⋆˚𝜗𝜚˚⋆

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Introduction to My Upcoming Book

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Concept:

A Question

If you were to take:

Abstract thinking:

which is the ability to consider and reason concepts, ideas and principles that are not physically present or obvious It involves understanding and working with ideas that are not tied to specific, concrete experiences. A skill that is crucial for creativity

And combine it with:

Associative thinking:

Which is connecting concepts and ideas in a seemingly random, free-flowing manner, allowing your mind to explore new connections

Connections like:

Biology and World Building

Can you create an alien civilization where biology provides the building blocks?

Chapter One

Chapter One is available for free online. In this chapter, I lay out all the necessary tools that I will be using to build my world 

The next phase will be in my upcoming book 

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How it is Written

This website and chapter one will be written in steps 

First I lay out all the science, in full detail until I can’t break it down any further.

Next, I will take the pieces and “link” them together, filling in any gaps with lore.

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Interphase Part One: Before Life

Creation Myth:

In the Beginning, all was dark, all was still. The world was there, yet unaware. All were sleeping, as their bodies were filled with energy, a spark for every being. 

Then came the first words, the first code for life. 

The words spread through the darkness and created all possibilities, like a tree with endless branches and many kinds of fruit.

Take your pick, take your choosing, what strikes your curiosity. Be warned that the fruit you pick cannot be put back. 

The fruit to sustain a hungry traveller, as they pick the fruits that interest them most. Some will be sweet, others foul. 

No time to taste them yet, but how to carry them?

Strings, woven together to make a cloth to carry them.

There is a decision to be made by a young traveller: Do I leave quickly and wander through the night? Or do I sleep until morning?

I don’t know what is out there in the night to find, but if I sleep, am I at the mercy of another?

Then something unexpected happens, the traveller is divided, and made in two equal bodies carrying the same amount of fruit. One traveller says to the other, “You can go wander in the night and work up an appetite, I will stay, feast and sleep.”

They say farewell, for they may never meet again.

As the curious traveller sets out into the night, something strange begins to happen in the sky.

One spark of light, and then another. Moving across the sky in one direction, and then the other. Faster, and faster, until it tears open the sky.

In the centre of the sky, was a body, a mind. Beginning as one and then becoming two.

Two realms were created:

One named Organelle and the other Lamina.

The traveller then felt a strange sensation as they became infused with the knowledge of their path that lays before them. To become two equal bodies with half the amount of fruit. They will try to speak to each other, but cannot understand.

The two travellers will part ways as they begin the rest of their life. 

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Origin:

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From the void, the sky gives birth to ten stars. As they descend towards the ground, they shed their dust. Creating a path to the city. 

A star for every man and every woman, as they appear to us one by one on our journey to Mito.

The dust that has been shed is then caught in the wind. A little storm of particles, glowing and golden, takes the form of a fight between wild animals, spilling dust instead of blood.

After the storm has settled, the animals are gone. The fallen particles have created a ring. A ring made of nothingness, void empty space cut away from existence.

In the centre, the platform for the fight, a circle of land now exists 

A floating realm, made of wilderness.

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G1 Phase (Gap 1): Parts 1, 2 and 3:

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In Organelle

(Organelle is Day Lamina is Night)

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.·:*¨༺ 1 ༻¨*:·.

Grouping:

 Escape Wheel

….

Linking:

Connecting what is in this group 

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.·:*¨༺ 2 ༻¨*:·.

Grouping:

 Pallet Fork

….

Linking:

Connecting what is in this group 

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.·:*¨༺ 3 ༻¨*:·.

Grouping:

Gear Train

….

Linking:

Connecting what is in this group 

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.·:*¨༺ 4 ༻¨*:·.

Grouping:

Balance Bridge

….

Linking:

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.·:*¨༺ 5 ༻¨*:·.

Grouping:

Balance Spring

….

Linking

Connecting what is in this group 

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.·:*¨༺ 6 ༻¨*:·.

Grouping:

 Balance Wheel

….

Linking:

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.·:*¨༺ 7 ༻¨*:·.

Grouping:

Hairspring

….

Linking:

Connecting what is in this group 

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.·:*¨༺ 8 ༻¨*:·.

Grouping:

Jewel Roller

….

Linking:

Connecting what is in this group 

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.·:*¨༺ 9 ༻¨*:·.

