How to Speak 'Protein'

 

A Dictionary: The AlphaFold Protein Structure Database

What are Proteins? (from Google AI):

Proteins are the workhorse molecules of life, essential for building, maintaining, and regulating almost every tissue and process in your body. Composed of amino acid chains, they control everything from your muscles to your metabolism.

Proteins carry out several vital, specialized functions in the body:

• Structure: They provide rigid or flexible support for your body, cells, and tissues. Examples include collagen (in skin, bones, and tendons) and keratin (in hair and nails).
• Enzymes: They act as biological catalysts, speeding up millions of essential chemical reactions, such as digestion and energy production.
• Immunity: They protect the body from foreign invaders. Antibodies are proteins that identify and clear out bacteria and viruses.
• Signaling: They act as chemical messengers. Many hormones (like insulin) are proteins that regulate metabolism and physiological processes.
• Transport: They carry vital materials throughout the body. Hemoglobin, for example, is a protein in red blood cells that transports oxygen to all your tissues.
• Movement: Motor and structural proteins (like actin and myosin) facilitate muscle contractions and enable cells to move internally.

To explore how proteins factor into your daily diet and overall wellness, you can visit the Harvard T.H. Chan School of Public Health for evidence-based nutritional guidelines.

Speaking Protein (from Google AI):

Proteins communicate by passing chemical and physical messages to one another. They "speak" using a sophisticated molecular language based on shape, charge, and structural movement, working together in relay races to control everything your body does.

The primary ways proteins transmit and receive information include:

1. Shape and Fit (The Lock-and-Key Mechanism)

Proteins don't talk with words; they interact through physical touch.

• The "Word": A signaling molecule (such as a hormone, neurotransmitter, or another protein) acts as the ligand (the message).
• The "Listener": A receptor protein on the cell surface or inside the cell has a highly specific 3D shape tailored to that molecule.
• The Interaction: When the signal protein fits into the receptor, it locks together, triggering the "conversation".

2. Shape-Shifting (Conformational Change)

When a message "touches" or binds to a protein, it changes the protein's shape (known as a conformational change). This structural shift acts like flipping a light switch—it activates or deactivates the protein.

3. Molecular Relays (Signal Transduction)

Once a protein is activated, it rarely does the final job itself. Instead, it passes the message to the next protein in a sequence called a signaling pathway.

Phosphorylation: A protein kinase (a specialized protein enzyme) will "speak" to the next protein by attaching a tiny phosphate group to it. This tag changes the target's shape and instructs it to start the next task.

Chain Reactions: This passes the message down the line like a molecular relay team. By the time the message reaches its final destination, the signal has been amplified, producing a massive cellular response.

4. Direct Physical Contact

Some proteins act like telegraph cables. Transmembrane proteins sit directly in the cell membrane and touch proteins on neighboring cells to pass instructions.

You can explore the fascinating world of Cellular Communication on the Khan Academy.

William Thurston's Geometry of Everything

from Google AI:

Hilbert spaces are the mathematical foundation of standard quantum mechanics and quantum field theory. In contrast, Cannon-Thurston maps are highly specialized topological tools from geometric group theory. While Hilbert spaces model quantum states and probability, Cannon-Thurston maps relate boundaries of hyperbolic spaces, finding niche applications in quantum gravity and string theory. [1, 2, 3, 4, 5, 6]

Hilbert Spaces

• Core Concept: Complete complex inner product spaces used to represent state vectors and operators in quantum systems. [1, 2, 3, 4]
• Advantages:
  • Allows the use of functional analysis (e.g., Fourier transforms, calculus) to model wave mechanics and continuous time evolution.
  • Provides an elegant probabilistic framework (Born rule) for measurement outcomes. [1, 2, 3]
• Disadvantages:
  • Introduces "unphysical" mathematical redundancies, like requiring the inclusion of states with infinite expectations.
  • By enforcing completeness and \(L^{2}\) normalizability, it excludes important continuous, non-normalizable states (e.g., plane waves), requiring extensions like rigged Hilbert spaces. [1, 2, 3, 4, 5]

