Variation and selection

[MarkE]

Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.

If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?

- generic drift
- symbiogenesis
- horizontal DNA transfer
- action of mobile DNA
- epigenetic modifications
- others

I.e., these all mix things up and create new configurations, possibly in sophisticated ways, but they are not a refining mechanism. In fact, without the action of natural selection, over time would result in a net degradation (randomisation)?

[Oxyaena]

On 10/3/2018 4:51 AM, MarkE wrote:
> Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
>

Why write "claimed"? Have you not even read the *Origin*?

> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?

Selection is just one of many mechanisms of evolution, and while it is a
major one, it's not the only one, and there are specifically two types
of selection, they are natural selection (the one that's most commonly
known) and sexual selection (wherein potential mates select their
partners based off of what they find most "endearing", and so the
opposite gender will start to evolve those features their mates find
"endearing" or "attractive").





[snip]

[RonO]

On 10/3/2018 3:51 AM, MarkE wrote:
> Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
>
> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
>
> - generic drift

Genetic drift can add to the variation of the population if you consider
factors such as the neutral theory and how some variants are not
selected for or against in the current environment and are left to drift
higher or lower in allele frequency.

Some factors in volved in genetic drift can decrease the variation.
Examples would be founder effects where a small initial population is
involved and a lot of alleles can be fixed just by chance.

> - symbiogenesis

Symbiosis does involve the transfer of genes between the organisms involved.

> - horizontal DNA transfer

This is something that happens after hybridization effects (our
interbreeding with Neanderthals resulted in around 20% of the
Neanderthal genome being represented in the extant human population.

It can happen if something like a virus picked up a bit of DNA from one
species and transferred it to another.

Bacteria can pick up DNA from the environment and use it.

> - action of mobile DNA

Mobile elements (transposons) just jump around the genome and create
insertion deletion mutations. They carry their own transcriptional
regulatory sequences so they can alter the gene regulation when they
jump into ta location.

> - epigenetic modifications

Life forms modify their DNA or the proteins associated with the DNA in a
way that alters the regulation of regions of DNA in terms of
transcription (making RNA). The modifications can be altered due to
environmental factors. This can alter which variants may be selected
for or against, and it can maintain variation in a population if the
environmental effect is consistent enough.

> - others

Mutation rate and population size are major factors. The existence of
night and day (different alleles being selected for or against). The
existence of seasons (different alleles selected in the winter than in
the summer). Things like predator prey cycles. Predators increase
their numbers as the prey increase their population size, but it is
cyclic so different alleles could be selected for at different points in
the cycle. Etc. Anything that changes the environment will affect
genetic variation in a population.

Ron Okimoto

[MarkE]

Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?

It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.

If this is the case, what can made of this claim?

“Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
http://www.thethirdwayofevolution.com/

[MarkE]

“Claimed” because I’m a creationist unconvinced of natural selection as an explanation for macro evolution.

Would you agree sexual selection is a subset of natural selection, given the definition of fitness as differential reproductive success?

[Ernest Major]

How you divide up evolutionary mechanisms is open to debate - for
example Oxyaena has just contrasted natural selection and sexual
selection, while I consider sexual selection (and artificial selection)
forms of natural selection. That said, I would count genetic drift
(differential reproductive success NOT causally correlated with
genotype) with natural selection (differential reproductive success
causally correlated with genotype) in the differential reproductive
success category, contrasting with the variation category.

Genetic drift and natural selection form somewhat of a continuum; in
large populations and with large selection coefficients natural
selection dominates; in small populations and with small selection
coefficients genetic drift dominates.

Natural selection typically reduces the amount of variation within a
population whether by negative (purifying) or positive (adaptive)
selection, but sometimes maintains variation in a population due to
heterosis or to frequency dependent selection. Genetic drift also tends
to reduce the amount of variation within a population by fixing alleles,
but increases variation between (sufficiently isolated) populations, and
can plausibly be argued makes a greater proportion of genome space
accessible to evolution (which makes the Discovery Institutes Dissent
from Darwin statement, which is merely skeptical that natural selection
and mutation can account for the diversity of life, is taken literally
an ultra-Darwinist position). In the short term genetic drift can
increase the frequency of an allele above its equilibrium level, which I
would count as an increase in variation in the population.

The simple breakdown in sources of variation is between gene flow and
mutation. The former can be broken down into gene flow between
populations of one species, and introgression between different species.
If conceived widely introgression and horizontal/lateral transfer are
the same, but I prefer to restrict introgression to variation arising
from reproduction, and horizontal transfer to variation arising from
non-reproductive processes. Also consider inter genomic transfer - the
transfer of genes between organelles and the nucleus - and the potential
of numts as a source of variation. Mutation includes point mutations,
and deletions and insertions (depending on where the inserted DNA comes
from this blurs the line between gene flow and mutation) and
duplications and inversions and other changes of chromosomal structure,
which includes the effects of the operation of mobile DNA, and changes
to the number of sets of chromosomes. I'm in two minds whether to count
recombination as mutation, but it's definitely a source of variation.

Symbiogenesis and diploidisation are emergent processes which involve
both variation and differential reproductive success. I'd add genomic
shock (my term) here.

Epigenetic modifications are principally a form of gene regulation -
it's a major part of how different cell types express a different set of
genes and hence display different phenotypes. It's been noted that some
epigenetic modifications aren't reset by oogenesis and spermatogenesis,
which makes them a source of phenotypic variation. On the one hand
there's not a form of genotypic variation; on the other hand they change
how selection acts on the genome - so it's subtle question as whether
it's a source of variation.

Population genetics deals with changes within a population, but I think
that processes that create novel populations such as dispersal (to an
unoccupied habitat), vicariance, extinction (of intermediates) and
polyploidisation should also be considered as members of the set of
evolutionary mechanisms.

With regards to your final question symbiogenesis does not occur in the
absence of natural selection; epigenetic modifications don't lead to
randomisation of populations in the absence of natural selection or
changes in population fitness; genetic drift doesn't lead to the
randomisation of populations but can be expected to result in reduce
fitness in the absence of natural selection, or even in its presence if
the population is small enough and the selection coefficent weak enough;
and horizontal transfer and the actions of mobile DNA would both
increase standing variation (which is what I interpret you to mean by
randomisation) and reduce fitness in the absence of natural selection.

--
alias Ernest Major

[Alan Kleinman MD PhD]

And you don't know how either "natural" or "sexual" selection works.
>
>
>
>
>
> [snip]

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 4:25:05 AM UTC-7, Ron O wrote:
> On 10/3/2018 3:51 AM, MarkE wrote:
> > Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
> >
> > If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
> >
> > - generic drift
>
> Genetic drift can add to the variation of the population if you consider
> factors such as the neutral theory and how some variants are not
> selected for or against in the current environment and are left to drift
> higher or lower in allele frequency.

You are completely confused SlowO. Using your grammar, mutations add to variation, genetic drift is due to random selection. And selection always reduces diversity whether random or directional. And you don't understand the mathematics of either process. If you think you do understand, explain how to use Haldane's math to compute the intensity of selection for the Lenski experiment.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 5:10:04 AM UTC-7, MarkE wrote:
> Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?

SlowO's summary is confusing and wrong. And the reason it is wrong is that he has no understanding of what natural selection is. Natural selection is measured in one of two ways. It can be measured as the relative fitness of variants in a population. This measure of natural selection is used when doing the mathematics of survival of the fittest. The other way natural selection is measured is by the absolute fitness to reproduce. This measure of natural selection is used when doing the mathematics of adaptation (improvement in fitness) to compute the probability of a beneficial mutation occurring.

[jillery]

On Wed, 3 Oct 2018 06:25:12 -0400, Oxyaena <oxy...@invalid.user>
wrote:

>On 10/3/2018 4:51 AM, MarkE wrote:
>> Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
>>
>
>Why write "claimed"? Have you not even read the *Origin*?

Technically, it *is* claimed. It also happens to be a correct claim.

>> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
>
>Selection is just one of many mechanisms of evolution, and while it is a
> major one, it's not the only one, and there are specifically two types
>of selection, they are natural selection (the one that's most commonly
>known) and sexual selection (wherein potential mates select their
>partners based off of what they find most "endearing", and so the
>opposite gender will start to evolve those features their mates find
>"endearing" or "attractive").

Don't forget artificial selection, which inspired Darwin to coin his
famous phrase.

And some people divide selection into even more categories, but I'm
not one of them.

--
I disapprove of what you say, but I will defend to the death your right to say it.

Evelyn Beatrice Hall
Attributed to Voltaire

[jillery]

All that you describe above are examples of different types mutations.
Mutations are the grist for the natural selection mill. Without them,
there would be nothing for natural selection to select.

[Ernest Major]

On 03/10/2018 13:09, MarkE wrote:
> Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?

The different processes act in concert and it is not really appplicable
to say that one process is solely responsible of the creation of "new
functionality, information and complexity" - a surprising amount of
change can be achieved by the action of natural (including artifical)
selection and recombination, but without a source of variation the
process would run out of steam as more and more loci became fixed.

