How can scientists possibly know ... ?? An open exploration thread

[holdon]

That is the process of evolution. There are two ways in which this produces new species:

1. Chronospecies A->a1->a2->a3->etc, etc, etc, where each a# is a variant of its predecessor. Carry this on long enough and aN may be different enough from A to be considered a different species. Note that in this scenario, we always have one species. It changes over time, with each variant replacing its predecessor.

What "variants" are you talking about? The phenotypes? Or the alleles?

2. Cladistics or sister species: Population A subdivides into two groups. Both evolve as above, but because they are separated from each other, they evolve in different directions. After a time the two populations do not, or even cannot, interbreed even when given opportunity to do so. In this case one species is ancestor to two species so the number of species is increased. We can also check that the new species do not interbreed with each other, and sometimes we can also check that they no longer interbreed with the parent species either.

In either case, you have a new species. This, by definition, is macro-evolution. It did not require any change in the process of evolution.

The process of evolution gives us both micro-evolution (change within the species) and macro-evolution (new species).




Why do you assume it is not measurable? What is there about the frequency at which alleles or character traits appear that is not measurable? What is there about a change in the size or placement of a bone (think about reptilian jaw bones becoming mammalian ear bones) that is not measurable? What is there about a DNA sequence or the amino acid sequence of a protein that is not measurable?

What is not measurable is what part natural selection contributed to any of those changes.

Natural selection has nothing to do with changing the genes themselves. What natural selection does is change the frequency with which certain versions of a gene (alleles) appear in a population.

So, natural selection cannot explain genes changing. Therefore it cannot be measured as to that aspect.

Natural selection does not create a gene for melanism. It does, however, determine whether moths that carry the gene will be rare or plentiful.

And as I told you before: n.s. apparently never wiped out the varietal breadth.

If we have changed from having 95% of the population with the gene to having it appear in only 5% of the population, that is a considerable change for that particular trait.

And I thought you said hereabove n.s. didn't change genes???

If we also have other character traits changing as well, (for natural selection acts on the whole organism at once, not just one character at a time) there can be considerable change over a few generations. And, of course, the more generations, the more change there may be.



Did he assume it or did he observe it? One does not call what has been observed an assumption.

And I thought there was no "biological advancement"? Are you now saying there is/was?

Actually, as far as I know, Darwin did not observe any simple forms. Micro-organisms had only recently been discovered and Darwin did not study them much if at all. All the examples he gives in his writings are of complex organisms. He was certainly totally unaware of micro-fossils.

So, he apparently did not observe a progression from simple to complex forms. Did he assume any such thing? Well, I have read Origin of Species, and I don't recall any passage in which he makes that assumption. Can you cite such a passage?

I cited this sentence by him already before: "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."

Now, since Darwin's time, we have explored the fossil record much more thoroughly and developed much more exhaustive studies of micro-organisms generally. It would be idiotic today to deny that simple organisms existed for a long time before any complex organisms appeared. The simpler prokaryotic cell is the only sort of fossil found in the first 2 billion years of the fossil record. And there is still another 700 million years before the eukaryotic cells developed complex multi-cellular forms. But all this is observation, not assumption.

And how was that fossil record established?

 

[holdon]

Well, that's exactly why you don't get what I'm saying. Why would I care what happens if I try to cut a loaf or brick in half infinite times? (You get atoms.) Why would I care what happens if I try to travel near the speed of light? (Relativity.) Why would I care about what makes the Moon go around the Earth? (Gravity.)

Why would I care about wanting to include lizards and cats in one class? Because trying to do so, and failing miserably without including a whole lot of other animals, demonstrates on the macroscopic level a unique cladistic system which lends itself powerfully to an evolutionary explanation.

Suppose I wanted to taxonomically classify motorcycles, bicycles, tricycles and cars. I could note, for example, that motorcycles and bicycles have two wheels, while tricycles have three and cars have four. I could then invent three clades: Bicyclidae, Tricyclidae, and Quadricyclae. I could also note that motorcycles and cars have internal combustion engines, while bicycles and tricycles don't. I could then invent two clades: Pyrodynamiae, and Pedodynamiae (Pig Latin for "moves with fire" and "moves with legs"). I could note that bicycles, tricycles and motorbikes are steered with handlebars, while cars employ a steering wheel. There's another possible taxonomy.

This demonstrates the general principle that no unique hierarchical principle needs to exist for groups of designed objects. It's not unique to transportation. When a computer has an AMD CPU, for example, that doesn't automatically guarantee that it will have a Samsung hard drive, a Sony LCD monitor, or Windows Vista.

Take a look, however, at life. Suppose I try to create a classification system in which I start by lumping cats and lizards together in a category, and everything else in a different category. How might I justify that? Absolutely no way. (Other than the trivial justification "I said so!") For in what morphological characteristics are cats and lizards more similar to each other than anything else? Are they both tetrapedal? But so are dogs and goannas and dinosaurs and rabbits and people. Do both have jaws? But so do all fish and all mammals. Do they have segmented bodies? (Yes, they do. Your fancy textbook should have something about that under embryonic development.)* So do all the other, uh, animals that have segmented bodies (can't remember the technical name offhand), all the way from whales to worms.

As a matter of fact, the smallest set of all living organisms that would contain both cats and lizards is the set Reptilia inclusive - namely the union of Reptilia, Aves, and Mammalia. Let's call this big set Felidasauri. (Heh heh.) [EDIT: The proper name for this taxonomic clade is Diapsida; nevertheless, I preserve the original "name" to show where it came from.]

