting aside questions of purpose, meaning, or ultimate origin.
This notion was advanced to make science more operationally powerful, espoused by thinkers such as Comte, Mill, and Huxley, and later adopted broadly by scientific institutions. The argument was that science should restrict itself to what is experimentally accessible in order to protect itself from speculation, theology, and unfalsifiable claims.
As I began reading about methodological naturalism, I initially found it both practical and reasonable. The scientific method is extraordinarily powerful within its domain, and it needs boundaries in order to function. What struck me only later was that, over time, gaps in understanding began to form as entire categories of scientific reasoning quietly disappeared.
What disappeared first was the permission to ask what a system is for. And once that permission narrowed, the further question of design—whether a system’s persistent organization toward an end reflects intention—was pushed even farther outside what was considered acceptable.
Teleology and design ask related but distinct questions, and those questions lead to different kinds of explanation. Teleology asks what a system is for, describing it in terms of the ends it serves or the functions it reliably accomplishes. Design asks whether such persistent organization toward an end is best understood as the product of intention. Mechanistic explanation, by contrast, confines itself to asking only how an outcome is produced and to describing the sequence of causes through which it occurs.
A strictly mechanistic description of the heart’s function would say that cardiac muscle contracts rhythmically in response to electrical signaling. A teleological explanation would say that the heart exists to pump blood through the body. A design-oriented account would say that a structure so precisely ordered toward that end suggests intention.
The same distinctions can be seen in cosmology. A mechanistic account would say that geological cycles redistribute elements through rock, water, and atmosphere in ways later used by biological systems. A teleological account would say that Earth’s mineral cycles are organized to sustain life. A design-oriented view would say that a system so precisely ordered toward life-enabling and life-sustaining ends is best understood as intended.
The problem is that, in the wake of methodological naturalism, modern science moved toward an almost exclusive focus on mechanism while resisting questions of purpose and largely avoiding questions of intention.
For most of human history, however, teleological and design-oriented reasoning were not treated as intellectual embarrassments. Aristotle called teleology “final causation.” Engineers use both forms of reasoning instinctively. Physicians rely on them constantly. You cannot practice medicine without asking what an organ is for, and, especially in medical school, you cannot fail to notice how precisely each organ’s structure is arranged to achieve that end.
Although the intellectual narrowing that began in the nineteenth century indeed made science extraordinarily powerful within its newly chosen domain, it also carried a cost: entire modes of reasoning were pushed outside the frame.
When Darwin’s Theory of Evolution Expanded Past Its Domain
Once teleology and design were removed, science went on describing systems that were unmistakably ordered, functionally coordinated, and often astonishingly well fitted to specific ends, but it did so in language that, to me in hindsight, now seems oddly evasive. Systems with clear functional orientation were said to have “emerged.” Architectures that looked purpose-built were redescribed as “self-organized.” Intricate coordination and governance were acknowledged only as “highly complex,” as though complexity could ever serve as an explanation.
The words changed, yet the systems they were describing did not. However, the explanatory work still had to be done by something, and that, in my view, is where evolution began expanding beyond its proper domain, at least conceptually. What had originally been a theory of change within living systems gradually became part of a broader habit of explaining everything as arising from prior conditions over time through incremental transformation.
I am not interested in debating evolution itself, though I have read some intriguing critiques of it. My point is narrower and, I think, more important: evolutionary theory was developed to explain how biological traits change over time within living systems, and yet we now use it, consciously or not, as part of a framework for explaining almost everything.
Even if one grants evolution all that it legitimately explains, the enormous prior structure that made it possible remains to be accounted for: a rock in space embedded with a mineral chemistry that, when carried by water, creates energy gradients, redox chemistry, and mineral cycling that power all life on Earth. Evolution unfolded atop those prior conditions. It explains how living systems change over time, but it does not explain where the system itself came from, why it exists, or why it is so precisely ordered.
I find it striking that this same conceptual posture appears to have subtly or overtly infiltrated our understanding of planets, stars, and even the universe itself, even though these domains are not alive, do not reproduce, and thus cannot undergo biological selection. It increasingly seems to me that many scientists now carry on their work guided by a broad assumption that change over time can stand in for origin, and that is why the deepest question keeps getting deferred rather than answered: what produced the initial conditions in the first place?