Cannon-Thurston Maps

• Core Concept: Continuous, surjective maps between the boundaries of hyperbolic spaces (often acting like space-filling curves). [1, 2]
• Advantages:
  • Captures the extreme geometric distortion of submanifolds in curved spaces.
  • Essential in understanding conformal field theories (CFTs) and their dualities in Anti-de Sitter (AdS) spaces, specifically in describing how boundary properties map to the bulk. [1, 2, 3]
• Disadvantages:
  • Highly abstract; not directly applicable to standard everyday quantum or classical mechanical predictions.
  • Mathematically pathological in some regimes (e.g., they can be non-Hölder continuous), making them difficult to compute or analyze for dynamical models. [1, 2]

To explore the mathematical underpinnings of wave mechanics, you can study the standard Hilbert Space framework. For geometric boundary theories, explore further into Cannon-Thurston Maps. [1]

Being Cellular - From Optical-Symbolic Learning to Electrical Pattern Learning to Learning Chemically by Diffusion & Osmosis

Lessons in Intelligence Environments from Cellular-Biological  MorphoSpaces

from Google AI:

"Learning by osmosis" refers to an informal, passive absorption of knowledge, habits, or culture. In science and biology, chemical and electrical refer to the fundamental driving forces behind cellular transport. 

Chemical forces rely on concentration gradients (particles moving from high to low). Electrical forces rely on membrane potentials (charged particles moving toward opposite charges). Together, they form an electrochemical gradient. 

Chemical vs. Electrical in Cellular Transport

• Chemical Gradient: Driven by a difference in the amount of a substance. Molecules naturally diffuse from areas of high concentration to areas of low concentration to achieve balance. 
• Electrical Gradient: Driven by a difference in charge. Because cell interiors are typically negatively charged, positive ions (Na+, K+) are naturally attracted into the cell. 
• Osmosis (Special Case): While diffusion moves any particle, osmosis refers exclusively to the movement of water (solvent) across a semipermeable barrier. Water moves toward the area with a higher solute concentration to equalize the concentrations on both sides. 

Chemical vs. Electrical in the Brain (Synapses)

In neuroscience, these concepts describe how neurons communicate: 

• Chemical Synapses: Information is transferred between cells via the release of neurotransmitters (chemicals). This is the most common form of synaptic communication in the brain. 
• Electrical Synapses: Cells are physically connected by gap junctions, allowing an electrical current (ions) to pass directly from one neuron to the next without a chemical intermediary. 

"Learning by Osmosis" in Cognitive Psychology

While biological osmosis involves the physical movement of molecules across a membrane (or Markov Blanket), the phrase is used metaphorically in psychology to describe absorbing knowledge: 

• Mechanism: It involves picking up nuances, office culture, or social behaviors by simply being immersed in a specific environment or observing peers. 
• Real-World Context: Learning a language through native immersion or picking up technical skills by sitting near experts are classic examples of this.

From Mythos to Logos: Meden Agan!

Within Any Given Set of Facts, Care (Relevance) Organizes the Facts (and builds a Hierarchy) in a Narrative/ Story"

from Google AI:

"Meden agan" (nothing in excess) represents the historical shift from myth to reason (logos) by replacing fear of capricious gods with a rational, self-regulated ethical framework. [1] In early Greek myth, breaking boundaries invited divine retribution (nemesis). [1] In the era of logos, moderation became a conscious, human-driven choice for psychological and social harmony. [1] 

The Mythological Roots: Divine Boundaries

• The Delphic Maxims: Inscribed at the Temple of Apollo at Delphi. [1]
• Divine Warning: Served as a literal reminder to humans that they are not gods. [1]
• Punishing Hubris: Mythical figures like Icarus or Phaethon ignored limits and suffered catastrophic destruction. [1]
• External Enforcement: Cosmic balance was maintained by the gods punishing human overreach. [1]

