Peez

Of course not. Not unless you are using these terms creatively. A population of 100 diploid individuals with 50 A alleles and 150 B alleles increases in size to a population of 200 diploid individuals with 100 A alleles and 300 B alleles. Allele frequencies have not changed (25% A and 75% B), there has been no evolution by the ‘allele-frequency' definition, but there has been evolution by the definition that you proposed. With respect, please reread the question. I did not ask about the host phenotype. Once again, I did not ask about the host's phenotype. Are you suggestion that the host cannot evolve without some change in the wolbachia phenotype? I do not see what "point of view" has to do with it. I am asking about inheritable change in wolbachia without any genetic change. I would argue that these are not "inherited" as such, but are rather learned. I presume by your choice of these examples that you know of no anatomical, physiological, cellular, subcellular, or unlearned behavioural traits that humans possess that are not inherited through DNA?

Peez

Peez

The biological species concept is typically expressed something like: (from Futuyma, 1998) I suppose that some here might wish to expand that to include the exchange of non-gene units of inheritance. The point is that the populations do not need to be actually interbreeding, they must only have the potential to interbreed successfully. Of course, I am also likely the only one here with a PhD in evolutionary biology . I certainly do not consider myself "Dawkinsonian", and I do not think of most evolution in terms of "selfish genes". Like every other evolutionary biologist that I have ever discussed it with, I define evolution in terms of changes in allele frequencies. This is hardly an unusual or extreme position.[quote][b]

Peez

Doubting Didymus

One of the things that always strikes me about this debate is the amount of agreement that goes on between the various veiwpoints. It is surprising that there is so much focus on the few small differences.

To clear things up, I have a few questions for peez.

If mitochondria had kept their genome intact and did not share it with the nuclear genome, would they count as heritable? If not, why not? For all intents and purposes they would perform the same function and have the same effects, so what difference does it make if they share their genes with the nucleus?

Would extraterrestrial life have DNA? No, the chances against it are astronomical. They would use some other method of heritability. Given this, isn't it more sensible to use a definition that speaks in terms of a more general 'heritable unit' that posesses the three (and a bit) characteristics that I listed above? That definition is the one that I most often come across from professional evolutionary biologists, including Dawkins. What do you think of it?

RufusAtticus

Doubting Didymus,
That’s what the “usually” is for.

Well, evolutionary units can be arranged into nested hierarchies, so it all depends on the question you are asking where you establish the units.

Peez,

Hmmmmm, let’s take a closer look at that example.

Assumptions:

• Panmictic sexually reproducing diploid population
• No migration, mutation, selection, or differential reproductive success
• One diallelic locus (A/B)
• When the population decreases, the individuals that die are chosen randomly.
• When the population increases, the individuals that are born are due to the random fusion of gametes.
• Only One population change event happens per time interval.

Terms:

p(t) = the current frequency of A alleles at time t
q(t) = 1.0-p(t)
N(t) = the population size at time t
Na(t) = the number of A alleles at time t, Na(t) =2* p(t)*N(t)
d(t) = |Na(t+1)-Na(t)|, the difference in the number of A alleles from t to t+1

Population Change:

1. More Common Case: Clearly if 2*p(t)*(N(t)-N(t+1)) is not an integer than there is no way to maintain the frequency.
2. Less Common Case: If 2*p(t)*(N(t)-N(t+1)) is an integer, then it is possible to maintain the same frequency, although it is rare. Because the alleles that are added or removed are sampled at random, the actual number of class A affected has a Binomial Probability, where

• P{d(t) = d} = [m!/d!/(m-d)!]*[p(t)^d]*[q(t)^(m-d)], where m = 2*|N(t+1)-Na(t)|.

So in this situation, what is the probability that p(t+1) = p(t)?

• P{p(t+1) = p(t)} = P{d(t) = p(t)*m}

This can be found by plugging into the above equation. So in your example, the probability that your population of 100 individuals doubles its size and maintains its allele frequency is 0.065. Now that is just at one diallelic locus. For n independent loci the probability would be 0.065^n. If n=20, the probability that the gene pool doesn’t change is 1.83E-24. It gets even less likely to stay constant if the loci have many segregating alleles.

Conclusion:

The probability of a change in population size not affecting the gene pool is very very very small.

Although your situation is an example of a population size change that doesn’t effect the gene pool, it is so unlikely to happen in real life that it is safe to say that a change in population size changes the nature of the gene pool. Thus it is evolution, even in your view.

