Answering....

[Ray Martinez]

On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman wrote:
> On 2/25/15, 5:55 PM, Ray Martinez wrote:

[Fifth reply; previous four, in a different topic, did not post--R.M.]

[....]

> > No, I'm asking about the cause of CD: is it falsifiable and if so
> > what is it? I don't see how reproduction is subject to falsification
> > requirements?
>
> The cause of common descent is reproduction, but that's by definition:
> that's what "descent" means. You clearly can't falsify one without
> simultaneously falsifying the other. I'm not clear what you're going for.

So reproduction (cause of common descent) exempt from falsification requirements?

[....]

> > Evolutionary explanations never rely on miracles (macro mutation or
> > single-step selection). Therefore the ToE is wholly reliant on slight
> > successive modifications, which must occur in order for CD to occur
> > (interdependence).
>
> Neither of those sentences is true, and I've warned you about using that
> word "therefore".

Could you please take the time to tell me why those sentences are not true? I see nothing wrong with them at all.

[....]

> >>> Here is how I think about evolutionary theory:
> >>>
> >>> I don't see why evolutionary scientists care about changes that don't
> >>> contribute to speciation. The only changes that matter are these
> >>> changes; therefore all change that contributes to speciation and/or
> >>> divergence is microevolution. Macroevolution, therefore, is
> >>> accumulated microevolution. The health of the ToE is wholly dependent
> >>> on explaining adaptation----namely, the evolution of reproductive
> >>> mechanisms. IF a solid core explanation exists then every other
> >>> problem or obstacle that the ToE faces is a downhill obstacle or
> >>> problem.
> >>
> >> You really have to stop using that term "therefore" or any of its
> >> synonyms, because it invariably precedes a non sequitur. Nor do you seem
> >> to understand what speciation is, or even what adaptation is. Anyway,
> >> not a single sentence above is true except the first one, i.e. that you
> >> don't see.
> >
> > You didn't feel like addressing. I understand.
>
> Would you like me to tell you what's wrong about each sentence?

Please.

> Or perhaps one or two particular ones?

Yes. I don't see anything wrong with what I said.

> It would take a while to explain the
> whole thing, and the rewards of explanation are minimal. Still, I'm
> willing if you ask.

I'm asking.

Thanks.

Ray

[Roger Shrubber]

Ray Martinez wrote:
> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
> wrote:
>> On 2/25/15, 5:55 PM, Ray Martinez wrote:

I'll jump in and do one of these.

>>> Evolutionary explanations never rely on miracles (macro mutation
>>> or single-step selection). Therefore the ToE is wholly reliant on
>>> slight successive modifications, which must occur in order for CD
>>> to occur (interdependence).
>>
>> Neither of those sentences is true, and I've warned you about using
>> that word "therefore".
>
> Could you please take the time to tell me why those sentences are not
> true? I see nothing wrong with them at all.

Speciation has been observed to occur through whole genome
duplication. That is a macromutation, single step selection
and renders your first claim false.
And genomic data suggests other historic whole genome duplication
events are part of the genetic heritage of the natural world.
Nothing about ToE precluded this. You claim of reliance is
clearly wrong. It also would not necessarily follow even if
your first claim were true. What the ToE is wholly reliant
on depends on the ToE and it's intrinsic nature. Further, CD
does not require slight successive modification. CD still
holds for cases of whole genome duplication and instantaneous
speciation as the new species still descended from a parent
species. Basically, you got so much wrong that it's hard to
address it all. You got the facts wrong, don't understand
logical inferences, and you don't seem to understand common
descent. It's rather impressive to pile that many mistakes
into two sentences.

[John Harshman]

On 2/26/15, 3:49 PM, Ray Martinez wrote:
> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman wrote:
>> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>
> [Fifth reply; previous four, in a different topic, did not post--R.M.]
>
> [....]
>
>>> No, I'm asking about the cause of CD: is it falsifiable and if so
>>> what is it? I don't see how reproduction is subject to falsification
>>> requirements?
>>
>> The cause of common descent is reproduction, but that's by definition:
>> that's what "descent" means. You clearly can't falsify one without
>> simultaneously falsifying the other. I'm not clear what you're going for.
>
> So reproduction (cause of common descent) exempt from falsification requirements?

Yes, just as you can't falsify the claim that triangles have three sides.

>>> Evolutionary explanations never rely on miracles (macro mutation or
>>> single-step selection). Therefore the ToE is wholly reliant on slight
>>> successive modifications, which must occur in order for CD to occur
>>> (interdependence).
>>
>> Neither of those sentences is true, and I've warned you about using that
>> word "therefore".
>
> Could you please take the time to tell me why those sentences are not true? I see nothing wrong with them at all.

Miracles are not the same as macromutations are not the same as
single-step selection. Nor, if that were true, would it imply what you
say next. Nor is the theory of evolution reliant on any single thing,
because it isn't a unitary entity but a bundle of various things. Common
descent is one of those things, and common descent doesn't rely on any
modification at all.

>>>>> Here is how I think about evolutionary theory:
>>>>>
>>>>> I don't see why evolutionary scientists care about changes that don't
>>>>> contribute to speciation. The only changes that matter are these
>>>>> changes; therefore all change that contributes to speciation and/or
>>>>> divergence is microevolution. Macroevolution, therefore, is
>>>>> accumulated microevolution. The health of the ToE is wholly dependent
>>>>> on explaining adaptation----namely, the evolution of reproductive
>>>>> mechanisms. IF a solid core explanation exists then every other
>>>>> problem or obstacle that the ToE faces is a downhill obstacle or
>>>>> problem.
>>>>
>>>> You really have to stop using that term "therefore" or any of its
>>>> synonyms, because it invariably precedes a non sequitur. Nor do you seem
>>>> to understand what speciation is, or even what adaptation is. Anyway,
>>>> not a single sentence above is true except the first one, i.e. that you
>>>> don't see.
>>>
>>> You didn't feel like addressing. I understand.
>>
>> Would you like me to tell you what's wrong about each sentence?
>
> Please.

The biggest problem is that you have no idea what speciation is; it's
the evolution of reproductive isolation between two populations. It
isn't the evolution of morphological novelty, as you seem to imagine.

Who are you to decide what matters? And you have another "therefore"
that leads into a non sequitur. I would go so far as to say that the
greatest contributor to macroevolution is accumulated microevolution,
bit it isn't the only contributor.

Nor does the theory of evolution have to do solely with adaptation.
That's what natural selection is about, but that's not all of evolution.
Nor is adaptation the evolution of reproductive mechanisms, though it's
not clear what you mean by "reproductive mechanisms".

The final sentence is just gibberish; I can't even tell if it's a non
sequitur, but that's the way to bet.

>> Or perhaps one or two particular ones?
>
> Yes. I don't see anything wrong with what I said.
>
>> It would take a while to explain the
>> whole thing, and the rewards of explanation are minimal. Still, I'm
>> willing if you ask.
>
> I'm asking.
>
> Thanks.

Sadly, I expect no comprehension.

[Ray Martinez]

On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber wrote:
> Ray Martinez wrote:
> > On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
> > wrote:
> >> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>
> I'll jump in and do one of these.

Good!

>
> >>> Evolutionary explanations never rely on miracles (macro mutation
> >>> or single-step selection). Therefore the ToE is wholly reliant on
> >>> slight successive modifications, which must occur in order for CD
> >>> to occur (interdependence).
> >>
> >> Neither of those sentences is true, and I've warned you about using
> >> that word "therefore".
> >
> > Could you please take the time to tell me why those sentences are not
> > true? I see nothing wrong with them at all.
>
> Speciation has been observed to occur through whole genome
> duplication. That is a macromutation, single step selection
> and renders your first claim false.

Absurd.

Whatever happened to Natura non facit saltum ('nature does not make jumps')? Dawkins has written how many books defending this bedrock Darwinian principle?

> And genomic data suggests other historic whole genome duplication
> events are part of the genetic heritage of the natural world.
> Nothing about ToE precluded this.

What about the "[morphological] heritage of the natural world"?

> You[r] claim of reliance is
> clearly wrong.

Evolution is not reliant on, or tethered to, slight successive modification? Of course my question is rhetorical.

> It also would not necessarily follow even if
> your first claim were true. What the ToE is wholly reliant
> on depends on the ToE and it's intrinsic nature. Further, CD
> does not require slight successive modification.

Apes morphing into human beings isn't reliant on slight successive modification? You're going to postulate leaps and bounds? and give aid to special creation?

> CD still
> holds for cases of whole genome duplication and instantaneous
> speciation as the new species still descended from a parent
> species.

When "whole genome duplication" occurs what is the morphological effect? And would you please define or explain "instantaneous speciation"?

> Basically, you got so much wrong that it's hard to
> address it all.

Yes, one of us has so much wrong, I agree.

> You got the facts wrong, don't understand
> logical inferences, and you don't seem to understand common
> descent. It's rather impressive to pile that many mistakes
> into two sentences.

My replies say different. Do continue into second rebuttal.

Ray

[Ray Martinez]

On Thursday, February 26, 2015 at 4:20:14 PM UTC-8, John Harshman wrote:
> On 2/26/15, 3:49 PM, Ray Martinez wrote:
> > On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman wrote:
> >> On 2/25/15, 5:55 PM, Ray Martinez wrote:
> >
> > [Fifth reply; previous four, in a different topic, did not post--R.M.]
> >
> > [....]
> >
> >>> No, I'm asking about the cause of CD: is it falsifiable and if so
> >>> what is it? I don't see how reproduction is subject to falsification
> >>> requirements?
> >>
> >> The cause of common descent is reproduction, but that's by definition:
> >> that's what "descent" means. You clearly can't falsify one without
> >> simultaneously falsifying the other. I'm not clear what you're going for.
> >
> > So reproduction (cause of common descent) exempt from falsification requirements?
>
> Yes, just as you can't falsify the claim that triangles have three sides.

Glad you said that because that was my belief. Neither reproduction nor triangles, the "things themselves," are theoretical. Both are observed to exist.

>
> >>> Evolutionary explanations never rely on miracles (macro mutation or
> >>> single-step selection). Therefore the ToE is wholly reliant on slight
> >>> successive modifications, which must occur in order for CD to occur
> >>> (interdependence).
> >>
> >> Neither of those sentences is true, and I've warned you about using that
> >> word "therefore".
> >
> > Could you please take the time to tell me why those sentences are not true? I see nothing wrong with them at all.
>
> Miracles are not the same as macromutations are not the same as
> single-step selection.

The history of accepted evolution says different. I will finish my reply ASAP.

Ray

[broger...@gmail.com]

On Thursday, February 26, 2015 at 7:50:15 PM UTC-5, Ray Martinez wrote:
> On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber wrote:
> > Ray Martinez wrote:
> > > On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
> > > wrote:
> > >> On 2/25/15, 5:55 PM, Ray Martinez wrote:
> >
> > I'll jump in and do one of these.
>
> Good!
>
> >
> > >>> Evolutionary explanations never rely on miracles (macro mutation
> > >>> or single-step selection). Therefore the ToE is wholly reliant on
> > >>> slight successive modifications, which must occur in order for CD
> > >>> to occur (interdependence).
> > >>
> > >> Neither of those sentences is true, and I've warned you about using
> > >> that word "therefore".
> > >
> > > Could you please take the time to tell me why those sentences are not
> > > true? I see nothing wrong with them at all.
> >
> > Speciation has been observed to occur through whole genome
> > duplication. That is a macromutation, single step selection
> > and renders your first claim false.
>
> Absurd.
>
> Whatever happened to Natura non facit saltum ('nature does not make jumps')? Dawkins has written how many books defending this bedrock Darwinian principle?

Speciation by polyploidy (involving whole genome duplication) has been observed in plants. It is well studied. Observations trump nifty Latin mottoes.

[Ray Martinez]

Macro mutation and single-step selection are essentially the same thing. Both are scientifically equivalent to creation miracles. The ToE renounced both a long time ago (since Goldschmidt). Darwinism has always considered both anathema.

>
> Ray
>
> > Nor, if that were true, would it imply what you
> > say next. Nor is the theory of evolution reliant on any single thing,
> > because it isn't a unitary entity but a bundle of various things.

