Punctuated Equilibrium On a Grand Scale

[nyi...@bellsouth.net]

We are used to thinking of individual Punctuated Equilibrium (PE)
events in terms of mere millions of years or less, but I am inviting readers
to step back and look at evolution throughout the history of the earth.

The way it was introduced by Gould and Eldredge, PE has to do with
stasis punctuated by speciations. The latter took place over relatively
short time periods. Here, however, the "punctuations" are far greater
jumps, involving dozens or hundreds of speciations [and what can be
thought of as "speciations" in pre-biotic evolution] along
single lineages, sometimes involving a huge number of parallel lineages.

For the first few hundred million years, the evolution was
pre-biotic, and may have only made real progress
towards life as we know it after the Late Heavy Bombardment (which
ended ca. 3.8gya [gya = billions (= 1000 millions) of years ago].
Some time before 3.5gya the first efficient replicators appeared,
and biological evolution commenced. It had definitely arrived with
the first prokaryotes, found in rocks of ca. 3.48gya.

In the next ca. 2.9 billion years, the main events on the way to
modern animal life were the advent of eukaryotes, then endosymbiosis
and sexual reproduction (meiosis and fertilization involving
homologous chromosomes), then the first multicellular animal,
and the first bilaterian.

Then came the Ediacaran fauna and the start of the Cambrian explosion,
which can be said to begin with the protostome-deuterostome split.
This could have been as recent as 570mya, which would confine the Cambrian
explosion to 40-45 million years duration. This was a "punctuation" on a
truly grand scale, with at least 13 protostome phyla and 3 deuterostome phyla
making their debut in this short period (along with 2 to 4 extinct
bilaterian phyla).

Compared to these perhaps 0.04 - 0.045gy, even the following ca. 0.52 gy
were relatively uneventful, with at most 14 new phyla making their debut.
And the preceding ca. 2.9gy were a long period of stasis interrupted
by only a very few "grand scale punctuations."

IMHO by far the biggest of these was to meiosis/fertilization,
but I've never seen any attempt to give a scenario for how this
came about, although there are scads of explanations for how
such a development could have been advantageous once it was in place.

I've already posted a great deal since December 2010 about the
far more impressive "prebiotic punctuation," so on this thread I
will be putting almost all my emphasis on the Cambrian explosion.

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

[nyi...@bellsouth.net]

On Monday, October 6, 2014 2:40:55 PM UTC-4, nyi...@bellsouth.net wrote:

> Then came the Ediacaran fauna and the start of the Cambrian explosion,
> which can be said to begin with the protostome-deuterostome split.
> This could have been as recent as 570mya, which would confine the Cambrian
> explosion to 40-45 million years duration.

There have been a lot of studies giving wildly varying results. The 570mya
figure is from a decade old study by Kevin J. Peterson *, Jessica B. Lyons,
Kristin S. Nowak, Carter M. Takacs, Matthew J. Wargo, and Mark A. McPeek,
"Estimating metazoan divergence times with a molecular clock,"
http://www.pnas.org/content/101/17/6536.long

Four years later, Peterson and a new batch of co-authors compared a lot
of different studies, and stuck by Peterson's 2004 guns with:
"Of course, many others have addressed these questions using
a similar approach, and it is worth comparing our results
against not only the fossil record but also with other
molecular clock estimates as well. It compares well with
some molecular analyses, notably Peterson et al. (2004)
and Peterson & Butterfield (2005), all of whom argued
that the last common ancestor of protostomes and deuterostomes
evolved not more than 635 Myr ago."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614224/

The second reference is to:
Peterson K.J, Butterfield N.J. "Origin of the Eumetazoa:
testing ecological predictions of molecular clocks against
the Proterozoic fossil record. Proc. Natl. Acad. Sci. USA.
2005;102:9547 - 9552.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172262/
Excerpt:
"Because of the difficulty in assigning maximum values to divergence times
based on an incomplete fossil record, all calibrations were fixed as minima
(contrary to ref. 23; see ref. 5 for further details). We note, however,
that setting the maximum of each of our calibrated nodes at 1.5 billion
years increases the protostome-deuterostome ancestor from 579 to just
646 Ma, still 100 myr younger than estimated by Blair and Hedges (23).
This discrepancy cannot be explored further due to the absence of
methods provided (23)."

[23] "Molecular clocks do not support the Cambrian explosion."
Blair JE, Hedges SB Mol Biol Evol. 2005 Mar; 22(3):387-90.

As readers can see, there is a lot of controversy here!

Peter Nyikos

[John Harshman]

Go on.

[Roger Shrubber]

According to internet memes:
<http://knowyourmeme.com/memes/ancient-aliens>

<http://suncoastskeptics.com/sites/default/files/notsayingaliens.png>

[Walter Bushell]

In article <6f1bc86c-0d32-4afb...@googlegroups.com>,

nyi...@bellsouth.net wrote:

>
> In the next ca. 2.9 billion years, the main events on the way to
> modern animal life were the advent of eukaryotes, then endosymbiosis
> and sexual reproduction (meiosis and fertilization involving
> homologous chromosomes), then the first multicellular animal,
> and the first bilaterian.

You forgot the invention of photosynthesis, which if not strictly in
the animal sphere was certainly important for all that followed. Hmm,
with the rise of oxygen in the air lead to the first mass extinction.

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

[nyi...@bellsouth.net]

You expect me to take sides? Dream on. Even if the Cambrian explosion
took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
Valentine put it [Do you have easy access to that book? I don't.]
it's a pretty darn "grand scale punctuation" compared to the
preceding ca. 2.9gy and the subsequent ca. 0.52 gy.

IIRC I had forgotten about the early date of that 2004 analysis
when I told you about it in that Prothero "skeptic"blog.
Remember how I criticized its choice of taxa?

It omitted both chaetognaths (which anatomists class as
deuterostomes, molecular biologists as protostomes) and acoelous
flatworms, whose LCA with us probably predates the protostome-deuterostome
split. Prothero, or one of his toadies, axed our whole discussion
and Prothero never told his fans where he got that 80 million year
figure or even what the starting point was as far as the tree of
eumetazoans goes.

However, since I know next to nothing about molecular clock methods,
I'm not sure how this affects the timing of the protostome-deuterostome
split. Not at all (I think) if chaetognaths predate the split, but
perhaps significantly if they are incorporated into calculating
the split.

What does your knowledge of molecular clock methods tell you?

Peter Nyikos

[John Harshman]

On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
> On Monday, October 6, 2014 3:46:40 PM UTC-4, John Harshman wrote:
>> On 10/6/14, 12:10 PM, nyi...@bellsouth.net wrote:
>
>>> As readers can see, there is a lot of controversy here!
>
>> Go on.
>
> You expect me to take sides?

I expect you to make some kind of point.

> Dream on.

Probably.

> Even if the Cambrian explosion
> took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
> Valentine put it [Do you have easy access to that book? I don't.]

I do.

> it's a pretty darn "grand scale punctuation" compared to the
> preceding ca. 2.9gy and the subsequent ca. 0.52 gy.

I'm assuming you realize this has nothing at all to do with punctuated
equilibria. Correct? You have borrowed a name and attached it to
something else. Now, what you have is somewhat similar to the concept in
paleontology of coordinated stasis, but only somewhat.

> IIRC I had forgotten about the early date of that 2004 analysis
> when I told you about it in that Prothero "skeptic"blog.
> Remember how I criticized its choice of taxa?
>
> It omitted both chaetognaths (which anatomists class as
> deuterostomes, molecular biologists as protostomes) and acoelous
> flatworms, whose LCA with us probably predates the protostome-deuterostome
> split. Prothero, or one of his toadies, axed our whole discussion
> and Prothero never told his fans where he got that 80 million year
> figure or even what the starting point was as far as the tree of
> eumetazoans goes.
>
> However, since I know next to nothing about molecular clock methods,
> I'm not sure how this affects the timing of the protostome-deuterostome
> split. Not at all (I think) if chaetognaths predate the split, but
> perhaps significantly if they are incorporated into calculating
> the split.
>
> What does your knowledge of molecular clock methods tell you?

If you just told me where you were trying to go, I would know what would
be relevant to talk about. There are potential reasons for leaving
certain taxa out and potential reasons to put certain other taxa in. One
way to attempt to improve accuracy is to remove taxa with unusually high
evolutionary rates, and another way is to insert taxa that break up long
branches. I believe that acoel flatworms fall into the first category. I
don't know about chaetognaths; but as you say their position is unclear.

[nyi...@bellsouth.net]

On Monday, October 6, 2014 5:33:17 PM UTC-4, Walter Bushell wrote:
> In article <6f1bc86c-0d32-4afb...@googlegroups.com>,
> nyi...@bellsouth.net wrote:

> > In the next ca. 2.9 billion years, the main events on the way to
> > modern animal life were the advent of eukaryotes, then endosymbiosis
> > and sexual reproduction (meiosis and fertilization involving
> > homologous chromosomes), then the first multicellular animal,
> > and the first bilaterian.

> You forgot the invention of photosynthesis, which if not strictly in
> the animal sphere was certainly important for all that followed.

Excellent observation. It was free oxygen, without a doubt, that made
animal life possible. But this in turn waited for the endosymbiosis
that produced mitochondria from free-living respiratory bacteria.

Since mitochondria have lost more of their genes than chloroplasts,
it is reasonable to think that the latter endosymbiosis took place
considerably after the first. Another reason is that, although I
listed sexual reproduction after endosymbiosis (see above) it
seems that this latter endosymbiosis took place later than the advent of
meiosis, which is essentially the same in all the eukaryotic kingdoms
that have it. OTOH mitochondria are important to all eukaryotes
except for certain parasitic ones, so I am not sure whether it came
earlier or later than meiosis.

> Hmm, with the rise of oxygen in the air lead to the first mass extinction.

Do you have in mind the wiping out of the Ediacaran fauna? I think several
mass extinctions took place earlier, out of the range (at least for
the time being) of our prying-into-fossils eyes. I'm thinking
of the Snowball Earth episodes, which are believed to have happened
in both the Paleoproterozoic (Huronian glaciation, 2.4 - 2.1 gya) and
the Neoproterozoic (Marinoan, ca. 650 mya, Sturtian ca. 715 mya). Both
precede the Ediacaran period.

In the Huronian, oxygen was probably the main culprit, oxydizing the
methane into less greenhouse-intensive CO2, while in the latter ones,
it was photosynthesis itself that was the prime suspect, converting
CO2+H20 indirectly to O2+ sugars.

http://en.wikipedia.org/wiki/Snowball_Earth

Peter Nyikos

[alias Ernest Major]

On 07/10/2014 04:21, nyi...@bellsouth.net wrote:
> On Monday, October 6, 2014 5:33:17 PM UTC-4, Walter Bushell wrote:
>> In article <6f1bc86c-0d32-4afb...@googlegroups.com>,
>> nyi...@bellsouth.net wrote:
>
>>> In the next ca. 2.9 billion years, the main events on the way to
>>> modern animal life were the advent of eukaryotes, then endosymbiosis
>>> and sexual reproduction (meiosis and fertilization involving
>>> homologous chromosomes), then the first multicellular animal,
>>> and the first bilaterian.
>
>> You forgot the invention of photosynthesis, which if not strictly in
>> the animal sphere was certainly important for all that followed.
>
> Excellent observation. It was free oxygen, without a doubt, that made
> animal life possible. But this in turn waited for the endosymbiosis
> that produced mitochondria from free-living respiratory bacteria.
>
> Since mitochondria have lost more of their genes than chloroplasts,
> it is reasonable to think that the latter endosymbiosis took place
> considerably after the first. Another reason is that, although I
> listed sexual reproduction after endosymbiosis (see above) it
> seems that this latter endosymbiosis took place later than the advent of
> meiosis, which is essentially the same in all the eukaryotic kingdoms
> that have it. OTOH mitochondria are important to all eukaryotes
> except for certain parasitic ones, so I am not sure whether it came
> earlier or later than meiosis.

There are better reasons than genome sizes to infer than plastids are
later symbionts than mitochondria. Plastid and mitochondrial genome
sizes are quite variable and the sizes overlap; it turns out that in
Arabidopsis thaliana the mitochondrial genome (366,924 bps) is larger
than the plastid genome (154,478 bps).

Although secondary plastids are obviously younger than either primary
plastids or mitochondria many of them have completely lost the genome
from their algal component. (On the other hand in the cases where it has
been retained the nucleomorph genome is relatively large.)

Even if the data were cleaner you would have to take into account the
relative sizes of the genomes of the ancestral symbionts.

>
>> Hmm, with the rise of oxygen in the air lead to the first mass extinction.
>
> Do you have in mind the wiping out of the Ediacaran fauna?

He obviously means the decimation of the anaerobic microbiota, inferred
to have occurred at 2.3 gya.

I think several
> mass extinctions took place earlier, out of the range (at least for
> the time being) of our prying-into-fossils eyes. I'm thinking
> of the Snowball Earth episodes, which are believed to have happened
> in both the Paleoproterozoic (Huronian glaciation, 2.4 - 2.1 gya) and
> the Neoproterozoic (Marinoan, ca. 650 mya, Sturtian ca. 715 mya). Both
> precede the Ediacaran period.
>
> In the Huronian, oxygen was probably the main culprit, oxydizing the
> methane into less greenhouse-intensive CO2, while in the latter ones,
> it was photosynthesis itself that was the prime suspect, converting
> CO2+H20 indirectly to O2+ sugars.
>
> http://en.wikipedia.org/wiki/Snowball_Earth
>
> Peter Nyikos
>

--
alias Ernest Major

[Jonathan]

<nyi...@bellsouth.net> wrote in message
news:6f1bc86c-0d32-4afb...@googlegroups.com...

> We are used to thinking of individual Punctuated Equilibrium (PE)
> events in terms of mere millions of years or less, but I am inviting
> readers
> to step back and look at evolution throughout the history of the earth.
>

I'm inviting people to step into the abstract when it comes
to evolution.

Asking whether evolution is dominated by incremental or sudden
and massive change is the very same question as asking whether
light is a particle or a wave.

Evolution is the result of the critical interaction, or simultaneous
maximums, of the opposite extremes in possible behavior.
Whether for physical, living or spiritual systems


s

[Jonathan]

"Jonathan" <wr...@gmail.com> wrote in message
news:qPOdnRvbVp9QVa7J...@giganews.com...

>
> <nyi...@bellsouth.net> wrote in message
> news:6f1bc86c-0d32-4afb...@googlegroups.com...
>
>> We are used to thinking of individual Punctuated Equilibrium (PE)
>> events in terms of mere millions of years or less, but I am inviting
>> readers
>> to step back and look at evolution throughout the history of the earth.
>>
>
>
> I'm inviting people to step into the abstract when it comes
> to evolution.
>
> Asking whether evolution is dominated by incremental or sudden
> and massive change is the very same question as asking whether
> light is a particle or a wave.
>
> Evolution is the result of the critical interaction, or simultaneous
> maximums, of the opposite extremes in possible behavior.

> Whether for physical, living or spiritual systems.



Whether for life, such as...
Genetics and selection!

The universe.....
Gravity and cosmic expansion

Or everything else....
Facts and imagination

Or more abstractly, the critical interaction or
simultaneous maximums of....

Rules of operation and the freedom of interaction.




s







>
> s
>

[nyi...@bellsouth.net]

On Tuesday, October 7, 2014 7:03:52 AM UTC-4, Jonathan wrote:
> <nyi...@bellsouth.net> wrote in message
> news:6f1bc86c-0d32-4afb...@googlegroups.com...
>
> > We are used to thinking of individual Punctuated Equilibrium (PE)
> > events in terms of mere millions of years or less, but I am inviting
> > readers
> > to step back and look at evolution throughout the history of the earth.

> I'm inviting people to step into the abstract when it comes
> to evolution.

Yeah, there is chemical evolution, stellar evolution and the evolution
of planetary systems, for starters. Then there is the age old question:
if there is a creator of our world, to what does that creator owe its
existence? The only answer our minds can really grasp is, "It evolved
in a universe that may have been infinitely old and of infinite extent,
but at any rate was so much grander than ours that even such `supernatural'
beings could have evolved in it, given enough time."

> Asking whether evolution is dominated by incremental or sudden
> and massive change is the very same question as asking whether
> light is a particle or a wave.

Sophomoric. In fact, finding some point of resemblance might be as
challenging as finding some point of resemblance between ravens
and writing desks. Even in _Alice in Wonderland_, the riddle wasn't
so ambitious as to go, "Why is a raven the very same thing as a
writing desk?"

> Evolution is the result of the critical interaction, or simultaneous
> maximums, of the opposite extremes in possible behavior.
> Whether for physical, living or spiritual systems

If you can explain what you've just said, perhaps we can find
something on which to communicate.

Let me tell you something about the wave/particle conundrum about
light (and other things along the electromagnetic spectrum): "wave"
and "particle" are two concepts our minds can grasp, but I believe
there is more to light than some of the effects on other things
and itself that we can measure. Similarly, I believe there is
MUCH more to dark matter than its behavior as a gravitational
attractor.

[nyi...@bellsouth.net]

On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
>
> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
> > On Monday, October 6, 2014 3:46:40 PM UTC-4, John Harshman wrote:
> >> On 10/6/14, 12:10 PM, nyi...@bellsouth.net wrote:
> >
> >>> As readers can see, there is a lot of controversy here!
> >
> >> Go on.
> >
> > You expect me to take sides?
>
> I expect you to make some kind of point.

"I am not in this world to live up to your expectations"
--from a popular prose poem of the sixties

Perhaps this the kind of point you were fishing for: I think that the title
of the Blair&Hedges paper [23], in the light of the quote below a Peterson et. al. paper, marks [23] as a propaganda piece rather than a serious work of
science.

"We note, however,
that setting the maximum of each of our calibrated nodes at 1.5 billion
years increases the protostome-deuterostome ancestor from 579 to just
646 Ma, still 100 myr younger than estimated by Blair and Hedges (23).
This discrepancy cannot be explored further due to the absence of
methods provided (23)."

[23] "Molecular clocks do not support the Cambrian explosion."
Blair JE, Hedges SB Mol Biol Evol. 2005 Mar; 22(3):387-90.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172262/

However, I will NOT jump to the conclusion that Peterson et. al's figures
are correct and Blair and Hedges's incorrect, not with so many other
estimates out there, such as Erwin & Valentine's [see below]. I think
about science like a scientist, not a propagandist.

Disappointed?

> > Even if the Cambrian explosion
> > took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
> > Valentine put it [Do you have easy access to that book? I don't.]
>
> I do.

Good. Then perhaps you can succeed where Christine Janis failed, and
figure out what kind of molecular clock analysis they used to support
their estimates.

__________________an Amazon blog post________________

Christine, recall that I had requested an example of a primary source for
the molecular studies that E&V used for their dating of pre-Atdabanian
evolutionary events. You gave me the following url:

http://onlinelibrary.wiley.com/doi/10.1002/bies.200900033/full

and you wrote:

"I suggest that you look at Figure 3, which maps the miRNA acquisition
onto a dated phylogeny."

I finally did get Figure 3 downloaded, and it has not the tiniest smidgin
of a hint as to how their dates were arrived at.

To make matters worse, they say something that seems to undermine
any effort to use their own data to arrive at a dating:

"In the time during which nephrozoans (i.e., protostomes and deuterostomes)
acquired 32 novel miRNA families, cnidarians acquired only a single miRNA
family; in the time during which vertebrates acquired 40 novel miRNA
families, pancrustaceans, annelids, gastropod molluscs, and eleutherozoan
echinoderms acquired only 5-8 novel families; and in the time during which
primates acquired 84 novel miRNA families, rodents only acquired 16 novel
families (Fig. 3, Table 1). Indeed, the addition of these 84 novel miRNA
families represents near the totality of miRNA innovation in the lineage
leading to the cepahlochordate Branchiostoma floridae (Fig. 3), and thus
primates evolved almost the same number of families as amphioxus in about
a tenth of the time."

Table 1 gives plenty of evidence for the topology of their tree, but I cannot
see any way of inferring dates from it.

Is this really the best you can do?

+++++++++++++++++++++ end of second post of ten archived at
http://www.amazon.com/review/R2HNOHERF138DU/ref=cm_cd_pg_pg219?ie=UTF8&asin=0062071475&cdForum=Fx3P3RC85LN3MPG&cdPage=219&cdThread=TxLRAUUZ3UBEFC&store=books#wasThisHelpful

It was. In a snippy reply further down in the page, she gave me the
link to the 2004 PNAS paper by Peterson et. al. that I've quoted from
in my second post, but gave no hint that it had ever been used by
Erwin & Valentine.

Can you do better, John?

Peter Nyikos

[nyi...@bellsouth.net]

Thank you for this interesting information. A question about terminology:
does "secondary plastids" include what remains of the genome of the algal,
etc., endosymbiont?

> >> Hmm, with the rise of oxygen in the air lead to the first mass extinction.
> >
> > Do you have in mind the wiping out of the Ediacaran fauna?
>
> He obviously means the decimation of the anaerobic microbiota, inferred
> to have occurred at 2.3 gya.

Thanks, I had forgotten about the many popular accounts I have read about how
the oxygen "poisoned" so many organisms not adapted to it. In fact, it
is an interesting question how so anaerobes have survived. How did the
methanogens get into mammalian intestines if exposure to oxygen is fatal
to them?

Peter Nyikos

[John Harshman]

On 10/7/14, 11:16 AM, nyi...@bellsouth.net wrote:
> On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
>>
>> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
>>> On Monday, October 6, 2014 3:46:40 PM UTC-4, John Harshman wrote:
>>>> On 10/6/14, 12:10 PM, nyi...@bellsouth.net wrote:
>>>
>>>>> As readers can see, there is a lot of controversy here!
>>>
>>>> Go on.
>>>
>>> You expect me to take sides?
>>
>> I expect you to make some kind of point.
>
> "I am not in this world to live up to your expectations"
> --from a popular prose poem of the sixties
>
> Perhaps this the kind of point you were fishing for: I think that the title
> of the Blair&Hedges paper [23], in the light of the quote below a Peterson et. al. paper, marks [23] as a propaganda piece rather than a serious work of
> science.

Perhaps you are right, but I also think you are in general oversensitive
to imagined subtleties.

> "We note, however,
> that setting the maximum of each of our calibrated nodes at 1.5 billion
> years increases the protostome-deuterostome ancestor from 579 to just
> 646 Ma, still 100 myr younger than estimated by Blair and Hedges (23).
> This discrepancy cannot be explored further due to the absence of
> methods provided (23)."
>
> [23] "Molecular clocks do not support the Cambrian explosion."
> Blair JE, Hedges SB Mol Biol Evol. 2005 Mar; 22(3):387-90.
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172262/
>
> However, I will NOT jump to the conclusion that Peterson et. al's figures
> are correct and Blair and Hedges's incorrect, not with so many other
> estimates out there, such as Erwin & Valentine's [see below]. I think
> about science like a scientist, not a propagandist.
>
> Disappointed?

Yes. This self-puffery always disappoints me.

Is it impossible for you to post without making gratuitous attacks on
someone who isn't present? But I'll look and see.

[Earle Jones27]

On 2014-10-07 11:03:52 +0000, Jonathan said:

> <nyi...@bellsouth.net> wrote in message
> news:6f1bc86c-0d32-4afb...@googlegroups.com...
>
>> We are used to thinking of individual Punctuated Equilibrium (PE)
>> events in terms of mere millions of years or less, but I am inviting readers
>> to step back and look at evolution throughout the history of the earth.
>>
>
>
> I'm inviting people to step into the abstract when it comes
> to evolution.
>
> Asking whether evolution is dominated by incremental or sudden
> and massive change is the very same question as asking whether
> light is a particle or a wave.
>
> Evolution is the result of the critical interaction, or simultaneous
> maximums, of the opposite extremes in possible behavior.
> Whether for physical, living or spiritual systems

*
Jonathan: If you really believe what you wrote above, you need two
very basic courses: One in biology and one in physics. No need for
any advanced work, just the first-order lectures in those fields.

"Evolution is the result of the critical interaction ...of opposite
extremes..."

Hogwash.

earle
*

[Roger Shrubber]

One of the special aspects of his scheme of things is that he
gets to skip all the little details and just assert his variously
mangled interpretations of his emergence dogma. It's a great time
saver for him, if nothing else. It also has the advantage of bypassing
a large set of dependencies, observations and logical development
for people to attack. It just is, provided you hold the end
result in the right way, squint with one eye while looking through
his special complexity kaleidoscope.

[Jonathan]

<nyi...@bellsouth.net> wrote in message
news:20fa2115-eb16-4001...@googlegroups.com...

> On Tuesday, October 7, 2014 7:03:52 AM UTC-4, Jonathan wrote:
>> <nyi...@bellsouth.net> wrote in message
>> news:6f1bc86c-0d32-4afb...@googlegroups.com...
>>
>> > We are used to thinking of individual Punctuated Equilibrium (PE)
>> > events in terms of mere millions of years or less, but I am inviting
>> > readers
>> > to step back and look at evolution throughout the history of the earth.
>
>> I'm inviting people to step into the abstract when it comes
>> to evolution.

>
> Yeah, there is chemical evolution, stellar evolution and the evolution
> of planetary systems, for starters.

There are only components and emergent system
properties. Yet every component is a whole unto itself.

So just like the duality of light, all of our observations of
reality are necessarily subjective, depending on whether...we
decide to treat something as a part or a whole.

You're still mired in the old way of observing, looking for
specific microphysical explanations for each and every
thing. That ends up with a thousand disciplines, one
for each and every type of 'thing'.

Complexity theory is about expanding to ever greater emergent
wholes (greater complexity) as a way of understanding how
each and every thing works. And that world-view ends up
with one discipline or concept for all things.

Which is better? Which can show us what is /common/
among those thousand disciplines? As the commonalties
among all things is where the secrets to nature are found.

>Then there is the age old question:
> if there is a creator of our world, to what does that creator owe its
> existence? The only answer our minds can really grasp is, "It evolved
> in a universe that may have been infinitely old and of infinite extent,
> but at any rate was so much grander than ours that even such
> `supernatural'
> beings could have evolved in it, given enough time."
>

Mathematicians are supposed to be noted for their
attention to detail, the only reason for the above
metaphysical guesswork is for the lack of a clear
definition of the word 'god'.

Darwin provides a perfectly good definition as
evolutionary systems problem-solve as a matter
of course. Such processes converge towards
the better adaptation or solution, towards the
ideal possible future....towards 'perfection'
for that system.

God is the goal towards which any self-organized
systems aspire or are attracted to. Our goals might be
heaven or profit while gravity or the Second law have
their own preferred 'states'.

The concept of god emerges from us, and is as real and
important as any other idea, perhaps far more so as it
defines the ideal possible future we can imagine.

God, in truth, comes at the top of the evolutionary hierarchy
not at the beginning. So a simple frame of reference error
has kept science and religion apart all this time.

>> Asking whether evolution is dominated by incremental or sudden
>> and massive change is the very same question as asking whether
>> light is a particle or a wave.
>
> Sophomoric. In fact, finding some point of resemblance might be as
> challenging as finding some point of resemblance between ravens
> and writing desks.
>Even in _Alice in Wonderland_, the riddle wasn't
> so ambitious as to go, "Why is a raven the very same thing as a
> writing desk?"
>

If you can't easily see the commonalties between
a bird and a table, then nature will remain a mystery.

They both evolve from the same evolutionary process
however at vastly different scales of complexity.

A table would be a type 1 self organized system
while a single bird a type 3.
http://www.calresco.org/lucas/quantify.htm

But the abstract process of 'creation' is the
same for both.

An evolving system is the result of the critical interaction
between the system 'rules of operation', and the 'freedom
of interaction' of it's components.

For a bird, the rules of operation can be represented
by 'genetics', and the freedom of interaction by 'selection'.

