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Colin Robinson
2012-Dec-31, 12:07 AM
from the thread "Copernican Fallacy and Numbers"


A serious question that I do not know the answer to:

Is there only one example of life on Earth? Could viral, eukarya, bacteria, and archaea be four examples of different types of life or are they definitively a single group?


These are organisms: (http://en.wikipedia.org/wiki/Organism)

They are classified as 'life'.
They all share a common biochemistry and genetic code: (http://en.wikipedia.org/wiki/Common_descent#Common_biochemistry_and_genetic_cod e) ...

This is also somewhat off-topic.

I agree with Solfe that this is a serious question. If it is off-topic for the thread it was asked in, why not a new thread for it?

It's true that viruses, eukarya, bacteria, and archaea have a common genetic code.

But viruses are not always classified as life. Even though they have the same sort of genetic code as cellular life (e.g. bacteria, archaea), their overall structure (morphology) is very different... Viruses don't metabolize, and they can only reproduce by using chemical machinery of the cells they infect.

Re the other three groups, eukarya, bacteria, and archaea, there are more similarities, though there are interesting differences too. For instance, bacteria and archaea have different sorts of cell walls. Many species of archaea produce methane, but no bacteria are known to do that. Some "metabolism first" models see the biochemical differences between bacteria and archaea as grounded in different cycles of pre-life chemistry.

The eukarya (amoebas, protozoa, sea-weed, humans etc) seem to be comparatively late arrivals. The mainstream view is that they (we) orginated from an archaea cell with a live bacterium inside it, in a symbiotic relationship.

Returning to the virus question, there are different theories of how they originated.

1. Are they cells which have become radically simplified?
2. Are they basically genetic material that escaped from cells, like a domestic animal which went feral?
3. Or were they originally self-replicating molecules in the primordial soup?

There has been a certain amount of debate re whether abiogenesis happened via a genes-first route (beginning with a self-replicating information-rich molecule such as RNA) or via a metabolism-first route (beginning with an auto-catalytic set of enzymes, or precursors of enzymes).

What if both theories are sorta right? Maybe proto-cells emerged via the metabolism-first route, but then viruses (based on nucleic acids) emerged via the genes-first route and began to use the catalytic materials in the proto-cells to make more viruses?

And perhaps the first bacteria and archaea appeared when some of the viruses took up permanent residence within some of the proto-cells, as internal symbionts?

Solfe
2012-Dec-31, 01:23 AM
Thanks Colin! My classes ended and I let all serious and deep thought go. :)

Paul Wally
2012-Dec-31, 12:02 PM
from the thread "Copernican Fallacy and Numbers"

I agree with Solfe that this is a serious question. If it is off-topic for the thread it was asked in, why not a new thread for it?

It's true that viruses, eukarya, bacteria, and archaea have a common genetic code.

But viruses are not always classified as life. Even though they have the same sort of genetic code as cellular life (e.g. bacteria, archaea), their overall structure (morphology) is very different... Viruses don't metabolize, and they can only reproduce by using chemical machinery of the cells they infect.

Re the other three groups, eukarya, bacteria, and archaea, there are more similarities, though there are interesting differences too. For instance, bacteria and archaea have different sorts of cell walls. Many species of archaea produce methane, but no bacteria are known to do that. Some "metabolism first" models see the biochemical differences between bacteria and archaea as grounded in different cycles of pre-life chemistry.

The eukarya (amoebas, protozoa, sea-weed, humans etc) seem to be comparatively late arrivals. The mainstream view is that they (we) orginated from an archaea cell with a live bacterium inside it, in a symbiotic relationship.

Returning to the virus question, there are different theories of how they originated.

1. Are they cells which have become radically simplified?
2. Are they basically genetic material that escaped from cells, like a domestic animal which went feral?
3. Or were they originally self-replicating molecules in the primordial soup?

There has been a certain amount of debate re whether abiogenesis happened via a genes-first route (beginning with a self-replicating information-rich molecule such as RNA) or via a metabolism-first route (beginning with an auto-catalytic set of enzymes, or precursors of enzymes).

What if both theories are sorta right? Maybe proto-cells emerged via the metabolism-first route, but then viruses (based on nucleic acids) emerged via the genes-first route and began to use the catalytic materials in the proto-cells to make more viruses?

And perhaps the first bacteria and archaea appeared when some of the viruses took up permanent residence within some of the proto-cells, as internal symbionts?

I think that symbiosis is the key. It's just one of those fundamental principles that explains a lot, much like evolution. My first guess is to work within the the metabolism first paradigm and then try to see how different kinds of symbiotic relationships can emerge within such a dynamic system. What I like about metabolism first is that it doesn't draw explicit distinction between organism and environment, i.e. everything is just one whole chemical system.

My inclination is therefore more towards option 3) Viruses were originally self-replicating molecules in the primordial soup. If 3) was indeed the case then what must have happened is that the primordial soup gradually became incorporated intra-cellularly within organisms because of the various symbiotic relations that began to emerge. This process then continued until there was no more extra-cellular primordial soup left for viruses to replicate themselves. It then follows that the only places where viruses can still find the much needed primordial soup are inside the cells of other organisms.

Colin Robinson
2013-Jan-01, 01:47 AM
I think that symbiosis is the key. It's just one of those fundamental principles that explains a lot, much like evolution.

It does. At the same time, it raises questions about how we think of the "tree of life". The way pictures of the tree of life have often been drawn, it's all about divergence, branching out, one species becoming many... But the Margulis concept of the origin of eukaryotes suggests that it sometimes goes the other way — two or more species become one, like multiple roots converging into a single stem.

If a similar, but earlier event gave rise to "life as we know it" — i.e., by a protocell with cytoplasm and enzyme-like catalysts but no nucleic acid, forming a symbiosis with a virus which had nucleic acid but no cytoplasm — then simplistic pictures of the "tree of life" would require further redrafting... And the origin of life would have to be thought of as a sequence of events rather than a single event.


My first guess is to work within the the metabolism first paradigm and then try to see how different kinds of symbiotic relationships can emerge within such a dynamic system. What I like about metabolism first is that it doesn't draw explicit distinction between organism and environment, i.e. everything is just one whole chemical system.

Yes, it is somewhat comparable to crystals emerging out of a solution...

Ara Pacis
2013-Jan-01, 07:07 PM
I prefer to think of viruses not as living but more like undead. The V is Z.

Selfsim
2013-Jan-01, 10:29 PM
I think that symbiosis is the key. It's just one of those fundamental principles that explains a lot, much like evolution.Symbiosis doesn't have to be 'key'.

Plasmids (http://en.wikipedia.org/wiki/Plasmids) aren't classified as 'life', but are capable of autonomous replication, (ie: no symbiosis is necessary in this case), and also carry genes necessary for survival, (as well)

'Replicons' (http://en.wikipedia.org/wiki/Replicon_(genetics)) are classified as DNA or RNA molecules, (or regions thereof), that replicate from a single centre, (or origin of replication (http://en.wikipedia.org/wiki/Origin_of_replication)). A common characteristic for replication seems to be a high 'AT' (Adenine-Thymine) content, (two hydrogen bonds), although this seems to be neither necessary nor sufficient, in order to infer causation .. (either in modern-day life, nor in pre-biotic models).