Would the existence of a unique clade Diapsida be logically necessary within an evolutionary framework? Almost certainly. And what do we observe in the real world?

(It's "tetrapodal", not tetrapedal. If you're talking Latin and such)
Anyway, so you think that because you can put "wheels" together, they must have evolved 1 from the other? Which one was first: the complex 4 wheeler, the less complex 3 wheeler, or the even less 2 wheeler or 1 wheeler? Or could you have one without the other?

 

[shernren]

(It's "tetrapodal", not tetrapedal. If you're talking Latin and such)
Anyway, so you think that because you can put "wheels" together, they must have evolved 1 from the other? Which one was first: the complex 4 wheeler, the less complex 3 wheeler, or the even less 2 wheeler or 1 wheeler? Or could you have one without the other?

Um, my entire point is that bicycles and tricycles and motorcycles and cars have no objective classification hierarchy.

Do you agree that life has an objective classification hierarchy? That there is one single smallest group that includes cats and lizards? That given any set of life-forms, there is one single smallest group that includes them all?

 

[gluadys]

What "variants" are you talking about? The phenotypes? Or the alleles?

The phenotypes. Alleles are only subject to natural selection when expressed in the phenotype.

What is not measurable is what part natural selection contributed to any of those changes.

That is like saying you cannot measure the contribution of red paint to the red colour on my walls.

The changes are the measure of natural selection.

So, natural selection cannot explain genes changing. Therefore it cannot be measured as to that aspect.

Which is like saying that a thermometer cannot measure acceleration. Obviously, you have to use the correct tools to get the correct measurement.

You want to look at genetic changes, you have to look at rates and types of mutation, not natural selection.

I expect one underlying difficulty here is that you are not differentiating between changes in individual organisms and changes in a species. Mutations cause the first; natural selection is the principal cause of the second.

And as I told you before: n.s. apparently never wiped out the varietal breadth.

So? I don't get your point here.

And I thought you said hereabove n.s. didn't change genes???

It doesn't. Did you think that the very genes of the moths changed? Did you think individual moths changed from white to black or back again? Or did you think that pairs of white moths produced black baby moths?

You would be wrong on all counts.

The genes did not change. What changed (and this is what natural selection is) was how frequently black or white moths reproduced. When black moths reproduced more frequently than white moths (because birds had eaten most of the white moths but fewer of the black), more of the next generation were black. When white moths reproduced more frequently than black moths (because in unpolluted areas, most black moths tended to be eaten while white moths were eaten less often) more of the next generation were white.

No change in the genes themselves was necessary. Only a change in which variant was able to reproduce more frequently.

And I thought there was no "biological advancement"? Are you now saying there is/was?

What did I say that suggested advancement? I said there would be considerable change over time as various traits were subjected to natural selection. In your lexicon does "change" always mean "advancement"?

I cited this sentence by him already before: "from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."

And what do you think he meant by "simple" in this context. (Hint: he was not speaking of micro-organisms.)

And how was that fossil record established?

By natural history.

 

[holdon]

Um, my entire point is that bicycles and tricycles and motorcycles and cars have no objective classification hierarchy.

Ok.

Do you agree that life has an objective classification hierarchy?

And what would that be then? Who was so objective as to come up with that one?

That there is one single smallest group that includes cats and lizards? That given any set of life-forms, there is one single smallest group that includes them all?

And based on what criteria? I don't think I understand you.

 

[holdon]

That is like saying you cannot measure the contribution of red paint to the red colour on my walls.

Yes, could be. Because your walls may be red brick or I don't know what.

The changes are the measure of natural selection.

Who is to say? You suppose that whatever changes there are compared to another population, that it must be because of natural selection. Why?

Which is like saying that a thermometer cannot measure acceleration. Obviously, you have to use the correct tools to get the correct measurement.

Yes!

You want to look at genetic changes, you have to look at rates and types of mutation, not natural selection.

To the extend that natural selection could influence rates and types of mutation, you would have to take that into consideration.

I expect one underlying difficulty here is that you are not differentiating between changes in individual organisms and changes in a species. Mutations cause the first; natural selection is the principal cause of the second.

I thought that in this discussion we were interested in the changing (evolution) of species into other new species or whatever.

So? I don't get your point here.

Just to make the point that n.s. doesn't influence that certain alleles exist or not.

It doesn't. Did you think that the very genes of the moths changed? Did you think individual moths changed from white to black or back again? Or did you think that pairs of white moths produced black baby moths?

You would be wrong on all counts.

The genes did not change. What changed (and this is what natural selection is) was how frequently black or white moths reproduced. When black moths reproduced more frequently than white moths (because birds had eaten most of the white moths but fewer of the black), more of the next generation were black. When white moths reproduced more frequently than black moths (because in unpolluted areas, most black moths tended to be eaten while white moths were eaten less often) more of the next generation were white.

No change in the genes themselves was necessary. Only a change in which variant was able to reproduce more frequently.

Precisely! And that's why natural selection does NOT bring about changes in the genes. As you point out here: the same still exist before and after the "dark days".
Therefore natural selection cannot do what you said hereabove: "natural selection is the principal cause of the second" (=change in species).

What did I say that suggested advancement?

Because of Darwin perceiving "simple going to more complex".

I said there would be considerable change over time as various traits were subjected to natural selection. In your lexicon does "change" always mean "advancement"?

No.

And what do you think he meant by "simple" in this context. (Hint: he was not speaking of micro-organisms.)

