Evolution of peptide synthesis Part 1
el cid
Focus on Evolution of of peptide synthesis
Part I
Translation overview
Translation is the term used for the biochemical process
of synthesizing polypeptides based on the sequence of
codons present on a messenger RNA molecule.
The mapping between anticodons and amino acids is
termed The Genetic Code. There are 64 anticodones
composed of triplets of 4 nucleotide bases that are
canonically mapped to 20 amino acids and a termination
signal.
Translation is accomplished a condensation reaction
that grows a polypeptide 1 amino acid at at time in
an extension that proceeds from the front (N-terminal)
to the back (C-terminal) of a linear amino acid polymer
called a polypeptide or protein.
The translation of mRNA to polypeptide sequence
occurs through a decoding mechanism that matches
specific amino acids to anticodon specific tRNA
molecules that are in turn matched to specific codons
in mRNA.
The condensation reaction is accomplished by amidolysis
of an ester attached to a tRNA molecule, an energetically
favored reaction. The ester attached to the tRNA molecule
which is attacked in the amidolysis reaction includes
the previously synthesized growing polypeptide which
is then released from that tRNA. The attacking amine
is itself attached by an ester bond to its own tRNA
molecule and thus the growing peptide is transferred from
one tRNA molecule to the next with a single amino
acid extension to the C-terminal end of the amino acid
polymer.
The specific mapping of amino acids to tRNAs is then
seen as both the chemical activation of an amino acid
to make the polymerization favorable and the translation
mechanism to match mRNA codon sequence (and ultimately
DNA gene sequences) to polypeptide sequences.
The combined mapping and activation function is
accomplished by enzymes known as amino acyl tRNA
transferases. The polymerization reaction takes place
within the ribosome, a large RNA protein complex though
the catalytic role has been revealed to be resident
within RNA making the ribosome one of the most
significant ribozymes in the cell.
Because protein enzymes are used to load modern
tRNA molecules with amino acids, a chicken and
egg puzzle presents itself in hypothesizing an
evolutionary origin for translation. How do tRNAs
get activated before there are enzymes to do so?
How do you get the enzymes without the activated
tRNAs?
The remainder of this series of posts will discuss
ideas focused on potential solutions to the chicken and
egg puzzle with observations on the natural history
of peptide synthesis and the implications for its
evolutionary past.
The genetic code is presented below.
T C A G
T TTT phe TCT ser TAT tyr TGT cys T
TTC phe TCC ser TAC tyr TGC cys C
TTA leu TCA ser TAA end TGA end A
TTG leu TCG ser TAG end TGG trp G
C CTT leu CCT pro CAT his CGT arg T
CTC leu CCC pro CAC his CGC arg C
CTA leu CCA pro CAA gln CGA arg A
CTG leu CCG pro CAG gln CGG arg G
A ATT ile ACT thr AAT asn AGT ser T
ATC ile ACC thr AAC asn AGC ser C
ATA ile ACA thr AAA lys AGA ser A
ATG met ACG thr AAG lys AGG ser G
G GTT val GCT ala GAT asp GGT gly T
GTC val GCC ala GAC asp GGC gly C
GTA val GCA ala GAA glu GGA gly A
GTG val GCG ala GAG glu GGG gly G
There is a long history of speculation regarding
the organization of the code extending back to
publications by Crick in 1968. Significant observations
about the code itself include the following.
Of the 3 nucleotides in the codon,changes in the
3rd position are least likely to change the amino acid.
AAs with similar properties tend to be near to each other.
Common AAs tend to have more codons. Multiple authors
have observed that codons beginning with G represent some
of the amino acids that are among the most abundant of
those found in abiotic synthesis experiments.
One model proposes the earliest version of the code
would have been a 4 amino acid code derived from the bottom,
GTx val GCx ala GAx asp GGx gly. [Ikehara 2002]
Multiple methods have been used to test hypotheses
about potential precursors of the current genetic code.
In particular, the explosion of genomic sequence
data has allowed a number of studies that fit
protein sequences in Last Universal Ancestor models.
“Relative to the modern protein set, LUA proteins
were found to be generally richer in those amino acids
that are believed to have been most abundant in the
prebiotic environment and poorer in those amino acids
that are believed to have been unavailable or scarce.
It is proposed that the inferred amino acid composition
of proteins in the LUA probably reflects historical
events in the establishment of the genetic code.
[Brooks, 2002]
Such studies are complex but a number of lines of evidence
are converging. A more recent analogous effort produced
very similar conclusions, namely that cys, glu, phe,
ile, lys, val, try and tyr are recent additions to the
code. Cys, trp and tyr are intriguingly clustered
together with the stop codons evoking know mechanisms
of codon replacement through suppressor tRNAs. This
study likewise found that val, ala, asp and gly appear
more frequently in canonical sequences of the oldest
proteins.
The curious case of gln and asn will be discusssed
separately.
Many criticisms may be levied at these studies, however,
it remains that extensive sequence data has been
tested that generally confirms early speculations.
There do appear to be patterns in the genetic code
that suggest a simpler precursor and protein sequence
data strongly suggests that the most ancient
protein sequences relied on a reduced amino acid
repertoire.
( continued in separate post )
DJ Brooks et al “Evolution of Amino Acid Frequencies
in Proteins Over Deep Time: Inferred Order of
Introduction of Amino Acids into the Genetic Code”
Mol Biol Evol (2002) 19 (10):1645-1655.
K Ikehara “Origins of gene, genetic code, protein and life:
comprehensive view of life systems from a GNC-SNS
primitive genetic code hypothesis”
J Biosci. (2002) 27 (3) : 165-186
el cid
> Focus on Evolution of of peptide synthesis
> Part I
Focus on Evolution of of peptide synthesis
Part 2
Amino acyl tRNA Synthetase (ARSs) and tRNA
This class of enzymes catalyzes the covalent attachment
of specific amino acids to specific tRNAs yielding
an energetically activated amino acid in the form
of an ester linkage to the tRNA.
Two classes of ARS enzymes exist, class I and II.
Most amino acids have a single ARS that works for
its complement of tRNAs. There is no recognizable
homology between class I and class II ARSs. The
homology between ARSs of the same class is mostly limited
to the catalytic domain responsible for acylating
tRNAs with an amino acid. Contrary to early assumptions,
all cellular genomes do not encode for all 20 ARSs
with one bacterial species apparently only encoding
16 [Bult 1996]. Asn and Gln are two ARSs that are most commonly
missing with the indirect pathway.
The indirect pathway for the synthesis of gln
and asn tRNA uses the corresponding acid ARS
forming a mismatched AA-tRNA {glu-tRNA(gln); asp-tRNA(asn)}
and subsequently amidotransferases [Curnow 1997]
converts glu-tRNA(gln) to gln-tRNA(gln) and/or asp-tRNA(asn)
to asn-tRNA(asn).
A direct pathway, with separation deep within the tree of
life, also exists for asn,gln. Thus gln and asn are frequently
considered some of the latest additions to the “universal”
genetic code. Analysis of the direct ARSs for asp and asn suggest that
asn-RS arose after the split of Eucarya and Archaea
though this is not reliable data that asn was not in use
owing to the indirect pathway. Extensive evidence of
horizontal transfer of ARS enzymes after the divergence
of the major kingdoms exists. Interestingly, EF-tu,
and enzyme that binds with tRNAs and then binds to the
ribosome, does not bind the 'misacylated' glu-tRNA(gln)
in some cell lineages that use the indirect loading method,
but this is the only editing function know for EF-tu.
Another ARS that is sometimes missing is cys-RS with an
indirect pathway that first loads the amino acid O-phospho-
ser with a subsequent conversion to cys. There exist some
intriguing speculations about the co-evolution of amino
acid metabolism and the evolution of the genetic code
using a parallel set of ribozymes with dual functionality
for amino acid biosynthesis and peptide synthesis. These
speculations take full consideration of the many ribozymes
that have been found to be capable of specifically acylating
tRNA molecules.
The relationships among ARS enzymes is also interesting.
Class I ARS enzymes can be subdivided according the
structural similarities.
Asn and asp ARSs are clearly related. Likewise, within
the class I group of ARSs, which are all related, closer
relationships are seen in the subset for val, leu, ile
and met with obvious similarities seen in these amino
acids. Indeed met-RS is known to load norleucine under
conditions of low met concentrations. Studies of ile-RS
reveal a misacylation rate of 1/300 though intrinsic
editing functions reduce the incorporation into peptides
to 1/3000 in modern cells. The codon motif XTX shared
by these 4 amino acids further points to an expansion
of a reduced genetic code, either specific for val or
partially promiscuous within this set. A class I subgroup
commonly denoted as subgroup IC encodes for trp and tyr,
the two large aromatic amino acids show are much more
closely related to each other than the rest of class I.
They share the T[A,G]X region of the genetic code taken
by the stop codons. Replacement of a stop codon by a
an amino acid codon is a process that is fairly well
documented and given the apparent late addition of
these amino acids (along with cys which shares the same
codon motif), it is suggested that the entire motiff
was originally a synthesis termination codon.
The relationships among the observable ARSs points
to a familiar mode of duplication and divergence
for these enzymes. It need be noted that the earliest
attempts to discover homology in ARSs was confounded
by the relatively low level of sequence identify
that made accurate alignment of sequences problematic.
More recent methods that take into account the crystal
structure of these enzymes aids the identification
of homologous regions to test the validity of alignment.
Alignments that match an alpha-helical stretch to a
beta sheet are clearly dubious. Catalytic domains
and active site provide clear anchors.
The duplication and divergence model is likewise
fortified by the way the relationships in synthetases
matches to relationships in the genetic code itself.
(I've grown lazy in citing references but anybody
can readily find support for all these points
within pubmed)
(end part 2)
CJ Bult et. al. (1996) Science 273, 1058-1073
AW Curnow et. al(1997) PNAS 94,11819–1182
John Harshman
[snippies]
I would like to point out that if I were for some reason designing the
whole protein synthesis system from scratch, and decided to make ARSs a
part of that system, it would make the most obvious sense to design them
all according to a single plan, with differences only in the small
motifs that a) recognize the specific amino acid and b) recognize the
specific tRNA to which the amino acid is to be attached. All other
portions of the protein, having identical function, might as well be
identical. Of course this is not what we see, even allowing for 4
billion years of subsequent evolution. Therefore the actual situation is
evidence against Peter's scenario (forget the number) in which protein
synthesis is designed.
el cid
Sometimes designers change specifications when they
run into a problem. Then there's the problem of specifications
changing the designers, though from what I've seen, for some
people, changing the specifications of the designers is no
problem at all.
John Harshman
the moment.
lucaspa
> tRNA molecules with amino acids, a chicken and
> egg puzzle presents itself in hypothesizing an
> evolutionary origin for translation. How do tRNAs
> get activated before there are enzymes to do so?
> How do you get the enzymes without the activated
> tRNAs?
It's easy to get enzymes by thermal polymerization of amino acids to
proteins. That's one way to get the first proteins. Another way is
to have ribozymes act as the enzymes and synthesize proteins. Both
mechanisms have been shown to work. So that is one solution to the
puzzle you posted.
Another is that uncatalyzed reactions WILL happen, but not as
specifically or as efficiently as when they are catalyzed. So yes, you
can get tRNA to react with amino acids without an enzyme. Other
papers you want to are:
1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J.
Molecular Evolution 46: 1-17, 1998. Describes Darwinian step-by-step
for evolution from RNA molecules to cells with directed protein
synthesis. All intermediate steps are useful.
http://awcmee.massey.ac.nz/people/dpenny/pdf/Poole_et_al_1998.pdf
2. P S Schimmel and R Alexander, All you need is RNA. Science
281:658-659, Jul. 31, 1998. Describes research showing that RNA in
ribosomes sufficient to make proteins. Intermediate step in going from
abiogenesis to genetic code.
4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a
transfer RNA gene through a point mutation in the anticodon. Science,
279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670
lucaspa
>
> If creationism is any guide, the designer is whatever fits the needs of
It was the negative conclusions about the nature of the designer that
caused Special Creation to be rejected by Christians in favor of
evolution in the period 1860-1880. Special Creation "created" some
very serious problems for the concept of the Christian god. Evolution
by natural selection -- by making natural selection the proximate
designer -- rescued God from creationism.
Always remember, :), however bad creationism is as science and
whatever danger it poses for science, creationism is even worse as
Christian theology and poses an even bigger danger for Christianity.
John Harshman
creationists want to avoid.
David Hare-Scott
Why?
David
pnyikos
I'm eagerly awaiting them. What you've posted so far seems to fif
right under the rubric of something you alleged about Julie Thomas:
> She would dig
> into a few systems and recite the names of various enzymes
> or proteins but it was clear she was looking this stuff up
> as she went along and pressing her own preconceptions
> on them.
I think it is pretty safe to conclude that you are not a professional
biochemist. A professional, while justly proud of all that
biochemistry has done, would also be keenly aware of its present day
limitations and not post something as bombastic as the claim you made
on the same thread where that quote from you was taken:
> And for what little it's worth, my sense of the current
> knowledge of protein folding is less pessimistic than
> yours. Fund me with 30 million and in 5 years I'll
> have a protein holoenzyme that replaces the ribosome.
Nor would he have posted the dismissive words about such a staggering
milestone that you did in the next sentence. Both can be found in the
excerpt below from a post from which you have run away:
---------------------------------- begin excerpt
> And for what little it's worth, my sense of the current
> knowledge of protein folding is less pessimistic than
> yours. Fund me with 30 million and in 5 years I'll
> have a protein holoenzyme that replaces the ribosome.
You and what team of Nobel Laureates?
I think you are seriously underestimating the difficulty of ensuring
fidelity; the casual, offhand way in which you breeze past it, both
here and in the post to which I replied just before this one, suggests
you haven't given it the attention it deserves.
> It's not a very interesting problem from a commercial
> or utilitarian perspective so I wouldn't really spend
> any money to do it, there being far better ways to
> spend the money
Oh, really? If you could do as you claim, then your remarks about the
"steep curve" in another post of yours strongly suggest that this
hypothetical holoenzyme would speed up the production of polypeptides
many-fold.
Picture the possibilities:
(1) replacing rRNA-producing DNA with holoenzyme-producing in seeds so
that you get several crops a year instead of just one.
(2) doing the same for the oocytes and sperm of vertebrates, with
livestock growing and maturing many times faster than in even the most
intensive factory farms today.
It would rival controlled thermonuclear fusion as the greatest
scientific advance of the 21st century.
Why, given a couple of centuries, humans could even rapidly evolve
mice to an intellingent species to where Theodore Sturgeon's short
story "MIcrocosmic God" becomes prophetic fiction!
Farfetched? no more so, IMHO, than your bombastic claim.
Peter Nyikos
================= end of excerpt from
http://groups.google.com/group/talk.origins/msg/be5b341179935ceb
[more "looking this stuff up" by "el cid" deleted]
Peter Nyikos
pnyikos
One thing is for sure: you aren't Keith Robison. Robison would never
have posted a childish insult based on an intentional misreading of
what any bright 8 year old can see is an analogy. [Keyword: sub-
basement, skyscraper.]
