Evolvability and more

From: Pim van Meurs <pimvanmeurs@yahoo.com>
Date: Sat Sep 24 2005 - 16:11:14 EDT

Cornelius Hunter wrote:

> Folks:
>
> It is not surprising that evolution, a theory not well grounded in
> science, continues to propagate credulous speculation.

This statement is begging the question. In fact, as I have shown it is
well founded in science as it not only provides credible and observable
mechanisms but it can be shown that these mechanisms are sufficient in
explaining much of the evolution of life.

> The inevitable response to questions of complexity and astronomical
> design spaces, is that evolution isn't random after all. It is really
> a guided search process, homing in on those functional designs.
> Furthermore, the evolutionary process itself evolves, fixing itself so
> that it works right.

This is a common confusion about evolution. Understanding the meaning of
randomness is essential if one wants to appreciate and understand
evolutionary theory beyond a strawman. Evolution is 'guided' by many
things, which is why it appears to be teleological. For instance,
natural selection leading to function is a good example of how evolution
is 'teleological'. Ayala and Ruse have commented on this in quite some
detail. Ruse also points out that evolution is constained not just by
selection but also by laws of nature, once again giving an appearance of
teleology.
A more recent understanding of evolutionary theory has resolved an early
paradox, how can evolution evolve itself? The answer is simple and yet
this evolvability of evolution is essential for its successes.

> The reason usually given for evolution being non random is natural
> selection. Natural selection guides the search process, right? Well
> actually, no it doesn't. All natural selection does is kill off the
> non competitive designs.

Another common confusion about evolution is that 'all natural selection
does is kill of the non competitive design'. In fact, as such it does
guide and inject a lot of information in the genome. But things get even
better, and while this may appear somewhat surprising to some, evolution
can in fact guide the search itself. This is what is meant by
evolvability. In other words, evolution can evolve search patterns which
are more likely to generate improvements. This does not mean that
evolution is guided in the sense that it provides the right variation
for a particular circumstance, just the evolution is biased by its own
history. Recent work on RNA and DNA has shown how neutrality is an
important concept not just for robustness, but also for evolvability. In
fact, it has been shown how neutrality is itself a selectable trait.
Imagine this.... While a more naive perspective would have rejected
neutrality as being selectable, a more indepth understanding of the
dynamics of evolution reveal that a static understanding based on
population dynamics is not sufficient to understand evolvability.

> That unguided biological variation still must luckily hit upon the
> right designs for natural selection to preserve (because it works
> better than the less competitive designs). So we're back to the
> problem of needing astronomically large populations, bigger than the
> all the electrons that could pack into the universe, by many orders of
> magnitude.

Nope and this is easily shown by adding selection to processes of random
variations. Without selection, indeed astronomically large populations
may be needed but selection makes all the differences. This is a well
known finding of evolutionary theory although it may be unfamiliar to
some and I can understand why a naive understanding of evolution may
lead one to reach conclusions as the one above. Luckily science is not
constrained by our ignorance or limits in our imagination.

> Nonetheless evolutionists speak of "selection pressure" as though
> natural selection was indeed influencing the biological variation. At
> the risk of sounding teleological, such language gets the complexity
> monkey off their back. Of course, the idea of evolution evolving
> itself is equally teleological and credulous. But this is in fact what
> evolutionists must conclude given what we now understand about
> adaptation.
>
> This is what happens when religion dabbles in science.

Evolution indeed may appear teleological but science understands why
this is the case. Of course, this has nothing to do with religion but
everything to do with good science.
I suggest that anyone interested in this topic familiarizes themselves
with the hot topic of evolvability and neutrality. Mark Toussaint has
some excellent work in this area and more recently work from Fontana and
others have addressed how evolvability in evolution takes place.

Selection indeed affects biological variation, nothing surprising about
this, many people have speculated about this and more recently we have
seen fascinating examples. For instance hypermutations, a response by
bacteria in times of increased stress shows how evolution has generated
a mechanism to create variation when needed. Other examples include
biases in nucleotide substitutions. Or the best example is neutrality.
Once one appreciates these aspects, it is trivial to show how these
mechanisms can recapture much of the observations and data found about
evolution. And that's why evolutionary science is such a powerful
testimony to scientific inquiry.

Nevertheless, some, often based on unfamiliarity with the present state
of scientific inquiry are quick to jump to conclusions which remain
largely unsupported by scientific evidence or logical arguments.

Links:

Robustness Mutational Robustness, Modularity and Evolvability
http://www.santafe.edu/research/mutationalRobustness.php

Plasticity, Evolvability, and Modularity in RNA (2000)
http://citeseer.csail.mit.edu/373009.html

"Neutral and nonneutral mutations: the creative mix--evolution of
complexity in gene interaction systems. Zuckerkandl E. J Mol Evol.
1997;44 Suppl 1:S2-8."

On the Possibility of Constructive Neutral Evolution Arlin Stoltzfus J
Mol Evol (1999) 49:169181

Andreas Wagner, Hypothesis Robustness, evolvability, and neutrality FEBS
Letters 579 (2005) 17721778
http://samba.unm.edu/~wagnera/FEBS05_Neutrality_published.pdf

Evolvability is a selectable trait David J. Earl and Michael W. Deem
PNAS | August 10, 2004 | vol. 101 | no. 32 | 11531-11536
http://www.pnas.org/cgi/content/full/101/32/11531

<quote> Concomitant with the evolution of biological diversity must^
have been the evolution of mechanisms that facilitate evolution,^
because of the essentially infinite complexity of protein sequence^
space. We describe how evolvability can be an object of Darwinian^
selection, emphasizing the collective nature of the process.^ We
quantify our theory with computer simulations of protein^ evolution.
These simulations demonstrate that rapid or dramatic^ environmental
change leads to selection for greater evolvability.^ The selective
pressure for large-scale genetic moves such as^ DNA exchange becomes
increasingly strong as the environmental^ conditions become more
uncertain. Our results demonstrate that^ evolvability is a selectable
trait and allow for the explanation^ of a large body of experimental
results.</quote>

Dr Toussaint publications at
http://homepages.inf.ed.ac.uk/mtoussai/publications/

C. Igel, M. Toussaint (2003): Neutrality and self-adaptation
<http://homepages.inf.ed.ac.uk/mtoussai/publications/igel-toussaint-03.pdf>
[ps.gz
<http://homepages.inf.ed.ac.uk/mtoussai/publications/igel-toussaint-03.ps.gz>].
*Natural Computation 2*, 117-132.

M. Toussaint, C. Igel (2002): Neutrality: A Necessity for
Self-Adaptation
<http://homepages.inf.ed.ac.uk/mtoussai/publications/toussaint-igel-02-cec.pdf>
[ps.gz
<http://homepages.inf.ed.ac.uk/mtoussai/publications/toussaint-igel-02-cec.ps.gz>].
/Congress on Evolutionary Computation (CEC 2002)/, 1354-1359.
[nlin.AO/0204038 <http://arXiv.org/abs/nlin.AO/0204038>, citeseer
<http://citeseer.ist.psu.edu/toussaint02neutrality.html>]

All one needs to do is follow the trail to either papers quoted by these
references or papers which quote these references and a vaste amount of
scientific research can be traced which has increased our understanding
of evolutionary processes in an almost revolutionary manner.
Received on Sat Sep 24 16:13:09 2005

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