Paul Wally
2013-Jan-01, 11:18 PM
It does. At the same time, it raises questions about how we think of the "tree of life". The way pictures of the tree of life have often been drawn, it's all about divergence, branching out, one species becoming many... But the Margulis concept of the origin of eukaryotes suggests that it sometimes goes the other way — two or more species become one, like multiple roots converging into a single stem.

Very interesting! I'm wondering now whether there are not game-theoretic models of this Margulis concept. Cooperation is as important a factor to consider as competition. Perhaps, from such a model it might be possible to see when and under what kind of conditions cooperation presents a greater evolutionary advantage.



If a similar, but earlier event gave rise to "life as we know it" — i.e., by a protocell with cytoplasm and enzyme-like catalysts but no nucleic acid, forming a symbiosis with a virus which had nucleic acid but no cytoplasm — then simplistic pictures of the "tree of life" would require further redrafting... And the origin of life would have to be thought of as a sequence of events rather than a single event.

I do tend to look at abiogenesis as a process rather than an event. Say for instance that it was a particular event occurring at some specific location like some particular deep sea vent, then this leads to the question of why there weren't several such events occurring at different deep sea vents, and this naturally leads to the question of why we seem to have only one origin. One solution to this problem would then be that there were several origins but somehow only one dominated. Another possible solution is that several of these original lines converged, as you say, to form one. But then there's viruses, a very interesting problem that you're raising here. They just don't seem to quite fit into this picture.

There is this idea that I've had for a while now. I'm wondering if we shouldn't look at abiogenesis as a global process, rather than some particular sequence of events that happened at some particular location. Yes, there are random local processes, but the statistics of these processes tend to play out on a global scale such that there is eventually some homogeneity in terms of the types that eventually emerge globally. So perhaps there wasn't an original first individual organism but more something like an original type or types that emerged globally. This global emergence would then be similar to a phase transition, only it occurs over geological timescales. Take for instance the Cambrian explosion. To me it really looks like a phase transition phenomenon.

Paul Wally
2013-Jan-01, 11:42 PM
Plasmids (http://en.wikipedia.org/wiki/Plasmids) aren't classified as 'life', but are capable of autonomous replication, (ie: no symbiosis is necessary in this case), and also carry genes necessary for survival, (as well)



They do say in the article that these plasmids require a "suitable host" in order to replicate. So it seems they cannot replicate in the external environment.

Selfsim
2013-Jan-02, 12:55 AM
They do say in the article that these plasmids require a "suitable host" in order to replicate. So it seems they cannot replicate in the external environment.True .. and a lot seems to depend on the defintion of 'symbiosis' which itself, seems to not be particularly well defined or agreed.

Eg: on Symbiosis: (http://en.wikipedia.org/wiki/Symbiosis)

The definition of symbiosis is controversial among scientists. Some believe symbiosis should only refer to persistent mutualisms, while others believe it should apply to any types of persistent biological interactions (i.e. mutualistic, commensalistic, or parasitic).

From the Wiki Plasmid page:

Microbial transformation with plasmid DNA is neither parasitic nor symbiotic in nature, because each implies the presence of an independent species living in a commensal or detrimental state with the host organism.

Given the difficulty in defining Symbosis, would it be a sound basis for a 'global' model? Why?

Colin Robinson
2013-Jan-02, 01:19 AM
Symbiosis doesn't have to be 'key'.

Plasmids (http://en.wikipedia.org/wiki/Plasmids) aren't classified as 'life', but are capable of autonomous replication, (ie: no symbiosis is necessary in this case), and also carry genes necessary for survival, (as well)

Thanks for the comment, and the link to the WP articles. According to the WP page about plasmids, it is not exactly a matter of symbiosis being unnecessary. The page says plasmids only replicate "within a suitable host". This is not considered symbiosis, simply because the plasmid is not considered an independent species, even though it replicates "autonomously" within its host cell. A plasmid cannot encase itself in protein to migrate from one cell to another, as a virus does.

Selfsim
2013-Jan-02, 01:28 AM
There is this idea that I've had for a while now. I'm wondering if we shouldn't look at abiogenesis as a global process, rather than some particular sequence of events that happened at some particular location. Yes, there are random local processes, but the statistics of these processes tend to play out on a global scale such that there is eventually some homogeneity in terms of the types that eventually emerge globally.

So perhaps there wasn't an original first individual organism but more something like an original type or types that emerged globally. This global emergence would then be similar to a phase transition, only it occurs over geological timescales. Take for instance the Cambrian explosion. To me it really looks like a phase transition phenomenon.Positing abiogenesis as a phase transition, doesn't necessarily allow for any better predictions at a global level.

The problem would then seem to merely shift to the problem of defining 'global' and 'local'(??)

Colin Robinson
2013-Jan-02, 01:33 AM
Very interesting! I'm wondering now whether there are not game-theoretic models of this Margulis concept. Cooperation is as important a factor to consider as competition. Perhaps, from such a model it might be possible to see when and under what kind of conditions cooperation presents a greater evolutionary advantage.

Yes, there has been work on application of game theory to cooperation between species. The WP page evolutionary game theory (http://en.wikipedia.org/wiki/Evolutionary_game_theory) has a section "Co-evolution" with information about this.


I do tend to look at abiogenesis as a process rather than an event. Say for instance that it was a particular event occurring at some specific location like some particular deep sea vent, then this leads to the question of why there weren't several such events occurring at different deep sea vents, and this naturally leads to the question of why we seem to have only one origin. One solution to this problem would then be that there were several origins but somehow only one dominated. Another possible solution is that several of these original lines converged, as you say, to form one. But then there's viruses, a very interesting problem that you're raising here. They just don't seem to quite fit into this picture.

If it's true (as the metabolism-first models suggest) that there were proto-cells contains enzyme-like catalysts before there were nucleic-acid genes, this means viruses as we know them (being nucleic acid based) appeared on the scene after proto-cells.

Maybe viruses (on one hand) and chromosomal DNA (on the other) can be thought of as related systems which, in the language of game theory, adopted two different strategies. The virus adopted a predatory strategy in relation to a proto-cell — using the proto-cell to help the virus replicate, and in the process destroying the proto-cell.

Meanwhile, the virus' relative which became the chromosomal DNA adopted a mutualistic strategy, where it too used a host proto-cell to help it replicate, but did so in a way that did not destroy the host but enhanced the host's survival.