Robison would not have posted a wildly false clam about what I had
said in the late 90's about lipid layers, and then aggressively
continued the way you did on being corrected.
On the other hand, PZ Myers loved to taunt me about the question I
asked about them.
And, just in case you ARE PZ Myers, I'd like to call your attention to
a generally favorable commentary by Joel McDurmon on a review you
did:
http://americanvision.org/1828/atheism-freemasonry-god-equation/
Here is the opening paragraph:
Brave atheist PZ Myers (the American Richard Dawkins wannabe) has
recently done humanity the favor of debunking the so-called “God
Equation”—a simple physics trick that purports to give “scientific
evidence that the creation of the Earth and Moon was a deliberate
act.” But what has begun to come out of the debunking is a
misunderstanding by some that this attempt at proving “intelligent
design” has somehow come from “Christian” creation scientists. So,
the story now needs debunking on two counts—the particular spin on
“intelligent design” given by the discoverers of the equation, and the
particular misapplication that some atheists on the web have added to
it. In the end, we will see the God Equation proponents and the
atheists are the ones in league.
=================== end of excerpt
I do believe the words "Brave atheist" were written tongue in cheek.
I'll believe PZ Myers to be brave when he burns a copy of the Koran
with as much publicity as he got when he desecrated of a Holy
Communion host.
Peter Nyikos
John Harshman
I suspect he's referring to the problem of natural evil, an exemplified
for Darwin by the ichneumon wasp larva that devours a caterpillar from
the inside, carefully preserving the vital organs until the last
possible moment. Or you may want to consider the careful design of
bubonic plague or malaria. If god did that, he has a nasty sense of
humor at best. But if he just let evolution take its course, he's off
the hook. (Unless he's actually omnipotent and omniscient, but that's
another discussion.)
el cid
> ================= end of excerpt fromhttp://groups.google.com/group/talk.origins/msg/be5b341179935ceb
>
> [more "looking this stuff up" by "el cid" deleted]
>
> Peter Nyikos
Fascinating how someone repeatedly whines about not getting
spoon fed a scenario whereby polypeptide synthesis could
evolve naturally but then reacts this way when somebody else
goes to the effort.
To respond to the only science I can find in the above, it is
misguided. Replacing ribosomal protein synthesis would
not provide for multiple crops a year and would not make
tasty beasties grow faster either. The rate of protein synthesis
does appear to be limiting for lab strains of bacteria growing
at their maximum rate in ideal media. Supposing a calf
would grow into a nice tasty steer simply because proteins
were synthesized faster is pure fantasy. And even simple
bacteria would require many additional changes if proteins
were made much faster than they are made now. You
would need to adjust half-lives of mRNA to keep multiple
regulator pathways working, you need to change all sorts
of protein breakdown pathways or proteins themselves
to retune their native half-lives.
Meanwhile, I've no inclination to finish posting about the
evidence that protein translation evolved. The only vocal
doubter of the plausibility isn't demonstrating comprehension,
even of things that directly refute specific opinions he
has cited about ARSs which appeared to be a linchpin
of his skepticism.
Too bad. There's some neat stuff out there: evidence
for tRNAs being hybrid constructs, structural evidence
and even trans=splicing in thermopiles; self-replicating
ribozymes that form specific polypeptides through amino
acid aceylated intermediates via either homodimeric
or heterodimeric pairings; ribozymes that function
like ARSs; analogues to primative ribosomes; and key
data that dovetails with previously presented results all
pointing toward an evolutionary history for ribosomal peptide
synthesis, metabolic functions for precursors, selective
advantages for protein coated ribozymes and more.
Though somebody is correct, anybody can look up the
details through pubmed. The real question is, why haven't
they done so if they are so keen on the roots of the
genetic code and polypeptide synthesis? Let him.
My time here is nearly at an end anyway.
Mark Isaak
Also, the fossil record shows change over time, indicating either
evolution or a deceitful creator of the fossil record.
--
Mark Isaak eciton (at) earthlink (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume
Mark Isaak
> [snip]
> I do believe the words "Brave atheist" were written tongue in cheek.
> I'll believe PZ Myers to be brave when he burns a copy of the Koran
> with as much publicity as he got when he desecrated of a Holy Communion
> host.
He *did* desecrate a Koran (and also _The God Delusion_) at the same
time as he did the host.
pnyikos
> On Dec 13, 4:17 pm, el cid <elcidbi...@gmail.com> wrote:
>
> > Because protein enzymes are used to load modern
> > tRNA molecules with amino acids, a chicken and
> > egg puzzle presents itself in hypothesizing an
> > evolutionary origin for translation. How do tRNAs
> > get activated before there are enzymes to do so?
> > How do you get the enzymes without the activated
> > tRNAs?
>
> It's easy to get enzymes by thermal polymerization of amino acids to
> proteins.
Enzymes? or even polypeptides? Aren't you talking about coacervates
[sp?] aka microspheres? Those don't figure in origin of life research
any more, do they?
> That's one way to get the first proteins. Another way is
> to have ribozymes act as the enzymes and synthesize proteins.
Yes, that's standard RNA World stuff. My main interest is how to get
from RNA World to polypeptide synthesis via translation.
> Both
> mechanisms have been shown to work. So that is one solution to the
> puzzle you posted.
No, not the one I posted. See below.
> Another is that uncatalyzed reactions WILL happen, but not as
> specifically or as efficiently as when they are catalyzed.
The universe can't wait that long.
> So yes, you
> can get tRNA to react with amino acids without an enzyme.
This is in RNA World, and not a step further.
> Other
> papers you want to are:
>
> 1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J.
> Molecular Evolution 46: 1-17, 1998. Describes Darwinian step-by-step
> for evolution from RNA molecules to cells with directed protein
> synthesis.
No, it does not. It skips completely over the part that I am most
interested in, and where I've said the greatest difficulty of all
lies: the protein takeover of charging tRNA with the right amino acids
in one-to-one fashion.
I've been saying that for almost a decade and a half now.
Sure, once an aminoacyl-tRNA synthetase that restricts itself to ONE
kind of tRNA and ONE amino acid, the organism that somehow codes for
it in its genome can be assumed to have a Darwinian advantage over one
that uses a ribozyme to do the same thing.
But where is the cellular Zeus-analogue from whose head-analogue this
is supposed to spring, full-grown as it were?
Oh, you say it evolved step by step?
I'd love to see ANYONE here find a scenario for THAT. Keep in mind
that if the average cell has a pretty reliable ribozyme for charging
one particular tRNA, and a protein starts doing it in a highly
UNreliable way, sometimes grabbing one amino, sometimes another, than
the cell where this happens has a huge evolutionary DISadvanage.
> All intermediate steps are useful.
http://awcmee.massey.ac.nz/people/dpenny/pdf/Poole_et_al_1998.pdf
Did you read the article thoroughly? The authors disarm casual
readers with the following words, which pinpoint the central problem:
The origin of the information in the
mRNAs is perhaps the most difficult
problem to resolve because we would not
expect these ribo-organisms to contain
meaningful information about future
protein sequences. [p. 5, column 2]
A casual reader would naturally assume they actually deal with this
problem, and seeing how long and dense the article is, might stop
reading at some point and never realize that after the authors
immediately drop the whole subject, they never even address it again.
> 2. P S Schimmel and R Alexander, All you need is RNA. Science
> 281:658-659, Jul. 31, 1998. Describes research showing that RNA in
> ribosomes sufficient to make proteins. Intermediate step in going from
> abiogenesis to genetic code.
Proteins that fold into enzymes, or just into structural proteins, or
just into "chaperone proteins" or just into coacervates, which mimic
true polypeptides but are not in any evolutionary relationship to
them?
"chaperone proteins" are a big item in the article by Massey et. al.,
but I could find nothing about them my 1990 Voet and Voet; can anyone
give me an accessible reference to what sort of functions they
perform?
> 4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a
> transfer RNA gene through a point mutation in the anticodon. Science,
> 279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670
A bit player in a gigantic drama, set squarely in RNA World.
Peter Nyikos
chris thompson
And the problem of evil wrt parasites has only gotten worse since
then. Consider _Sacculina_, the barnacle that has begun to plague the
left coast. The female enters a crab (unfortunately, it's now entering
Dungeness crabs- another fishery gone) and sterilizes it- the crab can
no longer reproduce. If the female barnacle enters a male crab, it
feminizes the male, so the male behaves like a female. This involves
waving fresh water over the spot, which, on a female crab, would be
where her egg sac would be. But now it's the egg sac of _Sacculina_.
The crab even waves water around to spread the barnacle's hatchlings.
I probably got some details wrong, but you get the point. Hey, is this
an example of a crab not reproducing after its own kind?
Chris
pnyikos
> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
>
>
> > If creationism is any guide, the designer is whatever fits the needs of
> > the moment.-
And if Massey et. al are any guide, a "path" is whatever "Mother Earth
did it" propagandists call it.
I call what they present a series of widely spaced columns like in
Colorado National Monument, with no sign of how one can build a bridge
between them.
> It was the negative conclusions about the nature of the designer that
> caused Special Creation to be rejected by Christians in favor of
> evolution in the period 1860-1880. Special Creation "created" some
> very serious problems for the concept of the Christian god. Evolution
> by natural selection -- by making natural selection the proximate
> designer -- rescued God from creationism.
Only to a deist. The typical Christian might wonder what God was up to
during the 13 billion years before the coming of Christ. In that
respect, I am a typical Christian.
Augustine had a conversation-stopper for what God did BEFORE making
the universe, but he didn't know about those 13 billion years.
> Always remember, :), however bad creationism is as science and
> whatever danger it poses for science, creationism is even worse as
> Christian theology and poses an even bigger danger for Christianity.
That depends on how narrowly one interprets "creationism". Does your
definition include a God who only intervenes occasionally with minute
Divine nudges as in the following passage from Loren Eiseley's _The
Immense Journey_?
``Perhaps there also, among rotting fish heads and blue,
night-burning bog lights, moved the eternal mystery,
the careful finger of God. The increase was not much.
It was two bubbles, two thin-walled little balloons at the
end of the Snout's small brain. The cerebral hemispheres
had appeared.''
It is my contention that this kind of God poses no danger for
Christianity, and requires no rescuing.
Peter Nyikos
John Harshman
> On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
>> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>
>>
>>
>>> If creationism is any guide, the designer is whatever fits the needs of
>>> the moment.-
>
> And if Massey et. al are any guide, a "path" is whatever "Mother Earth
> did it" propagandists call it.
>
> I call what they present a series of widely spaced columns like in
> Colorado National Monument, with no sign of how one can build a bridge
> between them.
That's nice. What is Massey et al.? And why are you defending the
intellectual integrity of creationism?
>> It was the negative conclusions about the nature of the designer that
>> caused Special Creation to be rejected by Christians in favor of
>> evolution in the period 1860-1880. Special Creation "created" some
>> very serious problems for the concept of the Christian god. Evolution
>> by natural selection -- by making natural selection the proximate
>> designer -- rescued God from creationism.
>
> Only to a deist.
Wrong rescue.
> The typical Christian might wonder what God was up to
> during the 13 billion years before the coming of Christ. In that
> respect, I am a typical Christian.
Do you have any answers to your question?
> Augustine had a conversation-stopper for what God did BEFORE making
> the universe, but he didn't know about those 13 billion years.
>
>> Always remember, :), however bad creationism is as science and
>> whatever danger it poses for science, creationism is even worse as
>> Christian theology and poses an even bigger danger for Christianity.
>
> That depends on how narrowly one interprets "creationism". Does your
> definition include a God who only intervenes occasionally with minute
> Divine nudges as in the following passage from Loren Eiseley's _The
> Immense Journey_?
>
> ``Perhaps there also, among rotting fish heads and blue,
> night-burning bog lights, moved the eternal mystery,
> the careful finger of God. The increase was not much.
> It was two bubbles, two thin-walled little balloons at the
> end of the Snout's small brain. The cerebral hemispheres
> had appeared.''
>
> It is my contention that this kind of God poses no danger for
> Christianity, and requires no rescuing.
I don't agree, but that kind of god does prevent the particular problem
the OP was discussing. Of course that kind of god is almost identical to
the god he came up with as a solution.
pnyikos
> On Dec 15, 5:53 pm, pnyikos <nyik...@bellsouth.net> wrote:
>
>
>
> > On Dec 13, 4:17 pm, el cid <elcidbi...@gmail.com> wrote:
> > I'm eagerly awaiting them. What you've posted so far seems to fif
> > right under the rubric of something you alleged about Julie Thomas:
>
> > > She would dig
> > > into a few systems and recite the names of various enzymes
> > > or proteins but it was clear she was looking this stuff up
> > > as she went along and pressing her own preconceptions
> > > on them.
[...]
> Meanwhile, I've no inclination to finish posting about the
> evidence that protein translation evolved.
How can you finish something you haven't even begun?
But don't let ME stop you. I'm sure Hershey, Gans, Isaac, and maybe
even Harshman will credit you with solving the riddle of an
evolutionary PATH to protein translation no matter what handwaving you
post.
Don't you think they will accuse me of doing exactly what you accused
me of up there?
> The only vocal
> doubter of the plausibility isn't demonstrating comprehension,
> even of things that directly refute specific opinions he
> has cited about ARSs which appeared to be a linchpin
> of his skepticism.
See, you are already claiming to have *directly* refuted specific
opinions -- which, of course, you couldn't name, hence don't name --
and I'm sure the people I've mentioned and MANY others will back you
to the hilt on this.
You see, shortly before I started posting again to talk.origins, I
caught sight of a thread, BLAST FROM THE PAST, whose title intrigued
me because I was going to start posting here, shortly after posting
again to sci.bio.palentology.
The people participating in that were complaining because they were
running out of people to "spank" and were even resorting to
resurrecting an old post. So I had a good idea what might be waiting
for me here, but I thought I'd take the plunge anyway, and the
"futility of intelligent design" thread was right down my alley, so I
picked that one.
> Too bad. There's some neat stuff out there: evidence
> for tRNAs being hybrid constructs, structural evidence
> and even trans=splicing in thermopiles; self-replicating
> ribozymes that form specific polypeptides through amino
> acid aceylated intermediates via either homodimeric
> or heterodimeric pairings; ribozymes that function
> like ARSs; analogues to primative ribosomes;
Yes, RNA World stuff. The article I discussed with "lucaspa" has
plenty of that in it. But as I told him, and as I told you before you
embarked on this thread, the part I have always been eager to hear
about is how ARSs arise from that RNA World.
[more of the same RNA World stuff deleted]
> Though somebody is correct, anybody can look up the
> details through pubmed. The real question is, why haven't
> they done so if they are so keen on the roots of the
> genetic code and polypeptide synthesis?
I have done so. But don't let that stop you from continuing to
misrepresent me.
After all, that's what spanking is all about, isn't it?
> Let him.
Run away, then, coward. You have already run away from the other
kitchens that I've made too hot for you:
The futility of intelligent design:
http://groups.google.com/group/talk.origins/browse_thread/thread/949b80db368cbdf6/0cab8fc8780939e2
The Protein Takeover. PN's scenario
http://groups.google.com/group/talk.origins/browse_thread/thread/2c15d26cb7c9f831/b7d5df28b106a0af
> My time here is nearly at an end anyway.