Information is a slippery term when applied to a genome. From an
classical information theory viewpoint natural selection mostly removes
information from a gene pool - it typically reduces the amount of
variation, so you need few bits to describe it.

Dawkins has argued that natural selection adds information to a gene
pool because it records imperfectly the past environment (i.e. selection
pressures) of a population. (Analogous to the transmission of radiation
from a stellar interior to space recording information about the
chemical composition of the upper layers of the stellar atmosphere.)

Creationist concepts of genetic information don't seem to be
well-defined, which makes the question unanswerable with respect to them.

I would reckon that much complexity in organisms occurs in spite of
natural selection, not because of it. (Defining an objective definition
of organismal complexity also turns out to be a non-trivial problem.
Look up Paul Nelson Day.)

Functionality is the one where the action of natural selection is pretty
nearly necessary though not sufficient.

>
> It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.

Natural selection allows the accumulation of beneficial change. If you
want to described that as natural selection doing the heavy lifting, OK,
but that's still not natural selection being solely responsible.

>
> If this is the case, what can made of this claim?
>
> “Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> http://www.thethirdwayofevolution.com/
>
>

I'd reckon it's a straw man.


--
alias Ernest Major

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 5:20:04 AM UTC-7, MarkE wrote:
> “Claimed” because I’m a creationist unconvinced of natural selection as an explanation for macro evolution.

And well you should remain unconvinced. The typical claim of the advocates of the ToE is that micro-evolutionary changes can add up to a macro-evolutionary change. The problem with this logic is that micro-evolutionary changes are not linked by the addition rule of probabilities. Micro-evolutionary changes are linked by the multiplication rule of probabilities. It is this principle which allows for the successful use of combination therapy for the treatment of hiv.

>
> Would you agree sexual selection is a subset of natural selection, given the definition of fitness as differential reproductive success?

Sexual selection has its own particular govening mathematics and can lead to an improvement in fitness but sexual selection without error cannot produce new alleles. For the production of new more fit alleles requires rmns. And the process is limited by the multiplication rule of probabilities.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 6:10:03 AM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 05:09:27 -0700 (PDT), MarkE
> <mark.w.e...@gmail.com> wrote:
>
> >Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
> >
> >It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.
> >
> >If this is the case, what can made of this claim?
> >
> >“Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> >http://www.thethirdwayofevolution.com/
>
>
> All that you describe above are examples of different types mutations.
> Mutations are the grist for the natural selection mill. Without them,
> there would be nothing for natural selection to select.

So when are you going to learn how rmns works?

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 5:25:03 AM UTC-7, Ernest Major wrote:
> On 03/10/2018 09:51, MarkE wrote:
> > Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
> >
> > If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
> >
> > - generic drift
> > - symbiogenesis
> > - horizontal DNA transfer
> > - action of mobile DNA
> > - epigenetic modifications
> > - others
> >
> > I.e., these all mix things up and create new configurations, possibly in sophisticated ways, but they are not a refining mechanism. In fact, without the action of natural selection, over time would result in a net degradation (randomisation)?
> >
>
> How you divide up evolutionary mechanisms is open to debate - for
> example Oxyaena has just contrasted natural selection and sexual
> selection, while I consider sexual selection (and artificial selection)
> forms of natural selection. That said, I would count genetic drift
> (differential reproductive success NOT causally correlated with
> genotype) with natural selection (differential reproductive success
> causally correlated with genotype) in the differential reproductive
> success category, contrasting with the variation category.
>
> Genetic drift and natural selection form somewhat of a continuum; in
> large populations and with large selection coefficients natural
> selection dominates; in small populations and with small selection
> coefficients genetic drift dominates.

So explain to us what hiv is doing when the population is subject to 3 drug combination therapy. And what happens to hiv populations if only 1 or 2 drugs are used. And explain to us the operation of the Lenski and Kishony experiments.

[MarkE]

EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.

There seems to be a trend with evolutionary theory to minimise/limit the role of NS, but without offering an alternative, or conflating variation with selection. The Third Way website I quoted (strongly not creationist) states that some have “elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”

But NS *is* the only “creative force” available to naturalistic evolution. Without NS, there can be no “appearance of design”, no “exquisite engineering”.

[Alan Kleinman MD PhD]

How does this accumulation of beneficial change work? Explain to us the Kishony experiment.

[Ernest Major]

Are you really claiming that the Kishony experiment does not show the
accumulation of benefical change? The experiment shows populations
expanding to lethality borders and then stalling until a mutation occurs
which makes the territory beyond the border non-lethal, and a
sub-population expanding to the next border, reiterated. That looks very
like the accumulation of beneficial changes to me.

>>>
>>> If this is the case, what can made of this claim?
>>>
>>> “Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
>>> http://www.thethirdwayofevolution.com/
>>>
>>>
>>
>> I'd reckon it's a straw man.
>>
>>
>> --
>> alias Ernest Major
>
>

--
alias Ernest Major

[jillery]

To quote someone you regard so highly, I already did. Prove me wrong.

[jillery]

On Wed, 3 Oct 2018 06:12:05 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:

>So explain to us what hiv is doing when the population is subject to 3 drug combination therapy. And what happens to hiv populations if only 1 or 2 drugs are used. And explain to us the operation of the Lenski and Kishony experiments.

You first.

[Ernest Major]

In my response to your 3rd post I expressed my objection to isolating
the "creative power" of evolution to the process of natural selection.

It's been known for 50 years that most evolutionary change at the level
of the genome is not the result of natural selection - look up Neutral
Theory and Nearly Neutral Theory. (I prefer Nearly Neutral Theory - I
doubt that many alleles have selection coefficients of exactly zero, but
a great many have selection coefficients so small that the effect of
genetic drift overwhelm those of selection.)

Where natural selection comes into play is the creation and maintenance
of adaptations (not increased functionality, not more information, nor
greater complexity, just better adaptation). But it doesn't do the
creative bit on its own; it's necessary but no sufficient.

You might like to try to articulate why you think natural selection
being the only creative force would be a problem. It might clarify your
thinking, and it might help people respond to your concerns.

--
alias Ernest Major

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 6:25:03 AM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 06:14:08 -0700 (PDT), Alan Kleinman MD PhD

> wrote:
>
> >On Wednesday, October 3, 2018 at 6:10:03 AM UTC-7, jillery wrote:
> >> On Wed, 3 Oct 2018 05:09:27 -0700 (PDT), MarkE
> >> <mark.w.e...@gmail.com> wrote:
> >>
> >> >Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
> >> >
> >> >It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.
> >> >
> >> >If this is the case, what can made of this claim?
> >> >
> >> >“Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> >> >http://www.thethirdwayofevolution.com/
> >>
> >>
> >> All that you describe above are examples of different types mutations.
> >> Mutations are the grist for the natural selection mill. Without them,
> >> there would be nothing for natural selection to select.
> >So when are you going to learn how rmns works?
>
>
> To quote someone you regard so highly, I already did. Prove me wrong.

Why don't you explain it to Ernest Major?

[Alan Kleinman MD PhD]

The Kishony experiment certainly does show the accumulation of beneficial mutations. It is an excellent demonstration of micro-evolution. I just thought you might want to give the mathematical explanation of how this process works. If you have trouble giving this explanation, that's ok. I'll explain it to MarkE. What do you think would happen if Kishony had used two drugs in his experiment instead of one? Can you explain the mathematics of this experiment?

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 6:25:03 AM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 06:12:05 -0700 (PDT), Alan Kleinman MD PhD

> wrote:
>
> >So explain to us what hiv is doing when the population is subject to 3 drug combination therapy. And what happens to hiv populations if only 1 or 2 drugs are used. And explain to us the operation of the Lenski and Kishony experiments.
>
>
> You first.

To quote someone you regard so highly, I already did. Prove me wrong. And don't forget, my explanation is peer-reviewed and published.

[John Harshman]

Evolution involves variation and selection, but it involves other things
too, like genetic drift, which is neither.

Genetic drift isn't "variation", and epigenetic modifications aren't
*genetic* variation. Variation is something that happens to individuals,
and drift, like selection, is something that happens to populations.
Epigenetic modifications happen to individuals, but since they aren't
heritable (except in the very short term) they are not subject to
natural selection and play no part in evolution.

The rest are legitimately considered sources of variation.

Yes, without selection genomes would degrade.

[John Harshman]

"Creative force" is a term of ambiguous meaning. Perhaps it's better to
say that natural selection is the only thing we know of that acts to
increase adaptation and thus capable of resulting in adaptive evolution.
You don't build an eye just by mutation and/or drift.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 7:05:04 AM UTC-7, John Harshman wrote:
> On 10/3/18 1:51 AM, MarkE wrote:
> > Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
> >
> > If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
> >
> > - generic drift
> > - symbiogenesis
> > - horizontal DNA transfer
> > - action of mobile DNA
> > - epigenetic modifications
> > - others
> >
> > I.e., these all mix things up and create new configurations, possibly
> > in sophisticated ways, but they are not a refining mechanism. In
> > fact, without the action of natural selection, over time would result
> > in a net degradation (randomisation)?
>
> Evolution involves variation and selection, but it involves other things
> too, like genetic drift, which is neither.

