Origins of life: The cooperative gene

[Mark Isaak]

There is a new "News and Views" article in the Oct. 17 _Nature_:
Origins of life: The cooperative gene.
by James Attwater & Philipp Holliger.
"The origin of life on Earth remains one of the great unsolved
mysteries. A new study suggests that cooperation among molecules could
have contributed to the transition from inanimate chemistry to biology."

Presumably it is a comment on this research article:
Spontaneous network formation among cooperative RNA replicators.
by Nilesh Vaidya et al.
"The origins of life on Earth required the establishment of
self-replicating chemical systems capable of maintaining and evolving
biological information. In an RNA world, single self-replicating RNAs
would have faced the extreme challenge of possessing a mutation rate low
enough both to sustain their own information and to compete successfully
against molecular parasites with limited evolvability. Thus theoretical
analyses suggest that networks of interacting molecules were more likely
to develop and sustain life-like behaviour. Here we show that mixtures
of RNA fragments that self-assemble into self-replicating ribozymes
spontaneously form cooperative catalytic cycles and networks. We find
that a specific three-membered network has highly cooperative growth
dynamics. When such cooperative networks are competed directly against
selfish autocatalytic cycles, the former grow faster, indicating an
intrinsic ability of RNA populations to evolve greater complexity
through cooperation. We can observe the evolvability of networks through
in vitro selection. Our experiments highlight the advantages of
cooperative behaviour even at the molecular stages of nascent life."


Both full articles, however, are paywalled, so I have not seen them.
Anyone here with access who can say whether they are any good?

--
Mark Isaak eciton (at) curioustaxonomy (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

[Richard Norman]

You must understand that "cooperativity" in relation to chemical
reactions bears absolutely no relation to "cooperativity" in relation
to behavioral interaction between organisms.

Wikipedia says: "In biochemistry, a macromolecule exhibits cooperative
binding if its affinity for its ligand changes with the amount of
ligand already bound."
http://en.wikipedia.org/wiki/Cooperative_binding

[Ernest Major]

In message <5pnu7857ddpji63o3...@4ax.com>, Richard Norman
<r_s_n...@comcast.net> writes

However, the abstract reads to me as if the authors are using the word
in the second sense.

I''ve been under the impression that Kaufmann's self-organisation
research programme has not as yet being particularly productive in
regards to abiogenesis and evolution (it seems to have been more
applicable to ecology). This abstract suggests that someone has now
found an instance relevant to abiogenesis.

>
>Wikipedia says: "In biochemistry, a macromolecule exhibits cooperative
>binding if its affinity for its ligand changes with the amount of
>ligand already bound."
> http://en.wikipedia.org/wiki/Cooperative_binding
>

--
alias Ernest Major

[Richard Norman]

Damn, now i am going to have to read the papers!

[Richard Norman]

Incidentally, the actual paper is

Spontaneous network formation among cooperative RNA replicators

Nilesh Vaidya et al.
Nature(2012) doi:10.1038/nature11549

and the news article about it is

Origins of life: The cooperative gene

James Attwater& Philipp Holliger
Nature(2012) doi:10.1038/nature11635

Mark Isaac did give the titles and authors names but the doi
references will give direct acces to anyone who has full access.

I will email the full texts to anyone who requests by email. Just
delete the two underscores in my listed email address.

[James Beck]

On Thu, 18 Oct 2012 09:57:31 -0400, Richard Norman

Sounds kind of obvious, in the same way that placing the last piece of
an almost-finished jigsaw puzzle together is faster than solving the
whole thing. What makes it interesting is that you can show that
that's true. This is also why I have trouble shaking the idea that
viruses are improperly defined as parasites.

[Paul J Gans]

Ernest Major <{$to$}@meden.demon.co.uk> wrote:

An enormous amount of work has been done on self-organization in
the last ten years. While it looked hard to arrange early on, it
has become easier and easier of late.

I have no idea where all this will end up, but it is one of the
major reasons why I feel that abiogenesis right here on earth may
have been much simpler than it appeared in the year 2000.

--
--- Paul J. Gans

[Richard Norman]

On reading the papers I see that I was wrong in my initial impression.
The authors are using "cooperative" in opposition to "selfish" in my
second type of meaning rather than in the biochemical sense given by
my first and by the Wikipedia reference.

The paper discusses an autocatalytic system: a substance helps
promote its own synthesis. Then, assuming mutations to produce a
family of very similar autocatalytic systems, the papers discuss the
difference between "selfish" catalysis where each mutant only helps
promote its own synthesis vs "cooperative" catalysis where one mutant
can also promote the synthesis of other variants.

[Richard Norman]

The question isn't whether abiogenesis in 2010 is easier than it was
in 2000 but rather whether it was easier in 3.5 billion BCE than in
2010 CE. (Sorry, couldn't help myself!)

[Paul J Gans]

Please do and give us your view.

[Paul J Gans]

Well, I don't know. We do know that abiogenesis succeeded in
3.5 billion BCE and we can't do it today.

Tentative hypothesis: it was easier back then... ;-)

[Richard Norman]

On Thu, 18 Oct 2012 22:34:28 +0000 (UTC), Paul J Gans

Probably because we didn't have those stifling corporate taxes and
opressive government regulation back then so innovators could succeed.

[Paul J Gans]

Exactly. Everything was easier. Women came in binders and
nobody died for lack of insurance. One and one can equal
three because I'm a business man and have experience in
these matters.

It is hard in 2012. Easy in -3.5 billion.

[pnyikos]

On Oct 18, 6:38 pm, Paul J Gans <gan...@panix.com> wrote:

> Richard Norman <r_s_nor...@comcast.net> wrote:
> >On Thu, 18 Oct 2012 20:04:10 +0000 (UTC), Paul J Gans
> ><gan...@panix.com> wrote:

> >>Ernest Major <{$t...@meden.demon.co.uk> wrote:
> >>>In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman
> >>><r_s_nor...@comcast.net> writes

That's Paul Gans for you. Tries to disarm me with acknowledging the
possibility of earth life being started by directed panspermia, then
when my back is turned he claims we DO KNOW that it started by
homegrown abiogenesis.

Peter Nyikos

[Michael Siemon]

In article
<cc1acac6-2f64-4f91...@g4g2000yqk.googlegroups.com>,

Peter,
Not everyone (indeed, hardly _anyone_!) rides your hobby-horses.
Paul acknowledges a non-zero possibility of panspermia. But, like
most half-way knowledgeable folks, thinks it is too much a longshot
to enter normal conversation. Your obsessions are not evidence.

