Evolution and abiogenesis

[Skeptic Ginger]

I never said it wasn't.

Then why did you inject it into the discussion?

 

[Fudbucker]

Then why did you inject it into the discussion?

I didn't.

 

[Skeptic Ginger]

I didn't.

Are you unaware Intelligent Design relies exclusively on evidence for irreducible complexity?

 

[Fudbucker]

Are you unaware Intelligent Design relies exclusively on evidence for irreducible complexity?

I don't know much about Intelligent Design (tm).

One could make the argument that intelligence(s) were involved in steering evolution away from biological dead-ends that wouldn't have resulted in intelligent creatures like us.

After looking at usual ID theories, I concede they use the complexity argument a lot. That was not MY argument though.

Point taken.

 

[SelfSim]

Abiogenesis has one answer. There is only one real answer that will ever be. "We don't know." Period the end.

I remember being a kid and one of the reasons I was so sold on the idea of Heaven was I thought when you died and went to heaven, they would answer all of your questions about life.

But that's never going to happen. Even if we THINK we've figured out, bar the ability of a time machine, it ain't ever going to happen. So we should not make up stories to make ourselves feel better.

To me, a sign of intelligence is the ability to say "I don't know" and be comfortable with not knowing. People who are emotional don't seem to be able to handle it. So they comfort themselves with theories and lies.

God did it
Aliens seeded the planet
If we do enough research we can figure it out.

I concur with this perspective.

This is why:

i) Abiogenesis of so-called precursor chemistry involves convergence towards a thermodynamic sink, (where a closed system ceases to undergo further change, and at that point, the system achieves a thermodynamically stable equilibrium state). We can predict where a regular chemical system is headed from known historical precursors (i.e., in a convergent direction toward its thermodynamic sink), but we cannot retrace from that sink point, to 'post-dict' precisely what those precursors were.

and;

ii) Evolution involves divergence, in replicator space, from a single common (dynamic) stability, which is based on change, (as opposed to lack of change). There is no single, unique pathway to subsequent values. The divergent topology here however, alllows retracing of pathways back to a common ancestor (ie: LUCA - as is evidence by the fossil record), but prevents prediction of where any one of the multiple evolutionary pathways into the future, will end up.

In case (i) above, thermodynamic stability, being a state function, is independent of factors extraneous to the system, whereas the stability of physical, chemical and biological systems, in (ii) above, may be dramatically affected by changing circumstances.

The difference is significant. Thermodynamic stability can be quantified because it is state based, (and can have state functions assigned). The stability in (ii) however, is circumstantial .. it cannot be formally quantified, and can only be assessed in a qualitative way, because it is primarily dependent on factors external to the system.

This 'qualitative way', (which is mirrored in the case of post-diction of Abiogenesis' precursors), then opens the floodgates to a world of philosophically based 'pre- (or post-) dictions' (ie: based on beliefs). A belief in unevidenced 'universal Determinism' then plays the key motivating factor in this regard, IMO.

 

[truethat]

I love it when smart people agree with me. Sigh.

 

[ThunderChunky]

What you call my assumptions, I call the best explanation for the evidence.

There are competing scientific theories, yours is probably not even the most popular at the moment.

Is a prion or a virus alive? Is the question settled?

A prion is not a Darwinian replicator and cannot evolve. A virus can evolve, but they depend on living things to replicate. The viral world is not separate from the living world.

Does it not suggest evolution is on a continuum from non-life to life with no clear place the division occurs?

Some non living systems can replicate and evolve (like self replicating rna), but can does not mean must. Self replicating rnas are implausible and certainly not the best theory of abiogenesis.

Even if you define life and draw your line on the continuum, is there evidence the mechanisms by which change occurs (random mutation and selection pressures) are different on either side of the line?

Yes, metabolism and chemical systems are not subject to Darwinian selection. This is roughly half the field of abiogenesis.



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[Darwin123]

Yes, metabolism and chemical systems are not subject to Darwinian selection.

I don't think that is true.

What we think of as metabolism in extant living things includes growth. Usually what we think of as reproduction includes copying in some form. There is no sharp line between growth and copying.

Imagine a prebiotic micelle that just keeps growing. The membrane is lipids plus proteins. Just a membrane which grows and grows. The structural stability decreases with size. The rate of assimilating materials in the growing micelle depends on the composition of that micelle. At some indefinite point, brownian motion breaks the large, unstable micelle in two. breaks into two asymmetric parts. It heals by surface tension.

This hypothetical micelle has metabolism, but not a reproduction per se. However, it has a rather inaccurate way of copying itself. As its rate of assimilating materials varies with its composition, the growth is subject to a type of Darwinian evolution. So there is a sort of heredity of composition through the accumulation of material. The composition of the micelle will is being selected.

