
                          Tree Shaped Chromosomes
                          =======================

This document discusses the virtues of employing tree-shaped chromosomes in
artificial life programs, and ones that use genetic modelling which includes
genetic recombination.

Index
~~~~~
Modern Life is Rubbish
Coloured Bodies

Modern Life is Rubbish
~~~~~~~~~~~~~~~~~~~~~~
In the process of presenting evidence for the theory of evolution, scientists
have drawn attention to the way in which some organisms seem to be adapted to
their environment in ways that seem to suggest that an historical development
has been instrumental in moulding their forms.

Such signs of history have been referred to as "Scars of Evolution" by Elaine
Morgan.  The word "scars" is well chosen as it implies that the signs are
almost always maladaptive to some degree or other, and that a designer would
avoid such features.

Many organisms display signs that one structure has been adapted from an
original use to a new role, signs of "lock in" of arbitrary or non-optimal
designs, vestiges of historical structures of no apparent utility, and
sometimes complete lack of features which it seems they would find
advantageous, but are not suggested by small variations in the embryological
development of their forms.

As well as being applied to specific phenotypic aspects of individual
organisms, the same technique of examining apparently imperfect adaptations
may be applied to the study of the genetic machinery in an attempt to trace
its history.

When examining multicellular organisms such as ourselves, one of the curious
features is that we seem to be colonies of millions of bacteria-like
organisms.  These creatures are all clones of one another, descended from a
single cell, and most of them are still capable of asexual reproduction. 
Amazingly, each of them contains a copy of the entire genetic heritage of the
organism.

There are undoubted advantages in storing the information locally to the
cell.  In particular, translation and transcription into amino acids can
occur adjacent to the information store, and when the cell decides to
reproduce in mitosis it has all the information it needs to pass to its new
sister cell.

It seems that there are also huge disadvantages to using local storage.  The
sheer quantity of redundant information involved is colossal, when it is
considered that there must be a cost in terms of the chemicals, time and
energy required to support all the information.

As organisms age their genetic homogeneity decreases due to mutations in the
individual cells.  In older people this results in cancers, as well as other
signs of cellular lack of harmony symptomatic of ageing.  Those cells in the
germ line responsible for gamete production are affected in the same manner
as other cells.  With all the copies of the genome available, you might have
thought that this resource could be used as a multiple back up device, or as
a gigantic error correction system, but in fact cells do not communicate with
their neighbours about genetic matters directly at all.

The question arises: would the organism be better off if it could maintain a
central genetic database and then network its cells together?

If this proved tp be possible then in principle a whole series of changes
could be made.  If, for example, the information store could be decoupled
from the two important processes of transcription and replication, then a
more energy-efficient and secure storage system could be developed.

If cells could communicate genetic information to one another then improved
error checking could be implemented and compression techniques would be
available if required.  Viruses could be virtually defeated from subverting
such communication channels by employing encryption techniques.  Better cell
to cell communications could also eliminate the physical substance transfer
involved in sex.  

The kind of network required need not be fast; indeed the speed of the
nervous system would be more than sufficient: genes do not control their
hosts in real time but via the slow-motion remote control of protein
manufacture.  Communications could even take the form of local transactions
between adjacent cells.

There is no proposal here to defend here the viability or otherwise of such
possible alternatives to the current arrangements, but that such
possibilities exist and may be greatly superior to existing systems is worthy
of consideration.  Because it is at the bottom so to speak of a series of
developmental stages, the genetic substrate may be helpfully seen as the most
ancient and primitive structure of modern life, and though there is a sense
in which it is immensely high technology, there are many ways in which its
'design' seems to bear witness to the nature of life's last common ancestor,
rather than modern utility.

If such a system was to be found to be superior, then the conclusion would
follow that the existing arrangement exists as a kind of local optimum of a
system with much better global maxima.  It would be a sign that developmental
constraints on the organism have limited it to the current system which
displays all too clearly its historical legacy, and that this design defect
had become "locked in" by all the subsequently constructed structures which
are built on top of it.

The phrase "The bathwater cannot be thrown out because of the baby" would
seem appropriate in this context.  Unfortunately, as time passes the dirt in
the bathwater is liable to accumulate as more and more "lock in"s occur on
different levels, until it is difficult to make out the baby at all.