There is this idea that I've had for a while now. I'm wondering if we shouldn't look at abiogenesis as a global process, rather than some particular sequence of events that happened at some particular location. Yes, there are random local processes, but the statistics of these processes tend to play out on a global scale such that there is eventually some homogeneity in terms of the types that eventually emerge globally. So perhaps there wasn't an original first individual organism but more something like an original type or types that emerged globally. This global emergence would then be similar to a phase transition, only it occurs over geological timescales. Take for instance the Cambrian explosion. To me it really looks like a phase transition phenomenon.

Yes, I agree it makes more sense to think of it as a global transition... Perhaps another analogy is the formation of the planets from their primordial nebula.

No-one seems to raise questions like why don't we observe new planets forming in the solar system now? or why haven't we created a new planet in a laboratory?

Colin Robinson
2013-Jan-02, 01:42 AM
True .. and a lot seems to depend on the defintion of 'symbiosis' which itself, seems to not be particularly well defined or agreed.

Eg: on Symbiosis: (http://en.wikipedia.org/wiki/Symbiosis)


From the Wiki Plasmid page:


Given the difficulty in defining Symbosis, would it be a sound basis for a 'global' model? Why?

Lots of scientific terms have multiple definitions. Have you ever looked at all the different definitions of the chemical term "acid"?

Paul Wally
2013-Jan-02, 02:10 AM
True .. and a lot seems to depend on the defintion of 'symbiosis' which itself, seems to not be particularly well defined or agreed.

Wikipedia
The definition of symbiosis is controversial among scientists. Some believe symbiosis should only refer to persistent mutualisms, while others believe it should apply to any types of persistent biological interactions (i.e. mutualistic, commensalistic, or parasitic).


I go with latter definition: "... any types of persistent biological interactions (i.e. mutualistic, commensalistic, or parasitic)" What I proposed earlier, is that we look at these interactions in terms of game theory, i.e. the dynamics of competitive behaviour vs cooperative behaviour.




Wikipedia
Microbial transformation with plasmid DNA is neither parasitic nor symbiotic in nature, because each implies the presence of an independent species living in a commensal or detrimental state with the host organism.
Given the difficulty in defining Symbosis, would it be a sound basis for a 'global' model? Why?

I think in this case what they mean by 'symbiotic' is mutualistic, and not the more general concept of 'persistent biological interactions'.

On the global model idea, I think, combining game theory and evolution through natural selection could yield interesting results, perhaps even for a very simple model. You see, environment does not only include the abiotic. It also includes other organisms, so this naturally means that we have to look at how organisms interact and what types of interactions would tend to persist. Viruses persisted because of a parasitic interaction, while cell organels persisted through mutual cooperation. Both types of interaction are instances of the broader definition of symbiosis.

whimsyfree
2013-Jan-02, 03:09 AM
I do tend to look at abiogenesis as a process rather than an event. Say for instance that it was a particular event occurring at some specific location like some particular deep sea vent, then this leads to the question of why there weren't several such events occurring at different deep sea vents, and this naturally leads to the question of why we seem to have only one origin. One solution to this problem would then be that there were several origins but somehow only one dominated. Another possible solution is that several of these original lines converged, as you say, to form one.


There are numerous reasons why all current organisms might appear to descend from a single abiogenesis:

Abiogenesis is very unlikely;
Conditions changed to ones unsuitable for abiogenesis (e.g. from a reducing to an oxidizing environment);
Abiogenesis occurred multiple times but subsequent generations of life were unable to compete with the established one.


Multiple early lines may have converged but this must have happened very early.


But then there's viruses, a very interesting problem that you're raising here. They just don't seem to quite fit into this picture.


They could be independent lines of replicators that failed to make the transition but nevertheless co-evolved with those that did.


There is this idea that I've had for a while now. I'm wondering if we shouldn't look at abiogenesis as a global process, rather than some particular sequence of events that happened at some particular location. Yes, there are random local processes, but the statistics of these processes tend to play out on a global scale such that there is eventually some homogeneity in terms of the types that eventually emerge globally. So perhaps there wasn't an original first individual organism but more something like an original type or types that emerged globally. This global emergence would then be similar to a phase transition, only it occurs over geological timescales.


AFAIK the evidence is that if this happened then this original type consolidated to become the LUCA fairly rapidly (in geological time).


Take for instance the Cambrian explosion. To me it really looks like a phase transition phenomenon.

Not sure what you mean. The idea that a large number of lines concurrently underwent a complexity explosion would be ATM, would it not?

Colin Robinson
2013-Jan-03, 02:27 AM
There are numerous reasons why all current organisms might appear to descend from a single abiogenesis:

Abiogenesis is very unlikely;
Conditions changed to ones unsuitable for abiogenesis (e.g. from a reducing to an oxidizing environment);
Abiogenesis occurred multiple times but subsequent generations of life were unable to compete with the established one.


Multiple early lines may have converged but this must have happened very early.

What if living cells as we know them (including bacteria and archaea) derive from a merger between

* a proto-cell (containing an autocatalytic set of enzyme-like molecules but no DNA or RNA of its own); and
* a virus-like agent (containing DNA and/or RNA) which found its way into the proto-cell and stayed there as an endo-symbiont?

Would that qualify as "very early"?

Paul Wally
2013-Jan-03, 11:47 PM
Positing abiogenesis as a phase transition, doesn't necessarily allow for any better predictions at a global level.

Maybe it could work. That strategy worked quite well with statistical thermodynamics where we are now able to predict the behavior of macroscopic observables like temperature change based on the statistics of large ensembles of microscopic particles in random motion.


The problem would then seem to merely shift to the problem of defining 'global' and 'local'(??)

It's still unclear, but for now, I'll define 'global' as the biosphere system level, consisting of species, their interactions with each other and with the general abiotic environment. 'Local' would be things like individual organisms, individual chemical processes, occurring at particular space-time locations within the biosphere.

Paul Wally
2013-Jan-04, 01:02 AM
There are numerous reasons why all current organisms might appear to descend from a single abiogenesis:

Abiogenesis is very unlikely;
Conditions changed to ones unsuitable for abiogenesis (e.g. from a reducing to an oxidizing environment);
Abiogenesis occurred multiple times but subsequent generations of life were unable to compete with the established one.



I would like to add another possibility. There appears to be one abiogenesis because there is one system. So what I'm really proposing is that abiogenesis is a system level emergent process rather than some localized event that just happened to have occurred at some particular place and time.



They could be independent lines of replicators that failed to make the transition but nevertheless co-evolved with those that did.

If viruses were independent lines of replicators then they must have been self-replicating, and then lost that capability somehow as they became dependent on other organisms for that function. But as I proposed earlier, the environment could have changed in such a way that it was no longer possible for viruses to self-replicate.


Not sure what you mean. The idea that a large number of lines concurrently underwent a complexity explosion would be ATM, would it not?

Why? Isn't that exactly what the Cambrian explosion was, a complexity explosion? Now I read up a bit on the Cambrian explosion in Wikipedia, after reading your post. There I found a link to an interesting paper, Sole,Fernandez and Kauffman (2003), Adaptive walks in a gene network model of morphogenesis: Insights into the Cambrian explosion .

