PDA

View Full Version : Models of abiogenesis: Stuart Kauffman and Addy Pross



Colin Robinson
2013-Sep-13, 04:37 AM
(from the thread "Did life here, start out there?")

Oh .. (and in all fairness), I should add that this is about when another particular LiS contributor usually 'chirps' up,

Are you talking about me by any chance, Selfsim? :)


and reminds us that Stuart Kauffman's interpretation from his studies on 'autocatalytic sets' is that, if this is the way abiogenesis proceeds, then in his view, life is an 'inevitable' outcome ... (whereupon I usually remind others, that this is his speculative opinion based on a bunch of assumptions ... which is fair enough too, I might add).


Dynamic Kinetic Stability: Toward a general theory of evolution: Extending Darwinian theory to inanimate matter. By Addy Pross, June 2011, Journal of Systems Chemistry. (http://cosmoquest.org/forum/showthread.php?146137-Abiogenesis-and-Evolution-Unified&p=2155836#post2155836)
I posted the topic in a new thread in the Science Forum, as its 'hardcore' mainstream science.

Very interesting paper by Addy Pross. You've described Kauffman's work as "speculative opinion" but Pross' work as " 'hardcore' mainstream science".

I'm posting this in the LiS forum because I want to compare the "mainstream" Addy Pross with the "speculative" Stuart Kauffman. And also because I'm interested in what their work suggests about life in universe.

I'd suggest that Kauffman and Pross actually have a lot in common, both in regard to their methods of enquiry (Kauffman's work is based on empirical chemistry as well as theoretical modelling, and Pross is the same) and also in regard to their conclusions.

As you've mentioned, Kauffman talks about "autocatalytic sets". Pross in section 2.1.2 of his paper talks about "cooperative cross-catalytic networks".

Pross, like Kauffman, sees the possibility that the systems with the characteristics of life could be based on chemical compounds unfamiliar to us — "life forms not related to the protein-nucleic acid format as we know it, would be possible" (Pross, section 2.3.2).

One difference between Pross and Kauffman is in relation to the debate between replicator-first and metabolism-first concepts. Kauffman's concept of abiogenesis can I think be fairly described as "metabolism first", while Pross' concept is "replication and metabolism together" (Pross, section 2.3.3).

Direct link to Addy Pross paper. (http://www.jsystchem.com/content/2/1/1#)

Selfsim
2013-Sep-13, 05:55 AM
You've duplicated a thread because I expressed an opinion?

Man, this place is beyond confusion!

Colin Robinson
2013-Sep-13, 06:45 AM
You've duplicated a thread because I expressed an opinion?

The opinions you've expressed in the thread "Did life here, start out there?" raised questions for me about whether Kauffman and Pross are as different as you seem to think. Would you like to clarify why you think that Kauffman's work about abiogenesis is "speculation", but that Pross is doing "mainstream science"?

Selfsim
2013-Sep-13, 11:24 AM
Kauffman invents terminologies which have no meaning. I'm not convinced he has his hands firmly around thermodynamics (as much as a theoretical physicist would). 'Closed' and 'isolated' systems are often confused in his works. He assumes biospheres are continuously in a nonequilibrium state .. but they aren't perpetually in such a state at all (on a rotating Earth). He tends to wax lyrical on more philosophical points, which gives the impression the philosophy has more significance, before he's actually nailed home the science parts. He seems to use distinctions of 'dead' and 'alive' molecules, but I've never seen a scientific definition for 'dead' or 'alive' molecules? He also brings religion and deities into his dissertations for no particular reasons other than to position them as place-holders for 'creativity in the abiotic and biotic universe'. He kind of anthropomorphises molecules, as thought they have 'free will', or consciousness, or something ... His 'self-sustaining network of reactions' never seems to be explained in terms of sources and sinks of energy. (One is sort of left with an image of a perpetual motion machine(?)). Don't get me wrong ... overall, I think he's made great in-roads into applying systems complexity to the abiogenesis and life issues .. but I also think he's done a pretty lousy job of communicating it all in a clear, objective and understandable way, suited for a mainstream scientific audience.

