Your cousin was a comb jelly

[TomS]

"� researchers conclude that ctenophores branched off first,
not sponges as many have thought. Yet ctenophores have muscles
and nerve cells, cell types that sponges lack, suggesting that
animal evolution did not proceed smoothly from the simple to
the more complex. Instead, the ancestor to all these animals
may have had a more complex nervous system that sponges and
cnidarians lost, and the mesodermal tissue that gives rise to
muscles may have arisen independently in ctenophores."

Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"

<http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>

About this research article:

(many authors)
The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
Implications for Cell Type Evolution
Science, volume 342 number 6164 (13 December 2013)
pages 1336ff
doi: 10.1126/science.124592


--
---Tom S.

[alias Ernest Major]

On 13/12/2013 12:32, TomS wrote:
> "� researchers conclude that ctenophores branched off first,

If I recall correctly there hasn't been a consistent topology obtained
for bilaterians, ctenophores, cnidarians, placozoans and the various
sponge groups.

This paper is paywalled, and there is very little informed comment as
yet. However see Carl Zimmer (which cites a 2008 article of his
confirming the correctness of my recollection - ctenophores basal was
reported then).


http://phenomena.nationalgeographic.com/2013/12/12/in-search-of-the-first-animals/

There also a comment article in Science, but this is paywalled as well.

http://www.sciencemag.org/content/342/6164/1327

The result is based on the genomes of 13 species, plus unspecified
outgroups. Small taxon samples are known to cause problems, and throwing
loci at the problem doesn't always help. However they also looked at
partial genomes of a several times greater number of species.

--
alias Ernest Major

[Darwin123]

Your quotation doesn't say what the groups branched off from. It
doesn't make sense to say a group "branched off first" unless
there are at least three groups in the discussion.

Suppose there were only two groups under discussion: the sponges
and the ctenophores. The only other group under discussion was the
lineage of ancestors common to both groups. This would be called the
common ancestor group. However, suppose that we knew nothing about the
morphology of the most recent common ancestor (MRCA). In order for any
group to "branch off first", there has to be a well defined trunk.

If we don't know the morphology of the MRCA, then we can't
decide which groups branched off "first". The ctenophores and
the sponges by definition branched off at the same time. Neither of
them came "first".

Suppose the MRCA of both ctenophores and sponges was a unicellular
organism. Suppose that we knew for sure that the MRCA was very similar to an extant dinoflagellate. Since both ctenophores and sponges are multicellular,
this would mean that the MRCA of both groups looked nothing like an individual
of either group. It still would not be possible to uniquely determine which
group branched off first. It would not be possible even in principle,
since there is no "trunk" specified.

I conjecture what the investigators really meant is that the MRCA of all
metazoans had a morphology more similar to a ctenophore than to a sponge.
Then, one would that the full article provides context with respect to what the word "first" means.

The snipped quotation does not challenge my confidence in the theory
of evolution because it does not contradict the models I have read about
concerning the evolution of metazoans.

According to my understanding of the theory, both sponges and animals
are descended from an MRCA that was a unicellular organism. This is
consistent with the model in the article, with maybe one important
detail added.

This is one model consistent with what the investigators have found.
The MRCA of all metazoans (MRCAM) was a unicellular organism. At one point, one population within the MRCAM species differentiated into a multicellular organism similar to an extant sponge. However, the complementary population continued to propagate for a while. Eventually, part or all of the complementary population differentiated into an organism similar to an extant ctenophore.

The implied trunk here is unicellular organisms. Hence, the sponges branched off from a unicellular organism a long time after the ctenophores branched off from a unicellular organism.

Here is what I think the investigators visualize. The MRCAM was a unicellular organism. At some point, one population of MRCAM differentiated
into a multicelled organism that resembled a ctenophore, complete with
nerves and muscle. This was the most recent common ancestor of all animals
(MRCAA). A population of MRCAA differentiated into an organism without
nerves or muscle. This was the most recent common ancestor of all sponges
(MRCAS). The MRCAS was similar to a modern day sponge.

The implied trunk here is animals. The sponges in this model branched
off from the other animals long after the ctenorpores had branched off
from the other animals.

Neither model contradicts the general theory of evolution. However,
there is a model that has been falsified. I imagined that the evolution of
metazoans occurred like this.

The investigators have falsified the following theory, if they are correct.
The possibility is that the unicellular MRCAM first branched off into
a sponge-like species and unicellular species. Then, one of the unicellar
species branched off into a ctenophore-like species.

I would have thought this the most likely, but I have no quantitative basis for this conjecture. I still think the MRCA of all metazoans may have
roughly resembled a dinoflagellate. However, it would have differed from an
extant dinoflagellate in a few important ways. Everything has evolved from
those ancient days.

[Richard Norman]

On Fri, 13 Dec 2013 12:08:49 -0800 (PST), Darwin123
<drose...@yahoo.com> wrote:

>On Friday, December 13, 2013 7:32:45 AM UTC-5, TomS wrote:

>> "? researchers conclude that ctenophores branched off first,

The whole gist of the article is indeed to determine the order of
branching. The ctenophora are shown from this data to be a sister
group to ALL the remaining animals including sponges and placophora.

I don't know the details to criticize or evaluate different methods of
phylogenetic analysis or bootstrapping, maximum likelihood analysis,
etc. Maybe John Harshman could help out here.

I do have both the full research paper and a companion more
explanatory piece, "My Oldest Sister Is a Sea Walnut?" by Antonis
Rokas in the same issue of Science. Both seem to be paywalled. Email
me if you want it by removing the two underscores in my address.

[R. Dean]

On 12/13/2013 7:32 AM, TomS wrote:
> "� researchers conclude that ctenophores branched off first,

This assumes too much. The viewpoint that similarity denotes common
ancestor is simply a premise without empirical evidence. The fact
that all organisms, extinct and extant have so much in common could
just as well indicate a unified plan by an intelligent designer.

[John Harshman]

Might, but I don't have a subscription to Science.

> I do have both the full research paper and a companion more
> explanatory piece, "My Oldest Sister Is a Sea Walnut?" by Antonis
> Rokas in the same issue of Science. Both seem to be paywalled. Email
> me if you want it by removing the two underscores in my address.

I will.

[John Harshman]

Why, yes. Anything at all could indicate such a unified plan. Isn't it
odd, though, that the unified plan the designer selected, out of all the
possible plans, is exactly the sort of thing you would expect from a
branching tree of common descent? What are the odds?

[Richard Norman]

It is sent.

AAAS membership is $150 per year. I was a member for several decades
and the issues of Science just piled up, one a week, with things I
wanted to read or told myself I really should read until it was so
overwhelming that I just started throwing the damn things out.

[Richard Norman]

On Fri, 13 Dec 2013 17:31:27 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/13/2013 7:32 AM, TomS wrote:

>> "� researchers conclude that ctenophores branched off first,

The paper is not at all about similarity in morphology. All that
discussion is based on genomic analysis and, especially, an analysis
of the genes responsible for development of nervous and mesodermal
cells.

[Robert Camp]

On 12/13/13 2:31 PM, R. Dean wrote:

> On 12/13/2013 7:32 AM, TomS wrote:
>> "� researchers conclude that ctenophores branched off first,
>> not sponges as many have thought. Yet ctenophores have muscles
>> and nerve cells, cell types that sponges lack, suggesting that
>> animal evolution did not proceed smoothly from the simple to
>> the more complex. Instead, the ancestor to all these animals
>> may have had a more complex nervous system that sponges and
>> cnidarians lost, and the mesodermal tissue that gives rise to
>> muscles may have arisen independently in ctenophores."
>>
>> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>>
>> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>>
>>
>> About this research article:
>>
>> (many authors)
>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>> Implications for Cell Type Evolution
>> Science, volume 342 number 6164 (13 December 2013)
>> pages 1336ff
>> doi: 10.1126/science.124592
>>
>>
> This assumes too much. The viewpoint that similarity denotes common
> ancestor is simply a premise without empirical evidence.

Have you ever actually taken the time to think about the role
"similarity" plays in virtually all of our knowledge-seeking endeavors?

How far down the road of nihilism are you willing to travel?

> The fact
> that all organisms, extinct and extant have so much in common could
> just as well indicate a unified plan by an intelligent designer.

Why would your putative "intelligent designer" design in such a way?
What do you know about this designer that suggests to you a unified plan
for similarity among extinct and extant animals would be one of
his/her/its design objectives?

[Darwin123]

On Friday, December 13, 2013 5:31:27 PM UTC-5, R. Dean wrote:
> On 12/13/2013 7:32 AM, TomS wrote:
>

> > "� researchers conclude that ctenophores branched off first,

>
> > not sponges as many have thought. Yet ctenophores have muscles
>
> > and nerve cells, cell types that sponges lack, suggesting that
>
> > animal evolution did not proceed smoothly from the simple to
>
> > the more complex. Instead, the ancestor to all these animals
>
> > may have had a more complex nervous system that sponges and
>
> > cnidarians lost, and the mesodermal tissue that gives rise to
>
> > muscles may have arisen independently in ctenophores."
>
> >
>
> > Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>
> >
>
> > <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>
> >
>
> > About this research article:
>
> >
>
> > (many authors)
>
> > The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>
> > Implications for Cell Type Evolution
>
> > Science, volume 342 number 6164 (13 December 2013)
>
> > pages 1336ff
>
> > doi: 10.1126/science.124592
>
> >
>
> >
>
> This assumes too much.

Actually, the results suggest almost the opposite. The results show
that similarity in morphology does not follow from similarity in
genome.

The investigators assumed that the general theory of evolution is
true. They accept the fact that the general theory of evolution, as
understood since Darwin, has been proven. However, Darwin did not
know anything about genes. Therefore, there are details involving
genes that are still not completely clear.

There is a hypothesis that similarity in genome automatically
implies similarity in morphology. This is a rule of thumb that has
many exceptions. It is this rule (model, scholium?) that is under
question.

The ctenophora and sponges are usually classified as animals.
However, the ctenophora resemble other animals in morphology more
than sponges. Ctenophora have muscles and nerves, similar to most "higher"
animals. In this way, ctenophora resemble mammals more than they
resemble sponges. Sponges don't have nerves and muscles.

The study showed that higher animals, including mammals, have
genomes that resemble the genomes of sponges more than the genomes of
ctenphora. If that is true, then similarity in genomes is not
required for the morphology to be the same. The genetic sequences
are not precisely unique to any given morphology.

This does not disprove the entire Creationist argument, but it does
disprove one assumption that many Creationists presents. A Creationist
will often claim that the reason that genomes are similar in animals
of the same morphology is that the Designer had no choice. In order
to make two animals with similar morphology, he had to make their
genomes similar.

>The viewpoint that similarity denotes common
> ancestor is simply a premise without empirical evidence. The fact
> that all organisms, extinct and extant have so much in common could
> just as well indicate a unified plan by an intelligent designer.

When two animals with have similar morphologies in the same
habitat, then one could ascribe it to a designer. He made their morphologies
similar in order to deal with the habitat. However, he doesn't have to make
their genomes the same.

This is not proof of a Creator one way or another. It does prove one very
specific argument used by some Creationists is wrong. There may be a designer.
However, he has a lot more freedom in choosing genomes than is commonly claimed.

The conclusions of the study are not firmly established. The assumption
that they used was that more similarity between genomes implies more recent
divergence between the corresponding species. They conclude that similarity
in genome is more reliable than similarity in morphology. This is independent
of the issue whether evolution has occurred. It is more a study of how it
occurred.

The more gene loci are examined, the more likely this hypothesis
is true. Other posters implied that the investigators did not look at
a sufficiently large number of gene loci. This may or may not be true.
I don't have the background to analyze their data myself, even if it
was given to me.

I do know that the investigators were not even considering the
hypothesis that an intelligent designer was responsible for the similarity
in genome between mammals, sponges and ctenophora.

If there was a Designer, their study would merely be indicating a
whim on the part of the Designer. He could have chosen some other
genome for sponges and ctenophora, but He decided that one similar to
mammals was better.

This was basically unpredictable, hence it was random. There is no way to predict His whim. Therefore, development of the genome was random, where random means a matter of His whim.

If the animals evolved from a common ancestor, then the study merely
shows that natural selection can remove structural features. The MRCA
of ctenophora and sponges may have had muscles and nerves which disappeared
in the sponges. The ancestors of the sponge happened to pass a habitat
where nerves and muscles weren't necessary for a very long time.

Again, this is basically unpredictable. Hence, the genome is random, where random means unpredictable.

So one way or another, we are stuck with random.

[John Harshman]

I read the phylogenetic analysis parts of the paper, and I didn't find
anything wrong with it. The trees to pay attention to are the ML
analyses of the "EST set", which seem to have a good taxonomic sample
and no other problems.

One thing that surprises me is the (comparatively) shallow divergence
among the three ctenophores analyzed. Either ctenophores had a
near-extinction bottleneck well into the Phanerozoic or the sampling has
been biased toward a few close relatives.