Why, have I blown your cover, PZ Myers? :-) :-) :-)
Peter Nyikos
pnyikos
There is no such "someone", and here is no such effort on this thread
so far by you as you hint at next:
>whereby polypeptide synthesis could
> evolve naturally but then reacts this way when somebody else
> goes to the effort.
The only person on this thread who has made that kind of effort was
"lucaspa". At the rate you are going, you will die of old age before
you even get around to producing the sort of analysis that Poole,
Jeffreys, and Penny did. They are very good at what they do, and I
didn't give them enough credit for that in my first reply to
"lucaspa". But even they do not address the central difficulty which
they so ably *described* and in which I am so very interested.
> To respond to the only science I can find in the above,
"the above" includes your bombastic claim, and your disparaging
remarks about a monumental breakthrough, of course.
But you aren't including all the science: you didn't address the key
concept of fidelity.
> it is
> misguided. Replacing ribosomal protein synthesis would
> not provide for multiple crops a year and would not make
> tasty beasties grow faster either.
And why not?
> The rate of protein synthesis
> does appear to be limiting for lab strains of bacteria growing
> at their maximum rate in ideal media.
Which is far faster than eukaryotic cells multiply. That article
"lucaspa" linked goes into this in some depth.
>Supposing a calf
> would grow into a nice tasty steer simply because proteins
> were synthesized faster is pure fantasy.
It's a huge step along the way. And of course, you are ignoring my
punch line in the included post.
Continued in next post.
Peter Nyikos
pnyikos
> On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
> > [snip]
> > I do believe the words "Brave atheist" were written tongue in cheek.
> > I'll believe PZ Myers to be brave when he burns a copy of the Koran
> > with as much publicity as he got when he desecrated of a Holy Communion
> > host.
>
> He *did* desecrate a Koran (and also _The God Delusion_) at the same
> time as he did the host.
Can you document that?
Peter Nyikos
pnyikos
> On Dec 13, 4:17�pm, el cid <elcidbi...@gmail.com> wrote:
>
> > Focus on Evolution of of peptide synthesis
> > Part I
>
> Focus on Evolution of of peptide synthesis
> Part 2
> Amino acyl tRNA Synthetase (ARSs) and tRNA
>
> This class of enzymes catalyzes the covalent attachment
> of specific amino acids to specific tRNAs yielding
> an energetically activated amino acid in the form
> of an ester linkage to the tRNA.
> Two classes of ARS enzymes exist, class I and II.
> Most amino acids have a single ARS that works for
> its complement of tRNAs. There is no recognizable
> homology between class I and class II ARSs. The
> homology between ARSs of the same class is mostly limited
> to the catalytic domain responsible for acylating
> tRNAs with an amino acid.
And so, it is no wonder that you ran away from the following expose by
me:
------------------- begin excerpt, me going first,
---------------------then you, then me again:
> >Voet and Voet said it twenty years ago: they are a very diverse
> > "order" of enzymes, no two of which resemble each other, EXCEPT the
> > ones that code for the same amino acids--the ones in what I call the
> > same "family".
Take away "very" in front of "diverse" and, if anything, I
understated what Voet and Voet wrote:
The similarity of the reactions catalyzed
by these enzymes and the structural
resemblance of all tRNA suggests that all
aminoacyl-tRNA synthetases evolved from a
common ancestor and should therefore be
structurally similar. This is not the
case, however. In fact,
*
the aminoacyl-tRNA synthetases form a
diverse group of enzymes.
*
The over 100 such enzymes that have been
characterized each have one of four
different types of subunit structures,
alpha, alpha_2, alpha_4 and alpha_2beta_2,
with subunit sizes ranging from 334 to
> 1000 residues. Moreover, although
synthetases specific for a given amino
acid exhibit considerable sequence
homology from organism to organism, there
is little similarity among synthetases
specific for different amino acids.
--_Biochemistry_, by Voet and Voet
John Wiley and Sons, 1990, p. 907
The two lines set apart by asterisks were italicized.
> You've got some bad information there. There are two classes
> of amino acyl tRNA synthetases. They recognizably belong
> to one of these two classes.
And how similar are the ones within each class, but not the same
family, to each other?
Trivia: I used the word "order" but you jumped all the way up to
"class". :-)
> I expect you misunderstood V&V
I expect I didn't. And I'd love to hear your opinion on the very next
sentence in the book:
Quite possibly, aminoacyl-tRNA synthetases
arose very early in evolution, before
the development of the modern protein
synthesis apparatus other than tRNAs.
--*ibid*
Is one of your scenarios going to start with "AA-tRNA came first, then
the AA-tRNA synthetases, then the rRNA and the mRNA?"
=============== end of excerpt from
http://groups.google.com/group/talk.origins/msg/7971496e2c5c006d
Note the put-down by el cid. And note the avoidance of any mention of
degrees of similarity by "el cid".
But most importantly, el cid hasn't hinted at his opinion of what Voet
and Voet wrote in that last sentence.
I've snipped almost all the rest, which speaks hopefully of how the
evidence "points to" "duplication and divergence" but the evidence for
it seems flimsy at best:
> It need be noted that the earliest
> attempts to discover homology in ARSs was confounded
> by the relatively low level of sequence identify
> that made accurate alignment of sequences problematic.
> More recent methods that take into account the crystal
> structure of these enzymes aids the identification
> of homologous regions to test the validity of alignment.
> Alignments that match an alpha-helical stretch to a
> beta sheet are clearly dubious. Catalytic domains
> and active site provide clear anchors.
I wonder whether the articles cited below do any better:
> (I've grown lazy in citing references but anybody
> can readily find support for all these points
> within pubmed)
>
> (end part 2)
>
> CJ Bult et. al. (1996) Science 273, 1058-1073
>
> AW Curnow et. al(1997) PNAS �94,11819�1182
Judging from the article "lucaspa" linked and I critiqued, I'm not too
optimistic, but I'll take a look during the Christmas break.
Peter Nyikos
Ernest Major
<d6cd725d-c9bc-4b16...@35g2000prt.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes
defamation falls under the prohibition against bearing false witness. If
you don't know what PZ Myers did it is your responsibility to make a
good faith effect to find out before badmouthing him.
As for the documentation, PZ Myers posted a photograph on his blog.
--
alias Ernest Major
pnyikos
And if the article by Poole, Jeffares, and Penny that "lucaspa" linked
for us is typical of U.of Ediacara thinking, an "evolutionary path" is
whatever the U. of Ediacara member says it is.
I said something similar in response to these words of yours in a
follow-up to "lucaspa" but had a strange "senior moment" where I wrote
"Massey et. al." when I meant the three authors I named above.
Peter Nyikos
pnyikos
> pnyikos wrote:
> > On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
> >> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> >>> If creationism is any guide, the designer is whatever fits the needs of
> >>> the moment.-
By the way, was the above meant to be a dig at me? It could be
construed that way, you know.
> > And if Massey et. al are any guide, a "path" is whatever "Mother Earth
> > did it" propagandists call it.
>
> > I call what they present a series of widely spaced columns like in
> > Colorado National Monument, with no sign of how one can build a bridge
> > between them.
>
> That's nice. What is Massey et al.?
See my reply to you of a moment ago.
> And why are you defending the
> intellectual integrity of creationism?
What makes you think I am doing that?
You aren't one of those people whose mindset includes "the enemy of my
enemy is my friend", are you?
> >> It was the negative conclusions about the nature of the designer that
> >> caused Special Creation to be rejected by Christians in favor of
> >> evolution in the period 1860-1880. �Special Creation "created" some
> >> very serious problems for the concept of the Christian god. �Evolution
> >> by natural selection -- by making natural selection the proximate
> >> designer -- rescued God from creationism.
>
> > Only to a deist.
>
> Wrong rescue.
>
> > The typical Christian might wonder what God was up to
> > during the 13 billion years before the coming of Christ. �In that
> > respect, I am a typical Christian.
>
> Do you have any answers to your question?
Not really. But the I haven't ruled out the Eiseley-style route.
> > Augustine had a conversation-stopper for what God did BEFORE making
> > the universe, but he didn't know about those 13 billion years.
>
> >> Always remember, :), however bad creationism is as science and
> >> whatever danger it poses for science, creationism is even worse as
> >> Christian theology and poses an even bigger danger for Christianity.
>
> > That depends on how narrowly one interprets "creationism". �Does your
> > definition include a God who only intervenes occasionally with minute
> > Divine nudges as in the following passage from Loren Eiseley's _The
> > Immense Journey_?
>
> > � � ``Perhaps there also, among rotting fish heads and blue,
> > � � night-burning bog lights, moved the eternal mystery,
> > � � the careful finger of God. �The increase was not much.
> > � � It was two bubbles, two thin-walled little balloons at the
> > � � end of the Snout's small brain. �The cerebral hemispheres
> > � � had appeared.''
>
> > It is my contention that this kind of God poses no danger for
> > Christianity, and requires no rescuing.
>
> I don't agree, but that kind of god does prevent the particular problem
> the OP was discussing. Of course that kind of god is almost identical to
> the god he came up with as a solution.
Why do you say that?
Peter Nyikos
el cid
Well at least you're finally half right about something. May it
bring you the pleasure your internet persona suggests it will.
el cid
> On Dec 13, 4:36 pm, el cid <elcidbi...@gmail.com> wrote:
> > On Dec 13, 4:17 pm, el cid <elcidbi...@gmail.com> wrote:
>
> > > Focus on Evolution of of peptide synthesis
> > > Part I
>
> > Focus on Evolution of of peptide synthesis
> > Part 2
> > Amino acyl tRNA Synthetase (ARSs) and tRNA
>
> > This class of enzymes catalyzes the covalent attachment
> > of specific amino acids to specific tRNAs yielding
> > an energetically activated amino acid in the form
> > of an ester linkage to the tRNA.
> > Two classes of ARS enzymes exist, class I and II.
> > Most amino acids have a single ARS that works for
> > its complement of tRNAs. There is no recognizable
> > homology between class I and class II ARSs. The
> > homology between ARSs of the same class is mostly limited
> > to the catalytic domain responsible for acylating
> > tRNAs with an amino acid.
>
> And so, it is no wonder that you ran away from the following expose by
> me:
>
> ------------------- begin excerpt, me going first,
snip
> =============== end of excerpt from http://groups.google.com/group/talk.origins/msg/7971496e2c5c006d
>
> Note the put-down by el cid. And note the avoidance of any mention of
> degrees of similarity by "el cid".
>
> But most importantly, el cid hasn't hinted at his opinion of what Voet
> and Voet wrote in that last sentence.
>
> I've snipped almost all the rest, which speaks hopefully of how the
> evidence "points to" "duplication and divergence" but the evidence for
> it seems flimsy at best:
You previously complained about nobody providing you anything,
and then that it's just details and apparently don't like summaries.
It was predictable and why I asked you to give you scenario for
what might have happened in that lucky 1 in a googol universes
but you refused to do so.
I am not going to dig into your every misconception. One can't
battle willful ignorance.
I will point out that the duplication and divergence in ARSs
clearly had to occur prior to the last universal ancestor and
so nobody expects high sequence identify. Structural identity
and homology that is only detectable with many many sequences
from across the tree is life is what you get. And you get the core
catalytic domain conserved in class. Other relationships are
observed and they make sense. When you finally get around
to reading about it, start with Woese's many publications.
Of course, you'll just focus on things new to you that fit
your preconceptions but that likely can't be helped. You've
not evidenced free will on that front.
> > It need be noted that the earliest
> > attempts to discover homology in ARSs was confounded
> > by the relatively low level of sequence identify
> > that made accurate alignment of sequences problematic.
> > More recent methods that take into account the crystal
> > structure of these enzymes aids the identification
> > of homologous regions to test the validity of alignment.
> > Alignments that match an alpha-helical stretch to a
> > beta sheet are clearly dubious. Catalytic domains
> > and active site provide clear anchors.
>
> I wonder whether the articles cited below do any better:
>
> > (I've grown lazy in citing references but anybody
> > can readily find support for all these points
> > within pubmed)
>
> > (end part 2)
>
> > CJ Bult et. al. (1996) Science 273, 1058-1073
>
> > AW Curnow et. al(1997) PNAS 94,11819 1182
John Harshman
> On Dec 16, 6:40 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
>>>> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>>> If creationism is any guide, the designer is whatever fits the needs of
>>>>> the moment.-
>
> By the way, was the above meant to be a dig at me? It could be
> construed that way, you know.
Only by the paranoid. Nobody was talking about you.
>>> And if Massey et. al are any guide, a "path" is whatever "Mother Earth
>>> did it" propagandists call it.
>>> I call what they present a series of widely spaced columns like in
>>> Colorado National Monument, with no sign of how one can build a bridge
>>> between them.
>> That's nice. What is Massey et al.?
>
> See my reply to you of a moment ago.
>> And why are you defending the
>> intellectual integrity of creationism?
>
> What makes you think I am doing that?
>
> You aren't one of those people whose mindset includes "the enemy of my
> enemy is my friend", are you?
No, but that's what you seem to be doing.
>>>> It was the negative conclusions about the nature of the designer that
>>>> caused Special Creation to be rejected by Christians in favor of
>>>> evolution in the period 1860-1880. Special Creation "created" some
>>>> very serious problems for the concept of the Christian god. Evolution
>>>> by natural selection -- by making natural selection the proximate
>>>> designer -- rescued God from creationism.
>>> Only to a deist.
>> Wrong rescue.
>>
>>> The typical Christian might wonder what God was up to
>>> during the 13 billion years before the coming of Christ. In that
>>> respect, I am a typical Christian.
>> Do you have any answers to your question?
>
> Not really. But the I haven't ruled out the Eiseley-style route.
And in fact, I can't think of a way in which that could conceivably be
ruled out. Is there any way at all to distinguish it, operationally,
from purely natural evolution?
>>> Augustine had a conversation-stopper for what God did BEFORE making
>>> the universe, but he didn't know about those 13 billion years.
>>>> Always remember, :), however bad creationism is as science and
>>>> whatever danger it poses for science, creationism is even worse as
>>>> Christian theology and poses an even bigger danger for Christianity.
>>> That depends on how narrowly one interprets "creationism". Does your
>>> definition include a God who only intervenes occasionally with minute
>>> Divine nudges as in the following passage from Loren Eiseley's _The
>>> Immense Journey_?
>>> ``Perhaps there also, among rotting fish heads and blue,
>>> night-burning bog lights, moved the eternal mystery,
>>> the careful finger of God. The increase was not much.
>>> It was two bubbles, two thin-walled little balloons at the
>>> end of the Snout's small brain. The cerebral hemispheres
>>> had appeared.''
>>> It is my contention that this kind of God poses no danger for
>>> Christianity, and requires no rescuing.
>> I don't agree, but that kind of god does prevent the particular problem
>> the OP was discussing. Of course that kind of god is almost identical to
>> the god he came up with as a solution.
>
> Why do you say that?
