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Spatial objects are things which occupy some piece of space (contrast 
integers and timeintervals). They typically have many properties 
which aren't spatial, but the purely spatial aspects of them can be 
divided into three kinds, all of which can change independently of 
the others. Not all spatial objects have all these properties and 
some may have others in addition.

1. The intrinsic shape of the object.
2. The location of the object in some larger reference space or region.
3. The orientation of the object in some larger reference space, or 
with respect to something else.

In order to be able to talk about orientation, we will adapt the 
notion of 'intrinsic shape' to include a set of intrinsic axes. So 
for example a cylinder with its main axis along the cylinder will be 
considered a different shape than the same cylinder with its main 
axis perpendicular to the cylinder. This requires us to split the 
notion of 'shape' into two distinct notions:

A directed shape is a shape with between one and three mutually 
perpendicular axes 'rigidly embedded' in it. Particular examples 
include a directed surface, which has one axis (locally) 
perpendicular to the surface and two axes in the surface,  and the 
shape of a Ford Thunderbird with axes in the forward, upward and 
left-to-right directions. (Exactly what is meant by a 'shape' and an 
'axis' is given in more detail later. ) One key property is that 
moving or rotating an object does not change the directed shape, but 
other transformations (folding, bending, compression, twisting, 
forced conformity to another object, impacts, etc.) may change the 
shape. In general, an operation which changes shape is classed as a 
deformation. If a directed shape has more than one axis then the axes 
are ordered as primary, secondary and tertiary, conventionally 
labelled by the letters a,b,c respectively. They always form a 
right-handed set (if one were standing facing the primary axis with 
the secondary axis vertical, then the tertiary axis is on the right.)

A spatial extent is the piece of space actually occupied by an 
object, ie the piece of space which is filled up with the material 
which comprises the object. This is supposed to be defined relative 
to some larger reference space, so such pieces of space do not move 
when the object is moved (though they may move when the larger 
reference space is moved.) Any directed shape in a given orientation 
(ie with its axes fixed in affine 3-space) and at a given location, 
occupies a unique spatial extent, but two different objects can have 
the same spatial extent (though not at the same time).

A directed shape is symmetric about an axis if it occupies the same 
spatial extent when rotated about that axis.

Shapes and axes

We define shape in terms of planar approximations. (Smooth shapes can 
be regarded as limits of this approach, but for RKF textbook 
applications the distinction isnt likely to be important.) The basic 
notion is the simplest kind of directed shape, a directed surface.

A directed surface (edge) is a roughly planar (linear) piece of 
surface with a unit vector  perpendicular to its tangent(s). Another 
name for this is a side. Each piece of 2Dsurface defines two directed 
surfaces which have their unit vectors in opposite directions. 
Intuitively, a directed surface is one side of an abstract piece of 
2D space. (Each piece of 1-D surface (ie a line) defines two directed 
edges in any containing plane similarly, but there are infinitely 
many directed edges surrounding each edge in 3space.) Basic facts 
about directed surfaces are that they come in pairs, have opposites, 
and that surfaces of solid things are always directed outwards. For 
example, a cell membrane consists of two opposite sheets each of 
which has a hydrophilic side and a hydrophobic one, which are in 
sheetlike contact across their hydrophobic directed surfaces. So the 
membrane has two outward directed surfaces which are both hydrophilic.

(Another way to think about a directed surface is as a very thin 
surface-like region of space immediately adjacent to the surface on 
one side of it. If I paint a directed surface, this region gets 
filled with paint. Mathematically this region is the product of the 
surface with  its first spatial differential in the direction of the 
vector. This is the sense of 'directed surface' I used in the 
'liquids' axioms)

A shape is a set of pieces of directed surface (or directed edge) in 
a specified 3-dimensional (or 2-dimensional) arrangment. Idea is that 
one can move a shape around and its still the same shape, but if you 
move its parts relative to each other then it becomes a different 
shape. Particular shapes include eg a facial mask of Adolf Hitler, 
the shape of the letter A, and a particular configuration of an 
Alexander Calder mobile. Often we will not need to describe a shape 
in detail, only know that it has some global properties and bears 
some useful relation to another shape. Examples of global properties 
of a shape include contiguity (theres a path in the surface from any 
part to any other part) smoothness, roughness, angularity and so on, 
and  flat where all the pieces are coplanar; spherical, etc..