As always, better taxon sampling will help test the hypothesis here. But
I'd have to say it's become my new default position.

[John S. Wilkins]

John Harshman <jhar...@pacbell.net> wrote:

> On 12/13/13 2:31 PM, R. Dean wrote:
> > On 12/13/2013 7:32 AM, TomS wrote:

> >> "… researchers conclude that ctenophores branched off first,

That is evidence that the creator wants us to believe in common descent.
--
John S. Wilkins, Associate, Philosophy, University of Sydney
http://evolvingthoughts.net
But al be that he was a philosophre,
Yet hadde he but litel gold in cofre

[William Morse]

I have been a member since the early seventies. I used to religiously
read the review articles and the few research articles that dealt with
something I understood. Now I throw most of them out unread, although I
do get to about one a month. But I can check out articles for those who
are interested if Richard is not available.

[jillery]

On Fri, 13 Dec 2013 17:31:27 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/13/2013 7:32 AM, TomS wrote:

>> "� researchers conclude that ctenophores branched off first,

Just to reply in kind to your oft-repeated but never supported
assertion, no it doesn't.

[Paul Ciszek]

In article <1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>,

John S. Wilkins <jo...@wilkins.id.au> wrote:
>> >
>> Why, yes. Anything at all could indicate such a unified plan. Isn't it
>> odd, though, that the unified plan the designer selected, out of all the
>> possible plans, is exactly the sort of thing you would expect from a
>> branching tree of common descent? What are the odds?
>
>That is evidence that the creator wants us to believe in common descent.

A creator who wants to trick as many people as possible into eternal
damnation is seriously messed up.

--
Please reply to: | "Try to imagine a row of computers programmed by
pciszek at panix dot com | hippies."
Autoreply is disabled | --Ayn Rand, The Anti-Industrial Revolution

[Paul Ciszek]

1) What happened to the "sponges are paraphyletic, with some sponges more
closely related to eumetazoans than they are to other sponges" model?

2) I thought I read that there is paleochemical evidence of some categories
of sponges going way, way back, older than any recognizable fossils of
animals. Wouldn't this model require ctenophores to be even older
than that?

3) Could this be explained by one single species with a very unusual
genome (at least as far as the genes they are looking at for this
study are concerned) that somehow became the sole surviving ctenophore,
and subsequently the ancestor of all extant ctenophores?

4) Ctenophores and cnidarians are diploblasts, bilateria are triploblasts,
and if I understand correctly sponges are monoblasts. Does this model
require sponges to have not only lost muscles and nerves, but
diploblasty as well?


--
Please reply to: | "Evolution is a theory that accounts
pciszek at panix dot com | for variety, not superiority."
Autoreply has been disabled | -- Joan Pontius

[eridanus]

El viernes, 13 de diciembre de 2013 22:31:27 UTC, R. Dean escribi�:

>
> > The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
> > Implications for Cell Type Evolution
> > Science, volume 342 number 6164 (13 December 2013)
> > pages 1336ff
>
> > doi: 10.1126/science.124592
>
> This assumes too much. The viewpoint that similarity denotes common
> ancestor is simply a premise without empirical evidence. The fact
> that all organisms, extinct and extant have so much in common could
> just as well indicate a unified plan by an intelligent designer.

Of course, Dean.
The most humans dig exploring how happened the evolution of living beings,
the more likely it looks that it was planned this way by a god creator.

Once the theory will be almost complete, you can come out reclaiming "this
was exactly the way that god made it. But he buried deep underground to
keep us busy working for five or seven centuries.
Eridanus

[eridanus]

El s�bado, 14 de diciembre de 2013 02:40:04 UTC, John S. Wilkins escribi�:

> John Harshman <jhar...@pacbell.net> wrote:
>
>
>
> > On 12/13/13 2:31 PM, R. Dean wrote:
>
> > > On 12/13/2013 7:32 AM, TomS wrote:
>

> > >> "� researchers conclude that ctenophores branched off first,

of course, John. But it happens that this god creator has not any relation
with the liars that wrote the bible. We keep calling this "god creator" a
little by inertia. It takes a lot to change our ways of speaking. Just you
discover one day, how the big bang started, then this was the way did it
our god creator. If our science one day discovers that a big bang never
occurred, this was exactly planed this way by a god creator. God creator
made the things so complex and so hidden, just to keep us entertained
working on digging and thinking.
Eridanus





,

[alias Ernest Major]

On 14/12/2013 01:12, Darwin123 wrote:
> The more gene loci are examined, the more likely this hypothesis
> is true. Other posters implied that the investigators did not look at
> a sufficiently large number of gene loci. This may or may not be true.
> I don't have the background to analyze their data myself, even if it
> was given to me.

I think you have misunderstood. They used whole genomes - that is every
gene locus available (probably limited by the ability to align them).

I did mention that 13 taxa, plus unspecified outgroups, is less than
ideal for addressing this question, and John Harshman wrote "better

taxon sampling will help test the hypothesis here".

--
alias Ernest Major

[TomS]

"On Sat, 14 Dec 2013 13:40:04 +1100, in article
<1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>, John S. Wilkins stated..."
[...snip...]

>That is evidence that the creator wants us to believe in common descent.

And, given how powerful they are, who am I to cross them?

BTW, they also dictated the Pentateuch to Moses so that it would look
like it was written by other people hundreds of years later.

Who knows why they do such things, but they go to so much effort that
they must really want us to believe such things.

Getting on the wrong side of Kim in North Korea would be less risky.


--
---Tom S.

[TomS]

"On Fri, 13 Dec 2013 17:31:27 -0500, in article
<_ULqu.20562$rg6....@fx06.fr7>, R. Dean stated..."
[...snip...]

>This assumes too much. The viewpoint that similarity denotes common
>ancestor is simply a premise without empirical evidence. The fact
>that all organisms, extinct and extant have so much in common could
>just as well indicate a unified plan by an intelligent designer.
>

Of course, if we assume that similarity indicates a unified plan by
an intelligent designer, that means that there is a very unified plan
for humans, chimps and other apes.

And a unified plan for them means that, in order to follow the
intentions of our common designers, we *ought* to behave like apes.

That's what you're saying that the intelligent designers want us to
do.

Oh, there are other possibilities:

It could be that the great similarities of the human body with those
of the other primates (and to somewhat lesser degrees, other mammals,
other tetrapods, other vertebrates, other animals, other living things)
is due to restrictions on what the intelligent designers are capable
of. What they can do with the raw material that they were given to work
with, and the laws of nature that they have to follow.

It could be that it's just a coincidence. It could be that it's just
a matter of chance that humans happen to have the same structure of eyes
as do other vertebrates, rather than like eyes of insects, of octopuses,
or of potatoes.

I don't know which of the three options the advocates of "Intelligent
Design" would select: The Morality of Apes, The Limits of Design, or
The Effectiveness of Chance.


--
---Tom S.

[eridanus]

El s�bado, 14 de diciembre de 2013 12:18:04 UTC, TomS escribi�:

that post was excellent. Thanks.
eri

[John Harshman]

On 12/13/13 11:45 PM, Paul Ciszek wrote:
> In article<1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>,
> John S. Wilkins<jo...@wilkins.id.au> wrote:
>>>>
>>> Why, yes. Anything at all could indicate such a unified plan. Isn't it
>>> odd, though, that the unified plan the designer selected, out of all the
>>> possible plans, is exactly the sort of thing you would expect from a
>>> branching tree of common descent? What are the odds?
>>
>> That is evidence that the creator wants us to believe in common descent.
>
> A creator who wants to trick as many people as possible into eternal
> damnation is seriously messed up.
>

Have you ever read the Old Testament?

[John Harshman]

On 12/14/13 2:20 AM, alias Ernest Major wrote:
> On 14/12/2013 01:12, Darwin123 wrote:
>> The more gene loci are examined, the more likely this hypothesis
>> is true. Other posters implied that the investigators did not look at
>> a sufficiently large number of gene loci. This may or may not be true.
>> I don't have the background to analyze their data myself, even if it
>> was given to me.
>
> I think you have misunderstood. They used whole genomes - that is every
> gene locus available (probably limited by the ability to align them).

Not whole genomes exactly. They had an amino acid data set and so were
limited to protein-coding exons. Which turn out to be an amazingly high
percentage of this tiny eukaryote genome.

> I did mention that 13 taxa, plus unspecified outgroups, is less than
> ideal for addressing this question, and John Harshman wrote "better
> taxon sampling will help test the hypothesis here".

The outgroups were specified: they used various combinations of
opisthokonts, including choanoflagellates. And they had two data sets,
one of just 13 taxa and one of 50+ taxa (but fewer sites).

[Paul Ciszek]

In article <2t6dnZY2x6mj5jHP...@giganews.com>,

Yes.

--
Please reply to: |"We establish no religion in this country, we command
pciszek at panix | no worship, we mandate no belief, nor will we ever.
dot com | Church and state are, and must remain, separate."
Autoreply disabled | --Ronald Reagan, October 26, 1984

[Paul Ciszek]

In article <l8h30a$j96$1...@reader1.panix.com>,

Paul Ciszek <nos...@nospam.com> wrote:
>
>3) Could this be explained by one single species with a very unusual
> genome (at least as far as the genes they are looking at for this
> study are concerned) that somehow became the sole surviving ctenophore,
> and subsequently the ancestor of all extant ctenophores?

According to Wiki, the last common ancestor of all modern Ctenophores
was recent, possibly as recent as the K-T event. I gotta wonder if the
"freak species becomes freak phylum" might be the Occam's razor
explanation here.

[Paul Ciszek]

In article <IZadnZ3Sx62B4THP...@giganews.com>,

John Harshman <jhar...@pacbell.net> wrote:
>
>The outgroups were specified: they used various combinations of
>opisthokonts, including choanoflagellates. And they had two data sets,
>one of just 13 taxa and one of 50+ taxa (but fewer sites).

Is this the sort of data set that you can keep adding to piecemeal?
i.e., "Hey, I just sequenced a priaplulid worm, you want it?"
Or, if you want a larger set of species, do you have go back and
"do" them all together?

[R. Dean]

Why would you think an intelligent designer would act in such an
unintelligible, irrational way as you suggest? Life is interconnected
interdependent in a logical way; all life is dependent on life - as in
the "food chain". If protein from species to species were radically
different, for example, life could not exist. IOW there very well may
not be other possible plans.
We human are able to make predictions based upon what we observe, indeed
the fact that life, the laws of physics and the universe itself is
understandable and predictable as the result. This would not be
the case if everything was the result of a whimsical capricious or
fickle designer. Indeed, such would not fit the definition of
intelligent design.

[R. Dean]

On 12/13/2013 6:17 PM, Richard Norman wrote:
> On Fri, 13 Dec 2013 17:31:27 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/13/2013 7:32 AM, TomS wrote:

>>> "� researchers conclude that ctenophores branched off first,

OK, but I was under the impression that by comparing the genomes
of several of these placozoans they determined their location in
the tree of life.

[Paul Ciszek]

In article <H10ru.28231$rg6....@fx06.fr7>,

According to wiki, there is genetic evidence to support the Epitheliozoa
hypothesis, the idea that the Placozoa are a sister group to Eumetazoa
and the "stomach side" of a placozoan is the precursor to the gut of
Eumetazoans:

http://en.wikipedia.org/wiki/Placozoa#Epitheliozoa_hypothesis

Perhaps someone who knows sponges can answer me this: How does the larval
form of a sponge differ from a placozoan?

[R. Dean]

On 12/13/2013 6:50 PM, Robert Camp wrote:
> On 12/13/13 2:31 PM, R. Dean wrote:
>> On 12/13/2013 7:32 AM, TomS wrote:
>>> "� researchers conclude that ctenophores branched off first,
>>> not sponges as many have thought. Yet ctenophores have muscles
>>> and nerve cells, cell types that sponges lack, suggesting that
>>> animal evolution did not proceed smoothly from the simple to
>>> the more complex. Instead, the ancestor to all these animals
>>> may have had a more complex nervous system that sponges and
>>> cnidarians lost, and the mesodermal tissue that gives rise to
>>> muscles may have arisen independently in ctenophores."
>>>
>>> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>>>
>>> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>>>
>>>
>>>
>>> About this research article:
>>>
>>> (many authors)
>>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>>> Implications for Cell Type Evolution
>>> Science, volume 342 number 6164 (13 December 2013)
>>> pages 1336ff
>>> doi: 10.1126/science.124592
>>>
>>>
>> This assumes too much. The viewpoint that similarity denotes common
>> ancestor is simply a premise without empirical evidence.
>
> Have you ever actually taken the time to think about the role
> "similarity" plays in virtually all of our knowledge-seeking endeavors?
>

Yes, if I found two books by two different authors and I found that
chapter after chapter in the two books were the same or almost the same
wording I would not assume two different writers had exactly the same
thoughts. I would call the work of one person; the other plagiarism.

