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BIO-CHEMISTRYof
<IN-FORMATION>: CHEMISTRY FOR LIFE SCIENCES Chemical bases of Biological Information Paolo Manzelli <LRE@UNIFI.IT>
The essential bases of biological “ IN-FORMATION ” (*) processing of
the
self-replicating bio-systems, can be researched by means the observation
of the chemical self-organizing reactions. In fact
DNA is not the unique
informational molecule but it is only the central part of an complex
networked communication of information of a catalyzed system, working
within the biochemical transformation of the living cells. Hence today
the flux of Bio- information
is not more considered as well as an unique accident of a DNA
molecular substance, but it is related to the complex changes of
molecular forms in the metabolic chemical dynamic of life.
As a matter
of facts any cell must be able to perform numerous chemical reactions in
the right order, in space and time, and this complex approach requires a
great number of specific catalysts (enzymes) as well as happen in the
Krebs Cycle. This dynamic situation implies that metabolic enzyme
networks including DNA molecule (named : “DNA-WORLD”, i.e. biological
catalyst self-assembly) , constitutes a genuine global “IN-FORMATION”
processing for several cellular problem solving, that will be based on
a transformational reproductive co-organization.
Looking in this perspective
of
“DNA-WORLD” the most probable and logical explanation for biological
information flow need to be revised , in a way to find a logical
connection to the chemical self-organization dynamics as well as is
possible to observe in the chemical transformation of the so called
“Oscillating Reactions”.
In conclusion
“ in-formation” related to the chemical and bio-chemical transformation
can be seen as well as a progressive development of different
evolutionary levers of catalytic self-organization of informational
channels between matter and energy, so that in this way of reasoning
we can understand the fundamental basis of “in-formation evolutionary
planning of nature” , starting from a deep analysis of chemical
self-organizing systems.
(*)- Footnote:
(
Semantic meaning of Information is equivalent to “taking a new form”
i.e. “ In-Formation” ; therefore Bio-Information needs to be not
confused of something having a meaning as well is included in the
concept of knowledge )
BOND//NO-BOND
OSCILLATING CHEMICAL DYNAMICS in transition state between high//low
catalytic barriers
Starting from
the above preliminary consideration the growth of living system needs
to be seen as well as a complex phenomena of “in-formation”
which lead to a high chemical collective organisation of constituted
atoms and molecules. In this way, we can understand, how the life system
of reproductive chemical-biology, develops by means a great deals of
chemical end bio-chemical examples of collective oscillating
informational behaviour.
At this
proposal we start to remember that two Russian biophysicists
Belousow (1951) and Zhabotinsky (1961) would
like to simulate the biological KREBS CYCLE , through a more simple
chemical (B-Z) reactions with a limited number of reactants, in a
way that can be easy to see how chemical transformation can
spontaneously organise themselves. As a matter of facts B-Z reactions
demonstrate how geometric patterns, such as concentric circles, can
propagate and diffuse information through an interactive interference
among spiral configuration diffusing across the chemical medium and
generating a complex oscillating system both in space and time. In
addition can be useful to take into account that before such B-Z
experiments some spatio-temporal oscillators are experimentally well
known as periodic reactions in gels, where the oscillating phenomena can
be followed in a range of a slower space-time diffusion ; those
oscillating precipitates are known as Liesegang Rings, because they was
firstly discovered in 1896 after the German chemist Z. Q. Liesegang.
Today these
two categories of oscillating reactions permits us to observe, directly
by the eyes , the self organization behaviour in chemistry and hence
they can be seen as an evident channels of informational diffusion
obtained by the co-organization of periodical interactive structures
associated with the period of transformation of any auto-catalytic
system of chemical reactants. In particular
it is easy to watch, without the use of instruments, the dynamics of
formation of the colourful indicators of Liesegang bands, in a way that
it become unproblematic to see the coupling between diffusion
of the front of the periodic precipitation
‘Liesegang rings’, are formed because the reactivity among reactants
assumes a rhythmic performance as it can be put in evidence by coloured
indicators. The alternating sedimentation in rings of “reaction
and not reaction products” can be understood by recognizing that
the self oscillating catalysis produces an intermittent
reactivity between a supercritical NO-Bonding Region, where the
reaction between reagents do not occur, and a sub-critical Bond
–Regime, in which the reaction between reactants can effectively
take place. A simple explanation of the space-time rhythmic
alternation of BOND//NO-BOND precipitates in Liesegang Rings can
be based on the consideration that the auto-catalyst phenomena permits
to generate an oscillation of the energy barrier on the reaction
coordinate (RC) during a molecular transformation between two critical
states respectively in relation to high and low activation energy
In a more deeper scientific approach , we can recognize that quantum
dynamical processes generates a cyclic splitting of the energy
barrier in a way that can separate the electron overlapping of
reactants and products . Therefore a range between higher and lower
activation energy bifurcations establish the rhythmic
reorganization energy barrier , in a way that it is changing the linear