Pross' work is more readable and understandable, when taken from a thermodynamics principles perspective. (I think the other thread is my test for what others might have to say about this). He doesn't invent things with no meaning. He uses simple analogies and examples. He explains the dynamic behaviours of self-replicating systems, and actually attempts to use mathematics to describe what he means. He doesn't wax lyrical using philosophical concepts to make his fundamental points.

I think the concepts they're both talking about aren't at 'odds' with eachother. I think they are both heading in similar directions. Its just that I've found Pross' paper to be way more readable when coming from a classical thermodynamics and systems complexity viewpoint, whereas Kauffman relies more on not-necessarily shared, philosophical speculation bases.

Paul Wally
2013-Sep-13, 02:29 PM
Kauffman invents terminologies which have no meaning. I'm not convinced he has his hands firmly around thermodynamics (as much as a theoretical physicist would). 'Closed' and 'isolated' systems are often confused in his works. He assumes biospheres are continuously in a nonequilibrium state .. but they aren't perpetually in such a state at all (on a rotating Earth). He tends to wax lyrical on more philosophical points, which gives the impression the philosophy has more significance, before he's actually nailed home the science parts. He seems to use distinctions of 'dead' and 'alive' molecules, but I've never seen a scientific definition for 'dead' or 'alive' molecules? He also brings religion and deities into his dissertations for no particular reasons other than to position them as place-holders for 'creativity in the abiotic and biotic universe'. He kind of anthropomorphises molecules, as thought they have 'free will', or consciousness, or something ... His 'self-sustaining network of reactions' never seems to be explained in terms of sources and sinks of energy. (One is sort of left with an image of a perpetual motion machine(?)). Don't get me wrong ... overall, I think he's made great in-roads into applying systems complexity to the abiogenesis and life issues .. but I also think he's done a pretty lousy job of communicating it all in a clear, objective and understandable way, suited for a mainstream scientific audience.



Could you reference an accessible sample of Kauffman's work so that I/we could also see what the fuss is all about?

Cougar
2013-Sep-13, 03:57 PM
Could you reference an accessible sample of Kauffman's work so that I/we could also see what the fuss is all about?

Well, I quite liked Kauffman's 1995 book At Home in the Universe, The Search for the Laws of Self-Organization and Complexity. He models a system of arbitrary molecules or chemicals. He assumes that any particular molecule may act as a catalyst for another's chemical reaction. (I don't think that's too unreasonable.) He gives this a very low probability. Then he adds different generic molecules - diversity. He found that once the diversity of molecules reaches a particular threshold, self-sustaining auto-catalytic sets of molecules emerge. As in most complex systems, the fine details are not important. It doesn't matter what the particular molecules are. What matters is that some molecules speed up a particular chemical reaction, and that the number and variety of molecules passes a certain threshold. He's not saying this results in life. It's more like the first step toward life. (He may not be the best writer, but he's not that bad.)

Colin Robinson
2013-Sep-13, 08:39 PM
Could you reference an accessible sample of Kauffman's work so that I/we could also see what the fuss is all about?

Here's a freely accessible sample of Kauffman's work on the topic of abiogenesis, from the journal Life (2011).

Approaches to the Origin of Life on Earth (http://www.mdpi.com/search?q=Origin+of+Life&journal=life&volume=&authors=Kauffman&section=&issue=&article_type=&special_issue=&page=&search=Search)

Selfsim
2013-Sep-13, 09:12 PM
Could you reference an accessible sample of Kauffman's work so that I/we could also see what the fuss is all about?The text I'm referencing comes form a bunch of his books. His most noted publication is probably his first:

1. "At Home in the Universe: the Search for the Laws of Self-Organization and Complexity", 1995, Oxford University Press;

Others are:
2. "Investigations" (pages x to xi, 4-5) (2000/2). Oxford University Press.
3. "Reinventing the Sacred: A New View of Science, Reason, and Religion" (2008). Basic Books. (One I find pretty far-fetched).
4. "Origins of Order: Self-Organization and Selection in Evolution", (1993). Oxford University Press. Technical monograph.

An enlightening commentary on Kauffman's theories is discussed in:

5. Thims, Libb. (2007). Human Chemistry (Volume One) (http://books.google.com.au/books?id=05E2V-LM-c8C&dq=human+chemistry+%28volume+one%29&q=Kauffman#v=snippet&q=Kauffman&f=false), (ch. 5: "Molecular Evolution", pages. 121-146, particularly 108, 132-33). (Morrisville, NC: LuLu).

