Lets Talk About The Inside
Brain: Provide an Interface of a Creatures Brain allowss the biochemistry to respond changes in the brain and also affects the dynamics of the brain.These Loci allow the biochemistry to model neurotransmitter chemicals in the brain that have various effects and vital for the learning mechanism inside Norns, Grendels, and Ettins. Creature: Allow the biochemistry to interface to the circulator, reproductive, immune, sensorimotor, and drive level systems inside creatures.Among other things, these loci allow the biochemisty to respond to enviormental changes such as air quality, heights, the gradient of slopes, and so fourth. Current Organ: Allow the Biochemisty interface to the organ system inside Creatures 2. Receptors can then monitor toxins inside the blood stream and adjust organs general state of health acordingly.
GENETICS OF NORNS
Unfortunately it is beyond the scope of current technology to model the process of genetics at a molecular level :-( . But the general principle of genetics-a set of instructions describing structures that create systems out of which behavior can emerge-is borrowed from nature in Creatures 2(yeah!!!:-))
Creatures Genotypes consist of a single haploid chromosome made up of about 800 genes (the genome). As a result of being haploid, the genome has to carry both male and female genes to avoid vital sex genes getting lost during the crossover process. When a creature is created,only the appropirately sexed genes are expressed :those from the other gender are carried but ignored.
Creatures 2 has 16 specific type of genes that handel biochemistry, organs, brain layout, and morphological specification.During successful mating between creatures, the chormosone from each parent is crossed and spliced to produce a new one made up of genes from both donors. To Prevent the loss of critical genes each gene is preceded by a standard header that indicates which of the following crossing over errors allowed in that gene.
Duplication: This indicates that a gene can be accidentally duplicated.
Mutation: This indicates that individual information pieces (codons) within the gene can be mutated.
Deletion: The gene can be deleted entirely.
The Probaility of mutation is also spectified in the header allowing for some genes to be more likely to be mutated than other genes. In addtion, the gene header contains another entry that allows genes to be carried but not expressed in either sex.
Bacteria and The Immune system
The immune/repair system inside a creature is handled by the spleen and the bones. The bones are responsible for repairing damged organs. The spleen responds to presence of bacteria in the bloodstream and pordouces antibodys to fight the infection. Bacteria in Creatures 2 can be directed by modern antigenes. Antigenes are a bit like flavors of bacteria, and a different antibody is required to defeat each one. Once the spleen has produced enough antibodys, the infection is defeated and the bacteria dies. The antibodys will remain for a long time, so the creature will be effictively immuned to the infection, just as we humans catch a diease such as chicken pox 2 times. There are 8 different antigenes in a creature, and 8 corresponding antibodies used to attack them. This Process is handeled by a number of chemical reactions, and it is possible to examine these genes using the advanced science kit. Obviously, if the spleen are the bones are damaged, the body is unable to fight infections are repair itself after damage. This is a Sort of Immune system Deficiency problems similar superficial effect to viral infection such AIDS where a creature can not defend itself from bacterial infection.
Toxins
As well as damage that can be caused by physical injury and bacterial infections, there are a number of other toxins that can cause specific damage. In the case of these toxins, the spleen is useless as a defense mechnasim because toxins do not emit antigenes.These toxins are shown in the tabel below.
TABLE OF TOXINS
Name: Descripton
Radiation: Creatures exposed to radiation will get heavy metals in their blood streams. Heavy metals damage the bones, and hence the organ repair mechanism. The Treatment for radation is a compound called EDTA, or ethylenediaminetetracetic acid.
Geddonase: This breaks down adipose>Adipose is a Creature's very long-term fat storage. This reaction releases a small amount of glucose./i>
Glycotoxin: This breaks down glycogen, which Creatures use as an emergency energy store. Injecting the infected creature with arnica acts as a cure.
