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Selfsim
2013-Oct-25, 06:33 AM
Take a look at this as a good example of a highly misleading article headline ...

Chemists show life on Earth was not a fluke (http://phys.org/news/2013-10-chemists-life-earth-fluke.html) ...

... They found that these molecular machines, which exist in living cells today, don't do much on their own. But as soon as they add fatty chemicals, which form a primitive version of a cell membrane, it got the chemicals close enough to react in a highly specific manner.
...
To make things simple, they chose an assembly that produces proteins. This assembly consists of 83 different molecules including DNA, which was programmed to produce a special green fluorescent protein (GFP) that could be observed under a confocal microscope.
...
The assembly can only produce proteins when its molecules are close enough together to react with each other. When the assembly is diluted with water, they can no longer react. This is one reason that the insides of living cells are very crowded, concentrated places: to allow the chemistry of life to work.
..
Stano reports in the journal Angewandte Chemie that many of these liposomes trapped some molecules of the assembly. But remarkably, five in every 1,000 such liposomes had all 83 of the molecules needed to produce a protein. These liposomes produced large amount of GFP and glowed green under a microscope.

Computer calculations reveal that even by chance, five liposomes in 1,000 could not have trapped all 83 molecules of the assembly. Their calculated probability for even one such liposome to form is essentially zero. The fact that any such liposomes formed and that GFP was produced means something quite unique is happening.

Stano and his colleagues do not yet understand why this happened. ... then the clincher ...
Regardless of the limitations, Stano's experiment has shown for the first time that self-assembly into simple cells may be an inevitable physical process. Finding out how exactly this self-assembly happens will mean taking a big step towards understanding how life was formed.So, these guys started out with: "an assembly that produces proteins. This assembly consists of 83 different molecules including DNA", and from that, the headline takes the quantum leap to: "Life on Earth was not a Fluke"??? ... (like, who ever said it was, anyway ??)

Gimme a break! .. Talk about building a huge strawman, and then failing on just about all counts to justify it!

Colin Robinson
2013-Oct-25, 09:53 AM
I'd agree that the article's headline overstates matters somewhat.

Very interesting experiment, all the same. It seems to show a mixture of DNA, enzymes, and the lipid POPC self-organizing in an unexpectedly non-random way into a cell-like structure that is simple, yet chemically active.

Selfsim
2013-Oct-25, 07:16 PM
I was a little confused about the approach these guys are taking, when compared with what was gained from the minimal genome project, (Ventner Institute), which figured out that a minimum of about 256 genes is required for metabolism and replication. (This was based on Mycoplasma genitalium).

Interestingly, 'the minimal set' varies from organism to organism, and even varies according to strain type within that organism class. It also varies depending on the environment the culture is developed in. Eg: if it is nutrient-scarce, more genes are needed to produce nutrients for food, etc.

It has also been found that some 'minimal gene sets', needed by some organisms for their survival are unique (chuckle, chuckle .. :p ). The Ventner crowd went on to design and construct a 'synthetic' organism .. but I think all of these needed components, (or at least, used them as templates) from already existing cells ..

Anyway, here is a related (and downloadable) paper (http://www.mul2.polito.it/smart13/mat_conf/paper_caricati/20130425234831_Full-length%20paper%20STANO%20SMART%20TORINO%202013.pdf ) explaining more clearly what's going on here ...


… The question therefore becomes: what is the minimal complexity necessary to display basic living functions, namely self-maintenance, self- reproduction, and the possibility to evolve? The experimental investigation on “minimal” cells foresees the creation of cell-like systems based on the encapsulation, within liposomes, of the minimal and sufficient number of components to reconstruct the living phenomenology. Clearly, it is very difficult to obtain the full set of the features that are typical of life, so that a stepwise approach is suggested. Practically it consists in reconstructing the essential cellular functions inside liposomes, with increasing complexity.They go on to discuss present issues:
Among the most important milestones still on the route to get fully functioning SSMCs, we recognize the production of ribosomes, the reconstitution of membrane-linked functions (i.e., membrane enzymes), the issue of energy production, the control of the chemistry and the physics of cell growth and division, and the synchronization between the various processes.

Biophysical issues are clearly related to the construction of synthetic cells, and the formation of liposomes as well as the encapsulation of solutes are two of the most important ones. In particular, an interesting issue concerns the interplay between the choice of the preparation method and the actual experimental outcome. As it will be specified in paragraph 3.2, although microfluidic technologies are quickly enter in the field and promise the reproducible and continuous production of synthetic cells with a programmable and desired composition, the spontaneous assembly of synthetic cells from their components has been widely used till now. Intriguingly, the so-called “overcrowding” effect, which will be discussed below in more details, has recently revealed how unexpected biophysical phenomena strongly impact on the theory and practice of cell models research.

Producing scientific knowledge by constructing/synthesizing biomimetic objects complements the traditional “analytic (taking apart)” strategy. The synthetic approach has stimulated recent epistemological discussionsSo, it looks like the study in the OP was addressing the encapsulation by liposomes and subsequent behaviours. Their choices in the design of their experiment, would have played a significant role in what eventuated, (or so it appears).

Paul Wally
2013-Oct-25, 08:42 PM
I was a little confused about the approach these guys are taking, when compared with what was gained from the minimal genome project, (Ventner Institute), which figured out that a minimum of about 256 genes is required for metabolism and replication. (This was based on Mycoplasma genitalium).

They are probably not investigating the same problem, so there's not much sense in comparing "approaches". The one is starting from existing life and makes it simpler whereas the other one attempts to arrive at life from something simpler than life itself. These are two completely different investigations.



Interestingly, 'the minimal set' varies from organism to organism, and even varies according to strain type within that organism class. It also varies depending on the environment the culture is developed in. Eg: if it is nutrient-scarce, more genes are needed to produce nutrients for food, etc.

It has also been found that some 'minimal gene sets', needed by some organisms for their survival are unique (chuckle, chuckle .. :p ). The Ventner crowd went on to design and construct a 'synthetic' organism .. but I think all of these needed components, (or at least, used them as templates) from already existing cells ..


Stano et al have a bottom up approach, so they're not working with 'organisms', only molecules. Since there are no organisms (yet), I doubt whether the whole notion of a 'gene' has any meaningful interpretation (yet). Also, from what I understand, their approach is biomemetic, meaning that they're merely attempting to imitate life-like processes in a very rudimentary way.



Their choices in the design of their experiment, would have played a significant role in what eventuated, (or so it appears).

Apparently they did discover something which then lead to an interesting puzzle: "How is it possible for 5 out of 1000 liposomes to encapsulate all 83 molecules?"

Selfsim
2013-Oct-25, 10:48 PM
They are probably not investigating the same problem, so there's not much sense in comparing "approaches". The one is starting from existing life and makes it simpler whereas the other one attempts to arrive at life from something simpler than life itself. These are two completely different investigations. Membrane functions, encapsulation of solutes, and "overcrowding" effects are the well-known areas for further investigation (see the Stano etal paper in my last post).