[Michael Siemon]

In article <fc2188p7t5cbv6vl2...@4ax.com>,

:-)

[pnyikos]

On Oct 18, 4:08 pm, Paul J Gans <gan...@panix.com> wrote:
> Ernest Major <{$t...@meden.demon.co.uk> wrote:
> >In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman

> ><r_s_nor...@comcast.net> writes

> >>On Wed, 17 Oct 2012 16:17:08 -0700, Mark Isaak
> >><eci...@curioustax.onomy.net> wrote:
>
> >>>There is a new "News and Views" article in the Oct. 17 _Nature_:
> >>>Origins of life: The cooperative gene.
> >>>by James Attwater & Philipp Holliger.
> >>>     "The origin of life on Earth remains one of the great unsolved
> >>>mysteries. A new study suggests that cooperation among molecules could
> >>>have contributed to the transition from inanimate chemistry to biology."
>
> >>>Presumably it is a comment on this research article:
> >>>Spontaneous network formation among cooperative RNA replicators.
> >>>by Nilesh Vaidya et al.
> >>>     "The origins of life on Earth required the establishment of
> >>>self-replicating chemical systems capable of maintaining and evolving
> >>>biological information. In an RNA world, single self-replicating RNAs
> >>>would have faced the extreme challenge of possessing a mutation rate low
> >>>enough both to sustain their own information and to compete successfully
> >>>against molecular parasites with limited evolvability. Thus theoretical
> >>>analyses suggest that networks of interacting molecules were more likely
> >>>to develop and sustain life-like behaviour. Here we show that mixtures
> >>>of RNA fragments that self-assemble into self-replicating ribozymes
> >>>spontaneously form cooperative catalytic cycles and networks.

Sounds like RNA world to me.

But wait...Gans got the PoTM for September because of hand-waving
which I thought referred to an article in Scientific American whose
author said that the difficulties of getting to RNA world were even
more formidable than most people think. So he was proposing small
molecules that were not "RNA fragments."

Gans was the very person who made me aware of the existence of that
Scientific American article, and he waxed enthusiastic about it, using
terms very much like the following:

[...]

> An enormous amount of work has been done on self-organization in
> the last ten years.  While it looked hard to arrange early on, it
> has become easier and easier of late.
>
> I have no idea where all this will end up, but it is one of the
> major reasons why I feel that abiogenesis right here on earth may
> have been much simpler than it appeared in the year 2000.

"Abiogenesis" needs to be understood here in the sense of "life as we
do not know it"--very much so if one goes by Gans's ostensible
foundation for that PoTM article. Getting from the small molecules of
that Scientific American article even as far as RNA world is something
the author of that article never broached, for reasons one might guess
from his comments about RNA world at the beginning.

Nobody here has even made a stab at imagining how "life as we know
it" evolved from even the RNA world in a mere half a billion years,
what with the necessity of inventing a genetic code, a reverse
transcriptase (either in protein or ribozyme form), a transcriptase, a
DNA polymerase, and a host of protein enzymes that almost totally
supplant the RNA-based enzymes of "life as we sort of know it."

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

[pnyikos]

On Oct 18, 7:03 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 18 Oct 2012 22:34:28 +0000 (UTC), Paul J Gans
>
>
>
>
>
> <gan...@panix.com> wrote:

> >Richard Norman <r_s_nor...@comcast.net> wrote:
> >>On Thu, 18 Oct 2012 20:04:10 +0000 (UTC), Paul J Gans
> >><gan...@panix.com> wrote:
>

> >>>Ernest Major <{$t...@meden.demon.co.uk> wrote:
> >>>>In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman

> >>>><r_s_nor...@comcast.net> writes

> >>>>>On Wed, 17 Oct 2012 16:17:08 -0700, Mark Isaak
> >>>>><eci...@curioustax.onomy.net> wrote:
>
> >>>>>>There is a new "News and Views" article in the Oct. 17 _Nature_:
> >>>>>>Origins of life: The cooperative gene.
> >>>>>>by James Attwater & Philipp Holliger.
> >>>>>>     "The origin of life on Earth remains one of the great unsolved
> >>>>>>mysteries. A new study suggests that cooperation among molecules could
> >>>>>>have contributed to the transition from inanimate chemistry to biology."
>
> >>>>>>Presumably it is a comment on this research article:
> >>>>>>Spontaneous network formation among cooperative RNA replicators.
> >>>>>>by Nilesh Vaidya et al.
> >>>>>>     "The origins of life on Earth required the establishment of
> >>>>>>self-replicating chemical systems capable of maintaining and evolving
> >>>>>>biological information. In an RNA world, single self-replicating RNAs
> >>>>>>would have faced the extreme challenge of possessing a mutation rate low
> >>>>>>enough both to sustain their own information and to compete successfully
> >>>>>>against molecular parasites with limited evolvability. Thus theoretical
> >>>>>>analyses suggest that networks of interacting molecules were more likely
> >>>>>>to develop and sustain life-like behaviour. Here we show that mixtures
> >>>>>>of RNA fragments that self-assemble into self-replicating ribozymes
> >>>>>>spontaneously form cooperative catalytic cycles and networks.

As I wrote in reply to Gans, it is hard to imagine how "life as we
know it" evolved from this kind of "RNA world" in a mere half a

billion years, what with the necessity of inventing a genetic code, a
reverse transcriptase (either in protein or ribozyme form), a
transcriptase, a DNA polymerase, and a host of protein enzymes that
almost totally supplant the RNA-based enzymes of "life as we sort of
know it."

But getting to this point is no mean task either. As Leslie Orgel and
co-author put it:

Scientists interested in the origins of life seem to
divide neatly into two classes. The first, usually
but not always molecular biologists, believe that
RNA must have been the first replicating molecule
and that chemists are exaggerating the difficulty
of nucleotide synthesis. ... The second group
of scientists is much more pessimistic. They believe
that the de novo appearance of oligonucleotides on
the primitive earth would have been a near miracle.
(The authors subscribe to this latter view). Time
will tell which is correct.
--G. F. Joyce and Leslie E. Orgel, "Prospects
for understanding the origin of the RNA
world," in: _The RNA World_, ed. R. F.
Gesteland and J. F. Atkins, Cold Spring
Harbor Press, 1993, p. 19.

And even today, there is no generally accepted production of a single
nucleotide under lab conditions scrupulously simulating the conditions
of early earth. [Purines and pyrimidines have been produced, but
these are relatively easy parts of nucleotides to synthesize.]

> >>>>>You must understand that "cooperativity" in relation to chemical
> >>>>>reactions bears absolutely no relation to "cooperativity" in relation
> >>>>>to behavioral interaction between organisms.
>
> >>>>However, the abstract reads to me as if the authors are using the word
> >>>>in the second sense.
>
> >>>>I''ve been under the impression that Kaufmann's self-organisation
> >>>>research programme has not as yet being particularly productive in
> >>>>regards to abiogenesis and evolution (it seems to have been more
> >>>>applicable to ecology). This abstract suggests that someone has now
> >>>>found an instance relevant to abiogenesis.
>
> >>>>>Wikipedia says: "In biochemistry, a macromolecule exhibits cooperative
> >>>>>binding if its affinity for its ligand changes with the amount of
> >>>>>ligand already bound."
> >>>>>  http://en.wikipedia.org/wiki/Cooperative_binding
>
> >>>>--
> >>>>alias Ernest Major
>
> >>>An enormous amount of work has been done on self-organization in
> >>>the last ten years.  While it looked hard to arrange early on, it
> >>>has become easier and easier of late.
>
> >>>I have no idea where all this will end up, but it is one of the
> >>>major reasons why I feel that abiogenesis right here on earth may
> >>>have been much simpler than it appeared in the year 2000.

Only in the sense of "live as we very much do not know it." As far as
getting up to the sophistication of the molecules used in the
experiments of the article, it does not seem much easier than it
appeared in the year 1993 [see above].