The core of his theories are formed by what he calls:
i) 'The Adjacent Possible' ((2) above) ;
ii) 'Auto-catalytic closure';
iii) 'Thermodynamic work cycles' ((2) above) and;
iv) 'The Fourth Law' of thermodynamics (which subsequently seems to get replaced by a what I'd sort of call: a 'religion-based version of thermodynamics (in (3 above)).

Swift
2013-Sep-13, 10:20 PM
Well, I quite liked Kauffman's 1995 book At Home in the Universe, The Search for the Laws of Self-Organization and Complexity. He models a system of arbitrary molecules or chemicals. He assumes that any particular molecule may act as a catalyst for another's chemical reaction. (I don't think that's too unreasonable.) He gives this a very low probability. Then he adds different generic molecules - diversity. He found that once the diversity of molecules reaches a particular threshold, self-sustaining auto-catalytic sets of molecules emerge. As in most complex systems, the fine details are not important. It doesn't matter what the particular molecules are. What matters is that some molecules speed up a particular chemical reaction, and that the number and variety of molecules passes a certain threshold. He's not saying this results in life. It's more like the first step toward life. (He may not be the best writer, but he's not that bad.)
I have to admit I have not read the book and my be speaking from a great state of ignorance. I may also be biased as an experimental chemist. But I have some troubles with the idea that once you get a particularly rich variety of molecules, that autocatalytic sets of molecules (reactions) emerge, for an undescribed, generic set of molecules. I think the specific set of molecules matters greatly, and one cannot make such a statement generic.

Selfsim
2013-Sep-14, 12:51 AM
I have to admit I have not read the book and my be speaking from a great state of ignorance. I may also be biased as an experimental chemist. But I have some troubles with the idea that once you get a particularly rich variety of molecules, that autocatalytic sets of molecules (reactions) emerge, for an undescribed, generic set of molecules. I think the specific set of molecules matters greatly, and one cannot make such a statement generic.In his book, "Investigations", he asserts the statement you mention, and then he goes about 'investigating' what qualities a physical system must have, in order to be to qualify as an 'autonomous agent'.1

In giving his definition of an 'autonomous agent', he then goes immediately to an example of a system where a bacterium is swimming upstream in a glucose gradient. The issue here, is that the bacterium is already a hugely complex molecule, (far from being a simple one) .. So, I guess he's sort of forgotten his original argument that: 'self-reproducing molecular systems will form in any large and sufficiently complex chemical reaction'?!? :confused:

This is classic Kauffman style-rationale .. and it is not at all clear. He then goes on to ask: "What must a physical system be, such that it can act on its own behalf?"2 Then he goes on to reason: "might there be a fourth law of thermodynamics for self-constructing open thermodynamic systems such as biospheres? " It all gets more complicated from that point onwards, and leads to the idea that a 'molecular autonomous agent', is a self-reproducing molecular system, capable of carrying out one or more work cycles. (Carnot work-cycles, that is).

(I always get confused from this point onwards ... )

Footnote:
1. This is sort of what I mean about how he seems to always introduce new 'verbage', to explain unintuitive concepts).
2.Well if ya ask me .. a bacterium swimming upstream in a glucose gradient is what he means .. :confused:

Hlafordlaes
2013-Sep-14, 03:57 AM
I have to admit I have not read the book and my be speaking from a great state of ignorance. I may also be biased as an experimental chemist. But I have some troubles with the idea that once you get a particularly rich variety of molecules, that autocatalytic sets of molecules (reactions) emerge, for an undescribed, generic set of molecules. I think the specific set of molecules matters greatly, and one cannot make such a statement generic.

I'd love to hear your take in the other thread on the Pross paper. I'd quote from it here, but would rather not derail this thread.

Colin Robinson
2013-Sep-14, 04:44 AM
I have to admit I have not read the book and my be speaking from a great state of ignorance. I may also be biased as an experimental chemist. But I have some troubles with the idea that once you get a particularly rich variety of molecules, that autocatalytic sets of molecules (reactions) emerge, for an undescribed, generic set of molecules. I think the specific set of molecules matters greatly, and one cannot make such a statement generic.