Stano et al have a bottom up approach, so they're not working with 'organisms', only molecules. Since there are no organisms (yet), I doubt whether the whole notion of a 'gene' has any meaningful interpretation (yet). Also, from what I understand, their approach is biomemetic, meaning that they're merely attempting to imitate life-like processes in a very rudimentary way.Metabolism covers a whole gamut of protein synthesis, (which is the end result of the experiment in the OP). The term 'metabolism' is quite non-specific in meaning, (in this context) ... All of which serves as a reminder about just how non-specific 'the hunt' for exo-'metabolism' really is ...

Apparently they did discover something which then lead to an interesting puzzle: "How is it possible for 5 out of 1000 liposomes to encapsulate all 83 molecules?"Well no-one ever said anything that leads to protein synthesis is a random process! This is why the implied surprise in the jouno article seems so misplaced.

Colin Robinson
2013-Oct-26, 03:37 AM
and from that, the headline takes the quantum leap to: "Life on Earth was not a Fluke"??? ... (like, who ever said it was, anyway ??)

The French biochemist Jacques Monod was a prominent scientist who considered life on Earth to be a low-probability outcome of random processes: in everyday language, a fluke. In his book "Chance and Necessity", Monod wrote…


The universe was not pregnant with life nor the biosphere with man. Our number came up in the Monte Carlo game.

Selfsim
2013-Oct-26, 06:17 AM
The French biochemist Jacques Monod was a prominent scientist who considered life on Earth to be a low-probability outcome of random processes: in everyday language, a fluke. In his book "Chance and Necessity", Monod wrote…He (http://en.wikipedia.org/wiki/Jacques_Monod#Professional_life) was also skewed by an atheistic ideology ... (from which such philosophical views should be taken .. Ie: as distinct from a scientific basis) ...
He was also a proponent of the view that life on earth arose by freak chemical accident and was unlikely to be duplicated even in the vast universe. "Man at last knows he is alone in the unfeeling immensity of the universe, out of which he has emerged only by chance. His destiny is nowhere spelled out, nor is his duty. The kingdom above or the darkness below; it is for him to choose", he wrote in 1971. He used the bleak assessment that forms the earlier part of the quote as a springboard to argue for atheism and the absurdity and pointlessness of existence. Monod stated we are merely chemical extras in a majestic but impersonal cosmic drama—an irrelevant, unintended sideshow. His views were in direct opposition to the religious certainties of his ancestor Henri's well-known brothers Frédéric Monod and Adolphe Monod. In 1973 he was one of the signers of the Humanist Manifesto II.Clearly there is no empirical evidence for any pure random chance ... just as there is no empirical evidence for any other views on the distribution of emergence .. (like a determinable outcome). All this is unknown ... and is nothing more than pure guesswork.

Colin Robinson
2013-Oct-26, 08:57 AM
He (http://en.wikipedia.org/wiki/Jacques_Monod#Professional_life) was also skewed by an atheistic ideology ... (from which such philosophical views should be taken .. Ie: as distinct from a scientific basis) ...Clearly there is no empirical evidence for any pure random chance ... just as there is no empirical evidence for any other views on the distribution of emergence .. (like a determinable outcome). All this is unknown ... and is nothing more than pure guesswork.

Empirical evidence is what scientific work is about.

For instance, the experiment you mentioned in the OP of this thread has given us some empirical evidence which we didn't have before.

It demonstrates that we can take a mechanism that produces protein in a cell, break that mechanism up into 83 chemical compounds, throw those 83 compounds into water, add a lipid, and we find lipid-enclosed systems in which those 83 molecules have put themselves back together into the protein-creating mechanism we started with.

Does that prove that "life on Earth was no fluke"?

Not quite. However, it does make the transition from a mixture of chemicals to a biological system look less random — less "flukey" — than it may have looked before.

Selfsim
2013-Oct-26, 10:34 AM
... It demonstrates that we can take a mechanism that produces protein in a cell, break that mechanism up into 83 chemical compounds, throw those 83 compounds into water, add a lipid, and we find lipid-enclosed systems in which those 83 molecules have put themselves back together into the protein-creating mechanism we started with.Take a look at exactly what 83 molecules they're talking about! ...

... In fact, by hydrating lipids in a solution containing the transcription-translation molecular machinery (DNA, RNA polymerase, t-RNA, ribosomes, etc., for a total of about 80 different macromolecules), it has been possible to synthesize proteins inside liposomes ... ... They haven't broken down any mechanisms at all!

All they've done, is basically relocate the various fully functional piece parts, of a fully functional mechanism, into a synthesised array of vesicles of 200nm diameter, and found .. surprise .. surprise (err not .!.) .. that it performs the same functions as it did in a natural cell membrane!

I still can't see the big deal about this. I mean what did they expect it to do?
Sit 'round and play tiddly-winks?


Does that prove that "life on Earth was no fluke"?

Not quite. However, it does make the transition from a mixture of chemicals to a biological system look less random — less "flukey" — than it may have looked before.No it doesn't. This is not just any old mixture of chemicals!

It never looked 'random' in the first place!
How could anyone say DNA, RNA polymerase, t-RNA and ribosomes ever looked like 'random' molecules?
They are probably the most specific, highly ordered molecules in the known universe!

Paul Wally
2013-Oct-26, 02:23 PM
... They haven't broken down any mechanisms at all!

All they've done, is basically relocate the various fully functional piece parts, of a fully functional mechanism...

Now explain how the parts got together again.



It never looked 'random' in the first place!

Yes, but in the second place it did look random, only less random than expected.



How could anyone say DNA, RNA polymerase, t-RNA and ribosomes ever looked like 'random' molecules?
They are probably the most specific, highly ordered molecules in the known universe!

Now you're just mentioning molecules and 'forget' that a system was taken apart which then reorganized itself with a higher than expected probability.

marsbug
2013-Oct-26, 02:43 PM
If i read the paper aright: They broke the chemical machinery into components, mixed them together randomly in an aqueos solution. Then they allowed vesicals to form, and those vesicals encapsulated some portion of the chemical-machinery components. They found that in 5 out of every 1000 vesicles the forming vesicle had encapsulated the right components to re-assemble the original molecular machinery. Over enough repetitions that would happen anyway, but the 5 out of 1000 number is statistically unlikely, even though the components are present in the solution.

Is that the gist of it? IF it's confirmed by subsequent experiments, and IF there are no systematic errors, then it does suggest something more than chance at work, although it is still a highly controlled and artificial situation. Have they unwittingly preselected the components to be selected by the vesicle encapsulation in the right amounts to rebuild the original machinery? Is my first question, although I don't have the biology background to answer it from reading the paper.

