35,000,000,000,000

[MarkE]

That's an estimate of the number of cells in the human body.

Apologies for labouring this point, but here's a different angle, in search of answers as yet not forthcoming.

An adult human is a highly integrated, autonomous, functional system. The human brain is recognised as "the most complex object known."

A single cell (the fertilised ovum) becomes 35,000,000,000,000 cells...including the most complex object known.

That's 100 times the number of stars in our galaxy.

It's the ultimate rabbit-out-of-a-hat trick.

This is not an argument from incredulity, or god of the gaps. It seems the 'gap' is only widening as science probes the alien intricacy of embryological development.

Belief that the blunt instrument of natural selection alone can explain this phenomonen is, starkly, a leap of faith.

References:

"Foremost among the unresolved problems confronting modern biology is the origin of biological complexity, most notably that of the shape and form of our own bodies."
http://www.sciencedirect.com/science/article/pii/S0079610716300542

'According to physicist, Roger Penrose, What’s in our head is orders of magnitude more complex than anything one sees in the Universe: "If you look at the entire physical cosmos," says Penrose, "our brains are a tiny, tiny part of it. But they're the most perfectly organized part. Compared to the complexity of a brain, a galaxy is just an inert lump." Each cubic millimeter of tissue in the neocortex, reports Michael Chorost in World Wide Mind, contains between 860 million and 1.3 billion synapses. Estimates of the total number of synapses in the neocortex range from 164 trillion to 200 trillion. The total number of synapses in the brain as a whole is much higher than that. The neocorex has the same number of neurons as a galaxy has stars: 100 billion. One researcher estimates that with current technology it would take 10,000 automated microscopes thirty years to map the connections between every neuron in a human brain, and 100 million terabytes of disk space to store the data.'
http://www.dailygalaxy.com/my_weblog/2015/12/human-brain-intelligence-networks-identified-.html

[MarkE]

PS

“[the zygote is] a few thousand genes and proteins, none of which can possibly hold any concept, in any language, of the structure and function of a human body....”
--"Life Unfolding: How the human body creates itself" by Jamie A. Davies

[MarkE]

PPS

Just to flesh out those 3.5x10^13 cells, fhe main systems of the human body are:

1.        Cardiovascular / Circulatory system:
- Circulates blood around the body via the heart, arteries and veins,        delivering oxygen and nutrients to organs and cells and carrying their waste products away.

2.        Digestive system / Excretory system:
- Mechanical and chemical processes that provide nutrients via the mouth, esophagus, stomach and intestines.
- Eliminates waste from the body.

3.        Endocrine system:
- Provides chemical communications within the body using hormones.

4.        Integumentary system/ Exocrine system:
- Skin, hair, nails, sweat and other exocrine glands.

5.        Lymphatic system / Immune system:
- The system comprising a network of lymphatic vessels that carry a clear fluid called lymph.
- Defends the body against disease-causing agents.

6.        Muscular system/Skeletal system:
- Enables the body to move using muscles.
- Bones supporting the body and its organs.

7.        Nervous system:
- Collects and processes information from the senses via nerves and the brain and tells the muscles to contract to cause physical actions.

8.        Renal system / Urinary system:
- The system where the kidneys filter blood.

9.        Reproductive system:
- The sex organs required for the production of offspring.

10.        Respiratory system
- The lungs and the trachea that bring air into the body.

11.        Sensory system
- Consists of sensory receptors, neural pathways, and parts of the brain involved in sensory perception.

The human body's cells, tissues, organs, and systems work together in remarkable harmony. Actions as simple as eating a piece of fruit involve numerous systems in complex coordination, whether the nervous system, with impulses traveling up to 248 mph, or the muscular system, with contracting and relaxation of some of the body's 600 muscles, or the endocrine system, involving hormones produced by glands in one part of the body that affect select cells with the correct receptors in other parts of the body. Should one organ or system of the body falter in performing its function, the entire body is affected. There are over 250 different kinds of cells in the human being (Baldi 2001) and Fukuyama (2002) states there are approximately 100 trillion cells in the average adult (although other sources list estimates of ten trillion or fifty trillion cells). These cells are generally performing 20 diverse reactions at any one time, involving repair, reproduction, communication, waste disposal, and nutrition, and including a purpose that aids the body as a whole. The human eye can distinguish up to one million color surfaces and human hearing is so sensitive it can distinguish hundreds of thousands of different sounds. The liver alone performs 500 different functions, and a square inch of skin contains on the average 650 sweat glands, 20 blood vessels, and more than a thousand nerve endings. The brain has been called "the most developed and complex system known to science" (Davis 1992).

[Bill Rogers]

It's true. There are a huge number of cells in the human body and they interact in complex ways to form organs with complex interacting functions. Within cells, there are huge numbers of different complex molecules that interact in complex ways. The human brain (any brain, really) is a remarkable object. That they are here in good working order, and keep reproducing themselves over millions of years is astounding. So what is your approach to figuring out how it all works and how it all got here?

[RonO]

A blue whale can weigh 190 tons and may have a thousand times the number
of cells as a human, so what?

A mouse has only a couple trillion cells that develop from a single
celled zygote, so what?

A nematode worm like C. elegans has only around 1,000 cells that develop
from the single celled zygote, so what?

We have fossilized embryos over half a billion years old. The Cambrian
started 540 million yeas ago when embryos were still developing into
organisms consisting of just a few thousand cells.

What hat trick is needed to keep building more and more complex
organisms from a single cell zygote. The really hard part seems to have
been creating the single celled zygote and haploid cells from the
zygote. That took billions of years. Some organisms still just have
the single celled diploid version that doesn't develop into more than
single cells and then goes through meiosis to create the single haploid
cells again.

Multicellular animals are most closely related to one lineage of sponge.
That means that there were a lot of sponge like species and one took
the path to us. We all evolved from that lineage whether the taxa are
vertebrates or invertebrates. How does that fit into your design
alternative? Something like a the cordate Amphioxus became a new
tetraploid species (doubled their genome) and evolved into all the
vertebrates that you see, and the doubling of the genome happened around
half a billion years ago.

Put what we know in your model and see what happens. If all you ever do
is muck around with what we do not fully understand, you will just end
up like the bogus and dishonest IDiot/creationists that came before you.

Ron Okimoto

[MarkE]

Bill, I appreciate your acknowledgment of my premise.

What is my approach to figuring out how it all works and how it all got here?

Continue to research this. It's important for better understanding and combating disease for starters.

As this research progresses, it will discover a greater percentage of the genome to be functional. It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.

These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.

Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.

At that point, science hands over to theology.

[Bill Rogers]

On Sunday, February 5, 2017 at 9:34:58 AM UTC-5, MarkE wrote:
> Bill, I appreciate your acknowledgment of my premise.
>
> What is my approach to figuring out how it all works and how it all got here?
>
> Continue to research this. It's important for better understanding and combating disease for starters.

So far, we agree.

>
> As this research progresses, it will discover a greater percentage of the genome to be functional. It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.

That's your prediction. I disagree, but the research needed to determine whether your prediction is correct is the same research I think should be done. So, on a practical level we agree.

>
> These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.

That's your prediction, but I doubt i will come to pass.

>
> Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.

First I'll wait to see whether your prediction about the failure of the theory of evolution comes true. Then if the theory of evolution turns out not be be right, I'll be expecting research to look for alternate theories that explain everything that the theory of evolution did explain AND whatever things that, hypothetically, it did not.

I'd be happy to consider specific, testable theories about a designer. A generalized, non-specified designer can explain any and all evidence, though, so it's not really a testable notion. If that's what you want, there's no need to wait for some predicted failure of evolution. Just plant the flag and say that a designer is responsible.

[Robert Camp]

On 2/5/17 4:15 AM, MarkE wrote:
> That's an estimate of the number of cells in the human body.
>
> Apologies for labouring this point, but here's a different angle, in
> search of answers as yet not forthcoming.
>
> An adult human is a highly integrated, autonomous, functional system.
> The human brain is recognised as "the most complex object known."
>
> A single cell (the fertilised ovum) becomes 35,000,000,000,000
> cells...including the most complex object known.
>
> That's 100 times the number of stars in our galaxy.

Let's consider the above observations,

- the human brain is very complex, possibly the "most" complex thing
known (this becomes less impressive when one considers both that we
don't know how complex everything else is, and that there must be
something that is the "most" complex thing known).

- there are oodles of cells in the human body, the numbers are difficult
for the human brain (you know, that "most" complex thing) to grasp, thus
they seem "unnatural" somehow.

- there are fewer stars in our galaxy (than cells in the brain), but
clearly there are a lot more galaxies out there, so the import of this
is quite lessened.

Now, it seems to me that these observations rely on facile comparisons
(stars in our galaxy), incredibly large numbers, and lofty conclusions
("most complex").

I look at these supposedly mind-boggling (in some metaphysically
important way, no less) ideas and wonder at the inherent assumptions.
What is it about the complexity of the human brain that seems so
meaningful to you? Is it that "most complex" business? If so, what if we
discovered or invented a more complex machine, does that immediately
change your attitude about what human brain complexity implies?

And why do you suppose that our inability to comprehend large numbers
suggests something metaphysically important about those things? What
reference do you use to tell you that 35 trillion is so big a number
that it must mean something above and beyond the simple fact?

> It's the ultimate rabbit-out-of-a-hat trick.

It obviously seems so to you. I see no reason or evidence that points to
such a conclusion.

> This is not an argument from incredulity, or god of the gaps.

It is clearly exactly those things - an argument from incredulity and a
gap argument.

> It seems the 'gap' is only widening as science probes the alien
> intricacy of embryological development.

One who does not invest these kind of observations with so much a priori
wishful thinking recognizes that gaps in our knowledge widen and narrow
all the time as new discoveries are made and research pushes into those
areas.

> Belief that the blunt instrument of natural selection alone can
> explain this phenomonen is, starkly, a leap of faith.

No one is walking around making metaphysical claims that NS can explain
anything and everything. Biologists do research, see how new data
comports with current theory, revise the theory as needed, and consider
the next step.

"Leap of faith?" The plank in your eye is huge (above, you outright deny
making the arguments you very clearly *are* making), and you appear to
be oblivious to it.

[Jonathan]

Why do the equally countless molecules in the universe
organize into equally wondrous stars, solar systems
and galaxies?

Answer: there is a mysterious, invisible, all pervasive
guiding force that gives everything a goal or a purpose
to organize.

It's called gravity of course. And it follows a very
simple inverse square law.

With life it's quite the same, on a different level of
complexity hierarchy of course. But with life there's
also an invisible, mysterious, all pervasive guiding
force that gives life a goal or purpose to organize.

It's called emergence, and it follows an equally simple
power law, which is very nearly the same as an
inverse square law.

Go ahead and keep bashing everything into little bitty
pieces cave-man reductionist style, you won't find
the universal laws of there in the crumbs.



The Universal Laws of Nature

The Hidden Power Laws of Ecosystems
As nature scales, complexity gives way to universal law.
http://nautil.us/issue/29/scaling/the-hidden-power-laws-of-ecosystems


THE ROYAL SOCIETY
The fractal nature of nature: power laws, ecological
complexity and biodiversity

aBSTRACT

Underlying the diversity of life and the complexity of ecology
is order that re flects the operation of fundamental physical
and biological processes. Power laws describe empirical
scaling relationships that are emergent quantitative features
of biodiversity.

These features are patterns of structure or dynamics that
are self-similar or fractal-like over many orders of magnitude.
Power laws allow extrapolation and prediction over a wide range
of scales. Some appear to be universal, occurring in virtually
all taxa of organisms and types of environments. They offer clues
to underlying mechanisms that powerfully constrain biodiversity.

We describe recent progress and future prospects for understanding
the mechanisms that generate these power laws, and for explaining
the diversity of species and complexity of ecosystems in terms
of fundamental principles of physical and biological science.
Keywords: biodiversity; ecology; fractal; power l
http://www.fractal.org/Bewustzijns-Besturings-Model/Fractal-Nature.pdf



Even Dickinson knew a century and a half ago that a gravity like
relationship was behind the creation of life. She knew that
the persistent competition among opposites cause the system
to evolve towards it's ideal form.

She knew the environment, or natural selection merely
fine-tunes what the internal emergent forces create.

She knew all the basics of modern self organizing theory, aka
complexity science, a century and a half ago.

What's your excuse?






Growth of Man -- like Growth of Nature
Gravitates within
Atmosphere, and Sun endorse it
But it stir -- alone

Each -- its difficult Ideal
Must achieve -- Itself
Through the solitary prowess
Of a Silent Life

Effort -- is the sole condition
Patience of Itself
Patience of opposing forces
And intact Belief

Looking on -- is the Department
Of its Audience
But Transaction -- is assisted
By no Countenance

[Jonathan]

The rules for self organization are exceedingly simple.

The 'rules-of-operation' for the components
must be critically interacting with their
'freedom-of-interaction'.



For a democracy or a healthy society to emerge:

The 'rules of operation' are represented by a strong constitution.
The 'freedom of interaction' are represented by a bill of rights.


For evolution, creation and life to emerge:

The 'rules of operation' are represented by genetics.
The 'freedom of interaction' are represented by natural selection.


For a universe to emerge:

The 'rules of operation' are represented by a gravity
The 'freedom of interaction' are represented by a
cosmic expansion or perhaps inertia.


For an idea to emerge:

The 'rules of operation' are represented by facts.
The 'freedom of interaction' are represented by imagination.



One example each from the 'unique' and broad realms of
physical systems, living, society and mind.



When those 'opposites' in possibility are critically
interacting with each other, so that like light which
is perceived as dominant depends on the...observer
then the whole can become more than it's sum, and
creation and evolution emerges.'

There can be no single or ultimate objective explanation
for life, there will always be at least two coequal
causes which can only be subjectively observed.

There is no such thing as an objective reality.



s

[RonO]

On 2/5/2017 8:25 AM, MarkE wrote:
> Bill, I appreciate your acknowledgment of my premise.
>
> What is my approach to figuring out how it all works and how it all got here?
>
> Continue to research this. It's important for better understanding and combating disease for starters.

This is nice. A lot of IDiots claim that it isn't worth studying how
everything evolved because the Designer did it and we will never know
how. It is their excuse for not looking for what they need in order to
make that claim. How do you know that you will know what evidence you
are looking for? Smaller and smaller areas of the unknown knowledge
isn't going to be anything worth waiting for.

>
> As this research progresses, it will discover a greater percentage of the genome to be functional. It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.

All the genome is functional if only to hold the other bits together. I
hate to break this news to you, but people have been looking for gene
regulatory sequences and predicting that they are in the DNA between
coding sequences for over half a century. It shouldn't be a surprise
that we are still discovering these regulatory sequences. We have made
great strides in learning more about them in the last 15 years of
genomic technology, but the bait and switch still goes down, so that
obviously hasn't meant much for IDiocy?

Alien intricacy? I hate to tell you this, but when you check these
regulatory sequences have been evolving in the lifeforms on earth for
billions of years. Do you know why Behe doesn't claim any IC systems
for the divergence of chimps and humans or any terrestrial vertebrate?
The regulation that you expect to find will obviously have been working
and evolving in lifeforms for a very long time and the same regulatory
mechanisms are found from mice to men.

What do you intend to do while waiting to find this out? You can
already check what I've told you and determine reality for yourself.

>
> These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.

Unfortunately for you, you don't have a clue as to what the limits are,
so when do you think that you will recognize them? Dembski and Behe
have put up their claims, but nothing has panned out and they never
verified that any such systems exist. What did IC, CSI, SC, and the
fourth law of thermodynamics amount to, and what do you have to replace
them?

>
> Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.

How can you make a statment like this when systems that could be claimed
to be irreducibly complex (systems with multiple dependent interacting
parts) were predicted to occur the way organisms were expected to have
evolved? What functional complexity do you think is impossible to
evolve? It isn't IC because Behe hasn't even determined if his type of
IC exists in nature.

Take the flagellum. Minnich did some work and used a decades old
technique to determine some of the parts of the flagellum. He used
knock out mutations to determine what genes were associated with the
function of the flagellum. About last thing that I found about that
research was taking some of the parts of the flagellum that he had
identified and determining how they were relatied. He compared the
protein sequences and created a phylogeny of the proteins. They had
obviously evolved by gene duplication over a very long period of time.
They even concluded that the order of the evolution of the proteins made
sense when the way that the flagellum is made was taken into
consideration. Minnich stopped that type of work, but what does that
tell you about your design? The flagellum may have evolved around 2
billion years ago. From the sequences of the parts it looked like it
took tens of millions of years to evolve the parts that Minnich looked at.

As more of this type of work gets done (apparently not by IDiots) and
more is learned about the evolution of these things what are you going
to look for?

>
> At that point, science hands over to theology.

Unfortunately such a point is so far into the future that it isn't worth
contemplating. You obviously do not know what you are talking about. A
lot of Theological questions will be the last unanswered questions
because Science can't address them. You have to wait until we
understand all of nature before that happens. You have a very long time
to wait.

Some theology has already been addressed by science and the theology
changed. We are no longer the center of the universe and god or the
gods do not pull the sun and moon across the sky. Newton was born the
year Galileo died under house arrest and Newton's work ended the church
burning people to death for claiming otherwise. It was likely the
biggest theological hit religion has taken. Biological evolution isn't
much by comparison. I don't think anyone was ever burned at the stake
for thinking that lifeforms could evolve. The earth is obviously older
than some theologies want it to be. There was never a world wide flood.
The germ theory of disease makes designer did it plaques a part of
history and a new type of designer plaques a possibility. Even IDiots
like Behe and Denton accept biological evolution as a fact of nature.
Eddies brand of creationists have gone from YEC to OEC. They used to
believe that each day of creation was 7,000 years long, but now the
length of a day could be billions of years long. Not only that, but
they claim that the sun and moon were not created on the fourth day like
the Bible says, but they were present at the beginning of the earth.

So what is going to happen to your theology by the time science has the
answers?

Ron Okimoto
>

[MarkE]

Ron, you're already in the sin-bin for talking and not listening. If this dry-retching of ID diatribe continues it'll be a red card.

[MarkE]

Robert, I’m picturing you in a dark, boozy cabaret, sitting with your pals around a table at the back of the room, and heckling the magician who has just pulled a rabbit out of his hat. You've got the crowd on your side at this point. He proceeds to extract a dozen more rabbits, but you only up the taunts. Then come dogs, cats, and an A to Z of animals, in their millions, all assembling on a nearby plain for a sublimely choreographed performance of The Lion King. You’re sitting there alone, still shouting for a refund, but everyone else including your friends have long since left to enjoy the spectacle.

But here's the real problem. I'm not saying gee-whiz isn't 35 trillion a big number. I'm saying it's a big *ratio*. A mind-boggling ratio. Somehow, that single cell, whose contents give no clue of the universe within, explodes into unmatched complexity and function.

> > It's the ultimate rabbit-out-of-a-hat trick.
>
> It obviously seems so to you. I see no reason or evidence that points to
> such a conclusion.
>
> > This is not an argument from incredulity, or god of the gaps.
>
> It is clearly exactly those things - an argument from incredulity and a
> gap argument.

There are two kinds of incredulity. One is due to ignorance or lack of imagination, leading to a probability underestimate.

The other is used by science all the time. Dawkins puts it this way: "we can accept a certain amount of luck in our explanations, but not too much." Too much, and others will rightly be incredulous.

This instance appropriately calls for the latter. I'm not suggesting it's an outright refutation, but at least a very large red flag.

To reflexively downplay and dismiss the potential significance and implications of this evidence is to protect materialism irrespective. Or you don't really get what we're looking at here?

> > It seems the 'gap' is only widening as science probes the alien
> > intricacy of embryological development.
>
> One who does not invest these kind of observations with so much a priori
> wishful thinking recognizes that gaps in our knowledge widen and narrow
> all the time as new discoveries are made and research pushes into those
> areas.
>
> > Belief that the blunt instrument of natural selection alone can
> > explain this phenomonen is, starkly, a leap of faith.
>
> No one is walking around making metaphysical claims that NS can explain
> anything and everything. Biologists do research, see how new data
> comports with current theory, revise the theory as needed, and consider
> the next step.

What naturalistic explanation is there, apart from NS, to explain an accumulation of functional complexity, even the most complex object known?

Dawkins again: "Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning."

[RonO]

Run away in denial. Denial is all IDiots have and you know it. I have
just demonstrated that what you are doing is what the ID perps have been
doing for a couple of decades and all IDiocy is, is a stupid scam that
creationists are running on themselves.

You obviously have to do something different. The same old same old
isn't going to amount to anything.

Do something that the ID perps never tried. Actually try to figure out
if there is any science that you can actually do. Science isn't just
sitting around and making baseless claims. The hard part is
verification of those claims. If you can't figure out any way to verify
them except to claim that some one else in the future will figure it out
you aren't doing any science today. You might as well wait and see how
it all turns out.

Why not do the sensible thing and put up your model of creation and try
to figure out if there is anything that you can do to verify any parts
of it? That isn't a trap. If you want to know if your model is valid
you have to verify it somehow. The only reason the ID perps don't do
that is because they already know that the answers are not what they
want. That is how sad the ID scam is at this time.

Why don't IDiots persue such research? What is the draw to keep doing
nothing except make assertions that you can't back up as meaning
anything to IDiocy?

Ron Okimoto

[Burkhard]

Well, drift for instance. Or they are the result of culture and similar
non-inheritable forces.

[Robert Camp]

Here's the distinction which obviates your analogy: a magic show is
about entertainment, the scientific enterprise is about revealing valid
data about the natural world. What that means, in the case of the
former, is that it's okay (in fact encouraged) for people to bring along
a willingness to accept extravagant assumptions up front. In the case of
the latter, people need to divest their reasoning of unwarranted
assumptions if they are to be successful.

> Then come dogs, cats, and an A
> to Z of animals, in their millions, all assembling on a nearby plain
> for a sublimely choreographed performance of The Lion King.

I have mentioned before that you seem to have trouble eliminating
assumed conclusions from your analogies. This one is quite the whopper.
It may be that your intention was to include a bit of self-parody here,
and if so then well done. If not, you really need to re-examine your
thought processes.

> You’re
> sitting there alone, still shouting for a refund, but everyone else
> including your friends have long since left to enjoy the spectacle.

This canard is getting a bit long in the tooth. Can't we all agree that
the, "Oh, you're too literal and detached to recognize the "magic" of it
all" trope is an unworthy approach?

> But here's the real problem. I'm not saying gee-whiz isn't 35
> trillion a big number. I'm saying it's a big *ratio*. A mind-boggling
> ratio. Somehow, that single cell, whose contents give no clue of the
> universe within, explodes into unmatched complexity and function.

It seemed to me that "isn't 35 trillion a big number" was exactly what
you were saying, but we can move on. So let me ask, how about 70
trillion cells from a single fertilized egg (in the case of identical
twins)? Is that twice as mind-boggling? Does that constitute twice the
compelling argument against natural selection? How about the notion that
bacteria can achieve the same ratios, does the fact that they're not
human diminish that feat?

The obvious point here is that these are all mere facts of nature. That
you choose to be boggled by them is much more a reflection of your own
assumptions and proclivities than anything inherent in those facts.

And choosing to believe that in making this observation I am somehow
inured to the wonder of nature is also a reflection of your
proclivities, but not in a good way.

>>> It's the ultimate rabbit-out-of-a-hat trick.
>>
>> It obviously seems so to you. I see no reason or evidence that
>> points to such a conclusion.
>>
>>> This is not an argument from incredulity, or god of the gaps.
>>
>> It is clearly exactly those things - an argument from incredulity
>> and a gap argument.
>
> There are two kinds of incredulity. One is due to ignorance or lack
> of imagination, leading to a probability underestimate.
>
> The other is used by science all the time. Dawkins puts it this way:
> "we can accept a certain amount of luck in our explanations, but not
> too much." Too much, and others will rightly be incredulous.

And in using that metric one must understand enough about the
observations being explained to know how much "luck" in involved or can
be accepted. My continued point is that you've imputed a judgement of
"too much luck" to a situation about which you simply don't have the
information to make that claim.

> This instance appropriately calls for the latter. I'm not suggesting
> it's an outright refutation, but at least a very large red flag.

I'm sorry. I don't see a red flag. I still just see incredulity.

> To reflexively downplay and dismiss the potential significance and
> implications of this evidence is to protect materialism irrespective.

The blame game is another unworthy tactic. No one is reflexively
downplaying or dismissing anything. Seems to me that what is happening
is (once again) you don't recognize all of the assumed conclusions with
which you invest your argument.

> Or you don't really get what we're looking at here?

So we can now add "You just don't get it" to the list of disappointing
equivocations. It would be much better if you just stick to explaining
your arguments. For example, I'm still waiting to hear specific claims
that don't just reduce to incredulity.

>>> It seems the 'gap' is only widening as science probes the alien
>>> intricacy of embryological development.
>>
>> One who does not invest these kind of observations with so much a
>> priori wishful thinking recognizes that gaps in our knowledge widen
>> and narrow all the time as new discoveries are made and research
>> pushes into those areas.
>>
>>> Belief that the blunt instrument of natural selection alone can
>>> explain this phenomonen is, starkly, a leap of faith.
>>
>> No one is walking around making metaphysical claims that NS can
>> explain anything and everything. Biologists do research, see how
>> new data comports with current theory, revise the theory as needed,
>> and consider the next step.
>
> What naturalistic explanation is there, apart from NS, to explain an
> accumulation of functional complexity, even the most complex object
> known?

Why "apart from NS"? Do you have evidence that something more is required?

In any case, there are other possible mechanisms (Burkhard has offered
one). But the important question here is, do you imagine the current
lack of a natural explanation (were this true) would somehow constitute
evidence for a non-natural explanation? If so, this is quite the logical
fallacy.

> Dawkins again: "Yet the living results of natural selection
> overwhelmingly impress us with the appearance of design as if by a
> master watchmaker, impress us with the illusion of design and
> planning."

Indeed. I happen to disagree with Dawkins on this point. I don't believe
the results of natural selection demonstrate even "the illusion" of
design, regardless of whether by a master or a simpleton. The results of
natural selection impress me with the appearance of a wasteful,
endlessly iterative, often brutal process that results in both beauty
and blight, but not the slightest hint of deliberation or intent.

But understand Dawkins' point here: in noting that people perceive an
illusion of design, he's saying that we're mistaking the design sense of
patterns for the design sense of purposeful agency. He's saying this is
something with which we (as a result of our evolutionary history of
pattern-detection) confound our observations - not something we actually
discover in nature.

So while I don't agree with how Dawkins expresses the idea, I do agree
with the final analysis, and it is one that lends no authority or
consequence to "theories" of Intelligent Design.


<snip>

[Peter Nyikos]

On Sunday, February 5, 2017 at 9:34:58 AM UTC-5, MarkE wrote:
> Bill, I appreciate your acknowledgment of my premise.
>
> What is my approach to figuring out how it all works and how it all got here?
>
> Continue to research this.

As should evolutionary theorists. By the way, I've come to realize
just how ambiguous that creationist catchword, "Darwinism" is. Depending
on the context [which may include a shell game between the various meanings]
it can either mean:

1. The naked fact that we vertebrates have evolved from a common ancestral
species, and the highly defensible hypothesis that all earth life is
descended from prokaryotes. [The logical alternative to creationism
in the sense of creation of species *de novo*.]

2. Modern evolutionary theory, a part of theoretical biology. [The logical
alternative to "ID theory".]

3. The philosophical/religious belief that abiogenesis and evolution
of life all happened without supernatural intervention.

> It's important for better understanding and combating disease for starters.

That's part of population genetics. Creationists have no problem with
that, and that includes that ideological purist, the "species immutabilist"
Ray Martinez.

I'm in the process of trying to find out how much of modern evolutionary
theory is dependent on wild extrapolations from population genetics.
I'm having a hard time finding out because anti-ID types favor the
ambiguous term "evolutionary biology." Depending on the context,
it could mean:

A. Population genetics.

B. The modern synthesis, which includes A.

C. Evidence that evolution has taken place, in the sense of 1. above.

> As this research progresses, it will discover a greater percentage of the genome to be functional.

Yes, and NOT just in the sense of coding for proteins, or the more general
sense of coding for RNA.

> It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.
>
> These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.

Here is another source of ambiguity. "Natural selection" is used by most
anti-ID types in the strictly population-genetics sense. But I think most
laymen think of it as the grand pageant of "origin of species" on the
one hand and extinction on the other. The mass extinctions of the distant
past exerted a profound influence on evolution by "naturally selecting"
certain orders and families to go extinct and others to survive. We humans
have "naturally selected" untold numbers of species to go extinct,
including so much of the megafauna of the Pleistocene.

> Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.

It is safe for you to say that at the present time because evolutionary
theory is still in its embryonic state ("infancy" would be too generous
a description). Thus, Bill Rogers is overly complacent in expecting
you to challenge evolutionary theory before being willing to entertain
arguments for ID. There is really very little in the way of concrete
results for anyone to challenge.

> At that point, science hands over to theology.

I often wonder how much of the behavior of anti-ID types is fueled either
by atheism or belief in what is inappropriately called "theistic evolution"
and should be renamed "deistic evolution" because it dogmatically
adheres to meaning 3. of "Darwinism" above.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

On Sunday, February 5, 2017 at 9:45:00 AM UTC-5, Bill Rogers wrote:

> First I'll wait to see whether your prediction about the failure of the theory of evolution comes true.

When you say "the theory of evolution" do you mean the present state of
evolutionary biology theory, known as "the modern synthesis"? Or do you
mean the naked fact of common descent? [See my reply to Mark E for more
on this.]

>Then if the theory of evolution turns out not be be right, I'll be expecting research to look for alternate theories that explain everything that the theory of evolution did explain.

What exactly does the modern synthesis adequately explain? Some red herrings:

1. Bacterial resistance to antibiotics is part of population genetics and
irrelevant to any real bone of contention between the conflicting claims of
ID and anti-ID.

2. The existence of transitional forms like *Ambulocetus* and *Tiktaalik*
requires no evolutionary theory, but only the naked fact of common descent
and the common sense observation that evolution doesn't proceed by the
production of "hopeful monsters" that differ radically in morphology
from the creatures giving them birth.

> AND whatever things that, hypothetically, it did not.

Does evolutionary theory predict the vast disparity of earthly biota?
Just how does it do that? How does it even account for there being
anything more sophisticated than prokaryotes, which monopolized earth
for what is believed to be the greater part of the history of earthly
biota?

> I'd be happy to consider specific, testable theories about a designer.
> A generalized, non-specified designer can explain any and all evidence,
> though, so it's not really a testable notion.

And a generalized, non-specified evolutionary theory can do the same,
with the same drawback.

But there do exist testable ID hypotheses. One that ID theorists
have largely neglected (because of the nature of their book-buying
audience) is the Crick-Orgel theory of Directed Panspermia.

If planet after planet is found with life, but that life invariably
turns out to have essentially the same genetic code as earth life,
then some form of panspermia would be the only tenable explanation for
the beginning of life ON EARTH,and directed panspermia -- seeding of
earth by intelligent extraterrestrials -- would probably win out
over the undirected kind because of the vast interstellar distances
and hostile interstellar environment.

Another testable, albeit farfetched, ID hypothesis that also does not involve
supernatural designers reads like pulp science fiction; and that may be
why ID theorists never mention it -- whereas directed panspermia does get
a brief mention in _Darwin's Black Box_ -- they are misrepresented enough
as it is.

It is that alien colonists, after drastically sterilizing earth of its
indigenous organisms (all microorganisms), brought some of their own
creatures with them -- prokaryotes, protists, algae, sea creatures
to populate the waters of the earth -- so as to colonize it.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

Univ. of South Carolina
http://people.math.sc.edu/nyikos/

[John Harshman]

On 2/6/17 11:54 AM, Peter Nyikos wrote:

> It is that alien colonists, after drastically sterilizing earth of its
> indigenous organisms (all microorganisms), brought some of their own
> creatures with them -- prokaryotes, protists, algae, sea creatures
> to populate the waters of the earth -- so as to colonize it.

