e-den biology

An Organism's Body

An organism's body provides the interface between the biological domain and the physical domain. Each organism's visible body is a chain of adjacent atoms with optional bends. Related to this, and inhabiting biological space, is a more abstract body, the skeleton. The skeleton is a string of digits in which digits 1-6 correspond to visible atoms and digits 7 or 8 constitute left- or right-hand bends or joints. Different skeletons can give rise to the same apparent body: for example, the sequences 1234 and 123784 both give rise to a straight chain of atoms (1-2-3-4) but, in the latter case, two joints are hidden, invisible for the moment because the left and right bends cancel each other out. The joints in a skeleton are moveable; they can be swapped with adjacent digits in either direction and the result is a change in the organism's shape. This action is known as 'wriggling'. For example, a body of the following structure:

......24444...

......2.....4...

......3.......

is likely to have the underlying skeleton: 3228444484.

The orientation for this body begins at 'north' (the default orientation) for the first digit and is changed to 'east' by the first right turn and then to 'south' by the next right turn. For this body, legitimate wriggling actions involving the first joint are as follows:

3228444484 > 3282444484 ( headwards wriggle )

3228444484 > 3224844484 ( tailwards wriggle )

For juvenile organisms, there is another fundamental difference between its physical body and its abstract skeleton. The physical body begins life as a single digit, even though the skeleton is completely developed during the organism's time as a spore. Gradually, digit by digit, the physical body is extended to match the hidden skeleton and when this process is complete the organism is an adult.

An Organism's Actions

At any one moment, an organism may move its body as a whole without changing shape, wriggle one of its joints or stay still. When the organism moves as a whole, it is usually limited to single space movements either vertically or horizontally. Typically, the result of a wriggle is that part of the organism moves one space diagonally while the rest stays still. Thus, almost whatever action the organism chooses, it stays within the zone cleared by its force field. The neurological control of movement and wriggling is discussed later but, in brief, all joints may be considered as having tension, a tendency to move either headwards or tailwards, and the joint with the strongest tension is allowed to move in its favoured direction whenever the organism passes up the chance to move as a whole.

There is an important exception to the general rule that all organisms move within the single space cleared by their force field. An organism may move two squares at once if it displays a very strong neurological tendency to move in a particular direction. More precisely, it is granted a double move if the tendency parameter for that direction exceeds 100, indicating that the relevant motor neuron has fired at least twice in one biological moment (as discussed on the neurology page ). This is known as sprinting and represents a recent modification of the e-den rules. It is useful for herbivores trying to flee a carnivore or, conversely, for carnivores chasing their prey. It comes at a cost, however. The second stage of the double-space sprint move carries twice the energy penalty of a normal move, so that the overall penalty for the two spaces is three times that of a single move. More seriously, for herbivores, their digestive mechanisms are disabled during sprinting, on the basis that, in real biology, it would be unlikely that any animal could graze and flee at the same time. Thus, as long as an organism is sprinting, it is burning energy rapidly with no chance of replenishing it. For herbivores that are crashing through digestible barriers, relying on their three-atoms to eat out a path for them, an accidental attempt to sprint might mean that the organism crashes into an otherwise digestible object. Recalling that three-atoms may push away inanimate fours, this leaves five and six atoms as potentially dangerous obstacles that have the curious property of allowing the passage of non-sprinting herbivores but not sprinters.

All movements, including sprinting, lead to a decrement of the organism's rest parameter. Conversely, staying still increments the parameter. This parameter ranges from zero (exhausted) to 1000 (fully rested). The rest parameter climbs rapidly between 0 and 500, with each still moment allowing it to increase by 5, but more slowly thereafter, with each still moment increasing it by only 2. Normal movement decrements it by 1 unit per space moved but srinting decrements it by 2 units per space.

The rest parameter reflects the immediate availability of energy to the organism and its decline represents a process of fatigue. At low values of rest, the organism has to pay a higher metabolic cost for its existance and also suffers a risk of 'movement failure' due to exhaustion. Movement failure is a probabilistic process and may prevent a normal single space move from succeeding or may prevent the second move of an attempted sprint. This becomes increasingly likely as rest falls below 100, becoming a certainty when rest is zero. If an organism tries to sprint but fails because it is exhausted, it still pays the higher energy premium. The steady decline of the rest parameter with sprinting means that all organisms have a limited sprint range and this is longer if the organism starts its sprint from the fully rested state.