Kauffman's theories are grounded in experimental chemistry as well as in systems theory. He would probably agree that "the specific set of molecules matters", in the sense that it makes a difference what range of catalytic properties they have.

His article mentioned in post 7 discusses whether the earliest self-catalysing systems on Earth were more likely based on RNA sequences or on peptides. He considers that "peptides are more chemically diverse than RNA sequences, hence might form CAS more readily". (CAS means "collectively autocatalytic sets".)

Paul Wally
2013-Sep-15, 12:13 PM
Well, I quite liked Kauffman's 1995 book At Home in the Universe, The Search for the Laws of Self-Organization and Complexity. He models a system of arbitrary molecules or chemicals. He assumes that any particular molecule may act as a catalyst for another's chemical reaction. (I don't think that's too unreasonable.) He gives this a very low probability. Then he adds different generic molecules - diversity. He found that once the diversity of molecules reaches a particular threshold, self-sustaining auto-catalytic sets of molecules emerge. As in most complex systems, the fine details are not important. It doesn't matter what the particular molecules are. What matters is that some molecules speed up a particular chemical reaction, and that the number and variety of molecules passes a certain threshold. He's not saying this results in life. It's more like the first step toward life. (He may not be the best writer, but he's not that bad.)

Thanks for that. I also prefer the more general or universal approach to the problem of how life emerges. Getting too entangled in particularities is not the way to go, in my opinion.


Here's a freely accessible sample of Kauffman's work on the topic of abiogenesis, from the journal Life (2011).

Approaches to the Origin of Life on Earth (http://www.mdpi.com/search?q=Origin+of+Life&journal=life&volume=&authors=Kauffman&section=&issue=&article_type=&special_issue=&page=&search=Search)

Thank you for that link. I read through it and I find that it's quite rich in interesting ideas. There are loads of possibilities in there for further research.


The text I'm referencing comes form a bunch of his books. His most noted publication is probably his first:

1. "At Home in the Universe: the Search for the Laws of Self-Organization and Complexity", 1995, Oxford University Press;

Others are:
2. "Investigations" (pages x to xi, 4-5) (2000/2). Oxford University Press.
3. "Reinventing the Sacred: A New View of Science, Reason, and Religion" (2008). Basic Books. (One I find pretty far-fetched).
4. "Origins of Order: Self-Organization and Selection in Evolution", (1993). Oxford University Press. Technical monograph.

An enlightening commentary on Kauffman's theories is discussed in:

5. Thims, Libb. (2007). Human Chemistry (Volume One) (http://books.google.com.au/books?id=05E2V-LM-c8C&dq=human+chemistry+%28volume+one%29&q=Kauffman#v=snippet&q=Kauffman&f=false), (ch. 5: "Molecular Evolution", pages. 121-146, particularly 108, 132-33). (Morrisville, NC: LuLu).

The core of his theories are formed by what he calls:
i) 'The Adjacent Possible' ((2) above) ;
ii) 'Auto-catalytic closure';
iii) 'Thermodynamic work cycles' ((2) above) and;
iv) 'The Fourth Law' of thermodynamics (which subsequently seems to get replaced by a what I'd sort of call: a 'religion-based version of thermodynamics (in (3 above)).

Thanks Selfsim, for clarifying your opinions of Kauffman. However, I do think you ought to evaluate each of his ideas on its own merit. His work on
autocatalytic sets does seem to be an important contribution to theoretical biology and it does have empirical support also, so it is really irrelevant what Kauffman's other views may be.

I see you have a new pet theory now. I'll have a look at the Pross paper and critically look at the content thereof, bearing in mind that any other views that Pross may hold do not detract from what is inside the paper.

Swift
2013-Sep-16, 01:56 AM
Kauffman's theories are grounded in experimental chemistry as well as in systems theory. He would probably agree that "the specific set of molecules matters", in the sense that it makes a difference what range of catalytic properties they have.

His article mentioned in post 7 discusses whether the earliest self-catalysing systems on Earth were more likely based on RNA sequences or on peptides. He considers that "peptides are more chemically diverse than RNA sequences, hence might form CAS more readily". (CAS means "collectively autocatalytic sets".)
I am somewhat familiar with the arguments about RNA and/or peptides as catalysts and their role in abiogenesis. I don't have a preference of one versus the other, or versus other schemes, but I think they are both legit systems for consideration.