An interesting theory. How would one test it? I would assume that it
would be tested from the fossil record, and we would expect some major
point of discontinuity in that record, pre-sterilization and
post-sterilization. I don't see such a thing. Do you have a candidate?

[John Harshman]

On 2/6/17 11:06 AM, Peter Nyikos wrote:
> On Sunday, February 5, 2017 at 9:34:58 AM UTC-5, MarkE wrote:
>> Bill, I appreciate your acknowledgment of my premise.
>>
>> What is my approach to figuring out how it all works and how it all got here?
>>
>> Continue to research this.
>
> As should evolutionary theorists. By the way, I've come to realize
> just how ambiguous that creationist catchword, "Darwinism" is. Depending
> on the context [which may include a shell game between the various meanings]
> it can either mean:
>
> 1. The naked fact that we vertebrates have evolved from a common ancestral
> species, and the highly defensible hypothesis that all earth life is
> descended from prokaryotes. [The logical alternative to creationism
> in the sense of creation of species *de novo*.]
>
> 2. Modern evolutionary theory, a part of theoretical biology. [The logical
> alternative to "ID theory".]
>
> 3. The philosophical/religious belief that abiogenesis and evolution
> of life all happened without supernatural intervention.
>
>> It's important for better understanding and combating disease for starters.
>
> That's part of population genetics. Creationists have no problem with
> that, and that includes that ideological purist, the "species immutabilist"
> Ray Martinez.

Ray actually has huge problems with population genetics. He doesn't
think there are any natural processes, for example. And many other
creationists have problems too. That's why they keep attacking the
peppered moth case, for example. Of course very few creationists have
any real understanding even of the basics of population genetics. That's
why they keep claiming that if most mutations are deleterious there can
be no evolution.

> I'm in the process of trying to find out how much of modern evolutionary
> theory is dependent on wild extrapolations from population genetics.

What sort of wild extrapolations did you have in mind here?

>> As this research progresses, it will discover a greater percentage of the genome to be functional.
>
> Yes, and NOT just in the sense of coding for proteins, or the more general
> sense of coding for RNA.

I doubt that much more of the human genome will be found to be
functional than is known to be now, but certainly a fair proportion of
the currently known functional DNA in the human genome doesn't code for
protein and isn't transcribed into functional RNA. No surprises there.

>> It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.
>>
>> These findings will become increasingly incompatible with the
>> limits of natural selection (especially as the selectionist
>> paradigm continues to be eroded by neutral theory, CNE, etc).
>> Natural selection will be shown to be an inadequate explanation.

> Here is another source of ambiguity. "Natural selection" is used by most
> anti-ID types in the strictly population-genetics sense. But I think most
> laymen think of it as the grand pageant of "origin of species" on the
> one hand and extinction on the other. The mass extinctions of the distant
> past exerted a profound influence on evolution by "naturally selecting"
> certain orders and families to go extinct and others to survive. We humans
> have "naturally selected" untold numbers of species to go extinct,
> including so much of the megafauna of the Pleistocene.

I'm with you there. Extinction and, perhaps, speciation rates, during
mass extinctions and otherwise, have had an influence on the course of
evolution.

>> Since there is no alternative naturalistic explanation for the
>> accumulation of functional complexity (ie Dawkins' "appearance of
>> design"), the only reasonable option will be to infer a designer.

> It is safe for you to say that at the present time because evolutionary
> theory is still in its embryonic state ("infancy" would be too generous
> a description). Thus, Bill Rogers is overly complacent in expecting
> you to challenge evolutionary theory before being willing to entertain
> arguments for ID. There is really very little in the way of concrete
> results for anyone to challenge.

How familiar are you with the literature on evolutionary biology and
evolutionary theory?

>> At that point, science hands over to theology.
>
> I often wonder how much of the behavior of anti-ID types is fueled either
> by atheism or belief in what is inappropriately called "theistic evolution"
> and should be renamed "deistic evolution" because it dogmatically
> adheres to meaning 3. of "Darwinism" above.

Good to know what you wonder about. Should we be interested?

[Peter Nyikos]

On Monday, February 6, 2017 at 3:09:58 PM UTC-5, John Harshman wrote:

Fascinating, how little time it took you to find me, John. The UTC-5
is Eastern Standard time. I've removed the ambiguity in the following
attribution line:

> On 2/6/17 11:54 AM, Pacific Standard Time, Peter Nyikos wrote:

Anyway, it's nice having you on this thread, because it was through
you that I first learned about the way population genetics seems
to be extrapolated all over the place by evolutionary theorists.
More about this in my reply to your second post, the one you
did in reply to my first post.

The first unambiguous evidence of multicellular organisms could be such a point.
What evidence have we that the unicellular organisms that preceded them
had anything like our genetic code? Stromatolite fossils billions of
years old don't give away the secrets of the individuals that produced them,
do they?

Reefs are an interesting parallel. In the last half-billion years there
have been eons where no evidence of reefs has been found, and several
distinct episodes of reef-building activity. And the first one was
by pleosponges, very different from any reef builders of today.

Peter Nyikos

[Peter Nyikos]

On Monday, February 6, 2017 at 3:19:58 PM UTC-5, John Harshman wrote:
> On 2/6/17 11:06 AM, Peter Nyikos wrote:
> > On Sunday, February 5, 2017 at 9:34:58 AM UTC-5, MarkE wrote:
> >> Bill, I appreciate your acknowledgment of my premise.
>>
> >> What is my approach to figuring out how it all works and how it all got here?
>>
> >> Continue to research this.
>
> > As should evolutionary theorists. By the way, I've come to realize
> > just how ambiguous that creationist catchword, "Darwinism" is. Depending
> > on the context [which may include a shell game between the various meanings]
> > it can either mean:
> >
> > 1. The naked fact that we vertebrates have evolved from a common ancestral
> > species, and the highly defensible hypothesis that all earth life is
> > descended from prokaryotes. [The logical alternative to creationism
> > in the sense of creation of species *de novo*.]
> >
> > 2. Modern evolutionary theory, a part of theoretical biology. [The logical
> > alternative to "ID theory".]
> >
> > 3. The philosophical/religious belief that abiogenesis and evolution
> > of life all happened without supernatural intervention.
> >
> >> It's important for better understanding and combating disease for starters.
> >
> > That's part of population genetics. Creationists have no problem with
> > that, and that includes that ideological purist, the "species immutabilist"
> > Ray Martinez.
>
> Ray actually has huge problems with population genetics. He doesn't
> think there are any natural processes, for example.

That's neither here nor there. He has no problems with the external
facts of bacterial resistance, etc. nor the change of frequencies of
alleles over time within a population.

>And many other
> creationists have problems too. That's why they keep attacking the
> peppered moth case, for example.

I fail to follow your reasoning. Part of it is that you don't explain
the form the attacks that you have in mind took. What I've seen are
two forms: 1, the two varieties were always there, so where's the
evidence of evolution? and 2. [the ad hominem form] Like Haeckel, the experimenters committed scientific fraud.

>Of course very few creationists have
> any real understanding even of the basics of population genetics. That's
> why they keep claiming that if most mutations are deleterious there can
> be no evolution.
>
> > I'm in the process of trying to find out how much of modern evolutionary
> > theory is dependent on wild extrapolations from population genetics.
>
> What sort of wild extrapolations did you have in mind here?

For one, the claim that genetic drift and natural selection are
legitimate rivals for the main force in evolution. [See Burkhard's
reply to MarkE and Camp's reply to the same post, backing Burkhard.]

Once you get past the scale of populations, it's a no-brainer:
natural selection wins hands down. See my comments to MarkE below.

> >> As this research progresses, it will discover a greater percentage of the genome to be functional.
> >
> > Yes, and NOT just in the sense of coding for proteins, or the more general
> > sense of coding for RNA.
>
> I doubt that much more of the human genome will be found to be
> functional than is known to be now,

Is this doubt just a WAG, to use a favorite expression of someone we
both know well?

> but certainly a fair proportion of
> the currently known functional DNA in the human genome doesn't code for
> protein and isn't transcribed into functional RNA. No surprises there.

Hindsight is 20/20. Where was the prediction that this would be found
to be the case, before the fact?

> >> It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.
> >>
> >> These findings will become increasingly incompatible with the
> >> limits of natural selection (especially as the selectionist
> >> paradigm continues to be eroded by neutral theory, CNE, etc).
> >> Natural selection will be shown to be an inadequate explanation.
>
> > Here is another source of ambiguity. "Natural selection" is used by most
> > anti-ID types in the strictly population-genetics sense. But I think most
> > laymen think of it as the grand pageant of "origin of species" on the
> > one hand and extinction on the other. The mass extinctions of the distant
> > past exerted a profound influence on evolution by "naturally selecting"
> > certain orders and families to go extinct and others to survive. We humans
> > have "naturally selected" untold numbers of species to go extinct,
> > including so much of the megafauna of the Pleistocene.
>
> I'm with you there. Extinction and, perhaps, speciation rates, during
> mass extinctions and otherwise, have had an influence on the course of
> evolution.

Right, and where is there a comparable role for genetic drift?

> >> Since there is no alternative naturalistic explanation for the
> >> accumulation of functional complexity (ie Dawkins' "appearance of
> >> design"), the only reasonable option will be to infer a designer.
>
> > It is safe for you to say that at the present time because evolutionary
> > theory is still in its embryonic state ("infancy" would be too generous
> > a description). Thus, Bill Rogers is overly complacent in expecting
> > you to challenge evolutionary theory before being willing to entertain
> > arguments for ID. There is really very little in the way of concrete
> > results for anyone to challenge.
>
> How familiar are you with the literature on evolutionary biology and
> evolutionary theory?

Not familiar enough to know whether a hypothesis we discussed in
December was in the mainstream of evolutionary theory, or a naive
extrapolation from it by you.

This was your conjecture that there was plenty of time for an essentially
unique genetic code to become ubiquitous. It was based on an extrapolation
of genetic drift from populations to the biota of an entire planet.

On the day I went on posting break, I posted a detailed rebuttal to
this hypothesis of yours. You never replied -- was this just out of
courtesy, holding back until my return?

> >> At that point, science hands over to theology.
> >
> > I often wonder how much of the behavior of anti-ID types is fueled either
> > by atheism or belief in what is inappropriately called "theistic evolution"
> > and should be renamed "deistic evolution" because it dogmatically
> > adheres to meaning 3. of "Darwinism" above.
>
> Good to know what you wonder about. Should we be interested?

If you want to know where Ken Miller and Ron O are coming from, you
should be interested in the issue of what fuels anti-ID behavior.

Also, you showed so much interest in my religious beliefs in
sci.bio.paleontology -- where they are off topic -- that you refused
to post anything on-topic along with your off-topic question.

I said I would only go off-topic in reply to posts with some on-topic
component, but you stubbornly kept wheedling for me to reply to your
question anyway.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://www.math.sc.edu/~nyikos/

[MarkE]

Ron, I'm not a scientist, I'm an amateur, with little likelihood of doing any science of my own. But it's a lifelong interest, and what I can do is discuss and interpret the science work done by others.

Not sure what your situation is. I can see you're passionate about your views and energetic in your opposition to ID in particular. If you don't mind me asking, what's your story, what are your areas of interest and reasons for posting here? Asking out of genuine interest - happy to reciprocate.

[John Harshman]

On 2/6/17 12:37 PM, Peter Nyikos wrote:
> On Monday, February 6, 2017 at 3:09:58 PM UTC-5, John Harshman wrote:
>
> Fascinating, how little time it took you to find me, John. The UTC-5
> is Eastern Standard time. I've removed the ambiguity in the following
> attribution line:
>
>> On 2/6/17 11:54 AM, Pacific Standard Time, Peter Nyikos wrote:
>
> Anyway, it's nice having you on this thread, because it was through
> you that I first learned about the way population genetics seems
> to be extrapolated all over the place by evolutionary theorists.
> More about this in my reply to your second post, the one you
> did in reply to my first post.
>
>>> It is that alien colonists, after drastically sterilizing earth of its
>>> indigenous organisms (all microorganisms), brought some of their own
>>> creatures with them -- prokaryotes, protists, algae, sea creatures
>>> to populate the waters of the earth -- so as to colonize it.
>>
>> An interesting theory. How would one test it? I would assume that it
>> would be tested from the fossil record, and we would expect some major
>> point of discontinuity in that record, pre-sterilization and
>> post-sterilization. I don't see such a thing. Do you have a candidate?
>
> The first unambiguous evidence of multicellular organisms could be such a point.
> What evidence have we that the unicellular organisms that preceded them
> had anything like our genetic code? Stromatolite fossils billions of
> years old don't give away the secrets of the individuals that produced them,
> do they?

Present a horizon you think might be the correct one and we'll discuss it.

> Reefs are an interesting parallel. In the last half-billion years there
> have been eons where no evidence of reefs has been found, and several
> distinct episodes of reef-building activity. And the first one was
> by pleosponges, very different from any reef builders of today.

I don't see why this would be considered a parallel. And what are the
eons in which there were no reefs? Not familiar.

[John Harshman]

Perhaps I don't know what you mean by "population genetics". Generally
it includes the various processes (natural processes, at that) by which
allele frequencies change. Ray rejects all those processes, and I don't
see what's left of population genetics is you remove them.

>> And many other
>> creationists have problems too. That's why they keep attacking the
>> peppered moth case, for example.
>
> I fail to follow your reasoning. Part of it is that you don't explain
> the form the attacks that you have in mind took. What I've seen are
> two forms: 1, the two varieties were always there, so where's the
> evidence of evolution? and 2. [the ad hominem form] Like Haeckel, the experimenters committed scientific fraud.

Why allege fraud in that case? The purpose is to discredit an example of
mutation in the first case and evolution in the second.

>> Of course very few creationists have
>> any real understanding even of the basics of population genetics. That's
>> why they keep claiming that if most mutations are deleterious there can
>> be no evolution.
>>
>>> I'm in the process of trying to find out how much of modern evolutionary
>>> theory is dependent on wild extrapolations from population genetics.
>>
>> What sort of wild extrapolations did you have in mind here?
>
> For one, the claim that genetic drift and natural selection are
> legitimate rivals for the main force in evolution. [See Burkhard's
> reply to MarkE and Camp's reply to the same post, backing Burkhard.]

What do you mean by "main force" here? Which is more important depends
on that meaning.

> Once you get past the scale of populations, it's a no-brainer:
> natural selection wins hands down. See my comments to MarkE below.

It's unclear what you mean by that, even with reference to your comments

below.

>>>> As this research progresses, it will discover a greater percentage of the genome to be functional.
>>>
>>> Yes, and NOT just in the sense of coding for proteins, or the more general
>>> sense of coding for RNA.
>>
>> I doubt that much more of the human genome will be found to be
>> functional than is known to be now,
>
> Is this doubt just a WAG, to use a favorite expression of someone we
> both know well?

No. There are a number of sorts of evidence that most of the human
genome is junk. Do you know of any of them?

>> but certainly a fair proportion of
>> the currently known functional DNA in the human genome doesn't code for
>> protein and isn't transcribed into functional RNA. No surprises there.
>
> Hindsight is 20/20. Where was the prediction that this would be found
> to be the case, before the fact?

Why would such a prediction be necessary? The existence of regulatory
sequences, targets of regulatory proteins, has been known since
discovery of the lac operon at least.

>>>> It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.
>>>>
>>>> These findings will become increasingly incompatible with the
>>>> limits of natural selection (especially as the selectionist
>>>> paradigm continues to be eroded by neutral theory, CNE, etc).
>>>> Natural selection will be shown to be an inadequate explanation.
>>
>>> Here is another source of ambiguity. "Natural selection" is used by most
>>> anti-ID types in the strictly population-genetics sense. But I think most
>>> laymen think of it as the grand pageant of "origin of species" on the
>>> one hand and extinction on the other. The mass extinctions of the distant
>>> past exerted a profound influence on evolution by "naturally selecting"
>>> certain orders and families to go extinct and others to survive. We humans
>>> have "naturally selected" untold numbers of species to go extinct,
>>> including so much of the megafauna of the Pleistocene.
>>
>> I'm with you there. Extinction and, perhaps, speciation rates, during
>> mass extinctions and otherwise, have had an influence on the course of
>> evolution.
>
> Right, and where is there a comparable role for genetic drift?

Why, random extinction and speciation, of course, meaning any such
events not strongly related to particular characters of the species.
Raup's "field of bullets" is the extreme case.

>>>> Since there is no alternative naturalistic explanation for the
>>>> accumulation of functional complexity (ie Dawkins' "appearance of
>>>> design"), the only reasonable option will be to infer a designer.
>>
>>> It is safe for you to say that at the present time because evolutionary
>>> theory is still in its embryonic state ("infancy" would be too generous
>>> a description). Thus, Bill Rogers is overly complacent in expecting
>>> you to challenge evolutionary theory before being willing to entertain
>>> arguments for ID. There is really very little in the way of concrete
>>> results for anyone to challenge.
>>
>> How familiar are you with the literature on evolutionary biology and
>> evolutionary theory?
>
> Not familiar enough to know whether a hypothesis we discussed in
> December was in the mainstream of evolutionary theory, or a naive
> extrapolation from it by you.
>
> This was your conjecture that there was plenty of time for an essentially
> unique genetic code to become ubiquitous. It was based on an extrapolation
> of genetic drift from populations to the biota of an entire planet.

> On the day I went on posting break, I posted a detailed rebuttal to
> this hypothesis of yours. You never replied -- was this just out of
> courtesy, holding back until my return?

No. I am not familiar with this detailed rebuttal.

>>>> At that point, science hands over to theology.
>>>
>>> I often wonder how much of the behavior of anti-ID types is fueled either
>>> by atheism or belief in what is inappropriately called "theistic evolution"
>>> and should be renamed "deistic evolution" because it dogmatically
>>> adheres to meaning 3. of "Darwinism" above.
>>
>> Good to know what you wonder about. Should we be interested?
>
> If you want to know where Ken Miller and Ron O are coming from, you
> should be interested in the issue of what fuels anti-ID behavior.

But should I be interested in your thoughts on that issue? That would
demand that your notions have some basis other than your own prejudices.

> Also, you showed so much interest in my religious beliefs in
> sci.bio.paleontology -- where they are off topic -- that you refused
> to post anything on-topic along with your off-topic question.

> I said I would only go off-topic in reply to posts with some on-topic
> component, but you stubbornly kept wheedling for me to reply to your
> question anyway.

I don't know what this refers to. Your memory of our past discussions is
clearly more detailed than mine. It might even be better than mine.

[Peter Nyikos]

Ray does not reject the natural process of sperm uniting with oocytes.
He doesn't claim that he owes his existence to a miracle the way at least
one conception is described in the Bible as being miraculous. He just
thinks God was connected with it in some ineffable way. The same ought to
go for mutations and all the reasons gene frequencies change in populations.

> and I don't
> see what's left of population genetics is you remove them.

I hope Ray joins this thread, so he can tell you firsthand what he rejects
and what he accepts.

> >> And many other
> >> creationists have problems too. That's why they keep attacking the
> >> peppered moth case, for example.
> >
> > I fail to follow your reasoning. Part of it is that you don't explain
> > the form the attacks that you have in mind took. What I've seen are
> > two forms: 1, the two varieties were always there, so where's the
> > evidence of evolution? and 2. [the ad hominem form] Like Haeckel, the experimenters committed scientific fraud.
>
> Why allege fraud in that case?

Why is the blogosphere full of charges of lying and fraud and other forms of
dishonesty, both by ID theorists and by their opponents? Just look at
the numerous accusations of a "bait and switch scam" by Ron O. Do you
know enough about them to know why they are dwarfed by the number of
accusations of a "switch scam"? [That's a real-life example of "the sound
of one hand clapping," figuratively speaking.]

> The purpose is to discredit an example of
> mutation in the first case

What mutation? The phenomenon was well known before any experiments
were undergone. The experiment was designed to show how one variety
or the other was naturally selected for. It didn't address the origin
of the varieties.

> and evolution in the second.

Yeah, but now you are leaving the domain of evolutionary theory and
entering the naked fact of evolution.

> >> Of course very few creationists have
> >> any real understanding even of the basics of population genetics. That's
> >> why they keep claiming that if most mutations are deleterious there can
> >> be no evolution.
> >>
> >>> I'm in the process of trying to find out how much of modern evolutionary
> >>> theory is dependent on wild extrapolations from population genetics.
> >>
> >> What sort of wild extrapolations did you have in mind here?
> >
> > For one, the claim that genetic drift and natural selection are
> > legitimate rivals for the main force in evolution. [See Burkhard's
> > reply to MarkE and Camp's reply to the same post, backing Burkhard.]
>
> What do you mean by "main force" here? Which is more important depends
> on that meaning.

Maybe I should have said "the more important force."

When "Roger Shrubber" tried to argue that genetic
drift was more important, he was talking on the level of populations.
He couldn't possibly have made a case on the

> > Once you get past the scale of populations, it's a no-brainer:
> > natural selection wins hands down. See my comments to MarkE below.
>
> It's unclear what you mean by that, even with reference to your comments
> below.

Why is it unclear? The comments below establish it as being a far
greater force than genetic drift, even with your attempt to make
a case for the latter below.

<snip of things to be dealt with in separate post, if appropriate>

> >>> Here is another source of ambiguity. "Natural selection" is used by most
> >>> anti-ID types in the strictly population-genetics sense. But I think most
> >>> laymen think of it as the grand pageant of "origin of species" on the
> >>> one hand and extinction on the other. The mass extinctions of the distant
> >>> past exerted a profound influence on evolution by "naturally selecting"
> >>> certain orders and families to go extinct and others to survive. We humans
> >>> have "naturally selected" untold numbers of species to go extinct,
> >>> including so much of the megafauna of the Pleistocene.
> >>
> >> I'm with you there. Extinction and, perhaps, speciation rates, during
> >> mass extinctions and otherwise, have had an influence on the course of
> >> evolution.
> >
> > Right, and where is there a comparable role for genetic drift?
>
> Why, random extinction and speciation, of course, meaning any such
> events not strongly related to particular characters of the species.

There are many things responsible for random extinction besides
genetic drift. Floods, fires, volcanic eruptions, a new predator
or disease hitting a population without natural defenses...

> Raup's "field of bullets" is the extreme case.

The Wikipedia entry makes no mention of genetic drift in connection
with it.

<snip of things to be dealt with in separate post, if appropriate>

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --
U. of South Carolina
http://www.math.sc.edu/~nyikos/

[RonO]

What do you think that I have been telling you to do. Instead of look
at what we don't know, why not explore what we do know and the things
that others are actually working on. What are scientists actually
working on. They are working on the gaps in our knowledge, but they are
working from what is known instead of relying on what we don't know at
this time. Reliance on what we do not know hasn't done any IDiot any
good for decades. It has been going on since before the modern ID scam.
The ID perps just decided that, that was the only thing that they were
going to do.

>
> Not sure what your situation is. I can see you're passionate about your views and energetic in your opposition to ID in particular. If you don't mind me asking, what's your story, what are your areas of interest and reasons for posting here? Asking out of genuine interest - happy to reciprocate.

What's your model? Maybe you can actually work on it instead of messing
around with junk that isn't going to get you anywhere.

I'm a scientist. I actually do what the ID perps claim to be doing, but
they can't seem to do any. I've been reading TO since 1993. When I
started reading TO the ID scam wasn't discussed. I've watched the end
game for scientific creationism. Why aren't you a scientific
creationist? ID is only the replacement. They needed to call it
something else for political purposes. That is why IDiots like Santorum
went back to calling it creationism after the IDiot court loss in Dover.

I was participating on the ARN board that was run by IDiots. When the
bait and switch went down in 2002 and it was apparent that no one was
going to get the promised ID science, there was just abject denial.
Mike Gene (the most scientific of the IDiot proponents) admitted that he
had given up on teaching ID in the public schools back in 1999. No
IDiot cared that they had been lied to about the ID science. The reason
was that it wasn't the science that they were interested in. It was
only their religious beliefs. ID turned into a creationist scam run by
creationists on their fellow creationists. It hasn't changed since.
The bait and switch will still go down on the next set of IDiot rubes
stupid enough to not know any better by now. I expected some of the
IDiots on ARN to be half way honest, but none of them were even half way
honest. Beats me how long it took, but now Mike Gene admits that there
never was any ID science. That admission was years too late, and likely
should have been made when he decided that ID was too bogus to teach in
the public schools. I am sure that Mike Gene is still a creationist, he
just doesn't claim that ID is science anymore.

The ISCID IDiot science organization is dead, and the ID Network quit,
and there are still IDiots.

Why would you keep putting up the junk as if it mattered?

IDiots should be working on fixing what is obviously broken, but
dishonesty is all they have left even if they are just lying to
themselves. That is the sad reality of IDiocy today. You likely know
that because you try to deny being an IDiot, but you keep using the same
lame arguments. Unless you have some fix why even try?

Instead of just using the same lame arguments, why not start of by
stating why they did not amount to anything, and try to figure out what
might be done to change that? Relying on what we don't know isn't going
to do anything. If you can't figure out how to make the argument into
anything worth talking about, try another. Once you run through them
all you will end up where I have been telling you reality is at, at this
time.

It is long past when some type of honest effort should be made. Put up
your model. Figure out what parts of the model that you can address
with what is already known and address those parts. Eddies group is
obviously changing their theology with what can't be denied any longer.

Frankly I would not base my theology on the current science. Why should
the science matter? Just because the Bible is wrong about the shape of
the earth or when the creation happened shouldn't be anything to deny.
There doesn't seem to be any reason to burn anyone at the stake because
the Bible is wrong about some aspect of nature. Creationists are the
first to admit that their god is outside of nature. A lot of your
theology cannot be addressed by science. Why let the parts that can be
addressed bother you? Why should a natural history lesson be the basis
of your belief? It is a lesson that is constantly being improved.

The IDiots at the Biologic Institute have started a project to
demonstrate that Adam and Eve could have existed. It is a stupid
project because they will find out that it wasn't worth doing the
project at all. Just by what is already known we know that such a pair
existed so long ago that any genetic variation that they had is pretty
much all gone. Genetic variation turns over in populations like clock
work. That is what makes the molecular clock viable. The vast majority
of the existing segregating variation in the human population is due to
new mutations that have occurred within the last half million years.
They do not have to figure out if the 4 chromosome sets that existed in
Adam and Eve could recombine to form all the millions of haplotypes
existing in the human population at this time because nearly all the
variation that exists in those haplotypes did not exist in Adam and Eve.
It is all new variation from new mutations.

The saddest thing is that these are the IDiots that claimed that it was
the science that they were interested in and not their religious beliefs.

Are you going to be different?

Ron Okimoto

[RSNorman]

I hope this post goes through -- my last four attempts to post here on
t.o. never showed up even though my newsreader says that posted
successfully.

I do not understand how you so casually parcel up "evolution" into
"population genetics", "evolutionary theory", and the actual "fact of
evolution" as observed in the world. These are all completely unified
and integrated concepts, biological evolution or, more simply in the
context of biology, just plain "evolution."

The "Theory of Evolution" is not part of theoretical biology. There
is extensive laboratory and field work done on the area and so it is
no more theoretical than, say, ecology or physiology. Both of these
latter areas include substantial mathematical theorizing and modelling
and computer simulations and the like. Evolution does, also. That
does not separate the mathematical developments from the field or
experimental studies. Population genetics provides the solid
foundation for evolutionary theory which is firmly based on the
observed "facts of evolution" as seen in the world. Some people work
more (or exclusively) in one realm; others span across the field.

Natural selection and neutral change are merely two different ways in
which evolutionary change occurs, both theoretically and in actuality.
The "selectionist paradigm" merely asserts one without the other. The
"erosion" of the paradigm does not replace selection with drift and
neutral mutation but allows for either or both to operate depending on
circumstance.

Evolutionary theory may still be in what you call an "embryonic" stage
simply because there are large problems still open. That is what we
biologists merely call an "active" area of study. The "Theory of
Natural Selection" originated some 150 years ago, was drastically
modified by developments from 100 to 50 years ago to create the
"modern synthesis". But things did not stop there. That was the very
onset of genomic analysis and that dramatically opened up new arenas
of study. Gould tried desperately to get his "Structure of
Evolutionary Theory" to form the basis for a new and "More Modern
Synthesis" but it didn't catch on. Still that doesn't mean that
evolutionary biology today is what it was 30 or 50 or 100 or 150 years
ago. Is that embryonic? It sure is an awful long gestation period!
It is simply how science develops.

[John Harshman]

It's conceivable that you are right.

>> and I don't
>> see what's left of population genetics is you remove them.
>
> I hope Ray joins this thread, so he can tell you firsthand what he rejects
> and what he accepts.

I hope Ray doesn't join this thread. He's a distraction from any issues
at hand other than the trivial one of what he himself believes, he
understands nothing, and he contributes nothing.

>>>> And many other
>>>> creationists have problems too. That's why they keep attacking the
>>>> peppered moth case, for example.
>>>
>>> I fail to follow your reasoning. Part of it is that you don't explain
>>> the form the attacks that you have in mind took. What I've seen are
>>> two forms: 1, the two varieties were always there, so where's the
>>> evidence of evolution? and 2. [the ad hominem form] Like Haeckel, the experimenters committed scientific fraud.
>>
>> Why allege fraud in that case?
>
> Why is the blogosphere full of charges of lying and fraud and other forms of
> dishonesty, both by ID theorists and by their opponents? Just look at
> the numerous accusations of a "bait and switch scam" by Ron O. Do you
> know enough about them to know why they are dwarfed by the number of
> accusations of a "switch scam"? [That's a real-life example of "the sound
> of one hand clapping," figuratively speaking.]

Why bring that up?

>> The purpose is to discredit an example of
>> mutation in the first case
>
> What mutation? The phenomenon was well known before any experiments
> were undergone. The experiment was designed to show how one variety
> or the other was naturally selected for. It didn't address the origin
> of the varieties.

Hey, you're the one that mentioned creationist attacks on the existence
of a mutation to the melanistic form. What did you mean if not that?

>> and evolution in the second.
>
> Yeah, but now you are leaving the domain of evolutionary theory and
> entering the naked fact of evolution.

There are no naked facts. The attack is on the existence of an example
of natural selection. Without the theory of natural selection, there is
no example.

>>>> Of course very few creationists have
>>>> any real understanding even of the basics of population genetics. That's
>>>> why they keep claiming that if most mutations are deleterious there can
>>>> be no evolution.
>>>>
>>>>> I'm in the process of trying to find out how much of modern evolutionary
>>>>> theory is dependent on wild extrapolations from population genetics.
>>>>
>>>> What sort of wild extrapolations did you have in mind here?
>>>
>>> For one, the claim that genetic drift and natural selection are
>>> legitimate rivals for the main force in evolution. [See Burkhard's
>>> reply to MarkE and Camp's reply to the same post, backing Burkhard.]
>>
>> What do you mean by "main force" here? Which is more important depends
>> on that meaning.
>
> Maybe I should have said "the more important force."

Still doesn't help unless you explain what "important" means here.

> When "Roger Shrubber" tried to argue that genetic
> drift was more important, he was talking on the level of populations.
> He couldn't possibly have made a case on the

That cut off in mid-sentence.

>>> Once you get past the scale of populations, it's a no-brainer:
>>> natural selection wins hands down. See my comments to MarkE below.
>>
>> It's unclear what you mean by that, even with reference to your comments
>> below.
>
> Why is it unclear? The comments below establish it as being a far
> greater force than genetic drift, even with your attempt to make
> a case for the latter below.

I'm afraid the comments below establish nothing. They just assert. How
do you know the extinction of certain taxa were selected rather than
random? It's a live question. You hint at it with a single word
"megafauna", but you need to do better than single words if you want to
make a case.