Why don't you explain the difference between "drift" and "selection". Under what circumstances does selection work and when does a population drift?

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 7:05:04 AM UTC-7, John Harshman wrote:

So take the ambiguity out of your explanation and explain how natural selection can make an eye. I'll even make it easier for you. Explain how the Kishony experiment works.

[jillery]

Since you asked, because he didn't ask me, nor does he need anybody to
explain it to him. You're welcome.

[jillery]

On Wed, 3 Oct 2018 06:40:50 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:

>On Wednesday, October 3, 2018 at 6:25:03 AM UTC-7, jillery wrote:
>> On Wed, 3 Oct 2018 06:12:05 -0700 (PDT), Alan Kleinman MD PhD
>> wrote:
>>
>> >So explain to us what hiv is doing when the population is subject to 3 drug combination therapy. And what happens to hiv populations if only 1 or 2 drugs are used. And explain to us the operation of the Lenski and Kishony experiments.
>>
>>
>> You first.
>To quote someone you regard so highly, I already did.

Those are your words. How conveniently you forget.

>Prove me wrong. And don't forget, my explanation is peer-reviewed and published.

Tell us to which falsehoods you will admit when I prove you wrong.

[jillery]

You first.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 8:25:03 AM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 06:39:14 -0700 (PDT), Alan Kleinman MD PhD

> wrote:
>
> >On Wednesday, October 3, 2018 at 6:25:03 AM UTC-7, jillery wrote:
> >> On Wed, 3 Oct 2018 06:14:08 -0700 (PDT), Alan Kleinman MD PhD
> >> wrote:
> >>
> >> >On Wednesday, October 3, 2018 at 6:10:03 AM UTC-7, jillery wrote:
> >> >> On Wed, 3 Oct 2018 05:09:27 -0700 (PDT), MarkE
> >> >> <mark.w.e...@gmail.com> wrote:
> >> >>
> >> >> >Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
> >> >> >
> >> >> >It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.
> >> >> >
> >> >> >If this is the case, what can made of this claim?
> >> >> >
> >> >> >“Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> >> >> >http://www.thethirdwayofevolution.com/
> >> >>
> >> >>
> >> >> All that you describe above are examples of different types mutations.
> >> >> Mutations are the grist for the natural selection mill. Without them,
> >> >> there would be nothing for natural selection to select.
> >> >So when are you going to learn how rmns works?
> >>
> >>
> >> To quote someone you regard so highly, I already did. Prove me wrong.
> >Why don't you explain it to Ernest Major?
>
>
> Since you asked, because he didn't ask me, nor does he need anybody to
> explain it to him. You're welcome.

Neither you nor Ernest Major understands how rmns works. And until you take a course in introductory probability theory and understand it, you won't.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 8:25:03 AM UTC-7, jillery wrote:

> On Wed, 3 Oct 2018 07:20:42 -0700 (PDT), Alan Kleinman MD PhD

> wrote:
>
> >On Wednesday, October 3, 2018 at 7:05:04 AM UTC-7, John Harshman wrote:
> >> On 10/3/18 6:17 AM, MarkE wrote:
> >> > EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
> >> >
> >> > There seems to be a trend with evolutionary theory to minimise/limit
> >> > the role of NS, but without offering an alternative, or conflating
> >> > variation with selection. The Third Way website I quoted (strongly
> >> > not creationist) states that some have “elevated Natural Selection
> >> > into a unique creative force that solves all the difficult
> >> > evolutionary problems without a real empirical basis.”
> >>
> >> > But NS *is* the only “creative force” available to naturalistic
> >> > evolution. Without NS, there can be no “appearance of design”, no
> >> > “exquisite engineering”.
> >>
> >> "Creative force" is a term of ambiguous meaning. Perhaps it's better to
> >> say that natural selection is the only thing we know of that acts to
> >> increase adaptation and thus capable of resulting in adaptive evolution.
> >> You don't build an eye just by mutation and/or drift.
> >So take the ambiguity out of your explanation and explain how natural selection can make an eye. I'll even make it easier for you. Explain how the Kishony experiment works.
>
>
> You first.

Don't be silly, natural selection can't make an eye. And I've already explained how the Kishony experiment works, many times. But you don't have the prerequisites to understand the explanation. And Harshman will not explain how the Kishony experiment works. He has already said he doesn't know how that experiment works and he has a PhD in evolutionary biology. When will biologists learn how evolution works?

[zencycle]

On Wednesday, October 3, 2018 at 4:55:03 AM UTC-4, MarkE wrote:

>
> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
>

> - others
>

"others"? You might want to be a bit more specific.

[John Harshman]

Nilsson D., Pelger S. A pessimistic estimate of the time required for an
eye to evolve. Proceedings of the Royal Society of London, Series B
1994; 256:53-58.

[zencycle]

On Wednesday, October 3, 2018 at 12:30:04 PM UTC-4, John Harshman wrote:
>
> Nilsson D., Pelger S. A pessimistic estimate of the time required for an
> eye to evolve. Proceedings of the Royal Society of London, Series B
> 1994; 256:53-58.

John, you know where this is going to go, why do you even bother?

[Alan Kleinman MD PhD]

That paper is the biggest collection on nonsense that only someone who thinks that reptile can grow feathers could believe. But if you actually believe that nonsense, use this to explain how the Kishony experiment works. The Royal Society of London has certainly gone downhill since they published Isaac Newton's Principia Mathematica.

[Alan Kleinman MD PhD]

Maybe ztupid wants to explain the Kishony experiment based on this paper?

[jillery]

On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), Alan Kleinman MD PhD
<klei...@sti.net> wrote:

>On Wednesday, October 3, 2018 at 8:25:03 AM UTC-7, jillery wrote:
>> On Wed, 3 Oct 2018 07:20:42 -0700 (PDT), Alan Kleinman MD PhD
>> wrote:
>>
>> >On Wednesday, October 3, 2018 at 7:05:04 AM UTC-7, John Harshman wrote:
>> >> On 10/3/18 6:17 AM, MarkE wrote:
>> >> > EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
>> >> >
>> >> > There seems to be a trend with evolutionary theory to minimise/limit
>> >> > the role of NS, but without offering an alternative, or conflating
>> >> > variation with selection. The Third Way website I quoted (strongly
>> >> > not creationist) states that some have “elevated Natural Selection
>> >> > into a unique creative force that solves all the difficult
>> >> > evolutionary problems without a real empirical basis.”
>> >>
>> >> > But NS *is* the only “creative force” available to naturalistic
>> >> > evolution. Without NS, there can be no “appearance of design”, no
>> >> > “exquisite engineering”.
>> >>
>> >> "Creative force" is a term of ambiguous meaning. Perhaps it's better to
>> >> say that natural selection is the only thing we know of that acts to
>> >> increase adaptation and thus capable of resulting in adaptive evolution.
>> >> You don't build an eye just by mutation and/or drift.
>> >So take the ambiguity out of your explanation and explain how natural selection can make an eye. I'll even make it easier for you. Explain how the Kishony experiment works.
>>
>>
>> You first.
>Don't be silly, natural selection can't make an eye.

So your question is not just silly, but pointless. Is anybody
surprised.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 10:20:03 AM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), Alan Kleinman MD PhD

There's a point here. It's just that you are unwilling or incapable of seeing the point. In your mind, you think that natural selection can create an eye when hiv cannot evolve efficiently to just 3 selection pressures targeting only two genes. I think it is both that you are unwilling and incapable.

[zencycle]

On Wednesday, October 3, 2018 at 1:05:04 PM UTC-4, Alan Kleinman MD PhD wrote:
>
> The Royal Society of London has certainly gone downhill since they published
> Isaac Newton's Principia Mathematica.

I don't normally respond to your vapid spew (and don't anticipate it again any time soon), but I though it was noteworthy to point out that drdr littleman PUIT finally admits his philosophy on science is stuck in the 17th century.

[Robert Camp]

On 10/3/18 1:51 AM, MarkE wrote:
> Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
>

> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
>

> - generic drift
> - symbiogenesis
> - horizontal DNA transfer
> - action of mobile DNA
> - epigenetic modifications
> - others
>
> I.e., these all mix things up and create new configurations, possibly in sophisticated ways, but they are not a refining mechanism.

If I take the proper inference here (and I may well not be doing so, so
correct me if you don't mean to imply that "refining" is important) I'd
suggest you consider that while "a refining mechanism" may be valuable
under static conditions, the natural environment is always changing. In
such circumstances being "refined" can mean having narrowed options.

Organisms are "optimised" to a degree, yes, but "mixing things up" lends
critical adaptability to populations trying (in an obviously
non-teleological sense) to survive a dynamic and unpredictable world.

[Alan Kleinman MD PhD]

ztupid finds calculus and the laws of motion a little out of date. That's why he is ztupid.

[Bob Casanova]

On Wed, 3 Oct 2018 06:25:12 -0400, the following appeared in
talk.origins, posted by Oxyaena <oxy...@invalid.user>:

>On 10/3/2018 4:51 AM, MarkE wrote:
>> Organisms are observed to be highly optimised and rich in information. NS is one claimed naturalistic mechanism to generate and maintain this.
>>
>

>Why write "claimed"? Have you not even read the *Origin*?