Colin Robinson
2013-Oct-26, 09:08 PM
If i read the paper aright: They broke the chemical machinery into components, mixed them together randomly in an aqueos solution. Then they allowed vesicals to form, and those vesicals encapsulated some portion of the chemical-machinery components. They found that in 5 out of every 1000 vesicles the forming vesicle had encapsulated the right components to re-assemble the original molecular machinery. Over enough repetitions that would happen anyway, but the 5 out of 1000 number is statistically unlikely, even though the components are present in the solution.

Is that the gist of it?

Yes, I agree that's the gist.


IF it's confirmed by subsequent experiments, and IF there are no systematic errors, then it does suggest something more than chance at work, although it is still a highly controlled and artificial situation.

As the article says, an important next step is to find out whether less complex molecules can self-assemble in a similar way into an active system within a vesicle.

Selfsim
2013-Oct-26, 09:16 PM
Now explain how the parts got together again.That is the real focus of the investigation.
This study is more about understanding how to develop synthetic organisms by inquiring into the interaction between forming vesicles and entrapment of sub cellular machinery.
I see very little to do with abiogenesis, frankly.
I don't think it has anything to do with it, the more I think about it ... maybe it might be of casual interest to the RNA first hypothesis(??)


Yes, but in the second place it did look random, only less random than expected.The entrapment frequency distribution followed more closely a power-law. It was originally assumed to be a Poisson distribution - that's where the randomness' inference came into all this. They were originally pursuing a hypothesis that vescile formation and subsequent entrapment were independent events. Clearly they aren't (and I can't see why they would ever assume this in the first place .. all the macromolecules involved are a highly complex structures containing both polar, non-polar, hydrophyllic and hydrophobic molecules and they knew this before they commenced).
Why would they assume what happens subsequently would be random?

This has virtually nothing to do with random compounds coming together to become life ..



Now you're just mentioning molecules and 'forget' that a system was taken apart which then reorganized itself with a higher than expected probability.So?

I can't see why they had the expectation in the first place!
The only surprise here is that their expectation was way out!

There must be other biologists working elsewhere, (like the Ventner Institute) who would be laughing at the naivity of the original hypothesis!

Selfsim
2013-Oct-26, 09:21 PM
If i read the paper aright: They broke the chemical machinery into components, mixed them together randomly in an aqueos solution. Then they allowed vesicals to form, and those vesicals encapsulated some portion of the chemical-machinery components. They found that in 5 out of every 1000 vesicles the forming vesicle had encapsulated the right components to re-assemble the original molecular machinery. Over enough repetitions that would happen anyway, but the 5 out of 1000 number is statistically unlikely, even though the components are present in the solution.Yep .. (thanks for reading the paper). :)


Is that the gist of it? IF it's confirmed by subsequent experiments, and IF there are no systematic errors, then it does suggest something more than chance at work, although it is still a highly controlled and artificial situation. Have they unwittingly preselected the components to be selected by the vesicle encapsulation in the right amounts to rebuild the original machinery? Is my first question, although I don't have the biology background to answer it from reading the paper.Or, was their preparation technique an influencing factor?

Because these molecules are inherently adaptive to external environments, just about anything can influence the end result - there should be no surprises about this.

Selfsim
2013-Oct-26, 09:30 PM
... As the article says, an important next step is to find out whether less complex molecules can self-assemble in a similar way into an active system within a vesicle.... Most of the net results of such an approach are already known to other researchers.
DNA repair mechanisms are a hugely complex topic unto itself. If they break apart a DNA or RNA chain ... then all that then comes into play. The mechanism they're playing around with, itself, is a highly active system. The relationships between the molecular piece-parts and the functioning of the mechanism is highly non-linear ... we already knwo this. So what would be the point of going down such a path if inquiry?

If this is what they're planning, these guys seem to be re-inventing the horse, (and wasting lots of time/effort in doing it).

Colin Robinson
2013-Oct-26, 10:44 PM
... Most of the net results of such an approach are already known to other researchers.

That statement makes a nice change from your usual litany of unknown, unknown, unknown... :)


DNA repair mechanisms are a hugely complex topic unto itself. If they break apart a DNA or RNA chain ... then all that then comes into play.

Repair of a broken biomolecule may be a complex topic, but is it the same topic?

The article we're discussing is about a number of molecules going from a state where they are not enclosed by any membrane, and cannot work together like a team, to a state where they are working together as a team within a liposome.

Another way of saying this: It is about the relation between chemistry and cellular morphology.

Selfsim
2013-Oct-26, 11:45 PM
That statement makes a nice change from your usual litany of unknown, unknown, unknown... :) I prefer 'Gregorian Chant' ... 'litanies' are reserved for advocacy platforms. I repeat facts ... not beliefs ... there is nothing untoward about repeating facts.


Repair of a broken biomolecule may be a complex topic, but is it the same topic?Well how else do fully functional cellular mechanisms respond to say, an incomplete strand of DNA? Such mechanisms don't care whether it was deliberately 'broken down' to a sub-strand, or not!


The article we're discussing is about a number of molecules going from a state where they are not enclosed by any membrane, and cannot work together like a team, to a state where they are working together as a team within a liposome. What this nonsense about 'teamwork'? Ya think these molecules possess consciousness now? :)


Another way of saying this: It is about the relation between chemistry and cellular morphology.Finally! (I agree!)
Further, its about modern-day macromolecular bio-chemistry! ... (Which is a far cry from just 'chemistry' ... which is the whole point about this ...)

Colin Robinson
2013-Oct-27, 12:40 AM
What this nonsense about 'teamwork'? Ya think these molecules possess consciousness now? :)

I mean than when the 83 different molecules are operating together, they can produce something which none of them operating separately could produce.


Finally! (I agree!)
Further, its about modern-day macromolecular bio-chemistry! ... (Which is a far cry from just 'chemistry' ... which is the whole point about this ...)

A aqueous solution of chemical compounds (even if they are modern-day macromolecular biochemical compounds), does not have a cell-like morphology. What Pasquale Stano et al appear to have shown, is that when the lipid POPC is added to the solution, a simple but functional morphology can emerge.

This seems to me like an important result.

And its importance is not affected at all by a somewhat exaggerated headline on an article which in any case was not written by Stano et al themselves. (The author's name is given at the top of the article as "Andrew Bissette".)

Paul Wally
2013-Oct-27, 01:34 AM
The article we're discussing is about a number of molecules going from a state where they are not enclosed by any membrane, and cannot work together like a team, to a state where they are working together as a team within a liposome.

Another way of saying this: It is about the relation between chemistry and cellular morphology.

Yep, and interestingly that relation appears to be quite flexible in the sense that even if the system is completely dismantled it has a statistically significant chance of reassembling itself. It is almost as if there is some kind of dynamic attractor.