I didn't get time to read the whole paper in detail yet, but here's an extract from p.629. I underlined the relevant concepts.


Sole,Fernandez and Kauffman (2003), Adaptive walks in a gene network model of morphogenesis: Insights into the Cambrian explosion

The jump in pattern diversity experienced at H = G = 2 indicates
that thresholds in network complexity, even at small-gene
numbers exist and can lead to combinatorial explosions. Such
explosions would open a whole spectrum of available structures.
Reaching such a threshold might require the formation
of a minimal regulatory network and might also require other
prerequisites dealing with body size, cellular interactions and
tissue specialization. However, once in place, the whole universe
of patterns can be made suddenly available.

Paul Wally
2013-Jan-04, 01:45 AM
Yes, there has been work on application of game theory to cooperation between species. The WP page evolutionary game theory (http://en.wikipedia.org/wiki/Evolutionary_game_theory) has a section "Co-evolution" with information about this.

Thanks for that Colin. Quite a rich literature on the subject. I'll try and find a game theory model specifically for Endosymbiosis, if/when I get time.




If it's true (as the metabolism-first models suggest) that there were proto-cells contains enzyme-like catalysts before there were nucleic-acid genes, this means viruses as we know them (being nucleic acid based) appeared on the scene after proto-cells.

A bit of a side issue: How did these proto-cells self-replicate without genetic material (If I understand you correctly)?

Another question: According to this hypothesis, did viruses and other nucleic acid based structures emerge from within the protocells or from the external environment.



Maybe viruses (on one hand) and chromosomal DNA (on the other) can be thought of as related systems which, in the language of game theory, adopted two different strategies. The virus adopted a predatory strategy in relation to a proto-cell — using the proto-cell to help the virus replicate, and in the process destroying the proto-cell.

Meanwhile, the virus' relative which became the chromosomal DNA adopted a mutualistic strategy, where it too used a host proto-cell to help it replicate, but did so in a way that did not destroy the host but enhanced the host's survival.

Interesting. So you think a chromosome is a type of virus? The only difficulty I have is that if both chromosomes and viruses used the proto-cell to replicate then how did they replicate before that? Surely if they were species, they must have been self-replicating, but why use the proto-cell for that function when they already have that function, or am I missing something here?

A.DIM
2013-Jan-04, 03:13 AM
Tangentially relevant: In Memoriam .... (http://www.astrobio.net/pressrelease/5240/in-memoriam-carl-woese)

The astrobiology community deeply mourns the loss of Dr. Carl Woese, the University of Illinois microbiology professor credited with the discovery of a “third domain” of life.
...
In 1977, Dr. Woese and his colleagues overturned a universally held assumption about the basic structure of the tree of life. Microbes known as archaea are as distinct from bacteria as plants and animals are, they wrote in a published paper. Prior to this finding, scientists had lumped archaea together with bacteria and asserted that the tree of life had two main branches — bacteria (called prokarya), and everything else (eukarya). Their discovery added archaea as a third main branch of the evolutionary family tree.


It wasn't so long ago mainstream thinking was overturned what regards life and its domains.
No doubt it, mainstream thinking, will be upended again; that's pretty much how it works.

Colin Robinson
2013-Jan-04, 04:30 AM
A bit of a side issue: How did these proto-cells self-replicate without genetic material (If I understand you correctly)?

The hypothesis is that they relied on what is called compositional information, rather than coded information. If you have a workshop containing various machines, and you want to make a duplicate of the workshop, you could do that in 2 different ways:

1. Keep a written list of all the different items, and work from that list to make a set of duplicate items. Also make a copy of the list, to go in the new worshop. (Coded information method)
2. Go through the workshop and just duplicate each piece of machinery without ever bothering to make a list. (Compositional information method)

Would gene-less reproduction work for a proto-cell?

Some recent discussion about this question is summarized in section 2.2 of the paper The algorithmic origins in life by Sara Walker and Paul Davies (http://rsif.royalsocietypublishing.org/content/10/79/20120869.full), which Selfsim brought to our attention in another thread:

"The heritable information in this case typically consists of the compositional ratios of the molecules in the organized assemblies. Although it has been suggested that such ‘composomes’ might provide a primitive inheritance mechanism [51,52], it is not clear that they are evolvable, since compositional information tends to degrade over successive generations inhibiting the capacity for open-ended evolution [53] (see [54] for a recent discussion of how such systems could be evolvable if possessing excess mutual catalysis)."


Another question: According to this hypothesis, did viruses and other nucleic acid based structures emerge from within the protocells or from the external environment.

It could conceivably have happened either way...


Interesting. So you think a chromosome is a type of virus? The only difficulty I have is that if both chromosomes and viruses used the proto-cell to replicate then how did they replicate before that? Surely if they were species, they must have been self-replicating,

If the first viruses appeared later than the first proto-cells, maybe the viruses never replicated without using proto-cells, just as viruses today don't replicate without using cells, although they can travel between cells in dormant form. The early viruses still would have been species, in the same sense as viruses today are species.

Alternatively, maybe there were enough chemical building blocks in the general environment that the early viruses could replicate outside cells, even though viruses today cannot.


but why use the proto-cell for that function when they already have that function, or am I missing something here?

Perhaps because, even if they could replicate outside the proto-cells, they could replicate faster and easier by using the proto-cells' catalytic resources.

Why did we humans ever start using horses for transport, when we already had legs?

Jens
2013-Jan-04, 05:13 AM
Maybe viruses (on one hand) and chromosomal DNA (on the other) can be thought of as related systems which, in the language of game theory, adopted two different strategies. The virus adopted a predatory strategy in relation to a proto-cell — using the proto-cell to help the virus replicate, and in the process destroying the proto-cell.

Meanwhile, the virus' relative which became the chromosomal DNA adopted a mutualistic strategy, where it too used a host proto-cell to help it replicate, but did so in a way that did not destroy the host but enhanced the host's survival.



I've never heard that about nuclear DNA, but I think that is a fairly well respected idea with regard to mitochondria, so I don't think it's all that far out as an idea.

Paul Wally
2013-Jan-05, 12:53 AM
The hypothesis is that they relied on what is called compositional information, rather than coded information. If you have a workshop containing various machines, and you want to make a duplicate of the workshop, you could do that in 2 different ways:

1. Keep a written list of all the different items, and work from that list to make a set of duplicate items. Also make a copy of the list, to go in the new worshop. (Coded information method)
2. Go through the workshop and just duplicate each piece of machinery without ever bothering to make a list. (Compositional information method)

Would gene-less reproduction work for a proto-cell?

Some recent discussion about this question is summarized in section 2.2 of the paper The algorithmic origins in life by Sara Walker and Paul Davies (http://rsif.royalsocietypublishing.org/content/10/79/20120869.full), which Selfsim brought to our attention in another thread:

"The heritable information in this case typically consists of the compositional ratios of the molecules in the organized assemblies. Although it has been suggested that such ‘composomes’ might provide a primitive inheritance mechanism [51,52], it is not clear that they are evolvable, since compositional information tends to degrade over successive generations inhibiting the capacity for open-ended evolution [53] (see [54] for a recent discussion of how such systems could be evolvable if possessing excess mutual catalysis)."