But that seems wholly different than a statement that any complex chemical system will develop autocatalytic behavior. I think he overreaches.

Colin Robinson
2013-Sep-16, 02:38 AM
I am somewhat familiar with the arguments about RNA and/or peptides as catalysts and their role in abiogenesis. I don't have a preference of one versus the other, or versus other schemes, but I think they are both legit systems for consideration.

But that seems wholly different than a statement that any complex chemical system will develop autocatalytic behavior. I think he overreaches.

I don't think Kauffman's point is that any complex chemical system will develop autocatalytic sets. As Cougar mentioned, a necessary condition is presence of molecules with catalytic properties.


What matters is that some molecules speed up a particular chemical reaction…

I've read accounts of abiogenesis (not by Kauffman) where the crucial event was considered to be formation of the first self-replicating molecule (e.g. the first DNA molecule, or the first RNA molecule).

Kauffman's theory of autocatalytic sets (as I understand it) says that the life does not emerge from any single molecule, but rather from a particular sort of system of inter-related molecules.

Selfsim
2013-Sep-16, 08:31 AM
Thanks Selfsim, for clarifying your opinions of Kauffman. However, I do think you ought to evaluate each of his ideas on its own merit. His work on autocatalytic sets does seem to be an important contribution to theoretical biology and it does have empirical support also, so it is really irrelevant what Kauffman's other views may be. AIUI, in Kauffman’s model, reactions consist of the concatenation and cutting of molecular sequences, up to some maximal (large) length, starting from small sequences (in length), where each molecule has a certain probability of (independently) catalysing any given reaction. He arbitrarily assigns the same probability of this happening to each molecule.

It has been shown (in theory) that these assumptions are critical to the conclusion formed. Kauffman has maintained that we should expect self-sustaining, autocatalytic networks to emerge in random chemical systems, once some threshold (in ‘complexity’, ‘connectivity’ or ‘catalysation rate’) is exceeded.

The above assumption calls for some scrutiny as to whether or not there is a requirement of fine-tuning of the underlying biochemistry for such networks to occur in the first place. I'm not sure whether or not this aspect has been actively investigated yet? (Although, perhaps the recent Urzymes research (http://www.science20.com/news_articles/rna_world_hypothesis_primordial_soup_may_need_new_ recipe-120456) demonstrates that such investigation is alive and healthy?)

It has been shown by others (Mossel/Steel1) that the probability that such a system contains an autocatalytic set, is entirely dependent on the average number of concatenation reactions in the system, divided by the length of the sequence doing the catalysing. If this figure is small, then the probability that the system contains an autocatalytic set will be small. If its big, then the probability approaches 1.

So, Kauffman's above assertion is balanced on his above (undistinguished) assumptions, but it seems it was left up to others to figure out the validity of them (or otherwise ... it wasn't Kauffman who did this). This leaves me with the view that Kauffman's assertions of 'inevitability' of the emergence of autocatalytic sets from a system, is still predicated on his subjective optimism, (which seems to be often overlooked).

Reference:
1. Random bio-chemical networks: The probability of self-sustaining autocatalysis. (http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/jtbnetworks.pdf) Mossel, Steel, Journal of Theoretical Biology, October 2004.



I see you have a new pet theory now. I'll have a look at the Pross paper and critically look at the content thereof, bearing in mind that any other views that Pross may hold do not detract from what is inside the paper.I think Pross' DKS actually helps to provide a possible universal generalised theory, which supports Kauffman's overall direction. As I said earlier, I don't necessarily see an either/or situation here. Their work seems to be in different spaces, and complementary(?)

KABOOM
2013-Sep-17, 03:30 PM
http://www.sciencedaily.com/releases/2013/09/130913185848.htm

Suggests that self-replicating peptides then led to self-replicating and proto-protein enzymens could translate genetic info before "life molecules"

A.DIM
2013-Sep-23, 05:40 PM
http://www.sciencedaily.com/releases/2013/09/130913185848.htm

Suggests that self-replicating peptides then led to self-replicating and proto-protein enzymens could translate genetic info before "life molecules"

Thanks; I saw that and thought of this thread.