Paul Wally
2013-Oct-27, 01:52 AM
There must be other biologists working elsewhere, (like the Ventner Institute) who would be laughing at the naivity of the original hypothesis!

I doubt that! Scientists don't refute a hypothesis by laughing at it.

Selfsim
2013-Oct-27, 02:27 AM
Yep, and interestingly that relation appears to be quite flexible in the sense that even if the system is completely dismantled it has a statistically significant chance of reassembling itself. It is almost as if there is some kind of dynamic attractor.... in the drive towards achieving a state of Dynamic Kinetic Stability via a process which involves the re-establishment of molecular complexification ... :eek:

Selfsim
2013-Oct-27, 02:29 AM
I doubt that! Scientists don't refute a hypothesis by laughing at it.Maybe not .. but it certainly (frequently) starts out that way ..

Selfsim
2013-Oct-27, 03:01 AM
I mean than when the 83 different molecules are operating together, they can produce something which none of them operating separately could produce. There are several different known mechanisms for protein synthesis. One of the less spectacular ones doesn't require ribosomes and follows a chemical pathway of organic synthesis (http://en.wikipedia.org/wiki/Organic_synthesis). Peptide synthesis operates in this way.

This would've been a closer-to-abiogenesis demonstration, than the inclusion of ribosomes and RNA molecules.


A aqueous solution of chemical compounds (even if they are modern-day macromolecular biochemical compounds), does not have a cell-like morphology. What Pasquale Stano et al appear to have shown, is that when the lipid POPC is added to the solution, a simple but functional morphology can emerge.

This seems to me like an important result. Simple functional protein synthesis pathways already exist in organic synthesis, and operate in the absence of liposome encapsulation .. all it takes is a higher than inorganic chemical level of molecular complexity.


And its importance is not affected at all by a somewhat exaggerated headline on an article which in any case was not written by Stano et al themselves. (The author's name is given at the top of the article as "Andrew Bissette".)I question 'the importance'.
The more I look at this, the more it looks like pure hype about something quite routine and already quite well-known.

Colin Robinson
2013-Oct-27, 04:19 AM
There are several different known mechanisms for protein synthesis. One of the less spectacular ones doesn't require ribosomes and follows a chemical pathway of organic synthesis (http://en.wikipedia.org/wiki/Organic_synthesis).

???

Proteins are a class of organic compounds. How could synthesis of a protein not be an "organic synthesis"?


Peptide synthesis operates in this way

As mentioned in the WP page Peptide (https://en.wikipedia.org/wiki/Peptides):


Proteins consist of one or more polypeptides arranged in a biologically functional way

Again, how could any synthesis of a protein not be a "peptide synthesis"?


and operate in the absence of liposome encapsulation. This would've been a closer-to-abiogenesis demonstration, than the inclusion of ribosomes and RNA molecules.

Even if you think the first protein synthesis happened in the absence of encapsulation, isn't the origin of encapsulation an important question in its own right? Don't all cells today have enclosing membranes?

Selfsim
2013-Oct-27, 05:06 AM
???

Proteins are a class of organic compounds. How could synthesis of a protein not be an "organic synthesis"?Proteins do not have to be produced by cellular based ribosomes performing normal translation/transcription from mRNA. They can be assembled by chemical ligation. This makes the resultant proteins different from bio-synthesised proteins translated by bio-cellular processes.


As mentioned in the WP page Peptide (https://en.wikipedia.org/wiki/Peptides):
...
Again, how could any synthesis of a protein not be a "peptide synthesis"?Peptide synthesis refers to non-cellular based protein synthesis. (See above).


Even if you think the first protein synthesis happened in the absence of encapsulation, isn't the origin of encapsulation an important question in its own right? Don't all cells today have enclosing membranes?I have no idea how the first protein came about.
My point is that the macromolecules Stano etal commenced with, are easily complex enough to produce proteins without involving liposome encapsulation inside a rudimentary cell (albeit via different means). The potential to form proteins already exists because of the complexity of the molecules.

In an abiogenesis context, the key issue is how such complex macromolecules were formed. From a synthetic biology engineering perspective however, the interaction between the vesicles and the encapsulated molcules, becomes significant if one is attempting to synthesise some kind of artificial life. (Which I see, is the primary driver behind this research .. not life origins ... the latter being 'spin' added to attract interest from gullible exo-life enthusiasts).

Colin Robinson
2013-Oct-27, 06:03 AM
In an abiogenesis context, the key issue is how such complex macromolecules were formed.

That is one key issue...

Colin Robinson
2013-Oct-27, 09:04 AM
The paper cited in the OP of the thread Global Abiogenesis Model has a section with the title "Concentration", which discusses the role in abiogenesis of lipid membranes and other structures which may possibly have done a similar job:


Concentration
Mechanisms of concentration increase the overall rates of chemical reactions.

A simple point, but one that deserves to be taken very seriously.


Concentration mechanisms in pore spaces, on mineral surfaces, or within non-biogenic lipid membranes could also have acted as prebiotic forms of encapsulation which prevented the diffusion of biochemically useful products or even provided the grounds for genetic heredity (Maynard-Smith & Szathmary, 1997; Sowerby et al., 2001, 2002).
Modern life utilizes lipid membranes as encapsulation mechanisms to prevent diffusion of cellular components, to generate concentration gradients, and to maintain a unit of heredity. Many researchers have focused on possible mechanisms for the formation of early lipid membranes, such as micelles (Deamer et al., 2002). There is dispute, however, regarding how early such encapsulating membranes would have played a role in the evolution of life; some argue that encapsulating membranes must have been an early feature of life, while others argue that it would have been a much later development. The latter point of view suggests that the earliest stages of life’s formation may have involved encapsulation through inorganic micro-compartments such as fluid inclusions, vesicles, porous sediments and hydro-thermal chimneys or sea-ice brine pockets (Section ‘Hadean micro-environments and their potential role in the origin of life’). If inorganic micro-compartments served as concentration points for prebiotic molecules, then it is possible that lipid membranes only became important at later stages in the origin and evolution of biochemicals (Koonin & Martin, 2005). However, it is also conceivable that non-biological lipid membranes played a more active role by transporting prebiotic compounds between different environmental settings.

In short, the role of lipid encapsulation and other forms of chemical concentration is an important unresolved question in the study of abiogenesis.

Paul Wally
2013-Oct-27, 09:46 AM
... in the drive towards achieving a state of Dynamic Kinetic Stability via a process which involves the re-establishment of molecular complexification ... :eek:

I don't think molecular complexification is what is under investigation here ... system complexity yes. With the organization of
molecules into a system it still remains the same complex molecules. The protein synthesis is just a kind of 'litmus' test for whether there is a functioning system.

Paul Wally
2013-Oct-27, 10:02 AM
My point is that the macromolecules Stano etal commenced with, are easily complex enough to produce proteins without involving liposome encapsulation inside a rudimentary cell (albeit via different means). The potential to form proteins already exists because of the complexity of the molecules.



