in article fqeu0n$156...@darwin.ediacara.org, Tom Hendricks at
tom-hendri...@att.net wrote on 3/2/08 11:09 AM:

On Feb 28, 12:49 pm, verulam <johnhewit...@yahoo.com> wrote:
Tom,
OK, you feel the nucleotide problem can be solved but I do not agree.
I think nucleotides can only arise as part of an established
metabolism, which is a "metabolism first" viewpoint.

"Metabolism first' is a fluke chemical event. Now when metabolism pops up is
it immediately adapted to the environment, or is it destroyed in that
environment? if not adapted immediately, we need another fluke. That's two, -
you'll need about 10 more before your'e done. And one is enough to rule out
life.

Tom,

I would count myself in the metabolism-first camp, and I think you are
missing the point of this view.  The emergence of a metabolism de novo is no
more of a fluke event than the emergence of a convection cell in the
atmosphere.  You could argue that a convection cell is initially spawned by
a fluke puff of wind that entrains the emergence of a full blown dissipative
structure, but that would also miss the point.  Like a convection cell, a
metabolism does thermodynamic work.  The structure of a dissipative
metabolism is fueled by local gradients (e.g., macromolecular structures,
thermal gradients, and so on) and could be sparked by chaotic chemical
dynamics (analogous to a puff of wind sparking a convection cell).  I
wouldn't call chemical dynamics a metabolisms until positive feedback loops
are established, which effectively sustain the structure of the metabolic
chemistry (again, analogous to positive feedback within a convection cell).

In other words, the metabolisms-first view envisions the prior existence of
a physical potential (e.g., a thermal and/or macromolecular gradient) that
pulled dynamic metabolic (chemical) structures into existence.  This is
different from a fluke.

Cheers,

Guy

On Mar 3, 12:22 pm, Guy A Hoelzer <hoel...@unr.edu> wrote:
in article fqeu0n$156...@darwin.ediacara.org, Tom Hendricks at
tom-hendri...@att.net wrote on 3/2/08 11:09 AM:

On Feb 28, 12:49 pm, verulam <johnhewit...@yahoo.com> wrote:
Tom,
OK, you feel the nucleotide problem can be solved but I do not agree.
I think nucleotides can only arise as part of an established
metabolism, which is a "metabolism first" viewpoint.

"Metabolism first' is a fluke chemical event. Now when metabolism pops up is
it immediately adapted to the environment, or is it destroyed in that
environment? if not adapted immediately, we need another fluke. That's two,
-
you'll need about 10 more before your'e done. And one is enough to rule out
life.

Tom,

I would count myself in the metabolism-first camp, and I think you are
missing the point of this view.  The emergence of a metabolism de novo is no
more of a fluke event than the emergence of a convection cell in the
atmosphere.  You could argue that a convection cell is initially spawned by
a fluke puff of wind that entrains the emergence of a full blown dissipative
structure, but that would also miss the point.  Like a convection cell, a
metabolism does thermodynamic work.  The structure of a dissipative
metabolism is fueled by local gradients (e.g., macromolecular structures,
thermal gradients, and so on) and could be sparked by chaotic chemical
dynamics (analogous to a puff of wind sparking a convection cell).  I
wouldn't call chemical dynamics a metabolisms until positive feedback loops
are established, which effectively sustain the structure of the metabolic
chemistry (again, analogous to positive feedback within a convection cell).

'"Sparked" by chaotic chemical dynamics'? That sounds like a fluke to
me.

And why would metabolism be important? Do chemicals want to eat?

I'm looking at my table. Does my salt want to eat and my pepper want
to replicate?
Do chemicals want to get to you - to metabolism, to replication?
I think you are trying to get to whatever your definition of what life
is, and you are starting
it out with some special out-of-the ordinary events - fluke events.

Fluke events would only lead to life processes if they were not fluke
events
but often-happening events. Then they would be events that fit that
environment
and happened often in that environment, and were stable in that
environment.

IF what you suggest happened often and was ordinary, then
it may have had a part. If it was rare, then it was a fluke.

And overall remember if water is involved - and it is necessary to
life - all of this is a response to the
sun temperature cycle that keeps the water in liquid form. Can anyone
invision a scenario without
water?

