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Selfsim
2012-Dec-14, 09:07 AM
So, hot on the tail of the Davies et al: 'Algorithmic' origins of life (the informational perspective), comes this:

The compositional and evolutionary logic of metabolism (http://iopscience.iop.org/1478-3975/10/1/011001/article), (published in Physical Biology, December 12, 2012)

... A somewhat daunting 62 page report, (of pretty hard reading), which argues the evolutionary case for the 'Metabolism first' origins of bio-chemistry.

An easier read is here:
Was life inevitable? New paper pieces together metabolism's beginnings (http://phys.org/news/2012-12-life-inevitable-paper-pieces-metabolism.html)

Some quotes follow (from the PhysOrg article):


... In other words, carbon fixation is the centerpiece of metabolism – the basic process by which cells take in chemicals from their environments and build them into products they need to live. It's also the link between the geochemistry of Earth and the biochemistry of life.
...
In a paper earlier this year, Smith and Santa Fe Institute Omidyar Fellow Rogier Braakman mapped the most primitive forms of carbon fixation onto major, early branching points in the tree of life (PLoS Computational Biology, April 18, 2012). Now, the two researchers have drawn from geochemistry, biochemistry, evolution, and ecology to detail the likeliest means by which molecules lurched their way from rocks to cells.So, all the exo-life, Earth-like planet hunters will love this bit ...

In mapping the chemical pathways to life's emergence, the researchers touch on a more existential question: How likely was it for life to have developed at all? Extraordinarily so, says Braakman. "Metabolism appears to be an 'attractor state' within organic chemistry, where it was likely to be selected regardless of earlier stages of chemical evolution" in the chaotic, high-energy conditions of prebiotic Earth, he says. Can it happen elsewhere? Possibly, even probably, he says. Rocky planets usually have cores chemically similar to ours, so if a planet is volcanically (and perhaps tectonically) active and has an ocean, it will probably have hydrothermal vents that spew chemicals, creating the potential conditions for life, Braakman says. In fact, the physics of star and planet formation make the chances of such conditions pretty reasonable. Smith cautions, however, that we still have much to learn about the chemical and physical conditions that might lead to life-like organization ...How likely?: 'Extraordinarily so' (not exactly sure of what that means ... its speculative speak, I think .. (I need a translator) :) ).

(Then there's the more recognisable, classic speculative speak ... "possibly, even probably", and even "pretty reasonable" :) )

Anyway, its a classic piece of work with a lot of valuable, well referenced, research material included. The Glossary in 'Appendix A', actually makes the whole report worthwhile (even if just from a communications aid perspective). More quotes to follow (once I've read 'em).

Comments welcome.

Selfsim
2012-Dec-14, 09:16 AM
So, I've read these words from the conclusion (http://iopscience.iop.org/1478-3975/10/1/011001/article#pb438384s8) (in the report), several times over. I'm still not quite sure of what to make of them, but they certainly generate some interesting thoughts ...


Properties of distributions, as in the use of network modules or the diversity of cofactors, should in turn be predictable from asymmetries in catalytic constraints that are likely to arise within a large and diverse possibility space of organic chemistry.

Moreover, this lawfulness should have been expected: the factors that reduce (or encrypt) the role of laws in biology, and lead to unpredictable historical contingencies, arise from long-range correlation. Correlation of multiple variables leads to large spaces of possibility and entangles the histories of different traits, making the space difficult to sample uniformly. But correlation in biology is in large part a constructed property; it has not been equally strong in all eras and its persistence depends on timescales.

Long-term evolution permits recombination even in modern integrated cells and genomes. Early life, in contrast, with its less-integrated cells and genomes, and its more loosely-coupled traits, had constructed less long-range correlation. These are the domains where the simpler but invariant constraints of underlying chemistry and physics should show through.
Translation attempts welcome.

BioSci
2012-Dec-14, 04:42 PM
So, I've read these words from the conclusion (http://iopscience.iop.org/1478-3975/10/1/011001/article#pb438384s8) (in the report), several times over. I'm still not quite sure of what to make of them, but they certainly generate some interesting thoughts ...
Translation attempts welcome.

Hows this:?


