

Hi Adam,
I haven't looked at the PDF, and I want to point out that your thoughts are similar to a topic I call the phenomenology of matter to humans, but it doesn't feature cups and birds. It's just geometric surfaces glowing in different colors in different places. By shifting our gaze from one place to another and from one object to another, we construct a 3D image in our minds of a piece of present existence. Every philosopher touches on this topic in their theory of existence. Some might recommend Peirce's Phaneroscopy, while I'll recommend Hegel's Science of Logic (doctrine of being).
We can discuss the structure of 3D images and the details of their construction, and then their movement and change of shape. There's a lot of interesting geometry there.
Alex
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Your approach reminds me of a certain strain of Phenomenalism in philosophy. You might want to look at:
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Hello Adam,
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One of my independent study topics in Cognitive Psych in college was ‘similarity’. It led to the thought that we think in metaphors, little contextual patterns (graphic connections, little ‘ontologies’) that we have stored somewhere, and when we perceive something (in a context), we walk the metaphor graph to the situation most similar in context.
Similarity was hard, and led to contextual patterns of thought. Example: if you have an orange, a banana, and a tennis ball, which two are most similar? The answer is contextual – if the context is fruit, then the orange and banana; if the context is shape, then the orange and tennis ball.
I had come to think that thought is metaphoric, involving metaphor in a context. I don’t recall any work around this, but that was a long time ago. There might be some…
Bobbin Teegarden
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next steps / building a picture:
Now ... the idea is that we can start representing this via a picture. We can represent a moment with a dot, and a correspondence with a line.
If you wake up and fall asleep in the same room, then notice that the moment of waking up and the moment of falling asleep have a stronger correspondence because you are in the same bedroom, with similar lighting, with a similar visual gaze.
recursion:
Think about the fact that in the last image you just saw, you were not just looking at pure reality itself. You were looking at a representation of reality, a picture I sketched to convey something.
But here's the thing ... this representation is still within a moment. And therefore it's now a thing to which correspondences can be built upon / between.
(I feel like people don't talk about this often ... usually there is a textbook explaining philosophical concepts, a theory of everything, topics about consciousness, but the fact of that experience of reading text scribbled on a page articulating things ... this itself is part of Reality as well, not an isolated thing that just sits by itself. It needs to be accounted for by that 'theory of everything')
Appreciation for making it this far!
Any advice, ideas, or insights would be immensely appreciated. 🙏
I am not working within academia, but am curious about connecting with like-minded people and branching within people whom this content resonates with.
Sincerely,
Adam
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Finally Logic and Genes may be connected but directly going to Math and genome is a step away ! even though we know that mathematics is important for genomics.
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Dear and respected colleagues,
Genetic reductionism is as dangerous as any other form of reductionism. The examples (bees, butterflies so far) are part of a larger body of empirical evidence of anticipatory action. I discussed many examples, in detail, in my book (no reason to advertise). Would be happy to provide details to those interested. Of bees and butterflies…superb title for a book on the subject. The data and information landscape of the living is MULTIVARIATE!.
Best wishes.
Mihai Nadin
next steps / building a picture:
Now ... the idea is that we can start representing this via a picture. We can represent a moment with a dot, and a correspondence with a line.
If you wake up and fall asleep in the same room, then notice that the moment of waking up and the moment of falling asleep have a stronger correspondence because you are in the same bedroom, with similar lighting, with a similar visual gaze.
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Genetic reductionism is as dangerous as any other form of reductionism.
To view this discussion visit https://groups.google.com/d/msgid/ontolog-forum/BL3PR01MB6897CB50EA962927655080CFDAB5A%40BL3PR01MB6897.prod.exchangelabs.com.