So here we have different replication mechanisms, and it seems they emerged independently and then combined into one later. This leads me to wonder that if evolution tends to produce diversity of forms then why didn't the same type of diversity happen in the case of different replication mechanisms. If it was indeed the case that the emergence of different replication mechanisms were possible within the primordial soup then why didn't they simply become more diverse instead of doing the exact opposite.


If the first viruses appeared later than the first proto-cells, maybe the viruses never replicated without using proto-cells, just as viruses today don't replicate without using cells, although they can travel between cells in dormant form. The early viruses still would have been species, in the same sense as viruses today are species.

So where do we put the original virus; inside or outside the proto-cell. Perhaps the proto-cell is the problem. Perhaps we should remove the cell membrane then there's no longer a topological problem of inside/ouside dichotomy :). But then we lose our concept of individual organism and then all we have is a vast chemical network. How do cell membranes/vacuoles emerge within a vast chemical network - another problem for another thread maybe. It's just that these vacuoles, they like to form.

Getting back to the proto-cell hypothesis: We could look at these proto-cells as accumulators of nutrients, whereas other replicators would just use what they need from their environment. But as the accumulators increase in number, the nutrients in the environment should become scarcer. That should then lead to increased competition between the non-accumulating replicators. Eventually they start competing for access to the accumulators. The cell membrane of the proto-cell is a selective mechanism, but in this case also a mechanism for natural selection. It follows then that only those replicators capable of getting through the proto-cell membrane gets selected.





Perhaps because, even if they could replicate outside the proto-cells, they could replicate faster and easier by using the proto-cells' catalytic resources.

Why did we humans ever start using horses for transport, when we already had legs?

Ok, got it.

Paul Wally
2013-Jan-05, 01:05 AM
The hypothesis is that they relied on what is called compositional information, rather than coded information. If you have a workshop containing various machines, and you want to make a duplicate of the workshop, you could do that in 2 different ways:

1. Keep a written list of all the different items, and work from that list to make a set of duplicate items. Also make a copy of the list, to go in the new worshop. (Coded information method)
2. Go through the workshop and just duplicate each piece of machinery without ever bothering to make a list. (Compositional information method)

Would gene-less reproduction work for a proto-cell?

Some recent discussion about this question is summarized in section 2.2 of the paper The algorithmic origins in life by Sara Walker and Paul Davies (http://rsif.royalsocietypublishing.org/content/10/79/20120869.full), which Selfsim brought to our attention in another thread:

"The heritable information in this case typically consists of the compositional ratios of the molecules in the organized assemblies. Although it has been suggested that such ‘composomes’ might provide a primitive inheritance mechanism [51,52], it is not clear that they are evolvable, since compositional information tends to degrade over successive generations inhibiting the capacity for open-ended evolution [53] (see [54] for a recent discussion of how such systems could be evolvable if possessing excess mutual catalysis)."


So here we have different replication mechanisms, and it seems they emerged independently and then combined into one later. This leads me to wonder that if evolution tends to produce diversity of forms then why didn't the same type of diversity happen in the case of different replication mechanisms. If it was indeed the case that the emergence of different replication mechanisms were possible within the primordial soup then why didn't they simply become more diverse instead of doing the exact opposite.


If the first viruses appeared later than the first proto-cells, maybe the viruses never replicated without using proto-cells, just as viruses today don't replicate without using cells, although they can travel between cells in dormant form. The early viruses still would have been species, in the same sense as viruses today are species.

So where do we put the original virus; inside or outside the proto-cell? Perhaps the proto-cell is the problem. Perhaps we should remove the cell membrane then there's no longer a topological problem of inside/ouside dichotomy :). But then we lose our concept of individual organism and then all we have is a vast chemical network. How do cell membranes/vacuoles emerge within a vast chemical network - another problem for another thread maybe. It's just that these vacuoles, they like to form.

Getting back to the proto-cell hypothesis: We could look at these proto-cells as accumulators of nutrients, whereas other replicators would just use what they need from their environment. But as the accumulators increase in number the nutrients in the environment should become scarcer. That should then lead to increased competition between the non-accumulating replicators. Eventually they start competing for access to the accumulators. The cell membrane of the proto-cell is a selective mechanism, but in this case also a mechanism for natural selection. It follows then that only those replicators capable of getting through the proto-cell membrane gets selected.





Perhaps because, even if they could replicate outside the proto-cells, they could replicate faster and easier by using the proto-cells' catalytic resources.

Why did we humans ever start using horses for transport, when we already had legs?

Ok, got it.

Colin Robinson
2013-Jan-05, 07:41 AM
So here we have different replication mechanisms, and it seems they emerged independently and then combined into one later. This leads me to wonder that if evolution tends to produce diversity of forms then why didn't the same type of diversity happen in the case of different replication mechanisms. If it was indeed the case that the emergence of different replication mechanisms were possible within the primordial soup then why didn't they simply become more diverse instead of doing the exact opposite.

Perhaps because one method of replication gave a clear advantage in efficiency compared to the other...

The trouble with a compositional method of replication is that to avoid loss of information you need information back-up (redundancy), which you can only achieve by means of "excess mutual catalysis".

But that presumably means you need extra catalytic machinery in your workshop.

Whereas a gene-based system gives you your information back-up in the form comparable to a concise written list of your machinery and how to replace it...

As the Sara Walker/Paul Davies article says, genes are a digital method of storing and processing information, whereas "composomes" are an analog method. In the history of technology, analog devices came first, because they are easier to invent, but digital devices have gradually taken over, because they are better information handlers.


Getting back to the proto-cell hypothesis: We could look at these proto-cells as accumulators of nutrients, whereas other replicators would just use what they need from their environment. But as the accumulators increase in number the nutrients in the environment should become scarcer. That should then lead to increased competition between the non-accumulating replicators. Eventually they start competing for access to the accumulators. The cell membrane of the proto-cell is a selective mechanism, but in this case also a mechanism for natural selection. It follows then that only those replicators capable of getting through the proto-cell membrane gets selected.

Maybe one way of looking at it, is that an enzyme-based protocell would have been good at concentrating nutrients, whereas an RNA-based replicator would have been good at concentrating information... When the two sorts of system began to work together, it was a winning combination.

However because replicators were (in a sense) smarter than the protocells, they also had another very attractive evolutionary strategy -- manoevre your way inside the protocell and reorganize it into a very short-lived replicator factory, which is what viruses do to cells today.

Paul Wally
2013-Jan-05, 12:00 PM
As the Sara Walker/Paul Davies article says, genes are a digital method of storing and processing information, whereas "composomes" are an analog method. In the history of technology, analog devices came first, because they are easier to invent, but digital devices have gradually taken over, because they are better information handlers.



