Threesology Research Journal

Threesology Research Journal Tripartite Aspects of Various Subjects 8

Series Contents (single page overview)
Aspects 1	Aspects 2	Aspects 3	Aspects 4	Aspects 5	Aspects 6
Aspects 7	Aspects 8	Aspects 9	Aspects 10	Aspects 11	Aspects 12

Visitors as of Sept. 3rd, 2025

On this page in order of appearance:

Tripartite Aspects of Life's Biological Origin: [1] (Re-wording of previous search query using the terms "Life's Origin".)
Tripartite Aspects of Abiogenesis: [2]
Tripartite Aspects of the Triplet Code origin: [3] (My theory of a solar influence is not yet mainstream biology.)
Originating Aspects of DNA's Tripartite Code: [4] (I used a rewording to see what came up.)
Tripartite Aspects of Earth's slowing rotation: [5]
Tripartite Aspects of Chirality: [6] (General reference not explicit to amino acid handedness.)
Tripartite Aspects of Molecular Chirality: [7]
Tripartite Aspects of Planetary Chirality [8] (Does not mention the direction of spin for each of the planets)

[1] Internet query: "Tripartite Aspects of Life's Biological Origin"

AI (overview) response: Three core aspects define the scientific understanding of life's biological origin: the formation of building block molecules, the evolution of self-replicating information, and the enclosure of these systems within membranes. The process, known as abiogenesis, describes how non-living matter transitioned into living organisms.

1. Formation of organic molecules

This first stage of abiogenesis focuses on how the simple chemical ingredients of early Earth transformed into the complex organic molecules necessary for life. Proposed sources for these building blocks include:

The "primordial soup" hypothesis: This theory, explored in the Miller-Urey experiment, posits that organic molecules were synthesized from inorganic compounds in Earth's early, oxygen-poor atmosphere. Electrical energy from sources like lightning would have fueled these reactions.
Deep-sea hydrothermal vents: Life could have originated in the protected, energy-rich environment of deep-sea vents. These undersea systems provide a constant supply of chemical precursors and the energy from redox (reduction-oxidation) reactions, which may have enabled the synthesis of more complex molecules.
Extraterrestrial delivery: Organic molecules, including amino acids, have been discovered in meteorites and comets. This suggests that some of life's ingredients may have been brought to Earth from outer space.

2. Evolution of self-replicating molecules

Once organic molecules were present, the next major hurdle was the emergence of a system that could store genetic information and replicate itself.

The RNA world hypothesis: This is a leading theory suggesting that RNA, not DNA, was the first genetic material. This is supported by the discovery that
- RNA can serve a dual purpose:
- Information storage: Like DNA, it can store genetic instructions.
- Catalytic activity: As a "ribozyme," it can catalyze its own replication and other chemical reactions, a function typically performed by protein enzymes in modern life.
Genes-first vs. metabolism-first: While the RNA world is a "genes-first" hypothesis, the "metabolism-first" hypothesis is an alternative idea. It suggests that self-sustaining metabolic reactions evolved first, perhaps near deep-sea vents, before the complex machinery for genetic replication emerged.

3. Enclosure within membranes (protocells)

For life to emerge, these replicating molecules needed to be contained and separated from the surrounding environment.

Formation of protocells: Scientists propose that the first living entities were "protocells," self-organized spheres of lipids that enclosed organic molecules and polymers.
The lipid world hypothesis: This theory suggests that the first self-replicating objects were lipid-like molecules that formed vesicles in water. These simple "cell membranes" could grow by absorbing more lipids and would spontaneously split into two, passing their stored information to the next generation.
Creation of an internal environment: This membrane enclosure was crucial because it allowed for the separation of internal and external environments. This created a distinct chemical identity, enabling a stable internal state (homeostasis) and the concentration of the molecules needed for early metabolic reactions.

[2] Internet query: "Tripartite Aspects of Abiogenesis"

AI (overview) response: The tripartite aspects of abiogenesis refer to the three major, and competing, hypotheses for how the fundamental components of life—self-replication, metabolism, and compartmentalization—first emerged on Earth. Each hypothesis attempts to resolve the question of which aspect came first.

1. "Replication-first" (or genes-first) hypothesis

This view suggests that a self-replicating molecule, likely RNA, was the first biological molecule to appear, enabling the start of evolution.

