01. The War to Save Science
A Love of Natural Philosophy Against the Little Darkage in Modern Science.
Welcome to my Substack!
My name is Geo.
I go by @Qastokes in most digital spaces, and when I take myself and my ideas a little more seriously, the pseudonym @CulturePhilos. A wording that originates in a style of thinking I’ve taken to calling — at least for myself — cultural philosophy.
The core intention of cultural philosophy is to consider being human in a deep sense, and culture in a serious way, by using the toolkit of Natural Philosophy — the classical and original methods of scientific inquiry. Natural Philosophy uses the toolkit of reason, hypothesis, experimental comparison, and the application of well-grounded scientific theories in one’s thinking about the world. I use these tools while considering the meaning of, and doing of, being human within the context of other humans — in a word: culture.
Let’s Talk About the Culture of Science.
I love science. I don’t mean this with that foaming at the mouth “I fucking love Science!” rabid zeal that’s shallow and easy to mock. I mean it in a more amateur sense, from the root of that word — for the love of it. My science is the science of natural philosophy. The science of Aristotle and Archimedes to the extent they discovered the Method. It is certainly the science of Galileo, Darwin, Einstein, Goodall, and Feynman. A science of thinking, and of discovering truth in the world by understanding that world. A science lost and half-forgotten as the culture surrounding it has fallen into a systemic intellectual decay and darkage.
I believe there is a deep set and fatal rot at the heart of modern science. Science is deep in crisis. One publicly known example of this is the Replication Crisis in Psychology. But we can simply ask, where has all the innovation gone? Where are the profound insights into the world and the human condition? Outside the often open-sourced digital realm, very little meaningful improvement has been made. Even a casual observer can sense the troubles throughout the fruits of the Academe. Much actual progress — and opportunities to improve human life — are discarded, mocked as pseudoscience, and rarely broadcast from respected institutions to the public. Instead, science has become a battleground for ideology.
We need to escape this crisis and repair the damage done to science. I want to communicate to you — and bring you to share in — my idealism that we can repair science and give ourselves and our species the clarity of thinking and scientific knowledge needed to overcome even the seemingly insurmountable problems of our modern times.
To that end, I want to contrast the Natural Philosophy approach to scientific inquiry, its general process — and intention of thinking — with the modern and currently established scientific paradigm. I would describe this now establishment scientific lineage as Laboratory Science.
Systems Compared.
What is Natural Philosophy? Put simply, it is a method of thinking. Specifically, it is the broader mental toolkit that both developed science, and for which science was developed. Natural Philosophy, put to words in a more periphrastic way — is the love of thinking about the nature of the natural world.
It is an accessible method of free thought and free inquiry that is entirely acquirable and resident in your mind. There is no certification for natural philosophy. It cannot be taken from you. It is your tool to exercise, your judgment, and your intellectual rigor to deploy. It is a powerful toolkit to combat the manipulation, deception, and confusion of your perspective. Natural Philosophy is augmented by technical processes and tools, by modern machines and technology — not defined and controlled by them. Nor is it controlled by the power, exclusive access, gatekeeping, patent trolling, and financial capital that have cultivated around deploying scientific apparatus in the modern laboratory setting.
This is the failure mode. The laboratory of Laboratory Science is not a researcher co-op. It is a hierarchical institution. It carries the baggage of our institutional paradigm. The laboratory is fueled by funding, not by research. Its purpose is to secure the funding to pay for its facilities, along with the personnel on salary. This structure and approach to research and science conforms to the interests of the financial decision makers in control of how the funding is spent. Money, now at the scientific bedrock, enforces incentive structures that powerfully compel the search for specific desired outcomes. Financial outcomes. In a competitive economic landscape where financial extraction is required for survival, Laboratory Science conforms towards the highest bidder.
It’s quite hard to permanently cure a disease when the perpetual treating of that disease — and those suffering from it — is far more profitable and economically reliable. Anything that doesn’t make money dies. A lab that focuses too much on solving problems with objectively effective solutions, but without a highly profitable business plan, won’t find funding. That lab will often face scientific push back as their research acts in direct competition with the incentives of the peers who review their findings before publication. The labs that do public-good oriented work easily fail, and there is little financial reason to invest in the large upfront cost of bootstrapping a new one.
Promising and fundamental research rarely gets the funding it needs in the system as is — as paradigm shifting discoveries are massive risks for vested interests. Innovation not chosen and supported by a player is easily seen as a threat by that player. A patent buyout is not equivalent to funding. Half-finished research sitting in a vault half-forgotten becomes a massive legal burden for new groups hoping to further human understanding. Consolidating explicit permission to both act on and expand human knowledge into a few litigious and financially driven organizations. Science effectively locked away, regardless of whether that knowledge could benefit all of us greatly.
