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

[gluadys]

There is no reason to believe that ancient birds did have teeth, because there is still a gene that can produce teeth.

But they did have teeth. The teeth are clearly visible in their fossil remains.

I hope you are not going to suggest they had teeth in spite of NOT having genes to induce the production of teeth.

And as I told you the tooth gene is still fully functional in birds.

We know that. But it's not expressed because another gene acts to stop the formation of the teeth.

And we have no evidence of that occuring.

Are you speaking generally or of one specific case? We know of species in which there is very little diversity and many genes are not polymorphic.

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.

I think you've gone off topic again.

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

Only on the hypothesis that the allele put in an appearance, disappeared and then put in an appearance again. The principle of parsimony would rule against that unless there is evidence to dispense with the principle.

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

There are hundreds of thousands of registered species without formal taxonomic names. The formal process of establishing a species name can't keep up with the rate of discovery.

Who knows what affects the spread of an allele in a population?

Biologists have a pretty good idea. Major influences are heredity and natural selection. Other factors include genetic drift, gene flow, speciation, hybridization, etc. It is complex, but not a huge mystery.

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.

You would have to explain some strange facts to account for the prolonged existence of this allele in such a small portion of the African population.

1. How did it come to remain in this population alone without effective isolation from the rest of the population of Burkina Faso and other nearby African nations?

2. Why did it not protect the population from malaria until recently?

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

You are going to have to explain your semantics. To me adding X, Y and Z to A, B and C is accumulation. Until junior was conceived, no one had that combination of alleles. Some had various combinations of A, B and C. Some had various combinations of X, Y and Z. But nobody had a combination which included A, B and C AND X, Y and Z. How do you get status quo from that?

But melanism isn't, I believe.No, but the dark and the white alleles would still keep coming from heterozygous ones. 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.

Well, again, are we talking specifics or general principles. In the specific case of the moth, yes melanism is the dominant trait and heterzygosity of black adults is a source of non-melanic alleles. (So is immigration from non-polluted areas of the country.)

But you said: n.s. does not explain why any of the alleles would disappear.

In fact, in theory natural selection can account for the disappearance of the allele. That is why I gave two possible scenarios: one in which the favored trait is dominant (as in the pepper moth) and a hypothetical case in which it is recessive. In the latter case, the dark adults would all be homozygous, so if, in fact, all white adults were eliminated, there would be no non-melanic allele to pass on.

It would be more difficult, but not theoretically impossible to eliminate the non-melanic allele even when the melanic allele is dominant.

To give an example. Suppose we began with a sample of 1000, divided in classic Mendelian proportions of 250MM, 500Mm, 250 mm. Allele frequency is even: 500M & 500m Phenotypically 750 melanic and 250 non-melanic individuals.

Assume the theoretical extreme of natural selection: All non-melanic individuals are wiped out, all melanic individuals survive to reproduce. (In nature you would never get such an extreme, but this keeps the math simple.) In this extreme scenario, the only source of non-melanic alleles for the next generation (assuming no immigration) are those from heterozygous survivors: 500 of them. Each contributes one non-melanic allele to the gene pool. But each also contributes one melanic allele and each homozygous survivor contributes two for a total of 1000M to 500 m.

Using the Hardy-Weinburg formula and rounding off to the nearest whole number of individuals, this gives a next generation of 444MM, 444Mm, 111mm

Again eliminate the 111mm individuals (and so 222 m alleles). Now our gene pool is 1332M to 444m. Apply Hardy-Weinberg again and in the next generation you get the distribution 563MM, 375Mm, 63mm.

Note that in each generation the number of MM individuals is rising while both the Mm and mm figures are falling. So in each generation there are fewer m alleles from which to derive mm individuals.

I calculated this out to eight generations by which time the ratio of M:m is 10:1 In a representative sample of 1000 individuals this gave a distribution of 810 MM, 180Mm, 10mm

Theoretically, there is no reason why the m allele should not disappear completely at some point, but it takes a while because even though it is rarer in each generation, the rate of reduction slows down. Over the eight generations the number of mm individuals declines as follows 250, 111, 63, 40, 28.20, 16, 12, 10 So from generation 1 to 2 you get over a 50% reduction but from generation 7 to 8 you get only a 16% reduction. Just like losing weight. It is a lot easier to get rid of the first 20 pounds than the last 2.

So even in this extreme scenario it would probably take another 20 or so generations to eliminate the allele, but it could happen. In real life, of course, it would take even longer unless the total population were much reduced.

A rare allele in a small population could be eliminated fairly quickly as only a very few individuals would carry it.

 

[holdon]

But they did have teeth. The teeth are clearly visible in their fossil remains.

No, you are reading me wrong. I said that if you believe ancient birds had teeth, because there is now still a gene that can produce them, that that is faulty reasoning.

You would have to explain some strange facts to account for the prolonged existence of this allele in such a small portion of the African population.

Or you would have to account for the much more prolonged existence of a toothmaking gene in birds. But I don't understand your conclusion: you have no way of knowing what existed when and where.

You are going to have to explain your semantics. To me adding X, Y and Z to A, B and C is accumulation. Until junior was conceived, no one had that combination of alleles. Some had various combinations of A, B and C. Some had various combinations of X, Y and Z. But nobody had a combination which included A, B and C AND X, Y and Z. How do you get status quo from that?

Because on the whole there is no new genetic information being produced.

In fact, in theory natural selection can account for the disappearance of the allele. That is why I gave two possible scenarios: one in which the favored trait is dominant (as in the pepper moth) and a hypothetical case in which it is recessive. In the latter case, the dark adults would all be homozygous, so if, in fact, all white adults were eliminated, there would be no non-melanic allele to pass on.
It would be more difficult, but not theoretically impossible to eliminate the non-melanic allele even when the melanic allele is dominant.

To give an example. Suppose we began with a sample of 1000, divided in classic Mendelian proportions of 250MM, 500Mm, 250 mm. Allele frequency is even: 500M & 500m Phenotypically 750 melanic and 250 non-melanic individuals.

Assume the theoretical extreme of natural selection: All non-melanic individuals are wiped out, all melanic individuals survive to reproduce. (In nature you would never get such an extreme, but this keeps the math simple.) In this extreme scenario, the only source of non-melanic alleles for the next generation (assuming no immigration) are those from heterozygous survivors: 500 of them. Each contributes one non-melanic allele to the gene pool. But each also contributes one melanic allele and each homozygous survivor contributes two for a total of 1000M to 500 m.

Using the Hardy-Weinburg formula and rounding off to the nearest whole number of individuals, this gives a next generation of 444MM, 444Mm, 111mm

Again eliminate the 111mm individuals (and so 222 m alleles). Now our gene pool is 1332M to 444m. Apply Hardy-Weinberg again and in the next generation you get the distribution 563MM, 375Mm, 63mm.

Note that in each generation the number of MM individuals is rising while both the Mm and mm figures are falling. So in each generation there are fewer m alleles from which to derive mm individuals.

I calculated this out to eight generations by which time the ratio of M:m is 10:1 In a representative sample of 1000 individuals this gave a distribution of 810 MM, 180Mm, 10mm

Theoretically, there is no reason why the m allele should not disappear completely at some point, but it takes a while because even though it is rarer in each generation, the rate of reduction slows down. Over the eight generations the number of mm individuals declines as follows 250, 111, 63, 40, 28.20, 16, 12, 10 So from generation 1 to 2 you get over a 50% reduction but from generation 7 to 8 you get only a 16% reduction. Just like losing weight. It is a lot easier to get rid of the first 20 pounds than the last 2.

So even in this extreme scenario it would probably take another 20 or so generations to eliminate the allele, but it could happen. In real life, of course, it would take even longer unless the total population were much reduced.

Well, you understand that theoretically the number never goes to zero.... And you understand then that for this white allele elimination to work absolutely ALL whites would have to eliminated by the birds; if not, only in few generations, a lot of moths would be heterozygous again, because the distribution numbers work very fast into the other direction. (inversely proportionate to what you call: because even though it is rarer in each generation, the rate of reduction slows down. ) It's a very far fetched scenario.

A rare allele in a small population could be eliminated fairly quickly as only a very few individuals would carry it.

But it wouldn't take much for it NOT to be eliminated, which is much more likely under a n.s. scenario: under that scenario it's hard to understand any absolutes.

 

[Mallon]

Here's a question for you, holdon:

You correctly acknowledge that modern birds have genes that code for teeth. Yet none of these birds possess teeth. So why do birds retain genetic coding for teeth if none of them express it?

Here's the answer from an evolutionary scenario: Birds have the genes for teeth because they are descended from reptiles. They simply do not express those genes because (a) they add needless weight in flight, and (b) they've evolved gizzards to replace the teeth. We can test this scenario scientifically by seeing whether our predictions stemming from this line of reasoning hold true. As it turns out, the fossil record agrees.

What scientific alternative would you espouse? And remember: "Because God wanted it that way" isn't a scientific explanation.

 

[holdon]

And remember: "Because God wanted it that way" isn't a scientific explanation.

And why not? Why would you be permitted to believe that birds have descended from reptiles and I am not permitted to believe "God wanted it that way? I think this is unfair!

But there are a lot of genes that may be found in other species, genuses, orders, etc... It could rather point in the direction of the same Architect, don't you think? If birds with teeth are extinct now, what prevented Him from making them in the beginning?

 

[Mallon]

And why not? Why would you be permitted to believe that birds have descended from reptiles and I am not permitted to believe "God wanted it that way? I think this is unfair!

Boohoo.
Again, we don't accept "God wanted it that way" in science because it is not a testable explanation. Furthermore, it is intellectual laziness and puts an end to scientific investigation.
Just imagine: What if someone suggested that the reason we have not yet found a cure for cancer is because "God wants it that way"? Would you then throw your hands up and stop looking for a cure?

But there are a lot of genes that may be found in other species, genuses, orders, etc... It could rather point in the direction of the same Architect, don't you think?

Again, the appeal to a "common designer" is an untestable claim. It's ad hoc. How would you falsify it?

If birds with teeth are extinct now, what prevented Him from making them in the beginning?

Good question. So: How could you test this claim with science?

See what I'm getting at?

 

[holdon]

Just imagine: What if someone suggested that the reason we have not yet found a cure for cancer is because "God wants it that way"? Would you then throw your hands up and stop looking for a cure?

No, of course not: God does not want that. We should know that.

Again, the appeal to a "common designer" is an untestable claim. It's ad hoc. How would you falsify it?

I don't have to. I believe it.

Good question. So: How could you test this claim with science?

See what I'm getting at?

Again, I believe it. And even the scientist believes:
"The decision to try to explain things rationally, cannot be a rational one itself." (Popper)

 

[Mallon]

No, of course not: God does not want that. We should know that.

And yet simply accepting that "God wants it that way" would keep us from trying.

I don't have to. I believe it. Again, I believe it.

Good. So we've established that what your faith in God doesn't stem from science.

And even the scientist believes:
"The decision to try to explain things rationally, cannot be a rational one itself." (Popper)

Certainly, the logic behind using science to make sense of world may be circular. But the assumptions of science work nonetheless and produce results. The productivity of science breaks down when we try to redefine it by chosing not to "explain things rationally" and instead use God to fill in the gaps.

 

[theFijian]

And why not? Why would you be permitted to believe that birds have descended from reptiles and I am not permitted to believe "God wanted it that way? I think this is unfair!

You are quite permitted to believe it, it just aint scientific that's all. It doesn't have to be scientific for it to be worhwhile believing does it?

 

[holdon]

And yet simply accepting that "God wants it that way" would keep us from trying.

Wait a minute. You were talking about whether God wanted birds to have teeth, and now you keep going on a tangent whether God wants diseases. This is not a very logical nor scientific process of yours.

Good. So we've established that what your faith in God doesn't stem from science.

Correct.

Certainly, the logic behind using science to make sense of world may be circular. But the assumptions of science work nonetheless and produce results.

What assumptions are you talking about?

The productivity of science breaks down when we try to redefine it by chosing not to "explain things rationally" and instead use God to fill in the gaps.

No, I think that if you use the concept of a Originator, Architect, Creator if you will, you have indeed a good basis to explore scientifically and rationally what He made.
If there is no such Being "behind it all", we may come up with all kinds of underlying assumptions according to our fantasies from alchemy and astrology to evolutionism. In my opinion we would then be more severly impaired in "getting results"

 

[holdon]

You are quite permitted to believe it, it just aint scientific that's all. It doesn't have to be scientific for it to be worhwhile believing does it?

No. Scientifically believing the resurrection would be quite a challenge, I imagine. But is it therefore not true? Is it only a good story, a nice myth?

 

[Mallon]

If there is no such Being "behind it all", we may come up with all kinds of underlying assumptions according to our fantasies from alchemy and astrology to evolutionism. In my opinion we would then be more severly impaired in "getting results"

It's ironic that you should put evolution in the same box as astrology. When Intelligent Design was put on trial in Dover, one of its key proponents, Michael Behe, admitted that redefining science to include Intelligent Design would open it up to astrology and other quackeries:

Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.

 

[holdon]

It's ironic that you should put evolution in the same box as astrology. When Intelligent Design was put on trial in Dover, one of its key proponents, Michael Behe, admitted that redefining science to include Intelligent Design would open it up to astrology and other quackeries:

I don't know who Michael Behe is, nor who was tried at Dover. I reasoned purely from the inclinations of the human mind.

 

[Mallon]

I don't know who Michael Behe is, nor who was tried at Dover. I reasoned purely from the inclinations of the human mind.

Evidently, at least one of the founders of ID disagrees with you.

 

[gluadys]

No, you are reading me wrong. I said that if you believe ancient birds had teeth, because there is now still a gene that can produce them, that that is faulty reasoning.

Well, of course it is. But given the heritability of genes, it makes sense to hypothesize an ancestor that had teeth. And to test the hypothesis via inspection of relevant fossils.

Historically, the connection was made the other way around. The fossils with teeth were found first and it was hypothesized that modern birds would still have the genes for producing teeth. That hypothesis was tested by genetic analysis and experiment and turned out to be accurate.

Or you would have to account for the much more prolonged existence of a toothmaking gene in birds.

I gave you specific facts you would have to account for. What facts would have to be accounted for in this case?

But I don't understand your conclusion: you have no way of knowing what existed when and where.

Sure we do. Because this allele produces a hemoglobin that protects from malaria, we can tell from the geographic and temporal distribution of malaria where it existed and exists. Because, unlike its more famous cousin, it does not induce sickle cells, it can be distinguished from the other form that also protects against malaria.

It was these characteristics that led to finding it in the first place.

Because on the whole there is no new genetic information being produced.

After all this conversation are you still not understanding that producing new genetic information is not what natural selection is about?

We were talking about the colour change in the moths and I commented that:

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

To which you responded: "What accumulation of changes brings about a new species?"

And I gave you an example of how a set of alleles confined to one family and another set of alleles confined to a different family could accumulate through mating a pair of individuals from these families.

Please remember we are talking natural selection, and how it changes the character of a species. Natural selection does not discriminate between an allele that appeared for the first time in mum's own DNA and one she inherited from ten generations back. Junior inherits half of mum's alleles no matter how old or young they are: and half of dad's.

So, he can inherit alleles from both families and combine them in ways that never happened before. While mum differs from most of the population in three ways and dad in three different ways, junior differs in all six ways.

Furthermore, since we are assuming favorable selection for all six, all six will continue to appear and re-appear not only in junior but in more and more of his siblings and cousins, and eventually in more distant relations.

Eventually, individuals who inherit only one or two (or none) of these alleles will be in a minority. Almost the whole population will be inheriting all six.

So now most of the population differs from its ancestors, not just in one respect (colour) but in six respects. And you can continue this for as many inheritable traits as the species possesses.

Theoretically, you could get very significant change in a species without any new alleles introduced by mutation at all, just by varying the frequency of existing alleles. On morphological grounds alone, that could be enough to justify a new species name.

If the changes also induce reproductive isolation, then you have a new species by definition.

In practice, due to the constancy of mutations occurring, some of the alleles affected will be new ones. So the production of new genetic information is a built-in given.

However, new genetic information is not going to change the species unless it is spread via natural selection. Whereas natural selection can change the species with or without new genetic information.

Well, you understand that theoretically the number never goes to zero....

No, I don't. Theoretically, given enough time, the number will go to zero. But realistically, this almost never occurs.

And you understand then that for this white allele elimination to work absolutely ALL whites would have to eliminated by the birds;

Yes. That would be true no matter whether the allele was dominant or recessive.

if not, only in few generations, a lot of moths would be heterozygous again, because the distribution numbers work very fast into the other direction. (inversely proportionate to what you call: because even though it is rarer in each generation, the rate of reduction slows down. )

Right.

It's a very far fetched scenario.

As I said at the outset.

But it wouldn't take much for it NOT to be eliminated, which is much more likely under a n.s. scenario: under that scenario it's hard to understand any absolutes.

Which is why I objected to the absolute statement that natural selection could not account for the disappearance of an allele. That scenario might be rare, but it is not absolutely out of the question.

In fact, it may be less rare that you suspect. Many populations, especially among the more specialized species, are quite small. And in small populations you can get significant genetic change, including the complete elimination of an allele, by sheer chance, without even needing natural selection.

Any significant reduction in the size of a population is likely to lead to a reduction in variability, especially when we remember that many character traits are not distributed evenly through a species' range and that a species itself may show different levels of population density from one locale to another. Picture a situation in which the 30% of the population which carry an allele are all found in a high-density area that covers only 10% of the species' total range. You only need a disaster occurring in that restricted area to wipe out that allele.

 

[holdon]

Picture a situation in which the 30% of the population which carry an allele are all found in a high-density area that covers only 10% of the species' total range. You only need a disaster occurring in that restricted area to wipe out that allele.

That's not natural selection, but artificial selection. While you may be able to picture it, it is very very remote from anything we know to have happened. It's an hypothesis, and a weak one in my view. That's evolutionism.

 

[Mallon]

That's not natural selection, but artificial selection.

Do you know what artificial selection is, holdon?

 

[holdon]

Do you know what artificial selection is, holdon?

Yes, something forced, not left to the random actions of nature.

 

[Mallon]

Yes, something forced, not left to the random actions of nature.

So can you please explain how gluadys' scenario was an example of artificial, rather than natural, selection?

 

[holdon]

So can you please explain how gluadys' scenario was an example of artificial, rather than natural, selection?

I'm surprised about that question frankly. I think we concluded that Natural Selection does not explain new species, and that Mutations do not explain new species. So, we're now onto something that is called "genetic drift". (I suspect the next thing will be "migrations")

But here is the example you asked for:
"Picture a situation in which the 30% of the population which carry an allele are all found in a high-density area that covers only 10% of the species' total range. You only need a disaster occurring in that restricted area to wipe out that allele."

 

[USincognito]

I'm surprised about that question frankly. I think we concluded that Natural Selection does not explain new species, and that Mutations do not explain new species.

So much CF storage space since this thread used up and it seems we're still back on page 2. Who admitted, and it would be nice if you could quote them, that neither natural selection nor mutation explains new species?

I hate to repeat what you've been told before, but random mutation allows the advent of new species and natural selection preserves them. They are the two halves to a whole, but together explain new species.