I think I remember now. This is where we had our little disgreement on information in living organisms. My view is still that the digital information idea is at best a useful analogy for modeling purposes. My reasoning is that it is not at all clear what constitutes information and what is not information within natural systems, whereas in technology we define what counts as information and what is irrelevant and then design the system according to that convention.

Xibalba
2013-Jan-05, 03:03 PM
I thought that maybe other forms of life appeared early on the Earth... but if that happened, it is now gone. Exterminated by our ancestors? Unable to adapt to its environment? I don't know, but if it was there, it is no more...

lpetrich
2013-Jan-10, 07:17 PM
So long, and thanks for all the Archaea » Pharyngula (http://freethoughtblogs.com/pharyngula/2012/12/30/so-long-and-thanks-for-all-the-archaea/)
Carl R. Woese: 1928 – 2012 | The Institute for Genomic Biology (http://www.igb.illinois.edu/news/carl-r-woese-1928-%E2%80%93-2012)

His greatest discovery was a major revision of the overall tree of life.

When he started to get to work on that question in the mid-1970's, he and his colleagues believed that the biggest distinction was between prokaryotes and eukaryotes. But he wanted to learn more. He looked for some biological molecule that might be ubiquitous and convenient to sequence, and he decided on small-subunit ribosomal RNA (SSU rRNA). Back then, it was difficult to sequence a whole strand, so he cut it up with an enzyme and then sequenced the fragments. But that proved good enough.

Typical sizes of ribosomal-RNA strands:
Escherichia coli bacterium: small: 1542 nt, large: 2906 nt
Human: small: 1869 nt, large: 5070 nt, some extras: 121 nt, 156 nt
nt = nucleotides

He put a lot of organisms' SSU rRNA through his sequencing setup, and he compared the sequences that he found.


He made a remarkable discovery, which he published in 1977. There was a deep split in the prokaryotes, a split so deep that it was comparable to the split with the eukaryotes that he also found.

On one side were most of the more familiar prokaryotes, like disease organisms. On the other side was a motley collection of mostly free-living organisms that are often averse to oxygen, and that sometimes inhabit extreme conditions like great heat and acidity. That other side seemed to CW to be the sort of organisms that would do well in the early Earth before the emergence of oxygen-releasing photosynthesis. He decided to named them "archaebacteria" or Archaea. The more familiar ones he named Eubacteria or Bacteria.

So he came up with a classification featuring three side-by-side domains: Eubacteria, Archaea, and Eukarya (eukaryotes).


At first, CW's split of the prokaryotes did not seem very well-supported to some biologists -- the Eubacteria and Archaea seemed more alike than different. However, subsequent research found other gene sequences and various phenotypic features that are consistent with this early split, and by the late 1980's, Woese's three-domain system had become generally accepted. Features like:

DNA-polymerase structure - that's the enzyme that replicates the DNA in the genome
Membrane-lipid structure

Opposite asymmetries of the glycerol's central carbon
Fatty acids -- A: isoprene polymer (branched-chain), B: straight chain
Fatty acids to glycerol -- A: ether-linked, B: ester-linked
Some Archaea have membrane lipids that extend across the cell membrane

Initial amino acid of a protein -- A: methionine, B: formylmethionine
Resistance to various antibiotics, diphtheria toxin, etc.


But over the last decade or so, a challenge has emerged to CW's three-domain system: the status of Eukarya. By the late 1980's, the endosymbiotic origin of mitochondria and chloroplasts had become well-established, but what about the rest of the cell?

As far as can be determined, the informational systems of Eukarya are much like those of Archaea, while many metabolic enzymes are closer to Eubacteria. So was the ancestral eukaryote an archaeon-eubacterium symbiosis?

Even more difficult for CW's three-domain system is where the eukaryote informational systems branched off from. The three-domain system would picture branching off before the diversification of the ancestors of the present-day Archaea. But there are some studies that claim that those systems branched off from inside Archaea. So we go from 3 to 2 taxa in the highest-level branching of the Tree of Life.

Let's see what's happened over the centuries.

Aristotle ~350 BCE, Carolus Linnaeus 1735: Plantae, Animalia
Ernst Haeckel 1866: Protista, Plantae, Animalia
Herbert F. Copeland 1938: Monera, Protista, Plantae, Animalia (Monera = prokaryotes)
Édouard Chatton, Roger Stanier, Cornelis van Niel 1960's: Prokaryota (Monera), Eukaryota (Protista, Plantae, Animalia)
Robert Whittaker 1969: Prokaryota (Monera), Eukaryota (Protista, Plantae, Fungi, Animalia)
Carl Woese 1977: Eubacteria / Bacteria, Archaebacteria / Archaea, Eukarya
James Lake 1984: The eocyte hypothesis: Eukarya info systems from inside Archaea

lpetrich
2013-Jan-10, 07:19 PM
Turning to viruses, they are information-system parasites, and there are 3 main hypotheses about their origins:

They are cellular organisms whose information systems have atrophied.
They are plasmids or transposons ("jumping genes") that move between cells.
They emerged alongside cellular organisms

Given the variety of viruses, they likely originated several times and by more than one of these mechanisms.

Some viruses are "slow viruses" that incorporate themselves into their hosts' genomes, meaning that a virus can become an ordinary transposon.

lpetrich
2013-Jan-10, 07:24 PM
A major confounding factor in studying the evolution of prokaryotes is Horizontal Gene Transfer (HGT) / Lateral Gene Transfer (LGT). Though common in prokaryotes, it is less common in eukaryotes, though it does happen there also.

How important is lateral gene transfer? « Why Evolution Is True (http://whyevolutionistrue.wordpress.com/2011/04/13/how-important-is-lateral-gene-transfer/)
Current Biology - Lateral gene transfer (http://www.cell.com/current-biology/abstract/S0960-9822(11)00101-1) - open access; not behind a paywall.


It's certainly possible that LGT has been so frequent that it scrambled up the genomes of many organisms, making an overall family tree meaningless. But did that happen? Some research has addressed that question.


I have found some papers of a way of doing whole-genome phylogenies: finding all substrings of a genome with a certain length, like 5 or 6, and then comparing their probability distributions. It's better to do this with predicted protein sequences than with the original nucleotides, in order to factor out nucleotide composition biases.

Whole-genome prokaryotic phylogeny (http://bioinformatics.oxfordjournals.org/content/21/10/2329.full) - uses the BLAST algorithm to compare genomes.
Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach - Springer (http://link.springer.com/article/10.1007%2Fs00239-003-2493-7) - fairly good agreement with SSU rRNA phylogenies, especially for the lower taxa.
Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from complete genomes without sequence alignment. | ResearchGate (http://www.researchgate.net/publication/7856990_Phylogeny_of_prokaryotes_and_chloroplasts_ revealed_by_a_simple_composition_approach_on_all_p rotein_sequences_from_complete_genomes_without_seq uence_alignment) - more good agreement. Also finds split between green algae and red algae.
Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution (http://www.pnas.org/content/107/1/133.full) - some more recent work, also has fairly good agreement with SSU rRNA results.