All these broken incentives and dynamics apply doubly to individual researchers. Researchers are filtered out of financially successful laboratory institutions if their work doesn’t provide a viable financial return on research investment dollars. Any honorable researcher faces the decision to either get with the financial incentive program, or become a pariah and an outsider to the establishment.
“It is difficult to get a man to Understand something when his Salary depends upon his not Understanding it.”
Thus the culture of the establishment system develops mechanisms of rationalization that avoid the Understandings that threaten Salary — the point the above classic adage from Upton Sinclair puts so well. A morass of faulty assumptions abounds, while paths to proper understanding are prematurely dead-ended and discarded.
Peer Review, Broken Culture.
Science was broken when, in the 1960s, the mechanisms meant to protect against this systemic self-deception were corrupted so as to reinforce the dysfunction rather than combat it. I don’t want to get overly caught up in the specifics of history and rhetoric in epistemology and philosophy that backdrop the transition of what we used to understand as science, into Laboratory Science.
(…But! In essence, for those interested — I consider Positivism at fault. The naive attempt to define an exclusive scientific correctness subverted all the actual mechanisms of truth-seeking while creating a self-serving scientistocratic class. Positivism in values, biases, and core ideas is the root of many and various problems, both subtle and explicit — all contributing to our scientific malaise.)
However, there is a singular linchpin that, if pulled, would drive a systemic resurgence of true science. That linchpin, the fundamental corruption, is the mechanism of Peer Review — as we know it today. Despite all its pomp and pretense, Peer Review is a mere ceremony of rigor. It is, in essence, just a process of running a scientific paper past a bunch of established members of the scientific field to ask if they want it published in a particular journal. There is nothing robust in that.
The process is usually done single blind — the reviewing Peers can see who is publishing, but the author does not know who is reviewing. This means there is no cost or risk to reputation for Peers who abuse the process to protect their incentive and financial interests. Furthermore, the reputational entity that carries the cost of any failures and faults in the system is Science itself. No one is held personally responsible, everyone can defer responsibility out of their hands to another locus of the system. The Journal editor is expected to, if not actively obliged to defer to the judgement of the Peer Review process, and disregard his own judgement. Zero accountability — systemically.
(Double unblinded, aka Open Peer Review, is nakedly political and still broken, as it carries formal weight in the process of scientific record.)
Its important to make understood: this criticism isn’t a dismissal of science, or of hard working scientists doing real work. Its a criticism of how science has been changed as a culture and process, and the damage that has been done to the work and ability to reach the public with that work, of scientists.
Most people who work in science do so in good faith, they try hard to correct for the broken dynamics of the system in which they work. This doesn’t change that the system is broken and corrupt, and that it is getting worse over time. With that said, just imagine how effective all that effort and good faith could be if the system were in fact correctly functional!
An Old Method of Status and Scientific Record.
Let’s compare this to the prior system, which we can call Review By Peers. In Review by Peers, the process of scientific record was a process of successive and gradual ratification, experimental replication, competition, and only after extensive and graduated rigor — acceptance into consensus opinion and journals of record. Not a rubber stamp of approval from establishment peers at the point of publication.
Review by Peers enforces a high standard of quality by laying both reputational risk and cost upon the publishing editor. Responsibility for publication choices laid directly upon the person who was the final decision maker on what went into the Journal. A hard job to be sure, but highly important, respected and highly leveraged. A position requiring exacting standards — difficulty to be expected.
Putting the locus of responsibility directly on the final decision makers of each editorial process established reputational competition between journals, editors, peers, and authors. Under this model, science developed into a selective evolutionary ecosystem that valued truth and scientific quality above political machinations and financial incentives. The editor would approach members of the scientific establishment, his personal acquaintances or a mystical scrying pool — the exact methods genuinely do not matter, outcomes do — for advice on the correct decision to make. His reputation depended on his judgment, his reputational risk could not be discarded from him to the whims of the Peer Review process. This informal but exacting system of direct responsibility is the system which built the scientific and technical culture that put us on the moon — and drove the standards of the editors who built the legendary journals of Science and Nature.
No matter how arcane their methods, editors who continued to publish high-quality, scientifically meaningful articles would become successful in the world of journals. There wasn’t a need for a systematic method of quality control, because selection forces and evolutionary dynamics within a reputational free market ecosystem did the work. In this structure, scientific culture had a frighteningly elegant solution for sorting papers, journals, scientists, and ideas into a self-managing hierarchy of importance and value. Making it possible for public-good oriented work to compete and win. A system capable of breaking down the rationalizations around financial incentives. Controversy to be settled by further science, not by committee fiat before publication. Science itself as the quality control, not opinion.