The Philosophical Shift: Internalized Logos

• Self-Regulation: Shifted the responsibility of balance from the gods to human reason. [1]
• Aristotle’s Golden Mean: Transformed the maxim into a systematic ethical framework where virtue is the middle ground between deficiency and excess. [1]
• Political Harmony: Applied to the Greek city-state (polis) to prevent the extremes of tyranny and anarchy. [1]
• Psychological Health: Framed emotional mastery as a rational necessity for living a good life (eudaimonia). [1]

Desert de Retz: Building a Home Within a Crumbling Folly 

Reality's Quantum Image-Generating Framework

Andrea Oldofredi, "Hume, Rovelli, and why the quantum world contains no objects"

Nothing exists on its own

Physicists have long known that quantum objects behave nothing like the solid, independent things of everyday experience. But the implications run deeper than strange behaviour. Carlo Rovelli's Relational Quantum Mechanics suggests that quantum systems have observer-dependent properties—what they are depends on their interactions with other systems. Drawing on a tradition running from Hume to contemporary metaphysics, philosopher Andrea Oldofredi explores this novel relational perspective on our world, arguing that objects are not the fundamental furniture of reality.

Quantum Mechanics is arguably one of the most successful theories in the history of science, for its predictions are confirmed by countless experiments, making it a cornerstone of contemporary physics. However, a century after its inception, the theory still challenges our classical worldview, offering a counterintuitive description of nature at microscopic scales. Contrary to classical mechanics, where objects are individually distinguishable and possess well-defined attributes at all times, QM speaks about indistinguishable systems with indeterminate properties, superposed states, and non-local interactions. Unsurprisingly, then, questions concerning its ontology, i.e., what fundamentally exists, are still vividly discussed to this day.

Despite its empirical success, however, physicists and philosophers alike enquire whether QM should be considered a true description of the natural world, because this theory is affected by conceptual conundrums and formal difficulties (e.g., the measurement problem). To address such issues, new quantum interpretations emerged from the 1950s. Among the many existing alternatives, here we consider a widely discussed framework that turns thirty this year, Carlo Rovelli’s Relational Quantum Mechanics (RQM).

RQM is motivated by Rovelli’s work in loop quantum gravity, where spacetime is not a substance existing per se, but rather it emerges from a dynamic network of relations, providing a relational perspective of it.

A new ontology for RQM

Now, with MBT in mind, let us introduce a new way to conceive objects in RQM. According to Rovelli, a physical system can be characterized “by a family of yes/no questions that can be meaningfully asked of it”, where such questions are measurements that can be performed on physical observables, i.e., properties, attributable to the system under consideration. An observer O may ask a set of potentially infinite questions Q1, Q2, …, Qn to the system s, obtaining the string

(e1, e2, …, en) (1)

where each ei;represents a specific answer. Nonetheless, RQM postulates that “there is a maximum amount of relevant information that can be extracted from a system”. Hence, Rovelli says, a complete description of a physical system s is given in terms of the string

[e1, e2, …, ek] (2)

with k < n , which is a subset of (1). Because in RQM information about systems is obtained through interactions, and questions are measurements on the system s performed by some observer O, (2) contains O’s knowledge about s. Clearly, this string represents the description of s relative to O; indeed, another observer P may ascribe to s a different list of properties/values.

Since in RQM physical systems are defined via a specific set of observables, it is then reasonable to characterize them as mereological bundles of qualities. In this way, RQM can be provided with a property-oriented ontology in which objects are defined straightforwardly, for in MBT they are reduced to properties. However, given that the values of the properties of quantum systems in Rovelli’s theory are observer-dependent, we can define the objects of RQM as mereological bundles of properties whose values depend on the perspective from which they are observed.

More precisely, one should say that there is a set of inherent properties characterizing a certain species of particles—such as mass, charge, spin, etc.—which are not observer-dependent, so that their value remains constant. On the contrary, the values of extrinsic properties (such as energy, position, momentum, etc.) are observer-dependent and change relative to specific observers. Additionally, in virtue of contextuality and the algebraic structure of QM, not all observables associated with a certain system can have definite values.

To give an example, in RQM, an electron is characterized by inherent properties such as mass, charge, and spin-1/2, and extrinsic properties such as momentum, energy, angular momentum, and position. These latter have relational and contextual values which depend on the specific interactions of the particle under consideration with different observers.

