abiogenesis via a metabolic network
Kent Paul Dolan
of abiogenesis here, as mentioned in this
introduction:
Among the many theories of the origin of life, two
major viewpoints can be identified; I refer to
these as the Genetic View and the Metabolic View.
These can be briefly described as follows:
* Genetic View: Template replicating molecules
or crystals were crucial for the origin of life,
and have from the outset been the carriers of
inherited information that makes evolution
possible
* Metabolic View: The first living entities were
metabolic systems, and they evolved by exploring
the possibilities for new kinds of metabolic
network.
to this recent paper:
http://www.simsoup.info/Network_Dynamics_In_SimSoup_V1.0.pdf
announcing incremental progress with the
SimSoup complex chemistry simulator.
Can anyone clarify how the two views differ, and
what relative validity they are considered to have
(both "who's winning", and "are both workable")?
Thanks for any insight.
xanthian.
Perplexed in Peoria
"Kent Paul Dolan" <xant...@well.com> wrote in message news:1157596714.2...@i42g2000cwa.googlegroups.com...
I'll start with full disclosure. I am a 'Metabolic View'
person, a Wachtershauser fan, and not a scientist. My
summary may be biased and not perfectly well informed.
As to "who's winning", I would say that metabolism-first
has the momentum and has almost caught up in popularity.
But neither is actually winning, and in fact neither *can*
win without some new ideas. Depending on what you mean
by 'workable', it might be said that neither is workable,
or that both are workable. Certainly neither one is
currently providing a coherent account of abiogenesis.
You have given an excellent capsule summary of the two
views above. But let me point out that there are two
competing schools of thought within the metabolism-first
camp, and 'SimSoup' represents only one of them.
SimSoup represents the 'heterotrophic' 'self-organization
from complexity' school of thought often associated with
the name of Stuart Kaufmann. These people think that
abiotic chemistry generated a soup, and that membranes
formed and life arose once the soup became dense and
complex enough.
The second school of thought is the 'autotrophic'
viewpoint often associated with the name of Gunter
Wachtershauser. This viewpoint denies that there
even was a soup. Instead, the origin of life was
a very local affair associated with solid mineral
catalysts which formed membranes locally from
CO2 or CO and some source of reducing power. It
says that metabolism started simple and only
gradually became complex.
There are two main schools within the genetics-first
viewpoint as well. One school is associated with
the name of Manfred Eigen and assumes that the
first lifeforms were replicating RNA molecules.
The RNA life then invented metabolism. Variants
claim that something like RNA (PNA for example)
came first.
The second genetics-first school is associated
with Graham Cairns-Smith, and claims that the first
genes and first lifeforms were clay crystals. These
lifeforms invented a simple metabolism; then the
clay genes+metabolism invented RNA; then the combination
of all three invented modern metabolism and lost the
clay somewhere along the way.
So there are really four theories here. And the best
way to compare them is to list the major problems
which each theory fails to address. But first, let
us note that none of the four address the classic
chicken-egg problem in the origin of life on Earth -
the origin of coded protein synthesis. And until
that problem is cracked, no theory of abiogenesis
can claim victory. There may be differences as
to which of the four is best able to deal with
this problem, but which is best on this point, if
any, is very murky now.
Other unsolved problems of the four theories:
Eigen - How can you get RNA molecules, let alone
replicating RNA molecules without a prior metabolism
to produce activated nucleotides? If the original
'organisms' were simple RNA molecules, how was the
transition made to a different unit-of-selection -
the cellular organism containing many species of
RNA molecules? Why would RNA molecules invent
metabolism before they became encapsulated? OTOH,
how could they reproduce without metabolism if they
became encapsulated first?
Cairns-Smith: How could clay crystals provide
enough specific catalysis to invent the first
metabolism? Having done so, why would they invent
RNA? (Encapsulation issues are less of a problem
here, because the 'old' metabolism can ease the
transition. But there are still issues related
to transitions of the unit-of-selection.)
Kaufmann: Why wouldn't the initial complex
metabolism be poisoned by all the stuff in the
soup which doesn't belong to the autocatalytic
set? Kaufmann's early models had no realistic
thermodynamics. How does encapsulation arise?