He merely postulated a god who works through evolution. No reason that
couldn't involve occasional direct tweaks. The rarer and smaller the
tweaks, the more closely one approaches a purely deist position. You are
arbitrarily dividing a continuum.
John Harshman
> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> el cid wrote:
>>> On Dec 13, 5:09 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>> el cid wrote:
>>>> [snippies]
>>>> I would like to point out that if I were for some reason designing the
>>>> whole protein synthesis system from scratch, and decided to make ARSs a
>>>> part of that system, it would make the most obvious sense to design them
>>>> all according to a single plan, with differences only in the small
>>>> motifs that a) recognize the specific amino acid and b) recognize the
>>>> specific tRNA to which the amino acid is to be attached. All other
>>>> portions of the protein, having identical function, might as well be
>>>> identical. Of course this is not what we see, even allowing for 4
>>>> billion years of subsequent evolution. Therefore the actual situation is
>>>> evidence against Peter's scenario (forget the number) in which protein
>>>> synthesis is designed.
I notice you have never responded to the above, by the way.
>>> Sometimes designers change specifications when they
>>> run into a problem. Then there's the problem of specifications
>>> changing the designers, though from what I've seen, for some
>>> people, changing the specifications of the designers is no
>>> problem at all.
>> If creationism is any guide, the designer is whatever fits the needs of
>> the moment.
>
> And if the article by Poole, Jeffares, and Penny that "lucaspa" linked
> for us is typical of U.of Ediacara thinking, an "evolutionary path" is
> whatever the U. of Ediacara member says it is.
Even assuming this is true, so what? This argument is on the level of a
5-year-old's challenge: "Bobby hit me first". But on the contrary, I
find creationists on the whole much less intellectually consistent than
evolutionists. Are you truly disagreeing with that?
> I said something similar in response to these words of yours in a
> follow-up to "lucaspa" but had a strange "senior moment" where I wrote
> "Massey et. al." when I meant the three authors I named above.
That's another reason you should actually explain what you mean, rather
than alluding to it cryptically. Some of your cryptic allusions are
impenetrable.
Jack Dominey
> On Dec 13, 5:29 pm, el cid <elcidbi...@gmail.com> wrote:
> And, just in case you ARE PZ Myers, I'd like to call your attention
No, he's not PZ Myers, PZ spends his time on his enormously popular blog.
He's Howard Hershey, just like everyone else here.
John Harshman
muse of fire, that ascends the brightest heaven of invention.
el cid
Not that I expect people to have charted my thinking on
any topic I've posted about, but confusing me with PZ is
probably not the most defensible confusion. I'm not a fan
of his stunts, general antagonism toward all religion and
tribalistic them vs. us mentality. As to the "winner" of any
exchanges between him and Peter, the posts are there
in the archive for anyone who somehow cares. If that
caring applies to any readers: you will be entertained;
seek professional help.
hersheyh
> On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
>
> > On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > > If creationism is any guide, the designer is whatever fits the needs of
> > > the moment.-
>
> And if Massey et. al are any guide, a "path" is whatever "Mother Earth
> did it" propagandists call it.
>
> I call what they present a series of widely spaced columns like in
> Colorado National Monument, with no sign of how one can build a bridge
> between them.
The columns for arguing for *in situ* abiogenesis and evolution of the
biochemical system seen on Earth has columns a lot closer together
with more ideas for how to span gaps without invoking miracles than
your arguments for the evolution, somehow, of a somehow similar but
different biochemical system that somehow evolved into a space-faring
civilization and somehow decided on implementing a program of
panspermy that somehow overcame the difficulties of both to somehow
seed the earth with organisms that are somehow different from the
original organisms (or not) and certainly dramatically different from
the multicellular civilization organisms that sent them. There is an
awful lot of handwaving in that hypothesis compared to even the
weakest explanation involving the evolution *in situ* of life into the
protein-based enzymology of today and the eubacterial flagella of
today. That is, there are better explanations of both systems you
assert, without evidence, cannot possibly have evolved here that do
not require handwaving mysterious aliens into existence.
hersheyh
If everyone Peter responds to is me, how am I also a nonperson he
won't respond to? Perhaps that's why he was absent from this forum so
long. He needed a Jesuit (or a rabbi) to parse out for him how it was
possible to respond to all the other names without responding to HH
sockpuppets.
John Harshman
> On Dec 16, 6:11 pm, pnyikos <nyik...@bellsouth.net> wrote:
>> On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
>>
>>> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>>> If creationism is any guide, the designer is whatever fits the needs of
>>>> the moment.-
>> And if Massey et. al are any guide, a "path" is whatever "Mother Earth
>> did it" propagandists call it.
>>
>> I call what they present a series of widely spaced columns like in
>> Colorado National Monument, with no sign of how one can build a bridge
>> between them.
When you think about it, that's actually an unfortunate metaphor for
Peter, since said columns are actually the remnants of a formerly
continuous surface.
> The columns for arguing for *in situ* abiogenesis and evolution of the
> biochemical system seen on Earth has columns a lot closer together
> with more ideas for how to span gaps without invoking miracles than
> your arguments for the evolution, somehow, of a somehow similar but
> different biochemical system that somehow evolved into a space-faring
> civilization and somehow decided on implementing a program of
> panspermy that somehow overcame the difficulties of both to somehow
> seed the earth with organisms that are somehow different from the
> original organisms (or not) and certainly dramatically different from
> the multicellular civilization organisms that sent them. There is an
> awful lot of handwaving in that hypothesis compared to even the
> weakest explanation involving the evolution *in situ* of life into the
> protein-based enzymology of today and the eubacterial flagella of
> today. That is, there are better explanations of both systems you
> assert, without evidence, cannot possibly have evolved here that do
> not require handwaving mysterious aliens into existence.
Actually, one of his hypotheses (3A?) proposes that the aliens were
approximately just like us, leaving the impression that he imagines that
P(A and B) could be greater than P(A), where A is the natural origin of
life rather like ours and B is the whole panspermy thing.
John Harshman
sockpuppet. He had a list...
pnyikos
> In message
> <d6cd725d-c9bc-4b16-9103-8ff7e1cdd...@35g2000prt.googlegroups.com>,
> pnyikos <nyik...@bellsouth.net> writes>On Dec 16, 4:14�pm, Mark Isaak <eci...@earthlink.net> wrote:
> >> On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
> >> > [snip]
> >> > I do believe the words "Brave atheist" were written tongue in cheek.
> >> > I'll believe PZ Myers to be brave when he burns a copy of the Koran
> >> > with as much publicity as he got when he desecrated of a Holy Communion
> >> > host.
>
> >> He *did* desecrate a Koran (and also _The God Delusion_) at the same
> >> time as he did the host.
>
> >Can you document that?
>
> >Peter Nyikos
>
> It is a common exegesis among both Jews and Christians that reckless
> defamation falls under the prohibition against bearing false witness.
I did no such thing, of course. All I did was to make a conditional
statement, a positive one at that, after posting my own personal
belief.
Are you Jewish or Christian?
>If
> you don't know what PZ Myers did it is your responsibility to make a
> good faith effect to find out before badmouthing him.
My asking Mark is just such a good faith effort. As is the question I
ask below.
> As for the documentation, PZ Myers posted a photograph on his blog.
Does the photo show reporters covering the event?
If not, I suggest you re-read what I wrote.
Peter Nyikos
pnyikos
> On Dec 17, 12:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > Jack Dominey wrote:
> > > On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
>
> > >> On Dec 13, 5:29 pm, el cid <elcidbi...@gmail.com> wrote:
>
> > >> And, just in case you ARE PZ Myers, I'd like to call your attention
>
> > > No, he's not PZ Myers, PZ spends his time on his enormously popular blog.
The first statement obviously does not follow from the second.
> > > He's Howard Hershey, just like everyone else here.
>
> > Let's remember that Peter invented that one.
Let's remember that I did no such thing. What I did do was to
suspect that there was more than one person, only one of whom was a
talk.origins figure, posting from the her...@indiana.edu address.
That one figure goes by the name of Howard Hershey.
Let's remember that Harshman earlier prefaced a much more realistic
but still wildly wrong statement along the same lines with "as I
recall."
Let's also remember that he immediately cautioned me against
"obsessive defensiveness."
I took that as a hint that what he said was meant to be a joke, and
that I should turn to more profitable avenues of discussion than to
correct him. So I didn't correct him.
Perhaps I was mistaken, and I should have corrected him. Perhaps he
is really that badly deluded about me, that he misremembers what I
wrote so completely.
Or perhaps Harshman has decided to "spank" me as mercilessly as anyone
here. Whether it is in the form of carrying a joke much further than
a mature person should carry it, or whether he is deliberately lying
about me, remains to be seen.
> >His paranoia is truly a
> > muse of fire, that ascends the brightest heaven of invention.
I thought Harshman was a responsible, sensible adult. It looks as
though I was mistaken.
> Not that I expect people to have charted my thinking on
> any topic I've posted about, but confusing me with PZ is
> probably not the most defensible confusion.
Actually, it is eminently defensible. The pool of people who argued
with Julie Thomas, and had sufficient knowledge of biochemistry to at
least do a convincing job of it, is not all that great.
Of course, you may have been lying through your teeth about having
been there and engaged her in that kind of discussion, but I prefer
not to assume that for this year (what's left of it) at least.
Peter Nyikos
pnyikos
I had several. But none of them was that kind of list.
But you knew that, didn't you?
And you knew that I never accused *anyone* of being an HH sockpuppet,
don't you?
See my reply to "el cid" of a few minutes ago for more details.
Peter Nyikos
el cid
Your sincere effort to discover if PZ had stopped beating his
wife should be recognized for exactly what it is.
> > As for the documentation, PZ Myers posted a photograph on his blog.
>
> Does the photo show reporters covering the event?
>
> If not, I suggest you re-read what I wrote.
The part about it being the same event?
el cid
> On Dec 17, 12:51 pm, el cid <elcidbi...@gmail.com> wrote:
>
> > On Dec 17, 12:12 pm, John Harshman <jharsh...@pacbell.net> wrote:
>
> > > Jack Dominey wrote:
> > > > On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
>
> > > >> On Dec 13, 5:29 pm, el cid <elcidbi...@gmail.com> wrote:
>
> > > >> And, just in case you ARE PZ Myers, I'd like to call your attention
>
> > > > No, he's not PZ Myers, PZ spends his time on his enormously popular blog.
>
> The first statement obviously does not follow from the second.
>
> > > > He's Howard Hershey, just like everyone else here.
>
> > > Let's remember that Peter invented that one.
>
> Let's remember that I did no such thing. � What I did do was to
> suspect that there was more than one person, only one of whom was a
How many ways are you going to try to have it? You already
accused me of BS'ing about having engaged her and now
you don your trusty plastic halo and make as if you didn't
do so. If you want to play such a crusader in pursuit of honesty
you really ought to start with yourself.
Ernest Major
<709a9b52-1dca-4269...@15g2000vbz.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes
>On Dec 16, 7:03 pm, Ernest Major <{$t...@meden.demon.co.uk> wrote:
>> In message
>> <d6cd725d-c9bc-4b16-9103-8ff7e1cdd...@35g2000prt.googlegroups.com>,
>> pnyikos <nyik...@bellsouth.net> writes>On Dec 16, 4:14 pm, Mark Isaak
>><eci...@earthlink.net> wrote:
>> >> On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
>> >> > [snip]
>> >> > I do believe the words "Brave atheist" were written tongue in cheek.
>> >> > I'll believe PZ Myers to be brave when he burns a copy of the Koran
>> >> > with as much publicity as he got when he desecrated of a Holy Communion
>> >> > host.
>>
>> >> He *did* desecrate a Koran (and also _The God Delusion_) at the same
>> >> time as he did the host.
>>
>> >Can you document that?
>>
>> >Peter Nyikos
>>
>> It is a common exegesis among both Jews and Christians that reckless
>> defamation falls under the prohibition against bearing false witness.
>
>I did no such thing, of course. All I did was to make a conditional
>statement, a positive one at that, after posting my own personal
>belief.
>
>Are you Jewish or Christian?
That's hardly relevant. I happen to think that not bearing false witness
is a good thing, and am pleased that some Christians agree with me.
>
>>If
>> you don't know what PZ Myers did it is your responsibility to make a
>> good faith effect to find out before badmouthing him.
>
>My asking Mark is just such a good faith effort. As is the question I
>ask below.
>
>> As for the documentation, PZ Myers posted a photograph on his blog.
>
>Does the photo show reporters covering the event?
>
>If not, I suggest you re-read what I wrote.
>
>Peter Nyikos
>
If you don't accept that photograph as evidence what evidence do you
have that PZ Myers desecrated a host? In your attempt to avoid
responsibility for the implication that PZ Myers was cowardly you have
effectively claimed that you were engaging in reckless defamation when
you accused him of desecrating a host? (To the best of my knowledge and
recollection that photograph and his word are the only evidence of said
desecration.)
--
alias Ernest Major
pnyikos
> pnyikos wrote:
> > On Dec 16, 6:40 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >> pnyikos wrote:
> >>> On Dec 15, 1:21 pm, lucaspa <luca...@optonline.net> wrote:
> >>>> On Dec 13, 8:01 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>>> If creationism is any guide, the designer is whatever fits the needs of
> >>>>> the moment.-
>
> > By the way, was the above meant to be a dig at me? It could be
> > construed that way, you know.
>
> Only by the paranoid.
You misuse the word. Try looking it up in the dictionary. Note the
word "unreasonable," and answer the following questions, if you
please.
Who else is talking here about designers BESIDES creationists and
myself, except to try and pooh-pooh their existence?
And what is your "If creationism is any guide," supposed to refer to?
More creationists talking about designers?
Anyway, you've posted much worse digs at me on this thread, than the
above statement.
> >> And why are you defending the
> >> intellectual integrity of creationism?
>
> > What makes you think I am doing that?
No answer.
> > You aren't one of those people whose mindset includes "the enemy of my
> > enemy is my friend", are you?
>
> No, but that's what you seem to be doing.
That mindset is foolish. Think of Hitler, Stalin, Roosevelt. {Yes,
I think Roosevelt went too far in praising "Uncle Joe"}
> >>>> It was the negative conclusions about the nature of the designer that
> >>>> caused Special Creation to be rejected by Christians in favor of
> >>>> evolution in the period 1860-1880. Special Creation "created" some
> >>>> very serious problems for the concept of the Christian god. Evolution
> >>>> by natural selection -- by making natural selection the proximate
> >>>> designer -- rescued God from creationism.
> >>> Only to a deist.
> >> Wrong rescue.
>
> >>> The typical Christian might wonder what God was up to
> >>> during the 13 billion years before the coming of Christ. In that
> >>> respect, I am a typical Christian.
> >> Do you have any answers to your question?
>
> > Not really. But the I haven't ruled out the Eiseley-style route.
>
> And in fact, I can't think of a way in which that could conceivably be
> ruled out. Is there any way at all to distinguish it, operationally,
> from purely natural evolution?
Only if we somehow could estimate the odds of evolution producing
intelligent life from prokaryotes in 4 billion years.