Well, an experiment was performed in this case where the addition of lipids lead to some chance of encapsulation and protein synthesis. If proteins
could quite easily have been produced without liposome encapsulation then where is the evidence for that in this experiment?

marsbug
2013-Oct-27, 12:19 PM
That is the real focus of the investigation.
This study is more about understanding how to develop synthetic organisms by inquiring into the interaction between forming vesicles and entrapment of sub cellular machinery.
I see very little to do with abiogenesis, frankly.
I don't think it has anything to do with it, the more I think about it ... .. all the macromolecules involved are a highly complex structures containing both polar, non-polar, hydrophyllic and hydrophobic molecules and they knew this before they commenced).
Why would they assume what happens subsequently would be random?



Perhaps the point is not that the re-assembly of the complex molecules is not random, but that the fashion in which it is not random is still unknown (the 'mechanics' of it). You say in an earlier post (post number 5, first line that isn't a quote) that effects like this are known to be areas that need investigating, so I imagine any data points wrt these phenomena have some value. I also imagine that there is some value to be had from this for both the A - life and abiogenesis community, although personally I can't say how much. If the authors have hyped the import of this study, well, that's only to be expected, it's what they need to do to ensure their work continues to get fundng. I don't like that that's how it is, but that [B]is[B] how it is.

marsbug
2013-Oct-27, 12:23 PM
Could a naturally forming vesicle have found itself in a soup chemical machinery components like this in a natural environment?

Selfsim
2013-Oct-27, 08:31 PM
I don't think molecular complexification is what is under investigation here ... system complexity yes. With the organization of molecules into a system it still remains the same complex molecules. The protein synthesis is just a kind of 'litmus' test for whether there is a functioning system.Your 'system' exists at multiple levels of scale. For example the ribosome molecule is comprised of many different complex components (it is thus a 'system' unto itself). One component relevant to the translational process, reads mRNA, and then then another component joins amino acids to form a polypeptide chain. Both components (or systems) come together at a specific time in the one molecule in order to perform the translation function. Each component is a 'system', as is the aggregated ribosome. All of these systems are complex systems.

System complexity measures vary over the time period during which the translation function is being performed.

Colin Robinson
2013-Oct-27, 09:11 PM
Could a naturally forming vesicle have found itself in a soup chemical machinery components like this in a natural environment?

Could such a situation arise without pre-existing life? Difficult to see how it could arise with chemical components as complex as the ones used in this experiment. But could a soup containing simpler chemical components undergo a similar process of non-random encapsulation?

Well, as the article says:


It may be that these particular molecules are suited to this kind of self-organisation because they are already highly evolved. An important next step is to see if similar, but less complex, molecules are also capable of this feat.

Selfsim
2013-Oct-27, 10:15 PM
My point is that the macromolecules Stano etal commenced with, are easily complex enough to produce proteins without involving liposome encapsulation inside a rudimentary cell (albeit via different means). The potential to form proteins already exists because of the complexity of the molecules.Well, an experiment was performed in this case where the addition of lipids lead to some chance of encapsulation and protein synthesis. If proteins
could quite easily have been produced without liposome encapsulation then where is the evidence for that in this experiment?Ok .. so I'm not arguing that encapsulation makes no difference to the chances of protein production. It certainly amplifies that chance, but it is not the only means facilitating protein synthesis by the sub-cellular translational apparatus. I am saying that the complexity of the molecules is what realises the potential for protein synthesis in the first instance. These molecules are prone to performing this function, by using whatever available means they can. Encapsulation, (clustered around a seemingly optimal size of vesicle and exhibiting a power law distribution), is one such means.
Whilst there is knowledge from outside this study of other means demonstrating this potential, (such as solid phase synthesis (http://en.wikipedia.org/wiki/Peptide_synthesis#Solid-phase_synthesis)), the evidence sourced from this particular study (within the established experimental bounds) is demonstrated in Figure #4 (page 25). Whilst its not particularly 'strong' evidence', it is nonetheless evidence of the potential of protein synthesis from the apparatus. There is synthesis of proteins shown in this graph, at very large vesicle sizes upwards of 10 \mum. The concentration of these proteins is still clustered around the average for the smaller vesicles. From the study, here is no reason to assume that the potential for protein synthesis ceases, as a result of increasing vesicle size, either.

Selfsim
2013-Oct-27, 10:42 PM
Could such a situation arise without pre-existing life? Difficult to see how it could arise with chemical components as complex as the ones used in this experiment. But could a soup containing simpler chemical components undergo a similar process of non-random encapsulation?

Well, as the article says:
It may be that these particular molecules are suited to this kind of self-organisation because they are already highly evolved. An important next step is to see if similar, but less complex, molecules are also capable of this feat."Minimal molecular complexity", eh?

Take a ribosome (http://en.wikipedia.org/wiki/Ribosome#Biogenesis). Its synthesis and processing involves the co-ordinated functioning of over 200 proteins. (Aside and interestingly: this takes place in both the cytoplasm and the cell nucleus (in modern-day prokaryotes and eukaryotes)). From this it seems that no matter how 'less complex' the sub-components might get .. those sub-components are still highly complex .. with certainty, when compared with inorganic compounds .. and even when compared with basic molecules classified as 'organic'.

Bissette's above words may seem 'reasonable' (from a logical viewpoint) but when one drills into those simple-to-write words, they are really quite meaningless when it comes to the practicality of the proposition. (This is another typical technique used by reporters for 'upping the hype' .. whilst coming from ignorance of the complexity what they're talking about).

Colin Robinson
2013-Oct-28, 12:45 AM
"Minimal molecular complexity", eh?

Take a ribosome (http://en.wikipedia.org/wiki/Ribosome#Biogenesis). Its synthesis and processing involves the co-ordinated functioning of over 200 proteins. (Aside and interestingly: this takes place in both the cytoplasm and the cell nucleus (in modern-day prokaryotes and eukaryotes)). From this it seems that no matter how 'less complex' the sub-components might get .. those sub-components are still highly complex .. with certainty, when compared with inorganic compounds .. and even when compared with basic molecules classified as 'organic'.

You are saying that cells today are a lot more complex that simple organic or inorganic molecules?

True enough. There is an oft-quoted statement by the cellular biologist Lynn Margulis:


To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

What I still don't understand, is why you think that this diminishes the relevance of experiments which study how organic molecules (simple or complex) become encapsulated (randomly or selectively) in lipid membranes.

Githyanki
2013-Oct-28, 02:34 AM
What gets me, is just how quickly life emerged on Earth; as soon as the conditions were right, life appeared. Now, life still could have come from space. What gets me, is that if it was THAT easy for life to emerge, it should emerge over and over again as conditions are still favorable for life.