How it works: This theory proposes a hypothetical "RNA world," where RNA molecules acted as both genetic information storage (like modern DNA) and catalysts for chemical reactions (like modern proteins).
Key evidence: The discovery of ribozymes (RNA enzymes) showed that RNA can catalyze chemical reactions, supporting the idea that it could have both replicated itself and performed early metabolic functions.
Challenges: A major hurdle is explaining how the first RNA molecules, which are complex, could have formed spontaneously from simpler precursors under early Earth conditions. RNA is also fragile, raising questions about its stability.

2. "Metabolism-first" hypothesis

This theory posits that a self-sustaining network of chemical reactions, a primitive metabolism, arose before complex genetic molecules.

How it works: These hypotheses suggest that life began with simple, autocatalytic (self-promoting) chemical cycles that could extract energy from the environment. Eventually, these cycles would have produced the complex organic molecules necessary for life.
Key evidence:
- Hydrothermal vents: The iron-sulfur world theory proposes that life began at deep-sea hydrothermal vents, where mineral surfaces and chemical gradients could have catalyzed a primitive, autotrophic metabolism.
- Metabolic fossils: Some core metabolic pathways, like portions of the Krebs cycle, can be mimicked in the lab under prebiotic conditions, suggesting they are remnants of ancient metabolic processes.
Challenges: Demonstrating how these chemical networks could transition to a genetically controlled system is difficult. The issue of chirality (the handedness of molecules) and how a random network could evolve to support specific, reproducible reactions also remains.

3. "Compartmentalization-first" (or cell-first) hypothesis

This view proposes that membranes or protocells formed first, creating a distinct internal chemical environment for the origin of life's building blocks.

How it works: In this scenario, simple lipid molecules, when placed in water, can spontaneously form vesicles (hollow spheres). These vesicles would have created a protected, concentrated environment where the chemical reactions of metabolism and replication could occur more efficiently.
Key evidence:
- Protocell experiments: Researchers like Jack Szostak have shown that simple fatty-acid vesicles can grow and divide under laboratory conditions. These vesicles can also encapsulate functional RNA, demonstrating a possible route toward the first primitive cells.
- Challenges: Like the other hypotheses, this model still needs to account for the origins of both metabolism and genetic replication inside the compartment. The challenge is showing how all three elements—a membrane, self-replication, and metabolism—could have come together.

Comparison of the three aspects
3 aspects of early biological activity

[3] Internet query: "Tripartite Aspects of the Triplet Code origin"

AI (overview) response: The tripartite aspects of the Triplet Code's origin are the three main theoretical models proposed to explain its emergence: the stereochemical theory, the coevolution theory, and the frozen accident theory. Though not mutually exclusive, these models emphasize different selective pressures and chemical interactions that could have shaped the genetic code as life developed.

1. Stereochemical theory

This theory posits that the relationship between codons and their associated amino acids is not arbitrary, but based on a direct, physical—or stereochemical—interaction.

Amino acid binding sites: The theory suggests that primordial RNA molecules, acting as both genetic material and catalysts, had specific binding sites for amino acids.
"Escaped triplets": According to the "escaped triplet" hypothesis, these specific binding triplets later "escaped" from their amino acid-binding role to become the modern codons and anticodons.
Evidence and significance: Experiments in which RNA aptamers (molecules that bind a specific target) are selected to bind particular amino acids have shown that these binding sites are often enriched for the amino acid's cognate codons. This provides statistical support that at least a portion of the code is based on fundamental chemical affinities.

2. Coevolution theory

The coevolution theory proposes that the genetic code expanded alongside the evolution of the metabolic pathways that synthesize amino acids.

Gradual expansion: The first codes would have used only a few simple, easily available amino acids from the prebiotic environment. Over time, as organisms developed metabolic pathways to create more complex amino acids from simpler precursors, the genetic code expanded to incorporate these new amino acids.
Codon assignment: The theory suggests that new codons were recruited to code for amino acids derived from the biosynthetic pathways of existing amino acids. For example, amino acids in the same biosynthetic family (such as serine, glycine, and cysteine) are often specified by codons that are chemically similar.
Error minimization: This model is compatible with the "error minimization" property of the modern genetic code, where chemically similar amino acids tend to have similar codons. This reduces the negative impact of translational errors, as a mutation is more likely to substitute a similar amino acid.

