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

[holdon]

But really, what other explanation is there other than genetic change? That's a downright simple question.

Ah, so you now assume there was "genetic change" in those flies. And before you said it was a clear case of new speciation.
Why would you assume that?

 

[gluadys]

Ah, so you now assume there was "genetic change" in those flies. And before you said it was a clear case of new speciation.
Why would you assume that?

First, I think, given the nature of genetic change, that the onus would be on the person who claims there is no genetic change to prove it. How can there possibly be no genetic change? Genetic change is happening all the time in individual organisms, introducing variety into the species.

Second, I think we need to be wary of the way we connect genetic change with speciation. The critical factor in speciation is isolation--whether that isolation be caused by intrinsic or extrinsic factors.

A genetic change can introduce an intrinsic isolating factor without any changes in the visible phenotype of the species. For example, in one type of fly, different species distinguish their proper mates by chemical scent---not because the females use different chemicals in the production of scent, but because they use the same chemicals in different proportions. It doesn't take much in the way of genetic change to change the proportion of a chemical ingredient used in scent production. But that is all that is needed by the male flies to determine whether they should pursue or ignore a particular female.

Now whether this is enough difference to make different populations incapable of interbreeding, it is enough to discourage interbreeding, so even if they are not separate species yet, they will likely become so as gene flow between the populations slows and eventually stops.

In this sort of case, the genetic factor initiated the speciation, even if it took behaviour to complete the speciation.

When the isolating factor is extrinsic, we get genetic divergence as a by-product of the isolation. Much of the genetics involved may have little to do with capacity to reproduce. It may relate to such superficial things as colour patches and patterns. Or a change in mating call.

But these in turn become intrinsic isolating factors if they affect how one recognizes a potential mate. If a female bird does not recognize a mating call, she will not choose the bird with the strange song. So again, even if the populations are not separate species yet, they are discouraged from mating, and speciation will be a by-product of that discouragement.

In short, the genetic difference need not be great, and may not be, in itself an inhibitor of interbreeding. But if it has a significant effect on mate choice, the populations will tend to separate, and the separation in itself will assure more and more genetic divergence until interbreeding becomes genetically as well as behaviourally problematical.

 

[holdon]

First, I think, given the nature of genetic change, that the onus would be on the person who claims there is no genetic change to prove it. How can there possibly be no genetic change? Genetic change is happening all the time in individual organisms, introducing variety into the species.

What do you mean by genetic change? The other person claimed that "genetic change" was the explanation for certain flies no longer to interbreed. You apparently don't agree with that.

Second, I think we need to be wary of the way we connect genetic change with speciation. The critical factor in speciation is isolation--whether that isolation be caused by intrinsic or extrinsic factors.

A genetic change can introduce an intrinsic isolating factor without any changes in the visible phenotype of the species. For example, in one type of fly, different species distinguish their proper mates by chemical scent---not because the females use different chemicals in the production of scent, but because they use the same chemicals in different proportions. It doesn't take much in the way of genetic change to change the proportion of a chemical ingredient used in scent production. But that is all that is needed by the male flies to determine whether they should pursue or ignore a particular female.

Now whether this is enough difference to make different populations incapable of interbreeding, it is enough to discourage interbreeding, so even if they are not separate species yet, they will likely become so as gene flow between the populations slows and eventually stops.

In this sort of case, the genetic factor initiated the speciation, even if it took behaviour to complete the speciation.

When the isolating factor is extrinsic, we get genetic divergence as a by-product of the isolation. Much of the genetics involved may have little to do with capacity to reproduce. It may relate to such superficial things as colour patches and patterns. Or a change in mating call.

But these in turn become intrinsic isolating factors if they affect how one recognizes a potential mate. If a female bird does not recognize a mating call, she will not choose the bird with the strange song. So again, even if the populations are not separate species yet, they are discouraged from mating, and speciation will be a by-product of that discouragement.

In short, the genetic difference need not be great, and may not be, in itself an inhibitor of interbreeding. But if it has a significant effect on mate choice, the populations will tend to separate, and the separation in itself will assure more and more genetic divergence until interbreeding becomes genetically as well as behaviourally problematical.