 

[ThunderChunky]

I don't think that is true.

What we think of as metabolism in extant living things includes growth. Usually what we think of as reproduction includes copying in some form. There is no sharp line between growth and copying.

Imagine a prebiotic micelle that just keeps growing. The membrane is lipids plus proteins. Just a membrane which grows and grows. The structural stability decreases with size. The rate of assimilating materials in the growing micelle depends on the composition of that micelle. At some indefinite point, brownian motion breaks the large, unstable micelle in two. breaks into two asymmetric parts. It heals by surface tension.

This hypothetical micelle has metabolism, but not a reproduction per se. However, it has a rather inaccurate way of copying itself. As its rate of assimilating materials varies with its composition, the growth is subject to a type of Darwinian evolution. So there is a sort of heredity of composition through the accumulation of material. The composition of the micelle will is being selected.

Growth can be a result of metabolism but you can have metabolism without growth (e.g. quiescent cells) and growth without metabolism (eg crystal growth, prion aggregate growth, etc). Metabolism involves chemical reactions. The micelle you describe has no metabolism although it might depend on a pre-existing one to make the amino acids/proteins for its membrane. The micelle is also not necessarily undergoing Darwinian selection. The composition would have to be favorable for growth and favorable for maintaining itself during growth and splitting for that to be the case.

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[Skeptic Ginger]

There are competing scientific theories, yours is probably not even the most popular at the moment.

Pray tell, what is the most popular theory and by which criteria are you making the claim?

A prion is not a Darwinian replicator and cannot evolve. ....

Really?

Darwinian Evolution of Prions in Cell Culture

REPORT
Darwinian Evolution of Prions in Cell Culture
Jiali Li*, Shawn Browning*, Sukhvir P. Mahal, Anja M. Oelschlegel, Charles Weissmann†
+ Author Affiliations
↵†To whom correspondence should be addressed. E-mail: charlesw@scripps.edu
Science 12 Feb 2010:
Vol. 327, Issue 5967, pp. 869-872
DOI: 10.1126/science.1183218

DNA-less Evolution

Prions are proteinaceous infectious elements involved in a variety of neurodegenerative diseases, including scrapie in sheep and so-called mad cow disease in cattle. Now Li et al. (p. 869, published online 31 December) show that, when propagated in tissue culture cells, cloned prion populations become diverse by mutational events and can undergo selective amplification. Thus, even though devoid of a coding genome, prions, when propagated under a particular selection regime, can be subject to rapid evolution.
Abstract

Prions are infectious proteins consisting mainly of PrPSc, a β sheet–rich conformer of the normal host protein PrPC, and occur in different strains. Strain identity is thought to be encoded by PrPSc conformation. We found that biologically cloned prion populations gradually became heterogeneous by accumulating “mutants,” and selective pressures resulted in the emergence of different mutants as major constituents of the evolving population. Thus, when transferred from brain to cultured cells, “cell-adapted” prions outcompeted their “brain-adapted” counterparts, and the opposite occurred when prions were returned from cells to brain. Similarly, the inhibitor swainsonine selected for a resistant substrain, whereas, in its absence, the susceptible substrain outgrew its resistant counterpart. Prions, albeit devoid of a nucleic acid genome, are thus subject to mutation and selective amplification.

Scientists at Scripps Institute are doing intensive research on abiogenesis.

Some non living systems can replicate and evolve (like self replicating rna), but can does not mean must. Self replicating rnas are implausible and certainly not the best theory of abiogenesis.

Yes, metabolism and chemical systems are not subject to Darwinian selection. This is roughly half the field of abiogenesis.

So say you?

Peptides and the origin of life

Abstract
Considering the state-of-the-art views of the geochemical conditions of the primitive earth, it seems most likely that peptides were produced ahead of all other oligomer precursors of biomolecules. Among all the reactions proposed so far for the formation of peptides under primordial earth conditions, the salt-induced peptide formation reaction in connection with adsorption processes on clay minerals would appear to be the simplest and most universal mechanism known to date. The properties of this reaction greatly favor the formation of biologically relevant peptides within a wide variation of environmental conditions such as temperature, pH, and the presence of inorganic compounds. The reaction-inherent preferences of certain peptide linkages make the argument of ‘statistical impossibility’ of the evolutionary formation of the ‘right’ peptides and proteins rather insignificant. Indeed, the fact that these sequences are reflected in the preferential sequences of membrane proteins of archaebacteria and prokaryonta distinctly indicates the relevance of this reaction for chemical peptide evolution. On the basis of these results and the recent findings of self-replicating peptides, some ideas have been developed as to the first steps leading to life on earth.