And I think we are much further from that than we are from calculating
the odds of the first protein aminoacyl-tRNA synthetase arising from a
RNA world where the only proteins were structural or
"chaperone" [whatever that means] and very weak catallysts hardly
deserving of the name "enzyme".
And, judging from what has transpired in these last two weeks here, we
are still very far even from that.
>
Here is that quote from Loren Eiseley's _The Immense Journey_ again:
> >>> ``Perhaps there also, among rotting fish heads and blue,
> >>> night-burning bog lights, moved the eternal mystery,
> >>> the careful finger of God. The increase was not much.
> >>> It was two bubbles, two thin-walled little balloons at the
> >>> end of the Snout's small brain. The cerebral hemispheres
> >>> had appeared.''
> >>> It is my contention that this kind of God poses no danger for
> >>> Christianity, and requires no rescuing.
> >> I don't agree, but that kind of god does prevent the particular problem
> >> the OP was discussing. Of course that kind of god is almost identical to
> >> the god he came up with as a solution.
>
> > Why do you say that?
>
> He merely postulated a god who works through evolution. No reason that
> couldn't involve occasional direct tweaks. The rarer and smaller the
> tweaks, the more closely one approaches a purely deist position. You are
> arbitrarily dividing a continuum.
Do the things I said about probabilities above help? If the first
probability turned out to be astronomical, the two best alternatives
become "evolution by divine nudges" and "evolution by aliens visiting
earth thousands of times to get evolution going the way they want it
to," with "unguided evolution" a distant third.
IMO, anyway. What's your take on this?
Peter Nyikos
Paul J Gans
Simple. Of all of us, YOU are the only one who is NOT Howard Hershey!
See what complex plots we howlers create!
--
--- Paul J. Gans
Paul J Gans
We Howard Hersheys are a diverse group.
John Harshman
> Let's also remember that he immediately cautioned me against
> "obsessive defensiveness."
[snip exercise in obsessive defensiveness]
John Harshman
>>>>>> It was the negative conclusions about the nature of the designer that
>>>>>> caused Special Creation to be rejected by Christians in favor of
>>>>>> evolution in the period 1860-1880. Special Creation "created" some
>>>>>> very serious problems for the concept of the Christian god. Evolution
>>>>>> by natural selection -- by making natural selection the proximate
>>>>>> designer -- rescued God from creationism.
>>>>> Only to a deist.
>>>> Wrong rescue.
>>>>> The typical Christian might wonder what God was up to
>>>>> during the 13 billion years before the coming of Christ. In that
>>>>> respect, I am a typical Christian.
>>>> Do you have any answers to your question?
>>> Not really. But the I haven't ruled out the Eiseley-style route.
>> And in fact, I can't think of a way in which that could conceivably be
>> ruled out. Is there any way at all to distinguish it, operationally,
>> from purely natural evolution?
>
> Only if we somehow could estimate the odds of evolution producing
> intelligent life from prokaryotes in 4 billion years.
Can we?
> And I think we are much further from that than we are from calculating
> the odds of the first protein aminoacyl-tRNA synthetase arising from a
> RNA world where the only proteins were structural or
> "chaperone" [whatever that means] and very weak catallysts hardly
> deserving of the name "enzyme".
Then there isn't any way at all to distinguish occasional tweaking from
purely natural evolution. Like I said.
> And, judging from what has transpired in these last two weeks here, we
> are still very far even from that.
> Here is that quote from Loren Eiseley's _The Immense Journey_ again:
>>>>> ``Perhaps there also, among rotting fish heads and blue,
>>>>> night-burning bog lights, moved the eternal mystery,
>>>>> the careful finger of God. The increase was not much.
>>>>> It was two bubbles, two thin-walled little balloons at the
>>>>> end of the Snout's small brain. The cerebral hemispheres
>>>>> had appeared.''
>>>>> It is my contention that this kind of God poses no danger for
>>>>> Christianity, and requires no rescuing.
>>>> I don't agree, but that kind of god does prevent the particular problem
>>>> the OP was discussing. Of course that kind of god is almost identical to
>>>> the god he came up with as a solution.
>>> Why do you say that?
>> He merely postulated a god who works through evolution. No reason that
>> couldn't involve occasional direct tweaks. The rarer and smaller the
>> tweaks, the more closely one approaches a purely deist position. You are
>> arbitrarily dividing a continuum.
>
> Do the things I said about probabilities above help?
It might if there were such a probability calculation. (I mean one that
actually meant something.) Since you don't have one, it's moot.
> If the first
> probability turned out to be astronomical, the two best alternatives
> become "evolution by divine nudges" and "evolution by aliens visiting
> earth thousands of times to get evolution going the way they want it
> to," with "unguided evolution" a distant third.
>
> IMO, anyway. What's your take on this?
My take is that absent a valid probability calculation there's no point.
And we would also need to have valid calculations for the other
scenarios. A likelihood ratio, in other words.
Stanley Friesen
>On Dec 17, 11:36 am, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>> > Not really. But the I haven't ruled out the Eiseley-style route.
>>
>> And in fact, I can't think of a way in which that could conceivably be
>> ruled out. Is there any way at all to distinguish it, operationally,
>> from purely natural evolution?
>
>Only if we somehow could estimate the odds of evolution producing
>intelligent life from prokaryotes in 4 billion years.
I am not sure this is even a well-defined question. To start with, what
counts as "intelligent life"? And I am not sure there is any meaningful
way to compute prior odds for any evolutionary sequence, since selection
and adaptation seriously alter the odds, in the direction of less
randomness.
>
>And I think we are much further from that than we are from calculating
>the odds of the first protein aminoacyl-tRNA synthetase arising from a
>RNA world where the only proteins were structural or
>"chaperone" [whatever that means] and very weak catallysts hardly
>deserving of the name "enzyme".
Actually, I suspect that the origin of the enzyme family of
aminoacyl-tRNA synthetases was quite a late event in the switch to
protein-based life. I suspect the earliest tRNA loaders were ribozymes
rather then proteins, and their replacement by protein tRNA synthetases
only occurred after the basic translation mechanism was fairly well
developed.
Query? How do tRNA synthetases recognize the correct tRNA to load? [I
probably knew once upon a time, but I have forgotten].
>>
>> He merely postulated a god who works through evolution. No reason that
>> couldn't involve occasional direct tweaks. The rarer and smaller the
>> tweaks, the more closely one approaches a purely deist position. You are
>> arbitrarily dividing a continuum.
>
>Do the things I said about probabilities above help? If the first
>probability turned out to be astronomical, the two best alternatives
>become "evolution by divine nudges" and "evolution by aliens visiting
>earth thousands of times to get evolution going the way they want it
>to," with "unguided evolution" a distant third.
Not necessarily. Given the utterly unimaginably vast number of solar
systems in the Universe, events with astronomical odds will assuredly
happen *somewhere*. Thus the soundest conclusion to make if the odds did
turn out to be so extreme is that we are the only intelligent life in
the Milky Way, and perhaps in the Local Grouo.
Only if the odds are bad *and* intelligent life turns out to be
relatively common are we in a situation where some sort of design might
become a valid conclusion from probabilities.
[BTW, given the way selection works, it is quite possible that evolution
follows a generally similar course on sufficiently old life-bearing
planet (even though particular shapes and ecologies will be quite
unique).]
--
The peace of God be with you.
Stanley Friesen
John Harshman
> Query? How do tRNA synthetases recognize the correct tRNA to load? [I
> probably knew once upon a time, but I have forgotten].
They bind to one of the loop regions, but not the anticodon loop.
Stanley Friesen
In that loop, do they recognize a base sequence, or the 3D conformation
of the loop. [I suspect it is the latter].
pnyikos
A figment of your imagination is what it is.
> > > As for the documentation, PZ Myers posted a photograph on his blog.
>
> > Does the photo show reporters covering the event?
>
> > If not, I suggest you re-read what I wrote.
>
> The part about it being the same event?
You and "Major" both missed the obvious connection between
"publicity" up there and "reporters"
down here.
Readers may have fun laying bets on whether one or both of these
"missings" was intentional, but I think the ones actually
participating on this thread are too considerate, too solicitous about
y'all's tender feelings to do something that callous.
Of course, betting EITHER way would be callous. After all, who wants
to choose between being an fool and being a knave? Better to keep mum
and hope someone comes up with a third alternative.
Peter Nyikos
el cid
http://scienceblogs.com/pharyngula/2008/07/the_great_desecration.php
You can scroll down to the picture if you like. You know, the one
with the host penetrated by a rusty nail. The self-same nail is
through pages of the Koran.
I happen to think PZ is an ass for the stunt but I defend his
right to do it just as I defend your right to be an ass by asking
questions loaded with innuendo and then denying that you
were doing exactly that. I don't defend those who threatened
PZ's family because of what he did.
Mark Isaak
> [snip context, not relevant to my point]
>
> Readers may have fun laying bets on whether one or both of these
> "missings" was intentional, but I think . . .
Readers may be interested that, last time Nyikos was here, whenever he
speculated about my motives, he was wrong. A very impressive 100%
failure rate.
--
Mark Isaak eciton (at) earthlink (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume
Ernest Major
<eci...@earthlink.net> writes
>On Mon, 20 Dec 2010 04:48:43 -0800, pnyikos wrote:
>
>> [snip context, not relevant to my point]
>>
>> Readers may have fun laying bets on whether one or both of these
>> "missings" was intentional, but I think . . .
>
>Readers may be interested that, last time Nyikos was here, whenever he
>speculated about my motives, he was wrong. A very impressive 100%
>failure rate.
>
"facts" he based them on are wrong as well.
--
alias Ernest Major
John Harshman
> John Harshman <jhar...@pacbell.net> wrote:
>
>> Stanley Friesen wrote:
>>
>>> Query? How do tRNA synthetases recognize the correct tRNA to load? [I
>>> probably knew once upon a time, but I have forgotten].
>> They bind to one of the loop regions, but not the anticodon loop.
>
> In that loop, do they recognize a base sequence, or the 3D conformation
> of the loop. [I suspect it is the latter].
I looked this up in Larry Moran's biochem text. It just says they
recognize the acceptor stem (not loop as I had remembered). But I'm not
sure we can easily distinguish between RNA structure and sequence,
especially since the binding region seems to be one sequential stem
region. Oh, and the book also mentions that in a few tRNA synthetases
the anticodon loop also plays a role in recognition, which might suggest
an evolutionary pathway.
Stanley Friesen
Yes, as is usual in biology there are lots of subtle variations on a
theme. And with that comes the difficulty in tracing the evolutionary
sequence leading to those variants (especially when, as is likely in
this case, the oldest version no longer exist)
It is certainly clear that the genetic code itself is subject to
selection, and that parts of it are older than others.
Paul J Gans
>On Mon, 20 Dec 2010 04:48:43 -0800, pnyikos wrote:
>> [snip context, not relevant to my point]
>>
>> Readers may have fun laying bets on whether one or both of these
>> "missings" was intentional, but I think . . .
>Readers may be interested that, last time Nyikos was here, whenever he
>speculated about my motives, he was wrong. A very impressive 100%
>failure rate.
Most readers here (I can think of one exception) are not much
impressed with our friend's ideas or explanations, not to mention
his math. And he seems uninterested to actually discussing his
own ideas.
In situations like this two options rise: one is to ignore him.
The other is to play with him.
I've chosen a Schroedinger-like combination of both... ;-)
pnyikos
> >> el cid wrote:
> >>> On Dec 13, 5:09 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>>> el cid wrote:
> >>>> [snippies]
> >>>> I would like to point out that if I were for some reason designing the
> >>>> whole protein synthesis system from scratch, and decided to make ARSs a
> >>>> part of that system, it would make the most obvious sense to design them
> >>>> all according to a single plan, with differences only in the small
> >>>> motifs that a) recognize the specific amino acid and b) recognize the
> >>>> specific tRNA to which the amino acid is to be attached. All other
> >>>> portions of the protein, having identical function, might as well be
> >>>> identical. Of course this is not what we see, even allowing for 4
> >>>> billion years of subsequent evolution. Therefore the actual situation is
> >>>> evidence against Peter's scenario (forget the number) in which protein
> >>>> synthesis is designed.
>
> I notice you have never responded to the above, by the way.
>
> >>> Sometimes designers change specifications when they
> >>> run into a problem. Then there's the problem of specifications
> >>> changing the designers, though from what I've seen, for some
> >>> people, changing the specifications of the designers is no
> >>> problem at all.
> >> If creationism is any guide, the designer is whatever fits the needs of
> >> the moment.
>
> > for us is typical of U.of Ediacara thinking, an "evolutionary path" is
> > whatever the U. of Ediacara member says it is.
>
> Even assuming this is true, so what?
So "el cid" is wrong in his claim that he has given me a "path", but
since he is a member in good standing in the U. of Ediacara, and I
explicitly rejected membership in that "committee", he can probably
get lots of people here to act as though he had provided one.
>This argument is on the level of a
> 5-year-old's challenge: "Bobby hit me first".
This rejoinder by you is so grotesquely inappropriate, I think Pagano
was really on to something when he called you the Clown Master of
talk.origins.
Note, it's inappropriate in a very strong way: it makes absolutely no
sense in the context of what you are responding to.
This, by the way, is one piece of behavior by you that I had in mind
on another thread when alluding to this one.
I was alluding to the complete falsehood that I had called some people
sock puppets of Hershey, and used it to "justify" a bizarre accusation
of paranoia by me:
"Let's remember that Peter invented that one.
His paranoia is truly a muse of fire, that ascends
the brightest heaven of invention."
I said that subsequent behavior by you and others on this thread made
it clear in my mind that you were just clowning around, having a
little fun.
I'd forgotten that this post of yours came just BEFORE that one.
Evidently you were already primed for some more clowning, when you
posted that "Let's remember..." bit.
>But on the contrary, I
> find creationists on the whole much less intellectually consistent than
> evolutionists. Are you truly disagreeing with that?
I lack the experience to make a judgment. For instance, from what I
have seen so far, your statement that Ron O "isn't the soul of reason"
while Ray Martinez is bordering on clinical insanity makes more sense
if the names are switched.
And you did nothing to counter that impression, alleging laziness when
I asked you for documentation on Ray that would support your claim.
I suppose you are also too lazy to even DESCRIBE some behavior by Ray
that would counter that impression.
Peter Nyikos
pnyikos
> On Mon, 20 Dec 2010 04:48:43 -0800, pnyikos wrote:
> > [snip context, not relevant to my point]
>
> > Readers may have fun laying bets on whether one or both of these
> > "missings" was intentional, but I think . . .
>
> Readers may be interested that, last time Nyikos was here, whenever he
> speculated about my motives, he was wrong.
So you allege.
> A very impressive 100%
> failure rate.
Can you document more than one of those "whenever"s?
If not, 100% isn't very impressive.