>
>
>> If evolution involves variation and then selection, is it correct to put all the following in the ‘variation’ category?
>

>Selection is just one of many mechanisms of evolution, and while it is a
> major one, it's not the only one, and there are specifically two types
>of selection, they are natural selection (the one that's most commonly
>known) and sexual selection (wherein potential mates select their
>partners based off of what they find most "endearing", and so the
>opposite gender will start to evolve those features their mates find
>"endearing" or "attractive").

I may be wrong, but AIUI sexual selection is usually
considered to be part of natural selection, potential mates
being part of the environment driving natural selection. Not
so?
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Bob Casanova]

On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), the following
appeared in talk.origins, posted by Alan Kleinman MD PhD
<klei...@sti.net>:

>...natural selection can't make an eye

So, since multiple types of eyes exist, why don't you
explain where each came from? Or even *one* type,
cephalopods, for instance?

And BTW, "It wasn't by X" isn't an explanation, nor is any
reference to Kishony or Lenski, or to your "paper".

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 12:30:02 PM UTC-7, Bob Casanova wrote:
> On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), the following
> appeared in talk.origins, posted by Alan Kleinman MD PhD

> :
>
> >...natural selection can't make an eye
>
> So, since multiple types of eyes exist, why don't you
> explain where each came from? Or even *one* type,
> cephalopods, for instance?
>
> And BTW, "It wasn't by X" isn't an explanation, nor is any
> reference to Kishony or Lenski, or to your "paper".

I've explained correctly how natural selection works, both for rmns and random recombination. Just because you don't have the skill or training to understand the correct explanation, don't blame me. Next time don't sleep through your two courses in statistics. Now if you think that natural selection created all the different types of eyes, turn on a light and you do the work, dimmy.

[jillery]

That's not it.


> In your mind,


You have no idea what's in my mind, and you don't care to know.

>you think that natural selection can create an eye when hiv cannot evolve efficiently to just 3 selection pressures targeting only two genes.

And yet eyes exist, and evolved independently in a dozen different
lineages. So how do you think that happened?

> I think it is both that you are unwilling and incapable.

You're entitled to your own opinions. You're not entitled to your own
facts.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 1:00:03 PM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 10:42:03 -0700 (PDT), Alan Kleinman MD PhD

Certainly, it is. You refuse to study introductory probability theory which is the mathematical foundation for stochastic processes. That's why you come up with these silly ideas like reptiles grow feathers and fish turn into mammals. If you learn nothing else about probability theory, learn about the multiplication rule. It's the reason combination therapy works for the treatment of hiv and it is the reason reptiles don't grow feathers no matter how cold they get.

[jillery]

Certainly it is not. Eyes exist, and evolved independently in a dozen
different lineages. So one more time, how do you think that happened?

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 1:45:04 PM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 13:05:15 -0700 (PDT), Alan Kleinman MD PhD

You don't understand the simplest examples of rmns and yet you claim that eyes evolved in a dozen different lineages? Why doesn't hiv get a dozen different resistant variants for its simple evolutionary problem? You are unwilling and incapable of understanding this principle.

[Oxyaena]

On 10/3/2018 8:16 AM, MarkE wrote:
> “Claimed” because I’m a creationist unconvinced of natural selection as an explanation for macro evolution.

The Archive is your friend:

http://talkorigins.org/

It will educate you on the subject of evolution that no creationist can,
or try the *Origin*, which I already recommended, and which is also
available on the Archive.


>
> Would you agree sexual selection is a subset of natural selection, given the definition of fitness as differential reproductive success?
>

Different authors disagree as to whether sexual selection is part of
natural selection, and I already explained that natural selection is
only one of the many mechanisms for evolution, even if it is the
*driving* mechanism for evolution. Evolution is a fact, common ancestry
is a fact, natural selection is a theory. Even in the unlikely event
that natural selection were to be disproven, evolution would still remain.

For the record, I think whether sexual selection is a subset of natural
selection or not is irrelevant, as I explained before that while NS is
the driving mechanism behind evolution, it's not the only factor at play.

[Mark Isaak]

On 10/3/18 6:17 AM, MarkE wrote:
> EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
>
> There seems to be a trend with evolutionary theory to minimise/limit the role of NS, but without offering an alternative, or conflating variation with selection. The Third Way website I quoted (strongly not creationist) states that some have “elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
>
> But NS *is* the only “creative force” available to naturalistic evolution. Without NS, there can be no “appearance of design”, no “exquisite engineering”.

Others have answered your original question well. I'll just add a
couple of my own thoughts.

First, it seems to me that questions about whether variation or
selection are the important part of evolution are akin to asking, "When
people walk, is it the left leg or the right leg which is important?"
Evolution would go nowhere without both.

Second, think of evolution as analogous (in some ways) to product
development. If you want to improve your product (say, coat hangers),
you start by brainstorming lots of different possible modifications:
shape it slightly different, make it from a different material, alter
its texture or weight or color, add an electronic app to destroy coats
that go out of style, etc. Most of these modifications will get
rejected, either quickly (such as, one presumes, the last one) or after
product testing, or even after being on the market for years. Others
will succeed in the market, perhaps to the point that inferior designs
stop being made. Evolution works much the same way. There are
important differences, to be sure (e.g., evolution cannot easily make
very large changes, and changes cannot be rejected before a complete
prototype is produced), but the process of variation and selection is
much the same.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Omnia disce. Videbis postea nihil esse superfluum."
- Hugh of St. Victor

[Alan Kleinman MD PhD]

Sexual reproduction introduces lateral transfer of genetic material. In some instances, this can lead to an improvement of fitness. That improvement in fitness is mathematically predictable. Another point you need to consider is that lateral transfer of genetic without error does not create new alleles. The creation of new alleles requires mutations. Now you need to consider why combination therapy still works for the treatment of hiv despite the fact that this virus does recombination.

[Alan Kleinman MD PhD]

Your analogy is ok to a point but too limited. If your product requires 2 changes to give improvement, it is going to much less likely for this to occur especially when the changes are random and occur at a frequency of e-9. That's why combination therapy works for the treatment of hiv. You need to improve both the reverse transcriptase and protease products before you have a more fit replicator.

[Mark Isaak]

Too bad you don't understand applied mathematics, especially since you
think you do.

[Alan Kleinman MD PhD]

The peer reviewers of my papers might disagree with you. Are you going to give me a chapter in the next edition of your book? I'd like to see how you explain away the multiplication rule of probabilities.

[RonO]

On 10/3/2018 7:09 AM, MarkE wrote:
> Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?

First off Natural selection is just that, something selected for by
nature. Your concept of design only comes in because evolution builds
on what came before. The organism still survives, but new things emerge
and people call these designs, but they are usually just variants of
duplicated genes that do something a little differently and result in
the organism being a little different.

They just gave the Nobel prize to researchers who started using
"directed" evolution.

https://www.the-scientist.com/news-opinion/directed-evolution-phage-display-nab-chemistry-nobel-64890

Original paper:
http://www.pnas.org/content/pnas/90/12/5618.full.pdf

They call it directed evolution because it is artificial selection. The
researchers still use random mutations, but they have an assay that
allows them to select the genes that are better at what they want to
select for, so they have artificial generations where they take an
existing functional enzyme or antibody that binds things and introduce
random mutations, selected out of the thousands of variants that they
produce and mutate again and select again until they get to whare they
want to go.

Nature doesn't know where it is going with any selection. If the
mutation has some advantage more organisms with that mutation will be
produced in the next generation, and other mutations can build on what
came before. So nature can only select for what works. The researchers
can have some goal in mind, and still use random mutations to get there.
as long as they can select for what they want. The researchers do not
have to know what mutations will work, they let their selection
procedure identify those mutations. Nature can only select for a
mutation if it has some type of reproductive advantage.

Natural selection is only the selection part. Other factors produce the
genetic variation. As you indicate genetic drift is a major factor in
accumulating genetic variation in a population, and some biologist think
that it might be more important to what the organism ends up looking
like than natural selection. If you take a population like Europeans
you can see a wide range of phenotypic variation (what the individuals
look like). Some look more like each other, but there is a broad range
of phenotypes drifting in the population. There may be some selection,
but it has been too weak to make everyone look the same. The variation
that makes each person an individual can drift in the population for a
long time and it might be fixed by chance and the population would have
to build what comes next on that foundation.

So before genetic drift or selection you have mutation. In terms of
base-pair substitution mutations, every site in the human genome has
been hit on the order of 100 times by new mutations in the existing
generation of humans. So there is a lot of new mutations, but when we
talk about the standing genetic variation in a population we talk about
the variants that have risen to the level of 1% allele frequency in the
population (over 100 million people have the same variant). It takes
selection or drift for a variant to reach this allele frequency. The
human population suffered a population bottle neck within the last
100,000 years so we have around 1/5 the standing genetic variation that
the average species has. Chimps have around 3 times more standing
genetic variation than humans.