I should also admit that, for most of my career, I did not explore questions of origin either and, in retrospect, had unconsciously accepted the easy notion that everything that currently exists came from things before, usually over some incomprehensibly long period of time. Part of what made that posture so easy to adopt was that, even if I had tried to pursue teleological or design questions, I would have had no way to produce the quantity or quality of evidence considered “sufficient” to prove anything.
Insufficient Evidence
Those words now bring a smile to my face, because they remind me that I have a single tattoo, acquired at the age of fifty-three in the middle of the global war on ivermectin. I got it partly on a whim and partly to bond with my then fifteen-year-old daughter, who wanted her first tattoo. On my left shoulder, in block print, are the words INSUFFICIENT EVIDENCE.
At the time, it was my own private rebuke to the entire world of academics, experts, and authorities that kept insisting that ivermectin did not work, and that anyone claiming otherwise was doing so on the basis of “insufficient evidence,” even though I knew from the first patient I treated that it worked. But in the context of this book, and this chapter, the phrase has now taken on a different meaning, and I find that interesting.
As a clinician-scientist, I never spent time pursuing teleological or design arguments because I assumed there was no point. Any argument along those lines would, by definition, never have sufficient evidence to satisfy the standards of modern science, and so the whole territory seemed futile before it was even entered.
And yet here we are. The next five chapters are, in effect, my attempt to marshal a historically unusual kind of evidence, one capable of supporting teleological and design arguments in a way I once would have assumed impossible. If I have changed, it is because I followed the evidence far enough that the old prohibitions no longer held, not because I “found religion.”
Where the Explanations Ran Out
As I worked through the mineral chemistry underlying ISAW, then followed that chemistry forward into biology and backward into geology, I found myself being pushed beyond mechanism and toward questions of function, teleology, and design. And the reason was simple: every field kept pointing back to the same architecture—iron, sulfur, aluminum, water, and charge. The same mineral logic repeated across scales. The same boundary principles governed rocks, microbes, plants, animals, and humans.
The deeper I went, the less randomness I saw. Instead, I kept finding systems that were internally consistent and remarkably well governed. At some point, I realized I was no longer just describing mechanisms. I was describing systems that behaved as though they were organized to do something, and that realization is what forced this chapter into existence.
What I am questioning, then, is something else entirely: the claim that evolution is sufficient as a total explanation of life and reality. During my months-long immersion in mineral science, I never came across examples of chaos or randomness accidentally producing order. What I saw, again and again, was order giving rise to more order. I found systems, from cosmology to biology, in which basic structure determined which processes could occur within them, and those processes, once underway, worked to keep that structure intact. In other words, the arrangement shaped the behavior, and the behavior continuously reinforced the arrangement. I was looking at systems that appeared built to sustain themselves.
And once I began developing a sense of what these systems were arranged to accomplish, I started to ask: how did such a system come into being at all? A serendipitous geochemical accident, a spontaneous arrangement of extraordinarily coordinated parts, cycling endlessly through time, with both minerals and water never exhausted, only redistributed, moving through different forms, locations, and functions before reentering the cycle?
Ultimately, the question became more literal: how does a universe governed by conserved energy, coherent order, and reusable architectures give rise to life at all—and then to systems so fertile, diverse, and self-sustaining that they emerge wherever conditions permit?
The next step in that inquiry comes from history. More specifically, it comes from a body of texts that carried forward, in symbolic form, a kind of knowledge I once would have dismissed as impossible to verify and therefore impossible to use. This is where the evidence changes category, and where this book moves into its real center.
*If you value the late nights and deep dives into all the “rabbit holes” I write about (or the Op-Eds and lectures I generate for the public), your support is greatly appreciated.
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I'm super glad I played this chapter again. Earlier I commented on what 'teleology' was. Your explanation as it pertains to evolution seems crisp & thought provoking. Can't wait to see where we/you go from here.
Your ventilator story shows how institutional rules can actually result in dangerous practices and it takes people with good judgment and courage to correct them which can become a huge task and the outcome is never certain.