> >>The question isn't whether abiogenesis in 2010 is easier than it was
> >>in 2000 but rather whether it was easier in 3.5 billion BCE than in
> >>2010 CE.  (Sorry, couldn't help myself!)

One of my sub-hypotheses, which has it that the panspermists had
ribozymes in place of protein enzymes, has them doing an
extensive designing of prokaryotes which could even take the form of
abiogenesis. Obviously, such panspermists would have
had to be somewhat more advanced technologically than we are at the
present time. So in that sense, yes, they would have had an easier
time back then than we have now.

> >Well, I don't know.  We do know that abiogenesis succeeded in
> >3.5 billion BCE and we can't do it today.

I think it more likely that the panspermists had less radical
designing to do. Even if their bodies used enzymes made of RNA rather
than protein enzymes, the more likely scenario is that they would have
begun with a unicellular organism of the same sort and replaced its
enzymes one at a time with protein enzymes. I would not call that
abiogenesis.

On the other hand, maybe their body cells were much, much simpler than
those of prokaryotes. If they were as simple as an individual
"cooperative catalytic cycle" then the invention by them of
prokaryotes would indeed qualify as abiogenesis.

> >Tentative hypothesis:  it was easier back then...  ;-)

> Probably because we didn't have those stifling corporate taxes and
> opressive government regulation back then so innovators could succeed.

I agree, if by "we" you mean "we intelligent creatures of the
universe."

By my hypothesis, abiogenesis in the sense that you and Paul are
speaking of happened much longer ago than 3.5 billlion BCE. It is the
seminal event of life in our galaxy, leading to the evolution of those
panspermists.

[Aside: I have no objection to "BCE" and "CE" if the C is understood
to stand for "Christian". The usual understanding "Common" is
somewhat ethnocentric. Muslims and Chinese, who number their years
differently from us, may together outnumber the "Common" people who
are accustomed to the Christian calendar.]

[Richard Norman]

I have no interest in arguing either panspermia. Abiogenesis is a
difficult problem but there is progress in understanding how it might
have happened. The paper under discussion is part of that effort.
Panspermia is conceptually possible but so is creation by an all
powerful deity in six 24 hour days some 6000 years ago. Both of these
explain the result without a shred of actual evidence other than that
we don't (yet) have a satisfactory scientific explanation.

As to BCE/CE -- as a Jew I find naming 2012 as the "Year of Our Lord"
whereas earlier times were 'Before Christ" exceptionally offensive.
Christ was not Lord in my thinking and certainly not my Lord. The
yeary numbering system we currently occupy is "commonly" adopted
world-wide even though the ancient Mayans and Romans and Assyrians
and modern Jews and Muslims and Chinese have locally used other
numbering systems.

[Burkhard]

Bit of a hazy memory from the few semesters where I studied history, ,
but is "common" in BCE/ACE not contrasted with "royal" (so, linked to
"commoner") rather than to "universal"? A traditional way to count
years was "in the third year of the reign of King X", and the "common
calendar" did away with this. I seem to remember this usage of "common
era" from some medieval documents.

[Richard Norman]

On Fri, 19 Oct 2012 05:25:15 -0700 (PDT), Burkhard
<b.sc...@ed.ac.uk> wrote:

>On 19 Oct, 12:23, Richard Norman <r_s_nor...@comcast.net> wrote:
>> On Thu, 18 Oct 2012 20:13:20 -0700 (PDT), pnyikos
>>

>> >[Aside: I have no objection to "BCE" and "CE" if the C is understood
>> >to stand for "Christian".  The usual understanding "Common" is
>> >somewhat ethnocentric.  Muslims and Chinese, who number their years
>> >differently from  us, may together outnumber the "Common" people who
>> >are accustomed to the Christian calendar.]
>>

>> As to BCE/CE -- as a Jew I find naming 2012 as the "Year of Our Lord"
>> whereas earlier times were 'Before Christ" exceptionally offensive.
>> Christ was not Lord in my thinking and certainly not my Lord.  The
>> yeary numbering system we currently occupy is "commonly" adopted
>> world-wide even though the ancient  Mayans and Romans and Assyrians
>> and modern Jews and Muslims and Chinese have locally used other
>> numbering systems.
>
>Bit of a hazy memory from the few semesters where I studied history, ,
>but is "common" in BCE/ACE not contrasted with "royal" (so, linked to
>"commoner") rather than to "universal"? A traditional way to count
>years was "in the third year of the reign of King X", and the "common
>calendar" did away with this. I seem to remember this usage of "common
>era" from some medieval documents.

I haven't researched this but isn't the word "common" meaning
commonplace also derived from "commoner" being the ordinary people as
opposed to the royals?

[Paul J Gans]

pnyikos <nyi...@bellsouth.net> wrote:

>On Oct 18, 6:38?pm, Paul J Gans <gan...@panix.com> wrote:
>> Richard Norman <r_s_nor...@comcast.net> wrote:
>> >On Thu, 18 Oct 2012 20:04:10 +0000 (UTC), Paul J Gans
>> ><gan...@panix.com> wrote:
>> >>Ernest Major <{$t...@meden.demon.co.uk> wrote:
>> >>>In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman
>> >>><r_s_nor...@comcast.net> writes
>> >>>>On Wed, 17 Oct 2012 16:17:08 -0700, Mark Isaak
>> >>>><eci...@curioustax.onomy.net> wrote:
>>
>> >>>>>There is a new "News and Views" article in the Oct. 17 _Nature_:
>> >>>>>Origins of life: The cooperative gene.
>> >>>>>by James Attwater & Philipp Holliger.

>> >>>>> ? ? "The origin of life on Earth remains one of the great unsolved

>> >>>>>mysteries. A new study suggests that cooperation among molecules could
>> >>>>>have contributed to the transition from inanimate chemistry to biology."
>>
>> >>>>>Presumably it is a comment on this research article:
>> >>>>>Spontaneous network formation among cooperative RNA replicators.
>> >>>>>by Nilesh Vaidya et al.

>> >>>>> ? ? "The origins of life on Earth required the establishment of

>> >>>> ?http://en.wikipedia.org/wiki/Cooperative_binding

>>
>> >>>--
>> >>>alias Ernest Major
>>
>> >>An enormous amount of work has been done on self-organization in

>> >>the last ten years. ?While it looked hard to arrange early on, it

>> >>has become easier and easier of late.
>>
>> >>I have no idea where all this will end up, but it is one of the
>> >>major reasons why I feel that abiogenesis right here on earth may
>> >>have been much simpler than it appeared in the year 2000.
>> >The question isn't whether abiogenesis in 2010 is easier than it was
>> >in 2000 but rather whether it was easier in 3.5 billion BCE than in

>> >2010 CE. ?(Sorry, couldn't help myself!)
>>
>> Well, I don't know. ?We do know that abiogenesis succeeded in

>> 3.5 billion BCE and we can't do it today.

>That's Paul Gans for you. Tries to disarm me with acknowledging the
>possibility of earth life being started by directed panspermia, then
>when my back is turned he claims we DO KNOW that it started by
>homegrown abiogenesis.

Wow! I thought even you'd conceded that life had developed
*somewhere* abiogenetically by -3.5 billion years. You want
to make that -5.0 billion years, be my guest. My point still
stands.