Genetic recombination is an important factor in genetic variation. Your
chromosomes get shuffled as the homologous chromosomes recombine to form
new haplotypes (order of alleles along a chromosome). Recombination is
important because you have just a few chromosomes, but thousands of
genes. Recombination allows different combinations of existing genetic
variants to be inherited.

You can see the evidence of genetic recombination in our genomes by
looking at the Neanderthal DNA that modern humans that made it out of
Africa around 80,000 years ago have in their genomes. Europeans, Asians
and native Americans have a couple percent Neanderthal DNA. The first
hybrids had one set of intact Neanderthal chromosomes, but in the time
since the hybridization event (soon after modern humans left Africa)
recombination has happened and the Neanderthal chromosomes have been
recombined with modern Human chromosomes so that the bits of Neanderthal
chromosome are only around 50,000 base-pairs. The rate of decrease in
size has gone down because at this point the Neandethal bits only have
around 1 in 5,000 chance to be involved in a recombination event. The
Neanderthal chromosomes started out on the order of 100 million
base-pairs and recombination has chopped them up to their current size.

Ron Okimoto

>
> It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.
>
> If this is the case, what can made of this claim?
>

> “Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> http://www.thethirdwayofevolution.com/
>
>

[August Rode]

We use mathematics to model natural phenomena. If there is a
disagreement between the mathematics and what is actually observed in
nature, don't you think it's most likely that the model is wrong?

[MarkE]

On Wednesday, October 3, 2018 at 10:40:03 PM UTC+9:30, Ernest Major wrote:

> On 03/10/2018 13:09, MarkE wrote:
> > Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
>

> The different processes act in concert and it is not really appplicable
> to say that one process is solely responsible of the creation of "new
> functionality, information and complexity" - a surprising amount of
> change can be achieved by the action of natural (including artifical)
> selection and recombination, but without a source of variation the
> process would run out of steam as more and more loci became fixed.
>
> Information is a slippery term when applied to a genome. From an
> classical information theory viewpoint natural selection mostly removes
> information from a gene pool - it typically reduces the amount of
> variation, so you need few bits to describe it.
>
> Dawkins has argued that natural selection adds information to a gene
> pool because it records imperfectly the past environment (i.e. selection
> pressures) of a population. (Analogous to the transmission of radiation
> from a stellar interior to space recording information about the
> chemical composition of the upper layers of the stellar atmosphere.)
>
> Creationist concepts of genetic information don't seem to be
> well-defined, which makes the question unanswerable with respect to them.

Information does appear to be a slippery concept. Dembski's CSI is an attempt to define it, though hasn't seemed to produce quantifiable results.

Dawkin's locating information in the environment and translated to genomes acknowledges the information issue, and possibly tacitly recognises conservation of information. If so, the question then is, how did information accumulate as the universe developed?

> I would reckon that much complexity in organisms occurs in spite of
> natural selection, not because of it. (Defining an objective definition
> of organismal complexity also turns out to be a non-trivial problem.
> Look up Paul Nelson Day.)

Agreed complexity is...complex. But I would say that non-NS processes, which have been previously deemed to alone degrade the genome (and the phenotype), will correspondingly reduce complexity--functional complexity--what the organism can do, and how well.

> Functionality is the one where the action of natural selection is pretty
> nearly necessary though not sufficient.

Agreed. As above, relate function to complexity. Though a specific 'functional' increase (fitness) can result from a complexity decrease, e.g. some bacterial antibiotic immunity results from loss of function.

> > It seems to me it is, by definition. The other factors provide the chance variations, the undirected experiments, but NS does the heavy lifting.
>

> Natural selection allows the accumulation of beneficial change. If you
> want to described that as natural selection doing the heavy lifting, OK,
> but that's still not natural selection being solely responsible.

For sure, sources of variation are needed, but it's important to recognise that these inherently degrade the organism. Which is why I'm curious about, for example, the debate between neutral theory and adaptationism - isn't this a category error? (i.e. variation vs selection?)

> >
> > If this is the case, what can made of this claim?
> >

> > “Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> > http://www.thethirdwayofevolution.com/
> >
> >
>
> I'd reckon it's a straw man.
>
>
> --
> alias Ernest Major

[MarkE]

On Thursday, October 4, 2018 at 10:00:02 AM UTC+9:30, Ron O wrote:
> On 10/3/2018 7:09 AM, MarkE wrote:
> > Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
>
> First off Natural selection is just that, something selected for by
> nature. Your concept of design only comes in because evolution builds
> on what came before. The organism still survives, but new things emerge
> and people call these designs, but they are usually just variants of
> duplicated genes that do something a little differently and result in
> the organism being a little different.
>
> They just gave the Nobel prize to researchers who started using
> "directed" evolution.
>
> https://www.the-scientist.com/news-opinion/directed-evolution-phage-display-nab-chemistry-nobel-64890
>
> Original paper:
> http://www.pnas.org/content/pnas/90/12/5618.full.pdf
>
> They call it directed evolution because it is artificial selection. The
> researchers still use random mutations, but they have an assay that
> allows them to select the genes that are better at what they want to
> select for, so they have artificial generations where they take an
> existing functional enzyme or antibody that binds things and introduce
> random mutations, selected out of the thousands of variants that they
> produce and mutate again and select again until they get to whare they
> want to go.

This example highlights I think a key aspect of the origins debate. That is, the proposed Darwinian mechanism is effective in searching some fitness landscapes. I've programmed genetic algorithms myself and seen them work. I think creationists need to acknowledge this.

So the debate correctly needs to address how far can the action of GAs be extrapolated, and under what conditions. That's a more nuanced discussion that easily gets lost when either side digs in.

Here's a response to the Nobel Prize announcement which exemplifies my point (even though you may disagree with Axe's assessment):

"It’s also fitting that words like “design” and “directed” be attached to their work. The truth is that by much hard work and careful thought, they accomplished what accidental processes would never accomplish on their own.

"Equally true is that even these stellar scientists have not found a way to invent from scratch proteins that rival the ones we see by the thousands in living cells. As Frances Arnold once said with admirable candor: “[E]fforts to date to generate novel catalysts have primarily demonstrated that we are getting good at making bad enzymes. Making good enzymes will require a whole new level of insight, or new methodologies altogether.”

"The problem these efforts face in the lab is exactly the problem faced by Darwin’s evolutionary mechanism in the wild: Nothing can be selected until it already exists. The fact that some clever thing would be enormously beneficial if it existed has no power to make that thing exist."

https://evolutionnews.org/2018/10/nobel-prize-in-chemistry-for-intelligent-design/

[MarkE]

On Wednesday, October 3, 2018 at 11:35:04 PM UTC+9:30, John Harshman wrote:
> On 10/3/18 6:17 AM, MarkE wrote:
> > EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
> >
> > There seems to be a trend with evolutionary theory to minimise/limit
> > the role of NS, but without offering an alternative, or conflating
> > variation with selection. The Third Way website I quoted (strongly

> > not creationist) states that some have “elevated Natural Selection

> > into a unique creative force that solves all the difficult
> > evolutionary problems without a real empirical basis.”
>

> > But NS *is* the only “creative force” available to naturalistic
> > evolution. Without NS, there can be no “appearance of design”, no
> > “exquisite engineering”.
>

> "Creative force" is a term of ambiguous meaning. Perhaps it's better to
> say that natural selection is the only thing we know of that acts to
> increase adaptation and thus capable of resulting in adaptive evolution.
> You don't build an eye just by mutation and/or drift.

It does have teleological overtones, and is somewhat vague, but it does capture the universally acknowledged observation of living things as having “the appearance of design” and “exquisite engineering”. The Third Way group who used the term are explicitly wary of creationists (like me :) misquoting them (not me, I trust).

But I wouldn't disagree with your alternative definition.

[MarkE]

On Thursday, October 4, 2018 at 7:15:02 AM UTC+9:30, Alan Kleinman MD PhD wrote:
> On Wednesday, October 3, 2018 at 2:30:03 PM UTC-7, Mark Isaak wrote:
> > On 10/3/18 6:17 AM, MarkE wrote:
> > > EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
> > >
> > > There seems to be a trend with evolutionary theory to minimise/limit the role of NS, but without offering an alternative, or conflating variation with selection. The Third Way website I quoted (strongly not creationist) states that some have “elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
> > >
> > > But NS *is* the only “creative force” available to naturalistic evolution. Without NS, there can be no “appearance of design”, no “exquisite engineering”.
> >
> > Others have answered your original question well. I'll just add a
> > couple of my own thoughts.
> >
> > First, it seems to me that questions about whether variation or
> > selection are the important part of evolution are akin to asking, "When
> > people walk, is it the left leg or the right leg which is important?"
> > Evolution would go nowhere without both.

I think it's a category question. Left and right legs are in same category ("propulsion units"), and the brain with walking program is in a separate category ("control function"). Similarly, NS is (uniquely) the selection category, all other elements are in the variation category.

My wondering is, are positions such as the quoted Third Way conflating categories in diminishing the place of NS?

