Doubting Didymus

Rufus:

Why would my wolbachia be copies of my grandmothers wolbachia? Surely it is because of the heritable features of the wolbachia? Equally as surely, changes in my phenotype due to wolbachia are due to those selfsame heritable features of the wolbachia.

I am willing to concede the focus on genes to a focus on heritablility. While it is true that my cell membranes have come from my grandmother, are you sure it is true that my membranes are copies of my grandmothers membranes? That is, if my grandmother had some unique feature of her membranes, do I have a copy of that feature, that I would not have otherwise had? If not, then neither can my generation pass on their own membranes, so evolution can not accumulate.

Evolution can only accumulate, as far as I can see, when fairly exact copies can be made of something. Evolution must therefore be tracable to heritable features. Therefore in turn, anything that is not heritable must be able to be traced to heritable factors, when considering evolution but not when considering organism development, where non heritable factors can play a new role in every individual. What am I missing, if anything?

Peez

Please provide an example of non-nucleotide inheritance. You have given us a number of examples of how various non-nucleotide factors can influence the expression of genes, but I have yet to see an example of non-nucleotide inheritance. I would be very interested in such an example. I disagree, but perhaps you could recommend an evolution text book that discusses non-nucleotide evolution. It is bizarre that you keep bringing up this straw man. Nobody here, to my knowledge, has suggested that there is no more to phenotype than genetics. As far as I know, no biologist holds this opinion. If you could provide an example, your argument would be much more compelling.

Peez

Peez

I am simply pointing out that evolution is defined by biologists as a change in allele frequency over time. This obviously tends to involve population genetics. If others wish to use a less specific definition of "evolution", that is fine, but the two definitions should not be confused. In what sense? Sure, they are alive. Why do you wish to include wolbachia reproduction in a definition of evolution?

Quote:

Ahh, but wolbachia-infection is an inharitable change, that isn't covered by the gene-pool defination.

I have not been convinced that wolbachia infection is inheritable. Could you please explain. If such inheritance could be demonstrated, then it might be relevant. This is going to become an argument about semantics shortly: is the wolbachia a "trait" of the organism? But before we go there, please explain how wolbachia is passed on from one generation to the next. As far as I can tell, that is a straw man. I have not noticed anyone claiming that "an organism can be reduced to it's genome or a population to it's gene pool". I ask again: who said that genes are responsible for everything?

Peez

[ October 28, 2002: Message edited by: Peez ]</p>

Doubting Didymus

Peez, run back over the middle pages of this thread for some links and discussions about wolbachia. It looks like the extended phenotype to me, focusing on the effects of the inheritable features of wolbachia that cause changes in the hosts phenotype.

RufusAtticus

I think you're getting it, but let me clarify what goes on.

Wolbachia are cytoplasmic parasites. When they infect a cell they feed off the metabolites in the host cell. They are living autonomous parasites that divide and proliferate within the host cell. When that cell divides, the wolbachia population is divided between the daughter host cells.

Because wolbachia infect multicellular organisms, they often cluster in the reproductive tissues where they are transmitted to gametes and the next generation. Furthermore, to facilitate their vertical transformation they routinely affect the reproductive phenotype of the host to their benefit.

Considering how most membranes are maintained and enlarged, such features would be diluted.

I think you’re getting it. But is there anyway to apply this to fossil evidence?

Peez,

I and pz have already showed that not all biologists see “evolution” as only change in allele frequency over time. In fact, last year in one of my introductorily graduate evolutionary biology classes we discussed at length the various definitions and descriptions proposed by biologists. I’ll see if I can find the literature that we read on it.

Please see above for my short synoposis. There are some more links floating around this thread. And, yes Wolbachia infection and the phenotypic results of it are a trait of the population.

Well, I think these discussions started when DD said on the first page that only genes are passed on from parent to offspring. I think both he and Oolon both made statements on the fourth page that suggested that organisms can be reduced or almost reduced to their genes. I don’t think you can take my comments as erecting a strawman to your position, since they weren’t meant to apply to what we are also discussing in this thread.

Sorry for any confusion.