Why do these organisms invent RNA? Without genes,
how do they evolve?
Wachtershauser: Life starts encapsulated, but
is a simple autotrophic metabolism really feasible?
Why do these organisms invent RNA? Without genes,
how do they evolve?
Well, that is the way I see it, anyhow.
Andrew McClure
It may be a bit early in the thread to do this, but I would like to
nominate this for post of the month. This is in general an interesting
topic for which surprisingly little information is readily available.
josephus
one samll equestion. Has anyone done any work on chemical equilibrium?
I dont know any techinical inforamtion about abiogenisis. Thanks, it
was great.
josephus
Perplexed in Peoria
"josephus" <dog...@earthlink.net> wrote in message news:teOLg.7581$bM....@newsread4.news.pas.earthlink.net...
I probably don't understand your question. Chemical equilibrium
is a well understood subject. It is in the departures from
equilibrium that the chemistry gets difficult and interesting.
Life is generally assumed to appear and thrive in a situation
far from chemical equilibrium.
seem...@cyberspace.org
[...]
> The second genetics-first school is associated
> with Graham Cairns-Smith, and claims that the first
> genes and first lifeforms were clay crystals. These
> lifeforms invented a simple metabolism; then the
> clay genes+metabolism invented RNA; then the combination
> of all three invented modern metabolism and lost the
> clay somewhere along the way.
[...]
> So there are really four theories here. And the best
> way to compare them is to list the major problems
> which each theory fails to address. But first, let
> us note that none of the four address the classic
> chicken-egg problem in the origin of life on Earth -
> the origin of coded protein synthesis. And until
> that problem is cracked, no theory of abiogenesis
> can claim victory.
That problem has nothing to do with the origin of
self-replicating, evolving systems - since it happened
***long*** after life first arose.
IMO, all that need be noted by anyone from the four
camps you mentioned is that "evolution did it" is a
highly satisfying explanation for this piece of
technology - or indeed practically any other subsequent
development.
> Other unsolved problems of the four theories:
>
> Cairns-Smith: How could clay crystals provide
> enough specific catalysis to invent the first
> metabolism?
/If/ we take "metabolism" to mean:
http://en.wikipedia.org/wiki/Metabolism
...then that's pretty much the question of how clay
organisms got to grips with the first organics - to
which the answer seems to be that they grabbed them
using grooves on their surfaces.
There's a big literature these days about clays'
abilities in this area - derived in part from the
literature on industrial catalysts - but also
because the fact that clays played a role in
the origin of life has become increasingly recognised.
Why would clay organisms have started messing with
organic chemistry?
That is easy to answer in general - since
use of organic compounds facilitate far more
sophisticated chemistry and better technology -
and evolution results in progressive technological
development, with important discoveries accumulating
over time.
It's non-trivial to answer if the question is
which aspects of organic chemistry came first -
since there are so many things organic chemistry
can be used for - and the specific details of
which came first have been brushed over for
almost the last four billion years.
My guess is that the first organics were
grabbed as glue:
http://originoflife.net/first_organics/
...however, there are no shortage of other
applications for organic molecules.
> Having done so, why would they invent RNA?
Probably structural reasons. My impression
is that this is the answer given in nearly
all theories of the origin of RNA that aren't
brain-dead ;-)
seem...@cyberspace.org
> I don't see much discussion of the "metabolic view"
> of abiogenesis here, as mentioned in this
> introduction:
>
> Among the many theories of the origin of life, two
> major viewpoints can be identified; I refer to
> these as the Genetic View and the Metabolic View.
> These can be briefly described as follows:
>
> * Genetic View: Template replicating molecules
> or crystals were crucial for the origin of life,
> and have from the outset been the carriers of
> inherited information that makes evolution
> possible
>
> * Metabolic View: The first living entities were
> metabolic systems, and they evolved by exploring
> the possibilities for new kinds of metabolic
> network.
>
> to this recent paper:
>
> http://www.simsoup.info/Network_Dynamics_In_SimSoup_V1.0.pdf
[...]