>
> How far down the road of nihilism are you willing to travel?
>

I think nihilism describes the mindless, thoughtless random actions
on irrational, non-intilligent processes. Better discriptive traits
would be chaos, confusion, disorder, anarchy, etc..

>
>> The fact
>> that all organisms, extinct and extant have so much in common could
>> just as well indicate a unified plan by an intelligent designer.
>
> Why would your putative "intelligent designer" design in such a way?
> What do you know about this designer that suggests to you a unified plan
> for similarity among extinct and extant animals would be one of
> his/her/its design objectives?
>

What else? It's what one would expect of intelligence. If what we
found was chaos, disorder, capricious laws of physics it would suggest
unintelligable processes.
>

[jillery]

On Sat, 14 Dec 2013 11:43:26 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/13/2013 5:53 PM, John Harshman wrote:
>> On 12/13/13 2:31 PM, R. Dean wrote:
>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>> "� researchers conclude that ctenophores branched off first,

On what basis do you suggest that he suggested is irrational?

> Life is interconnected
>interdependent in a logical way; all life is dependent on life - as in
>the "food chain". If protein from species to species were radically
>different, for example, life could not exist. IOW there very well may
>not be other possible plans.

Sounds pretty rational to me.

>We human are able to make predictions based upon what we observe, indeed
>the fact that life, the laws of physics and the universe itself is
>understandable and predictable as the result. This would not be
>the case if everything was the result of a whimsical capricious or
>fickle designer. Indeed, such would not fit the definition of
>intelligent design.

And it would not fit the definition of unguided design. So the real
question is how does one tell the difference? Care to answer it?

[jillery]

On Sat, 14 Dec 2013 12:12:45 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/13/2013 6:50 PM, Robert Camp wrote:
>> On 12/13/13 2:31 PM, R. Dean wrote:
>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>> "� researchers conclude that ctenophores branched off first,

It's what we expect of human intelligence. On what basis do you
assume other intelligences would follow suit.

More to the point, your argument assumes intelligence is the only way
such similarity can happen. Science shows that to be not the case.

> If what we
>found was chaos, disorder, capricious laws of physics it would suggest
>unintelligable processes.

No it would not. It would suggest a capricious deity or multiple
deities with conflicting motives and goals, as in ancient mythologies.

[R. Dean]

Yes, I read as much. The development of certain organs or limbs in
"closely related species" sometimes takes different pathways controlled
by the same genes.

>
> The ctenophora and sponges are usually classified as animals.
> However, the ctenophora resemble other animals in morphology more
> than sponges. Ctenophora have muscles and nerves, similar to most "higher"
> animals. In this way, ctenophora resemble mammals more than they
> resemble sponges. Sponges don't have nerves and muscles.
>
> The study showed that higher animals, including mammals, have
> genomes that resemble the genomes of sponges more than the genomes of
> ctenphora. If that is true, then similarity in genomes is not
> required for the morphology to be the same. The genetic sequences
> are not precisely unique to any given morphology.
>
> This does not disprove the entire Creationist argument, but it does
> disprove one assumption that many Creationists presents. A Creationist
> will often claim that the reason that genomes are similar in animals
> of the same morphology is that the Designer had no choice. In order
> to make two animals with similar morphology, he had to make their
> genomes similar.
>

This is an argument I've never heard. Morphology is controlled (more
like set in a cascading motion) by the homeobox genes.

>
>> The viewpoint that similarity denotes common
>> ancestor is simply a premise without empirical evidence. The fact
>> that all organisms, extinct and extant have so much in common could
>> just as well indicate a unified plan by an intelligent designer.
> When two animals with have similar morphologies in the same
> habitat, then one could ascribe it to a designer. He made their morphologies
> similar in order to deal with the habitat. However, he doesn't have to make
> their genomes the same.
>

There may be overriding considerations and usually is where new
and expermental processes are found. But generally speaking, in
design work, one will use tried and true methods where possible
rather than go with experimental or untried designs, unless one is in
research and development; and even then one resorts to incorporating
known processes where possible rather than go entirely into experimental
areas.

>
> This is not proof of a Creator one way or another. It does prove one very
> specific argument used by some Creationists is wrong. There may be a designer.
> However, he has a lot more freedom in choosing genomes than is commonly claimed.
>

I don't understand how this falsifies anything. Proof is not an issue.
Another point. There is a distinction between creationism as in
"scientific creationism" and intelligent design. For example, the
Creationism is genesis based, whereas I.D. is not. Creationism
attempts to name the creator but I.D. looks at design which they
believe is observable and testable but the idenity of the designer
is unknown and unknowable. But in the same sense as I can determine
the expertise of an engineer by his design, it may be possible to
determine something of the characteristics and the mind of the
designer. But not by me, by some much smarter than I am.

>
> The conclusions of the study are not firmly established. The assumption
> that they used was that more similarity between genomes implies more recent
> divergence between the corresponding species. They conclude that similarity
> in genome is more reliable than similarity in morphology. This is independent
> of the issue whether evolution has occurred. It is more a study of how it
> occurred.
>
> The more gene loci are examined, the more likely this hypothesis
> is true. Other posters implied that the investigators did not look at
> a sufficiently large number of gene loci. This may or may not be true.
> I don't have the background to analyze their data myself, even if it
> was given to me.
>
> I do know that the investigators were not even considering the
> hypothesis that an intelligent designer was responsible for the similarity
> in genome between mammals, sponges and ctenophora.
>
> If there was a Designer, their study would merely be indicating a
> whim on the part of the Designer. He could have chosen some other
> genome for sponges and ctenophora, but He decided that one similar to
> mammals was better.
>

I fail to understand why some people think of a designer in terms of
whimsical, capricious, fickle etc. These traits are not the
characteristics of intelligence.

>
> This was basically unpredictable, hence it was random. There is no way to predict His whim. Therefore, development of the genome was random, where random means a matter of His whim.
>

Are you capable of determining that there are no overriding
considerations. The different modes of making a living, of locomotion
reproduction etc.

>
> If the animals evolved from a common ancestor, then the study merely
> shows that natural selection can remove structural features. The MRCA
> of ctenophora and sponges may have had muscles and nerves which disappeared
> in the sponges. The ancestors of the sponge happened to pass a habitat
> where nerves and muscles weren't necessary for a very long time.
>
> Again, this is basically unpredictable. Hence, the genome is random, where random means unpredictable.
>
> So one way or another, we are stuck with random.
>

You may be correct. I don't know. It's also possible that where we
say may have, or could have, or if we consider... then it implies
we don't know enough to arrive at valid conclusions. The very
next discovery may completely alter our present theory.

[R. Dean]

On 12/14/2013 2:45 AM, Paul Ciszek wrote:
> In article <1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>,
> John S. Wilkins <jo...@wilkins.id.au> wrote:
>>>>
>>> Why, yes. Anything at all could indicate such a unified plan. Isn't it
>>> odd, though, that the unified plan the designer selected, out of all the
>>> possible plans, is exactly the sort of thing you would expect from a
>>> branching tree of common descent? What are the odds?
>>
>> That is evidence that the creator wants us to believe in common descent.
>
> A creator who wants to trick as many people as possible into eternal
> damnation is seriously messed up.
>

Totally unrelated, a non-sequitur.

[Robert Camp]

You're right, it's similarity that leads you to suspect a relationship
between the two books. That's the kind of observation that forms
patterns in our heads, that allows us to put pieces of a puzzle together
to form a greater understanding.

But you're wrong to think that it's just similarity that leads you to a
conclusion of plagiarism. You infer plagiarism only because you're
considering artifacts that you know to be intelligently devised, and
because you already know that humans are responsible for such things.

Humans have historically tended toward intuiting purpose upon noticing
similarity between objects/structures/functions of unknown origin. But
we've developed methods like science and critical analysis, so that
today we can get beyond mistakes like looking at rounded pebbles in a
stream and concluding that some designer must have rounded them all.

Your example makes both my points: the earlier one about similarity
being fundamental to understanding natural phenomena, and the recent one
about mistakes of intuition.

You need to be willing to examine the consequences of your arguments.

>> How far down the road of nihilism are you willing to travel?
> >
> I think nihilism describes the mindless, thoughtless random actions
> on irrational, non-intilligent processes. Better discriptive traits
> would be chaos, confusion, disorder, anarchy, etc..

Consult a dictionary.

>>> The fact
>>> that all organisms, extinct and extant have so much in common could
>>> just as well indicate a unified plan by an intelligent designer.
>>
>> Why would your putative "intelligent designer" design in such a way?
>> What do you know about this designer that suggests to you a unified plan
>> for similarity among extinct and extant animals would be one of
>> his/her/its design objectives?
>>
> What else? It's what one would expect of intelligence. If what we
> found was chaos, disorder, capricious laws of physics it would suggest
> unintelligable processes.

To suggest that you know what to expect of a non-human designing
intelligence, or that we have no reason to expect something "else," is
to presume that there cannot be an intelligence so much greater than, or
different from, our own that it might act very differently.

There are many possible reasons one could expect a designer to create by
way of a unified plan of similarity - conservation of resources for
example. But how do you know the designer has any need to conserve
resources? An omnipotent designer, for instance, can do anything, and
therefore has no need to worry about profligacy.

And how do you know that what we limited humans perceive as "chaos,
disorder, capricious laws of physics" isn't simply the designed, ordered
product of a much more advanced entity working on scales we cannot
imagine? Are you really so presumptuous as to assume that any possible
non-human intelligence *must* be utterly like our own?

You simply cannot support inference to supernatural, transcendental or
even just natural-but-so-advanced-as-to-seem-like-magic intelligent
design by way of analogy with human design. It's not a coherent argument.

You're trying to discuss really big issues without having really thought
about them.

[jillery]

On Sat, 14 Dec 2013 13:01:50 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/13/2013 8:12 PM, Darwin123 wrote:

<snip to point>

>> This is not proof of a Creator one way or another. It does prove one very
>> specific argument used by some Creationists is wrong. There may be a designer.
>> However, he has a lot more freedom in choosing genomes than is commonly claimed.
>>
>I don't understand how this falsifies anything. Proof is not an issue.
>Another point. There is a distinction between creationism as in
>"scientific creationism" and intelligent design. For example, the
>Creationism is genesis based, whereas I.D. is not. Creationism
>attempts to name the creator but I.D. looks at design which they
>believe is observable and testable but the idenity of the designer
>is unknown and unknowable. But in the same sense as I can determine
>the expertise of an engineer by his design, it may be possible to
>determine something of the characteristics and the mind of the
>designer. But not by me, by some much smarter than I am.

You can determine the expertise of an engineer by his design, because
you recognize the nature of the designer, a human. You share similar
experiences and behavioral traits. So even if you know nothing other
than the designer is human, you can make a lot of reasonable
assumptions.

OTOH you know nothing of your presumptive designer independent of its
presumptive design, so you have no basis for making any reasonable
assumptions about it.

[R. Dean]

But you must realize that modern evolutionary theory is a late comer
to the question of origins, an alternative explanation, if you will.
Before the appearance of Darwinism there were people who saw design
in nature as evidence of a designer. The most famous would be
William Paley. In fact an argument could be advanced that Darwin was
influenced by Paley and synonymously challenged by his work to find an
alternative explanation for origins.


> Eridanus
>
>

[R. Dean]

On 12/14/2013 7:18 AM, TomS wrote:
> "On Fri, 13 Dec 2013 17:31:27 -0500, in article
> <_ULqu.20562$rg6....@fx06.fr7>, R. Dean stated..."
> [...snip...]
>> This assumes too much. The viewpoint that similarity denotes common
>> ancestor is simply a premise without empirical evidence. The fact
>> that all organisms, extinct and extant have so much in common could
>> just as well indicate a unified plan by an intelligent designer.
>>
>
> Of course, if we assume that similarity indicates a unified plan by
> an intelligent designer, that means that there is a very unified plan
> for humans, chimps and other apes.
>

Of course, I was speaking in terms of life itself, rather than specific
groups, species or individual persons of individual animals ie my dog
or cat.

[R. Dean]

The Old Testament has been fulfilled, obsoleted and set aside by the New
Testament, for _believers_. Or haven't you heard.

[Paul Ciszek]

In article <OQ1ru.130$9g...@fx31.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>>
>The Old Testament has been fulfilled, obsoleted and set aside by the New
>Testament, for _believers_. Or haven't you heard.

So we can ignore those douchebags who keep quoting Leviticus 18 and 20?

[Paul Ciszek]

In article <171ru.81$S73...@fx17.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>On 12/14/2013 2:45 AM, Paul Ciszek wrote:
>> In article <1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>,
>>

>> A creator who wants to trick as many people as possible into eternal
>> damnation is seriously messed up.
>>
>Totally unrelated, a non-sequitur.

Nope. This creator has built evidence of an old earth into everything,
down to the isotopic level. And yet he sends anyone who believes the
version of events that he has so carefully framed up straight to hell.

[Burkhard]

Your bible doesn't have Matthew 5:18 then?