So no matter the chemistry it is all
a response to the environmental forces of the sun/uv/heat cycle. That
is where we should
be looking, not at metabolism, replication, or any of the other OOL
fluke scenarios.

On Mar 3, 6:22 pm, Guy A Hoelzer <hoel...@unr.edu> wrote:



in article fqeu0n$156...@darwin.ediacara.org, Tom Hendricks at
tom-hendri...@att.net wrote on 3/2/08 11:09 AM:

On Feb 28, 12:49 pm, verulam <johnhewit...@yahoo.com> wrote:
Tom,
OK, you feel the nucleotide problem can be solved but I do not agree.
I think nucleotides can only arise as part of an established
metabolism, which is a "metabolism first" viewpoint.

"Metabolism first' is a fluke chemical event. Now when metabolism pops up is
it immediately adapted to the environment, or is it destroyed in that
environment? if not adapted immediately, we need another fluke. That's two, -
you'll need about 10 more before your'e done. And one is enough to rule out
life.

Tom,

I would count myself in the metabolism-first camp, and I think you are
missing the point of this view.  The emergence of a metabolism de novo is no
more of a fluke event than the emergence of a convection cell in the
atmosphere.  You could argue that a convection cell is initially spawned by
a fluke puff of wind that entrains the emergence of a full blown dissipative
structure, but that would also miss the point.  Like a convection cell, a
metabolism does thermodynamic work.  The structure of a dissipative
metabolism is fueled by local gradients (e.g., macromolecular structures,
thermal gradients, and so on) and could be sparked by chaotic chemical
dynamics (analogous to a puff of wind sparking a convection cell).  I
wouldn't call chemical dynamics a metabolisms until positive feedback loops
are established, which effectively sustain the structure of the metabolic
chemistry (again, analogous to positive feedback within a convection cell).

In other words, the metabolisms-first view envisions the prior existence of
a physical potential (e.g., a thermal and/or macromolecular gradient) that
pulled dynamic metabolic (chemical) structures into existence.  This is
different from a fluke.

Cheers,

Guy

Yes, I would agree with Guy's comments here - at least insofar as they
apply to the mechanism for the origin of a metabolism advanced by
myself.

The point is that one can describe *an* origin for metabolism that
begins, essentially,  with just our present perception of the
prebiotic earth and some standard physical and organic chemistry. You
then that the resulting, thermally driven oscillations would be
subject to selective evolution. By considering how you might expect
that evolution to progress, you can get something resembling
metabolism to emerge. That is not a "Pop and adapt" view and I have no
idea how Tom comes by the notion.

By contrast Tom is, himself, assuming that nucleotides will simply pop
into existence and then defy chemistry by behaving in whatever way he
finds convenient. I don't think so but I cannot put the responsibility
entirely on Tom. Currently, the most popular theory for the origin of
life is the "RNA world" theory and that entire program does exactly
what Tom is doing.

Sincerely

John Hewitt

Currently, the most popular theory for the origin of
life is the "RNA world" theory and that entire program does exactly
what Tom is doing.

in article fqo5ra$6m...@darwin.ediacara.org, Tom Hendricks at
tom-hendri...@att.net wrote on 3/5/08 11:18 PM:



On Mar 3, 12:22 pm, Guy A Hoelzer <hoel...@unr.edu> wrote:
in article fqeu0n$156...@darwin.ediacara.org, Tom Hendricks at
tom-hendri...@att.net wrote on 3/2/08 11:09 AM:

On Feb 28, 12:49 pm, verulam <johnhewit...@yahoo.com> wrote:
Tom,
OK, you feel the nucleotide problem can be solved but I do not agree.
I think nucleotides can only arise as part of an established
metabolism, which is a "metabolism first" viewpoint.

"Metabolism first' is a fluke chemical event. Now when metabolism pops up is
it immediately adapted to the environment, or is it destroyed in that
environment? if not adapted immediately, we need another fluke. That's two,
-
you'll need about 10 more before your'e done. And one is enough to rule out
life.