For a table, the rules of operation are typically called
carpentry, and the freedom of interaction represented
by our imagination in the design.

Any complex or organized system can be defined in this
way, any system, whether living, physical or even spiritual.
And the optimum combination of those opposites defines
the best 'natural' outcome.

Try it and see for yourself.

>> Evolution is the result of the critical interaction, or simultaneous
>> maximums, of the opposite extremes in possible behavior.
>> Whether for physical, living or spiritual systems
>


> If you can explain what you've just said, perhaps we can find
> something on which to communicate.
>

Every word is chosen carefully and means exactly as the
dictionary says they mean. What words do you find confusing?
The longer version is here, where each word is explained
in detail.

Self Organized System Faq
http://calresco.org/sos/sosfaq.htm#1.3

> Let me tell you something about the wave/particle conundrum about
> light (and other things along the electromagnetic spectrum): "wave"
> and "particle" are two concepts our minds can grasp, but I believe
> there is more to light than some of the effects on other things
> and itself that we can measure.

Why try to unravel the behavior of a system displaying
such duality only at the smallest and least approachable scales
of all, such as light?

When all self organized or evolving systems also display
critical behavior at far easier ways to observe.

A cloud constantly transitions between condensation
and evaporation, it's opposing states of matter.
Just as evolution is an unstable combination of
incremental and massive change.

As you go up the complexity ladder, the picture clears
from the ability to compare numerous 'duality's and
their common behaviors.

>Similarly, I believe there is
> MUCH more to dark matter than its behavior as a gravitational
> attractor.
>

Steinhardt bases his new cyclic cosmology on dark energy.
And dark energy is an....emergent system property.

It's the common global properties that define existence.
Not the physical details. Downward causation, or the 'goal'
is the defining variable for the future of all organized systems.

Objective methods are for building the damn thing~

[Jonathan]

"Earle Jones27" <earle...@comcast.net> wrote in message
news:2014100713395256597-earlejones@comcastnet...

Then you tell me what evolution is the result of.....?

A cloud is the result of the critical interaction between
condensation and evaporation, it's opposite extremes
in possible states.

Neo-Darwinism is the result of the opposites of
genetics (rules of operation) and selection (freedom
of interaction)

An idea is the result of the critical interaction between
facts and imagination. Rules and freedom.
Order and chaos.

Any and all organized systems can be defined in this
abstract way. I provided one example each from
life, the universe and everything else.

Can ...you think in abstract terms?


>
> Hogwash.
>
> earle
> *
>

[nyi...@bellsouth.net]

In my first post to this thread, I wrote the following about the phyla
that made their debut in the Cambrian explosion.

"Then came the Ediacaran fauna and the start of the Cambrian explosion,
which can be said to begin with the protostome-deuterostome split.
This could have been as recent as 570mya, which would confine the Cambrian
explosion to 40-45 million years duration. This was a "punctuation" on a
truly grand scale, with at least 13 protostome phyla and 3 deuterostome phyla
making their debut in this short period (along with 2 to 4 extinct
bilaterian phyla)."

This is an estimate just of the protostome and deuterostome phyla that made
their debut before the end of the Lower Cambrian. It does not include
Chaetognatha, which might have branched off from Bilateria before the LCA of
protostomes and deuterostomes.

As I said in my second post, the 570mya figure is controversial, but
even if earlier figures are adopted, the contrast between the time
the Cambrian unfolding took, and the number of phyla it involved, and what
happened in the next 515 million years to the present is striking.

I probably was too generous when I wrote:

" the following ca. 0.52 gy
were relatively uneventful, with at most 14 new phyla making their debut."

In fact, only five of those phyla are found in the fossil record: Bryozoa,
Nemertea, Nematoda, Platyhelminthes, and Rotifera; and as for the others,
most of them are quite obscure and only Acanthocephala, Kinoryncha,
and Gastrotricha are well known. Moreover, Bryozoa made its debut no later
than the early Ordovician and so may well have existed as early as the other
phyla I have named. So too, for that matter, might a number of the others.
If anyone knows of molecular studies that shed light on when the divergence
might have occurred, I'd be very interested.

One way of minimizing this contrast is to claim that the concept of "phylum"
is an artificial one, but it has been used for well over a century to
be roughly synonymous with "unique body plans." So it is an indicator
of disparity, the idea being that animals within a phylum are less
different in some fundamental way from each other than any in one phylum
are from any in another phylum. And so perhaps the real question about
the Cambrian explosion is this: why did so much disparity blossom in so
short a time, while later in earth history it happened on a smaller scale
in a much longer time?

Peter Nyikos

[nyi...@bellsouth.net]

On Tuesday, October 7, 2014 9:18:41 PM UTC-4, Jonathan wrote:
> "Earle Jones27" <earle...@comcast.net> wrote in message
> news:2014100713395256597-earlejones@comcastnet...
>
> > On 2014-10-07 11:03:52 +0000, Jonathan said:

> > Jonathan: If you really believe what you wrote above, you need two very
> > basic courses: One in biology and one in physics. No need for any
> > advanced work, just the first-order lectures in those fields.

> > "Evolution is the result of the critical interaction ...of opposite
> > extremes..."

> Then you tell me what evolution is the result of.....?

Any good biology text (except those written by creationists) will answer
that in detail. It gives details where you are content with a simple
formula below that explains neither genetics nor selection, nor makes
a case for them being opposites.

> A cloud is the result of the critical interaction between
> condensation and evaporation,

It is a condensation. When it dissolves into thin air, as the saying
goes, that is evaporation.

>it's opposite extremes in possible states.

> Neo-Darwinism is the result of the opposites of
> genetics (rules of operation) and selection (freedom
> of interaction)

The things in parentheses can be construed as opposites. Genetics and
selection are even less "opposite" than agriculture and cooking.

> An idea is the result of the critical interaction between
> facts and imagination. Rules and freedom.
> Order and chaos.

Thesis and antithesis.

Ever read Hegel? Ever read William James's essay, "On some Hegelisms"?
Do the philosophical speculators who have inspired you talk about Hegel
and his "system"?

They could be on some altered state of consciousness, such as William James
underwent when he breathed a hefty dose of nitrous oxide and for a while
felt that Hegel was right after all, even though he had written brilliantly
in opposition to Hegel.

But when the nitrous oxide wore off, he saw that the notes he had furiously
written down, and which he had felt "were fused in the fire of infinite
rationality," were complete drivel, and was even able to strengthen his case
against Hegel as a result.

> Any and all organized systems can be defined in this
> abstract way. I provided one example each from
> life, the universe and everything else.

> Can ...you think in abstract terms?

We all can. But we don't get lost in metaphysical fogs the way you do.

Peter Nyikos

[John Harshman]

It should be easy for you to find.

> One way of minimizing this contrast is to claim that the concept of "phylum"
> is an artificial one, but it has been used for well over a century to
> be roughly synonymous with "unique body plans." So it is an indicator
> of disparity, the idea being that animals within a phylum are less
> different in some fundamental way from each other than any in one phylum
> are from any in another phylum. And so perhaps the real question about
> the Cambrian explosion is this: why did so much disparity blossom in so
> short a time, while later in earth history it happened on a smaller scale
> in a much longer time?

Back when I paid attention to the literature on this, there were three
main ideas. 1) The empty barrel theory: at no other time have so many
major niches been vacant, so the adaptive radiation would likewise have
been unmatched. 2) The loose genes theory: developmental pathways were
initially quite changeable but became developmentally canalized over
time. 3) Yes, phyla are arbitrary units that by definition must have
arisen before the classes and orders that make them up.

[Josko Daimonie]

I can, but randomly combining terms into "critical interaction" and
"opposite extremes" isn't "thinking abstract". If you think it is, then
that is a critical superposition of random things in an arbitrary manner
given the basket cookies of limited coconuts.

Seriously. If two genes are competing in, say, an environment of mice,
and one allele is slightly better at surviving and resulting offspring,
then there's selection.

I don't see how that's two extremes. You might attach the word
"critical" in the sense of one succeeding and the other not, but if it's
3 reproducing offspring for the allele 1 and 2 for allele 2, I really
don't see the word critical applying.

[alias Ernest Major]

As a counterargument to the claim that phyla represent unique body plans
there is the observation that the phyla Pogonophora and Vestimentifera
are now considered to make up parts of the annelid family Siboglinidae,
the phylum Pentastomida is now considered a crustacean subclass (with
Crustacea promoted to subphylum), and the phylum Echiura is now
considerd an annelid class. Myxozoa (formerly not even recognised as
animals in the modern sense) are derived Cnidaria, and elsewhere
Microsporidia are derived Fungi.

If someone wants to argue that the Cambrian Explosion represents
something unique in terms of the production of disparsity that someone
needs a more objective measure of disparity than taxonomic rank.

PS: It appears that (Upper) Cambrian Bryozoans were found a few years back.

http://geology.gsapubs.org/content/38/6/547.short

--
alias Ernest Major

[nyi...@bellsouth.net]

On Tuesday, October 7, 2014 11:26:19 PM UTC-4, John Harshman wrote:
> On 10/7/14, 7:43 PM, nyi...@bellsouth.net wrote:

> > One way of minimizing this contrast is to claim that the concept of "phylum"
> > is an artificial one, but it has been used for well over a century to
> > be roughly synonymous with "unique body plans." So it is an indicator
> > of disparity, the idea being that animals within a phylum are less
> > different in some fundamental way from each other than any in one phylum
> > are from any in another phylum. And so perhaps the real question about
> > the Cambrian explosion is this: why did so much disparity blossom in so
> > short a time, while later in earth history it happened on a smaller scale
> > in a much longer time?

> Back when I paid attention to the literature on this, there were three
> main ideas.

How long ago was that? Can you recall any websites (or at least
articles or books) where the following ideas were advanced?

>1) The empty barrel theory: at no other time have so many
> major niches been vacant, so the adaptive radiation would likewise have
> been unmatched.

The niches hardly would explain the different body plans. The niche of
free-living terrestrial life was filled by members of relatively few
phyla, none of which arose there as far as we know.

>2) The loose genes theory: developmental pathways were
> initially quite changeable but became developmentally canalized over
> time.

The issue is, when, and what were the limits of that changeability
back in the Cambrian, and what are they today? Is there a serious genetic
foundation for this idea?

Why, for example, has no other phylum developed a flexible extensive
endoskeleton? Could not a large number of phyla even today develop something
as simple as the notochord of the lancelet (Branchiostoma a.k.a. Amphioxus)?
The closest any other phylum has come is the Hemichordata, but the
analogue there is only a small part of body length; in the lancelet it
stretches from one end to the other.

In contrast, flexible extensive exoskeletons are found in quite a number
of phyla and have developed independently several times in the subphylum
Vertebrata alone: placoderms, ankylosaurs, Henodus, armadillos.

> 3) Yes, phyla are arbitrary units that by definition must have
> arisen before the classes and orders that make them up.

But how artificial? Is it not noteworthy that practically every
one of the classical phyla, as defined in the 20th century up to
1970 is a clade, and that most if not all of the exceptions are
paraphyletic? This despite the fact that phylogeny of invertebrates
was very poorly known from the fossil record.

Peter Nyikos

[nyi...@bellsouth.net]

On Wednesday, October 8, 2014 4:05:45 AM UTC-4, alias Ernest Major wrote:

> As a counterargument to the claim that phyla represent unique body plans
> there is the observation that the phyla Pogonophora and Vestimentifera
> are now considered to make up parts of the annelid family Siboglinidae,
> the phylum Pentastomida is now considered a crustacean subclass (with
> Crustacea promoted to subphylum), and the phylum Echiura is now
> considerd an annelid class. Myxozoa (formerly not even recognised as
> animals in the modern sense) are derived Cnidaria, and elsewhere
> Microsporidia are derived Fungi.

With the exception of Pogonophora and Echiua, these are not mentioned
in the quite comprehensive 1967 book _General Zoology_ by Gabriel Moment,
and he recognizes the Annelid affinities of the latter. As for the former,
the posterior parts which show the telltale segmentation were not even
recovered until 1964:

http://www.ucmp.berkeley.edu/annelida/pogonophora.html

IIRC, the Vestimentifera are were what "Pogonophora"
designated before the discovery of giant tube worms.

It might well be that several of the more obscure phyla, consisting
exclusively of parasites, were made into phyla not because of the
uniqueness of body plan, but because they did not fit into the well
known phyla which, in some cases, had had their membership shifted
to turn them into clades. Platyhelminthes is one example of which
I know.

> If someone wants to argue that the Cambrian Explosion represents
> something unique in terms of the production of disparsity that someone
> needs a more objective measure of disparity than taxonomic rank.

Yes, taxonomic rank is only a very rough first approximation. More about
this later today or tomorrow.

> PS: It appears that (Upper) Cambrian Bryozoans were found a few years back.

> http://geology.gsapubs.org/content/38/6/547.short

Since then, there has been a re-evaluation of the genus described:

Taylor, P.D.; Berning, B.; Wilson, M.A. (2013). "Reinterpretation of the Cambrian 'bryozoan' Pywackia as an octocoral". Journal of Paleontology 87 (6): 984-990. doi:10.1666/13-029.

Secondary source:

http://en.wikipedia.org/wiki/Bryozoa#cite_note-Taylor2013-1

Peter Nyikos

[nyi...@bellsouth.net]

On Wednesday, October 8, 2014 9:35:28 AM UTC-4, nyi...@bellsouth.net wrote:

> It might well be that several of the more obscure phyla, consisting
> exclusively of parasites,

This should have read, "several phyla, especially some obscure ones
that consist exclusively of parasites," since Platyhelmithes was
anything but obscure. The acoelomic flatworms have caused some
shifing around with the advent of molecular methods.

>were made into phyla not because of the
> uniqueness of body plan, but because they did not fit into the well
> known phyla which, in some cases, had had their membership shifted
> to turn them into clades. Platyhelminthes is one example of which
> I know.

Peter Nyikos

[John Harshman]

Such as this: Lee et al., Rates of Phenotypic and Genomic Evolution
during the Cambrian Explosion, Current Biology (2013)

http://dx.doi.org/10.1016/j.cub.2013.07.055

> PS: It appears that (Upper) Cambrian Bryozoans were found a few years back.
>
> http://geology.gsapubs.org/content/38/6/547.short
>

I believe that's controversial. If you will note, the very first listed
paper that cites your reference reinterprets it as an octocoral.

[John Harshman]

On 10/8/14, 5:56 AM, nyi...@bellsouth.net wrote:
> On Tuesday, October 7, 2014 11:26:19 PM UTC-4, John Harshman wrote:
>> On 10/7/14, 7:43 PM, nyi...@bellsouth.net wrote:
>
>>> One way of minimizing this contrast is to claim that the concept of "phylum"
>>> is an artificial one, but it has been used for well over a century to
>>> be roughly synonymous with "unique body plans." So it is an indicator
>>> of disparity, the idea being that animals within a phylum are less
>>> different in some fundamental way from each other than any in one phylum
>>> are from any in another phylum. And so perhaps the real question about
>>> the Cambrian explosion is this: why did so much disparity blossom in so
>>> short a time, while later in earth history it happened on a smaller scale
>>> in a much longer time?
>
>> Back when I paid attention to the literature on this, there were three
>> main ideas.
>
> How long ago was that? Can you recall any websites (or at least
> articles or books) where the following ideas were advanced?

Here is something I wrote for a seminar on the subject back in the
mid-'90s. The references should get you into the literature.

The Cambrian Explosion

What do we see?
The first unquestioned metazoans appear in the late Riphean or early
Vendian, loosely termed the Ediacaran fauna. They are all soft, and are
mostly preserved as molds in coarse sandstones. There are also trace
fossils, all (?) surface trails. Near the end of the Ediacaran, the
Ediacaran fauna fades out, trace fossils diversify, and the first
"small, shelly fossils" appear. The Tommotian is a period of gradual
increase in diversity of the shelly types, including the first examples
of modern phyla, and of trace fossils. The first trilobites appear in
the Atdabanian, as do (?) the first post-Ediacaran unmineralized
metazoans. All modern phyla are known by the end of the Cambrian, all
classes (of marine invertebrates) by the end of the Ordovician (not
counting those without fossil records).

What needs explanation?
Why didn't this happen earlier? Why not later? Why so fast? Why only
once? The fourth question is the only one I intend to worry about here:
why did almost all the animal phyla (apparently) arise in the Cambrian,
and none since then? (Say, what about plants? What about land animals?)

Explosion? What Explosion?
Maybe the supposed explosion is due to taxonomic or taphonomic effects.
Taxonomic: Raup has a complicated simulation, but I think it boils down
to the idea that in a nested hierarchy, deep nodes have to come before
shallow nodes. If higher taxa are not defined cladistically, is this
relevant?
Conway Morris (1985, mostly) has another idea. Maybe these perceived
radical differences in bauplan are artifacts of the big gaps between
modern groups; a Cambrian systematist would see only low-level taxa
where we see phyla and classes. Briggs & Fortey suggest something
similar in reference to the arthropods.
Taphonomic: Do the various groups have invisible Precambrian histories?
Valentine & Erwin examine various ways for this to happen: ancestors
were soft & squishy, teeny, rare or localized, lived in unpreserved
environments; the fossil record sucks. They reject all of them.
Are we looking in the right place for Precambrian ancestors? Where are
the animals that made Precambrian trace fossils? Were Ediacaran fossils
especially preservable or were the rules of preservation different then?
See Seilacher, Fedonkin.
Butterfield examines in detail the factors involved in preservation of
the Burgess Shale. Animals are preserved as films of original carbon. An
extracellular cuticle with various means of keeping its proteins from
attack (crosslinks, e. g.) is almost universal. Since animals carry the
means of their own destruction within their guts (proteolytic enzymes
and intestinal biota), filling of coelomic spaces with fine clay both
adsorbs enzymes and blocks spread of decomposers. How about a late
evolution of cuticle? Of coeloms? (But what about body plans that just
won't work at all without rigid parts?)

The Empty Barrel
You know the story: when the starting gun goes off, everyone races to
fill vacant ways of life. With plenty of room and no competition,
selection is relaxed and experiments are possible. When the barrel is
full, there's no room for experiment. In the end Permian, species
diversity crashed but ecological diversity was still high: the barrel
was still mostly full, thus no room for new phyla (Erwin et al.) How
does this scenario cover the invasion of the land?
McMenamin's variant makes the origin of predation the cause, with no
required relaxation of selection (quite the opposite). Once the noise
died down, it would take a new stimulus to set things going again, which
has not happened yet.
Kauffman sort of fits here, although he requires no biotic
intereactions. He envisages adaptive landscapes, with species starting
in valleys. At the beginning, a big jump is as likely to improve fitness
as a small jump, but this ends soon. Why are species starting in valleys?

Loose Genes
The basic loose gene theory waves its arms and talks about
canalization. Epistatic effects were less common then. (Is this
possible?) Maybe epigenetic homeostatic mechanisms (say it three times
fast) weren't as fully evolved as they are now. (Would this result in
greater embryonic mortality? Is there a way to look for that?) Jablonski
& Bottjer suggest a test by examining deviations from bilateral symmetry.
Jacobs at least tries to elaborate his mechanism enough to be testable.
In arthropods, in some systems, at least, serial genes divide the
developing body into identical segments, while selector genes, with
regional patterns of expression, differentiate the segments. He supposes
this to be the ancestral development pattern
of coelomates, which are thus primitively segmented. He divides phyla
into two groups: segmented taxa which have presumably retained the
ancestral system, and non-segmented taxa which have not. In segmented
types, selector genes were once closely linked and were open to all
sorts of simple rearrangements with big phenotypic effects. Now they are
scattered over the genome and big changes are no longer easy. Ordinal
originations of segmented animals show such a historical pattern, while
non-segmented animals do not.
Problems? Patel et al. come to a different conclusion on ancestral
states: the ancestor had a serially ordered central nervous system, but
body segmentation evolved separately in arthropoda, annelida, and
chordata. Jacob explains why segmented animals used to have loose genes,
but why should unsegmented animals still have loose genes just because
regulation of development is conceptually more complicated? And of
course this pattern only explains the ordinal level, not class or
phylum. How well does Lake's phylogeny match Jacob's theories? Patel et al.?



The Cambrian Explosion: Bibliography

Anderson, M. M. and S. Conway Morris. 1982. A review, with descriptions
of four unusual forms, of the soft-bodied fauna of the Conception and
St. John's Groups (late-Precambrian), Avalon Peninsula, Newfoundland.
Third North American Paleontological Convention, Proceedings vol. I, 1-8.
Possibly the oldest known diverse fauna, perhaps as old as late Riphean,
and grossly resembling the Ediacaran fauna.

Briggs, D. E. G. and R. A. Fortey. 1989. The early radiation and
relationships of the major arthropod groups. Science 246:241-243.
Cladistic analysis of Burgess Shale and other arthropods shows
trilobites as highly derived, crustaceans as possibly paraphyletic, and
disparity within Burgess arthropods not especially high.

Butterfield, N. J. 1990a. Organic preservation of non-mineralizing
organisms and the taphonomy of the Burgess Shale. Paleobiology 16:272-286.
Talks about reasons for preservation of "soft-bodied" animals, including
a decay-resistant, extracellular cuticle and interior coelomic spaces
which can be permeated with clay particles. To add to hypotheses of
multiple, simultaneous skeletonization events, can we try
cuticle-ization and coelomization?

Butterfield, N. J. 1990b. A reassessment of the enigmatic Burgess Shale
fossil Wiwaxia corrugata (Matthew) and its relationship to the
polychaete Canadia spinosa Walcott. Paleobiology 16:287-303.
Wiwaxia is a polychaete, reducing the number of funny phyla by one.

Chen, J. 1988. Precambrian metazoans of the Huai River drainage area
(Anhui, E. China): their taphonomic and ecological evidence.
Senckenbergiana Lethaea 69:189-215.
Another candidate for oldest metazoans, this time annulated, coelomate,
burrowing worms, dated at 740ma. Big implications if so. But see Conway
Morris 1990.

Conway Morris, S. 1985. Cambrian Lagerstatten: their distribution and
significance. Philosophical Transactions of the Royal Society of London
B311 ꌴ9-65.
Survey of Cambrian soft-bodied fossil localities. Considers the
explosion of phyla as an artifact of hindsight: we see the Cambrian
world through a filter of living groups.

-----------. 1989a. Burgess Shale faunas and the Cambrian explosion.
Science 246:339-346.
Description of the Burgess Shale fauna. No useful input on the
uniqueness of the Cambrian explosion.

-----------. 1989b. The persistence of Burgess Shale-type faunas:
implications for the evolution of deeper-water faunas. Transactions of
the Royal Society of Edinburgh: Earth Sciences 80:271-283.
At least some of the Burgess genera have very long duration (stasis?),
some from ?Tommotian (more likely early Atdabanian -- see Dzik and
Lendzion), arguing for a rapid Cambrian explosion. (The main subject of
the paper is some gibberish about taxa originating in shallow shelf
environments.)

-----------. 1990. Late Precambrian and Cambrian soft-bodied faunas.
Annual Review of Earth and Planetary Sciences 18:101-122.
A short review of Ediacaran and Burgess fossils.

Donovan, S. K. 1987. The fit of the continents in the late Precambrian.
Nature 327:139-141.
Just thought you might wonder what the world looked like; three theories
evaluated from a biogeographic perspective.

Dzik, J. and K. Lendzion. 1988. The oldest arthropods of the East
European Platform. Lethaia 21:29-38.
A third species of anomalocarid and a naraoid trilobite from the
?Atdabanian are the earliest Burgess-like fossils known.

Erwin, D. H., J. W. Valentine, and J. J. Sepkoski, Jr. 1986. A
comparative study of diversification events: the early Paleozoic versus
the Mesozoic. Evolution 41:1177-1186.
Documents the explosion and gives a classic statement of the empty
barrel theory.

Fedonkin, M. A. 1985. Precambrian metazoans: the problems of
preservation, systematics and evolution. Philosophical Transactions of
the Royal Society of London B311:27-45.
An interesting view of Ediacaran taphonomy. That's the good part. The
rest is weird morphological evolutionary models based on superficial
resemblances. Annelida from Cnidaria in two easy steps?

Field, K. G., G. J. Olsen, D. J. Lane, S. J. Giovannoni, M. T. Ghiselin,
E. C. Raff, N. R. Pace, and R. A. Raff. 1988. Molecular phylogeny of the
animal kingdom. Science 239:748-753.
18s RNA-derived phylogeny presents several mutually inconsistent trees
containing different combinations of taxa. A consensus tree of this
unintended jackknifing would show very little structure at the phylum
level. Maybe this suggests the coelomate radiation was very fast
(Cambrian explosion?). Or maybe it's just garbage.

Gehling, J. G. 1987. Earliest known echinoderm -- a new Ediacaran fossil
from the Pound Subgroup of South Australia. Alcheringa 11:337-345.
This replacement for Tribrachidium at least has five-fold symmetry. This
is here because the accompanying photos show how hard it is to tell much
from Ediacaran fossils.

Glaessner, M. F. 1984. The dawn of animal life: a biohistorical study.
Cambridge: Cambridge University Press.
A paleontologist/morphologist of the old school interprets Ediacaran
life, assigning everything to modern groups. Could be, but it sounds
like a suspicious coincidence to me.

Gould, S. J. 1989. Wonderful Life: The Burgess Shale and the Nature of
History. New York: W. W. Norton & Company.
Plenty of drama and great pictures. The explosion itself is not central
to his personal ax-grinding, but he has a nice summary on pp. 228-233.
Gould could perhaps use a short course in phylogenetic systematics.

Hoffman, A. and M. H. Nitecki (eds.). 1986. Problematic Fossil Taxa. New
York: Oxford University Press.
Authors tackle various weird groups, most of them relevant to the
Cambrian explosion. Lots of good photos and reconstructions. Bengston's
introduction has an interesting discussion of what we mean by "phylum".

Jacobs, D. K. 1990. Selector genes and the Cambrian radiation of
Bilateria. Proceedings of the National Academy of Sciences 87:4406-4410.
A previously unrecognized pattern in the evolution of novelties and a
"loose genes" explanation to account for it. This may be testable.

Kauffman, S. A. 1989. Cambrian explosion and Permian quiescence:
implications of rugged fitness landscapes. Evolutionary Ecology 3:274-281.
A third hypothesis, probably not testable. On an adaptive landscape with
many local maxima, assuming a species begins with low fitness, big
mutations are as likely to improve fitness as little ones. As a species
finds higher peaks, big mutations no longer work well. Thus phylum-sized
changes go away. There is a vague implication that the landscape gets
smoother too, which also makes big mutations unprofitable. But why
assume low fitness at the start?

Lake, J. A. 1990. Origin of the Metazoa. Proceedings of the National
Academy of Sciences 87:763-766.
Reanalysis of Field et al. using Lake's own parsimony method makes
arthropods paraphyletic (?) to a big group including Annelida, Mollusca,
and Brachiopoda. Some basal branch lengths are long, implying
considerable undiscovered Precambrian history of coelomates. Weird
stuff, but food for thought.

Matthews, S. C. and V. V. Missarzhevsky. 1975. Small shelly fossils of
late Precambrian and early Cambrian age: a review of recent work.
Journal of the Geological Society of London 131:289-304.
I picked this one because it has photos of most of the "small, shelly
fossils" you hear so much about. Plate 4 figs. 2, 5, 8 is Microdictyon,
unnamed until 1981.

McMenamin, M. A. S. 1989. The origins and radiation of the early
Metazoa. In: K. C. Allen and D. E. G. Briggs, eds. Evolution and the
fossil record. London: Belhaven Press, 73-98.
The Reader's Digest version of his book, below.