The main object of explanation of accepted evolution is adaptive complexity. If this explanation were to suffer falsification then the ToE is gutted. You're portraying the ToE as too large and too complex to suffer falsification. You refuse to stick your neck out and clearly spell out as to what entails and constitutes theory falsification. Good thing the history of accepted evolution says different.

Will finish ASAP.

Ray

[Ray Martinez]

On Thursday, February 26, 2015 at 5:20:15 PM UTC-8, broger...@gmail.com wrote:
> On Thursday, February 26, 2015 at 7:50:15 PM UTC-5, Ray Martinez wrote:
> > On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber wrote:
> > > Ray Martinez wrote:
> > > > On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
> > > > wrote:
> > > >> On 2/25/15, 5:55 PM, Ray Martinez wrote:
> > >
> > > I'll jump in and do one of these.
> >
> > Good!
> >
> > >
> > > >>> Evolutionary explanations never rely on miracles (macro mutation
> > > >>> or single-step selection). Therefore the ToE is wholly reliant on
> > > >>> slight successive modifications, which must occur in order for CD
> > > >>> to occur (interdependence).
> > > >>
> > > >> Neither of those sentences is true, and I've warned you about using
> > > >> that word "therefore".
> > > >
> > > > Could you please take the time to tell me why those sentences are not
> > > > true? I see nothing wrong with them at all.
> > >
> > > Speciation has been observed to occur through whole genome
> > > duplication. That is a macromutation, single step selection
> > > and renders your first claim false.
> >
> > Absurd.
> >
> > Whatever happened to Natura non facit saltum ('nature does not make jumps')? Dawkins has written how many books defending this bedrock Darwinian principle?
>
> Speciation by polyploidy (involving whole genome duplication) has been observed in plants. It is well studied. Observations trump nifty Latin mottoes.
>

What about animal species (the main object of explanation)? Did you forget?

Ray

[John Harshman]

On 2/26/15, 4:59 PM, Ray Martinez wrote:
> On Thursday, February 26, 2015 at 4:20:14 PM UTC-8, John Harshman wrote:
>> On 2/26/15, 3:49 PM, Ray Martinez wrote:
>>> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman wrote:
>>>> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>>>
>>> [Fifth reply; previous four, in a different topic, did not post--R.M.]
>>>
>>> [....]
>>>
>>>>> No, I'm asking about the cause of CD: is it falsifiable and if so
>>>>> what is it? I don't see how reproduction is subject to falsification
>>>>> requirements?
>>>>
>>>> The cause of common descent is reproduction, but that's by definition:
>>>> that's what "descent" means. You clearly can't falsify one without
>>>> simultaneously falsifying the other. I'm not clear what you're going for.
>>>
>>> So reproduction (cause of common descent) exempt from falsification requirements?
>>
>> Yes, just as you can't falsify the claim that triangles have three sides.
>
> Glad you said that because that was my belief. Neither reproduction nor triangles, the "things themselves," are theoretical. Both are observed to exist.

That was very confused. It isn't the observation that counts, it's the
tautology. The fact that your parents reproduced causes you to be
descended from them. Now extend that back in time for as many
generations as you like.

>>>>> Evolutionary explanations never rely on miracles (macro mutation or
>>>>> single-step selection). Therefore the ToE is wholly reliant on slight
>>>>> successive modifications, which must occur in order for CD to occur
>>>>> (interdependence).
>>>>
>>>> Neither of those sentences is true, and I've warned you about using that
>>>> word "therefore".
>>>
>>> Could you please take the time to tell me why those sentences are not true? I see nothing wrong with them at all.
>>
>> Miracles are not the same as macromutations are not the same as
>> single-step selection.
>
> The history of accepted evolution says different. I will finish my reply ASAP.

Sigh.

[John Harshman]

Could be. I'm not actually familiar with the term "single-step
selection" and it isn't clear to me what you mean by it. Nothing is
scientifically equivalent to a creation miracle. There is nothing in
principle against macromutation, though it seems a very unlikely source
of any complex adaptation, if that's what you're trying to say.

None of that has anything to do with common descent.

>> Ray
>>
>>> Nor, if that were true, would it imply what you
>>> say next. Nor is the theory of evolution reliant on any single thing,
>>> because it isn't a unitary entity but a bundle of various things.
>
> The main object of explanation of accepted evolution is adaptive
> complexity. If this explanation were to suffer falsification then the
> ToE is gutted. You're portraying the ToE as too large and too complex
> to suffer falsification. You refuse to stick your neck out and
> clearly spell out as to what entails and constitutes theory
> falsification. Good thing the history of accepted evolution says
> different.

What do you mean by "this explanation"? Evolution? No, evolution is not
the explanation for adaptation. Natural selection is the explanation for
adaptation. Natural selection is one feature of evolution. Common
descent is a completely separate feature of evolution.

I am not protraying the theory of evolution as too large and complex to
suffer falsification; I'm not sure what you misread to give you that
impression. The rest of that paragraph is incomprehensible.

[Roger Shrubber]

Ray Martinez wrote:
> On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber
> wrote:
>> Ray Martinez wrote:
>>> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John
>>> Harshman wrote:
>>>> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>>
>> I'll jump in and do one of these.
>
> Good!
>
>>
>>>>> Evolutionary explanations never rely on miracles (macro
>>>>> mutation or single-step selection). Therefore the ToE is
>>>>> wholly reliant on slight successive modifications, which must
>>>>> occur in order for CD to occur (interdependence).
>>>>
>>>> Neither of those sentences is true, and I've warned you about
>>>> using that word "therefore".
>>>
>>> Could you please take the time to tell me why those sentences are
>>> not true? I see nothing wrong with them at all.
>>
>> Speciation has been observed to occur through whole genome
>> duplication. That is a macromutation, single step selection and
>> renders your first claim false.
>
> Absurd.
>
> Whatever happened to Natura non facit saltum ('nature does not make
> jumps')? Dawkins has written how many books defending this bedrock
> Darwinian principle?

Eppur si muove
I'm not responsible for the ways you misinterpret things.
The fact remains that whole genome duplications have been
observed and they result in speciation. It's a fact. And in
comparative genomics we observe cases where an apparently
diverged species has twice the chromosomes of its sister
species with strong correspondences between sister chromosomes.
Whole genome duplication is rather common in plants. There's
strong evidence for two rounds of whole genome duplication
in the line leading to vertebrates. It's standard stuff.

To the extent that your representation of Dawkins is
accurate, Dawkins is wrong. But I think you misrepresent
Dawkins, or have run too far with his oversimplification.

>> And genomic data suggests other historic whole genome duplication
>> events are part of the genetic heritage of the natural world.
>> Nothing about ToE precluded this.

> What about the "[morphological] heritage of the natural world"?

I have no idea what you are talking about. I deal in
actual observations of the world, not in attempts to
deconstruct language. Put another way, I understand
what people write because I look at the data.

>> You[r] claim of reliance is clearly wrong.

> Evolution is not reliant on, or tethered to, slight successive
> modification? Of course my question is rhetorical.

Not wholly, no. Yes it happens and is an important part but
that does not make it exclusive to slight successive modifications
as you claimed. Whole genome duplications are just one example
of an exception. That exception alone renders both of your
sentences in question wrong.

>> It also would not necessarily follow even if your first claim were
>> true. What the ToE is wholly reliant on depends on the ToE and it's
>> intrinsic nature. Further, CD does not require slight successive
>> modification.
>
> Apes morphing into human beings isn't reliant on slight successive
> modification? You're going to postulate leaps and bounds? and give
> aid to special creation?

Logic Ray. Logic.

You made a claim that evolution is _ONLY_ small successive
modifications. Examples of whole genome duplication demonstrate
that _ONLY_ is wrong. That makes your claim wrong.

That does not mean that evolution does not usually work by
small successive modifications. Sometimes, evolution involves
big leaps. Whole genome duplication is probably the biggest
sort. That doesn't say that things like whole genome duplication
are common. In fact, they are somewhat rare. But they do
happen. We know they happen. Nothing about ToE says they
should not happen. It's not that hard. Nevertheless, you
apparently don't understand, and nevertheless you resist
understanding.

>> CD still holds for cases of whole genome duplication and
>> instantaneous speciation as the new species still descended from a
>> parent species.

> When "whole genome duplication" occurs what is the morphological
> effect? And would you please define or explain "instantaneous
> speciation"?

It varies. You might not be able to tell. Many agricultural
crops have fairly recent duplications, the same for many
flowers. Wheat have many distinct ploidy levels. Duploid
is what you are most familiar with. Many agricutural
wheats are hexaploid (a simple duplication is quadraploid).
It's still wheat.

>> Basically, you got so much wrong that it's hard to address it all.

> Yes, one of us has so much wrong, I agree.

The facts are on my side Ray. Your ignorance of whole genome
duplication is clear. It's been observed.

>> You got the facts wrong, don't understand logical inferences, and
>> you don't seem to understand common descent. It's rather impressive
>> to pile that many mistakes into two sentences.

> My replies say different. Do continue into second rebuttal.

It's probably pointless. You'll resort to some bizarre interpretation
of somebody else's words. But watching you evade the obvious has
a certain type of entertainment value.

[broger...@gmail.com]

As far as I know, polyploid speciation event have only been observed in plants, not in animals. So what? The theory of evolution covers plants as well as animals. Why not just admit you're wrong on this point (since you clearly ARE wrong about it)? It's not a point that's essential to your argument, anyway.

[Ray Martinez]

Likewise. I assumed that you knew we were talking about animal species and how the complexity seen evolved----that we were not talking about plants.

> The fact remains that whole genome duplications have been
> observed and they result in speciation.

What about animal species?

> It's a fact. And in
> comparative genomics we observe cases where an apparently
> diverged species has twice the chromosomes of its sister
> species with strong correspondences between sister chromosomes.
> Whole genome duplication is rather common in plants.

Yet we weren't talking about plants, but the origin of sexually reproducing animal species. Neither macro mutation nor single-step selection has any role in the production of adaptive complexity.

> There's
> strong evidence for two rounds of whole genome duplication
> in the line leading to vertebrates. It's standard stuff.

So what are you saying? Macro mutation occurs in species?

>
> To the extent that your representation of Dawkins is
> accurate, Dawkins is wrong. But I think you misrepresent
> Dawkins, or have run too far with his oversimplification.

I'm conveying standard Darwinian stuff, which you seem wholly ignorant. Who cares about plants? Plants are NOT the main object of explanation in the origins debate. The fact that you first thought macro mutation was about plants indicates much ignorance of basic history of science.

>
> >> And genomic data suggests other historic whole genome duplication
> >> events are part of the genetic heritage of the natural world.
> >> Nothing about ToE precluded this.
>
> > What about the "[morphological] heritage of the natural world"?
>
> I have no idea what you are talking about.

Because we are not on the same page. Will finish ASAP.

Ray

[Ray Martinez]

I never have a problem admitting when I'm wrong or in error. If you review the context I assumed topic (origin of animal species) and not auxiliary phenomena (origin of plants). The point is that macro mutation and single-step selection are anathema to explaining the existence of adaptive complexity.

In this context I beg to differ with John Harshman. Common descent, that is, connected biodiversity (species-to-species), is dependent on speciation occurring, and speciation or divergence is dependent on micro-modification occurring.

Ray

[Roger Shrubber]

The Theory of Evolution applies to plants as well as animals.
This little discussion relates to your comments about the Theory
of Evolution. Why would anyone presume the discussion was specific
to animals? Did you think there was a different ToE with respect
to plants? Biologists don't.

>> The fact remains that whole genome duplications have been observed
>> and they result in speciation.

> What about animal species?

There is evidence of historic genome duplication events leading to
vertebrates. As these are events in the past they involve more
sophisticated analysis. I'm not interested in trying to prove
the validity of the inferences to you because it would be a great
deal of effort on my part. I brought up the actually observed
cases because they are quite simple and direct. And they are
sufficient to disprove your claim. Again, the ToE applies to all
life, not just animals.

>> It's a fact. And in comparative genomics we observe cases where an
>> apparently diverged species has twice the chromosomes of its
>> sister species with strong correspondences between sister
>> chromosomes. Whole genome duplication is rather common in plants.