A key relationship between shapes is opposite, gotten by reversing 
the directions of all the directed surfaces and edges in the shape. 
Two shapes which are opposite can fit perfectly against each other so 
that each part of one shape is in contact with a part of the other 
and vice versa. A key fits part of the interior of a lock in this 
sense.

This concept of 'fitting' arises in the idea of  'conformity': one 
surface/object conforms to another if it takes its opposite shape 
when they are forced into contact. This is the essential core of the 
the soft/hard contrast: when you push 2 things together, the soft one 
distorts to fit the hard one. Examples include wrapping a statue in 
clingwrap, pouring paint onto a surface, and pushing clay into a 
mold. (May need to generalise this to a degree of fit, ie more pieces 
of surface are in contact than not. Good fit provides more contact 
places than poor fit. Perfect fit has them all. Example of perfect 
fit is liquid against a surface, as in making a casting from a mold, 
or making a cast of a face.)

An axis or direction vector is a vector which has a direction but no 
particular location or length (it is a unit vector in affine space). 
This means that it does not make sense to ask where in a directed 
shape its axes are located (through the middle or along the edge, 
etc.); they define only a direction and nothing else.

The set of all such directions forms a mathematical group with 
several generators, including normalised vector addition, rotations 
and reflection. The inverse operation in this group is called 
opposite. There is a tractable subgroup generated by clockwise pi/2 
rotations about an axis plus reflections, and this can be given a 
neat axiomatisation. This 'right-angle' group is sufficient to 
describe notions of parallelism, perpendicularity and some kinds of 
symmetry.  Using this we should be able to describe things like 
perpendicular attachement, lying parallel to a surface, rotation, and 
motions such as sliding, rotating, and tumbling.

Suppose opposite directions are denoted by the function opp and 
CR(x,y, z) means a pi/2 clockwise rotation about x transforms y into 
(what was) z. Anticlockwise rotation is got by applying opp to the 
last argument. The axioms are:
(opp (opp x)) = x
(implies  CR(x,y, z) (not (x=y or x=z or y=z)) )
(implies CR(x,y,z) CR(x, z, opp(y)))
(implies CR(x,y,z) CR(y, x, z))
(implies CR(x,y,z) CR(z, y, x))
(and maybe some more which I will try to get straight soon.)
  It follows from these for example that a pi rotation sends the other 
two axes to their opposites, and that a 2pi rotation is the identity 
function, and that if you face north, lie on your back, turn 
clockwise by pi/2 and then stand up, you will be facing west.

Some suggestions for assigning primary axes to shapes (all pretty obvious):
cylinder or rod - along axis of cylinder
plane - perpendicular to plane
hexalateral object - backtofrontaxis
blob - through object perpendicular to main side (ie use axis of main 
side as a surface)



Extents and locations and pieces of space.

We think of space as basically consisting of a collection of 
locations where something can be placed. These locations are defined 
with respect to a larger reference space which contains them all, 
called a region. Regions may themselves be places in some larger 
region, and locations or objects located in a region may themselves 
define other  regions for smaller locations. For example, the back 
right passenger seat may be a location in a region consisting of the 
interior of a car, which is itself located in geographical space on 
the surface of the planet, which is moving within the solar system.