McMenamin, M. A. S. and D. L. S. McMenamin. 1990. The Emergence of
Animals: the Cambrian Breakthrough. New York: Columbia University Press.
A good semi-popular account of metazoan history through the Cambrian,
including his variation on the ecological explanation for the explosion:
the invention of predation caused a revolution, devices for avoiding
predators becoming exapted for new ways of life. Things settled down
soon, and permanently, for reasons that aren't clear to me, but the
implication is that only in periods of ecological chaos are there
opportunities for new body plans.

Patel, N. H., E. Martin-Blanco, K. G. Coleman, S. J. Poole, M. C. Ellis,
T. B. Kornberg, and C. S. Goodman. 1989. Expression of engrailed
proteins in arthropods, annelids, and chordates. Cell 58:955-968.
This is a whole new world. I picked this as representative of numerous
papers cited by Jacobs because it covers the widest ground and draws
some phylogenetic conclusions for itself, which conflict somewhat with
Jacobs. Note especially what the annelids are doing. For an interesting
time, try to reconcile this paper with Lake.

Raup, D. A. 1983. On the early origins of major biologic groups.
Paleobiology 9:107-115.
Divergence time between >90% of major groups is predicted to be >500ma,
given the model of stochastically constant evolutionary rates. If we're
talking about evolutionary novelties rather than branching pattern,
divergence time is probably not a relevant measure.

Seilacher, A. 1984. Late Precambrian and early Cambrian Metazoa:
preservational or real extinctions? In: H. D. Holland and A. F.
Trendall, eds., Patterns of Change in Earth Evolution, Berlin:
Springer-Verlag.
Discusses the taphonomy of Ediacaran organisms, coming to the conclusion
developed in more detail in the next paper.

-----------. 1989. Vendozoa: organismic construction in the
Proterozoic biosphere. Lethaia 22:229-239.
Interpretation of the Ediacaran fauna as the separate phylum Vendozoa,
making the Cambrian explosion more explosive than ever.

Valentine, J. W. and D. H. Erwin. 1987. Interpreting great developmental
experiments: the fossil record. In: R. A. Raff and E. C. Raff, eds.,
Development as an Evolutionary Process. New York: A. R. Liss, 71-108.
Contains an analysis of various processes which might produce an
apparent (or real) Cambrian explosion and concludes that something weird
was going on, but makes no firm statement about what, finding all
current theories inadequate. Joel Cracraft memorial quibble: I wish they
wouldn't talk about "ancestral clades".

[John Harshman]

On 10/8/14, 5:56 AM, nyi...@bellsouth.net wrote:

> On Tuesday, October 7, 2014 11:26:19 PM UTC-4, John Harshman wrote:
>> On 10/7/14, 7:43 PM, nyi...@bellsouth.net wrote:
>
>>> One way of minimizing this contrast is to claim that the concept of "phylum"
>>> is an artificial one, but it has been used for well over a century to
>>> be roughly synonymous with "unique body plans." So it is an indicator
>>> of disparity, the idea being that animals within a phylum are less
>>> different in some fundamental way from each other than any in one phylum
>>> are from any in another phylum. And so perhaps the real question about
>>> the Cambrian explosion is this: why did so much disparity blossom in so
>>> short a time, while later in earth history it happened on a smaller scale
>>> in a much longer time?
>
>> Back when I paid attention to the literature on this, there were three
>> main ideas.
>
> How long ago was that? Can you recall any websites (or at least
> articles or books) where the following ideas were advanced?
>
>> 1) The empty barrel theory: at no other time have so many
>> major niches been vacant, so the adaptive radiation would likewise have
>> been unmatched.
>
> The niches hardly would explain the different body plans. The niche of
> free-living terrestrial life was filled by members of relatively few
> phyla, none of which arose there as far as we know.

There is no "niche of free-living terrestrial life"; there are many such
niches. Apparently no new body plans were needed, though, if you think
phyla are body plans. But "body plan" is in the eye of the beholder anyhow.

>> 2) The loose genes theory: developmental pathways were
>> initially quite changeable but became developmentally canalized over
>> time.
>
> The issue is, when, and what were the limits of that changeability
> back in the Cambrian, and what are they today? Is there a serious genetic
> foundation for this idea?

Not sure. I haven't been following it lately.

> Why, for example, has no other phylum developed a flexible extensive
> endoskeleton? Could not a large number of phyla even today develop something
> as simple as the notochord of the lancelet (Branchiostoma a.k.a. Amphioxus)?
> The closest any other phylum has come is the Hemichordata, but the
> analogue there is only a small part of body length; in the lancelet it
> stretches from one end to the other.

Actually, echinoderms have endoskeletons (ophiuroids even have
"vertebrae"), and many "worms" have hydrostatic skeletons, just not
separate structures that embody them.

> In contrast, flexible extensive exoskeletons are found in quite a number
> of phyla and have developed independently several times in the subphylum
> Vertebrata alone: placoderms, ankylosaurs, Henodus, armadillos.

Why don't flexible exoskeletons count as new body plans?

>> 3) Yes, phyla are arbitrary units that by definition must have
>> arisen before the classes and orders that make them up.
>
> But how artificial? Is it not noteworthy that practically every
> one of the classical phyla, as defined in the 20th century up to
> 1970 is a clade, and that most if not all of the exceptions are
> paraphyletic? This despite the fact that phylogeny of invertebrates
> was very poorly known from the fossil record.

No, I don't think it's that noteworthy.

[Tim Norfolk]

On Tuesday, October 7, 2014 11:26:19 PM UTC-4, John Harshman wrote:

<snip>

> Back when I paid attention to the literature on this, there were three
> main ideas. 1) The empty barrel theory: at no other time have so many
> major niches been vacant, so the adaptive radiation would likewise have
> been unmatched. 2) The loose genes theory: developmental pathways were
> initially quite changeable but became developmentally canalized over
> time. 3) Yes, phyla are arbitrary units that by definition must have
> arisen before the classes and orders that make them up.

Here's a thought. Are the mass extinctions that we are seeing going to contribute to a large rush into vacated niches, or are we filling them all (with the rats, cockroaches, etc)?

[John Harshman]

All the vacated niches will be filled by something that's already
nearby, requiring no big changes in body plan. That's in contrast to the
Cambrian, when it was a wide-open race. Or so the theory goes.

[Nick Roberts]

In message <-82dnc4njomGDKnJ...@giganews.com>

To which the inevitable reply is:

Can ... you think?

You seem to be of the opinion that reading poetry and an obsession with
woo is a substitute for self-discipline in thinking. It isn't - unless
you actually understand the basics of the science in the things you
talk about, any attempt to apply complexity theory to real problems is
an exercise in futility.

And in answer to your question...

(Biological) evolution is the inevitable consequence of imperfect
replication, inheritance and non-random selection imposed by the
interaction of the phenotype with the environment.

What "freedom of interaction" is supposed to mean in this context is not
clear to me. I'm not sure it's clear to you, beyond it being a
cool-sounding collection of words.

--
Nick Roberts tigger @ orpheusinternet.co.uk

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

[erik simpson]

Fine set of references, several of which I'd missed. Thanks.

[John Harshman]

On 10/8/14, 12:47 PM, erik simpson wrote:

> Fine set of references, several of which I'd missed. Thanks.
>

Well, it was a fine set as of 1993 or so.

[jillery]

Don't hold back, Nick. Say how you really feel ;-)

--
Intelligence is never insulting.

[Jonathan]

<nyi...@bellsouth.net> wrote in message
news:4353d224-f68e-4a31...@googlegroups.com...

> On Tuesday, October 7, 2014 9:18:41 PM UTC-4, Jonathan wrote:
>> "Earle Jones27" <earle...@comcast.net> wrote in message
>> news:2014100713395256597-earlejones@comcastnet...
>>
>> > On 2014-10-07 11:03:52 +0000, Jonathan said:
>
>> > Jonathan: If you really believe what you wrote above, you need two
>> > very
>> > basic courses: One in biology and one in physics. No need for any
>> > advanced work, just the first-order lectures in those fields.
>
>> > "Evolution is the result of the critical interaction ...of opposite
>> > extremes..."
>
>> Then you tell me what evolution is the result of.....?
>
> Any good biology text (except those written by creationists) will answer
> that in detail.

That's a cop-out. This ng seems devoted to debunking
creationism more than explaining evolution.

Creationists, due to their literal interpretations, are
low hanging fruit, debunking them is plucking the
wings off flies, and does nothing to further the
understanding of evolution to the general public.

And your biology books, none of them, can explain
evolution in a way that can be applied to....non-living
evolving systems.

Complexity theory can, and that universal application shows us
the commonalties they all share, which allows universal laws
to be derived, at last.

Any good mathematician should practice translating
equations/concepts into plain English, if they can't they
probably don't understand the relationships very well.

> It gives details where you are content with a simple
> formula below that explains neither genetics nor selection, nor makes
> a case for them being opposites.

Opposites in possible ...behavior, is the word /behavior/
not registering?

>
>> A cloud is the result of the critical interaction between
>> condensation and evaporation,
>
> It is a condensation. When it dissolves into thin air, as the saying
> goes, that is evaporation.
>

But while /organized/, while a cloud, how are the
molecules ....behaving? Aren't they residing at the
phase transition point between water and vapor?

The only two possible 'states of matter' for that system?
Just as light has only two possible states.

Condensation is subcritical behavior, (static attractor)
/converging to order/ or simplicity over time, such as
matter, gravity, facts, laws, genetics or

Evaporation is supracritical behavior (chaotic attractor)
/diverging to disorder/ or dissipating such as a gas, energy,
cosmic expansion, imagination, freedom, selection or

Two opposing directions is behavior.

When at the subcritical/supercritical boundary, evolution
or self-organization spontaneously emerges.

For instance, for the emergent systems called....

Ideas, the sub/supracritical boundary would be
facts (static) and imagination (chaotic). When
both are at simultaneous maximums the better
idea or 'genius' is likely to emerge.

Or for the emergent system called....

Democracy, the sub/supra boundary would be
the 'rule of law' and freedom. The ideal democracy
should emerge when both are at simultaneous
maximums.

Genetics (fixed rules of operation is subcritical behavior.
Selection is supracritical behavior, characterized by
highly unconstrained or random interactions.

Incremental change is static, punctuated equilibria
is chaotic. Any organized system...must have both
behaviors present and critically interacting, so that
one can't tell which dominates the output, as with light
or the Mona Lisa smile

That's the source of evolution for all things.

/When the opposites in possible behavior at critically interacting/

>>it's opposite extremes in possible states.
>
>> Neo-Darwinism is the result of the opposites of
>> genetics (rules of operation) and selection (freedom
>> of interaction)
>
> The things in parentheses can be construed as opposites.
>Genetics and selection are even less "opposite" than
>agriculture and cooking.
>

Each system is broken down internally between their own static
and chaotic behaviors. Just humor me and list two or three
quite different, but still naturally evolving systems at random, and
let's see how they can be defined in this universal way?

It's good practice, like practicing how to anti-differentiate.

>> An idea is the result of the critical interaction between
>> facts and imagination. Rules and freedom.
>> Order and chaos.
>
> Thesis and antithesis.
>

That's not a proper analogy. Static and chaotic
attractors are qualitative opposites, as in one
is a fact, the other a system tendency.

As in one is classical behavior, the other quantum.

The two can't be expressed by a common mathematical
relationship when using a reductionist or objective frame
of reference. However, the ...output is a result of the
interactions of both, so the mathematics of system behavior
renders the brick-wall of the uncertainty principle, or vexing
duality in physics irrelevant.

As just such an inherent duality is a prerequisite for evolution.
The duality of static and chaotic behavior standing poised
at the boundary between them.

So that one can't tell which is more important to the whole.

> Ever read Hegel? Ever read William James's essay, "On some Hegelisms"?
> Do the philosophical speculators who have inspired you talk about Hegel
> and his "system"?
>

My 'inspiration' is complexity theory, nothing speculative about it.
Although complexity theory handles philosophical questions
as easily as any other.

> They could be on some altered state of consciousness, such as William
> James
> underwent when he breathed a hefty dose of nitrous oxide and for a while
> felt that Hegel was right after all, even though he had written
> brilliantly
> in opposition to Hegel.
>
> But when the nitrous oxide wore off, he saw that the notes he had
> furiously
> written down, and which he had felt "were fused in the fire of infinite
> rationality," were complete drivel, and was even able to strengthen his
> case
> against Hegel as a result.
>

Hegel was right in the sense we can't separate the outside world
from our perception of it. Which is clearly a co-evolutionary
approach where object and ecosystem can't be defined in isolation
from each other. And that this duality is the primary
obstacle to understanding nature.

If we can't separate object from environment, reality from
mind, how can we define anything? Because of this our instincts
tell us to separate everything from each other first, the exact
....wrong way to understand (co-evolving) systems or natural laws.

But what Hegel couldn't figure out is a testable, mathematically based
way to jump over the brick-wall of inherent incompatible duality.

Instead of becoming mired in all kinds of metaphysical vagueness
like consciousness and inner self etc, you simply observe the....effects
the object has on it's environment, instead of the object, as the primary
source of knowledge.

When an evolving system is disturbed in certain ways, the...effects
show us the logical or internal structure of the system.
An evolving system responds differently than a top down
control system, for instance.

So by disturbing a system we can discern it's internal or
logical structure even if it's internal details are completely
unknown or even unknowable.

>> Any and all organized systems can be defined in this
>> abstract way. I provided one example each from
>> life, the universe and everything else.
>
>> Can ...you think in abstract terms?
>
> We all can. But we don't get lost in metaphysical fogs the way you do.
>

I'm not the one lost in a fog, I can express the underlying process
of evolution for all that exists, physical, living or spiritual in
fifty words or less, at least that's my goal <g>. I tend to
go on and on, but the idea can be stated in a single sentence.

Even less if one has the skill of a good poet.


s




> Peter Nyikos
>

[Jonathan]

"Jonathan" <wr...@gmail.com> wrote in message
news:iOqdnRfD6Zv7W6jJ...@giganews.com...

> Two opposing directions is behavior.
>

What? Huh?

Oh wait, two opposing directions in behavior!



s

[nyi...@bellsouth.net]

On Wednesday, October 8, 2014 10:25:13 AM UTC-4, John Harshman wrote:

I'll be addressing your reply to points 1 and 2 later, hopefully today.
Right now I have time just for this.

> >> 3) Yes, phyla are arbitrary units that by definition must have
> >> arisen before the classes and orders that make them up.

> > But how artificial? Is it not noteworthy that practically every
> > one of the classical phyla, as defined in the 20th century up to
> > 1970 is a clade, and that most if not all of the exceptions are
> > paraphyletic? This despite the fact that phylogeny of invertebrates
> > was very poorly known from the fossil record.

> No, I don't think it's that noteworthy.

I would have preferred a less laconic reply, but at least this one
segues nicely into one of the many pieces of "fine print" in the
massive endnotes section of _Darwin's Doubt_, a section that a scientist
would study carefully were [s]he not predisposed, as most scientists
are, to dismissing Stephen Meyer as an intellectual lightweight.

Endnote 8 to Chapter 2:

If anything, using a "rank-free" classification system may actually
intensify the mystery of the Cambrian explosion. A single phylum
may include many unique modes of organizing tissues, organs, and
body parts, and these differences in organization may deserve to
be recognized as different body plans as much as the differences
that distinguish different phyla. As one proponent of the rank-free
approach put it to me, "Why shouldn't clams and squids [both of whom
belong to the single phylum Mollusca] be recognized as exemplifying
every bit as much as trilobites and starfish [...]?" In the traditional
system, however, both clams and squids, and many other animals that
exemplify equally pronounced differences in form within other phyla,
will all fall within their respective individual phyla. For this
reason, measuring the explosiveness of the Cambrian radiation solely
by reference to the number of phyla that appear in the Cambrian
may actually minimize the severity of the problem, whereas dispensing
with taxonomic ranking may actually tend to accentuate it.
____________________end of endnote on p. 419________________

Peter Nyikos

[John Harshman]

On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:
> On Wednesday, October 8, 2014 10:25:13 AM UTC-4, John Harshman wrote:
>
> I'll be addressing your reply to points 1 and 2 later, hopefully today.
> Right now I have time just for this.
>
>>>> 3) Yes, phyla are arbitrary units that by definition must have
>>>> arisen before the classes and orders that make them up.
>
>>> But how artificial? Is it not noteworthy that practically every
>>> one of the classical phyla, as defined in the 20th century up to
>>> 1970 is a clade, and that most if not all of the exceptions are
>>> paraphyletic? This despite the fact that phylogeny of invertebrates
>>> was very poorly known from the fossil record.
>
>> No, I don't think it's that noteworthy.
>
> I would have preferred a less laconic reply, but at least this one
> segues nicely into one of the many pieces of "fine print" in the
> massive endnotes section of _Darwin's Doubt_, a section that a scientist
> would study carefully were [s]he not predisposed, as most scientists
> are, to dismissing Stephen Meyer as an intellectual lightweight.

But Stephen Meyer is an intellectual lightweight. He's a creationist.

> Endnote 8 to Chapter 2:
>
> If anything, using a "rank-free" classification system may actually
> intensify the mystery of the Cambrian explosion. A single phylum
> may include many unique modes of organizing tissues, organs, and
> body parts, and these differences in organization may deserve to
> be recognized as different body plans as much as the differences
> that distinguish different phyla. As one proponent of the rank-free
> approach put it to me, "Why shouldn't clams and squids [both of whom
> belong to the single phylum Mollusca] be recognized as exemplifying
> every bit as much as trilobites and starfish [...]?" In the traditional
> system, however, both clams and squids, and many other animals that
> exemplify equally pronounced differences in form within other phyla,
> will all fall within their respective individual phyla. For this
> reason, measuring the explosiveness of the Cambrian radiation solely
> by reference to the number of phyla that appear in the Cambrian
> may actually minimize the severity of the problem, whereas dispensing
> with taxonomic ranking may actually tend to accentuate it.
> ____________________end of endnote on p. 419________________

That might be a point if there actually were a problem. Do you agree
with Meyer on this question? I think it's a problem for Meyer. He wants
there to be no ancestors for the various groups, but if we agree that
cephalopods and bivalves are both molluscs, and share a common ancestor
despite their quite different body plans, his idea of sudden appearance
of body plans without ancestors goes away, since relationship implies
ancestors.

[nyi...@bellsouth.net]

On Wednesday, October 8, 2014 3:52:49 PM UTC-4, John Harshman wrote:
> On 10/8/14, 12:47 PM, erik simpson wrote:

> > Fine set of references, several of which I'd missed. Thanks.

What really sets them apart is the annotations. They should help
in deciding which references are most relevant.

> Well, it was a fine set as of 1993 or so.

You gave a lot of food for thought in them and preceding them.
Are the question marks in parentheses the way the original read, or are they
afterthoughts occasioned by developments in the intervening two decades?

Just scratching the bottom surface: you wrote:

Joel Cracraft memorial quibble: I wish they
wouldn't talk about "ancestral clades".

Did Joel Cracraft say that, or did you think that would have
been an especially apropos thing for him to say?

Anyway, the term could make sense as shorthand for "clades the way
they were in Cambrian times, with forms ancestral to organisms
in the clade as it has developed to the present."

Is that the way it was actually used by Erwin and Valentine?

[Erwin and Valentine are getting to seem as inseparable as Gilbert and
Sullivan or Rogers and Hammerstein.] :-)

Peter Nyikos

[nyi...@bellsouth.net]

I haven't had time to study it in detail, but it looks like
it is more about diversity (number of speciations) rather than
disparity (magnitude of morphological changes). Don't forget that
nuclear genes tell only part of the story; a lot depends on which
ones are expressed, and that has to do with the enzymes in the
cytoplasm of gametes.

By the way, have you had any luck with finding the dates
for protostome-deuterostome split that Erwin & Valentine
espouse in that book? More importantly, have you found the
molecular clock studies that they use to back this and other
dates up?

Perhaps relevant: a recent paper, "Early vertebrate evolution"
by Philip C. J. Donoghue and Joseph N. Keating, which talks a lot about
molecular clocks and their wide variance of dates.

http://onlinelibrary.wiley.com/enhanced/doi/10.1111/pala.12125/

They cite a paper co-authored by Erwin and Peterson and a number of others
[but not Valentine, hence my smiley in my preceding post to this
thread] in talking about a diagram where they put the LCA of Chordata
all the way back in the Cryogenian:

"Node dates, where applicable, correspond with divergence estimates from
Erwin et al. (2011). Geological timescale based on Gradstein et al.
(2012)."
...
Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D.
and Peterson, K. J. 2011. The Cambrian conundrum: early divergence and later
ecological success in the early history of animals. Science, 334, 1091-1097.
...
Gradstein, F. M., Ogg, J. G., Schmitz, M. and Ogg, G. (eds). 2012.
The geological timescale 2012. Elsevier, Oxford, 1144 pp.

Trivia: Donoghue and Keating write:

"*Haikouichthys* (Fig. 2K, and its likely junior synonym *Myllokunmingia*"

...but Fig. 2K shows a very familiar picture which other sources
identify with a fossil of Myllokunmingia, [the type specimen, perhaps?]
whereas Donoghue and Keating caption says
"Haikouichthys ercaicunensis (YKLP (RCCBYU)-00195)"

Peter Nyikos

[Nick Roberts]

In message <ee6b3a1psr2q3uhmc...@4ax.com>

8-)

Well, jonathon annoys me. Or more correctly, his obsession with
lecturing people about subjects in which they are vastly more expert
than he is annoys me. Every now and again I one of his more vacuous
posts annoy me to the extent that I respond.

I've asked him several times to try to put the case for complexity
theory in some concrete example, and using his own words rather than a
screed copied wholesale from a web site. So far he has never responded.
I suppose it's possible that he has me killfiled.

[John Harshman]

On 10/9/14, 9:46 AM, nyi...@bellsouth.net wrote:
> On Wednesday, October 8, 2014 3:52:49 PM UTC-4, John Harshman wrote:
>> On 10/8/14, 12:47 PM, erik simpson wrote:
>
>>> Fine set of references, several of which I'd missed. Thanks.
>
> What really sets them apart is the annotations. They should help
> in deciding which references are most relevant.
>
>> Well, it was a fine set as of 1993 or so.
>
> You gave a lot of food for thought in them and preceding them.
> Are the question marks in parentheses the way the original read, or are they
> afterthoughts occasioned by developments in the intervening two decades?

The original.

> Just scratching the bottom surface: you wrote:
>
> Joel Cracraft memorial quibble: I wish they
> wouldn't talk about "ancestral clades".
>
> Did Joel Cracraft say that, or did you think that would have
> been an especially apropos thing for him to say?

Cracraft is one of the early fanatical cladists, who would be aghast at
the term. Of course he's still alive, but at the time he had recently
left Chicago.

> Anyway, the term could make sense as shorthand for "clades the way
> they were in Cambrian times, with forms ancestral to organisms
> in the clade as it has developed to the present."

No it couldn't.

> Is that the way it was actually used by Erwin and Valentine?

I hope not. But I would have to look.

[John Harshman]

On 10/9/14, 10:35 AM, nyi...@bellsouth.net wrote:
> On Wednesday, October 8, 2014 10:11:01 AM UTC-4, John Harshman wrote:
>> On 10/8/14, 1:05 AM, alias Ernest Major wrote:
>
>>> If someone wants to argue that the Cambrian Explosion represents
>>> something unique in terms of the production of disparsity that someone
>>> needs a more objective measure of disparity than taxonomic rank.
>
>> Such as this: Lee et al., Rates of Phenotypic and Genomic Evolution
>> during the Cambrian Explosion, Current Biology (2013)
>
>> http://dx.doi.org/10.1016/j.cub.2013.07.055
>
> I haven't had time to study it in detail, but it looks like
> it is more about diversity (number of speciations) rather than
> disparity (magnitude of morphological changes). Don't forget that
> nuclear genes tell only part of the story; a lot depends on which
> ones are expressed, and that has to do with the enzymes in the
> cytoplasm of gametes.

I'm sorry, but that paragraph just shows that you have no clue. It's
about rates of molecular and morphological evolution (like the title
says), not about speciations. Nor do the enzymes (wouldn't call them
enzymes; transcription factors would be the better term) in gametes
(eggs, really) affect more than the very initial stages of gene
expression, and so have only a small part to do with the big picture of
developmental evolution.

One might argue that the number of morphological character changes is a
reasonable estimate of disparity. Would you disagree?

> By the way, have you had any luck with finding the dates
> for protostome-deuterostome split that Erwin & Valentine
> espouse in that book? More importantly, have you found the
> molecular clock studies that they use to back this and other
> dates up?

Haven't looked yet.

> Perhaps relevant: a recent paper, "Early vertebrate evolution"
> by Philip C. J. Donoghue and Joseph N. Keating, which talks a lot about
> molecular clocks and their wide variance of dates.
>
> http://onlinelibrary.wiley.com/enhanced/doi/10.1111/pala.12125/
>
> They cite a paper co-authored by Erwin and Peterson and a number of others
> [but not Valentine, hence my smiley in my preceding post to this
> thread] in talking about a diagram where they put the LCA of Chordata
> all the way back in the Cryogenian:
>
> "Node dates, where applicable, correspond with divergence estimates from
> Erwin et al. (2011). Geological timescale based on Gradstein et al.
> (2012)."
> ...
> Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D.
> and Peterson, K. J. 2011. The Cambrian conundrum: early divergence and later
> ecological success in the early history of animals. Science, 334, 1091-1097.
> ...
> Gradstein, F. M., Ogg, J. G., Schmitz, M. and Ogg, G. (eds). 2012.
> The geological timescale 2012. Elsevier, Oxford, 1144 pp.
>
> Trivia: Donoghue and Keating write:
>
> "*Haikouichthys* (Fig. 2K, and its likely junior synonym *Myllokunmingia*"
>
> ...but Fig. 2K shows a very familiar picture which other sources
> identify with a fossil of Myllokunmingia, [the type specimen, perhaps?]
> whereas Donoghue and Keating caption says
> "Haikouichthys ercaicunensis (YKLP (RCCBYU)-00195)"

That's why it's a junior synonym, eh?

[nyi...@bellsouth.net]

On Tuesday, October 7, 2014 9:00:57 PM UTC-4, Jonathan wrote:
> <nyi...@bellsouth.net> wrote in message

> news:20fa2115-eb16-4001...@googlegroups.com...

> >Then there is the age old question:
> > if there is a creator of our world, to what does that creator owe its
> > existence? The only answer our minds can really grasp is, "It evolved
> > in a universe that may have been infinitely old and of infinite extent,
> > but at any rate was so much grander than ours that even such
> > `supernatural' beings could have evolved in it, given enough time."

> Mathematicians are supposed to be noted for their
> attention to detail,

...as well as to the big picture. Beauties such as the
Goedel Incompleteness theorems and the Goedel Completeness
Theorem [yes, there is such a thing] and the Goedel-Cohen
proof of the independence of the Continuum Hypothesis are
the result of both abilities.

> the only reason for the above
> metaphysical guesswork is for the lack of a clear
> definition of the word 'god'.

You are changing the subject from "creator of our world"
[i.e., creator of our universe, or perhaps our multiverse,
and possibly things within it] to "god", to which you
feel free to attach your own favorite meaning.

That meaning owes a lot [perhaps indirectly] to
Teilhard de Chardin.

> Darwin provides a perfectly good definition as
> evolutionary systems problem-solve as a matter
> of course.

What problem was the human vermiform appendix supposed
to solve? What problem was the strangely "backwards"
retina of vertebrates [now a frozen fixture, along
with the inevitable blind spot] supposed to solve?

Oh, wait. You are a holistic thinker *par excellence*
and think these are the wrong kinds of questions to
ask, don't you? All that matters to you is what
Teilhard de Chardin called "the Omega point," isn't it?

> Such processes converge towards
> the better adaptation or solution, towards the
> ideal possible future....towards 'perfection'
> for that system.

Hmmm...little omega points on the way to the Omega
Point, eh?