Cyanide: This stops the Creatures heart. The cure for this is sodium thiosulpthite (big words in here isnt a bit complicated dont worry youll get used to it :-))You can normally keep a Creature alive by continuously injecting the defibrillant mixture using the Syringe tab in the Science kit applet until cyanide decays (about 15 secs). A better treatment is a combination of defibrillant and sodium thiosulphite.
SleepToxin: The name speaks for itself no cure for it do it just makes them sleep no damage and it wears off pretty quick.
Fever Toxin:This shuts down the skin organ, making it hard for the creature to cool itself which leads to overheating and finally dehydration which is not good :-(. This is a Result of Bacterial infection No cure at this time :0.
Belladonna:This slows down the heart.This reduces the rate of which ATP is produced, and can be fatal.
Adipose:This is not a toxin in normal conditions because it is a long-term fat store. However, In great quanities, The Creature is effectively obese, and this can lead to heart diease. Cure: Make your Creature work out and give him a diet!!!!
Gene Reference Chart
Creatures has 16 separate gene types divided amongst four separate groups. These groups are: Brain Genes, Biochemistry Genes, Creature Genes and Organ Genes. All gene types share some basic header information: § Sex. Norn D-DNA carries both male and female genes. Some genes can be active for one particular sex only (i.e., the reproductive system), and others are for both (such as the digestive system, immune system, etc.) § Mutability. Most genes can be mutated, deleted or duplicated during the breeding process. Some critical genes may not be manipulated in some ways, specified in the mutability box. Those that can be mutated can be mutated to varying degrees. § Switch-on time. This dictates which of the seven life stages switches on this gene. To be on at birth, it should be set to “Embryo”. § Do not express. A gene can be ‘silent’, or carried. This means that it does not contribute to the creature’s phenotype at all, but is potentially available for future generations through mutation of the ‘do not express’ option. The gene types and their descriptions are shown in the table below. Type and sub-type numbers are shown in parentheses after the name: Gene Type Gene Sub-Type Gene Description Brain Genes (0) Lobe (0) Defines a brain lobe. (10 in generation 1 creature)The Brain Lobe is the most complex gene type. Click here for further information. Organ (1) The brain organ. (1 in generation 1 creature)Only one of these is allowed per creature. This organ is similar to the body organs, but contains the brain lobes. When this organ’s life force reaches zero the creature dies. Bio- chemistry Genes (1) Receptor (0) Chemical receptor. (183 in generation 1 creature)This binds to a named location and “fires” that location according to the concentration of the chemical it monitors. Receptors are used throughout a creature’s systems. Emitter (1) Chemical emitter. (63 in generation 1 creature)Binds to a named location and emits an amount of a specified chemical—the concentration depending on the value of the locus to which it is attached. Reaction (2) Chemical reaction. (117 in generation 1 creature)Specifies a chemical reaction and the amounts involved. Chemical reactions are in the form IA + JB => KC + LD, where A, B, C and D are chemical numbers and I, J, K and L are the concentrations involved. All reactions are allowed except nothing => something. The reaction rate can also be specified, the approximate half-life of which is shown in the status bar. Half Lives (3) Chemical Half-lives. (1 in generation 1 creature)There is normally only one of these genes, and it specifies the approximate half-life (the time in which it takes for a chemical to decay to half its initial concentration) for each chemical. Initial Concentration (4) Chemical initial concentration. (22 in generation 1 creature)This gene allows a fixed dose of a chemical to be present when the gene switches on. It is these genes that allow us to give newborn Norns energy (glucose and glycogen) and natural immunity (a low dose of antibodies). Creature Genes (2) Stimulus (0) Stimulus. (39 in generation 1 creature)Emit variable amounts of up to four chemicals when a given stimulus occurs. This allows a creature to feel pain when it bumps into a wall, for example. Genus (1) Species. (1 in generation 1 creature)The only compulsory gene (although many others are required to make a viable life-form). This gene specifies the species of creature and the mother and father’s genetic moniker.) Graphic appearance ID. (5 in generation 1 Appearance (2creature)Describes which of the possible graphic sets are used to make up any given area of the body. Initially, five are specified: Head, arms, body, legs and tail. Pose (3) (242 in