Apart from wriggling or moving as described above, a juvenile organism has another option, that of growing by one digit at its tail end. This action is known as 'extending'. A new organism begins life as a spore (*9), hatches into a single digit juvenile and then gradually extends its physical body to match that of its hidden skeleton, paying for the creation of the necessary atoms by burning metabolic fuel. The hidden skeleton may be wriggled even before it is incarnated into physical atoms, so the juvenile may extend into shapes that differ from its genetic siblings. The actual sequence of atoms cannot be altered, however.

Once an organism reaches adulthood (its body is fully extended and matches the skeleton specified by its genes), it may attempt to sporulate or mate. Sporulation involves the creation of a single asexual spore a few spaces south of the organism's body. Mating involves the transfer of genetic information through a point of contact with another consenting organism and the production of a shared spore below the mating pair. Both processes are discussed in more detail later.

Adults may also convert stored energy into atoms, depositing the new atoms near their tails. The new atoms are placed one space outside the clear zone in whatever direction the tail is currently pointing, but only if the square is empty or contains grass. This action is called "dropping" and can be used to create food dumps, barriers or even messages. An organism may drop any atom in the range 1 to 6 (the edible atoms) and can also drop a zero, thereby erasing the current contents of the selected space (provided the erased atom is in the range 1 to 7).

At any one moment, then, an organism faces the following major choices, most of which are mutually exclusive: move, wriggle, extend, drop, sporulate or mate. All of these have visible effects on the physical world of the Grid. The organism's other effects on the Grid are as follows:

It may knock atoms aside, or destroy them if there is no vacant space to receive them.

It may consume matter adjacent to its *3 atoms.

It may kill other organisms if its force field is unfriendly, or be killed in the attempt.

It may change the appearance (but not the actual mass) of its *5 atoms.

Functions of Individual Body Segments

In many ways, the digits of an organism are not really analogous to atoms because they each enable specific activities: *3s digest, *4s wound or kill, *5s signal and so on. In many ways, charged atoms are more like cells or even whole organs, as summarised below:

one hearing

two eye

three digestive organ

four weapon

five signalling

six bone or armour

seven left-joint

eight right-joint

nine spore

zero not allowed

In other ways, though, the atoms of an organism are not like organs. They are the simplest indivisible elements of e-den and their basic features are not modifiable by the arrangement of smaller parts. For example, no amount of evolution can improve upon the 90% efficiency of a *3-atom's energy conversion. What evolution can do, however, is improve upon a species' grazing techniques or alter the physical shape of an organism to maximise the chance that the *3-atoms are brought into proximity to the food. Similarly, the range of colour values a *5-atom may adopt is limited to integers between *1 and *8, and no *5-atom can ever do better than that. An organism is free, however, to use that capability for camouflage or communication or any other purpose evolution can discover. The amount of visual information striking each 'eye' cannot be increased but the sophistication of the visual processing can be improved indefinitely.1

With that in mind, the features of each possible body segment can be considered...

Ones are the cheapest bodily segment to produce, in terms of metabolic cost, and are useful for connecting more important parts of the organism. To be sensitive to the vibrations produced by other organisms - to hear, in other words - an organism must contain at least one one-atom. As the lightest possible body segment, however, they render an organism vulnerable. When an organism attempts to move against an atom it cannot push away, it faces a loss of physical integrity and subsequent death. A *1-atom is unable to push away any neutral atom more massive than a 2 and thus represents a weak area of the organism's field. When any other body segment is injured, by virtue of a breach in the organism's force field by an atom too massive to repel, the injured segment degenerates into a *1-atom, losing any special attributes it had previously.

Twos allow an organism to 'see', provided they have the appropriate neurological wiring to make use of the information. Conceptually, we could think of each atom in the Grid as emitting four information rays, one in each of the cardinal directions, and the eyes of an organism intercepting these rays. Or we could think of the eyes sending out their own rays in the four cardinal directions and reading the reflections that bounce back to them, like radar. The programming corresponds more closely with the second mechanism but the two mechanisms are operationally equivalent.

It should be apparent that Bugs cannot see along diagonals. Thus, it is not hard for one Bug to hide from another. (Hearing, which works in all directions, can compensate for this limitation to some extent.) As the second lightest possible body segment, two-atoms are almost as vulnerable as one-atoms when it comes to collisions. Thus, it is not generally wise for an organism to lead with its eyes when it moves, unless it is confident no obstacles lie immediately ahead.