> Can anyone clarify how the two views differ, and
> what relative validity they are considered to have
> (both "who's winning", and "are both workable")?
I see two splits here:
There's disagreement over how the heritable information is stored,
with one camp thinking it was written down somehow (as it is in
todays organisms), and the other promoting less 'tangible'
information storage strategies.
...and there's disagreement over which /types/ of clues are
important when identifying our earliest ancestors. Should
we concentrate on the phenotype or the genotype? Should
the focus be on nutrient sources or exhaust pipes? Is the
source of power important? What about how the first organisms
dissipated heat? How did the first organisms detect and
correct heritable errors?
For the first split, the folk promoting the "less tangible"
media have quite an uphill battle on their hands, IMO.
That's not how life works today - and there's little more
than computer simulations exist to suggest that it could
ever realistically have worked differently.
The second split is largely hot air IMO. The first
organisms degraded a source of energy while passing
on an inheritance. Clues about how they did this
may come from all over the place.
Different researchers may differ about the significance
of these clues - but at the end of the day, the same
clues are available to everyone, and we ought to all
reach the same conclusion - *if* those clues are
interpreted correctly.
One of the problems at the moment is that researchers
have different backgrounds, exaggerate the importance
of some clues at the expense of other ones - and reach
different conclusions from each other.
This has been going on for decades now - *long* after
the solution to the problem was found - and extremely
clearly explained - way back in the 1960s.
Historically, very few other scientific mysteries
have persisted for so long after the correct soultion
was found and explained.
I wish that everyone involved would just pull them
selves together, and snap out of the dream worlds
they have been wandering around in ;-)
chris.li...@gmail.com
Second.
Chris
Kent Paul Dolan
> Perplexed in Peoria wrote:
> [...]
>> The second genetics-first school is associated
>> with Graham Cairns-Smith, and claims that the
>> first genes and first lifeforms were clay
>> crystals.
My understanding of this was that the genes or
lifeforms (which were the same thing at the time,
the "lifeforms" were so simple) were _assembled on
the surfaces of_ clay crystals, with the assistance
of convenient grooves characteristic of those
crystals, not that the crystals were themselves
included as part of those "lifeforms".
>> These lifeforms invented a simple metabolism;
>> then the clay genes+metabolism invented RNA; then
>> the combination of all three invented modern
>> metabolism and lost the clay somewhere along the
>> way.
Right. The clay is a substrate in which a free
floating replicator stub can embed itself, then,
using the grooves of that substrate, elongate itself
(the on-screen actions of some of Chris Langton's
Virtual Ants
http://www.google.com/search?q=chris.langton+virtual.ants
are extremely evocative here) eventually perhaps
spalling off stubs into the surrounding medium
which are sufficiently organized to set up
housekeeping in an unoccupied "nearby in time and
space" clay crystal groove.
One would guess that the success of this spalling
would be highly dependent on the length of the
underlying groove, and speculate that the evolution
of replicators which could succeed in many of the
available groove lengths would involve that
replicator looping a fraction of itself out of the
groove to adjust its in-groove length to the
distance to the groove's endpoint. This, in turn,
would lead to replicators evolving complex,
nonlinear structures while still elongating
themselves, at their growth points, in linear
grooves.
This, in turn, would allow for the evolving now
non-linear form to ingest one of its ends in that
enzyme-behaving "loop" and replicate enough
of its initial "sufficient" stub to seed lots of grooves.
Going a bit further, a cooperation, where one
RNA-like enitity feeds itself through the loop of
a sister, while relaxing its own loop to feed through
freely and be fully replicated, gives cooperative,
more complex structures. This could happen either
with both RNA-like structures initially still
(partially?) embedded in a clay crystal substrate
groove, one of them so embedded and one floating
free, or both floating free, so there is some time
independence as to which way and in which order this
part of the evolution might have occurred.
> [...]
>> So there are really four theories here. And the
>> best way to compare them is to list the major
>> problems which each theory fails to address. But
>> first, let us note that none of the four address
>> the classic chicken-egg problem in the origin of
>> life on Earth - the origin of coded protein
>> synthesis. And until that problem is cracked, no
>> theory of abiogenesis can claim victory.
> That problem has nothing to do with the origin of
> self-replicating, evolving systems - since it
> happened ***long*** after life first arose.
Agreed. Protein is a long way downstream of a
successful RNA-like self-replicator.
> IMO, all that need be noted by anyone from the
> four camps you mentioned is that "evolution did
> it" is a highly satisfying explanation for this
> piece of technology - or indeed practically any
> other subsequent development.
>> Other unsolved problems of the four theories:
>> Cairns-Smith: How could clay crystals provide
>> enough specific catalysis to invent the first
>> metabolism?
> /If/ we take "metabolism" to mean:
> http://en.wikipedia.org/wiki/Metabolism
I'd take almost none of that as given, it is too
descriptive of things as they are "today".
At the time point of the abiogenesis event, we don't
have stuff like enzymes yet.
Just cater for the bit: "dynamic energy budget",
that the available radiant energy, thermal energy,
and chemical potential energy get consumed in ways
that make the replication assembly versus
disassembly process run in the direction that favors
assembly and spawning of new replicators.
Only that much "metabolism" seems to be supportable
at the point in time of the abiogenesis event.
[Hmm, "point in time of the abiogenesis"
acronyms in the usual manner to PITA; bad, bad
idea, Kent. Even "PITOTAE" for "point in time
of the abiogenesis event" has great suckitude.
It looks too much like Dan Quayle trying to
spell something tuberous.]
> ...then that's pretty much the question of how
> clay organisms
I'll re-object here to the clay being characterized
as "organisms"; the clay substrate seems to be a
fairly passive catalyst rather than something whose
own, crystaline mode of reproduction is being in any
way enhanced by its interaction with organics at its
groove instances. That's a separate issue, it seems
to me. It _could_ have occurred that the organics
fed back replication enhancement to the crystal's
replication, creating an evolutionary cooperation,
but that idea of feedback doesn't seem _necessary_
to theorizing about clay crystal grooves evoking
abiogenesis.
> got to grips with the first organics - to which
> the answer seems to be that they grabbed them
> using grooves on their surfaces.
> There's a big literature these days about clays'
> abilities in this area - derived in part from the
> literature on industrial catalysts - but also
> because the fact
That's not a good place for the word "fact". Better
would be "advanced evidence-driven speculation".
> that clays played a role in the origin of life has
> become increasingly recognised.
> Why would clay organisms have started messing with
> organic chemistry?
No, again, to "clay organisms".
By the time some somethings are "organisms", they
are long past "starting" to mess with organic
chemistry, they are in it up to their nose-flaps.
> That is easy to answer in general - since use of
> organic compounds facilitate far more
> sophisticated chemistry and better technology -
> and evolution results in progressive technological
> development, with important discoveries
> accumulating over time.
This sounds a lot like teleological muddle-think.
Please try to say whatever you intended without any
of the "intensionality" you've put into that
paragraph.
> It's non-trivial to answer if the question is
> which aspects of organic chemistry came first -
That is an inherently nonsense phrase. "Organic
chemistry" is part of the structure of the universe
and its physical constants; none of it "came first".
Some organic _chemicals_ preceded others in time, a
whole different discussion.
> since there are so many things organic chemistry
> can be used for
That again suffers from smelling of teleology --
abiogenesis is no more purposeful than is evolution.
> and the specific details of which came first have
> been brushed over for almost the last four billion
> years.
Sorry, that's nonsense. To "brush over" something
requires a presiding intelligence. WHO has been
"brushing over" stuff during any but the last few
hundred years, since the atomic nature of matter was
first discovered, once again?
> My guess is that the first organics were grabbed
> as glue:
> http://originoflife.net/first_organics/
While Tim's page is pretty, it isn't too evocative
of what other folks think of with clay crystal
groove abiogenesis. For example, his "organics"
don't connect to one another via organic molecules
in that initial concept, they're just daubs of paste
at corners, and there's nothing visible to push them
to interconnect. In the case, there don't even need
to be grooves at all for the paste mechanism to
work, just pits. Mostly, he's just grasping for
some mechanism to lend the speed-up of evolution at
a point before abiogenesis has happened, to the
splendid amount of chemical energy, and reactive
chemical compound density, available at "hot smoker"
ocean benthic vents. I want that too, and have
posted about it here already, but I don't see that
he's got one yet with his "floating pile of pick-up
sticks" proposal.