> Yet we weren't talking about plants, but the origin of sexually
> reproducing animal species. Neither macro mutation nor single-step
> selection has any role in the production of adaptive complexity.

Says who? Your claim was about the ToE. It applies to plants
as well as animals and to bacteria and archae. What makes you think
that evolution in animals is a distinctly different process? Strange.

>> There's strong evidence for two rounds of whole genome duplication
>> in the line leading to vertebrates. It's standard stuff.

> So what are you saying? Macro mutation occurs in species?

Yes. Did I stutter? It isn't common but it happens.

>> To the extent that your representation of Dawkins is accurate,
>> Dawkins is wrong. But I think you misrepresent Dawkins, or have run
>> too far with his oversimplification.

> I'm conveying standard Darwinian stuff, which you seem wholly
> ignorant. Who cares about plants? Plants are NOT the main object of
> explanation in the origins debate. The fact that you first thought
> macro mutation was about plants indicates much ignorance of basic
> history of science.

No, it isn't standard Darwinian stuff. It's your very strange
misunderstanding of the ToE. The ToE applies to plants and
animals and microbes. The breadth of misconceptions you hold
make it difficult to converse.

[Ray Martinez]

The **concept** of speciation entails one species gradually changing into a different species; hence "speciation." And don't forget you have had great trouble understanding the conceptual.

> > >
> > > Who are you to decide what matters? And you have another "therefore"
> > > that leads into a non sequitur. I would go so far as to say that the
> > > greatest contributor to macroevolution is accumulated microevolution,
> > > bit it isn't the only contributor.

Fine. At least you said something definitive.

> > >
> > > Nor does the theory of evolution have to do solely with adaptation.
> > > That's what natural selection is about, but that's not all of evolution.

You don't seem to understand that if irreplaceable concepts suffer falsification the whole suffers falsification as well. Without a valid explanation for adaptive complexity the ToE, like I said, is gutted. Do you know what "gutted" means?

> > > Nor is adaptation the evolution of reproductive mechanisms, though it's
> > > not clear what you mean by "reproductive mechanisms".

The mechanism that disallows an ape to successfully impregnate a human female, for example.

> > >
> > > The final sentence is just gibberish; I can't even tell if it's a non
> > > sequitur, but that's the way to bet.
> > >
> > > >> Or perhaps one or two particular ones?
> > > >
> > > > Yes. I don't see anything wrong with what I said.
> > > >
> > > >> It would take a while to explain the
> > > >> whole thing, and the rewards of explanation are minimal. Still, I'm
> > > >> willing if you ask.
> > > >
> > > > I'm asking.
> > > >
> > > > Thanks.
> > >
> > > Sadly, I expect no comprehension.

Likewise.

You're excused.

Ray

[Roger Shrubber]

John Harshman wrote:
> On 2/26/15, 4:59 PM, Ray Martinez wrote:


>> Glad you said that because that was my belief. Neither reproduction
>> nor triangles, the "things themselves," are theoretical. Both are
>> observed to exist.
>
> That was very confused. It isn't the observation that counts, it's the
> tautology. The fact that your parents reproduced causes you to be
> descended from them. Now extend that back in time for as many
> generations as you like.

At the risk of getting into something interesting, I've been thinking
about this. Running backwards that way in sexually reproducing organisms
isn't so trivial.

When I think of common descent respective to evolution, I think about
the branching nested hierarchy. That's easy with things like bacteria
where two daughter cells are spawned from a single common ancestor,
and 4 granddaughter cells are spawned from a single common ancestor.
That's a direct nested hierarchy. But things get messy with sex.

Your family tree is an inverted nested hierarchy. You are spawned
from two individuals, and hopefully you have 4 distinct grandparents,
8 distinct great grandparents. That's not common descent.

If we integrate heredity over many generations we get something that
is, I claim, non trivial. To state the obvious, at 20 generations
back we have 2^20 (~1,000,000) virtual ancestors but quite certainly
orders of magnitude fewer real ancestors. And going back 100 generations
the compression of real ancestors versus 'virtual' ancestors is greater.

And thus in this integrated sense, the current population of humans
collapses their ancestry to a small population of distant ancestors.
None of this is especially interesting or novel as insights go
but I do think it is in many respects non-trivial (granted that
people will have different notions of what is or isn't trivial).

Essentially, one needs to shift their thinking into populations,
and understand the dynamics of sexually reproducing populations,
and that isn't completely trivial. It's easy to think in terms
of an individual's family tree. It's much more complex to think
in terms of populations with ancestor trimming. I rather expect
that many who think they understand it have rather incomplete
understanding.

My point, such as it exists, is that understanding common descent
requires more sophistication than some might suggest.

[Ray Martinez]

I have now informed you of the main object of explanation.

>
> >> The fact remains that whole genome duplications have been observed
> >> and they result in speciation.
>
> > What about animal species?
>
> There is evidence of historic genome duplication events leading to
> vertebrates. As these are events in the past they involve more
> sophisticated analysis. I'm not interested in trying to prove
> the validity of the inferences to you because it would be a great
> deal of effort on my part. I brought up the actually observed
> cases because they are quite simple and direct. And they are
> sufficient to disprove your claim. Again, the ToE applies to all
> life, not just animals.
>
> >> It's a fact. And in comparative genomics we observe cases where an
> >> apparently diverged species has twice the chromosomes of its
> >> sister species with strong correspondences between sister
> >> chromosomes. Whole genome duplication is rather common in plants.
>
> > Yet we weren't talking about plants, but the origin of sexually
> > reproducing animal species. Neither macro mutation nor single-step
> > selection has any role in the production of adaptive complexity.
>
> Says who?

Almost all evolutionary authorities. You don't know that?

> Your claim was about the ToE. It applies to plants
> as well as animals and to bacteria and archae. What makes you think
> that evolution in animals is a distinctly different process? Strange.

Truck loads of books published by evolutionary authorities.

>
> >> There's strong evidence for two rounds of whole genome duplication
> >> in the line leading to vertebrates. It's standard stuff.
>
> > So what are you saying? Macro mutation occurs in species?
>
> Yes. Did I stutter? It isn't common but it happens.

Show me two examples! Waiting! Then tell me how said examples effect the standard Darwinian explanation of adaptive complexity? Do you even know what the standard explanation is? You seem to think that current evolutionary concepts just popped into existence, not having a historical context of replacing or complimenting previously accepted concepts.

>
> >> To the extent that your representation of Dawkins is accurate,
> >> Dawkins is wrong. But I think you misrepresent Dawkins, or have run
> >> too far with his oversimplification.
>
> > I'm conveying standard Darwinian stuff, which you seem wholly
> > ignorant. Who cares about plants? Plants are NOT the main object of
> > explanation in the origins debate. The fact that you first thought
> > macro mutation was about plants indicates much ignorance of basic
> > history of science.
>
> No, it isn't standard Darwinian stuff.

IOW, you're ignorant, no surprise here.

> It's your very strange
> misunderstanding of the ToE.

The misunderstanding card.

> The ToE applies to plants and
> animals and microbes. The breadth of misconceptions you hold
> make it difficult to converse.

That's exactly what I've been saying about your knowledge.

Ray

[Dana Tweedy]

On 2/26/15 5:46 PM, Ray Martinez wrote:
> On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber wrote:
>> Ray Martinez wrote:
>>> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
>>> wrote:
>>>> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>>
>> I'll jump in and do one of these.
>
> Good!
>
>>
>>>>> Evolutionary explanations never rely on miracles (macro mutation
>>>>> or single-step selection). Therefore the ToE is wholly reliant on
>>>>> slight successive modifications, which must occur in order for CD
>>>>> to occur (interdependence).
>>>>
>>>> Neither of those sentences is true, and I've warned you about using
>>>> that word "therefore".
>>>
>>> Could you please take the time to tell me why those sentences are not
>>> true? I see nothing wrong with them at all.
>>
>> Speciation has been observed to occur through whole genome
>> duplication. That is a macromutation, single step selection
>> and renders your first claim false.
>
> Absurd.

Yes, what you wrote below is absurd, Ray. But you really don't need to
call your shots.

>
> Whatever happened to Natura non facit saltum ('nature does not make jumps')?

The same thing that happened to "If man was meant to fly, he'd have
wings" Science moves on.

> Dawkins has written how many books defending this bedrock Darwinian principle?

How many? Approximately 0, or maybe less. I don't know of any book
Dawkins has written that denies that polyplody happens.

>
>> And genomic data suggests other historic whole genome duplication
>> events are part of the genetic heritage of the natural world.
>> Nothing about ToE precluded this.
>
> What about the "[morphological] heritage of the natural world"?

What about it? Morphology is a consequence of genes. Genetic change is
what matters in evolution. Morphology is a side effect. Large genetic
changes can produce little outward morphological changes, and small
genetic changes can cause large morphological changes. It all depends
on where in the genome the changes take place.

>
>> You[r] claim of reliance is
>> clearly wrong.
>
> Evolution is not reliant on, or tethered to, slight successive modification?

Evolution most often produces slight, successive modification, but it's
not "tethered" to it. Large changes in morphology are usually selected
against by the environment, but not always.

> Of course my question is rhetorical.

Of course, your question reveals your lack of understanding.

>
>> It also would not necessarily follow even if
>> your first claim were true. What the ToE is wholly reliant
>> on depends on the ToE and it's intrinsic nature. Further, CD
>> does not require slight successive modification.
>
> Apes morphing into human beings isn't reliant on slight successive modification?

Ray, human beings *are* apes, and remained apes all through the split
from our last common ancestor with other apes. Saying "apes morphed
into human beings" is like saying "birds morphed into chickens".

Also, you have missed the point. Common descent does not require
slight successive modification. It only requires reproduction and
survival of the offspring. In practice, evolution tends to produce
small successive changes in a population, but there is no requirement
for such changes always be small. Offspring with large genetic and
morphological changes would be common descent as well.

You seem to be conflating the evolution of humans with common
descent. Humans did evolve (according to the fossil and genetic
evidence) in fairly small steps. But it wouldn't matter to the issue if
the changes were large.

> You're going to postulate leaps and bounds? and give aid to special creation?

"Leaps and bounds" wouldn't give any aid to special creation because
there still isn't any mechanism of special creation, and no observation
of special creation happening, any time, or in any place.

>
>> CD still
>> holds for cases of whole genome duplication and instantaneous
>> speciation as the new species still descended from a parent
>> species.
>
> When "whole genome duplication" occurs what is the morphological effect?

Usually not a great deal of morphological effect. As already
mentioned, it's most common in plants. One effect seen is seedless
fruits, such as Bananas and Watermelons. Those plants propagate by
sending out shoots, so they don't reproduce like their ancestors did.
For examples see:

https://genomevolution.org/wiki/index.php/Whole_genome_duplication

> And would you please define or explain "instantaneous speciation"?

It's just like it sounds, Ray. Speciation in a single generation. It
happens when a large genetic change produces offspring that can't
reproduce with the parent population. Speciation is usually a gradual
process, but not always.
for more info, see:

http://www.yourarticlelibrary.com/biology/mechanisms-of-speciation-gradual-speciation-and-abrupt-of-instantaneous-speciation/27223/

>
>> Basically, you got so much wrong that it's hard to
>> address it all.
>
> Yes, one of us has so much wrong, I agree.

and to see that person, you would need to look in a mirror, Ray.

>
>> You got the facts wrong, don't understand
>> logical inferences, and you don't seem to understand common
>> descent. It's rather impressive to pile that many mistakes
>> into two sentences.
>
> My replies say different.

But you are wrong. Your "replies" are a symptom of your ignorance.

> Do continue into second rebuttal.

Why? You were obliterated in the first one.

DJT

[Dana Tweedy]

Plants are living things too, Ray, and species. They evolved like
animals species have evolved. If you limit yourself to just animal
species, you are cutting out the vast majority of species on Earth.

>
>> The fact remains that whole genome duplications have been
>> observed and they result in speciation.
>
> What about animal species?

What about them? Whole genome duplication hasn't been observed in
animals, (yet,) but that doesn't mean it never happens in living species.