On Dec 23, 2025, at 6:49 PM, Michael DeBellis <mdebe...@gmail.com> wrote:
One last thing: when I first read this post I knew there was something I had read a while ago that I thought was relevant but I couldn't remember what it was and I just stumbled over it while looking for something else. It's a paper by an evolutionary psych anthropologist named Pascal Boyer. If you are ever interested in the scientific study of religion read his book Religion Explained. It's an amazing discussion of the role religion played in our hunter gatherer ancestors and how different that was from modern religion and what the evolutionary drivers of religion may have been. It's a fascinating topic because religion is one of those things that from a purely evolutionary perspective doesn't seem to make sense. Tribe members spend all sorts of resources in the form of sacrifices (animals and people), lopping off body parts, rituals, etc. for no obvious evolutionary benefit. Actually, it always amazed me that Dawkins of all people could just dismiss religion as a "mind virus" because if that is all it is (i.e., if there was no benefit to ancient hunter gatherers from religion) then there would be strong selection pressure for atheism. Boyer's hypothesis (this is of course gross over simplification) is that religion served to 1) Increase tribal cohesion, to differentiate our tribe (which is the good people) from the other tribes (the bad people) and 2) to serve as a check against "cheaters" in the game theoretic sense. Scott Atran's In Gods We Trust came to similar conclusions. Anyway, this paper by Boyer is I think relevant to the questions the OP was posing about memory and our sense of self. What Are Memories For? Functions of Recall in Cognition and Culture by Pascal Boyer.
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next steps / building a picture:
Now ... the idea is that we can start representing this via a picture. We can represent a moment with a dot, and a correspondence with a line.If you wake up and fall asleep in the same room, then notice that the moment of waking up and the moment of falling asleep have a stronger correspondence because you are in the same bedroom, with similar lighting, with a similar visual gaze.
John,
I advised Michael to pay attention to a collection of articles on the logic of religious texts. I emphasized that they, too, can be formalized, although the rules of inference differ greatly from both mathematical logic and from religion to religion.
The topic of perception is not even orthogonal, but rather opposed to the topic of religious feeling and thought.
If we touch on this, then speaking of "our perceptions" is completely naive – we can only speak of our own perceptions; we only guess about others' perceptions by analogy with ours, or by receiving messages.
Merry Xmas
Alex
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On Dec 26, 2025, at 1:09 AM, Alex Shkotin <alex.s...@gmail.com> wrote:
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On Dec 26, 2025, at 1:56 PM, jsi...@measures.org wrote:
Peirce recognized that diagrammatic logic was *iconic* and therefore superior for conveying thirdness relations compared to serialized statements using *symbolic* conventions. These latter could never capture the simultaneity, continuity, reciprocity and mutual dependence of true thirdness, no matter how many statements were accumulated.
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John,
Let's discuss the most important perception for our civilization – vision. It's impossible to verify that one person sees the same color as another. But it seems possible that we see the same shape of objects. And here, definitions play a significant role. But practical definitions. For example,
A surface is what we see around us – what our gaze rests on. Our gaze can move along it lengthwise and widthwise, but not depthwise.
A line is the boundary of a surface that curves back on itself.
A point is how we see a receding object before it disappears.
These are the practical principles of Euclidean geometry.
A line is considered straight if looking along it turns it into a point.
An infinite straight line is rarely seen, but easily imagined. Hilbert took it and an infinite flat surface, in addition to a point, as fundamental entities to formulate the axiomatics of Euclidean geometry. Some have taken other entities as primary entities, for example, Weyl, vectors. The structure of a definition as a unit of knowledge is nontrivial, and understanding and agreeing with it, or presenting one's own, requires mental effort.
For example, what do you think of this definition [1]? There's room for formal languages: rcl is Rocq, and I might add col for Common Logic. All it takes is enthusiasm.
The system of definitions is a gem of theory.
Alex
[1] lHaob1 rus:расположено шарнирно eng:located on a hinge
Alex, Michael, and Adam,
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Janet,
I'm on the road today, so I'll answer without diving.
-EG is a mathematical construction using the geometry of labeled objects, i.e., some kind of mathematics.
-What distinguishes Eastern icons is that they don't have letter or word marks. Christian icons usually do. Is it possible to formalize the shapes of icons? Of course, there's usually an established canon for their drawing. The experience of contemplating religious paintings is a separate topic. As Landau said, "Personal experience cannot be transferred."
-Gelfand said in his Kyoto lecture, and this still seems true: we don't have mathematics for biology.
The use of visual thinking is not only natural, but almost inevitable:
-the text we read is two-dimensional,
-any more or less complex formula is two-dimensional.
Visual thinking about forms is Euclidean.
Alex
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On Dec 26, 2025, at 10:20 PM, Alex Shkotin <alex.s...@gmail.com> wrote:

Hi Adam,
I looked at your substack and was amazed to read:
"About a month ago, I had joined the Ontolog Forum, an open forum dedicated to a particular branch of philosophy that aligns most closely with what I write: Ontology."