[Paul Ciszek]

In article <e21ru.80$S73...@fx17.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>>
>There may be overriding considerations and usually is where new
>and expermental processes are found. But generally speaking, in
>design work, one will use tried and true methods where possible
>rather than go with experimental or untried designs, unless one is in
>research and development; and even then one resorts to incorporating
>known processes where possible rather than go entirely into experimental
>areas.

Experiment? Research? Untried?

I thought this Creator was all knowing, and never made mistakes.

[R. Dean]

On 12/14/2013 12:24 PM, jillery wrote:
> On Sat, 14 Dec 2013 11:43:26 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/13/2013 5:53 PM, John Harshman wrote:
>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>> "� researchers conclude that ctenophores branched off first,

The alternative, as I see it would be chaos, disorder, whimical.

>
>
>> Life is interconnected
>> interdependent in a logical way; all life is dependent on life - as in
>> the "food chain". If protein from species to species were radically
>> different, for example, life could not exist. IOW there very well may
>> not be other possible plans.
>
>
> Sounds pretty rational to me.
>
>
>> We human are able to make predictions based upon what we observe, indeed
>> the fact that life, the laws of physics and the universe itself is
>> understandable and predictable as the result. This would not be
>> the case if everything was the result of a whimsical capricious or
>> fickle designer. Indeed, such would not fit the definition of
>> intelligent design.
>
>
> And it would not fit the definition of unguided design. So the real
> question is how does one tell the difference? Care to answer it?
>

Real design I think would be the opposite of chaotic, random mindless
meandering without plan, purpose, function or order. By contrast
design has purpose, function order and increasing interdependent
levels of complexity, all of which contribute to the functionality of
the unit. I know this sounds like irreduciable complexity, but it's
a step beyond.

[R. Dean]

On 12/14/2013 12:55 PM, jillery wrote:
> On Sat, 14 Dec 2013 12:12:45 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/13/2013 6:50 PM, Robert Camp wrote:
>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>> "� researchers conclude that ctenophores branched off first,

We can make predictions about intelligence in general, based upon human
intelligence. The same characterastics of intelligence should, be
ubiqious throughout, but not necessarily the same degree or levels of
intelligence.

>
> More to the point, your argument assumes intelligence is the only way
> such similarity can happen. Science shows that to be not the case.
>

It's a choice based upon which you personally see as the most reasonable
conclusion based upon the evidence.

>
>> If what we
>> found was chaos, disorder, capricious laws of physics it would suggest

>> unintelligible processes.

>
>
> No it would not. It would suggest a capricious deity or multiple
> deities with conflicting motives and goals, as in ancient mythologies.
>

This is true, which supports my contention which is that the opposite of
the scenario you describe, is the most reasonable.

[R. Dean]

On 12/14/2013 1:31 PM, jillery wrote:
> On Sat, 14 Dec 2013 13:01:50 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/13/2013 8:12 PM, Darwin123 wrote:
>
> <snip to point>
>
>>> This is not proof of a Creator one way or another. It does prove one very
>>> specific argument used by some Creationists is wrong. There may be a designer.
>>> However, he has a lot more freedom in choosing genomes than is commonly claimed.
>>>
>> I don't understand how this falsifies anything. Proof is not an issue.
>> Another point. There is a distinction between creationism as in
>> "scientific creationism" and intelligent design. For example, the
>> Creationism is genesis based, whereas I.D. is not. Creationism
>> attempts to name the creator but I.D. looks at design which they
>> believe is observable and testable but the idenity of the designer
>> is unknown and unknowable. But in the same sense as I can determine
>> the expertise of an engineer by his design, it may be possible to
>> determine something of the characteristics and the mind of the
>> designer. But not by me, by some much smarter than I am.
>
>
> You can determine the expertise of an engineer by his design, because
> you recognize the nature of the designer, a human. You share similar
> experiences and behavioral traits. So even if you know nothing other
> than the designer is human, you can make a lot of reasonable
> assumptions.
>

You missed my point it's the characteristic of the engineer that is
reflected in his design. I have known engineers whose designs are
elegant, and others who's designs are sloppy, but even the sloppy
engineers usually manage to accomplish their task; indeed if not in the
most desirable fashion. By this one can determine something about
the engineer.

>
> OTOH you know nothing of your presumptive designer independent of its
> presumptive design, so you have no basis for making any reasonable
> assumptions about it.
>

I think intelligence wherever you find it possesses most of the same
characteristics. Can I _prove_ it? No! But it's reasonable to conclude
as much.

[R. Dean]

On 12/14/2013 2:15 PM, Paul Ciszek wrote:
> In article <OQ1ru.130$9g...@fx31.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>>>
>> The Old Testament has been fulfilled, obsoleted and set aside by the New
>> Testament, for _believers_. Or haven't you heard.
>
> So we can ignore those douchebags who keep quoting Leviticus 18 and 20?
>

The Old Testament has been set aside for believers. So, yes you can
since you are a believer.

[R. Dean]

On 12/14/2013 2:18 PM, Paul Ciszek wrote:
> In article <171ru.81$S73...@fx17.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>> On 12/14/2013 2:45 AM, Paul Ciszek wrote:
>>> In article <1ldvf9v.61x0rgqo9p4vN%jo...@wilkins.id.au>,
>>>
>>> A creator who wants to trick as many people as possible into eternal
>>> damnation is seriously messed up.
>>>
>> Totally unrelated, a non-sequitur.
>
> Nope. This creator has built evidence of an old earth into everything,
> down to the isotopic level. And yet he sends anyone who believes the
> version of events that he has so carefully framed up straight to hell.
>

This is not something I am interested in. There is nothing that gives
the identified the intelligent designer. Furthermore, I don't think the
designer cares what one believes regarding the age of the universe,
or planet or anything else. There is reason to believe he apparently
washed his hands of his "creation".

[R. Dean]

I have no interest in discussing religion when science is the topic.
Matt 5:18 is religious, and not of interest in the scientific discussion
on origins. I've pointed out that the Old Testament has been obsoleted
for believers, in the hopes of pushing religion off the stage and out of
the picture.

[Robert Camp]

Go back and re-read. You are the one who missed the point.

>> OTOH you know nothing of your presumptive designer independent of its
>> presumptive design, so you have no basis for making any reasonable
>> assumptions about it.
>>
> I think intelligence wherever you find it possesses most of the same
> characteristics. Can I _prove_ it? No! But it's reasonable to conclude
> as much.

Why? What is the reason behind such a conclusion?

[R. Dean]

On 12/14/2013 2:21 PM, Paul Ciszek wrote:
> In article <e21ru.80$S73...@fx17.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>>>
>> There may be overriding considerations and usually is where new
>> and expermental processes are found. But generally speaking, in
>> design work, one will use tried and true methods where possible
>> rather than go with experimental or untried designs, unless one is in
>> research and development; and even then one resorts to incorporating
>> known processes where possible rather than go entirely into experimental
>> areas.
>
> Experiment? Research? Untried?
>
> I thought this Creator was all knowing, and never made mistakes.
>

I think you are relating to the Biblical concept of God.
There is nothing in the Intelligent Design hypothesis that suggest the
designer is the Biblical God. Indeed, I believe there is evidence of
design in nature, but absolutely no evidence which suggest the identity
of the designer. For all I know the designer may be Zeus.
>

[Richard Norman]

On Sat, 14 Dec 2013 17:11:55 +0000 (UTC), nos...@nospam.com (Paul
Ciszek) wrote:

>
>In article <H10ru.28231$rg6....@fx06.fr7>,
>R. Dean <"R. Dean"@gmail.com> wrote:
>>>
>>OK, but I was under the impression that by comparing the genomes
>>of several of these placozoans they determined their location in
>>the tree of life.
>
>According to wiki, there is genetic evidence to support the Epitheliozoa
>hypothesis, the idea that the Placozoa are a sister group to Eumetazoa
>and the "stomach side" of a placozoan is the precursor to the gut of
>Eumetazoans:
>
>http://en.wikipedia.org/wiki/Placozoa#Epitheliozoa_hypothesis
>
>Perhaps someone who knows sponges can answer me this: How does the larval
>form of a sponge differ from a placozoan?

Well, for one thing, a larval sponge develops into a mature sponge; a
placozoan does not. But I guess this doesn't satisfy you.

A nice description of sponge development and a very short section on
Placozoa is Chapter 5 of Ruppert, Fox, and Barne's "Invertebrate
Zoology"

http://www.fcnym.unlp.edu.ar/catedras/invertebrados/ruppert%26fox%26barnes_ch05_porifera%26placozoa.pdf

Here is more on Placozoa
http://www.ucmp.berkeley.edu/phyla/placozoa/placozoa.html

Placozoa have fewer and simpler cell types than sponges but do have a
particular intercellular junction found in all metazoa except sponges.
Both sponge larvae and placozoa have epithelial-like cell assemblages
but the placazoan type seems more "advanced". All the evidence
points to placozoa being intermediate (in terms of sequence of
branching) between sponges and cnidaria. The big thing now is where
to put the Ctenophora.

Larval placozoa have not been observed since reproduction seems to be
primarily asexual. Eggs have long been known but not sperm, although
a 2011 paper identifies a number of genes involved in sperm
production.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019639
Without larval forms, the developmental pattern of placozoa can't be
guessed.

Here is one comment on larval sponges: "Six major steps in animal
evolution: are we derived sponge larvae?", a paper from 2008.
http://www.ncbi.nlm.nih.gov/pubmed/18315817

http://www.newscientist.com/article/mg20227061.300-sponge-larvae-your-unlikely-ancestors.html

The notion of nervous-system-like cells is not absent from sponges.
Here is a paper from 2012 about light sensing cells in sponge larvae:
http://jeb.biologists.org/content/215/8/ii
That "eye" differs from all other animal eyes in not using opsin but
rather something akin to cryptochrome.

Also the larval sponge has an anterior-posterior orientation as well
as a development from a blastula stage. So sponge-like organisms at
the base of the animals is quite reasonable.

[Richard Norman]

On Sat, 14 Dec 2013 15:38:44 -0500, "R. Dean" <"R. Dean"@gmail.com>

wrote:

>On 12/14/2013 2:15 PM, Paul Ciszek wrote:
>> In article <OQ1ru.130$9g...@fx31.fr7>, R. Dean <"R. Dean"@gmail.com> wrote:
>>>>
>>> The Old Testament has been fulfilled, obsoleted and set aside by the New
>>> Testament, for _believers_. Or haven't you heard.
>>
>> So we can ignore those douchebags who keep quoting Leviticus 18 and 20?
>>
>The Old Testament has been set aside for believers. So, yes you can
>since you are a believer.

There seems to be inordinate number of "believers" insistent on
pushing the ten commandments into all sorts of public places. And
these same people also pick and choose very selected levitical and
deuteronomic bits and pieces about which "abominations" are truly
abominable.

[John Harshman]

So your answer would be "no", then?

[John Harshman]

On 12/14/13 8:43 AM, R. Dean wrote:

> On 12/13/2013 5:53 PM, John Harshman wrote:
>> On 12/13/13 2:31 PM, R. Dean wrote:
>>> On 12/13/2013 7:32 AM, TomS wrote:
>>>> "� researchers conclude that ctenophores branched off first,
>>>> not sponges as many have thought. Yet ctenophores have muscles
>>>> and nerve cells, cell types that sponges lack, suggesting that
>>>> animal evolution did not proceed smoothly from the simple to
>>>> the more complex. Instead, the ancestor to all these animals
>>>> may have had a more complex nervous system that sponges and
>>>> cnidarians lost, and the mesodermal tissue that gives rise to
>>>> muscles may have arisen independently in ctenophores."
>>>>
>>>> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>>>>
>>>> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>>>>
>>>>
>>>>
>>>>
>>>> About this research article:
>>>>
>>>> (many authors)
>>>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>>>> Implications for Cell Type Evolution
>>>> Science, volume 342 number 6164 (13 December 2013)
>>>> pages 1336ff
>>>> doi: 10.1126/science.124592
>>>>
>>>>
>>> This assumes too much. The viewpoint that similarity denotes common

>>> ancestor is simply a premise without empirical evidence. The fact

>>> that all organisms, extinct and extant have so much in common could
>>> just as well indicate a unified plan by an intelligent designer.
>>>

>> Why, yes. Anything at all could indicate such a unified plan. Isn't it
>> odd, though, that the unified plan the designer selected, out of all the
>> possible plans, is exactly the sort of thing you would expect from a
>> branching tree of common descent? What are the odds?
>>

> Why would you think an intelligent designer would act in such an

> unintelligible, irrational way as you suggest? Life is interconnected

> interdependent in a logical way; all life is dependent on life - as in
> the "food chain". If protein from species to species were radically
> different, for example, life could not exist. IOW there very well may
> not be other possible plans.

Your assumption is incorrect. If proteins were entirely different from
species to species, the food chain would work just fine as long as they
were made from the same 20 amino acids.