This underlying system, the organic Review By Peers method of sorting science, has in part, been rediscovered by the recent explosion of interest in preprint publication of scientific papers. The counterproductive gatekeeping of establishment systems is being circumvented by an informal network making early offerings of scientific findings. Rediscovering the dynamics of the old system. An old system conducive to innovation and clarity — what we all need to navigate the complexity of the modern world.
Without the “quality control” of Peer Review, the analytical toolkit of Natural Philosophy is an important component of scientific investigation, the building blocks of a culture directed towards understanding the world. Science and quality of work stands and falls on the standards of all who consider it. A correct hypothesis stands up against adversarial experiment — more science — not the whims of a cabal behind the scenes making judgments from self-interest. Ideas that before would be shot down and go unpublished can scale as they face and overcome the continual scrutiny of successive scientists, investigators, and members of the public exercising their faculties of free thought. A culture of replicated and open science, without a centralizing control mechanism — manipulation masquerading as quality control.
To overcome the intellectual decay and rebuild our knowledge systems out from under the damage done to science by Peer Review, we need to take our understanding back to bedrock. Science is a process of comparing the expected outcomes of a model of how reality works with a precisely defined and repeatable experiment. Experiment is not the whole of the scientific method, it is simply a formalized and technical method of clearly exposing a facet of reality. Detached from its origins, science is no longer a method of checking the implications of a hypothesis against reality, but rather a method of collecting factoids that interest power. Experiment without a hypothesis wrought from model is just bias aggregation, not science.
Laboratory Science doesn’t have a proper place or mechanism for integrating theorists. It’s institutions don’t value the people who dedicate their lives to exploring, understanding, and contemplating the nature of the world — modeling reality in overarching Scientific Theories. Nor is its purpose exposing mechanisms for access to scientific apparatus, allowing people to express and test their understanding against reality, hypothesis testing through experiment.
Instead, Laboratory Science is a closed-off and inaccessible system of compartmentalized labcoat technicians, testing ideas that serve financial incentives. It is not the open process — of exploring and expanding our human knowledge, testing our ideas for the sake of discovering and sharing truth — that we need. What we call science today is not science, rather, it operates as something akin to the propaganda arm of whatever funds active research. There is “science” that aggressively supports every ideological perspective, or at least those with access to funding.
There is a lot of lofty rhetoric around the word science. Let’s put it in simple and direct terms. At its best, a scientific paper is a formalized eyewitness report of a specific facet of reality. Anyone can and should write one. Anyone can form a hypothesis, as in develop a model of reality from observation and contemplation. Anyone can craft and perform an experiment based on the implications of that hypothesis and present its process and outcome formally. That is the entirety of definitional science encapsulated. Nearly everything else is our cultural processing of the outcome of this Scientific Method.
The Scientific Method.
Our modern Laboratory Science style understanding of the method, at least as commonly described, is a flawed rendering of the fundamental idea. Take any of the 5 or 6 or 7 or 8 steps of the scientific method approaches. You know: Question, Research, Hypothesis Prediction, Experiment, Analysis, Conclusions. Or the worse version: Question, Prediction, Gather Data, Analyze Data, Conclusions. Which was, by the way, the top google result (which is both horrifying and fascinating to me.) This set of steps doesn’t resemble anything I experience as meaningfully scientific. These steps are a shallow cargo cult of Method. I want to communicate the profundity of the real Scientific Method.
Let’s zoom out and give ourselves a clear perspective. The locus of science to me is in Explanatory Model. Theory. A mental model of reality that accurately represents and predicts the way the world around us works. A model with which to reason about the world, a way to know it. An intimate relationship with the processes of reality that bring form to all that exists around us. A way of looking at the world where seeing the world how it is, is the goal. Approaching the world as a naturalist and as a philosopher. The point is to understand the world, not to collect a dubious list of facts that can be rearraigned in nearly any way for the sake of argument. So, let’s dive into a deeper formulation of the scientific method, bringing in some of the sensibilities of a natural philosopher as we do.
The Principles of True Science.
There are four steps in the approach to natural philosophy I find appropriate in the modern day.
The First Step is nurturing a model. A coherent system of explanation and suite of answers for how the world works, and why. This nurturing is a deep skill, looking for and comparing fundamental abstractions, first principles, and complexity seeds that are the story of how things work. For a model to be any good, it needs to explain more than the other models, with less initial complexity and fewer assumptions. The trick to this is to become unbiased, learn many models, along with working examples and run them in parallel. Juggling many ideas and bringing them all together into one picture. It was not for nothing that Einstein was a patent clerk.