Bacteria, Archaea, and Eukarya emerge as well-defined groups, though it finds
((Bacteria, Archaea), Eukarya)
instead of a lot of other work finding
(Bacteria, (Archaea, Eukarya))
or
(Bacteria, Archaea containing Eukarya)
That may be an effect of all the proteins that early eukaryotes got from various sources. Informational systems are what support the close relationship with Archaea.

Towards a Genome-Based Taxonomy for Prokaryotes (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1236649/) - finds that LSU / 23S rRNA is as good as SSU / 16S rRNA, and that several widely-distributed protein-coding genes are also good.
PLOS Biology: From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria (http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0000019) - certain sorts of genes do not get laterally transferred very much.

This and other research shows that prokaryotes have a well-defined "average-gene" phylogeny, one that is apparent despite all the prokaryotes' LGT.

lpetrich
2013-Jan-10, 08:46 PM
I thought that maybe other forms of life appeared early on the Earth... but if that happened, it is now gone. Exterminated by our ancestors? Unable to adapt to its environment? I don't know, but if it was there, it is no more...
That is certainly possible.

But if such organisms *had* survived, how would we be able to recognize them?

I think that the first hint would be failing to find any recognizable genes in such an organism. There's a standard procedure for searching for genes: the Polymerase Chain Reaction with primers for whatever genes one is looking for.

However, this is a negative criterion, and it won't help find such organisms in environment samples. One has to isolate the organism before it becomes meaningful.

The next would be failing to find DNA or RNA in it, with upper limits like (say) a few thousand nucleobases per organism, much smaller than any that are known for cellular organisms.

After that, we must determine what's what in it, like what is its molecule of heredity. If that molecule can be established to be something other than DNA or RNA, then we've got it made.

Otherwise, we are likely to have some organism that shares an origin with all well-studied organisms, but that branched off very early. Something like

(this organism, (Archaea, Bacteria))

That would still be interesting, even if not a separate origin.

Selfsim
2013-Jan-10, 11:54 PM
… One has to isolate the organism before it becomes meaningful.I whole-heartedly agree … and I'm so happy to see this finally recognised, (by another), as a fundamental.

I might add that I'm yet to see how this can be done remotely over, (for eg), light year distances.


The next would be failing to find DNA or RNA in it, with upper limits like (say) a few thousand nucleobases per organism, much smaller than any that are known for cellular organisms.

After that, we must determine what's what in it, like what is its molecule of heredity. If that molecule can be established to be something other than DNA or RNA, then we've got it made.

Otherwise, we are likely to have some organism that shares an origin with all well-studied organisms, but that branched off very early. Something like

(this organism, (Archaea, Bacteria))

That would still be interesting, even if not a separate origin.Same comment as above …

I completely agree .. and I'm yet to see how this can be done remotely .. over, (for eg), light year distances(??)

IsaacKuo
2013-Jan-11, 12:33 AM
I whole-heartedly agree … and I'm so happy to see this finally recognised, (by another), as a fundamental.
Huh? He was simply noting that the Polymerase Chain Reaction procedure was not useful for finding organisms in the first place, and that the Polymerase Chain Reaction procedure is only meaningful after first isolating the organism in question. "It" refers to the Polymerase Chain Reaction procedure.

I might add that I'm yet to see how this can be done remotely over, (for eg), light year distances.
What does this have to do with anything? Anyway, there is one obvious method, which is to send some sort of exploration probe. Exploration probes with hardware designed to perform chemistry test procedures have, in fact, been designed and flown. Another obvious method with historical precedent is to search for traces of of life forms in meteorites. In fact, we have already sent a mission which collected interstellar dust.

One proposed mission builds on the technique used in Stardust to collect samples from Enceladus geysers and return them to Earth. If there are life forms in subsurface oceans other than Earth, this mission could be the our best shot at physically collecting them in the near term. Unlike other missions, it doesn't require landers or ascent vehicles or drilling.

lpetrich
2013-Jan-11, 06:42 AM
(me: … One has to isolate the organism before it becomes meaningful.)

I whole-heartedly agree … and I'm so happy to see this finally recognised, (by another), as a fundamental.

I might add that I'm yet to see how this can be done remotely over, (for eg), light year distances.
I had in mind an organism on the Earth.

The question I was addressing was how one would find an organism that had an origin completely separate from the origin of every organism that we've studied in any detail. Absence of known genes is not a good way to do it if there are other organisms that could supply copies of them to sequencing equipment. Likewise for DNA and RNA in general. Those molecules are not prebiotic, and it's not very apparent that there is any reason to use (deoxy)ribose instead of something else.

However, I don't expect a separate-origin organism to have no amino acids, because some amino acids can form prebiotically, and thus would be available for an early organism. But full-scale proteins are another story, since the RNA-world stage of our biota likely had only very simple proteins, if any at all.

Likewise for membrane lipids, since they are a convenient way to separate the interior and the exterior of a cell. However, they need not have compositions much like known cells' membrane lipids. They would likely be mostly straight and mostly hydrocarbon, since that is a fairly simple way to build membrane lipids, but that still leaves plenty of room for variation. The differences in membrane lipids between Bacteria/Eukarya and Archaea ought to make that evident.

Selfsim
2013-Jan-11, 08:43 AM
(me: … One has to isolate the organism before it becomes meaningful.)

I had in mind an organism on the Earth.Sure.
Apologies for the slight diversion, but I think isolation of the organism, (from its environment), is still a fundametal for testing .. and this should apply regardless of where its found. And that's not necessarily as straightforward as it may seem to be. A lot depends on the nature of the find itself and isolating it, (under controlled conditions), would seem to be the first step in determining what 'it' actually is.


The question I was addressing was how one would find an organism that had an origin completely separate from the origin of every organism that we've studied in any detail. Absence of known genes is not a good way to do it if there are other organisms that could supply copies of them to sequencing equipment. Likewise for DNA and RNA in general. Those molecules are not prebiotic, and it's not very apparent that there is any reason to use (deoxy)ribose instead of something else.

However, I don't expect a separate-origin organism to have no amino acids, because some amino acids can form prebiotically, and thus would be available for an early organism. But full-scale proteins are another story, since the RNA-world stage of our biota likely had only very simple proteins, if any at all.

Likewise for membrane lipids, since they are a convenient way to separate the interior and the exterior of a cell. However, they need not have compositions much like known cells' membrane lipids. They would likely be mostly straight and mostly hydrocarbon, since that is a fairly simple way to build membrane lipids, but that still leaves plenty of room for variation. The differences in membrane lipids between Bacteria/Eukarya and Archaea ought to make that evident.Sure.
A recent example, given here a few weeks ago, was about trying to figure out whether or not nanobacteria were 'living entities', or not. There were some 15 or so detailed tests applied, which eventually convinced the authors that they had sufficient cause to declare them to be not living entities (although the conclusion still seems controversial, to some folk). These things seem to be autonmously replicating, self-propagating 'complexes', but one of the original studies which treated them as microorganisms, was overturned by a subsequent one, on the basis that they showed no signs of the presence of, specifically, nucleic acids (in spite of the paradoxical presence of proteins).