> We human are able to make predictions based upon what we observe, indeed
> the fact that life, the laws of physics and the universe itself is
> understandable and predictable as the result. This would not be
> the case if everything was the result of a whimsical capricious or
> fickle designer. Indeed, such would not fit the definition of
> intelligent design.

There is a big difference between randomness and absence of the
particular pattern that results from common descent. God would have a
choice of many, many regular patterns that had no relationship to an
evolutionary tree. And yet he chose the tree.

[John Harshman]

On 12/14/13 8:19 AM, Paul Ciszek wrote:
> In article<IZadnZ3Sx62B4THP...@giganews.com>,
> John Harshman<jhar...@pacbell.net> wrote:
>>
>> The outgroups were specified: they used various combinations of
>> opisthokonts, including choanoflagellates. And they had two data sets,
>> one of just 13 taxa and one of 50+ taxa (but fewer sites).
>
> Is this the sort of data set that you can keep adding to piecemeal?
> i.e., "Hey, I just sequenced a priaplulid worm, you want it?"
> Or, if you want a larger set of species, do you have go back and
> "do" them all together?
>
The former. Sequences are sequences, not comparisons. If you add a new
one, you can just put it into the database with all the old ones.

[Inyo]

"TomS" <TomS_...@newsguy.com> wrote in message
news:396937965.000...@drn.newsguy.com...

> ". researchers conclude that ctenophores branched off first,

> not sponges as many have thought. Yet ctenophores have muscles
> and nerve cells, cell types that sponges lack, suggesting that
> animal evolution did not proceed smoothly from the simple to
> the more complex. Instead, the ancestor to all these animals
> may have had a more complex nervous system that sponges and
> cnidarians lost, and the mesodermal tissue that gives rise to
> muscles may have arisen independently in ctenophores."

That last part perplexes me: "mesodermal tissue that gives rise to muscles
may have arisen independently in ctenophores." So, when the ctenophores
first branched off from the foundational ancestral organism, ctenophores had
not yet developed the necessary mesodermal tissue to give rise to muscles
and a more complex nervous system?

But the porifera and cnidarians did indeed possess such biological
complexities when they branched off, only to lose them later on--never
advancing to higher plateaus of biological organization (AKA, humans), while
the poor ctenophores, which traipsed away first from that ancestral
organism, had to find a way to recreate the identical essential tissues they
(ctenopores) lacked to begin with--although such complex genetics were
already present in the foundational animal--in order to provide biological
lines that eventually developed into humans?

Just askin', that's all. I suppose one potential answer could very well
be--"in a word...yes." OK. Flippancy accepted. The thing of it is is--while
I'm willing to follow the line of evidence wherever it leads, to whatever
conclusion, no matter the first-blush improbability, or even ostensible
logical absurdity of it, how does one go about proving either from the
fossil record, or even through genetic analyses, perhaps, that the porifera
and cnidarians lost mesodermal complexity advantages, tissues present when
they departed from the their ancestor?

At any rate, I fully expect the "Ancient Aliens" program to pick up on this
latest news. A pregnant line of investigation might be that Ancient Aliens
injected those ctenophores with the necessary genetic material to assure a
favorable biological outcome--videlicet, an animal that they could
eventually, millions of years later, with additional direct genetic
manipulation, steer toward the creation of modern humans, understanding as
they did that the ctenophore provided optimal genetic combinations, whereas
utilization of the porifera to such ends would have resulted in an organism
less malleable to their agenda.

http://inyo.coffeecup.com/site/manix/manixmypages.html
Web pages I have created: paleontology and music.

[jillery]

On Sat, 14 Dec 2013 15:05:34 -0500, "R. Dean" <"R. Dean"@gmail.com>

wrote:

>On 12/14/2013 12:55 PM, jillery wrote:
>> On Sat, 14 Dec 2013 12:12:45 -0500, "R. Dean" <"R. Dean"@gmail.com>
>> wrote:
>>
>>> On 12/13/2013 6:50 PM, Robert Camp wrote:
>>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>>> "� researchers conclude that ctenophores branched off first,

Predictions based on a sample of one are statistically unreliable.
When that's all there is, one can make plausible predictions, but it
supposed to be understood they are not evidence for anything.

>> More to the point, your argument assumes intelligence is the only way
>> such similarity can happen. Science shows that to be not the case.
>>
>It's a choice based upon which you personally see as the most reasonable
>conclusion based upon the evidence.

Wrong. What you describe is pure illogic and ignores evidence. Your
claimed evidence is that some aspects of human design are similar to
some aspects of life. You conveniently ignore the other aspects of
human design and other aspects of life are not at all similar. IOW
you cherrypick your evidence for ID and ignore the evidence against
it. That's not how good science is done.

And even if your claimed evidence was valid, it still wouldn't show
that all designed objects must have a designer. It can only show that
objects designed by humans have a designer.

>>> If what we
>>> found was chaos, disorder, capricious laws of physics it would suggest
>>> unintelligible processes.
>>
>>
>> No it would not. It would suggest a capricious deity or multiple
>> deities with conflicting motives and goals, as in ancient mythologies.
>>
>This is true, which supports my contention which is that the opposite of
>the scenario you describe, is the most reasonable.

You claim capricious law of physics implies unintelligence. I claim
capricious laws of physics implies capricious gods. So the opposite
is (not) (capricious laws of physics) implies (not) (capricious gods)
or (not) (gods). Since you seem to think reality is a democracy, I
vote for (not) gods.

[alias Ernest Major]

On 14/12/2013 16:19, Paul Ciszek wrote:
> In article <IZadnZ3Sx62B4THP...@giganews.com>,
> John Harshman <jhar...@pacbell.net> wrote:
>>
>> The outgroups were specified: they used various combinations of
>> opisthokonts, including choanoflagellates. And they had two data sets,
>> one of just 13 taxa and one of 50+ taxa (but fewer sites).

I misspoke. I meant unspecified in the abstract and press release. My
apologies for the sloppiness.

>
> Is this the sort of data set that you can keep adding to piecemeal?
> i.e., "Hey, I just sequenced a priaplulid worm, you want it?"
> Or, if you want a larger set of species, do you have go back and
> "do" them all together?
>

--
alias Ernest Major

[jillery]

On Sat, 14 Dec 2013 15:36:40 -0500, "R. Dean" <"R. Dean"@gmail.com>

No, I replied directly to your point. Regardless of the differences,
what you recognize of their designs you do because of your common
humanity. It's not the personal differences you describe that lets
you recognize the design as design.

>> OTOH you know nothing of your presumptive designer independent of its
>> presumptive design, so you have no basis for making any reasonable
>> assumptions about it.
>>
>I think intelligence wherever you find it possesses most of the same
>characteristics. Can I _prove_ it? No! But it's reasonable to conclude
>as much.

Not only is it unreasonable, but it's illogical and incorrect as well.

[Darwin123]

On Saturday, December 14, 2013 1:06:59 PM UTC-5, R. Dean wrote:

> > A creator who wants to trick as many people as possible into eternal
> > damnation is seriously messed up.
>
> >
>

> Totally unrelated, a non-sequitur.
But possibly true ! It may even be a tautology!

[Free Lunch]

On Sat, 14 Dec 2013 14:17:29 -0700, Richard Norman
<r_s_n...@comcast.net> wrote in talk.origins:

You'll never catch them quoting long sections from Jesus' Sermon on the
Mount, however.

[Darwin123]

On Saturday, December 14, 2013 1:37:30 PM UTC-5, R. Dean wrote:
> On 12/14/2013 3:15 AM, eridanus wrote:
>
> > El viernes, 13 de diciembre de 2013 22:31:27 UTC, R. Dean escribi�:

>
> >
>
> >>
>
> >>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>
> >>> Implications for Cell Type Evolution
>
> >>> Science, volume 342 number 6164 (13 December 2013)
>
> >>> pages 1336ff
>
> >>
>
> >>> doi: 10.1126/science.124592
>
> >>
>
> >> This assumes too much. The viewpoint that similarity denotes common
>

> >> ancestor is simply a premise without empirical evidence. The fact

>
> >> that all organisms, extinct and extant have so much in common could
>
> >> just as well indicate a unified plan by an intelligent designer.
>
> >
>

> > Of course, Dean.
>
> > The most humans dig exploring how happened the evolution of living beings,
>
> > the more likely it looks that it was planned this way by a god creator.
>
> >
>
> > Once the theory will be almost complete, you can come out reclaiming "this
>
> > was exactly the way that god made it. But he buried deep underground to
>
> > keep us busy working for five or seven centuries.
>
> >
>
> But you must realize that modern evolutionary theory is a late comer
>
> to the question of origins, an alternative explanation, if you will.
>
> Before the appearance of Darwinism there were people who saw design
>
> in nature as evidence of a designer. The most famous would be
>
> William Paley. In fact an argument could be advanced that Darwin was
>
> influenced by Paley and synonymously challenged by his work to find an
>
> alternative explanation for origins.

The Greek Xenophon, in his book Memorabilia (circa 380 BC) used almost
the exact same argument about 2.1 KY before Paley. Xenophon was quoting
Socrates, so it would seem that Socrates beat Paley. However, Socrates
and Xenophon were probably more logical than Paley.

One of the ways that Paley's argument fails is that his metaphorical
Designer is singular. In fact, the watch he found on the beach has multiple
designers. There is a whole lineage of clock makers who were designing
clocks before his watch was built. The knowledge that the final designer
had was an accumulation of knowledge from hundreds of designers.

The watch was effectively designed by a committee. The watch is the
final product of a number of designs, each slightly different from the
first. Some of the steps may have been bigger than others. However, there
was no one designer who said, "Okay, I just came up with all the components
and the integrated plans for the first clock in the world".

In fact, each component of the watch had its own designer. The metal
used to make the watch was designed by a different person than the glass on
the face. In fact, there is no one designer for anything that humans make.
The watch was basically designed by committee. If you don't believe it, then
take out some books on the history of clock design.

Socrates and Xenophon were pagans. They believed in many gods. This means
that they would have been comfortable with the idea of a world built by
committee.

Anyway, it really should have been called Xenophon's argument, not
Paley's argument.

[Darwin123]

On Saturday, December 14, 2013 11:43:26 AM UTC-5, R. Dean wrote:

> On 12/13/2013 5:53 PM, John Harshman wrote:
>
> > On 12/13/13 2:31 PM, R. Dean wrote:
>
> >> On 12/13/2013 7:32 AM, TomS wrote:
>
> >>> "� researchers conclude that ctenophores branched off first,
>
> >>> not sponges as many have thought. Yet ctenophores have muscles
>
> >>> and nerve cells, cell types that sponges lack, suggesting that
>
> >>> animal evolution did not proceed smoothly from the simple to
>
> >>> the more complex. Instead, the ancestor to all these animals
>
> >>> may have had a more complex nervous system that sponges and
>
> >>> cnidarians lost, and the mesodermal tissue that gives rise to
>
> >>> muscles may have arisen independently in ctenophores."
>
> >>>
>
> >>> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>
> >>>
>
> >>> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>
> >>>
>
> >>>
>
> >>>
>
> >>> About this research article:
>
> >>>
>
> >>> (many authors)
>

> >>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>
> >>> Implications for Cell Type Evolution
>
> >>> Science, volume 342 number 6164 (13 December 2013)
>
> >>> pages 1336ff
>
> >>> doi: 10.1126/science.124592
>
> >>>
>
> >>>
>
> >> This assumes too much. The viewpoint that similarity denotes common
>
> >> ancestor is simply a premise without empirical evidence. The fact
>
> >> that all organisms, extinct and extant have so much in common could
>
> >> just as well indicate a unified plan by an intelligent designer.
>
> >>
>

> > Why, yes. Anything at all could indicate such a unified plan. Isn't it
>
> > odd, though, that the unified plan the designer selected, out of all the
>
> > possible plans, is exactly the sort of thing you would expect from a
>
> > branching tree of common descent? What are the odds?
>
> >
>
> Why would you think an intelligent designer would act in such an
>
> unintelligible, irrational way as you suggest? Life is interconnected
>
> interdependent in a logical way; all life is dependent on life - as in
>
> the "food chain". If protein from species to species were radically
>
> different, for example, life could not exist. IOW there very well may
>
> not be other possible plans.

Which means that you are missing the point about genome similarity.

The genomic code is redundant. The morphology and chemistry of an
organism is somewhat insensitive to the sequence of base pairs on the DNA
molecule. One could construct a creature with nearly identical to any
individual, with the same proteins and the same morphology, using a vastly
different sequence.

Evidence exists in the types of common mutations that cause large
changes in genome but small changes in both chemistry and morphology. Transpositions can change large DNA sequences without affecting the
phenotype severally. Even gene duplications can occur without changing
the phenotype. Hence, the organism is fairly robust to changes in genome.

Hence, similarity in genome is not necessary for similarity in phenotype.
One could build the same species (phenotypically) using genes that have
been scrambled relative to the original.