But even then it doesn't mean there is a new species....

The production of genetic material is programmed so that reliable copies of the genetic information carriers are made. This excludes to a great extend that new readable information is added. Because what can't be read, won't be copied. That's the so called stasis, observed by many geneticists. It means that the genetic material is extremely constant within a species. It is not that it doesn't allow for varietal differences. On the contrary: seemingly endless combination of different alleles that can get expressed or not under different circumstances. But the overall genetic information (expressed or not) is the same. This is of course because the factories and transporters in the cell that re-produce the genetic information are themselves coded by that same genetic information (chemically expressed as a sequence of bases). So, that it is virtually impossible that a sequence would deviate from its master model.

 

[gluadys]

What do you mean by genetic change? The other person claimed that "genetic change" was the explanation for certain flies no longer to interbreed. You apparently don't agree with that. But even then it doesn't mean there is a new species....

Good point. Obviously speciation and genetic change are connected. My point was that you can go in either direction. The initial reason the flies did not interbreed was because they were artificially separated. At this point no genetic change had occurred.

When they were first permitted to intermingle again (and remember by now it is not the same generation of flies we began with), the major reason for not interbreeding may have been behavioral rather than genetic. Or the behaviour of avoiding flies from a different group may have been induced by genetic change.

In the last analysis, you have both the behaviour of avoiding hybrid matings and genetic change. Genetic change is inevitable in any population. Divergence is inevitable if the populations are kept separate because there is no gene flow between the isolated groups to allow sharing of new mutations. Each group accumulates a different set of mutations and each group may adapt according to a different set of selection pressures.

The production of genetic material is programmed so that reliable copies of the genetic information carriers are made. This excludes to a great extend that new readable information is added. Because what can't be read, won't be copied. That's the so called stasis, observed by many geneticists.

Actually stasis is not a genetic phenomenon. The term was used to refer to apparent lack of change in fossil species for which we have no genetic information. In fact, there are many fossil sequences which show no stasis either, although some do. But since fossils only show mostly shells or bones, not the whole organism, we have no way of determining how much phenotypic or genetic change was not preserved in the fossils.

It means that the genetic material is extremely constant within a species. It is not that it doesn't allow for varietal differences. On the contrary: seemingly endless combination of different alleles that can get expressed or not under different circumstances.

Actually, evolution doesn't pay a lot of attention to combinations of different alleles affecting different traits. Sure, you can get a lot of unique organisms when you look at combinations, as the combinations pile up geometrically.

But the important matter in evolution is "how many versions are there of one gene in the gene pool and how are these distributed in the population?"

Check out this thread where I have noted the difference in these perspectives:

http://foru.ms/t5536798-variation-and-variability.html

But the overall genetic information (expressed or not) is the same. This is of course because the factories and transporters in the cell that re-produce the genetic information are themselves coded by that same genetic information (chemically expressed as a sequence of bases). So, that it is virtually impossible that a sequence would deviate from its master model.

Everyone agrees that mutations are rare per gene, per cell. But that fact has to be balanced against the huge number of base pairs in the genome. When one is dealing with huge numbers, even a very rare occurrence happens many times. There are as many base pairs in a human cell as there are human beings in the whole current global population. So even a mutation rate of only one in a hundred million means you get around 100 mutations per cell replication. IOW you probably have about 100 unique sequences in your DNA that did not occur in either of your parents. Same for most mammals.

For the flies, it would depend on how large their genome is. A smaller genome would show fewer mutations per individual.


The other matter you are not considering is the impact of natural selection. Even if no new mutations had occurred at all, natural selection, by changing the frequency of alleles in different directions, would create genetic difference. Of course, it is highly improbable that there would be no new mutations, so mutations and natural selection would operate in tandem to differentiate the populations and set up species barriers between them.

 

[holdon]

Good point. Obviously speciation and genetic change are connected. My point was that you can go in either direction. The initial reason the flies did not interbreed was because they were artificially separated. At this point no genetic change had occurred.

When they were first permitted to intermingle again (and remember by now it is not the same generation of flies we began with), the major reason for not interbreeding may have been behavioral rather than genetic. Or the behaviour of avoiding flies from a different group may have been induced by genetic change.