Actually you did. If you did not want “the wolbachia phenotype in the host's great-grandchildren” to mean “the host phenotype due to wolbachia,” then you should have said “wolbachia’s” or simply “the host’s wolbachia’s phenotype.” Now to answer your new question, if the mutation doesn’t change the wolbachia’s phenotype, then its descendents’ phenotype doesn’t change either, ceteris paribus.

No, I’m saying that the host’s traits will only evolve due to wolbachia evolution, if said wolbachia evolution produces a phenotype that effects the host. Of course, the host can still evolve from other pressures.

Point of view makes a big difference. We’re not looking for an inheritable change in wolbachia, but rather an inheritable change in the host. Wolbachia are one such inheritable change.

You’re shifting your goal posts. You asked for non-nucleotide inheritance in humans. I gave you some great examples from evolutionary biology. Now you ask for non-nucleotide inheritance that is not a “learned” trait. Inheritance is inheritance, whether it is vertical or horizontal. Why does a trait that is acquired after conception, not count as an inherited trait? Why does it matter whether I inherit my mother’s language via auditory communication instead of from the ovum?

Not me. As long as the primary units of inheritance can’t be exchanged, the populations will still drift apart.

Well I’m in the second year of my doctoral work towards one.

See above, QED.

~~RvFvS~~

[ November 12, 2002: Message edited by: RufusAtticus ]

[ November 12, 2002: Message edited by: RufusAtticus ]</p>

Peez

I believe that this is a question of semantics. It is a question of what constitutes an individual organism. Since mitochondrial proteins are largely constructed using ‘plans' from the nucleus, I do not consider them independent organisms. Rather, I consider them a part of the cell. Note that this is a tangent, and even if wolbachia were considered in the same way as mitochondria, the inheritance would remain genetic (as far as I have been able to determine). But to answer your question, I do consider mitochondria to be heritable in the same sense that I consider arms to be heritable. The distinction is whether they are considered separate organisms, but I stress that this is irrelevant to the issue of whether or not the inheritance is through nucleic acids. Who knows? I would tend to agree that, at the very least, there would be some differences. On the other hand, I would hesitate to make such a comment with certainty. Probably. I scanned back a bit but could not find it. I do seem to remember seeing it, but could you post it again? Meanwhile, please note that I am not adverse to a more general definition of inheritance, and I do not think that inheritance must occur only through nucleic acids. I am merely saying that, with the exception of one unusual and very limited example (cilia orientation in a certain group of protists), I have seen no indication that it does occur through anything other than nucleic acids. Thus, the "allele-frequency" definition of evolution is practical. I suppose that one could easily generalize this definition by taking a more general definition of "allele", so as to include non-nucleotide information that is inherited. After all, "allele" does not have to be explicitly nucleic acids.