Threes are virtually essential for any member of the Grid. They allow an organism to convert adjacent neutral atoms into energy and thus provide the organism with fuel for its various activities. (The only other way an organism can obtain energy is by coming into contact with a second organism and killing it, gaining the victim's energy stores in the process). Three-atoms perform their mass-energy conversion with 90% efficiency, so that 90% of the energy units associated with each consumed atom are made available to the organism as energy. These units are initially stored within the organism as a parameter called 'energy' which is interconverted with a more long term form of energy storage, known as 'metabolic fuel' or, more simply, as 'metab'. When the short term stores of energy are full, a conversion to metab takes place with 50% efficiency. For each moment of its existence, an organism pays an energy cost based on its size and the extent of its recent activity. When the short term stores are empty, the long term metabolic fuel is reconverted to energy, again with imperfect efficiency (70%). An organism can minimise these costly conversions by topping up its short term stores more frequently.

Fours are the principle weapon available to Bugs in conflict. They specifically interfere with the force field of other organisms, rendering them up to 100-fold weaker in the event of a conflict. They must be part of the 'primary contact' to have their maximal effect, however. When one organism contacts another, and multiple segments of each organism are adjacent to multiple segments of the other, the most headwards segment of the older organism is considered the first segment to make contact. This first segment, and the nearest segment of the other organism, constitute the primary contact between the organisms. If both organisms have non-permissive or minimally permissive force fields (i.e. are unfriendly), then the primary contact is used to determine which organism survives the encounter. The presence of a four-atom anywhere in the organism's body weakens its neighbours field by a factor of 10. If it is part of the primary contact it weakens it by a further factor of 10. The mass of the contacting segments, the size of each organism and their metabolic well-being also contribute to strength of each field. If one field is highly permissive (friendly) and the other is frankly unfriendly (friendliness<0), then the highly permissive field will be damaged and the friendly organism will die. It is much safer, then, for any single organism to maintain a highly unfriendly force field. Such a strategy, though, would inevitably kill siblings and would make sexual reproduction impossible. If all the organisms in a region are friendly, then contact between them is harmless and the fours they bear are irrelevant. Furthermore, if two or more consenting organisms touch, their combined forcefield is strengthened as though they each had claim on the total stored energy between them (known as the 'pact' effect). Two or more weaker organisms could therefore potentially resist attack by a larger organism.

Fives are signalling elements that can adopt the colour of any charged atom from *1 to *8. An organism can control up to ten different five-atoms, any of which may adopt a different appearance (software extensions will probably increase this limit). Five-atoms may be put to many uses, most obviously for communication or camouflage. It should be noted, though, that fives cannot adopt the same signal as neutral matter, and so cannot completely mimic the inanimate environment.

Sixes, by virtue of their high mass and charge, are the least susceptible body components to damage. Also, in the event of contact with another organism, they are, after a four-atom, the most advantageous segments to have as part of a primary contact. They may push away any inanimate matter that has been left behind when another organism dies (1-6, or 'organic matter'), and even push away the lightest of the 'inorganic matter' 7s. They also have a specific ability to momentarily increase their repulsive force, allowing the repulsion of 8s. Unlike their ability to push away atoms of mass 1 to 7, this ability must be recruited, at significant energy cost, by the firing of a particular neuron in the organism's brain.

Sevens and eights constitute the organism's joints. They allow the organism to wriggle, to change shape, or to sweep its tail end through a region without paying the metabolic cost of a whole body move. Each joint is associated with two 'muscles', a headwards muscle and a tailwards muscle, which ratchet up the tension in either the headwards or tailwards direction each time they contract. Whenever an organism elects not to move as a whole, the joint with the greatest tension at that moment moves in the appropriate direction to reduce the tension. The body changes shape as described previously. Sensory neurons ('proprioceptors') keep track of each joint's displacement from its starting position so that the organism, if it is wired appropriately, can maintain an awareness of its current shape. Sevens and eights never appear as charged atoms, and do not leave behind neutral atoms in the event of an organism's death. Any apparent *7 or *8 in the Grid, therefore, must actually be a *5-atom.