3. Frozen accident theory

First proposed by Francis Crick, this theory suggests that the current genetic code was fixed early in the history of life and its exact mapping is a "frozen accident" of that time.

Early fixation: The theory states that once a coding system was established in the last universal common ancestor (LUCA), it could not be easily changed. The fitness cost of reassigning codons in an organism with an already-large and complex set of proteins would be prohibitively high.
The cost of change: To alter the code, a cell would need to simultaneously change its codon assignments, its tRNAs, and its aminoacyl-tRNA synthetases, while also surviving the deleterious effects of recoding all existing genes. This makes any significant evolutionary modification to the established code extremely difficult.
Controversy and context: While suggesting the code is random, Crick also acknowledged that stereochemical influences could have shaped its initial formation. The theory is not intended to explain how the code formed, but rather why it is nearly universal and resistant to change once established. It argues that any early advantage a particular code may have had was subsequently locked in place.

[4] Internet query: "Originating aspects of DNA's tripartite code"

AI (overview) response: The originating aspects of DNA's tripartite (triplet) code are explained by a combination of logical necessity, evolutionary theories, and experimental evidence. The tripartite code is based on using three nucleotides, called a codon, to specify one of the 20 amino acids used to build proteins. The evolution of this system is a central question in molecular biology, with several theories proposing how this structure became nearly universal.

The logical necessity of a triplet code

The fundamental reason for a triplet code is combinatorial. With only four nucleotide bases—adenine (A), cytosine (C), guanine (G), and thymine (T)— a coding system must be able to specify at least 20 different amino acids.

Single-base code: A code using single nucleotides would provide only four possible combinations, which is insufficient to represent 20 amino acids.
Doublet code: A two-base code would provide 4² = 16 possible combinations, still not enough to cover all 20 amino acids.
Triplet code: A three-base code provides 4³ = 64 possible combinations, which is more than enough for 20 amino acids. The extra capacity provides
redundancy, meaning some amino acids are encoded by multiple codons.

Evolutionary and theoretical origins

The specific arrangement and origin of the triplet code are subjects of various hypotheses that are not mutually exclusive.

Coevolution theory

This theory posits that the structure of the genetic code coevolved with the metabolic pathways for synthesizing amino acids.

Amino acid recruitment: Amino acids were not all added to the genetic code at once. The first amino acids were likely those produced by prebiotic chemical synthesis. Later, additional amino acids were incorporated into the code as new biochemical synthesis pathways evolved.
Minimizing errors: The organization of the standard genetic code supports this theory. Codons that differ by a single base, especially at the third or "wobble" position, often code for chemically similar amino acids. This arrangement helps minimize the impact of point mutations.

H.O.B. Note: We can see this "wobbling" activity in multiple subjects involving a tripartite modeling. It is clearly recognizable with the advent of an additional item where the first three are separated with a word such as "and" (e.g. North-South-East "and" West; which we could alternatively describe as North-South-East ...a cognitive "wobble" is inserted in the form of a word written as "and"... West.), or as a symbol labeled "comma" seen in number value notation: ones-tens-hundreds... (comma)... thousands. The grouping in threes followed by a comma can be discerned as a cognitive metaphor of the "wobble" occurring at the 3rd spot in amino acid genetics. These examples are otherwise noted as 3 to 1 ratios.

Stereochemical hypothesis

The stereochemical theory proposes that codon assignments were not random but were based on a physical or chemical affinity between amino acids and the nucleotides in their corresponding codons or anticodons.

While initially not widely accepted, Francis Crick explicitly noted that stereochemical interactions should be pursued and that simple thermodynamic processes would be insufficient to explain the code's specificity. Later research has provided some evidence of interactions between amino acids and their cognate tRNAs.

H.O.B. Note: The solar theory I have proposed for the triplet code origin involves a stereo/photo-chemistry alignment. The "stereo" refers to light emanations and vibrations in the electromagnetic spectrum and not someone's boom-box blaring rap... unless of course it's a 3-part rap. A central question akin to the chicken and egg controversy is which came first? Stereochemical (in darkness) molecular reactions or Photochemical (in light) molecular reactions?

Frozen accident hypothesis

Proposed by Francis Crick, this hypothesis suggests the genetic code is a "frozen accident." It proposes that the code was fixed early in the evolution of the last universal common ancestor (LUCA).