"Moreover, this lawfulness should have been expected: the factors that reduce (or encrypt) the role of laws in biology, and lead to unpredictable historical contingencies, arise from long-range correlation. Correlation of multiple variables leads to large spaces of possibility and entangles the histories of different traits, making the space difficult to sample uniformly. But correlation in biology is in large part a constructed property; it has not been equally strong in all eras and its persistence depends on timescales."

Translation:: Evolution of complex, inter-related, coordinated, and self-reproducing chemistry (Life) can be seen as a logical and necessary result of chemistry and physics applied to a very complex chemical system - pre-biotic development and biology. The rate of such evolution is also dependent on the environment and the status of the current biology.


"Long-term evolution permits recombination even in modern integrated cells and genomes. Early life, in contrast, with its less-integrated cells and genomes, and its more loosely-coupled traits, had constructed less long-range correlation. These are the domains where the simpler but invariant constraints of underlying chemistry and physics should show through."

Translation:: early life was less complex than current, more evolved, organisms and the plausible impact of chemistry and physics is easier to model.

Your mileage may vary! :)

Selfsim
2012-Dec-14, 06:58 PM
Hows this:?

Translation:: Evolution of complex, inter-related, coordinated, and self-reproducing chemistry (Life) can be seen as a logical and necessary result of chemistry and physics applied to a very complex chemical system - pre-biotic development and biology. The rate of such evolution is also dependent on the environment and the status of the current biology.Hi BioSci;
Thanks for that - (much appreciated).
Seems consistent with what they're arguing.
The part about correlation in biology being mostly a 'construction' I find interesting.
Does this mean that as we correlate and categorise certain characteristics, (in true reductionist style), we introduce parasitic effects in the predictions?


Translation:: early life was less complex than current, more evolved, organisms and the plausible impact of chemistry and physics is easier to model.Once again, the desire to model in simplistic terms, (in order to 'postdict' the origin mechanism), seems to dominate thinking?
Could early life have been just as complex (or of similar complexity) as it is now? This might make sense if it arose from chemical complexity and other contingent events. (Eg: a single cell is still highly complex, and it seems that's what came first, (etc))?

I keep coming back to the view that something as complex as life, (even in its early stages), could easily be inferred to have originated from something equally or of greater complexity, (not necessarily just lots of simple inorganic chemical reactions). There doesn't seem to be much consideration of other less obvious contingent factors. (Not sure what they might be, mind you .. which is why I personally keep being drawn back to pondering the 'possible' general characteristics of the mechanism .. whatever they might be).

Cheers

BioSci
2012-Dec-14, 10:07 PM
Hi BioSci;
Thanks for that - (much appreciated).
Seems consistent with what they're arguing.
The part about correlation in biology being mostly a 'construction' I find interesting.
Does this mean that as we correlate and categorise certain characteristics, (in true reductionist style), we introduce parasitic effects in the predictions?

Not sure what you mean by parasitic. I understand it more as the biochemistry of life that we have studied (Earth) is a single result of a very large potential biochemical space. DNA, RNA, amino acids, carbohydrates, proteins, etc. are all solutions to life problems that are selected from many possible outcomes - but are not the only or even "best" solutions - they are just a solution.


Once again, the desire to model in simplistic terms, (in order to 'postdict' the origin mechanism), seems to dominate thinking?
Could early life have been just as complex (or of similar complexity) as it is now? This might make sense if it arose from chemical complexity and other contingent events. (Eg: a single cell is still highly complex, and it seems that's what came first, (etc))?

I keep coming back to the view that something as complex as life, (even in its early stages), could easily be inferred to have originated from something equally or of greater complexity, (not necessarily just lots of simple inorganic chemical reactions). There doesn't seem to be much consideration of other less obvious contingent factors. (Not sure what they might be, mind you .. which is why I personally keep being drawn back to pondering the 'possible' general characteristics of the mechanism .. whatever they might be).

Cheers

I do not agree that excess "reductionist" thinking is really involved - rather it is very hard to hypothesize the development of life from a prior lifeless state other than through a progression of increasingly complex chemistry > organic chemistry > biochemistry > pre-biotic chemistry > "proto-life" > reproducing "life."
It is when one gets to the stage of a reproducing "life-like" organism that evolution becomes a powerful process that can further expand what initially may be a "barely" functioning "life-like" chemical process into a world full of diverse living organisms.