generation 1 creature)Describes the graphic location information for a Norn to get into any given “pose”. There are four walking poses, for example, which are cycled in an animation specified with a “gait” gene (see below). Gait (4) Specify pose sequence. (15 in generation 1 creature)Specifies the poses required to move through a given sequence. For example, there is a gait for normal walking. Different poses switch on at different times to replace these with “older looking” walking sequences as the creature ages. Instinct (5) Creature instinct. (44 in generation 1 creature)Instincts encourage creatures to perform a certain action at a certain time. An example instinct is the one that helps creatures to avoid overcrowding. Instincts are “taught” to creatures whilst they sleep. Click here for a detailed explanation. Pigment (6) Pigmentation. (12 in generation 1 creature)Refers to a colour and the concentration of that colour. Colours can be red, green or blue. Pigment bleed (7) Pigmentation modification. (12 in generation 1 creature)Allows the colours of a newborn Norn to differ slightly from its parents, while still being based on inherited characteristics. Organ Genes (3) Organ (0) Organ. (20 in generation 1 creature)Organs house the chemistry genes – reactions, receptors and emitters. They regulate the rate at which these chemical functions run. TOTALS: 16 separate types 787 genes total in generation 1 creatureFemale specific genes: 30 Male specific genes: 12In most cases, existing Norns use the sex specific genes for reproductive systems.
Terms and Words Used
Macro When the Creatures program is running, it is possible to issue it commands and instructions from outside the program. The same language used for this, is also used by the agents (Norns, plants, toys – in fact, every object in Creatures is an agent) inside Creatures to define their properties and behaviours. It is therefore possible to create new agents, and inject them into Creatures without Creatures having to know anything about the agents in advance. Macros can be issued from the Export page. Caption File Creatures genetics are long sequences of numbers that are interpreted as construction details for biological structures. These numbers are not easily interpretable by human eyes, so the Genetics Kit provides a way of creating “Caption Files” that allow individual user-typed descriptions to be viewed along side individual genes. The Genetics Kit gives you the option to store a separate caption file for each genome, or use the default caption file for the current species (Norn, Grendel, etc.). To use default caption files, select Advanced Options from the Advanced menu and check the appropriate check-box:As shipped, the Genetics Kit will attempt to use unique caption files wherever they exist, falling back to the default files if necessary.Caption files are stored on disk with the “.GNO” extension. The default files are called “species.GNO” where species is either “Norn”, “Ettin” or “Grendel”. They are stored in the Genetics Kit application folder. Unique caption files are stored in the Creatures Genetics folder, and are “moniker.gno” where moniker is the four character genetic ID.
Digital DNA
Digital DNA describes the genetic system used in Creatures. It differs from real DNA, which is a biochemical construction, but achieves the same thing: a set of simple instructions that can be used to construct a complex biological system. Genome A complete set of Digital DNA genes to describe the construction of an entire creature. Genomes are stored as files on disk with the “.GEN” extension. They are kept in the Creatures Genetics folder. Each creature (from the ones on the egg disk to the Grendels) has its own separate “.GEN” file. Gene One single individual instruction. In the case of nature, a gene is made up of nucleotides, which in sets of three specify the amino acids that construct one protein. Many of these will be required to build one living cell. In Creatures, there are 16 different gene types, in three classes. These are used to construct different biological systems ranging from chemical receptors to brain lobes. A typical Norn will have around 790 genes, whereas a human being has around 100,000. Moniker Genomes are identified with a 4 character alphanumeric code called the Genetic Moniker. You can identify the moniker for a creature using the Science Kit applet inside Creatures by using the “Genetics” page:Having identified the moniker (in the case of the above illustration, 1UEV), that genome can then easily be loaded into the Genetics Kit:1. Select Load Genome from the File menu.2. Find the file “Moniker.GEN”. With the Norn in the above picture, that would be “1UEV.GEN”.3. Select and load that file.The above procedure can be used to load the genome for any Norn you have or have previously had in Albia.