Any watching designers would wring their hands in frustration, desperate to
be able to start on a fresh new drawing board, and use the old evolved design
as the basis for a completely new organism with all such constraints designed
out.

Coloured Bodies
~~~~~~~~~~~~~~~
The invention of sex may be a usefully considered to be a major landmark in
the development of modern organisms.  One of the reasons for this is that it
probably marks the end of the evolution of the main structure of the genetic
code, the reason for this being that any major structural changes are likely
to be incompatible with existing organisms, and so would be incapable of
interbreeding with them.  If a new variation upon a genetic mechanism is good
enough that its organisms can afford to abandon the rest of the gene pool in
which they find themselves, then it may prevail.  Otherwise the majority are
likely to win out over any innovations in the genetic system.  Sex could be
described as a heavy subsequently constructed structure, built on top of the
genetic mechanism which tends to fix it in position.

The above description applies to small, gradual changes in the genetic
structure, but is not relevant to theories of genetic takeover of the kind
described by A. G. Cairns-Smith, which remain possible for as long as a
superior genetic substrate can be envisaged.

Having mentioned Cairns-Smith's work, another of his metaphors seems
appropriate to the discussion.   He describes the "lock in" phenomena
concisely, using the metaphor of building a stone arch.  This is a classic
metaphor illustrating that the initial stages of final constructions may be
best seen by envisaging preliminary supporting structures; in the example of
the stone arch, this may be a mound of earth.  If the mound of earth is then
removed, the arch becomes suddenly brittle and "locked in" to a state where
all the stones depend on each other.  Once this dropping away of preliminary
structures has occurred, there is often no going back, even if the resulting
construction contains aspects which are no longer appropriate to the use to
which it is being put.

It seems unfortunate that Cairns-Smith's work has not found a wider audience
within the A-life community.  One problem may be that a well known A-life
enthusiast Stuart Kauffman has proposed a conflicting theory of the origin of
life to the one Cairns-Smith proposes, involving autocatalytic sets.  The
author believes that this barrier may eventually be resolved by problems
within the autocatalytic theory.  Cairns-Smith's own critique of models of
"chemical evolution" seems to be applicable, as autocatalytic sets would seem
to have a "low ceiling" in terms of information storage.

Turning back to chromosomes, meiosis will now be examined.  Although there
seems to be some control by the structure of chromosomes over meiosis, in
that some parts of the genome are more sexy than others and different parts
have different baseline mutation rates, these effects provides very little
structure to meiosis.  Apart from the near immunity of that genetic
wasteland, the Y chromosome, and inversions, no parts of the genome which are
treated with additional respect by the process.

Meiosis' lack of discrimination may be an aspect of its even-handedness.  If
the meiotic process can be influenced by a particular gene in a manner that
makes that gene more likely than its alles to find its way into gametes, then
that gene will come to dominate, even it it has other severe side-effects on
individuals who bear it.  This kind of gene is often referred to as an outlaw
gene.  There is subsequent pressure on meiosis from the other genes in the
organism which all suffer from the adverse effects of outlaw genes.  It has
been theorised that under some conditions the outlaws are fairly effectively
suppressed.   It may be that the form of the suppression forces meiosis to be
simple, as any structural complexity offers outlaws opportunities for
subverting the process to their own ends.

The "some conditions" under which the outlaws are suppressed are theorised to
be as follows:

Outlaws that act by subverting meiosis or around the point of conception are
known as segregation distorters.  They may act at other points in the
lifecycle of the organism, as in the example of a behaviour pattern,
influenced by a gene on the Y-chromosome, causing parents to invest more
resources in bringing up sons than daughters.

Outlaw genes not only help themselves to a larger slice of the genetic pie
than they would normally receive, they usually help their chromosomal
neighbours too.  Sometimes the entire chromosome containing the gene is
helped.  If an organism has a large number of chromosomes then a larger
proportion of the organism's genes suffer as a result of their association
with the outlaw than would if the organism had fewer chromosomes.  These are
more likely to act in unison to suppress the effects of the outlaw genes,
than if there are, for example, only two chromosome pairs, in which case one
of them may want the outlaw to succeed because its genes will directly be
levered into the next generation by the outlaw's mechanism.  It will try to
block any suppression effects which the other chromosome pair would like to
impose on the outlaw.