Tom,

I would count myself in the metabolism-first camp, and I think you are
missing the point of this view.  The emergence of a metabolism de novo is no
more of a fluke event than the emergence of a convection cell in the
atmosphere.  You could argue that a convection cell is initially spawned by
a fluke puff of wind that entrains the emergence of a full blown dissipative
structure, but that would also miss the point.  Like a convection cell, a
metabolism does thermodynamic work.  The structure of a dissipative
metabolism is fueled by local gradients (e.g., macromolecular structures,
thermal gradients, and so on) and could be sparked by chaotic chemical
dynamics (analogous to a puff of wind sparking a convection cell).  I
wouldn't call chemical dynamics a metabolisms until positive feedback loops
are established, which effectively sustain the structure of the metabolic
chemistry (again, analogous to positive feedback within a convection cell).

'"Sparked" by chaotic chemical dynamics'? That sounds like a fluke to
me.

I don't think so, because the underlying chaotic chemical dynamics are
omnipresent.   The source of the "spark" may not be predictable, but the
input of "sparks" is both predictable and abundant.  The "sparks" are still
happening constantly today, although there is not enough fuel left to catch
fire (new origins of life), because it is already being tapped by the
biosphere.  It is also possible that the biosphere has reshaped local
(earthly) material constraints in such a way that new origins have been
suppressed.  At least this paragraph aims to explain my personal view a
little further, and why I don't see this model as requiring a fluke.

And why would metabolism be important? Do chemicals want to eat?

No, but thermodynamics "wants" to dissipate gradients.  This can be
accomplished by favoring the emergence of dynamical, dissipative
autocatalytic sets of chemicals (a metabolism), which do "eat".

I'm looking at my table. Does my salt want to eat and my pepper want
to replicate?
Do chemicals want to get to you - to metabolism, to replication?
I think you are trying to get to whatever your definition of what life
is, and you are starting
it out with some special out-of-the ordinary events - fluke events.

I hope my responses above convince you that these points are not relevant.

Fluke events would only lead to life processes if they were not fluke
events
but often-happening events. Then they would be events that fit that
environment
and happened often in that environment, and were stable in that
environment.

The metabolic pathways would have to become stable, but the constant
sparking of chaotic chemical dynamics would be and could be far from stable.

IF what you suggest happened often and was ordinary, then
it may have had a part. If it was rare, then it was a fluke.

OK.

And overall remember if water is involved - and it is necessary to
life - all of this is a response to the
sun temperature cycle that keeps the water in liquid form. Can anyone
invision a scenario without
water?

It does seem that water has special properties that facilitate life but I,
for one, remain open to the possibility that our limited imaginings about
alternatives leaves open the possibility of life without water.

So no matter the chemistry it is all
a response to the environmental forces of the sun/uv/heat cycle. That
is where we should
be looking, not at metabolism, replication, or any of the other OOL
fluke scenarios.

I think you are being too defensive about the importance of your cycles.
Personally, I think the existence of cycles facilitates the de novo origins
of metabolisms, because they can make it easier to connect the extremes of a
gradient with channeled flows.

Guy

On Mar 3, 12:22 pm, Guy A Hoelzer <hoel...@unr.edu> wrote:

'"Sparked" by chaotic chemical dynamics'? That sounds like a fluke to
me.
Fluke and chaos have nothing to do with each other. Turbulent

On Mar 6, 3:18 am, Tom Hendricks <tom-hendri...@att.net> wrote:

On Mar 3, 12:22 pm, Guy A Hoelzer <hoel...@unr.edu> wrote:
'"Sparked" by chaotic chemical dynamics'? That sounds like a fluke to
me.

      Fluke and chaos have nothing to do with each other. Turbulent
fluids follow chaotic dynamics, but the "evolution" of a turbulent
fluid is almost independent of initial conditions. As long a energy is
pumped into a turbulent fluid, it continues in the same state
regardless of the exact microscopic state of the fluid. I suspect that
is what you call "stable."

    Note: turbulence needs a spark. That right, even if the Reynolds
number exceeds the critical Reynolds number, some "seed" vortex is
necessary to start the process going. The vortex gets amplified, but
the phase is lost. A turbulent system is not "cyclic" in the usual
sense (try periodic). The seed in your language would be a "fluke."