> God is the goal towards which any self-organized
> systems aspire or are attracted to. Our goals might be
> heaven or profit while gravity or the Second law have
> their own preferred 'states'.

omega points of all shapes and sizes, eh?

> The concept of god emerges from us, and is as real and
> important as any other idea, perhaps far more so as it
> defines the ideal possible future we can imagine.

Yup, you get to define "god" your way, making up the
rules as you go along. As an ancient Greek wag put it,
man makes the gods in his own image.

<snip remaining bomfoggery>

I'll comment on the rest of your bomfoggery if you face the
issue of meanings of words in a mature way.

Peter Nyikos
Professor, Department of Mathematics -- standard disclaimer--
U. of South Carolina

[jillery]

On Thu, 09 Oct 2014 18:35:17 +0100, Nick Roberts

IIRC I have asked him something similar, and his reply in paraphrase
was that Complexity Theory is complex and so needs complex words to
explain it.

He also posted a "proof" where he claimed to have predicted with
complexity theory a sharp rise (or maybe it was a drop) in the price
of a particular stock. Of course, he provided nothing that could be
authenticated, nor did he discuss any cases where his predictions were
wrong.

I might feel different about Jonathan if I liked Emily Dickinson's
poetry, but I don't hold out much hope for either.

[nyi...@bellsouth.net]

On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:
> On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:
> > On Wednesday, October 8, 2014 10:25:13 AM UTC-4, John Harshman wrote:

> >>> Is it not noteworthy that practically every
> >>> one of the classical phyla, as defined in the 20th century up to
> >>> 1970 is a clade, and that most if not all of the exceptions are
> >>> paraphyletic? This despite the fact that phylogeny of invertebrates
> >>> was very poorly known from the fossil record.

> >> No, I don't think it's that noteworthy.

> > I would have preferred a less laconic reply, but at least this one
> > segues nicely into one of the many pieces of "fine print" in the
> > massive endnotes section of _Darwin's Doubt_, a section that a scientist
> > would study carefully were [s]he not predisposed, as most scientists
> > are, to dismissing Stephen Meyer as an intellectual lightweight.

> But Stephen Meyer is an intellectual lightweight. He's a creationist.

Hardly the kind of ignorant creationist that R. Norman dug up for me.
I wonder why he hasn't participated here yet--he opened my eyes to
just how ignorant it is possible for creationists [he dug up three
of them] to be and still to command a following.

To say that these three thought there were no animals before the Cambrian
is only to scratch the surface of their ignorance. I'm afraid all
too many scientists, reading put-downs of Meyer by other scientists,
get the impression that he is no better than these infamous three.

Meyer has never been shown to be the kind of "creation ex nihilo"
creationist that these three, and almost all other creationists, are.
For example, Meyer has never come out and claimed that trilobites
did not have biological ancestors; nor does he pretend to be staying
within the bounds of science when he states his personal belief
that God played a major hand in the Cambrian explosion--but his
friend Michael Behe believes this took the form of producing
a great many mutations spread out over a few million year's time,
and Meyer certainly isn't going to gainsay him.

> > Endnote 8 to Chapter 2:

> > If anything, using a "rank-free" classification system may actually
> > intensify the mystery of the Cambrian explosion. A single phylum
> > may include many unique modes of organizing tissues, organs, and
> > body parts, and these differences in organization may deserve to
> > be recognized as different body plans as much as the differences
> > that distinguish different phyla. As one proponent of the rank-free
> > approach put it to me, "Why shouldn't clams and squids [both of whom
> > belong to the single phylum Mollusca] be recognized as exemplifying
> > every bit as much as trilobites and starfish [...]?" In the traditional
> > system, however, both clams and squids, and many other animals that
> > exemplify equally pronounced differences in form within other phyla,
> > will all fall within their respective individual phyla. For this
> > reason, measuring the explosiveness of the Cambrian radiation solely
> > by reference to the number of phyla that appear in the Cambrian
> > may actually minimize the severity of the problem, whereas dispensing
> > with taxonomic ranking may actually tend to accentuate it.
>
> > ____________________end of endnote on p. 419________________
>
>
>
> That might be a point if there actually were a problem. Do you agree
> with Meyer on this question?

It's a toughie as to whether I would agree with the actual words I've
quoted just now. And even more so as to whether you would agree with them,
because you have yet to address them.

Here's a question that might help both of us to discuss the actual
quote intelligently, as opposed to what you are doing below.

Does the existence of a notochord as scaffolding for vertebrae prevent
the vertebral column from being the kind of "new body plan" that
the "loose genes theory" tried to minimize the probability of?
I'm referring to something you wrote earlier:

"2) The loose genes theory: developmental pathways were
initially quite changeable but became developmentally canalized over
time.

As I'm sure you know, the notochord is not a primordium for the vertebral
column, but only a scaffolding for it.

> I think it's a problem for Meyer. He wants
> there to be no ancestors for the various groups,

Balderdash. Like I said, he certainly isn't going to gainsay
Michael Behe on common descent.

> but if we agree that
> cephalopods and bivalves are both molluscs, and share a common ancestor
> despite their quite different body plans, his idea of sudden appearance
> of body plans

"sudden" here means "within about 5 million years." At least, according
the actual data Meyer presents, and even the way he presents it.
Creationists will read between the lines, and so will anti-creationists
trying to prop up a strawman Meyer.

>without ancestors goes away, since relationship implies
> ancestors.

Sure. Looks to me like you've been reading too many canards about
Meyer without investigating his actual writings carefully enough.

Peter Nyikos

[erik simpson]

You do a lot of reading of scripture from the Book of Doubt. Whatever your
problem with some of the reviews you've reviled, 'Darwin's Doubt' can't be
considered to be a authoritative source for current paleontological science.
In the presence of much better accounts, why do lean so heavily on Meyer's
misleading tome? You're at a university, but you claim you don't have easy
access to Erwin & Valentine? That's preposterous.

[John Harshman]

On 10/9/14, 3:16 PM, nyi...@bellsouth.net wrote:
> On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:
>> On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:
>>> On Wednesday, October 8, 2014 10:25:13 AM UTC-4, John Harshman wrote:
>
>>>>> Is it not noteworthy that practically every
>>>>> one of the classical phyla, as defined in the 20th century up to
>>>>> 1970 is a clade, and that most if not all of the exceptions are
>>>>> paraphyletic? This despite the fact that phylogeny of invertebrates
>>>>> was very poorly known from the fossil record.
>
>>>> No, I don't think it's that noteworthy.
>
>>> I would have preferred a less laconic reply, but at least this one
>>> segues nicely into one of the many pieces of "fine print" in the
>>> massive endnotes section of _Darwin's Doubt_, a section that a scientist
>>> would study carefully were [s]he not predisposed, as most scientists
>>> are, to dismissing Stephen Meyer as an intellectual lightweight.
>
>> But Stephen Meyer is an intellectual lightweight. He's a creationist.
>
> Hardly the kind of ignorant creationist that R. Norman dug up for me.

Indeed. He's a different kind of ignorant creationist, and his ignorance
is in part apparently calculated.

> I wonder why he hasn't participated here yet--he opened my eyes to
> just how ignorant it is possible for creationists [he dug up three
> of them] to be and still to command a following.
>
> To say that these three thought there were no animals before the Cambrian
> is only to scratch the surface of their ignorance. I'm afraid all
> too many scientists, reading put-downs of Meyer by other scientists,
> get the impression that he is no better than these infamous three.

I will agree that he is slightly better. Would that please you?

> Meyer has never been shown to be the kind of "creation ex nihilo"
> creationist that these three, and almost all other creationists, are.
> For example, Meyer has never come out and claimed that trilobites
> did not have biological ancestors; nor does he pretend to be staying
> within the bounds of science when he states his personal belief
> that God played a major hand in the Cambrian explosion--but his
> friend Michael Behe believes this took the form of producing
> a great many mutations spread out over a few million year's time,
> and Meyer certainly isn't going to gainsay him.

Yes, Meyer does try to avoid saying anything about what he actually
thinks happened. But he can't avoid it altogether. His book makes no
sense unless he's trying to show that trilobites had no ancestors.

Thank you for your condescension.

> Does the existence of a notochord as scaffolding for vertebrae prevent
> the vertebral column from being the kind of "new body plan" that
> the "loose genes theory" tried to minimize the probability of?
> I'm referring to something you wrote earlier:
>
> "2) The loose genes theory: developmental pathways were
> initially quite changeable but became developmentally canalized over
> time.
>
> As I'm sure you know, the notochord is not a primordium for the vertebral
> column, but only a scaffolding for it.

Unfortunately, "body plan" is in the eye of the beholder. But I see
nothing prevents a vertebral column from being a new body plan, if you like.

>> I think it's a problem for Meyer. He wants
>> there to be no ancestors for the various groups,
>
> Balderdash. Like I said, he certainly isn't going to gainsay
> Michael Behe on common descent.

Yes, for political reasons. Behe has stated his views, and Meyer won't.
Though I've shown you quotes in which he came very, very close. He,
after all, sees no scientific evidence contradicting the separate
creation of humans and apes.

>> but if we agree that
>> cephalopods and bivalves are both molluscs, and share a common ancestor
>> despite their quite different body plans, his idea of sudden appearance
>> of body plans
>
> "sudden" here means "within about 5 million years." At least, according
> the actual data Meyer presents, and even the way he presents it.
> Creationists will read between the lines, and so will anti-creationists
> trying to prop up a strawman Meyer.

No, that's the period during which a number of body plans suddenly
(really) appeared. Apparently, not every creation act was simultaneous.
I find it amusing that you use "Meyer" and "data" in the same sentence.
So, why do you think Meyer is so coy about what he thinks?

>> without ancestors goes away, since relationship implies
>> ancestors.
>
> Sure. Looks to me like you've been reading too many canards about
> Meyer without investigating his actual writings carefully enough.

We've been over this before. What things look like to you and what
actually happens are not closely related. I read the damn book. I'm not
sure you did.

[Roger Shrubber]

erik simpson wrote:
> On Thursday, October 9, 2014 3:16:08 PM UTC-7, nyi...@bellsouth.net wrote:
>> On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:


>>> But Stephen Meyer is an intellectual lightweight. He's a creationist.


>> Hardly the kind of ignorant creationist that R. Norman dug up for me.
>> I wonder why he hasn't participated here yet--he opened my eyes to
>> just how ignorant it is possible for creationists [he dug up three
>> of them] to be and still to command a following.

https://www.youtube.com/watch?v=nn4KFzX6Ywg
Wherein Meyer attempts to play peace maker with creationists
about the age of the Earth. While he claims he is "old Earth",
he dismisses arguments about the age of the Earth as rather
insignificant. What's important, he says, is that you can look
at the world and see evidence of the creator.

To me, somebody who claims that his interpretation of evidence
demonstrates a creator (he does not hedge here with "designer")
but at the same time can look at the same evidence and not
be decisive about the age of the Earth is a light weight. He
sacrifices decisiveness in favor of "the big tent" because,
as he makes clear, the first and most important thing is to
attack the dominance of a secular world view and affirm the
existence of God. He also mentions Philip Johnson as the leader
of their approach which to me acknowledges the explicit
strategy outlined in The Wedge Document: attack secularism,
defend God the creator by pretending we are not creationists
so we can get past the courts.

>> To say that these three thought there were no animals before the Cambrian
>> is only to scratch the surface of their ignorance. I'm afraid all
>> too many scientists, reading put-downs of Meyer by other scientists,
>> get the impression that he is no better than these infamous three.

He is not much better than these three. He still simply begins with
"God exists and is the creator" and then tried to fit the evidence
to his conclusion.

>> Meyer has never been shown to be the kind of "creation ex nihilo"
>> creationist that these three, and almost all other creationists, are.
>> For example, Meyer has never come out and claimed that trilobites
>> did not have biological ancestors; nor does he pretend to be staying
>> within the bounds of science when he states his personal belief
>> that God played a major hand in the Cambrian explosion--but his
>> friend Michael Behe believes this took the form of producing
>> a great many mutations spread out over a few million year's time,
>> and Meyer certainly isn't going to gainsay him.

What an incredibly bizarre thing to say. Would Behe no longer be
his friend if he disagreed with him? Could he not be friends with
Behe if he disagreed? Or are you just that convinced that everybody
colludes and hides the truth of what they think to put on some
united front. Though I must grant, Meyer did go pretty far in
the cited video in demonstrating that he just might do that.
Of course people who do that are intellectual light weights.

[erik simpson]

On Thursday, October 9, 2014 3:16:08 PM UTC-7, nyi...@bellsouth.net wrote:

> <...>

>
>
> Meyer has never been shown to be the kind of "creation ex nihilo"
> creationist that these three, and almost all other creationists, are.
> For example, Meyer has never come out and claimed that trilobites
> did not have biological ancestors; nor does he pretend to be staying
> within the bounds of science when he states his personal belief
> that God played a major hand in the Cambrian explosion--but his
> friend Michael Behe believes this took the form of producing
> a great many mutations spread out over a few million year's time,
> and Meyer certainly isn't going to gainsay him.
>

What exactly is the difference between "creation ex nihilo" and chemical
meddling over a period of millions of years? Chemical reactions are covered
by quantum electrodynamics, one of the most precise and exhaustively tested
theories we have. Does Behe mean to suggest that some magical being introduces
extra interactions in the Hamiltonian describing the chemical system, or would
he prefer a "demon" (like, perhaps, Maxwell's) to nudge a reaction in the
preferred direction? Sounds pretty "ex nihilo" to me. That the magic is
spread out in time (so we wouldn't notice?) makes it sound like God might be
embarrassed if he were caught trying to fix up His creation on the sly.

[nyi...@bellsouth.net]

On Thursday, October 9, 2014 6:26:28 PM UTC-4, erik simpson wrote:

I see you ignored my advice on how to stop extra lines from being
inserted into copied text. Do you not have easy access to Thunderbird?

> You do a lot of reading of scripture from the Book of Doubt.

Is this kind of sneer all you can contribute to the on-topic discussion?
I'm disappointed in you.

> Whatever your
> problem with some of the reviews you've reviled, 'Darwin's Doubt' can't be
> considered to be a authoritative source for current paleontological science.

I never claimed it was. And so far I have only quoted ONE passage from it,
whose content seems to have left you speechless. I would have left it
in my reply for you to gawk at again, but you ignored my advice about
Thunderbird and even snipped it from your reply in the thread where
I made it.

> In the presence of much better accounts, why do lean so heavily on Meyer's
> misleading tome?

"So heavily." How subjective can you get?

Next thing you know, you will be blaming ME for reducing the signal-to-noise
ratio on this thread. Just remember, YOUR signal to noise ratio here was zero until your penultimate sentence:

> You're at a university, but you claim you don't have easy
> access to Erwin & Valentine? That's preposterous.

The only copy in the university system is at USC Upstate. I could have it
delivered to the Thomas Cooper Library here at USC Columbia for a couple
of weeks if the USC Upstate librarians are willing, but I wouldn't call
that EASY access.

By the way, do YOU have easier access to E & V yourself? If so, how
about lending Harshman a hand in finding where they place the
protostome-deuterostome split, and what molecular studies they
are using as a basis?

Peter Nyikos

[nyi...@bellsouth.net]

On Thursday, October 9, 2014 6:42:48 PM UTC-4, John Harshman wrote:
> On 10/9/14, 3:16 PM, nyi...@bellsouth.net wrote:
>
> > On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:
>
> >> On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:

[about Richard Norman:

> > I wonder why he hasn't participated here yet--he opened my eyes to
> > just how ignorant it is possible for creationists [he dug up three
> > of them] to be and still to command a following.

> > To say that these three thought there were no animals before the Cambrian
> > is only to scratch the surface of their ignorance. I'm afraid all
> > too many scientists, reading put-downs of Meyer by other scientists,
> > get the impression that he is no better than these infamous three.

> I will agree that he is slightly better. Would that please you?

That's like saying that Poul Anderson is a slightly better writer
of science fiction than Zenna Henderson. [Ms. Henderson is very good
at writing about human emotions, but her aptitude for science seems close
to zero in the "science fiction" stories of hers that I have read.]

In case you haven't guessed, the answer to your question is No.

> > Meyer has never been shown to be the kind of "creation ex nihilo"
> > creationist that these three, and almost all other creationists, are.
> > For example, Meyer has never come out and claimed that trilobites
> > did not have biological ancestors; nor does he pretend to be staying
> > within the bounds of science when he states his personal belief
> > that God played a major hand in the Cambrian explosion--but his
> > friend Michael Behe believes this took the form of producing
> > a great many mutations spread out over a few million year's time,
> > and Meyer certainly isn't going to gainsay him.

> Yes, Meyer does try to avoid saying anything about what he actually
> thinks happened.

What Meyer privately believes and what he endorses when speaking *qua* ID
theorist are two utterly different things. We've been through this
MANY times before.

<snip rest of irrelevant comment>

> But he can't avoid it altogether. His book makes no
> sense unless he's trying to show that trilobites had no ancestors.

With this completely unsupported allegation, you have revealed just why
you completely ignored the actual issues Meyer is writing about in the
passage I quoted, as did Erik Simpson:

Endnote 8 to Chapter 2:

If anything, using a "rank-free" classification system may actually
intensify the mystery of the Cambrian explosion. A single phylum
may include many unique modes of organizing tissues, organs, and
body parts, and these differences in organization may deserve to
be recognized as different body plans as much as the differences
that distinguish different phyla. As one proponent of the rank-free
approach put it to me, "Why shouldn't clams and squids [both of whom
belong to the single phylum Mollusca] be recognized as exemplifying
every bit as much as trilobites and starfish [...]?" In the traditional
system, however, both clams and squids, and many other animals that
exemplify equally pronounced differences in form within other phyla,
will all fall within their respective individual phyla. For this
reason, measuring the explosiveness of the Cambrian radiation solely
by reference to the number of phyla that appear in the Cambrian
may actually minimize the severity of the problem, whereas dispensing
with taxonomic ranking may actually tend to accentuate it.
____________________end of endnote on p. 419________________


> >> That might be a point if there actually were a problem. Do you agree
> >> with Meyer on this question?

> > It's a toughie as to whether I would agree with the actual words I've
> > quoted just now. And even more so as to whether you would agree with them,
> > because you have yet to address them.

I'm still a long way from deciding whether rank-free classification
will actually tend to accentuate the unusualness of the Cambrian
explosion. But I have decided that the examples given are quite
plausible, e.g., that squids and clams may well represent different
body plans.

And one benefit that may come from the likes of Meyer bringing
up these questions is that scientists with open minds might actually
start wondering just what insights the naturalists of the first half of the
20th century brought to the concept of "body plan" when they made the phyla
what they were.

Problem is, are there any mainstream scientists who care about such things?

> > Here's a question that might help both of us to discuss the actual
> > quote intelligently, as opposed to what you are doing below.

> Thank you for your condescension.

Condescension is very much in keeping with the *ad hominem* attack you
did. But at least you have now revealed the unspoken, unsupported
assumption behind it. That's progress.

["I read the damn book. I'm not sure you did." (snipped below)
is not support.]

> > Does the existence of a notochord as scaffolding for vertebrae prevent
> > the vertebral column from being the kind of "new body plan" that
> > the "loose genes theory" tried to minimize the probability of?
>
> > I'm referring to something you wrote earlier:

> > "2) The loose genes theory: developmental pathways were
> > initially quite changeable but became developmentally canalized over
> > time.

By the way, it strikes me as strange that you haven't mentioned anything
from Erwin and Valentine about this, but just reposted something from
1993 or so. How much of their book have you read?

> Unfortunately, "body plan" is in the eye of the beholder.

Do you think all those early 20th century naturalists weren't really
talking about something objective?

> But I see
> nothing prevents a vertebral column from being a new body plan, if you like.

It has always struck me as strange that an elaborate skeleton such as
we have is not as much of a "new body plan" when compared to the notochord
as the notochord is over the "body plan" of hemichordates or echinoderms,
but I really don't know what reasoning those old fashioned naturalists used.

Remainder deleted. You asked a question there involving coyness, but I have
no insight into why you are as coy as you are, so don't expect me
to have any into why Meyer is as coy as he is.

Peter Nyikos

[John Harshman]

On 10/9/14, 7:56 PM, nyi...@bellsouth.net wrote:
> On Thursday, October 9, 2014 6:42:48 PM UTC-4, John Harshman wrote:
>> On 10/9/14, 3:16 PM, nyi...@bellsouth.net wrote:
>>
>>> On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:
>>
>>>> On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:
>
> [about Richard Norman:
>>> I wonder why he hasn't participated here yet--he opened my eyes to
>>> just how ignorant it is possible for creationists [he dug up three
>>> of them] to be and still to command a following.
>
>>> To say that these three thought there were no animals before the Cambrian
>>> is only to scratch the surface of their ignorance. I'm afraid all
>>> too many scientists, reading put-downs of Meyer by other scientists,
>>> get the impression that he is no better than these infamous three.
>
>> I will agree that he is slightly better. Would that please you?
>
> That's like saying that Poul Anderson is a slightly better writer
> of science fiction than Zenna Henderson. [Ms. Henderson is very good
> at writing about human emotions, but her aptitude for science seems close
> to zero in the "science fiction" stories of hers that I have read.]
>
> In case you haven't guessed, the answer to your question is No.

You are constitutionally unable to make a point without insulting some
third party not present, in this case Zenna Henderson. So we disagree on
how much of a bozo Mr. Meyer has shown himself to be.

>>> Meyer has never been shown to be the kind of "creation ex nihilo"
>>> creationist that these three, and almost all other creationists, are.
>>> For example, Meyer has never come out and claimed that trilobites
>>> did not have biological ancestors; nor does he pretend to be staying
>>> within the bounds of science when he states his personal belief
>>> that God played a major hand in the Cambrian explosion--but his
>>> friend Michael Behe believes this took the form of producing
>>> a great many mutations spread out over a few million year's time,
>>> and Meyer certainly isn't going to gainsay him.
>
>> Yes, Meyer does try to avoid saying anything about what he actually
>> thinks happened.
>
> What Meyer privately believes and what he endorses when speaking *qua* ID
> theorist are two utterly different things. We've been through this
> MANY times before.

Never while confronting reality, though. There is no such thing as an ID
theorist. He's a creationist who wants to avoid public recognition of
that fact.

> <snip rest of irrelevant comment>
>
>> But he can't avoid it altogether. His book makes no
>> sense unless he's trying to show that trilobites had no ancestors.
>
> With this completely unsupported allegation, you have revealed just why
> you completely ignored the actual issues Meyer is writing about in the
> passage I quoted, as did Erik Simpson:

Have you read the book? The whole book? His chapter on the fossil record
makes it clear. If trilobites had ancestors, we would see them in the
fossil record, and we don't. Again, did you actually read the book?

There are probably no mainstream scientists who agree that the concept
of "body plan" had much to do with phyla. This is your fantasy. There is
no benefit to Meyer bringing up fake questions.

>>> Here's a question that might help both of us to discuss the actual
>>> quote intelligently, as opposed to what you are doing below.
>
>> Thank you for your condescension.
>
> Condescension is very much in keeping with the *ad hominem* attack you
> did. But at least you have now revealed the unspoken, unsupported
> assumption behind it. That's progress.

How can I have revealed an unspoken assumption? Wouldn't that require
you to read between the lines? And we know how bad you are at that sort
of thing. What was my unspoken assumption, for the record?

> ["I read the damn book. I'm not sure you did." (snipped below)
> is not support.]

Did you read the book? Did you read the whole book?

>>> Does the existence of a notochord as scaffolding for vertebrae prevent
>>> the vertebral column from being the kind of "new body plan" that
>>> the "loose genes theory" tried to minimize the probability of?
>>
>>> I'm referring to something you wrote earlier:
>
>>> "2) The loose genes theory: developmental pathways were
>>> initially quite changeable but became developmentally canalized over
>>> time.
>
> By the way, it strikes me as strange that you haven't mentioned anything
> from Erwin and Valentine about this, but just reposted something from
> 1993 or so. How much of their book have you read?

All of it. You should read it too.

>> Unfortunately, "body plan" is in the eye of the beholder.
>
> Do you think all those early 20th century naturalists weren't really
> talking about something objective?

Yes.

>> But I see
>> nothing prevents a vertebral column from being a new body plan, if you like.
>
> It has always struck me as strange that an elaborate skeleton such as
> we have is not as much of a "new body plan" when compared to the notochord
> as the notochord is over the "body plan" of hemichordates or echinoderms,
> but I really don't know what reasoning those old fashioned naturalists used.
>
> Remainder deleted. You asked a question there involving coyness, but I have
> no insight into why you are as coy as you are, so don't expect me
> to have any into why Meyer is as coy as he is.

Here, let me restore it:

> Balderdash. Like I said, he certainly isn't going to gainsay
> Michael Behe on common descent.

Yes, for political reasons. Behe has stated his views, and Meyer won't.
Though I've shown you quotes in which he came very, very close. He,
after all, sees no scientific evidence contradicting the separate
creation of humans and apes.

>> but if we agree that cephalopods and bivalves are both molluscs,
>> and share a common ancestor despite their quite different body
>> plans, his idea of sudden appearance of body plans

> "sudden" here means "within about 5 million years." At least,
> according the actual data Meyer presents, and even the way he
> presents it. Creationists will read between the lines, and so will
> anti-creationists trying to prop up a strawman Meyer.

No, that's the period during which a number of body plans suddenly
(really) appeared. Apparently, not every creation act was simultaneous.
I find it amusing that you use "Meyer" and "data" in the same sentence.
So, why do you think Meyer is so coy about what he thinks?

>> without ancestors goes away, since relationship implies
>> ancestors.
>
> Sure. Looks to me like you've been reading too many canards about
> Meyer without investigating his actual writings carefully enough.

We've been over this before. What things look like to you and what

actually happens are not closely related. I read the damn book. I'm not
sure you did.

Did you?

[nyi...@bellsouth.net]

On Thursday, October 9, 2014 11:17:46 PM UTC-4, John Harshman wrote:
> On 10/9/14, 7:56 PM, nyi...@bellsouth.net wrote:
> > On Thursday, October 9, 2014 6:42:48 PM UTC-4, John Harshman wrote:
> >> On 10/9/14, 3:16 PM, nyi...@bellsouth.net wrote:
> >>
> >>> On Thursday, October 9, 2014 10:36:26 AM UTC-4, John Harshman wrote:
> >>
> >>>> On 10/9/14, 7:03 AM, nyi...@bellsouth.net wrote:
> >
> > [about Richard Norman:
> >>> I wonder why he hasn't participated here yet--he opened my eyes to
> >>> just how ignorant it is possible for creationists [he dug up three
> >>> of them] to be and still to command a following.
> >
> >>> To say that these three thought there were no animals before the Cambrian
> >>> is only to scratch the surface of their ignorance. I'm afraid all
> >>> too many scientists, reading put-downs of Meyer by other scientists,
> >>> get the impression that he is no better than these infamous three.
> >
> >> I will agree that he is slightly better. Would that please you?
> >
> > That's like saying that Poul Anderson is a slightly better writer
> > of science fiction than Zenna Henderson. [Ms. Henderson is very good
> > at writing about human emotions, but her aptitude for science seems close
> > to zero in the "science fiction" stories of hers that I have read.]
> >
> > In case you haven't guessed, the answer to your question is No.
>
> You are constitutionally unable to make a point without insulting some
> third party not present, in this case Zenna Henderson.

First of all, that is such an outrageous hyperbole that it qualifies
as a bare-faced lie.

Secondly, you have NO inhibitions against MASSIVELY and repeatedly
insulting third parties not present, including Meyer and Feduccia.
And the research and publication and honors record of Feduccia
dwarfs yours, and he has impeccable "evolutionist" credentials,
but you treat him with contempt, as do Prum and Prothero.

Thirdly, you are moving the goalposts with:

> So we disagree on
> how much of a bozo Mr. Meyer has shown himself to be.