Well, I don't know what simple forms he exactly had in mind. He spoke about God creating a few or even one, but not saying exactly what it was.

By natural history.

And what is that?

 

[shernren]

Who was so objective as to come up with that one? And based on what criteria? I don't think I understand you.

Gah.

Suppose I try to create a classification system in which I start by lumping cats and lizards together in a category, and everything else in a different category. How might I justify that? Absolutely no way. (Other than the trivial justification "I said so!")

For in what morphological characteristics are cats and lizards more similar to each other than anything else?

Are they both tetrapedal? But so are dogs and goannas and dinosaurs and rabbits and people.

Do both have jaws? But so do all fish and all mammals.

Do they have segmented bodies? (Yes, they do. Your fancy textbook should have something about that under embryonic development.)* So do all the other, uh, animals that have segmented bodies (can't remember the technical name offhand), all the way from whales to worms.

As a matter of fact, the smallest set of all living organisms that would contain both cats and lizards is the set Reptilia inclusive - namely the union of Reptilia, Aves, and Mammalia. Let's call this big set Felidasauri. (Heh heh.) [EDIT: The proper name for this taxonomic clade is Diapsida; nevertheless, I preserve the original "name" to show where it came from.]

 

[gluadys]

Yes, could be. Because your walls may be red brick or I don't know what.

I just told you they had red paint on them. You don't get to change the analogy.

Who is to say? You suppose that whatever changes there are compared to another population, that it must be because of natural selection. Why?

Well, given that you don't seem to understand that mutations and natural selection are different processes, perhaps we need to define what changes we are talking about.

A change in a gene generates a new allele of the gene. This is not caused by natural selection. Natural selection has nothing to do with the appearance of a new allele in a population.

If the new allele affects the relative rate of reproduction, that will change the frequency of appearance of the allele in the population. That, by definition, is evolution by natural selection.

If there are several alleles already in the population, and a new factor in the environment (e.g. pollution) makes reproduction more likely for those with one allele than another, that allele will appear more frequently in subsequent generations. That is also, by definition, evolution by natural selection.

So, if by change, you mean the appearance of a new version of a gene---then, no--natural selection does not cause that. But if by change, you mean that the species in which allele A was more common changes so that allele X is more common, because of an environmental factor, that is natural selection.

Note that the first change occurs in an individual. The second is a change in the population and does not require any change in any individual.

Yes! To the extend that natural selection could influence rates and types of mutation, you would have to take that into consideration.

It doesn't. Mutation and natural selection occur independently of each other. Mutation is an event in the nucleus of a cell. The cell is found in only one organism. Only if the cell is a germ-line cell can the mutation even be passed to another organism.

Natural selection is a population-level phenomenon. One organism is not a population. You can't have ratios of variants when you have only one individual to consider. You can't measure the statistical frequency of alleles in just one organism. These figures which relate to natural selection only have meaning in a population of many individuals.

I thought that in this discussion we were interested in the changing (evolution) of species into other new species or whatever.

Mutation and natural selection are the principal mechanisms of evolution. But evolution should not be equated solely with the appearance of new species. A new species can be, and often is, a consequence of evolution, but a lot of evolution occurs within a species too. Evolution is the changing character of a species, whether or not that leads to a new species. When it does lead to a new species, that is speciation.

Just to make the point that n.s. doesn't influence that certain alleles exist or not.

What ever made you think that point had to be made? That's pretty basic to anyone who understands the process of evolution.

Precisely! And that's why natural selection does NOT bring about changes in the genes.

And where did I ever claim otherwise? Of course it does not bring about changes in the genes. Natural selection brings about changes in the species. It is mutations that bring about changes in the genes.

As you point out here: the same still exist before and after the "dark days".
Therefore natural selection cannot do what you said hereabove: "natural selection is the principal cause of the second" (=change in species).

Are you not overlooking the fact that the species did change?

The problem here is that you are looking for a new species instead of a change in the species. But a new species is not an essential outcome of evolution. Sure, we can and do observe speciation. But we also observe changes in species without speciation. That is the case with the pepper moth. It is a good example of natural selection changing the characteristics of a species. And that is what evolution is: a change in the predominant character of a species (in this case a colour change).

Given the right circumstances, the accumulation of such changes (or even a single change) can also produce speciation. My point is that it is still evolution even when no new species is generated. It is evolution because the character of the species changed.

Now, if you want to go to a different example than the pepper moth, to one in which speciation did occur, we can do that as well, and show how the sort of change that occurred in the pepper moth is the same sort of change that can lead to speciation.

Because of Darwin perceiving "simple going to more complex". No. Well, I don't know what simple forms he exactly had in mind. He spoke about God creating a few or even one, but not saying exactly what it was. And what is that?

Yes, the references is to God creating a few forms or even one. In another passage of Origin, Darwin speculates that all the species of animals known today could have arisen from as few as six original creations, and likewise for plants. He was thinking in terms of what creationists call "fully-formed" complex creatures; perhaps one arthropod, one mollusc, one chordate, one angiosperm, one fern, etc.

So the simplicity was not simplicity of form, but simplicity of ecosystem: a very few, but already complex, species to begin with branching over the generations into the web of diversity we see today, with thousands of species of each type. Nothing to suggest that one type is more advanced than another. Just that each gives rise to endless new forms.

Today, of course, biologists agree that all current species did originate from simple micro-organisms (simplicity of form). But that is a discovery that came later than Darwin. So it would be an anachronism to impose that view on Darwin.