     I think the words that you are confusing are episodic and
chaotic. Just because a system is chaotic doesn't mean that it is
episodic. The some of the parameters of a chaotic system can be
determined. Some of the details chaotic system is highly sensitive to
small perturbations. In fact, living things currently are full of
chaotic systems.

     Chaotic systems are rather robust against periodic disturbances.
Periodic disturbances tend to destroy order, ironically. Complex
systems are often destroyed by chance resonances with periodic
disturbances. Our hearts do not beat periodically, at best they beat
quasiperiodically. Our heart beat is chaotic. If our hearts beat in a
truly periodic fashion, you could blow up your heart just by running
at the right slow cadence.

    When you say that the sun cycle is in every cell of our bodies, is
it possible that you are thinking of some type of chaos? I really
don't see the 23'54'' diurnal cycle as being common in our cells. I
see fractals all over the place, however. That implies chaotic
dynamics.

      And again, why UV? What is so magical about UV radiation? Life
most probably started in the sea, although even this isn't known for
sure. UV can't penetrate far below the surface. Liquid water strongly
absorbs UV. Are you implying that UV started near the surface of the
ocean?

On Mar 12, 11:32 pm, Lorentz <drosen0...@yahoo.com> wrote:

Having water in liquid form is proof of a sun temperature cycle.
Absolute nonsense. Liquid water is a proof that there is a heat

Sea as origin? Problems - no dry phase means no polymerization,
Total nonsense. Polymers form in liquids. They sometime

and
most
chemistry is too diluted in the sea.
Your half truth is accepted. Your exact statement is wrong.

Plus many more problems.
Tidal pool or shores - maybe - they would have both a dry hot phase
and a
cool wet phase.
Okay. Maybe tidal pools had a role. But this is sand in the eyes.

UV is flooding the earth and growing stronger from 4.5 - 1.5. How can
you not talk about it? If not the sea, and not the vents (same
problems
with an added one - vents sterilize the ocean)
Illogical argument. Vents don't sterilize the ocean.Vents don't

then you are left with
places that are flooded with UV.
Okay, your nonsequitor is done. Back to my original question. What

The sun is the strongest source of
energy at this time. It is also the most constant.
I thought you said it cycled? In any case, geothermal energy has

It is also the
thing
that keeps the earth at the temperature of liquid water.
Agreed. Without the sun to keep water liquid, other models don't

It seems to
be both the most damaging force, and the most powerful force for
change and for chemical selection - that whichis not destroyed,
survives..
Duh.
There are other energy sources but they are not constant and cyclical.
Not true. For one thing, the two statements logically contradict

How can you build a stable chemistry system on unstable energy events?
One catch about Miller's experiment is that his recreated lightning
was
a constant and predictable energy source in the LAB. But in nature
lighting is not so regimented. Neither is any other energy source
except the SUN.
What are you talking about? Lightning occurs every time there is a

Note that though everyone tries to devise a scenario to avoid
the damage of UV, we have photosynthesis (and probably our oldest
real evidence of life at 3.5 is very similar to bacteria that
photosynthesize.)
And very similar to autotrophic bacteria that digest sulfuric acid.

The toughest question for you is why would first life
a. run from UV because of its damaging affect, but at the same time
b. get its power source from UV/sun as photosynthesis.
That doesn't make a bit of sense.

There is that study (see my UV recent posts and my paper's referendes)
that UV was actually helpful in
the development of nucleotides.
Some nucleotides have an absorption band in the near UV. I give the

If we look at life as my definition -
that chemistry which
best stabilizes under the UV bombardment and in that environment, you
see that every definition of life
is just that. Cell's, metabolism, replication, coding, they are all
just tricks to help
survive the UV infested environment.
Or the acidic environment?
No origin scenario can go on without talking about UV. Like I said
it's the
500 pound gorilla in the room.
Which probably couldn't live in strong UV.

On Mar 14, 4:34 pm, Tom Hendricks <tom-hendri...@att.net> wrote:

On Mar 12, 11:32 pm, Lorentz <drosen0...@yahoo.com> wrote:
Having water in liquid form is proof of a sun temperature cycle.

    Absolute nonsense. Liquid water is a proof that there is a heat
source, regardless of cycle. There doesn't have to be any cycle to
melt ice.

