Chapter One

This is Where our story begins 

Opening Scene 

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Organelle is our world. One more sophisticated than the one that once belonged to our visitors. One more civilized than the cruel world from which they came. This is the beginning of our story.

It was a cold clear night Organelle was shaken, the sky disturbed by strange flashing lights as a loud boom would wake even the heaviest of sleepers. 

Those curious enough to look to the sky got the sight of a large pink fireball as it comes down and crashing into a nearby forest. 

“What the hell was that!” Was the general response from the residents who were awakened

In Plas nothing is accidental, nothing is random, everything has a reason so what is the reason for this?

The event sparked curiosity from onlookers as a few questioned if Organelle is under attack and the authorities are called to respond 

Those who could not contain their curious nature decided to investigate for themselves and as they followed the path of charred and broken branches they were met with an even more confusing sight.

A white disc. Standing five feet high and roughly twelve feet across. One side appears to be torn open  while inside lay three comatose bodies, seen by those who dared to approach the object.

As the authorities arrive with rifles in hand peering inside. “They are alive but the crash seems to have knocked them unconscious. We will take them to the military hospital and question them later.” “What if they are enemies?” Asked an onlooker. With little hesitation the officer calmly answered “We will make sure they are heavily guarded in case they are hostile. Now everyone.. go home and get some rest the situation will be handled properly and we will update the public on the situation as it develops”. 

The following day the incident is the talk of the nation. Speculation, rumours, everything from conspiracy theories to the assumption that the entire thing is a hoax. A hoax that is part of a conspiracy theory and such talk as the residents try to dissect the event to understand why it took place and the meaning behind it

In Plas there everything has an underlying purpose. This being the result of conditioning from the entertainment industry. Organelle’s celebrities live underground in a secret society and have made careers out of hinting at what goes on in their art. The magazines people in Plas read are all speculation so they have adopted this into mainstream culture.

Soon I will post a scientifically accurate conversation between Felix and Winifred 

I decided to redo the conversation because I was unhappy with the result 

Culture 

selective permeability - these processes can be passive or active

The ability to differentiate between different types of molecules, only allowing some molecules through while blocking others

The surface nation Plas is the largest of all the nations of Organelle and covers the entire surface.  Plas is the least respected of nations and belongs to the general public. The higher classes live in underground nations and secret societies while the public is often kept in the dark about what goes on inside the world

The surface nation has for lack of better words a bubble around it which is to protect the nation from either large scale invasions or objects. The pod that has crashed was small enough to enter Plas’s atmosphere. The purpose of this bubble is to protect Organelle from the giant insects that float around the universe. That and Organelle does business with other worlds that are adversaries and are not trusted 

endocytosis

Endocytosis is an active transport process. Active transport is a process that requires energy to move molecules and ions across a cell membrane against a concentration gradient

a concentration gradient occurs when there is a higher concentration of solute in one area and a lower concentration in another

The culture of Plas is that one group of people in Plas are not better than other residents of Plas even though Organelle has elites that live underground including celebrities they are not necessarily idolized. They might have influence over the public but they are still just people, this is the attitude in Plas

Endocytosis is a cellular process in which substances are brought into the cell

This happens in steps:

Invagination The plasma membrane folds inward to form a cavity

Once the object is found the authorities open a portal that leads to the underground nations. This is done secretly as the crowd returns to their homes

Vesicle formation

The membrane folds back on itself until the ends meet, trapping fluid inside

Once the import is complete the portal closes again 

 The cell processes the internalized vesicle

There is to be an investigation of the object and the people inside 

or exocytosis

 a process for moving large molecules out of the cell to the cell exterior

Once everything is cleared will be sent back to Plas where they can do the least amount of damage and only know things on a need to know basis. The people of Plas are curious about the visitors and what the event all means. Why did they come to us? 

There are steps to this:

Vesicle trafficking

initiates from vesicle formation via membrane budding, process that transforms flat membranes into vesicles

This is an important concept in Plas that a person needs to form an identity that is a higher dimension and the realization that viewing something as either good or bad is what they call two dimensional thinking. This type of thinking doesn’t allow there to be more depth and insight into what is in front of them and it simplifies the perception that something either is one or the other. This type of thinking is frowned upon in well, everywhere in Organelle 

Membrane budding is a key step in vesicular transport, 

To remove oneself from this way of thinking is rewarded with the freedom to explore the world around them that they were not able to see before 

multivesicular body and exosome biogenesis

Multivesicular bodies are organelles that contain many small vesicles and are involved in the transport, storage, and recycling of substances