Problems with this reasoning are

1. Perhaps life can only emerge in a non-oxygen environment were the temperature is near 200F (conditions of Earth 3.8BYA)
2. the chances of life being created is one in five-million; say if life gets a chance to form, once every five-million years, that's a lot of time for us, but in geological time, nothing really.

Colin Robinson
2013-Oct-28, 03:59 AM
What gets me, is just how quickly life emerged on Earth; as soon as the conditions were right, life appeared. Now, life still could have come from space. What gets me, is that if it was THAT easy for life to emerge, it should emerge over and over again as conditions are still favorable for life.

Problems with this reasoning are

1. Perhaps life can only emerge in a non-oxygen environment were the temperature is near 200F (conditions of Earth 3.8BYA)
2. the chances of life being created is one in five-million; say if life gets a chance to form, once every five-million years, that's a lot of time for us, but in geological time, nothing really.

Oxygen (O2) is definitely a factor. Variants of the Miller/Urey experiment have shown that simple organic compounds such as amino acids form easily in hydrogen-rich conditions, but not in oxygen-rich conditions.
The high temperatures (by our standards) of Hadean Earth may also have been a plus for abiogenesis. Formation of peptide bonds (which link amino acids into protein-like chains) is not thermodynamically favoured at what we think of as "room temperature", but becomes so (at least for certain combinations of amino acids) around 60 degrees Celsius, which is 140 Fahrenheit. See Flegmann AW Energetics of peptide bond formation at elevated temperatures (http://www.ncbi.nlm.nih.gov/pubmed/448749).

pzkpfw
2013-Oct-28, 04:01 AM
What gets me, is just how quickly life emerged on Earth; as soon as the conditions were right, life appeared. Now, life still could have come from space. What gets me, is that if it was THAT easy for life to emerge, it should emerge over and over again as conditions are still favorable for life.

Problems with this reasoning are

1. Perhaps life can only emerge in a non-oxygen environment were the temperature is near 200F (conditions of Earth 3.8BYA)
2. the chances of life being created is one in five-million; say if life gets a chance to form, once every five-million years, that's a lot of time for us, but in geological time, nothing really.

Or, the life that's already here trumps (eats?) any "new" life that appears?

Colin Robinson
2013-Oct-28, 04:10 AM
Or, the life that's already here trumps (eats?) any "new" life that appears?

Yes, Charles Darwin made that suggestion in his famous letter of 1871, where he imagined formation of the first protein in a "warm little pond". (It is quoted on the WP page Abiogenesis (https://en.wikipedia.org/wiki/Abiogenesis).)


at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.

Paul Wally
2013-Oct-28, 02:40 PM
I am saying that the complexity of the molecules is what realises the potential for protein synthesis in the first instance. These molecules are prone to performing this function, by using whatever available means they can.

It's not just molecular complexity that is required. The various types of molecules have co-evolved to produce proteins, so what realizes that potential is the relation between the molecules rather than the intrinsic complexity of the molecules.

kevin1981
2013-Oct-28, 06:50 PM
I have only recently started to learn about molecular biology but it is very interesting. I was wondering about past education and what jobs do Colin Robinson, Selfsim and Paul Wally do.. ? I hope i am not being to rude, it is just that you all have a great understanding about these subjects and i am interested in how you have acquired it.

For 3 billion years all life was microscopic and unicellular, why did it change ?

Selfsim
2013-Oct-28, 08:08 PM
I have only recently started to learn about molecular biology but it is very interesting. I was wondering about past education and what jobs do Colin Robinson, Selfsim and Paul Wally do.. ? I hope i am not being to rude, it is just that you all have a great understanding about these subjects and i am interested in how you have acquired it. Oh I'm an Astrophysicist working as an Astrobiologist.
(… Just kidding! :p :) What I am, is as I appear to be, from the words I write ..)


For 3 billion years all life was microscopic and unicellular, why did it change ?It changed - that's what's known.

Why it changed, is explained by a lot of developed reasoning, but the increased complexity, facilitated by the environment, has improved the chances of survival for organisms on Earth, and resulted in their persistence in that environment over time.

kevin1981
2013-Oct-28, 08:28 PM
It changed - that's what's known.

Why it changed, is explained by a lot of developed reasoning, but the increased complexity, facilitated by the environment, has improved the chances of survival for organisms on Earth, and resulted in their persistence in that environment over time.

Thanks, i guess it is a common sense answer really. I just like asking these questions to people who know what they are talking about to see what they say. I take it you are a biologist, molecular biologist type person !

Selfsim
2013-Oct-28, 08:30 PM
It's not just molecular complexity that is required. The various types of molecules have co-evolved to produce proteins, so what realizes that potential is the relation between the molecules rather than the intrinsic complexity of the molecules.Compounds form from elements because of the electrostatic force of attraction between opposite charges (or dipole attraction). Such forces are established by differences in the population of electron orbits amongst the elements. Van der Waals forces are akin to the totality of intermolecular forces. All of these are caused by the makeup of the base units (elements, other molecules, electron orbital populations, etc).

What happens between the large bio-molecules we're talking about, is a function of their shape and composition.

Colin Robinson
2013-Oct-28, 08:33 PM
I have only recently started to learn about molecular biology but it is very interesting. I was wondering about past education and what jobs do Colin Robinson, Selfsim and Paul Wally do.. ? I hope i am not being to rude, it is just that you all have a great understanding about these subjects and i am interested in how you have acquired it.

I think these threads are for talking about the topics, rather than for talking about ourselves. Did you know that you can connect with any contributor's profile, or send a message to them, by moving your mouse over the underlined name at the top of a post, and then clicking?


For 3 billion years all life was microscopic and unicellular, why did it change ?

During the period when life on Earth was entirely unicellular and microscopic, a couple of things happened which helped make multicellular life possible later on. One was emergence of the cyanobacteria, which perform photosynthesis and produce oxygen. Another was the appearance of the eukaryotic cell, which is more complex than the cells of bacteria and archaea.

Have you looked at the WP page Evolutionary History of Life (https://en.wikipedia.org/wiki/Evolutionary_history_of_life)?

KABOOM
2013-Oct-28, 08:46 PM
You are saying that cells today are a lot more complex that simple organic or inorganic molecules?

True enough. There is an oft-quoted statement by the cellular biologist Lynn Margulis:



What I still don't understand, is why you think that this diminishes the relevance of experiments which study how organic molecules (simple or complex) become encapsulated (randomly or selectively) in lipid membranes.

Nick Lane in his book, "Oxygen", took the opposite view from Margulis in that "to go from bacterium to people is MORE of a step than to go from a mixture of amino acids to a bacterium. His premise seemed to hone on how "un-probable" it seemed for single celled entities to meld together and form more complex entities given the increased difficulty that could be encountered in terms of reproduction. I've seen this view posited by many "Rare Earth" proponents as well.