> <snip of things to be dealt with in separate post, if appropriate>
>
>
>>>>> Here is another source of ambiguity. "Natural selection" is used by most
>>>>> anti-ID types in the strictly population-genetics sense. But I think most
>>>>> laymen think of it as the grand pageant of "origin of species" on the
>>>>> one hand and extinction on the other. The mass extinctions of the distant
>>>>> past exerted a profound influence on evolution by "naturally selecting"
>>>>> certain orders and families to go extinct and others to survive. We humans
>>>>> have "naturally selected" untold numbers of species to go extinct,
>>>>> including so much of the megafauna of the Pleistocene.
>>>>
>>>> I'm with you there. Extinction and, perhaps, speciation rates, during
>>>> mass extinctions and otherwise, have had an influence on the course of
>>>> evolution.
>>>
>>> Right, and where is there a comparable role for genetic drift?
>>
>> Why, random extinction and speciation, of course, meaning any such
>> events not strongly related to particular characters of the species.
>
> There are many things responsible for random extinction besides
> genetic drift. Floods, fires, volcanic eruptions, a new predator
> or disease hitting a population without natural defenses...

Genetic drift doesn't cause extinction. Nor does natural selection. We
were talking about analogs of these population-level phenomena at a
higher level. There is species drift as well as species selection.

>> Raup's "field of bullets" is the extreme case.
>
> The Wikipedia entry makes no mention of genetic drift in connection
> with it.

I don't know why you got the idea that genetic drift was literally involved.

[Peter Nyikos]

On Monday, February 6, 2017 at 4:19:58 PM UTC-5, MarkE wrote:

> > > Ron, you're already in the sin-bin for talking and not listening. If this dry-retching of ID diatribe continues it'll be a red card.
> > >
> >
> > Run away in denial. Denial is all IDiots have and you know it. I have
> > just demonstrated that what you are doing is what the ID perps have been
> > doing for a couple of decades and all IDiocy is, is a stupid scam that
> > creationists are running on themselves.

It is no more of a scam than Ron O ranting about "IDiocy" and yet
hardly giving any information on how evolutionary theory has
explained the evolution that has actually taken place on earth.

> > You obviously have to do something different. The same old same old
> > isn't going to amount to anything.

Ironic, this spiel from someone who has been regurgitating the same old
same old talk about a scam since 2002. And recycling whole paragraphs
of rant in the process.

> > Do something that the ID perps never tried. Actually try to figure out
> > if there is any science that you can actually do.

Ron O is ignoring the elephant in the room -- Minnich, who testified
in Dover about the experiments he and his students did on the bacterial
flagellum.

Not only did they show that the flagellum they were testing
was irreducibly complex -- each and every one of its 30+ parts was
essential to the function of swimming -- but they also did experiments
that suggested that the Type III mechanism might have evolved from the
flagellum through loss of parts, rather than the flagellum evolving from
the type III mechanism through addition of parts.

<snip irrelevant lecture by Ron O>

> > Why not do the sensible thing and put up your model of creation

ID theory doesn't hypothesize creation; it hypothesizes intelligent
design, as its name implies.

> > to figure out if there is anything that you can do to verify any parts
> > of it? That isn't a trap. If you want to know if your model is valid
> > you have to verify it somehow. The only reason the ID perps don't do
> > that is because they already know that the answers are not what they
> > want. That is how sad the ID scam is at this time.

Ron O has no reason whatsoever for thinking this. Part of his problem
is that he doesn't realize that the ID emphasis on the weaknesses of
evolutionary theory is just the other side of the coin on anti-ID folks
like him harping on the weaknesses of ID theory.

> > Why don't IDiots persue such research?

See above about Minnich.

> > What is the draw to keep doing
> > nothing except make assertions that you can't back up as meaning
> > anything to IDiocy?
> >
> > Ron Okimoto
>
> Ron, I'm not a scientist, I'm an amateur, with little likelihood of doing any science of my own. But it's a lifelong interest, and what I can do is discuss and interpret the science work done by others.
>
> Not sure what your situation is. I can see you're passionate about your views and energetic in your opposition to ID in particular.
> If you don't mind me asking, what's your story, what are your areas of interest and reasons for posting here?
> Asking out of genuine interest - happy to reciprocate.

Well, you got another long spiel in reply, but did he tell you anything
along the lines which you had in mind?

I first encountered Ron O back in 2010 and have seen innumerable
long spiels from him since then -- but none that really got to the
root of his motivations.

Did you ever get a clue as to how his fanatical opposition to intelligent
design squares with what he claims to be his religious beliefs? I've
learned essentially nothing along these lines -- next to nothing about
his religious beliefs, and nothing whatsoever about the connection.
Nobody else here seems to know more about this than I do.

I, on the other hand, have been very forthcoming about my beliefs. I
am an agnostic who has reluctantly concluded that the evidence for
a designer/creator of our world is rather slim -- but who nevertheless
clings to a hope that the basics of Christianity are true. This includes a
life after death, but I hope that heaven and hell are much more like
they are depicted in C.S. Lewis's _The Great Divorce_ than like the horrible
image of hell as depicted in olden days.

Where do you stand, if you don't mind telling?

Peter Nyikos
Professor of Mathematics -- standard disclaimer--
University of South Carolina

[Peter Nyikos]

On Monday, February 6, 2017 at 7:24:58 PM UTC-5, RSNorman wrote:
> On Mon, 6 Feb 2017 11:06:19 -0800 (PST), Peter Nyikos
> <nyi...@bellsouth.net> wrote:

> > I've come to realize
> >just how ambiguous that creationist catchword, "Darwinism" is. Depending
> >on the context [which may include a shell game between the various meanings]
> >it can either mean:
> >
> >1. The naked fact that we vertebrates have evolved from a common ancestral
> >species, and the highly defensible hypothesis that all earth life is
> >descended from prokaryotes. [The logical alternative to creationism
> >in the sense of creation of species *de novo*.]
> >
> >2. Modern evolutionary theory, a part of theoretical biology. [The logical
> >alternative to "ID theory".]
> >
> >3. The philosophical/religious belief that abiogenesis and evolution
> >of life all happened without supernatural intervention.

MarkE wrote:
> >> It's important for better understanding and combating disease for starters.
> >
> >That's part of population genetics. Creationists have no problem with
> >that, and that includes that ideological purist, the "species immutabilist"
> >Ray Martinez.
> >
> >I'm in the process of trying to find out how much of modern evolutionary
> >theory is dependent on wild extrapolations from population genetics.
> >I'm having a hard time finding out because anti-ID types favor the
> >ambiguous term "evolutionary biology." Depending on the context,
> >it could mean:
> >
> >A. Population genetics.
> >
> >B. The modern synthesis, which includes A.
> >
> >C. Evidence that evolution has taken place, in the sense of 1. above.

<snip for focus>

> >> Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.
> >
> >It is safe for you to say that at the present time because evolutionary
> >theory is still in its embryonic state ("infancy" would be too generous
> >a description). Thus, Bill Rogers is overly complacent in expecting
> >you to challenge evolutionary theory before being willing to entertain
> >arguments for ID. There is really very little in the way of concrete
> >results for anyone to challenge.
> >
> >> At that point, science hands over to theology.
> >
> >I often wonder how much of the behavior of anti-ID types is fueled either
> >by atheism or belief in what is inappropriately called "theistic evolution"
> >and should be renamed "deistic evolution" because it dogmatically
> >adheres to meaning 3. of "Darwinism" above.
> >
>
> I hope this post goes through -- my last four attempts to post here on
> t.o. never showed up even though my newsreader says that posted
> successfully.

It got through, and I'm glad it did. Nice to hear from you, Richard.

> I do not understand how you so casually parcel up "evolution" into
> "population genetics", "evolutionary theory", and the actual "fact of
> evolution" as observed in the world.

It isn't casual. It comes from witnessing innumerable failures of
communication, and whether a given one is due to honest misunderstandings
or deliberate shell games is immaterial. They often take the form of someone
"refuting" a creationist or ID supporter's claim about "Darwinism"
by giving evidence of actual evolution from fossils or from molecular systematics.

And yet it is clear from the creationist/ID supporter's
previous behavior, or at least from his rejoinder to the "refutation"
that what he was disputing was the alleged explanation of this
actual evolution by evolutionary theory.

> These are all completely unified
> and integrated concepts, biological evolution or, more simply in the
> context of biology, just plain "evolution."

Concepts are one thing, the actual events are another.

> The "Theory of Evolution" is not part of theoretical biology. There
> is extensive laboratory and field work done on the area and so it is
> no more theoretical than, say, ecology or physiology.

There is lots of work in population genetics, but that is a minuscule
part of evolution, and not the part about which there are disputes.

Similarly, when I talk about experiments to verify irreducible
complexity (IC), the response I often get is that the REAL issue
is whether it is evidence for intelligent design (ID) and that
the concept of IC is of no intrinsic interest.

> Both of these
> latter areas include substantial mathematical theorizing and modelling
> and computer simulations and the like. Evolution does, also.

That is one weird use of the word "Evolution."

> That
> does not separate the mathematical developments from the field or
> experimental studies. Population genetics provides the solid
> foundation for evolutionary theory which is firmly based on the
> observed "facts of evolution" as seen in the world.

What do you mean by the "observed facts of evolution"? Do they
include the details of the evolution of vertebrates from humble
beginnings to the ones we see all around us, as is inferred from
fossils, and more indirectly from molecular evidence?

Population genetics does not provide THE foundation for
explaining all that, not without bringing chemistry and
geology and physics into the picture. You may even need
astronomy to account fully for the K-T extinction.

> Some people work
> more (or exclusively) in one realm; others span across the field.

The field of science? or just the field of biology?

> Natural selection and neutral change are merely two different ways in
> which evolutionary change occurs, both theoretically and in actuality.

Genetic drift is ONE form of neutral change. There are
many others, including the ones I listed for John Harshman.

> The "selectionist paradigm" merely asserts one without the other. The
> "erosion" of the paradigm does not replace selection with drift and
> neutral mutation but allows for either or both to operate depending on
> circumstance.

You are still talking about population genetics, aren't you?

> Evolutionary theory may still be in what you call an "embryonic" stage
> simply because there are large problems still open. That is what we
> biologists merely call an "active" area of study. The "Theory of
> Natural Selection" originated some 150 years ago, was drastically
> modified by developments from 100 to 50 years ago to create the
> "modern synthesis". But things did not stop there.

Ok, so what is the proper term for the present state of affairs?
We've had "Darwinism," "Neo-Darwinism," "evo-devo" "the modern
synthesis" and goodness knows how many other terms.

> That was the very
> onset of genomic analysis and that dramatically opened up new arenas
> of study. Gould tried desperately to get his "Structure of
> Evolutionary Theory" to form the basis for a new and "More Modern
> Synthesis" but it didn't catch on. Still that doesn't mean that
> evolutionary biology today is what it was 30 or 50 or 100 or 150 years
> ago. Is that embryonic? It sure is an awful long gestation period!

As it should be.

> It is simply how science develops.

Yes. Even physics is having growing pains, and it doesn't have to
deal with the incredibly complicated issues posed by the messiness
of the history of earth life. For instance, stellar evolution is
far simpler, by untold orders of magnitude, than biological evolution
as it has played out over the eons of earth history.

Peter Nyikos
Professor, Dept. of Mathematics

U. of South Carolina -- standard disclaimer--
http://people.math.sc.edu/nyikos

[RSNorman]

On Mon, 6 Feb 2017 19:27:26 -0800 (PST), Peter Nyikos

I do realize you are trying to analyze the misunderstandings of
creationists/IDers about biological evolution. But my perspective is
from biology and I just think that they are simply illiterate
(deliberately or inadvertently) about what real evolution is.
Sometimes people here argue (incorrectly from my perspective) with
them not really helping. Yes, evolution "is" a change in the allele
frequency in a population over generations. Yes, evolution "is" the
development of all extant life from a common ancestor (or ancestral
pool of microbes). But these are simply different aspects of the
subject and the whole thing about modern biology is that when you
understand molecular biology, developmental biology, physiology,
ecology,..., then you know why those two aspects are intimately
connected.

>> These are all completely unified
>> and integrated concepts, biological evolution or, more simply in the
>> context of biology, just plain "evolution."
>
>Concepts are one thing, the actual events are another.

Yes. There is also a difference between "results" of an experimental
paper and "discussion". But the two are inextricably interwoven.

>
>> The "Theory of Evolution" is not part of theoretical biology. There
>> is extensive laboratory and field work done on the area and so it is
>> no more theoretical than, say, ecology or physiology.
>
>There is lots of work in population genetics, but that is a minuscule
>part of evolution, and not the part about which there are disputes.
>
>Similarly, when I talk about experiments to verify irreducible
>complexity (IC), the response I often get is that the REAL issue
>is whether it is evidence for intelligent design (ID) and that
>the concept of IC is of no intrinsic interest.
>

I don't know about biological experiments "to verify irreducible
complexity". I do not know what you are talking about here. If there
were such experiments that DID verify it then that would constitute
evidence.

It is quite true that the concept of IC is of no intrinsic interest to
biologists. It is not something we work on or worry about except to
answer people ignorant of modern biology.

>> Both of these
>> latter areas include substantial mathematical theorizing and modelling
>> and computer simulations and the like. Evolution does, also.
>
>That is one weird use of the word "Evolution."

"Evolution" is simply what that whole area is called. Just like
"physiology" represents a whole range of rather different areas from
cellular biophysics to ecological adaptation. Physiology is based on
how the machinery of the organism works, from cellular to whole
organismal. Evolution is based on change over time, from molecular to
whole groups of organisms.

>> That
>> does not separate the mathematical developments from the field or
>> experimental studies. Population genetics provides the solid
>> foundation for evolutionary theory which is firmly based on the
>> observed "facts of evolution" as seen in the world.
>
>What do you mean by the "observed facts of evolution"? Do they
>include the details of the evolution of vertebrates from humble
>beginnings to the ones we see all around us, as is inferred from
>fossils, and more indirectly from molecular evidence?

I used that phrase because it seemed that you raised that point. The
existence of extant organisms with similarities and differences in
morphology, behavior, development, ecology, biochemistry along with
the enormous database of genomic sequencing plus the fossil record:
these constitute observed facts. Evolution is the general name both
for the well developed idea about how it all happened (the process of
evolution) and the organisms themselves (the results of evolution).

>Population genetics does not provide THE foundation for
>explaining all that, not without bringing chemistry and
>geology and physics into the picture. You may even need
>astronomy to account fully for the K-T extinction.

Population genetics IS the foundation for the changes that occur. That
the dynamics of genetic change depends on external factors is sort of
obvious. The nuclear reactions in a distant star are necessary to
explain animal migration by celestial navigation, just as the nuclear
reactions in our sun are necessary to explain photosynthesis. But
that really is pushing it. The details of specific evolutionary
changes are clearly influenced by geological factors controlling the
environment. That does not mean that geology should be considered a
mechanism of evolutionary change.

>> Some people work
>> more (or exclusively) in one realm; others span across the field.
>
>The field of science? or just the field of biology?

Biology is a pretty big field. OK, many people in animal behavior or
paleontology work in departments outside of biology. Doesn't matter.

>> Natural selection and neutral change are merely two different ways in
>> which evolutionary change occurs, both theoretically and in actuality.
>
>Genetic drift is ONE form of neutral change. There are
>many others, including the ones I listed for John Harshman.

I did not specify genetic drift because, as you say, there are other
non-selectionist mechanisms of evolutionary change.

>> The "selectionist paradigm" merely asserts one without the other. The
>> "erosion" of the paradigm does not replace selection with drift and
>> neutral mutation but allows for either or both to operate depending on
>> circumstance.
>
>You are still talking about population genetics, aren't you?

Yes. And I am talking about evolutionary change.

>> Evolutionary theory may still be in what you call an "embryonic" stage
>> simply because there are large problems still open. That is what we
>> biologists merely call an "active" area of study. The "Theory of
>> Natural Selection" originated some 150 years ago, was drastically
>> modified by developments from 100 to 50 years ago to create the
>> "modern synthesis". But things did not stop there.
>
>Ok, so what is the proper term for the present state of affairs?
>We've had "Darwinism," "Neo-Darwinism," "evo-devo" "the modern
>synthesis" and goodness knows how many other terms.

I have been retired for well over a decade now and don't have contact
with the community of people who called themselves "evolutionary
biologists." But my recollection is that they simply say
"evolutionary biology". "Evo-devo" is a particular subdivision.
"Neo-Darwinism" was coined to counter the strictly selectionist
paradigm. Some people argue that epigenetics will totally revamp
evolutionary biology. Most geneticists and molecular biologists and
evolutionary biologists say that epigenetics will simply become just
one more mechanism at work in controlling the relationship between the
hereditary material passed from generation to generation, the essence
of biological evolution, and the formation of a particular phenotype
with a particular morphology, ecology, behavior, physiology.

>> That was the very
>> onset of genomic analysis and that dramatically opened up new arenas
>> of study. Gould tried desperately to get his "Structure of
>> Evolutionary Theory" to form the basis for a new and "More Modern
>> Synthesis" but it didn't catch on. Still that doesn't mean that
>> evolutionary biology today is what it was 30 or 50 or 100 or 150 years
>> ago. Is that embryonic? It sure is an awful long gestation period!
>
>As it should be.
>
>> It is simply how science develops.
>
>Yes. Even physics is having growing pains, and it doesn't have to
>deal with the incredibly complicated issues posed by the messiness
>of the history of earth life. For instance, stellar evolution is
>far simpler, by untold orders of magnitude, than biological evolution
>as it has played out over the eons of earth history.
>

Biological objects play by very different rules from chemical or
physical objects. They tend to do what they want to do rather than
obey fixed and simple laws. Try to absolutely control the situation
so thoroughly to try to eliminate variation and you destroy the
biological context and get absolutely aberrant results.

[jillery]

Peter Nyikos is ignoring the elephant in the room, that Minnich's
experiments merely showed the existence of Behe's IC, but did nothing
to show Behe's claims about IC, specifically that such systems could
not have evolved. More telling, neither has Behe. To the best of my
knowledge, nobody in the IC community has done any experiments which
showed the implausibility of evolved IC. OTOH Muller described
evolved IC decades before Behe wrote DBB.

><snip irrelevant lecture by Ron O>

<snip remaining irrelevant noise by Peter Nyikos>

--
This space is intentionally not blank.

[jillery]

On Mon, 06 Feb 2017 21:43:22 -0700, RSNorman <r_s_n...@comcast.net>

Based on his other posts, my impression is he's referring to the
experiments Minnich described in his Dover trial testimony.

If by "it" you mean ID, I must disagree. Behe's bald assertions
notwithstanding, biological IC is not evidence against biological
evolution, nor is it evidence for Design,

[Peter Nyikos]

On Tuesday, February 7, 2017 at 12:44:57 AM UTC-5, jillery wrote:
> On Mon, 06 Feb 2017 21:43:22 -0700, RSNorman <r_s_n...@comcast.net>
> wrote:

> >>Similarly, when I talk about experiments to verify irreducible
> >>complexity (IC), the response I often get is that the REAL issue
> >>is whether it is evidence for intelligent design (ID) and that
> >>the concept of IC is of no intrinsic interest.

IIRC this was your stance on the Minnich experiments, jillery. Correct?

> >I don't know about biological experiments "to verify irreducible
> >complexity". I do not know what you are talking about here. If there
> >were such experiments that DID verify it then that would constitute
> >evidence.
>
>
> Based on his other posts, my impression is he's referring to the
> experiments Minnich described in his Dover trial testimony.

Indeed, one need look no further than the post I did in reply to
MarkE yesterday evening. There might, of course, have been other
experiments to verify IC that I haven't learned about.

> If by "it" you mean ID, I must disagree. Behe's bald assertions
> notwithstanding, biological IC is not evidence against biological
> evolution, nor is it evidence for Design,

Behe's assertions are nuanced: the more complex the IC structure/system,
the stronger the case for meeting Darwin's criterion
of not being attainable through "numerous, successive, slight modifications".
See pp. 39-40 of _Darwin's Black Box_.

And so, you've reminded me of yet a fourth meaning for "Darwinism":
the belief in evolutionary gradualism as set forth in the quote from
_Origin of Species_.

Peter Nyikos
Professor, Dept. of Math. -- standard disclaimer--
Univ. of South Carolina
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

The question I asked up there was:

"Right, and where is there a comparable role for genetic drift?"

What question did you THINK you were answering?

Peter Nyikos

[Peter Nyikos]

Yes, it does, and populations with too little genetic diversity are
prime targets for extinction by natural selection. Just as evolution
within a population is also affected by natural selection.

> We
> were talking about analogs of these population-level phenomena at a
> higher level. There is species drift as well as species selection.

Natural selection is not an analog. It is both a population-level
phenomenon and a phylum-level phenomenon, as in the case of
some enigmatic Ediacaran organisms, believed to have succumbed
to the development of predation by eumetazoans.

It could well be that all the peer-reviewed studies of natural selection
were done on the level of populations; but it would not follow that
natural selection is a population-genetics phenomenon.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of South Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[John Harshman]

It's an exactly comparable role. Species selection is not literally the
same as natural selection, just analogous. The stochastic processes that
happen above the population level are not the same as genetic drift,
just analogous. I thought that was clear.

[MarkE]

Analogies are like bicycles, you can ride them too far. This analogy is partly for fun (the bits where the analogy doesn't hold), but also as a broad interpretation of your response (all the other bits).

Okay, that's a thoughtful set of responses which deserve a serious reply.

I concede it is tricky to decisively demonstrate "argument from legitimate scientific incredulity" (to use the positive form). Dembski proposed a "universal probability bound" of 1 in 10^150 for this purpose - a number which "corresponds to an upper limit on the number of physical events that could possibly have occurred in the observable part of the universe since the big bang." He has quantified Dawkins' "too much luck".

Would you agree with this approach, in principle if not Dembski's number?

Can this be applied to my 1 to 35 trillion observation? I don't think so, not directly. I'm not even offering a fully-formed argument (you can go now, I've got this). Rather, I'm raising a flag, and saying this doesn't seem to add up in a big way...How do others see it?

Is that hopelessly subjective? Well, it's not going to published in Nature any time soon. But here's the logic of it which I think has merit:

The 1 to 35 trillion ratio would be unremarkable if it were a single bacterium multiplying thus. Nothing particularly novel created, i.e. low algorithmic complexity. However, with human development, we have very, very high functional complexity. I can't put a number on it, but there's wide agreement to describe our brain as the most complex object known. Both structural and functional complexity.

So here's my first claim: we can say there must be a very high information content within that single parent cell. I'm proposing a broad definition information here, which is the capability to produce the structure that is a human, via the constrained process of cell division and differentiation.

Now if 8% of our DNA is functional, that's 64MB of data in the genome. So we can safely conclude that by any known means, that's nowhere near enough information to specify the most complex object known. The cell is an integrated physicochemical system, but again it seems safe to say that the only viable alternative source of this information in the cell is the proteins it can produce.

I'm assuming that development occurs naturally, i.e. without a need for divine intervention.

Therefore, the information (as defined) must reside in:

1. The genome, but be much more than 8% being functional, and/or employ storage with efficiency well beyond what our current technology or understanding;

2. The information is in the 2 million proteins the body is capable of producing; i.e. as more than a linear polymer, rather the complex specific binding properties of these intricately folded 3D molecules;

3. A combination or 1 and 2.

The median protein length in H. sapiens is 375 amino acids, of say 5 bits each, giving about 0.5GB of "linear" (pre-folding) information.

Jamie A. Davies interprets this as: “[the zygote is] a few thousand genes and proteins, none of which can possibly hold any concept, in any language, of the structure and function of a human body....”

Is he correct? He locates the extra information needed outside the parent cell, as "adaptive self-organization".

It's now 1am, and I have work tomorrow...to be continued!

[John Harshman]

On 2/7/17 6:39 AM, Peter Nyikos wrote:
> On Monday, February 6, 2017 at 9:00:00 PM UTC-5, John Harshman wrote:
>> On 2/6/17 3:27 PM, Peter Nyikos wrote:
>>> On Monday, February 6, 2017 at 4:34:58 PM UTC-5, John Harshman wrote:
>
>>>>>> I'm with you there. Extinction and, perhaps, speciation rates, during
>>>>>> mass extinctions and otherwise, have had an influence on the course of
>>>>>> evolution.
>>>>>
>>>>> Right, and where is there a comparable role for genetic drift?
>>>>
>>>> Why, random extinction and speciation, of course, meaning any such
>>>> events not strongly related to particular characters of the species.
>>>
>>> There are many things responsible for random extinction besides
>>> genetic drift. Floods, fires, volcanic eruptions, a new predator
>>> or disease hitting a population without natural defenses...
>>
>> Genetic drift doesn't cause extinction. Nor does natural selection.
>
> Yes, it does, and populations with too little genetic diversity are
> prime targets for extinction by natural selection. Just as evolution
> within a population is also affected by natural selection.

Sorry, but that isn't natural selection. It's species selection.

>> We
>> were talking about analogs of these population-level phenomena at a
>> higher level. There is species drift as well as species selection.
>
> Natural selection is not an analog. It is both a population-level
> phenomenon and a phylum-level phenomenon, as in the case of
> some enigmatic Ediacaran organisms, believed to have succumbed
> to the development of predation by eumetazoans.

That's competition, not natural selection. You do not appear to know the
definition.

> It could well be that all the peer-reviewed studies of natural selection
> were done on the level of populations; but it would not follow that
> natural selection is a population-genetics phenomenon.

It would if you knew the definition of the term. I suppose you want to
substitute your idiosyncratic definition for the one commonly understood
by biologists. What give you license to do that?

[John Harshman]

On 2/7/17 6:12 AM, Peter Nyikos wrote:

> Behe's assertions are nuanced: the more complex the IC structure/system,
> the stronger the case for meeting Darwin's criterion
> of not being attainable through "numerous, successive, slight modifications".
> See pp. 39-40 of _Darwin's Black Box_.

Why would you think that assertion to be true? Would that not be
assuming a particular model of evolution, by the sequential addition of
invariant parts?

[Greg Guarino]

On 2/5/2017 7:28 AM, MarkE wrote:
> PS

>
> “[the zygote is] a few thousand genes and proteins, none of which can possibly hold any concept, in any language, of the structure and function of a human body....”

> --"Life Unfolding: How the human body creates itself" by Jamie A. Davies
>
You seem to be making the assumption that the zygote must contain a
blueprint for the finished organism; that every neural connection, every
organ, every vessel must somehow be specified in DNA.

I doubt that biologists think that (and the biologists among us can
correct me if I'm wrong).

My (extremely inexpert) take on it is that DNA helps determine the
chemical makeup of the cell. As cells reproduce, they produce somewhat
different configurations depending on their "environment"; said
environment notably including the other cells around them. In every case
what happens violates no laws of chemistry.

Cells in different parts of an embryo develop differently not because
there is an overarching blueprint, but simply because the chemical and
physical "neighborhood" around them is different. Certain genes switch
on or off, or at different times, or for different amount of time. Their
own "history" also plays a role. The configuration of a cell's ancestors
limit what kind of cell it can become.

That the finished creature is a squirrel, or begonia or sponge is
dependent on how DNA has set up the cells to grow and reproduce in their
"environment".





---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus

[Peter Nyikos]

On Tuesday, February 7, 2017 at 12:24:58 AM UTC-5, jillery wrote:
> On Mon, 6 Feb 2017 18:18:37 -0800 (PST), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Monday, February 6, 2017 at 4:19:58 PM UTC-5, MarkE wrote:
> >
> >> > > Ron, you're already in the sin-bin for talking and not listening. If this dry-retching of ID diatribe continues it'll be a red card.
> >> > >
> >> >
> >> > Run away in denial. Denial is all IDiots have and you know it. I have
> >> > just demonstrated that what you are doing is what the ID perps have been
> >> > doing for a couple of decades and all IDiocy is, is a stupid scam that
> >> > creationists are running on themselves.
> >
> >It is no more of a scam than Ron O ranting about "IDiocy" and yet
> >hardly giving any information on how evolutionary theory has
> >explained the evolution that has actually taken place on earth.
> >
> >> > You obviously have to do something different. The same old same old
> >> > isn't going to amount to anything.
> >
> >Ironic, this spiel from someone who has been regurgitating the same old
> >same old talk about a scam since 2002. And recycling whole paragraphs
> >of rant in the process.
> >
> >
> >> > Do something that the ID perps never tried. Actually try to figure out
> >> > if there is any science that you can actually do.
> >
> >Ron O is ignoring the elephant in the room -- Minnich, who testified
> >in Dover about the experiments he and his students did on the bacterial
> >flagellum.

To add to the irony, Ron O actually DID talk about Minnich in
the part I snipped, but here he suffered from a lapse of memory.

> >Not only did they show that the flagellum they were testing
> >was irreducibly complex -- each and every one of its 30+ parts was
> >essential to the function of swimming -- but they also did experiments
> >that suggested that the Type III mechanism might have evolved from the
> >flagellum through loss of parts, rather than the flagellum evolving from
> >the type III mechanism through addition of parts.
>
>
> Peter Nyikos is ignoring the elephant in the room, that Minnich's
> experiments merely showed the existence of Behe's IC, but did nothing
> to show Behe's claims about IC, specifically that such systems could
> not have evolved.

Behe never made such a claim. Re-read that item at the top of p. 40
of _Darwin's Black Box_ to see what claim he did make. You've quoted
it yourself and had it re-quoted to you.

As for the elephant -- well, Ron O was ignoring the elephant of
needing to show that the various experiments which supposedly
showed the latest version of evolutionary theory to be true,
actually did show that.

Oh, wait, I'm just falling in line with your "show" jargon.
What Ron O failed to do was to show that various experiments
provided evidence for this or that feature of evolutionary theory.
He is doing the opposite of the alleged "switch scam": attacking the
weaknesses of ID theory instead of presenting the case for
evolutionary theory.

> More telling, neither has Behe. To the best of my
> knowledge, nobody in the IC community has done any experiments which
> showed the implausibility of evolved IC.

Nor has anyone in the anti-ID community, or even the biological
community [1] done any experiments to show that the bacterial
flagellum could have evolved by the usual processes studied
in evolutionary biology, within the time it seems to have taken
to evolve.

[1] What percentage of the biological community knows enough about ID theory
to take an informed stand on it? My estimate: less than 1 percent. And
the reason is the distorted picture of IC and ID that has become the
virtual reality in which most biologists work. You are presenting
part of that distorted picture, both above and below:

> OTOH Muller described
> evolved IC decades before Behe wrote DBB.

This misconception is part of that virtual reality. Muller never
described any IC systems. He merely described systems to which
ONE OR MORE PARTS are essential. The definition of IC is
that EACH AND EVERY PART is essential to the basic function.

And yes, it stands to reason that biological organisms won't do
backup systems for each and every part. You could suffer amputation
of a leg and still be able to function at almost everything you do.

>
> ><snip irrelevant lecture by Ron O>
>
> <snip remaining irrelevant noise by Peter Nyikos>

What I wrote above was highly relevant to Ron O's blather,
and so was the following part that you snipped:

_____________________________ repost ____________________

> > Why not do the sensible thing and put up your model of creation

ID theory doesn't hypothesize creation; it hypothesizes intelligent
design, as its name implies.

> > to figure out if there is anything that you can do to verify any parts
> > of it? That isn't a trap. If you want to know if your model is valid
> > you have to verify it somehow. The only reason the ID perps don't do
> > that is because they already know that the answers are not what they
> > want. That is how sad the ID scam is at this time.

Ron O has no reason whatsoever for thinking this. Part of his problem
is that he doesn't realize that the ID emphasis on the weaknesses of
evolutionary theory is just the other side of the coin on anti-ID folks
like him harping on the weaknesses of ID theory.

> > Why don't IDiots persue such research?

See above about Minnich.

========================== end of repost ++++++++++++++++

Also, I do believe that what I wrote later on was relevant to MarkE's
questions that he posed to Ron O, which were:

"If you don't mind me asking, what's your story, what are your
areas of interest and reasons for posting here?
Asking out of genuine interest - happy to reciprocate."

So far, MarkE hasn't posted a "reciprocation" and so it is very unclear
whether Ron O answered his questions the way MarkE had in mind. And
that was the issue which I was addressing with the opening comment
of the rest of my post:

"Well, you got another long spiel in reply, but did he
tell you anything along the lines which you had in mind?"