Plas’s culture is made up of a multitude of subcultures that involve creating different traditions that stretch across the nation most of them are based on different forms of entertainment and the arts. Looking for a deeper meaning behind an artist’s work. The artists in Organelle have a secret society and live underground. Their work however is allowed to hint at what is going on. Different artists have a following and the traditions inspired by them are a fun thing for the public to entertain themselves with

biogenesis is the development of life from preexisting life

When Plas is evolving as a culture the people look to the past. The ancient civilizations so that they can take old ideas and incorporate them into modern society 

followed by vesicle transport among intracellular organelles,

The information collected by the elite is passed down from every society as it is tweaked by the people in the higher societies to the point it’s completely different when it finally reaches Plas. The people of Plas understand this so they don’t take ANY of the information literally 

ferrying material from one organelle to another or between regions of the same organelle

Information is passed around freely between subcultures and also between individuals within those groups 

and is accomplished by vesicle fusion with the target membrane

vesicle fusion happens in steps:

Cargo molecules are trapped in carriers on intracellular membrane compartments. This process involves several organelles

The pod carrying Lucy, Harlow and Dalton is taken to the main underground military base that is occupied by leaders representing several nations 

Vesicle targeting and fusion

Snare proteins are part of the machinery that mediates vesicle targeting and fusion

a family of proteins that mediate membrane fusion in eukaryotes. SNARE proteins are molecular motors that help bring two membranes together for fusion

Beings that live very different lifestyles in the diverse culture of Plas come together to discuss the news of the crash. There is much speculation over the purpose of the event and what it all means from every understanding 

Vesicle fusion passes through a fusion pore, which is a metastable intermediate with a small aqueous opening

Underneath the surface of Plas while those on the surface speculate, Lucy and the others are taken down an underground tunnel 

The vesicle fuses with the cell membrane, and the vesicle's contents are expelled. Exocytosis is important for transporting neurotransmitters

What Plas refers to as three dimensional thinking is brought into the speculation and the rumours begin 

the merging of a vesicle with other vesicles or a part of a cell membrane

The different people decide to combine their theories and in less than 24 hours the UFO crash is all over the news

The receptors (aka complex proteins) on the surface assist in cell recognition/binding and other intracellular processes

The news has caught the attention of the elite in Nuc as well as the other underground nations. The elite of Nuc contact other worlds begging for information on who these aliens are and where they came from 

receptors on the cell surface of one cell bind to glycoproteins

molecules that comprise protein and carbohydrate chains that are involved in many physiological functions including immunity. Many viruses have glycoproteins that help them enter bodily cells

The possibility of these aliens being being sent as a weapon against Organelle is brought to attention. It is decided that as a precaution the aliens will be put through intense screening processes which include a memory scan and a session inside the Dream Machine 

 a large and diverse group of proteins to which one or more sugar molecules have been attached through covalent bonding

the mutual sharing of one or more pairs of electrons between two atoms

The memory scan looks at the last images the aliens have to remember and the emotions from the images. Once that information is received then the information is made into a spectrum of possibilities from those images using artificial intelligence and recording the emotion that arises from these images

The results of the test show they are from a world that has destroyed itself and as they were getting into the pod to be sent off there was panic, fear and dread

on the cell surface of another cell, allowing the two cells to communicate

Using remote communication the elite of Organelle and otherworldly elites suggest that they be sent to Plas while watched closely 

Cell signaling

The process by which a cell responds to substances outside the cell through signaling molecules found on the surface of and inside the cell

The news of the crash spreads quickly and within hours it is all over Organelle, pictures of the crash site and speculation spread throughout the nations

Cell recognition

identify cells as either self or non-self with their specific tertiary structure

Self cells are cells that belong to the body and are recognized by the immune system as part of the body, while non-self cells are foreign cells or substances that are recognized as not part of the body. The immune system's ability to differentiate between self and non-self cells is called self/non-self discrimination

It is up to the military to find out what world they came from and if they are a threat. Worlds are classified into groups of allies and adversaries. Familiar and unfamiliar

Cell adhesion

the ability of a single cell to stick to another cell or an extracellular matrix

Like earth Organelle has an international space station that communicates between worlds 

Parts of the plasma membrane include Phospholipids that form the bilayer; a membrane with two molecular layers

There are two separate dimensions in Plas civilians live on the upper surface and then there are those who live underneath. The under layer is home to military personnel and border patrol and is a multitude of bases That is where Lucy, Harlow and Dalton have been taken

integral proteins form transporters;

Transport proteins are integral transmembrane proteins; that is they exist permanently within and span the membrane across which they transport substances 

The equivalent to our internet, it spans all across Plas and connects everyone. Within two hours of the crash the news is all over Plas

peripheral proteins are part of the cell's recognition sites

Every home in Plas is a floating structure that is tethered to the ground at night when all the lights are on its a beautiful sight. The purpose is to protect homes from animals, flooding and mild earthquakes. Trees are not cut down and cities float, the people have their space and so do the animals

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Taking them to the military base 

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At the site of the crash the crowd has cleared and the authorities are to transport the pod down to the military hospital. One person takes out a small hand held device used to open a portal down to the lower dimension of Plas. 