The Second Step is prediction, but can be more technically described as formulating a hypothesis by calculating the implications of the model. Put another way, what is the story that the model tells? If you’re preparing an experiment, what part of the story is unique? That is a good place for a hypothesis experiment. But, we’re quite concerned with models in Natural Philosophy, so there’s another vital question to resolve. Explanatory Power. Explain more with less. What other models does this model consume? Does it give more confident and clarifying answers to the working examples? Does it elegantly explain things you thought would be unrelated, but which are adjacent? As you calculate a hypothesis consider the implications of the model. If it starts to spread in many directions and light off new ideas and explanations you weren’t expecting, that is a powerful and positive sign you are on the right track.
The Third Step is to checksum, as in error check your model. This is the part of Natural Philosophy, of science properly understood, where experiment is directly relevant. What evidence would prove this wrong? Or better said, what is the explanatory boundary of this model? Most models are incomplete. The softer the sciences, the more incomplete the models. That’s perhaps a good concept of what soft means in science. Sciences where the checksums have outpaced the models, or as the case might be, where neither model nor checksums are particularly well understood or coherent. See, the actual idea is to compare model with nature; experiment can be a precision tool to achieve that end. But experiments can be poorly designed and misapplied. A good model can show where experiments are broken, just as much as a good experiment can show where models are broken. All layers in the whole process of science need more serious error correction and consideration.
Which brings us to the Fourth Step. Sharing the findings for others to replicate, and if convinced of its truth, broadcast it broadly. Even though this particular step isn’t formally scientific, it is the linchpin of the process. It is the science we experience. Its working principles recurse back into the nature of the other steps, shaping them. It is the vital node we need to repair. What gets broadcast becomes science — for the majority of us. From a distance any peer-reviewed paper is as good as any other. That is tragic as science shouldn’t be akin to a pass/fail 101 class. Science shouldn’t work such that good and world-changing work is easily sidelined and ignored, while bad work can be easily highlighted and substantiated by Peer Review corrupting science for use by political interests in their rhetoric.
We should base our sense of scientific quality on scientific quality. We should base it on the clarity of the model and the reproducibility of that model’s relationship to the natural world across many predictions. What we attend to in published science should be driven in part by the competition of editors for reputation. The people we trust to get it right and publish the important, high quality papers, should be the people we look to for important, high quality papers.
It is time to restore the old system. Now, in that refurbished system, let’s suppose peer reviewing bodies do want to form and apply standards of public methodological analysis to research papers (essentially replicating the concept of modern peer review.) They would be establishing review databases of papers that they are willing to stand behind — a fantastic way to start a new journal! The review dynamics will be quite different, and the standards of peer review science much higher. Reviewing bodies would compete with each other to source the best reviews and methods of analysis, and papers fight to get reviewed by the best bodies. The pain of Peer Review for authors gone with a change in dynamics. The reputation of the entire reviewing body would be clearly at stake for each paper they choose to publish and stand behind.
We should replace the question of: “Is it peer reviewed?”
Instead we should ask: “Show me the methodological analysis. Who was the publishing editor and Journal? What’s the publication track record according to a person or a judging body I trust?” In other words, a multivariate, specific, and adaptive sanity check, not a single generic & branded signal of official quality.
On the fourth step, I started with the broadcast of results and our public understanding of what’s true, because that is so important to how the social dynamics of the system have gone wrong. But science isn’t complete without reproduction of the experiment, of many experiments confirming various implications of the model. In this confirmation process both reproduction by people we trust and by people who don’t like the results of the experiment — end up serving important roles. A scientific paper really is simply a formalized eyewitness report — it is entirely possible, perhaps even common, to lie in one. Certainly to deceive in the relationship of model, or experimental outcome to reality and how we think of it. The power of science is in confirming the model with a hypothesis experiment. The trustworthiness of science comes from the replication of proper hypothesis testing. A properly designed experiment can be repeated for the same outcome by anyone with the ability to perform it.
Reproducibility of experiment gives us one of the most profound and powerful concepts in the classical perspective of natural philosophy — adversarial experiment. Adversarial experiments are powerful because it is possible for people who don’t believe the results of an experiment to perform it themselves and gain confidence in the outcome of it. This facility of proper science is one of the most powerful discoveries humanity has yet made, as it grants us the ability to resolve disputes between ourselves about mental models having proper alignment with reality.
End the Darkage.