If this reasoning is correct then it follows that multiple chromosomes and
sex go together.  No suggestion is being made here as to which of these
adaptations came first.  There may be other pressures favouring multiple
chromosomes (including structural and engineering considerations).  However,
organisms using sex with a low chromosome count may need some variations in
its style of meiotic division if they are not to become prey to outlaw genes.

The reason for interest here in the structure of chromosomes is as follows.
Genes display associations with other genes in the genome, in that some
groups of genes are more likely than others to find themselves sharing bodies
in offspring.  These genes are described as being linked to one another.

The mechanism behind linkage is very simple: genes that are on the same
chromosome are linked roughly in proportion to the distance they are from one
another along it.  This distance is related to the probability that meiosis
or mutation will act to cleave the two genes involved.  Genes on different
chromosomes are considered not to be linked at all - their probability of
sharing a body in the next generation is ½.

At first sight the ends of chromosomes look like interesting places in terms
of linkage as the distance only goes in one direction so to speak.  This
interest rapidly diminishes upon closer examination.

Linkage is important.  Even in asexual organisms where genetic shuffling is
not the norm, it may play some role.  Characters which are developmentally
related or inter-dependant would gravitate towards close linkage.  Genes that
need one another for their mutual well being would be inclined to find
themselves next door to one another.  Within linkage groups, genes would tend
to cooperate more with their neighbours than with the rest of their
particular genome when they encounter copies of them in other bodies. 
Recognising a copy of your close neighbour out in the world may be exactly
equivalent to recognising a copy of yourself.

The means by which genes are brought together is of course natural selection,
but of a slightly unusual type.  Usually selection may be thought of acting
on the phenotypes of organisms, but in any individual organism genetic
linkage displays no obvious signs of its effects.  It is only when the
organism reproduces that some important groups may be separated if they are
not closely linked.  The selection pressures may be thought of as being
towards evolvability, and away from rapid genetic decay in descendants.  For
a justification of the plausability of such selection pressures I refer you
to the chapter named "Kaleidoscopic Embryos" in Richard Dawkins' book,
"Climbing Mount Improbable".

Linkage comes to follow and mirror the structure of the organism.  This is 
not meant literally, in the sense that genes associated with different adult
bodily parts would like to form an isomorphic structure on the genome, but
giving due consideration to the developmental history of the organism.  In
the complex and mysterious growth processes of embryology, genes can be seen
as waltzing with other genes, and their partners tend to become their eternal
soulmates.

The main point to be made here is that distance is a very crude
one-dimensional symmetrical measure.  If an organism could have
multi-dimensional asymmetrical, conditional, with complex interdependencies
as relationships portrayed by links, then it would benefit in that the
complex relationship between genes in embryological processes could be
captured more clearly.

Tree-shaped chromosomes are referred to here.  This is for a number of
reasons.  Heirarchical trees are familiar data structures to many.  They are
easy to implement on existing computers.  A simple representation can be
imagined as a one-dimensional string of characters using nested brackets to
indicate the branching depth.  There is no need to imagine anything as
complex as branching in the physical DNA used to encode genes.  A simple
one-dimensional structure may be used, but it should contain markers (serving
the same function as the brackets referred to above) which encode information
relating to the tree structure, and which influence meiosis.  It is easy to
imagine the sexual process as being represented by a pruning and grafting
process between chromosomes.

I do not claim that "tree-shaped" is in any sense an optimal structure and it
may be preferable to consider genes as being related to groups of linkage
properties in an orthodox object-oriented manner.

With the existing state of the genetic substrate, the advantage of having a
better map between genetic and developmental/phenotypic structure may be
counterbalanced by a corresponding high cost of implementation.  The existing
genome is one-dimensional and complex links would probably have to be
represented physically on it in some manner, and then read in the process of
meiosis.  This kind of selective meiosis would be just the kind of mechanism
outlaw genes would love to get their hands on in pursuit of their own
subversive goals.  These disadvantages may contribute to the apparent absence
of such geometries from modern organisms.  However, messianic A-life heads
should not allow themselves to be constrained by such considerations.