The Norn Genome
A “Generation One” Norn (from an egg in the Hatchery) consists of approximately 790 genes. Unlike human beings, who carry two of each gene (one from the mother, and one from the father), a Norn carries only one of each gene. Some of these genes are specific to a certain sex, so in a male Norn, the female genes will be carried, but not actually used. The “Generation One” Norns have 12 female specific genes, and 8 male specific genes. When Norns breed in the wild, the genomes from the mother and father are laid out next to each other, and genetic material from one parent is exchanged with material from the other. The points along the genome where the exchanges take place, and the number of genes exchanged are random and occasionally there will be “crossover errors” which could result in individual genes being lost or duplicated. This process generates two new genomes, one of which is male, and the other is female. During natural births, the choice of which of these to use is random, whilst a Genetics Kit birth leaves the choice to you. The result of this is that a new Norn egg inherits a combination of genes from the father and mother together with some potential mutations and errors. Norns have 16 different gene types, each containing varying amounts of genetic information. Genes are broken down into four basic categories: 1. Brain Gene. Definition of brain lobes, neural dynamics and dendrite properties. 2. Biochemistry Genes. Chemical receptors, emitters, reactions, half-life and initial concentrations. 3. Creature Genes. Stimulus, species, appearance, poses, gaits, instincts and pigments. 4. Organ Genes. Organs contain biochemistry components such as reactions, emitters and receptors. The Genetics Kit allows all of these Genes to be viewed, and most can be edited. In addition, genes can also be either added to the genome, or removed entirely. Click here for a summary of the different gene types.
Creating New Genes
To create a new gene, click on the New Gene button from the Gene Editor page: If you are starting from a clean genome (i.e., no genes loaded), the Genetics Kit will ask you if you wish to create a species gene (the only compulsory gene). Read the notes before trying to create your own genome from scratch. If you are adding new genes to a genome that contains at least one gene, the following window will be opened: Clicking on the drop down box will reveal a complete list of gene types that you can create. These fall into four categories, Brain Genes, Creature Genes, Biochemistry Genes and Organ genes. You can use the Create button to make new genes whilst leaving the new gene window open. This allows many genes to be added at once. Example: Making a green Norn As a demonstration of the Genetics Kit, here are the instructions to creating a green Norn: 1. Load up any D-DNA file into the Genetics Kit 2. Go to the Gene Editor page and click on the Type line to sort the list by type. Scroll down the list until you find the “Creature: Pigment” genes. There should be twelve of these in a generation one creature 3. Edit all of the “Green pigment” genes (See under the “description” column) and move the slider up to “bright” (the right hand side) in each case: 1. Now edit all of the “Blue pigment” and “Red pigment” genes (four of each) and turn the slider right down to “muted” (the left-hand side) in each case. 2. Click on the Export tab, check Virgin Birth, ensure Creatures is running and click on the Lay Egg button. 3. Drop this egg in the incubator, and in a few seconds you’ll have a very bright Kermit green Norn!
Creatures: Chemicals Summary
The biochemical modelling system inside Creatures supports 256 arbitrary chemicals, each of which can vary from being not present (a level of zero) to maximum concentration (a level of 255). To help keep track of these chemicals, each can be assigned with a name and description. These names are then used to select chemicals on the biochemical monitor page in the Science Kit applet, and also here in the Genetics Kit. Out of the possible chemicals, just over half are used in “generation one” creatures. Over several generations, it is possible for some of the other chemicals to come into use by mutation. New chemical names can be assigned in the Genetics Kit using the Biochemistry Page, and then used for new chemical reaction genes. You can also edit their names and descriptions. Be careful when deleting chemicals, as you may lose the ability to see them in the Science Kit if they were already in use. New objects/agents can also make use of any new chemicals.