I've remarked on the "too little time" issue what regards abiogenesis on Earth hypotheses, and this research, I think, highlights it:

But for the hypothesis (RNA world) to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. That's a hard sell; scientists calculate that it would take much longer than the age of the universe for randomly generated RNA molecules to evolve sufficiently to achieve the modern level of sophistication. Given Earth's age of 4.5 billion years, living systems run entirely by RNA could not have reproduced and evolved either fast or accurately enough to give rise to the vast biological complexity on Earth today.

"The RNA world hypothesis is extremely unlikely," said Carter. "It would take forever."

And from the abstract:
These new data allow us to demonstrate statistically indistinguishable catalytic profiles for Class I and II aaRSs in both amino acid activation and tRNA acylation, over a time period extending to well before the assembly of full-length enzymes and even further before the Last Universal Common Ancestor. Both Urzymes also exhibit ∼60% of the contemporary catalytic proficiencies. Moreover, they are linked by ancestral sense/antisense genetic coding, and their evident modularities suggest descent from even simpler ancestral pairs also coded by opposite strands of the same gene. Thus, aaRS Urzymes substantially pre-date modern aaRS but are, nevertheless, highly evolved. Their unexpectedly advanced catalytic repertoires, sense/antisense coding, and ancestral modularities imply considerable prior protein-tRNA co-evolution.

Abiogenesis, wherever it occurred appears to have need much more time (and ingredients) than what is found on Earth.

Colin Robinson
2013-Sep-23, 09:04 PM
Thanks; I saw that and thought of this thread.

I've remarked on the "too little time" issue what regards abiogenesis on Earth hypotheses, and this research, I think, highlights it:

But for the hypothesis (RNA world) to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. That's a hard sell; scientists calculate that it would take much longer than the age of the universe for randomly generated RNA molecules to evolve sufficiently to achieve the modern level of sophistication. Given Earth's age of 4.5 billion years, living systems run entirely by RNA could not have reproduced and evolved either fast or accurately enough to give rise to the vast biological complexity on Earth today.

"The RNA world hypothesis is extremely unlikely," said Carter. "It would take forever."

And from the abstract:
These new data allow us to demonstrate statistically indistinguishable catalytic profiles for Class I and II aaRSs in both amino acid activation and tRNA acylation, over a time period extending to well before the assembly of full-length enzymes and even further before the Last Universal Common Ancestor. Both Urzymes also exhibit ∼60% of the contemporary catalytic proficiencies. Moreover, they are linked by ancestral sense/antisense genetic coding, and their evident modularities suggest descent from even simpler ancestral pairs also coded by opposite strands of the same gene. Thus, aaRS Urzymes substantially pre-date modern aaRS but are, nevertheless, highly evolved. Their unexpectedly advanced catalytic repertoires, sense/antisense coding, and ancestral modularities imply considerable prior protein-tRNA co-evolution.

Abiogenesis, wherever it occurred appears to have need much more time (and ingredients) than what is found on Earth.

Carter's argument seems to be that abiogenesis would have taken too much time IF it happened via an "RNA world" route, i.e. with variants of RNA doing all the catalytic work, as well as storing information. But could have happened more quickly if RNA and simple peptide catalysts developed together.

R.A.F.
2013-Sep-23, 09:31 PM
Abiogenesis, wherever it occurred appears to have need much more time (and ingredients) than what is found on Earth.

Interestingly enough, that is about the only thing I remember from my very short read of The 12 Planet.

A.DIM
2013-Sep-24, 01:19 AM
Carter's argument seems to be that abiogenesis would have taken too much time IF it happened via an "RNA world" route, i.e. with variants of RNA doing all the catalytic work, as well as storing information. But could have happened more quickly if RNA and simple peptide catalysts developed together.

I think most OOL hypotheses run into the too-little-time problem, though I may be wrong. Carter's hypothesis too, intimates as much: "Thus, aaRS Urzymes substantially pre-date modern aaRS but are, nevertheless, highly evolved. Their unexpectedly advanced catalytic repertoires, sense/antisense coding, and ancestral modularities imply considerable prior protein-tRNA co-evolution."

And we're back to the hardware / software problem.

To the contrary though, I'd rather think abiogenesis is an inevitable, easily achieved consequence of the make up of our universe.