Grouping:

Shock Protector Mechanism 

….

Linking:

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.·:*¨༺ 10 ༻¨*:·.

Grouping:

 Balance Shaft

….

Linking:

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Grouping:

 Case

….

Linking: 

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.·:*¨༺ 12 ༻¨*:·.

Grouping:

Balance Wheel Axis 

Linking:

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.·:*¨༺ 13 ༻¨*:·.

Grouping:

 Barrel Bridge

Linking:

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.·:*¨༺ 14 ༻¨*:·.

Grouping:

Barrel

Linking:

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.·:*¨༺ 15 ༻¨*:·.

Grouping:

Ratchet Wheel

Linking:

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Grouping:

Arbor

Linking:

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.·:*¨༺ 17 ༻¨*:·.

Grouping:

Click

Linking:

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.·:*¨༺ 18 ༻¨*:·.

Grouping:

Crown Wheel

Linking:

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.·:*¨༺ 19 ༻¨*:·.

Grouping:

Cannon Pinion

Linking:

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.·:*¨༺ 20 ༻¨*:·.

Grouping:

 Driving Wheel

Linking:

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.·:*¨༺ 21 ༻¨*:·.

Grouping:

Stem

Linking:

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Grouping:

Winding Pinion

Linking:

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Grouping:

Sliding Pinion

Linking:

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.·:*¨༺ 24 ༻¨*:·.

Grouping:

Setting Wheel

Linking:

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.·:*¨༺ 25 ༻¨*:·.

Grouping:

Yoke

Linking:

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.·:*¨༺ 26 ༻¨*:·.

Grouping:

Setting Lever Jumper

Linking:

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Grouping:

Jumper

Linking:

Connecting what is in this group 

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Crown

Linking:

Connecting what is in this group 

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Part 1 Interphase Continued: G1 Phase (Gap 1): Part 1:

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Growth Phase:

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Primary metabolites: 

These are essential for growth, development, and reproduction

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Carbohydrates:

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Monosaccharides:

 Simple sugars are the primary energy sources

They cannot be further broken down. They are the simplest form of carbohydrates and the building blocks for more complex sugars

Cyclic forms:

Monosaccharides primarily exist in a ring-like structure, rather than a linear chain, due to the formation of hemiacetals or hemiketals, organic compounds. 

The cyclic form arises when a carbonyl group, group composed of a carbon atom double-bonded, where two atoms share two pairs of electrons, to an oxygen atom, reacts with a hydroxyl group, denoting the radical -OH, that has one or more unpaired electrons, present in alcohols, on the same molecule

When a monosaccharide forms a cyclic structure, a new chiral center, an atom that has four different groups bonded to it in such a manner that it has a non-superimposable mirror image, is created at the carbon that was part of the carbonyl group

Common Ring Sizes:

The most common cyclic forms of monosaccharides involve five-membered ring (furanose) or a six-membered (pyranose) rings

The term "furanose" is derived from its similarity to the furan molecule, while "pyranose" is derived from pyran

The linear and cyclic forms, and it’s conversion of into each other between the α and β anomers, Alpha and Beta, is a process called mutarotation

Alpha (α) Anomer:

In the α-anomer, the hydroxyl group on the anomeric carbon is positioned trans to the CH2OH group (the hydroxymethyl group on the last chiral carbon) when viewed from the perspective of the ring

Beta (β) Anomer:

In the β-anomer, the hydroxyl group on the anomeric carbon is positioned cis to the CH2OH group, This means they are on the same side of the ring plane

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During the:

Cyclization:

a chemical reaction that involves the formation of a ring from a linear molecule through the creation of a new bond

Ring Formation:

Cyclization reactions involve the intramolecular formation of a ring structure, where a molecule's ends or specific parts connect to create a closed loop

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monosaccharide, sugars that cannot be broken down into simple sugars,

the carbonyl carbon:

 carbonyl carbon carries a partial positive charge and is electron-seeking

aldehyde:

a class of organic compounds in which a carbon atom shares a double bond with an oxygen atom, a single bond with a hydrogen atom, and a single bond with another atom

ketone:

characterized by a carbonyl group (C=O) bonded to two carbon atoms, distinguishing them from related compounds like aldehydes

organic compounds that contain a:

carbonyl group:

carbonyl group is a functional group with the formula C=O, composed of a carbon atom double-bonded to an oxygen atom, and it is divalent at the C atom

becomes a chiral center

Chiral Center

The key characteristic of a chiral center is that the atom is bonded to four different:

substituents:

an atom taking the place of another atom or group, or occupying a specified position. 