 

[holdon]

I just told you they had red paint on them. You don't get to change the analogy.

Even so, how good is the red paint? Does the stone shine through or not? Or: to someone with red glasses all is red...
Of course analogies are never perfect. But that doesn't change the question: in what measure does n.s. change the species?

Well, given that you don't seem to understand that mutations and natural selection are different processes, perhaps we need to define what changes we are talking about.

A change in a gene generates a new allele of the gene. This is not caused by natural selection. Natural selection has nothing to do with the appearance of a new allele in a population.

If the new allele affects the relative rate of reproduction, that will change the frequency of appearance of the allele in the population. That, by definition, is evolution by natural selection.

If there are several alleles already in the population, and a new factor in the environment (e.g. pollution) makes reproduction more likely for those with one allele than another, that allele will appear more frequently in subsequent generations.

As long as the same environment and its effect on reproduction persist.

So, if by change, you mean the appearance of a new version of a gene---then, no--natural selection does not cause that. But if by change, you mean that the species in which allele A was more common changes so that allele X is more common, because of an environmental factor, that is natural selection.

No problem with that; just to note that n.s. does not explain why any of the alleles would disappear.

Note that the first change occurs in an individual. The second is a change in the population and does not require any change in any individual.

??? How can there be change in a population without change in the individual? (white or dark moths) To have a predominant dark population of moths you must have individual dark moths, no?

It doesn't. Mutation and natural selection occur independently of each other. Mutation is an event in the nucleus of a cell. The cell is found in only one organism. Only if the cell is a germ-line cell can the mutation even be passed to another organism.

Natural selection is a population-level phenomenon. One organism is not a population. You can't have ratios of variants when you have only one individual to consider. You can't measure the statistical frequency of alleles in just one organism. These figures which relate to natural selection only have meaning in a population of many individuals.

Ok

A new species can be, and often is, a consequence of evolution

When is it not?

What ever made you think that point had to be made? That's pretty basic to anyone who understands the process of evolution.

Maybe it wasn't so basic, or you would have gotten it the first time.

And where did I ever claim otherwise? Of course it does not bring about changes in the genes. Natural selection brings about changes in the species. It is mutations that bring about changes in the genes.

Ok, for changes in the species to show, mustn't there be different alleles (= change in genes) in the individuals. Call it mutations if you wish, fine.

Are you not overlooking the fact that the species did change?

Oh my goodness. What do you mean "species did change". I guess we're having a semantics problem here. I thought we were talking about Biston betularia for example.

The problem here is that you are looking for a new species instead of a change in the species. But a new species is not an essential outcome of evolution. Sure, we can and do observe speciation.

Where?

But we also observe changes in species without speciation. That is the case with the pepper moth. It is a good example of natural selection changing the characteristics of a species. And that is what evolution is: a change in the predominant character of a species (in this case a colour change).

Ok, but we're not talking about a new species then. How do you think that could come about?

Given the right circumstances, the accumulation of such changes (or even a single change) can also produce speciation.

What accumulation of changes brings about a new species?

My point is that it is still evolution even when no new species is generated. It is evolution because the character of the species changed.

Now, if you want to go to a different example than the pepper moth, to one in which speciation did occur, we can do that as well, and show how the sort of change that occurred in the pepper moth is the same sort of change that can lead to speciation.

By all means do tell.

Yes, the references is to God creating a few forms or even one. In another passage of Origin, Darwin speculates that all the species of animals known today could have arisen from as few as six original creations, and likewise for plants. He was thinking in terms of what creationists call "fully-formed" complex creatures; perhaps one arthropod, one mollusc, one chordate, one angiosperm, one fern, etc.

Yes, what did he know eh?

Today, of course, biologists agree

Who agrees here?

 

[gluadys]

Even so, how good is the red paint? Does the stone shine through or not? Or: to someone with red glasses all is red...

I specified red paint. I could have used the red glasses analogy instead for the same purpose. But that would be a different analogy. The only time the question of "how much does this contribute to the red colour" would come up is if you mix the analogies and specify that both red paint and red glasses were contributing factors.

But that doesn't change the question: in what measure does n.s. change the species?

By the measure of the change in the frequency at which given alleles occur.

As long as the same environment and its effect on reproduction persist.

Correct. "Environmental pressures" is basically a synonym for "natural selection".

No problem with that; just to note that n.s. does not explain why any of the alleles would disappear.

Why not? Alleles, especially if they are recessive, can fall under the radar of natural selection and so not be easy to eliminate entirely, but it's not beyond possibility either. One way in which an allele could disappear from a species is when a genetic bottleneck occurs.

??? How can there be change in a population without change in the individual? (white or dark moths) To have a predominant dark population of moths you must have individual dark moths, no?

Sure. But you don't have to have any individual white moth change into a black moth. The change in the species occurs without any individual changing.

When is it not?

When no reproductive isolation occurs. The species changes in characteristics, but does not split into separately breeding groups.

Maybe it wasn't so basic, or you would have gotten it the first time.

But i knew that long before we began this conversation, so there has been nothing for me to "get".

Ok, for changes in the species to show, mustn't there be different alleles (= change in genes) in the individuals. Call it mutations if you wish, fine.

A change in a gene (or any genetic material) is a mutation. That is what the word "mutation" means.

The result of a mutation in a gene is a revised version of the gene. Most genes exist in several versions. An allele is one particular version of a gene which exists in two or more versions in the population.