>
>> It's a fact. And in
>> comparative genomics we observe cases where an apparently
>> diverged species has twice the chromosomes of its sister
>> species with strong correspondences between sister chromosomes.
>> Whole genome duplication is rather common in plants.
>
> Yet we weren't talking about plants, but the origin of sexually reproducing animal species.

Again, if you limit your view of nature to just sexually reproducing
animal species you are cutting out the vast majority of living things.
There's no rational excuse for doing os.

> Neither macro mutation nor single-step selection has any role in the production of adaptive complexity.

Plants are just as complex, and adaptive as animal species, if not more
so. You seem to be retreating and dragging the goal posts along with
you.

>
>> There's
>> strong evidence for two rounds of whole genome duplication
>> in the line leading to vertebrates. It's standard stuff.
>
> So what are you saying? Macro mutation occurs in species?

Yes, it does. It has been observed in plants, and there's nothing that
would in principle, stop it from happening in animals, or other Kingdoms.

>
>>
>> To the extent that your representation of Dawkins is
>> accurate, Dawkins is wrong. But I think you misrepresent
>> Dawkins, or have run too far with his oversimplification.
>
> I'm conveying standard Darwinian stuff, which you seem wholly ignorant.

No, Ray. You are "conveying" your own misunderstanding of Darwinian
evolution. You are the one who is ignorant, and too arrogant to admit
your ignorance.


> Who cares about plants?

Many of the greatest scientists of the Victorian era were
Botanists. Linnaeus, Burbidge, von Gesner, Henslow, Mendel, etc. Even
a county parson by the name of William Paley wrote: "Botany is
extremely important and entertaining part of the science of nature"

The Works of William Paley, D.D.: And An Account of the Life and ...,
Volume 4, page 197

> Plants are NOT the main object of explanation in the origins debate.

Plants are living things, Ray, and plants are just as much a part of the
science of origins as animals are.

> The fact that you first thought macro mutation was about plants indicates much ignorance of basic history of science.

Ray, this is probably the most bizarre, and utterly false thing you have
ever said, which takes some doing.. It stands as a monument to your
ignorance of science, and history.

>
>>
>>>> And genomic data suggests other historic whole genome duplication
>>>> events are part of the genetic heritage of the natural world.
>>>> Nothing about ToE precluded this.
>>
>>> What about the "[morphological] heritage of the natural world"?
>>
>> I have no idea what you are talking about.
>
> Because we are not on the same page. Will finish ASAP.

Ray, if you have any sense at all, you'll quit while you are behind.

snip the rest.

DJT

[Dana Tweedy]

On 2/26/15 5:59 PM, Ray Martinez wrote:
> On Thursday, February 26, 2015 at 4:20:14 PM UTC-8, John Harshman wrote:
>> On 2/26/15, 3:49 PM, Ray Martinez wrote:
>>> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman wrote:

snip

>>> Could you please take the time to tell me why those sentences are not true? I see nothing wrong with them at all.
>>
>> Miracles are not the same as macromutations are not the same as
>> single-step selection.
>
> The history of accepted evolution says different. I will finish my reply ASAP.

Ray, no "accepted evolution" has ever claimed that macromutations are
the same thing as miracles. You are being even more opaque than usual.

DJT

[Roger Shrubber]

Then you still need to rewrite your claim about the ToE
to be specific to the evolution of animals (which it isn't).
And you would still be wrong. You wrote

>>>>>>>>> Evolutionary explanations never rely on miracles
>>>>>>>>> (macro mutation or single-step selection). Therefore

If you want that to be specific to the evolution of animals,
then you need to state it because biologists don't think
evolution works in significantly different ways in animals
and plants.

Also, as I've said we have evidence of genome duplications
in the natural history of vertibrates. That evidence doesn't
bother evolutionary biologists. It isn't a violation of the
principles of evolution like you claim. So you remain wrong.

>>>> The fact remains that whole genome duplications have been
>>>> observed and they result in speciation.
>>
>>> What about animal species?
>>
>> There is evidence of historic genome duplication events leading to
>> vertebrates. As these are events in the past they involve more
>> sophisticated analysis. I'm not interested in trying to prove the
>> validity of the inferences to you because it would be a great deal
>> of effort on my part. I brought up the actually observed cases
>> because they are quite simple and direct. And they are sufficient
>> to disprove your claim. Again, the ToE applies to all life, not
>> just animals.
>>
>>>> It's a fact. And in comparative genomics we observe cases where
>>>> an apparently diverged species has twice the chromosomes of
>>>> its sister species with strong correspondences between sister
>>>> chromosomes. Whole genome duplication is rather common in
>>>> plants.
>>
>>> Yet we weren't talking about plants, but the origin of sexually
>>> reproducing animal species. Neither macro mutation nor
>>> single-step selection has any role in the production of adaptive
>>> complexity.
>>
>> Says who?

> Almost all evolutionary authorities. You don't know that?

Actually I know that you are wrong.
Most evolution takes place in small steps. That does not
preclude some big steps. I've noted that you have an
affinity for all or none thinking. That's your problem.
The actual theory of evolution is not encumbered by your
misconceptions.

>> Your claim was about the ToE. It applies to plants as well as
>> animals and to bacteria and archae. What makes you think that
>> evolution in animals is a distinctly different process? Strange.

> Truck loads of books published by evolutionary authorities.

No Ray, no. It boggles the mind that you believe this.
The underlying biochemistry is the same. The molecular
genetics is the same. There are some differences in the
details of egg and sperm in animals versus how things
occur in plants but they don't change things overall.

>>>> There's strong evidence for two rounds of whole genome
>>>> duplication in the line leading to vertebrates. It's standard
>>>> stuff.
>>
>>> So what are you saying? Macro mutation occurs in species?
>>
>> Yes. Did I stutter? It isn't common but it happens.
>
> Show me two examples! Waiting! Then tell me how said examples effect
> the standard Darwinian explanation of adaptive complexity? Do you
> even know what the standard explanation is? You seem to think that
> current evolutionary concepts just popped into existence, not having
> a historical context of replacing or complimenting previously
> accepted concepts.

You are avoiding simple logic.
You made a claim that said evolution was exclusively the result of
small incremental change. You're wrong. Occasionally there are
big changes. Whole genome duplication is one example. Occasional
large changes render your claim false. Got it? If you claims
that X occurs only by Y, and somebody shows that occasionally
X occurs by Z, your claim is falsified. Got it? That does not
mean that Y isn't the most common means of producing X. Got it?

So our view of natural history isn't significantly changed
by the observation that sometimes whole genomes have been
duplicated. And whatever you may think, there has never been
anything in the ToE that prohibited whole genome duplication.

>>>> To the extent that your representation of Dawkins is accurate,
>>>> Dawkins is wrong. But I think you misrepresent Dawkins, or have
>>>> run too far with his oversimplification.
>>
>>> I'm conveying standard Darwinian stuff, which you seem wholly
>>> ignorant. Who cares about plants? Plants are NOT the main object
>>> of explanation in the origins debate. The fact that you first
>>> thought macro mutation was about plants indicates much ignorance
>>> of basic history of science.
>>
>> No, it isn't standard Darwinian stuff.
>
> IOW, you're ignorant, no surprise here.

Well it's a special sort of ignorance based on being a
practicing biologists, discussing biology with other
professional biologists, and being an active part of the
scientific community. Except most people would think that
such a background rendered someone informed about the
standard view of evolution amongst biologists.

Ray, the things you think about evolution are very often
not what biologists think about evolution. You attempt to
deconstruct language in the most tortured ways and produce
utter gibberish. It's painful to watch. I'm sure that's
hard for you to accept but it's true. You just get things wrong.

>> It's your very strange misunderstanding of the ToE.

> The misunderstanding card.

>> The ToE applies to plants and animals and microbes. The breadth of
>> misconceptions you hold make it difficult to converse.

> That's exactly what I've been saying about your knowledge.

And you are unanimous in your view. You are also alone.

[Dana Tweedy]

Except when it's something you don't want to admit...

> If you review the context I assumed topic (origin of animal species) and not auxiliary phenomena (origin of plants).

Origin of plants is not an "auxiliary phenomena", Ray. It's all
evolution.

> The point is that macro mutation and single-step selection are anathema to explaining the existence of adaptive complexity.

That is simply not true, Ray.

>
> In this context I beg to differ with John Harshman. Common descent, that is, connected biodiversity (species-to-species),

Plants are species, Ray.

> is dependent on speciation occurring, and speciation or divergence is dependent on micro-modification occurring.

Speciation usually involves small changes in populations, but there is
no reason it must. You are just wrong yet again, and you won't admit
your error.


DJT

[chris thompson]

Why are plants so much less important for evolution than animals? Why does it matter they speciate in different manners? You might just as well say animals don't count as much because animals don't photosynthesize.

But you're mistaken in any case. It seems _Xenopus_ in particular has an array of species that came into being through genome duplication. Abstract at:

http://www.ncbi.nlm.nih.gov/pubmed/18006297

Full-text article available free to registered users (registration is free).

Chris

[Nashton]

On 2015-02-27 8:19 AM, chris thompson wrote:


<snip>

Do you even know what occurs during photosynthesis?

[John Harshman]

I know what I and the rest of the world mean. I'm not sure what you
mean. There is much about evolution that doesn't require that we explain
the origin of adaptation. Common descent, for example.

>>>> Nor is adaptation the evolution of reproductive mechanisms, though it's
>>>> not clear what you mean by "reproductive mechanisms".
>
> The mechanism that disallows an ape to successfully impregnate a human female, for example.

Those are called "isolating mechanisms". They may or may not be
adaptations, and adaptations may or may not be isolating mechanisms. So
your initial premise is just wrong.

[Greg Guarino]

On 2/26/2015 9:43 PM, Ray Martinez wrote:

> You don't seem to understand that if irreplaceable concepts suffer
> falsification the whole suffers falsification as well. Without a
> valid explanation for adaptive complexity the ToE, like I said, is
> gutted. Do you know what "gutted" means?

Rather than use metaphors let's be specific. Without selection (I assume
that's the "irreplaceable" concept you are referring to), we would need
another explanation for adaptation. But the evidence for Common Descent
is separate and would would remain undiminished.

In fact, we could have adaptation via mutation and selection, and yet
NOT have universal common descent. There could have been several origin
of life events, each of which would have its own separate sets of
descendants.

And we could have universal common descent without mutation and
selection as well; the divergence in that case would be as yet
unexplained, but the evidence for common descent would remain too strong
to ignore.

[Burkhard]

You mean you have expressed your personal preference or interest? The
theory of evolution does not discriminate between the kingdoms, how
could it, given common descent?

>
>>
>>>> The fact remains that whole genome duplications have been observed
>>>> and they result in speciation.
>>
>>> What about animal species?
>>
>> There is evidence of historic genome duplication events leading to
>> vertebrates. As these are events in the past they involve more
>> sophisticated analysis. I'm not interested in trying to prove
>> the validity of the inferences to you because it would be a great
>> deal of effort on my part. I brought up the actually observed
>> cases because they are quite simple and direct. And they are
>> sufficient to disprove your claim. Again, the ToE applies to all
>> life, not just animals.
>>
>>>> It's a fact. And in comparative genomics we observe cases where an
>>>> apparently diverged species has twice the chromosomes of its
>>>> sister species with strong correspondences between sister
>>>> chromosomes. Whole genome duplication is rather common in plants.
>>
>>> Yet we weren't talking about plants, but the origin of sexually
>>> reproducing animal species. Neither macro mutation nor single-step
>>> selection has any role in the production of adaptive complexity.
>>
>> Says who?
>
> Almost all evolutionary authorities. You don't know that?

You mean like this one:


Smartt, Joseph, and Norman Willison Simmonds. Evolution of crop plants.
No. Ed. 2. Longman scientific & technical, 1995.

Cronquist, Arthur. "The evolution and classification of flowering
plants." The evolution and jclassification of flowering plants. (1968).

Graham, Linda E. Origin of land plants. John Wiley & Sons, Inc., 1993.

Taylor, Edith L., Thomas N. Taylor, and Michael Krings. Paleobotany: the
biology and evolution of fossil plants. Academic Press, 2009.

Soltis, Douglas E., et al. Phylogeny and evolution of angiosperms.
Sinauer Associates Incorporated, 2005.