[Paul J Gans]

pnyikos <nyi...@bellsouth.net> wrote:

>On Oct 18, 4:08?pm, Paul J Gans <gan...@panix.com> wrote:
>> Ernest Major <{$t...@meden.demon.co.uk> wrote:
>> >In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman
>> ><r_s_nor...@comcast.net> writes
>> >>On Wed, 17 Oct 2012 16:17:08 -0700, Mark Isaak
>> >><eci...@curioustax.onomy.net> wrote:
>>
>> >>>There is a new "News and Views" article in the Oct. 17 _Nature_:
>> >>>Origins of life: The cooperative gene.
>> >>>by James Attwater & Philipp Holliger.

>> >>> ? ? "The origin of life on Earth remains one of the great unsolved

>> >>>mysteries. A new study suggests that cooperation among molecules could
>> >>>have contributed to the transition from inanimate chemistry to biology."
>>
>> >>>Presumably it is a comment on this research article:
>> >>>Spontaneous network formation among cooperative RNA replicators.
>> >>>by Nilesh Vaidya et al.

>> >>> ? ? "The origins of life on Earth required the establishment of

>> >>>self-replicating chemical systems capable of maintaining and evolving
>> >>>biological information. In an RNA world, single self-replicating RNAs
>> >>>would have faced the extreme challenge of possessing a mutation rate low
>> >>>enough both to sustain their own information and to compete successfully
>> >>>against molecular parasites with limited evolvability. Thus theoretical
>> >>>analyses suggest that networks of interacting molecules were more likely
>> >>>to develop and sustain life-like behaviour. Here we show that mixtures
>> >>>of RNA fragments that self-assemble into self-replicating ribozymes
>> >>>spontaneously form cooperative catalytic cycles and networks.

>Sounds like RNA world to me.

>But wait...Gans got the PoTM for September because of hand-waving
>which I thought referred to an article in Scientific American whose
>author said that the difficulties of getting to RNA world were even
>more formidable than most people think. So he was proposing small
>molecules that were not "RNA fragments."

> Gans was the very person who made me aware of the existence of that
>Scientific American article, and he waxed enthusiastic about it, using
>terms very much like the following:

>[...]

>> An enormous amount of work has been done on self-organization in

>> the last ten years. ?While it looked hard to arrange early on, it

>> has become easier and easier of late.
>>
>> I have no idea where all this will end up, but it is one of the
>> major reasons why I feel that abiogenesis right here on earth may
>> have been much simpler than it appeared in the year 2000.

>"Abiogenesis" needs to be understood here in the sense of "life as we
>do not know it"--very much so if one goes by Gans's ostensible
>foundation for that PoTM article. Getting from the small molecules of
>that Scientific American article even as far as RNA world is something
>the author of that article never broached, for reasons one might guess
>from his comments about RNA world at the beginning.

>Nobody here has even made a stab at imagining how "life as we know
>it" evolved from even the RNA world in a mere half a billion years,
>what with the necessity of inventing a genetic code, a reverse
>transcriptase (either in protein or ribozyme form), a transcriptase, a
>DNA polymerase, and a host of protein enzymes that almost totally
>supplant the RNA-based enzymes of "life as we sort of know it."

I'm not going to bother with a detailed analysis of this, but
you have conflated two different papers. The Scientific American
one was by Robert Shapiro who believed that "small molecule"
abiogenesis was much more likely than most of the alternative
theories.

The second paper reflected current progress in self-assembly.
Just google on "molecular self assembly" for a good sampling
of what has been going on in the past decade. Repeat by
googling on "nanotechnology self assemply.

I'll add that this field is in its infancy.

[pnyikos]

Where is your sense of proportion? Panspermia is a scientific
hypothesis, using only scientific/mathematical methodology and
philosophy-of-science reasoning. YEC flies in the face of gargantuan
evidence.

> Both of these
> explain the result without a shred of actual evidence

The result at issue is the beginning of life ON EARTH, and there
isn't a shred of actual evidence that abiogenesis took place HERE.

>other than that
> we don't (yet) have a satisfactory scientific explanation.

Panspermia does not, repeat, NOT have anything to do with the ultimate
origins of life.

> As to BCE/CE -- as a Jew I find naming 2012 as the "Year of Our Lord"
> whereas earlier times were 'Before Christ" exceptionally offensive.

I respect that. However, I once wrote a half serious pair of
questions that you may want to ponder:

With "BC" ("Before Christ") rapidly giving way to "BCE"
("Before the Common Era"), why isn't there a similar
move to replace "July" with something else (say, "Thermidor")?

Could it be because modern society finds Jesus Christ
more objectionable than Julius Caesar?

> Christ was not Lord in my thinking and certainly not my Lord.  The
> yeary numbering system we currently occupy is "commonly" adopted
> world-wide even though the ancient  Mayans and Romans and Assyrians
> and modern Jews and Muslims and Chinese have locally used other
> numbering systems.

"locally"? Do you have any idea how Ramadan is computed? How the
Chinese new year is computed? Do you really think the Chinese new
year is a local curiosity?

Peter Nyikos

[Richard Norman]

On Fri, 19 Oct 2012 11:49:40 -0700 (PDT), pnyikos
<nyi...@bellsouth.net> wrote:

>On Oct 19, 7:23áam, Richard Norman <r_s_nor...@comcast.net> wrote:
>> On Thu, 18 Oct 2012 20:13:20 -0700 (PDT), pnyikos
>>
>>
>>
>>
>>
>> <nyik...@bellsouth.net> wrote:

>> >On Oct 18, 7:03ápm, Richard Norman <r_s_nor...@comcast.net> wrote:
>> >> On Thu, 18 Oct 2012 22:34:28 +0000 (UTC), Paul J Gans
>>
>> >> <gan...@panix.com> wrote:
>> >> >Richard Norman <r_s_nor...@comcast.net> wrote:
>> >> >>On Thu, 18 Oct 2012 20:04:10 +0000 (UTC), Paul J Gans
>> >> >><gan...@panix.com> wrote:
>>
>> >> >>>Ernest Major <{$t...@meden.demon.co.uk> wrote:
>> >> >>>>In message <5pnu7857ddpji63o36c872n4rooo0qe...@4ax.com>, Richard Norman
>> >> >>>><r_s_nor...@comcast.net> writes
>> >> >>>>>On Wed, 17 Oct 2012 16:17:08 -0700, Mark Isaak
>> >> >>>>><eci...@curioustax.onomy.net> wrote:
>>
>> >> >>>>>>There is a new "News and Views" article in the Oct. 17 _Nature_:
>> >> >>>>>>Origins of life: The cooperative gene.
>> >> >>>>>>by James Attwater & Philipp Holliger.

>> >> >>>>>> á á "The origin of life on Earth remains one of the great unsolved

>> >> >>>>>>mysteries. A new study suggests that cooperation among molecules could
>> >> >>>>>>have contributed to the transition from inanimate chemistry to biology."
>>
>> >> >>>>>>Presumably it is a comment on this research article:
>> >> >>>>>>Spontaneous network formation among cooperative RNA replicators.
>> >> >>>>>>by Nilesh Vaidya et al.

