Self-Organization and Canalization

From: Michael Ragland (ragland37_at_webtv.net)
Date: 09/21/04 

Date: Tue, 21 Sep 2004 18:00:35 +0000 (UTC)

Computational Geneticists Revisit A Mystery In Evolution
Science Daily ^ | Date:Posted 8/8/2002 | Editorial Staff
Posted on 08/16/2002 10:27:48 AM PDT by vannrox
Reprinted from ScienceDaily Magazine ...
Source:             Stanford University
Date Posted:    Thursday, August 08, 2002
Web
Address:   http://www.sciencedaily.com/releases/2002/08/020807065302htm

Computational Geneticists Revisit A Mystery In Evolution

You and I are both human, with hearts that beat at roughly the same
rates, nervous systems that churn out just about the same chemicals,
bodies that are similar enough to peg us as people and not chimpanzees.
But despite the fact that we both belong to the same species, our genes
are pretty different. Only half the genes are identical among siblings
who aren't twins, for example, and for most of us, the degree of genetic
relatedness is much smaller.

Why, biologists first asked 60 years ago, do members of the same species
have such similar traits, or phenotypes, despite the fact that they have
such diverse genes, or genotypes? They couldn't fully explore that
question until now - when, aided by computers, they can sift through
mountains of experimental data. In the June 24 issue of the Proceedings
of the National Academy of Sciences, senior research scientist Aviv
Bergman of Stanford's Center for Computational Genetics and Biological
Modeling (CCGBM) and postdoctoral scholar Mark Siegal of the Department
of Biological Sciences provide a surprisingly simple answer.

Invariant traits - such as having five fingers to a hand instead of four
or six - don't become universal because Nature has somehow selected
special genotypes that faithfully direct development of the trait under
a wide variety of conditions, the researchers argue. Instead, they show,
it is the complexity of our genotypes - the many genes that interact in
networks during development, inhibiting and activating each other and
even regulating themselves - that provides fidelity. Indeed, Bergman and
Siegal show that any functional genetic network that is complex enough
has this built-in property of fidelity. This is true whether natural
selection on the phenotype produced by the network during development is
strong, weak or absent. Natural selection may be important in shaping
traits that aid in reproduction and survival, but Bergman and Siegal
show that it doesn't matter much during development, when, biologically
speaking, all roads lead to Rome.

''We're taking a more sophisticated view of evolution as a process,''
says Bergman, who co-directs the CCGBM with Marcus Feldman, the Burnet
C. and Mildred Finley Wohlford Professor in the School of Humanities and
Sciences. ''We need to take into account not only the genetic system by
which the hereditary information is passed on from one generation to the
next, but also the developmental system by which the information
contained in the fertilized egg is expanded into the functioning
structure of the reproducing individuals.'' Researchers at CCGBM,
established in 1997 with a grant from the Paul G. Allen Foundation,
conduct interdisciplinary research into quantitative problems of
biology.

''Evolutionary biologists tend to think of natural selection as the
first possibility of a mechanism for explaining most things that they
observe,'' says Siegal. ''So it's natural that the first attempts to
explain this disconnect between great genotypic variation and little
phenotypic variation was through natural selection.''

In 1942, even before it was known that genes were made of DNA, British
biologist Conrad H. Waddington coined the term canalization to describe
the ''funneling'' that occurs during development to produce just a few
end products, or traits, such as the beautifully patterned wings of a
butterfly. He envisioned development proceeding the way a ball rolls
down a mountain, traveling mainly along well-worn grooves and having the
option of rolling one way or the other at only a few forks in the road.
The ball rolls to the right, and the result is, say, development of an
elaborately patterned forewing. It rolls left, and a different-looking
hindwing forms. The puzzle that attracted Bergman and Siegal was not so
much the nature of the genetic switches that operate at the ''forks''
but instead what causes the ''grooves'' that keep development faithfully
rolling along when both environmental disturbance and genetic mutation
could potentially set it off course.

''You can throw a lot of insults at an organism - either genetic ones by
mutation or environmental ones by changing the temperature or changing
the chemical composition of the food - and in spite of all of those
insults, development is pretty robust,'' explains Siegal, who also
conducts evolutionary research on fruit flies in the laboratory of Bruce
Baker, the Dr. Morris Herzstein Professor in Biology. From larvae
incubated in a lab at 18 or 28 degrees Celsius, for instance,
similar-looking flies will develop, even though chemical reactions are
twice as fast at hotter temperatures than colder ones. The developmental
pathway and end products (traits) seem immune to such insults.
Indeed, some biologists argue that canalization may have evolved as a
response to environmental change. Under this scenario, Bergman explains,
''When mechanisms evolved to dampen the effect of environmental
variation on the phenotype, as a side effect they also happened to
buffer genetic variation.'' But the results of Bergman and Siegal
suggest that environmental perturbation is not necessary for
canalization to evolve. ''We don't know all the details of what makes
that funneling process work,'' Siegal admits. ''But our contribution to
it is giving one possible reason that hasn't in our view been considered
enough.''