Are prions related to the emergence of early life?

Summary
DNA and RNA are the modern cellular molecules related to the storage and processing of the genetic information. However, in the Earth primeval environment conditions, these two molecules are far from being the best option for this function due to their great complexity and sensibility to heat. Experiments have been showing that proteins are very stable and reliable molecules even in very extreme conditions and, under certain circumstances, could be related to the transmission of certain phenotypes that are inherited in a non-Mendelian manner.

Prions, infective proteins that are associated to several neurological diseases among mammals by replacing their dominant native state of prion protein by a misfolded one, are remarkably resistant to even the most extreme environments. Furthermore, prions are also associated to the transmission of certain fungal traits in an epigenetical model. These two characteristics support the hypothesis that prions are a possible relic of early stage peptide evolution and may represent the reminiscence of a very ancient analogical code of biological transmission of information rather than the digital one represented by modern nucleic acids.

Are prions a relic of an early stage of peptide evolution?

Abstract
The rather unique properties of prions and their presence in very different kinds of living species suggest that this type of molecule was created at a very early stage of evolution and may even represent a relic from a time where peptide evolution was ongoing and RNA/DNA did not yet exist. A comparison of the most frequently occurring amino acid sequences in known prions with the sequences preferentially formed in the salt-induced peptide formation reaction, the most simple mechanism enabling the formation of peptides under primitive earth conditions, shows a remarkable coincidence that strongly supports this hypothesis.

Molecular Evolution of Prions

The disturbing link between the prions that cause Bovine Spongiform Encephalopathy (BSE) in cattle and Creutzfeld-Jakob disease (CJD) in humans comes from a study of the evolutionary relationships of prions in a wide variety of mammals. The normal prion found in cattle shares two biochemical features with the prion found in humans and apes. Crucially, neither of these features are found in the prion of sheep -- the prion which, when mutated, causes the disease called 'scrapie'. These biochemical features -- changes in the amino-acid sequence of the prion protein -- occur in a part of the protein thought to be involved in the onset of prion-mediated diseases such as CJD and BSE.

The discovery is a shattering blow for the evolutionary argument that because humans seem unable to contract prion diseases from sheep infected with scrapie, they would be unlikely to contract CJD from contaminated beef. The study, published in the 25 April issue ofNature comes from a team of researchers based in Oxford, in the UK, including Professor T. R. E. Southwood, a former advisor to the British Government on BSE.

This line of research supports what I've been saying about the continuum. It also goes hand in hand with the link I posted earlier hypothesizing the role of rRNA (ribosomal RNA).

 

[Skeptic Ginger]

I concur with this perspective.

This is why:

i) Abiogenesis of so-called precursor chemistry involves convergence towards a thermodynamic sink, (where a closed system ceases to undergo further change, and at that point, the system achieves a thermodynamically stable equilibrium state). We can predict where a regular chemical system is headed from known historical precursors (i.e., in a convergent direction toward its thermodynamic sink), but we cannot retrace from that sink point, to 'post-dict' precisely what those precursors were.

You are making an unsupported assumption that the chemical reactions occurring in the prebiotic soup are unchanging at the end of the reaction. That's just not true with either prions or ribosomal RNA.

ii) Evolution involves divergence, in replicator space, from a single common (dynamic) stability, which is based on change, (as opposed to lack of change). There is no single, unique pathway to subsequent values. The divergent topology here however, alllows retracing of pathways back to a common ancestor (ie: LUCA - as is evidence by the fossil record), but prevents prediction of where any one of the multiple evolutionary pathways into the future, will end up.

In case (i) above, thermodynamic stability, being a state function, is independent of factors extraneous to the system, whereas the stability of physical, chemical and biological systems, in (ii) above, may be dramatically affected by changing circumstances.

The difference is significant. Thermodynamic stability can be quantified because it is state based, (and can have state functions assigned). The stability in (ii) however, is circumstantial .. it cannot be formally quantified, and can only be assessed in a qualitative way, because it is primarily dependent on factors external to the system.

This 'qualitative way', (which is mirrored in the case of post-diction of Abiogenesis' precursors), then opens the floodgates to a world of philosophically based 'pre- (or post-) dictions' (ie: based on beliefs). A belief in unevidenced 'universal Determinism' then plays the key motivating factor in this regard, IMO.

Looks like you've put this same hypothesis forward on the CosmoQuest forum.

Care to cite any research putting this collection of complex word salad to the test? Your bibliography has no links.