If any two of these groups are the same, the atom is not a chiral center

Monosaccharides with the same molecular formula can be:

structural isomers (different bonding arrangements):

molecules that have the same molecular formula (same number and type of atoms) but differ in the way their atoms are connected or bonded together

stereoisomers (same bonding, different spatial arrangement):

molecules that have the same molecular formula and the same connectivity of atoms, but they differ in the three-dimensional arrangement of those atoms in space

Disaccharides: 

Disaccharides are formed when two monosaccharides are linked together. Monosaccharides are simple sugars

Reducing vs. Non-Reducing:

Disaccharides can be classified as reducing or non-reducing, depending on whether they have a free anomeric carbon (the carbon involved in the glycosidic bond) that can act as a reducing agent. Lactose and maltose are reducing sugars, while sucrose is a non-reducing sugar

Glycosidic Bond:

Glycosidic bonds are formed when a hydroxyl group on one sugar molecule reacts with a hydroxyl group of another sugar

This reaction involves the elimination of a water molecule (dehydration synthesis)

Polysaccharides: 

They are long-chain polymeric carbohydrates, chemically bonding together many small:

repeating units:

the smallest structural unit that, when repeated, forms the larger structure of a polymer or crystal

Enzymes: 

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Recombinases:

Enzymes like recombinases are critical for the process of crossing over, where genetic material is exchanged between homologous chromosomes

Homologous Recombination (HR) Enzymes:

They work with recombinases to ensure proper crossover formation and prevent non-crossovers during meiosis

Managing DNA Topology:

Topoisomerases: 

These enzymes are involved in controlling the topological state of DNA, including the formation and resolution of knots and catenanes. Topoisomerase II, for example, is important for chromosome condensation and segregation during meiosis

Microtubule-severing enzymes: 

Enzymes like spastin and fidgetin play a role in severing microtubules, which are essential components of the spindle apparatus that separates chromosomes during meiosis

Structural proteins: 

Play a role in chromosome behaviour, particularly in the formation of the synaptonemal complex (SC) it’s proteins include:

SYCP1:

A central protein in the SC, forming a filamentous structure that connects the lateral elements (containing SYCP2 and SYCP3) to the central element

SYCP2 and SYCP3:

Part of the lateral elements, which are protein structures that form the backbone of the SC and are associated with chromatin loops

HOP1:

Another protein found in the lateral elements, contributing to the structural organization of the SC

SKR-1 and SKR-2:

These proteins are localized to the central region of the SC in C. elegans and are involved in its structure and function

SYCE3:

This protein actively remodels the SYCP1 lattice during synapsis

TEX12:

This protein, part of the central element, forms a complex with SYCE2 and contributes to the SC's fibrous backbone

Transport proteins:

 Kinesins and Dyneins:

The kinesin gene family is a group of motor proteins that play a critical role in intracellular transport, particularly in the movement of cellular cargo along microtubules

KIF3A 

KIF3A is a key component of the kinesin-II motor protein complex, which is essential for building and maintaining cilia and flagella. These cellular appendages are involved in various processes, including cell signaling and movement

Dynein, another motor protein, is involved in various meiotic processes, including

Axonal Transport:

KIF3A, along with its partners KIF3B and KAP3, forms a complex that moves along microtubules, facilitating the transport of various cargo, including vesicles, within neurons

Spindle Assembly Checkpoint (SAC):

The SAC is a crucial quality control mechanism that monitors spindle assembly. It ensures that chromosomes are correctly attached to the spindle before the cell proceeds to separate them. If any chromosomes are not properly attached or aligned, the SAC delays cell division until the issue is resolved

Regulatory proteins:

 Controlling gene expression and cellular processes

Secondary metabolites: 

These have various roles, including signaling, defense, and other functions not directly related to the life cycle

Terpenoids:

Composed of repeating isoprene units

Include a wide range of compounds like monoterpenes, diterpenes, triterpenes, and carotenoids

Phenylpropanoids:

Contain a phenolic ring, often derived from phenylalanine

Include phenolic acids, flavonoids, tannins, and lignin

Alkaloids:

Nitrogen-containing compounds with diverse structures

Polyketides:

Synthesized from acetate or propionate units

Include a wide variety of compounds like antibiotics, pigments, and toxins

Role: defence against pathogens

Biosynthesis:

It is the longest phase of the cycle, but also the most variable in duration

the process of making complex products from simpler components through chemical reactions at the cellular level

Precursor Acquisition:

Living organisms obtain the necessary building blocks, or precursors, for biosynthesis. These can be obtained from the environment or synthesized from other molecules within the organism

Activation:

Precursors may need to be activated before they can be incorporated into the larger molecule. This often involves attaching the precursor to a carrier molecule or modifying it with an energy-rich molecule like ATP

Condensation/Elongation:

The activated precursors are then linked together through chemical reactions to form the desired molecule

For instance, in protein synthesis, amino acids are joined together by peptide bonds, forming a polypeptide chain

This process is highly regulated by enzymes

Modification and Processing:

These modifications, often referred to as post-translational modifications in proteins, can involve adding chemical groups, trimming parts of the molecule, or folding it into a specific three-dimensional structure

Proteins for DNA replication:

Cells produce the necessary proteins and enzymes required for DNA replication in the subsequent S phase

DNA Polymerase:

This enzyme is the main DNA builder. It adds new nucleotides to the growing DNA strand, matching them to the template strand. There are different types of DNA polymerases with specific functions, like leading strand synthesis and lagging strand synthesis

Helicase:

This protein unwinds the double helix structure of DNA, separating the two strands to create a replication fork where replication can begin

Primase:

Primase synthesizes short RNA primers that provide a starting point for DNA polymerase. DNA polymerase can only add nucleotides to an existing 3' end, so the primer acts as a "primer" for replication

Single-Strand Binding Proteins (SSB):

These proteins bind to the separated DNA strands, preventing them from re-forming a double helix and stabilizing them for replication

Topoisomerase:

This enzyme helps relieve the torsional stress that builds up ahead of the replication fork as the DNA unwinds. It does this by creating temporary nicks in the DNA, allowing it to rotate and relieve the tension, and then resealing the nicks

Ligase:

After the RNA primers are replaced with DNA, ligase is responsible for joining the small DNA fragments (Okazaki fragments) together on the lagging strand, creating a continuous DNA strand

Sliding Clamp:

Proteins like PCNA (in eukaryotes) and the beta subunit (in E. coli) form a ring around the DNA and bind to DNA polymerase, increasing its processivity (ability to synthesize long stretches of DNA)

Clamp Loader:

Proteins like RFC (in eukaryotes) and the gamma complex (in E. coli) are involved in loading the sliding clamp onto the DNA

Replisome:

This is a large complex of proteins that coordinates the activities of all the enzymes involved in DNA replication

Proteins for cell growth:

G1 is a growth phase, so cells synthesize proteins that contribute to overall cell size and mass

Centrosome proteins:

Centrosomes, which play a crucial role in cell division, are assembled during G1, requiring the synthesis of specific proteins

Proteins involved in G1/S checkpoint:

The G1 phase also involves the synthesis of proteins that regulate the G1/S checkpoint, ensuring proper DNA replication and cell cycle progression

Proteins involved in metabolism:

Cells synthesize enzymes and other proteins involved in various metabolic pathways to support growth and energy production

RNA:

RNA is a nucleic acid, like DNA, composed of nucleotides

Sugar molecule:

 RNA uses ribose sugar, while DNA uses deoxyribose

Nitrogenous base:

 RNA contains uracil instead of thymine (found in DNA)

Structure: 

RNA is typically single-stranded, while DNA is double-stranded

Single-stranded: 

Unlike the double helix structure of DNA, RNA is typically single-stranded

Types:

Messenger RNA (mRNA): 

Carries genetic information from DNA to the ribosomes, where proteins are made

Transfer RNA (tRNA): 

Delivers amino acids to the ribosomes during protein synthesis

Ribosomal RNA (rRNA): 

A major component of ribosomes, the protein-making machinery of the cell

Regulatory RNAs:

Involved in controlling gene expression

Nucleotides:

and other molecules needed for its functions preparing for: