Right now I"m rereading David Darlings book 'Life
Everywhere'
because it suggests so many ideas about astrobiology.

He talks about what life is and tries to get a basic
definition.
"One of the things life does - that underpins its very
existence - is
metabolize. Biologists and astrobiologists are unanimous
that metabolism
has to be a linchpin of life everywhere....

Thus instead of the incredibly complex chemical processes
of
metabolism popping up from nothing, they were forced into
existence and forced to use that energy to further fit
the
environment and survive the environment.

Metabolism by itself is way too complex to even consider
as one step (or one group of steps). But breaking it down
we see that it is possible if and only if life is seen
as a reaction to and an adaptation to its environment.

Comment on metabolism and the origin of life?
Tom Hendricks

Wikipedia
http://en.wikipedia.org/wiki/Tom_Hendricks
Paper on UV/Origin of Life

http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html

Comment on metabolism and the origin of life?
Tom Hendricks

I would say that the origin of life can simply be explained
similar to the way Dawkins explains the evolution of the
eye. It's one small step at a time, building on
others--plus, a _lot_ of time!
....tonyC

Tony,

Wikipedia
http://en.wikipedia.org/wiki/Tom_Hendricks
Paper on UV/Origin of Life

http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html

Right now I"m rereading David Darlings book 'Life Everywhere'
because it suggests so many ideas about astrobiology.

He talks about what life is and tries to get a basic definition.
"One of the things life does - that underpins its very existence - is
metabolize. Biologists and astrobiologists are unanimous that metabolism
has to be a linchpin of life everywhere....
A pivotal aspect of metabolism is the harnessing of energy.... Energy must
be available on demand for essential biological tasks such as building complex
substances from simpler starting materials, effecting repairs to living
structures, and reproducing."

True enough - but the first thing I see is how incredibly complex this
process is. There are at least two aspects to metabolism - with each
one as big a breakthrough as any aspect of life.
1. harnessing energy. (And no one answers why chemicals would want
energy - or be chemically selected for having a desire for energy).
2. utilizing energy for work (And no one answers why chemicals would
want to change or work or be chemically selected for having a desire
to improve or change or do anything).

To me I see no reason why any of this would happen out of nothing.
It is simply incomprehensible that either step would happen , let
alone both, let alone both at the same time in support of each other.
No wonder no one has a reasonable idea about the origin.

.....

Comment on metabolism and the origin of life?
Tom Hendricks

Wikipedia
http://en.wikipedia.org/wiki/Tom_Hendricks
Paper on UV/Origin of Life
http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html

On Thu, 1 Feb 2007 17:46:27 -0500 (EST), TomHendricks474@cs.com wrote:

Right now I"m rereading David Darlings book 'Life Everywhere'
because it suggests so many ideas about astrobiology.

He talks about what life is and tries to get a basic definition.
"One of the things life does - that underpins its very existence - is
metabolize. Biologists and astrobiologists are unanimous that metabolism
has to be a linchpin of life everywhere....
A pivotal aspect of metabolism is the harnessing of energy.... Energy must
be available on demand for essential biological tasks such as building complex
substances from simpler starting materials, effecting repairs to living
structures, and reproducing."

True enough - but the first thing I see is how incredibly complex this
process is. There are at least two aspects to metabolism - with each
one as big a breakthrough as any aspect of life.
1. harnessing energy. (And no one answers why chemicals would want
energy - or be chemically selected for having a desire for energy).
2. utilizing energy for work (And no one answers why chemicals would
want to change or work or be chemically selected for having a desire
to improve or change or do anything).

To me I see no reason why any of this would happen out of nothing.
It is simply incomprehensible that either step would happen , let
alone both, let alone both at the same time in support of each other.
No wonder no one has a reasonable idea about the origin.

....
[snip for brevity}
....
Comment on metabolism and the origin of life?
Tom Hendricks

Wikipedia
http://en.wikipedia.org/wiki/Tom_Hendricks
Paper on UV/Origin of Life
http://www.daviddarling.info/encyclopedia/U/UV_origin_of_life.html


Some comments on metabolism. I think you, as do most people, put an
overemphasis on polymers in your OOL scenarios. If someone talks about
what life might look like when and if found elsewhere, they will be
talking about whether the polymers will look similiar to the RNA, DNA
and polypetides of all our life. They won't be talking about the small
molecules that are fundamental to the metabolism of all our life.
There are also properties to a metabolism. For instance, there is a
near identical frequency distribution for all organisms that plots
number of carbon atoms in the organic molecules vs the number of
different kinds of molecules. Would life somewhere else show this
pattern or is this just some kind of "frozen accident"?
A metabolism is an autocatalytic set of different molecules in which
all the more complex molecules are maintained because there is some
reaction pathway within the set of molecules that produces each one.
Once running it maintains itself. How it begins seems to be
fundamentally different than the incremental process of natural
selection. It is an "emergent property" of a set of different
molecules. Either the set of molecules is autocatalytic or it isn't.
It is an all or nothing thing.
Some questions. What is the smallest set that will form a metabolism?
Unknown.
Must long ordered polymers be included in the set of molecules? Many
think they must. I don't think so but this is just speculation until
someone finds such a set of molecules. Then the case would be closed
and we would know it is possible. From your emphasis on polymers I
infer you think polymers are required. But you are sometimes a little
fuzzy on these points. Of course, if there can be metabolism without
ordered polymers, by implication there could be organisms without
polymers or any genome whatsoever.
The pertinent question is what is the smallest size set where one can
be certain some smaller subset forms an autocatalytic set. Unknown but
it will be an order of magnitude or more above the smallest possible
set. And it will much larger if long polymers are required.
In any case, then the question becomes - are there natural processes
that will create enough diffent kinds of molecules to reach this
number? These processes are similiar but not exactly the same as what
you often discuss. Any energetic source creates more complex molecules
from smaller ones. Lightning, UV, molecules from space, volcanic hot
surfaces, etc. All do this. A further requirement is that the
molecules must be concentrated since they only react when in contact.
They can't be diluted. There are various ways proposed to concentrate
molecules but, to me, hydration seems most plausible if not the only
plausible method.
Anyway if there are natural processes that create and concentrate
enough different molecules to pass this lower limit then metabolism
will "emerge". And it will do so everywhere and all the time.
Otherwise it would never "emerge".

"William L Hunt" <wlhunt@earthlink.net> wrote in message
news:eqaio7$2rp9$1@darwin.ediacara.org...
On Thu, 1 Feb 2007 17:46:27 -0500 (EST), TomHendricks474@cs.com wrote:
(Heavily snipped)

Anyway if there are natural processes that create and concentrate
enough different molecules to pass this lower limit then metabolism
will "emerge". And it will do so everywhere and all the time.
Otherwise it would never "emerge".

Sounds like you have been reading Stuart Kauffman and/or his Santa Fe
cohorts. Be careful - that kind of reading can be hazardous to
clear thinking. ;-)

Your argument can be caricatured as: "A sufficiently large set of
molecular
species will always contain an autocatalytic subset. So all we need to
do is to place a sufficiently large variety of molecules in close contact
and life will inevitably start up."

There are several things wrong with this line of thought:

1. It is just not true that "Either the set of molecules is autocatalytic
or it isn't. It is an all or nothing thing." It is a bit closer to the
truth to say that a set of molecules is autocatalytic or not in a
particular environment. The environment needs to supply the right kinds
of raw materials, and those raw materials need to be far from chemical
equilibrium. Tom has a tendency to assign a 'driving' role to the
environment. That is probably a mistake, but in your account it is given
no role at all. That is also a mistake. I would say that the environment
plays a 'gating' role in the origin - either it permits an autocatalytic
set to thrive, or it doesn't.

2. Your account assigns no role to the molecules that are not part of
the autocatalytic set - except perhaps as dilutants. But that is probably
not realistic. Unwanted molecules can easily 'gum up the works' of an
autocatalytic cycle by reacting with and inactivating cycle constituents,
by catalyzing dissipative side reaction pathways, etc. It seems to
me that it is as important to specify the molecules that may not be
present in an autocatalytic set as to specify the molecules that must
be present. This is why I find the notion of life emerging from
complexity
so unsatisfying.

3. Autocatalytic cycles are necessary for a metabolic lifeform, but they
are not sufficient. It is not enough that each molecular species has a
positive population growth rate. It must also be the case that each
species in the cycle (or connected network of cycles) must have exactly
the same growth rate. If there is only one cycle, then a steady state
is reached and my identical growth rate criterion is achieved
automatically.
But if you have a more complicated situation, with two subordinate cycles
acting parasitically on a primary cycle, say, then it must be the case
that each of those two subordinate cycles cross-inhibit the other.
Otherwise the system as a whole cannot be homeostatic and stable.

4. In order for this primitive form of life to evolve into something
more complicated, with genetic polymers and all that neat stuff, the
primitive life probably needs to be subject to something like natural
selection. This means that you need to have some kind of spontaneous
containerization, so that you have organisms that can be selected. It
also means that the chemical possibilities must be rich enough so that
variant complex cycles can arise and compete. Furthermore, these
intricate evolvable metabolisms must be able to outcompete any pelagic
non-evolvable autocatalytic cycles which might otherwise drain the ocean
of raw materials and chemical disequilibrium. (These last points,
incidentally, are the reasons why I like Wachtershauser's ideas. Not
only does he have spontaneous formation of lipid membrane organisms,
he also has these lipid films forming a protective coating over the
key raw material and thus inhibiting other processes which might dissipate
the dis-equilibrium.

Some comments on metabolism. I think you, as do most people, put an
overemphasis on polymers in your OOL scenarios. If someone talks about
what life might look like when and if found elsewhere, they will be
talking about whether the polymers will look similiar to the RNA, DNA
and polypetides of all our life.

molecules that are fundamental to the metabolism of all our life.
There are also properties to a metabolism. For instance, there is a
near identical frequency distribution for all organisms that plots
number of carbon atoms in the organic molecules vs the number of
different kinds of molecules. Would life somewhere else show this
pattern or is this just some kind of "frozen accident"?

A metabolism is an autocatalytic set of different molecules in which
all the more complex molecules are maintained because there is some
reaction pathway within the set of molecules that produces each one.

Once running it maintains itself. How it begins seems to be
fundamentally different than the incremental process of natural
selection. It is an "emergent property" of a set of different
molecules. Either the set of molecules is autocatalytic or it isn't.

It is an all or nothing thing.

Some questions. What is the smallest set that will form a metabolism?
Unknown.
Must long ordered polymers be included in the set of molecules? Many
think they must. I don't think so but this is just speculation until
someone finds such a set of molecules. Then the case would be closed
and we would know it is possible. From your emphasis on polymers I
infer you think polymers are required. But you are sometimes a little
fuzzy on these points.

ordered polymers, by implication there could be organisms without
polymers or any genome whatsoever.
The pertinent question is what is the smallest size set where one can
be certain some smaller subset forms an autocatalytic set.

it will be an order of magnitude or more above the smallest possible
set. And it will much larger if long polymers are required.
In any case, then the question becomes - are there natural processes
that will create enough diffent kinds of molecules to reach this
number? These processes are similiar but not exactly the same as what
you often discuss. Any energetic source creates more complex molecules
from smaller ones. Lightning, UV, molecules from space, volcanic hot
surfaces, etc. All do this. A further requirement is that the
molecules must be concentrated since they only react when in contact.
They can't be diluted. There are various ways proposed to concentrate
molecules but, to me, hydration seems most plausible if not the only
plausible method.
Anyway if there are natural processes that create and concentrate
enough different molecules to pass this lower limit then metabolism
will "emerge". And it will do so everywhere and all the time.
Otherwise it would never "emerge".
William L Hunt

Anyway if there are natural processes that create and concentrate
enough different molecules to pass this lower limit then metabolism
will "emerge". And it will do so everywhere and all the time.
Otherwise it would never "emerge".

Sounds like you have been reading Stuart Kauffman and/or his Santa Fe
cohorts. Be careful - that kind of reading can be hazardous to
clear thinking. ;-)

Your argument can be caricatured as: "A sufficiently large set of molecular
species will always contain an autocatalytic subset. So all we need to
do is to place a sufficiently large variety of molecules in close contact
and life will inevitably start up."

There are several things wrong with this line of thought:

1. It is just not true that "Either the set of molecules is autocatalytic
or it isn't. It is an all or nothing thing." It is a bit closer to the
truth to say that a set of molecules is autocatalytic or not in a
particular environment. The environment needs to supply the right kinds
of raw materials, and those raw materials need to be far from chemical
equilibrium. Tom has a tendency to assign a 'driving' role to the
environment. That is probably a mistake, but in your account it is given
no role at all. That is also a mistake. I would say that the environment
plays a 'gating' role in the origin - either it permits an autocatalytic
set to thrive, or it doesn't.

2. Your account assigns no role to the molecules that are not part of
the autocatalytic set - except perhaps as dilutants. But that is probably
not realistic. Unwanted molecules can easily 'gum up the works' of an
autocatalytic cycle by reacting with and inactivating cycle constituents,
by catalyzing dissipative side reaction pathways, etc. It seems to
me that it is as important to specify the molecules that may not be
present in an autocatalytic set as to specify the molecules that must
be present. This is why I find the notion of life emerging from complexity
so unsatisfying.

3. Autocatalytic cycles are necessary for a metabolic lifeform, but they
are not sufficient. It is not enough that each molecular species has a
positive population growth rate. It must also be the case that each
species in the cycle (or connected network of cycles) must have exactly
the same growth rate. If there is only one cycle, then a steady state
is reached and my identical growth rate criterion is achieved automatically.
But if you have a more complicated situation, with two subordinate cycles
acting parasitically on a primary cycle, say, then it must be the case
that each of those two subordinate cycles cross-inhibit the other.
Otherwise the system as a whole cannot be homeostatic and stable.

4. In order for this primitive form of life to evolve into something
more complicated, with genetic polymers and all that neat stuff, the
primitive life probably needs to be subject to something like natural
selection. This means that you need to have some kind of spontaneous
containerization, so that you have organisms that can be selected. It
also means that the chemical possibilities must be rich enough so that
variant complex cycles can arise and compete. Furthermore, these
intricate evolvable metabolisms must be able to outcompete any pelagic
non-evolvable autocatalytic cycles which might otherwise drain the ocean
of raw materials and chemical disequilibrium. (These last points,
incidentally, are the reasons why I like Wachtershauser's ideas. Not
only does he have spontaneous formation of lipid membrane organisms,
he also has these lipid films forming a protective coating over the
key raw material and thus inhibiting other processes which might dissipate
the dis-equilibrium.