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

On Monday, February 6, 2017 at 4:24:57 PM UTC-5, John Harshman wrote:
> On 2/6/17 12:37 PM, Peter Nyikos wrote:
> > On Monday, February 6, 2017 at 3:09:58 PM UTC-5, John Harshman wrote:
> >
> > Fascinating, how little time it took you to find me, John. The UTC-5
> > is Eastern Standard time. I've removed the ambiguity in the following
> > attribution line:
> >
> >> On 2/6/17 11:54 AM, Pacific Standard Time, Peter Nyikos wrote:

> >>> It is that alien colonists, after drastically sterilizing earth of its
> >>> indigenous organisms (all microorganisms), brought some of their own
> >>> creatures with them -- prokaryotes, protists, algae, sea creatures
> >>> to populate the waters of the earth -- so as to colonize it.
> >>
> >> An interesting theory. How would one test it? I would assume that it
> >> would be tested from the fossil record, and we would expect some major
> >> point of discontinuity in that record, pre-sterilization and
> >> post-sterilization. I don't see such a thing. Do you have a candidate?
> >
> > The first unambiguous evidence of multicellular organisms could be such a point.
> > What evidence have we that the unicellular organisms that preceded them
> > had anything like our genetic code? Stromatolite fossils billions of
> > years old don't give away the secrets of the individuals that produced them,
> > do they?
>
> Present a horizon you think might be the correct one and we'll discuss it.

Unlike directed panspermia, this is not a hypothesis I take seriously.
I only brought it up to demonstrate how Meyer's book _Darwin's Doubt_
does not necessarily entail a supernatural source of ID in the Cambrian
explosion.

And Meyer never claims in the book that it does entail that.
[Yes, you might well be surprised in view of the incredible amount of
wasted words on the blogosphere that assert that it does entail that,
and/or use that assertion as a foundation for further GIGO.]

> > Reefs are an interesting parallel. In the last half-billion years there
> > have been eons where no evidence of reefs has been found, and several
> > distinct episodes of reef-building activity. And the first one was
> > by pleosponges, very different from any reef builders of today.
>
> I don't see why this would be considered a parallel.

Why would reefs NOT be a parallel to stromatolites?

>And what are the
> eons in which there were no reefs? Not familiar.

There was a fascinating article in _Scientific American_ about that, some time
in the 1960's. This was back at the time when that magazine was far better
from a scientific viewpoint than it is now. IIRC it identified four widely
separated reef building episodes, each with different animals as their
foundation.

Unfortunately, I don't remember reading anything more recent about this.
All I can add is that it appears that the coral reefs of the present time
are vulnerable to global warming, and the earth has generally been
warmer than it is now.

I recently saw a fascinating graphic on the temperatures of the Cenozoic
at the student center of the University of Cincinnati. It filled
a whole wall and showed that even present-day temperatures are nowhere
near what prevailed at the beginning of the Miocene, which in turn were
nowhere near the Paleocene Maximum.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of S. Carolina at Columbia
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

On Tuesday, February 7, 2017 at 10:34:57 AM UTC-5, John Harshman wrote:
> On 2/7/17 6:39 AM, Peter Nyikos wrote:
> > On Monday, February 6, 2017 at 9:00:00 PM UTC-5, John Harshman wrote:
> >> On 2/6/17 3:27 PM, Peter Nyikos wrote:
> >>> On Monday, February 6, 2017 at 4:34:58 PM UTC-5, John Harshman wrote:
> >
> >>>>>> I'm with you there. Extinction and, perhaps, speciation rates, during
> >>>>>> mass extinctions and otherwise, have had an influence on the course of
> >>>>>> evolution.
> >>>>>
> >>>>> Right, and where is there a comparable role for genetic drift?
> >>>>
> >>>> Why, random extinction and speciation, of course, meaning any such
> >>>> events not strongly related to particular characters of the species.
> >>>
> >>> There are many things responsible for random extinction besides
> >>> genetic drift. Floods, fires, volcanic eruptions, a new predator
> >>> or disease hitting a population without natural defenses...
> >>
> >> Genetic drift doesn't cause extinction. Nor does natural selection.
> >
> > Yes, it does, and populations with too little genetic diversity are
> > prime targets for extinction by natural selection. Just as evolution
> > within a population is also affected by natural selection.
>
> Sorry, but that isn't natural selection. It's species selection.

All you are doing here is showing how unnatural the official
population genetics definition of "natural selection" is. It is as
unnatural as the definition of "evolution" as the change in allele
frequencies WITHIN a population.

When was the term "natural selection" restricted to population genetics?

> >> We
> >> were talking about analogs of these population-level phenomena at a
> >> higher level. There is species drift as well as species selection.
> >
> > Natural selection is not an analog. It is both a population-level
> > phenomenon and a phylum-level phenomenon, as in the case of
> > some enigmatic Ediacaran organisms, believed to have succumbed
> > to the development of predation by eumetazoans.
>
> That's competition, not natural selection.

Another unnatural definition. The competition was not between the
ediacaran organisms and their predators. If anything, the
competition was between the various predators for this wonderful
food supply.

> You do not appear to know the
> definition.

Speaking of definitions, have you ever found a published paper in biology,
peer-reviewed or not, that endorses your definition of
"X is in the same population as Y"? I refer to the one whereby every
eukaryote on earth is in the same population as the LCA of all
eukaryotes?

At one point, you tried to back away from it by saying, that if
"population" is the problem, then I should substitute "lineage".
But you never officially repudiated your definition of
"population", did you?

> > It could well be that all the peer-reviewed studies of natural selection
> > were done on the level of populations; but it would not follow that
> > natural selection is a population-genetics phenomenon.
>
> It would if you knew the definition of the term.

There is no difference between predators reducing a population
of prey and them reducing various scattered populations of
prey of the same species. Or to take an example from botany:
the chestnut blight destroyed the main population of American
chestnuts and would have caused the whole [sub?]species to become
eventually extinct if humans had not intervened to take drastic
steps against the blight that earlier humans had introduced.

> I suppose you want to
> substitute your idiosyncratic definition for the one commonly understood
> by biologists.

pot: kettle :: population : natural selection

>What give you license to do that?

Reason and common sense, as well as the general public perception
of the term. None of which apply to your idiosyncratic definition
of "population".

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

Univ. of South Carolina (Columbia)
http://www.math.sc.edu/~nyikos/

[Peter Nyikos]

No, Behe explicitly allows for indirect, circuitous routes at the top
of page 40.

You've been misled by yet another part of the virtual reality
that has grown up around Behe in the blogosphere.

Peter Nyikos

[Robert Camp]

On 2/7/17 7:32 AM, MarkE wrote:
> On Tuesday, February 7, 2017 at 2:30:00 AM UTC+9:30, Robert Camp
> wrote:
>> On 2/6/17 3:43 AM, MarkE wrote:
>>> On Monday, February 6, 2017 at 2:15:00 AM UTC+9:30, Robert Camp
>>> wrote:
>>>> On 2/5/17 4:15 AM, MarkE wrote:

<snip>

Depends upon the context. There are legitimate conclusions to be based
upon low probability calculations. Here, in both yours and Dembski's
cases, we have an illegitimate use (we have discussed this before).
There is no logic or rationale that supports using low probability
events or calculations (which are obligately dependent upon natural law)
to infer non-natural agency. It's a blatant category error. It just
doesn't follow.

Yes, there is such a thing as useful (or "scientific" if you will)
incredulity. And low probability events are ones in which legitimate
questions may be raised. But for something to be an argument from
incredulity one must, first, be making an argument. "Scientific"
incredulity takes the form of hypothesis, test, and repeat. It doesn't
assert an unwarranted inference to unevidence, untestable agency.

I may be reading you incorrectly, but your incredulity in the preceding
posts doesn't seem to be a call for more research, it seems to be a call
to think of these events as presenting a dichotomy: if there is no
natural explanation, then non-natural inference is justified.

There's nothing scientific about that kind of incredulity.

> Can this be applied to my 1 to 35 trillion observation? I don't think
> so, not directly. I'm not even offering a fully-formed argument (you
> can go now, I've got this). Rather, I'm raising a flag, and saying
> this doesn't seem to add up in a big way...How do others see it?

I have to wonder if you've asked yourself what I consider to be the
obvious critical questions before raising that flag, e.g., Do I know
enough about this to say that something doesn't add up?, Have I examined
my own convictions, some of which may confound my interpretation of the
data? Does this "flag" actually exist as an important conundrum in the
minds of those I consider experts, or are they merely expressing their
own human tendency for wonder?

For myself, I see nothing that doesn't add up. That doesn't mean I know
everything, or even much at all. It simply means I'm not assuming I know
enough to know how, or if, things *should* add up. I'm human, my mind is
easily boggled. There is intellectual freedom in recognizing and
accepting my own cognitive limitations.

> Is that hopelessly subjective? Well, it's not going to published in
> Nature any time soon. But here's the logic of it which I think has
> merit:
>
> The 1 to 35 trillion ratio would be unremarkable if it were a single
> bacterium multiplying thus. Nothing particularly novel created, i.e.
> low algorithmic complexity. However, with human development, we have
> very, very high functional complexity. I can't put a number on it,
> but there's wide agreement to describe our brain as the most complex
> object known. Both structural and functional complexity.

I'm going to accept the above for the purposes of discussion. But I just
want to note some of the possible difficulties with it,

- "Nothing novel" is a judgement that I don't necessarily consider
accurate or defensible
- complexity ("high functional" or "low algorithmic) can be a
problematic concept if not stringently defined, human intuition is not a
great guide (e.g, which is more complex, a perfectly spherical metal orb
or an irregular river stone?)
- the assumed import of the human brain being "the most complex object
known", which argument I'm guessing you'd drop like a hot rock if we
discover that something else is more complex

> So here's my first claim: we can say there must be a very high
> information content within that single parent cell. I'm proposing a
> broad definition information here, which is the capability to produce
> the structure that is a human, via the constrained process of cell
> division and differentiation.

I don't think you can say that at all, unless you are including all of
biochemistry within your broad definition of information. No one thinks
there's a tiny, incredibly complex and specific blueprint buried in the
cell's "information." DNA makes proteins, proteins fold and combine in
certain predictable ways. Those simple processes propagate and replicate
within expected environmental constraints to produce predictably complex
structures and functions.

It's all incredibly wondrous, but that wonder (mine, at least) is a
reaction to the ability of fundamental physics and chemistry to result
in intricate and elaborate aggregations capable of functions that go far
beyond their simple beginnings.

> Now if 8% of our DNA is functional, that's 64MB of data in the
> genome. So we can safely conclude that by any known means, that's
> nowhere near enough information to specify the most complex object
> known.

No, we cannot safely conclude that. It is, in fact a rash conclusion
based upon assumptions and misconceptions.

The problem, once again, is that you are looking at the final product
and assuming there must be a direct one-to-one correspondence of
structural and functional complexity to some kind of information
specification in the original cell. That's not what happens. That is, in
fact the way a designer might do things. Natural selection has happened
upon a more efficient and elegant process. Simple, iterative chemical
operations can give rise to biological complexity. We know this to be a
fact, we see it happen every minute of every day.

> The cell is an integrated physicochemical system, but again it
> seems safe to say that the only viable alternative source of this
> information in the cell is the proteins it can produce.

That is reasonable, though seemingly a contradiction of your previous
statement.

> I'm assuming that development occurs naturally, i.e. without a need
> for divine intervention.
>
> Therefore, the information (as defined) must reside in:
>
> 1. The genome, but be much more than 8% being functional, and/or
> employ storage with efficiency well beyond what our current
> technology or understanding;

> 2. The information is in the 2 million proteins the body is capable
> of producing; i.e. as more than a linear polymer, rather the complex
> specific binding properties of these intricately folded 3D
> molecules;
>
> 3. A combination or 1 and 2.

Leaving out the whole "well beyond what our current technology or
understanding" thing, sure.

> The median protein length in H. sapiens is 375 amino acids, of say 5
> bits each, giving about 0.5GB of "linear" (pre-folding) information.
>
> Jamie A. Davies interprets this as: “[the zygote is] a few thousand
> genes and proteins, none of which can possibly hold any concept, in
> any language, of the structure and function of a human body....”

I haven't read anything he's written so I don't know the context in
which he's speaking here, but I'd have to agree. Anyone looking for a
language, or a "concept", of the structure and function of a human body
inside a zygote, as you seem to be doing, is missing the point by a wide
margin.

There's no blueprint or complex specification code down there in the
depths of the cell, there is just chemistry.


<snip>

[scienceci...@gmail.com]

MarkE wrote:
>( 3.5x10^13 )

>That's an estimate of the
>number of cells in the
>human body.

...Snip to 'hat trick' point

>A single cell (the fertilised
>ovum) becomes

>35,000,000,000,000 >cells...including the most
>complex object known.

>That's 100 times the number
>of stars in our galaxy.

>It's the ultimate rabbit-out-
>of-a-hat trick.

That's misdirected logic. Go atomic not galactic: there are 4.8 X 10^27 atoms in the human body.

The 'hat trick' is roughly a flow chart of energy: solar production of energy to earth, energy absorption by earth, energy absorption by living things, the simple additive principle of eating for two during pregnancy for the "becoming" one to 3.5x10^13.

And to place this in a broader related context; about 10,000 years ago there were about 40,000 humans living on earth. Today there are about 7.4 billion humans. Lots of energy production going on (including red shift) at the atomic level. Proof is that this population expansion happened.

SC RED

[John Harshman]

But it doesn't demonstrate that. It's clear from the fossil record and
from genetic data that the Cambrian explosion was not an instance of the
scenario you describe.

> And Meyer never claims in the book that it does entail that.
> [Yes, you might well be surprised in view of the incredible amount of
> wasted words on the blogosphere that assert that it does entail that,
> and/or use that assertion as a foundation for further GIGO.]

Of course he doesn't. His last chapter includes a statement that he
doesn't, but it's a nudge-nudge, wink-wink sort of thing. Plausible
deniability.

>>> Reefs are an interesting parallel. In the last half-billion years there
>>> have been eons where no evidence of reefs has been found, and several
>>> distinct episodes of reef-building activity. And the first one was
>>> by pleosponges, very different from any reef builders of today.
>>
>> I don't see why this would be considered a parallel.
>
> Why would reefs NOT be a parallel to stromatolites?

I had no idea that's the parallel you intended. Yes, reefs and
stromatolites are both sorts of bioherms, but there the similarity ends.
I don't see the relevance of this to anything we were talking about.

>> And what are the
>> eons in which there were no reefs? Not familiar.
>
> There was a fascinating article in _Scientific American_ about that, some time
> in the 1960's. This was back at the time when that magazine was far better
> from a scientific viewpoint than it is now. IIRC it identified four widely
> separated reef building episodes, each with different animals as their
> foundation.

True. But in the intervals between these, are you sure there were no
reefs? There have been algal, archaeocyathan, tabulate, octacoral,
rudist, and hexacoral reefs, at least. But no reefs? When?

> Unfortunately, I don't remember reading anything more recent about this.
> All I can add is that it appears that the coral reefs of the present time
> are vulnerable to global warming, and the earth has generally been
> warmer than it is now.

Warming, per se, is not the cause of coral reef problems. Those are
rapid sea rise and ocean acidification. Reefs in general have done just
fine during warm periods.

> I recently saw a fascinating graphic on the temperatures of the Cenozoic
> at the student center of the University of Cincinnati. It filled
> a whole wall and showed that even present-day temperatures are nowhere
> near what prevailed at the beginning of the Miocene, which in turn were
> nowhere near the Paleocene Maximum.

True, but again irrelevant.

[John Harshman]

Well, it's what Darwin was talking about (I mean within-population
processes, not population genetics per se, which of course he had no
knowledge of), so I suppose it would be from the beginning.

Sorry if you don't like standard biological language. Why?

>>>> We
>>>> were talking about analogs of these population-level phenomena at a
>>>> higher level. There is species drift as well as species selection.
>>>
>>> Natural selection is not an analog. It is both a population-level
>>> phenomenon and a phylum-level phenomenon, as in the case of
>>> some enigmatic Ediacaran organisms, believed to have succumbed
>>> to the development of predation by eumetazoans.
>>
>> That's competition, not natural selection.
>
> Another unnatural definition. The competition was not between the
> ediacaran organisms and their predators. If anything, the
> competition was between the various predators for this wonderful
> food supply.

You have your personal definition of "competition" too. We aren't going
to get very far if you insist on all your own words. Impenetrability.

>> You do not appear to know the
>> definition.
>
> Speaking of definitions, have you ever found a published paper in biology,
> peer-reviewed or not, that endorses your definition of
> "X is in the same population as Y"? I refer to the one whereby every
> eukaryote on earth is in the same population as the LCA of all
> eukaryotes?

I haven't looked. And I doubt that such a thing exists. I was merely
pointing out that if we consider a population as extending over time,
there is no point at which we can say "this is a different population
from the previous generation".

> At one point, you tried to back away from it by saying, that if
> "population" is the problem, then I should substitute "lineage".
> But you never officially repudiated your definition of
> "population", did you?

It isn't my definition. It isn't a definition at all.

>>> It could well be that all the peer-reviewed studies of natural selection
>>> were done on the level of populations; but it would not follow that
>>> natural selection is a population-genetics phenomenon.
>>
>> It would if you knew the definition of the term.
>
> There is no difference between predators reducing a population
> of prey and them reducing various scattered populations of
> prey of the same species. Or to take an example from botany:
> the chestnut blight destroyed the main population of American
> chestnuts and would have caused the whole [sub?]species to become
> eventually extinct if humans had not intervened to take drastic
> steps against the blight that earlier humans had introduced.

True. But I don't see how that relates to your claim about natural
selection. Your points are almost never clear unless you actually state
them, which you seldom do.

>> I suppose you want to
>> substitute your idiosyncratic definition for the one commonly understood
>> by biologists.
>
> pot: kettle :: population : natural selection

I do not want to change the standard definition of population and never
have.

>> What give you license to do that?
>
> Reason and common sense, as well as the general public perception
> of the term. None of which apply to your idiosyncratic definition
> of "population".

The general public has no real clue about what natural selection is, and
at any rate should not be considered the judge of scientific terms. And
as for reason and common sense, so far I haven't seen either.

[John Harshman]

On 2/7/17 10:19 AM, Peter Nyikos wrote:
> On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
>> On 2/7/17 6:12 AM, Peter Nyikos wrote:
>>
>>> Behe's assertions are nuanced: the more complex the IC structure/system,
>>> the stronger the case for meeting Darwin's criterion
>>> of not being attainable through "numerous, successive, slight modifications".
>>> See pp. 39-40 of _Darwin's Black Box_.
>>
>> Why would you think that assertion to be true? Would that not be
>> assuming a particular model of evolution, by the sequential addition of
>> invariant parts?
>
> No, Behe explicitly allows for indirect, circuitous routes at the top
> of page 40.

Which indirect routes does he allow for, and why don't such routes
destroy his argument?

[Peter Nyikos]

On Tuesday, February 7, 2017 at 3:54:57 PM UTC-5, John Harshman wrote:
> On 2/7/17 10:19 AM, Peter Nyikos wrote:
> > On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
> >> On 2/7/17 6:12 AM, Peter Nyikos wrote:
> >>
> >>> Behe's assertions are nuanced: the more complex the IC structure/system,
> >>> the stronger the case for meeting Darwin's criterion
> >>> of not being attainable through "numerous, successive, slight modifications".
> >>> See pp. 39-40 of _Darwin's Black Box_.
> >>
> >> Why would you think that assertion to be true? Would that not be
> >> assuming a particular model of evolution, by the sequential addition of
> >> invariant parts?
> >
> > No, Behe explicitly allows for indirect, circuitous routes at the top
> > of page 40.

NOTE TO ALL READERS:

I would be interested in hearing of ANY experiments or scenarios bearing
on indirect, circuitous routes to the various IC systems that
are described in _Darwin's Black Box_.

Ironically, the only route of which I know is a DIRECT route
involving "numerous, successive, slight modifications"
to a short clotting system to produce the long clotting cascade.
It was described by Kenneth Miller and also by Keith Robison in the
Talk.Origins Archive. It also applies to the "complement pathway"
of the immune system.

Before you answer, though, please read what I write below about the
bacterial flagellum.

> Which indirect routes does he allow for, and why don't such routes
> destroy his argument?

He makes no restrictions, and his nuanced argument up there is not
easily destroyed. Did you have in mind the nonexistent virtual-reality
argument that the IC systems prove intelligent design?

Behe's nuanced argument could, of course, be weakened by specific examples
of circuitous routes to the various systems in _DBB_.
However, the usual anti-ID mantra at this point, "exaptation," is
too general a concept to be an indirect route for specific examples
like the bacterial flagellum.

For that, you would need some candidates for exaptation that
(1) don't pose big problems for their own evolution and
(2) can be exapted in concretely describable ways.

In the case of the bacterial flagellum, Minnich's testimony at Dover
included describing experiments addressing point (2) where the
candidate every anti-ID blogger and scientist puts forth
-- the type III mechanism -- is concerned. His experiments
ended in failure to attach the long flagellin filament
("tail" or "propeller").

I know of no experiments that succeeded in producing that effect,
do you? And yet, I think a publishable paper could result from success.


As to (1), I know of no effort by anti-ID types to show that the
Type III mechanism, which also looks to be IC, was exapted from
something else. Nor have I seen any scenario for its assembly,
either by a direct or circuitous route. Of course, there is always
the possibility, suggested by Minnich at Dover, that it evolved
from the bacterial flagellum through LOSS of the "propeller" and
the "hook."

But I don't think you want to go there, John.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/
nyikos "at" math.sc.edu

[Peter Nyikos]

Is this supposed to be a satire on jonathan's notion that all you need to
explain the existence of us human beings and all other living things
is self-organization and a bit of chaos theory?

If not, are you trying to outdo jonathan in some way?

Peter Nyikos

[John Harshman]

I wasn't asking about restrictions but about what sorts of scenarios he
mentions. There is, for example, the scaffolding pathway, in which parts
go away until the ones that remain are IC. And there is the addition
with modification of function pathway, in which parts that make an
original function better are added, and the original parts gradually
lose that aspect of their function. How many of those does he mention,
and which ones?

> Did you have in mind the nonexistent virtual-reality
> argument that the IC systems prove intelligent design?

No. I had in mind what I said.

> Behe's nuanced argument could, of course, be weakened by specific examples
> of circuitous routes to the various systems in _DBB_.
> However, the usual anti-ID mantra at this point, "exaptation," is
> too general a concept to be an indirect route for specific examples
> like the bacterial flagellum.
>
> For that, you would need some candidates for exaptation that
> (1) don't pose big problems for their own evolution and
> (2) can be exapted in concretely describable ways.
>
> In the case of the bacterial flagellum, Minnich's testimony at Dover
> included describing experiments addressing point (2) where the
> candidate every anti-ID blogger and scientist puts forth
> -- the type III mechanism -- is concerned. His experiments
> ended in failure to attach the long flagellin filament
> ("tail" or "propeller").
>
> I know of no experiments that succeeded in producing that effect,
> do you? And yet, I think a publishable paper could result from success.

Sorry, what effect? Are you saying that if laboratory experiments fail
to reproduce a particular evolutionary pathway, that argues that the
pathway doesn't exist?

> As to (1), I know of no effort by anti-ID types to show that the
> Type III mechanism, which also looks to be IC, was exapted from
> something else. Nor have I seen any scenario for its assembly,
> either by a direct or circuitous route. Of course, there is always
> the possibility, suggested by Minnich at Dover, that it evolved
> from the bacterial flagellum through LOSS of the "propeller" and
> the "hook."
>
> But I don't think you want to go there, John.

I have no interest in talking about the bacterial flagellum at all. Must
you constantly introduce digressions that then take over the conversation?

[Peter Nyikos]

Nice to see you keeping the rest of the readers in mind with this
otherwise blatantly "preaching to the choir" comment.

> It's clear from the fossil record and
> from genetic data that the Cambrian explosion was not an instance of the
> scenario you describe.

Now THIS part is not preaching to the choir! In fact the only
reason I can see any sense in this part is that you seem to be
assuming just one attempt at colonization instead of three
separate ones: one at the time of Doushanto, one at the beginnig
of the Ediacara mini-explosion, and one at the beginning of
the "main pulse of the Cambrian explosion," as Meyer puts it.

All three would have to be by colonists with (essentially) our genetic code,
but that could be explained by hypothesized by assuming they arose via
directed panspermia.

> > And Meyer never claims in the book that it does entail that.
> > [Yes, you might well be surprised in view of the incredible amount of
> > wasted words on the blogosphere that assert that it does entail that,
> > and/or use that assertion as a foundation for further GIGO.]
>
> Of course he doesn't. His last chapter includes a statement that he
> doesn't, but it's a nudge-nudge, wink-wink sort of thing. Plausible
> deniability.

By a similar reasoning, your innumerable put-downs of me
over the years would be a nudge-nudge, wink-wink sort of sign that
you want people to think I am a closet creationist and a
closet Feduccia partisan. This is especially true of the way you
you kept unfairly accusing me of bending over backwards beyond all
reason to defend Meyer and Feduccia.

But what has really been happening all these years is that I keep
applying the philosophy behind the 6th amendment to the US Constitution.
And you are playing the role of prosecuting attorney to the hilt,
including REAL bending over backwards to shield their two most outrageous
critics, Prothero and Prum, from getting what's coming to them.

> >>> Reefs are an interesting parallel. In the last half-billion years there
> >>> have been eons where no evidence of reefs has been found, and several
> >>> distinct episodes of reef-building activity. And the first one was
> >>> by pleosponges, very different from any reef builders of today.
> >>
> >> I don't see why this would be considered a parallel.
> >
> > Why would reefs NOT be a parallel to stromatolites?
>
> I had no idea that's the parallel you intended. Yes, reefs and
> stromatolites are both sorts of bioherms, but there the similarity ends.

Wrong. Just as reefs can be built by very different organisms, it
stands to reason that stromatolites could too. And my point up
there is that, while we know enough about the reef builders of the
last 520 million years to accurately place them in the Tree of Life,
we know nothing about the stromatolite-builders of 3.5 billion years
ago, except that they were microorganisms.

> >> And what are the
> >> eons in which there were no reefs? Not familiar.
> >
> > There was a fascinating article in _Scientific American_ about that, some time
> > in the 1960's. This was back at the time when that magazine was far better
> > from a scientific viewpoint than it is now. IIRC it identified four widely
> > separated reef building episodes, each with different animals as their
> > foundation.
>
> True. But in the intervals between these, are you sure there were no
> reefs? There have been algal, archaeocyathan, tabulate, octacoral,
> rudist, and hexacoral reefs, at least. But no reefs? When?

Alas, I haven't the time to undertake a search for that _Scientific

American_ article. And as I said:
>
> > Unfortunately, I don't remember reading anything more recent about this.

Peter Nyikos
Professor, Dept. of Maths -- standard disclaimer--

[Peter Nyikos]

NONE. He leaves all that up to his critics. And you've come up with
some general categories of scenarios below, but no actual scenarios.

> There is, for example, the scaffolding pathway, in which parts
> go away until the ones that remain are IC. And there is the addition
> with modification of function pathway, in which parts that make an
> original function better are added, and the original parts gradually
> lose that aspect of their function. How many of those does he mention,
> and which ones?

None, and AFAIK his critics have come up with a goose egg as far
as actual scenarios for indirect evolution of the IC systems in his book.
Hence my NOTE TO ALL READERS above.

> > Behe's nuanced argument could, of course, be weakened by specific examples
> > of circuitous routes to the various systems in _DBB_.
> > However, the usual anti-ID mantra at this point, "exaptation," is
> > too general a concept to be an indirect route for specific examples
> > like the bacterial flagellum.
> >
> > For that, you would need some candidates for exaptation that
> > (1) don't pose big problems for their own evolution and
> > (2) can be exapted in concretely describable ways.
> >
> > In the case of the bacterial flagellum, Minnich's testimony at Dover
> > included describing experiments addressing point (2) where the
> > candidate every anti-ID blogger and scientist puts forth
> > -- the type III mechanism -- is concerned. His experiments
> > ended in failure to attach the long flagellin filament
> > ("tail" or "propeller").
> >
> > I know of no experiments that succeeded in producing that effect,
> > do you? And yet, I think a publishable paper could result from success.
>
> Sorry, what effect?

Genetically attaching a hook and filament to a Type III mechanism to
produce an organelle analogous (but not necessarily homologous) to
bacterial flagellae.

> Are you saying that if laboratory experiments fail
> to reproduce a particular evolutionary pathway, that argues that the
> pathway doesn't exist?

Of course not. I don't have the tremendous confidence some people
seem to have in the ability of 21st century scientists to duplicate
things that took eons to evolve, if evolve they did.

> > As to (1), I know of no effort by anti-ID types to show that the
> > Type III mechanism, which also looks to be IC, was exapted from
> > something else. Nor have I seen any scenario for its assembly,
> > either by a direct or circuitous route. Of course, there is always
> > the possibility, suggested by Minnich at Dover, that it evolved
> > from the bacterial flagellum through LOSS of the "propeller" and
> > the "hook."
> >
> > But I don't think you want to go there, John.
>
> I have no interest in talking about the bacterial flagellum at all. Must
> you constantly introduce digressions that then take over the conversation?

I wrote for the general readership this time, as my all-caps note at
the very beginning indicated. Here in NGG, these all-caps hit the reader
in the usual display of part of one line from the post.

Your shoot-from-the-hip questions, desirous of being spoon-fed details
from Behe's book, were too gradualist for my taste, and I decided the
topic needed quicker development.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

University of South Carolina, Columbia
http://people.math.sc.edu/nyikos/

[Peter Nyikos]

On Tuesday, February 7, 2017 at 10:34:57 AM UTC-5, MarkE wrote:
> On Tuesday, February 7, 2017 at 2:30:00 AM UTC+9:30, Robert Camp wrote:
> > On 2/6/17 3:43 AM, MarkE wrote:
> > > On Monday, February 6, 2017 at 2:15:00 AM UTC+9:30, Robert Camp
> > > wrote:
> > >> On 2/5/17 4:15 AM, MarkE wrote:
> > >>> That's an estimate of the number of cells in the human body.
> > >>>
> > >>> Apologies for labouring this point, but here's a different angle,
> > >>> in search of answers as yet not forthcoming.
> > >>>
> > >>> An adult human is a highly integrated, autonomous, functional
> > >>> system. The human brain is recognised as "the most complex object
> > >>> known."

The brain of a sperm whale is about four times as big, but we have
no idea whether it could duplicate all the feats that the human mind
has accomplished.

And so it would seem that heckling someone who is enthusiastic about
the wonders of the world revealed by science is to be discouraged
more than heckling a stage magician. For some reason, Camp seems to
draw the opposite conclusion with his behavior all through this post.

> > What that means, in the case of the
> > former, is that it's okay (in fact encouraged) for people to bring along
> > a willingness to accept extravagant assumptions up front. In the case of
> > the latter, people need to divest their reasoning of unwarranted
> > assumptions if they are to be successful.
> >
> > > Then come dogs, cats, and an A
> > > to Z of animals, in their millions, all assembling on a nearby plain
> > > for a sublimely choreographed performance of The Lion King.
> >
> > I have mentioned before that you seem to have trouble eliminating
> > assumed conclusions from your analogies. This one is quite the whopper.
> > It may be that your intention was to include a bit of self-parody here,
> > and if so then well done. If not, you really need to re-examine your
> > thought processes.

Camp here shows how he has no sense of humor when the joke is on him.