Peez

Peez

Actually, no. I only assumed that the numbers that I gave were correct, nothing more. Again, no. I made no assumptions about why the numbers were the way they were, only that the numbers given were accurate. I did not assume that this was the only locus in the organism, or even that influenced a particular trait. Indeed, I did not even assume that any trait was influenced at all. I also did not assume that there were no other alleles in other populations. It should be obvious that the same argument can be made for multiple alleles and multiple loci. No, certainly not. It is plain from my example that it is unlikely that the individuals "are chosen to die randomly", since such random selection with such a sample size would usually change allele frequencies to some extent (i.e. genetic drift). If anything, the individuals that die were chosen to represent the original allele frequency (and therefore decidedly non-randomly). However, more to the point, it is absolutely irrelevant how the allele frequencies remain the same. No, see above. No, again the only thing relevant to whether or not evolution has occurred (according to the ‘allele frequency' definition) is the change in allele frequency over time. With respect, you have completely missed the point. I am perfectly aware of the issues that you are raising, but they are entirely irrelevant to the point that I was making. Essentially what you are arguing, if I understand you correctly, is that it is unlikely that a small population will not evolve at all (given the ‘allele frequency' definition). I agree. This does not contradict my position at all. I am not claiming that evolution cannot or even does not occur when a population increases in size, I am arguing that a population increase in and of itself is not evolution. In fact, you can do the same math to show that it is extremely unlikely that a small population will not evolve even if the population size remains the same. It is also safe to say that directional selection on a heritable trait will produce evolution, but that does not make natural selection the same thing as evolution. The point was that a change in population size in and of itself is not evolution as I understand it, but is would be evolution under the definition that you supplied. It was clear to me . Let's not get into a spat about this. I apologize again, as you still do not seem to be getting the question that I am trying to ask. I did not say that the mutation would not change the phenotype. I am asking about a situation in which we change the genetic material (DNA that is expressed, that influences the phenotype of the wolbachia cell) only in the wolbachia (all wolbachia cells in the host), and look at the descendant wolbachia (wolbachia that have descended from the wolbachia in the host, that is the wolbachia that we have genetically manipulated) a few host generations later (for example, in the great-grandchildren of the aforementioned host). Then we change the wolbachia phenotype without changing the DNA, and look at the descendant wolbachia a few host generations later. In each case, is the wolbachia's phenotype (the phenotype of the wolbachia themselves, the ones in the great-grandchildren of the original host) changed due to our manipulation? I think that I understand. I also disagree, of course. The mere fact that the hosts phenotype has been changed does not constitute evolution as I understand it. Only if you use "inherit" in a certain way, but this is still not relevant to the issue of evolution without any change in allele frequencies. The wolbachia themselves carry alleles. If you wish to include the passing on of wolbachia as "inheritance", then I would argue that this inheritance (as it applies to evolution) is ultimately through the wolbachia genes. Please be polite. I am not denying that these can be considered "traits" of humans. In that sense, these certainly can evolve without any change in allele frequency. Please slow down. Traits like language and culture certainly do evolve, but including these as examples from "evolutionary biology" is not necessarily valid. That being said, I am not trying to deny this here. Yes, I am. It has been claimed that such inheritance occurs, e.g.: and and and (quotes from pz) This paints a picture of a substantial role of non-nucleotide inheritance in the evolution of the morphology and biochemistry of organisms. I have no problem with the evolution of culture and language, but I believe that different theory is involved. Thus I do not see the utility in extending the definition of "evolution" in biology to necessarily include such phenomena. Meanwhile, I am looking for some indication that our understanding of the evolution of morphology, physiology, and cellular biology may be enhanced by using a more broad definition of evolution. I realize that you may not share pz's opinion in this particular case, but if you do I would be grateful for an example. You can define it that way, of course. It does count as an inherited trait if you use one definition, it does not count as an inherited trait if you use another. The issue here (unless I am mistaken) is the definition of evolution in biology. I do not see how the evolution of culturally transmitted traits (memes?) should be treated the same as genetically transmitted traits. The theory that covers these phenomena appears to be different, so I don't understand why they should be lumped together. I am sorry, I don't understand you here. Congratulations. The worst is over (I am assuming that you have completed your comprehensive exam by now). I was not trying to "pull rank" by mentioning my qualifications, I was only responding to the suggestion that I was taking a different point of view than others here, and that this point of view was rather extreme. I thought that my qualifications would put my point of view in context, that is all.

Peez

RufusAtticus

Peez,

Re: The Model
The model I presented was based on the situation you outlined. When ver I do a model, I state up front what assumptions I am using. Those assumptions establish a typical population with no evolutionary forces except drift due to change in population size. Sure you can posit that other evolutionary forces restore the allele frequencies after a population size change, but that doesn't change the fact that any change in population size is virtually gaurenteed to change the make up of the gene pool. The model shows that evolution due to drift will occur in any finite population, not just small ones. The point was to show why the situation you outlined is not an adequate rebutal to my points because it is guarenteed to almost never happen.

Re: Wolbachia Question
If the wolbachia genes are modified, which in turn changes the wolbachia phenotype, then its desendents' phenotypes are also modified, ceteris paribus. If the wolbachia phenotype is changed, without modifying its genes, then its descendents' phenotypes could either change or not, depending on how the wolbachia phenotype is changed and wheather such a change is passed on to daughter cells.

Re: "Learned" Traits
Can you please provide me a defination of an inherited trait that makes no assumption about the mode of inheritance, but still disqualifies "learned" traits?

Re: Speciation
My point is that I see no necessary reason to expand speciation mechanisms to account for anything other than isolation of genepools. Of course, if a population primarially transmits its traits in some non-nucleotide form, then speciation mechanisms would have to account for this difference.

~~RvFvS~~

[ November 14, 2002: Message edited by: RufusAtticus ]</p>

Doubting Didymus

Peez wanted me to repost this. It is the most robust definiton I have come across.