Selfsim
2013-Oct-28, 10:23 PM
What I still don't understand, is why you think that this diminishes the relevance of experiments which study how organic molecules (simple or complex) become encapsulated (randomly or selectively) in lipid membranes.Well, good question .. :)

See, the physics of modern-day bio-macromolecules, (whilst still following the fundamental physical and chemical laws), is complexified to such a degree, that new and unexpected behaviours emerge. These identical behaviours, in totality, could not possibly have existed if the precursor molecules were vastly simpler, (ie: as the story goes). Studying the behaviours of modern-day cells and sub-components, leads to greater assumptions, (and thereby increased uncertainty), about molecules in the ancient past. To believe that the behaviour of modern-day bio-molecules is somehow similar to behaviours in the past, requires a huge leap of faith, and vast oversimplification of the influences driving the outcomes emergent from the complexity of the 'evolved' molecules. Retracing the history (past information) of adaptive complex systems, is not possible because the information about influences and causes, has been lost in the surrounding environment. Whilst the end result is repeatably observable today, the way that result came about, starting from its origin, is not. Its a pity, because the molecules themselves are a record of the end results of all those influences, but the information they contain about what formed them, is not decodable (from the molecules themselves).

I think this is where my discontent about all this is coming from.

Bissette's suggested 'next step' of studying 'similar, but less complex molecules', is almost an oxymoron because doing so, removes the complexity which is the source of the behaviour being studied. Far less complex and simpler bio-molecular behaviours, is already well known, and well studied (eg: the kinetics of enzyme reactions). His words might flow nicely off the end of a journalist's the fingers at the keyboard, but the suggestion also fundamentally changes the problem being studied, which in this case, was not abiogenesis .. it was always bio-engineering starting with modern cells.

Noclevername
2013-Oct-28, 10:33 PM
"Minimal molecular complexity", eh?


See, the physics of modern-day bio-macromolecules, (whilst still following the fundamental physical and chemical laws), is complexified to such a degree, that new and unexpected behaviours emerge. These identical behaviours, in totality, could not possibly have existed if the precursor molecules were vastly simpler, (ie: as the story goes).

I see "'similar, but less complex molecules". Nowhere did I read "vastly" simpler or any synonyms, and certainly not "Minimal molecular complexity".

I may have read it wrong, or skipped something. Can you show me where the article said or implied these things?

Selfsim
2013-Oct-28, 11:20 PM
I see "'similar, but less complex molecules". Nowhere did I read "vastly" simpler or any synonyms, and certainly not "Minimal molecular complexity".

I may have read it wrong, or skipped something. Can you show me where the article said or implied these things?...

It may be that these particular molecules are suited to this kind of self-organisation because they are already highly evolved. An important next step is to see if similar, but less complex, molecules are also capable of this feat.'Tis I who have interpreted the above words and responded to the intent with the terms denoted inside inverted commas. Ie: "minimal molecular complexity", etc. This is to do draw analogy with projects such as the "Minimal Genome" project, and the ensuing concept of "Essential genes", both of which have been shown to result in non-intuitive complexity. What would the "minimal molecular complexity" measure be, in order to produce fluorescent proteins as the end product, following encapsulation in the lipid membrane compounds which were used in this study?

If your issue is that the terms I used, were not explicitly used in the article or paper, then you're welcome to be right about that .. and … that would be a trivial matter compared with the point I'm making.

Githyanki
2013-Oct-29, 05:21 AM
Or, the life that's already here trumps (eats?) any "new" life that appears?


Thanks: I totally forgot one of my earliest thoughts, that any new life that emerges simply gets eaten by the more advanced life...

Colin Robinson
2013-Oct-29, 09:04 AM
Well, good question .. :)

Thanks!


See, the physics of modern-day bio-macromolecules, (whilst still following the fundamental physical and chemical laws), is complexified to such a degree, that new and unexpected behaviours emerge. These identical behaviours, in totality, could not possibly have existed if the precursor molecules were vastly simpler, (ie: as the story goes). Studying the behaviours of modern-day cells and sub-components, leads to greater assumptions, (and thereby increased uncertainty), about molecules in the ancient past. To believe that the behaviour of modern-day bio-molecules is somehow similar to behaviours in the past, requires a huge leap of faith,

There is no need to rely on a "leap of faith".

The extent of similarities and differences between complex biomolecules and their simpler chemical relatives, in terms of how they interact with membranes made of lipids and similar compounds, can be researched through experiments.

There was another recent empirical study, cited in a quite recent thread in this forum Natural affinities may have helped RNA life (http://cosmoquest.org/forum/showthread.php?145496-Natural-affinities-may-have-helped-RNA-life) , about interaction between a fatty acid (fatty acids being compounds closely related to lipids) and the bases and sugars which are components of RNA. Please note: this study was not about RNA itself, but about simple building blocks of RNA.

The study found that the binding process is selective — some related bases bind chemically to the fatty acid, while others do not. The researchers concluded:


Thus, aggregates of a prebiotic amphiphile bind certain heterocyclic bases and sugars, including those found in RNA, and this binding stabilizes the aggregates against salt. These mutually reinforcing mechanisms might have driven the emergence of protocells.

marsbug
2013-Oct-29, 11:36 AM
Fascinateing! I've done some reading and gotten the distinct impression that lipid vesicles are a few steps along the road to 'life', even without any internal chemical machinery - they maintain a constant internal environment, reproduce by binary fission, etc. If there is evidence that lipid molecules might also preferentially bind with the type of compound that goes into constructing said machinery that seems a fairly big coincidence..... how many compounds that could also be used to build this kind of chemical machinery are there? And how many other kinds of membrane/vesicle forming molecule are there that don't exhibit such preferential binding? And, yes, I realise Colin was posting about fatty acids preferentially binding, and fatty acids are only related to lipids, but it's still an interesting (to me) line of thought.....

Paul Wally
2013-Oct-29, 07:22 PM
Compounds form from elements because of the electrostatic force of attraction between opposite charges (or dipole attraction). Such forces are established by differences in the population of electron orbits amongst the elements. Van der Waals forces are akin to the totality of intermolecular forces. All of these are caused by the makeup of the base units (elements, other molecules, electron orbital populations, etc).

What happens between the large bio-molecules we're talking about, is a function of their shape and composition.

Yes, that's all right, but it represents an incomplete picture. As I'm saying, it's not just molecular complexity that makes something like
protein synthesis possible, it's also system complexity, i.e. the system of molecules both simple and complex. A large molecule would be unable to perform its usual function in isolation from the larger system. It will even break down or become modified when not exposed to the right physical and chemical conditions.