> > > You’re
> > > sitting there alone, still shouting for a refund, but everyone else
> > > including your friends have long since left to enjoy the spectacle.
> >
> > This canard is getting a bit long in the tooth. Can't we all agree that
> > the, "Oh, you're too literal and detached to recognize the "magic" of it
> > all" trope is an unworthy approach?
>
> Analogies are like bicycles, you can ride them too far. This analogy is partly for fun (the bits where the analogy doesn't hold), but also as a broad interpretation of your response (all the other bits).
>
> > > But here's the real problem. I'm not saying gee-whiz isn't 35
> > > trillion a big number. I'm saying it's a big *ratio*. A mind-boggling
> > > ratio. Somehow, that single cell, whose contents give no clue of the
> > > universe within, explodes into unmatched complexity and function.
> >
> > It seemed to me that "isn't 35 trillion a big number" was exactly what
> > you were saying, but we can move on. So let me ask, how about 70
> > trillion cells from a single fertilized egg (in the case of identical
> > twins)? Is that twice as mind-boggling? Does that constitute twice the
> > compelling argument against natural selection? How about the notion that
> > bacteria can achieve the same ratios, does the fact that they're not
> > human diminish that feat?
> >
> > The obvious point here is that these are all mere facts of nature. That
> > you choose to be boggled by them is much more a reflection of your own
> > assumptions and proclivities than anything inherent in those facts.

This one-size-fits-all formula can be used to pooh-pooh any
natural phenomenon at all, depending on Camp's proclivities.

> > And choosing to believe that in making this observation I am somehow
> > inured to the wonder of nature is also a reflection of your
> > proclivities, but not in a good way.

Of course, Camp is leaving us completely in the dark as to
what natural phenomena he COULD be awestruck by. But he still
can't resist indulging in pompous pontification.

> > >>> It's the ultimate rabbit-out-of-a-hat trick.
> > >>
> > >> It obviously seems so to you. I see no reason or evidence that
> > >> points to such a conclusion.
> > >>
> > >>> This is not an argument from incredulity, or god of the gaps.
> > >>
> > >> It is clearly exactly those things - an argument from incredulity
> > >> and a gap argument.
> > >
> > > There are two kinds of incredulity. One is due to ignorance or lack
> > > of imagination, leading to a probability underestimate.
> > >
> > > The other is used by science all the time. Dawkins puts it this way:
> > > "we can accept a certain amount of luck in our explanations, but not
> > > too much." Too much, and others will rightly be incredulous.

<snip for focus>

> Okay, that's a thoughtful set of responses which deserve a serious reply.
>
> I concede it is tricky to decisively demonstrate "argument from legitimate scientific incredulity" (to use the positive form). Dembski proposed a "universal probability bound" of 1 in 10^150 for this purpose - a number which "corresponds to an upper limit on the number of physical events that could possibly have occurred in the observable part of the universe since the big bang." He has quantified Dawkins' "too much luck".
>
> Would you agree with this approach, in principle if not Dembski's number?

As an agnostic who would love to see more evidence of a benevolent God,
I do agree with this approach in principle. The fine-tuning of the
physical constants is another set of phenomena that call for "legitimate scientific incredulity." But I reluctantly agree with Martin Rees, the
Cambridge physicist and Astronomer Royal, that the existence of a
superastronomical number of parallel universes, most of which are
pure garbage, is more likely than the existence of a supernatural
creator/designer.

> Can this be applied to my 1 to 35 trillion observation? I don't think so, not directly. I'm not even offering a fully-formed argument (you can go now, I've got this). Rather, I'm raising a flag, and saying this doesn't seem to add up in a big way...How do others see it?

I think you do well to raise the flag. But you still have to work to
make a case as good as the one Rees made for rejecting the 19th
century atheistic axiom that said our universe (now known to be less than
15 billion years old) is all there is.

> Is that hopelessly subjective? Well, it's not going to published in Nature any time soon. But here's the logic of it which I think has merit:
>
> The 1 to 35 trillion ratio would be unremarkable if it were a single bacterium multiplying thus. Nothing particularly novel created, i.e. low algorithmic complexity. However, with human development, we have very, very high functional complexity. I can't put a number on it, but there's wide agreement to describe our brain as the most complex object known. Both structural and functional complexity.

Like I suggested, the sperm whale brain might be more complex, but that
is an irrelevant quibble.

> So here's my first claim: we can say there must be a very high information content within that single parent cell. I'm proposing a broad definition information here, which is the capability to produce the structure that is a human, via the constrained process of cell division and differentiation.
>
> Now if 8% of our DNA is functional, that's 64MB of data in the genome. So we can safely conclude that by any known means, that's nowhere near enough information to specify the most complex object known. The cell is an integrated physicochemical system, but again it seems safe to say that the only viable alternative source of this information in the cell is the proteins it can produce.

I think Greg Guarino did a good job of summarizing how the proteins
come into play to do the seemingly impossible. Have you seen his post?

>
> I'm assuming that development occurs naturally, i.e. without a need for divine intervention.

Of course, it's an everyday occurrence. But a truly wonderful one.

> Therefore, the information (as defined) must reside in:
>
> 1. The genome, but be much more than 8% being functional, and/or employ storage with efficiency well beyond what our current technology or understanding;
>
> 2. The information is in the 2 million proteins the body is capable of producing; i.e. as more than a linear polymer, rather the complex specific binding properties of these intricately folded 3D molecules;

As usual, enzymes can be expected to play the key role. And folding
into just the right shape is vital to their usefulness.

The chemical environment in which the folding takes place makes all the
difference. Too high or too low a pH is deadly.

> 3. A combination or 1 and 2.
>
> The median protein length in H. sapiens is 375 amino acids, of say 5 bits each, giving about 0.5GB of "linear" (pre-folding) information.
>
> Jamie A. Davies interprets this as: “[the zygote is] a few thousand genes and proteins, none of which can possibly hold any concept, in any language, of the structure and function of a human body....”
>
> Is he correct? He locates the extra information needed outside the parent cell, as "adaptive self-organization".

Yes, see Guarino's post again.

> It's now 1am, and I have work tomorrow...to be continued!

Your post is dated 10:34 Eastern Standard time, which suggests that
you are in Australia. Correct?

If so, would you have said "15 milliard years" instead of
"15 billion years"? [The British "billion" is the American "trillion".]

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--

[jillery]

On Tue, 7 Feb 2017 06:12:41 -0800 (PST), Peter Nyikos
<nyi...@bellsouth.net> wrote:

>On Tuesday, February 7, 2017 at 12:44:57 AM UTC-5, jillery wrote:
>> On Mon, 06 Feb 2017 21:43:22 -0700, RSNorman <r_s_n...@comcast.net>
>> wrote:
>
>> >>Similarly, when I talk about experiments to verify irreducible
>> >>complexity (IC), the response I often get is that the REAL issue
>> >>is whether it is evidence for intelligent design (ID) and that
>> >>the concept of IC is of no intrinsic interest.
>
>IIRC this was your stance on the Minnich experiments, jillery. Correct?

Since you asked, an important point you conveniently excluded is that
IC has no intrinsic *biological* interest. Based on those who claim
IC as evidence against biological evolution and for ID, it has lots of
intrinsic interest with them.

>> >I don't know about biological experiments "to verify irreducible
>> >complexity". I do not know what you are talking about here. If there
>> >were such experiments that DID verify it then that would constitute
>> >evidence.
>>
>>
>> Based on his other posts, my impression is he's referring to the
>> experiments Minnich described in his Dover trial testimony.
>
>Indeed, one need look no further than the post I did in reply to
>MarkE yesterday evening. There might, of course, have been other
>experiments to verify IC that I haven't learned about.
>
>> If by "it" you mean ID, I must disagree. Behe's bald assertions
>> notwithstanding, biological IC is not evidence against biological
>> evolution, nor is it evidence for Design,
>
>Behe's assertions are nuanced: the more complex the IC structure/system,
>the stronger the case for meeting Darwin's criterion
>of not being attainable through "numerous, successive, slight modifications".
>See pp. 39-40 of _Darwin's Black Box_.

Of course, your distinctive interpretation of Behe's "nuance" isn't
shared by most authorities on the subject, of which you should admit
are not one, your association below notwithstanding.

>And so, you've reminded me of yet a fourth meaning for "Darwinism":
>the belief in evolutionary gradualism as set forth in the quote from
>_Origin of Species_.
>
>Peter Nyikos
>Professor, Dept. of Math. -- standard disclaimer--
>Univ. of South Carolina
>http://people.math.sc.edu/nyikos/

[jillery]

So you learned a new polemical label during your leave of absence.
Give yourself a gold star.

[jillery]

On Tue, 7 Feb 2017 08:59:54 -0800 (PST), Peter Nyikos

It's not irony to snip out relevant commentary, but is instead
unintended self-parody.

>> >Not only did they show that the flagellum they were testing
>> >was irreducibly complex -- each and every one of its 30+ parts was
>> >essential to the function of swimming -- but they also did experiments
>> >that suggested that the Type III mechanism might have evolved from the
>> >flagellum through loss of parts, rather than the flagellum evolving from
>> >the type III mechanism through addition of parts.
>>
>>
>> Peter Nyikos is ignoring the elephant in the room, that Minnich's
>> experiments merely showed the existence of Behe's IC, but did nothing
>> to show Behe's claims about IC, specifically that such systems could
>> not have evolved.
>
>Behe never made such a claim. Re-read that item at the top of p. 40
>of _Darwin's Black Box_ to see what claim he did make. You've quoted
>it yourself and had it re-quoted to you.

An irony here is that you acknowledge I have posted multiple times
Behe's exact words from DBB, but then you fail to post them here.

And then you continue to baldly assert a distinctive interpretation of
Behe's words.

>As for the elephant -- well, Ron O was ignoring the elephant of
>needing to show that the various experiments which supposedly
>showed the latest version of evolutionary theory to be true,
>actually did show that.

That would be those articles and books presented to Behe during his
testimony in the Dover trial, the ones he claimed he didn't have the
time to read. Behe's claim to lack the time to back up his arguments
has a familiar ring to it.

>Oh, wait, I'm just falling in line with your "show" jargon.
>What Ron O failed to do was to show that various experiments
>provided evidence for this or that feature of evolutionary theory.
>He is doing the opposite of the alleged "switch scam": attacking the
>weaknesses of ID theory instead of presenting the case for
>evolutionary theory.

Of course, Ron O does show the case for evolutionary theory, just not
necessarily in the same posts you complain about.

>> More telling, neither has Behe. To the best of my
>> knowledge, nobody in the IC community has done any experiments which
>> showed the implausibility of evolved IC.
>
>Nor has anyone in the anti-ID community, or even the biological
>community [1] done any experiments to show that the bacterial
>flagellum could have evolved by the usual processes studied
>in evolutionary biology, within the time it seems to have taken
>to evolve.

Behe claims that it's practically impossible for evolution to produce
IC systems like the bacterial flagellum. To counter that bald
assertion, all that is neccessary is to show that it's plausible for
evolution to produce IC systems like a bacterial flagellum. Science
has met its burden. Behe and IC advocates have not.

>[1] What percentage of the biological community knows enough about ID theory
>to take an informed stand on it? My estimate: less than 1 percent.

Thanks for sharing. I filed your opinion appropriately, along with
all of your other meaningless "estimates" you posted to T.O.

>And
>the reason is the distorted picture of IC and ID that has become the
>virtual reality in which most biologists work. You are presenting
>part of that distorted picture, both above and below:

That's not the reason. Instead, it's your passion for treating
estimates pulled out of your ass as fact.

>> OTOH Muller described
>> evolved IC decades before Behe wrote DBB.
>
>This misconception is part of that virtual reality. Muller never
>described any IC systems. He merely described systems to which
>ONE OR MORE PARTS are essential. The definition of IC is
>that EACH AND EVERY PART is essential to the basic function.
>
>And yes, it stands to reason that biological organisms won't do
>backup systems for each and every part. You could suffer amputation
>of a leg and still be able to function at almost everything you do.

Tell that to the guy trying to run away from a hungry bear.

>> ><snip irrelevant lecture by Ron O>
>>
>> <snip remaining irrelevant noise by Peter Nyikos>
>
>What I wrote above was highly relevant to Ron O's blather,
>and so was the following part that you snipped:

I snipped all that followed your bald assertion of "Ron O's irrelevant
lecture". Are you now retracting that bald claim?

[MarkE]

On Tuesday, February 7, 2017 at 4:39:58 AM UTC+9:30, Peter Nyikos wrote:
> On Sunday, February 5, 2017 at 9:34:58 AM UTC-5, MarkE wrote:
> > Bill, I appreciate your acknowledgment of my premise.
> >
> > What is my approach to figuring out how it all works and how it all got here?
> >
> > Continue to research this.
>
> As should evolutionary theorists. By the way, I've come to realize
> just how ambiguous that creationist catchword, "Darwinism" is. Depending
> on the context [which may include a shell game between the various meanings]
> it can either mean:
>
> 1. The naked fact that we vertebrates have evolved from a common ancestral
> species, and the highly defensible hypothesis that all earth life is
> descended from prokaryotes. [The logical alternative to creationism
> in the sense of creation of species *de novo*.]
>
> 2. Modern evolutionary theory, a part of theoretical biology. [The logical
> alternative to "ID theory".]
>
> 3. The philosophical/religious belief that abiogenesis and evolution
> of life all happened without supernatural intervention.
>
> > It's important for better understanding and combating disease for starters.
>
> That's part of population genetics. Creationists have no problem with
> that, and that includes that ideological purist, the "species immutabilist"
> Ray Martinez.

>
> I'm in the process of trying to find out how much of modern evolutionary
> theory is dependent on wild extrapolations from population genetics.

> I'm having a hard time finding out because anti-ID types favor the
> ambiguous term "evolutionary biology." Depending on the context,
> it could mean:
>
> A. Population genetics.
>
> B. The modern synthesis, which includes A.
>
> C. Evidence that evolution has taken place, in the sense of 1. above.
>
>
> > As this research progresses, it will discover a greater percentage of the genome to be functional.
>
> Yes, and NOT just in the sense of coding for proteins, or the more general
> sense of coding for RNA.
>
> > It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.
> >
> > These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.

>
> Here is another source of ambiguity. "Natural selection" is used by most
> anti-ID types in the strictly population-genetics sense. But I think most
> laymen think of it as the grand pageant of "origin of species" on the
> one hand and extinction on the other. The mass extinctions of the distant
> past exerted a profound influence on evolution by "naturally selecting"
> certain orders and families to go extinct and others to survive. We humans
> have "naturally selected" untold numbers of species to go extinct,
> including so much of the megafauna of the Pleistocene.
>

> > Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.
>
> It is safe for you to say that at the present time because evolutionary
> theory is still in its embryonic state ("infancy" would be too generous
> a description). Thus, Bill Rogers is overly complacent in expecting
> you to challenge evolutionary theory before being willing to entertain
> arguments for ID. There is really very little in the way of concrete
> results for anyone to challenge.

Biology itself could be said to be in its relatively early days. But it seems to be growing at a faster rate that evolutionary theory, uncovering new data so fast that the theory is struggling to adapt (e.g. ENCODE results). I thought a good theory was meant to be predictive, not reactive?

> > At that point, science hands over to theology.
>
> I often wonder how much of the behavior of anti-ID types is fueled either
> by atheism or belief in what is inappropriately called "theistic evolution"
> and should be renamed "deistic evolution" because it dogmatically
> adheres to meaning 3. of "Darwinism" above.
>
> Peter Nyikos

> Professor, Dept. of Mathematics -- standard disclaimer--

> University of South Carolina
> http://people.math.sc.edu/nyikos/

[MarkE]

On Tuesday, February 7, 2017 at 11:50:00 AM UTC+9:30, Peter Nyikos wrote:
> On Monday, February 6, 2017 at 4:19:58 PM UTC-5, MarkE wrote:
>
> > > > Ron, you're already in the sin-bin for talking and not listening. If this dry-retching of ID diatribe continues it'll be a red card.
> > > >
> > >
> > > Run away in denial. Denial is all IDiots have and you know it. I have
> > > just demonstrated that what you are doing is what the ID perps have been
> > > doing for a couple of decades and all IDiocy is, is a stupid scam that
> > > creationists are running on themselves.
>
> It is no more of a scam than Ron O ranting about "IDiocy" and yet
> hardly giving any information on how evolutionary theory has
> explained the evolution that has actually taken place on earth.
>
> > > You obviously have to do something different. The same old same old
> > > isn't going to amount to anything.
>
> Ironic, this spiel from someone who has been regurgitating the same old
> same old talk about a scam since 2002. And recycling whole paragraphs
> of rant in the process.
>
>
> > > Do something that the ID perps never tried. Actually try to figure out
> > > if there is any science that you can actually do.
>
> Ron O is ignoring the elephant in the room -- Minnich, who testified
> in Dover about the experiments he and his students did on the bacterial
> flagellum.
>

> Not only did they show that the flagellum they were testing
> was irreducibly complex -- each and every one of its 30+ parts was
> essential to the function of swimming -- but they also did experiments
> that suggested that the Type III mechanism might have evolved from the
> flagellum through loss of parts, rather than the flagellum evolving from
> the type III mechanism through addition of parts.
>

> <snip irrelevant lecture by Ron O>
>

> > > Why not do the sensible thing and put up your model of creation
>
> ID theory doesn't hypothesize creation; it hypothesizes intelligent
> design, as its name implies.
>
> > > to figure out if there is anything that you can do to verify any parts
> > > of it? That isn't a trap. If you want to know if your model is valid
> > > you have to verify it somehow. The only reason the ID perps don't do
> > > that is because they already know that the answers are not what they
> > > want. That is how sad the ID scam is at this time.
>
> Ron O has no reason whatsoever for thinking this. Part of his problem
> is that he doesn't realize that the ID emphasis on the weaknesses of
> evolutionary theory is just the other side of the coin on anti-ID folks
> like him harping on the weaknesses of ID theory.
>
> > > Why don't IDiots persue such research?
>
> See above about Minnich.
>

> > > What is the draw to keep doing
> > > nothing except make assertions that you can't back up as meaning
> > > anything to IDiocy?
> > >
> > > Ron Okimoto
> >
> > Ron, I'm not a scientist, I'm an amateur, with little likelihood of doing any science of my own. But it's a lifelong interest, and what I can do is discuss and interpret the science work done by others.
> >
> > Not sure what your situation is. I can see you're passionate about your views and energetic in your opposition to ID in particular.

> > If you don't mind me asking, what's your story, what are your areas of interest and reasons for posting here?
> > Asking out of genuine interest - happy to reciprocate.
>

> Well, you got another long spiel in reply, but did he tell you anything
> along the lines which you had in mind?

Hello Peter, unfortunately no he didn't, not even between the lines. (The offer stands though Ron.)

>
> I first encountered Ron O back in 2010 and have seen innumerable
> long spiels from him since then -- but none that really got to the
> root of his motivations.
>
> Did you ever get a clue as to how his fanatical opposition to intelligent
> design squares with what he claims to be his religious beliefs? I've
> learned essentially nothing along these lines -- next to nothing about
> his religious beliefs, and nothing whatsoever about the connection.
> Nobody else here seems to know more about this than I do.

I'm beginning to wonder if Ron O is an early AI bot which was never decommissioned. Ron, it's time to come in from the cold.

> I, on the other hand, have been very forthcoming about my beliefs. I
> am an agnostic who has reluctantly concluded that the evidence for
> a designer/creator of our world is rather slim -- but who nevertheless
> clings to a hope that the basics of Christianity are true. This includes a
> life after death, but I hope that heaven and hell are much more like
> they are depicted in C.S. Lewis's _The Great Divorce_ than like the horrible
> image of hell as depicted in olden days.
>
> Where do you stand, if you don't mind telling?

Not at all. I'm a mainstream Christian, with an elec eng/software dev background. I encountered Australian creation science in my late teens, met with some of its leaders, attended conferences etc. I found they had a neat package, convincing to lay people, but selective and simplistic. I still appreciate them doing some of the heavy lifting critiquing evolution (with caveats).

The YEC position scientifically problematic (understatement intended), and theistic evolution has theological difficulties (e.g. fall/death relationship). Progressive creation attempts a resolution of both. Deism isn't compatible with Christianity I don't think.

Abiogenesis and the limits of evolutionary mechanisms are areas I am drawn to question.

>
> Peter Nyikos
> Professor of Mathematics -- standard disclaimer--
> University of South Carolina

[RonO]

Why lie to yourself like this? What more of a story do you need. I am
a scientists. I am still doing the science even if it is for private
industry. In many ways I do the same type of research I did before.
What about my story did you not get?

What is your story? You just have to fill it out as much as I did mine.

I did start reading TO since 1993 when IDiocy wasn't even on the radar
for creationists such as yourself. I've watched the entire ID scam
unfold and fall apart. The bait and switch is your reality. IDiot
organizations like the ISCID and ID Networks no longer exist.

>
>>
>> I first encountered Ron O back in 2010 and have seen innumerable
>> long spiels from him since then -- but none that really got to the
>> root of his motivations.
>>
>> Did you ever get a clue as to how his fanatical opposition to intelligent
>> design squares with what he claims to be his religious beliefs? I've
>> learned essentially nothing along these lines -- next to nothing about
>> his religious beliefs, and nothing whatsoever about the connection.
>> Nobody else here seems to know more about this than I do.
>
> I'm beginning to wonder if Ron O is an early AI bot which was never decommissioned. Ron, it's time to come in from the cold.

Why lie to yourself like this? Is it some type of defense mechanism?

I will tell you if you don't already know that you shouldn't get tangled
up with Nyikos.

Nyikos just means that he was wrong about some junk (it was about the
bait and switch and the Discovery Institute's involvement) and has been
lying about it ever since. As stupid as it may seem Nyikos denied that
the Discovery Institute was involved with the Ohio bait and switch that
was the initiation of the bait and switch scam. The Discovery Insitute
had sold the teach ID scam to the rubes, but when it came time to put up
or shut up the ID perps at the Discovery Institute decided to run the
bait and switch. Nyikos couldn't deal with the evidence that Meyer and
Wells ran the bait and switch personally. It was a big deal for the
Disovery Institute. It was the first major case where ID was going to
shine or flop and they decided to run, and they have been running every
single subsequent instance. Have you seen Wells' report on the first
bait and switch. He admits that the ID perps got together before going
to Ohio and decided to run the bait and switch. The dog and pony show
that he and Meyer put up was only for show. The president and an other
Discovery Institute players also attended the event. Nyikos has been in
denial of those simple facts since 2010. That is what he is referring to.

This is why your use of the IDiocy is stupid unless you have some means
to do better.

>
>> I, on the other hand, have been very forthcoming about my beliefs. I
>> am an agnostic who has reluctantly concluded that the evidence for
>> a designer/creator of our world is rather slim -- but who nevertheless
>> clings to a hope that the basics of Christianity are true. This includes a
>> life after death, but I hope that heaven and hell are much more like
>> they are depicted in C.S. Lewis's _The Great Divorce_ than like the horrible
>> image of hell as depicted in olden days.
>>
>> Where do you stand, if you don't mind telling?
>
> Not at all. I'm a mainstream Christian, with an elec eng/software dev background. I encountered Australian creation science in my late teens, met with some of its leaders, attended conferences etc. I found they had a neat package, convincing to lay people, but selective and simplistic. I still appreciate them doing some of the heavy lifting critiquing evolution (with caveats).
>
> The YEC position scientifically problematic (understatement intended), and theistic evolution has theological difficulties (e.g. fall/death relationship). Progressive creation attempts a resolution of both. Deism isn't compatible with Christianity I don't think.
>
> Abiogenesis and the limits of evolutionary mechanisms are areas I am drawn to question.

Creationist critiques of biological evolution are just tragically lame
at this time. IDiots like Denton have given up and admitted that
biological evolution is just fact. Guys like Behe do not deny the fact
of biological evolution. Behe is only claiming that somewhere in the
mess the designer tweeks things. We obviously had an ape like ancestor.
IDiots have to figure out how they can verify the tweeking.

Abiogenesis? Abiogenesis is among the weakest of sciences, and it is so
much better than anything that the creationists have that it is
laughable. Just because we don't know everything or much of anything
does not mean we know nothing. We have all of chemistry (no impossible
chemical reactions involved), we have all the elements (no special
creation of the elements needed, they have verified the creation of
heavy elements in super nova). What do you have by comparison? No
creator, no means of creation, nothing. That is what you face when you
compare abiogenesis to your beliefs. Not only that, but those are just
two things going for abiogenesis. What do you make of such observations
that lipids make bilayer membranes spontaneously, or that minerals and
simple organic molecular combinations can have enzymatic activity? This
is what all religious people face that are creationists. Nyikos doesn't
believe that there are religious people like me that are just more
honest than he is (do you really believe Nyikos is an IDiot agnostic
that goes to church regularly). They don't call it faith for no reason.
This is something most creationists that oppose science do not
understand about their beliefs. You obviously do not have to base your
religious beliefs on anything tangible that can be studied in nature.

You definitely do not have to resort to a bogus creationist scam to
perpetuate your religious beliefs or instigate dishonest, stupid and
irrational political schemes.

Nyikos and you can likely benefit by reading about the clergy that
signed the clergy letter against stupidity like IDiocy and anti science
creationist activities.

http://www.theclergyletterproject.org/Resources/Faces2.htm

To honest religious people a scam is just a scam, and stupidity is just
stupid.

Ron Okimoto

[Peter Nyikos]

On Wednesday, February 8, 2017 at 1:04:58 AM UTC-5, jillery wrote:
> On Tue, 7 Feb 2017 10:19:24 -0800 (PST), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
> >> On 2/7/17 6:12 AM, Peter Nyikos wrote:
> >>
> >> > Behe's assertions are nuanced: the more complex the IC structure/system,
> >> > the stronger the case for meeting Darwin's criterion
> >> > of not being attainable through "numerous, successive, slight modifications".
> >> > See pp. 39-40 of _Darwin's Black Box_.
> >>
> >> Why would you think that assertion to be true? Would that not be
> >> assuming a particular model of evolution, by the sequential addition of
> >> invariant parts?
> >
> >No, Behe explicitly allows for indirect, circuitous routes at the top
> >of page 40.
> >
> >You've been misled by yet another part of the virtual reality
> >that has grown up around Behe in the blogosphere.

Harshman, as usual, did an unmarked deletion of the preceding two lines
and kept on as though he had asked a telling pair of questions.

However, as can me seen by your reply, those two lines didn't
go unremarked:

>
> So you learned a new polemical label during your leave of absence.

I've used it many times before, including uses in talk.abortion
well before I returned to talk.origins in 2010. But now I've
found a specific use for it.

It provides a convenient keyword for people to do a
Google search on, whether an internal NGG one or an external one
that could also make use of other search engines.

I intend to use it this way from now on whenever I see
misrepresentations of Behe which I've already seen more times
than I care to count. You posted at least two yourself:
about Muller having written about IC long before Behe; and the
following whopper:

"Behe's claims about IC, specifically that such systems could
not have evolved."

> Give yourself a gold star.

I will, but not for any reason you are suggesting. If I see
the same piece more than twice, I will start building a
catalogue of them -- the ones that shape the form that
the virtual reality takes here in talk.origins.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
at the original USC, in South Carolina

[MarkE]

We did reach a stalemate on this. To clarify: you rule out inferring external agency through vanishingly low probability as a category error. Is there any event, phenomena or argument you can think of (in this life) that you might conceivably interpret as evidence for external agency? (I recall you would question the reliability of your sensory processing or mental state instead?)

> I may be reading you incorrectly, but your incredulity in the preceding
> posts doesn't seem to be a call for more research, it seems to be a call
> to think of these events as presenting a dichotomy: if there is no
> natural explanation, then non-natural inference is justified.

I'd always advocate more research, out of curiosity, and for the expected and surprising benefits it brings. Christians with a firm belief in creation have been a driving force in science over centuries. Unless one's conception of God is constant capricious intervention, belief brings to science the added delight of "thinking God's thoughts after him."

>
> There's nothing scientific about that kind of incredulity.
>
> > Can this be applied to my 1 to 35 trillion observation? I don't think
> > so, not directly. I'm not even offering a fully-formed argument (you
> > can go now, I've got this). Rather, I'm raising a flag, and saying
> > this doesn't seem to add up in a big way...How do others see it?
>
> I have to wonder if you've asked yourself what I consider to be the
> obvious critical questions before raising that flag, e.g., Do I know
> enough about this to say that something doesn't add up?, Have I examined
> my own convictions, some of which may confound my interpretation of the
> data? Does this "flag" actually exist as an important conundrum in the
> minds of those I consider experts, or are they merely expressing their
> own human tendency for wonder?

Why do you think I post here? To do precisely that!

>
> For myself, I see nothing that doesn't add up. That doesn't mean I know
> everything, or even much at all. It simply means I'm not assuming I know
> enough to know how, or if, things *should* add up. I'm human, my mind is
> easily boggled. There is intellectual freedom in recognizing and
> accepting my own cognitive limitations.

If your mind is easily boggled, how can you be confident about its conclusions regarding the complex and diverse issue of origins?

>
> > Is that hopelessly subjective? Well, it's not going to published in
> > Nature any time soon. But here's the logic of it which I think has
> > merit:
> >
> > The 1 to 35 trillion ratio would be unremarkable if it were a single
> > bacterium multiplying thus. Nothing particularly novel created, i.e.
> > low algorithmic complexity. However, with human development, we have
> > very, very high functional complexity. I can't put a number on it,
> > but there's wide agreement to describe our brain as the most complex
> > object known. Both structural and functional complexity.
>
> I'm going to accept the above for the purposes of discussion. But I just
> want to note some of the possible difficulties with it,
>
> - "Nothing novel" is a judgement that I don't necessarily consider
> accurate or defensible
> - complexity ("high functional" or "low algorithmic) can be a
> problematic concept if not stringently defined, human intuition is not a
> great guide (e.g, which is more complex, a perfectly spherical metal orb
> or an irregular river stone?)

Agreed complexity can be a problematic concept, full stop. Here's a stab: "Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction. Random and Ordered Sequence Complexities lie at opposite ends of the same bi-directional sequence complexity vector."
https://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-2-29

Goldilocks complexity (FSC) can't be too random (unspecified) and can't be too be ordered (uncomplex). Where have I heard this before?

> - the assumed import of the human brain being "the most complex object
> known", which argument I'm guessing you'd drop like a hot rock if we
> discover that something else is more complex

Not at all. The argument doesn't depend on it being the most complex; plain old mind-bogglingly is sufficient.

I keep banging on about information in the cell necessarily being compressed beyond known technology, employing fractal specification mechanisms, etc - the antithesis of one-to-one correspondence. I'm surprised you think I'm making any such assumption?

And yet from it the most complex object known emerges. Do we infer physics and chemistry have been pre-designed to allow life as we know it? Those atoms and molecules seem to be very special Lego bricks. I'm not being facetious - there are hints here of a form of front-loading and /or fine-tuning.

But let me instead argue against myself. A few hundred megabytes of DNA code produce proteins, which fold into complex, three-dimensional structures by virtue of their physicochemical properties alone, and spontaneously combine with other proteins to form cellular machines. The degree of specificity of these large molecules and the implications of that are debated of course, but there's no hidden magic in the chemistry itself, amazing as it is.

So why don't I just consider this behaviour at this level (intracellular), and allow for similar complex behaviour to emerge at subsequent higher levels (intercellular)?

There's no master blueprint tucked inside the cell that we could roll out and view as a complete anatomical diagram. But it's there implicitly. Proteins forming specific molecular machines etc is one thing. But proteins, RNA etc dormant or expressed differently at various stages of embryo development create layers of complexity to the requirement of specifying each step. It's a kind of "butterfly effect", a highly non-linear process with a vast cascade of stages, regulation, signalling, overlaying error correction and error tolerance as well.

I'm not arguing that this is so complex that it proves a designer (though I personally think it does). Rather, I'm saying that what's going here is actually so much more wound up in itself, recursive, fractal, etc (I don't even have concepts to describe it - remember, one cell becomes 35 trillion and the most structurally and functionally complex object known), that as research begins to grapple with this more and more, my prediction is it will have major implications for our understanding of the genome, proteins, RNA etc and place fatal contraints upon evolution.

You read it here first.