Creatures: Poses Summary
Creatures supports a total of 256 different “poses” for creatures. These are numerical representations for the positions that creatures can get into in order to interact with their environment. Pose 77, for example, describes the body position for death. A total of 155 poses are used in first generation Norns. The Genetics Kit has a specific page for editing and viewing the pose names. Adding a new pose name will not create a new pose. A new pose must be specified genetically. The pose naming system simply provides a method for assigning human-friendly tags to pose numbers. For new poses to be valid, appropriate genes must also be created. The pose sequence requires each body part’s position to be specified numerically, a task made much simpler by the Creatures Pose Editor. For poses then to be used by a creature, they have to either be incorporated in a gait that is used by the muscle organ, or used by a macro script that acts on the creature. Brain lobe Defines a brain lobe. (10 in generation 1 creature) Information stored in this gene includes the number of neurones and their individual dynamics. This is the most complex gene type to set up. Each neurone has two classes of dendrites, which can have different dynamic and connection properties. There are two pages per dendrite class, one for the growth and one for dendrite dynamics. Two further pages (General and Cell Body) describe properties of the entire lobe, such as the number of neurones, and neurone state rule:
General
Defines general properties for this brain lobe, and has the common mutation controls. The positioning and dimensions of the brain lobe can be specified here. A lobe number is automatically calculated and shown top right.
Cell Body
Specifies neurone properties. A neurone will fire if its state rises above the threshold. A special rule called an SVRule (State Variable Rule) is applied to calculate the new state of every neurone each “tick” (about 4 times a second in Creatures). Flags 2 to 4 are un-used. WTA stands for “Winner Takes All”. This means that all but the strongest-firing cell in the lobe is suppressed. Used for Decision and Attention lobes to decide which action or object wins the vote.
Dendrites
Each of the two classes of dendrite have the following two pages: (D0 is Dendrite Class 0, and D1 is Dendrite Class 1): Dendrite Growth · Source Lobe. Specifies the source lobe for the dendrite connections for these dendrites. · Dendrite Properties. Specifies the distribution of dendrites, and the minimum and maximum allowed. · Initial Attachment. Specifies properties for how dendrites wire themselves to neurones. · Migration Rules. Specifies the conditions under which dendrites migrate and find new connections. Dendrite Dynamics · Atrophy and Consolidation. Information covering the atrophy and strengthening properties for dendrite connections. · SVRules. SVRules specifying an optional expression that affects the reinforcement, susceptibility, back propagation and forward propagation of the dendrite. · Strength Adjustment. SVRules to adjust strength of dendrites.
SVRULES
State Variable Rules (or SVRules) are genetically defined functions that are used throughout a brain lobe structure to control several aspects of synaptic behaviour, as well as to compute a neurone’s state.
State Variable Rules are composed of interpreted opcodes and operands. Each SVRule expression is designed to be interpreted extremely fast (as each neurone’s state needs to be calculated, as well as other synaptic behaviours such as the dendrite relaxation functions, for example), non-brittle and “fail-safe”—genetic mutations must never cause syntax errors.
SVRules can compute new state values in many ways. A considerable amount of the possible functions go well beyond the present needs of the brain model in Creatures, giving great scope for alternative brain structures.
SVRules for brain lobes are defined on the various pages of the brain lobe gene. When a State Variable Rule is edited, this window appears:
The SVRule can then be edited by using the drop-down boxes. The expression can consist of up to twelve operands and opcodes, with the “
Brain organ
There is one brain organ per creature, which contains a number of brain lobes, specified in the lobe genes. The organ gene is responsible for specifying the physical structure that holds the brain, and is the target of any injury to the brain. A creature is defined as dead when this organ dies.
Instincts Summary
Instincts allow creatures to be taught that doing a particular action given a certain situation is either bad or good, without the creature having to go through the experience itself. This allows important concepts to be “pre-taught” to Norns, Ettins and Grendels to affect their initial behaviour.