> ...however, there are no shortage of other
> applications for organic molecules.
Again, you are talking as if _intent_ were involved.
[copied forward for further response]
>> Cairns-Smith:
>> How could clay crystals provide enough specific
>> catalysis to invent the first metabolism?
Perhaps that "catalysis" was merely providing a
substrate along which molecules aligned themselves
and attached, that constituted, with that alignment,
metabolisms in and of themselves? If you accept the
very limited version of "metabolism" I sketched
above, then the demands merely that the bookkeeping
come out favoring further assembly aren't all _that_
outlandish. Some fraction of all possible organic
compound assembly steps are already exothermic,
after all.
>> Having done so, why would they invent RNA?
They probably "invented" scads of stuff that
replicated "in the groove", some direct RNA
precursor happening to be the first one that
replicated successfully enough to free itself of the
substrate as a replicator. Had some other molecule
family come first to the post by a significant
timespan, life on earth would likely be very
different today; certainly the existing chirality
choices are mostly blind luck.
> Probably structural reasons. My impression is
> that this is the answer given in nearly all
> theories of the origin of RNA that aren't
> brain-dead ;-)
Well, if "something very like RNA" happens best to
fit some modestly likely particular groove, that's
likely to be as good a guess as we're going to get.
One thing I feel fairly confident about is that
before chemists and geophysicists are done, we will
have _several to many_ workable scenarios for
abiogenesis, and not a clue how to decide among
them. We are much closer now than we were even
twenty years ago to at least _one_ abiogenesis
scenario. Progress toward an abiogenesis
scenario since the first proofs that "lightning in a
feasible early earth atmosphere" made "interesting"
organic compounds looking very much like bits of
life, back in the 1950's, has been rapid and shows
no sign of slowing.
Much like densification of the human fossil record
in the same timespan has put Creationist crowing
about "missing links" on "mute", the few missing
parts still to be explained in abiogenesis scenarios
should make naysayers very careful what words they
put on record today only to eat them soon indeed.
FWIW
xanthian.
seem...@cyberspace.org
> > Perplexed in Peoria wrote:
> >> The second genetics-first school is associated
> >> with Graham Cairns-Smith, and claims that the
> >> first genes and first lifeforms were clay
> >> crystals.
>
> My understanding of this was that the genes or
> lifeforms (which were the same thing at the time,
> the "lifeforms" were so simple) were _assembled on
> the surfaces of_ clay crystals, with the assistance
> of convenient grooves characteristic of those
> crystals, not that the crystals were themselves
> included as part of those "lifeforms".
Cairns-Smith's theory is that the first
organisms were made entirely of clay minerals.
Their genetic information was encoded in
fault structures in the crystals, extended
via the processes of crystal growth and
reproduced by the crystals breaking at
right angles to their direction of growth.
By far the best resource for this theory is
Cairns-Smith's books, starting with:
Seven Clues to the Origin of Life -
a scientific detective story
- A. G. Cairns-Smith, Cambridge University Press, 1985;
There is /also/ the independent theory that clays
catalysed formation of organic polymers which were
used by early organisms.
That idea has been pursued particularly single-mindedly
by James P. Ferris - see the references to his work
on my links page:
http://originoflife.net/links/
Though the resulting research fits neatly with
Cairns-Smith's original idea, not all the supporters
of the "OOL clay catalyst" ideas buy into his original,
much-more-radical theory.
> > Why would clay organisms have started messing with
> > organic chemistry?
>
> No, again, to "clay organisms".
>
> By the time some somethings are "organisms", they
> are long past "starting" to mess with organic
> chemistry, they are in it up to their nose-flaps.
Not so - to emphasize in the point, in the Cairns-Smith
scenario the first organisms probably contained
no organic molecules whatsoever.
Organic molecules have all the wrong properties
for an early ancestor - in particular most organic
reactions are nowhere near reversible enough.
The presence of many carbon atoms would have
just gummed up the works.