[Peter Nyikos]

On Wednesday, February 8, 2017 at 6:29:58 AM UTC-5, MarkE wrote:
> On Tuesday, February 7, 2017 at 11:50:00 AM UTC+9:30, Peter Nyikos wrote:
> > On Monday, February 6, 2017 at 4:19:58 PM UTC-5, MarkE wrote:
> >
> > > > > Ron, you're already in the sin-bin for talking and not listening. If this dry-retching of ID diatribe continues it'll be a red card.
> > > > >
> > > >
> > > > Run away in denial. Denial is all IDiots have and you know it. I have
> > > > just demonstrated that what you are doing is what the ID perps have been
> > > > doing for a couple of decades and all IDiocy is, is a stupid scam that
> > > > creationists are running on themselves.

Note the word "creationists." Ron O has bought into the scam that
ID is just a branch of creationism. And to cast as wide a net
as possible, Ron O calls anyone a "creationist" who believes in
the existence of a creator. He even claims to believe in one
himself, but has consistently avoided even hinting at what this
creator is supposed to have created.

> > It is no more of a scam than Ron O ranting about "IDiocy" and yet
> > hardly giving any information on how evolutionary theory has
> > explained the evolution that has actually taken place on earth.
> >
> > > > You obviously have to do something different. The same old same old
> > > > isn't going to amount to anything.
> >
> > Ironic, this spiel from someone who has been regurgitating the same old
> > same old talk about a scam since 2002. And recycling whole paragraphs
> > of rant in the process.
> >
> >
> > > > Do something that the ID perps never tried. Actually try to figure out
> > > > if there is any science that you can actually do.
> >
> > Ron O is ignoring the elephant in the room -- Minnich, who testified
> > in Dover about the experiments he and his students did on the bacterial
> > flagellum.
> >
> > Not only did they show that the flagellum they were testing
> > was irreducibly complex -- each and every one of its 30+ parts was
> > essential to the function of swimming -- but they also did experiments
> > that suggested that the Type III mechanism might have evolved from the
> > flagellum through loss of parts, rather than the flagellum evolving from
> > the type III mechanism through addition of parts.
> >
> > <snip irrelevant lecture by Ron O>
> >
> > > > Why not do the sensible thing and put up your model of creation
> >
> > ID theory doesn't hypothesize creation; it hypothesizes intelligent
> > design, as its name implies.

Note how completely Ron O has bought into the scam: he is playing
a standard trick which falls under two very similar rubrics:
"The Woodsawyer's Dare" and "The Mouse Deer Trick". The former
is easily explained as daring the opponent to saw off the limb
on which he is sitting. The latter takes longer to explain; it
goes back to a Southeast Asian folk tale of a clever mouse deer.

> > > > to figure out if there is anything that you can do to verify any parts
> > > > of it? That isn't a trap.

Of course it is: it is a trap to get you to reveal that you are
the creationist that Ron O has already decided you are, come
hell or high water.

Unfortunately for Ron O, that trap can never work with me.

<snip for focus>

> > > > Ron Okimoto
> > >
> > > Ron, I'm not a scientist, I'm an amateur, with little likelihood of doing any science of my own. But it's a lifelong interest, and what I can do is discuss and interpret the science work done by others.
> > >
> > > Not sure what your situation is. I can see you're passionate about your views and energetic in your opposition to ID in particular.
> > > If you don't mind me asking, what's your story, what are your areas of interest and reasons for posting here?
> > > Asking out of genuine interest - happy to reciprocate.
> >
> > Well, you got another long spiel in reply, but did he tell you anything
> > along the lines which you had in mind?
>
> Hello Peter, unfortunately no he didn't, not even between the lines. (The offer stands though Ron.)
>
> >
> > I first encountered Ron O back in 2010 and have seen innumerable
> > long spiels from him since then -- but none that really got to the
> > root of his motivations.
> >
> > Did you ever get a clue as to how his fanatical opposition to intelligent
> > design squares with what he claims to be his religious beliefs? I've
> > learned essentially nothing along these lines -- next to nothing about
> > his religious beliefs, and nothing whatsoever about the connection.
> > Nobody else here seems to know more about this than I do.
>
> I'm beginning to wonder if Ron O is an early AI bot which was never decommissioned. Ron, it's time to come in from the cold.

I've made the comment a number of times that certain posts read
like the author could not pass the Turing test. There are others
to whom this applies, of course.

> > I, on the other hand, have been very forthcoming about my beliefs. I
> > am an agnostic who has reluctantly concluded that the evidence for
> > a designer/creator of our world is rather slim -- but who nevertheless
> > clings to a hope that the basics of Christianity are true. This includes a
> > life after death, but I hope that heaven and hell are much more like
> > they are depicted in C.S. Lewis's _The Great Divorce_ than like the horrible
> > image of hell as depicted in olden days.
> >
> > Where do you stand, if you don't mind telling?
>
> Not at all. I'm a mainstream Christian, with an elec eng/software dev background. I encountered Australian creation science in my late teens, met with some of its leaders, attended conferences etc. I found they had a neat package, convincing to lay people, but selective and simplistic. I still appreciate them doing some of the heavy lifting critiquing evolution (with caveats).

This is true if you substitute "evolutionary theory" for "evolution."
Much to my surprise, Richard Norman uses "evolution" in this way.

> The YEC position scientifically problematic (understatement intended), and theistic evolution has theological difficulties (e.g. fall/death relationship).

I've recently remarked that "theistic evolutionists" like Kenneth Miller
should really call themselves "deistic evolutionists." I've called
Miller a Neo-Deist under the natural assumption that -- inasmuch as
he is a Roman Catholic who seems proud of the fact -- he believes
in at least some of the Biblical accounts of God acting in history,
including Jesus's Resurrection. But now I am not so sure this is true.
If it isn't, then Miller is a deist, pure and simple.

> Progressive creation attempts a resolution of both.

Are you referring to God moving evolution along by sporadic
interventions in the course of earth's history?

> Deism isn't compatible with Christianity I don't think.

Not traditional Christianity at any rate. I intend to learn more
about Miller's beliefs one way or the other.

> Abiogenesis and the limits of evolutionary mechanisms are areas I am drawn to question.

Ever since 1996, I have been impressed by the incredible difficulty
of abiogenesis. The best scientific minds have been unable to
come up with a hypothesis that would make it more than a
once-in-a-galaxy occurrence. And that is just to the level
of the simplest prokaryotes.

[Peter Nyikos]

On Monday, February 6, 2017 at 11:44:58 PM UTC-5, RSNorman wrote:
> On Mon, 6 Feb 2017 19:27:26 -0800 (PST), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Monday, February 6, 2017 at 7:24:58 PM UTC-5, RSNorman wrote:

> >> On Mon, 6 Feb 2017 11:06:19 -0800 (PST), Peter Nyikos
> >> <nyi...@bellsouth.net> wrote:
> >
> >> > I've come to realize
> >> >just how ambiguous that creationist catchword, "Darwinism" is. Depending
> >> >on the context [which may include a shell game between the various meanings]
> >> >it can either mean:
> >> >
> >> >1. The naked fact that we vertebrates have evolved from a common ancestral
> >> >species, and the highly defensible hypothesis that all earth life is
> >> >descended from prokaryotes. [The logical alternative to creationism
> >> >in the sense of creation of species *de novo*.]
> >> >
> >> >2. Modern evolutionary theory, a part of theoretical biology. [The logical
> >> >alternative to "ID theory".]
> >> >
> >> >3. The philosophical/religious belief that abiogenesis and evolution
> >> >of life all happened without supernatural intervention.

<snip for focus>

> >> >I'm in the process of trying to find out how much of modern evolutionary
> >> >theory is dependent on wild extrapolations from population genetics.
> >> >I'm having a hard time finding out because anti-ID types favor the
> >> >ambiguous term "evolutionary biology." Depending on the context,
> >> >it could mean:
> >> >
> >> >A. Population genetics.
> >> >
> >> >B. The modern synthesis, which includes A.
> >> >
> >> >C. Evidence that evolution has taken place, in the sense of 1. above.

<snip to get to you, Richard>

> >> I do not understand how you so casually parcel up "evolution" into
> >> "population genetics", "evolutionary theory", and the actual "fact of
> >> evolution" as observed in the world.
> >
> >It isn't casual. It comes from witnessing innumerable failures of
> >communication, and whether a given one is due to honest misunderstandings
> >or deliberate shell games is immaterial. They often take the form of someone
> >"refuting" a creationist or ID supporter's claim about "Darwinism"
> >by giving evidence of actual evolution from fossils or from molecular systematics.

See post below, where Christine Janis seems to be doing
something similar:

> >And yet it is clear from the creationist/ID supporter's
> >previous behavior, or at least from his rejoinder to the "refutation"
> >that what he was disputing was the alleged explanation of this
> >actual evolution by evolutionary theory.
>
> I do realize you are trying to analyze the misunderstandings of
> creationists/IDers about biological evolution.

AND the confusions their opponents are also guilty of. Here is a
example on Amazon.com, with Christine Janis, a renowned paleontologist
and colleague of Kenneth Miller at Brown U., correcting some aspects
of a claim while adding a bit to the confusion herself:

She is quoting Togtman at the outset of the following post:

_______________________included post____________________
In reply to an earlier post on Jan 21, 2015, 2:13:59 PM PST
Christine M. Janis says:
'As I said, "If Darwin's theory were taught his way, as a
hypothesis, professors wouldn't lose their chance at tenure or be
dismissed for teaching students to be skeptical of his theory." '

I think that you're mixing the words "Theory" and "hypothesis" here.
I teach the various facts that we know of in anatomy,
paleontology, evolutionary development, etc. I teach how these fit
into an overarching theory of common descent. Where is the "hypothesis"?
=========================end of included post

Actually the common descent IS a hypothesis, one so well supported
as to be unassailable at least where animals are concerned.

And Christine is not talking about evolutionary theory but the way
all these sources are EVIDENCE for this hypothesis. One doesn't even need
to read Darwin's masterpiece to know this -- Lamarck already
knew enough about it to come up for his own explanation of how
it might have happened.


> But my perspective is
> from biology and I just think that they are simply illiterate
> (deliberately or inadvertently) about what real evolution is.

Real evolution is the way the biota of earth changed from
numerous and sundry causes all through ca. 3.5
billion years. But you are too much the "Man is the measure
of all things" sort to leave it at that.

> Sometimes people here argue (incorrectly from my perspective) with
> them not really helping. Yes, evolution "is" a change in the allele
> frequency in a population over generations. Yes, evolution "is" the
> development of all extant life from a common ancestor (or ancestral
> pool of microbes). But these are simply different aspects of the
> subject

To coin a word, you are being too "pedagogiacentric" here.

> and the whole thing about modern biology is that when you
> understand molecular biology, developmental biology, physiology,
> ecology,..., then you know why those two aspects are intimately
> connected.

Like saying "two aspects of human knowledge, set
theory and the whole of mathematics and its applications,
are intimately related."

Face it: even Harshman leaves the cozy realm of population genetics
once he tries to put an artificial barrier between the term
"natural selection" within a population and the same identical
process on bigger scales, affecting even the extinction of
whole phyla.

IN contrast, Harshman tore down the colossal "barrier" between
"genetic drift" and "random extinctions" by blatantly asserting
that the two barriers are exactly of the same sort.

> >> These are all completely unified
> >> and integrated concepts, biological evolution or, more simply in the
> >> context of biology, just plain "evolution."

> >Concepts are one thing, the actual events are another.
>
> Yes. There is also a difference between "results" of an experimental
> paper and "discussion". But the two are inextricably interwoven.

Pathetic analogy. The discussion should explain exactly what the
experiment was designed to do. The relation between the
state of evolutionary biology in 2017 and what it
purports to explain is utterly different.

Continued in next reply to this post.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/
Specialty: set-theoretic topology

[Peter Nyikos]

The very title, "On the Origin of Species by Means of Natural Selection,
or the Preservation of Favoured Races in the Struggle for Life)" suggests
otherwise: natural selection isn't something that takes place exclusively
WITHIN populations, but acts to produce new ("Origin") species.

And "the preservation of favoured races" hints at much more: the races
that are preserved have special qualities which make them survive
natural disasters to which less adapted species succumb.

And unless Wikipedia is badly in need of fixing, Darwin had that and
much more in mind about natural selection:

Darwin emphasizes that he used the phrase "struggle for existence"
in "a large and metaphorical sense, including dependence of one
being on another"; he gives examples ranging from plants struggling
against drought to plants competing for birds to eat their fruit
and disseminate their seeds.

INTERLUDE: note the use of "competing": it isn't the birds in competition
with the fruit, it is the plants in competition with each other for
birds to disseminate their seeds. But you claimed that "competition" is the
proper word for the ediacaran organisms becoming extinct by falling
prey to overactive predators.

Calling that "competition" between the organisms and their prey reminds
me of the immortal words of Mr. Spock in the movie Star Trek IV:

"To hunt a species to extinction is illogical."

But back to the Wikipedia entry:


He describes the struggle resulting from population growth:
"It is the doctrine of Malthus applied with manifold force
to the whole animal and vegetable kingdoms." He discusses
checks to such increase including complex ecological
interdependencies, and notes that competition is most
severe between closely related forms "which fill nearly
the same place in the economy of nature".[125]

"nearly the same place" doesn't sound like it's restricted to populations.
It could just as easily refer to Homo sapiens and Homo erectus. But now
comes the most telling part:


Chapter IV details natural selection under the "infinitely complex
and close-fitting ... mutual relations of all organic beings
to each other and to their physical conditions of life".[126]
Darwin takes as an example a country where a change in conditions
led to extinction of some species, immigration of others and,
where suitable variations occurred, descendants of some species
became adapted to new conditions.

...

Natural selection was expected to work very slowly in forming
new species, but given the effectiveness of artificial selection,
he could "see no limit to the amount of change, to the beauty
and infinite complexity of the coadaptations between all
organic beings, one with another and with their physical
conditions of life, which may be effected in the long course
of time by nature's power of selection".

You don't get such big changes without numerous extinctions, all
part of nature's power of selection. The forming of new species
is slow, but the culling of old species can be instantaneous.

Using a tree diagram and calculations, he indicates the
"divergence of character" from original species into
new species and genera. He describes branches falling off
as extinction occurred, while new branches formed in
"the great Tree of life ... with its ever branching
and beautiful ramifications".[130]
https://en.wikipedia.org/wiki/On_the_Origin_of_Species

> Sorry if you don't like standard biological language. Why?

Again I ask: just when did "natural selection" become standardly
restricted to populations by biologists OUTSIDE the specialty of
population genetics? Darwin would qualify if you could make a case for him,
but you need to do some HOMEWORK to do that.

Remainder deleted, to be replied to later as appropriate.

Peter Nyikos
Professor, Department of Math. -- standard disclaimer --

U. of South Carolina

[Robert Camp]

On 2/8/17 5:32 AM, MarkE wrote:
> On Wednesday, February 8, 2017 at 3:50:01 AM UTC+9:30, Robert Camp
> wrote:
>> On 2/7/17 7:32 AM, MarkE wrote:
>>> On Tuesday, February 7, 2017 at 2:30:00 AM UTC+9:30, Robert Camp
>>> wrote:
>>>> On 2/6/17 3:43 AM, MarkE wrote:
>>>>> On Monday, February 6, 2017 at 2:15:00 AM UTC+9:30, Robert
>>>>> Camp wrote:
>>>>>> On 2/5/17 4:15 AM, MarkE wrote:

<snip>

Your clarification is incomplete and confusing. I dismiss inferring
*supernatural* external agency as a category error.

That difference is the point. If you've missed it, that may explain why
you mistakenly interpreted our previous discussion as a stalemate (if I
used emojis I'd put a smiley face right there).

> Is there any event, phenomena or argument you can think of (in
> this life) that you might conceivably interpret as evidence for
> external agency? (I recall you would question the reliability of your
> sensory processing or mental state instead?)

Yes, that's true (providing we add the qualifier "supernatural" to
external agency). And it's at this point that I have to ask - even
though it's a digression - shouldn't you? Were you to have a waking
vision of Elvis Presley telling you to slick back your hair and become a
pop singer you'd likely question your mental state. Have you asked
yourself why you'd grant greater cognitive license to a vision of an
angel, or Jesus?

I absolutely do think you post here to test your ideas and consider the
responses. I think you are forthright and thoughtful.

But the point I keep emphasizing is that, despite your obviously
superior intellectual approach, you make a lot of the same mistakes
creationists and IDists make - you confuse your assumptions and
heartfelt beliefs for reliable guides to interpretation of empirical
facts (or lack thereof).

It's admirable to get the facts straight. It's creditable that you
appreciate and are amazed at scientific reality. But if you are
continually lead astray in your interpretations by unwarranted
assumptions, opportunities for real understanding are lost.

>> For myself, I see nothing that doesn't add up. That doesn't mean I
>> know everything, or even much at all. It simply means I'm not
>> assuming I know enough to know how, or if, things *should* add up.
>> I'm human, my mind is easily boggled. There is intellectual freedom
>> in recognizing and accepting my own cognitive limitations.
>
> If your mind is easily boggled, how can you be confident about its
> conclusions regarding the complex and diverse issue of origins?

My confidence initially comes from an understanding that the
evolutionary process has equipped me (us) to be good at certain kinds of
information gathering. And it is bolstered by checking what I think I
know against what the people who are experts think they know - who
themselves are constantly checking their knowledge against what
colleagues know.

I see it as a dead-end to expect, or look for, some kind of existential
certainty.

Well, that's why I keep wondering if I'm getting what you're saying
right. Sometimes your statements seem contradictory.

Here's the crux - if you're not claiming a need for some kind of direct
informational correlation between a specifying mechanism in the initial
cell and all of the structures and functions in the final product (e.g.
brain) then I can see no logic in continually wondering at the inability
of the initial cell to contain all the requisite "information."

No one says it contains all the "information" (depending, as usual, upon
what you are calling information), it contains all the requisite
chemistry; those processes needed to eventually produce the "information."

Well, that's a different question. One that we've discussed here many
times in the context of supposed fine-tuning (and others).

> Those atoms and molecules seem to be very special Lego bricks.
> I'm not being facetious - there are hints here of a form of
> front-loading and /or fine-tuning.

Again, I don't see any hints. And yet again (perhaps frustratingly, from
your perspective), I don't see any explanation for your perception of
those "hints" except an _a priori_ belief that something like that must
be required.

> But let me instead argue against myself. A few hundred megabytes of
> DNA code produce proteins, which fold into complex, three-dimensional
> structures by virtue of their physicochemical properties alone, and
> spontaneously combine with other proteins to form cellular machines.
> The degree of specificity of these large molecules and the
> implications of that are debated of course, but there's no hidden
> magic in the chemistry itself, amazing as it is.
>
> So why don't I just consider this behaviour at this level
> (intracellular), and allow for similar complex behaviour to emerge at
> subsequent higher levels (intercellular)?
>
> There's no master blueprint tucked inside the cell that we could roll
> out and view as a complete anatomical diagram. But it's there
> implicitly.

[I'm with you up to this point. And perhaps I can even agree with that
last comment, as long as you allow me to note that that "implicitly" is
wholly dependent upon contingency. The "anatomical diagram" could be
very different, or even non-existent, had one of an uncountable number
of events in the evolutionary history of that structure or function's
development happened differently. Your "implicitly" is a reflection of
the grand sweep of evolutionary history, and should not be seen as some
sort of cellular "magic."]

> Proteins forming specific molecular machines etc is one
> thing. But proteins, RNA etc dormant or expressed differently at
> various stages of embryo development create layers of complexity to
> the requirement of specifying each step. It's a kind of "butterfly
> effect", a highly non-linear process with a vast cascade of stages,
> regulation, signalling, overlaying error correction and error
> tolerance as well.
>
> I'm not arguing that this is so complex that it proves a designer
> (though I personally think it does).

Kudos. Even that seemingly minor recognition and differentiation is
something of which most theists we see here are incapable.

> Rather, I'm saying that what's
> going here is actually so much more wound up in itself, recursive,
> fractal, etc (I don't even have concepts to describe it - remember,
> one cell becomes 35 trillion and the most structurally and
> functionally complex object known), that as research begins to
> grapple with this more and more, my prediction is it will have major
> implications for our understanding of the genome, proteins, RNA etc
> and place fatal contraints upon evolution.
>
> You read it here first.

I look forward to your speculation's resolution. Hopefully we'll both be
around to see it.

[Peter Nyikos]

On Monday, February 6, 2017 at 9:00:00 PM UTC-5, John Harshman wrote:
> On 2/6/17 3:27 PM, Peter Nyikos wrote:
> > On Monday, February 6, 2017 at 4:34:58 PM UTC-5, John Harshman wrote:

> >> On 2/6/17 1:11 PM, Peter Nyikos wrote:
> >>> On Monday, February 6, 2017 at 3:19:58 PM UTC-5, John Harshman wrote:

> >>>> And many other
> >>>> creationists have problems too. That's why they keep attacking the
> >>>> peppered moth case, for example.
> >>>
> >>> I fail to follow your reasoning. Part of it is that you don't explain
> >>> the form the attacks that you have in mind took. What I've seen are
> >>> two forms: 1, the two varieties were always there, so where's the
> >>> evidence of evolution? and 2. [the ad hominem form] Like Haeckel, the experimenters committed scientific fraud.
> >>
> >> Why allege fraud in that case?
> >
> > Why is the blogosphere full of charges of lying and fraud and other forms of
> > dishonesty, both by ID theorists and by their opponents? Just look at
> > the numerous accusations of a "bait and switch scam" by Ron O. Do you
> > know enough about them to know why they are dwarfed by the number of
> > accusations of a "switch scam"? [That's a real-life example of "the sound
> > of one hand clapping," figuratively speaking.]
>
> Why bring that up?

To make you aware that charges of fraud are made right under your nose,
and NOT just by people who are creationists in the sense that is
standard for talk.origins.

And you ducked both of my questions.

> >> The purpose is to discredit an example of
> >> mutation in the first case
> >
> > What mutation? The phenomenon was well known before any experiments
> > were undergone. The experiment was designed to show how one variety
> > or the other was naturally selected for. It didn't address the origin
> > of the varieties.
>
> Hey, you're the one that mentioned creationist attacks on the existence
> of a mutation to the melanistic form.

What on earth are you referring to here? I never suspected that this
was the purpose of creationist charges of fraud. Can you find even
one source that claims that this was their purpose?

It makes no sense: even creationists have abandoned the claim that
very dark-skinned people are not of the same biblical "kind" as
nordic blondes.

> What did you mean if not that?

I meant exactly what I said: that it was a purely *ad hominem* fallacy.
See above. [OK, I didn't use the word "fallacy," but do you need to
be spoon-fed everything?]

> >> and evolution in the second.
> >
> > Yeah, but now you are leaving the domain of evolutionary theory and
> > entering the naked fact of evolution.
>
> There are no naked facts. The attack is on the existence of an example
> of natural selection. Without the theory of natural selection, there is
> no example.

By "the second" I thought you meant Haeckel, with the peppered moth charge
of fraud the first. You never addressed point (1), only point (2).

But it's clear now that you weren't being clear.


> >>>> Of course very few creationists have
> >>>> any real understanding even of the basics of population genetics. That's
> >>>> why they keep claiming that if most mutations are deleterious there can
> >>>> be no evolution.

> >>>>
> >>>>> I'm in the process of trying to find out how much of modern evolutionary
> >>>>> theory is dependent on wild extrapolations from population genetics.
> >>>>

> >>>> What sort of wild extrapolations did you have in mind here?
> >>>
> >>> For one, the claim that genetic drift and natural selection are
> >>> legitimate rivals for the main force in evolution. [See Burkhard's
> >>> reply to MarkE and Camp's reply to the same post, backing Burkhard.]
> >>
> >> What do you mean by "main force" here? Which is more important depends
> >> on that meaning.
> >
> > Maybe I should have said "the more important force."
>
> Still doesn't help unless you explain what "important" means here.
>
> > When "Roger Shrubber" tried to argue that genetic
> > drift was more important, he was talking on the level of populations.
> > He couldn't possibly have made a case on the [level of higher taxa].
>
> That cut off in mid-sentence.

Fixed now.

> >>> Once you get past the scale of populations, it's a no-brainer:
> >>> natural selection wins hands down. See my comments to MarkE below.
> >>
> >> It's unclear what you mean by that, even with reference to your comments
> >> below.
> >
> > Why is it unclear? The comments below establish it as being a far
> > greater force than genetic drift, even with your attempt to make
> > a case for the latter below.
>
> I'm afraid the comments below establish nothing. They just assert.

I refuse to let digs like this goad me into doing 500+ line posts
where I explain reasoning by more reasoning explained by yet more
reasoning...

> How do you know the extinction of certain taxa were selected rather than
> random?

First, as Richard Norman could tell you, "random" is not definable
mathematically. It's a statistical concept, using various "tests for
randomness" which test for crude approximations and give different
results according to how refined the test is. Statistics is not
a branch of mathematics and never can be.

Second, in light of this fact, I see no reason to restrict the
term "natural selection" to processes that are random
under one test and "un-random" under another.

> It's a live question. You hint at it with a single word
> "megafauna", but you need to do better than single words if you want to
> make a case.

A case for what?

<snip of things dealt with in first reply to this post of yours>

[John Harshman]

The production of new species happens through population genetic
processes within species.

> And "the preservation of favoured races" hints at much more: the races
> that are preserved have special qualities which make them survive
> natural disasters to which less adapted species succumb.

You made that part up. By "races" he meant "varieties", i.e. different
phenotypes within populations.

> And unless Wikipedia is badly in need of fixing, Darwin had that and
> much more in mind about natural selection:
>
> Darwin emphasizes that he used the phrase "struggle for existence"
> in "a large and metaphorical sense, including dependence of one
> being on another"; he gives examples ranging from plants struggling
> against drought to plants competing for birds to eat their fruit
> and disseminate their seeds.

All true. But how does it support any point you make?

> INTERLUDE: note the use of "competing": it isn't the birds in competition
> with the fruit, it is the plants in competition with each other for
> birds to disseminate their seeds. But you claimed that "competition" is the
> proper word for the ediacaran organisms becoming extinct by falling
> prey to overactive predators.

Of course it isn't the birds in competition with the fruit. The fruit
wants the birds to eat it. Intraspecific competition results in natural
selection within that species. Interspecific competition can result in
natural selection within either or both species, or neither. But
competition is not, per se, natural selection.

> Calling that "competition" between the organisms and their prey reminds
> me of the immortal words of Mr. Spock in the movie Star Trek IV:
>
> "To hunt a species to extinction is illogical."

Was that another pointless digression or was it in any way relevant?

You just made that part up again. None of what you quoted supports your
point. If you think it does, explain how.

> The forming of new species
> is slow, but the culling of old species can be instantaneous.
>
> Using a tree diagram and calculations, he indicates the
> "divergence of character" from original species into
> new species and genera. He describes branches falling off
> as extinction occurred, while new branches formed in
> "the great Tree of life ... with its ever branching
> and beautiful ramifications".[130]
> https://en.wikipedia.org/wiki/On_the_Origin_of_Species

Note that this says nothing about instantaneous culling.

>> Sorry if you don't like standard biological language. Why?
>
> Again I ask: just when did "natural selection" become standardly
> restricted to populations by biologists OUTSIDE the specialty of
> population genetics? Darwin would qualify if you could make a case for him,
> but you need to do some HOMEWORK to do that.

Biologists outside the specialty of population genetics generally don't
talk about natural selection. Nothing you have quoted is relevant to
your claims.

You have a habit of failing to make an explicit point, assuming that it
should be obvious. It is seldom obvious. When you do make a point, you
often argue for it by presenting a mass of statements with no clear
connection to your point, assuming that connection should be obvious. It
is seldom obvious. Please try to remember that I am not you, and the
only access I have to your thought processes is what you write. If you
reread your posts from the point of view of a reader who is not you, it
might help you clarify what you're saying.

[John Harshman]

I have no interest in your questions. I want to resist your constant
derailment of every thread.

>>>> The purpose is to discredit an example of
>>>> mutation in the first case
>>>
>>> What mutation? The phenomenon was well known before any experiments
>>> were undergone. The experiment was designed to show how one variety
>>> or the other was naturally selected for. It didn't address the origin
>>> of the varieties.
>>
>> Hey, you're the one that mentioned creationist attacks on the existence
>> of a mutation to the melanistic form.
>
> What on earth are you referring to here? I never suspected that this
> was the purpose of creationist charges of fraud. Can you find even
> one source that claims that this was their purpose?

No, no, no. You brought it up with #1, "the two varieties were always
there". If the two varieties were always there, there was no mutation.
Nothing to do with fraud.

[remainder of that misunderstanding snipped]

>>>>>> Of course very few creationists have
>>>>>> any real understanding even of the basics of population genetics. That's
>>>>>> why they keep claiming that if most mutations are deleterious there can
>>>>>> be no evolution.
>>>>>>
>>>>>>> I'm in the process of trying to find out how much of modern evolutionary
>>>>>>> theory is dependent on wild extrapolations from population genetics.
>>>>>>
>>>>>> What sort of wild extrapolations did you have in mind here?
>>>>>
>>>>> For one, the claim that genetic drift and natural selection are
>>>>> legitimate rivals for the main force in evolution. [See Burkhard's
>>>>> reply to MarkE and Camp's reply to the same post, backing Burkhard.]
>>>>
>>>> What do you mean by "main force" here? Which is more important depends
>>>> on that meaning.
>>>
>>> Maybe I should have said "the more important force."
>>
>> Still doesn't help unless you explain what "important" means here.

That was a request to explain what "important" means here.

>>> When "Roger Shrubber" tried to argue that genetic
>>> drift was more important, he was talking on the level of populations.
>>> He couldn't possibly have made a case on the [level of higher taxa].
>>
>> That cut off in mid-sentence.
>
> Fixed now.

OK. So what relevance does this have?

>>>>> Once you get past the scale of populations, it's a no-brainer:
>>>>> natural selection wins hands down. See my comments to MarkE below.
>>>>
>>>> It's unclear what you mean by that, even with reference to your comments
>>>> below.
>>>
>>> Why is it unclear? The comments below establish it as being a far
>>> greater force than genetic drift, even with your attempt to make
>>> a case for the latter below.
>>
>> I'm afraid the comments below establish nothing. They just assert.
>
> I refuse to let digs like this goad me into doing 500+ line posts
> where I explain reasoning by more reasoning explained by yet more
> reasoning...

Have it your way. But you tend to make huge leaps that others can't
follow. Do you want others to follow your reasoning or not?

>> How do you know the extinction of certain taxa were selected rather than
>> random?
>
> First, as Richard Norman could tell you, "random" is not definable
> mathematically. It's a statistical concept, using various "tests for
> randomness" which test for crude approximations and give different
> results according to how refined the test is. Statistics is not
> a branch of mathematics and never can be.
>
> Second, in light of this fact, I see no reason to restrict the
> term "natural selection" to processes that are random
> under one test and "un-random" under another.

Why the digression into what "random" means? Surely we have a
common-sense understanding that will serve here. I don't know what you
are referring to with "random under one test and un-random under another".

>> It's a live question. You hint at it with a single word
>> "megafauna", but you need to do better than single words if you want to
>> make a case.
>
> A case for what?

A case for what you are supposedly attempting to show, that the
extinctions of certain taxa were selected rather than random, on the way
to demonstrating that selection is a far greater force than genetic
drift. Isn't that what you were going for?

[Rolf]

"Peter Nyikos" <nyi...@bellsouth.net> wrote in message
news:d46152de-aebc-4153...@googlegroups.com...

> On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
>> On 2/7/17 6:12 AM, Peter Nyikos wrote:
>>
>> > Behe's assertions are nuanced: the more complex the IC
>> > structure/system,
>> > the stronger the case for meeting Darwin's criterion
>> > of not being attainable through "numerous, successive, slight
>> > modifications".
>> > See pp. 39-40 of _Darwin's Black Box_.
>>
>> Why would you think that assertion to be true? Would that not be
>> assuming a particular model of evolution, by the sequential addition of
>> invariant parts?
>
> No, Behe explicitly allows for indirect, circuitous routes at the top
> of page 40.
>
> You've been misled by yet another part of the virtual reality
> that has grown up around Behe in the blogosphere.
>

> Peter Nyikos
>

Behe runs amok in the first paragraph on p.40, with one of his
characteristic eurekas:
"our confidence that Darwin's criterion of failure has been met skyrockets
towards the maximum that science allows."