Hence, the Creator doesn't have to always use similar genomes. He
could build robust species using different genomes. Since the chemistry
would nearly be the same, the creatures could eat each other with no
difficulty.

Animals digest their food. Proteins are broken up into amino acids,
carbohydrate polymers into carbohydrate monomers, fats into fatty acids.
There is no need to make proteins similar. We could all survive, eating
each other, with different genomes.

Similarity in DNA sequences have a random element, with or without
a Designer. He could have chosen to have different species with completely
different genomes, but with the same forms we see today. Thus, he had a choice. The fact we see such similarities in genome today, not required for
survival, indicates whim on the part of the Creator. Not that this is impossible.

Consider watches. There are quartz crystal watches, spring watches,
and all sorts of clock works. Some of the clocks seem identical on the
outside, but are completely different inside. This is because every
clock has a history. There is an entire lineage of clock makers behind
every clock. There is no one watch maker to Paley's watch.

[Burkhard]

On Saturday, December 14, 2013 10:58:46 PM UTC, Darwin123 wrote:
>
>
> > > The most humans dig exploring how happened the evolution of living beings,

>

> > But you must realize that modern evolutionary theory is a late comer
> > to the question of origins, an alternative explanation, if you will.
> > Before the appearance of Darwinism there were people who saw design
> > in nature as evidence of a designer. The most famous would be
>
> > William Paley. In fact an argument could be advanced that Darwin was
>

> > influenced by Paley and synonymously challenged by his work to find an
> > alternative explanation for origins.
>
>
>
> The Greek Xenophon, in his book Memorabilia (circa 380 BC) used almost
> the exact same argument about 2.1 KY before Paley. Xenophon was quoting
> Socrates, so it would seem that Socrates beat Paley. However, Socrates
> and Xenophon were probably more logical than Paley.
>
>
> One of the ways that Paley's argument fails is that his metaphorical
> Designer is singular. In fact, the watch he found on the beach has multiple
> designers. There is a whole lineage of clock makers who were designing
> clocks before his watch was built. The knowledge that the final designer
> had was an accumulation of knowledge from hundreds of designers.
>
>
>
> The watch was effectively designed by a committee. The watch is the
> final product of a number of designs, each slightly different from the

> first. Some of the steps may have been bigger than others. However, tre

> was no one designer who said, "Okay, I just came up with all the components
> and the integrated plans for the first clock in the world".

> In fact, each component of the watch had its own designer. The metal
> used to make the watch was designed by a different person than the glass on
> the face. In fact, there is no one designer for anything that humans make.
> The watch was basically designed by committee. If you don't believe it, then
> take out some books on the history of clock design.
>

> Socrates and Xenophon were pagans. They believed in many gods. This means >
> that they would have been comfortable with the idea of a world built by
> committee.
>

> Anyway, it really should have been called Xenophon's argument, not >
> Paley's argument.

Furthermore, a significant number of features in biology are results of an
obvious arms, race, predator -prey dynamics. So the designers not just
work in teams, but opposing teams with shifting alliances. another data
point for the Greek pantheon as the designers - though of course they
never claimed such a thing for themselves

[John Harshman]

A matter of parsimony, one supposes. Either they were gained
independently or sponges lost them. There are two reasons to believe the
former, only one of which the paper mentions. The genes responsible for
development of the same sorts of tissues are considerably different
between ctenophores and the other metazoans that have them. The other
reason is that sponges have often been reconstructed as paraphyletic,
meaning that multiple losses would be required.

> At any rate, I fully expect the "Ancient Aliens" program to pick up on this
> latest news. A pregnant line of investigation might be that Ancient Aliens
> injected those ctenophores with the necessary genetic material to assure a
> favorable biological outcome--videlicet, an animal that they could
> eventually, millions of years later, with additional direct genetic
> manipulation, steer toward the creation of modern humans, understanding as
> they did that the ctenophore provided optimal genetic combinations, whereas
> utilization of the porifera to such ends would have resulted in an organism
> less malleable to their agenda.

That scenario works less well if there are different genes involved in
the two taxa.

[R. Dean]

That all life on the planet uses the same 20 amino acids is by itself,
curious given how many amino acids are found in nature.

>
>> We human are able to make predictions based upon what we observe, indeed
>> the fact that life, the laws of physics and the universe itself is
>> understandable and predictable as the result. This would not be
>> the case if everything was the result of a whimsical capricious or
>> fickle designer. Indeed, such would not fit the definition of
>> intelligent design.
>
> There is a big difference between randomness and absence of the
> particular pattern that results from common descent. God would have a
> choice of many, many regular patterns that had no relationship to an
> evolutionary tree. And yet he chose the tree.
>

Here you are making unjustified assumptions. We humans found these
tree patterns. If the I.Der had chosen a different pattern; you
could have detected the pattern and made the same observation.
Of course, you realize the "evolutionary trees" were seen before
Darwin. And I'm sure you are aware of the late Stephen J. Gould's
view of the evolutionary tree.

[R. Dean]

On 12/14/2013 5:12 PM, jillery wrote:
> On Sat, 14 Dec 2013 15:05:34 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/14/2013 12:55 PM, jillery wrote:
>>> On Sat, 14 Dec 2013 12:12:45 -0500, "R. Dean" <"R. Dean"@gmail.com>
>>> wrote:
>>>
>>>> On 12/13/2013 6:50 PM, Robert Camp wrote:
>>>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>>>> "� researchers conclude that ctenophores branched off first,

Yes, I believe this is true.

You conveniently ignore the other aspects of
> human design and other aspects of life are not at all similar. IOW
> you cherrypick your evidence for ID and ignore the evidence against
> it. That's not how good science is done.
>

This is an extremely broad claim you are making for me. Can you be more
specific.

>
> And even if your claimed evidence was valid, it still wouldn't show
> that all designed objects must have a designer. It can only show that
> objects designed by humans have a designer.
>

In an earlier post I described in some detail what I consider
intelligent design Vs unintelligible design.

>
>>>> If what we
>>>> found was chaos, disorder, capricious laws of physics it would suggest
>>>> unintelligible processes.
>>>
>>>
>>> No it would not. It would suggest a capricious deity or multiple
>>> deities with conflicting motives and goals, as in ancient mythologies.
>>>
>> This is true, which supports my contention which is that the opposite of
>> the scenario you describe, is the most reasonable.
>
>
> You claim capricious law of physics implies unintelligence. I claim
> capricious laws of physics implies capricious gods. So the opposite
> is (not) (capricious laws of physics) implies (not) (capricious gods)
> or (not) (gods). Since you seem to think reality is a democracy, I
> vote for (not) gods.
>

Maybe it's too late here. This at the moment is a riddle which I'm too
tired to try to solve. - Thanks Jill

[eridanus]

El s�bado, 14 de diciembre de 2013 18:14:23 UTC, Robert Camp escribi�:

> On 12/14/13 9:12 AM, R. Dean wrote:
>
> > On 12/13/2013 6:50 PM, Robert Camp wrote:
>
> >> On 12/13/13 2:31 PM, R. Dean wrote:
>
> >>> On 12/13/2013 7:32 AM, TomS wrote:
>

> >>>> "� researchers conclude that ctenophores branched off first,

>
> >>>> not sponges as many have thought. Yet ctenophores have muscles
>
> >>>> and nerve cells, cell types that sponges lack, suggesting that
>
> >>>> animal evolution did not proceed smoothly from the simple to
>
> >>>> the more complex. Instead, the ancestor to all these animals
>
> >>>> may have had a more complex nervous system that sponges and
>
> >>>> cnidarians lost, and the mesodermal tissue that gives rise to
>
> >>>> muscles may have arisen independently in ctenophores."
>
> >>>>
>
> >>>> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>
> >>>>
>
> >>>> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>
> >>>>
>
> >>>>
>
> >>>>
>
> >>>>
>
> >>>> About this research article:
>
> >>>>
>
> >>>> (many authors)
>
> >>>> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
>
> >>>> Implications for Cell Type Evolution
>
> >>>> Science, volume 342 number 6164 (13 December 2013)
>
> >>>> pages 1336ff
>
> >>>> doi: 10.1126/science.124592
>
> >>>>
>
> >>>>
>
> >>> This assumes too much. The viewpoint that similarity denotes common
>
> >>> ancestor is simply a premise without empirical evidence.
>
> >>
>
> >> Have you ever actually taken the time to think about the role
>
> >> "similarity" plays in virtually all of our knowledge-seeking endeavors?
>
> > >
>
> > Yes, if I found two books by two different authors and I found that
>
> > chapter after chapter in the two books were the same or almost the same
>
> > wording I would not assume two different writers had exactly the same
>
> > thoughts. I would call the work of one person; the other plagiarism.
>
>
>

> You're right, it's similarity that leads you to suspect a relationship
>
> between the two books. That's the kind of observation that forms
>
> patterns in our heads, that allows us to put pieces of a puzzle together
>
> to form a greater understanding.
>
>
>
> But you're wrong to think that it's just similarity that leads you to a
>
> conclusion of plagiarism. You infer plagiarism only because you're
>
> considering artifacts that you know to be intelligently devised, and
>
> because you already know that humans are responsible for such things.
>
>
>
> Humans have historically tended toward intuiting purpose upon noticing
>
> similarity between objects/structures/functions of unknown origin. But
>
> we've developed methods like science and critical analysis, so that
>
> today we can get beyond mistakes like looking at rounded pebbles in a
>
> stream and concluding that some designer must have rounded them all.
>
>
>
> Your example makes both my points: the earlier one about similarity
>
> being fundamental to understanding natural phenomena, and the recent one
>
> about mistakes of intuition.
>
>
>
> You need to be willing to examine the consequences of your arguments.

>
>
>
> >> How far down the road of nihilism are you willing to travel?
>
> > >
>
> > I think nihilism describes the mindless, thoughtless random actions
>
> > on irrational, non-intilligent processes. Better discriptive traits
>
> > would be chaos, confusion, disorder, anarchy, etc..
>
>
>

> Consult a dictionary.

>
>
>
> >>> The fact
>
> >>> that all organisms, extinct and extant have so much in common could
>
> >>> just as well indicate a unified plan by an intelligent designer.
>
> >>
>
> >> Why would your putative "intelligent designer" design in such a way?
>
> >> What do you know about this designer that suggests to you a unified plan
>
> >> for similarity among extinct and extant animals would be one of
>
> >> his/her/its design objectives?
>
> >>
>

> > What else? It's what one would expect of intelligence. If what we

>
> > found was chaos, disorder, capricious laws of physics it would suggest
>

> > unintelligable processes.
>
>
>
> To suggest that you know what to expect of a non-human designing
>
> intelligence, or that we have no reason to expect something "else," is
>
> to presume that there cannot be an intelligence so much greater than, or
>
> different from, our own that it might act very differently.
>
>
>
> There are many possible reasons one could expect a designer to create by
>
> way of a unified plan of similarity - conservation of resources for
>
> example. But how do you know the designer has any need to conserve
>
> resources? An omnipotent designer, for instance, can do anything, and
>
> therefore has no need to worry about profligacy.
>
>
>
> And how do you know that what we limited humans perceive as "chaos,
>
> disorder, capricious laws of physics" isn't simply the designed, ordered
>
> product of a much more advanced entity working on scales we cannot
>
> imagine? Are you really so presumptuous as to assume that any possible
>
> non-human intelligence *must* be utterly like our own?
>
>
>
> You simply cannot support inference to supernatural, transcendental or
>
> even just natural-but-so-advanced-as-to-seem-like-magic intelligent
>
> design by way of analogy with human design. It's not a coherent argument.
>
>
>
> You're trying to discuss really big issues without having really thought
>
> about them.

a wonderful reply. Thanks,
eridanus

[RonO]

On 12/13/2013 6:32 AM, TomS wrote:
> "� researchers conclude that ctenophores branched off first,

> not sponges as many have thought. Yet ctenophores have muscles
> and nerve cells, cell types that sponges lack, suggesting that
> animal evolution did not proceed smoothly from the simple to
> the more complex. Instead, the ancestor to all these animals
> may have had a more complex nervous system that sponges and
> cnidarians lost, and the mesodermal tissue that gives rise to
> muscles may have arisen independently in ctenophores."
>
> Elizabeth Pennisi, "ScienceShot: Your Cousin Was a Comb Jelly"
>
> <http://news.sciencemag.org/biology/2013/12/scienceshot-your-cousin-was-comb-jelly?rss=1>
>
> About this research article:
>
> (many authors)
> The Genome of the Ctenophor _Mnemiopsis leidyi_ and Its
> Implications for Cell Type Evolution
> Science, volume 342 number 6164 (13 December 2013)
> pages 1336ff
> doi: 10.1126/science.124592
>
>

The article that I read on this finding said that they got this result
in 2 out of the 3 analyses that they did. If they did a fourth what
would they get? This tells me that the results are probably too close
to call at this time, and they have to figure out all the confounding
details before they can be more sure of this claim.