Stewart, Wilson Nichols. Paleobotany and the evolution of plants.
Cambridge University Press, 1993.

>
>> Your claim was about the ToE. It applies to plants
>> as well as animals and to bacteria and archae. What makes you think
>> that evolution in animals is a distinctly different process? Strange.
>
> Truck loads of books published by evolutionary authorities.
>
>>
>>>> There's strong evidence for two rounds of whole genome duplication
>>>> in the line leading to vertebrates. It's standard stuff.
>>
>>> So what are you saying? Macro mutation occurs in species?
>>
>> Yes. Did I stutter? It isn't common but it happens.
>
> Show me two examples! Waiting! Then tell me how said examples effect the standard Darwinian explanation of adaptive complexity? Do you even know what the standard explanation is? You seem to think that current evolutionary concepts just popped into existence, not having a historical context of replacing or complimenting previously accepted concepts.
>
>>
>>>> To the extent that your representation of Dawkins is accurate,
>>>> Dawkins is wrong. But I think you misrepresent Dawkins, or have run
>>>> too far with his oversimplification.
>>
>>> I'm conveying standard Darwinian stuff, which you seem wholly
>>> ignorant. Who cares about plants? Plants are NOT the main object of
>>> explanation in the origins debate. The fact that you first thought
>>> macro mutation was about plants indicates much ignorance of basic
>>> history of science.

This quote from Friedman, William E., and Pamela K. Diggle. "Charles
Darwin and the origins of plant evolutionary developmental biology." The
Plant Cell Online 23.4 (2011): 1194-1207 says otherwise:

"Perhaps most surprisingly, we show that the first person to carefully
read and internalize the remarkable advances in the understanding of
plant morphogenesis in the 1840s and 1850s is none other than Charles
Darwin, whose notebooks, correspondence, and (then) unpublished
manuscripts clearly demonstrate that he had discovered the developmental
basis for the evolutionary transformation of plant form."


As does this one:

"It was a botanist called John Stevens Henslow that first inspired
Darwin, introduced him to the concept of variation and arranged his
place on the Beagle. Plants were as important as animals in Darwin’s
original theses on selection and variation in On the Origin of Species
and The Variation of animals and plants under domestication."

"When Darwin first proposed his theory of evolution by natural selection
many people collected orchids. Their complicated and delicate flowers
were held up by some as an example of nature’s beauty which natural
selection could not explain. Darwin himself addressed this criticism
with his work on orchids"

The work by Darwin on plant evolution is this one here:
"On the various contrivances by which British and foreign orchids are
fertilised by insects, and on the good effects of intercrossing. John
Murray, London 1862;

Darwin wrote several books on plants, including

On the movements and habits of climbing plants. In: Journal of the
Linnean Society of London (Botany) Bd. 9, S. 1–118

Insectivorous Plants. John Murray, London 1875;

The effects of cross and self fertilisation in the vegetable kingdom.
John Murray, London 1876;

The different forms of flowers on plants of the same species. John
Murray, London 1877;

The power of movement in plants. John Murray, London 1880;

The formation of vegetable mould, through the action of worms, with
observations on their habits. John Murray, London 1881

That he saw plant and animal evolution as inherently connected is shown
by another of his books that discusses them together:

"The variation of animals and plants under domestication. John Murray,
London 1868

[Ymir]

In article <ofmdnd-_FfLXR3LJ...@giganews.com>,

Roger Shrubber <rog.sh...@gmail.com> wrote:

> John Harshman wrote:
> > On 2/26/15, 4:59 PM, Ray Martinez wrote:
>
>
> >> Glad you said that because that was my belief. Neither reproduction
> >> nor triangles, the "things themselves," are theoretical. Both are
> >> observed to exist.
> >
> > That was very confused. It isn't the observation that counts, it's the
> > tautology. The fact that your parents reproduced causes you to be
> > descended from them. Now extend that back in time for as many
> > generations as you like.
>
> At the risk of getting into something interesting, I've been thinking
> about this. Running backwards that way in sexually reproducing organisms
> isn't so trivial.
>
> When I think of common descent respective to evolution, I think about
> the branching nested hierarchy. That's easy with things like bacteria
> where two daughter cells are spawned from a single common ancestor,
> and 4 granddaughter cells are spawned from a single common ancestor.
> That's a direct nested hierarchy. But things get messy with sex.
>
> Your family tree is an inverted nested hierarchy. You are spawned
> from two individuals, and hopefully you have 4 distinct grandparents,
> 8 distinct great grandparents. That's not common descent.

Major point of clarification:

Family trees and nested hierarchies aren't quite the same thing -- a
family tree directly encodes ancestry whereas a nested hierarchy groups
organisms according to their similarities.

This is a common point of confusion. Nested hierarchies, by definition,
involved grouping items into progressively larger, non-overlapping sets.
So in the following nested hierarchy (represented as a tree):

A
/ \
B C
/ \ / \
d e f g

the terminal elements {d, e, f, g} are grouped into three sets: B = {d,
e}, C = {f, g} and A = {d, e, f, g}. In other words, every non terminal
node *must* be a set.

In a family tree, that is not the case -- non-terminals are not sets,
but rather entities of the same type as the terminals. You're correct
that 'family tree' is a bit of a misnomer since, unless you restrict
yourself to either matrilineal descent, patrilineal descent, or are
discussing asexual organisms, you don't actually get a tree.

A 'tree of life' in which ancestors dominate their descendents does not
actuall constitute a nested hierarchy. A tree which groups organisms
into clades, on the other hand, does constitute a nested hierarchy.

If ancestral forms are included in a nested hierarchy, they will occupy
terminal nodes alongside their descendants (in other words they will be
elements rather than sets), not nonterminals as they would in a family
tree.

[Ymir]

In article <330b4670-457e-4c01...@googlegroups.com>,

Ray Martinez <pyram...@yahoo.com> wrote:

> The **concept** of speciation entails one species gradually changing into a
> different species; hence "speciation." And don't forget you have had great
> trouble understanding the conceptual.

That would be true only where chronospecies are concerned.

The concept of speciation entails one populations splitting into two or
more reproductively isolated subpopulations. The morphological and/or
genetic divergence of these subpopulations will generally be gradual,
but that's not part of the concept of speciation.

Andre

[jillery]

I'm glad you asked:

<http://en.wikipedia.org/wiki/Photosynthesis>


--
Intelligence is never insulting.

[Roger Shrubber]

You have an important point but I think you've oversimplified.
There is a nested hierarchy of common descent where the A, B and
C in your diagram are actual nodes and not set descriptors.
And we have to be careful (more careful than I was) in making
it clear which type of nested hierarchy we are referring to.
In one diagram, the lines indicated "is a subset of". In the
other the lines indicated "is a descendent of".
Such a nested hierarchy is readily found in tracing Y chromosome
inheritance in humans. Actual fathers spawn actual sons.

As species do have ancestors, both types of nested hierarchies
are meaningful. In practice, it is extremely difficult to
confidently assign specific ancestors. Worse still, because
our biological species concept is problematic, we get things
like neanderthals crossing back into human lineages so by
some expanded resolution there is merging as well as splitting.

[John Harshman]

Still, he has a point. The nested hierarchy is not in the internal nodes
but in the states of the terminal nodes. In a nested hierarchy, groups
nest within groups, but ancestors don't include descendants. Nested
hierarchy isn't the ancestry and descent itself, it's the pattern in the
descendants caused by that ancestry and descent. The hierarchy of
ancestors and descendants is a non-nested hierarchy. A phylogenetic tree
represents a nested hierarchy only if you think of the nodes as
indicators of set membership.

> As species do have ancestors, both types of nested hierarchies
> are meaningful. In practice, it is extremely difficult to
> confidently assign specific ancestors. Worse still, because
> our biological species concept is problematic, we get things
> like neanderthals crossing back into human lineages so by
> some expanded resolution there is merging as well as splitting.

This is true wherever you look closely enough. The lines and nodes on
phylogenetic trees are abstractions that usually work well enough. And
the lines are evolving populations. But if you look closely enough you
see the level of individuals within populations, and a tree turns into a
complex network of ancestry and descent within and between populations.
There are plenty of graphics online showing this sort of thing.

[Sneaky O. Possum]

Roger Shrubber <rog.sh...@gmail.com> wrote in
news:ofmdnd-_FfLXR3LJ...@giganews.com:
>> John Harshman wrote:
[snip]

>> That was very confused. It isn't the observation that counts, it's
>> the tautology. The fact that your parents reproduced causes you to be
>> descended from them. Now extend that back in time for as many
>> generations as you like.
>
> At the risk of getting into something interesting, I've been thinking
> about this. Running backwards that way in sexually reproducing
> organisms isn't so trivial.
>
> When I think of common descent respective to evolution, I think about
> the branching nested hierarchy. That's easy with things like bacteria
> where two daughter cells are spawned from a single common ancestor,
> and 4 granddaughter cells are spawned from a single common ancestor.
> That's a direct nested hierarchy. But things get messy with sex.
>
> Your family tree is an inverted nested hierarchy. You are spawned
> from two individuals, and hopefully you have 4 distinct grandparents,
> 8 distinct great grandparents. That's not common descent.

I apologize in advance for being obtuse, but I don't understand what you
mean by 'common descent' here. Am I wrong in thinking that common
descent is the same thing as descent from a common ancestor? As long as
each generation has at least one ancestor in common with each preceding
generation, that's common descent as I understand it. What am I missing?

> If we integrate heredity over many generations we get something that
> is, I claim, non trivial. To state the obvious, at 20 generations
> back we have 2^20 (~1,000,000) virtual ancestors but quite certainly
> orders of magnitude fewer real ancestors. And going back 100
> generations the compression of real ancestors versus 'virtual'
> ancestors is greater.

That's fairly well-known, yes.

> And thus in this integrated sense, the current population of humans
> collapses their ancestry to a small population of distant ancestors.
> None of this is especially interesting or novel as insights go
> but I do think it is in many respects non-trivial (granted that
> people will have different notions of what is or isn't trivial).
>
> Essentially, one needs to shift their thinking into populations,
> and understand the dynamics of sexually reproducing populations,
> and that isn't completely trivial. It's easy to think in terms
> of an individual's family tree. It's much more complex to think
> in terms of populations with ancestor trimming. I rather expect
> that many who think they understand it have rather incomplete
> understanding.

There's a regrettably widespread tendency to imagine that an individual
can evolve by mutating, but I don't think that affects our understanding
of common descent. Regardless of how many or how few ancestors any given
individual has, it's hypothetically possible to trace a line from that
individual back to the speciation event for the entire population - and
all the way back to the LCA of all extant life on Earth, for that
matter. Isn't that what common descent implies?

> My point, such as it exists, is that understanding common descent
> requires more sophistication than some might suggest.

I still don't see how. Is it inaccurate to say that all extant birds,
all extinct birds, and all other extinct dinosaurs descend from a common
ancestor? Evolution takes place in populations, but it begins with
mutations in the genes of individual organisms. If it were feasible to
sequence the genome of every dinosaur and every protodinosaur that ever
lived, it would be possible in principle to identify the first mutation
that started the process of differentiation: the organism with that
mutation would be the first dinosaur.

This ur-dino would mate with protodinos, but all of their offspring
would be dinosaurs, and all of those offspring's offspring would also
be dinosaurs. Eventually the dinosaurian genome would diverge
from the protodinosaurian to the point that the two groups could no
longer interbreed, and it would be comparatively easy to distinguish
protodinos from dinos, but it would be hypothetically possible to
differentiate them in all of the earlier generations as well.
--
S.O.P.

[Ymir]

In article <_OudnS6_JcfSL23J...@giganews.com>,

If the dominance relations in a tree are interpreted as representing
descendency, then you're dealing with a hierarchy, not a nested
hierarchy. To illustrate this, lets imagine that we know *exactly* what
species was ancestral to both chimps and humans, and what species was
ancestral to both that species and Gorillas. A tree of ancestry might
look like:
(1)
Y
/ \
X Gorillas
/ \
H. sapiens P. trog.


The nested hierarchy associated with the above family tree would look
something like the following:
(2)
A
/ | \
/ | \
B | \
/ C | \
/ / \ | \
X H.s. P.t. G.g. Y

Where A, B, and C are sets.