Are you competent enough at math to figure out why? :-)
Peter Nyikos
pnyikos
wrote:
> In message
> <709a9b52-1dca-4269-9813-93680a500...@15g2000vbz.googlegroups.com>,
> pnyikos <nyik...@bellsouth.net> writes
>
>
>
> >On Dec 16, 7:03�pm, Ernest Major <{$t...@meden.demon.co.uk> wrote:
> >> In message
> >> <d6cd725d-c9bc-4b16-9103-8ff7e1cdd...@35g2000prt.googlegroups.com>,
> >><eci...@earthlink.net> wrote:
> >> >> On Wed, 15 Dec 2010 15:17:48 -0800, pnyikos wrote:
> >> >> > [snip]
> >> >> > I do believe the words "Brave atheist" were written tongue in cheek.
> >> >> > I'll believe PZ Myers to be brave when he burns a copy of the Koran
> >> >> > with as much publicity as he got when he desecrated of a Holy Communion
> >> >> > host.
>
> >> >> He *did* desecrate a Koran (and also _The God Delusion_) at the same
> >> >> time as he did the host.
>
> >> >Can you document that?
>
> >> >Peter Nyikos
>
> >> It is a common exegesis among both Jews and Christians that reckless
> >> defamation falls under the prohibition against bearing false witness.
>
> >I did no such thing, of course. �All I did was to make a conditional
> >statement, a positive one at that, after posting my own personal
> >belief.
>
> >Are you Jewish or Christian?
>
> is a good thing,
By everyone? Or only -- as far as Usenet is concerned -- by people
with a minority opinon in the relevant newsgroup?
AFAIK, I am a minority of one here: pro-evolution, anti-homegrown-
abiogenesis.
> and am pleased that some Christians agree with me.
I am a Christian who agrees that not bearing false witness is a good
thing, but I don't think that will please you.
> >>If
> >> you don't know what PZ Myers did it is your responsibility to make a
> >> good faith effect to find out before badmouthing him.
>
> >My asking Mark is just such a good faith effort. �As is the question I
> >ask below.
>
> >> As for the documentation, PZ Myers posted a photograph on his blog.
>
> >Does the photo show reporters covering the event?
>
> >If not, I suggest you re-read what I wrote.
>
> >Peter Nyikos
>
> If you don't accept that photograph as evidence
of widespread publicity? Of course I don't accept it. If "el cid"
hadn't posted the url photo, I would not have known about it, and i
only looked at Myers's blog a long time ago, and couldn't recall
anything being said there about this desecration incident.
Both he and you confused the issue, even AFTER I suggested that you re-
read what I wrote. I can think of the following possible
explanations for this amazing coincidence:
1. You played "monkey see, monkey do" on seeing "el cid" confuse the
issue.
2. The two of you decided in e-mail (or some other private
communication) to have some fun and confuse the issue.
3. You were both incompetent at making a simple connection between
"publicity" and "reporters".
I rule out 2. because I think y'all have better things to do than to
communicate such trivial things to each other. Can you think of a
fourth alternative?
> what evidence do you
> have that PZ Myers desecrated a host?
It was widely publicized by Roman Catholic magazines and websites
before it happened, that he would desecrate one. Donohue, for
example, said a good bit about it.
> In your attempt to avoid
> responsibility for the implication that PZ Myers was cowardly
Weasel word "implication" noted. There is a huge middle ground
between "brave" and "cowardly." In the present political climate, it
takes no real bravery to desecrate Holy Communion hosts, but neither
would I call it a cowardly act. It's just nasty.
Now, I agree that it did take some bravery to desecrate the Koran, but
the degree of bravery depends on the degree of publicity.
Peter Nyikos
pnyikos
> Mark Isaak <eci...@earthlink.net> wrote:
> >On Mon, 20 Dec 2010 04:48:43 -0800, pnyikos wrote:
> >> [snip context, not relevant to my point]
>
> >> Readers may have fun laying bets on whether one or both of these
> >> "missings" was intentional, but I think . . .
> >Readers may be interested that, last time Nyikos was here, whenever he
> >speculated about my motives, he was wrong. �A very impressive 100%
> >failure rate.
So Isaak claims. But as I pointed out to him, if "whenever" only
includes one instance, 100% is not impressive at all.
> Most readers here (I can think of one exception) are not much
> impressed with our friend's ideas or explanations, not to mention
> his math.
Methinks Gans is just sore because I criticized his clumsy, amateurish
attempt to talk about conditional probability. Even John Harshman
picked holes in his presentation, and there's plenty more where those
came from.
>�And he seems uninterested to actually discussing his
> own ideas.
Gans is pulling a Ken Cox here, ignoring the umpteen posts where I DO
discuss my ideas.
> In situations like this two options rise: �one is to ignore him.
> The other is to play with him.
>
> I've chosen a Schroedinger-like combination of both... � ;-)
Gans's attitude is perfectly summarized by some things David Soestrom
said about "spoof," which is his word for "a new kind of playful,
ironic attitude toward the old conflict between good and evil":
Spoof is not true to itself. It cheats at
its own game. It only pretends to take life
as a game, but then inadvertently lets
earnest break in and govern it. Although
pretending to be above and beyond it all,
spoof cares, and cares very much. This
unconscious hypocrisy lies at the root of
all that I find objectionable in spoof ...
--"An Animadversion upon Spoof," The Midwest
Quarterly_ VIII (Spring 1967) 239-246]
Robert Paul Dye commented on this in "The Death of Silence" [_Journal
of Broadcasting, vol. 12 no. 3
(Summer 1968). Reprinted in _Language Awareness_,Paul Eschholtz,
Alfred Rosa, and Virginia Clark,
ed., St. Martin's Press, 1978] with the following words:
...spoofers...lack the courage to be moral and
at the same time cannot deny the desire to be
moral. The result is that the audience is
cheated and deceived. It is neither shocked into
moral consciousness, nor freed, for the moment,
from moral considerations. It is mired in
ambivalence, and the result is malaise.
Peter Nyikos
Ernest Major
<5c6c576a-a15f-4238...@l22g2000vbp.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes
>> >> It is a common exegesis among both Jews and Christians that reckless
>> >> defamation falls under the prohibition against bearing false witness.
>>
>> >I did no such thing, of course. All I did was to make a conditional
>> >statement, a positive one at that, after posting my own personal
>> >belief.
>>
>> >Are you Jewish or Christian?
>>
>> That's hardly relevant. I happen to think that not bearing false witness
>> is a good thing,
>
>By everyone? Or only -- as far as Usenet is concerned -- by people
>with a minority opinon in the relevant newsgroup?
You might salve your conscience with the thought that you were *only*
asking a question, but you're bearing false witness again.
>
>AFAIK, I am a minority of one here: pro-evolution, anti-homegrown-
>abiogenesis.
According to the theory of evolution the universal common descent of the
contemporary biosphere is a provisional and contigent fact. Given that
you have made statements disagreeing with that you are in conflict with
the theory of evolution to at least that degree.
>
>> and am pleased that some Christians agree with me.
>
>I am a Christian who agrees that not bearing false witness is a good
>thing, but I don't think that will please you.
>
You might salve your conscience with the thought that you were *only*
stating your opinion, but you're bearing false witness again.
--
alias Ernest Major
pnyikos
> pnyikos <nyik...@bellsouth.net> writes
>
> >> >> It is a common exegesis among both Jews and Christians that reckless
> >> >> defamation falls under the prohibition against bearing false witness.
>
> >> >I did no such thing, of course. �All I did was to make a conditional
> >> >statement, a positive one at that, after posting my own personal
> >> >belief.
>
> >> >Are you Jewish or Christian?
>
> >> That's hardly relevant. I happen to think that not bearing false witness
> >> is a good thing,
>
> >By everyone? �Or only -- as far as Usenet is concerned -- by people
> >with a minority opinon in the relevant newsgroup?
>
> You might salve your conscience with the thought that you were *only*
> asking a question, but you're bearing false witness again.
On the contrary, I think YOU have been salving your conscience over
totally ignoring the accusations Harshman leveled at me about alleged
"paranoia", and about how many people I have alleged to be sock
puppets for Howard Hershey. It happened right on this thread. THAT
is why I asked the question I did.
And your unequivocal accusation reveals a great deal about you. Do
you care about that, or are you a spoofer like Gans?
>
> >AFAIK, I am a minority of one here: pro-evolution, anti-homegrown-
> >abiogenesis.
>
> According to the theory of evolution the universal common descent of the
> contemporary biosphere is a provisional and contigent fact.
"provisional fact"? what meaning do you attach to that?
By "contingent fact," do you mean it is contingent on the existence of
living things at the outset?
> Given that
> you have made statements disagreeing with that
Please identify said statements.
>you are in conflict with
> the theory of evolution to at least that degree.
I wonder if John Harshman finds these last two sentences (broken up
into three pieces because I have trouble comprehending them) of yours
perfectly clear and transparent.
> >> and am pleased that some Christians agree with me.
>
> >I am a Christian who agrees that not bearing false witness is a good
> >thing, but I don't think that will please you.
>
> You might salve your conscience with the thought that you were *only*
> stating your opinion, but you're bearing false witness again.
Your concept of "bearing false witness" is alien to Judeo-Christian
thinking. That's one reason I didn't think what I said will please
you.
Peter Nyikos
Ernest Major
<f03b6d9e-55e3-4082...@q40g2000prh.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes
>On Jan 19, 5:03 am, Ernest Major <{$t...@meden.demon.co.uk> wrote:
>> In message
>> <5c6c576a-a15f-4238-b63b-28285e93d...@l22g2000vbp.googlegroups.com>,
>> pnyikos <nyik...@bellsouth.net> writes
>>
>> >> >> It is a common exegesis among both Jews and Christians that reckless
>> >> >> defamation falls under the prohibition against bearing false witness.
>>
>> >> >I did no such thing, of course. All I did was to make a conditional
>> >> >statement, a positive one at that, after posting my own personal
>> >> >belief.
>>
>> >> >Are you Jewish or Christian?
>>
>> >> That's hardly relevant. I happen to think that not bearing false witness
>> >> is a good thing,
>>
>> >By everyone? Or only -- as far as Usenet is concerned -- by people
>> >with a minority opinon in the relevant newsgroup?
>>
>> You might salve your conscience with the thought that you were *only*
>> asking a question, but you're bearing false witness again.
>
>On the contrary, I think YOU have been salving your conscience over
>totally ignoring the accusations Harshman leveled at me about alleged
>"paranoia", and about how many people I have alleged to be sock
>puppets for Howard Hershey. It happened right on this thread. THAT
>is why I asked the question I did.
If you would clarify a point for me. Are you claiming that during your
previous activity in talk.origins that you did not allege that many
people were sock puppets of Howard Hershey? (I was a lurker at the
time.)
Also, in I believe this very thread, did you or did you not speculate
that the late El Cid and myself were in collusion with respect to our
responses to your claims about PZ Myers?
>
>And your unequivocal accusation reveals a great deal about you. Do
>you care about that, or are you a spoofer like Gans?
It reveals that I think I know more about my opinions that you do.
>
>>
>> >AFAIK, I am a minority of one here: pro-evolution, anti-homegrown-
>> >abiogenesis.
>>
>> According to the theory of evolution the universal common descent of the
>> contemporary biosphere is a provisional and contigent fact.
>
>"provisional fact"? what meaning do you attach to that?
Subject to refutation by subsequent observation.
>
>By "contingent fact," do you mean it is contingent on the existence of
>living things at the outset?
No. It means that it is not an a priori requirement that life on earth
has a single origin. Abiogenesis could have occurred more than once, and
both lineages survived to the present day. (There are reasons to suspect
that this is unlikely, but that doesn't make it impossible.)
>
>> Given that
>> you have made statements disagreeing with that
>
>Please identify said statements.
You have claimed that the earth was seeded with multiple different
organisms. The statement I was thinking about when I wrote the above
(approaching a month ago) was to the effect that eukaryotes, archaea and
one or more lineages of prokaryotes were separately seeded.
>
>>you are in conflict with
>> the theory of evolution to at least that degree.
>
>I wonder if John Harshman finds these last two sentences (broken up
>into three pieces because I have trouble comprehending them) of yours
>perfectly clear and transparent.
I'm sure that he does.
>
>> >> and am pleased that some Christians agree with me.
>>
>> >I am a Christian who agrees that not bearing false witness is a good
>> >thing, but I don't think that will please you.
>>
>> You might salve your conscience with the thought that you were *only*
>> stating your opinion, but you're bearing false witness again.
>
>Your concept of "bearing false witness" is alien to Judeo-Christian
>thinking. That's one reason I didn't think what I said will please
>you.
I find this incomprehensible. I presume you didn't intend to claim that
the concept of bearing false witness is alien to Judeo-Christian
thinking. But, even if you intended a claim that my conception of
bearing false witness differs from the various conceptions found in
Judeo-Christian thinking, I fail to understand why that would lead you
to a conclusion that I would be displeased that you think that not
bearing false witness is a good thing. I note that I originally
referenced Jewish and Christian exegesis on the topic, though admittedly
on the point of reckless defamation, rather on point of insinuations
"disguised" as questions and opinions. But I doubt that the
incorporation of the latter into the concept of bearing false witness is
alien to Judeo-Christian thinking.
>
>Peter Nyikos
>
--
alias Ernest Major
pnyikos
> pnyikos <nyik...@bellsouth.net> writes
>
>
>
> >On Jan 19, 5:03�am, Ernest Major <{$t...@meden.demon.co.uk> wrote:
> >> In message
> >> <5c6c576a-a15f-4238-b63b-28285e93d...@l22g2000vbp.googlegroups.com>,
> >> pnyikos <nyik...@bellsouth.net> writes
>
> >> >> >> It is a common exegesis among both Jews and Christians that reckless
> >> >> >> defamation falls under the prohibition against bearing false witness.
>
> >> >> >I did no such thing, of course. �All I did was to make a conditional
> >> >> >statement, a positive one at that, after posting my own personal
> >> >> >belief.
You did not contest this.
> >> >> >Are you Jewish or Christian?
>
> >> >> That's hardly relevant. I happen to think that not bearing false witness
> >> >> is a good thing,
>
> >> >By everyone? �Or only -- as far as Usenet is concerned -- by people
> >> >with a minority opinon in the relevant newsgroup?
>
> >> You might salve your conscience with the thought that you were *only*
> >> asking a question, but you're bearing false witness again.
>
> >On the contrary, I think YOU have been salving your conscience over
> >totally ignoring the accusations Harshman leveled at me about alleged
> >"paranoia", and about how many people I have alleged to be sock
> >puppets for Howard Hershey. �It happened right on this thread. �THAT
> >is why I asked the question I did.
>
> If you would clarify a point for me. Are you claiming that during your
> previous activity in talk.origins that you did not allege that many
> people were sock puppets of Howard Hershey? (I was a lurker at the
> time.)
That is an understatement. As I told John Harshman RIGHT ON THIS
THREAD, two days before the post you made on Dec. 19:
"And you knew that I never accused *anyone* of being an
HH sockpuppet, don't you?"
http://groups.google.com/group/talk.origins/msg/3b48a91ae46b2d04
> Also, in I believe this very thread, did you or did you not speculate
> that the late El Cid and myself were in collusion with respect to our
> responses to your claims about PZ Myers?