They are using genome sequence, but they have to pick the "right" genes
for the analysis. They don't want to pick genes that are subject to
things like duplication and loss or that are prone to things like gene
conversion. They want to use single copy genes that were present in the
common ancestor. They have to avoid genes that duplicated and one copy
does the original function, but the others do other things (derived
functions that evolved since the last common ancestor of all metazoans
(multicellular animals)).

My guess is that mitochondrial functional genes might be the ones to
look at. Nuclear encoded mitochondrial genes such as the cytochrome
oxidase complex proteins. Ribosomal protein genes would do, and
specific tRNA synthases probably haven't changed since the last common
ancestor.

They can compare genomes, but if they pick the wrong genes they are
going to get the wrong answers. If they just pick as many genes as they
can they will likely get a mess. This ancestor existed so long ago
(hundreds of millions of years before the Cambrian explosion) that there
is a lot of noise in the data, and they have to try to reduce the noise
to see if there is enough signal left to make conclusions. To reduce
the noise they will likely resort to using conserved parts of genes
where they can rule out multiple small indels. When multiple insertions
and deletions have occurred in regions of the protein that isn't well
conserved you can't tell what amino acid residues align and the protein
alignments are just guessing. If these regions are not removed they
just produce spurious data.

So my guess is that the jury isn't in and the race hasn't even started, yet.

Ron Okimoto

[jillery]

Excellent point and well stated. I particularly like your last
allusion.

[jillery]

On Sat, 14 Dec 2013 16:08:39 -0500, "R. Dean" <"R. Dean"@gmail.com>

Then your presumption of a designer is useless, because you have no
way to say what your designer can and can't do.

[John Harshman]

You have changed the subject, but that still doesn't help you. The fact
you now bring up makes sense given common descent, but once again it
isn't at all necessary given creation.

>>> We human are able to make predictions based upon what we observe, indeed
>>> the fact that life, the laws of physics and the universe itself is
>>> understandable and predictable as the result. This would not be
>>> the case if everything was the result of a whimsical capricious or
>>> fickle designer. Indeed, such would not fit the definition of
>>> intelligent design.
>>
>> There is a big difference between randomness and absence of the
>> particular pattern that results from common descent. God would have a
>> choice of many, many regular patterns that had no relationship to an
>> evolutionary tree. And yet he chose the tree.
>>
> Here you are making unjustified assumptions. We humans found these
> tree patterns. If the I.Der had chosen a different pattern; you
> could have detected the pattern and made the same observation.

Nope. There is only one pattern consistent with common descent. Some
other pattern wouldn't have been.

> Of course, you realize the "evolutionary trees" were seen before
> Darwin. And I'm sure you are aware of the late Stephen J. Gould's
> view of the evolutionary tree.

Your first sentence is incorrect. Darwin was the first to present what
is clearly an evolutionary tree. If you're thinking of Lamarck, it's
apparent to me that he meant something different. Anyway, what does it
matter who was first? I have no idea what you mean by bringing up Gould,
but you are almost certainly mistaken about his views.

[TomS]

"On Sun, 15 Dec 2013 09:06:22 -0500, in article
<6odra9tdhnii1sbq5...@4ax.com>, jillery stated..."

>
>On Sat, 14 Dec 2013 15:18:36 -0800 (PST), Darwin123
><drose...@yahoo.com> wrote:

[...snip...]

>> Consider watches. There are quartz crystal watches, spring watches,
>>and all sorts of clock works. Some of the clocks seem identical on the
>>outside, but are completely different inside. This is because every
>>clock has a history. There is an entire lineage of clock makers behind
>>every clock. There is no one watch maker to Paley's watch.
>
>
>Excellent point and well stated. I particularly like your last
>allusion.
>

I wonder in Paley's day, whether each watch was individually
designed and made, one by one, by an artisan.

Unlike today, when watches are made on assembly lines, and the
watches are not individually designed and made, but are mass
produced.


--
---Tom S.

[RMcBane]

Or if there is one or many designers. Not to mention that designers
often aren't the maker of the designed object. And the makers don't
always follow the design.



--
Richard McBane

[jillery]

On Sun, 15 Dec 2013 00:46:06 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

>On 12/14/2013 4:39 PM, John Harshman wrote:
>> On 12/14/13 8:43 AM, R. Dean wrote:
>>> On 12/13/2013 5:53 PM, John Harshman wrote:
>>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>>> "� researchers conclude that ctenophores branched off first,

What do you mean by "found in nature"? There are few other sources of
amino acids except from life. If you really mean "all possible amino
acids, your conjecture is only superficially curious. Yes, there are
many possible amino acids, most of which are not used for life. But
of the 20 most commonly used amino acids used by life, they represent
the chemically simplest ones, from glycine to tryptophan. That's not
surprising at all.

There are larger, synthetic amino acids, some of which have been
incorporated into the DNA code for research purposes.

>>> We human are able to make predictions based upon what we observe, indeed
>>> the fact that life, the laws of physics and the universe itself is
>>> understandable and predictable as the result. This would not be
>>> the case if everything was the result of a whimsical capricious or
>>> fickle designer. Indeed, such would not fit the definition of
>>> intelligent design.
>>
>> There is a big difference between randomness and absence of the
>> particular pattern that results from common descent. God would have a
>> choice of many, many regular patterns that had no relationship to an
>> evolutionary tree. And yet he chose the tree.
>>
>Here you are making unjustified assumptions. We humans found these
>tree patterns. If the I.Der had chosen a different pattern; you
>could have detected the pattern and made the same observation.

Do you really think the scientists who found that pattern didn't know
that? That's why they didn't just observe the pattern and think their
job done. Instead, they used that pattern to predict what they would
find in the future. Every known species has been tested against the
pattern they found, with high correlation. That wouldn't happen if
the pattern they "found" was just happenstance.

>Of course, you realize the "evolutionary trees" were seen before
>Darwin. And I'm sure you are aware of the late Stephen J. Gould's
>view of the evolutionary tree.

Gould certainly didn't accept ID, or any version of designed life. Any
cite you have that you think suggests otherwise is almost certainly a
quotemine.

[TomS]

"On Sun, 15 Dec 2013 06:14:17 -0800, in article
<LKmdnd90YsGmJDDP...@giganews.com>, John Harshman stated..."
[...snip...]

>Nope. There is only one pattern consistent with common descent. Some
>other pattern wouldn't have been.

[...snip...]

The pattern of a nested hierarchy is indicative of common descent.

This pattern is also seen as indicative of common descent in the
field of linguistics, and in textual criticism. In fact, the very
same computer-baeed algorithms that have been developed for biology
have been applied to languages and to texts.

And, as it happens, no one has suggested an alternative explanation
for the nested hierarchy of biological variations (similarities
and differences), an explanation which accounts for that pattern
without involving common descent with modification. To be sure,
there were some suggestions which differ from Darwin's main one
(that is, undirected variation and differential reproductive
success: aka natural selection); I'd mention inheritance of
acquired characteristics and neutral drift among others. But I'm
not aware of any attempt at an explanation which does not involve
common descent. (And I don't count "that's the way it happens to
be" as an attempt at an explanation. Thus I rule out Omphalism
as an attempt at an explanation.)

And I'd also note that there is a *prediction* to this "tree of
life". Whenever we discover or investigate a new biological
specimen, whether extant or extinct, it will find its place in
the tree of life. This is not often explicitly noted, but it is
certainly there in every new sequencing of DNA and in every new
fossil discovery.


--
---Tom S.

[jillery]

On Sun, 15 Dec 2013 01:01:47 -0500, "R. Dean" <"R. Dean"@gmail.com>

wrote:

>On 12/14/2013 5:12 PM, jillery wrote:
>> On Sat, 14 Dec 2013 15:05:34 -0500, "R. Dean" <"R. Dean"@gmail.com>
>> wrote:
>>
>>> On 12/14/2013 12:55 PM, jillery wrote:
>>>> On Sat, 14 Dec 2013 12:12:45 -0500, "R. Dean" <"R. Dean"@gmail.com>
>>>> wrote:
>>>>
>>>>> On 12/13/2013 6:50 PM, Robert Camp wrote:
>>>>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>>>>> "� researchers conclude that ctenophores branched off first,

Odd that you accept my first claim so easily and then object to this
corollary. Or did you not understand its implication? By "some
aspects" I mean that you focus on specific aspects, and so ignore
others by definition.

>Can you be more specific.

More specific about what? If you mean about the evidence you ignore,
it has been specified many times by many posters. Some obvious
examples are the recurrent laryngeal nerve, lungs in sea mammals, and
wisdom teeth in humans. Without bogging down in specifics, all of
these are examples of poor "design", but are readily explained by
contingent evolution. For another group, try cancer, autoimmune and
hereditary diseases, which illustrate the imperfections of cellular
"design", but are read lily explained by molecular biology.

>> And even if your claimed evidence was valid, it still wouldn't show
>> that all designed objects must have a designer. It can only show that
>> objects designed by humans have a designer.
>>
>In an earlier post I described in some detail what I consider
>intelligent design Vs unintelligible design.

Do you refer to your post where you wrote:
***********************************

Why would you think an intelligent designer would act in such an
unintelligible, irrational way as you suggest? Life is interconnected
interdependent in a logical way; all life is dependent on life - as in
the "food chain". If protein from species to species were radically
different, for example, life could not exist. IOW there very well may
not be other possible plans.

************************************

You haven't yet supported your claim that the suggestion to which you
refer above describes an unintelligible or irrational way. Will you
do so now?

And other posters handily corrected your assertion about "radically
different proteins".

[jillery]

Not to beat this dead horse beyond reincarnation, but if one has
absolutely no evidence of the identity of a presumptive designer,
there's nothing that anybody can reasonably say about it, or it's
designs, or even if it's capable of designs. Such a conjecture
literally can't predict anything.

[jillery]

Given that most watches and clocks today are strictly electronic, and
their function incorporated into smartphones, it's hard to appreciate
what a challenge it was to make accurate timepieces when even spring
steel was rare and expensive.

I find the story of John Harrison inspiring.

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

[jillery]

On Sun, 15 Dec 2013 01:01:47 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

[...]

>>>>> If what we
>>>>> found was chaos, disorder, capricious laws of physics it would suggest
>>>>> unintelligible processes.
>>>>
>>>>
>>>> No it would not. It would suggest a capricious deity or multiple
>>>> deities with conflicting motives and goals, as in ancient mythologies.
>>>>
>>> This is true, which supports my contention which is that the opposite of
>>> the scenario you describe, is the most reasonable.
>>
>>
>> You claim capricious law of physics implies unintelligence. I claim
>> capricious laws of physics implies capricious gods. So the opposite
>> is (not) (capricious laws of physics) implies (not) (capricious gods)
>> or (not) (gods). Since you seem to think reality is a democracy, I
>> vote for (not) gods.
>>
>Maybe it's too late here. This at the moment is a riddle which I'm too
>tired to try to solve. - Thanks Jill

I understand. I too get tired when asked to consider the opposite of
capricious deities.

[Mitchell Coffey]

Lamarck didn't believe in an evolutionary tree, but rather a small
number of strait, thin, non-bushy trees, each with a limited amount of
branching.

Mitchell Coffey

[Darwin123]

On Sunday, December 15, 2013 9:16:11 AM UTC-5, TomS wrote:
> "On Sun, 15 Dec 2013 09:06:22 -0500, in article
>
> <6odra9tdhnii1sbq5...@4ax.com>, jillery stated..."
>
> >
>
> >On Sat, 14 Dec 2013 15:18:36 -0800 (PST), Darwin123

>

> [...snip...]
>
> >> Consider watches. There are quartz crystal watches, spring watches,
>
> >>and all sorts of clock works. Some of the clocks seem identical on the
>
> >>outside, but are completely different inside. This is because every
>
> >>clock has a history. There is an entire lineage of clock makers behind
>
> >>every clock. There is no one watch maker to Paley's watch.
>
> >
>
> >
>
> >Excellent point and well stated. I particularly like your last
>
> >allusion.
>
> >
>
>
>
> I wonder in Paley's day, whether each watch was individually
>
> designed and made, one by one, by an artisan.

I think this is the case. However, artisans require an education.
They usually received their education by first being an apprentice.
The master artisan would teach them the "state of the art" in clock
technology.

The "state of the art" looked "finely tuned" for its function. However,
there had been a long period of trial and error to develop this state. The
clock went through generations of generations of artisans, making variations
on older designs and even borrowing ideas from contemporary artisans.

I assure you that Paleys watch looked much different from clocks that
had been made a hundred years before. The artisan himself would try out
different ideas in his lifetime. There was no way an individual human could
have designed a "fine tuned" watch at his first effort.

Read the book "Longitude" or the TV program based on the book to see
how long it took one artisan to develop a Naval chronometer, even while borrowing ideas from others. There were a lot of designs for a Naval
chronometer that failed for one reason or another. It took at least 7 trials,
same artisan, to make something that would work a reasonable number of times.