Instincts are used for many purposes. These include teaching Norns to retreat when overcrowded, or to do something when bored and eat when seeing food. A typical instinct gene may look like this:
Instincts are processed when creatures sleep. If a creature does not sleep, its instincts will not be learnt.
During sleep, Creatures detaches the brain from any outside stimulation. The sensory inputs specified in the Instinct gene (“When this is true” frame, in the picture above) are then fed directly into the creature’s brain. The action specified in the instinct gene is then fired, and the action connected dendritically through the concept lobe to the sensory inputs. The dendrites involved are then strengthened, and the weights increased according to the reward or punishment specified in the instinct gene.
The creature will then form neural connections that are likely to respond should the scenario specified in the instinct actually arise when the creature is awake. This allows many scenarios to be presented to the creature’s brain, in advance of them occurring in real life.
Many instincts switch on at different life stages. Instincts are used to influence and encourage mating behaviour, for example.
An instinct will not guarantee certain behaviour in a given situation, it can only influence and encourage, as it will integrate itself with the existing neural structure the creature has.
Organs How they Work
Organs are a new feature of Creatures2. Just like real-life organs, they contain biochemical functions, and can be damaged by disease, and repair themselves. In a generation one Norn there are 20 organs, although one of these is female-only. The more organs a Norn has, the more ATP it will use up.
Just like the other genes, the organ genes can be mutable, allowing Creatures to accumulate new organs for new functions. The gene appears like this:
The “Clockrate” determines how frequently the contained biochemistry will be updated. The further to the right the slider bar is, the more frequently the biochemistry will be updated. It is possible for a receptor to speed this up, or slow it down.
The “Organ vulnerability” sets how fast the Long Term Life Force moves towards the Short Term Lifeforce. The lower it is the more resistant the organ will be to damage (see below for a more complete description of this system).
The “Lifeforce start value” determines how sturdy the organ is at birth, and how much damage it can take before it dies.
The “Biotick start” is a way to co-ordinate the genesis of organs during development, so their functions switch on in the right order.
The “ATP damage coefficient” defines how dependent on ATP the organ is. ATP is the energy source for chemical reactions, receptors and emitters, and when it runs out the Creature becomes unconscious, and the organs start to degrade, being injured at a speed determined by their damage coefficient.
Organs allow biochemistry genes to be regulated in groups based on their common function. An organ will “contain” and regulate all the biochemistry genes following it in the genome, up until the next organ gene. The organ clockrate has a locus which receptors can attach to, and so it can be regulated according to a chemical level for instance. This allows reactions to be sped up or slowed down to maintain a constant chemical concentration, and deal with fluctuating conditions.
NOTE: if an organ’s clockrate ever falls to zero, the biochemistry that it contains will never be updated again, so the organ will be effectively dead. It is therefore important when setting up organs that their clockrate can never fall to zero.
Organs can be in a healthy or damaged state, determined by their Short Term and Long Term Life Force values. Organs can take damage from diseases or physical injury, lowering their Short Term Life Force, and producing Injury chemical as a signal to the immune system. When Short Term and Long Term Life Forces are apart, they move towards each other at a certain rate. The rate at which Short Term Life Force moves is generally faster than Long Term Life Force, and is open to regulation through a locus. This allows for organs to heal, at a rate which can be influenced by the biochemistry.
If an organ’s Long Term Life Force falls to zero the organ is declared dead, and the biochemistry it contains will never be updated again. In this way Creatures can lose some functions before others. For instance, it is possible for a Norn to catch a disease which kills their reproductive system, rendering the Norn infertile, but otherwise healthy. Once an organ has died there is no way to bring it back to life.
To increase the rate of healing, each organ has a locus called the ‘Repair rate’, which a receptor can attach to. The effect of this locus is to regulate the rate at which Short Term Life Force returns towards Long Term Life Force. In hatchery Norns this locus is regulated by prostaglandin, which is produced by the bones in response to Injury chemical.
COMING SOON RESPIRATION AND CARDIOVASCULAR SYSTEMS
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