>> >> >>>>>> á á "The origins of life on Earth required the establishment of

>> >> >>>>>>self-replicating chemical systems capable of maintaining and evolving
>> >> >>>>>>biological information. In an RNA world, single self-replicating RNAs
>> >> >>>>>>would have faced the extreme challenge of possessing a mutation rate low
>> >> >>>>>>enough both to sustain their own information and to compete successfully
>> >> >>>>>>against molecular parasites with limited evolvability. Thus theoretical
>> >> >>>>>>analyses suggest that networks of interacting molecules were more likely
>> >> >>>>>>to develop and sustain life-like behaviour. Here we show that mixtures
>> >> >>>>>>of RNA fragments that self-assemble into self-replicating ribozymes
>> >> >>>>>>spontaneously form cooperative catalytic cycles and networks.
>>
>> >As I wrote in reply to Gans, it is hard to imagine how "life as we
>> >know it" evolved from this kind of "RNA world" in a mere half a
>> >billion years, what with the necessity of inventing a genetic code, a
>> >reverse transcriptase (either in protein or ribozyme form), a
>> >transcriptase, a DNA polymerase, and a host of protein enzymes that
>> >almost totally supplant the RNA-based enzymes of "life as we sort of
>> >know it."
>>

>> >But getting to this point is no mean task either. áAs Leslie Orgel and
>> >co-author put it:
>>
>> > á áScientists interested in the origins of life seem to
>> > á á á ádivide neatly into two classes. áThe first, usually
>> > á á á ábut not always molecular biologists, believe that
>> > á á á áRNA must have been the first replicating molecule
>> > á á á áand that chemists are exaggerating the difficulty
>> > á á á áof nucleotide synthesis. á... The second group
>> > á á á áof scientists is much more pessimistic. áThey believe
>> > á á á áthat the de novo appearance of oligonucleotides on
>> > á á á áthe primitive earth would have been a near miracle.
>> > á á á á(The authors subscribe to this latter view). áTime
>> > á á á áwill tell which is correct.
>> > á á á á á á á á--G. F. Joyce and Leslie E. Orgel, "Prospects
>> > á á á á á á á á áfor understanding the origin of the RNA
>> > á á á á á á á á áworld," in: _The RNA World_, ed. R. F.
>> > á á á á á á á á áGesteland and J. F. Atkins, Cold Spring
>> > á á á á á á á á áHarbor Press, 1993, p. 19.

>>
>> >And even today, there is no generally accepted production of a single
>> >nucleotide under lab conditions scrupulously simulating the conditions

>> >of early earth. á[Purines and pyrimidines have been produced, but

>> >these are relatively easy parts of nucleotides to synthesize.]
>>
>> >> >>>>>You must understand that "cooperativity" in relation to chemical
>> >> >>>>>reactions bears absolutely no relation to "cooperativity" in relation
>> >> >>>>>to behavioral interaction between organisms.
>>
>> >> >>>>However, the abstract reads to me as if the authors are using the word
>> >> >>>>in the second sense.
>>
>> >> >>>>I''ve been under the impression that Kaufmann's self-organisation
>> >> >>>>research programme has not as yet being particularly productive in
>> >> >>>>regards to abiogenesis and evolution (it seems to have been more
>> >> >>>>applicable to ecology). This abstract suggests that someone has now
>> >> >>>>found an instance relevant to abiogenesis.
>>
>> >> >>>>>Wikipedia says: "In biochemistry, a macromolecule exhibits cooperative
>> >> >>>>>binding if its affinity for its ligand changes with the amount of
>> >> >>>>>ligand already bound."

>> >> >>>>> áhttp://en.wikipedia.org/wiki/Cooperative_binding

>>
>> >> >>>>--
>> >> >>>>alias Ernest Major
>>
>> >> >>>An enormous amount of work has been done on self-organization in

>> >> >>>the last ten years. áWhile it looked hard to arrange early on, it

>> >> >>>has become easier and easier of late.
>>
>> >> >>>I have no idea where all this will end up, but it is one of the
>> >> >>>major reasons why I feel that abiogenesis right here on earth may
>> >> >>>have been much simpler than it appeared in the year 2000.
>>

>> >Only in the sense of "live as we very much do not know it." áAs far as

>> >getting up to the sophistication of the molecules used in the
>> >experiments of the article, it does not seem much easier than it
>> >appeared in the year 1993 [see above].
>>
>> >> >>The question isn't whether abiogenesis in 2010 is easier than it was
>> >> >>in 2000 but rather whether it was easier in 3.5 billion BCE than in

>> >> >>2010 CE. á(Sorry, couldn't help myself!)
>>
>> >One of my sub-hypotheses, which has it that áthe panspermists had

>> >ribozymes in place of protein enzymes, has them doing an
>> >extensive designing of prokaryotes which could even take the form of

>> >abiogenesis. áObviously, such panspermists would have

>> >had to be somewhat more advanced technologically than we are at the

>> >present time. áSo in that sense, yes, they would have had an easier

>> >time back then than we have now.
>>

>> >> >Well, I don't know. áWe do know that abiogenesis succeeded in

>> >> >3.5 billion BCE and we can't do it today.
>>
>> >I think it more likely that the panspermists had less radical

>> >designing to do. áEven if their bodies used enzymes made of RNA rather

>> >than protein enzymes, the more likely scenario is that they would have
>> >begun with a unicellular organism of the same sort and replaced its

>> >enzymes one at a time with protein enzymes. áI would not call that

>> >abiogenesis.
>>
>> >On the other hand, maybe their body cells were much, much simpler than

>> >those of prokaryotes. áIf they were as simple as an individual

>> >"cooperative catalytic cycle" then the invention by them of
>> >prokaryotes would indeed qualify as abiogenesis.
>>

>> >> >Tentative hypothesis: áit was easier back then... á;-)

>>
>> >> Probably because we didn't have those stifling corporate taxes and
>> >> opressive government regulation back then so innovators could succeed.
>>
>> >I agree, if by "we" you mean "we intelligent creatures of the
>> >universe."
>>
>> >By my hypothesis, abiogenesis in the sense that you and Paul are

>> >speaking of happened much longer ago than 3.5 billlion BCE. áIt is the

>> >seminal event of life in our galaxy, leading to the evolution of those
>> >panspermists.
>>
>> >[Aside: I have no objection to "BCE" and "CE" if the C is understood

>> >to stand for "Christian". áThe usual understanding "Common" is
>> >somewhat ethnocentric. áMuslims and Chinese, who number their years
>> >differently from áus, may together outnumber the "Common" people who

>> >are accustomed to the Christian calendar.]
>>

>> I have no interest in arguing either panspermia. áAbiogenesis is a

>> difficult problem but there is progress in understanding how it might

>> have happened. áThe paper under discussion is part of that effort.