The apprentice would first help the master artisan make the master
artisan pieces. The artisan would already have made dozens of clocks on his
own, some of which didn't work. The artisan learned from his mentor. Meanwhile,
artisans would be looking at each others work. They exchanged ideas.

There was no one clock designer who knew everything there was to know about clocks. Further, no clock designer was born with the knowledge of how
clocks work. It would take a year or two from birth just to be able to read a clock.

>
>
>
> Unlike today, when watches are made on assembly lines, and the
> watches are not individually designed and made, but are mass
> produced.

I think there is a lack of appreciation in the creativity and
study involved in making an assembly line. There are teams of people
working together to design assembly lines, each using the knowledge
of past generations of designers. Note that there was no one inventor
of the "assembly line", just as there is no one designer for the watch.

So maybe the camel was made by a committee. There would be nothing
wrong with that. A committee of experts can be much more effective than a single, uneducated designer.

Sorry. I have been spending too much time at an Asatru website. Those
heathens made too many good arguments!!

[Darwin123]

Our own brains work on a cellular level in terms of random impulses. Coherent thoughts are the result of feedback loops that amplify some of the random impulses. Hence, even intelligent animals apparently make decisions that are random. If you believe in deities, then you can imagine that the deity work this way.

I also think some clergy are confused by the concept of "free will". Their definition of free will looks a lot like the mathematical definition of random. The mathematical definition of random is usually associated with lack of correlation. Some would say that it is the lack of logical consistency. This is the way some clergy define free will.

So maybe the Designer has free will in the sense of randomness. Many of his
decisions are initiated by random signals.

By this argument, evolution is merely the free will of the Designer! Evolution studies prove that there is an abundance of free will for every organism.

[eridanus]

El domingo, 15 de diciembre de 2013 13:40:16 UTC, Ron O escribi�:

> On 12/13/2013 6:32 AM, TomS wrote:
>

> > "� researchers conclude that ctenophores branched off first,

the hell is not written in the constitution; it is hidden below.

Some theoretical analysis are a little like the constitution. Fine on
the surface and dubious if you keep digging in.

Eridanus

[jillery]

On Sun, 15 Dec 2013 12:34:46 -0800 (PST), Darwin123
<drose...@yahoo.com> wrote:


[...]

> Our own brains work on a cellular level in terms of random impulses. Coherent thoughts are the result of feedback loops that amplify some of the random impulses. Hence, even intelligent animals apparently make decisions that are random. If you believe in deities, then you can imagine that the deity work this way.
>
> I also think some clergy are confused by the concept of "free will". Their definition of free will looks a lot like the mathematical definition of random. The mathematical definition of random is usually associated with lack of correlation. Some would say that it is the lack of logical consistency. This is the way some clergy define free will.
>
> So maybe the Designer has free will in the sense of randomness. Many of his
>decisions are initiated by random signals.
>
> By this argument, evolution is merely the free will of the Designer! Evolution studies prove that there is an abundance of free will for every organism.

So what other characteristics besides free will has this Designer of
yours?

[R. Dean]

On 12/14/2013 5:28 PM, jillery wrote:
> On Sat, 14 Dec 2013 15:36:40 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/14/2013 1:31 PM, jillery wrote:
>>> On Sat, 14 Dec 2013 13:01:50 -0500, "R. Dean" <"R. Dean"@gmail.com>
>>> wrote:
>>>
>>>> On 12/13/2013 8:12 PM, Darwin123 wrote:
>>>
>>> <snip to point>
>>>
>>>>> This is not proof of a Creator one way or another. It does prove one very
>>>>> specific argument used by some Creationists is wrong. There may be a designer.
>>>>> However, he has a lot more freedom in choosing genomes than is commonly claimed.
>>>>>
>>>> I don't understand how this falsifies anything. Proof is not an issue.
>>>> Another point. There is a distinction between creationism as in
>>>> "scientific creationism" and intelligent design. For example, the
>>>> Creationism is genesis based, whereas I.D. is not. Creationism
>>>> attempts to name the creator but I.D. looks at design which they
>>>> believe is observable and testable but the idenity of the designer
>>>> is unknown and unknowable. But in the same sense as I can determine
>>>> the expertise of an engineer by his design, it may be possible to
>>>> determine something of the characteristics and the mind of the
>>>> designer. But not by me, by some much smarter than I am.
>>>
>>>
>>> You can determine the expertise of an engineer by his design, because
>>> you recognize the nature of the designer, a human. You share similar
>>> experiences and behavioral traits. So even if you know nothing other
>>> than the designer is human, you can make a lot of reasonable
>>> assumptions.
>>>
>> You missed my point it's the characteristic of the engineer that is
>> reflected in his design. I have known engineers whose designs are
>> elegant, and others who's designs are sloppy, but even the sloppy
>> engineers usually manage to accomplish their task; indeed if not in the
>> most desirable fashion. By this one can determine something about
>> the engineer.
>
>
> No, I replied directly to your point. Regardless of the differences,
> what you recognize of their designs you do because of your common
> humanity. It's not the personal differences you describe that lets
> you recognize the design as design.
>
I didn't say I could determine anything from personal differences, but
rather from the designs, I can tell something about the engineers from
their designs. I think this applies to just about any work.
>
>>> OTOH you know nothing of your presumptive designer independent of its
>>> presumptive design, so you have no basis for making any reasonable
>>> assumptions about it.
>>>
>> I think intelligence wherever you find it possesses most of the same
>> characteristics. Can I _prove_ it? No! But it's reasonable to conclude
>> as much.
>
>
> Not only is it unreasonable, but it's illogical and incorrect as well.
>
You are entitled to your opinion, but I disagree.

[R. Dean]

Of course! This could apply to just about anything manufactured: the
chair I'm setting on, the computer, keyboard, the refrigator from which
I just got soda. But I'm saying That Darwin was influenced and
challenged by Darwin.

>
> Socrates and Xenophon were pagans. They believed in many gods. This means
> that they would have been comfortable with the idea of a world built by
> committee.
>
> Anyway, it really should have been called Xenophon's argument, not
> Paley's argument.
>

We know Darwin read Paley even claimed he could almost recall him word for
word. Whether or not Darwin knew of Socrates and Xenophon, I don't
know. But
he was definitely aware of Paley's "Evidences".

[R. Dean]

On 12/15/2013 9:04 AM, jillery wrote:

This is very true. Only what I observer that he/she/it _has_ done.

[jillery]

On Sun, 15 Dec 2013 17:48:15 -0500, "R. Dean" <"R. Dean"@gmail.com>

Ok. Whatever you infer about the designer from their designs, you do
so because you know the designers are human, and you are familiar with
human characteristics. You can't reasonably do that with non-human
designers.

>>>> OTOH you know nothing of your presumptive designer independent of its
>>>> presumptive design, so you have no basis for making any reasonable
>>>> assumptions about it.
>>>>
>>> I think intelligence wherever you find it possesses most of the same
>>> characteristics. Can I _prove_ it? No! But it's reasonable to conclude
>>> as much.
>>
>>
>> Not only is it unreasonable, but it's illogical and incorrect as well.
>>
>You are entitled to your opinion, but I disagree.

Non sequitur. You are not entitled to your own facts.

[jillery]

On Sun, 15 Dec 2013 18:08:59 -0500, "R. Dean" <"R. Dean"@gmail.com>

You don't know what your designer has done. You just admitted to
presuming your conclusion.

[R. Dean]

I know there only one tree, but from Ernst Haeckel to the present the
tree changes.

>
Darwin was the first to present what
> is clearly an evolutionary tree. If you're thinking of Lamarck, it's
> apparent to me that he meant something different. Anyway, what does it
> matter who was first? I have no idea what you mean by bringing up Gould,
> but you are almost certainly mistaken about his views.
>

How can you say this when you have no idea regarding how I see Gould's
views?

[Robert Camp]

Think it through, man. You cannot assert that an unevidenced designer
*has* done something until you demonstrate what he *can* do. In other
words it is your burden to establish the existence and capacity of your
designer *before* you get to assert, as part of an argument, that he has
done anything.

[John Harshman]

So? Are you saying it isn't real? If so, what happened to that pattern
you claimed would show god's design? If not, why bring it up?

> Darwin was the first to present what
>> is clearly an evolutionary tree. If you're thinking of Lamarck, it's
>> apparent to me that he meant something different. Anyway, what does it
>> matter who was first? I have no idea what you mean by bringing up Gould,
>> but you are almost certainly mistaken about his views.
>>
> How can you say this when you have no idea regarding how I see Gould's
> views?

Just a hunch. Go ahead and explain, and we'll see if I'm right.

[R. Dean]

On 12/15/2013 11:30 AM, jillery wrote:
> On Sun, 15 Dec 2013 00:46:06 -0500, "R. Dean" <"R. Dean"@gmail.com>
> wrote:
>
>> On 12/14/2013 4:39 PM, John Harshman wrote:
>>> On 12/14/13 8:43 AM, R. Dean wrote:
>>>> On 12/13/2013 5:53 PM, John Harshman wrote:
>>>>> On 12/13/13 2:31 PM, R. Dean wrote:
>>>>>> On 12/13/2013 7:32 AM, TomS wrote:

>>>>>>> "� researchers conclude that ctenophores branched off first,

There are 100's of naturally occurring amino acids. But only 20
are utalized by life.
>
class.fst.ohio-state.edu/FST822/lecturesab/AAcids.htm

[R. Dean]

On 12/15/2013 12:06 PM, TomS wrote:
> "On Sun, 15 Dec 2013 06:14:17 -0800, in article
> <LKmdnd90YsGmJDDP...@giganews.com>, John Harshman stated..."
> [...snip...]
>> Nope. There is only one pattern consistent with common descent. Some
>> other pattern wouldn't have been.
> [...snip...]
>
> The pattern of a nested hierarchy is indicative of common descent.
>
> This pattern is also seen as indicative of common descent in the
> field of linguistics, and in textual criticism. In fact, the very
> same computer-baeed algorithms that have been developed for biology
> have been applied to languages and to texts.
>

I've read about this. Several European languages are derived from
the Latin language, and changes occur over the centuries.
And I agree this is analogical to the concept of change over
time.

[jillery]

On Mon, 16 Dec 2013 01:15:03 -0500, "R. Dean" <"R. Dean"@gmail.com>
wrote:

[...]

>There are 100's of naturally occurring amino acids. But only 20
>are utalized by life.
> >
>class.fst.ohio-state.edu/FST822/lecturesab/AAcids.htm

That's not what your cite says:

"While there are hundreds of amino acids in nature, only 20 are
commonly found in *proteins* [emphasis mine]"

More specifically they are the monomers that are specified in the DNA
code to produce proteins. The other "hundreds of amino acids in
nature" are found in non-protein molecules, and as metabolic
intermediates:

<http://en.wikipedia.org/wiki/Amino_acids#Occurrence_and_functions_in_biochemistry>
<http://en.wikipedia.org/wiki/Amino_acids#Non-protein_functions>

So, even though these "hundreds of amino acids in nature" aren't all
used for proteins, they are all utilized by life, apart from the
synthetic amino acids I mentioned earlier.

So how is any of this surprising or odd?

[alias Ernest Major]

That is badly stated. 20 amino acids are encoded by the canonical
genetic code. 1 more amino acid (selenocysteine) is encoded by a kludge.
If I understand correctly these 21 amino acids are used universally
(unless some organisms have secondarily lost it).

Pyrolysine is also encoded by a kludge, but it only used by some
organisms. It is used by some archaea.

Selenemethionine is incorporated into proteins as an alternative to
methionine. (This looks as if it is a case of inadequate discrimination
by the translational machinery.)

Several other amino acids are incorporated in proteins by
post-translational modification. These include hydroxyproline, cystine,
hypusine, pyroglutamic acid and gamma-carboxy-glutamic acid.

In humans (and presumably a large clade of organisms) hydroxyproline is
more used than several of the canonical amino acids.

Cystine, formed by spontaneous post-translation oxidation of pairs of
cysteine, has an important role in the stabilisation of protein tertiary
structure.

Hypusine is used in a single protein by eukaryotes and archaea, but not
bacteria.

Pyroglutamic acid is used in a few proteins, included bacteriorhodopsin.
gamma-Carboxy-glutamic acid is also used in a few proteins, including
clotting factors.

Aminomalonic acid is reported to turn up in proteins, but it appears
that it is not known how it gets there, or if it has any function.

That's 28 amino acids. Beyond that other amino acids have biological
roles. gamma-Amino-butyric acid is a neurotransmitter. Carnitine has a
role in lipid transport. Several more occur as intermediates in
metabolism, or as anti-feedants in plants.

Beyond that, the implication that the limited diversity (several
hundred) of amino-acids in life is evidence for design, in your
statement that all life uses the same 20 amino acids, is incorrect.
Rather it is evidence for common descent. Common descent predicts that a
limited repertoire of amino acids will be used be in proteins, but the
observation is only consistent with design, not predicted.


--
alias Ernest Major