Scientists used to think that developmental fidelity evolved via natural
selection, principally through survival and reproduction of organisms
with redundant genetic systems - that is, ones with copies of important
gene sequences. But Siegal and Bergman's results indicate that
redundancy may only be one small manifestation of a bigger theme: the
complexity of gene networks. In short, more complex systems are more
resistant to change in their outputs.

''It is typically assumed that important properties of organisms are
crafted by natural selection,'' says Dmitri Petrov, assistant professor
of biological sciences. ''What Siegal and Bergman show is that
robustness in the face of mutation, or canalization, may be a byproduct
of complexity itself and therefore that robustness may be only very
indirectly a product of natural selection.''

Says Siegal: ''It might be that the complex nature of the genetic system
itself is going to give you canalization independent of natural
selection. This complexity goes beyond mere redundancy, incorporating
all kinds of elaborate connections in the gene network.''

That doesn't mean natural selection doesn't play an important role.
Continues Petrov: ''Natural selection has shaped the genetic networks of
complex organisms so that they produce appropriate phenotypes - the more
highly interconnected these networks are, the more robust the
corresponding phenotypes are. The importance of this result is that it
shifts the focus of the field away from abstract models of natural
selection and toward actual genetic networks. In so doing, it will
provide a new perspective for analyzing and understanding the current
outpouring of genetic data in model organisms.''

A new perspective could prove useful - because invoking natural
selection to explain the disparity between genotypic and phenotypic
variation has several problems. First, a prerequisite for canalization
is genetic variation - but if selection for a trait is too strong, it
shrinks the gene pool. ''Once that limits the genetic variation, it
removes the pressure to have canalization,'' Bergman says.

Second, modeling has shown that if nature ''selects'' a trait,
canalization evolves - but very, very slowly, over millions and millions
of generations. ''When you start thinking about time scales like that,''
Siegal says, ''you have to wonder whether any evolutionary force can be
consistent over that amount of time to actually cause the outcome that
you see.''

And third, what's ''optimal'' today may not be optimal tomorrow. Says
Bergman: ''As [scientist Stephen Jay] Gould said, as the environment
changes what was once fit may not be fit today, and with further change
in the environment could become fit again.''

For their project, Siegal and Bergman chose to model an abstract system
that is important in the development of most organisms - transcription
factors, or proteins that regulate the expression of genes. In the model
they developed, 10 genes each encode a protein that in principle is
capable of regulating the expression of each of the other nine genes, as
well as itself. To compare the complexity of the abstract system with
that of an actual system, consider that yeast, for example, has about
6,000 genes, around 500 of which regulate each other.

Bergman and Siegal's collaboration comes at a time when - thanks to the
use of microarray technology in a new field known as functional genomics
- scientists have greater knowledge about sophisticated gene
interactions during development. This technology helps scientists
analyze the functions of genes in an organism's genome - all the genes
that make up its genetic blueprint - and allows them to look closer than
ever before at the intricacies of heredity. So, although the song
remains the same as that sung by previous giants of biology, such as
Darwin and Gould, Bergman and Siegal are studying the individual musical
notes to better understand how evolution's song plays out.

''The evolution of genetic robustness is a whole new game now that we
have the results from Drs. Bergman and Siegal,'' says Gunter Wagner,
professor of ecology and evolutionary biology at Yale University. ''[It]
shows that selection against lethal mutations [those that make the
network incapable of producing any phenotype] can lead to the evolution
of mutational robustness of any character state, even in the absence of
stabilizing selection for that character state itself.''

Says Siegal: ''In many ways canalization was sort of a smokescreen that
was dividing evolutionary biologists and developmental biologists. The
developmental biologists were studying their genetic networks and the
evolutionary biologists were in the abstract saying, 'Well, these
networks must have evolved to produce certain properties, like
robustness in the face of mutational insult.' But since we have shown in
our model that it's actually the nature of the developmental system that
can give you this property, they're really not two separate things to
study. They're the same thing to study. I think a lot will come out of
looking at actual genetic networks and how the structure of those
networks gives them the property of being robust.''