I suppose tha actual definition would be: 'a change in the frequency of evolutionary units', requiring the following backup information:

My earlier post:
"I define evolution in terms of any units with three properties:
Heritability: the units must get themselves copyied with enough precision to overcome information loss.
Mutability: A unit that cannot change its nature in any way can never change over time.
Differential replication efficacy: Some units must be capable of becoming better at copying themselves than other units (or technically, simply better at copying than they once were). Without this, units can be heritable and mutable, but selection can achieve nothing and evolution is severely limited.

For evolution to be interesting, I would add a fourth attribute, which I read about in "levels of selection" by someone or other. That is: the unit must have a large future potential. To illustrate this I like to think of the clay crystal replicator theory. Clay crystals (might) exhibit heritability, mutability, and the ability to become better replicators, but I doubt (though I may be wrong) that they have the potential for this evolution to ever acheive anything much more complex than a clay crystal. Technically, this last is not nessecary for evolution to theoretically occur, but it is certainly neccesary for evolution that produces something like us.

Dawkins defines this unit as the gene, and I would agree, but the above definition is a little broader. Certainly this unit was not always the gene, and an alien species would probably have a totally different kind of unit."

Peez

You are still missing the point. I did not present that example as a model of how evolution might or might not occur. I was merely trying to explain why your definition seemed to me to be much too general. In particular, if you submit a paper to a journal and claim to have demonstrated evolution just by showing that population size has changed, the paper is not likely to be taken very well. The issue that I was raising was not that evolution will not occur when population size increases. In fact, by the same argument, evolution will almost always occur with or without any change in population size. Nevertheless, a change in population size in itself is not evolution (as far as I understand it). O.K., now please explain how the wolbachia phenotype could be passed on to daughter cells over several generations. Why? The definitions that I have seen goes something like (Drickamer et al. 2002. Animal Behaviour, Fifth Edition. McGraw-Hill. pp. 396-397)or (Futuyma. 1998. [i[Evolutionary Biology, Third Edition[/i]. p. 579) I am not the one trying to avoid specifying the "mode" of inheritance, and I am perfectly happy with these definitions. Certainly they are not perfect, but they seem very workable to me. This was my point.

Peez

Peez

Thank you for posting it again. This is fairly good, but since you asked I will offer my critical assessment:

In principle I do not see a problem with evolution without "mutability" in the units that you describe. Certainly evolution will not go very far without such "mutability", but I don't see it as necessary in the definition of evolution. Perhaps this relates to the "large future potential" (LFP) that is discussed. At first glance LFP seems like an awkward patch rather than an integral part of the definition. I do not think that it is necessary, since we already have to distinguish between biological evolution and other types (e.g. stellar evolution). Since clay crystals are not alive (let's not get into a ‘definition of life' debate), the definition of biological evolution does not need to be concerned with it. I think that you recognized the distinction, but I think that it is more elegantly dealt with by referring to living organisms. This is not a perfect solution, as there are shades of grey with regards to "life", but it seems a practical approach.

The qualification "Some units must be capable of becoming better at copying themselves than other units" is imprecise, or at least possibly misleading. Evolution occurs when some units are copied more than others, but not necessarily because they are "better at copying themselves" (which implies superior copying ability). A unit with the same copying ability as other units, or sometimes even with an inferior copying ability than others, can increase in frequency just by chance ("unit drift" ). I am not sure why you included "(or technically, simply better at copying than they once were)." I can imagine a scenario in which a unit is poorer at copying itself than it once was, and yet is becoming more common in the population (the other units in the population are doing even worse). Then the line "Without this, units can be heritable and mutable, but selection can achieve nothing and evolution is severely limited." seems to relate again to the LFP concept.

Genes were not always the units of heredity, but that is trivial. We simply did not know how heredity worked until Mendel worked out "particulate inheritance". Although he didn't use the same term, Mendel was talking about genes. Of course inheritance is often much more complex than simple Mendelian genetics, but I have yet to see any evidence that we need to define evolution in terms of loosely-defined "units" of inheritance rather than genes. For that matter, why not just define "genes" more loosely? This would make much more sense to me, since it would take into account non-nucleotide inheritance outside of the context of evolution as well. Perhaps "allele" could be defined as a unit of information that is inherited. This would allow us to discuss inheritance without having to work out what the particles of inheritance are, and would allow us to define evolution in a simple and general way. Meanwhile, since I have only seen one very limited example of non-nucleotide inheritance, it does not seem to be a pressing issue.

Thanks again for reposting that stuff, it is appreciated.

Peez