>> Panspermia is conceptually possible but so is creation by an all
>> powerful deity in six 24 hour days some 6000 years ago.
>
>Where is your sense of proportion? Panspermia is a scientific
>hypothesis, using only scientific/mathematical methodology and
>philosophy-of-science reasoning. YEC flies in the face of gargantuan
>evidence.
>

>>áBoth of these

>> explain the result without a shred of actual evidence
>
>The result at issue is the beginning of life ON EARTH, and there
>isn't a shred of actual evidence that abiogenesis took place HERE.
>
>>other than that
>> we don't (yet) have a satisfactory scientific explanation.
>
>Panspermia does not, repeat, NOT have anything to do with the ultimate
>origins of life.
>
>> As to BCE/CE -- as a Jew I find naming 2012 as the "Year of Our Lord"
>> whereas earlier times were 'Before Christ" exceptionally offensive.
>
>I respect that. However, I once wrote a half serious pair of
>questions that you may want to ponder:
>
> With "BC" ("Before Christ") rapidly giving way to "BCE"
> ("Before the Common Era"), why isn't there a similar
> move to replace "July" with something else (say, "Thermidor")?
>
> Could it be because modern society finds Jesus Christ
> more objectionable than Julius Caesar?
>

>> Christ was not Lord in my thinking and certainly not my Lord. áThe

>> yeary numbering system we currently occupy is "commonly" adopted

>> world-wide even though the ancient áMayans and Romans and Assyrians

>> and modern Jews and Muslims and Chinese have locally used other
>> numbering systems.
>
>"locally"? Do you have any idea how Ramadan is computed? How the
>Chinese new year is computed? Do you really think the Chinese new
>year is a local curiosity?

You confuse two issues. Holidays can be computed by various calendar
methods. Yet international business and discourse is conducted in the
"common era" calendar. I have been to China and Egypt and Jordan and
Turkey, places you correctly say use other calendars for many
purposes, and hotel and airline reservations were done using the
"common" calendar. I have just looked at several arabic language
newspapers and chinese language newspapers and although I can't read
the writing at all I find numerous references to dates in the common
calendar.

The "common era" calendar is indeed common all across the world.

[pnyikos]

If it contained more original text, I'd nominate this for October
PoTM. Unlike the prospective September winner, it actually spells out
what the line of research actually is.

Also unlike it, it describes a stage which may well be intermediate
between the miserably rudimentary molecules and molecule aggregates
that so far are shown to be possible under early earth conditions, and
the first prokaryote. In fact it seems to be intermediate between
those rudimentary molecules and any kind of extraterrestrial life we
can imagine; in particular, the directed panspermists of 3.5 - 4
billion years ago.

The prospective September winner had previously written about
something that went off on a tangent completely, towards "life as we
don't know it and can't imagine it" and the author seemed to be very
pessimistic about the kind of precursor to life that is being studied
here.

I second the motion.

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

[pnyikos]

On Oct 19, 12:23 pm, Paul J Gans <gan...@panix.com> wrote:

You missed the point of what I wrote here.

> >"Abiogenesis" needs to be understood here in the sense of "life as we
> >do not know it"--very much so if one goes by Gans's ostensible
> >foundation for that PoTM article.  Getting from the small molecules of
> >that Scientific American article even as far as RNA world is something
> >the author of that article never broached, for reasons one might guess
> >from his comments about RNA world at the beginning.

I'm afraid I have to paraphrase below what I wrote above. You seem to
have not even been aiming at the point.

> >Nobody here has even made a stab at  imagining how "life as we know
> >it" evolved from even the RNA world in a mere half a billion years,
> >what with the necessity of inventing a genetic code, a reverse
> >transcriptase (either in protein or ribozyme form), a transcriptase, a
> >DNA polymerase, and a host of protein enzymes that almost totally
> >supplant the RNA-based enzymes of "life as we sort of know it."
>
> I'm not going to bother with a detailed analysis of this, but
> you have conflated two different papers.

No, I have drawn a sharp distinction between them. OTOH anyone
reading that ostensible September PotM winner can't be sure as to
which of these two kinds of research you were talking about.

>  The Scientific American
> one was by Robert Shapiro who believed that "small molecule"
> abiogenesis was much more likely than most of the alternative
> theories.

Alternative theories of what? Alternative theories as to what is
likely to evolve into life as we know it? That article wasn't playing
that game. It didn't even play the game of getting over to the things
to which Mark Isaak alerted us.

> The second paper reflected current progress in self-assembly.
> Just google on "molecular self assembly" for a good sampling
> of what has been going on in the past decade.  Repeat by
> googling on "nanotechnology self assemply.
>
> I'll add that this field is in its infancy.

So is everything connected with abiogenesis.

Peter Nyikos

[Mark Isaak]

On 10/19/12 11:49 AM, pnyikos wrote:
> On Oct 19, 7:23 am, Richard Norman <r_s_nor...@comcast.net> wrote:

>> I have no interest in arguing either panspermia. Abiogenesis is a
>> difficult problem but there is progress in understanding how it might
>> have happened. The paper under discussion is part of that effort.
>> Panspermia is conceptually possible but so is creation by an all
>> powerful deity in six 24 hour days some 6000 years ago.
>
> Where is your sense of proportion? Panspermia is a scientific
> hypothesis, using only scientific/mathematical methodology and
> philosophy-of-science reasoning. YEC flies in the face of gargantuan
> evidence.

For panspermia to be scientific, it should make testable predictions.
The only predictions I can think of it making are "We might find the
remains of the spacecraft someday" or of that ilk, which is marginally
better than nothing, but by an extremely small margin.

>> Both of these
>> explain the result without a shred of actual evidence
>
> The result at issue is the beginning of life ON EARTH, and there
> isn't a shred of actual evidence that abiogenesis took place HERE.

First, there is not a shred of evidence that abiogenesis did *not* take
place here.

Second, there is slight evidence that panspermia is false. Not finding
those spacecraft remains is more likely if the remains do not exist in
the first place, so it counts as evidence against panspermia. The other
evidence we might expect to be more likely from pansperia than
terra-spermia (life on other planets of the Solar System, direct contact
with the alien home world) likewise provide evidence against panspermia
by their failure to appear. Granted, that evidence is quite weak, but
it is evidence.

Third, there is Occham's razor. Pansperia multiplies entities without
giving anything in return.

>>> [Aside: I have no objection to "BCE" and "CE" if the C is understood
>>> to stand for "Christian". The usual understanding "Common" is

>>> somewhat ethnocentric. ...]

And "Christian" isn't?!??

Try to think forward through issues, rather than looking for
justifications of your own prejudices and arguing backwards.

>> As to BCE/CE -- as a Jew I find naming 2012 as the "Year of Our Lord"
>> whereas earlier times were 'Before Christ" exceptionally offensive.
>
> I respect that. However, I once wrote a half serious pair of
> questions that you may want to ponder:
>
> With "BC" ("Before Christ") rapidly giving way to "BCE"
> ("Before the Common Era"), why isn't there a similar
> move to replace "July" with something else (say, "Thermidor")?
>
> Could it be because modern society finds Jesus Christ
> more objectionable than Julius Caesar?

It is not Jesus Christ which is objectionable. It is how he is wielded.

[pnyikos]

On Oct 19, 8:43 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 10/19/12 11:49 AM, pnyikos wrote:
>
> > On Oct 19, 7:23 am, Richard Norman <r_s_nor...@comcast.net> wrote:
> >> I have no interest in arguing either panspermia.  Abiogenesis is a
> >> difficult problem but there is progress in understanding how it might
> >> have happened.  The paper under discussion is part of that effort.
> >> Panspermia is conceptually possible but so is creation by an all
> >> powerful deity in six 24 hour days some 6000 years ago.
>
> > Where is your sense of proportion?  Panspermia is a scientific
> > hypothesis, using only scientific/mathematical methodology and
> > philosophy-of-science reasoning. YEC flies in the face of gargantuan
> > evidence.
>
> For panspermia to be scientific, it should make testable predictions.