TooMany
2012-Dec-14, 10:18 PM
I do not agree that excess "reductionist" thinking is really involved - rather it is very hard to hypothesize the development of life from a prior lifeless state other than through a progression of increasingly complex chemistry > organic chemistry > biochemistry > pre-biotic chemistry > "proto-life" > reproducing "life."
It is when one gets to the stage of a reproducing "life-like" organism that evolution becomes a powerful process that can further expand what initially may be a "barely" functioning "life-like" chemical process into a world full of diverse living organisms.

This was also discussed in the "How small can life be?" thread. Presuming that the first form of life was as complex as a modern bacterium is to presume creation and deny evolution. Yes, bacteria are that complex.

Selfsim
2012-Dec-15, 12:57 AM
"Moreover, this lawfulness should have been expected: the factors that reduce (or encrypt) the role of laws in biology, and lead to unpredictable historical contingencies, arise from long-range correlation. Correlation of multiple variables leads to large spaces of possibility and entangles the histories of different traits, making the space difficult to sample uniformly. But correlation in biology is in large part a constructed property; it has not been equally strong in all eras and its persistence depends on timescales."
Does this mean that as we correlate and categorise certain characteristics, (in true reductionist style), we introduce parasitic effects in the predictions?
Not sure what you mean by parasitic. I understand it more as the biochemistry of life that we have studied (Earth) is a single result of a very large potential biochemical space. DNA, RNA, amino acids, carbohydrates, proteins, etc. are all solutions to life problems that are selected from many possible outcomes - but are not the only or even "best" solutions - they are just a solution.Hmm .. upon re-reading the original quote, I kind of interpret them as commenting about how present day traits may not be accurately retraceable because it leads to large numbers of possibilities, making correlation techniques subject to large uncertainties (or errors).
(Maybe I'm completely misinterpreting it though … I'll come back to it again after a bit of a break (and a think)).


I do not agree that excess "reductionist" thinking is really involved - Excuse my comment in parentheses: ("in true reductionist style") .. I didn't mean to imply excessive reductionism in biology … (although that is a frequent criticism by 'alternativists' attempting build more 'holistic' approaches).

… rather it is very hard to hypothesize the development of life from a prior lifeless state other than through a progression of increasingly complex chemistry > organic chemistry > biochemistry > pre-biotic chemistry > "proto-life" > reproducing "life." Oh, I agree.
After reading the other report in the other thread, about the Davies' information model approach to abiogenesis, they kind of speculate about other influences other than pure chemistry .. (and I guess I've carried some of that thinking into my above comments). Just what those other influences might be, seems to be kind of 'shaded out' in this report, although I do to get a flavour of the more classical idea of 'stacked contingent events'. (I guess that's not surprising though, as they are building the 'pure' case for metabolism first, after all …)


It is when one gets to the stage of a reproducing "life-like" organism that evolution becomes a powerful process that can further expand what initially may be a "barely" functioning "life-like" chemical process into a world full of diverse living organisms.Sure .. no issues at all with that ...

Selfsim
2012-Dec-15, 01:02 AM
This was also discussed in the "How small can life be?" thread. Presuming that the first form of life was as complex as a modern bacterium is to presume creation and deny evolution. Yes, bacteria are that complex.That's one interpretation .. but Davies et al have another realised by viewing abiogenesis from an information model perspective.

Colin Robinson
2012-Dec-16, 09:47 PM
I keep coming back to the view that something as complex as life, (even in its early stages), could easily be inferred to have originated from something equally or of greater complexity, (not necessarily just lots of simple inorganic chemical reactions).

I'd agree that the chemical environment life emerged from wasn't necessarily simple...

For instance, supposing Kauffman is right about autocatalytic sets being the earliest life, or proto-life... Then what sort of chemistry would have been going on prior to the autocatalytic sets?

Logic suggests it would have been a more diverse organic chemistry, because autocatalytic sets tend to reduce diversity by transforming molecules which aren't members of the set, into copies of the molecules which are members.

Selfsim
2012-Dec-16, 11:13 PM
I'd agree that the chemical system life emerged from wasn't necessarily simple...

For instance, supposing Kauffman is right about autocatalytic sets being the earliest life, or proto-life... Then what sort of chemistry would have been going on prior to the autocatalytic sets?