According to this idea, subsequent changes to the code were mostly prevented because a change to any single codon's meaning would lethally disrupt the sequences of many different proteins, making the code resistant to further alteration.

Experimental breakthroughs

The definitive experimental evidence that confirmed the genetic code was a triplet, non-overlapping code came from several key experiments in the 1960s.

Crick, Brenner, et al. experiment (1961): This team used "frameshift mutations" in bacteriophages to demonstrate that the genetic code is read in triplets, starting from a fixed point. When they added or removed one or two nucleotides, the reading frame was shifted, causing the rest of the protein to be nonfunctional. When they added or removed three nucleotides, the reading frame was restored, and the gene was only minimally affected.
Nirenberg and Matthaei experiment (1961): Using a cell-free system, these researchers synthesized a messenger RNA composed only of uracil (poly-U). When this poly-U was added to the system, it produced a protein chain made exclusively of the amino acid phenylalanine. This demonstrated that the RNA codon UUU codes for phenylalanine and provided the first experimental proof of a specific codon assignment.

Ultimately, the universal nature and specific structure of the genetic code are likely the result of a combination of these principles: a mathematical need for a triplet system, followed by a refinement process influenced by coevolution and error minimization, with the resulting pattern frozen into place by early evolutionary history.

[5] Internet query: "Tripartite Aspects of Earth's slowing rotation"

AI (overview) response: The three primary factors in the slowing of Earth's rotation are tidal friction, post-glacial rebound, and internal core-mantle dynamics. This cumulative, long-term deceleration is a complex phenomenon driven by the continuous interplay of gravitational forces, geophysical processes, and climate-related mass shifts.

1. Tidal friction (gravitational)

Tidal friction is the dominant and longest-running cause of Earth's rotational slowdown.

The Moon's gravitational pull: The Moon's gravity creates tidal bulges in Earth's oceans on both the near and far sides of the planet.
Rotational drag: Because Earth rotates on its axis faster than the Moon orbits, the planet's spin drags these tidal bulges ahead of the Moon's position.
Braking effect: The Moon's gravity then pulls back on the nearest bulge, creating a braking torque that saps angular momentum from Earth's rotation, slowing it down. In accordance with the conservation of angular momentum, this process simultaneously causes the Moon to be accelerated into a higher orbit, moving it farther away from Earth.
Magnitude: This effect has gradually increased the length of a day by about 1.7 to 2.3 milliseconds per century over billions of years.

2. Post-glacial rebound (crustal)

Post-glacial rebound is the ongoing uplift of landmasses that were once compressed by the immense weight of Ice Age glaciers.

Mass redistribution: As the glaciers melted, a significant amount of mass (water) was relocated from the polar regions towards the equator. This is analogous to a figure skater who slows their spin by extending their arms.
Moment of inertia: This shift of mass away from Earth's axis of rotation increases the planet's moment of inertia, causing its rotational speed to decrease, and thus lengthening the day.
Opposing force: While the overall long-term trend is a slowdown, this process can actually cause a slight increase in rotation speed at certain points. The Earth's mantle is still flowing back to fill the void left by the ice sheets, which can subtly affect the planet's shape and distribution of mass.

3. Core-mantle dynamics (internal)

The interactions between Earth's different internal layers produce measurable, though small, variations in the planet's rotation rate.

Differential rotation: Earth's solid inner core is surrounded by a liquid outer core, and the two rotate independently of each other and the solid mantle. Recent studies have detected that the inner core's rotation has been slowing down relative to the mantle.
Gravitational and electromagnetic coupling: This differential rotation is influenced by gravitational and electromagnetic coupling between the core and mantle. Gravitational tugs from dense areas of the rocky mantle can slow the inner core, while the fluid outer core can also produce electromagnetic forces that affect its rotation.
Multidecadal oscillation: Evidence suggests this phenomenon may be part of an approximate 70-year cycle where the inner core speeds up and slows down relative to the rest of the planet. These dynamic interactions can cause small changes in the length of a day and affect Earth's magnetic field.

[6] Internet query: "Tripartite Aspects of Chirality"

AI (overview) response: In a broad sense that applies across disciplines, the tripartite aspects of chirality can be understood as: intrinsic chirality, extrinsic chirality, and the chirality of the probing mechanism. While the term "tripartite" is also used in specific, advanced physics contexts like quantum entanglement, this broader framework offers a more general understanding.

