This model was proposed in the 1970s
I must first remind the reader that the model I intend to
postulate is purely speculative and is open to whatever criticisms and
modifications that time and hard scientific evidence might demand. It seems to
me that the basic strength of the scientific perspective is the use of the
paradigm and the willing openness to allow empirical data to decide the
ultimate usefulness of any conceptual model.
However, science like any other modern human institution has
the tendency to become rigid in its outlook. I believe that at the present time
there is a strong tendency to take a narrow and unbending stand concerning the
evolution of life on the planet earth. No one who accepts the basic premise of
scientific investigation is about to deny the existence of DNA, its inherent structure,
and the role it plays in heredity. Also it is quite apparent that we as human
beings coexist on the planet with a vast variety of living things each with its
unique structures and adaptations. Various theories of evolution have attempted
to explain the mechanism by which these forms have come into existence. Darwin,
Mendel, and the brilliant work of modern molecular geneticists have elucidated the
molecular structure and function of the actual genetic material. It has been clearly
demonstrated how DNA by the very nature of its structure is capable of holding
the biochemical information necessary for life; how it conserves this information,
and how living things are able to call upon this information to organize the
functions that are the definitive prerequisites for life. These mechanisms are
not open to dispute since they represent hard data demonstrated over and over
again.
However, it is my intention to show that there are certain
explanations of phenomena that are strongly held but in fact rely on tenuous
proofs. It is currently held that evolution has proceeded on planet earth
through a process of spontaneous mutation of genetic material in which the
resulting changes in characteristics of living forms are either rejected or
reinforced by natural selection pressures. Allow me to give some examples.
There exists now a variety of bacteria, Neisseria gonorrhoeae, that is the causative
agent for the disease referred to as gonorrhea in humans that has become immune
to penicillin. The argument to explain this event would be the following: a
fortuitous mutation of the genetic material in this organism produced the
ability to negate the effect of the antibiotic. This event was independent of
the presence of penicillin in the environment of the organism. With this new
characteristic the particular strain of bacteria that held the immunity of
course would survive where its cohorts would perish. Hence the new natural
condition selected for the organism with the immunity. This same rationale has
been extended to encompass the entire evolution of living organisms on planet
earth.
The contemporary view is that the information contained in
the DNA is carefully conserved and fixed and is not generally subject to
alteration by its environment except in the limited area of fortuitous
mutational events. In my estimation A rigid model forbidding any sort of
adaptive mechanism in the genetic material itself and if living structures
actually adhered to such a model the planet earth would be probably be devoid
of the richness and variety of the life that it in fact supports.
This perspective is not an original view of mine. It is conceivable that within the
organization of DNA there exists an inherent mechanism to allow for a non-random
interaction between the environment and the structure of the information store.
It is with this thought in mind that I
propose the following model:
1 -that there is a portion of the DNA that is rigidly fixed
in information content in what is now referred to as genes in general and in
the so-called introns in particular. Billions of years in the biosphere have
established this information as being essential for life and substantial changes
in this structure can prove deleterious.
2-there is a large portion of the DNA in organisms that has
no apparent information content by nature of its seeming random and repetitive
sequences. This DNA is far from trivial and some of this structure represents
the basic language store from which the genetic material responds to
environmental signals; allow me to elaborate.
Proteins, especially enzymes, are the intermediaries between
the information stored in the DNA and the expression of this information into
discrete characteristics. In point of fact discrete genes hold the information
for the structure of discrete proteins. The genetic code has of course been
definitely worked out. It is these proteins that act on the cellular
environment of living things. Enzymes are specialized proteins and are
responsible for the catalysis of all the diverse chemical reactions taking place
within each and every living cell. Enzymes mediate cellular activity.
3 -The model I am proposing predicts the existence of quite
another mechanism operating within the genetic material. The specificity of
enzymes for their substrates has been well established. This specificity cannot
be accidental but must rely on discrete and well-established chemical laws. In
other words, there exists a particular relationship between amino acid
sequences of enzymes and the exact structure of a particular enzyme allowing it
to act upon a particular substrate, and also establishes the nature of that
reactivity i.e. whether oxidative cleavage, reduction, synthesis etc.
This relationship will be found to be quite simple -
computer analysis of amino acid sequences of different categories of enzymes i.e.
proteases and oxidases as an example will reveal certain relationships. It is
my prediction that it will eventually be shown that there exists particular
patterns, arrangement and spacings of amino acids that give rise to certain
classes of enzymes and that these patterns since they occur in proteins will be
represented in the DNA of the gene having the information for the synthesis of
that enzyme as is already understand.
It is my contention that the exact structure of a particular
substrate contains enough information for the synthesis of a protein that can
interact with it - there are only a limited number of ways cellular enzymatic
systems can chemically modify substrates in its environment. Examples of these are pathways for synthesis,
degradation, oxidation or reduction, cleavage, methylation etc. It is my contention that DNA sequences that
correspond to the relationships between amino acid sequence and enzymatic activity
are pre-existing within the seemingly random array of sequences within the
genome that have no known purpose.
Such arrays can be mobilized and activated by the appearance
of new substrates in the cellular environment. Such a mechanism proposes the
de-novo synthesis of a novel gene that has the information to create a novel
enzyme to interact with the new substrate presented to the cellular
environment. This particular aspect of
the model as of yet cannot fully explain the relationship between environmental
change, the appearance of new substrates and enzymatic populations as related
to gross characteristics. In multicellular organisms the degree of complexity
is exceedingly high.
The above model describes a transient mechanism for adaptive
change in genetic material . In
addition, I propose that there exists a mechanism for transferring these
de-novo genes to the conserved population of DNA in other words into inheritable
genes. If the environmental change persists then the new messenger RNA
containing the information for the protein designed to interact with the novel
substrate will exist over a prolonged time frame and therefore allowing reverse
transcriptases the opportunity to integrate this new sequence within the genome.
It is at this stage that selection
pressures play a significant role.
- The
following is a modification in part three of my proposition - dated July
19, 1982
Within the intervening sequences, the exons are composed of
sequences of DNA that code for pieces of the primary sequence of proteins that
are essential for determining the overall three-dimensional configuration of the
resulting protein which in the case of an enzyme such as cytochrome P-450 or an
antibody will also determine its specificity. Although these essential pieces
can be fit together in innumerable ways there are only a finite number of mini
sequences of amino acids probably containing highly conserved hydrophobic
residues that produce configurational patterns resulting in active proteins.
The most essential feature of this model as I see it is that
the capacity to respond to any new environmentally introduced signal i.e. to
produce a novel protein with the required specificity that relies upon the
existence of preformed genetic units, exons, that with the appropriate
environmental signal can be recombined to allow for the synthesis of a de-novo
protein. The advantage of this model is that it allows for more than merely a
random selection process for the evolution of new biological activity.
The weakness of this model however lies with the fact that
it rests upon the assumption that there exists a pre-existing mechanism that
can be activated upon the appearance of a novel substrate and that can
ultimately lead to the production of a particular sequence of amino acids and
therefore into reproducible 3 dimensional configurations with discrete
specificities that can bind to the new substrate.
However the existence or non-existence of such a mechanism
is experimentally accessible either by direct synthesis of model sequences or
sophisticated computer analysis of the many, many proteins in which both the
three-dimensional configurations and primary sequences are already known. If
such a language were indeed uncovered the possibilities would be endless for it
would then be plausible to synthesize a protein de-novo with novel and
predictable activity which in collaboration with genetic engineering could lead
to the production of novel synthetic genes.
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