In fact, our forum is a forum for IT specialists dedicated to products existing in the computing environment and called ontologies, following the tradition of borrowing terms from random sources during technology development.
It's a shame that even our website doesn't clarify this crucial distinction between the concerns of engineers and those of philosophers.
Each of us is a philosopher to some extent. Some can even say which philosophical doctrine they adhere to.
I have friends who are professional philosophers https://llfp.hse.ru/en/. But they hang out elsewhere.
Perhaps you should check out SCOR https://swissonto.ch/: there are both philosophers and engineers there.
I wonder who among us, other than JFS, would say they're a professional philosopher within the framework of any particular philosophical system, or at least their own. Barry Smith is a philosopher, but he's not philosophizing here.
Again, our community isn't "dedicated to a particular branch of philosophy"; it's focused on the creation and application of a specific type of IT object: formal ontologies.
Alex
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Dear João Paulo,
For me, the term "Applied Ontology" itself primarily refers to https://journals.sagepub.com/overview-metric/APO, and it actually says:
"As the subtitle makes clear, two broad kinds of content-based research activities are envisioned: ontological analysis and conceptual modeling. The former includes any attempt to investigate the nature and structure of a domain of interest using rigorous philosophical or logical tools; the latter concerns the cognitive and linguistic structures we use to model the world, as well as the various analysis tools and methodologies we adopt for producing useful computational models, such as information systems schemes or knowledge structures."
The fact is that any scientist and engineer applies ontological analysis, philosophical and logical tools when necessary.
As a result, we have a multitude of sciences and even more technologies. To create "useful computational models," one must be well-versed in theories already created for a given subject area.
After all, for now, our formal ontologies are mostly structured explanatory dictionaries with a small number of formulas.
But theories need to be formalized entirely.
Best regards,
Alex
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|
Feature |
Philosophical Ontology |
Applied Ontology |
Computational Ontology |
|
Primary Goal |
To understand the fundamental nature of reality (Being). |
To facilitate data interoperability and human-human, human-machine and machine-machine communication |
To facilitate data interoperability and human-machine communication |
|
Output |
Theoretical treatises and logical arguments. |
Computational artifacts (code, databases, OWL files, FOL files) and human-readable artifacts (for example natural language definitions (see ISO/IEC 21838-1)) |
Computational artifacts (code, databases, OWL files). |
|
Constraint |
Truth and metaphysical accuracy. |
Truth, computational tractability and practical utility, grounded in the premise that ontologies achieve maximum practical utility when they most accurately represent reality. |
Computational tractability and practical utility. |
|
Scope |
Often universal (everything that exists). |
Both top-level and domain-specific (e.g., industry, defense, medicine, geography, law). |
Often domain-specific (e.g., medicine, geography, law). |
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Thank you Barry! That is very useful.
And I’m assuming it all has the primary intention of humankind’s surviving, thriving, and flourishing sustainably for a few more generations...
As a luddite I Love the work you all do for us attempting to bring sanity to humanity! 😉
Cw
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“Today the most important thing, in my view, is to study the reasons why humankind does nothing to avert the threats about which it knows so much, and why it allows itself to be carried onward by some kind of perpetual motion. It cannot suffice to invent new machines, new regulations, new institutions. It is necessary to change and improve our understanding of the true purpose of what we are and what we do in the world. Only such an understanding will allow us to develop new models of behavior, new scales of values and goals, and thereby invest the global regulations, treaties, and institutions with a new spirit and meaning.” President Vaclav Havel, Czech Republic.
Here’s a video of optimism if you dare watch it https://www.rethinkx.com/videos
"A human being is part of the whole, called by us 'Universe'; a part limited in time and space. He experiences himself, his thoughts and feelings, as something separated from the rest - a kind of optical delusion of his consciousness. This delusion is a kind of prison for us, restricting us to our personal desires and affection for a few persons nearest us. Our task must be to free ourselves from this prison by widening our circle of compassion to embrace all living creatures and the whole nature in its beauty. Nobody is able to achieve this completely, but striving for such achievement is, in itself, a part of the liberation, and a foundation for inner security." -Albert Einstein. As quoted in Quantum Reality, Beyond the New Physics, p. 250.