Fourthly, this outpouring of contempt dwarfs the "insult" I
delivered to Ms. Henderson. I even had some good words for
her, but I've seen nothing comparable from you about Meyer
or Feduccia.

Fifthly, you are being very revealing in your failure to analyze
my analogy. Someone less hell-bent on insulting Meyer AS A PERSON
might have cleverly said it was very apt, because Meyer's book is
pure science fiction on the same scientifically adept level as
Poul Anderson's science fiction.

And guess what? I would have largely agreed. It has massive amounts
of biological data [I won't make my sixth point something
you said about that, so you can relax] and lots of documentation
of opposing points of view, but his way of treating them is
rather one-sided and uses a legal-document format of the "the foregoing
clauses notwithstanding..." variety.

Sixthly and finally, I'm sure Erik Simpson will again attack me for
the way every thread I'm in sees a lowering of the signal-to-noise
ratio, but he ignores the role you and Erik himself play in that.

> >>> Meyer has never been shown to be the kind of "creation ex nihilo"
> >>> creationist that these three, and almost all other creationists, are.
> >>> For example, Meyer has never come out and claimed that trilobites
> >>> did not have biological ancestors; nor does he pretend to be staying
> >>> within the bounds of science when he states his personal belief
> >>> that God played a major hand in the Cambrian explosion--but his
> >>> friend Michael Behe believes this took the form of producing
> >>> a great many mutations spread out over a few million year's time,
> >>> and Meyer certainly isn't going to gainsay him.
> >
> >> Yes, Meyer does try to avoid saying anything about what he actually
> >> thinks happened.
> >
> > What Meyer privately believes and what he endorses when speaking *qua* ID
> > theorist are two utterly different things. We've been through this
> > MANY times before.
>
> Never while confronting reality, though. There is no such thing as an ID
> theorist.

That is a canard that is constantly promoted by innumerable scientists,
some writing in anthologies purporting to give a true picture
of the ID movement, and most of them using the question-begging
formula "ID creationism" and various minor paraphrasals.

Were Meyer to stoop so low, he would be doing what many hack
creationists do: denounce all evolution biologists as atheists.

Bottom line: All but the last chapter of _Darwin's Doubt_
is pure ID theory, using the methodology of science even when
talking about the far-out ideas of Dembski about complexity.
Were he to talk about them differently, he would be like Jonathan.

And everything you've written on this thread about that book
is worded in a way that grossly misleads anyone who hasn't
looked at it carefully into thinking that this book is utterly
different from what it is.

Even this:

> He's a creationist who wants to avoid public recognition of
> that fact.

He makes his personal beliefs pretty clear in the last chapter.
What ambiguity remains was being actively pooh-poohed by
Erik Simpson on this thread three hours before you posted this.

> > <snip rest of irrelevant comment>
> >
> >> But he can't avoid it altogether. His book makes no
> >> sense unless he's trying to show that trilobites had no ancestors.
> >
> > With this completely unsupported allegation, you have revealed just why
> > you completely ignored the actual issues Meyer is writing about in the
> > passage I quoted, as did Erik Simpson:
>
> Have you read the book? The whole book? His chapter on the fossil record
> makes it clear.

There are TWO chapters almost completely devoted to it. One on the
Burgess bestiary and one on the Chengliang fauna. [And he talks about
it in other chapters too.]

I've read those two chapters, word for word. Have you?

> If trilobites had ancestors, we would see them in the
> fossil record, and we don't.

Pure editorializing on your part, this last sentence.

You can brag all you want about having read "the damn book" [I've read
about half, word for word] but this thread shows that you've
carefully gathered the creationist chaff of the last chapter,
given it your own spin, and cast the wheat of the preceding
chapters to the winds.

Remainder deleted, to be dealt with next week. I have to carefully
ration my time for dealing with off-topic propaganda by you and others
to one a day (or less) per thread I'm involved in, starting today
and lasting until mid-November at the earliest.

So Erik, etc. will just have to post on-topic if they want special
treatment from me. They're mighty small fry compared to Big Fish
Harshman.

By the way, you may be tempted to pull your usual stunt of saying
"I see nothing in this post that deserves an answer," and deleting
everything in it, but I'm sure Erik Simpson would be able to see
through that if he bothered to read my post. The great unknown is
whether that would affect his treatment of you.

Peter Nyikos

[John Harshman]

I meant to say "gratuitously insulting". It is of course proper to
insult those whose work is the topic of conversation. But I don't treat
Feduccia with contempt. I treat his views with contempt, with good
reason. His publication record, honors, and credentials are irrelevant.
It's the quality of his arguments and ideas that matter.

> Thirdly, you are moving the goalposts with:
>
>> So we disagree on
>> how much of a bozo Mr. Meyer has shown himself to be.
>
> Fourthly, this outpouring of contempt dwarfs the "insult" I
> delivered to Ms. Henderson. I even had some good words for
> her, but I've seen nothing comparable from you about Meyer
> or Feduccia.
>
> Fifthly, you are being very revealing in your failure to analyze
> my analogy. Someone less hell-bent on insulting Meyer AS A PERSON
> might have cleverly said it was very apt, because Meyer's book is
> pure science fiction on the same scientifically adept level as
> Poul Anderson's science fiction.

No it isn't. The words "scientifically adept" can't properly be applied
to Meyer's work.

You mean "imitating, on a surface level, the methodology of science".

> And everything you've written on this thread about that book
> is worded in a way that grossly misleads anyone who hasn't
> looked at it carefully into thinking that this book is utterly
> different from what it is.
>
> Even this:
>
>> He's a creationist who wants to avoid public recognition of
>> that fact.
>
> He makes his personal beliefs pretty clear in the last chapter.
> What ambiguity remains was being actively pooh-poohed by
> Erik Simpson on this thread three hours before you posted this.

He makes a couple of beliefs clear but hides the rest, in particular
what he thinks actually happened in the Cambrian.

>>> <snip rest of irrelevant comment>
>>>
>>>> But he can't avoid it altogether. His book makes no
>>>> sense unless he's trying to show that trilobites had no ancestors.
>>>
>>> With this completely unsupported allegation, you have revealed just why
>>> you completely ignored the actual issues Meyer is writing about in the
>>> passage I quoted, as did Erik Simpson:
>>
>> Have you read the book? The whole book? His chapter on the fossil record
>> makes it clear.
>
> There are TWO chapters almost completely devoted to it. One on the
> Burgess bestiary and one on the Chengliang fauna. [And he talks about
> it in other chapters too.]
>
> I've read those two chapters, word for word. Have you?

Yes. His main point is that the fossil record can't be incomplete enough
to hide the ancestors of the Burgess and Chengjiang faunas. No ancestors.

>> If trilobites had ancestors, we would see them in the
>> fossil record, and we don't.
>
> Pure editorializing on your part, this last sentence.

It's his takehome message from the fossil chapter.

> You can brag all you want about having read "the damn book" [I've read
> about half, word for word] but this thread shows that you've
> carefully gathered the creationist chaff of the last chapter,
> given it your own spin, and cast the wheat of the preceding
> chapters to the winds.

Ah, so you haven't actually read the book. Thanks for admitting that.
And no, I'm pretty much ignoring the last chapter. Once again your
powers of discernment fail.

> Remainder deleted, to be dealt with next week. I have to carefully
> ration my time for dealing with off-topic propaganda by you and others
> to one a day (or less) per thread I'm involved in, starting today
> and lasting until mid-November at the earliest.
>
> So Erik, etc. will just have to post on-topic if they want special
> treatment from me. They're mighty small fry compared to Big Fish
> Harshman.
>
> By the way, you may be tempted to pull your usual stunt of saying
> "I see nothing in this post that deserves an answer," and deleting
> everything in it, but I'm sure Erik Simpson would be able to see
> through that if he bothered to read my post. The great unknown is
> whether that would affect his treatment of you.

So, was the point of your initial post to investigate a possible defense
of Meyer? Why did you bring him up?

[Mark Isaak]

On 10/9/14 7:56 PM, nyi...@bellsouth.net wrote:
> [big snip]

> I'm still a long way from deciding whether rank-free classification
> will actually tend to accentuate the unusualness of the Cambrian
> explosion. But I have decided that the examples given are quite
> plausible, e.g., that squids and clams may well represent different
> body plans.

Caterpillars and butterflies also may well represent different body
plans. Can you (or anyone) give any objective use for "body plan"
beyond basic phylogeny?

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Keep the company of those who seek the truth; run from those who have
found it." - Vaclav Havel

[erik simpson]

This is an outstanding example of a post where S/N tends to zero. And no, I'm
not taking your advice to use another newsreader. You don't need to expand the
previous material, since you wrote most of it yourself. Accusing me and others
of being off-topic is ludicrous in the light of your own contributions.

This isn't a thread about PunkEq, and it isn't even about the Cambrian
explosion. It seems that your principle interest is Meyers "as a person".
(I note the implausible appearance of Fudducia as well, presumably also as a
person.)

I don't have much interest in these topics, and even less interest in the
disingenuous efforts of those at the DI and their rear-guard defense of the
"god of the gaps", or other meddlesome deities.

[erik simpson]

On Thursday, October 9, 2014 6:01:14 PM UTC-7, nyi...@bellsouth.net wrote:
> On Thursday, October 9, 2014 6:26:28 PM UTC-4, erik simpson wrote:

> <..>

>
> By the way, do YOU have easier access to E & V yourself? If so, how
> about lending Harshman a hand in finding where they place the
> protostome-deuterostome split, and what molecular studies they
> are using as a basis?
>
>
> Peter Nyikos

I own a copy. It costs about as much as a tank of gas. The estimate given for
the P-D divergence is in the Cryogenian, around or somewhat before 700 Mya.
The primary reference is Erwin et. al.

http://www.sciencemag.org/content/334/6059/1091.full
(Science 25 November 2011: 1091-1097)

[John Harshman]

On 10/10/14, 9:46 AM, erik simpson wrote:

> This is an outstanding example of a post where S/N tends to zero. And no, I'm
> not taking your advice to use another newsreader.

If it's your newsreader that's putting in the extra lines, it would be
nice if you changed. Peter isn't wrong about everything. Not quite.

[Sneaky O. Possum]

John Harshman <jhar...@pacbell.net> wrote in
news:2KGdnYiVYbHIhKXJ...@giganews.com:

It's not his newsreader. In fact, it's not a newsreader at all: that's the
problem. Erik's posting from Google Groups.
--
S.O.P.

[jillery]

As has been pointed out many times before, GG users can't just change
their "newsreader". They have to also subscribe to a real newsserver
as well.

[John Harshman]

Agreed. There are however a number of free or very cheap news servers.
Mine is $2.99/month, well worth it just to get rid of the annoying line
returns.

[nyi...@bellsouth.net]

Sandwiched immediately between a post by Harshman and a post by Simpson,
both of which have zero signal to (aggressive) noise ratio, Mark comes
through with something on topic.

On Friday, October 10, 2014 12:21:51 PM UTC-4, Mark Isaak wrote:
> On 10/9/14 7:56 PM, nyi...@bellsouth.net wrote:
>
> > [big snip]
>
> > I'm still a long way from deciding whether rank-free classification
> > will actually tend to accentuate the unusualness of the Cambrian
> > explosion. But I have decided that the examples given are quite
> > plausible, e.g., that squids and clams may well represent different
> > body plans.

> Caterpillars and butterflies also may well represent different body
> plans. Can you (or anyone) give any objective use for "body plan"
> beyond basic phylogeny?

The difference in body plans actually may depend on the details
of the metamorphosis. When we compare the beginning with the end,
the difference seems large to our eyes, due to the change in
proportions of leg length to body size, the change in mouth parts,
and the addition of wings. But the wings do not involve internal
organs the way the wings of vertebrates do, and they are thus
better compared to the feathers of birds rather than to their wings.
And the other two changes don't involve really major changes in
body plan either.

And so, I would need to study the details of metamorphosis
carefully to come to a decision on this one way or the other.

Peter Nyikos

[jillery]

On Fri, 10 Oct 2014 13:11:09 -0700, John Harshman

That's an argument I have used, among others. The counter-arguments
given was that not everybody has access to a computer on which they
can install a newsreader, and I'm incredibly fucking stupid, and my
maternal ancestry is closely related to dogs.

I don't know if any of these points are relevant to Erik's situation.

[John Harshman]

This may become moot if Google really fixes that problem. (Most other
Google Groups problems are annoying only to those who post from it.)

[nyi...@bellsouth.net]

On Friday, October 10, 2014 3:54:12 PM UTC-4, jillery wrote:
> On Fri, 10 Oct 2014 10:37:23 -0700, John Harshman
> <jhar...@pacbell.net> wrote:

> >If it's your newsreader that's putting in the extra lines, it would be

> >nice if you changed. <snip derogatory comment>

> As has been pointed out many times before, GG users can't just change
> their "newsreader". They have to also subscribe to a real newsserver
> as well.

They may not have to subscribe to a newsserver (a.k.a. netserver).

If they have Thunderbird e-mail, they do not even have to use Thunderbird
to get NGG access. All the commands I told Erik about yesterday are
done in Thunderbird e-mail. But you don't send the e-mail; you just copy
what you pasted in your message, paste it in your New Google Groups
posting window, and cancel the e-mail message.

Here is the procedure:

highlight and
copy the text in the post to which you are replying, hit "Write" in
Thunderbird, click on the place where text is to be inserted,
right-click and select "Paste as Quotation," and it will put
a bright colored line to the left of the text you paste in.

Hit <enter> at the top to make sure there is an extra line
at the top of the text you've entered, copy the text below,
and you are good to go: when you paste the text in the Google window,
the bright colored line will be replaced by an extra column
of > symbols, and so attributions will be exactly the way they
should be. And the payoff is that there will be no blank
lines that weren't in the original.

Excerpted from:
https://groups.google.com/forum/#!original/talk.origins/pxU8DjYMuDQ/-MEgpPRtk2gJ
a direct reply to Erik Simpson.

Other e-mail clients may do the same, but Yahoo e-mail doesn't and
neither does Microsoft outlook e-mail the way these are set up for me.

As SOP pointed out, the extra lines are right there in Erik's messages,
and NGG is the culprit. Even when I use the Thunderbird e-mail trick,
those extra lines stay there--it's just that they aren't replaced by three.

Peter Nyikos

[John Harshman]

On 10/10/14, 6:43 AM, nyi...@bellsouth.net wrote:

> And the research and publication and honors record of Feduccia
> dwarfs yours, and he has impeccable "evolutionist" credentials,
> but you treat him with contempt, as do Prum and Prothero.

I have belatedly decided that this claim pisses me off enough to respond
to. I will match my research and publication record up against
Feduccia's any time. I personally doubt that you have read any
significant fraction of Feduccia's publications. Or mine. You have no
basis for comparison except, perhaps, raw numbers. I freely admit that
Feduccia has published more papers than I have. But I think I've made a
bigger contribution to science than he has.

None of this is at all relevant to anything we were talking about.

[jillery]

I see how that would work, but what an incredible amount of effort to
avoid not getting your own computer.

[nyi...@bellsouth.net]

On Thursday, October 9, 2014 1:44:27 PM UTC-4, John Harshman wrote:
> On 10/9/14, 10:35 AM, nyi...@bellsouth.net wrote:
>
> > On Wednesday, October 8, 2014 10:11:01 AM UTC-4, John Harshman wrote:
> >> On 10/8/14, 1:05 AM, alias Ernest Major wrote:

> >>> If someone wants to argue that the Cambrian Explosion represents
> >>> something unique in terms of the production of disparsity that someone
> >>> needs a more objective measure of disparity than taxonomic rank.

> >> Such as this: Lee et al., Rates of Phenotypic and Genomic Evolution
> >> during the Cambrian Explosion, Current Biology (2013)

> >> http://dx.doi.org/10.1016/j.cub.2013.07.055

> > I haven't had time to study it in detail, but it looks like
> > it is more about diversity (number of speciations) rather than
> > disparity (magnitude of morphological changes). Don't forget that
> > nuclear genes tell only part of the story; a lot depends on which
> > ones are expressed, and that has to do with the enzymes in the
> > cytoplasm of gametes.

> I'm sorry, but that paragraph just shows that you have no clue. It's
> about rates of molecular and morphological evolution (like the title
> says), not about speciations.

I said "more about diversity". Call it speciations, call it "number
of morphological and/or molecular changes," that is still diversity,
not disparity, which talks about the *magnitude* of the changes.

And these changes are strongly correlated. Each speciation involves
molecular changes, and the morphological changes we see in fossils
are what gives us clues about the number of speciations that might
have been involved.

> Nor do the enzymes (wouldn't call them
> enzymes; transcription factors would be the better term) in gametes
> (eggs, really) affect more than the very initial stages of gene
> expression, and so have only a small part to do with the big picture of
> developmental evolution.

Mitochondria (which code for some enzymes) and centrioles are inherited
from the the maternal oocyte (to give it its biological name) in all animals
that I know of. Also the lipid component in cell membranes in most animals, no?

> One might argue that the number of morphological character changes is a
> reasonable estimate of disparity. Would you disagree?

Yes. You would have to point to a place in that article where it is made
clear that these morphological and molecular changes are measured by
a standard that is very poorly correlated with speciations. Otherwise, the
following statistics are highly suggestive.

In one insect order, Coleoptera, there are about a quarter of all
known species of animals. In one family within that order, Staphylinidae,
there are about as many species as in all of Vertebrata:

Vertebrates, 62,305 according to this website:
http://www.currentresults.com/Environment-Facts/Plants-Animals/number-species.php

Staphylinidae, about 58,000 described species in about 3,200 genera:
http://en.wikipedia.org/wiki/Rove_beetle

Each rove beetle species has a distinct molecular genetic component
from all others. In all but a handful of cases, the difference
shows up in morphology. And yet the disparity in Vertebrata is
vastly greater.

Here I snipped a question about the molecular clock study Erwin and
Valentine used in their book. Erik Simpson answered it, and it turns
out to be the Science paper by Erwin et. al that I referenced:

> > Perhaps relevant: a recent paper, "Early vertebrate evolution"
> > by Philip C. J. Donoghue and Joseph N. Keating, which talks a lot about
> > molecular clocks and their wide variance of dates.
> > http://onlinelibrary.wiley.com/enhanced/doi/10.1111/pala.12125/

> > They cite a paper co-authored by Erwin and Peterson and a number of others
> > [but not Valentine, hence my smiley in my preceding post to this
> > thread] in talking about a diagram where they put the LCA of Chordata
> > all the way back in the Cryogenian:

> > "Node dates, where applicable, correspond with divergence estimates from
> > Erwin et al. (2011). Geological timescale based on Gradstein et al
> > (2012)."
> > ...
> > Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D.
> > and Peterson, K. J. 2011. The Cambrian conundrum: early divergence and later
> > ecological success in the early history of animals. Science, 334, 1091-1097.

Erik has provided us with the url:

http://www.sciencemag.org/content/334/6059/1091.full

No longer paywalled, only hoopwalled: you have to jump through hoops to
get free access, but at least the hoops are free.

> > Trivia: Donoghue and Keating write:
> > "*Haikouichthys* (Fig. 2K, and its likely junior synonym *Myllokunmingia*"

> > ...but Fig. 2K shows a very familiar picture which other sources
> > identify with a fossil of Myllokunmingia, [the type specimen, perhaps?]
> > whereas Donoghue and Keating caption says
> > "Haikouichthys ercaicunensis (YKLP (RCCBYU)-00195)"

> That's why it's a junior synonym, eh?

Not my point. If it is the type specimen of Haikouichthys ercaicunensis,
it should not have been labeled Myllokunmingia in the other sources
I have seen. On the other hand, if it is the type specimen of
Myllokunmingia then, in view of the "likely" qualifier, a differently
worded caption would have been in order.

That's enough quibbling for one post, so I decided not to quibble above
about what an enzyme is.

Peter Nyikos

[erik simpson]

On another thread I note that the bug is GG has been diagnosed, and supposedly
will be fixed. Until the, I'll try to be good. I'll be away for a while, which
will make it easier.

[John Harshman]

I'm afraid you're just digging a hole here. Speciation and the number of
evolutionary changes are not very well correlated at all. Speciation
involves a tiny number of molecular changes to a tiny number of genes.
Nor is the degree of morphological change at all correlated with the
degree of molecular change, except as both are sometimes roughly
correlated with time.

Yes, speciation in fossils is usually inferred from morphological
change, but that's a problem; it is in fact difficult to recognize
speciation in the fossil record.

Finally, the number of changes is a good estimate of the magnitude of
change.

>> Nor do the enzymes (wouldn't call them
>> enzymes; transcription factors would be the better term) in gametes
>> (eggs, really) affect more than the very initial stages of gene
>> expression, and so have only a small part to do with the big picture of
>> developmental evolution.
>
> Mitochondria (which code for some enzymes) and centrioles are inherited
> from the the maternal oocyte (to give it its biological name) in all animals
> that I know of. Also the lipid component in cell membranes in most animals, no?

Maternal inheritance of mitochondria is the rule for most, but not all,
taxa, but that's a trivial point. The number of genes in the
mitochondrion is tiny compared to the nuclear genome. Inheritance of
centrioles and lipids means about as much for evolution as the
inheritance of water molecules.

>> One might argue that the number of morphological character changes is a
>> reasonable estimate of disparity. Would you disagree?
>
> Yes. You would have to point to a place in that article where it is made
> clear that these morphological and molecular changes are measured by
> a standard that is very poorly correlated with speciations. Otherwise, the
> following statistics are highly suggestive.

Can't. Nor can I point out the place where it's made clear that they
aren't correlated with the phases of the moon or the price of cheese,
for similar reasons.

> In one insect order, Coleoptera, there are about a quarter of all
> known species of animals. In one family within that order, Staphylinidae,
> there are about as many species as in all of Vertebrata:
>
> Vertebrates, 62,305 according to this website:
> http://www.currentresults.com/Environment-Facts/Plants-Animals/number-species.php
>
> Staphylinidae, about 58,000 described species in about 3,200 genera:
> http://en.wikipedia.org/wiki/Rove_beetle
>
> Each rove beetle species has a distinct molecular genetic component
> from all others. In all but a handful of cases, the difference
> shows up in morphology. And yet the disparity in Vertebrata is
> vastly greater.

First off, that's your opinion, based on you being a vertebrate. Second,
you will note that the genetic disparity of Coleoptera is much greater
than that of vertebrates, which makes my point. Second, do you
understand that the total number of changes in a clade isn't at all what
Lee et al. are talking about, but the number of changes along a single
lineage?

That's wise of you.

[nyi...@bellsouth.net]

It turns out that the "Paste as Quotation" trick on Thunderbird e-mail
can be used more than once on the same text. I used it twice on the text
to which Erik was replying (back in my original post, before Erik let
NGG add extra lines in between any two original lines). I used
it once on the text Erik added, and the result is no unwanted lines below.

People who have no interest in how much integrity Erik has (either because
they don't care about integrity or because they are determined to wear
blinkers where "faithful team players" like Erik are concerned) might
as well stop reading here.

Erik himself might already be on posting break, but if so, I will let
him know about this post on his return.

<snip for focus>

>> Sixthly and finally, I'm sure Erik Simpson will again attack me for
>> the way every thread I'm in sees a lowering of the signal-to-noise

>> ratio, but he ignores the the role you and Erik himself play in that.

This prediction came true--all of it--in spades. See below, where
Erik bottom-posted.

<snip for focus>

>> Bottom line: All but the last chapter of _Darwin's Doubt_
>> is pure ID theory, using the methodology of science even when
>> talking about the far-out ideas of Dembski about complexity.
>> Were he to talk about them differently, he would be like Jonathan.
>>
>> And everything you've written on this thread about that book
>> is worded in a way that grossly misleads anyone who hasn't
>> looked at it carefully into thinking that this book is utterly
>> different from what it is.
>>
>> Even this:
>>
>> > He's a creationist who wants to avoid public recognition of
>> > that fact.
>>
>> He makes his personal beliefs pretty clear in the last chapter.
>> What ambiguity remains was being actively pooh-poohed by
>> Erik Simpson on this thread three hours before you posted this.

Erik didn't bother to address this, perhaps because he realizes
how wretchedly strained his pooh-poohing was but doesn't want
to face this fact.

<snip for focus>

>> By the way, you may be tempted to pull your usual stunt of saying
>> "I see nothing in this post that deserves an answer," and deleting
>> everything in it, but I'm sure Erik Simpson would be able to see
>> through that if he bothered to read my post. The great unknown is
>> whether that would affect his treatment of you.
>>
>> Peter Nyikos

And now we come to your added text, Erik:

> This is an outstanding example of a post where S/N tends to zero.

IOW, Harshman and I have gone from being on-topic to being off-topic
(both of us). So what? You are off-topic all through this post. I'd
say the majority of posts to talk.origins have a S/N ratio of zero,
including almost all pun cascades. Why do you bother making an
issue of this?

Now, what WOULD be significant would be the concept of a NEGATIVE
signal-to-noise ratio, which would give negative scores for
communicating things that are not. A sure way of doing that is
to post derogatory claims about someone that have no rational
basis.

Harshman thus racked up a negative S/N ratio in the post
to which I was replying. I maintain that my response has a zero
score, being off topic but having a rational basis for everything
I wrote. At least, you made no attempt to rebut anything I wrote,
nor to buttress anything Harshman had written.

In your first direct reply to me on this thread, you racked up
a high negative score (close to -1, in fact) by ignoring the
on-topic issues in a quote I did. Instead, the fact that the
quote was from _Darwin's Doubt_ made you see red and something
akin to xenophobia set in. The resulting tirade against me
had no basis in reality. [I also said some things mildly favorable
to _Darwin's Doubt_, but you never contested them.]

> And no, I'm
> not taking your advice to use another newsreader.

I never gave you that advice; my advice works for anyone who has
Thunderbird e-mail. If you don't have it, all you had to do
was say so, and I wouldn't have even brought it up on this thread.

By the way, it took me only a minute or two to apply my Thunderbird
"Paste as Quotation" trick twice to the post to which you are replying.
Voila! no unwanted blank lines (but a wanted double column of > marks)
even though your own post had every other line there blank.

> You don't need to expand the
> previous material, since you wrote most of it yourself. Accusing me and others
> of being off-topic is ludicrous in the light of your own contributions.

Strange use of value-loaded words. You might as well say "it is ludicrous to
accuse me and others of posting to talk.origins."

Had you stopped here, I would have let you off by saying your S/N ratio
in this post was zero. But now you resume your xenophobic tirade
against me, sending it well below zero according to my suggested
concept:

> This isn't a thread about PunkEq, and it isn't even about the Cambrian
> explosion.

+++++++++++++++++++ sarcasm on
No, it is about enabling you and Harshman to display your dishonesty,
hypocrisy, and hostility. And you have taken full advantage of it.
+++++++++++++++++++ sarcasm off

> It seems that your principle interest is Meyers "as a person".
> (I note the implausible appearance of Fudducia as well, presumably also as a
> person.)

You are just sore because I showed (see above) how hypocritical Harshman
was in criticizing me for insults of absent people.

> I don't have much interest in these topics,

The Cambrian explosion and PunkEq? You certainly have shown
less interest on this thread in them than in attacking me and Myers.

> and even less interest in the
> disingenuous efforts of those at the DI and their rear-guard defense of the
> "god of the gaps", or other meddlesome deities.

If that were all _Darwin's Doubt_ were good for, I'd say this last
comment was on-topic. As it is, it hardly affects your
negative S/N ratio for this post at all.

Peter Nyikos

[nyi...@bellsouth.net]

On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:

> > Even if the Cambrian explosion
> > took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
> > Valentine put it [Do you have easy access to that book? I don't.]
>
> I do.

Can you recall whether it addresses any of the three ideas you mentioned
(and reposted on, from something you wrote about two decades ago?) for
explaining the uniqueness of the Cambrian explosion?