It can. Here is something I told John Harshman about that back in
July, centered on what I call the Throomian" sub-hypothesis: that the
first prokaryote was designed by aliens whose biochemistry resembled
ours with this exception, that their sophisticated enzymes were all
RNA based rather than polypeptide-based:

________________ excerpts from post_____________________

if we ever colonize the galaxy, as you seem to
think is an easy thing to do, and we find life in many stages of
"protein takeover", all with reasonably similar genetic codes, that
would be a big argument in favor of the Throomian sub-hypothesis.


On the other hand, if the takeover is in essentially the same stage
as
that of earth, and the genetic code is very similar, that would
strongly support the overall hypothesis of directed panspermia while
all but falsifying the Throomian sub-hypothesis.

A third possible outcome is that we encounter lots of life with
genetic codes all very different from ours. That would all but
falsify all three main sub-hypotheses of directed panspermia,.

And finally, if we find no life after searching a million likely
planets, that would falsify the hypothesis that WE are the result of
evolution from unicellular organisms sent here by directed
panspermists, but would still leave my general hypothesis about the
frequency of directed panspermia largely unscathed.
================ end of excerpt
from http://groups.google.com/group/talk.origins/msg/90027d90c58f7b4c

> The only predictions I can think of it making are "We might find the
> remains of the spacecraft someday" or of that ilk, which is marginally
> better than nothing, but by an extremely small margin.

You are just too unused to "thinking outside the box", whereas I am
quite adept at it. See above. And below.

In another thread, someone who resembles you a lot asked, "If there
were directed panspermists, why didn't they leave evidence of
themselves?" I cannot imagine what he had in mind that could possibly
have survived meteor bombardments on the moon, or plate tectonics and
weathering on earth, over close to 4 billion years.

But he may have been begging the question. They might have invented
the highly unusual device called the bacterial flagellum, which is
useful enough to have a good chance of staying in existence all those
years through being handed down from one generation to the next.

I once suggested that it may partly have been designed as a sort of
analogue of "Kilroy was here": intelligent beings eventually evolving
from the microscopic life they sent might look at it and begin to
suspect that their existence is due to another species having sent
life to earth, and be suitably appreciative of the gift of life to the
unknown beings that sent it.

The person to whom I suggested this professed to be disgusted with the
idea, saying it reminded him of gods that demanded worship, but I've
seen how you are able to grasp the difference between that and
gratitude.

> >>   Both of these
> >> explain the result without a shred of actual evidence
>
> > The result at issue is the beginning of life ON  EARTH, and there
> > isn't a shred of actual evidence that abiogenesis took place HERE.
>
> First, there is not a shred of evidence that abiogenesis did *not* take
> place here.

And there is not a shred of evidence that directed panspermia is *not*
the way life on earth began.

As I never tire of saying, the playing field is level here.

> Second, there is slight evidence that panspermia is false.  Not finding
> those spacecraft remains is more likely if the remains do not exist in
> the first place, so it counts as evidence against panspermia.

See above about 4 billion years. Your "slight evidence" is on very
shaky ground.

> The other
> evidence we might expect to be more likely from pansperia than
> terra-spermia (life on other planets of the Solar System, direct contact
> with the alien home world)

Their sun might well have swallowed up their planet by now, and they
may never have colonized other solar systems themselves. You know how
much harder it is to send intelligent beings like us to other
planetary systems than to send microorganisms.

>likewise provide evidence against panspermia
> by their failure to appear.

The jury is still out on Mars, Europa, and Titan. But none of these
places is as well situated as earth, nor as well stocked with a
variety of environments.

> Granted, that evidence is quite weak, but
> it is evidence.
>
> Third, there is Occham's razor.  Pansperia multiplies entities without
> giving anything in return.

It gives plenty in return -- good ideas about what it is worth looking
for if we send probes to other worlds, as in the excerpt above.

> >>> [Aside: I have no objection to "BCE" and "CE" if the C is understood
> >>> to stand for "Christian".  The usual understanding "Common" is
> >>> somewhat ethnocentric.  ...]
>
> And "Christian" isn't?!??

It puts the explanation for the dating front and center.

Peter Nyikos

[pnyikos]

On Oct 18, 9:43�pm, Michael Siemon <mlsie...@sonic.net> wrote:
> In article
> <cc1acac6-2f64-4f91-aabc-5d6fcbe81...@g4g2000yqk.googlegroups.com>,

No one here besides me advocates the Crick-Orgel hypothesis, and
that's why I do it so much: if the arguments aren't posted by me, they
simply aren't posted. Were it not for me, a promising avenue of
reasoning and (eventually, see my reply to Isaak today) research would
be totally neglected here.

> Paul acknowledges a non-zero possibility of panspermia.

"we know" is not an acknowledgement. It doesn't even leave room for
an acknowledgement.

> But, like
> most half-way knowledgeable folks, thinks it is too much a longshot
> to enter normal conversation.

That is a symptom of his halfway knowledgeability. He will never
progress beyond that, and, judging from your ZERO contribution to the
scientific issues, neither will you.

Gans's contribution is simply laughable: snow jobs about planetary
orbits being "chaotic" without a clue as to what "chaotic" means in
terms of 10,000 years, etc. See:

http://groups.google.com/group/talk.origins/msg/a6a8c8032c25abec

> Your obsessions are not evidence.

What obsessions? Take a look at my reply to Mark Isaak earlier today,
and learn how to think outside the box for a change.

Peter Nyikos

[Mark Isaak]

The ones above are very distinctly of the same ilk as finding the
spacecraft remains. Or worse; I do not consider exploring millions of
extrasolar planets to be a remotely reasonable test.

> And below.
>
> In another thread, someone who resembles you a lot asked, "If there
> were directed panspermists, why didn't they leave evidence of
> themselves?" I cannot imagine what he had in mind that could possibly
> have survived meteor bombardments on the moon, or plate tectonics and
> weathering on earth, over close to 4 billion years.

It must have weathered worse simply to get here. A spacecraft in
distant solar orbit could have survived and might charge up on solar
energy enough to send a "Hello world" signal every few years.

> But he may have been begging the question. They might have invented
> the highly unusual device called the bacterial flagellum, which is
> useful enough to have a good chance of staying in existence all those
> years through being handed down from one generation to the next.
>
> I once suggested that it may partly have been designed as a sort of
> analogue of "Kilroy was here": intelligent beings eventually evolving
> from the microscopic life they sent might look at it and begin to
> suspect that their existence is due to another species having sent
> life to earth, and be suitably appreciative of the gift of life to the
> unknown beings that sent it.

Except that is not a prediction of panspermia; it is your own special
pleading.