While you still are enamored by the excitement he express at the concept of
Irreducible Complexcity, it has been debunked in so many ways. Not that it
may not be a concept in its own right, but hardly of any consequence where
he and his creationist followers needs it the most.

Sorry, I remain unimpressed.
While you still really believe all the worlds leading biologists throughout
about 160 years have been, or are dead wrong. My mind boggles.
Nothing to suggest that Behe was right has surfaced in the 20 + years since
DBB was written.

[Rolf]

"MarkE" <mark.w.e...@gmail.com> wrote in message
news:65383bc7-7132-49a8...@googlegroups.com...

The best argument against creationism, a designer et cetera must be that
they just don't make sense. Current understanding - I underscore "current"
as the most up-to-date thoughts on both the natural evolution of the
biosphere as well as pathways for the development of the first
self-replicating molecules. I am at present reading "Reinventing the Sacred"
by Stuart A. Kauffman and it takes time, it is not an easy read - but very
interesting. I wonder if and when Nyikos, Behe, (Ray Martinez excepted for
obvious reasons.) will be able to respond to what Kauffman writes?

Rolf

[eridanus]

El domingo, 5 de febrero de 2017, 14:34:58 (UTC), MarkE escribió:
> Bill, I appreciate your acknowledgment of my premise.
>
> What is my approach to figuring out how it all works and how it all got here?
>

> Continue to research this. It's important for better understanding and combating disease for starters.
>
> As this research progresses, it will discover a greater percentage of the genome to be functional. It will also reveal deep complexity within this parent cell (that "alien intricacy"), such as codes within codes, recursive regulation and control, fractal specifications, cascades of protein marshalling, etc.

>
> These findings will become increasingly incompatible with the limits of natural selection (especially as the selectionist paradigm continues to be eroded by neutral theory, CNE, etc). Natural selection will be shown to be an inadequate explanation.
>

> Since there is no alternative naturalistic explanation for the accumulation of functional complexity (ie Dawkins' "appearance of design"), the only reasonable option will be to infer a designer.
>

> At that point, science hands over to theology.

Even in the probably case that we could not explain the damn thing,
what implies? Only one thing. That we are ignorants. Are you not?
Can explain why is this possible by saying "god did it"? Do you think
this is an explanation?
God did it. Well, why he did it? Do you know?
What was purpose of god to make all those impossible things?
You know that?

Then, other than god did it, what else do you know?
eri

[Peter Nyikos]

On Tuesday, February 7, 2017 at 10:34:57 AM UTC-5, John Harshman wrote:

> On 2/7/17 6:19 AM, Peter Nyikos wrote:
> > On Monday, February 6, 2017 at 9:00:00 PM UTC-5, John Harshman wrote:
> >> On 2/6/17 3:27 PM, Peter Nyikos wrote:
> >>> On Monday, February 6, 2017 at 4:34:58 PM UTC-5, John Harshman wrote:
> >>>> On 2/6/17 1:11 PM, Peter Nyikos wrote:

> >>>>>>> Here is another source of ambiguity. "Natural selection" is used by most
> >>>>>>> anti-ID types in the strictly population-genetics sense. But I think most
> >>>>>>> laymen think of it as the grand pageant of "origin of species" on the
> >>>>>>> one hand and extinction on the other. The mass extinctions of the distant
> >>>>>>> past exerted a profound influence on evolution by "naturally selecting"
> >>>>>>> certain orders and families to go extinct and others to survive. We humans
> >>>>>>> have "naturally selected" untold numbers of species to go extinct,
> >>>>>>> including so much of the megafauna of the Pleistocene.
> >>>>>>

> >>>>>> I'm with you there. Extinction and, perhaps, speciation rates, during
> >>>>>> mass extinctions and otherwise, have had an influence on the course of
> >>>>>> evolution.
> >>>>>
> >>>>> Right, and where is there a comparable role for genetic drift?
> >>>>
> >>>> Why, random extinction and speciation, of course, meaning any such
> >>>> events not strongly related to particular characters of the species.
> >>>
> >>> There are many things responsible for random extinction besides
> >>> genetic drift. Floods, fires, volcanic eruptions, a new predator
> >>> or disease hitting a population without natural defenses...
> >>

> >> Genetic drift doesn't cause extinction. Nor does natural selection. We
> >> were talking about analogs of these population-level phenomena at a
> >> higher level. There is species drift as well as species selection.
> >>
> >>>> Raup's "field of bullets" is the extreme case.
> >>>
> >>> The Wikipedia entry makes no mention of genetic drift in connection
> >>> with it.
> >>
> >> I don't know why you got the idea that genetic drift was literally involved.
> >
> > The question I asked up there was:

> >
> > "Right, and where is there a comparable role for genetic drift?"
> >

> > What question did you THINK you were answering?
>
> It's an exactly comparable role.

Only "exactly" if you are completely sold on Raup's "Field of Bullets."

> Species selection is not literally the
> same as natural selection, just analogous.

A distinction without a difference. As I told Richard Norman:

Face it: even Harshman leaves the cozy realm of population genetics
once he tries to put an artificial barrier between the term
"natural selection" within a population and the same identical
process on bigger scales, affecting even the extinction of
whole phyla.

And, LO! The deservedly popular biology textbook for beginning biology
majors puts up no such artificial barrier [caps substitute for boldface]:

NATURAL SELECTION A process in which organisms with certain
inherited characteristics are more likely to survive and
reproduce than organisms with other characteristics.
--_Biology_, by Campbell, Reece et.al., Eighth ed.,
Pearson Benjamin Cummings, 2008, p. G-24

> The stochastic processes that
> happen above the population level are not the same as genetic drift,
> just analogous. I thought that was clear.

How could something so counterintuitive be clear? As I told
Norman in the next paragraph:

IN contrast, Harshman tore down the colossal "barrier"
between "genetic drift" and "random extinctions"
by blatantly asserting that the two barriers are
exactly of the same sort.

Earth is too small for the same theory of stochastic processes
to make sense on large scales like the extinctions that took
place at the end of the Ediacaran, the Permian, the Triassic,
the Cretaceous, etc.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina

http://people.math.sc.edu/nyikos/

[Peter Nyikos]

On Wednesday, February 8, 2017 at 4:39:58 PM UTC-5, Rolf wrote:
> "Peter Nyikos" <nyi...@bellsouth.net> wrote in message
> news:d46152de-aebc-4153...@googlegroups.com...
> > On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
> >> On 2/7/17 6:12 AM, Peter Nyikos wrote:
> >>
> >> > Behe's assertions are nuanced: the more complex the IC
> >> > structure/system,
> >> > the stronger the case for meeting Darwin's criterion
> >> > of not being attainable through "numerous, successive, slight
> >> > modifications".
> >> > See pp. 39-40 of _Darwin's Black Box_.
> >>
> >> Why would you think that assertion to be true? Would that not be
> >> assuming a particular model of evolution, by the sequential addition of
> >> invariant parts?
> >
> > No, Behe explicitly allows for indirect, circuitous routes at the top
> > of page 40.
> >
> > You've been misled by yet another part of the virtual reality
> > that has grown up around Behe in the blogosphere.
> >
> > Peter Nyikos
> >
>
> Behe runs amok in the first paragraph on p.40, with one of his
> characteristic eurekas:

There is no "eureka" once the context has been restored.

> "our confidence that Darwin's criterion of failure has been met skyrockets
> towards the maximum that science allows."

Cherry-picking, Rolf? The first part of the sentence you are
quoting is excruciatingly general and gives no hint of whether
any of the actual examples in the book meet the criterion for
this level of confidence.

> While you still are enamored by the excitement he express at the concept of
> Irreducible Complexcity,

Rolf, I never was excited about it in the first place. Back in 1996 I
already wrote my verdict on the concept: "More bang for the buck," but
nothing much more. By seemingly necessitating bigger, redundant systems
that lose parts to arrive at IC, it moved the problem over to explaining
how the bigger systems evolve.

Since then, though, I've also come to appreciate a very indirect role:
it focuses our attention on exquisitely intricate molecular machines
and systems whose evolution SHOULD be explainable by current evolutionary
theory, but is not.

> it has been debunked in so many ways.

Really? I know only the debunking of long cascades involving autocatalytic
factors. Can you name me any other debunkings?

> Not that it
> may not be a concept in its own right, but hardly of any consequence where
> he and his creationist followers needs it the most.

And where would that be?

> Sorry, I remain unimpressed.
> While you still really believe all the worlds leading biologists throughout
> about 160 years have been, or are dead wrong.

Sorry, you have been misled by scuttlebutt and guilt by association.

I never believed anything remotely resembling what you are ascribing
to me.

> My mind boggles.

And it well should, about anyone who fits that grotesque fantasy
that you've ascribed to me.

> Nothing to suggest that Behe was right has surfaced in the 20 + years since
> DBB was written.

Behe has made myriads of statements over the years. Which ones did you
have in mind with "right"? right about what?

Peter Nyikos
Professor of Mathematics -- standard disclaimer--
University of South Carolina (in Columbia)
http://people.math.sc.edu/nyikos/

[John Harshman]

Not at all. All that's necessary is for extinction and speciation to
have some stochastic element.

>> Species selection is not literally the
>> same as natural selection, just analogous.
>
> A distinction without a difference. As I told Richard Norman:
>
> Face it: even Harshman leaves the cozy realm of population genetics
> once he tries to put an artificial barrier between the term
> "natural selection" within a population and the same identical
> process on bigger scales, affecting even the extinction of
> whole phyla.

Once again you make a claim and support it with something I can't see as
connecting to that claim. No, it isn't the same identical process. There
are numerous differences. And "the same" is not "analogous".

> And, LO! The deservedly popular biology textbook for beginning biology
> majors puts up no such artificial barrier [caps substitute for boldface]:
>
> NATURAL SELECTION A process in which organisms with certain
> inherited characteristics are more likely to survive and
> reproduce than organisms with other characteristics.
> --_Biology_, by Campbell, Reece et.al., Eighth ed.,
> Pearson Benjamin Cummings, 2008, p. G-24

Again, you support your claim with something that doesn't support your
claim.

>> The stochastic processes that
>> happen above the population level are not the same as genetic drift,
>> just analogous. I thought that was clear.
>
> How could something so counterintuitive be clear?

I thought I had stated it clearly. I don't know why it's
counterintuitive either.

> As I told
> Norman in the next paragraph:
>
> IN contrast, Harshman tore down the colossal "barrier"
> between "genetic drift" and "random extinctions"
> by blatantly asserting that the two barriers are
> exactly of the same sort.

I tore down a barrier by asserting that it's the same as another
barrier? That makes no sense at all. What argument are you trying to
make here?

> Earth is too small for the same theory of stochastic processes
> to make sense on large scales like the extinctions that took
> place at the end of the Ediacaran, the Permian, the Triassic,
> the Cretaceous, etc.

What does the size of the earth have to do with any of this? Are you
saying there's no stochastic element in mass extinctions?

[John Harshman]

Defend your claim that your scenario demonstrates what you say. Wouldn't
that be true only if your scenario were a plausible explanation of the
Cambrian explosion? I maintain that it isn't.

>> It's clear from the fossil record and
>> from genetic data that the Cambrian explosion was not an instance of the
>> scenario you describe.
>
> Now THIS part is not preaching to the choir! In fact the only
> reason I can see any sense in this part is that you seem to be
> assuming just one attempt at colonization instead of three
> separate ones: one at the time of Doushanto, one at the beginnig
> of the Ediacara mini-explosion, and one at the beginning of
> the "main pulse of the Cambrian explosion," as Meyer puts it.

Whoa, now you're changing the scenario. This new one is even less
plausible. And I don't know which one we should be arguing about. Is
this addition now your standard scenario or not?

This new scenario is unclear. Are we still saying that each attempt
wipes out all previous life?

> All three would have to be by colonists with (essentially) our genetic code,
> but that could be explained by hypothesized by assuming they arose via
> directed panspermia.

So many problems. Not only our genetic code but apparently all the same
sorts of organisms, but successively more similar to the modern ones.
What are the odds of that? And wouldn't each colonization attempt have
to be more or less instantaneous in geological terms? Doushantuo, a
single deposit, might come closest, but the Cambrian explosion, which
you claim to be explaining, took many millions of years.

>>> And Meyer never claims in the book that it does entail that.
>>> [Yes, you might well be surprised in view of the incredible amount of
>>> wasted words on the blogosphere that assert that it does entail that,
>>> and/or use that assertion as a foundation for further GIGO.]
>>
>> Of course he doesn't. His last chapter includes a statement that he
>> doesn't, but it's a nudge-nudge, wink-wink sort of thing. Plausible
>> deniability.

[snipping an attempt to derail the discussion into one about the various
wrongs done to you]

>>>>> Reefs are an interesting parallel. In the last half-billion years there
>>>>> have been eons where no evidence of reefs has been found, and several
>>>>> distinct episodes of reef-building activity. And the first one was
>>>>> by pleosponges, very different from any reef builders of today.
>>>>
>>>> I don't see why this would be considered a parallel.
>>>
>>> Why would reefs NOT be a parallel to stromatolites?
>>
>> I had no idea that's the parallel you intended. Yes, reefs and
>> stromatolites are both sorts of bioherms, but there the similarity ends.
>
> Wrong. Just as reefs can be built by very different organisms, it
> stands to reason that stromatolites could too.

Could, but that isn't the evidence for the stromatolites we know of.

> And my point up
> there is that, while we know enough about the reef builders of the
> last 520 million years to accurately place them in the Tree of Life,
> we know nothing about the stromatolite-builders of 3.5 billion years
> ago, except that they were microorganisms.

Not true. We know that they closely resembled cyanobacteria in
morphology. Anyway, please make some kind of connection to a point.

>>>> And what are the
>>>> eons in which there were no reefs? Not familiar.
>>>
>>> There was a fascinating article in _Scientific American_ about that, some time
>>> in the 1960's. This was back at the time when that magazine was far better
>>> from a scientific viewpoint than it is now. IIRC it identified four widely
>>> separated reef building episodes, each with different animals as their
>>> foundation.
>>
>> True. But in the intervals between these, are you sure there were no
>> reefs? There have been algal, archaeocyathan, tabulate, octacoral,
>> rudist, and hexacoral reefs, at least. But no reefs? When?
>
> Alas, I haven't the time to undertake a search for that _Scientific
> American_ article. And as I said:
>>
>>> Unfortunately, I don't remember reading anything more recent about this.

I'm going to provisionally doubt that the article said that there were
periods in the Phanerozoic when reefs were completely absent.

[John Harshman]

True. The question at hand is what sort of processes we might expect to
be able to produce IC, and whether Behe has thought about any of them.
It isn't about the bacterial flagellum, specifically, or about any
particular instance of a process.

Have you thought about any of them? If so, which ones?

>> There is, for example, the scaffolding pathway, in which parts
>> go away until the ones that remain are IC. And there is the addition
>> with modification of function pathway, in which parts that make an
>> original function better are added, and the original parts gradually
>> lose that aspect of their function. How many of those does he mention,
>> and which ones?
>
> None, and AFAIK his critics have come up with a goose egg as far
> as actual scenarios for indirect evolution of the IC systems in his book.
> Hence my NOTE TO ALL READERS above.

Before declaring IC of complex systems to preclude evolution, shouldn't
he have considered the various mechanisms by which IC might have
evolved? How can you consider any of them implausible without first
examining them?

>>> Behe's nuanced argument could, of course, be weakened by specific examples
>>> of circuitous routes to the various systems in _DBB_.
>>> However, the usual anti-ID mantra at this point, "exaptation," is
>>> too general a concept to be an indirect route for specific examples
>>> like the bacterial flagellum.
>>>
>>> For that, you would need some candidates for exaptation that
>>> (1) don't pose big problems for their own evolution and
>>> (2) can be exapted in concretely describable ways.
>>>
>>> In the case of the bacterial flagellum, Minnich's testimony at Dover
>>> included describing experiments addressing point (2) where the
>>> candidate every anti-ID blogger and scientist puts forth
>>> -- the type III mechanism -- is concerned. His experiments
>>> ended in failure to attach the long flagellin filament
>>> ("tail" or "propeller").
>>>
>>> I know of no experiments that succeeded in producing that effect,
>>> do you? And yet, I think a publishable paper could result from success.
>>
>> Sorry, what effect?
>
> Genetically attaching a hook and filament to a Type III mechanism to
> produce an organelle analogous (but not necessarily homologous) to
> bacterial flagellae.

Right. Why should these experiments be relevant to evolution?

>> Are you saying that if laboratory experiments fail
>> to reproduce a particular evolutionary pathway, that argues that the
>> pathway doesn't exist?
>
> Of course not. I don't have the tremendous confidence some people
> seem to have in the ability of 21st century scientists to duplicate
> things that took eons to evolve, if evolve they did.

So, again, why bring those experiments up if they don't show anything
other than the inability of 21st Century scientists (well, Minnich)?

>>> As to (1), I know of no effort by anti-ID types to show that the
>>> Type III mechanism, which also looks to be IC, was exapted from
>>> something else. Nor have I seen any scenario for its assembly,
>>> either by a direct or circuitous route. Of course, there is always
>>> the possibility, suggested by Minnich at Dover, that it evolved
>>> from the bacterial flagellum through LOSS of the "propeller" and
>>> the "hook."
>>>
>>> But I don't think you want to go there, John.
>>
>> I have no interest in talking about the bacterial flagellum at all. Must
>> you constantly introduce digressions that then take over the conversation?
>
> I wrote for the general readership this time, as my all-caps note at
> the very beginning indicated. Here in NGG, these all-caps hit the reader
> in the usual display of part of one line from the post.
>
> Your shoot-from-the-hip questions, desirous of being spoon-fed details
> from Behe's book, were too gradualist for my taste, and I decided the
> topic needed quicker development.

You say development, I say derailing. But I think we've established that
Behe doesn't consider or discuss any mechanisms by which IC systems
might evolve. Wouldn't you consider that a flaw?

[RonO]

Note how Nyikos runs away in denial. The silly and sad assoholic menace
just can't cope with reality.

https://groups.google.com/d/msg/talk.origins/b4eNYHIncSY/Zw0DAKbDvGEJ

REPOST:
It looks like Nyikos has started to run again and there is no doubt that
�tomorrow� has not come in terms of the posts that Nyikos claimed that
he would relentlessly pursue. The pattern has been the same for years,
and it has been stupid and ridiculous for years. Nyikos has some weird
insane notion that he has never lied on the internet and that he has
never lost an exchange on the internet. These stupid lies seem to drive
him to keep going back to his old stupidity where he has lied or just
been plain wrong so that he can continue some weird type of denial of
reality. Nyikos has a personal definition of running that includes not
answering a post for over two months, so he has to keep pestering me
every couple of months in order for him to continue his insane denial of
reality. This is the boob who early on (years ago) accused me of
running from a post for two whole weeks when there was no reason that I
should have even known that the post existed because he had posted it to
someone else. This is the type of projection of his own stupidity that
Nyikos has to indulge in, in order to continue his senseless denial.

I have decided that instead of having to deal with the same old, same
old over and over that I will just take advantage of the latest Nykosian
denial to put together a post that I can just repost when Nyikos starts
posting to me again. I have had to look up and link to some of the
first material that Nyikos had to run from and deny so instead of
continuing to have to look the junk up just to have Nyikos run again, I
will just start reposting this post.

Nyikos started to harass me again after months of running in this thread:
Why do the ID perps run the bait and switch scam on their own
creationist (9/10/14)
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/VLf_vGDImnIJ

He had to start lying about the past as usual, so I demonstrated that he
was lying and he decided to run, but as is also usually the case he had
to pretend to be addressing the posts so he lied to Glenn that he would
address the material that he is still running from �tomorrow,� but
tomorrow obviously has not come. It is like his ploy where he claims
that he will "continue" but runs from the material that he has deleted.

One of the posts Nyikos had run from (9/13/14):
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/00GyMLoAhDcJ

It is obvious that Nyikos had to run from this post because when the
same evidence has been put up in other posts he has snipped it out and
run or just run. He has failed to address this evidence multiple times.

The Nyikosian lie to Glenn about tomorrow (9/16/14):
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/vOPLiVKsp4kJ

QUOTE:
Ron O has really ramped up his campaign of deceit against me on this
thread. I won't have time for it until tomorrow, Glenn, but I will
relentlessly pursue him on this thread. One thing I should explain
now, though. Back at a time when Hemidactylus gave the appearance of
sincerity, I promised him I would only reply to Ron O very sparingly
from that point on.

But Hemidactylus has gone off the deep end, and he now is completely
on Ron O's side despite having tried to look above it all in the past.

So I consider myself released from my promise: it is quite possible
that he only held off revealing what a toady he is of Ron O because
I kept to my promise, but his irrational hatred for me caused him to cast
caution to the winds.

Peter Nyikos
END QUOTE:

Poor Hemi. Nyikos harassed him for years with his claims that his
knockdowns were still coming, and Nyikos will not even tell me what the
last knockdown was supposed to be and give me a link to the post. Now
Glenn will have to deal with the tomorrow that never came.

Instead of address the posts that Nyikos claimed that he would
relentlessly pursue Nyikos started to lie about the issues in new posts
even after I noted his claim above, so I took some time and looked up
the old evidence that Nyikos had run from years ago.

Wells on the Ohio Bait and Switch in 2002 (9/21/14)
https://groups.google.com/d/msg/talk.origins/H2Sw6NFIi4s/c7cRQzCvA2YJ

It wasn�t a futile exercise because I learned something that I had not
known before. I found a report that Wells had written (likely for the
other ID perps at the Discovery Institute) where he admits that Meyer
and he in consultation with others had decided to run the bait and
switch on the Ohio rubes before they went to Ohio. Their presentation
on the science of intelligent design was just for show, and Wells�
comment to the Ohio board that there was enough scientific support for
ID that it could be required to be taught in the Ohio public schools was
just bogus propaganda because they had no intention of providing the ID
science for the creationist rubes to teach. The ID perps sold the rubes
the ID scam and then only gave them a stupid obfuscation switch scam
that did not even mention that ID had ever existed. I will also note
that the addition to the Discovery Institute�s education policy
qualifier, that they did not want ID required to be taught in the public
schools, was not added until after the Ohio bait and switch. I noticed
that they had added it sometime around the Dover fiasco. The copy of
their education policy that was in their 2007 Dover propaganda pamphlet
definitely had the �required� qualification.

This is a post where I link to the old posts where Nyikos was running in
denial about being wrong about the Ohio bait and switch and the
Discovery Institute�s involvement from 2011.
https://groups.google.com/d/msg/talk.origins/H2Sw6NFIi4s/IfNy4J5a4pEJ

Dover propaganda pamphlet on why intelligent design science could still
be taught in the public schools:
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1453


Trying to find new issues to misdirect the argument to, Nyikos started
making bogus claims about another old thread even after he had snipped
and ran from the obvious explanation twice.

Unnoted change in policy at the Discovery Institute. (9/1/13)
https://groups.google.com/d/msg/talk.origins/_UKCQLy_THM/LS3yPcug9t8J

The issue was what I believed that Glenn was arguing in this thread. I
at first thought that Glenn was adding to the evidence that the
education policy had changed from what it was. The pamphlet that he put
up had the old education policy in it and contained the paragraph about
teaching the scientific theory of intelligent design that the Discovery
Institute had removed. It was the perfect example of how the education
policy had changed. When he started some weird negative campaign I
thought that he was claiming that the education policy had not changed
and he was using the Dover pamphlet to do it. I informed him that he
could not use a document that had been updated in 2009 to deny something
that the Discovery Institute had recently done, but he kept up his
nonsensical argument. Glenn now claims that he was not talking about
the education policy shift, but was only trying to claim that the ID
perps were still selling the ID is science scam. How could he use a 4
year old document to claim that? It also makes no sense to me because I
would have agreed with Glenn that the ID scam was going to continue.
There would have been no reason for us to argue if Glenn had been
clearer on what he was doing. It doesn�t matter for Nyikos because
Nyikos denies that the ID perps claim to have the ID science in that
pamphlet, so he is wrong no matter what Glenn was arguing.

Nyikos Snipping and running from this reality:
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/FawHtAIHPFoJ

Nyikos removing what he cannot deal with again in a post manipulation
that you have to compare to the above post to understand the stupidity
of what Nyikos does. This post really is a monument to the stupidity
that Nyikos indulges in.
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/TeXllwSwW0MJ

Nyikos has not addressed this post in the original policy change thread:
https://groups.google.com/d/msg/talk.origins/_UKCQLy_THM/NLk50v_IujsJ

Nyikos claims that I did not respond to his post, but I gave him the link:
https://groups.google.com/d/msg/talk.origins/38nQm79NC94/mR2PtcMGS_8J

It has been a vacation of sorts for me, but likely hell for other
posters in the months that Nyikos was running and just lying about his
escapades to other posters. I will just note the last instance of
harassment that Nyikos should try to deal with instead of running like
he did.

Nyikos� previous harassment thread:
By their Fruits May 2014 (5/22/14)
https://groups.google.com/d/msg/talk.origins/ttHhTTke_zE/3eaOhuIMGm8J

Nyikos started the above thread to harass me, but it backfired on him
because of his own stupid dishonesty, and he had to delete his post that
he started the thread with from my responses in order to keep lying. He
removed his original post twice from the discussion because he could not
defend his bogus tactics. Nyikos is that sad. Nyikos really has the
toddler mentality that if he pulls the blanket over his head no one can
see him. It is a weird delusional quirk that drives him to remove the
evidence from a post so that he can continue to deny reality.

By their Fruits March 2014
The thread that spawned the harassment thread.
Giving Nyikos some advice that he should have taken:
https://groups.google.com/d/msg/talk.origins/1MGKcHaFVtI/6fiXahJH9fMJ

My response to what Nyikos did:
https://groups.google.com/d/msg/talk.origins/1MGKcHaFVtI/vKg4Lu0kxB0J

Nyikos ran and started the harassment thread.

I realize that Nyikos is likely going to run and just harass other
posters with his stupid denial of reality, but I can�t do anything about
Nyikos except to expose the liar when he posts to me and get him to
leave me alone for a few weeks or months. Just imagine what a hell it
would be if I followed Nyikos around TO with a pooper scooper and set
him straight whenever he started lying about me to some other posters.
I am going to save this document onto my desktop for the next time
Nyikos can�t keep himself from his stupid sadistic harassment. I plan
to just repost it and tell the loon that he can address what he has
already run from before starting something else or lying about the past
some other way.

Ron Okimoto
END REPOST:

[Peter Nyikos]

On Wednesday, February 8, 2017 at 1:04:57 AM UTC-5, jillery wrote:
> On Tue, 7 Feb 2017 06:12:41 -0800 (PST), Peter Nyikos
> <nyi...@bellsouth.net> wrote:
>
> >On Tuesday, February 7, 2017 at 12:44:57 AM UTC-5, jillery wrote:
> >> On Mon, 06 Feb 2017 21:43:22 -0700, RSNorman <r_s_n...@comcast.net>
> >> wrote:
> >
> >> >>Similarly, when I talk about experiments to verify irreducible
> >> >>complexity (IC), the response I often get is that the REAL issue
> >> >>is whether it is evidence for intelligent design (ID) and that
> >> >>the concept of IC is of no intrinsic interest.
> >
> >IIRC this was your stance on the Minnich experiments, jillery. Correct?
>
>
> Since you asked, an important point you conveniently excluded is that
> IC has no intrinsic *biological* interest.

Norman put it that way, but did you? And even if you did, why should
Muller's very different but more rudimentary concept of NERC
(Not Everywhere Reducible Complexity) be so intensely interesting
biologically? or is it?

> Based on those who claim
> IC as evidence against biological evolution and for ID, it has lots of
> intrinsic interest with them.

Similarly, does NERC only hold interest for those who are so desperate
to discredit IC that they will misrepresent NERC as though it were IC?

>
> >> >I don't know about biological experiments "to verify irreducible
> >> >complexity". I do not know what you are talking about here. If there
> >> >were such experiments that DID verify it then that would constitute
> >> >evidence.
> >>
> >>
> >> Based on his other posts, my impression is he's referring to the
> >> experiments Minnich described in his Dover trial testimony.
> >
> >Indeed, one need look no further than the post I did in reply to
> >MarkE yesterday evening. There might, of course, have been other
> >experiments to verify IC that I haven't learned about.
> >
> >> If by "it" you mean ID, I must disagree. Behe's bald assertions
> >> notwithstanding, biological IC is not evidence against biological
> >> evolution, nor is it evidence for Design,
> >
> >Behe's assertions are nuanced: the more complex the IC structure/system,
> >the stronger the case for meeting Darwin's criterion
> >of not being attainable through "numerous, successive, slight modifications".
> >See pp. 39-40 of _Darwin's Black Box_.
>
>
> Of course, your distinctive interpretation of Behe's "nuance" isn't
> shared by most authorities on the subject,

Such "authorities" have to be talking about something not on pp. 39-40
if they have a shred of integrity.

Your oh-so-confident "Of course..." is therefore a naked
Appeal to Authority fallacy.

> of which you should admit
> are not one, your association below notwithstanding.

You are far less of one than I am, and I note that you don't even
have the minimal backbone to name one of these "authorities," let
alone to (heaven forbid!) quote one of them.

Did you, perhaps, have Kenneth Miller in mind? He has been quoted
as saying a most amateurish thing in response to why he is so
adamantly opposed to God having anything to do with evolution:

"Who is the better pool player? Somebody who, with a single
initial shot, hits all of the balls into the correct pockets?
Or, somebody who, after using the initial shot to scatter
the balls, then has to pot them all individually?"

Atoms aren't like billiard balls. Hasn't Prof. Miller ever heard of quantum
indeterminacy? Does he actually think there IS such a thing as the precise
location AND the precise momentum of every subatomic particle? And that they
were already present at the "single initial shot" of the Big Bang?

If so, he is hopelessly mired in 19th century physics.

[Mark Isaak]

On 2/8/17 5:31 AM, Peter Nyikos wrote:
> [...]

> Note the word "creationists." Ron O has bought into the scam that
> ID is just a branch of creationism.

To everyone except 0.000000014% of humanity, ID *is* just a branch of
creationism.

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"We are not looking for answers. We are looking to come to an
understanding, recognizing that it is temporary--leaving us open to an
even richer understanding as further evidence surfaces." - author unknown

[rsNorman]

Peter Nyikos <nyi...@bellsouth.net> Wrote in message:

As John points out you simply misunderstood how words are used.
The extinction of an entire phylum is hard to reconcile with the
notion of natural selection. And genetic drift represents merely
one very specific stochastic process by which populations change.
The important point is whether the extinction process is
correlated with fitness.
--


----Android NewsGroup Reader----
http://usenet.sinaapp.com/

[Mark Isaak]

On 2/7/17 10:19 AM, Peter Nyikos wrote:
> On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
>> On 2/7/17 6:12 AM, Peter Nyikos wrote:
>>

>>> Behe's assertions are nuanced: the more complex the IC structure/system,
>>> the stronger the case for meeting Darwin's criterion
>>> of not being attainable through "numerous, successive, slight modifications".
>>> See pp. 39-40 of _Darwin's Black Box_.
>>

>> Why would you think that assertion to be true? Would that not be
>> assuming a particular model of evolution, by the sequential addition of
>> invariant parts?
>
> No, Behe explicitly allows for indirect, circuitous routes at the top
> of page 40.

And he explicitly disallows it in the very next sentence.

(Why do you keep omitting that bit?)

[rsNorman]

Peter Nyikos <nyi...@bellsouth.net> Wrote in message:

Frankly I am confused about what point you are trying to make here.