Exactly what counts as a location is left open, but it should be 
precise enough to count as an answer to a question of the form 'where 
is x?'. Different notions of precision may be suitable in different 
contexts. We can allow only three-dimensional locations, or can allow 
things like 2d surfaces and lines and even points as locations. 
Locations may overlap and be included in one another, and may be 
hollow or arbitrarily shaped; or we may impose a coarse grid-like 
discipline on a set of locations in a region if that is more 
suitable. One basic relation between locations or pieces of space 
generally is 'inside', meaning that one location is entirely included 
in the other, and 'adjacent', meaning that the two pieces of space 
are immediately adjacent with no space between them. There are 
several alternative axiomatisations of thse notions already 
available, and we can probably get by with a fairly simple algebraic 
version like RCC8. Motion of an object (within a region) is 
conceptualised as change of its location in that region; notice that 
the region may itself be moving, so whether or not a thing is moving 
depends on the region (eg one can be moving at hundreds of miles an 
hour while asleep in an airplane seat).

(This ignores such issues as whether the reference region is an 
inertial frame, whether or not it has a gravity vector, and so on. 
Many of the Cyc concepts seem to have an implicit assumption that the 
reference frame is geographical space, but we cannot make this 
assumption for RKF.)

An extent is the most precise version of a location. The extent of a 
spatial object is the precise piece of space occupied by the stuff 
which comprises the object. For example, the extent of an ocean is 
the space completely filled with water (plus fish and other detria), 
while the extent of a plastic coffee cup is a thin, concave volume 
entirely filled with solid plastic. Extents may have a complicated 
structure; in particular they may have holes, cavities, etc, and may 
be not simply connected. Like locations in general, extents do not 
move: when an object moves it leaves one extent behind and fills up a 
new one. That is, we think of objects as moving through the larger 
space in which they move; but if they define a region (eg the space 
inside the empty cup) then that region moves with them. A 
prototypical example of this is a container, which when moved takes 
its contents with it. Relative to the container they remain in the 
same place, but that place itself moves along with the container.

We need extents to be able to talk about  rotational symmetry. An 
object is symmetric with respect to an axis if it occupies the same 
extent when rotated about that axis. For example, a cylinder with a 
longitudinal axis is symmetric wrt that axis. (Limited forms of 
symmetry can be described by the CR group, which cannot distinguish 
between the symmetry of a cube and that of a sphere. Neverthless I 
suspect this will be good enough for most of the cellular chemistry 
reasoning.)

Assemblies

Spatial things can often be made up from assemblies of other spatial 
things. A general thoery of this wojuld encompass all of structural 
engineering and solid geometry, but we can make some useful basic 
descriptions based on some simple shapes. For example consider the 
following shape classifications:
rod
ribbon
spiral
tube
2Dsheet
3Dblob
These can be assembled together in a variety of ways.. All the 
following arise in protein folding and membrane structure for example:

A rod can twist into a spiral
A spiral can be a tube
Several parallel rods can make a tube (with the same axis and length 
as the rods)
A folded ribbon can make a blob (with same width as ribbon but much shorter)
A folded rod or ribbon can make a 2Dsheet (like weaving)
A 2Dsheet can be rolled into a tube
A series of pieces can be linked by hinged or flexible joints end to 
end to form a foldable structure
A tube can pass through a 2Dsheet (ie be embedded in the sheet with 
its axis perpendicular to the sheet and each end in contact with the 
space on either side of the sheet.)
A foldable structure can be woven through a sheet from one side to 
the other and back again.

Detailed descriptions of these various possibilities can be given 
using the concpets developed earlier. For example, a hinge is a 
shared linear edge about which the two pieces can rotate. If they 
begin coplanar  then a pi rotation about the hinge will bring their 
original parallel faces into opposite orientation and adjacent. If 
they fit, then many pieces of these directed surfaces will be exactly 
opposite and adjacent, so any attraction between them will be 
reinforced (we here need an axiom about how many small forces can add 
up to a strong force, which may be tricky to state!) and this 
position will be stable. If this is repeated, many layers will be 
added to form a layered structure consisting of a 3dblob made of many 
2dsheets.

We are currently formalising a catalog of various geometric assembly 
and deformation processes which can be used to describe the cellular 
structures and processes in the text.