Waiting for them are a number of professionals in various fields including one named Luna, a military psychiatrist and psychologist, she has been called to study the three visitors as they are taken in on stretchers. Even though they are unconscious they will be put into an induced coma during the study.

The first test performed is a memory scan which brings up the last images and emotions that were experienced by the visitors. As they watch what looks to be an apocalyptic end and feelings of fear and dread and confusion gives insight that what has happened was an act of desperation for a world that has destroyed itself. 

“It appears these beings are searching to recolonize” says Luna “However it’s apparent they have a destructive nature. We will need to do further screening. Individual sessions in the Dream Machine will tell us everything we need to know.”

“Are you sure about how ethical this is Luna? Given they have just been through a traumatic experience, the Dream Machine might be too much and traumatizing for them not knowing it’s just a simulation.” 

Luna paused. Considering such a thing. “We know they are destructive creatures, and from the memory scan they appear vicious. We need to know what type of threat they pose before they wake up. You’re asking me if empathy towards a potential threat is more important than safety? My heart wants to be empathetic but my mind wants no part in such a risk.”

“We will program the beings from their memory to discourage ANY form of aggression and see if they can be made civilians. We will try our best to give them a home in Plas if they can learn how to behave like an average citizen.”

Developing Character Personalities 

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The setting for the simulation is based on Paramecium and its anatomy 

A little world I will try to keep it basic. Let’s see what effect Lucy, Harlow and Dalton have 

The macronucleus is responsible for the day-to-day operations of the cell,

The day to day activities include going out into the forest to find and collect water for both drinking and for cleaning 

contractile vacuole is made up of interconnected tubules and vesicles that collect fluid from the cell's cytosol. The CV then expels the fluid through pores in the plasma membrane

The body plasma membrane converts sensory stimuli into receptor potentials

an electrical signal that occurs when a sensory receptor is activated. It's also known as a generator potential or transduction current

The ability to sense and respond to signals that are otherworldly 

Transduction is the process of converting a stimulus into an electrical signal that the brain can interpret. In the case of hearing, transduction is the conversion of sound waves into electrical signals that the brain can process.

When they are able to sense these signals in a way that is acceptable the next step will be to send one out 

while the micronucleus is primarily involved in genetic material exchange during conjugation

Conjugation is the process by which one bacterium transfers genetic material to another through direct contact

one bacterium serves as the donor of the genetic material, and the other serves as the recipient. The donor bacterium carries a DNA sequence called the fertility factor

Can they handle basic communication with other worlds and successfully send out a message to another parallel world? What will be their message?

The macronucleus undergoes direct division without mitosis

During reproduction, the macronucleus disintegrates and is replaced by a new one formed from the micronuclei

The macronucleus contains a somatic genome that is actively transcribed and translated during the cell's vegetative growth phase

The information from the signals are grouped together into a report on the experience lived for each “day” in the simulation (one hour) 

Here I will map out the science behind the Dream Machine 

Dendritic cells

DCs patrol the body for pathogens, either directly or indirectly. 

The first part of the experience a person is taken from their memory and tells them “They’re looking for you. Who? They. You’re in a lot of trouble if they find you.”

They use pattern recognition receptors (PRRs) like Toll-like receptors (TLRs) and C-type lectin receptors (CLRs) to recognize pathogen-associated molecular patterns

The patient’s thought patterns will be recorded during the experience to see how they respond to the simulation. This simulation requires that the patient experiences it alone as they do the job of collecting water and learning how to properly interact with their environment 

DCs mature after recognizing pathogens, upregulating MHC molecules and costimulatory receptors to activate T cells

These receptors mediate the internalization of antigen–IgG complexes and promote antigen presentation

Recognize and Respond 

Simulated people exist in the environment and give different interactions each “day” (hour)

To begin the simulation process there are steps leading up to one major choice for the patient to make on a subconscious level 

Steps:

T cell activation is a stepwise process that involves a complex interplay of signals, some positive and some negative. The sum of these signals determines the fate of the T cell

The simulation is an experience with both positive and negative stimuli and choices made

Let the Simulation Begin

Steps:

antigen presenting

Antigen recognition: The T cell recognizes the antigen-class II MHC molecule complex on the antigen-presenting cell (APC) membrane

MHC class II molecules bind to peptides from proteins that have entered the endocytic pathway

The first signal sent to them is urgency. The need for food to eat and water to drink. They are to spend their first day learning to forage for food and water. They will receive some basic instructions delivered to them by a familiar face and told to listen carefully 

Phagocytosis Cells ingest large particles like bacteria or cell debris. This process is also known as "cell eating". 