That was only one of three (3) alternatives that I expressed, for what
is surely an astounding coincidence given the high degree of
intelligence I ascribe to both of you, and I rejected it out of hand,
and even gave reasons why.
And you deleted it in your reply, without even answering my question
of whether you could think of a fourth alternative.
As though the coincidence were a completely ho-hum affair for you.
All I can say is, I do believe the author of _Inherit the Wind_ could
equally well have put one piece of sarcasm into the mouth of the
creationist that he put into the mouth of the evolutionist/agnostic,
with a different setup of course.
After the creationist professed himself never to have wondered about a
certain remarkable thing in the bible, the agnostic says something
like this: "I hate to think where mankind would be if everyone were
gifted with your driving curiosity!"
> >And your unequivocal accusation reveals a great deal about you. �Do
> >you care about that, or are you a spoofer like Gans?
>
> It reveals that I think I know more about my opinions that you do.
And are keeping mum about them, just as you kept mum about any fourth
alternative.
> >> >AFAIK, I am a minority of one here: pro-evolution, anti-homegrown-
> >> >abiogenesis.
>
> >> According to the theory of evolution the universal common descent of the
> >> contemporary biosphere is a provisional and contigent fact.
It is clear from what you say below that this is only ONE theory of
evolution. I don't think any professional evolutionary biologist
would call someone who disagreed any less a pro-evolutionist for not
embracing it. See my remarks about Woese.
> >"provisional fact"? �what meaning do you attach to that?
>
> Subject to refutation by subsequent observation.
Thanks for the clarification.
> >By "contingent fact," do you mean it is contingent on the existence of
> >living things at the outset?
>
> No. It means that it is not an a priori requirement that life on earth
> has a single origin. Abiogenesis could have occurred more than once, and
> both lineages survived to the present day. (There are reasons to suspect
> that this is unlikely, but that doesn't make it impossible.)
Actually, I believe that is one way one might interpret Woese's
theory. "Multiple origins" could refer to there being three
independent cell lines (corresponding to the three domains) coming out
of a pre-cellular "annealing".
>
>
> >> Given that
> >> you have made statements disagreeing with that
>
> >Please identify said statements.
>
> You have claimed that the earth was seeded with multiple different
> organisms.
That is merely a theory I am advocating at present. A provisional and
contingent one, by your terminology.
But more importantly, I do believe that once the seeding (by
unicellular organisms) took place, then evolution did the rest, with
us as one crowning achievement, the eusocial insects as another, the
cetaceans another...
> The statement I was thinking about when I wrote the above
> (approaching a month ago) was to the effect that eukaryotes, archaea and
> one or more lineages of prokaryotes were separately seeded.
That is one possibility, but I think it more likely that eukaryotes
were not included. As Francis Crick loved to say, "Prokaryotes travel
farther."
Remainder deleted, to be replied to later.
Peter Nyikos
John Harshman
> That is an understatement. As I told John Harshman RIGHT ON THIS
> THREAD, two days before the post you made on Dec. 19:
>
> "And you knew that I never accused *anyone* of being an
> HH sockpuppet, don't you?"
I didn't actually know you didn't. Though memory is unreliable, I do
remember you as having done so. And I have no real interest in checking.
If you say you didn't, I'm willing to accept that. So, do you you know
how the legend got started?
Do you realize that nearly all your current traffic is devoted to
off-topic argument about who said what to whom?
Paul J Gans
>pnyikos wrote:
>> That is an understatement. As I told John Harshman RIGHT ON THIS
>> THREAD, two days before the post you made on Dec. 19:
>>
>> "And you knew that I never accused *anyone* of being an
>> HH sockpuppet, don't you?"
>I didn't actually know you didn't. Though memory is unreliable, I do
>remember you as having done so. And I have no real interest in checking.
>If you say you didn't, I'm willing to accept that. So, do you you know
>how the legend got started?
IIRC, and I may not, Howard Hershey was accused of having many
pseudonyms on this newsgroup. The clear implication was that
some regular posters here were actually Howard Hershey.
>Do you realize that nearly all your current traffic is devoted to
>off-topic argument about who said what to whom?
Beats arguing data.
John Harshman
> John Harshman <jhar...@pacbell.net> wrote:
>> pnyikos wrote:
>
>>> That is an understatement. As I told John Harshman RIGHT ON THIS
>>> THREAD, two days before the post you made on Dec. 19:
>>>
>>> "And you knew that I never accused *anyone* of being an
>>> HH sockpuppet, don't you?"
>
>> I didn't actually know you didn't. Though memory is unreliable, I do
>> remember you as having done so. And I have no real interest in checking.
>> If you say you didn't, I'm willing to accept that. So, do you you know
>> how the legend got started?
>
> IIRC, and I may not, Howard Hershey was accused of having many
> pseudonyms on this newsgroup. The clear implication was that
> some regular posters here were actually Howard Hershey.
No, that can't be right, because that would mean Peter had claimed that
many posters were Hershey's sock puppets. Or is it possibly that he's
taking refuge in the word "accusation", since he never named any
specific posters? No, that would be too weaselly; no honorable person
would do that, and sure, he is an honorable man.
Walter Bushell
Paul J Gans <gan...@panix.com> wrote:
> IIRC, and I may not, Howard Hershey was accused of having many
> pseudonyms on this newsgroup. The clear implication was that
> some regular posters here were actually Howard Hershey.
Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
this.
--
The Chinese pretend their goods are good and we pretend our money
is good, or is it the reverse?
John Harshman
> In article <ijkiog$7k9$2...@reader1.panix.com>,
> Paul J Gans <gan...@panix.com> wrote:
>
>> IIRC, and I may not, Howard Hershey was accused of having many
>> pseudonyms on this newsgroup. The clear implication was that
>> some regular posters here were actually Howard Hershey.
>
> Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> this.
>
John S. Wilkins
> In article <ijkiog$7k9$2...@reader1.panix.com>,
> Paul J Gans <gan...@panix.com> wrote:
>
> > IIRC, and I may not, Howard Hershey was accused of having many
> > pseudonyms on this newsgroup. The clear implication was that
> > some regular posters here were actually Howard Hershey.
>
> Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> this.
Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
so my mind is working once more.
--
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
richardal...@gmail.com
> Walter Bushell <pr...@panix.com> wrote:
> > Paul J Gans <gan...@panix.com> wrote:
>
> > > IIRC, and I may not, Howard Hershey was accused of having many
> > > pseudonyms on this newsgroup. The clear implication was that
> > > some regular posters here were actually Howard Hershey.
>
> > Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> > this.
>
> Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
> so my mind is working once more.
Surely that's an impossible combination?
RF
> --
> John S. Wilkins, Associate, Philosophy, University of Sydneyhttp://evolvingthoughts.net
John S. Wilkins
> On Feb 21, 8:25 am, j...@wilkins.id.au (John S. Wilkins) wrote:
> > Walter Bushell <pr...@panix.com> wrote:
> > > In article <ijkiog$7k...@reader1.panix.com>,
> > > Paul J Gans <gan...@panix.com> wrote:
> >
> > > > IIRC, and I may not, Howard Hershey was accused of having many
> > > > pseudonyms on this newsgroup. The clear implication was that
> > > > some regular posters here were actually Howard Hershey.
> >
> > > Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> > > this.
> >
> > Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
> > so my mind is working once more.
>
> Surely that's an impossible combination?
>
Not when the two are coterminous.
Walter Bushell
jo...@wilkins.id.au (John S. Wilkins) wrote:
> Walter Bushell <pr...@panix.com> wrote:
>
> > In article <ijkiog$7k9$2...@reader1.panix.com>,
> > Paul J Gans <gan...@panix.com> wrote:
> >
> > > IIRC, and I may not, Howard Hershey was accused of having many
> > > pseudonyms on this newsgroup. The clear implication was that
> > > some regular posters here were actually Howard Hershey.
> >
> > Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> > this.
>
> Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
> so my mind is working once more.
But somebody is always on the froup, so there will always be a Wilkins.
Paul J Gans
>> In article <ijkiog$7k9$2...@reader1.panix.com>,
>> Paul J Gans <gan...@panix.com> wrote:
>>
>> > IIRC, and I may not, Howard Hershey was accused of having many
>> > pseudonyms on this newsgroup. The clear implication was that
>> > some regular posters here were actually Howard Hershey.
>>
>> Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
>> this.
>Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
>so my mind is working once more.
Amazing how our advances are self-limiting. A few days of
internet and your mind will once again be gone.
Walter Bushell
Paul J Gans <gan...@panix.com> wrote:
> John S. Wilkins <jo...@wilkins.id.au> wrote:
> >Walter Bushell <pr...@panix.com> wrote:
>
> >> In article <ijkiog$7k9$2...@reader1.panix.com>,
> >> Paul J Gans <gan...@panix.com> wrote:
> >>
> >> > IIRC, and I may not, Howard Hershey was accused of having many
> >> > pseudonyms on this newsgroup. The clear implication was that
> >> > some regular posters here were actually Howard Hershey.
> >>
> >> Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> >> this.
>
> >Until a few minutes ago, *I* wasn't Wilkins. But I have internet again,
> >so my mind is working once more.
>
> Amazing how our advances are self-limiting. A few days of
> internet and your mind will once again be gone.
These say it very well.
Our sense of self is basically illusionary and fabulous anyway and based
on confabulations.
<http://9gag.com/gag/56183/>
<http://www.smbc-comics.com/index.php?db=comics&id=2067#comic>
pnyikos
> pnyikos wrote:
> > That is an understatement. As I told John Harshman RIGHT ON THIS
> > THREAD, two days before the post you made on Dec. 19:
>
> > "And you knew that I never accused *anyone* of being an
> > HH sockpuppet, don't you?"
>
> I didn't actually know you didn't. Though memory is unreliable, I do
> remember you as having done so.
Maybe you got confused by the crack made by hit-and-run artist Jack
Dominey, to which you replied.
> And I have no real interest in checking.
> If you say you didn't, I'm willing to accept that. So, do you you know
> how the legend got started?
AFAIK, it started with Jack Dominey. I think the people around in the
1990's were too close to the actual events to cook up that kind of
legend. But I could be wrong on this.
Dominey in turn may have been confused by a memory of me publicly
suspecting that there were several people posting from the
hers...@indiana.edu address. But I don't think I ever suspected
anyone posting under a different name in talk.origins of being one of
them; my suspicions had more to do with Indiana U. students lending
Hershey a hand.
> Do you realize that nearly all your current traffic is devoted to
> off-topic argument about who said what to whom?
That's not what it is all about. See what I said about not wanting
talk.origins to go the way of talk.abortion.
Peter Nyikos
pnyikos
> John Harshman <jharsh...@pacbell.net> wrote:
> >pnyikos wrote:
> >> That is an understatement. As I told John Harshman RIGHT ON THIS
> >> THREAD, two days before the post you made on Dec. 19:
>
> >> "And you knew that I never accused *anyone* of being an
> >> HH sockpuppet, don't you?"
> >I didn't actually know you didn't. Though memory is unreliable, I do
> >remember you as having done so. And I have no real interest in checking.
> >If you say you didn't, I'm willing to accept that. So, do you you know
> >how the legend got started?
>
> IIRC, and I may not, Howard Hershey was accused of having many
> pseudonyms on this newsgroup.
He was not.
> The clear implication was that
> some regular posters here were actually Howard Hershey.
GIGO.
Peter Nyikos
pnyikos
> > Paul J Gans <gan...@panix.com> wrote:
>
> >> IIRC, and I may not, Howard Hershey was accused of having many
> >> pseudonyms on this newsgroup. The clear implication was that
> >> some regular posters here were actually Howard Hershey.
>
> > Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
> > this.
>
> It's all the same. Wilkins is Hershey.
Could you steer me towards some substantive talk.origins posts of
yours, John? I haven't seen any in quite a while.
[Yes, I owe you quite a few replies in sci.bio.paleontology to
substantive posts of yours there. Unfortunately I've got too much on
my plate this week, but next week should be another story.]
Peter Nyikos
pnyikos
> >> pnyikos wrote:
>
> >>> That is an understatement. As I told John Harshman RIGHT ON THIS
> >>> THREAD, two days before the post you made on Dec. 19:
>
> >>> "And you knew that I never accused *anyone* of being an
> >>> HH sockpuppet, don't you?"
>
> >> I didn't actually know you didn't. Though memory is unreliable, I do
> >> remember you as having done so. And I have no real interest in checking.
> >> If you say you didn't, I'm willing to accept that. So, do you you know
> >> how the legend got started?
>
> > IIRC, and I may not, Howard Hershey was accused of having many
> > pseudonyms on this newsgroup. The clear implication was that
> > some regular posters here were actually Howard Hershey.
>
> No, that can't be right, because that would mean Peter had claimed that
> many posters were Hershey's sock puppets. Or is it possibly that he's
> taking refuge in the word "accusation", since he never named any
> specific posters? No, that would be too weaselly; no honorable person
> would do that, and sure, he is an honorable man.
Marcus Antonius, as he was known to his contemporaries, is a very poor
role model. Even Shakespeare doesn't try to whitewash him all the
way: in a scene after the famous "Friends, Romans, countrymen" speech,
he participates in a discussion about who is to be killed and who
should be spared, based not on actual crimes but on the ambitions of
the people in the discussion, including Marcus and Octavian.
Peter Nyikos
John Harshman
> On Feb 18, 12:56 am, John Harshman <jharsh...@pacbell.net> wrote:
>> Walter Bushell wrote:
>>> In article <ijkiog$7k...@reader1.panix.com>,
>>> Paul J Gans <gan...@panix.com> wrote:
>>>> IIRC, and I may not, Howard Hershey was accused of having many
>>>> pseudonyms on this newsgroup. The clear implication was that
>>>> some regular posters here were actually Howard Hershey.
>>> Aren't we all? Or are we Dr. Wilkins? Sometimes I get confused about
>>> this.
>> It's all the same. Wilkins is Hershey.
>
> Could you steer me towards some substantive talk.origins posts of
> yours, John? I haven't seen any in quite a while.
I would consider the great majority of my posts substantive. Try
choosing three at random. This assumes you consider arguments with
creationists to be substantive.
John Harshman
It would be nice if, instead of just demonstrating that you got the
Shakespeare reference, you would actually clarify the matter at hand.
What did you do? What didn't you do? How did the idea that you accused
people of being sock puppets arise?
John Harshman
> On Feb 17, 6:37 pm, John Harshman <jharsh...@pacbell.net> wrote:
>> pnyikos wrote:
>>> That is an understatement. As I told John Harshman RIGHT ON THIS
>>> THREAD, two days before the post you made on Dec. 19:
>>> "And you knew that I never accused *anyone* of being an
>>> HH sockpuppet, don't you?"
>> I didn't actually know you didn't. Though memory is unreliable, I do
>> remember you as having done so.
>
> Maybe you got confused by the crack made by hit-and-run artist Jack
> Dominey, to which you replied.
Perhaps. I can't remember anything from that far back.
>> And I have no real interest in checking.
>> If you say you didn't, I'm willing to accept that. So, do you you know
>> how the legend got started?
>
> AFAIK, it started with Jack Dominey. I think the people around in the
> 1990's were too close to the actual events to cook up that kind of
> legend. But I could be wrong on this.
