Re: [asa] FYI: Arrogance, dogma and why science - not faith - is the new enemy of

From: PvM <pvm.pandas@gmail.com>
Date: Thu Aug 23 2007 - 12:41:45 EDT

I sent this example offlist toJohn but others may be interested as
well. There are quite a few similar papers available to anyone
interested

<quote>
Although some have called systems biology a 'friend of Intelligent
Design', reality is that systems biology is all but a friend of what
is best known as 'ignorance'.

In a recent article in BioSystems 88 (2007) 163–172, titled
"Alternative routes and mutational robustness in complex regulatory
networks", Andreas Wagner and Jeremiah White describe how

<quote Abstract> Alternative pathways through a gene regulation
network connect a regulatory molecule to its (indirect) regulatory
target via different intermediate regulators. We here show for two
large transcriptional regulation networks, and for 15 different signal
transduction networks, that multiple alternative pathways between
regulator and target pairs are the rule rather than the exception. We
find that in the yeast transcriptional regulation network intermediate
regulators that are part of many alternative pathways between a
regulator and target pair evolve at faster rates. This variation is
not solely explicable by higher expression levels of such regulators,
nor is it solely explicable by their variable usage in different
physiological or environmental conditions, as indicated by their
variable expression. This suggests that such pathways can continue to
function despite amino acid changes that may impair one intermediate
regulator. Our results underscore the importance of systems biology
approaches to understand functional and evolutionary constraints on
genes and proteins.
</quote>

So while ID proponents are arguing for an 'edge' to evolution, real
science is uncovering a remarkable richness for evolution.

So let me ask the following question: Who has contributed to
scientific knowledge here?

The question now becomes, how can such robustness evolve?

The answer, not surprisingly, is via Darwinian pathways…

<quote> The topology of cellular circuits (the
who-interacts-with-whom) is key to understand their robustness to both
mutations and noise. The reason is that many biochemical parameters
driving circuit behavior vary extensively and are thus not fine-tuned.
Existing work in this area asks to what extent the function of any one
given circuit is robust. But is high robustness truly remarkable, or
would it be expected for many circuits of similar topology? And how
can high robustness come about through gradual Darwinian evolution
that changes circuit topology gradually, one interaction at a time? We
here ask these questions for a model of transcriptional regulation
networks, in which we explore millions of different network
topologies. Robustness to mutations and noise are correlated in these
networks. They show a skewed distribution, with a very small number of
networks being vastly more robust than the rest. All networks that
attain a given gene expression state can be organized into a graph
whose nodes are networks that differ in their topology. Remarkably,
this graph is connected and can be easily traversed by gradual changes
of network topologies. Thus, robustness is an evolvable property. This
connectedness and evolvability of robust networks may be a general
organizational principle of biological networks. In addition, it
exists also for RNA and protein structures, and may thus be a general
organizational principle of all biological systems.
</quote>

Ciliberti, S, Martin, OC, Wagner, A. (2007) Robustness can evolve
gradually in complex regulatory networks with varying topology. PLoS
Computational Biology 3(2): e15.

</quote>

Let me repeat

This connectedness and evolvability of robust networks may be a
general organizational principle of biological networks. In addition,
it exists also for RNA and protein structures, and may thus be a
general organizational principle of all biological systems.

Wow

Remind me again of this edge? And how ID explains these data?
John? Anyone else?

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Received on Thu Aug 23 12:42:00 2007

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