Nines, both charged and neutral, are special entities in the Grid. Charged nines, or spores, have the highest force field of any single atom and protect valuable packets of metabolic fuel and biological information deposited by other organisms. After a few moments they 'hatch' into single-digit juveniles. Prior to hatching, they are passive, motionless entities with maximally unfriendly force-fields. They contain no energy but usually have generous supplies of longer-term metabolic fuel, provided by their parent(s) during sporing or mating. They behave as local sinks for similar concentrations of metab and genetic information, so that, if an organism attempts to deposit a new spore in the close vicinity of an existing spore, the attempt will lead, instead, to the donation of metab and information to the existing spore. The new metab is simply added to the old; the new genetic information, however, is merged with the old to produce a new genome derived from both of the original genomes. This process is exactly the same as that which occurs in mating and thus represents an alternative method for organisms to reproduce sexually: they can simply lay their spores close together and the spores will combine automatically. No gender is inherent in this process and the sequence in which the spores are deposited is irrelevant.

If spores die before they hatch, they degenerate into *6s, and thus leave behind an edible piece of matter. (They are, in that sense, really *6s with their force fields temporarily boosted to provide them with a protective shell).

Neutral 9s, then, are not dead spores. They are a special entity that cannot be generated, moved or destroyed by any organic process except, on rare occasions, to make way for a *9 which displaces them. They thus represent an essentially fixed feature of the Grid and are used, when the Grid is not connected to the internet, to construct its retaining border.

An Organism's Life Cycle

A new organism is either placed in the Grid by the user, in which case it is known as an orphan and begins life with the default metab of 10000, or it is deposited by one or two parents, in which case it begins with whatever fuel its parents donate. The size of its parents' donation is determined by their genes and, in particular, the value of a parameter known as metab-child. Once set, this parameter cannot be changed and so all of an organism's asexual offspring start with the same metabolic reserves.

The new spore hatches after a few moments (genetically determined), and becomes a single-digit juvenile that may at once begin to move, wriggle, fight and feed. The juvenile may also extend, upon the firing of a specific neuron, thereby increasing its body length by one digit at a time. When it is fully extended and its physical body matches its internal (genetically-derived) body plan, the juvenile becomes an adult.

An adult organism may similarly move, wriggle, fight or feed or, if it chooses - and if it has sufficient metabolic fuel - breed by one of three methods:

As a single parent. It may sporulate by depositing a spore a few spaces below it and transferring metabolic fuel and genetic information to that spore. The genetic information may or may not mutate during the transfer.

As a second parent. It may sporulate near an existing spore, so that the metabolic fuel normally passed into a new spore is instead added to the existing spore. The spore's existing genome, derived from its first parent, is then merged with a copy of the second parent's genome (This does not require consent from the first parent but all sexual reproduction requires that the organisms share the same "species designator" or name; this name is genetically determined).

As a co-parent. With force field set to friendly, it may make contact with another friendly adult organism and produce a shared spore by mating. The shared spore's genome is a merged copy of its two parents' genomes.

In theory, an organism may produce offspring indefinitely, topping up its metab between breeding sessions, but most organisms eventually die by one of the following mechanisms:

Starvation. If an organism's metab falls below a critical level (100 units per body segment), it cannot maintain its force field or other functions and dies.

Collision. If an organism attempts to move into a space occupied by a neutral atom and does not succeed in pushing it away, because the segment at the point of contact is not sufficiently high in mass, then its structural integrity is compromised, leading to death.

Conflict. If an organism comes into contact with another organism and either of them has an unfriendly force field, the conflict is resolved according to the segments at the point of contact and the size and metabolic well-being of each organism. One organism invariably dies, surrendering its energy reserves to the victor. If an organism with an unfriendly field contacts another with a highly permissive field, the permissive organism is killed. Contact is considered to have occurred if the two organisms have atoms adjacent to each other or if only a single space separates their closest atoms.

Organisms do not age in a metabolic sense, although they may accumulate injuries by moving close to objects that cannot be cleared from their force field. Provided the organism does not move further towards the offending object, the contact will not be fatal but the organism may acquire a wound in the compromised body segment. Such a wound leaves that segment with the mass and charge of *1, rendering the organism even more susceptible to collision injuries in future and impairing the organism's ability to fend off neighbouring organisms. The wounding process also removes any prior special functions that the wounded segment had: eyes are permanently blinded, fours are disabled and so on. In the absence of such wounds, death is not more likely in older organisms. In fact, adults of any one species are larger than juveniles and therefore have a slight advantage in the event of an unfriendly contact. In the Grid, a cautious organism could potentially live forever.