I harp on this issue due to the fact that this has become an issue in
recent threads where several of our more obstinate posters are convinced
that nested hierarchies presuppose common descent when in fact they
simply describe similarities. Once we add the assumption of common
descent, A, B, and C become clades, but this isn't how the hierarchy is
determined. I think some of this confusion results from the fact that
people often think of the family tree in (1) when discussing the nested
hierarchy in (2).

Family trees can easily be used to predict what the nested hierarchy
should look like, but nested hierarchies don't necessarily allow us to
infer the actual family tree.

Andre

[John Harshman]

Well, that's what universal common descent implies. The word itself
merely implies that at least two things are descended from a third thing.

>> My point, such as it exists, is that understanding common descent
>> requires more sophistication than some might suggest.
>
> I still don't see how. Is it inaccurate to say that all extant birds,
> all extinct birds, and all other extinct dinosaurs descend from a common
> ancestor? Evolution takes place in populations, but it begins with
> mutations in the genes of individual organisms. If it were feasible to
> sequence the genome of every dinosaur and every protodinosaur that ever
> lived, it would be possible in principle to identify the first mutation
> that started the process of differentiation: the organism with that
> mutation would be the first dinosaur.

An interesting thought-experiment, but of course there would be no such
mutation. There is no one mutation that identifies the first dinosaur,
unless we make an arbitrary identification.

It may or may not be inaccurate to say that all X descend from a common
ancestor, depending on what we mean by "ancestor". Except for clonal
organisms, that ancestor isn't an individual but a population or
species. Sure, any given mutation originates in some individual (though
in a large population it's fairly likely to originate in several
individuals at different times), but there are a lot of spots in a
genome, and various differences between ancestor and descendant
populations originated at various times and places before later
spreading through the population.

Of course, if a mutation becomes fixed, and if it did indeed originate
in an individual, everybody in the population is descended from that one
individual, among others. Thus we are all descended from mitochondrial
Eve, Y-chromosome Adam, position 237 of cytochrome c Charlie, and so on.

> This ur-dino would mate with protodinos, but all of their offspring
> would be dinosaurs, and all of those offspring's offspring would also
> be dinosaurs.

That supposes that the mutant allele would be inherited every time. But
it started out with one copy in your ur-dino, and the number of copies
would increase gradually. Best-case scenario: all of the ur-dino's
immediate descendants would inherit one copy. With strong enough
selection, we'd start seeing homozygotes in the second generation.

> Eventually the dinosaurian genome would diverge
> from the protodinosaurian to the point that the two groups could no
> longer interbreed, and it would be comparatively easy to distinguish
> protodinos from dinos, but it would be hypothetically possible to
> differentiate them in all of the earlier generations as well.

Only if we arbitrily declared that one allele was the crucial allele,
and it was expressed in the heterozygote, and had a clear phenotypic
effect, and we allowed that there could be dinos and protodinos in a
single population, in fact in a single family. It's as if we had decreed
that brown eyes are what distinguishes H. sapiens from H. whatever.

[Roger Shrubber]

I think I understand where I'm wrong.
What then is the proper generic term for the structure of
a patralineal hierarchy? Is there something more generic than
'ancestral tree'?

[Ymir]

In article <NoqdnbvVVorNXm3J...@giganews.com>,

Roger Shrubber <rog.sh...@gmail.com> wrote:

> I think I understand where I'm wrong.
> What then is the proper generic term for the structure of
> a patralineal hierarchy? Is there something more generic than
> 'ancestral tree'?

'Hierarchy' (without the 'nested' part). Or tree. Or directed graph.

Andre

[Ymir]

In article <agisaak.spamblock-EDA022.12114427022015@shawnews>,

Ymir <agi...@gmail.com> wrote:

> The nested hierarchy associated with the above family tree would look
> something like the following:
> (2)
> A
> / | \
> / | \
> B | \
> / C | \
> / / \ | \
> X H.s. P.t. G.g. Y
>
> Where A, B, and C are sets.

Probably remove set 'C' from that tree. B should simply have three
terminals below it.

Andre

[Roger Shrubber]

The problem is that a child has two parents, and 4 grandparents.
The tree is growing in the wrong direction.
As I understand it, common descent rejects the idea of wide scale
hybrids. Once the set of the cat family is distinct from the
dog family, we don't expect cat-dog hybrids.
But we get 'hybrids' between the Smith clan and the Jones clan.

I'm ignoring the rest as I don't want to compound some errors
I made.

[John Harshman]

Which is to say that if you did an analysis that happened to include an
ancestor, it would appear in a trichotomy with its two descendants. And
if you put branch lengths on the tree, the length of the branch leading
to the ancestor would be zero or close to it.

[John Harshman]

Geneticists call it a pedigree. I think "non-nested hierarchy" is a
reasonable term. Once, trees in which ancestors occupied internal nodes
were called "phylogenetic trees" as distinct from cladograms, in which
they didn't. But this usage has died out. Now "phylogenetic tree" just
means a cladogram with branch lengths having a meaning. Nobody sticks
ancestors onto nodes any more.

[Ymir]

In article <agisaak.spamblock-D0CDB4.12295327022015@shawnews>,

And one further clarification: While the tree provides a convenient
visual representation of a nested hierarchy, it can be formally
misleading. In a nested hierarchy, elements are grouped into sets such
that:

1) For any two sets in the hierarchy, either
a) one is a proper subset of the other
or
b) the intersection of the two sets is the empty set.
and
2) there is one set which contains all elements as members.

What that entails in the above case is that

A = {X, H.s., P.t., G.g., Y}

rather than

A = {{X, H.s., P.t}, G.g., Y}

Of course, that elements are grouped into multiple, progressively larger
sets, rather than sets being grouped together into higher-order sets
isn't terribly important to any of the arguments made in this forum, but
nested hierarchies are formally defined as the former rather than the
latter (just in case you or anyone else cares).

Andre

[Ernest Major]

On 27/02/2015 01:59, broger...@gmail.com wrote:
> On Thursday, February 26, 2015 at 8:30:14 PM UTC-5, Ray Martinez wrote:
>> On Thursday, February 26, 2015 at 5:20:15 PM UTC-8, broger...@gmail.com wrote:

>>> On Thursday, February 26, 2015 at 7:50:15 PM UTC-5, Ray Martinez wrote:
>>>> On Thursday, February 26, 2015 at 4:15:15 PM UTC-8, Roger Shrubber wrote:
>>>>> Ray Martinez wrote:
>>>>>> On Wednesday, February 25, 2015 at 6:20:20 PM UTC-8, John Harshman
>>>>>> wrote:
>>>>>>> On 2/25/15, 5:55 PM, Ray Martinez wrote:
>>>>>
>>>>> I'll jump in and do one of these.
>>>>
>>>> Good!
>>>>
>>>>>
>>>>>>>> Evolutionary explanations never rely on miracles (macro mutation
>>>>>>>> or single-step selection). Therefore the ToE is wholly reliant on
>>>>>>>> slight successive modifications, which must occur in order for CD
>>>>>>>> to occur (interdependence).
>>>>>>>
>>>>>>> Neither of those sentences is true, and I've warned you about using
>>>>>>> that word "therefore".
>>>>>>
>>>>>> Could you please take the time to tell me why those sentences are not
>>>>>> true? I see nothing wrong with them at all.
>>>>>
>>>>> Speciation has been observed to occur through whole genome
>>>>> duplication. That is a macromutation, single step selection
>>>>> and renders your first claim false.
>>>>
>>>> Absurd.
>>>>
>>>> Whatever happened to Natura non facit saltum ('nature does not make jumps')? Dawkins has written how many books defending this bedrock Darwinian principle?
>>>

>>> Speciation by polyploidy (involving whole genome duplication) has been observed in plants. It is well studied. Observations trump nifty Latin mottoes.
>>>
>>
>> What about animal species (the main object of explanation)? Did you forget?
>>
>> Ray
>
> As far as I know, polyploid speciation event have only been observed in plants, not in animals. So what? The theory of evolution covers plants as well as animals. Why not just admit you're wrong on this point (since you clearly ARE wrong about it)? It's not a point that's essential to your argument, anyway.
>

Polyploids are rare in amniotes, but Tympanoctomys barrerae and
Pipanacoctomys aureus are hypotetraploid rodents, but there are triploid
Cnemidophorus lizards, as well as heterodiploid species.

They are commoner among fish and amphibians. Hyla versicolor is a fairly
recent polyploid (tetraploid) animal species, but probably doesn't
qualify as observed under Ray's nihilistic epistemology. Allotriploid
carp populations have been produced in the laboratory.

Polyploids are also known in insects, fungi and green algae, and
probably in other groups.

--
alias Ernest Major

[Ernest Major]

On 27/02/2015 03:50, Dana Tweedy wrote:
> What about them? Whole genome duplication hasn't been observed in
> animals, (yet,) but that doesn't mean it never happens in living species.

Actually it has been seen.

http://life.scichina.com:8082/sciCe/fileup/PDF/03yc0595.pdf

How long before Ray's position becomes absolutely no evolution (in
primates)?

--
alias Ernest Major

[Dana Tweedy]

I think that's Ray's position already, but I'll let him speak for
himself on that.


DJT
>

[Walter Bushell]

In article <79329d00-b699-4646...@googlegroups.com>,

chris thompson <chris.li...@gmail.com> wrote:

> Why are plants so much less important for evolution than animals?

Because we are animals.

--
Never attribute to stupidity that which can be explained by greed. Me.

[Walter Bushell]

In article <mcpq55$b14$1...@dont-email.me>, Nashton <no...@nana.ca>
wrote:

> On 2015-02-27 8:19 AM, chris thompson wrote:
>
>
> <snip>
>
> Do you even know what occurs during photosynthesis?

The name is a misnomer because photons are not synthesized. Ou
contraire they are destroyed.

Furthermore it hasn't been until recently that we discovered what
happens.

[Chris Thompson]

On 2/26/2015 10:15 PM, Ray Martinez wrote:

> On Thursday, February 26, 2015 at 6:40:16 PM UTC-8, Roger Shrubber wrote:
>> Ray Martinez wrote:

>>> On Thursday, February 26, 2015 at 5:50:18 PM UTC-8, Roger Shrubber

>>>> Eppur si muove I'm not responsible for the ways you misinterpret
>>>> things.
>>>
>>> Likewise. I assumed that you knew we were talking about animal
>>> species and how the complexity seen evolved----that we were not
>>> talking about plants.
>>
>> The Theory of Evolution applies to plants as well as animals.
>> This little discussion relates to your comments about the Theory
>> of Evolution. Why would anyone presume the discussion was specific
>> to animals? Did you think there was a different ToE with respect
>> to plants? Biologists don't.
>
> I have now informed you of the main object of explanation.
>

Translation: I have moved the goalposts.

>>
>>>> The fact remains that whole genome duplications have been observed
>>>> and they result in speciation.
>>
>>> What about animal species?

Ernest Major listed some, such as _Hyla versicolor_. _Xenopus_ also has
a history of speciation by polyploidy.

Are you now going to shift the goalposts even further and claim you were
only talking about mammals?

>>
>> There is evidence of historic genome duplication events leading to
>> vertebrates. As these are events in the past they involve more
>> sophisticated analysis. I'm not interested in trying to prove
>> the validity of the inferences to you because it would be a great
>> deal of effort on my part. I brought up the actually observed
>> cases because they are quite simple and direct. And they are
>> sufficient to disprove your claim. Again, the ToE applies to all
>> life, not just animals.
>>
>>>> It's a fact. And in comparative genomics we observe cases where an
>>>> apparently diverged species has twice the chromosomes of its
>>>> sister species with strong correspondences between sister
>>>> chromosomes. Whole genome duplication is rather common in plants.
>>
>>> Yet we weren't talking about plants, but the origin of sexually
>>> reproducing animal species. Neither macro mutation nor single-step
>>> selection has any role in the production of adaptive complexity.
>>
>> Says who?
>
> Almost all evolutionary authorities. You don't know that?
>

>> Your claim was about the ToE. It applies to plants
>> as well as animals and to bacteria and archae. What makes you think
>> that evolution in animals is a distinctly different process? Strange.
>
> Truck loads of books published by evolutionary authorities.
>
>>
>>>> There's strong evidence for two rounds of whole genome duplication
>>>> in the line leading to vertebrates. It's standard stuff.
>>
>>> So what are you saying? Macro mutation occurs in species?
>>
>> Yes. Did I stutter? It isn't common but it happens.
>
> Show me two examples! Waiting! Then tell me how said examples effect the standard Darwinian explanation of adaptive complexity? Do you even know what the standard explanation is? You seem to think that current evolutionary concepts just popped into existence, not having a historical context of replacing or complimenting previously accepted concepts.
>

_Xenopus_ and _Hyla versicolor_. You could have found that with Google
in about 4 seconds.