Conclusion

Elaborating on Paul’s MBT, we saw in this piece that RQM is compatible with an ontology of properties. This fact has interesting consequences, since it shows that quantum objects need neither be thought of as bare particulars nor as Aristotelian substances. On the contrary, following Hume’s tradition, we can define them as bundles of qualities, where intrinsic properties characterizing a certain species of particles have constant values, extrinsic qualities take definite values relative to particular observers, and not every observable defining a system can have a definite value in virtue of the quantum formalism. Additionally, from our perspective on RQM, we can properly speak about material objects in motion and interacting in spacetime. Hence, we can enrich and clarify its event ontology, making it a full-fledged realist interpretation of quantum theory.

Let’s step back from the technical details for a moment and consider what this picture is really telling us. We live our lives taking for granted that objects exist. This seems an obvious fact. The chair you are sitting on, the phone in your hand, the body you inhabit, the most solid and unquestionable features of reality. But what Rovelli’s quantum mechanics suggests is that this intuition, while practically indispensable, is not the deepest truth about our world. Underneath the solid, stable objects of everyday experience, there is no hidden substance giving things their identity and independence. There are only properties, interactions, and the relational facts that such interactions generate. What we call an object is not a “thing in itself,” but a bundle of properties that holds together reliably enough at the scales we inhabit to function as a thing. But zoom in far enough, and the thing dissolves into its relationships and qualities.

From NEETS to Hikikomori to Cloud-Serfs...

 

from Google AI:

NEET is an acronym that stands for Not in Education, Employment, or Training. It is a socioeconomic classification that refers to young adults or teenagers who are unemployed and not enrolled in school or vocational training.

The Social and Economic Phenomenon

Originally coined in the United Kingdom in the late 1990s, the term has become a widely used metric for economists and sociologists globally to track the health of youth labor markets.

The Classification: It applies to individuals, typically between the ages of 16 and 24, who are either actively looking for work or have stopped participating in the labor force entirely.

Global Scope:

• The phenomenon exists globally, with higher percentages often exacerbated by complex factors such as mental health struggles, caregiving responsibilities, or difficulties transitioning from school to work.
• Cultural Slang: In internet culture and some countries like Japan, the term can sometimes be colloquially used to describe individuals who intentionally retreat from society, often spending their time at home.

Other Meanings

If you are not referring to the socioeconomic acronym, you might be thinking of the National Eligibility cum Entrance Test (NEET). This is a massive, highly competitive medical entrance examination in India required for students seeking admission to undergraduate medical and dental programs.

The Commodification of Information

...from Leisure to unpaid Labour

and BACK!  Everything is Kayfabe Now!

Avoiding Civilizational Collapse - 3 Strategies

If man wants to progress, he must create new forms of energy of greater and greater densities.

-Lazare Carnot (1784)

Why Complex Societies Collapse

Can Catastrophic Collapse (ie Bronze Age Collapse) be Mitigated thru Simplification?

Hands Up! Georges Bataille: The Threadless Minotaur Living Inside Goedel's Labyrinth

Heidegger's hand is tied to the terrestrial order. Thus, it does not grasp the human future. Human beings have long since stopped dwelling between 'earth' and 'sky'. On the way towards the un-thinged [Unbedingtheit], they will also leave the 'mortals' and the 'divinities' behind. The last things (τὰ ἔσχατα) will also have to be eliminated. Human beings soar up towards the un-thinged, the unconditioned. We are headed towards a trans-human and post-human age in which human life will be a pure exchange of information. Human beings shed their being be-thinged, their facticity, even though this is precisely what makes them what they are. 'Human' is derived from humus, that is, soil. Digitalization is a resolute step along the way towards the abolition Of the humanum. The future Of humans seems mapped out: humans will abolish themselves in order to posit themselves as the absolute .

Byung-Chul Han, "Heidegger's Hand"

Losing Ipseity in the Second-Order Observation Perspective of Profilicity.

from Google AI:

Ipseity is the quintessential element of identity, derived from the Latin word ipse (meaning "self"). It refers to selfhood, individuality, or the unique quality and nature of being yourself.

