Evolution: time for some change?

A great idea. It allows some space for what we don't yet know.

 

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when scientists first started using the word evolution, they were actually referring to the development of an organism and not at all to the process of descent with modification as charles darwin postulated. Even darwin only mentions the word evolution only once in his book on the origin of species i think.

Evolutionary developmental biology strives to explain the diversity of life. Population biology strives to explain the distribution of genetic information in a population. Population biology cannot explain the evolution of a straucture such as an eye. Evo-devo can. Development can tell you how a duck got webbed feet or how a bord got feathers. Development is at the origin of any phenotypical change. There is no gene for webbed feet after all.

 

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Spurious

"There is no gene for webbed feet after all."

Can you explain that a bit.

 

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Ducks have webbed feet because a gene that is already expressed in this area has extended its expression domain (or chickens lost it, depending who was first, the chicken or the duck).

In this case gremlin, a BMP inhibitor, is expressed in the interdigital space (the space between your toes) in ducks, but not in chickens. This prevents the apoptosis (regulated cell death) of the cells between the digits. Hence the duck never loses the tissue between its toes.

You can similate this by putting a bead loaded with gremlin protein inthe interdigital space of the foot of a chicken embryo. This mimicks the effect of gremlin in the duck. There is no apoptosis and you end up with a chicken with webbing between the digits where the bead was placed.

The question then becomes how this expression pattern was changed, and although we do not know exactly, developmental biology has the theories to explain this. Which are tested and proven in other systems.

in conclusion, there is no specific gene for webbed feet. We are dealing with a slight alteration of an existing system, with rather beneficial consequences if you are fond of a pond.

and of course, this cannot be measure in terms of gene frequency. This is on the level of combinatorial control of gene expression.

 

Thanks. Does this mean that inhibitors are not part of the gene?

 

no gremlin is a gene that codes for a protein. This protein inhibits the action of the BMP gene.

But this doesn't mean that ducks have a different gene for gremlin than chickens. If you would put the coding region of the gremlin gene of a chicken into a duck, the duck would still produce webbed feet.

 

That confused me. Gremlin (is it really called that?) is a gene, but you say ducks and chickens have the same genes. Sorry to be thick. Do they both have the gene but it is not expressed as a protein in a chicken for some reason?

 

There's no webbed feet without genes though

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[edit] So how would you define evolution?

 

there are no webbed feet without an egg either.

there are no male crododiles if it is too hot either.

 

gremlin is expressed in both chick and duck in many different organs and at many different time points.

What is important is the alteration of temporal and spatial expression, not the gene itself. What we are looking for are changes in enhancer sites and changes in modulation of upstream signals.

 

I'm still not quite with you. Are you saying that the mechanisms that determine when and where gremlin will be expressed in ducks is not genetically determined? Or are you saying that there is no gene for webbed feet because they are caused by a complex of interacting genes? Or am I missing the point?

 

correct. Although the basis is genetic, i doubt we could measure this meaningfully in terms of changes in gene frequency. We because we do not know what we should measure, if we do not understand the development. Development gives us therefore a window on evolution.

 

Ah, got it. Thanks.

 

A question we could ask is whether evolutionary genetics provide a sufficient theory of morphological change?

 

Any question about a definition has two aspects -
1) simply the linguistic act of deciding what a specific word means
2) the act of deciding what the essence of some general idea is

The basic idea of evolution, in a non-biological sense, is the set of changes in a system that take it from one state to another. The essential problem that I think spurious monkey wants to highlight is that there is something unsatisfying about defining it simply as change without any consideration of what type of change will occur. A directionality perhaps.

In a biological sense I think the discussion should be overlayed strongly by statistical mechanical/thermodynamical conceptions.

To make an example if one has two chambers, one containing gas and one not, separated by divider and removes the divider the gas will expand and fill both chambers. The reverse will not occur, there are statistical reasons why the process will move in one direction when considering the possible paths available to the molecules (the exceedingly small number of paths leading the molecules to return to a single chamber are negligible among the multitude of paths where they remain filling the two chambers).

By the same token if one considers the set of mutations that occurs in a species over time there is an inherent directionality. We will never retrace the path we have so far followed or one close to it. Even though we know there is a set of molecular operations that could take us on that path.

The reason is close to a creationist confusion regarding irreducible complexity (though I shudder to get anyone started on this topic). Once a component that has been added to a genetic system, for instance a duplicated gene, has acquired some new useful function, it is difficult to imagine it being removed.