activity of the reaction coordinate (RC). In fact outstanding the
bifurcation of the activation energy the
upper limit of the higher position of double transition state the
Liesegang reaction works in the irreversible reactions throughout an
negative bonding activation ( NO-BOND OVERLAPPING REGION) . After
quantum changes of the energy barrier, the Lieserang precipitates can
work in a “Bonding regime” , in correspondence to a reduction of
the power of the barrier; so that the molecular reactivity can shift to
toward the effective bonding of end -products. Ultimately we can also
observe Liasegang Band thickness will change during the development of
the reaction as a function of progressive enlargement of BOND//NO-BOND
fluctuation , that probably can be associated to a tunnelling effect of
the energy barrier modifying the RC catalytic path profiles. Similar
influence of energy barrier fluctuations are recently detailed in the
case of some elementary chemical reactions , where the effect to the
reaction consists also to produce a chemical oscillation along the
reaction coordinate generated by slowing down the top of the reaction
barrier to the bonding region. An comparable approach was recently
experimented and calculated in relation to the more simple case of the
H + HD
Changing of Bond // No-Bond
barriers by means catalytic effect hence represents a multidimensional
cyclic -contraction of the activation energy, that alters the matrix
entropy/entalphy during the RC patting, coming from the initial chaos to
a new-molecular order formation . In this manner we can establish a
correlation between “In-Formation” dynamics and the control of
free-energy defined by the physical structure in time and space of the
Liesegang Rings realized during the diffusion of irreversible chemical
oscillating process . Therefore the study of these oscillating
phenomena , is very important because first it could be used as model
for the comprehension of the concrete “Chemical bases of Biological
In-formation flows” . As a matter of facts the Liesegang bands and
more in general the spiral patterns across the chemical medium
generating an oscillating reactions , can be seen as a substrate
No-Bond- channels for developing an organized patterns of
“in-formation” dissemination , so that we can interpret the spiral
oscillating structures as well as chemical pathways generated for
developing an effective informational planning of the self-catalyst
control of free-energy during the complex relationships between chaos
and new-molecular order occurring far from the thermodynamic equilibrium
Certainly the
catalyst activity in biology responds to the higher complexity so that
it will be co-organized with more specialized coherent planning of
“in-formation”. Thus passing from chemical reaction to bio-chemical
self–organized promotion of metabolic transformation, we can
distinguish an accurate number of specific auxiliary enzymes as well as
it is needed for following the mainly accurate metabolic pathway of
bio-chemical transformations as well as take place in
the citric
acid Krebs Cycle – where a "ring" of metabolic processes
producing. the specific energy transfer molecule (ATP) it is utilized
for regulating the energy-transfer the cellular metabolism.
Anyhow it is a pity to
consider that the disciplinary division of biology from chemistry and
physics till now has no taken in serious consideration the “Chemical
bases of Biological In-formation” .
As a final consideration it
is important to remember that
Alan Turing (1912-1954) made
foundational contributions to philosophy, mathematics, biology,
artificial intelligence, computer science and, in this
trans-disciplinary context in
(1952) develops a fundamental
study of no liner spatial patterns diffusion in chemistry, generated by
a symmetry breaking bifurcation of energy perturbation. In this
pioneering works of Chemical Morphogenesis (from morphê shape
and genesis creation). Alan Turing demonstrates by mathematical
calculations how the bifurcation perturbation shows a characteristic
crossover changes between two critical regimes. Therefore a “no-linear
perturbation of reaction energy” produces an interval where, the
front velocity vanishes , as a result of a interference effect the
interacting wave-fronts underlying dynamical structure of
informational channels , as well as it is previously considered in
relation to the interpretation of bond//no-Bond periodic precipitates
of Liesegang Rings where it can be easy to understand how the no-bond
interactive structures can be considered the pathway of information
throughout the irreversible reactions .
In conclusion
of this brief article on the title : BIO-CHEMISTRYof <IN-FORMATION> , I
hope that successive studies of pattern catalysis can be developed in a
interdisciplinary bio-chemical research network focused about the
studies of oscillating reactions, in a way that this research can
represent in the next future a key understanding of the fundamental
chemical basis of biological information
OSCILLATING
REACTIONS :
http://www.faidherbe.org/site/cours/dupuis/oscil.htm ;
Belousow-Zhabotinsky reactions:
http://www.hermetic.ch/pca/bz.htm ;
B-Z experiment in
internet:
http://www.pc.chemie.uni-siegen.de/pci/versuche/v57-3.html
;
REACTION DIFFUSION
:
http://www.complex-systems.northwestern.edu/publications/SoftMatter.pdf
Liesegang
Rings :
http://www.sas.org/tcs/weeklyIssues/2004-04-30/chem/;
Wave Optics and
LR
http://dysa.northwestern.edu/Pubs/PRLFialkowski.pdf
Activation
Energy:
http://en.wikipedia.org/wiki/Activation_energy
H +
HD
KREBS CYCLE :
http://www.life-enhancement.com/LE/article_template.asp?ID=454
Alan Turing :
http://www.turing.org.uk/turing/;
Morphogenesis calculations:
http://sd.ist.utl.pt/Awareness/ST/ST.html
Patterns Formation :
http://hopf.chem.brandeis.edu/yanglingfa/pattern/HopfTuringWave.htm |
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