Doubting Didymus

You do? I was under the impression that I was running contrary to your opinion. I knew about wolbachia already, and I agree that this kind of infection is both heritable and phenotype altering. My point is that, since the wolbachia inherited (through adaptation or some for some other reason) the ability to change the host phenotype, that ability can be thought of in terms of hertiable units when considering the evolution of that ability.

Diluted a lot or diluted a little? If diluted a little, does the 'fading' of the membranes mutant feature occur slowly enough for natural selection to maintain it? I would not say so at a guess. I strongly suspect that membranes can not be adequately copied to the next generation.

If the features of my mothers membranes are faded in me, they must fade even more in the next generation. Thus: evolution can not accumulate by the copying of cell membranes.

I do not see your point. If we hypothetically agreed that evolution is driven by the inheritance, mutation and selection (or drift) of genes then we can apply that knowledge to any fossil record evolutionary patterns we can see.

As a small example, if phylogenetics establishes which lineages possess that famous gene that influences eye development (the technical name of which I have forgotten. Hox something?), Then we can veiw the fossil record and have a look at what the ancestral fossils of the appropriate period had. If we could find a gene or set of genes that, when removed, caused a bird to grow scale structures instead of feathers, then similarly, we can establish when and in what lineage those genes began to develop and then see what the fossil record says about that time and that lineage. If we see that that is the time that feathered lizards began appearing, then we could make the historical judgement about when and where the genes for feathers arose, and what they were.

In short, we can apply genetic knowledge to fossils by examining the 'effects' of those genes on the bones of the now fossilised species.

On another note: what does it matter? If evolution is driven by genes than we can talk about that without knowing exactly what those genes were. In the blind watchmaker dawkins constructs a sexual selection positive feedback theory of weaverbird tail length from a gene centric veiwpoint without naming the genes responsible or attempting to extract and veiw them. Similarly, even if there was no way of establishing the exact times, locations, or causes of historical mass extinctions we could still theorise that they play a part in evolutionary history.

If I said that, it is not what I meant. All I was expressing was the standard gene centric veiw of evolution, that phenotypes evolve by changes in genes and not through any other factor that an individual recieves from its parent.

I said that proteins can be 'reduced' to genes.

Look, using the word 'reduced' is annoying. I would prefer to say that genes have 'power' over the development of features. Thinking about it this way, we are no longer talking about reducing features to the actions of genes, we are talking about attributing the evolution of those features to historical alterations in genes. Environment effects evolution. How? By influencing the gene pool. You could say that we gene centrists are 'reducing' the evolutionary process to genes, but not reducing the development of organisms to genes.

I will also add my voice to Peez's in request of examples of heritable factors that are not genes. I am sure they exist, but have not yet seen any examples applicable to humans. Wolbachia may be heritable, it is true, but what is it about wolbachia that makes them copies of my parent's wolbachia? I suggest that it is the wolbachia genes that make them copies, or at least some other fairly permanent heritable phenotype altering factor, though I cannot imagine what this other factor might be.

RufusAtticus

Yes, but that ability is not part of the gene pool of the host. It is part of the gene pool of the parasite, but it affects the host.

Yes, this is true in humans.

Your example works well if we have extant populations related to the fossil series, but what happens if we have a fossil series with no such living relatives? How do you apply knowledge of extant genes to trilobites? What happens if we are looking at a trait of a fossils for which we have no genetic evidence for?

But if evolution is only the change in allele frequencies in a gene pool, how are you going to say that evolution happened if you don't have a gene pool to look at?

Like you said, the environment influences gene pools. How then can you reduce evolution to genes without the environment to go with it? By colapasing everything to genes, you are removing key historical non-genetic and abiotic factors that influenced the "path" that the gene pool took.

Wolbachia is one such heritable factor that is not genetic. Yes, Wolbachia have genes and gene pools, but that applies to Wolbachia evolution not the hosts'. Wolbachia are not part of the hosts' gene pool although they are vertically transmitted from parent to offspring. They also change the traits of the population sometimes even causing speciation in the host.

If we observed an asexual population being descended from a sexual population we would consider that evolution. Right? Why does it matter if the heritable mechanism of that trait it part of the population's gene pool, or due some other factor?

Doubting Didymus

Then we agree; the evolution of changed phenotypes in the host is the result of the evolution of the genes of the parasite.

