The Datafile PD-CD 5/DATAFILE_PDCD5.iso/utilities/t/texturegnd/Docs/TreeShaped

Text File | 1996-11-30 | 16KB | 282 lines

                          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