Re: molecuar biology (fwd)

Pat Pun (
Thu, 9 May 1996 17:39:43 -0500 (CDT)

Dear Ken,

Thank you for getting onto this video project with full force. James
Valentine is one of the outspoken scientists in defense of the Darwinian
model of evolution and therefore has deep faith in the naturalistic
paradigm that somehow one can explain everything by the gradual
accumulation of mutations selected by the favorable environmental factors.
The tone of his remarks from your attachment seemed to reflect the same optimism
he expressed in his earlier book, "Evolution", which he coauthored with the
leading NeoDarwinists in 1977. I can summarize several issues that
molecular biologists have to deal with when they attempt to explain the

(1) There is a widely accepted consensus among molecular evolutionists
that the rate of molecular evolution, i.e. the rate of change in the
macromolecules that define life such as nucleic acid and protein, and
the rate of macroevolution, i.e. the rate of appearance of new phyla as
judged by their first appearance in the fossils and the advancement of
fossil features, are independent of each other. The former proceeds at a
relatively constant rate, according to most accounts, and the latter
proceeds at an erratic rate, (i.e. the Cambrian explosion). This is an
enigma for modern biology which by and large depends on the Central Dogma
of Molecular biology, i.e. gene determines morphology or genetic changes
reflect morphological changes.

(2) To resort to the relatively rare genetic loci which are involved in
regulation to account for the above discrepancy, neoDarwinists still have
to wrestle with the following problems:

1. Regulatory elements well defined in bacterial system only
control the synthesis of proteins that are involved in a single
function, i.e. the utilization of a specific sugar when its is present.
To account for the sudden explosion of the Cambrian fossils, regulatory
mutations will have to account for the wholesale CREATION of not only new
body plands but NEW LIFE (single cell to multicellular organisms).
Moreover, regulatory system in bacteriaphage works in a self regulating
fashion in which mutliple mechanisms use the same region of DNA, i.e. the
same trigger can turn on two mutually exclusive genetic pathways such as
bursting the cell or keeping the cell alive by burrowing inside the
chromosome. The entire system will have to be changed drastically in
order for the system to evolve to a differnent regulatory stage.
Regulatory systems in higher form of life including the HOX system are
tightly coordinated such that the whole system work together as a unit,
i.e. the products of one gene or one cell turns on a serious of other
gene or cells. Again an integration of these system cannot be changed by
a stepwise small mutations. Drastic changes such as the loss of gain of an
entire system is necessary. However, such changes are always lethal to
the organisms.

2.There was hardly any living systems before the Cambrian explosion for
the regulatory mutations to occur. The more enigmatic problem is to
account for the abiogenesis of the first cell in the absence of genetic
mechanisms that only occur in living systems. 4 unsolved problems have
to be dealt with when neoDarwinists tackle with the molecular evolution
of the first cell:

i. polymerization of molecules is only an assembly but not
the source of information.

ii. no account for the switch from EXTERNAL control in
the primordial condition to INTERNAL control of the first cell, which can
adapt to the different environments.

iii. primordial conditions of synthesis is metastable and
does not persist to facilitate building up of complexity necessary for
the evolution of the first cell.

iv. thermodynamics favors the destruction rather than
build up of order in the absence of living systems.

3. Comparisons of various macromolecular sequences lead to many
erratic groupings of living systems, i.e. rRNA sequencing lead to only 3
groups in the living world, groups as disparaging as worm, horse, pigeon,
turtle, carp, lamprey can be all close relatives to each other. Only 1%
genetic difference separates human from Rhesus Monkey. The majority of the
DNA sequences in higher forms of life are repetitive and non-functional.
What mechanisms can be postulated to include the minute genetic
differences among these groups to account their vast morphological and
physiological differences.

The molecular tools only allow us to amplify and magnify our genetic
materials. Without an ideological breakthrough such as polyphylectism
where different blue prints are used for groups of life, they will only
lead to more blind alleys.

I am hoping to write something up along these lines of argument sometime

Let me know what further help you may need from me.