I'd ask Erik Simpson, who owns a copy, but he's probably on posting break.
By the way, Erik came through with the information on what E&V had said
about the date of the protostome-deuterostome split, and provided their
source: a 2011 paper co-authored by Erwin which just might reflect
the state of the art [and the word "art" is not out of place,
even though there is a lot of science involved] on molecular dating.

> > it's a pretty darn "grand scale punctuation" compared to the
> > preceding ca. 2.9gy and the subsequent ca. 0.52 gy.
>
> I'm assuming you realize this has nothing at all to do with punctuated
> equilibria. Correct?

The Gould and Eldredge concept, basically correct. To minimize confusion
I'll be using the term "PE writ large" from now on.

> You have borrowed a name and attached it to
> something else.

So what?

> Now, what you have is somewhat similar to the concept in
> paleontology of coordinated stasis, but only somewhat.

Where's the difference? By the way, is there a term for what
might be called "huge numbers of correlated punctuations"?

"An explosion"? Nah, that invites amendments like "a slow fuse."

> > IIRC I had forgotten about the early date of that 2004 analysis
> > when I told you about it in that Prothero "skeptic"blog.
> > Remember how I criticized its choice of taxa?
> >
> > It omitted both chaetognaths (which anatomists class as
> > deuterostomes, molecular biologists as protostomes) and acoelous
> > flatworms, whose LCA with us probably predates the protostome-deuterostome
> > split. Prothero, or one of his toadies, axed our whole discussion
> > and Prothero never told his fans where he got that 80 million year
> > figure or even what the starting point was as far as the tree of
> > eumetazoans goes.
> >
> > However, since I know next to nothing about molecular clock methods,
> > I'm not sure how this affects the timing of the protostome-deuterostome
> > split. Not at all (I think) if chaetognaths predate the split, but
> > perhaps significantly if they are incorporated into calculating
> > the split.
> >
> > What does your knowledge of molecular clock methods tell you?
>
> If you just told me where you were trying to go, I would know what would
> be relevant to talk about.

You did a pretty good job below without needing to know that I have been
trying to learn what the best source is for dating of various Precambrian
events. All you need to know here is that I didn't have the E&V source
in my hands at the time I wrote the earlier things, so I hadn't
read what turned out to be their source all along.

Now I have read enough to note that it, too, leaves out those two taxa,
which might affect their results to some extent.

> There are potential reasons for leaving
> certain taxa out and potential reasons to put certain other taxa in. One
> way to attempt to improve accuracy is to remove taxa with unusually high
> evolutionary rates, and another way is to insert taxa that break up long
> branches. I believe that acoel flatworms fall into the first category.

That's assuming they are descended from more "advanced" organisms,
doesn't it? [If "more advanced" means nothing to you, despite its
clear morphological connotations, try "in a clade within one of the
known classes of one protostome phylum."]

>I don't know about chaetognaths; but as you say their position is unclear.

Yes, but if they split off before the protostome-deuterostome split,
that would probably affect the dating of the LCA of bilateria.
The only way to find out for sure is to include them in some
future analysis.

Peter Nyikos
Professor, Dept. of Math., -- standard disclaimer --
University of South Carolina at Columbia

[John Harshman]

On 10/13/14, 6:58 AM, nyi...@bellsouth.net wrote:
> On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
>> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
>
>>> Even if the Cambrian explosion
>>> took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
>>> Valentine put it [Do you have easy access to that book? I don't.]
>>
>> I do.
>
> Can you recall whether it addresses any of the three ideas you mentioned
> (and reposted on, from something you wrote about two decades ago?) for
> explaining the uniqueness of the Cambrian explosion?

It does.

> I'd ask Erik Simpson, who owns a copy, but he's probably on posting break.
> By the way, Erik came through with the information on what E&V had said
> about the date of the protostome-deuterostome split, and provided their
> source: a 2011 paper co-authored by Erwin which just might reflect
> the state of the art [and the word "art" is not out of place,
> even though there is a lot of science involved] on molecular dating.

Yes, I'd say it does, more or less. The import is that molecular and
fossil dates have converged.

>>> it's a pretty darn "grand scale punctuation" compared to the
>>> preceding ca. 2.9gy and the subsequent ca. 0.52 gy.
>>
>> I'm assuming you realize this has nothing at all to do with punctuated
>> equilibria. Correct?
>
> The Gould and Eldredge concept, basically correct. To minimize confusion
> I'll be using the term "PE writ large" from now on.
>
>> You have borrowed a name and attached it to
>> something else.
>
> So what?

That's likely to cause confusion.

>> Now, what you have is somewhat similar to the concept in
>> paleontology of coordinated stasis, but only somewhat.
>
> Where's the difference? By the way, is there a term for what
> might be called "huge numbers of correlated punctuations"?
>
> "An explosion"? Nah, that invites amendments like "a slow fuse."

There is no technical term that I know of, though it's more or less the
corollary to coordinated stasis. But what exactly do you mean by
"punctuation" here? You probably aren't referring to speciation.

Why?

>> There are potential reasons for leaving
>> certain taxa out and potential reasons to put certain other taxa in. One
>> way to attempt to improve accuracy is to remove taxa with unusually high
>> evolutionary rates, and another way is to insert taxa that break up long
>> branches. I believe that acoel flatworms fall into the first category.
>
> That's assuming they are descended from more "advanced" organisms,
> doesn't it? [If "more advanced" means nothing to you, despite its
> clear morphological connotations, try "in a clade within one of the
> known classes of one protostome phylum."]

No. It assumes they have unusually high evolutionary rates of molecular
evolution. Nothing more.

>> I don't know about chaetognaths; but as you say their position is unclear.
>
> Yes, but if they split off before the protostome-deuterostome split,
> that would probably affect the dating of the LCA of bilateria.
> The only way to find out for sure is to include them in some
> future analysis.

Ah, I see what you were trying (unsuccessfully) to get at. What you mean
has nothing to do with the accuracy of dating particular nodes but with
the correctness of which node to attach the name "Bilateria" to. Yes, if
you leave out bilaterians that are outside protostomes and
deuterostomes, you will be dating the wrong node. The question is
whether that node is good enough for your purposes.

[nyi...@bellsouth.net]

On Monday, October 13, 2014 12:34:45 PM UTC-4, John Harshman wrote:

> On 10/13/14, 6:58 AM, nyi...@bellsouth.net wrote:
> > On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
> >> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
> >
> >>> Even if the Cambrian explosion
> >>> took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
> >>> Valentine put it [Do you have easy access to that book? I don't.]
> >>
> >> I do.
> >
> > Can you recall whether it addresses any of the three ideas you mentioned
> > (and reposted on, from something you wrote about two decades ago?) for
> > explaining the uniqueness of the Cambrian explosion?
>
> It does.

So why didn't you mention this when you gave 1), 2) and 3) in your last
Oct 7 post, nor when you reposted that long post from two decades ago
on Oct 8 about 1), 2) and 3)?
And what is stopping you from summarizing what it says about these
three ideas now?

> > I'd ask Erik Simpson, who owns a copy, but he's probably on posting break.
> > By the way, Erik came through with the information on what E&V had said
> > about the date of the protostome-deuterostome split, and provided their
> > source: a 2011 paper co-authored by Erwin which just might reflect
> > the state of the art [and the word "art" is not out of place,
> > even though there is a lot of science involved] on molecular dating.
>
> Yes, I'd say it does, more or less. The import is that molecular and
> fossil dates have converged.

Have you actually looked at the article? On the one hand, both the
cephalochordate-urochordate&vertebrate split, and the
lophotrochozoan-ecdysozoan split took place BEFORE the beginning
of the Ediacaran (ca. 635 Ma) according to them.
On the other hand, we get this:

"Numerous eukaryotic taxa, including the first example of
multicellularity with complex development (24), are represented
in rocks assigned to the later (i.e., <580 Ma) Ediacaran Period.
Among these fossils should be organisms that can be unambiguously
assigned to the Metazoa and to more inclusive lineages
(e.g., Bilateria), but mostly these fossils are enigmatic
and lineages with diagnostic bilaterian apomorphies have
not been identified."

http://www.sciencemag.org/content/334/6059/1091.full

Are you usually this <ahem> reliable about what your sources say?

> >>> it's a pretty darn "grand scale punctuation" compared to the
> >>> preceding ca. 2.9gy and the subsequent ca. 0.52 gy.
> >>
> >> I'm assuming you realize this has nothing at all to do with punctuated
> >> equilibria. Correct?
> >
> > The Gould and Eldredge concept, basically correct. To minimize confusion
> > I'll be using the term "PE writ large" from now on.

Or, rarely, "Punctuated Equilibrium writ large," or more commonly
"PuncEq writ large." [I dislike the expression "Punk Eek."

<snip>

> >> There are potential reasons for leaving
> >> certain taxa out and potential reasons to put certain other taxa in. One
> >> way to attempt to improve accuracy is to remove taxa with unusually high
> >> evolutionary rates, and another way is to insert taxa that break up long
> >> branches. I believe that acoel flatworms fall into the first category.
> >
> > That's assuming they are descended from more "advanced" organisms,
> > doesn't it? [If "more advanced" means nothing to you, despite its
> > clear morphological connotations, try "in a clade within one of the
> > known classes of one protostome phylum."]
>
> No. It assumes they have unusually high evolutionary rates of molecular
> evolution. Nothing more.

And how do we know that? Anyway, do you think it would also affect
the topology of the phylogenetic tree?

> >> I don't know about chaetognaths; but as you say their position is unclear.
> >
> > Yes, but if they split off before the protostome-deuterostome split,
> > that would probably affect the dating of the LCA of bilateria.
> > The only way to find out for sure is to include them in some
> > future analysis.
>
> Ah, I see what you were trying (unsuccessfully) to get at. What you mean
> has nothing to do with the accuracy of dating particular nodes but with
> the correctness of which node to attach the name "Bilateria" to. Yes, if
> you leave out bilaterians that are outside protostomes and
> deuterostomes, you will be dating the wrong node. The question is
> whether that node is good enough for your purposes.

My purposes in this post are, presumably, yours as well: to get a
really clear picture of both the phylogeny and the dating. Since
sci.bio.paleontology has been essentially destroyed by you-know-who,
this is the best place for doing it.

Once we get back to 1), 2) and 3) my purposes become broader,
and I've been quite forthright about them in the post to which
you replied when you listed 1), 2) and 3).

Peter Nyikos
Professor, Dept. of Math. -- standard disclaimer --
U of South Carolina

[John Harshman]

On 10/14/14, 12:57 PM, nyi...@bellsouth.net wrote:
> On Monday, October 13, 2014 12:34:45 PM UTC-4, John Harshman wrote:
>
>> On 10/13/14, 6:58 AM, nyi...@bellsouth.net wrote:
>>> On Monday, October 6, 2014 7:17:25 PM UTC-4, John Harshman wrote:
>>>> On 10/6/14, 2:42 PM, nyi...@bellsouth.net wrote:
>>>
>>>>> Even if the Cambrian explosion
>>>>> took 0.08 gy as Prothero put it, or a bit over 0.1gy as Erwin and
>>>>> Valentine put it [Do you have easy access to that book? I don't.]
>>>>
>>>> I do.
>>>
>>> Can you recall whether it addresses any of the three ideas you mentioned
>>> (and reposted on, from something you wrote about two decades ago?) for
>>> explaining the uniqueness of the Cambrian explosion?
>>
>> It does.
>
> So why didn't you mention this when you gave 1), 2) and 3) in your last
> Oct 7 post, nor when you reposted that long post from two decades ago
> on Oct 8 about 1), 2) and 3)?
> And what is stopping you from summarizing what it says about these
> three ideas now?

Nothing more than a disinclination to bother. Better you should buy a
copy. Anyone interested in the Cambrian explosion should really have
that book.

>>> I'd ask Erik Simpson, who owns a copy, but he's probably on posting break.
>>> By the way, Erik came through with the information on what E&V had said
>>> about the date of the protostome-deuterostome split, and provided their
>>> source: a 2011 paper co-authored by Erwin which just might reflect
>>> the state of the art [and the word "art" is not out of place,
>>> even though there is a lot of science involved] on molecular dating.
>>
>> Yes, I'd say it does, more or less. The import is that molecular and
>> fossil dates have converged.
>
> Have you actually looked at the article? On the one hand, both the
> cephalochordate-urochordate&vertebrate split, and the
> lophotrochozoan-ecdysozoan split took place BEFORE the beginning
> of the Ediacaran (ca. 635 Ma) according to them.
> On the other hand, we get this:
>
> "Numerous eukaryotic taxa, including the first example of
> multicellularity with complex development (24), are represented
> in rocks assigned to the later (i.e., <580 Ma) Ediacaran Period.
> Among these fossils should be organisms that can be unambiguously
> assigned to the Metazoa and to more inclusive lineages
> (e.g., Bilateria), but mostly these fossils are enigmatic
> and lineages with diagnostic bilaterian apomorphies have
> not been identified."
>
> http://www.sciencemag.org/content/334/6059/1091.full
>
> Are you usually this <ahem> reliable about what your sources say?

I may possibly have misremembered. Or you may be misinterpreting. It's
possible I will take another look. But you have to consider that several
prior estimates ran back before a billion years.

>>>>> it's a pretty darn "grand scale punctuation" compared to the
>>>>> preceding ca. 2.9gy and the subsequent ca. 0.52 gy.
>>>>
>>>> I'm assuming you realize this has nothing at all to do with punctuated
>>>> equilibria. Correct?
>>>
>>> The Gould and Eldredge concept, basically correct. To minimize confusion
>>> I'll be using the term "PE writ large" from now on.
>
> Or, rarely, "Punctuated Equilibrium writ large," or more commonly
> "PuncEq writ large." [I dislike the expression "Punk Eek."

I think any use of the term displays a distorted understanding of what
it means and of the phenomenon you're trying to describe.

>>>> There are potential reasons for leaving
>>>> certain taxa out and potential reasons to put certain other taxa in. One
>>>> way to attempt to improve accuracy is to remove taxa with unusually high
>>>> evolutionary rates, and another way is to insert taxa that break up long
>>>> branches. I believe that acoel flatworms fall into the first category.
>>>
>>> That's assuming they are descended from more "advanced" organisms,
>>> doesn't it? [If "more advanced" means nothing to you, despite its
>>> clear morphological connotations, try "in a clade within one of the
>>> known classes of one protostome phylum."]
>>
>> No. It assumes they have unusually high evolutionary rates of molecular
>> evolution. Nothing more.
>
> And how do we know that? Anyway, do you think it would also affect
> the topology of the phylogenetic tree?

One infers rates of evolution from a tree. Long branches do indeed have
the potential to affect the topology of the tree. Whether they do in any
particular case is a matter for analysis.

>>>> I don't know about chaetognaths; but as you say their position is unclear.
>>>
>>> Yes, but if they split off before the protostome-deuterostome split,
>>> that would probably affect the dating of the LCA of bilateria.
>>> The only way to find out for sure is to include them in some
>>> future analysis.
>>
>> Ah, I see what you were trying (unsuccessfully) to get at. What you mean
>> has nothing to do with the accuracy of dating particular nodes but with
>> the correctness of which node to attach the name "Bilateria" to. Yes, if
>> you leave out bilaterians that are outside protostomes and
>> deuterostomes, you will be dating the wrong node. The question is
>> whether that node is good enough for your purposes.
>
> My purposes in this post are, presumably, yours as well: to get a
> really clear picture of both the phylogeny and the dating. Since
> sci.bio.paleontology has been essentially destroyed by you-know-who,
> this is the best place for doing it.
>
> Once we get back to 1), 2) and 3) my purposes become broader,
> and I've been quite forthright about them in the post to which
> you replied when you listed 1), 2) and 3).

I'm not sure your purposes are actually as forthright as you maintain.
How did Stephen Meyer enter the conversation, for example?

[nyi...@bellsouth.net]

On Tuesday, October 14, 2014 4:32:36 PM UTC-4, John Harshman wrote:
> On 10/14/14, 12:57 PM, nyi...@bellsouth.net wrote:
> > On Monday, October 13, 2014 12:34:45 PM UTC-4, John Harshman wrote:
> >> On 10/13/14, 6:58 AM, nyi...@bellsouth.net wrote:

> >>> By the way, Erik came through with the information on what E&V had said
> >>> about the date of the protostome-deuterostome split, and provided their
> >>> source: a 2011 paper co-authored by Erwin which just might reflect
> >>> the state of the art [and the word "art" is not out of place,
> >>> even though there is a lot of science involved] on molecular dating.

Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D.
and Peterson, K. J. 2011. The Cambrian conundrum: early divergence
and later ecological success in the early history of animals.
Science, 334, 1091-1097.

> >> Yes, I'd say it does, more or less. The import is that molecular and
> >> fossil dates have converged.
> >
> > Have you actually looked at the article? On the one hand, both the
> > cephalochordate-urochordate&vertebrate split, and the
> > lophotrochozoan-ecdysozoan split took place BEFORE the beginning
> > of the Ediacaran (ca. 635 Ma) according to them.
> > On the other hand, we get this:
> >
> > "Numerous eukaryotic taxa, including the first example of
> > multicellularity with complex development (24), are represented
> > in rocks assigned to the later (i.e., <580 Ma) Ediacaran Period.
> > Among these fossils should be organisms that can be unambiguously
> > assigned to the Metazoa and to more inclusive lineages
> > (e.g., Bilateria), but mostly these fossils are enigmatic
> > and lineages with diagnostic bilaterian apomorphies have
> > not been identified."
> >
> > http://www.sciencemag.org/content/334/6059/1091.full
> >
> > Are you usually this <ahem> reliable about what your sources say?
>
> I may possibly have misremembered. Or you may be misinterpreting.

There is NO WAY I could have misinterpreted Figure 1
on those two splits:

http://www.sciencemag.org/content/334/6059/1091/F1.large.jpg

The first split is especially far back, and very close to the
protostome-deuterostome split [ca. 675 Ma, see Figure 3].
It makes for Chordata being a "ghost taxon" for well over
100 million years.

>It's possible I will take another look.

Here is something to spur you along. What I quoted on fossils is
of a negative sort; the positive information further heightens
the discrepancy:

"A recompilation (SOM text 1 and table S1) of the first
occurrences of all metazoan phyla, classes, and stem-classes
(extinct clades) of equivalent morphologic disparity
(Fig. 2, D and E) shows their first occurrences in the
latest Ediacaran (by 555 Ma), with a dramatic rise over
about 25 million years in the first several stages of
the Cambrian, and continuing into the Ordovician
(Figs. 1 and 3 and table S3).
...
Definitive evidence for the presence of bilaterian
animals in the Ediacaran comes from surficial trace fossils.
Putative trace fossils have been reported from 565 Ma (42),
but otherwise most are found in rocks <560 Ma (6, 43)."

> But you have to consider that several
> prior estimates ran back before a billion years.

In contrast, a paper seven years earlier, whose lead author is
a co-author of the 2011 paper, showed how one could estimate a 573 Ma
protostome-deuterostome split (but also, at the opposite extreme,
a 653Ma split, still noticeably after the estimate in the 2011 paper):

Kevin J. Peterson, Jessica B. Lyons, Kristin S. Nowak, Carter M. Takacs,
Matthew J. Wargo, and Mark A. McPeek,
"Estimating metazoan divergence times with a molecular clock,"
Proc. Natl Acad. Sci. USA. 2004;101:6536--6541.

http://www.pnas.org/content/101/17/6536.long

From Peterson's POV, the 2011 paper features DIvergence, not CONvergence
of the molecular estimates and fossil records from "prior estimates".
As I remarked in my second post to this thread, he stuck by his
"prior estimates" in:

"The Ediacaran emergence of bilaterians: congruence between
the genetic and the geological fossil records"
Kevin J Peterson, James A Cotton, James G Gehling, and Davide Pisani,
Philos Trans R Soc Lond B Biol Sci. Apr 27, 2008; 363(1496): 1435--1443.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614224/

Note that this 2008 paper and the 2011 paper had another
co-author, Pisani.

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

[John Harshman]

Yes. Please, when quoting, add your own interpretation of what point you
are making. It may have been the 2004 paper I was thinking of, not the
2011 one. There are clearly difficulties in calibrating molecular
clocks, and these grow larger as we approach the root.

The figure you show is a point estimate. Better to consider the
confidence intervals, which I see appear only in the supplemental
information ("database S2"). It isn't exactly clear which of the 36
different analyses Fig. 1 (and therefore Fig. 3) is based on, but for
the one that seems to come closest to the date given for Bilateria, the
point estimate is 670ma, with 95% confidence limits 640-755. Some other
analyses put the point estimate as low as 656ma, with confidence limits
632-798. Still, there seems a significant gap between bilaterian
divergence point and first fossil evidence.

So, what lesson from this? Either the molecular time-calibration
analysis is overestimating the age of some nodes or there are some
substantial ghost lineages. Do you see a third alternative?

[John Harshman]

I should point out that there is at least one hypothesis to explain the
long ghost lineages: Butterfield, N. J. 1994. Secular distribution of
Burgess‐Shale‐type preservation. Lethaia 28: 1-13.

ABSTRACT Burgess-Shale-type preservation is defined as a taphonomic
pathway involving the exceptional organic preservation of
non-mineralizing organisms in fully marine siliciclastic sediments. In
the Phanerozoic it occurs widely in Lower and Middle Cambrian sequences
but subsequently disappears as a significant taphonomic mode. The
hypothesis that this distribution derives solely from a secular increase
in the depth of bioturbation is falsified: low bioturbation indices do
not prevent the rapid enzymatic degradation of organic structure, nor do
they account for the conspicuous absence of comparable preservation
during the Vendian. An earlier, Late Riphean (ca. 750–850 Ma), interval
of enhanced organic-walled fossil preservation suggests a long-term
recurrence in Burgess-Shale-type taphonomy that is independent of
metazoan activity. A model based on the potentially powerful
anti-enzymatic and/or stabilizing effects of clay minerals on organic
molecules is proposed to account for Burgess-Shale-type preservation.
Long-term changes in average clay mineralogies and the ocean chemistry
that determines their interaction with organic molecules are likely to
have induced the pronounced secular distribution of these fossil biotas,
while regional variations in tectonism, weathering, etc., explain their
non-uniform geographic distribution; the close correlation between
exceptional, organic-walled fossil preservation and volcano-genic
sedimentation in Tertiary lake deposits provides a compelling analogue.
Recognition of a temporal control on Burgess-Shale-type preservation
constrains the evolutionary scenarios that can be drawn from such
biotas; significantly, neither the initial rate of appearance, nor the
ultimate fate of Burgess-Shale-type taxa can be directly assessed.

[nyi...@bellsouth.net]

On Wednesday, October 15, 2014 11:35:41 AM UTC-4, John Harshman wrote:
> On 10/15/14, 6:28 AM, nyi...@bellsouth.net wrote:
> > On Tuesday, October 14, 2014 4:32:36 PM UTC-4, John Harshman wrote:

> - hide quoted text -

> >> On 10/14/14, 12:57 PM, nyi...@bellsouth.net wrote:
> >>> On Monday, October 13, 2014 12:34:45 PM UTC-4, John Harshman wrote:
> >>>> On 10/13/14, 6:58 AM, nyi...@bellsouth.net wrote:
> >
> >>>>> By the way, Erik came through with the information on what E&V had said
> >>>>> about the date of the protostome-deuterostome split, and provided their
> >>>>> source: a 2011 paper co-authored by Erwin which just might reflect
> >>>>> the state of the art [and the word "art" is not out of place,
> >>>>> even though there is a lot of science involved] on molecular dating.
> >
> > Erwin, D. H., Laflamme, M., Tweedt, S. M., Sperling, E. A., Pisani, D.
> > and Peterson, K. J. 2011. The Cambrian conundrum: early divergence
> > and later ecological success in the early history of animals.
> > Science, 334, 1091-1097.
> >
> >>>> Yes, I'd say it does, more or less. The import is that molecular and
> >>>> fossil dates have converged.

NOTE that even before I gave the full reference, I specifically said
it was a 2011 paper, and I used the expression "co-authored by Erwin".

NOTE also your agreement (more or less) with it being state of the
art.

> >>> Have you actually looked at the article? On the one hand, both the
> >>> cephalochordate-urochordate&vertebrate split, and the
> >>> lophotrochozoan-ecdysozoan split took place BEFORE the beginning
> >>> of the Ediacaran (ca. 635 Ma) according to them.
> >>> On the other hand, we get this:
> >>>
> >>> "Numerous eukaryotic taxa, including the first example of
> >>> multicellularity with complex development (24), are represented
> >>> in rocks assigned to the later (i.e., <580 Ma) Ediacaran Period.
> >>> Among these fossils should be organisms that can be unambiguously
> >>> assigned to the Metazoa and to more inclusive lineages
> >>> (e.g., Bilateria), but mostly these fossils are enigmatic
> >>> and lineages with diagnostic bilaterian apomorphies have
> >>> not been identified."
> >>>
> >>> http://www.sciencemag.org/content/334/6059/1091.full
> >>>
> >>> Are you usually this <ahem> reliable about what your sources say?
> >>
> >> I may possibly have misremembered. Or you may be misinterpreting.
> >
> > There is NO WAY I could have misinterpreted Figure 1
> > on those two splits:
> >
> > http://www.sciencemag.org/content/334/6059/1091/F1.large.jpg

<snip for focus>

> >> But you have to consider that several
> >> prior estimates ran back before a billion years.
> >
> > In contrast, a paper seven years earlier, whose lead author is
> > a co-author of the 2011 paper, showed how one could estimate a 573 Ma
> > protostome-deuterostome split (but also, at the opposite extreme,
> > a 653Ma split, still noticeably after the estimate in the 2011 paper):
> >
> > Kevin J. Peterson, Jessica B. Lyons, Kristin S. Nowak, Carter M. Takacs,
> > Matthew J. Wargo, and Mark A. McPeek,
> > "Estimating metazoan divergence times with a molecular clock,"
> > Proc. Natl Acad. Sci. USA. 2004;101:6536--6541.
> >
> > http://www.pnas.org/content/101/17/6536.long

NOTE that Erwin was not a co-author.

> > From Peterson's POV, the 2011 paper features DIvergence, not CONvergence
> > of the molecular estimates and fossil records from "prior estimates".
> > As I remarked in my second post to this thread, he stuck by his
> > "prior estimates" in:
> >
> > "The Ediacaran emergence of bilaterians: congruence between
> > the genetic and the geological fossil records"
> > Kevin J Peterson, James A Cotton, James G Gehling, and Davide Pisani,
> > Philos Trans R Soc Lond B Biol Sci. Apr 27, 2008; 363(1496): 1435--1443.
> >
> > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614224/
> >
> > Note that this 2008 paper and the 2011 paper had another
> > co-author, Pisani.
>
> Yes. Please, when quoting, add your own interpretation of what point you
> are making.

I refuse to do what my grade school and high school teachers called
"spoon-feeding." The point was crystal clear: I was disputing your
claim,

"The import is that molecular and
fossil dates have converged."

> It may have been the 2004 paper I was thinking of, not the
> 2011 one.

Scroll back up to the three places where I wrote "NOTE" in caps.
Would your 7th grade teacher have allowed you to get away
with such an excuse?

A pattern is beginning to emerge: when you are in a tight spot,
you preface unreasonable "requests" with "Please." Other times,
you treat me with an attitude many if not most whites in the
Jim Crow South had towards "uppity" blacks.

> There are clearly difficulties in calibrating molecular
> clocks, and these grow larger as we approach the root.
>
> The figure you show is a point estimate. Better to consider the
> confidence intervals, which I see appear only in the supplemental
> information ("database S2"). It isn't exactly clear which of the 36
> different analyses Fig. 1 (and therefore Fig. 3) is based on, but for
> the one that seems to come closest to the date given for Bilateria, the
> point estimate is 670ma, with 95% confidence limits 640-755.