[MarkE]

'Refining' is perhaps too imprecise. The summary of my position is, NS is the only 'creative force' (to use the Third Way term), i.e. uniquely in the 'selection' category; all other elements are in the 'variation' category, and in and of themselves all degrade the genotype and phenotype over time (though variation is of course necessary).

[jillery]

So if you don't think it impertinent to ask a direct question, do you
regard creationism as more compelling than, and conflicting with,
Evolution? If so, how?

[jillery]

You posted no answer to my question. That suggests to me you have no
idea how so many different kinds of eyes came to be, which explains
why you post nothing but noise.

[zencycle]

On Thursday, October 4, 2018 at 1:30:03 AM UTC-4, MarkE wrote:

> Here's a response to the Nobel Prize announcement which exemplifies my point (even though you may disagree with Axe's assessment):
>
> "It’s also fitting that words like “design” and “directed” be attached to their work. The truth is that by much hard work and careful thought, they accomplished what accidental processes would never accomplish on their own.
>

A lot of work has been done recently in showing how the RNA world model had help vis a vis lipids or peptides. REsearch like this shows that replicase structures could have happened on their own,

https://arxiv.org/ftp/arxiv/papers/1211/1211.0413.pdf

from the conclusion:

"we have tried to provide a
molecular mechanism of protein synthesis in Lipid-RNA World,
which would eventually take up the Lipid-RNA World to the next
stage of chemical evolution: the Protein-RNA World. This model
suggests that proto-ribosome could have polymerized amino acids
without the need of any chemical energy source, just by utilizing
physical forces generated by thermal fluctuations. Our ribosomal
evolution model can explain the contemporary 23S rRNA structure
and supports the previous predictions about its ancient regions."

Here's a link _a_ paper on peptide/RNA interactions:

"Sequence and Structure Space of RNA-Binding Peptides"

https://pdfs.semanticscholar.org/49ba/30eeea68633b86448616da088ee4fdd385bb.pdf

From the conclusion:
" The high frequency at which RNA-binding peptides
can be found for some RNA structures suggests
that specific binders may have readily evolved from a
relatively small sequence space, perhaps reflecting the
early transition from an RNA world."

[RonO]

On 10/4/2018 12:25 AM, MarkE wrote:
> On Thursday, October 4, 2018 at 10:00:02 AM UTC+9:30, Ron O wrote:
>> On 10/3/2018 7:09 AM, MarkE wrote:
>>> Hi Ron, good summary. My question here concerns the status of NS in view of the modern synthesis (and extensions of it), i.e., does NS nevertheless remain the only mechanism responsible for the creation of new functionality, information and complexity? For the “appearance of design”?
>>
>> First off Natural selection is just that, something selected for by
>> nature. Your concept of design only comes in because evolution builds
>> on what came before. The organism still survives, but new things emerge
>> and people call these designs, but they are usually just variants of
>> duplicated genes that do something a little differently and result in
>> the organism being a little different.
>>
>> They just gave the Nobel prize to researchers who started using
>> "directed" evolution.
>>
>> https://www.the-scientist.com/news-opinion/directed-evolution-phage-display-nab-chemistry-nobel-64890
>>
>> Original paper:
>> http://www.pnas.org/content/pnas/90/12/5618.full.pdf
>>
>> They call it directed evolution because it is artificial selection. The
>> researchers still use random mutations, but they have an assay that
>> allows them to select the genes that are better at what they want to
>> select for, so they have artificial generations where they take an
>> existing functional enzyme or antibody that binds things and introduce
>> random mutations, selected out of the thousands of variants that they
>> produce and mutate again and select again until they get to whare they
>> want to go.
>
> This example highlights I think a key aspect of the origins debate. That is, the proposed Darwinian mechanism is effective in searching some fitness landscapes. I've programmed genetic algorithms myself and seen them work. I think creationists need to acknowledge this.

The fitness landscape is not searched. The new mutation either improves
the reproductive ability of the organism, makes it worse, or doesn't do
much of anything under the current environmental conditions. Fitness
landscapes are not searched, nature just selects for variants that do
better under the fitness landscape that exists that would affect the
reproduction of the organism in the environment that the organism exists
in. There is some fitness landscape and any new mutation has a chance
of changing the position of the organism with the new mutation in that
landscape. Previous evolution can limit the movement in the landscape
because most mutations don't change much and it may be difficult to go
from one peak to another.

>
> So the debate correctly needs to address how far can the action of GAs be extrapolated, and under what conditions. That's a more nuanced discussion that easily gets lost when either side digs in.

GAs are limited because they do not simulate the conditions that we find
in nature. There isn't just one type of fitness in terms of
environments that real organisms find themselves in.

>
> Here's a response to the Nobel Prize announcement which exemplifies my point (even though you may disagree with Axe's assessment):
>
> "It’s also fitting that words like “design” and “directed” be attached to their work. The truth is that by much hard work and careful thought, they accomplished what accidental processes would never accomplish on their own.

They actually just acted as the selective agents and it was the
techniques of combining the methods of generating random mutations and
coupling that with methods of detecting the phenotypes that they wanted
to select for that got them the Nobel. The process was directed in that
they put the random mutations into specific genes, but they didn't care
what mutations were put in so they were able to identify which
"accidents" resulted in a better phenotype using their selection
methods. This is what nature does, but nature has a different selection
mechanism and the researchers could select for the phenotypes that they
wanted even if nature would not have done that.

>
> "Equally true is that even these stellar scientists have not found a way to invent from scratch proteins that rival the ones we see by the thousands in living cells. As Frances Arnold once said with admirable candor: “[E]fforts to date to generate novel catalysts have primarily demonstrated that we are getting good at making bad enzymes. Making good enzymes will require a whole new level of insight, or new methodologies altogether.”

They just did what nature does. In nature evolution builds on what came
before. If a new mutation doesn't work in the context of the existing
genetics it gets selected against. If it improves things it gets
selected for. So it is true that in this way they did not improve on
what nature does. They were able to develop specific selection
procedures that allowed them to select for what they wanted.

>
> "The problem these efforts face in the lab is exactly the problem faced by Darwin’s evolutionary mechanism in the wild: Nothing can be selected until it already exists. The fact that some clever thing would be enormously beneficial if it existed has no power to make that thing exist."

Natural selection doesn't depend on knowing what will work. Random
mutations either improve things or not. The researchers did not have to
predict which mutations did something. All they had to do was put in a
bunch of random mutations and use their selection procedures to identify
what they wanted. Here, like in nature, selection is the nonrandom part.

Ron Okimoto

[MarkE]

No problem, it’s relevant and interesting I think to discuss personal perspectives and what informs them.

I’ve always had a deep interest in and respect for science. I find myself challenging global warming sceptics who, as nonscientists, blithely take a position contrary to the large majority of scientists. But here I am, taking a similar stance myself in this area.

I’ve dropped in to t.o over many years to test my own thinking and position. If you can avoid flamethrowers at ten paces, it’s a good place to (ironically) evolve and refine ideas. I appreciate the expertise on tap here; it is there amidst the noise.

My Christian faith is ultimately a spiritual conviction based on special revelation (the Bible) and personal experience. Fundamental in this is a belief that “God created...”

However, regardless of that, my own assessment of scientific evidence leaves me to view naturalistic explanations for the following as unsatisfactory. I’d argue these are not a god-of-the-gaps recourse, but real issues for materialism. Not in order, and without explanation here:

- First cause
- Fine tuning
- Abiogenesis
- Macroevolution
- Consciousness

There are of course Christians who seek to harmonise creation and evolution as theistic evolution. I’ve been open to that possibility myself. My questioning is, what are the limits of NS as naturalistic “creative force”, along with known sources of variation.

[Don Cates]

I think 'drift' is being misrepresented in this thread. It is also in
the 'selection' category. The difference is that the 'selection' is by
chance and not by any effect on differential reproductive success. It
also does not 'degrade' the genotype or phenotype. This leads to the
problem that many 'obviously adaptive' characteristics may really be due
to drift. to be known to be adaptive, there should be good evidence for
a direct link to differential reproductive success, not only a
convincing 'just so' story.

>>> In fact, without the action of natural selection, over time would result in a net degradation (randomisation)?
>>>
>

--
--
Don Cates ("he's a cunning rascal" PN)

[John Harshman]

On 10/4/18 6:35 AM, MarkE wrote:

> However, regardless of that, my own assessment of scientific evidence
> leaves me to view naturalistic explanations for the following as
> unsatisfactory.

Do you find supernatural explanations satisfactory? If so, why?

> I’d argue these are not a god-of-the-gaps recourse, but real issues for materialism.

Go ahead and make that argument, then.

> Not in order, and without explanation here:
>
> - First cause

That seems like a problem for theists too. It merely pushes the question
back one stage, and you can't avoid it by just declaring that God is
uncaused. That would leave you to explain why the universe can't also be
uncaused.

> - Fine tuning

Is there really such a thing? The arguments for it aren't really very good.

> - Abiogenesis

What leads you to suppose that, because we don't currently know how that
happens, God must have been involved? I can't see anything in that claim
other than God of the gaps. But perhaps you can explain.