Then we can say nothing specific about the genes of that fossil species. So what? That does not mean that the fossil species' evolution was not the same gene driven evolution that we see in modern species today. You do not need to see the actual genes in order to think about evolution in terms of genes. I gave the example of Dawkins' theorising on the weaverbird tail. Dawkins has not performed phylogenetic analyses on the weaverbird, nor on any of its relatives. In fact, for all intents and purposes the weaverbird may as well have been known only by fossils, and yet it is possible to theorise about its evolution in terms of its genes.

I don't understand your point. We cannot see the gene pool today, therefore the gene pool was not very relevant in the evolution of the fossil species? If evolution is to do with genes today, then evolution was to do with genes in the far past. I don't see what difference it makes if we can see the genes or not, we have no reason to suspect that evolutionary mechanisms were different for species that do not have extant descendants.

Not a bit of it! When did I ever imply that genes are the only factors that influence evolutionary history? Saying that evolution is the history of gene lineages does not presuppose that nothing but the genes themselves can influence that history.

I am not removing key historical non-genetic and abiotic factors at all. Surely you can see that?

All gene centrism implys is that for non-genetic and abiotic factors to effect evolution, they must be having effects on the genes. That makes them just as important to the gene centric perspective as they are to every other perspective of evolution.

Who said the genes have to be my genes? The phenotypic changes in me are a part of the extended phenotype of the wolbachia and are therefore fue to the genes of the wolbachia.

Ah, you say, but my own genes are being altered by the wolbachia as well! This is true, but it is also perfectly consistant with gene centrism. Wolbachia induces speciation by creating an infected population that loses or reduces the ability to breed with non infected populations. In this way, wolbachia infection is very similar to geographical isolation. It is an environmental factor that is influencing the evolution of the gene pools of wolbachia hosts.

I reiterate: Why has my phenotype changed?
Because of the genes that make up the phenotype of my parasite.

Why have my genes changed, and my population speciated?
Because environmental factors (a population of parasites) have induced reproductive isolation, and thereby, my genes have become too different from my parent species to reproduce with them.

RufusAtticus

DD,

Put it this way, Wolbachia have evolved the ability to affect the reproduction of their hosts. As such this can have extreme repercussions on the evolution of the host populations. I restate this because your above statement can be read as arguing that after Wolbachia infect their hosts, they evolve the ability to screw with its reproduction.

But if evolution is only the change in allele frequencies, then how can you know the weaverbird evolved without knowing its gene pool? You can’t do allozymes, RFLPs, or microsatellites on fossils. Obviously, since you say that evolution has happened here there is something else you are using other than the change in allele frequencies to determine that. What is it?
Because if we define “evolution” as the change in allele frequencies in a gene pool, then we can’t detect “evolution” if we don’t have the gene pool. I’m not saying that we can’t detect evolution without a gene pool, I’m just pointing out the inadequacies of the allele-centric definition when applied to fossil series.
Okay, that is clearer than your previous statement, “You could say that we gene centrists are 'reducing' the evolutionary process to genes, but not reducing the development of organisms to genes.”
Well if you say that a population evolves by changes to the allele frequency of its gene pool, then the genes must be those of individuals in the population.
Please describe what you mean by “extended phenotype” in this context.
But wolbachia don’t modify the genes of the host (AFAIK). For example, some wolbachia make insects produce only daughters by destroying spindle fibers in meiosis so that diploid gametes form.
Yes, but that factor itself is a phenotype of the population and not part of geography or environment of the organism.
Actually, speciation due to wolbachia is not due to changes in the hosts’ genome, but rather that having wolbachia prevents the gene exchange. In some instances this is due to wolbachia destroying “hybrid” zygotes. In others it is due to the wolbachia preventing “cross” fertilization from occurring. Yes such barriers do eventually cause drift to affect the hosts’ genome, but there is no reason that we should wait until that happens to say that the host population has changed.

~~RvFvS~~

Peez

I have scanned a number of the sites linked to, but I saw nothing that suggested that wolbachia infection should be considered evolution. Instead, there were comments that made it clear that such infection is not considered evolution. If I missed something specific, please direct me to the right place.

Peez