640 is barely below the UPPER limit in that 2004 paper of 653.

> Some other
> analyses put the point estimate as low as 656ma, with confidence limits
> 632-798. Still, there seems a significant gap between bilaterian
> divergence point and first fossil evidence.

And it will seem that way for a long time, unless new Lagerstatten
are found in the Ediacaran. More about this in my reply to your
other post so far today.

> So, what lesson from this? Either the molecular time-calibration
> analysis is overestimating the age of some nodes or there are some
> substantial ghost lineages. Do you see a third alternative?

Nope. Do you?

Peter Nyikos

[John Harshman]

On 10/15/14, 10:36 AM, nyi...@bellsouth.net wrote:

Allow me to snip the childish point-scoring.

>> Some other
>> analyses put the point estimate as low as 656ma, with confidence limits
>> 632-798. Still, there seems a significant gap between bilaterian
>> divergence point and first fossil evidence.
>
> And it will seem that way for a long time, unless new Lagerstatten
> are found in the Ediacaran. More about this in my reply to your
> other post so far today.
>
>> So, what lesson from this? Either the molecular time-calibration
>> analysis is overestimating the age of some nodes or there are some
>> substantial ghost lineages. Do you see a third alternative?
>
> Nope. Do you?

No. Do you have an opinion on which is more likely?

[Mitchell Coffey]

On 10/15/2014 1:36 PM, nyi...@bellsouth.net wrote:
> On Wednesday, October 15, 2014 11:35:41 AM UTC-4, John Harshman wrote:

[snip]

>> It may have been the 2004 paper I was thinking of, not the
>> 2011 one.
>
> Scroll back up to the three places where I wrote "NOTE" in caps.
> Would your 7th grade teacher have allowed you to get away
> with such an excuse?
>
> A pattern is beginning to emerge: when you are in a tight spot,
> you preface unreasonable "requests" with "Please." Other times,
> you treat me with an attitude many if not most whites in the
> Jim Crow South had towards "uppity" blacks.

You mean he shotguns you and buries you under a levee?

Mitchell Coffey

[nyi...@bellsouth.net]

Don't be ridiculous. Only a tiny fraction of whites participated
in lynchings. Did the "many if not most whites" not register
somehow?

Here is an example right on this thread where he treated
something I wrote as if I were being "uppity."

________________excerpt from a reply by John to me____________

> However, I will NOT jump to the conclusion that Peterson et. al's figures
> are correct and Blair and Hedges's incorrect, not with so many other
> estimates out there, such as Erwin & Valentine's [see below]. I think
> about science like a scientist, not a propagandist.
>
> Disappointed?

Yes. This self-puffery always disappoints me.
=============== end of excerpt ===============================

It was "uppity" ("self-puffery") of me to spell out something that should
be expected of anyone in my position. Harshman has often made accusations
against me that insinuate that I do NOT think about science like a
scientist, and I believe he made the charge of "self-puffery" to
give him a freer hand at making such insinuations in the future.

Since you are not averse to talking about things that happened in
2001, I could give you an example from 2010, if you are interested,
of a very strong insinuation of that sort.

By the way, here is a reply to deadrat on the thread "Peter Nyikos"
in which you take center stage:

https://groups.google.com/forum/#!original/talk.origins/pxU8DjYMuDQ/7R5B79-vB-cJ

I posted it about half an hour ago.

Peter Nyikos

[nyi...@bellsouth.net]

On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:

> I should point out that there is at least one hypothesis to explain the
> long ghost lineages: Butterfield, N. J. 1994. Secular distribution of
> Burgess‐Shale‐type preservation. Lethaia 28: 1-13.
>
> ABSTRACT Burgess-Shale-type preservation is defined as a taphonomic
> pathway involving the exceptional organic preservation of
> non-mineralizing organisms in fully marine siliciclastic sediments.

Other types of Konservat-Lagerstatten have been found, haven't they?
The following website draws a distinction between siliciclastic
and phosphatic, the latter including the Chengjiang deposits.

http://en.wikipedia.org/wiki/Sedimentary_rock

Here is a wiki stub which draws some sort of a distinction,
perhaps within the concept of "silliciclastic sediments"
[I don't know enough geology to tell.]

Bitter Springs is a Precambrian fossil locality in
Australia, which preserves microorganisms in silica.[1]
Its preservational mode ceased in the late Precambrian
with the advent of silicifying organisms.[2]

http://en.wikipedia.org/wiki/Bitter_Springs_%28fossil_locality%29

This is one of four Ediacaran Konservat-Lagerstatten (and the oldest)
referenced here:

http://en.wikipedia.org/wiki/Lagerst%C3%A4tte

The other three are: Doushantuo Formation, 600–555 Mya;
Mistaken Point 565 Mya Newfoundland, Canada and the best known:
Ediacara Hills 550-545? Mya South Australia

How is it that the last two preserved so many organisms, yet
so few acknowledged bilaterians? They also are later than where
the 2004 study, the one with the "shallowest" molecular date
for the protostome-deuterostome split, put this split (573 mya).

> In the Phanerozoic it occurs widely in Lower and Middle Cambrian sequences
> but subsequently disappears as a significant taphonomic mode. The
> hypothesis that this distribution derives solely from a secular increase
> in the depth of bioturbation is falsified: low bioturbation indices do
> not prevent the rapid enzymatic degradation of organic structure, nor do
> they account for the conspicuous absence of comparable preservation
> during the Vendian.

How "incomparable" were the Mistaken Point and the Ediacara Hills
Lagerstatten? Do you dispute the following claim in the wiki
site on the Ediacara biota?

"The Ediacaran biota had soft bodies and no skeletons,
making their abundant preservation surprising."

Don't get sidetracked by the "no skeletons" when there are
such strained concepts as fluid in the coelom forming a "skeleton."
I'm interested in the "soft bodies" part.

<snip>

> A model based on the potentially powerful
> anti-enzymatic and/or stabilizing effects of clay minerals on organic
> molecules is proposed to account for Burgess-Shale-type preservation.
> Long-term changes in average clay mineralogies and the ocean chemistry
> that determines their interaction with organic molecules are likely to
> have induced the pronounced secular distribution of these fossil biotas,
> while regional variations in tectonism, weathering, etc., explain their
> non-uniform geographic distribution; the close correlation between
> exceptional, organic-walled fossil preservation and volcano-genic
> sedimentation in Tertiary lake deposits provides a compelling analogue.

Does the following describe the same "analogue" from the Ediacaran
period?

"S.B. Misra's discovery of fossiliferous ash-beds at the
Mistaken Point assemblage in Newfoundland changed all this
as the delicate detail preserved by the fine ash allowed
the description of features that were previously undiscernible."
http://en.wikipedia.org/wiki/Ediacara_biota

> Recognition of a temporal control on Burgess-Shale-type preservation
> constrains the evolutionary scenarios that can be drawn from such
> biotas; significantly, neither the initial rate of appearance, nor the
> ultimate fate of Burgess-Shale-type taxa can be directly assessed.

Not from the Burgess shales themselves, obviously.

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

U. of South Carolina at Columbia

[John Harshman]

On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:
> On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:
>
>> I should point out that there is at least one hypothesis to explain the
>> long ghost lineages: Butterfield, N. J. 1994. Secular distribution of
>> Burgess‐Shale‐type preservation. Lethaia 28: 1-13.
>>
>> ABSTRACT Burgess-Shale-type preservation is defined as a taphonomic
>> pathway involving the exceptional organic preservation of
>> non-mineralizing organisms in fully marine siliciclastic sediments.
>
> Other types of Konservat-Lagerstatten have been found, haven't they?
> The following website draws a distinction between siliciclastic
> and phosphatic, the latter including the Chengjiang deposits.
>
> http://en.wikipedia.org/wiki/Sedimentary_rock

No, the Chengjiang is not phosphatic. Where did you get that idea? Its
preservation resembles the Burgess. Yes, there are other sorts of
preservation. Did you have a point?

> Here is a wiki stub which draws some sort of a distinction,
> perhaps within the concept of "silliciclastic sediments"
> [I don't know enough geology to tell.]
>
> Bitter Springs is a Precambrian fossil locality in
> Australia, which preserves microorganisms in silica.[1]
> Its preservational mode ceased in the late Precambrian
> with the advent of silicifying organisms.[2]

No, not siliciclastic. More like precipitation. Again, did you have a point?

> http://en.wikipedia.org/wiki/Bitter_Springs_%28fossil_locality%29
>
> This is one of four Ediacaran Konservat-Lagerstatten (and the oldest)
> referenced here:
>
> http://en.wikipedia.org/wiki/Lagerst%C3%A4tte
>
> The other three are: Doushantuo Formation, 600–555 Mya;
> Mistaken Point 565 Mya Newfoundland, Canada and the best known:
> Ediacara Hills 550-545? Mya South Australia
>
> How is it that the last two preserved so many organisms, yet
> so few acknowledged bilaterians? They also are later than where
> the 2004 study, the one with the "shallowest" molecular date
> for the protostome-deuterostome split, put this split (573 mya).

To put it briefly: different conditions, different preservation,
different things preserved. One problem with Ediacara is that they
preserve molds and casts in coarse sandstone, so detail is limited. It's
consequently hard to tell what many Ediacaran organisms are. Mistaken
Point is yet another mode of preservation with its own characteristics
and biases.

>> In the Phanerozoic it occurs widely in Lower and Middle Cambrian sequences
>> but subsequently disappears as a significant taphonomic mode. The
>> hypothesis that this distribution derives solely from a secular increase
>> in the depth of bioturbation is falsified: low bioturbation indices do
>> not prevent the rapid enzymatic degradation of organic structure, nor do
>> they account for the conspicuous absence of comparable preservation
>> during the Vendian.
>
> How "incomparable" were the Mistaken Point and the Ediacara Hills
> Lagerstatten? Do you dispute the following claim in the wiki
> site on the Ediacara biota?
>
> "The Ediacaran biota had soft bodies and no skeletons,
> making their abundant preservation surprising."

No.

> Don't get sidetracked by the "no skeletons" when there are
> such strained concepts as fluid in the coelom forming a "skeleton."
> I'm interested in the "soft bodies" part.

In what way are you interested? You seem to be trying to get at
something, but what?

>> A model based on the potentially powerful
>> anti-enzymatic and/or stabilizing effects of clay minerals on organic
>> molecules is proposed to account for Burgess-Shale-type preservation.
>> Long-term changes in average clay mineralogies and the ocean chemistry
>> that determines their interaction with organic molecules are likely to
>> have induced the pronounced secular distribution of these fossil biotas,
>> while regional variations in tectonism, weathering, etc., explain their
>> non-uniform geographic distribution; the close correlation between
>> exceptional, organic-walled fossil preservation and volcano-genic
>> sedimentation in Tertiary lake deposits provides a compelling analogue.
>
> Does the following describe the same "analogue" from the Ediacaran
> period?
>
> "S.B. Misra's discovery of fossiliferous ash-beds at the
> Mistaken Point assemblage in Newfoundland changed all this
> as the delicate detail preserved by the fine ash allowed
> the description of features that were previously undiscernible."
> http://en.wikipedia.org/wiki/Ediacara_biota

No.

>> Recognition of a temporal control on Burgess-Shale-type preservation
>> constrains the evolutionary scenarios that can be drawn from such
>> biotas; significantly, neither the initial rate of appearance, nor the
>> ultimate fate of Burgess-Shale-type taxa can be directly assessed.
>
> Not from the Burgess shales themselves, obviously.

Obviously. But his point is that we should not expect to see the same
sort of preservation very much before or very much after, and so should
not draw lessons of non-existence from the absence of such lagerstatten.
Again, are you trying to make any sort of point?

[nyi...@bellsouth.net]

On Wednesday, October 15, 2014 2:20:24 PM UTC-4, John Harshman wrote:
> On 10/15/14, 10:36 AM, nyi...@bellsouth.net wrote:

> Allow me to snip the childish point-scoring.

What you ACTUALLY snipped was a bunch of childish excuses YOU made
for your misleading claim...

Yes, I'd say it does, more or less. The import is that molecular and
fossil dates have converged.

...about a 2011 paper lead-authored by Erwin, AND me calling you on it...

...AND a lot of meaty information about the various estimates
in that 2011 paper and a 2004 paper lead-authored by Peterson.

Specifically, you snipped the information that the 2011 paper, to which
you were referring as "state of the art..." with your "Yes...more or less",
puts the mean estimate for the protostome-deuterostome split at ca 670 Ma,
and the first undoubted bilaterian fossils at < 560 Ma.

To appreciate the magnitude of the difference, if you add the difference
in dates (110 M even ignoring that <) to 560 Ma, you get 450 Ma, which is
UPPER ORDOVICIAN!

Somewhere in the 560-450 interval, all but four (4) of the ca. 25
bilaterian phyla known from fossils had appeared, and all but one
of those had appeared by 515 Ma. In every phylum that didn't
go extinct, there was at least one class with many representatives
in essentially modern form. Within Chordata, for example,
you can count the cephalochordates and perhaps tunicates, and Agnatha.

If you can't stomach paraphyletic classes, the "ostracoderms," whose
evolution was well underway by 450 Ma, make nice stand-ins for
Cyclostomata.

> >> Some other
> >> analyses put the point estimate as low as 656ma, with confidence limits
> >> 632-798. Still, there seems a significant gap between bilaterian
> >> divergence point and first fossil evidence.

To say the least.

> > And it will seem that way for a long time, unless new Lagerstatten
> > are found in the Ediacaran. More about this in my reply to your
> > other post so far today.

I read your skimpy reply, and will reply to it on Monday.

You could have given us references more recent than 1994, talking
about other kinds of Lagerstatten besides the siliciclastic
sediments with which that 1994 paper is concerned, but you
didn't give any other references at all, not even wiki links.

You seem far more interested in fishing for something that isn't there
than in serious discussion of biological and geological issues related
to the Cambrian explosion.

> >> So, what lesson from this? Either the molecular time-calibration
> >> analysis is overestimating the age of some nodes or there are some
> >> substantial ghost lineages. Do you see a third alternative?
> >
> > Nope. Do you?
>
> No. Do you have an opinion on which is more likely?

That depends on what you mean by "substantial". If 110 my is
only slightly substantial in your eyes, as your snipped and
reposted comment suggests, then I would say it is a mixture of
the two, but have no idea what the contribution of each factor is.

Maybe if you were more helpful, we would get somewhere with that issue.

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

[Mitchell Coffey]

On 10/16/2014 10:08 AM, nyi...@bellsouth.net wrote:
> On Wednesday, October 15, 2014 2:56:35 PM UTC-4, Mitchell Coffey wrote:
>> On 10/15/2014 1:36 PM, nyi...@bellsouth.net wrote:
>>
>>> On Wednesday, October 15, 2014 11:35:41 AM UTC-4, John Harshman wrote:
>>
>> [snip]
>>
>>>> It may have been the 2004 paper I was thinking of, not the
>>>> 2011 one.
>
>>> Scroll back up to the three places where I wrote "NOTE" in caps.
>>> Would your 7th grade teacher have allowed you to get away
>>> with such an excuse?
>
>>> A pattern is beginning to emerge: when you are in a tight spot,
>>> you preface unreasonable "requests" with "Please." Other times,
>>> you treat me with an attitude many if not most whites in the
>>> Jim Crow South had towards "uppity" blacks.
>
>> You mean he shotguns you and buries you under a levee?
>
> Don't be ridiculous. Only a tiny fraction of whites participated
> in lynchings. Did the "many if not most whites" not register
> somehow?

[More of your self-involvement, snipped.]

It's predictable that you didn't recognize sarcasm when you read it.

I'll add this post - where you compare your treatment on Usenet to that
of African-Americans under Jim Crow (and by a guy whom you yourself
treat abusively) - to my file for the next time you deny being a narcissist.

Mitchell Coffey

[nyi...@bellsouth.net]

On Friday, October 17, 2014 4:31:31 PM UTC-4, Mitchell Coffey wrote:

> On 10/16/2014 10:08 AM, nyi...@bellsouth.net wrote:
> > On Wednesday, October 15, 2014 2:56:35 PM UTC-4, Mitchell Coffey wrote:
> >> On 10/15/2014 1:36 PM, nyi...@bellsouth.net wrote:
> >>
> >>> On Wednesday, October 15, 2014 11:35:41 AM UTC-4, John Harshman wrote:
> >>
> >> [snip]

> >>>> It may have been the 2004 paper I was thinking of, not the
> >>>> 2011 one.
> >
> >>> Scroll back up to the three places where I wrote "NOTE" in caps.
> >>> Would your 7th grade teacher have allowed you to get away
> >>> with such an excuse?
> >
> >>> A pattern is beginning to emerge: when you are in a tight spot,
> >>> you preface unreasonable "requests" with "Please." Other times,
> >>> you treat me with an attitude many if not most whites in the
> >>> Jim Crow South had towards "uppity" blacks.

Harshman snipped all of the above and MUCH MORE in his reply,
and that "much more" made his claim about what he had snipped
into a grotesque half-truth, and even what little truth remained
was misleading. See the real truth in my reply to that post by
Harshman. That reply to him included lots of on-topic information:

https://groups.google.com/forum/#!original/talk.origins/nhhRXy0BtBA/R_I9Dk5DaYsJ

Watch Coffey flatter Harshman ["Imitation is the sincerest form
of flattery"] below by doing a similarly deceitful snip and not
showing any interest in the on-topic issues.

> >> You mean he shotguns you and buries you under a levee?

> > Don't be ridiculous. Only a tiny fraction of whites participated
> > in lynchings. Did the "many if not most whites" not register
> > somehow?

> [More of your self-involvement, snipped.]

The "involvement" had to do with Harshman, not me. With this comment
and the rest of what you write here, you have solidified your
solidarity with Harshman.

> It's predictable that you didn't recognize sarcasm when you read it.

Your sarcasm was laid on so thick, only an idiot would fail to
realize it. But it had so little to do with what I had said that you
came across as being very clumsy. And you still come across as being
very clumsy, all through this post.

What bozos like you don't understand is that I don't like to belabor
the obvious. Instead, I gave a reason as to WHY the sarcasm was so clumsy,
but your behavior shows that I should have said more.

The words "many if not most whites" did not register in your CONSCIENCE,
and neither did the word "attitude" as your last sentence makes
clear:

> I'll add this post - where you compare your treatment on Usenet to that
> of African-Americans under Jim Crow (and by a guy whom you yourself
> treat abusively) - to my file for the next time you deny being a narcissist.

You are dumb as a fox with the unqualified word "treatment" as applied
to African-Americans. It is a blanket word that encompasses even
your sarcastic "shotguns [them] and buries [them] under a levee."

The issue has to do exclusively with VERBAL treatment, and the attitude
of only a small fraction "many if not most whites" saw expression in
threats of violence. The rest expressed itself in chronic belittlement,
and you have illustrated your own attitude right here, starting with your
mislabeled snip and intensifying it with "It's predictable..." and
with this last sentence of yours.

Clearly, you look upon my behavior as "uppity" by labeling all efforts
to show what dirty tactics Harshman indulges in as "narcissism."

By the way, when you said "I'll add this post..." were you referring
to the post to which you are replying, or only your prejudice-dripping
reply? If the former, it is a safe bet that you will never
repost it in full alongside your description of what you snipped.

Peter Nyikos

[erik simpson]

Peter, that last several exchanges you've had with John have been concerned with
two subjects.

1) John's (and my) lack of character, acuity and general dishonesty.

2) Many raised-eyebrow comments about fossils that should have been found in
the Ediacaran but haven't, and much disagreement about the dates of divergence
within the deep metazoan lineages. I'm sure you're aware that the various
Ediacaran lagerstatte represent quite different environmental and taphonomic
circumstances, and lacking fossils that can be assigned to crown groups, the
molecular clock point-date estimates have very large ranges of uncertainty.

If you were a creationist or a standard-issue IDiot, it would be clear where
you were going with this, but since I doubt you are either, I share John's
puzzlement about what point you are leading up to. Are you being coy
deliberately, or is there something else you have to say?

[Mitchell Coffey]

Yet you behaved has if I actually thought most southern Whites were
involved in violently terrorizing African-Americans:

> But it had so little to do with what I had said that you
> came across as being very clumsy. And you still come across as being
> very clumsy, all through this post.
>
> What bozos like you don't understand is that I don't like to belabor
> the obvious. Instead, I gave a reason as to WHY the sarcasm was so clumsy,
> but your behavior shows that I should have said more.
>
> The words "many if not most whites" did not register in your CONSCIENCE,
> and neither did the word "attitude" as your last sentence makes
> clear:
>
>> I'll add this post - where you compare your treatment on Usenet to that
>> of African-Americans under Jim Crow (and by a guy whom you yourself
>> treat abusively) - to my file for the next time you deny being a narcissist.

Many and in fact most whites in the Jim Crow south had the attitude
toward African-Americans that you decry. Taken literally, your "many if
not most whites" implied otherwise, but I'll just calk this up to
thoughtlessness on your part.

By the way, while most white southerners were not directly involved in
violence against African-Americans, even in the rare event that
prosecutors prosecuted Whites involved in violence against
African-Americans it was virtually impossible to empanel an all-white
jury willing to convict a White man when the victim was Black. Your
average southerner was complicit in the system of anti-Black violence,
if not directly involved themselves.

Furthermore, support for the lynching of of Blacks had greater support
among Whites under Jim Crow than you seem to think. Lynchings usually
involved large groups of people. Lynching was seldom prosecuted. Public
officials seldom even decried it, and southern representatives
consistently attempted to block Federal anti-lynching legislation.

> You are dumb as a fox with the unqualified word "treatment" as applied
> to African-Americans. It is a blanket word that encompasses even
> your sarcastic "shotguns [them] and buries [them] under a levee."
>
> The issue has to do exclusively with VERBAL treatment, and the attitude
> of only a small fraction "many if not most whites" saw expression in
> threats of violence. The rest expressed itself in chronic belittlement,
> and you have illustrated your own attitude right here, starting with your
> mislabeled snip and intensifying it with "It's predictable..." and
> with this last sentence of yours.
>
> Clearly, you look upon my behavior as "uppity" by labeling all efforts
> to show what dirty tactics Harshman indulges in as "narcissism."

I look upon them as criticism of Harshman, as you criticize him. You've
now introduced the term "uppity" as a synonym for criticism of you.

As I've noted, comparing your treatment in T.O. - where participation is
voluntary, where you are allowed to say whatever your want, and where
you both give and receive criticism and insults - to the treatment of
Blacks under Jim Crow, is narcissism. You don't seem to understand why.

> By the way, when you said "I'll add this post..." were you referring
> to the post to which you are replying, or only your prejudice-dripping
> reply? If the former, it is a safe bet that you will never
> repost it in full alongside your description of what you snipped.
>
> Peter Nyikos

I was referring to your post.

Sure, Kid, if you want your narcissism indulged, here's what I snipped
from your post:

<snipped material>

Here is an example right on this thread where he treated
something I wrote as if I were being "uppity."

________________excerpt from a reply by John to me____________

> However, I will NOT jump to the conclusion that Peterson et. al's figures
> are correct and Blair and Hedges's incorrect, not with so many other
> estimates out there, such as Erwin & Valentine's [see below]. I think
> about science like a scientist, not a propagandist.
>
> Disappointed?

Yes. This self-puffery always disappoints me.
=============== end of excerpt ===============================

It was "uppity" ("self-puffery") of me to spell out something that should
be expected of anyone in my position. Harshman has often made accusations
against me that insinuate that I do NOT think about science like a
scientist, and I believe he made the charge of "self-puffery" to
give him a freer hand at making such insinuations in the future.

Since you are not averse to talking about things that happened in
2001, I could give you an example from 2010, if you are interested,
of a very strong insinuation of that sort.

By the way, here is a reply to deadrat on the thread "Peter Nyikos"
in which you take center stage:

https://groups.google.com/forum/#!original/talk.origins/pxU8DjYMuDQ/7R5B79-vB-cJ

I posted it about half an hour ago.

</snipped material>

"I think about science like a scientist, not a propagandist" /is/
self-puffery, bragging about yourself, while implying your opponent is a
propagandist.

And, to repeat what I said above, comparing your treatment in T.O. -
where participation is voluntary, where you are allowed to say whatever
your want, and where you both give and receive criticism and insults -
to the treatment of Blacks under Jim Crow, is narcissism.


Mitchell Coffey

[nyi...@bellsouth.net]

On Thursday, October 16, 2014 12:17:59 PM UTC-4, John Harshman wrote:
> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:
>
> > On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:

> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:
> > On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:
> >
> >> I should point out that there is at least one hypothesis to explain the
> >> long ghost lineages: Butterfield, N. J. 1994. Secular distribution of
> >> Burgess‐Shale‐type preservation. Lethaia 28: 1-13.
> >>
> >> ABSTRACT Burgess-Shale-type preservation is defined as a taphonomic
> >> pathway involving the exceptional organic preservation of
> >> non-mineralizing organisms in fully marine siliciclastic sediments.
> >
> > Other types of Konservat-Lagerstatten have been found, haven't they?
> > The following website draws a distinction between siliciclastic
> > and phosphatic, the latter including the Chengjiang deposits.
> >
> > http://en.wikipedia.org/wiki/Sedimentary_rock
>
> No, the Chengjiang is not phosphatic. Where did you get that idea?

Faulty memory. I remembered that there was a lot of phosphate mining
in that county, but forgot that the shales where the exquisite fossils
have been found were not on those strata. Turns out that those
shales are sandwiched in between two layers of phosphate-rich rock.

> Its preservation resembles the Burgess. Yes, there are other
> sorts of preservation. Did you have a point?

Isn't it obvious? The 1994 reference you gave is inadequate for
coming to even tentative conclusions about whether the Cambrian
diversification is better called an "explosion" or a "short fuse."
Unless we know more about the various kinds of Konservat Lagerstatten,
we can't judge how remarkable the absence of confirmed bilaterian
fossils before 560 Ma. really is.

> > Here is a wiki stub which draws some sort of a distinction,
> > perhaps within the concept of "silliciclastic sediments"
> > [I don't know enough geology to tell.]
> >
> > Bitter Springs is a Precambrian fossil locality in
> > Australia, which preserves microorganisms in silica.[1]
> > Its preservational mode ceased in the late Precambrian
> > with the advent of silicifying organisms.[2]
>
> No, not siliciclastic. More like precipitation. Again, did you have a point?

See above. Then there is the broader issue that I wrote about in my
first post to this thread, one you didn't even RECOGNIZE when I
gave the url for it on another thread. Perhaps you should read it
again--assuming you've read it at all.

Key: The shorter the Cambrian explosion, the more remarkable it
is in contrast to the ca. 3 billion years (gy) of comparative "stasis"
that preceded it and the ca. 0.5 gy that followed it.
Although these dwarf the ca. 0.02 gy of the molecularly timed
calculation and the ca. 0.04 gy of the fossil record calculation,
the difference between the latter two is nontrivial.

> > http://en.wikipedia.org/wiki/Bitter_Springs_%28fossil_locality%29
> >
> > This is one of four Ediacaran Konservat-Lagerstatten (and the oldest)
> > referenced here:
> >
> > http://en.wikipedia.org/wiki/Lagerst%C3%A4tte
> >
> > The other three are: Doushantuo Formation, 600–555 Mya;
> > Mistaken Point 565 Mya Newfoundland, Canada and the best known:
> > Ediacara Hills 550-545? Mya South Australia
> >
> > How is it that the last two preserved so many organisms, yet
> > so few acknowledged bilaterians? They also are later than where
> > the 2004 study, the one with the "shallowest" molecular date
> > for the protostome-deuterostome split, put this split (573 mya).
>
> To put it briefly: different conditions, different preservation,
> different things preserved. One problem with Ediacara is that they
> preserve molds and casts in coarse sandstone, so detail is limited. It's
> consequently hard to tell what many Ediacaran organisms are. Mistaken
> Point is yet another mode of preservation with its own characteristics
> and biases.