So mutations produce new alleles.

Mutations occur independently of natural selection. That is why the allele favored by natural selection need not be the product of a recent mutation. The allele could have been formed by a mutation that occurred several dozen or even hundreds of generations ago. Or it could indeed be a new allele just created by a recent mutation.

But you are right. There need to be at least two versions of a gene in the population for any selection to occur. Can't have selection when there is nothing to select.

Furthermore, the difference in the alleles needs to be expressed in the phenotype and it needs to make a difference, however slight, in reproductive success. Alleles can generate different characteristics which don't impact on reproductive success. In that case, both variants will occur in the population in a steady Mendelian proportion.

Oh my goodness. What do you mean "species did change". I guess we're having a semantics problem here. I thought we were talking about Biston betularia for example.

Yes, and the predominant colour of the species changed, didn't it? Twice in fact. Once from white to black and then again from black to white.

Ok, but we're not talking about a new species then.

Yes, we are talking evolution and natural selection, but not new species.

What accumulation of changes brings about a new species?

OK. In the moth we looked at a change in one characteristic: colour. Melanism (black colour) in this case was controlled by one gene.

Every creature has many genes controlling many traits and sometimes in many complex ways.

Mutation can occur in any of these genes and affect any of these traits at any time. I think we have already mentioned that on average a newly-conceived mammal has about 100 mutations.

So over time, many characteristics can exhibit variations. And through sexual reproduction, variations from mum get added to variations from dad, so junior gets an accumulation of variations which first appeared in separate families.

Then we get natural selection acting on two or more of these variations, making both of them more frequent than their counterparts: say favoring both a colour change and a change in food supply. Now the species differs overall from its ancestors in two major ways. Just keep adding more of the same and eventually you get a species which is significantly different from its ancestors.


Mind you, this is what biologists call a chrono-species. We can't actually test out whether the current population could have or would have mated with the 100th generation before it. What separates them is time and character traits, enough so that for convenience, biologists give them a different species name.

A clearer case for speciation is cladistic speciation, where one population gives rise to two or more daughter populations, and you can determine by their mating habits whether they are or are not different species.

By all means do tell.

OK. Here is a fairly simple example of cladistic speciation. A new species formed through isolation from its parent species.

http://findarticles.com/p/articles/mi_m1134/is_1_110/ai_70770157Yes,

Isolation is the key ingredient in cladistic speciation. It can begin, as here, with geographic isolation. But there are all sorts of other isolating factors that can come into play.

However, the separated populations are not considered new species until there is evidence of reproductive isolation.

Reproductive isolation may result from a single change in behaviour. Or it may be the consequence of a long sequence of accumulated changes in the separated populations over time. In the second case, one or both populations may have changed enough that they no longer recognize the other as potential mates. In the first case, they may look so similar to the human eye that we cannot differentiate them easily, but somehow they differentiate themselves. What we can expect in the case of such species, is that eventually they will develop physical differences we can perceive without a DNA analysis.

Who agrees here?

I already said: biologists. Pretty well all of them all over the world.

btw, here we have touched on another facet of evolution, and usually the one that draws the most objections, namely the common descent not just of two species of mosquitoes or even of animals as diverse as foxes and wolves, but of all current species from a single universal common ancestor.

That is a topic of its own. But I want only to mention it and not discuss it yet, because the processes of evolution and speciation need to be understood before one can get a handle on common descent.

 

[holdon]

By the measure of the change in the frequency at which given alleles occur.

But that doesn't change the species: B. betularia remained B. betularia before, during and after environmental pressures.

Why not? Alleles, especially if they are recessive, can fall under the radar of natural selection and so not be easy to eliminate entirely, but it's not beyond possibility either. One way in which an allele could disappear from a species is when a genetic bottleneck occurs.

Alleles are variants of genes. Even if all "light" moths disappear, the genes are still there in the "dark" moths. And therefore the light allele (not sure such a thing exists; because several factors may be involved) can resurface anytime.

Sure. But you don't have to have any individual white moth change into a black moth. The change in the species occurs without any individual changing.

Of course. But what I am interested in is if somehow through n.s. genetic information in the population fundamentally changes.

A change in a gene (or any genetic material) is a mutation. That is what the word "mutation" means.

The result of a mutation in a gene is a revised version of the gene. Most genes exist in several versions. An allele is one particular version of a gene which exists in two or more versions in the population.

So mutations produce new alleles.

Mutations occur independently of natural selection. That is why the allele favored by natural selection need not be the product of a recent mutation. The allele could have been formed by a mutation that occurred several dozen or even hundreds of generations ago. Or it could indeed be a new allele just created by a recent mutation.

What example do have of the last case?

But you are right. There need to be at least two versions of a gene in the population for any selection to occur. Can't have selection when there is nothing to select.

Furthermore, the difference in the alleles needs to be expressed in the phenotype and it needs to make a difference, however slight, in reproductive success. Alleles can generate different characteristics which don't impact on reproductive success. In that case, both variants will occur in the population in a steady Mendelian proportion.

Wasn't there a study (or rather several) that showed the majority of alleles did not contribute to any reproductive success? Something about "neutral theory"?

Yes, and the predominant colour of the species changed, didn't it? Twice in fact. Once from white to black and then again from black to white.

Yes, but it remained all the time still good old B. betularia.

OK. In the moth we looked at a change in one characteristic: colour. Melanism (black colour) in this case was controlled by one gene.

Was it? Not that it matters much here, but I'm just wondering if that was ever confirmed.