>>>> Both of these
>>>> explain the result without a shred of actual evidence
>>
>>> The result at issue is the beginning of life ON EARTH, and there
>>> isn't a shred of actual evidence that abiogenesis took place HERE.
>>
>> First, there is not a shred of evidence that abiogenesis did *not* take
>> place here.
>
> And there is not a shred of evidence that directed panspermia is *not*
> the way life on earth began.
>
> As I never tire of saying, the playing field is level here.
>
>> Second, there is slight evidence that panspermia is false. Not finding
>> those spacecraft remains is more likely if the remains do not exist in
>> the first place, so it counts as evidence against panspermia.
>
> See above about 4 billion years. Your "slight evidence" is on very
> shaky ground.

I never said otherwise. Still, it is on steadier ground than anything
else relevant to panspermia.

>> The other
>> evidence we might expect to be more likely from pansperia than
>> terra-spermia (life on other planets of the Solar System, direct contact
>> with the alien home world)
>
> Their sun might well have swallowed up their planet by now, and they
> may never have colonized other solar systems themselves. You know how
> much harder it is to send intelligent beings like us to other
> planetary systems than to send microorganisms.
>
>> likewise provide evidence against panspermia
>> by their failure to appear.
>
> The jury is still out on Mars, Europa, and Titan. But none of these
> places is as well situated as earth, nor as well stocked with a
> variety of environments.

Don't forget Jupiter and Saturn; no reason they could not harbor life.
Life is one thing we have had several reasonable chances to detect, and
we have not detected it. This counts as a strike against panspermia.
If we find it, and if it matches your predictions, then we can count
evidence for panspermia, but unless and until that happens, this
evidence counts against.

>> Third, there is Occham's razor. Pansperia multiplies entities without
>> giving anything in return.
>
> It gives plenty in return -- good ideas about what it is worth looking
> for if we send probes to other worlds, as in the excerpt above.

We already know, when we reach an extrasolar world, that *everything*
will be worth looking at.

[pnyikos]

Oh, dear. I forgot about this thread. And I have lots to say here,
too!

On Oct 20, 4:18 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 10/19/12 7:35 PM, pnyikos wrote:

> > On Oct 19, 8:43 pm, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> >> On 10/19/12 11:49 AM, pnyikos wrote:
>
> >>> On Oct 19, 7:23 am, Richard Norman <r_s_nor...@comcast.net> wrote:
> >>>> I have no interest in arguing either panspermia.  Abiogenesis is a
> >>>> difficult problem but there is progress in understanding how it might
> >>>> have happened.  The paper under discussion is part of that effort.
> >>>> Panspermia is conceptually possible but so is creation by an all
> >>>> powerful deity in six 24 hour days some 6000 years ago.
>
> >>> Where is your sense of proportion?  Panspermia is a scientific
> >>> hypothesis, using only scientific/mathematical methodology and
> >>> philosophy-of-science reasoning. YEC flies in the face of gargantuan
> >>> evidence.
>
> >> For panspermia to be scientific, it should make testable predictions.

I've addressed this very question today, in a new FAQ entry, after
reading what transpired between us here.

See:

http://groups.google.com/group/talk.origins/msg/bfe2b431094912d4

> > It can.  Here is something I told John Harshman about that back in
> > July, centered on what I call the Throomian" sub-hypothesis: that the
> > first prokaryote was designed by aliens whose biochemistry resembled
> > ours with this exception, that their sophisticated enzymes were all
> > RNA based rather than polypeptide-based:

A lot of today's FAQ entry is copied from what I said here, next:

> > ________________ excerpts from post_____________________
>
> > if we ever colonize the galaxy, as you seem to
> > think is an easy thing to do, and we find life in many stages of
> > "protein takeover", all with reasonably similar genetic codes, that
> > would be a big argument in favor of the Throomian sub-hypothesis.
>
> > On the other hand, if the takeover is in essentially the same stage
> > as
> > that of earth, and the genetic code is very similar, that would
> > strongly support the overall hypothesis of directed panspermia while
> > all but falsifying the Throomian sub-hypothesis.
>
> > A third possible outcome is that we encounter lots of life with
> > genetic codes all very different from ours.  That would all but
> > falsify all three main sub-hypotheses of directed panspermia,.
>
> > And finally, if we find no life after searching a million likely
> > planets, that would falsify the hypothesis that WE are the result of
> > evolution from unicellular organisms sent here by directed
> > panspermists, but  would still leave my general hypothesis about the
> > frequency of directed panspermia largely unscathed.
> > ================ end of excerpt

> > fromhttp://groups.google.com/group/talk.origins/msg/90027d90c58f7b4c

>
> >> The only predictions I can think of it making are "We might find the
> >> remains of the spacecraft someday" or of that ilk, which is marginally
> >> better than nothing, but by an extremely small margin.
>
> > You are just too unused to "thinking outside the box", whereas I am
> > quite adept at it.  See above.

You recovered quite nicely from being surprised by implicit
predictions of the Throomian hypothesis that you hadn't thought of:

> The ones above are very distinctly of the same ilk as finding the
> spacecraft remains.  Or worse; I do not consider exploring millions of
> extrasolar planets to be a remotely reasonable test.

It would certainly test the hypothesis that the panspermists carried
out something on the order of a million seedings. By now the planetary
systems may be pretty evenly scattered throughout the spiral arms of
our galaxy, so that after searching a mere 10,000 planets we may be
expected to have encountered one of the others they seeded. [Assume
maybe 1 out of 10 planetary systems to have planets worth taking a
close look at.]

Or we might encounter all kinds of life forms just in the first
thousand, and then have to decide between a truly gargantuan project
or abiogenesis, depending on what the biochemistry of those life forms
was.

> >  And below.
>
> > In another thread, someone who resembles you a lot asked, "If there
> > were directed panspermists, why didn't they leave evidence of
> > themselves?" I cannot imagine what he had in mind that could possibly
> > have survived meteor bombardments on the moon, or plate tectonics and
> > weathering on earth, over close to 4 billion years.
>
> It must have weathered worse simply to get here.

The space beyond the Kuiper belt is much more like a vacuum than what
you get in our little neighborhood. Of course, the probes will be
covering a huge amount of space in a short time (10,000 years tops,
the way I see it) but you have to weigh that against almost 4 billion
years of inhabiting this relatively crowded neighborhood while not
being kicked out of the solar system in all that time.

>  A spacecraft in
> distant solar orbit could have survived and might charge up on solar
> energy enough to send a "Hello world" signal every few years.

Over 4 billion years? That would be some feat of engineering.

> > But he may have been begging the question.  They might have invented
> > the highly unusual device called the bacterial flagellum, which is
> > useful enough to have a good chance of staying in existence all those
> > years through being handed down from one generation to the next.
>
> > I once suggested that it may partly have been designed as a sort of
> > analogue of "Kilroy was here":  intelligent beings eventually evolving
> > from the microscopic life they sent might look at it and begin to
> > suspect that their existence is due to another species having sent
> > life to earth, and be suitably appreciative of the gift of life to the
> > unknown beings that sent it.
>
> Except that is not a prediction of panspermia; it is your own special
> pleading.

Anyone can label any argument they don't like as "special
pleading" (or "ad hoc," or whatever). The trick is to back up the
label with reasoned argument.

And I don't think you are up to the task.

[Granted, it isn't a *prediction*. But then, I was just explaining
why another argument isn't all that damaging to directed panspermia.]

Remainder deleted, to be replied to tomorrow [I hope].

Peter Nyikos