Where You'll Encounter the Word

• Philosophy: Used in phenomenology and existentialism to describe the first-person perspective, "mineness," or the foundation of human consciousness.
• Psychology: "Ipseity disturbance" (or self-disorder) is a term used to describe a foundational rupture in an individual's sense of existing as a distinct subject.
• Theology: Often contrasted with aseity (existing entirely of and from oneself)

Emile Durkheim: Sociology, Suicide, and the Nature of Religion

Social Ecosystem: environment, population, technology, and social organization

Marcel Mauss: A Century of Symbolic Gift Giving

The 'Gift' of 9/11

The twin towers were not destroyed by terrorists. The twin towers committed suicide. They collapsed under their own weight. When the two towers collapsed, you had the impression that they were responding to the suicide of the suicide planes with their own suicide. It has been said that even God cannot declare war on himself. Well he can. The West in the position of God, divine omnipotence and absolute moral legitimacy has become suicidal and declared war on itself.

-Jean Baudrillard, "The Spirit of Terrorism"

from Google AI:

Continental Philosophy (The Event as Rupture)

In Continental philosophy, an "event" is often viewed as a sudden, unpredictable rupture or breakthrough that changes everything—it alters how we perceive truth, language, or history. 

• Alain Badiou: A French philosopher who defines an event as an unpredictable, ground-breaking rupture that brings forth new truths. According to Badiou, an event shatters established norms and forces individuals to take a leap of faith to remain faithful to this new truth (e.g., a revolutionary political movement or falling in love).
• Gilles Deleuze: Drawing from the ancient Stoics, Deleuze viewed events as "incorporeal" entities. Rather than physical actions, events are the meaning or sense of what happens, which subsist at the surface of things and transform how we understand ourselves and our realities.
• Martin Heidegger: In his later work (Contributions to Philosophy), Heidegger conceptualizes the event (or Ereignis) as a moment of appropriation, where human beings and the meaning of "Being" come into a mutually revealing relationship.

The End of Pure Positivity

Adjusting the Markov Blanket (It's Location And/Or Transparency)

More on Plur1bus

More on Markov Blankets

Valentin Turchin: Meta-Systems Transition Theory - A Case for Anti-Fragility?

Chapters:

00:00 The night the bronze age went silent 

07:10 The world before the crash 

15:00 Egypt’s records and the sea peoples name 

23:36 The last letters from ugarit 

36:55 Hatti collapses and hattusa burns 

51:34 Mycenaean greece and the end of palace life 

1:08:45 Cities along the levantine coast fall 

1:24:18 Cyprus and the broken copper highway 

1:39:51 Anatolia in motion 

1:54:27 What the battles might have looked like 

2:08:15 Earthquakes, drought, and the climate question 

2:22:22 Piracy, refugees, and a sea full of desperation 

2:36:14 Why the great powers couldn’t bounce back 

2:50:30 Where did the mystery army go 

3:03:39 What the collapse left behind 

3:19:32 A mystery that still breathes

What?  No "Sea Peoples" from Atlantis? 

Peter Turchin (Valentin's son): Elite Surplus Theory -

Sovereignty...

Jean-Luc Godard, "A Bande Apart" (1964)

Hector Goes to War

Friedrich Schiller, "Hector and Andromache"

Andromache
Will you, my Hector, forever go away
to where with unmatched hands Achilles makes
Patroclus bloody off’rings?
____________________Who will teach
your little one with strength to throw the spear,
or how to honor the gods, if what I fear
occurs and Orcus devours you?

Hector
Dear wife, enough of tears, for go I must,
for love of you I burn with battle-lust
my arms sustain Pergamus.
____________________If now I fall,
I’ll fall in the Trojan gods’ and your defense
as a pious hero, then make my descent
to grim, to Stygian Dis.

Andromache
I’ll never hear the clash of your weapons again,
unused, your iron will rust in the halls of men,
and Priam’s line will die.
__________________You’ll go to where
no sun, no day e’er shines his golden face,
to where the Cocytus slithers through the waste,
your love will die in the Lethe.