Colin Robinson
2013-Oct-29, 07:58 PM
Fascinateing! I've done some reading and gotten the distinct impression that lipid vesicles are a few steps along the road to 'life', even without any internal chemical machinery - they maintain a constant internal environment, reproduce by binary fission, etc. If there is evidence that lipid molecules might also preferentially bind with the type of compound that goes into constructing said machinery that seems a fairly big coincidence..... how many compounds that could also be used to build this kind of chemical machinery are there? And how many other kinds of membrane/vesicle forming molecule are there that don't exhibit such preferential binding? And, yes, I realise Colin was posting about fatty acids preferentially binding, and fatty acids are only related to lipids, but it's still an interesting (to me) line of thought.....

When I wrote that fatty acids were related to lipids, I was thinking of lipids as fats, which are compounds (esters) of fatty acids and glycerol. I just did some checking, and it seems the accepted definition of lipid includes not only fats but also a range of other substances including the fatty acids themselves.

In short, I was wrong — fatty acids are lipids!

See the WP page Lipid (https://en.wikipedia.org/wiki/Lipid), where there is a definition taken from the Journal of Lipid Research.

Selfsim
2013-Oct-29, 10:04 PM
There is no need to rely on a "leap of faith".

The extent of similarities and differences between complex biomolecules and their simpler chemical relatives, in terms of how they interact with membranes made of lipids and similar compounds, can be researched through experiments.

There was another recent empirical study, cited in a quite recent thread in this forum Natural affinities may have helped RNA life (http://cosmoquest.org/forum/showthread.php?145496-Natural-affinities-may-have-helped-RNA-life) , about interaction between a fatty acid (fatty acids being compounds closely related to lipids) and the bases and sugars which are components of RNA. Please note: this study was not about RNA itself, but about simple building blocks of RNA.

The study found that the binding process is selective — some related bases bind chemically to the fatty acid, while others do not. The researchers concluded:This study was focused on an abiogenesis hypothesis (RNA first, from what I can see). The study in the OP was not. The 'affinities' study was thus able to add some small statements to the abiogenesis hypothesis. The OP study returned information about the relationships between vesicle sizes, their contents and their comparative formation dynamics, given the initial conditions of modern molecular machinery, specific modern-day lipids, and pre-defined lab preparation procedures.

The sub-molecular inhibition of the salt sourced flocculation of an amphiphile (hypothesised to be pre-biotically available) by RNA ribose, in the Black etal study, is non-intuitively associated with the power-law observations and subsequent protein synthesis in the Stano etal study. RNA frequently interacts with cell membranes during many cellular processes. How and under what specific conditions it does this, are unknowns and answers are needed for bio-engineering purposes. Stano etal make no references to the Black et al mechanisms. In fact in explaining their own observations, they say:
These fascinating preliminary observations unveil an underlying complexity that is based on the interplay between vesicle formation mechanisms and solute encapsulation, a signature of the “individuality” in the assemblage of cells from their components. Ultimately, the roots of this “diversity” derive from the fact that lipid vesicles are not formed under thermodynamic control, rather they are “kinetic traps”. Each liposome follows its own assembly mechanism that is determined by stochastically unique micro/local conditions.They go on (see section 4) to explain that:
Very little is known a priori on distributions of size, lamellarity, membrane rigidity, membrane permeability, lipid patches, single- or multi-solute concentration, between-solutes ratios, pore and membrane-protein density, multi-vesicle architecture etc. Similarly, the relation between the statistic distributions of these properties is not well known, as well as how they are related with each other. From a careful analysis of these distributions, however, it is possible to get insights into the physical mechanisms of liposome formation.In other words, there is a lot more to consider above and beyond simple chemical thermodynamic affinities between RNA ribose and lipid membranes .. and that would go for prebiotics and modern molecules, (as long as one accepts that fundamental physics has not changed since life's emergence and the present day).

Frankly, the idea of going from the encapsulation of some ribose molecule inside some pre-biotic fatty acid (>~2.4Gya), to a living cell, is way MORE of a step than going from modern-day RNA and lipids, to a protein producing cell, because of the vast difference in molecular complexity.

Selfsim
2013-Oct-29, 10:31 PM
Yes, that's all right, but it represents an incomplete picture. As I'm saying, it's not just molecular complexity that makes something like protein synthesis possible, it's also system complexity, i.e. the system of molecules both simple and complex. A large molecule would be unable to perform its usual function in isolation from the larger system. It will even break down or become modified when not exposed to the right physical and chemical conditions.The "large molecule" contains the information for building the larger system … Otherwise: where else did all this other 'machinery' come from?

I can see we need to start a new thread to explore what is meant by "system complexity". 'Uniqueness' is one extreme degree of a measure of system complexity .. 'self-similarity' might be the other. One doesn't need to know anything about the mechanisms in a given system to discuss its complexity though. (… Although I can see that knowledge of what goes on in such a system, does help ideologically challenged reductionists in temporarily abandoning their skepticism).

Paul Wally
2013-Oct-29, 11:17 PM
The "large molecule" contains the information for building the larger system … Otherwise: where else did all this other 'machinery' come from?

I assume you're referring to DNA. Now DNA already finds itself within a system supporting its functionalities within the system. There is mutual inter-dependence between the various components of the system. It's a closed loop chicken-egg situation. We don't know which came first; DNA or cell chemistry or whether it even makes sense to ask that question.



I can see we need to start a new thread to explore what is meant by "system complexity". 'Uniqueness' is one extreme degree of a measure of system complexity .. 'self-similarity' might be the other. One doesn't need to know anything about the mechanisms in a given system to discuss its complexity though. (… Although I can see that knowledge of what goes on in such a system, does help ideologically challenged reductionists in temporarily abandoning their skepticism).

I've got a better idea. Why don't you look up the term 'system complexity' then we don't have to quibble about semantics in a science forum.

Selfsim
2013-Oct-30, 08:00 PM
… I've got a better idea. Why don't you look up the term 'system complexity' then we don't have to quibble about semantics in a science forum.Hmm … I feel no need for quibbling about semantics … do you?

Selfsim
2013-Oct-30, 09:23 PM
I've started a new thread (http://cosmoquest.org/forum/showthread.php?147057-Self-Dissimilarity-and-Complexity) in the Science Forum (SF) about Self-Dissimilarity measures as a way of distinguishing Complex Systems. (The topic is way broader than just about living systems or life's fundamental (various) complex systems. Comments about the life aspects could be discussed here, however .. (we might need a new LiS thread for that .. or just add 'em onto the SF thread).

This approach is a more formalised method which relies less heavily on terms, definitions, and trying to shove things into some hypothesized model which is labelled: 'life'. In the author's words:
Puzzles like how to decide whether a system “is alive” are rendered moot if approached from the perspective of self-dissimilariy. We argue that such puzzles arise from trying to squeeze physical phenomena into pre-existing theoretical models (e.g., for models concerning “life” one must identify the atomic units of the physical system, define what is meant for them to reproduce, etc.). We instead view life as a characteristic signature of a system’s self-dissimilarity over a range of spatio-temporal scales. In this view life is more than a yes/no bit, and even more than a real number signifying a degree—it is an entire signature.