This increase in complexity is similarly tracked on the morphological level, as in the case of Williston's law (the number of serially homologous elements tends to decrease while the individual elements tend to become more different and specialized). As each component becomes more specialized it becomes more difficult to do without it. One must follow a very specific set of molecular changes to remove elements and maintain function, whereas the system is more robust to adding elements which then are the object of selection until they become an integral component of the system.

In the long run evolution is about the choice of what path is taken on the road to increasing complexity. Not in a conscious sense - although one could argue populations lead to a certain amount of democracy in weighting various choices. The road most traveled to success for a single individual helps set the path of the population.

 

I would like to make a sidenote that it is not truly difficult to make developmental changes. It is just difficult to make them for certain structures. The developmental importance of these structures is reflected in the concept of bauplan and phylotypic stage.

If we look at the phylotypic stage we may note that it is possible to make enormous changes in development before and after this stage. The important structures that hardly change (such as the notochord) function to instruct other structures, organs and tissues.

 

Do you mean it's not difficult to have mutations that change development? Or ones that change development and are workable evolutionarily?

Also how would you define difficult? There are obviously a large fraction of mutations possible in each protein that don't even alter the protein generated in addition to the buffering you mentioned in the actual developmental processes. Do you mean difficulty defined as some fraction of mutations that alter development? Or more like the fraction of such changes that are viable? or ...

I must admit I'm also curious as to whether I was on the right track to answering your question in my previous response ... were you trying to get at a metric of evolution beyond simple changes in frequency. Fixation of duplications being one possibility from my response (which hallmarks arrival of a qualitatively different individual).

Of course one experimental issue with this definition is that one would need full genome sequences to identify such changes and most evolutionary studies currently sample from single genes. Then again duplicated genes could be found if one makes intelligent use of reduced stringency screening processes. Still the exact quantification procedure is much more ill-defined when one is forced to look at the greater range of possibilities when dealing with more complicated global changes.

 

I meant that changes in gene frequencies is a really unsatisfactory definition of evolutin. Even darwin did better than that with his descent with modification. It left more room open.

We could know exactly how a gene frequency changed and still not know anything about evolution. A favourite quote would be that ontogeny does not recapitulate phylogeny, but ontogeny creates phylogeny. The developmental process is therefore a means to make evolutionary change possible. It should be at the center of evolutionary thought.

 

I knew you meant that (indeed Williston's law has strong similarity to descent with modification). What I tossed out was a very general conceptual framework regarding for thinking about sets of genes and their inter-dependencies. SInce evolution occurs on the level of the organism one clearly has to start thinking about how the elemental building blocks of genes fit together into functional systems.

Development is certainly a good system for doing so since it elaborates spatially and the end goal is fairly apparent. For a detailed metric concerning effects on development, people need to experimentally determine and then compare complete gene networks in different organisms.

Other biological systems are reasonable as well though. I'd be interested if anyone has made an evolutionary comparison of transcriptional or other networks in bacteria where it's considerably more feasible (I don't think development is a necessary part of moving forward, just considering networks/systems that have a specific function). In development, it's certainly a goal of many like Tautz and Carroll, but it's not that easy and it's not surprising with the paucity of data that it hasn't taken over the evolutionary field. There aren't enough instances to do any interesting stats on relative rates of evolution.

If you have access to development check out:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9716530&dopt=Abstract

I also recommend reading stuff by CH Waddington (a bit old, but he had many intelligent thoughts on the matter). If you have any good refs on people working on this subject, I'd be interested as well.

 

For tooth development Jukka Jernvall is on the cutting edge of evo-devo

Salazar-Ciudad, I. & Jernvall, J. (2002) A gene network model accounting for development and evolution of mammalian teeth. Proceedings of the National Academy of Sciences, U.S.A. 99: 8116-8120.

for a evo-devo model on tooth shape

and because I know Isaac and nobody reads his crap volentarilyI will also recommend his review article.
Salazar-Ciudad, I., Jernvall, J. & Newman, S. A. (2003) Mechanisms of pattern formation in development and evolution. Development 130: 2027-2037

Let me introduce myself, this is my own shit:
Development 130, 1049-1057 (2003)
Root or crown: a developmental choice orchestrated by the differential regulation of the epithelial stem cell niche in the tooth of two rodent species
Mark Tummers* and Irma Thesleff

but that is not really relevant here, although the article contains the word evolution.