The report outlining the tests applied is here, (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242841/) (if its of interest).

Whilst the end conclusion was that they are pre-biotic complexes, this wasn't at all clear before the tests were applied, (quite the opposite, actually). Might this approach be taken as an example of how modern science might go about testing some new find, which initially appears to be a separate abiogenesis candidate?

Paul Wally
2013-Jan-11, 10:22 AM
I thought that maybe other forms of life appeared early on the Earth... but if that happened, it is now gone. Exterminated by our ancestors? Unable to adapt to its environment? I don't know, but if it was there, it is no more...

Maybe with some future understanding or theory of abiogenesis and evolution we might be able to infer that such organisms must have existed, even though we may never find actual fossil evidence. It is the idea of looking for a missing link in evolution. We infer from theory that it must have existed, but we might not actually find it, and not finding it doesn't necessarily mean it didn't exist.

Xibalba
2013-Jan-11, 08:37 PM
The fact is, as some pointed out, that we don't know what we are looking for.

For example, a silicon-based organic chemistry "could" be possible, even here on Earth. But how do these silicon organisms live? What do they look like? Do they even have something similar to heredity, or is it a concept restricted to Earth's carbon-based life?

For all we know, rocks could be some strange, and pretty dull, form of life.

Xibalba
2013-Jan-11, 08:38 PM
double post, sorry

Colin Robinson
2013-Feb-25, 01:38 AM
I've just learned of a book by Freeman Dyson, called Origins of Life (http://www.amazon.com/Origins-Life-Freeman-Dyson/dp/0521626684), which hypothesizes a two-fold beginning something like the one I suggested in this thread's OP. (But Dyson got there before me.)

Selfsim
2013-Feb-25, 06:09 AM
Hmm interesting ... he might cite Erwin Schrödinger's maxim, but it seems he's actually following Schrödinger's lead, (in so far as switching from Physics to ponder the origins of biology).

He builds a mathematical model following on from ten key assumptions (apparently).

I'd be interested to know exactly what those assumptions might be. Any ideas?

Also, this book was originally written in 1985 and then re-released in 1999. Has anyone followed through with his recommended tests?

Cheers

Selfsim
2013-Feb-25, 06:18 AM
In the meantime, the RNA first camp seems to have made a rather interesting 'discovery' just the other day ....

Molecules assemble in water, hint at origins of life (http://phys.org/news/2013-02-molecules-hint-life.html)

The base pairs that hold together two pieces of RNA, the older cousin of DNA, are some of the most important molecular interactions in living cells. Many scientists believe that these base pairs were part of life from the very beginning and that RNA was one of the first polymers of life. But there is a problem. The RNA bases don't form base pairs in water unless they are connected to a polymer backbone, a trait that has baffled origin-of-life scientists for decades. If the bases don't pair before they are part of polymers, how would the bases have been selected out from the many molecules in the "prebiotic soup" so that RNA polymers could be formed?
... then the discovery ...

Hud's group knew that they were on to something when they added a small chemical tail to a proto-RNA base and saw it spontaneously form linear assemblies with another proto-RNA base. In some cases, the results produced 18,000 nicely ordered, stacked molecules in one long structure.
...
The proto-RNA's two-component, self-assembling system consisted of cyanuric acid (CA) and TAPAS, a derivative of triaminopyrimidine (TAP).
...
His next goal is to determine whether the proto-RNA bases can be linked by a backbone to form a polymer that could have functioned as a genetic material.Its certainly getting interesting ...

Cheers

Selfsim
2013-Feb-25, 06:53 AM
Found Dyson's assumptions ... (summarised below):


Assumption 1. (Oparin Theory). Cells came first, enzymes second, genes much later.
Assumption 2. A cell is a confined volume of fluid containing small organic molecules (monomers) in solution. The monomers are free to diffuse in and out of the cell. Inside the cell is a chemically active surface with a fixed number N of sites exposed to the fluid. The surface may be the boundary membrane of the cell, or it may be a separate structure in the cell’s interior.
Assumption 3. Cells do not interact with one another. There is no Darwinian selection. Evolution of the population of molecules within a cell proceeds by random drift. Darwinian selection only begins after the model ends,
Assumption 4. Changes of population occur by discrete steps, each step consisting of an adsorption or desorption of a single monomer
at a single site of the surface. This assumption is unnecessarily restrictive and is imposed only for the sake of simplicity ...
Assumption 5. Each of the N sites on the surface adsorbs and desorbs monomers with equal probability. This assumption is also unrealistic and is made to keep the calculations simple.
Assumption 6. Themonomers bound to the surface can be divided into two classes, active and inactive. This assumption appears to be uncontroversial, but it actually contains the essential simplification that makes the model mathematically tractable.
Assumption 7. The active monomers are those that happen to be of the right species at the right sites, where they and their neighbors make a polymer that can act as an enzyme. To act as an enzyme means to catalyze the adsorption of other monomers in a selective manner so that monomers of the correct species are chosen preferentially to be adsorbed at other sites where they can be active.
Assumption 8. The monomers belong to (n+1) chemical species, all present in the fluid with equal abundance. At each site, only one species is active, and the remaining n species are inactive ... Assumption 8 is a drastic approximation ...
Assumption 9. The curve y=phi(x) is S-shaped, crossing the line y=x at three points, alpha, beta gamma, between zero and one.
This assumption is again borrowed from the Curie–Weiss model of a ferromagnet. It means that the population of molecules has three possible equilibrium states...
Assumption 10. Here we make a definite choice for the function psi(x), basing the choice on a simple thermodynamic argument. It will turn out happily that the function phi(x) derived from thermo-dynamics has the desired S-shaped form to produce the three equilibrium states required by Assumption 9....

Hmm ... some tradeoffs made for the sake of simplicity of computation ...

My view: its just another model. I'd rather see a more empirical mechanistic basis, rather than purely theoretical.

Rgds

Colin Robinson
2013-Feb-25, 10:51 PM
Found Dyson's assumptions ... (summarised below):


Hmm ... some tradeoffs made for the sake of simplicity of computation ...

My view: its just another model. I'd rather see a more empirical mechanistic basis, rather than purely theoretical.

Rgds

It may be just another model. But if we think of the origin of life on Earth as a single one-off event (rather than a sequence of two or more smaller events) isn't that also is model?

Selfsim
2013-Feb-25, 11:50 PM
It may be just another model. But if we think of the origin of life on Earth as a single one-off event (rather than a sequence of two or more smaller events) isn't that also is model?Sure … they're all reasonably serious attempts at speculative models .. All worthy of consideration from a strengths and weaknesses perspective .. and when one does that, they tend to balance out in the final analysis, eh?