Can you elaborate on that last sentence? see quote near the end where
"fine detail" is mentioned.

> > How "incomparable" were the Mistaken Point and the Ediacara Hills
> > Lagerstatten? Do you dispute the following claim in the wiki
> > site on the Ediacara biota?
> >
> > "The Ediacaran biota had soft bodies and no skeletons,
> > making their abundant preservation surprising."
>
> No.

I took that to refer not only to Ediacara hills but the other three
as well. By the way, are you of the opinion that the notorious
Doushanto microfossils are embryos of eumetazoans?

> > Don't get sidetracked by the "no skeletons" when there are
> > such strained concepts as fluid in the coelom forming a "skeleton."
> > I'm interested in the "soft bodies" part.
>
> In what way are you interested? You seem to be trying to get at
> something, but what?

See above. You seem to be fishing for something quite different from
the rather obvious things I wrote, but what?

> >> A model based on the potentially powerful
> >> anti-enzymatic and/or stabilizing effects of clay minerals on organic
> >> molecules is proposed to account for Burgess-Shale-type preservation.
> >> Long-term changes in average clay mineralogies and the ocean chemistry
> >> that determines their interaction with organic molecules are likely to
> >> have induced the pronounced secular distribution of these fossil biotas,
> >> while regional variations in tectonism, weathering, etc., explain their
> >> non-uniform geographic distribution; the close correlation between
> >> exceptional, organic-walled fossil preservation and volcano-genic
> >> sedimentation in Tertiary lake deposits provides a compelling analogue.
> >
> > Does the following describe the same "analogue" from the Ediacaran
> > period?
> >
> > "S.B. Misra's discovery of fossiliferous ash-beds at the
> > Mistaken Point assemblage in Newfoundland changed all this
> > as the delicate detail preserved by the fine ash allowed
> > the description of features that were previously undiscernible."
> > http://en.wikipedia.org/wiki/Ediacara_biota
>
> No.

Why doesn't "volcano-genic" describe the "ash-beds"?

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

[John Harshman]

If it were obvious I would not have asked. Thanks, however, for finally
stating something clearly. You are wrong. The reference is still valid.
Different means of preservation have different characteristics and
preserve different sorts of organisms. Burgess-type preservation is
particularly good for organisms with organic cuticles, not so great for
things without, like cnidarians. Ediacaran-type preservation seems
particularly good for cnidarian-grade, benthic organisms and perhaps
isn't so good for other sorts, like bilaterians. Doushantuo-type
preservation seems good for very small things; not sure what else. So
the sort of preservation that would be best at recovering soft-bodied
bilaterians is found in the Atdabanian but not for a long time before that.

>>> Here is a wiki stub which draws some sort of a distinction,
>>> perhaps within the concept of "silliciclastic sediments"
>>> [I don't know enough geology to tell.]
>>>
>>> Bitter Springs is a Precambrian fossil locality in
>>> Australia, which preserves microorganisms in silica.[1]
>>> Its preservational mode ceased in the late Precambrian
>>> with the advent of silicifying organisms.[2]
>>
>> No, not siliciclastic. More like precipitation. Again, did you have a point?
>
> See above. Then there is the broader issue that I wrote about in my
> first post to this thread, one you didn't even RECOGNIZE when I
> gave the url for it on another thread. Perhaps you should read it
> again--assuming you've read it at all.
>
> Key: The shorter the Cambrian explosion, the more remarkable it
> is in contrast to the ca. 3 billion years (gy) of comparative "stasis"
> that preceded it and the ca. 0.5 gy that followed it.
> Although these dwarf the ca. 0.02 gy of the molecularly timed
> calculation and the ca. 0.04 gy of the fossil record calculation,
> the difference between the latter two is nontrivial.

Your use of "stasis" is counter to the usual meaning in paleontology;
well, at least you used scare quotes. Sure, the difference between a
literal interpretation of the fossil record that leaves out various
important parts of it is significantly different from an estimate from
molecular data with big error bars. But what's the point behind your
point? Are you perhaps trying to edge up to an unknown evolutionary
mechanism?

>>> http://en.wikipedia.org/wiki/Bitter_Springs_%28fossil_locality%29
>>>
>>> This is one of four Ediacaran Konservat-Lagerstatten (and the oldest)
>>> referenced here:
>>>
>>> http://en.wikipedia.org/wiki/Lagerst%C3%A4tte
>>>
>>> The other three are: Doushantuo Formation, 600–555 Mya;
>>> Mistaken Point 565 Mya Newfoundland, Canada and the best known:
>>> Ediacara Hills 550-545? Mya South Australia
>>>
>>> How is it that the last two preserved so many organisms, yet
>>> so few acknowledged bilaterians? They also are later than where
>>> the 2004 study, the one with the "shallowest" molecular date
>>> for the protostome-deuterostome split, put this split (573 mya).
>>
>> To put it briefly: different conditions, different preservation,
>> different things preserved. One problem with Ediacara is that they
>> preserve molds and casts in coarse sandstone, so detail is limited. It's
>> consequently hard to tell what many Ediacaran organisms are. Mistaken
>> Point is yet another mode of preservation with its own characteristics
>> and biases.
>
> Can you elaborate on that last sentence? see quote near the end where
> "fine detail" is mentioned.

I don't know as much about preservation at Mistaken Point as at the
other places. But I think you're trying to say that if fine detail was
preserved we should have seen lots of clear bilaterians. Is that it? But
there are all sorts of potential taphonomic biases, none of which you
are considering.

>>> How "incomparable" were the Mistaken Point and the Ediacara Hills
>>> Lagerstatten? Do you dispute the following claim in the wiki
>>> site on the Ediacara biota?
>>>
>>> "The Ediacaran biota had soft bodies and no skeletons,
>>> making their abundant preservation surprising."
>>
>> No.
>
> I took that to refer not only to Ediacara hills but the other three
> as well. By the way, are you of the opinion that the notorious
> Doushanto microfossils are embryos of eumetazoans?

I have no strong opinions. That seems to be the common, recent view of
those who are best equipped to have views.

>>> Don't get sidetracked by the "no skeletons" when there are
>>> such strained concepts as fluid in the coelom forming a "skeleton."
>>> I'm interested in the "soft bodies" part.
>>
>> In what way are you interested? You seem to be trying to get at
>> something, but what?
>
> See above. You seem to be fishing for something quite different from
> the rather obvious things I wrote, but what?

Nothing above seems to clarify. And I do think there's something behind
what you wrote that you aren't saying and seem unwilling to say.

>>>> A model based on the potentially powerful
>>>> anti-enzymatic and/or stabilizing effects of clay minerals on organic
>>>> molecules is proposed to account for Burgess-Shale-type preservation.
>>>> Long-term changes in average clay mineralogies and the ocean chemistry
>>>> that determines their interaction with organic molecules are likely to
>>>> have induced the pronounced secular distribution of these fossil biotas,
>>>> while regional variations in tectonism, weathering, etc., explain their
>>>> non-uniform geographic distribution; the close correlation between
>>>> exceptional, organic-walled fossil preservation and volcano-genic
>>>> sedimentation in Tertiary lake deposits provides a compelling analogue.
>>>
>>> Does the following describe the same "analogue" from the Ediacaran
>>> period?
>>>
>>> "S.B. Misra's discovery of fossiliferous ash-beds at the
>>> Mistaken Point assemblage in Newfoundland changed all this
>>> as the delicate detail preserved by the fine ash allowed
>>> the description of features that were previously undiscernible."
>>> http://en.wikipedia.org/wiki/Ediacara_biota
>>
>> No.
>
> Why doesn't "volcano-genic" describe the "ash-beds"?

Sorry, of course it does. But it seems to have no relevance to any point
you're trying to make. Are you trying to equate those ash-beds with
Burgess-type preservation?

[Sneaky O. Possum]

nyi...@bellsouth.net wrote in
news:2ba86ffd-63e6-4ad1...@googlegroups.com:

> On Wednesday, October 15, 2014 2:56:35 PM UTC-4, Mitchell Coffey
> wrote:
>> On 10/15/2014 1:36 PM, nyi...@bellsouth.net wrote:
>> > On Wednesday, October 15, 2014 11:35:41 AM UTC-4, John Harshman
>> > wrote:
[snip]

>> > Scroll back up to the three places where I wrote "NOTE" in caps.
>> > Would your 7th grade teacher have allowed you to get away
>> > with such an excuse?
>
>> > A pattern is beginning to emerge: when you are in a tight spot,
>> > you preface unreasonable "requests" with "Please." Other times,
>> > you treat me with an attitude many if not most whites in the
>> > Jim Crow South had towards "uppity" blacks.
>
>> You mean he shotguns you and buries you under a levee?
>
> Don't be ridiculous. Only a tiny fraction of whites participated
> in lynchings. Did the "many if not most whites" not register
> somehow?

Speaking of ridiculous, where did you get the impression that shooting
someone and burying him under a levee qualifies as a lynching? That's
just a straightforward example of murder - and many white people in the
Jim Crow South were indeed willing to murder a black man or woman who
had the temerity to assert their rights.

Of course, there were other options besides physical violence available
to white people who wanted to teach assertive black people a lesson: one
could take away their jobs, refuse them access to public transportation,
refuse to serve them at a restaurant or lunch counter, etc.

One option that was *never* representative of the attitude white people
had towards assertive black people in the Jim Crow South was 'express
critical opinions about things they post in a moderated newsgroup.' If
John had made an attempt to get your ass banned from talk.origins, that
still wouldn't be very close to treating you with with an attitude many
if not most whites in the Jim Crow South had towards "uppity" blacks,
but it would arguably be in the same hemisphere.

If one is going to claim that one has been treated with the same
attitude that an assertive black person was treated by white people in
the Jim Crow South, one need not produce evidence of actual violence
upon one's person, but one had better have evidence of
treatment significantly more hostile than an admonition against
self-puffery.

> Here is an example right on this thread where he treated
> something I wrote as if I were being "uppity."
>
> ________________excerpt from a reply by John to me____________
>
>> However, I will NOT jump to the conclusion that Peterson et. al's
>> figures are correct and Blair and Hedges's incorrect, not with so
>> many other estimates out there, such as Erwin & Valentine's [see
>> below]. I think about science like a scientist, not a propagandist.
>>
>> Disappointed?
>
> Yes. This self-puffery always disappoints me.
> =============== end of excerpt ===============================
>
> It was "uppity" ("self-puffery") of me to spell out something that
> should be expected of anyone in my position. Harshman has often made
> accusations against me that insinuate that I do NOT think about
> science like a scientist, and I believe he made the charge of
> "self-puffery" to give him a freer hand at making such insinuations in
> the future.

If you honestly think John's use of the term 'self-puffery' to describe
your assertion that you 'think about science like a scientist, not a
propagandist' is in any way comparable to the attitudes expressed by
white people towards 'uppity' black people in the Jim Crow South, you're
beyond hope. If you *don't* honestly think that, you're beneath contempt.
Either way, you're not worth another moment of anyone's time.
--
S.O.P.

[nyi...@bellsouth.net]

On Monday, October 20, 2014 2:55:48 PM UTC-4, John Harshman wrote:

> On 10/20/14, 11:28 AM, nyi...@bellsouth.net wrote:
> > On Thursday, October 16, 2014 12:17:59 PM UTC-4, John Harshman wrote:

> - hide quoted text -

> >> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:
> >>
> >>> On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:
> >
> >> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:
> >>> On Wednesday, October 15, 2014 12:06:14 PM UTC-4, John Harshman wrote:
> >>>
> >>>> I should point out that there is at least one hypothesis to explain the
> >>>> long ghost lineages: Butterfield, N. J. 1994. Secular distribution of
> >>>> Burgess‐Shale‐type preservation. Lethaia 28: 1-13.
> >>>>
> >>>> ABSTRACT Burgess-Shale-type preservation is defined as a taphonomic
> >>>> pathway involving the exceptional organic preservation of
> >>>> non-mineralizing organisms in fully marine siliciclastic sediments.
> >>>
> >>> Other types of Konservat-Lagerstatten have been found, haven't they?

<snip>

> >> Yes, there are other
> >> sorts of preservation. Did you have a point?
> >
> > Isn't it obvious? The 1994 reference you gave is inadequate for
> > coming to even tentative conclusions about whether the Cambrian
> > diversification is better called an "explosion" or a "short fuse."
> > Unless we know more about the various kinds of Konservat Lagerstatten,
> > we can't judge how remarkable the absence of confirmed bilaterian
> > fossils before 560 Ma. really is.
>
> If it were obvious I would not have asked.

Not obvious to whom?

<snip implicit put-down>

> You are wrong. The reference is still valid.

What you said next did not support this claim. Except for the
first sentence, you talk about things not in the abstract.

> Different means of preservation have different characteristics and
> preserve different sorts of organisms. Burgess-type preservation is
> particularly good for organisms with organic cuticles, not so great for
> things without, like cnidarians. Ediacaran-type preservation seems
> particularly good for cnidarian-grade, benthic organisms and perhaps
> isn't so good for other sorts, like bilaterians. Doushantuo-type
> preservation seems good for very small things; not sure what else.

This last sentence is so subjective, it actually sheds doubt on
what went before, because you provide no references.

> So
> the sort of preservation that would be best at recovering soft-bodied
> bilaterians is found in the Atdabanian but not for a long time before that.

You left out Mistaken Point here, and played with the cards very close
to your chest about it later on in the post, as will be clear from
my next reply.

> >>> Here is a wiki stub which draws some sort of a distinction,
> >>> perhaps within the concept of "silliciclastic sediments"
> >>> [I don't know enough geology to tell.]
> >>>
> >>> Bitter Springs is a Precambrian fossil locality in
> >>> Australia, which preserves microorganisms in silica.[1]
> >>> Its preservational mode ceased in the late Precambrian
> >>> with the advent of silicifying organisms.[2]
> >>
> >> No, not siliciclastic. More like precipitation. Again, did you have a point?
> >
> > See above. Then there is the broader issue that I wrote about in my
> > first post to this thread, one you didn't even RECOGNIZE when I
> > gave the url for it on another thread. Perhaps you should read it
> > again--assuming you've read it at all.

<crickets>

> > Key: The shorter the Cambrian explosion, the more remarkable it
> > is in contrast to the ca. 3 billion years (gy) of comparative "stasis"
> > that preceded it and the ca. 0.5 gy that followed it.
> > Although these dwarf the ca. 0.02 gy of the molecularly timed
> > calculation and the ca. 0.04 gy of the fossil record calculation,
> > the difference between the latter two is nontrivial.
>
> Your use of "stasis" is counter to the usual meaning in paleontology;
> well, at least you used scare quotes.

If you are using this to avoid discussing anything about the intended
meaning, then you may have lost a great deal of your love of science
for the sake of science.

For sure, you avoided mentioning anything about the intended
meaning in what you wrote later. That's why I put in "<crickets>"
up there.

Peter Nyikos

[nyi...@bellsouth.net]

On Monday, October 20, 2014 2:55:48 PM UTC-4, John Harshman wrote:
> On 10/20/14, 11:28 AM, nyi...@bellsouth.net wrote:
> > On Thursday, October 16, 2014 12:17:59 PM UTC-4, John Harshman wrote:
> >> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:

Repeating some from my first reply, for continuity:

> So the sort of preservation that would be best at recovering soft-bodied
> bilaterians is found in the Atdabanian but not for a long time before that.

You left out Mistaken Point here, and played with the cards very close

to your chest about it later on in the post.

...

> > Key: The shorter the Cambrian explosion, the more remarkable it
> > is in contrast to the ca. 3 billion years (gy) of comparative "stasis"
> > that preceded it and the ca. 0.5 gy that followed it.
> > Although these dwarf the ca. 0.02 gy of the molecularly timed
> > calculation and the ca. 0.04 gy of the fossil record calculation,
> > the difference between the latter two is nontrivial.
>
> Your use of "stasis" is counter to the usual meaning in paleontology;
> well, at least you used scare quotes.

If you are using this to avoid discussing anything about the intended
meaning, then you may have lost a great deal of your love of science
for the sake of science.

> Sure, the difference between a
> literal interpretation of the fossil record that leaves out various
> important parts of it

...assuming there is something to leave out. But that is begging
the question of the reason for the discrepancy between molecular
estimates and fossil evidence.

> is significantly different from an estimate from
> molecular data with big error bars. But what's the point behind your
> point?

Try taking the intended meaning of "stasis" seriously, and my use
of the word "dwarf".

> Are you perhaps trying to edge up to an unknown evolutionary
> mechanism?

No. I am fascinated by the riddle posed by the huge contrast between
3gy and at most 0.3 gy that I talked about. You apparently are not,
and are more interested in looking for cards up my sleeve than in
"playing the card game," [see above and below about cards held
close to the chest] which I find more fascinating even than
bridge or poker.

> >>> http://en.wikipedia.org/wiki/Bitter_Springs_%28fossil_locality%29
> >>>
> >>> This is one of four Ediacaran Konservat-Lagerstatten (and the oldest)
> >>> referenced here:
> >>>
> >>> http://en.wikipedia.org/wiki/Lagerst%C3%A4tte
> >>>

> >>> The other three are: Doushantuo Formation, 600-555 Mya;

> >>> Mistaken Point 565 Mya Newfoundland, Canada and the best known:
> >>> Ediacara Hills 550-545? Mya South Australia
> >>>
> >>> How is it that the last two preserved so many organisms, yet
> >>> so few acknowledged bilaterians?

<snip for focus>

> >> Mistaken
> >> Point is yet another mode of preservation with its own characteristics
> >> and biases.
> >
> > Can you elaborate on that last sentence? see quote near the end where
> > "fine detail" is mentioned.
>
> I don't know as much about preservation at Mistaken Point as at the
> other places. But I think you're trying to say that if fine detail was
> preserved we should have seen lots of clear bilaterians. Is that it? But
> there are all sorts of potential taphonomic biases, none of which you
> are considering.

More of holding the cards close to your chest. You failed to
elaborate on either "characteristics" or "[potential] biases."
Even your little error about "volcano-genic" at the end
[deleted, but I will deal with it in my next reply]
gave you insufficient incentive to do so.

Concluded in next reply.

Peter Nyikos

[nyi...@bellsouth.net]

On Monday, October 20, 2014 2:55:48 PM UTC-4, John Harshman wrote:
> On 10/20/14, 11:28 AM, nyi...@bellsouth.net wrote:
> > On Thursday, October 16, 2014 12:17:59 PM UTC-4, John Harshman wrote:
> >> On 10/16/14, 7:56 AM, nyi...@bellsouth.net wrote:

> >>> How "incomparable" were the Mistaken Point and the Ediacara Hills
> >>> Lagerstatten? Do you dispute the following claim in the wiki
> >>> site on the Ediacara biota?
> >>>
> >>> "The Ediacaran biota had soft bodies and no skeletons,
> >>> making their abundant preservation surprising."
> >>
> >> No.
> >
> > I took that to refer not only to Ediacara hills but the other three
> > as well. By the way, are you of the opinion that the notorious
> > Doushanto microfossils are embryos of eumetazoans?
>
> I have no strong opinions. That seems to be the common, recent view of
> those who are best equipped to have views.

Do any of them explain why such fragile things would be preserved, but
not the wide range of bilaterian soft bodies, including Chordates with
a notochord running the length of the body? [Cephalochordates and
Vertebrates, which Erwin et. al. had diverging from each other BEFORE
the beginning of the Ediacaran period in their 2011 molecular analyses.]

> >>> Don't get sidetracked by the "no skeletons" when there are
> >>> such strained concepts as fluid in the coelom forming a "skeleton."
> >>> I'm interested in the "soft bodies" part.
> >>
> >> In what way are you interested? You seem to be trying to get at
> >> something, but what?
> >
> > See above. You seem to be fishing for something quite different from
> > the rather obvious things I wrote, but what?
>
> Nothing above seems to clarify. And I do think there's something behind
> what you wrote that you aren't saying and seem unwilling to say.

You can allay these persistent suspicions. To continue the card
game metaphor, I am wearing a sleeveless tank top.

From a very early age (no later than 8) I've had a deep love
of science for the sake of science, although for about five years
it was in the realm of "stamp collecting rather than physics". But
the "physics" aspect soon came to the fore and has been dominant since
the age of 20, but "stamp collecting" still is a good part of that
love, as you found out during our three years of trying to resurrect
sci.bio.paleontology.

And so, as I told you in my second reply, I am fascinated by a
riddle that seems to interest you not at all.

You have shown very little love of science for the sake of science
in this thread, with your laconic replies, the paucity of references
[star billing: a 1994 paper whose abstract promises revelations about
only ONE kind of preservation method] and your relentless fishing
expeditions for cards up my sleeve. And you are the best of a
bad bunch.

> >>>> A model based on the potentially powerful
> >>>> anti-enzymatic and/or stabilizing effects of clay minerals on organic
> >>>> molecules is proposed to account for Burgess-Shale-type preservation.
> >>>> Long-term changes in average clay mineralogies and the ocean chemistry
> >>>> that determines their interaction with organic molecules are likely to
> >>>> have induced the pronounced secular distribution of these fossil biotas,
> >>>> while regional variations in tectonism, weathering, etc., explain their
> >>>> non-uniform geographic distribution; the close correlation between
> >>>> exceptional, organic-walled fossil preservation and volcano-genic
> >>>> sedimentation in Tertiary lake deposits provides a compelling analogue.
> >>>
> >>> Does the following describe the same "analogue" from the Ediacaran
> >>> period?
> >>>
> >>> "S.B. Misra's discovery of fossiliferous ash-beds at the
> >>> Mistaken Point assemblage in Newfoundland changed all this
> >>> as the delicate detail preserved by the fine ash allowed
> >>> the description of features that were previously undiscernible."
> >>> http://en.wikipedia.org/wiki/Ediacara_biota
> >>
> >> No.
> >
> > Why doesn't "volcano-genic" describe the "ash-beds"?
>
> Sorry, of course it does. But it seems to have no relevance to any point
> you're trying to make. Are you trying to equate those ash-beds with
> Burgess-type preservation?

Obviously not. The difference is clear just from the abstract, which
uses "analogue" rather than "example." Note how I picked up on "analogue"
in my question. But the point is, I am in the dark about the differences,
and you are of no help whatsoever despite what seems to be a far better
knowledge of geology.

By the way, I seem to detect an ulterior motive in your last question, going
beyond mere fishing for cards up my sleeve. And for this post anyway, I am
going to be as coy about it as you've been in your fishing. If you start
being more open about what you are fishing FOR, I will elaborate.

Peter Nyikos

[erik simpson]

I'll take you at your word that you're not 'hiding cars up your sleeve', and are
genuinely interested in the early phylogenies. If so, have you sprung for getting
yourself a copy of E&V? If not, why not? You'll find illuminating discussion of
exactly the questions of interest. In particular, you will be disabused of the
notion that "stasis" characterized the environment prior to the Atdabanian. The
chemistry of the ocean varied widely during the Ediacaran, particularly with
regard to oxygenation. Mistaken Point represents a deep-water environment (too
deep for photosythesis), and is dominated by microbial mats and successive layers of Rangeomorphs. The other prominent Ediacaran lagerstatte are shallow-water and display a much more varied biota.

Undisputed bilateria aren't known before the late Ediacaran, the best example
being Kimberella, which has been suggested as a stem mollusc, based mainly on
'looking molluscy' and possibly possessing something resembling a radula. There
isn't any disagreement with molecular and fossil dates for the divergence of
protostomes and deuterostomes, or even subsequent divergences of ecdysozoans,
lophotrocozoans, etc. because the fossil dates don't exist. That is, of course,
the reason for the very uncertain guidance provided by the molecular studies.

Bitter Springs cherts are earlier than is generally considered Ediacaran.

It is of course interesting to speculate on why the early bilaterian clades
haven't been found in the fossil record, but the probable reasons of small
size and problematic preservation environments seem to be good provisional
explanations for their absence. Bilateral symmetry would be easy to diagnose
if found, but the subsequent early divergences might not be. There is
considerable controversy over how 'complex' the Ur-bilaterian may have been,
the apomorphies that distinguished them might not be the characters we use
to distinguish crown phyla.

[nyi...@bellsouth.net]

Coffey's latest personal attacks and obfuscation, and S.O.P.'s more
studied response to me will remain unanswered today,
and perhaps all week, because or Fall break starts at the end of
Wednesday class and I'm looking forward to quantity and quality
time with my family.

I did have a lot to say about these two on another thread, though:

Subject: Re: Peter Nyikos
Date: Tue, 21 Oct 2014 09:22:34 -0700 (PDT)
Message-ID: <f51e8d6d-016f-4da1...@googlegroups.com>
https://groups.google.com/forum/#!original/talk.origins/pxU8DjYMuDQ/ofQygYbQF3AJ

Erik, in contrast, seems willing to bury the hatchet after some
over-the-top rhetoric, both on this thread and on that "Peter Nyikos"
thread, and so I will do him the courtesy of a reply despite having a
great deal of mathematics-related work to do today.

On Monday, October 20, 2014 12:54:41 PM UTC-4, erik simpson wrote:

> Peter, that last several exchanges you've had with John have been
> concerned with two subjects.
>
> 1) John's (and my) lack of character, acuity and general dishonesty.

John has persisted in providing lots of raw material for this subject,
as you can see from my three replies to him today.

> 2) Many raised-eyebrow comments about fossils that should have been found
> in the Ediacaran but haven't, and much disagreement about the dates of
> divergence within the deep metazoan lineages.

This begs the question on an issue which is very much open,
and which Harshman and I touched on in our earlier exchanges:
how to explain the discrepancy between the earliest accepted
bilaterian fossils (< 560 mya) and what seems to be state of
the art on the molecular clocks, a 2011 paper which puts its
best guess at ca. 670 for the protostome-deuterostome split WITHIN
bilateria and a very high confidence for an interval with a later date
but still more than 630 mya.

What do YOU think? Is it ghost lineages or is it a flaw in the latest
molecular analyses?

> I'm sure you're aware that the various
> Ediacaran lagerstatte represent quite different environmental and taphonomic
> circumstances,

Harshman is being very unhelpful about two of them so far. See comments
about Danger Point in all three replies to him today.

> and lacking fossils that can be assigned to crown groups, the
> molecular clock point-date estimates have very large ranges of uncertainty.

The relevant crown group here is bilateria. For some strange reason,
Erwin et. al. leave out all analysis and all references to molecular
research on Chaetognatha, yet have the following to say:

"The only protostome phyla whose crown-group ancestor was likely
carnivorous are the chaetognaths and the nemerteans, and both the
fossil record (73) and molecular clock results (Fig. 3)
suggest that their ancestor appeared in the late Ediacaran
to early Cambrian."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614224/

Fig. 3 makes no mention of Chaetognatha, only Nemertea.

I've speculated that, inasmuch as Chaetognaths have both protostome
and deuterostome characters, and opinion is divided as to which they
are [see the Wikipedia entry], that they might have split off from
other bilateria BEFORE the protostome-deuterostome split.

In that case a molecular phylogenetic analysis could give a THIRD estimate
of when the phylum split off.

> If you were a creationist or a standard-issue IDiot, it would be clear where
> you were going with this, but since I doubt you are either, I share John's
> puzzlement about what point you are leading up to.

I think he has very definite ideas on what he would LIKE me to be leading
up to. As to what I think those are--well, that's the ONLY thing about
which I am coy here.

> Are you being coy
> deliberately, or is there something else you have to say?

Nothing to add to what I wrote above and what I wrote about my love of
science for the sake of science in my third and last reply to Harshman
today. Perhaps you should read what I wrote to him there, and
in my second reply, about how coy HE is being and how I'm "playing cards
with a sleeveless tank top," so to speak.

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