Comment:
This is an article which flirts with self-organization of complex
biological systems although the term isn't used. It acknowledges, "That
doesn't mean natural selection doesn't play an important role. Continues
Petrov: ''Natural selection has shaped the genetic networks of complex
organisms so that they produce appropriate phenotypes - the more highly
interconnected these networks are, the more robust the corresponding
phenotypes are. The importance of this result is that it shifts the
focus of the field away from abstract models of natural selection and
toward actual genetic networks. In so doing, it will provide a new
perspective for analyzing and understanding the current outpouring of
genetic data in model organisms.''

But the article states, "Second, modeling has shown that if nature
''selects'' a trait, canalization evolves - but very, very slowly, over
millions and millions of generations. ''When you start thinking about
time scales like that,'' Siegal says, ''you have to wonder whether any
evolutionary force can be consistent over that amount of time to
actually cause the outcome that you see.'' To back this up the article
states, "And third, what's ''optimal'' today may not be optimal
tomorrow. Says Bergman: ''As [scientist Stephen Jay] Gould said, as the
environment changes what was once fit may not be fit today, and with
further change in the environment could become fit again.'' IMHO this is
nonsense. I would argue that for millions and millions of years despite
intermittent dramatic changes in environment there were traits which
were naturally selected (in conjuction with developmental genetic
regulatory networks) which were canalized and conserved across species.
Some animals became extinct for various reasons but these traits were
canalized and conserved across species.
 
Siegel states, "In many ways canalization was sort of a smokescreen that
was dividing evolutionary biologists and developmental biologists. The
developmental biologists were studying their genetic networks and the
evolutionary biologists were in the abstract saying, 'Well, these
networks must have evolved to produce certain properties, like
robustness in the face of mutational insult.' But since we have shown in
our model that it's actually the nature of the developmental system that
can give you this property, they're really not two separate things to
study. They're the same thing to study. I think a lot will come out of
looking at actual genetic networks and how the structure of those
networks gives them the property of being robust.''

I agree although not alot of information was given on their model and
the results of it. But I would not call canalization a "smokescreen".
The idea of certain traits being evolutionarily conserved [canalized]
via natural selection and developmental genetic networks contributing to
this canalization is IMHO very real.

The article leans very much against natural selection. It states,
"Scientists used to think that developmental fidelity evolved via
natural selection, principally through survival and reproduction of
organisms with redundant genetic systems - that is, ones with copies of
important gene sequences. But Siegal and Bergman's results indicate that
redundancy may only be one small manifestation of a bigger theme: the
complexity of gene networks. In short, more complex systems are more
resistant to change in their outputs." This is very troubling to me if
true. I wouldn't characterize redundancy as a small manifestation in the
sense such canalized traits which have been conserved across species
[such as aggression] allowed many species to survive, reproduce and
evolve over millions and millions of years. But it worries me if these
canalized traits are part of the developmental complexity of gene
networks and are more resistant to change in their outputs. I've stated
aggression in humans is no longer an adaptive trait but if it is a part
of the complexity of gene networks and more resistant to change in
output than that means a much greater understanding of these
developmental gene networks in complex biological systems will be
necessary before possibly being able to remove aggression through
genetic engineering.

Along the lines of self-organization the article states, ''It is
typically assumed that important properties of organisms are crafted by
natural selection,'' says Dmitri Petrov, assistant professor of
biological sciences. ''What Siegal and Bergman show is that robustness
in the face of mutation, or canalization, may be a byproduct of
complexity itself and therefore that robustness may be only very
indirectly a product of natural selection.''

It states, "Natural selection may be important in shaping traits that
aid in reproduction and survival, but Bergman and Siegal show that it
doesn't matter much during development, when, biologically speaking, all
roads lead to Rome." Who has said natural selection is divorced from
development. It goes on to say, "The puzzle that attracted Bergman and
Siegal was not so much the nature of the genetic switches that operate
at the ''forks'' [canalization] but instead what causes the ''grooves''
that keep development faithfully rolling along when both environmental
disturbance and genetic mutation could potentially set it off course." I
don't subscribe to the Garden of Adam and Eve. At one time we were
invertebrates and over millions and millions of years we evolved to the
present Homo Sapien. During that time there were innumerable
environmental disturbances and mutations and we evolved. We share
"genes" with flies, mice and many other creatures. But I don't believe
Siegel the complex nature of the genetic system itself is going to give
you canalization independent of natural selection. Yes, this complexity
goes beyond mere redundancy, incorporating all kinds of elaborate
connections in the gene network but this doesn't negate natural
selection.
 
 

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