There are the products of evolution the organisms that now or
previously did exist. There are the processes and mechanisms
that are well established to produce evolutionary change. There
is the theory or hypothesis that those processes and mechanisms
produced the products. But, frankly, nobody mentions the terms
theory or hypothesis in talking about the orbit of a planet or
the way lenses focus light or that table salt is NaCl.


Incidentally I wrote that population genetics is the foundation of
modern evolution. I didn't say it was the only thing. Evolution
is descent with modification; a change in the heritable nature of
a population, the genotype. That is exactly what pop-gen is
about. Natural selection is based on differences incapabilities
of organisms, the phenotype. That is where evo-devo comes in. It
is also dependent on the environment, physical and biological.
You do not understand evolution without understanding the whole.


You may continue but I can only do so sporadically and less
thoroughly than I would wish. I am again on the road with only a
tablet to work on and probably infrequent Internet access for
almost two weeks.

Oh, you mentioned in another post (my limited software makes it
very hard to search posts) about set theory vs. all mathematics.
Back some 60+ years ago when I took "foundations of mathematics"
we did not only mathematical logic but also axiomatic set theory.
Isn't set theory really the foundation for mathematics (just as
pop-gen for evolution}?

[jillery]

On Wed, 8 Feb 2017 04:59:01 -0800 (PST), Peter Nyikos

<nyi...@bellsouth.net> wrote:

>On Wednesday, February 8, 2017 at 1:04:58 AM UTC-5, jillery wrote:
>> On Tue, 7 Feb 2017 10:19:24 -0800 (PST), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>> >On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
>> >> On 2/7/17 6:12 AM, Peter Nyikos wrote:
>> >>
>> >> > Behe's assertions are nuanced: the more complex the IC structure/system,
>> >> > the stronger the case for meeting Darwin's criterion
>> >> > of not being attainable through "numerous, successive, slight modifications".
>> >> > See pp. 39-40 of _Darwin's Black Box_.
>> >>
>> >> Why would you think that assertion to be true? Would that not be
>> >> assuming a particular model of evolution, by the sequential addition of
>> >> invariant parts?
>> >
>> >No, Behe explicitly allows for indirect, circuitous routes at the top
>> >of page 40.
>> >
>> >You've been misled by yet another part of the virtual reality
>> >that has grown up around Behe in the blogosphere.
>>

>> So you learned a new polemical label during your leave of absence.
>
>I've used it many times before, including uses in talk.abortion
>well before I returned to talk.origins in 2010. But now I've
>found a specific use for it.

What you post to other froups is of no interest to me, nor I suspect
to other posters to T.O.

>It provides a convenient keyword for people to do a
>Google search on, whether an internal NGG one or an external one
>that could also make use of other search engines.

I accept the above as your admission to using polemical labels. So
you have no basis for complaining about other's alleged use of same.

>I intend to use it this way from now on whenever I see
>misrepresentations of Behe which I've already seen more times
>than I care to count. You posted at least two yourself:
>about Muller having written about IC long before Behe; and the
>following whopper:

A whopper is a sandwich from BurgerKing. Any personal definitions you
use here for that word are equally irrelevant.

>"Behe's claims about IC, specifically that such systems could
> not have evolved."

The distinction you claim between Muller's interlocking complexity and
Behe's irreducible complexity is irrelevant to the issue under
discussion, but it's no surprise that you baldly assert otherwise.
Muller's two-step as he described it decades before Behe wrote DBB is
entirely capable of removing all unnecessary parts.

In the very quote to which you refer but conveniently don't post, Behe
says explicitly that the methods he allows evolution might have
evolved IC are for very simple systems, and not for anything as
complex as the bacterial flagellum or even immune systems. If in fact
Behe allowed meaningful possibilities, then his claim that IC is
strong evidence against evolution would be logically incoherent, and
his entire line of reasoning about IC would unravel.

>> Give yourself a gold star.

The above sentence is not from the post to which you replied. Your
use of alternate facts is as dishonest as Trump's.

>I will, but not for any reason you are suggesting. If I see
>the same piece more than twice, I will start building a
>catalogue of them -- the ones that shape the form that
>the virtual reality takes here in talk.origins.
>
>Peter Nyikos
>Professor, Dept. of Mathematics -- standard disclaimer--
>at the original USC, in South Carolina

I had hoped that you would use your leave of absence from T.O. as a
clean break from your compulsive habit of posting repetitive
irrelevant spew from your puckered sphincter. Based on your comments
above, that hope is in vain.

[jillery]

On Wed, 8 Feb 2017 16:44:11 -0800 (PST), Peter Nyikos

<nyi...@bellsouth.net> wrote:

>On Wednesday, February 8, 2017 at 1:04:57 AM UTC-5, jillery wrote:
>> On Tue, 7 Feb 2017 06:12:41 -0800 (PST), Peter Nyikos
>> <nyi...@bellsouth.net> wrote:
>>
>> >On Tuesday, February 7, 2017 at 12:44:57 AM UTC-5, jillery wrote:
>> >> On Mon, 06 Feb 2017 21:43:22 -0700, RSNorman <r_s_n...@comcast.net>
>> >> wrote:
>> >
>> >> >>Similarly, when I talk about experiments to verify irreducible
>> >> >>complexity (IC), the response I often get is that the REAL issue
>> >> >>is whether it is evidence for intelligent design (ID) and that
>> >> >>the concept of IC is of no intrinsic interest.
>> >
>> >IIRC this was your stance on the Minnich experiments, jillery. Correct?
>>
>>
>> Since you asked, an important point you conveniently excluded is that
>> IC has no intrinsic *biological* interest.
>
>Norman put it that way, but did you?

If you won't accept what I say I said, why bother to even ask me?

>And even if you did, why should
>Muller's very different but more rudimentary concept of NERC
>(Not Everywhere Reducible Complexity) be so intensely interesting
>biologically? or is it?

Of course, nobody but you suggested Muller's observations are
"intensely interesting biologically".

>> Based on those who claim
>> IC as evidence against biological evolution and for ID, it has lots of
>> intrinsic interest with them.
>
>Similarly, does NERC only hold interest for those who are so desperate
>to discredit IC that they will misrepresent NERC as though it were IC?

Since you asked, Behe's IC discredits itself. You're welcome.

>> >> >I don't know about biological experiments "to verify irreducible
>> >> >complexity". I do not know what you are talking about here. If there
>> >> >were such experiments that DID verify it then that would constitute
>> >> >evidence.
>> >>
>> >>
>> >> Based on his other posts, my impression is he's referring to the
>> >> experiments Minnich described in his Dover trial testimony.
>> >
>> >Indeed, one need look no further than the post I did in reply to
>> >MarkE yesterday evening. There might, of course, have been other
>> >experiments to verify IC that I haven't learned about.
>> >
>> >> If by "it" you mean ID, I must disagree. Behe's bald assertions
>> >> notwithstanding, biological IC is not evidence against biological
>> >> evolution, nor is it evidence for Design,
>> >
>> >Behe's assertions are nuanced: the more complex the IC structure/system,
>> >the stronger the case for meeting Darwin's criterion
>> >of not being attainable through "numerous, successive, slight modifications".
>> >See pp. 39-40 of _Darwin's Black Box_.
>>
>>
>> Of course, your distinctive interpretation of Behe's "nuance" isn't
>> shared by most authorities on the subject,
>
>Such "authorities" have to be talking about something not on pp. 39-40
>if they have a shred of integrity.
>
>Your oh-so-confident "Of course..." is therefore a naked
>Appeal to Authority fallacy.

Of course you're incorrect. I don't appeal to anything. Instead I
merely note your claim to authority on the subject, and your complete
lack of said authority, an example of Dunning-Kruger.

>> of which you should admit
>> are not one, your association below notwithstanding.
>
>You are far less of one than I am, and I note that you don't even
>have the minimal backbone to name one of these "authorities," let
>alone to (heaven forbid!) quote one of them.

Your failure to quote Behe's comments to which you repeatedly allude
disqualifies you from complaining about my alleged association with
invertebrates.

>> >Peter Nyikos
>> >Professor, Dept. of Math. -- standard disclaimer--
>> >Univ. of South Carolina
>> >http://people.math.sc.edu/nyikos/

You are a poster child for eliminating tenure.

[zencycle]

On Monday, February 6, 2017 at 6:49:57 AM UTC-5, MarkE wrote:
>
> To reflexively downplay and dismiss the potential
> significance and implications of this evidence is
> to protect materialism irrespective.

You're confusing 'evidence' with 'interpretation'.

> What naturalistic explanation is there, apart from NS,
> to explain an accumulation of functional complexity,
> even the most complex object known?

Natural selection best fits the evidence. If you have another suggestion (and I suspect that you do), present it with proof (you know, that pesky "testable, falsifiable, verifiable" thingie).

> Dawkins again: "Yet the living results of
> natural selection overwhelmingly impress us
> with the appearance of design as if by a master
> watchmaker, impress us with the illusion of design
> and planning."

You do see how Dawkins uses the terms 'appearance' and 'illusion'? Dawkins does not support your premise - in fact he does the opposite.

[Michael James]

I'm going to trim...a lot.

On 2017-02-08, MarkE <mark.w.e...@gmail.com> wrote:
> On Wednesday, February 8, 2017 at 3:50:01 AM UTC+9:30, Robert Camp wrote:
>> On 2/7/17 7:32 AM, MarkE wrote:
>> > On Tuesday, February 7, 2017 at 2:30:00 AM UTC+9:30, Robert Camp
>> > wrote:
>> >> On 2/6/17 3:43 AM, MarkE wrote:
>> >>> On Monday, February 6, 2017 at 2:15:00 AM UTC+9:30, Robert Camp
>> >>> wrote:
>> >>>> On 2/5/17 4:15 AM, MarkE wrote:

[huge snip]

>> > Now if 8% of our DNA is functional, that's 64MB of data in the
>> > genome. So we can safely conclude that by any known means, that's
>> > nowhere near enough information to specify the most complex object
>> > known.
>>
>> No, we cannot safely conclude that. It is, in fact a rash conclusion
>> based upon assumptions and misconceptions.
>>
>> The problem, once again, is that you are looking at the final product
>> and assuming there must be a direct one-to-one correspondence of
>> structural and functional complexity to some kind of information
>> specification in the original cell. That's not what happens. That is, in
>> fact the way a designer might do things. Natural selection has happened
>> upon a more efficient and elegant process. Simple, iterative chemical
>> operations can give rise to biological complexity. We know this to be a
>> fact, we see it happen every minute of every day.
>
> I keep banging on about information in the cell necessarily being compressed beyond known technology, employing fractal specification mechanisms, etc - the antithesis of one-to-one correspondence. I'm surprised you think I'm making any such assumption?

How much information or unique configurations can be contained in your 64 MB?
Have you thought about this or computed it?
Let's take 2bits. The number of unique states is 4
0 0
1 0
0 1
1 1
OK, let's add another bit, 3 bits can contain 8 unique states. (This is left as an
exercise for the reader).
Each added bit doubles the number of unique states of the string.

How many unique states can be contained in a 64MB string? Easy.
2^64e6 (yes 1e6 /= mega, I know. Just go with it)
According to Google, there are between 10^78 to 10^82 atoms in the known
universe.
Do you want to take a guess on which number is larger and by how much?

You seem to labor under the misapprehension that the amount of information that
can be communicated in a 64MB strong is small. And leaving aside the fact that you
have excluded large parts of the genome in your "estimate". Areas which I
believe are known to contain precisely the sorts of regulatory switches which
also contain "information" for the genome.

[snips]

>
> There's no master blueprint tucked inside the cell that we could roll out and view as a complete anatomical diagram. But it's there implicitly. Proteins forming specific molecular machines etc is one thing. But proteins, RNA etc dormant or expressed differently at various stages of embryo development create layers of complexity to the requirement of specifying each step. It's a kind of "butterfly effect", a highly non-linear process with a vast cascade of stages, regulation, signalling, overlaying error correction and error tolerance as well.
>
> I'm not arguing that this is so complex that it proves a designer (though I personally think it does). Rather, I'm saying that what's going here is actually so much more wound up in itself, recursive, fractal, etc (I don't even have concepts to describe it - remember, one cell becomes 35 trillion and the most structurally and functionally complex object known), that as research begins to grapple with this more and more, my prediction is it will have major implications for our understanding of the genome, proteins, RNA etc and place fatal contraints upon evolution.
>
> You read it here first.

Not really. And not for the last time either I'm sure.

mike

P.S. A very crude estimate of 2^6.4e7 ~ 10^2000000. A ten followed by 10
million zeros.
P.P.S. Corrections welcome.

--
mrj...@swcp.com http://www.swcp.com/~mrjames/
"When you can measure what you are speaking about and express it in
numbers you know something about it; but when you cannot express it in
numbers your knowledge is a meagre and unsatisfactory kind" - Lord Kelvin

[Öö Tiib]

On Thursday, 9 February 2017 04:54:58 UTC+2, Mark Isaak wrote:
> On 2/8/17 5:31 AM, Peter Nyikos wrote:
> > [...]
> > Note the word "creationists." Ron O has bought into the scam that
> > ID is just a branch of creationism.
>
> To everyone except 0.000000014% of humanity, ID *is* just a branch of
> creationism.

I suspect that you have missed at least one order of magnitude there
since 0.000000014% feels close to just single person.

[Mark Isaak]

Is there a second one?

[Peter Nyikos]

On Wednesday, February 8, 2017 at 10:19:57 PM UTC-5, Mark Isaak wrote:
> On 2/7/17 10:19 AM, Peter Nyikos wrote:
> > On Tuesday, February 7, 2017 at 10:39:58 AM UTC-5, John Harshman wrote:
> >> On 2/7/17 6:12 AM, Peter Nyikos wrote:
> >>
> >>> Behe's assertions are nuanced: the more complex the IC structure/system,
> >>> the stronger the case for meeting Darwin's criterion
> >>> of not being attainable through "numerous, successive, slight modifications".
> >>> See pp. 39-40 of _Darwin's Black Box_.
> >>
> >> Why would you think that assertion to be true? Would that not be
> >> assuming a particular model of evolution, by the sequential addition of
> >> invariant parts?
> >
> > No, Behe explicitly allows for indirect, circuitous routes at the top
> > of page 40.
>
> And he explicitly disallows it in the very next sentence.

No, he does not. Behe talks like a scientist, and in this case he,
with typical scientific caution, does not try to quantify what
he says next.

"As the complexity of an interacting system increases, though,
the likelihood of such an indirect route drops precipitously."

"precipitously" refers to the well known fact that as each new
factor is added, the increase in difficulty of production
is exponential unless there is something unusual about the system.

But there is no quantification, because addition of a new factor could
be with probability very close to 1 or close to 0 or close to anywhere
in between. And this has to be determined on a case by case basis.

BOTTOM LINE: I am still looking for one, just ONE example of an
actual purported evolution of a *specific* IC system by an indirect
route. Until one is produced, there is no way anyone can quantify Behe's
statement.

Behe isn't foolish enough to try, and his critics apparently think
simplistic statements like the one you've made are enough to sink him.

As I said before, we DO have two examples which arise by DIRECT
routes, the clotting systems and immune systems described in _DBB_.
Kenneth Miller and Keith Robison have very cleverly devised
a process where they could have arisen by "small, Darwinian steps."

But here is another piece of virtual reality: the misconception
that all one needs to say in these two cases is,
"it arose by the usual method of gene duplication and subsequent
divergence." People who think this have never studied the
absolutely crucial role autocatalycity plays in the Miller-Robison
scenario.

> (Why do you keep omitting that bit?)

I don't carry the book with me every time I travel between home
and university. And my time for posting is limited.

[It is 5:18pm, I have a meeting to attend at 5:30 and then have to rush to
a 7:00 meeting, and this may be the only post I can do today.]

If talk.origins weren't like a basketball game in which the
home crowd loudly heckles the opponent trying to make a free throw,
any number of people could have corrected you by now.

But you are on the home team, and thereby hangs a tale.

> --
> Mark Isaak eciton (at) curioustaxonomy (dot) net

> "We are not looking for answers. [We are looking for ways
to make Peter Nyikos waste his time by us making comments that
could have been avoided by us thinking like mature adults.]

Fixed it for you. :-)

[Peter Nyikos]

Why do you think that?

"He's a credit to his race -- the human race."
--oft-quoted praise for Joe Louis, African-American who was
boxing heavyweight champion for a record number of years.

> > And unless Wikipedia is badly in need of fixing, Darwin had that and
> > much more in mind about natural selection:
> >
> > Darwin emphasizes that he used the phrase "struggle for existence"
> > in "a large and metaphorical sense, including dependence of one
> > being on another"; he gives examples ranging from plants struggling
> > against drought to plants competing for birds to eat their fruit
> > and disseminate their seeds.
>
> All true. But how does it support any point you make?

Drought affects all plants to some extent. The difference between wining
and losing the struggle for survival is not confined to individual populations. Whole clades could lose.

> > INTERLUDE: note the use of "competing": it isn't the birds in competition
> > with the fruit, it is the plants in competition with each other for
> > birds to disseminate their seeds. But you claimed that "competition" is the
> > proper word for the ediacaran organisms becoming extinct by falling
> > prey to overactive predators.
>
> Of course it isn't the birds in competition with the fruit. The fruit
> wants the birds to eat it. Intraspecific competition results in natural
> selection within that species. Interspecific competition can result in
> natural selection within either or both species, or neither. But
> competition is not, per se, natural selection.

Thanks for explaining the first part of what I wrote to any lurkers on the
middle-school level. But you are ignoring the second part, starting with
"But you claimed...." And even the following didn't get you to address it:

> > Calling that "competition" between the organisms and their prey reminds
> > me of the immortal words of Mr. Spock in the movie Star Trek IV:
> >
> > "To hunt a species to extinction is illogical."
>
> Was that another pointless digression or was it in any way relevant?

So, let me get this straight: if Species A is the sole food of Species B,
and Species A is driven to extinction by excessive predation by Species B,
the official biological language has it that Species B was COMPETING
against Species A all along??? despite the fact that Species B is
doomed to extinction in short order???

Remainder deleted, to be replied to later.

[jillery]

On Thu, 9 Feb 2017 13:13:21 -0800, Mark Isaak
<eciton@curiousta/xyz/xonomy.net> wrote:

>On 2/9/17 12:33 PM, 嘱 Tiib wrote:
>> On Thursday, 9 February 2017 04:54:58 UTC+2, Mark Isaak wrote:
>>> On 2/8/17 5:31 AM, Peter Nyikos wrote:
>>>> [...]
>>>> Note the word "creationists." Ron O has bought into the scam that
>>>> ID is just a branch of creationism.
>>>
>>> To everyone except 0.000000014% of humanity, ID *is* just a branch of
>>> creationism.
>>
>> I suspect that you have missed at least one order of magnitude there
>> since 0.000000014% feels close to just single person.
>
>Is there a second one?

Steady Eddie. And he has claimed other strange bedfellows.

[John Harshman]

Please stop these irrelevant digressions. You know that Darwin didn't
mean "species" when he said "race".

>>> And unless Wikipedia is badly in need of fixing, Darwin had that and
>>> much more in mind about natural selection:
>>>
>>> Darwin emphasizes that he used the phrase "struggle for existence"
>>> in "a large and metaphorical sense, including dependence of one
>>> being on another"; he gives examples ranging from plants struggling
>>> against drought to plants competing for birds to eat their fruit
>>> and disseminate their seeds.
>>
>> All true. But how does it support any point you make?
>
> Drought affects all plants to some extent. The difference between wining
> and losing the struggle for survival is not confined to individual populations. Whole clades could lose.

Go on.

>>> INTERLUDE: note the use of "competing": it isn't the birds in competition
>>> with the fruit, it is the plants in competition with each other for
>>> birds to disseminate their seeds. But you claimed that "competition" is the
>>> proper word for the ediacaran organisms becoming extinct by falling
>>> prey to overactive predators.
>>
>> Of course it isn't the birds in competition with the fruit. The fruit
>> wants the birds to eat it. Intraspecific competition results in natural
>> selection within that species. Interspecific competition can result in
>> natural selection within either or both species, or neither. But
>> competition is not, per se, natural selection.
>
> Thanks for explaining the first part of what I wrote to any lurkers on the
> middle-school level. But you are ignoring the second part, starting with
> "But you claimed...." And even the following didn't get you to address it:
>
>>> Calling that "competition" between the organisms and their prey reminds
>>> me of the immortal words of Mr. Spock in the movie Star Trek IV:
>>>
>>> "To hunt a species to extinction is illogical."
>>
>> Was that another pointless digression or was it in any way relevant?
>
> So, let me get this straight: if Species A is the sole food of Species B,
> and Species A is driven to extinction by excessive predation by Species B,
> the official biological language has it that Species B was COMPETING
> against Species A all along??? despite the fact that Species B is
> doomed to extinction in short order???

Yes. Competition is a struggle over a limiting resource. I this
particular case the individuals of species a were a limiting resource
for both species. Why is that a problem?

[jillery]

Of course, Behe's "precipitously" provides the qualification you deny.

>BOTTOM LINE: I am still looking for one, just ONE example of an
>actual purported evolution of a *specific* IC system by an indirect
>route. Until one is produced, there is no way anyone can quantify Behe's
>statement.

Of course, there's no need for science to quantify Behe's statement.
That's Behe's job. Why is it that IDiots insist on fobbing off that
obligation onto their opponents?

>Professor, Department of Willful Stupidity -- standard disclaimer --
>U. of South Carolina


Fixed it for you.

[Peter Nyikos]

You're deliberately misreading "quantification," aren't you?


What's more, Behe doesn't qualify his statement; instead he moves
to a whole new level. And that's why YOU didn't quote the alleged
qualification, isn't it?

> >BOTTOM LINE: I am still looking for one, just ONE example of an
> >actual purported evolution of a *specific* IC system by an indirect
> >route. Until one is produced, there is no way anyone can quantify Behe's
> >statement.
>
>
> Of course, there's no need for science to quantify Behe's statement.

Yes, but there is a need for anti-Behe non-scientists, especially
militant atheists like yourself, to back up their alleged "refutations"
of what Behe wrote by giving actual examples -- or even actual WAGs --
of the indirect routes to Behe's examples of IC systems --
indirect routes which supposedly "refute" him.

> That's Behe's job. Why is it that IDiots insist on fobbing off that
> obligation onto their opponents?

Why is it that you pretend that Behe has to do the job of refuting Behe?

Behe explicitly acknowledged the *possible* existence of indirect routes,
you know. Why don't his opponents need to do the job of REALLY refuting him
instead of saying things like "the fact that there are indirect routes
obviously refutes him"? Until someone comes up with a PLAUSIBLE indirect
route, this "fact" is not in evidence, and may actually be false.

>
> >Behe isn't foolish enough to try, and his critics apparently think
> >simplistic statements like the one you've made are enough to sink him.

"I'm not Mark Isaak" is your excuse for ignoring these last two
lines, isn't it?

> >As I said before, we DO have two examples which arise by DIRECT
> >routes, the clotting systems and immune systems described in _DBB_.
> >Kenneth Miller and Keith Robison have very cleverly devised
> >a process where they could have arisen by "small, Darwinian steps."
> >
> >But here is another piece of virtual reality: the misconception
> >that all one needs to say in these two cases is,
> >"it arose by the usual method of gene duplication and subsequent
> >divergence." People who think this have never studied the
> >absolutely crucial role autocatalycity plays in the Miller-Robison
> >scenario.

"I never claimed that" might be your excuse for ignoring the irony
that direct routes have been found for two of Behe's IC examples
in _DBB_, but there don't even seem to be WAGs of indirect routes
for any of his other examples.

> >> (Why do you keep omitting that bit?)
> >
> >I don't carry the book with me every time I travel between home
> >and university. And my time for posting is limited.
> >
> >[It is 5:18pm, I have a meeting to attend at 5:30 and then have to rush to
> >a 7:00 meeting, and this may be the only post I can do today.]
> >
> >If talk.origins weren't like a basketball game in which the
> >home crowd loudly heckles the opponent trying to make a free throw,
> >any number of people could have corrected you by now.
> >
> >But you are on the home team, and thereby hangs a tale.

You too are on the "home team," jillery, your minor tiffs with
Harshman, Casanova, Norman, "deadrat," and Vince Maycock notwithstanding.
And you take full advantage of that both above and below.

> >> --
> >> Mark Isaak eciton (at) curioustaxonomy (dot) net
> >> "We are not looking for answers. [We are looking for ways
> >to make Peter Nyikos waste his time by us making comments that
> >could have been avoided by us thinking like mature adults.]
> >
> >Fixed it for you. :-)
> >
> >Peter Nyikos
> >Professor, Department of Willful Stupidity -- standard disclaimer --
> >U. of South Carolina

Looks like I really hit home with that "Fixing" in the form
of an accusation wasting of time: the champion time-waster
plays "monkey see, monkey do something superficially similar".

>
> Fixed it for you.

...with a blatant act of projection on your part.

Are you frustrated because I didn't waste any time in quoting
something that you've seen and quoted yourself? That "something" PROVES
that you wrote a blatant falsehood about Behe. Creationists are
regularly accused of lying for a lot less: repeating false statements
whose falsehood has not been recognized by said creationists
in the past.

Peter Nyikos
Professor, a position you cannot aspire to except for some
cute "humanities" special courses, like the one studying
the influence of Lady Gaga on popular culture.

[Peter Nyikos]

In what sense of the word "sense"? Keep in mind that a designer need not
have actually created the stuff of our universe. The ability to manipulate
it with skill, and the great longevity and intelligence entailed, is all
that is required.

> Current understanding - I underscore "current"
> as the most up-to-date thoughts on both the natural evolution of the
> biosphere as well as pathways for the development of the first
> self-replicating molecules.

"self-replicating" is ambiguous. Were it not for enzymes, the ability of
DNA or RNA to spontaneously self-replicate would not have advanced
the biosphere past the pre-prokaryote stage after a mere 4 billion years.

> I am at present reading "Reinventing the Sacred"
> by Stuart A. Kauffman and it takes time, it is not an easy read - but very
> interesting. I wonder if and when Nyikos, Behe, (Ray Martinez excepted for
> obvious reasons.) will be able to respond to what Kauffman writes?
>
> Rolf

In that particular book? I haven't seen it. Perhaps Behe has. I can ask him if you wish.

Would you like to post your impressions of how good a job Kauffman does?
For instance, does he explain how "the protein takeover" might have
happened en route to the first prokaryotes?

Peter Nyikos

Professor, Dept. of Mathematics -- standard disclaimer--

University of South Carolina
http://people.math.sc.edu/nyikos/
nyikos "AT" math.sc.edu

[Peter Nyikos]

On Thursday, February 9, 2017 at 3:19:58 PM UTC-5, Michael James wrote:
> I'm going to trim...a lot.

And disappear from this thread, never to return to it?

Note to readers: according to the "show activity" resource in NGG,
Michael James has done a grand total of four (4) posts in the last
three years to talk.origins, and never two to the same thread.

Anyway, this is for the general readership, as are all my posts
where I "sign" more than just my name at the end.

> On 2017-02-08, MarkE <mark.w.e...@gmail.com> wrote:
> > On Wednesday, February 8, 2017 at 3:50:01 AM UTC+9:30, Robert Camp wrote:
> >> On 2/7/17 7:32 AM, MarkE wrote:

>
> >> > Now if 8% of our DNA is functional, that's 64MB of data in the
> >> > genome. So we can safely conclude that by any known means, that's
> >> > nowhere near enough information to specify the most complex object
> >> > known.

Mark is here talking about the body of a human individual, I believe.

> >> No, we cannot safely conclude that. It is, in fact a rash conclusion
> >> based upon assumptions and misconceptions.
> >>
> >> The problem, once again, is that you are looking at the final product
> >> and assuming there must be a direct one-to-one correspondence of
> >> structural and functional complexity to some kind of information
> >> specification in the original cell. That's not what happens. That is, in
> >> fact the way a designer might do things. Natural selection has happened
> >> upon a more efficient and elegant process. Simple, iterative chemical
> >> operations can give rise to biological complexity. We know this to be a
> >> fact, we see it happen every minute of every day.
> >
> > I keep banging on about information in the cell necessarily being compressed beyond known technology, employing fractal specification mechanisms, etc - the antithesis of one-to-one correspondence. I'm surprised you think I'm making any such assumption?
>
> How much information or unique configurations can be contained in your 64 MB?
> Have you thought about this or computed it?
> Let's take 2bits. The number of unique states is 4
> 0 0
> 1 0
> 0 1
> 1 1

This seems to represent the 4 DNA nucleotides. But below, it turns
out that Michael James is NOT counting the number of bits encoded
in an individual's genome, but in counting ALL the possible sequences
that can be encoded by the 64mb bits.

That's like addressing some comments about the information contained
in a single bridge deal of 4 hands, by talking about the grand total of all
the possible bridge deals.

> OK, let's add another bit, 3 bits can contain 8 unique states. (This is left as an
> exercise for the reader).
> Each added bit doubles the number of unique states of the string.
>
> How many unique states can be contained in a 64MB string? Easy.
> 2^64e6 (yes 1e6 /= mega, I know. Just go with it)
> According to Google, there are between 10^78 to 10^82 atoms in the known
> universe.
> Do you want to take a guess on which number is larger and by how much?

Do readers want to take a guess on which is the larger of the two:
the number of atoms in the universe, versus the number of possible
bridge deals?

> You seem to labor under the misapprehension that the amount of information that
> can be communicated in a 64MB strong is small. And leaving aside the fact that you
> have excluded large parts of the genome in your "estimate". Areas which I
> believe are known to contain precisely the sorts of regulatory switches which
> also contain "information" for the genome.
>
> [snips]
>
> >
> > There's no master blueprint tucked inside the cell that we could roll out and view as a complete anatomical diagram. But it's there implicitly. Proteins forming specific molecular machines etc is one thing. But proteins, RNA etc dormant or expressed differently at various stages of embryo development create layers of complexity to the requirement of specifying each step. It's a kind of "butterfly effect", a highly non-linear process with a vast cascade of stages, regulation, signalling, overlaying error correction and error tolerance as well.
> >
> > I'm not arguing that this is so complex that it proves a designer (though I personally think it does). Rather, I'm saying that what's going here is actually so much more wound up in itself, recursive, fractal, etc (I don't even have concepts to describe it - remember, one cell becomes 35 trillion and the most structurally and functionally complex object known), that as research begins to grapple with this more and more, my prediction is it will have major implications for our understanding of the genome, proteins, RNA etc and place fatal contraints upon evolution.
> >
> > You read it here first.
>
> Not really. And not for the last time either I'm sure.
>
> mike
>
> P.S. A very crude estimate of 2^6.4e7 ~ 10^2000000. A ten followed by 10
> million zeros.
> P.P.S. Corrections welcome.

No corrections, just the fact that Michael James's number in turn is dwarfed
by something that has been around for a long time: googolplex,
defined rigorously as 10^googol, where googol = 10^100, 1 followed by
a hundred 0's. [So googolplex is 1 followed by googol zeros.]

You read it many times before you read it here. ;-)

And if that is small potatoes to you, I can tell you about much
bigger finite numbers.

But I don't think anyone wants me to really get into infinite
numbers here.

> --
> mrj...@swcp.com http://www.swcp.com/~mrjames/
> "When you can measure what you are speaking about and express it in
> numbers you know something about it; but when you cannot express it in
> numbers your knowledge is a meagre and unsatisfactory kind" - Lord Kelvin

Wrong. Topology does beautiful, rigorously definable things that do
not require numbers. And the numbers in which my branch of topology
deals are almost all infinite. In fact, I was very pleased when I
could justify putting the number 7/8 into the research paper
for which I am best known, and a bit embarrassed that I wasn't
the one who justified putting 11/12 into a joint paper I did
with John Kulesza and Ronnie Levy. It was John who did it.

Peter Nyikos
Professor, Dept. of Mathematics -- standard disclaimer--
University of South Carolina
http://people.math.sc.edu/nyikos/

Specialty since 1977: set-theoretic topology