“The sad truth...is that most evil is done by people who never made up their minds to be or do either evil or good.” Hannah Arendt quoted in The Bulwork.
What are you doing to ensure the funding and achievement of the 17 Sustainable Development Goals by or before the year 2030? Connect the dots! See the web of life! Achieve ‘justice for all’. Or, prepare for the catastrophic consequences. cw
From: ontolo...@googlegroups.com <ontolo...@googlegroups.com> On Behalf Of Barry Smith
Sent: Sunday, January 11, 2026 8:18 AM
To: ontolo...@googlegroups.com
Subject: Re: [ontolog-forum] Re: Curious Question: Is someone else working on something like this?
Or try this:
Feature | Philosophical Ontology | Applied Ontology | Computational Ontology |
Primary Goal | To understand the fundamental nature of reality (Being). | To facilitate data interoperability and human-human, human-machine and machine-machine communication | To facilitate data interoperability and human-machine communication |
Output | Theoretical treatises and logical arguments. | Computational artifacts (code, databases, OWL files, FOL files) and human-readable artifacts (for example natural language definitions (see ISO/IEC 21838-1)) | Computational artifacts (code, databases, OWL files). |
Constraint | Truth and metaphysical accuracy. | Truth, computational tractability and practical utility, grounded in the premise that ontologies achieve maximum practical utility when they most accurately represent reality. | Computational tractability and practical utility. |
Scope | Often universal (everything that exists). | Both top-level and domain-specific (e.g., industry, defense, medicine, geography, law). | Often domain-specific (e.g., medicine, geography, law). |
On Sun, Jan 11, 2026 at 2:20 AM Alex Shkotin <alex.s...@gmail.com> wrote:
IN ADDITION: Just to get Gemini point of view, please, look here https://gemini.google.com/share/1a90345b0fb2
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Hi Ferenc!
My direct answer to your question is: I do something similar, as it manifests itself in my work of systematizing, concentrating, and formalizing theoretical knowledge. Well, except for poetry—that requires a gift.
But I couldn't resist asking Gemini Thinking mode, and I found the answer interesting https://gemini.google.com/share/0f14680b76b0
Regards,
Alex
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Barry,
Thanks for the crucial clarification that Gemini missed: "human-readable artifacts"!
This addresses a crucial aspect of storing knowledge units within a theory framework: a knowledge unit must be represented in a human-readable manner and, if possible, formalized.
For example, lHaob1 rus:расположено шарнирно eng:located on a hinge
This definition from the geometry framework is human-readable twice, and is waiting for enthusiasts to formalize it in YAFOLL or Rocq.
This framework is not described yet, but as an example of described framework look at (PDF) Theory framework - knowledge hub message #1
Alex
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"I have friends who are professional philosophers https://llfp.hse.ru/en/. But they hang out elsewhere."
Hi Barry,
Nice!
Here's a transposed variant of the table for additional effect.
| Ontology Type | Primary Goal | Output | Constraint | Scope |
|---|---|---|---|---|
| Philosophical Ontology |
| To understand the fundamental nature of reality (Being). |
| Theoretical treatises and logical arguments. |
| Truth and metaphysical accuracy. |
| Often universal (everything that exists). |
| Applied Ontology | To facilitate data interoperability and human–human, human–machine, and machine–machine communication. | Computational artifacts (code, databases, OWL files, FOL files) and human-readable artifacts (e.g., natural language definitions; see ISO/IEC 21838-1). | Truth, computational tractability, and practical utility, grounded in the premise that ontologies achieve maximum practical utility when they most accurately represent reality. |
| Both top-level and domain-specific (e.g., industry, defense, medicine, geography, law). |
| Computational Ontology | To facilitate data interoperability and human–machine communication. |
| Computational artifacts (code, databases, OWL files). |
| Computational tractability and practical utility. |
| Often domain-specific (e.g., medicine, geography, law). |
Kingsley
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Hi Chris,
I wonder why Applied Ontology addresses human–human, human–machine, and machine–machine communication.And Computational Ontology only addresses human–machine communication - apparently not interested in machine–machine communication.Maybe a typo?
I think so, but Barry should have the final word since I just
repurposed his original table :)
Kingsley
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