In a proper scientific culture, good ideas demonstrate their worth, whereas bad ideas fail in the face of adversarial experiment and successive scrutiny. Bad incentives and structures running amuck in our society must show their hand and face off against adversarial experiments. With the results before us all, no one can lie. A process that forces the biases of humanity to face down the results of reality. Malformed experimental design can be analyzed, and erroneous results discarded in shared analysis, building public-good faith as we all explore and deepen our understanding of the world. Proper science belongs to all of us, not a bespectacled, labcoated few.
We can, and in a very tangible and existential sense must, meaningfully improve our system and culture of science. The current model is broken. Its problems are systemic and derive from bastardizations made nearly a lifetime ago. We can see the darkage, and we can correct the errors driving it.
I’ve expressed much of the broad strokes of the thinking that will need to be applied in detail to restore a culture of science based on reason and natural philosophy. It is time to build the entire system of science into a new and yet old form, a form capable of addressing and solving the problems of the modern day. The initial steps are happening organically, via the preprint movement, because circumventing Peer Review is so obviously necessary to people doing real work. But that culture shift is only temporary and will be curbed by administrative oversight if a deep-rooted and philosophically robust movement of real science, of natural philosophy, doesn’t emerge and organize itself.
So join me! It’s up to all of us. Together let’s organize to rebuild science into the system of investigation and knowledge we need to solve the problems of the world. It is time to end the darkage.
The Time IS Now! Now is the time to take reality and the tools of understanding it back into our own hands. Because if we take a moment to think it through, the alternative is a fragmented and compartmentalized tyranny, a pseudo-technocratic bureaucracy, ‘science’ serving the interests of the wealthiest financiers of our impending cyberpunk dystopia. A muddied and incoherent tower of Babel growing ever more convoluted — until one day when the entire idea of science as a method of discovering truth becomes laughable to all the reasonably sane people who see through the facade of what it has become. At which point the whole world will surely collapse into a darkage black as pitch cast in shadow, a fatal death spiral.
Proper Science must be an open process: working from the hypothesis experiment method, utilizing Review By Peer to empower our editorial broadcast mechanisms, with error contradicted by adversarial experiment — more science. A scientific system based on the foundational tenants of Natural Philosophy, a toolkit accessible to all and in which we can all be equal participants. A system of developing human knowledge in which the free intellect is sovereign and truth the highest standard.
Again, Welcome to CulturePhilos! Together let’s challenge ourselves with our best ideas, at our individual best, as the best Humans we can be, building the best culture we can build, free in mind, spirit, and philosophy — as sovereign and free intellects.
Insights on how to develop and participate in a truly better world coming weekly.
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Congratulations on your new Substack. My intuition is that we will agree in a lot of ways and that we share the desire to see science well grounded and fruitful to the benefit of mankind. To that end, I have some well-intended comments and pushback for you. I won’t be able to do these points justice here because these topics could be, and have been, the subject of entire books, and because I intend to go into more depth in my own future articles on the subject.
It seems like what you’re calling Natural Philosophy is just science using different, not necessarily better, words. An example of this is your first step, nurturing a model. Nurturing a model is the same as developing a model except that to nurture feels more like a human trait. Nurturing. Like what a parent does to make their children grow. It’s also one of the major problems in modern science; people become too attached to their ideas and fall to confirmation bias. We don’t need people who nurture ideas. Scientists have to be willing to strangle their hypothesis in the cradle if it doesn’t map to reality. This is hard to do and even harder to learn. Unfortunately, the same pattern is repeated throughout your section on True Science in that your descriptions of a better scientific method include the very same foundational flaws that laid low our current attempt.
Given that Max Planck is supposed to have said something along the lines of, “science advances one funeral at a time”, and he died in the 1940’s, I feel like this problem has a deeper root than peer review. I’m not a fan of peer review as it stands. I know people who have or would have if they had the chance held back competitors by poorly reviewing their papers. It is definitely an issue. Any resurgence of Review by Peers would be damned from its first breath unless it were set up to deal with the very real threat of corruption which you rightly point to in your article. How we would design a system resilient to corruption and how we would transfer to said system are genuinely difficult questions.
I think you’re right in the spirit of what you say, and I’m glad to have other people thinking on this, but if we could snap our fingers and replace current science with your system, it would suffer the same fate, for the same reasons. Maybe at a faster pace. There’s a lot I want to say about your take on laboratory science, but this is getting long enough. I hope you take this comment in the spirit it is meant. Thanks for the article.
Some minute issues:
Extra period in the phrase Explanatory Model Theory.
All models of reality are incomplete. To have a complete model, you’d have to recreate reality.