> - Macroevolution

So far it isn't clear what you mean by "macroevolution". Why do you
think macroevolution is physically inexplicable?

> - Consciousness

What makes you think this is fundamentally inexplicable other than by
invoking God?

> There are of course Christians who seek to harmonise creation and
> evolution as theistic evolution. I’ve been open to that possibility
> myself. My questioning is, what are the limits of NS as naturalistic
> “creative force”, along with known sources of variation.

We don't know of any such limits, or at least we don't know of anything
we observe that can't be the result of known processes. Of course there
is much whose explanation we don't know. But you have disdained "God of
the gaps".

One thing that can't reasonably be doubted is common descent. Can you
accept that?

[Bob Casanova]

On Wed, 3 Oct 2018 12:47:19 -0700 (PDT), the following

appeared in talk.origins, posted by Alan Kleinman MD PhD

<klei...@sti.net>:

>On Wednesday, October 3, 2018 at 12:30:02 PM UTC-7, Bob Casanova wrote:
>> On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), the following
>> appeared in talk.origins, posted by Alan Kleinman MD PhD
>> :
>>
>> >...natural selection can't make an eye
>>
>> So, since multiple types of eyes exist, why don't you
>> explain where each came from? Or even *one* type,
>> cephalopods, for instance?
>>
>> And BTW, "It wasn't by X" isn't an explanation, nor is any
>> reference to Kishony or Lenski, or to your "paper".

>I've explained correctly how natural selection works, both for rmns and random recombination. Just because you don't have the skill or training to understand the correct explanation, don't blame me. Next time don't sleep through your two courses in statistics. Now if you think that natural selection created all the different types of eyes, turn on a light and you do the work, dimmy.

So you can't explain it, and can only post more
irrelevancies and ad hominems in a futile attempt to
disguise your incompetence? OK.

[jillery]

For the sake of avoiding confusing conflation, please don't discuss
first cause, fine tuning, and abiogenesis with natural selection.
Natural selection is a mechanism of biological evolution, and has
nothing to do with those topics.

If by consciousness you mean an awareness of being aware, my
impression is it's an emergent property of memory and intelligence. So
it's biological, but it's not the kind of property which would be
selected directly by natural selection. It's arguable whether
consciousness is even adaptive. So again, to avoid confusing
conflation, it ought not be discussed with natural selection.

So we are left with macroevolution. If by macroevolution you mean
evolutionary change resulting in new species, I still wonder how you
think creationism provides a better explanation than natural
selection.

Since you specify macroevolution, that suggests to me you accept
microevolution, genetic variation within species. If so, I wonder
what you think stops microevolution from making changes to a species
over time until it's too different from the original to be called the
same species.

As to your question, of course natural selection has limits. One is,
it has no foresight. It can't adapt organisms to what will be, but
only to the current environment.

Another is, it's limited to variations within the population. It
can't select variations which don't exist. That's where mutations
come in.

Another is, it has to compromise among competing demands. For
example, as the cheetah runs faster, it puts more stress on its body.
Adaptation could make bones and muscles stronger, and lungs larger,
but all that also makes a cheetah heavier, which slows it down.

Another is, it's limited by the body plan of the species. Natural
selection can't make a Pegasus, a horse with four legs and functional
wings.

[Robert Camp]

If, in the process of equating variation and degradation you mean to
cast optimization and variation as antithetical, it is important to note
(as others have already done) that selection and environmental fluidity
change that calculus significantly.

As such, variation, in the proper context, becomes a boon as well as a
potential burden.

Evolution is like that - a collection of cobbled-together trade-offs and
shifting equilibria.

Design is not like that.

[Mark Isaak]

On 10/3/18 10:46 PM, MarkE wrote:
> On Thursday, October 4, 2018 at 7:15:02 AM UTC+9:30, Alan Kleinman MD PhD wrote:
>> On Wednesday, October 3, 2018 at 2:30:03 PM UTC-7, Mark Isaak wrote:
>>> On 10/3/18 6:17 AM, MarkE wrote:
>>>> EM, we probably have fundamentally opposing viewpoints, but your response is concise and informative - appreciated.
>>>>
>>>> There seems to be a trend with evolutionary theory to minimise/limit the role of NS, but without offering an alternative, or conflating variation with selection. The Third Way website I quoted (strongly not creationist) states that some have “elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.”
>>>>
>>>> But NS *is* the only “creative force” available to naturalistic evolution. Without NS, there can be no “appearance of design”, no “exquisite engineering”.
>>>
>>> Others have answered your original question well. I'll just add a
>>> couple of my own thoughts.
>>>
>>> First, it seems to me that questions about whether variation or
>>> selection are the important part of evolution are akin to asking, "When
>>> people walk, is it the left leg or the right leg which is important?"
>>> Evolution would go nowhere without both.
>
> I think it's a category question. Left and right legs are in same category ("propulsion units"), and the brain with walking program is in a separate category ("control function"). Similarly, NS is (uniquely) the selection category, all other elements are in the variation category.
>
> My wondering is, are positions such as the quoted Third Way conflating categories in diminishing the place of NS?

I think your Third Way website quote is being very sloppy with the word
"creative" and somewhere between hyperbolic and wrong with their claim
about lack of empirical basis, but I don't think they commit a category
error.

Evolution (the whole package) needs two things: variation and direction.
Without selection, evolution can and does continue to happen, but not
in "interesting" ways. Changes happen, but not changes that affect
survival; they might change in new or opposite ways starting tomorrow,
so the changes don't add up much. With selection, the changes
accumulate in the same direction and build upon one another, so cheetahs
don't get just a little faster, they get lots faster, and a beetle's
slightly smelly exudation gets refined into the bombardier beetle's
firing mechanism. I suspect that is what the quote refers to as "all
the difficult evolutionary problems."

The part of the quote I most disagree with is "without a real empirical
basis." There is lots of empirical evidence showing that natural
selection causes adaptive changes. Granted, the direct evidence applies
only very recently (though the record for maize goes quite a ways back),
but it is still, along with fossil evidence, an empirical basis for
wider conclusions.

[Mark Isaak]

On 10/4/18 6:35 AM, MarkE wrote:

> [...]

> My Christian faith is ultimately a spiritual conviction based on special revelation (the Bible) and personal experience. Fundamental in this is a belief that “God created...”
>
> However, regardless of that, my own assessment of scientific evidence leaves me to view naturalistic explanations for the following as unsatisfactory. I’d argue these are not a god-of-the-gaps recourse, but real issues for materialism. Not in order, and without explanation here:
>
> - First cause

As others have noted, positing a god does not solve the problem.

> - Fine tuning

What do you find so compelling about a universe which is fine-tuned for
a little hydrogen in mostly-empty space, almost everywhere hostile to life?

> - Abiogenesis
> - Consciousness

Both of these, I think, can be firmly considered god-of-the-gaps issues.
Both have made astounding progress in the half or so of my lifetime
that I began paying serious attention to them. If you have not read
recent books and articles on those subjects, you owe it to yourself to
do so.

> - Macroevolution

What could possibly *prevent* it?

> There are of course Christians who seek to harmonise creation and evolution as theistic evolution. I’ve been open to that possibility myself. My questioning is, what are the limits of NS as naturalistic “creative force”, along with known sources of variation.

Here's a question I have never seen a creationist take seriously; maybe
you will: Does evolution look designed?

[MarkE]

To summarise: I find creation compelling for reasons within science and beyond science.

Beyond science, my Christian faith.

Within science, what I see as inadequacies of naturalistic explanations, e.g. lack of fossil intermediates, genetic burden, concurrent multivariable optimisation, irreducable complexity, origin of information, etc.

Here’s a good empirical case: Lenski’s failed E. coli evolution in a flask: https://www.darwinthenandnow.com/2018/01/longest-evolution-experiment-dead-end/

[MarkE]

I meant to say, lack of naturalistic explanations for macroevolution.

[jillery]

On Thu, 4 Oct 2018 16:18:10 -0700 (PDT), MarkE
<mark.w.e...@gmail.com> wrote:

>I meant to say, lack of naturalistic explanations for macroevolution.

Then start with that. Do you accept microevolution? If so, what do
you think is it about microevolution that doesn't explain
macroevolution?

[Oxyaena]

On 10/4/2018 7:06 PM, MarkE wrote:
> To summarise: I find creation compelling for reasons within science and beyond science.
>
> Beyond science, my Christian faith.
>
> Within science, what I see as inadequacies of naturalistic explanations, e.g. lack of fossil intermediates,

You've obviously never even looked at a simple Wiki page for
paleontology, then, have you? Not to mention the innumerable papers in
the scientific literature describing intermediate forms. We know of
hundreds.

Look up *Australopithecus* if you catch my drift, or just go to this site:

http://talkorigins.org/faqs/homs/

> genetic burden, concurrent multivariable optimisation, irreducable complexity,

IC isn't real, and irreducibly complex systems have been shown to
evolve. Take blood clotting for example, which Behe used as an example
of IC, but we now know that whales and dolphins lack an important part
of the blood clot cascade and they still undergo blood clots, and we've
known about this since the 60's. This demonstrates that Behe's
definition of "IC" is false, for a supposedly IC system has been reduced
in parts and still functions.