---------------------------------------------------------------------
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--============_-1243689214==_ma============
Content-Type: text/enriched; charset="us-ascii"

<italic><fontfamily><param>Times</param><bigger>Spatial objects
</bigger></fontfamily></italic><fontfamily><param>Times</param><bigger>are
things which occupy some piece of space (contrast integers and
timeintervals). They typically have many properties which aren't
spatial, but the purely spatial aspects of them can be divided into
three kinds, all of which can change independently of the others. Not
all spatial objects have all these properties and some may have others
in addition. 


1. The intrinsic shape of the object.

2. The location of the object in some larger reference space or
region.

3. The orientation of the object in some larger reference space, or
with respect to something else.


In order to be able to talk about orientation, we will adapt the notion
of 'intrinsic shape' to include a set of intrinsic axes. So for example
a cylinder with its main axis along the cylinder will be considered a
different shape than the same cylinder with its main axis perpendicular
to the cylinder. This requires us to split the notion of 'shape' into
two distinct notions:


A <italic>directed shape</italic> is a shape with between one and three
mutually perpendicular axes 'rigidly embedded' in it. Particular
examples include a directed surface, which has one axis (locally)
perpendicular to the surface and two axes in the surface,  and the
shape of a Ford Thunderbird with axes in the forward, upward and
left-to-right directions. (Exactly what is meant by a 'shape' and an
'axis' is given in more detail later. ) One key property is that moving
or rotating an object does not change the directed shape, but other
transformations (folding, bending, compression, twisting, forced
conformity to another object, impacts, etc.) may change the shape. In
general, an operation which changes shape is classed as a
<italic>deformation</italic>. If a directed shape has more than one
axis then the axes are ordered as primary, secondary and tertiary,
conventionally labelled by the letters a,b,c respectively. They always
form a right-handed set (if one were standing facing the primary axis
with the secondary axis vertical, then the tertiary axis is on the
right.)


A <italic>spatial extent </italic>is the piece of space actually
occupied by an object, ie the piece of space which is filled up with
the material which comprises the object. This is supposed to be defined
relative to some larger reference space, so such pieces of space do not
move when the object is moved (though they may move when the larger
reference space is moved.) Any directed shape in a given orientation
(ie with its axes fixed in affine 3-space) and at a given location,
occupies a unique spatial extent, but two different objects can have
the same spatial extent (though not at the same time). 


A directed shape is <italic>symmetric</italic> about an axis if it
occupies the same spatial extent when rotated about that axis.


Shapes and axes


We define shape in terms of planar approximations. (Smooth shapes can
be regarded as limits of this approach, but for RKF textbook
applications the distinction isnt likely to be important.) The basic
notion is the simplest kind of directed shape, a directed surface. 


A directed surface (edge) is a roughly planar (linear) piece of surface
with a unit vector  perpendicular to its tangent(s). Another name for
this is a <italic>side</italic>. Each piece of 2Dsurface defines two
directed surfaces which have their unit vectors in opposite directions.
Intuitively, a directed surface is one side of an abstract piece of 2D
space. (Each piece of 1-D surface (ie a line) defines two directed
edges in any containing plane similarly, but there are infinitely many
directed edges surrounding each edge in 3space.) Basic facts about
directed surfaces are that they come in pairs, have opposites, and that
surfaces of solid things are always directed outwards. For example, a
cell membrane consists of two opposite sheets each of which has a
hydrophilic side and a hydrophobic one, which are in sheetlike contact
across their hydrophobic directed surfaces. So the membrane has two
outward directed surfaces which are both hydrophilic. 


(Another way to think about a directed surface is as a very thin
surface-like region of space immediately adjacent to the surface on one
side of it. If I paint a directed surface, this region gets filled with
paint. Mathematically this region is the product of the surface with 
its first spatial differential in the direction of the vector. This is
the sense of 'directed surface' I used in the 'liquids' axioms)


A <italic>shape</italic> is a set of pieces of directed surface (or
directed edge) in a specified 3-dimensional (or 2-dimensional)
arrangment. Idea is that one can move a shape around and its still the
same shape, but if you move its parts relative to each other then it
becomes a different shape. Particular shapes include eg a facial mask
of Adolf Hitler, the shape of the letter A, and a particular
configuration of an Alexander Calder mobile. Often we will not need to
describe a shape in detail, only know that it has some global
properties and bears some useful relation to another shape. Examples of
global properties of a shape include contiguity (theres a path in the
surface from any part to any other part) smoothness, roughness,
angularity and so on, and  <italic>flat </italic>where all the pieces
are coplanar; <italic>spherical</italic>, etc.. 