Every creature has many genes controlling many traits and sometimes in many complex ways.

Mutation can occur in any of these genes and affect any of these traits at any time. I think we have already mentioned that on average a newly-conceived mammal has about 100 mutations.

Do you mean "new mutations", "new alleles"?

So over time, many characteristics can exhibit variations. And through sexual reproduction, variations from mum get added to variations from dad, so junior gets an accumulation of variations which first appeared in separate families.

Or you could say, the variations from dad and mom decreased.....!

Then we get natural selection acting on two or more of these variations, making both of them more frequent than their counterparts: say favoring both a colour change and a change in food supply. Now the species differs overall from its ancestors in two major ways. Just keep adding more of the same and eventually you get a species which is significantly different from its ancestors.

If the environmental pressues were thus maintained you will see that most moths that survive are dark moths: the others are always eaten. But it does not necessarily follow that no "light" moths were born.

Mind you, this is what biologists call a chrono-species. We can't actually test out whether the current population could have or would have mated with the 100th generation before it. What separates them is time and character traits, enough so that for convenience, biologists give them a different species name.

Ah, so the "new species" criterium basically follows the opinion of biologists. Not that this is new, but it is important to note.

A clearer case for speciation is cladistic speciation, where one population gives rise to two or more daughter populations, and you can determine by their mating habits whether they are or are not different species.

Now, the Great Dane and the Chihuahua don't mate. But they are not a different species. So who determines that?

OK. Here is a fairly simple example of cladistic speciation. A new species formed through isolation from its parent species.

http://findarticles.com/p/articles/mi_m1134/is_1_110/ai_70770157Yes,

Sorry, link don't work.

I already said: biologists. Pretty well all of them all over the world.

What if some don't? Are they to be burned at the stake of the "science inquisition"?

 

[gluadys]

But that doesn't change the species: B. betularia remained B. betularia before, during and after environmental pressures.

That is what I have been saying for sometime now. This is an instance of evolution within the species, not evolution leading to speciation.

The process of evolution is the same whether speciation happens or not, but speciation only occurs when you also get isolated populations. The two variants of moths were never isolated and never avoided interbreeding, so although the species changed, there was no speciation i.e. no new species as a result.

Alleles are variants of genes. Even if all "light" moths disappear, the genes are still there in the "dark" moths. And therefore the light allele (not sure such a thing exists; because several factors may be involved) can resurface anytime.

In this case, yes. In fact in many cases that is the situation. Birds still have the genes to grow teeth, but they don't.

However, there are also situations in which the allele itself can disappear from the population, e.g. a genetic bottleneck or a founder's event.

Of course. But what I am interested in is if somehow through n.s. genetic information in the population fundamentally changes.

The function of natural selection is to spread (or prevent the spread) of genetic information that has changed. When changed genetic information is spread repeatedly though a species, the genome of the species is fundamentally changed although natural selection did not generate the new alleles. Mutation did that.

What example do have of the last case?

Do a google on the "nylon bug". There is also a recent mutation affecting human hemoglobin that has shown up in North Africa. Like that which produces sickle-cell trait and sickle-cell anemia, it provides protection against malaria, but without the anemic side effects. Last I heard, geneticists expect it to replace the hemoglobin-S allele in about 50 years in Burkina Faso where it originated.

Wasn't there a study (or rather several) that showed the majority of alleles did not contribute to any reproductive success?

The vast majority of mutations have no impact on reproductive success. So I expect most variations don't either. Which comes down to saying that it doesn't matter which allele you get in the case of many character traits--not from an evolutionary standpoint.

Yes, but it remained all the time still good old B. betularia.

That is why it is called evolution within the species.

Was it? Not that it matters much here, but I'm just wondering if that was ever confirmed.

IIRC

Do you mean "new mutations", "new alleles"?

I would say mutations in this case because not all of them would occur in genes.

Or you could say, the variations from dad and mom decreased.....!

What?!?! Decreased where? Not in mum and not in dad, and since in junior we are adding mum's to dad's not in junior either.

If Mum is passing on alleles A, B and C which do not exist in dad's family and dad is passing on alleles X, Y and Z which don't exist in mum's family, junior is the recipient of alleles A, B, C, X, Y and Z. How is that anything other than accumulation?

If the environmental pressues were thus maintained you will see that most moths that survive are dark moths: the others are always eaten. But it does not necessarily follow that no "light" moths were born.

That is likely true if melanism is the dominant trait, for then there will probably be a source of non-melanic alleles in heterzygous individuals. But if melanism is recessive, all the dark moths will have only the gene for melanism, no non-melanic allele. In that case, if all the white moths were eaten, all the white alleles would also be destroyed.

Ah, so the "new species" criterium basically follows the opinion of biologists.

In the case of chrono-species where there is no practical way to apply the biological species test of reproductive isolation.

Now, the Great Dane and the Chihuahua don't mate. But they are not a different species. So who determines that?

Gene flow. Domestic dogs have basically become a ring species. The two breeds you mention cannot mate directly, but they can still exchange genetic information indirectly via intermediate breeds.

Sorry, link don't work.

Try again. I have checked this twice in preview and it works for me.

http://findarticles.com/p/articles/mi_m1134/is_1_110/ai_70770157

What if some don't? Are they to be burned at the stake of the "science inquisition"?

Actually, if they come up with evidence to support their alternate position, they would probably win the Nobel Prize.

 

[holdon]

That is what I have been saying for sometime now. This is an instance of evolution within the species, not evolution leading to speciation.

