Re: Addressing Scientific Reductionism

Jim writes:

I don't deny that examples of strong intra-module cohesion and weak
intermodule coupling can be found in organisms. One good example is
the prokaryote 'operon' as an organizing principle for the genetic
material. It is very interesting that there is growing evidence that
much of 'horizontal gene transfer' actually happens as 'horizontal
operon transfer'. That is, microbes typically don't swap single genes.
They swap entire metabolic pathways consisting of multiple protein-coding
genes plus a lot of regulatory information. See, for example, the paper
"The Natural History of Nitrogen Fixation" available through this
Wiki article:
http://wiki.cotch.net/index.php/Nitrogen_fixation

But there are also examples in which Nature apparently did not
follow Microsoft's good advice and came up with a solution I would
consider very non-modular. (Or perhaps, my sensibilities as to
what a module should look like are different than Nature's.) My
favorite example is attenuation in the tryptophan operon. Another
is the weird way in which the seleno-cysteine codon is recognized.

One of the reasons I resist the ideology that life is inherently
modular is that it sometimes closes minds in advance of the evidence.
If we already 'know' that life is modular, then we will not find
the exceptions to the rule. Lipmann, for example, provided a nice
modular model for the production and use of cellular energy. But
it actually made it more difficult for Mitchell to convince people
that the situation is more complicated than that.

For any system that was naturally evolved, you would be foolish, as you
rightly imply, to push any single philosophical point of view too far.
Modularity clearly has great advantages to the design and competitive
evolvability of a species, but it isn't the only attribute of evolution
that's self-evident.

Although Darwin and Cope both recognized the value and basic nature of
"mosaic evolution" (modular evolution) in the latter half of the 19th
Century, the cross-coupling effects of pleiotropy came to be well
recognized in the early half of the 20th Century.

The Microsoft text that I quoted argued strongly against "sprawling
namespaces." By that, they meant the re-use of global variables. If a
global variable isn't carefully maintained as a single-point,
authoritative state variable, it has every possibly of degenerating into
something that means, as Humpty Dumpty said, "precisely what I mean it
to mean, no more, no less."

While global state variables are rare in natural designs, the reuse of
basal code isn't. Once a functional protein exists, its code can be
preferentially replicated and used in a great variety of contexts, a
situation which works at complete counter-purposes to the evolution of
modular structures.

The first to clearly demonstrate the implicit pleiotropy associated with
code re-use was Hans Gruneberg in the 1930's. Gruneberg used the phrase
"spurious pleiotropy" to describe those pleiotropic effects that
permeate much of the phenotype due to the obvious re-use of code.
Gruneberg found that a single mutation in the rat caused thickened ribs,
a narrowing of the lumen of the trachea, emphysema of the lungs,
hypertropy of the heart, blocked nostrils, blunt snout, and low
viability. Congenital medical "syndromes" such as these are virtually
always the pleiotropic effects of a single gene's mutation ? and
hundreds of similar conditions for humans are now well known.

Sewall Wright preferred the term "universal pleiotropy," to especially
emphasize the same point that Mayr makes. Change any one gene ? and if
that change is expressed ? then that change will almost certainly have
effects that resonate throughout the phenome. Essentially all modern
evidence suggests that Wright was correct: all expressed genes tend to
be universally pleiotropic. Non-pleiotropic gene products simply don't
exist. But that moral is just as prevalent from all engineering
experience also.

The bottom line is therefore exactly as you say: "One of the reasons I
resist the ideology that life is inherently modular is that it sometimes
closes minds in advance of the evidence." On one hand we have powerful
evidence that there is great evolutionary advantage to the evolution of
modular structures, and that such a design is essentially inevitable,
while on the other hand, we similarly have powerful evidence that
modular-destroying pleiotropic effects are pervasive, if not universal,
in both human and natural systems.

While it may not be standard human practice to clearly keep such
counterveiling views in mind simultaneously, a proper understanding of
evolutionary design demands that you do.

Wirt Atmar


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Relevant Pages

  • Re: Hamiltons rule
    ... >>lack of the dimA gene results in exclusion from spores. ... We propose that the evolution of pleiotropic ... that in fact it wasn't a cheater, because of this pleiotropy. ...
    (sci.bio.evolution)
  • Re: Population genetics question regarding sexual selection
    ... it seems to me that pleiotropy is just an extreme case of close ... genetic linkage. ... Pleiotropy refers to the case where one gene influences the ... them as a single pleiotropic gene. ...
    (sci.bio.evolution)
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