Chris

>>
>>>> To the extent that your representation of Dawkins is accurate,
>>>> Dawkins is wrong. But I think you misrepresent Dawkins, or have run
>>>> too far with his oversimplification.
>>
>>> I'm conveying standard Darwinian stuff, which you seem wholly
>>> ignorant. Who cares about plants? Plants are NOT the main object of
>>> explanation in the origins debate. The fact that you first thought
>>> macro mutation was about plants indicates much ignorance of basic
>>> history of science.
>>

[Nick Roberts]

In message <3KudnSUfFstE6mnJ...@earthlink.com>

And to respond before the event...

The plains (or red) viscacha rat, Tympanoctomys barrerae is indeed a
tetraploid mammal, as is the golden viscacha rat, Pipanacoctomys
aureus.

--
Nick Roberts tigger @ orpheusinternet.co.uk

Hanlon's Razor: Never attribute to malice that which
can be adequately explained by stupidity.

[Ray Martinez]

My position is the position of science before the rise of Darwinism (species immutability).

The evolution of adaptive complexity is impossible. The needs of Atheism requires the impossible to be possible.

Ray

[Ray Martinez]

On Friday, February 27, 2015 at 8:05:03 AM UTC-8, Greg Guarino wrote:
> On 2/26/2015 9:43 PM, Ray Martinez wrote:
>
> > You don't seem to understand that if irreplaceable concepts suffer
> > falsification the whole suffers falsification as well. Without a
> > valid explanation for adaptive complexity the ToE, like I said, is
> > gutted. Do you know what "gutted" means?
>
> Rather than use metaphors let's be specific. Without selection (I assume
> that's the "irreplaceable" concept you are referring to), we would need
> another explanation for adaptation. But the evidence for Common Descent

> is separate and would remain undiminished.

Yet macroevolution extrapolated true based on accumulated microevolution. If the latter is false then the former falls with it. Without either common descent cannot occur.

And I've finally figured out what John Harshman is talking about. Your comment about CD has him written all over it. John has been defining common descent by the lowest common denominator. I, on the other hand, understand the claim conceptually: species-to-species, as opposed to each individual in a species or genus.

CD says species are related/connected to other species; this is how the public understands the concept. The understanding is correct. Without modification evolution, speciation and divergence, common descent, as explained, cannot occur.

>
> In fact, we could have adaptation via mutation and selection, and yet
> NOT have universal common descent. There could have been several origin
> of life events, each of which would have its own separate sets of
> descendants.

But CD is merely reproduction. Are you suggesting reproduction causes the evolution of higher taxa (LOL)?

>
> And we could have universal common descent without mutation and
> selection as well; the divergence in that case would be as yet
> unexplained, but the evidence for common descent would remain too strong
> to ignore.

Without selection you have nothing. The ToE is gutted. Your observations presuppose the ToE as an octopus: Lose an arm AND leg? No big deal. It's still valid science.

Ray

[Dana Tweedy]

On 3/2/15 3:29 PM, Ray Martinez wrote:
> On Sunday, March 1, 2015 at 11:14:57 AM UTC-8, Ernest Major wrote:
>> On 27/02/2015 03:50, Dana Tweedy wrote:
>>> What about them? Whole genome duplication hasn't been observed in
>>> animals, (yet,) but that doesn't mean it never happens in living species.
>>
>> Actually it has been seen.
>>
>> http://life.scichina.com:8082/sciCe/fileup/PDF/03yc0595.pdf
>>
>> How long before Ray's position becomes absolutely no evolution (in
>> primates)?
>>
>> --
>> alias Ernest Major
>
> My position is the position of science before the rise of Darwinism (species immutability).

Your position has nothing to do with science, Ray. Species immutability
was assumed, due to religious beliefs.

>
> The evolution of adaptive complexity is impossible.

Why would it be impossible?

> The needs of Atheism requires the impossible to be possible.

Science doesn't care about the "needs of atheism". Your claim that
it's impossible comes from your own need to oppose reason and learning.


DJT

[Dana Tweedy]

On 3/2/15 3:51 PM, Ray Martinez wrote:
> On Friday, February 27, 2015 at 8:05:03 AM UTC-8, Greg Guarino wrote:
>> On 2/26/2015 9:43 PM, Ray Martinez wrote:
>>
>>> You don't seem to understand that if irreplaceable concepts suffer
>>> falsification the whole suffers falsification as well. Without a
>>> valid explanation for adaptive complexity the ToE, like I said, is
>>> gutted. Do you know what "gutted" means?
>>
>> Rather than use metaphors let's be specific. Without selection (I assume
>> that's the "irreplaceable" concept you are referring to), we would need
>> another explanation for adaptation. But the evidence for Common Descent
>> is separate and would remain undiminished.
>
> Yet macroevolution extrapolated true based on accumulated microevolution.

No, macroevolution has been observed. Microevolution is essentially the
same process as macroevolution, only it does not result in speciation.

> If the latter is false then the former falls with it. Without either common descent cannot occur.

Incorrect, as has been explained to you many times. Speciation does not
necessarily depend on microevolution. Common descent occurs whenever
there is offspring from the same parents.

>
> And I've finally figured out what John Harshman is talking about. Your comment about CD has him written all over it. John has been defining common descent by the lowest common denominator. I, on the other hand, understand the claim conceptually: species-to-species, as opposed to each individual in a species or genus.
>

It really doesn't matter, Ray. Common descent is a fact, whether it is
within species, or leads to new species. You continue to misunderstand
simple things like common descent and natural selection.

> CD says species are related/connected to other species;

The evidence shows this to be true.

> this is how the public understands the concept.

What the public understands, or does not understand is irrelevant.


> The understanding is correct.

At best, it's partially correct. Many of the things the public
'understands' are wrong. The idea of the "chain of being" is a common
misconception.

> Without modification evolution, speciation and divergence, common descent, as explained, cannot occur.

Common descent can occur without modification, as it's just descent from
common ancestors. No need for change. But change in populations is
commonly observed, so denying it is foolish.

>
>>
>> In fact, we could have adaptation via mutation and selection, and yet
>> NOT have universal common descent. There could have been several origin
>> of life events, each of which would have its own separate sets of
>> descendants.
>
> But CD is merely reproduction.

Common descent is reproduction from a common ancestor.

> Are you suggesting reproduction causes the evolution of higher taxa (LOL)?

Reproduction is part of the process that causes the evolution of higher
taxa. Evolution happens at the nodes, not at the "higher" branches.
Higher taxa are the result of population splits happening long ago.

>
>>
>> And we could have universal common descent without mutation and
>> selection as well; the divergence in that case would be as yet
>> unexplained, but the evidence for common descent would remain too strong
>> to ignore.
>
> Without selection you have nothing.

Selection is not necessary for either micro, or macroevolution. It is
necessary to explain adaptive evolution, but not all evolutionary change
is adaptive. There are at least four other factors in evolution
besides selection. There is drift, mutations, selective mating, and
gene flow. All of those can operate without natural or artificial
selection.



> The ToE is gutted.


Actually, the Theory of evolution stands quite well. Nothing has
"gutted" it. Your misunderstanding, and ignorance are not problems for
evolution.

> Your observations presuppose the ToE as an octopus: Lose an arm AND leg? No big deal. It's still valid science.

The theory of evolution is a useful scientific theory. Like many
theories, there are different aspects of the theory. Common descent is
different from the mechanisms of evolution. Natural selection is
different from drift. Drift is different from gene flow, etc, etc.
Evolution is valid science. Creationism is not.


DJT

[Ernest Major]

Your position changes with the wind. You just conceded speciation in
plants - i.e. that species are not immutable.

--
alias Ernest Major

[Chris Thompson]

On 3/2/2015 11:56 PM, Dana Tweedy wrote:
> On 3/2/15 3:51 PM, Ray Martinez wrote:
>> On Friday, February 27, 2015 at 8:05:03 AM UTC-8, Greg Guarino wrote:
>>> On 2/26/2015 9:43 PM, Ray Martinez wrote:
>>>
>>>> You don't seem to understand that if irreplaceable concepts suffer
>>>> falsification the whole suffers falsification as well. Without a
>>>> valid explanation for adaptive complexity the ToE, like I said, is
>>>> gutted. Do you know what "gutted" means?
>>>
>>> Rather than use metaphors let's be specific. Without selection (I assume
>>> that's the "irreplaceable" concept you are referring to), we would need
>>> another explanation for adaptation. But the evidence for Common Descent
>>> is separate and would remain undiminished.
>>
>> Yet macroevolution extrapolated true based on accumulated microevolution.
>
> No, macroevolution has been observed. Microevolution is essentially the
> same process as macroevolution, only it does not result in speciation.
>

Only if we define macroevolution as to exclude speciation. John's point,
if I read it correctly, is that accumulated macroevolution results in
speciation. It's really just an arbitrary line we draw at the "point" of
speciation. I use quotes because "species" tends to be a fuzzy concept
in many cases, especially early on in the process.

>
>> If the latter is false then the former falls with it. Without either
>> common descent cannot occur.
>
> Incorrect, as has been explained to you many times. Speciation does not
> necessarily depend on microevolution. Common descent occurs whenever
> there is offspring from the same parents.
>
>
>>
>> And I've finally figured out what John Harshman is talking about. Your
>> comment about CD has him written all over it. John has been defining
>> common descent by the lowest common denominator. I, on the other hand,
>> understand the claim conceptually: species-to-species, as opposed to
>> each individual in a species or genus.
>>

John is not saying every individual is a species. He's saying, "Trace
your ancestry back far enough, through all the reproductive events, and
you'll eventually come to an organism that is decidedly and obviously
not human." The same is true for all of us.

Chris

[Greg Guarino]

On 3/2/2015 5:51 PM, Ray Martinez wrote:
>> And we could have universal common descent without mutation and
>>> selection as well; the divergence in that case would be as yet
>>> unexplained, but the evidence for common descent would remain too
>>> strong to ignore.

> Without selection you have nothing. The ToE is gutted. Your
> observations presuppose the ToE as an octopus: Lose an arm AND leg?
> No big deal. It's still valid science.

You should never use analogies Ray; you evidently have no understanding
of them.

Common descent is among the most strongly supported science known;
enough so as to be essentially undeniable. If we had no explanation for
how the diversification of species came about, then it would be an
unexplained, yet undeniable, phenomenon.

The lack of an explanation doesn't make a phenomenon go away, it just
makes it unexplained. Such is often the case in science. and in our
daily experience.

I know this is central for you Ray; the reason you constantly harp on
Darwin as the true "owner" of evolutionary theory. You figure you have
some refutation of natural selection, and the rest will fall with it.
Nether of those things is true. You refuting Natural Selection would be
akin to me refuting Quantum Mechanics; the difference being that I am
aware of my own ignorance in that area. But even if you were to stumble
on someone else's successful refutation of Natural Selection, there
would still be no reasonable explanation for the patterns we see in
biology other than Common Descent.

---
This email is free from viruses and malware because avast! Antivirus protection is active.
http://www.avast.com

[Ray Martinez]

On Tuesday, March 3, 2015 at 4:34:52 AM UTC-8, Greg Guarino wrote:
> On 3/2/2015 5:51 PM, Ray Martinez wrote:
> >> And we could have universal common descent without mutation and
> >>> selection as well; the divergence in that case would be as yet
> >>> unexplained, but the evidence for common descent would remain too
> >>> strong to ignore.
>
> > Without selection you have nothing. The ToE is gutted. Your
> > observations presuppose the ToE as an octopus: Lose an arm AND leg?
> > No big deal. It's still valid science.
>
> You should never use analogies Ray; you evidently have no understanding
> of them.