I understand. The confusion stems from when you say "change in species". This can mean that the species changed to another one, or that something in the species changed.

In this case, yes. In fact in many cases that is the situation. Birds still have the genes to grow teeth, but they don't.

See, your "still have" is quite an interesting statement. Because do you mean they had those genes from the beginning? (whatever "beginning" means) or is it the fact that the genes are still there, even if "not used"? In either case it proves a remarkable stability of gene information that persists whether expressed or not. By they way as most know, birds do develop a little tooth to hammer through the eggshell, so I am not surprised at all that some gene is found that is responsible for that.

However, there are also situations in which the allele itself can disappear from the population, e.g. a genetic bottleneck or a founder's event.

Again, I have to ask: what do you mean by "allele disappearing"? Do you mean that that allele is not longer (re) produced?

The function of natural selection is to spread (or prevent the spread)

Interesting: if it is both then no change?

of genetic information that has changed.

Again, what exactly do you mean by "genetic information that has been changed"? We know so little as to why certain alleles are made (produced) and retained in reproduction and then whether they are expressed or not and under what conditions. What we do know increasingly is that quite complex control systems are in place as to what exactly gets done in DNA reproduction, so that nothing gets done without "their permission". This explains by the way why "teeth genes" or any others are still there. (of course teeth genes are needed in birds or they won't hatch).

When changed genetic information is spread repeatedly though a species, the genome of the species is fundamentally changed although natural selection did not generate the new alleles. Mutation did that.

How do you know they are indeed "new alleles"? For a certain gen locus, you may find a number of different alleles, but that number is by no means infinite. On the contrary, it seems that the allele variety itself is part of other controlled processes and therefore somehow determined.

Do a google on the "nylon bug".

OK, from what I have read rapidly is that the species is still the same Flavobacterium K172, or something like that. So, no new speciation. It seems just a new variety. But of course if "biologists" want to give it a new species name that may occur. Problem with bacteria is the crossing of course....

There is also a recent mutation affecting human hemoglobin that has shown up in North Africa.

Again, subjective statement: Who knows it wasn't there before? See discovery is not new generation.

What?!?! Decreased where? Not in mum and not in dad, and since in junior we are adding mum's to dad's not in junior either.

If Mum is passing on alleles A, B and C which do not exist in dad's family and dad is passing on alleles X, Y and Z which don't exist in mum's family, junior is the recipient of alleles A, B, C, X, Y and Z. How is that anything other than accumulation?

But what about the alleles that Mom or Dad are not passing on?

That is likely true if melanism is the dominant trait, for then there will probably be a source of non-melanic alleles in heterzygous individuals. But if melanism is recessive, all the dark moths will have only the gene for melanism, no non-melanic allele. In that case, if all the white moths were eaten, all the white alleles would also be destroyed.

No, because the "white" alleles will "keep coming" from heterozygous dark parents. No genetic information is destroyed. Remember Hardy-Weinberg?

Try again. I have checked this twice in preview and it works for me.

http://findarticles.com/p/articles/mi_m1134/is_1_110/ai_70770157

Thanks it works now. From that article: "And the insects continue to evolve. Byrne and Nichols have identified three genetically distinct subvarieties of C. molestus, each one unique to a different subway line: Victoria, Bakerloo, and Central." But what is evident is that from their piece is that the researchers "evolved", the insects are just subvarieties that they discovered.

Actually, if they come up with evidence to support their alternate position, they would probably win the Nobel Prize.

Not so sure about that. Especially since Al Gore got his.... and on what grounds?

 

[gluadys]

I understand. The confusion stems from when you "change in species". This can mean that the species changed to another one, or that something in the species changed.

Basically, the process of evolution is one of changing something in the species. If that change results in reproductive isolation, then one also has a new species.

See, your "still have" is quite an interesting statement. Because do you mean they had those genes from the beginning? (whatever "beginning" means) or is it the fact that the genes are still there, even if "not used"?

It means that the genes continue to be inherited even though they are not being expressed. And that they can be expressed when the inhibiting factor is removed. It also means that since there is an inhibiting factor preventing expression of the genes, it is probable that this came into existence after the genes did, and that earlier versions of birds did have a full set of teeth. The latter supposition is borne out by the fact that fossils of ancient birds did have teeth. So, clearly the genes were inherited from a time when they were expressed and the inhibiting factor is a newer phenomenon that took over from the older condition. IOW the toothlessness of modern birds is a product of natural selection.

Again, I have to ask: what do you mean by "allele disappearing"? Do you mean that that allele is not longer (re) produced?

I mean that no member of the population carries the allele, even in an recessive, unexpressed form. There is no longer any copy of allele in the population to be inherited.

Interesting: if it is both then no change?

Obviously natural selection does not operate in contradictory fashion on the same allele at the same time. It may spread an allele affecting thickness of fur while suppressing an allele affecting the number of teeth. Or it may promote a colour change in one time period and suppress it in another time period.

Again, what exactly do you mean by "genetic information that has been changed"?

DNA sequences that have been changed by mutations or chromosomal rearrangements.

How do you know they are indeed "new alleles"?

Because they did not appear in earlier generations.

OK, from what I have read rapidly is that the species is still the same Flavobacterium K172, or something like that. So, no new speciation. It seems just a new variety.

You didn't ask about a new species. You asked for an example of an allele created by a recent mutation.

Nevertheless, by the criteria used to identify bacterial species, it is also a new species. (Bacterial reproduction is asexual so the biological species test of interbreeding cannot be used.)