Logic suggests it would have been a more diverse organic chemistry, because autocatalytic sets tend to reduce diversity by transforming molecules which aren't members of the set, into copies of the molecules which are members.See, I don't have a problem with the idea that some complex state may have already existed, as a result of some mundane, perfectly explainable circumstances. (Chemical, or Physics Law, or whatever ..)

Its the role of the hypothesised catalyst, (or trigger), which also introduces the vast implications of unpredictability, (through the phenomenon of sensitivity to the 'initial' conditions), which leads me away from inferences such as 'inevitability', which is the issue.

The idea that the environment imposes order on organisms is really more a metaphor for our benefit, and isn't necessarily so. What's more, the connection we have decided to be solely attributable the environment which we think existed at the time of our own hypothesised emergence, is only guesswork, at best.

See, the complexity view; that selection acts on systems whose structure has already self-organised, combined with a catalytic event leading to unpredictability, aligns more closely with the more formal origins of complexity theory. Scientists like Kauffman might alter their views upon pondering some more on what it was that 'brought him to the dance' .. and yet, he still ends up coming up with the shakier, more philosophically oriented view of 'inevitability'.

Autocatalysis might still play a role … but why should we think that such a factor necessarily dominates the outcome?

Paul Wally
2012-Dec-16, 11:42 PM
Autocatalysis might still play a role … but why should we think that such a factor necessarily dominates the outcome?

I don't think we have to think that autocatalysis necessarily dominates the outcome, as you say. We just have to suppose that it does, but then the
problem is still to come up with exactly how it does. I think this is the problem with many of these abiogenesis hypotheses, it doesn't satisfactorily answer the how-question. It merely hints at the possibility that it could lead to self-replication, but it doesn't actually demonstrate theoretically how it is supposed to happen. Or maybe it's just me missing that part of the explanation. :)

Selfsim
2012-Dec-17, 03:51 AM
Autocatalysis might still play a role … but why should we think that such a factor necessarily dominates the outcome?I don't think we have to think that autocatalysis necessarily dominates the outcome, as you say. We just have to suppose that it does, .. well 'supposing' is thinking, isn't it? :)


I think this is the problem with many of these abiogenesis hypotheses, it doesn't satisfactorily answer the how-question. It merely hints at the possibility that it could lead to self-replication, but it doesn't actually demonstrate theoretically how it is supposed to happen. Or maybe it's just me missing that part of the explanation. :)I agree with what you say about the abiogenesis hypotheses, (in general).
And yet, they do influence many real aspects, (ie: they have consequences), which some somehow end up as science 'lore' (a slight play on words intended there …).

The only reality which remains is: 'we don't know'.

So why does the conclusion of: 'inevitability of exo-life' persist, over the fact of incompleteness of a hypothesis which clearly lacks a mechanism, (ie: the 'how')?

I still maintain that we'll only ever find out 'the how' by making a fortuitous discovery. Deliberate, directed searches underwritten by incomplete hypotheses, cannot be taken as anything other than an 'intellectual excursions', which may serve to educate on the method, but says very little about their chosen subject(s).

Colin Robinson
2012-Dec-17, 09:30 AM
I think perhaps we've been missing a very important point in the OP article.

The fact that the simplest bacterium is incredibly complex is something we keep being reminded of...

But I think the article is actually arguing that complexity is not the whole story. That the chemistry of life on Earth is based on a core network which is far from complex.


3.1.3 "Almost all anabolic pathways in extant organisms originate in one of five intermediates in the TCA cycle—acetate (as acetyl-CoA), pyruvate, oxaloacetate, succinate (or succinyl-CoA) or α-ketoglutarate—which have been dubbed the 'pillars of anabolism' [51]. "

OK, the way they explain it may not sound all that simple to those unfamiliar with the terminology!

However, the technical term "anabolic" refers to the whole field of metabolism which builds stuff up, rather than breaking stuff down. (Breaking stuff down is called "catabolism".)

And (as their accompanying diagram shows) the substances mentioned such as acetate, pyruvate etc are all carboxylic acid groups 2 to six carbons long — very uncomplex indeed, by the standards of biochemistry!

They go on to suggest that this not-so-complex life-building network had a not-so-complex origin...

They hypothesize that it began in a pre-life chemistry, facilitated by catalysts that were either minerals or relatively simple compounds of metals and organics.