A.DIM
2013-Sep-24, 01:23 AM
Oh yeah, while we're at it: Did Autocells Lead to Life? (http://www.astrobio.net/exclusive/5703/did-autocells-lead-to-life)

Selfsim
2013-Sep-24, 03:17 AM
Oh yeah, while we're at it: Did Autocells Lead to Life? (http://www.astrobio.net/exclusive/5703/did-autocells-lead-to-life)I actually agree with the underlined part of this:

Deacon emphasizes that, in our search for life elsewhere in the Cosmos, we need to stop thinking about how life was created on Earth, and the specific molecules needed, and instead focus our attention on the general principles involved in the creation of life. However, we don't know what the general principles involved in the creation of life are, at the scales which would lead us to the conclusion that we actually understand this process, so how can we focus on what is unknown, (other than by exploration of our local surrounds and subsequent discovery)?

That spontaneous order can arise from lots of basic molecules, following simple rules is fair enough .. but there's more to it than just that. Otherwise, life would've been synthesised from scratch in the lab. Deacon's 'reciprocal' catalysis and self-assembly, has been known for years (no news there).

The idea that "whole Solar (stellar?) Systems are needed to generate life", is not evidenced. It may be just co-incident in our case, for all we know.
Who would've thought massive planets could form as close to their host stars as some recent observations indicate?
His adamant assertion in this is regard is way too premature. We don't know in detail the full diversity of element and compound combinations possible on other planets/moons, at scales and conditions which may prove to be optimal for pre-biotic molecular assembly and self-replication .. and we probably won't, until we find self-replicating molecules having origins from other than Earth.

Colin Robinson
2013-Sep-24, 09:08 AM
Oh yeah, while we're at it: Did Autocells Lead to Life? (http://www.astrobio.net/exclusive/5703/did-autocells-lead-to-life)

Thanks for the link to this article. It is an interesting suggestion that the precursors of proteins were organic polymers (polyamidines) produced in an environment without water, such as the atmosphere of a gas giant.

So many accounts of the origin of life are focused on bodies of water: either a warm little pond, or a prebiotic soup or a hot spring... which is reasonable enough considering that all known life has liquid water in its cells... On the other hand water has a tendency to break up complex organics by hydrolysis. So the suggestion that the precursors of proteins come from a waterless environment makes sense too.

Selfsim
2013-Sep-24, 11:35 PM
Thanks for the link to this article. It is an interesting suggestion that the precursors of proteins were organic polymers (polyamidines) produced in an environment without water, such as the atmosphere of a gas giant.

So many accounts of the origin of life are focused on bodies of water: either a warm little pond, or a prebiotic soup or a hot spring... which is reasonable enough considering that all known life has liquid water in its cells... On the other hand water has a tendency to break up complex organics by hydrolysis. So the suggestion that the precursors of proteins come from a waterless environment makes sense too.Hmm .. I agree .. (interesting).

The common genetic code amino acids can be classified by their behaviours with respect to water (hydrophilic-"ness", hydrophobic-"ness", etc). Both attributes play essential roles in the production of proteins and thence, the functions of those proteins within a cell. The position of those amino groups, within a protein molecule, seems consistent:

A high fraction of the hydrophobic amino acids in a protein, are buried within the core of the structure

From: The 20 Amino Acids and Their Role in Protein Structures (http://www.proteinstructures.com/Structure/Structure/amino-acids.html):

Most protein molecules have a hydrophobic core, which is not accessible to solvent and a polar surface in contact with the environment (although membrane proteins do not follow this pattern).

While the core is built up by hydrophobic amino acid residues, polar and charged amino acids preferentially cover the surface of the molecule and are in contact with solvent due to their ability to form hydrogen bonds (by donating or accepting a proton from an electronegative atom). Very often they also interact with each other: positively and negatively charged amino acids form so called salt bridges, while polar amino acid side chains may form side chain-side chain or side chains-main chain hydrogen-bonds (with polar amide carbonyl groups).

It has been observed that all polar groups capable of forming hydrogen bonds in proteins do form such bonds. And since these interactions are often crucial for the stabilization of the protein three-dimensional structure, they are normally conserved.
Given that both hydrophobic-"ness" and hydrophilic-"ness" of amino acids play vital roles in the functioning of a modern protein, can we really infer anything at all about water's apparent presence or absence during abiogenesis, when both types of amino acids were almost certainly around prior to the formation of the first proteins?