Sea as origin? Problems - no dry phase means no polymerization,

     Total nonsense. Polymers form in liquids. They sometime
precipitate out of the water, but not always.

and
most
chemistry is too diluted in the sea.

    Your half truth is accepted. Your exact statement is wrong.
    Chemistry is too diluted in the BULK liquid of the sea. There are
solid objects that form surfaces. Even a liquid hydrocarbon floating
on the surface of the water can form a surface where chemisticals can
be concentrated. Colloids in the sea can concentrate chemicals on
their surface.

       Do you know what micelles are? Please look them up. There is
plenty of surface area on colloidal particles, such as micelles.

Plus many more problems.
Tidal pool  or shores - maybe - they would have both a dry hot phase
and a
cool wet phase.

    Okay.
Snipped
UV is flooding the earth and growing stronger from 4.5 - 1.5. How can
you not talk about it? If not the sea, and not the vents (same
problems
with an added one - vents sterilize the ocean)

    Illogical argument. Vents don't sterilize the ocean.Vents don't
sterilize ALL life. Just some life.
    It the same problem up or down. Either life started elsewhere and
moved into the vents, or life started in the vents and moved
elsewhere. In either case, your premise is wrong. Any arguement
starting with that premise is wrong, regardless of where life
started.

      Many forms of life not only live in the vents, they can't live
anywhere else. Where in the vents is life sterilized? Only deep down.
It is actually the sulfuric acid, the chemicals generated by
geothermal heat, that allows life to live down there.

    So I go back to my original questions. Why is UV magical? Why is
the solar cycle so magical?

then you are left with
places that are flooded with UV.


     Just for nostalgia, I will refute an argument you once made long
ago. The aromatic amino acids happen to have an absorption band in the
UV spectral range. Your idea (which was never developed fully) is that
the existence of such an absorption band implies that UV started
life.
     This argument is irrational for several reasons. One reason is
that most amino acids are completely transparent to the UV that could
reach the ground in ANY atmosphere. The aromatic amino acids are an
exception, not the rule. Glutamic acid (of Chines restaurant fame) is
completely transparent to UV. Another reason: the absorption band may
have helped the pioneers that reached the surface of the oceans
survive. Life could have developed and evolved in a vent, and then
some brave procaryotes with tryptophan colonized the surface. The
tryptophan is very likely to be the earliest form of sun screen.

The sun is the strongest source of
energy at this time. It is also the most constant.

    I thought you said it cycled?

    Agreed. Without the sun to keep water liquid, other models don't
work. However, the visible and infrared energy of the sun could keep
us just as warm. And there doesn't have to be a cycle to keep us warm.
The cycle, if one is needed, can come from something other than the
sun.
       
snipped
There are other energy sources but they are not constant and cyclical.

    Not true. For one thing, the two statements logically contradict
each other. For another thing, there are many energy sources that
cycle independently of the solar cycle, and have cycles that are as
persistent or more as the solar cycle. I have mentioned them before,
when you made the same incorrect statement before. Are you reading
anything I write?

How can you build a stable chemistry system on unstable energy events?
One catch about Miller's experiment is that his recreated lightning
was
a constant and predictable energy source in the LAB. But in nature
lighting is not so regimented. Neither is any other energy source
except the SUN.

    What are you talking about? Lightning occurs every time there is a
thunderstorm, which in my area is several times a year.

snipped

The toughest question for you is why would first life
a. run from UV because of its damaging affect,  but at the same time
b. get its power source from UV/sun as photosynthesis.
That doesn't make a bit of sense.

There is that study (see my UV recent posts and my paper's referendes)
that UV was actually helpful in
the development of nucleotides.

   Some nucleotides have an absorption band in the near UV. I give the
same counterarguments I offered for amino acids.>If we look at life as my definition -
that chemistry which
best stabilizes under the UV bombardment and in that environment, you
see that every definition of life
is just that. Cell's, metabolism, replication, coding, they are all
just tricks to help
survive the UV infested environment.

   Or the acidic environment?> No origin scenario can go on without talking about UV. Like I said
it's the
500 pound gorilla in the room.

      Which probably couldn't live in strong UV.
OR develop photosynthesis?