> origin of information, etc.

This website will answer all of your questions:

http://talkreason.org/

>
> Here’s a good empirical case: Lenski’s failed E. coli evolution in a flask: https://www.darwinthenandnow.com/2018/01/longest-evolution-experiment-dead-end/
>

https://rationalwiki.org/wiki/Leski_affair

[Oxyaena]

On 10/4/2018 7:18 PM, MarkE wrote:
> I meant to say, lack of naturalistic explanations for macroevolution.
>

Read the *Origin*, as I've already told you.

[Alan Kleinman MD PhD]

The math that I've presented agrees with all real, measurable and repeatable examples of rmns (for example, the Weinreich paper, the Kishony Experiment, the Lenski experiment, combination therapy for the treatment of hiv,...). If you have any real, measurable and repeatable examples of rmns that contradicts this math, post them. But you won't because they don't exist.

[Alan Kleinman MD PhD]

On Wednesday, October 3, 2018 at 11:20:03 PM UTC-7, jillery wrote:
> On Wed, 3 Oct 2018 13:58:43 -0700 (PDT), Alan Kleinman MD PhD

I've given the correct explanation of how rmns works. If you want to claim that this mechanism of genetic transformation can make reptiles grow feathers, fish turn into mammals and create eyes, you would once again be wrong.

[Alan Kleinman MD PhD]

Well said. And what makes selection random is multiple selection pressures acting simultaneously on a population. For example, some members of a population are selected out by starvation, others by thermal stress, others by predation,... This leads to a far more complex evolutionary trajectory that is multiplicatively more difficult to adapt to. If the combined selection pressures don't drive the population to extinction, the only thing the population can do is drift. This is what hiv is doing to the combination selection pressures used to treat this virus.

[Alan Kleinman MD PhD]

On Thursday, October 4, 2018 at 9:25:03 AM UTC-7, John Harshman wrote:
> On 10/4/18 6:35 AM, MarkE wrote:
>
> > However, regardless of that, my own assessment of scientific evidence
> > leaves me to view naturalistic explanations for the following as
> > unsatisfactory.
>
> Do you find supernatural explanations satisfactory? If so, why?

Do you find mathematically irrational explanations satisfactory? If so, why? What is pathetic about you John is that you have a PhD in evolutionary biology yet have no understanding of the mechanisms of genetic transformation.

[Alan Kleinman MD PhD]

On Thursday, October 4, 2018 at 10:15:03 AM UTC-7, Bob Casanova wrote:
> On Wed, 3 Oct 2018 12:47:19 -0700 (PDT), the following
> appeared in talk.origins, posted by Alan Kleinman MD PhD

> :
>
> >On Wednesday, October 3, 2018 at 12:30:02 PM UTC-7, Bob Casanova wrote:
> >> On Wed, 3 Oct 2018 08:41:15 -0700 (PDT), the following
> >> appeared in talk.origins, posted by Alan Kleinman MD PhD
> >> :
> >>
> >> >...natural selection can't make an eye
> >>
> >> So, since multiple types of eyes exist, why don't you
> >> explain where each came from? Or even *one* type,
> >> cephalopods, for instance?
> >>
> >> And BTW, "It wasn't by X" isn't an explanation, nor is any
> >> reference to Kishony or Lenski, or to your "paper".
>
> >I've explained correctly how natural selection works, both for rmns and random recombination. Just because you don't have the skill or training to understand the correct explanation, don't blame me. Next time don't sleep through your two courses in statistics. Now if you think that natural selection created all the different types of eyes, turn on a light and you do the work, dimmy.
>
> So you can't explain it, and can only post more
> irrelevancies and ad hominems in a futile attempt to
> disguise your incompetence? OK.

My level of competence is to correctly explain how rmns works. dimmy, you don't have the competence to understand this explanation. I can tell you with mathematical certainty that rmns can't make reptiles grow feathers, turn fish into mammals and make eyes.

[MarkE]

Let me guess - you’ve just read How to Win Friends and Influence People?

[Oxyaena]

On 10/5/2018 9:33 AM, MarkE wrote:
> Let me guess - you’ve just read How to Win Friends and Influence People?
>

This is how I know you're not sincere at wanting to learn, for if you
were you wouldn't be such a dishonest coward by snipping what I wrote
and then making a flippant remark. Why are there no *honest*
creationists anymore?

[Mark Isaak]

https://www.thegunnysack.com/wp-content/uploads/2018/06/Boiled-Corn-On-The-Cob-Recipe.jpg

[MarkE]

Yes with with qualifications. The relationship between micro and macroevolution is a large part of the debate, with no simple answer, but here’s an example: https://evolutionnews.org/2018/05/more-on-alien-octopi-new-paper-admits-failure-of-evolution-to-explain-life/

[Alan Kleinman MD PhD]

On Friday, October 5, 2018 at 8:55:04 AM UTC-7, MarkE wrote:
> Yes with with qualifications. The relationship between micro and macroevolution is a large part of the debate, with no simple answer, but here’s an example: https://evolutionnews.org/2018/05/more-on-alien-octopi-new-paper-admits-failure-of-evolution-to-explain-life/

There is a simple answer MarkE. Microevolutionary steps are linked by the multiplication rule of probabilities. You probably don't understand the ramifications of this.

[Alan Kleinman MD PhD]

Apparently, they didn't teach you this in your graduate-level course in population genetics:
https://blog.nationalgeographic.org/2009/03/23/corn-domesticated-from-mexican-wild-grass-8700-years-ago/
That's not rmns, that's recombination and selection (also called breeding).

[John Harshman]

You need to stop citing creationist web sites. They don't tend to
correctly interpret the science they're reporting on. Nor is there a
debate within science that involves creationist web sites.

[MarkE]

Something like this?

Pmacro = P1micro x P2micro x ... Pnmicro

If Pmicro << 1, Pmacro is << 1 to the nth power

[Alan Kleinman MD PhD]

Elmer Fudd thinks he's the only one who can correctly interpret data. Why don't you interpret the Kishony experiment for us.

[Alan Kleinman MD PhD]

Good! So how does natural selection improve the probability of a particular Pmicro occurring?

[Oxyaena]

On 10/5/2018 11:51 AM, MarkE wrote:
> Yes with with qualifications. The relationship between micro and macroevolution is a large part of the debate, with no simple answer, but here’s an example: https://evolutionnews.org/2018/05/more-on-alien-octopi-new-paper-admits-failure-of-evolution-to-explain-life/
>
>

If you rely on "Evolution News" then you automatically lose the
argument, see Scopie's Law for more, and we *do* know how octopi came
about, they evolved from snail-like ancestors and lost their outer
shells sometime in the mid-Mesozoic, but I wouldn't expect *you* to know
that.

[Oxyaena]

You read my mind. I invoke Scopie's Law for this.

[zencycle]

On Friday, October 5, 2018 at 11:55:04 AM UTC-4, MarkE wrote:
> Yes with with qualifications. The relationship between micro and macroevolution is a large part of the debate, with no simple answer, but here’s an example: https://evolutionnews.org/2018/05/more-on-alien-octopi-new-paper-admits-failure-of-evolution-to-explain-life/

So Mark, did you read the paper that the evolution.org article links to? It's here:

https://www.sciencedirect.com/science/article/pii/S0079610718300798

First off, the evolution.org article completely mischaracterizes the paper it references (no surprise there). The article states "In fact, the complexity and sophistication of life cannot originate from non-biological matter under any scenario, over any expanse of space and time, however vast."

The paper makes no such claim, nor even the implication.

The paper is making the claim that there is a reasonable amount of evidence to suggest that organic molecules were seeded extraterrestrially - panspermia. It makes the claim that abiogenesis has no evidential support - this of course is blatantly false (and pay no attention to alan kleinman).

The paper makes a few serious errors, much like a 'god of the gaps argument', such as here :

"The transformative genes leading from the consensus ancestral Nautilus (e.g. Nautilus pompilius) to the common Cuttlefish (Sepia officinalis) to Squid (Loligo vulgaris) to the common Octopus (Octopus vulgaris, Fig. 5) are not easily to be found in any pre-existing life form – it is plausible then to suggest they seem to be borrowed from a far distant “future” in terms of terrestrial evolution, or more realistically from the cosmos at large."

So, because we have no transitional evidence, it's impossible that transitional creatures ever existed, therefore, space octopi. Hmmmmm.

There'a a lot more evidence out there, Mark, you just have to be ready to view it with an open mind.

[John Harshman]

Do we know that? Highly dubious. First, what do you mean by
"snail-like"? Second, how do you know when octopus ancestors lost their
shells? I think you are way over-interpreting the meager data.

[Alan Kleinman MD PhD]

You know who octopi came about? And you know how mammals came about? And you know how reptiles turn into birds? You are a blithering idiot who does not understand the simplest principles of genetic transformation. But I should not blame you when PhD evolutionary biologists like Elmer Fudd knows no better.