1. Intrinsic chirality

Intrinsic chirality is the inherent, built-in "handedness" of an object's geometry. A structure is intrinsically chiral if it cannot be superimposed on its mirror image through any combination of rotation and translation.

At the molecular level (chemistry): Many molecules are intrinsically chiral due to the three-dimensional arrangement of their atoms. A classic example is a carbon atom with four different substituents, known as a chiral center.
- Enantiomers: The two non-superimposable mirror-image forms are called enantiomers. They have identical physical properties (e.g., melting point, boiling point) but can interact differently with polarized light and other chiral molecules.
At the macroscopic level (biology and physics): Larger structures can also be intrinsically chiral.
- Helices: DNA molecules and protein alpha-helices are prime examples of intrinsically chiral, helical structures.
- Organisms: Many animals and plants exhibit intrinsic handedness, such as the coiling of snail shells or the asymmetric arrangement of internal organs.

>br> 2. Extrinsic chirality

Extrinsic chirality refers to a chiral arrangement created by the relative orientation between an achiral object and its environment, such as the direction of light incidence. The object itself is not chiral, but the experimental setup makes the overall system chiral.

Metamaterials and photonics: This concept is crucial in the design of metamaterials, where the chiral optical response (circular dichroism) is produced by illuminating an achiral planar nanostructure at an oblique angle.
- Example: When a planar, symmetric pattern is tilted relative to the incident light, the full system lacks a mirror plane, creating an extrinsic chiral response.
Reconfigurability: A key feature of extrinsic chirality is that the chiral response can be reconfigured or reversed simply by changing the angle of incidence or the orientation of the object, without altering the object's physical structure.

3. Chirality of the probing mechanism

The third aspect relates to the chiral nature of the method or "probe" used to detect and measure chirality.

Circularly polarized light: One of the most common probes for molecular chirality is circularly polarized light, which has its electric field vector rotating in either a right-handed (right circularly polarized, RCP) or left-handed (left circularly polarized, LCP) spiral.
- Circular Dichroism (CD): Chiral molecules absorb LCP and RCP light differently, a phenomenon known as circular dichroism. Measuring this difference is a primary method for characterizing molecular chirality.
Chiral recognition: Chiral probing can also involve using another chiral entity to distinguish between two enantiomers.
- Enzyme-substrate interactions: In biology, an intrinsically chiral enzyme will only bind to or react with one specific enantiomer of a substrate molecule, demonstrating chiral recognition.
- Separation of enantiomers: This principle is used in chromatography, where a chiral stationary phase is used to separate enantiomers from a racemic mixture.

[7] Internet query: "Tripartite Aspects of Molecular Chirality"

AI (overview) response: The tripartite aspects of molecular chirality refer to the three primary ways that chirality manifests in molecules: point, axial, and planar chirality. All three forms describe a molecule that is non-superimposable upon its mirror image, similar to a left and right hand.

1. Point chirality

Point chirality is the most common form, arising from a central atom, or chiral center, that is bonded to four different atoms or groups.

Chiral center: A carbon atom with four unique substituents is the most common example of a chiral center.
Stereoisomers: Molecules with one chiral center exist as a pair of non-superimposable mirror-image isomers called enantiomers. More complex molecules can have multiple chiral centers, leading to other types of stereoisomers, such as diastereomers.
Example: In the molecule 2-butanol, the second carbon is a chiral center because it is bonded to a hydrogen atom, a hydroxyl group (-OH), a methyl group (-CH₃), and an ethyl group (-CH₂CH₃).

2. Axial chirality

Axial chirality occurs when a molecule has an axis about which a set of substituents is arranged in a non-superimposable, helical pattern.

Lack of a chiral center: Axially chiral molecules may not have a traditional chiral center but still possess chirality due to their overall three-dimensional shape.
Chiral axis: This type of chirality is often found in substituted allenes, biphenyls with restricted rotation, and spiranes. In these structures, an axis of chirality is created by the spatial arrangement of the atoms, resulting in distinct enantiomers.
Example: In some ortho-substituted biphenyls, steric hindrance around the bond connecting the two phenyl rings prevents free rotation. If the substituents on each ring are different, the molecule becomes axially chiral.