>
> Dominey in turn may have been confused by a memory of me publicly
> suspecting that there were several people posting from the
> hers...@indiana.edu address. But I don't think I ever suspected
> anyone posting under a different name in talk.origins of being one of
> them; my suspicions had more to do with Indiana U. students lending
> Hershey a hand.
Ah, that explains it. I doubt that you were correct about the hershey
address, but it's certainly distinct from the claim being bandied about
here.
>> Do you realize that nearly all your current traffic is devoted to
>> off-topic argument about who said what to whom?
>
> That's not what it is all about. See what I said about not wanting
> talk.origins to go the way of talk.abortion.
That may be your purpose, but I was talking about your posts.
Paul J Gans
I explained that. I'll repeat it here:
"IIRC, and I may not, Howard Hershey was accused of having many
pseudonyms on this newsgroup. The clear implication was that
some regular posters here were actually Howard Hershey."
It was a running joke here for some months.
Given my deep involvement with the List Maker, I may be the only
one who remembers, though there are plenty of folks still around
from those days.
Roger Shrubber
His listness displayed a fascination with the Hersey. At times, he
accused
him of being a meager technician and reminisced about some perceived
abuse at the hands of a dis-fondly remember TA that dared to confound
his
self-asserted eminence. And then there were times he seemed awed by
the volume of erudite criticisms of the list-monger's absurdities,
asserting
a conspiracy of multitudes to produce the volume of refutations of his
frequent malapros. Whither Howard was incompetent or a conspiracy
of multitudes? Ours was not to resolve the innate contradiction of
the
accusations. Regardless the foil painted the clown with comic paint
unless
one had a conscience and so felt sorry for the Nikosian delusions and
further
lacked the wherewithall to laugh at the clown.
His current manifestation appears to have married some sing-song
notion
that anyone who accepts Earth-bound abiogenesis is devoted to the same
rather than simply following the data. Nobody actually sings his song,
but
it echos in his mind. Reality stands no chance against the echoes of
the
listmaker's mind. If you speculate on his motivations for aligning
himself
with the 'intelligent design' crown, he will accuse you of distorting
his very
different motivations. He is not one of the apologists who are
motivated by
the Wedge Document and you have his word on it. However, if you dare
to
think that energy finds chemistry to realize life, he will assert
motivations to
you even if you never espouse them yourself, something about mother
earth
that likely never entered your mind. And his ineffable surety will
carry conviction.
Thus you will be transformed into a Howard Hershey Zombie. It will not
matter what you say, what you cite, and certainly not that you think.
The
listmaster will have a place for you and within the expanses of his
grand
intellect your every action will only nest you deeper within your
appointed
well. So it has been written. So it shall be done.
Ernest Major
<jhar...@pacbell.net> writes
>pnyikos wrote:
>> On Feb 17, 6:37 pm, John Harshman <jharsh...@pacbell.net> wrote:
>>> pnyikos wrote:
>>>> That is an understatement. As I told John Harshman RIGHT ON THIS
>>>> THREAD, two days before the post you made on Dec. 19:
>>>> "And you knew that I never accused *anyone* of being an
>>>> HH sockpuppet, don't you?"
>>> I didn't actually know you didn't. Though memory is unreliable, I do
>>> remember you as having done so.
>> Maybe you got confused by the crack made by hit-and-run artist Jack
>> Dominey, to which you replied.
>
>Perhaps. I can't remember anything from that far back.
>
>>> And I have no real interest in checking.
>>> If you say you didn't, I'm willing to accept that. So, do you you know
>>> how the legend got started?
>> AFAIK, it started with Jack Dominey. I think the people around in
>>the
>> 1990's were too close to the actual events to cook up that kind of
>> legend. But I could be wrong on this.
The "we are all Howard Hershey" meme has been part of talk.origins
culture for a long time. That particular phrase turns up as least as
earlier as 2004, in response to an April Fools reference to the meme by
DIG.
>> Dominey in turn may have been confused by a memory of me publicly
>> suspecting that there were several people posting from the
>> hers...@indiana.edu address. But I don't think I ever suspected
>> anyone posting under a different name in talk.origins of being one of
>> them; my suspicions had more to do with Indiana U. students lending
>> Hershey a hand.
>
>Ah, that explains it. I doubt that you were correct about the hershey
>address, but it's certainly distinct from the claim being bandied about
>here.
The "we are all Howard Hershey" meme is obviously hyperbole, and not an
accurate rendition of Peter's record, but may well have contributed to a
distortion of people's memory of his posts. I do doubt that Peter
specifically accused many people of being sock puppets of Howard. A
conflation of the above with otherwise directed accusations of
sockpuppetry is certainly a plausible explanation. (Peter's reference to
Ken Cox as Howard's sock puppet might have been intended as a joke.)
>
>>> Do you realize that nearly all your current traffic is devoted to
>>> off-topic argument about who said what to whom?
>> That's not what it is all about. See what I said about not wanting
>> talk.origins to go the way of talk.abortion.
>
>That may be your purpose, but I was talking about your posts.
>
--
alias Ernest Major
Robert Grumbine
You've got company in remembering. Even though I never had
much to do with the maker of lists, the 'we are all howard hershey'
comment was amusing enough for me to remember where it came from.
--
Robert Grumbine http://moregrumbinescience.blogspot.com/ Science blog
Sagredo (Galileo Galilei) "You present these recondite matters with too much
evidence and ease; this great facility makes them less appreciated than they
would be had they been presented in a more abstruse manner." Two New Sciences
pnyikos
False, and what folows is not an explanation but a mis-remembered (at
most half true) DESCRIPTION of a "running joke":
> I'll repeat it here:
>
> "IIRC, and I may not, Howard Hershey was accused of having many
> pseudonyms on this newsgroup.
That may or may not have been the running joke. It is certainly not
what happened.
> The clear implication was that
> some regular posters here were actually Howard Hershey."
The running joke may have been that THIS was the clear implication
from my having what is in some sense the OPPOSITE suspicion about
Hershey.
And that indeed is a joke, and just the kind of joke one would expect
a leftist clown like Gans to embrace enthusiastically:
> It was a running joke here for some months.
>
> Given my deep involvement with the List Maker, I may be the only
> one who remembers,
Howard Hershey, who was far more involved with me in 1997-2001 than
Gans was, probably remembers a lot better. And I only expressed my
suspicions somewhere in that interval.
IIRC Mark Isaak, John Stockwell, and John Wilkins were also more
involved with me in that time period than Gans was.
> though there are plenty of folks still around
> from those days.
>
> --
> --- Paul J. Gans
Some deep involvement: Gans has not followed up to a single one of my
posts since I resumed posting to talk.origins in December. He seems
to think that his involvement in 1995-6 made him an expert in my ways--
but he either was clueless about my ways or he was completely
insincere in expressing his opinion about them back then. And the
same applies to my ways since I resumed posting in December.
IIRC, Gans had very little involvement with me in talk.origins in
1997-2001, although we tangled numerous times in the newsgroup
soc.history.medieval in 2001-2.
Peter Nyikos
pnyikos
> His current manifestation appears to have married some sing-song
> notion
> that anyone who accepts Earth-bound abiogenesis is devoted to the same
> rather than simply following the data.
There is no data that anyone has posted that would put Earth-bound
abiogenesis above directed panspermy. The arguments for that all boil
down to the invocation of Ockham's Razor, which is not a datum, and
speculation about the motivations of other intelligent species, which
are not data either.
Hence my "sing-song", which is poetic license, same as the poetic
license Shrubber is using throughout the post [most of which has been
deleted] to which I am following up.
> However, if you dare
> to
> think that energy finds chemistry to realize life, he will assert
> motivations to
> you
Utterly false. I am quite happy with the idea that it happened on
another planet, and maybe it happened on earth, but I think the odds
are against it, and no one has been able to refute my main argument
for that.
[Doggerel with the keyword Zombie deleted. I chalk it up to poetic
license, and hold no animus towards Shrubber for it. I don't expect
to encounter him again.]
pnyikos
> In article <ilmno6$6f...@reader1.panix.com>, Paul J Gans wrote:
He never did; see my reply to Gans's post.
> I'll repeat it here:
>
> > "IIRC, and I may not,
Gans did not.
> Howard Hershey was accused of having many
> > pseudonyms on this newsgroup. The clear implication was that
> > some regular posters here were actually Howard Hershey."
>
> > It was a running joke here for some months.
>
> > Given my deep involvement with the List Maker, I may be the only
> > one who remembers, though there are plenty of folks still around
> > from those days.
>
> You've got company in remembering.
Remembering what exactly?
> Even though I never had
> much to do with the maker of lists, the 'we are all howard hershey'
> comment was amusing enough for me to remember where it came from.
So who originated it? Not I, nor was it an extrapolation from
anything I posted.
Peter Nyikos
pnyikos
> In message <DvadnRPhvaZMNuPQRVn_...@giganews.com>, John Harshman
> <jharsh...@pacbell.net> writes
>
>
>
> >pnyikos wrote:
> >> On Feb 17, 6:37 pm, John Harshman <jharsh...@pacbell.net> wrote:
> >>> pnyikos wrote:
> >>>> That is an understatement. As I told John Harshman RIGHT ON THIS
> >>>> THREAD, two days before the post you made on Dec. 19:
> >>>> "And you knew that I never accused *anyone* of being an
> >>>> HH sockpuppet, don't you?"
> >>> I didn't actually know you didn't. Though memory is unreliable, I do
> >>> remember you as having done so.
> >> Maybe you got confused by the crack made by hit-and-run artist Jack
> >> Dominey, to which you replied.
>
> >Perhaps. I can't remember anything from that far back.
>
> >>> And I have no real interest in checking.
> >>> If you say you didn't, I'm willing to accept that. So, do you you know
> >>> how the legend got started?
> >> AFAIK, it started with Jack Dominey. I think the people around in
> >>the
> >> 1990's were too close to the actual events to cook up that kind of
> >> legend. But I could be wrong on this.
>
> The "we are all Howard Hershey" meme has been part of talk.origins
> culture for a long time. That particular phrase turns up as least as
> earlier as 2004,
LONG after I was gone from talk.origins!!!
In fact that was right about the middle of my posting break from all
of Usenet.
By the way, I never posted to talk.origins before 1995, so that can't
be a typo for 1994.
> in response to an April Fools reference to the meme by
> DIG.
> >> Dominey in turn may have been confused by a memory of me publicly
> >> suspecting that there were several people posting from the
> >> hersh...@indiana.edu address. But I don't think I ever suspected
> >> anyone posting under a different name in talk.origins of being one of
> >> them; my suspicions had more to do with Indiana U. students lending
> >> Hershey a hand.
>
> >Ah, that explains it. I doubt that you were correct about the hershey
> >address, but it's certainly distinct from the claim being bandied about
> >here.
>
> The "we are all Howard Hershey" meme is obviously hyperbole,
But John Harshman was fooled by it to the extent of basing a
hyperbolic accusation of paranoia on it, right on this thread.
>I do doubt that Peter
> specifically accused many people of being sock puppets of Howard. A
> conflation of the above with otherwise directed accusations of
> sockpuppetry is certainly a plausible explanation. (Peter's reference to
> Ken Cox as Howard's sock puppet might have been intended as a joke.)
I recall no such reference. Please provide documentation.
Peter Nyikos
Ernest Major
<d14bbb93-4617-4767...@a11g2000pri.googlegroups.com>,
pnyikos <nyi...@bellsouth.net> writes
<URL:http://groups.google.com/group/talk.origins/msg/454fbfa0b3cf1e90?dmo
de=source>
>
>Peter Nyikos
>
--
alias Ernest Major
Roger Shrubber
> In article <ilmno6$6f...@reader1.panix.com>, Paul J Gans wrote:
From Nov. 30, 1998, in a thread titled "Focus on Howard Hershey"
the Nyikos wrote:
<quote>
I make no secret of the fact that I am making an
attack on a highly dishonest entity, perhaps a whole
team of persons posting from hersh...@indiana.edu,
one of whom might even be Henry Barwood posting with
the permission of the real Howard Hershey--or it
might all be the work of the one-man team consisting
of the Lab Coordinator and Lecturer, Howard Hershey.
Since "howard hershey" has repeatedly refused to
either confirm or deny either description of the
"howard hershey" entity, yet has NEVER signed any
of his posts with "Howard Hershey" or even "howard hershey,"
the foregoing paragraph
represents my attempt to come to terms with this issue.
</quote>
He actively imagined a conspiracy of people behind
Howard's posts and suggested that at least one regular
was part of The Cabal. He ought to be careful about
denying things for which there are records.
John Harshman
accused Howard of being a sock puppet of Henry Barwood and unnamed
others. This of course fits the idea of the Hershey Collective better
than any alternatives.
pnyikos
> pnyikos <nyik...@bellsouth.net> writes
Now that I see it, I'm pretty sure it was a fishing expedition to try
and find out what the term "sock puppet" meant. Back in those days I
generally figured I'd have a better chance learning things indirectly
than asking point-blank about them.
> >I recall no such reference. Please provide documentation.
>
> <URL:http://groups.google.com/group/talk.origins/msg/454fbfa0b3cf1e90?dmo
> de=source>
------------------------------- begin excerpt
>When did I complain about Peter's habit of not dropping a subject?
Maybe Joe had in mind your "sock puppet" Ken Cox.
[Actually I don't know what the term "sock puppet" means,
but I believe Joe used it to describe Ken.]
==========================end of excerpt
I certainly wasn't accusing Ken Cox of being Howard Hershey by another
name. I knew the habits of the two well and knew they were well
established figures in talk.origins and that their approaches to
reality were utterly different.
Is Ken Cox still around, by the way?
Peter Nyikos
pnyikos
I never denied making such a tentative suggestion as the one about
Barwood there. The allegation was that I had ACCUSED someone of being
hh's sock puppet, and this suggestion is worlds apart from that.
I know my own ways, and I know what sorts of things are completely out
of character for me. Back in those days I fought almost all the time
with both hands tied behind my back, figuratively speaking: I almost
never accused anyone of lying outright.
Now I only fight with one hand behind my back, and that stays there,
figuratively speaking, to my dying day: I will never accuse anyone of
anything of which I know he is innocent, or even of which I think the
preponderance of evidence is that he is innocent. But I am far freer
with accusations of lying than I used to be.
Peter Nyikos
pnyikos
Too bad, John -- your mask of scientific objectivity has self-
destructed. See my own reply to Shrubber a few minutes ago.
It'll be interesting to see how many other traits of yours are masks
you are wearing.
> and unnamed
> others. This of course fits the idea of the Hershey Collective better
> than any alternatives.-
By the way, Hershey never claimed sole authorships of all those posts
from hers...@indiana.edu, did he?
Peter Nyikos
John Harshman
On the bright side, I am granted a second, convenient example of you
accusing me of dishonesty. Thanks.
>> and unnamed
>> others. This of course fits the idea of the Hershey Collective better
>> than any alternatives.-
>
> By the way, Hershey never claimed sole authorships of all those posts
> from hers...@indiana.edu, did he?
I don't know. Why should he have to?