Again, subjective statement: Who knows it wasn't there before? See discovery is not new generation.

If it was there before, it would not be presently confined to one small region of Africa. It would have already spread to other malaria-infested regions just as it is doing now.

But what about the alleles that Mom or Dad are not passing on?

That has no effect on the ones they are passing on. Junior is still adding alleles from mum's family line to alleles from dad's family line. (Also, any alleles mum and dad are not passing on are probably being passed on by their siblings to junior's cousins. Even junior's siblings will get a different assortment.)

No, because the "white" alleles will "keep coming" from heterozygous dark parents.

Incorrect. If melanism is recessive all dark parents are homozygous. Heterozygous individuals would not be dark in this case. So there would be no "white" alleles to come from dark parents.

"White" alleles can only come from dark parents when melanism is dominant.

From that article: "And the insects continue to evolve. Byrne and Nichols have identified three genetically distinct subvarieties of C. molestus, each one unique to a different subway line: Victoria, Bakerloo, and Central." But what is evident is that from their piece is that the researchers "evolved", the insects are just subvarieties that they discovered.

Yes, the three sub-varieties in the underground are varieties, not (yet) species. They could become species, time will tell.

However, all the underground mosquitoes are a new species relative to their above-ground ancestors C. pipiens. It is the speciation of the underground population from C. pipiens that I want to focus on.

Not so sure about that. Especially since Al Gore got his.... and on what grounds?

Al Gore is not a scientist and although his cause comes out of scientific research, he is not the researcher, but the promoter of the cause. Hence his prize, appropriately, is not for scientific research but for peace.

A Nobel Prize in biology would require actual scientific research.

Makes me wonder if any of the climatologists who discovered climate change have been nominated or given a prize in their field. It would be very difficult to single out one person's work, but perhaps a prize could be given to the International Panel.

 

[USincognito]

Remember Hardy-Weinberg?

Didn't you read the responses that explained how you were misunderstanding Hardy-Weinburg a few pages back?

 

[holdon]

Didn't you read the responses that explained how you were misunderstanding Hardy-Weinburg a few pages back?

Good that you're following this thread. And what is it exactly that I don't understand about Hardy-Weinberg? Because screaming randomly doesn't help the discussion.

 

[holdon]

It means that the genes continue to be inherited even though they are not being expressed. And that they can be expressed when the inhibiting factor is removed. It also means that since there is an inhibiting factor preventing expression of the genes, it is probable that this came into existence after the genes did, and that earlier versions of birds did have a full set of teeth. The latter supposition is borne out by the fact that fossils of ancient birds did have teeth. So, clearly the genes were inherited from a time when they were expressed and the inhibiting factor is a newer phenomenon that took over from the older condition. IOW the toothlessness of modern birds is a product of natural selection.

There is no reason to believe that ancient birds did have teeth, because there is still a gene that can produce teeth. And as I told you the tooth gene is still fully functional in birds.

I mean that no member of the population carries the allele, even in an recessive, unexpressed form. There is no longer any copy of allele in the population to be inherited.

And we have no evidence of that occuring.

DNA sequences that have been changed by mutations or chromosomal rearrangements.

That is not necessarily "loss of information". Even if DNA 'sequences' are rearranged and therefore 'accepted' by the control mechanisms in place, they can still be functional.

Because they did not appear in earlier generations.

But you have no way of knowing that, because you would have to know all the previous generations.

You didn't ask about a new species. You asked for an example of an allele created by a recent mutation.

Nevertheless, by the criteria used to identify bacterial species, it is also a new species. (Bacterial reproduction is asexual so the biological species test of interbreeding cannot be used.)

Only nobody seem to have given it a new species name...

If it was there before, it would not be presently confined to one small region of Africa. It would have already spread to other malaria-infested regions just as it is doing now.

Who knows what affects the spread of an allele in a population? It is simply not true that if an allele is only to be found a portion of a species, that it is therefore a new allele.

That has no effect on the ones they are passing on. Junior is still adding alleles from mum's family line to alleles from dad's family line. (Also, any alleles mum and dad are not passing on are probably being passed on by their siblings to junior's cousins. Even junior's siblings will get a different assortment.)

But then it is not "accumulation" but status quo at best.

Incorrect. If melanism is recessive all dark parents are homozygous.

But melanism isn't, I believe.

Heterozygous individuals would not be dark in this case. So there would be no "white" alleles to come from dark parents.

No, but the dark and the white alleles would still keep coming from heterozygous ones.

"White" alleles can only come from dark parents when melanism is dominant.

Like I said, I thought this was the case, but I am not sure. I think it comes from the fact that expressed melanism is often dominant in other species. But then there are often other factors at play as well than MC1R alleles.

Makes me wonder if any of the climatologists who discovered climate change have been nominated or given a prize in their field. It would be very difficult to single out one person's work, but perhaps a prize could be given to the International Panel.

No that would be unfair as well. Climatologists do ALWAYS discover climate change by definition; in the same way as you say evolution is always occuring.

 

[USincognito]

Good that you're following this thread. And what is it exactly that I don't understand about Hardy-Weinberg? Because screaming randomly doesn't help the discussion.

Who is screaming?

And you might go back and read this post.

 

[holdon]

And you might go back and read this post.

Yes, with "genetic drift" you can explain anything you want.

 

[USincognito]

Yes, with "genetic drift" you can explain anything you want.

A dismissive "response" is not an answer or argument.