In this scenario, the first organisms were made
*entirely* of kaolinite, montmorillite - or
some other clay mineral.
Their genome took the form of fault structures in
the crystal. Their phenotype consisted of properties
crystals have: brittleness, shape, texture - and so on.
When I refer to the theory as "crystalline ancestry"
I mean it *completely* literally - the idea is that
we are direct descendants of organisms which were
made entirely of inorganic crystals.
seem...@cyberspace.org
> seem...@cyberspace.org wrote:
[...]
> > use of organic compounds facilitate far more
> > sophisticated chemistry and better technology -
> > and evolution results in progressive technological
> > development, with important discoveries
> > accumulating over time.
>
> This sounds a lot like teleological muddle-think.
> Please try to say whatever you intended without any
> of the "intensionality" you've put into that
> paragraph.
[...]
> > since there are so many things organic chemistry
> > can be used for
>
> That again suffers from smelling of teleology --
> abiogenesis is no more purposeful than is evolution.
IMO, the exercise of trying to rid biology of teleological
language is pointless - and indeed counter-productive.
Worse, these days, the evolutionary process is directional
in nature, and contains embedded elements which include
intensionality and the ability to make reliable predictions.
This raises the possibility that physical evolution itself may
be well characterised as being a teleological process - and
this is an interpretation which I tend to favour.
I have a section on teleology towards the bottom of:
Dick
>Kent Paul Dolan wrote:
>> seem...@cyberspace.org wrote:
>
>[...]
>
>> > use of organic compounds facilitate far more
>> > sophisticated chemistry and better technology -
>> > and evolution results in progressive technological
>> > development, with important discoveries
>> > accumulating over time.
>>
>> This sounds a lot like teleological muddle-think.
>> Please try to say whatever you intended without any
>> of the "intensionality" you've put into that
>> paragraph.
>
>[...]
>
>> > since there are so many things organic chemistry
>> > can be used for
>>
>> That again suffers from smelling of teleology --
>> abiogenesis is no more purposeful than is evolution.
>
>IMO, the exercise of trying to rid biology of teleological
>language is pointless - and indeed counter-productive.
>
I think more discipline in word choice would be beneficial. Either
there is 'intent' or not. If Natural Selection cannot be expressed
without teleology, then there is a problem with the theory. Science
requires "discipline."
As an amateur, not even, I find myself confused by 'teleological
language.'
>Worse, these days, the evolutionary process is directional
>in nature, and contains embedded elements which include
>intensionality and the ability to make reliable predictions.
>
>This raises the possibility that physical evolution itself may
>be well characterised as being a teleological process - and
>this is an interpretation which I tend to favour.
There will always be alternative interpretations. Careful use of
words is an important step to exchanges of perspective. Sloppy word
definition leads to arguments where the substance of the argument is
forgotten.
>
>I have a section on teleology towards the bottom of:
>
>http://originoflife.net/direction/
Sorry, your article reads like a jumble of abstractions, the
conclusion is not supported by the abstractions. I throw out similar
distorted abstractions. I have an idea, but the words I choose are
not good containers for the thought and the thought may not be worth
the statement. I rely on responses to guide corrections in my mind.
I would offer specifics to your article, but I am too lazy.
dick
seem...@cyberspace.org
I suspect biology is not the field for you, then.
Biology is *full* of teleological language - selfish genes,
blind watchmakers, adaptations with functions - and so on.
There are several types of justification:
One is Mayr's:
``Mayr argues very strongly that the common use of teleological
language
by biologists is legitimate because it recognizes the
goal-directedness
of biological processes.''
- http://telicthoughts.com/?p=701
Another is that our language is intrinsically teleological -
and attempting to remove the teleological component makes
expressing things more tedious, long winded and complex.
Lastly, it should not be forgetten that the universe itself may
*literally* have a purpose. It appears that the universe is
running something a lot like like a large genetic algorithm.
That genetic algorithm may be running in order to caluclate
the result of an optimisation problem. That is what most
genetic algorithms I've encountered do.
If correct, that hypothesis would be a kind of ultimate justification
for the use of teleological language in biology.