In the last analysis, you have both the behaviour of avoiding hybrid matings and genetic change. Genetic change is inevitable in any population. Divergence is inevitable if the populations are kept separate because there is no gene flow between the isolated groups to allow sharing of new mutations.

You assume here that divergence is based on mutations. It is not in a great majority of the cases. Divergence is rather exhibited by selection pressures.

Actually stasis is not a genetic phenomenon.

It is from a geneticist standpoint. This is what Hardy-Weinberg is based on among others.

But the important matter in evolution is "how many versions are there of one gene in the gene pool and how are these distributed in the population?"

And if you look at that, you find yourself looking a varietal differences: not new species.

Everyone agrees that mutations are rare per gene, per cell. But that fact has to be balanced against the huge number of base pairs in the genome. When one is dealing with huge numbers, even a very rare occurrence happens many times. There are as many base pairs in a human cell as there are human beings in the whole current global population. So even a mutation rate of only one in a hundred million means you get around 100 mutations per cell replication. IOW you probably have about 100 unique sequences in your DNA that did not occur in either of your parents. Same for most mammals.

Here you assume that mutations (=chemical "mutilations") are reproduced. The majority will never be reproduced, because they can't be "read".

The other matter you are not considering is the impact of natural selection. Even if no new mutations had occurred at all, natural selection, by changing the frequency of alleles in different directions, would create genetic difference. Of course, it is highly improbable that there would be no new mutations, so mutations and natural selection would operate in tandem to differentiate the populations and set up species barriers between them.

But the genetic re-production apparatus, makes sure that the alleles are inherited (=copied and transferred). Even if they are not "phenotypically" expressed.

 

[shernren]

Divergence is rather exhibited by selection pressures.

But selection pressures have got to have heritable variation in the population to work on in the first place. And heritable variation comes either from mutations, or from something that acts so darn well like mutations in the genome that biologists haven't been able to tell the difference for the past century.

But the genetic re-production apparatus, makes sure that the alleles are inherited (=copied and transferred). Even if they are not "phenotypically" expressed.

Not true. Meiosis during sexual reproduction, and later fertilization, ensures that a random half of your genetic material comes from your mother and another random half comes from your father. To put it bluntly, half of the alleles your mother had on her non-sex chromosomes are missing from yours.

 

[holdon]

But selection pressures have got to have heritable variation in the population to work on in the first place. And heritable variation comes either from mutations, or from something that acts so darn well like mutations in the genome that biologists haven't been able to tell the difference for the past century.

If parents with bleu eyes have a child with brown eyes, it doesn't mean the the genes of the child mutated at all. That's the reasoning you're having here. But the "brown" gene was there all the time....

 

[gluadys]

You assume here that divergence is based on mutations. It is not in a great majority of the cases. Divergence is rather exhibited by selection pressures.

Actually, you are still overlooking isolation and the restriction/absence of gene flow. As long as you have a single population, mutations alone simply increase variability in the species.

But split the population into two isolated groups, and the mutations that occur and are preserved in each group will be a different set of mutations. This introduces a measure of divergence.

Divergence will be re-inforced by differing selective pressures on the two groups.

It is from a geneticist standpoint. This is what Hardy-Weinberg is based on among others.

Ah, that is what you are getting at. I hadn't heard it called "stasis" before. Such stasis occurs when there is little or no selective pressure or when the selective pressure is in favour of the status quo. After all, when a species is well adapted to its niche, any change is more likely to be negative than positive.

And if you look at that, you find yourself looking a varietal differences: not new species.

Yes, if a butterfly population changes from 40% with blue wings to 60% with blue wings over 5 generations, we have evolution on a small scale within the species, but not likely speciation.

Speciation requires that 1) the population be divided into two or more relatively isolated groups, 2) many such changes occurring in many traits, and 3) the development of intrinsic isolating factors that discourage/prevent interbreeding even when there is opportunity to do so.

If these factors result in two (or more) populations which 1) are genetically different from each other and 2) do not interbreed successfully when given the opportunity to do so, would you not agree that speciation has occurred?

Here you assume that mutations (=chemical "mutilations") are reproduced. The majority will never be reproduced, because they can't be "read".

I am not sure what you are saying here. Are you saying that most mutations will be caught and corrected before the cell reproduces? That is true enough.

Furthermore, uncorrected mutations often produce cell death and/or problems with embryological development that lead to spontaneous abortion.

Obviously such mutations have no impact on the evolution of a species. Mutations that appear in a viable organism tend not to have a major effect, positive or negative, on the organism. That is why most mutations are rated "neutral" in respect to fitness.

But the genetic re-production apparatus, makes sure that the alleles are inherited (=copied and transferred). Even if they are not "phenotypically" expressed.

True. But since the phenotype is an expression of the underlying genotype, a change in the ratio in which the phenotypes occurs signals an accompanying change in the ratio of the alleles.

Check out this post in which I have looked at the mathematics of phenotype and genotype change.

http://foru.ms/showpost.php?p=14449626&postcount=5

It is part of a debate with a creationist I had some time ago. The whole thread is here:

http://www.christianforums.com/t1368403-natural-selection-and-genetics.html

Remember that change in ratio (or the frequency at which an allele appears in the gene pool) is the definition of evolution.

Very often I think we focus too much on mutations, and especially on whether they are beneficial or harmful. This draws attention to the host organism. But evolution is not what happens to individual organisms. It is about population level changes: about which genomes are reproduced most frequently and which tend to disappear. One really needs to think in terms of the statistics of the gene pool above all else.

 

[gluadys]

If parents with bleu eyes have a child with brown eyes, it doesn't mean the the genes of the child mutated at all. That's the reasoning you're having here. But the "brown" gene was there all the time....

No, we understand what you are saying. Certainly it is true today that the alleles which produce different colour eyes are both distributed widely in the population and genetics explains nicely why a couple of brown-eyed parents can have a blue-eyed child.

But what about a few million years ago before there was any allele for blue eyes in the human population? Where did the first allele for blue eyes come from?

This is what we mean when we say mutations are the source of variation. Naturally, once a mutation has occurred, (provided natural selection does not eliminate it), it will continue to be inherited generation after generation. When they alter the expression of a gene, the variant forms of the affected genes are called alleles.

Natural selection operates independently of the timing of a mutation. The variation it favours or rejects may be the result of a brand new mutation or may be the consequence of an allele that has been in the population for many generations, but was not significant for survival until new selective pressures emerged.

When you say "the brown gene was there all the time...." you are just saying that the mutation which produced that gene occurred many generations ago instead of in the current generation. Natural selection works equally well with both old and new mutations.

 

[holdon]

But what about a few million years ago before there was any allele for blue eyes in the human population? Where did the first allele for blue eyes come from?

Well, you don't know where it came from.

When you say "the brown gene was there all the time...." you are just saying that the mutation which produced that gene occurred many generations ago instead of in the current generation.

You are assuming that a mutation was at the basis for "brown" and/or "blue". But you don't know. Nor can you. Nor do those things tend to depend on just one chemical difference. It's more complex than that.

 

[gluadys]

Well, you don't know where it came from. You are assuming that a mutation was at the basis for "brown" and/or "blue". But you don't know. Nor can you. Nor do those things tend to depend on just one chemical difference. It's more complex than that.

I agree it is more complex. There are actually many genes that work together to determine the exact colour and shade of the eye. As well as many other factors influencing gene expression. And every single one of them is subject to mutation and natural selection.

As for where the alleles came from in the first place, science doesn't know of any source other than mutation (change) in the genes that affect eye colour. And that applies to all other traits too. In all species.

If you want to present another option, go ahead.

 

[sfs]

You assume here that divergence is based on mutations. It is not in a great majority of the cases. Divergence is rather exhibited by selection pressures.

The great majority of divergence (at least for humans and closely related species) is the result of the random accumulation of mutations.

It is from a geneticist standpoint. This is what Hardy-Weinberg is based on among others.

?? Hardy-Weinberg says nothing about the origins of divergence.

Here you assume that mutations (=chemical "mutilations") are reproduced. The majority will never be reproduced, because they can't be "read".

All of the mutations that are being discussed (germ-line mutations) are passed on to offspring, and all can be read.

 

[sfs]

If parents with bleu eyes have a child with brown eyes, it doesn't mean the the genes of the child mutated at all. That's the reasoning you're having here. But the "brown" gene was there all the time....

True, but not really relevant. With human pigmentation, what we see is that the source population (all of sub-Saharan Africa) completely lacks the alleles for blue eyes and pale skin, and there is strong evidence that any mutations in that direction are weeded out by natural selection. In populations farther north, there is also strong evidence for recent selection for less pigmentation (certainly in the case of skin color, and probably with side-effects in eye color).

 

[holdon]

The great majority of divergence (at least for humans and closely related species) is the result of the random accumulation of mutations.

So, you say..... but you don't have any evidence for that. So, it's an assumption; a belief. That's all.

?? Hardy-Weinberg says nothing about the origins of divergence.

Nor did I say that.

All of the mutations that are being discussed (germ-line mutations) are passed on to offspring, and all can be read.

How can you be so sure they are "all" passed on to offspring?

 

[holdon]

True, but not really relevant. With human pigmentation, what we see is that the source population (all of sub-Saharan Africa) completely lacks the alleles for blue eyes and pale skin,

Really? How do you know?

 

[holdon]

And every single one of them is subject to mutation and natural selection.

Potentially yes. Probably no.

As for where the alleles came from in the first place, science doesn't know of any source other than mutation (change) in the genes that affect eye colour. And that applies to all other traits too. In all species.

That's why "science" has to preach the gospel of mutation.

 

[gluadys]

So, you say..... but you don't have any evidence for that. So, it's an assumption; a belief.

I wouldn't bet on there being no evidence. What have you read in popular literature or scientific journals that would lead you to think scientists are working with blind assumptions instead of evidence?

Most of what has been said in this thread on speciation and divergence and the mechanisms which produce them are well documented.

How can you be so sure they are "all" passed on to offspring?

Because the whole genome is passed on every time an organism reproduces. Any uncorrected change in DNA will be passed on.

Really? How do you know?

What do you think anthropologists are doing in Africa? One of the things they are doing is taking DNA samples.

I just read a report recently on the Human Genographic Project. They are specializing in study of the Y chromosome in males and mitochondrial DNA in females in order to trace the migration patterns of human beings since the origin of the species in Africa.

There is a great deal of evidence easily accessible if you take a moment to look for it.

Potentially yes. Probably no.

Not potentially. Actually. It is unavoidable.

That's why "science" has to preach the gospel of mutation.

Like I said, if you have another option to propose, go ahead.

 

[shernren]

Yup, holdon: how, in your view, does new genetic material emerge?

 

[holdon]

I wouldn't bet on there being no evidence. What have you read in popular literature or scientific journals that would lead you to think scientists are working with blind assumptions instead of evidence?

Of course I almost forgot. "The scientific journals" and "scientists".

Most of what has been said in this thread on speciation and divergence and the mechanisms which produce them are well documented.

Well documented how? What newly developed species has been well documented? And how?

What do you think anthropologists are doing in Africa?

Yes tell me: what exactly are they doing there?

One of the things they are doing is taking DNA samples.

I just read a report recently on the Human Genographic Project. They are specializing in study of the Y chromosome in males and mitochondrial DNA in females in order to trace the migration patterns of human beings since the origin of the species in Africa.

And what was their conclusion?

There is a great deal of evidence easily accessible if you take a moment to look for it.

Of course.

Not potentially. Actually. It is unavoidable.

Really? Then please explain to me how it is possible that organisms that have not evolved since "millions of years" are still here today exactly the same and unaltered (at least from what we can tell) despite all the environmental selective pressures they must have gone through like all other life forms.

Like I said, if you have another option to propose, go ahead.

What you call "science" assumes that all life forms must have evolved through an infinite number of mutations, requiring therefore an infinite space of time.....

 

[Mallon]

Yup, holdon: how, in your view, does new genetic material emerge?

You expect too much. holdon only asks questions. He doesn't answer them.