A key relationship between shapes is <italic>opposite</italic>, gotten
by reversing the directions of all the directed surfaces and edges in
the shape. Two shapes which are opposite can fit perfectly against each
other so that each part of one shape is in contact with a part of the
other and vice versa. A key fits part of the interior of a lock in this
sense. 


This concept of 'fitting' arises in the idea of  'conformity': one
surface/object conforms to another if it takes its opposite shape when
they are forced into contact. This is the essential core of the the
soft/hard contrast: when you push 2 things together, the soft one
distorts to fit the hard one. Examples include wrapping a statue in
clingwrap, pouring paint onto a surface, and pushing clay into a mold.
(May need to generalise this to a <italic>degree</italic> of fit, ie
more pieces of surface are in contact than not. Good fit provides more
contact places than poor fit. Perfect fit has them all. Example of
perfect fit is liquid against a surface, as in making a casting from a
mold, or making a cast of a face.)


An axis or direction vector is a vector which has a direction but no
particular location or length (it is a unit vector in affine space).
This means that it does not make sense to ask <italic>where</italic> in
a directed shape its axes are located (through the middle or along the
edge, etc.); they define only a direction and nothing else.


The set of all such directions forms a mathematical group with several
generators, including normalised vector addition, rotations and
reflection. The inverse operation in this group is called
<italic>opposite</italic>. There is a tractable subgroup generated by
clockwise pi/2 rotations about an axis plus reflections, and this can
be given a neat axiomatisation. This 'right-angle' group is sufficient
to describe notions of parallelism, perpendicularity and some kinds of
symmetry.  Using this we should be able to describe things like
perpendicular attachement, lying parallel to a surface, rotation, and
motions such as sliding, rotating, and tumbling. 


Suppose opposite directions are denoted by the function opp and CR(x,y,
z) means a pi/2 clockwise rotation about x transforms y into (what was)
z. Anticlockwise rotation is got by applying opp to the last argument.
The axioms are:

(opp (opp x)) = x

(implies  CR(x,y, z) (not (x=y or x=z or y=z)) )

(implies CR(x,y,z) CR(x, z, opp(y)))

(implies CR(x,y,z) CR(y, x, z))

(implies CR(x,y,z) CR(z, y, x))

(and maybe some more which I will try to get straight soon.)

 It follows from these for example that a pi rotation sends the other
two axes to their opposites, and that a 2pi rotation is the identity
function, and that if you face north, lie on your back, turn clockwise
by pi/2 and then stand up, you will be facing west. 


Some suggestions for assigning primary axes to shapes (all pretty
obvious):

cylinder or rod - along axis of cylinder

plane - perpendicular to plane

hexalateral object - backtofrontaxis

blob - through object perpendicular to main side (ie use axis of main
side as a surface)




Extents and locations and pieces of space.


We think of space as basically consisting of a collection of
<italic>locations</italic> where something can be placed. These
locations are defined with respect to a larger reference space which
contains them all, called a <italic>region</italic>. Regions may
themselves be places in some larger region, and locations or objects
located in a region may themselves define other  regions for smaller
locations. For example, the back right passenger seat may be a location
in a region consisting of the interior of a car, which is itself
located in geographical space on the surface of the planet, which is
moving within the solar system. 