Chemotaxis:

Chemotaxis is the movement of an organism in response to a chemical stimulus. It is a process that allows cells to sense chemicals in their environment and move towards or away from them

In the forest you will find what you need to use as either bait for hunting or to threaten the wildlife so it runs away. You need to eat but you also need to protect yourself. Can you find these items? 

Particle recognition: 

The signal recognition particle (SRP) is a ribonucleoprotein

a complex of RNA and proteins that regulates gene expression in cells

the process by which the information encoded in a gene is turned into a function

Listen carefully, you need to learn how to create tools and weapons using what is in your environment that you can carry quite a distance with. Only the most efficient tools and weapons are acceptable 

that directs proteins to the endoplasmic reticulum (ER) or plasma membrane. It's found in all three domains of life

The three domains of life in biology are Archaea, Bacteria, and Eukarya

You will take these items with you as you travel through three regions 

Archaea

unicellular, prokaryotic organisms, are capable of living in extreme environments they do not have a nucleus, membrane-bound organelles, and have a single circular chromosome

This region only has one area safe to stay in for a period of time. This region has no government or established cities yet it has one law to follow at all times and unquestioned 

unlike the linear chromosome of most eukaryotes. A circular chromosome, showing DNA replication proceeding bidirectionally,

moving or functioning in two directions, usually in opposite directions

This law holds two directions you can take to find “The Beginning”

with two replication forks generated at the "origin"

are Y-shaped structures that form during DNA replication

Circular chromosomes have no free ends to the DNA

Bacteria

The second region is much smaller area that you need to work with what is in your environment with no further instruction 

Rod-shaped bacteria that are gram-positive, meaning they have a thin outer coating 

Spherical bacteria that are non-motile and don't have flagella. They can grow in chains, clusters, or pairs

Spiral-shaped bacteria that are long and thick, and move using flagella

Eukarya

Eukaryotic cells have a true nucleus, which means the cell's DNA is surrounded by a membrane. Therefore, the nucleus houses the cell's DNA and directs the synthesis of proteins and ribosomes

Present at least one fact that you have learned so far in your journey 

Engulfment: The cell membrane engulfs the particle, forming a phagosome 

The patients experience being taken to an underground base while in the simulation 

Phagosome sealing: The phagosome fuses with a lysosome 

Digestion: The lysosome releases enzymes that break down the particle 

Absorption: The phagocyte absorbs the digestive products

The patient gets their first meal and is advised to make it last as long as possible. Now it’s time to find water

Pinocytosis Cells take in small molecules and liquid. This process is also known as "cell drinking".

Initiation: 

Pinocytosis begins when molecules in the extracellular fluid bind to receptors on the cell membrane. This binding triggers the cell membrane to fold and form a pocket around the fluid

Using what is in your environment create yourself a bowl to collect water 

Pocket creation: The cell membrane folds to create small pockets around the fluid 

Something that will not leak or break down too quickly, if you’re smart you will figure out how to make a bag to carry a larger amount of water 

Invagination: The cell membrane connects at the open end of the pocket 

Pinching off: The pocket pinches off to form a vesicle 

Vesicle movement: The vesicle moves into the cell's cytoplasm 

You will be travelling quite a distance into a desert like environment 

Vesicle fusion: The vesicle fuses with a lysosome or endosome 

Content breakdown: Enzymes in the lysosome break down the vesicle's contents

I hope you took the extra challenge to make a bag for the water you collected you will walk all night 

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The two-signal hypothesis is an immunological model that explains how T-cells are activated. It states that T-cells are only activated when they receive two signals: one from the T-cell receptor, and one from costimulatory molecules

two signals formation:

When only signal 1 is present, T-cells can become tolerant, lacking energy, or undergo apoptosis. 

After your walk you will feel as if you’re dying but you must listen to two messages 

T cells receive two independent signals for full activation. The first signal is an antigen-specific signal from the T-cell receptor (TCR) binding to an antigen. 

the ability of an immune system to distinguish between antigens and to identify "self" from "non-self"

One message is something that originated in the mind and was forgotten and the other is foreign

Keep your wits about you

The second signal is mediated by cytokines or co-stimulatory molecules. 

Co-stimulatory molecules are targets for immune modulation

the process of changing the body's immune system to make it more effective or less effective

The First of Three Stages is Complete 

Now to make changes to one’s character

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