Evasion. Analogy stands.

>
> Common descent is among the most strongly supported science known;
> enough so as to be essentially undeniable.

Among Evolutionists, yes, of course.

What's the point?

> If we had no explanation for
> how the diversification of species came about, then it would be an
> unexplained, yet undeniable, phenomenon.
>
> The lack of an explanation doesn't make a phenomenon go away, it just
> makes it unexplained. Such is often the case in science. and in our
> daily experience.
>
> I know this is central for you Ray; the reason you constantly harp on
> Darwin as the true "owner" of evolutionary theory. You figure you have
> some refutation of natural selection, and the rest will fall with it.
> Nether of those things is true. You refuting Natural Selection would be
> akin to me refuting Quantum Mechanics; the difference being that I am
> aware of my own ignorance in that area. But even if you were to stumble
> on someone else's successful refutation of Natural Selection, there
> would still be no reasonable explanation for the patterns we see in
> biology other than Common Descent.

All this commentary says is that evolution cannot be falsified; even if NS were to fall, it doesn't matter.

Creationists already know the world of evolution is lying when it talks about falsification. You've just proven that point.

But sober and fair minded persons on the evolution side understand that IF natural selection were to fall the ToE is gutted. Over the years you've shown yourself ignorant concerning the history of natural selection. You really have no idea how important the concept is to the health of the overall theory. **Every** major AND notable Evolutionist since 1950 has published literature that plainly says NS is the MAIN agent causing evolution and is the answer to the riddle of the origin of complexity. There are no exceptions. For example: Every book Richard Dawkins has written on the subject of evolution, except one, has been about the importance of NS as the key to our existence.

Yet here you are yawning concerning the importance of NS. I've always said what ordinary Evolutionists believe and what evolution scholars write are two completely different things. Your commentary here supports what I've always said spectacularly.

Ray

[Burkhard]

You keep confusing the part for the whole. Common descent is a part of
the theory of evolution, but not identical with it. If NS were to fail,
then the theory of evolution as we now understand it would indeed be
falsified with it. But not common descent, that is Greg's point. So
any theory that takes the place of the ToE in this case - and I have no
idea how such a theory would look like, possibly like the neutral theory
of evolution - would still have to explain common descent.

[Ray Martinez]

Common descent, according to a resident scholar, is caused by ordinary reproduction. Yet all the ordinary reproduction in the world doesn't cause common descent, that is, the connectedness of species to other species. Sexually reproducing animal species are only connected to one another on the contingency that micro-modification evolution occurs, speciation, and divergence. The first concept (micro-modification) is wholly dependent on the veracity of natural selection. So everything is dependent on natural selection. And this is what evolution authorities tell the public in their popular publications. Natural selection is the answer to our existence, not the God of Archdeacon Paley.

Ray

[Roger Shrubber]

Ray Martinez wrote:

> Common descent, according to a resident scholar, is caused by
> ordinary reproduction. Yet all the ordinary reproduction in the world
> doesn't cause common descent, that is, the connectedness of species
> to other species. Sexually reproducing animal species are only
> connected to one another on the contingency that micro-modification
> evolution occurs, speciation, and divergence. The first concept
> (micro-modification) is wholly dependent on the veracity of natural
> selection. So everything is dependent on natural selection. And this
> is what evolution authorities tell the public in their popular
> publications. Natural selection is the answer to our existence, not
> the God of Archdeacon Paley.

Nobody has ever claimed or implied that the process or reproduction
acting within currently extant species retrospectively produced
the pattern of common descent. Your words above imply that
such was claimed. It wasn't. The claim is that the pattern of
common descent as observed in, for example carnivores, is the
result of all carnivores having arisen from a common ancestor.
Further, relying on the history of natural sciences, this was
observed before anybody knew anything about DNA, or genes, how
base pair in DNA change during copying, how phenotypic traits
are produced from inherited DNA and all the other details of
molecular biology.

The point being, you don't need to know the molecular details
to recognize the pattern of common descent that follows the readily
observable nature in which offspring share characteristics of
their parents. You don't need to understand how natural selection
works to see this pattern. You don't need to understand population
genetics or molecular genetics to see this pattern.

Is it becoming clear? The observation of common descent requires
nothing but a general understanding of how offspring resemble
(and differ from) their parents, and observation of existing animals,
an observation of animals that exist in the fossil record and
the dates associated with these observations. In that sense, common
descent and a biological observation of a chain of beings does
not require detailed mechanistic molecular or genetic understanding
of how traits develop. You just need a broad high level understanding
of reproduction.

And that's why, even before Darwin, people were hypothesizing
common descent and a united chain of species.

[Greg Guarino]

On 3/4/2015 7:32 PM, Ray Martinez wrote:
> On Tuesday, March 3, 2015 at 4:34:52 AM UTC-8, Greg Guarino wrote:
>> On 3/2/2015 5:51 PM, Ray Martinez wrote:
>>>> And we could have universal common descent without mutation
>>>> and
>>>>> selection as well; the divergence in that case would be as
>>>>> yet unexplained, but the evidence for common descent would
>>>>> remain too strong to ignore.
>>
>>> Without selection you have nothing. The ToE is gutted. Your
>>> observations presuppose the ToE as an octopus: Lose an arm AND
>>> leg? No big deal. It's still valid science.
>>
>> You should never use analogies Ray; you evidently have no
>> understanding of them.
>
> Evasion. Analogy stands.

You don't have any talent for recognizing evasion either. Here's a hint:
it's never necessary in a discussion of any facet of evolution with you.

>> Common descent is among the most strongly supported science known;
>> enough so as to be essentially undeniable.
>
> Among Evolutionists, yes, of course.

Among biologists.

> What's the point?
>
>> If we had no explanation for how the diversification of species
>> came about, then it would be an unexplained, yet undeniable,
>> phenomenon.
>>
>> The lack of an explanation doesn't make a phenomenon go away, it
>> just makes it unexplained. Such is often the case in science. and
>> in our daily experience.
>>
>> I know this is central for you Ray; the reason you constantly harp
>> on Darwin as the true "owner" of evolutionary theory. You figure
>> you have some refutation of natural selection, and the rest will
>> fall with it. Nether of those things is true. You refuting Natural
>> Selection would be akin to me refuting Quantum Mechanics; the
>> difference being that I am aware of my own ignorance in that area.
>> But even if you were to stumble on someone else's successful
>> refutation of Natural Selection, there would still be no reasonable
>> explanation for the patterns we see in biology other than Common
>> Descent.
>
> All this commentary says is that evolution cannot be falsified; even
> if NS were to fall, it doesn't matter.

Nope. First it says is that "evolution" is not a single "edifice".

Modern biology makes a number of claims that fall under the rubric of
"evolution". One of those is that all life on Earth stems from a common
set of ancestors; all life is thus related. We have a large and growing
body of evidence that this is true, but each new genome that is
sequenced could be the one that falsifies that claim. demonstrating that
one species - at least - is NOT related to all the rest.

A second claim is that adaptation is due largely to mutation and
selection. We have other sorts of evidence that supports this claim. But
the first time we find a population that does NOT come to have the
traits of those members that leave the most surviving progeny, we will
know that - at least in that species - some unknown process is in play.

> Creationists already know the world of evolution is lying when it
> talks about falsification. You've just proven that point.

> But sober and fair minded persons on the evolution side understand
> that IF natural selection were to fall the ToE is gutted.

Imprecise language is one of your problems. "Gutted" means nothing. Be
specific. Or perhaps you simply can't; you're actually constitutionally
unable to understand separate concepts.

The evidence for Common Descent is separate from the evidence for
mutation and selection as the chief agent of adaptation. Either could be
falsified, but falsifying Natural Selection would do nothing to shake
the concept of Common Descent.

You can call that "gutted" if you like, and it would be a sea change to
be without the mechanism of adaptation, but Common Descent would be
untouched.

Over the
> years you've shown yourself ignorant concerning the history of
> natural selection. You really have no idea how important the concept
> is to the health of the overall theory. **Every** major AND notable
> Evolutionist since 1950 has published literature that plainly says NS
> is the MAIN agent causing evolution and is the answer to the riddle
> of the origin of complexity.

None of which has anything to do with the foundation and evidence for
Common Descent.

There are no exceptions. For example:
> Every book Richard Dawkins has written on the subject of evolution,
> except one, has been about the importance of NS as the key to our
> existence.

Sure. But without it, we would know that life diversified from a pool of
common ancestors, changing over time; We just wouldn't know how.

> Yet here you are yawning concerning the importance of NS.

It is fundamental for the explanation of adaptation; but not for
determining the accuracy of Universal Common Descent. And there's no
yawning; perhaps a bemused grin that you might be the person to falsify
Natural Selection, a topic I have spent hours trying to teach you the
basics of. A guy on your end of those discussions should trad lightly
with the word "ignorant", especially when used to describe the - very
patient - person on the other end.

I've always
> said what ordinary Evolutionists believe and what evolution scholars
> write are two completely different things. Your commentary here
> supports what I've always said spectacularly.

You are easily confused.

[Dana Tweedy]

Ray, all descent is caused by ordinary reproduction. That's how every
living thing on Earth got here. We are all the products of reproduction.

> Yet all the ordinary reproduction in the world doesn't cause common descent,

Actually, that's exactly what does cause common descent, ie "all the
ordinary reproduction in the world" There's no other way common descent
can happen.

> that is, the connectedness of species to other species.

Exactly what do you mean by the "connectedness" of species to other
species. I know what people who understand and use English mean by
this, but what do you mean, Ray?

> Sexually reproducing animal species are only connected to one another on the contingency that micro-modification evolution occurs, speciation, and divergence.

Sexually reproducing animals are only a part of the connectedness of
life. All life is connected through having common ancestors. Why are
you trying to limit things to just one group of organisms? Some groups
of sexually reproducing organisms have populations that reproduce
asexually. So, why the artificial distinction?

> The first concept (micro-modification) is wholly dependent on the veracity of natural selection.

That is where you are wrong. Small scale changes in populations do not
require natural selection, and even accumulation of those changes does
not require natural selection to produce a population that's
reproductively isolated. Natural selection is only one of the several
mechanisms that produce evolution.

> So everything is dependent on natural selection.

While natural selection is an important part of evolution, it's not
dependent on natural selection. This has been explained to you over,
and over. Why do you keep clinging to this misconception?

> And this is what evolution authorities tell the public in their popular publications.

This is another one of your unsupported claims. You can't seem to
understand that "authorities" are not what determines science, or
scientific theories. Whatever you imagine "evolution authorities" tell
people, it's clear you don't know what you are talking about when it
comes to the real science involved.

> Natural selection is the answer to our existence, not the God of Archdeacon Paley.

Natural selection is one of the mechanisms by which populations evolve.
Mr. Paley had the misfortune of living before science discovered the
way God creates. Paley's idea was that God is a designer. Darwin and
Wallace led the way in figuring out how God carried out his designs.


DJT



>
> Ray
>

[Burkhard]

Sure does. Without reproduction, no common descent - how do you imagine
CD comes about?

>that is, the connectedness of species to other species.

That however is a different question. Not "is CD true"? But"Given CD,
how do we arrive at the specific pattern of species that we observe? For
this, you need indeed specific forms of reproduction, in particular
reproduction with modification.

Sexually reproducing animal species are only connected to one another

on the contingency that micro-modification evolution occurs,
speciation, and divergence. The first concept (micro-modification)

is wholly dependent on the veracity of natural selection.

Not really, no. "Micro-modification", that is changes in the genetic
makeup from one generation to another, is something we know happens
simply by comparing DNA between parents and offspring. Mutation rates
can then be estimated statistically. That's true whether or not natural
selection is true (and neutral mutations by definition are not subject
to NS, yet they make up a significant part of all mutations)

So everything is dependent on natural selection. And this is what
evolution authorities tell the public in their popular publications.

Natural selection is the answer to our existence, not the God of
Archdeacon Paley.

NS is indeed needed in the standard model of the ToE to fix mutations in
a population. It is therefore necessary to produce the specific pattern
of species that we observe. But that does not imply entail that common
descent is dependent in natural selection.
>
> Ray
>