Exactly what counts as a location is left open, but it should be
precise enough to count as an answer to a question of the form 'where
is x?'. Different notions of precision may be suitable in different
contexts. We can allow only three-dimensional locations, or can allow
things like 2d surfaces and lines and even points as locations.
Locations may overlap and be included in one another, and may be hollow
or arbitrarily shaped; or we may impose a coarse grid-like discipline
on a set of locations in a region if that is more suitable. One basic
relation between locations or pieces of space generally is
'<italic>inside</italic>', meaning that one location is entirely
included in the other, and '<italic>adjacent</italic>', meaning that
the two pieces of space are immediately adjacent with no space between
them. There are several alternative axiomatisations of thse notions
already available, and we can probably get by with a fairly simple
algebraic version like RCC8. Motion of an object (within a region) is
conceptualised as change of its location in that region; notice that
the region may itself be moving, so whether or not a thing is moving
depends on the region (eg one can be moving at hundreds of miles an
hour while asleep in an airplane seat). 


(This ignores such issues as whether the reference region is an
inertial frame, whether or not it has a gravity vector, and so on. Many
of the Cyc concepts seem to have an implicit assumption that the
reference frame is geographical space, but we cannot make this
assumption for RKF.)


An extent is the most precise version of a location. The
<italic>extent</italic> of a spatial object is the precise piece of
space occupied by the stuff which comprises the object. For example,
the extent of an ocean is the space completely filled with water (plus
fish and other detria), while the extent of a plastic coffee cup is a
thin, concave volume entirely filled with solid plastic. Extents may
have a complicated structure; in particular they may have holes,
cavities, etc, and may be not simply connected. Like locations in
general, extents do not move: when an object moves it leaves one extent
behind and fills up a new one. That is, we think of objects as moving
<italic>through</italic> the larger space in which they move; but if
they define a region (eg the space inside the empty cup) then that
region moves with them. A prototypical example of this is a container,
which when moved takes its contents with it. Relative to the container
they remain in the same place, but that place itself moves along with
the container. 


We need extents to be able to talk about  rotational symmetry. An
object is symmetric with respect to an axis if it occupies the same
extent when rotated about that axis. For example, a cylinder with a
longitudinal axis is symmetric wrt that axis. (Limited forms of
symmetry can be described by the CR group, which cannot distinguish
between the symmetry of a cube and that of a sphere. Neverthless I
suspect this will be good enough for most of the cellular chemistry
reasoning.)


Assemblies


Spatial things can often be made up from assemblies of other spatial
things. A general thoery of this wojuld encompass all of structural
engineering and solid geometry, but we can make some useful basic
descriptions based on some simple shapes. For example consider the
following shape classifications:

rod

ribbon

spiral

tube

2Dsheet

3Dblob

These can be assembled together in a variety of ways.. All the
following arise in protein folding and membrane structure for example:


A rod can twist into a spiral

A spiral can be a tube

Several parallel rods can make a tube (with the same axis and length as
the rods)

A folded ribbon can make a blob (with same width as ribbon but much
shorter)

A folded rod or ribbon can make a 2Dsheet (like weaving)

A 2Dsheet can be rolled into a tube

A series of pieces can be linked by hinged or flexible joints end to
end to form a foldable structure

A tube can pass through a 2Dsheet (ie be embedded in the sheet with its
axis perpendicular to the sheet and each end in contact with the space
on either side of the sheet.)

A foldable structure can be woven through a sheet from one side to the
other and back again. 


Detailed descriptions of these various possibilities can be given using
the concpets developed earlier. For example, a hinge is a shared linear
edge about which the two pieces can rotate. If they begin coplanar 
then a pi rotation about the hinge will bring their original parallel
faces into opposite orientation and adjacent. If they fit, then many
pieces of these directed surfaces will be exactly opposite and
adjacent, so any attraction between them will be reinforced (we here
need an axiom about how many small forces can add up to a strong force,
which may be tricky to state!) and this position will be stable. If
this is repeated, many layers will be added to form a layered structure
consisting of a 3dblob made of many 2dsheets. 


We are currently formalising a catalog of various geometric assembly
and deformation processes which can be used to describe the cellular
structures and processes in the text. 


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