3. Planar chirality

Planar chirality arises when a molecule contains a plane that is not symmetric and contains a group that is restricted from rotating through the plane.

Defining elements: A planarly chiral molecule typically has a plane of substituents and an atom not in the plane that, together, create a non-superimposable mirror image.
Restricted rotation: The key feature is the inability of the molecule to freely rotate and form its mirror image, due to some sort of conformational constraint.
Examples: Some examples include certain substituted ferrocenes and trans-cyclooctene. In these compounds, the arrangement of substituents on a ring or planar system creates a chiral molecule.

Importance of tripartite chirality

Understanding these three forms of chirality is critical in many fields of chemistry and biology:

Drug discovery: Many biological processes, including drug-receptor binding, are highly specific and depend on a molecule's chirality. A drug enantiomer with the correct three-dimensional structure can bind to a receptor and produce a therapeutic effect, while its mirror image may be inactive, toxic, or cause unintended side effects.
Asymmetric synthesis: Chemists use specialized methods to selectively synthesize one enantiomer over the other, a process known as asymmetric synthesis. This is particularly important for pharmaceuticals, where producing a single enantiomer is often necessary to avoid negative side effects associated with the other.
Materials science: Chiral molecules can be used to create materials with unique properties, such as liquid crystals and metamaterials. The specific handedness of the molecules can influence the overall structure and behavior of the material.

[8] Internet query: "Tripartite Aspects of Planetary Chirality"

AI (overview) response: The tripartite aspects of planetary chirality describe the three main origins and forms of "handedness," or directional asymmetry, observed in astrophysical systems, including planets.

1. External factors

This form of chirality arises from the influence of external forces on a planet's large-scale phenomena.

Atmospheric and oceanic circulation: The Coriolis effect, caused by a planet's rotation, is a primary driver of this extrinsic chirality. It dictates the direction of rotation for large-scale weather patterns, such as cyclones and anticyclones, which spin in opposite directions in the northern and southern hemispheres. The Coriolis force also influences the large gyres in Earth's oceans.
Helical magnetic fields: The fluid dynamics in a star or planet can produce a twisted, or helical, magnetic field. While driven by internal processes, the overall structure of this magnetic helicity is a macroscopic manifestation of chirality. On Earth, the magnetic field also plays a role in how cosmic radiation influences surface chemistry.

2. Microphysical origins At a fundamental level, chirality is introduced by the weak nuclear force, which violates parity symmetry.

Parity violation: The weak force, one of the four fundamental forces, treats left-handed and right-handed particles differently. Neutrinos, for instance, are observed to be exclusively left-handed, while antineutrinos are right-handed. This asymmetry provides a tiny but universal chiral bias.
Chiral influence on chemistry: Scientists hypothesize that this microphysical bias may have been amplified over time, influencing the selection of one "handedness" for prebiotic molecules. While the effect is extremely subtle, its universal nature could imply that any life arising from this mechanism would share a common chirality, a phenomenon known as homochirality.

3. Spontaneous self-organization

The third aspect involves the spontaneous emergence of chirality during the development of a planetary system or life itself.

Nonlinear processes: Spontaneous chirality does not require an external chiral influence but arises from the interplay of instability and nonlinearity in a system. For example, the non-linear processes in magnetohydrodynamics can generate helical structures.
Origin of biomolecular homochirality: A key mystery in astrobiology is how terrestrial life came to use almost exclusively left-handed amino acids and right-handed sugars. This biological "homochirality" is a prominent example of spontaneous chiral organization. Scientists are exploring multiple scenarios for this, including:
- External delivery: Meteorites and comets have been found to contain chiral molecules, which could have been delivered to Earth with a slight chiral excess.
- Circularly polarized light: Circularly polarized light from stars in regions of space with a strong magnetic field can induce a chiral bias in organic molecules.
- Mineral surfaces: Chiral mineral surfaces could act as templates, selectively catalyzing the formation of one enantiomer over another.

The "Tripartite Aspects" framework highlights that planetary chirality is a multi-scale phenomenon, originating from universal physics, macroscopic planetary dynamics, and spontaneous self-organization critical to the origin of life.

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Initial posting: Wednesday, Sept. 3rd, 2025.... 2:52 AM