Hector
Though all my hopes and all my thoughts will sink,
from the gentle flow of the Lethe, my love won’t drink,
no, my love won’t drink.
__________________Listen! The Greeks
are blustering at Ilium’s walls. Now gird my sword,
hold back your tears, and listen to my word;
My love won’t die in the Lethe.

 

Georges Bataille: The Solar Anus & Sovereignty

I Am the Je Suis!

Just Follow the Plan!

THE PLAN

In the beginning was The Plan.
And then came the assumptions.
And the assumptions were without merit.
And The Plan was without substance.

And darkness was upon the face of the workers.
And they spoke among themselves, saying, “It is
a crock of shit, and it stinketh.”

And the workers went unto their supervisors and said,
“It is a pail of dung, and none may abide the odor thereof.”

And the supervisors went unto their managers, saying, “It is
a container of excrement and it is very strong, such that
none may abide by it.”

And the managers went unto their directors, saying,
“It contains that which aids plant growth, and it is very strong.”

And the directors went unto the VPs, saying unto them,
“It promotes growth and it is very powerful.”

And the VPs went unto the Prez, saying unto him, “This plan
will actively promote the growth and vigor of the company,
with powerful effects.”

And the Prez looked upon the plan, and saw that it was good.
And The Plan became Policy.
This is how shit happens!

On Lamaism vs. Islam: Where to Invest a Society's Surplus?

What is Life? 

Life is a chemical System that uses energy to keep itself from reaching chemical equilibrium. Equilibrium is the situation in which chemicals no longer have a tendency to react over time.

What are a Society's Eschatological Goals for the End Times.   To Immanentize it, or to Catechize it?  And to serving and achieving what 'ends' should a Society devote its' Surplus (Luxury - Necessity) energies?

from Google AI:

While Marx seeks to understand and optimize the production of wealth through human effort [Anthropogenic Energy?}. Bataille seeks to understand the necessary destruction of wealth through energy expenditure [Energy in all its' forms?].

Are you on Kronos Time? Or Kairos Time?

...Either way, the Quality of Times are Not Strained!

Shakespeare, "Merchant of Venice"

Portia: I pray you tarry, pause a day or two

Before you hazard, for in choosing wrong
I lose your company; therefore forbear a while.
There’s something tells me (but it is not love)
I would not lose you, and you know yourself
Hate counsels not in such a quality.
But lest you should not understand me well
(And yet a maiden hath no tongue but thought)
I would detain you here some month or two
Before you venture for me. I could teach you
How to choose right, but then I am forsworn.
So will I never be. So may you miss me.
But if you do, you’ll make me wish a sin,
That I had been forsworn. Beshrew your eyes,
They have o’erlooked me and divided me.
One half of me is yours, the other half yours—
Mine own, I would say—but if mine, then yours,
And so all yours. O, these naughty times
Puts bars between the owners and their rights!
And so though yours, not yours. Prove it so,
Let Fortune go to hell for it, not I.
I speak too long, but ’tis to peize the time,
To eche it, and to draw it out in length,
To stay you from election.

from Google AI:

Spoken by Portia in Shakespeare's The Merchant of Venice, "peize the time, to eche it" refers to intentionally slowing or extending time to delay a critical moment. The phrase combines weighing down the pace with stretching it out, illustrating her desire to postpone Bassanio's casket choice.

Not all decisions must be made at the Speed of Causality!?  ;) 

Laibach, "Musick": AI Generated Noise... When Every Copy Becomes Original

Hans-Georg Moeller: The Dark Psychology behind the West's Anti-Universalist "Affirmative-Semitism"

Shifting from an "Authentically felt" guilt for the holocaust (by actual Nazi's), to an Inauthentic, Profilic  and "Performative" guilt (by Descendants of Nazis) and transforming Affirmative-Semitism into the new "Civic Religion" of Germany, German sense of pride in "self".

“There is no such thing as collective guilt or collective innocence; guilt and innocence make sense only if applied to individuals.”

–Hannah Arendt, "Personal Responsibility Under Dictatorship"