References:
20. Kauffman, S.A. Investigations; Oxford University Press: USA, 2000.
27. Wagner, N.; Pross, A.; Tannenbaum, E. Selection advantage of metabolic over non-metabolic
replicators: a kinetic analysis. Biosystems 2010, 99, 126–129.
28. Monod,J.Chance and Necessity;Random,NY,USA,1972.
29. Pross, A. How can a chemical system act purposefully? Bridging between life and non-life. J. Phys. Org. Chem. 2008, 21, 724–730.Interesting stuff!

Surely in the modern age of computers you might post some links

I'll just point to KenG's response to you there since it echoes my thoughts.

Ken G
2013-Sep-15, 10:27 PM
This all seems pretty reasonable, but there are two issues that I remain unconvinced about:
1) I echo BioSci's basic skepticism that there really is a "gulf" between Darwinian thinking about life and abiogenetic processes. Darwinian evolution is not strictly about survival (which implies life), it is really about propagation, but in the context of life that is called survival. There is no reason why Darwinian principles cannot be applied generally, and indeed I have heard many references to evolutionary approaches to non-living things, like finding good game strategies or solving complicated equations. So although Pross may have a point that the differences can be overstressed, they can also be understressed-- if there are aspects of life that are not present in simple molecular chemistry, then it would be a mistake to overlook those differences.
...

You seem to think that an hypothesis equals accepted theory. You don't have much more than an hypothesis which is undermined by the fact prions and rRNA are indeed subject to random mutation and selection pressures.

 

[Hlafordlaes]

I concur with this perspective.

I don't.

We can share this statement: "This is why:"

I believe you to be correct that reverse engineering precursors would rely on a fully deterministic process, which is not the case. However, given that, if we take the examples Skeptic Ginger has been putting out there in the thread, we have clear examples of molecular replication with changes over generations, yet pre-biotic.

However, "all it will take" (could be a while) to establish the operating principles behind abiogenesis is to fess out one of the probably several ways in which molecular evolution might transition to encoded evolution. That is, not only is a similar molecule replicated, but also other 'parts' that are not directly present in the code, but are manufactured by it. This, for me, is the gap from pre-biotic to life that needs to be closed, but I see no reason why it may not be in future.

In fact, our first contact with a non-Earth life form might be in the lab, when a man-made code-based molecular system shows it can replicate and evolve. It most likely will not share some aspects of standard Earth life, such as varying along free parameters that are arbitrary.

So, would this result in the ability to reverse engineer original Earth abiogenesis? No, given your constraint. However, it would demonstrate a general principle that would operate in any chance chemical soup under the proper conditions.

 

[truethat]

I don't.

We can share this statement: "This is why:"

I believe you to be correct that reverse engineering precursors would rely on a fully deterministic process, which is not the case. However, given that, if we take the examples Skeptic Ginger has been putting out there in the thread, we have clear examples of molecular replication with changes over generations, yet pre-biotic.

However, "all it will take" (could be a while) to establish the operating principles behind abiogenesis is to fess out one of the probably several ways in which molecular evolution might transition to encoded evolution. That is, not only is a similar molecule replicated, but also other 'parts' that are not directly present in the code, but are manufactured by it. This, for me, is the gap from pre-biotic to life that needs to be closed, but I see no reason why it may not be in future.

In fact, our first contact with a non-Earth life form might be in the lab, when a man-made code-based molecular system shows it can replicate and evolve. It most likely will not share some aspects of standard Earth life, such as varying along free parameters that are arbitrary.

So, would this result in the ability to reverse engineer original Earth abiogenesis? No, given your constraint. However, it would demonstrate a general principle that would operate in any chance chemical soup under the proper conditions.

But how can we determine if those "chemical soups" and "proper conditions" reflect the way the earth was at the time that abiogenesis occurred?

 

[Belz...]

I am. I'm talking about defining evolution and abiogenesis to suit either argument, they are separate things, or, they are not.

And you keep insisting that they could be separate, something I am not arguing against.

What I am saying is that they are separate questions which could, in principle, have entirely different processes. It will most probably turn out that they are related processes, but the two questions are different, like "how did this person get conceived?" and "how did they grow up this way?" are related but different.

Upon what evidence are you supporting your 'it could be' hypothesis? Because I am not arguing against the premise that theoretically they could be different processes.

Then you are not arguing against what I said, as I suspected. We're actually in agreement, I think.

 

[Hlafordlaes]

But how can we determine if those "chemical soups" and "proper conditions" reflect the way the earth was at the time that abiogenesis occurred?

The argument does not make that assertion if you examine it. Difference between an operating principle and an arbitrary instance of its functioning.

 

[truethat]

The argument does not make that assertion if you examine it. Difference between an operating principle and an arbitrary instance of its functioning.

What I'm saying is that even if we can replicate everything. Or even if we found a planet that just started developing life on the planet in the very beginning stages, we have no way of knowing if that is the same condition in which abiogenesis occurred for life on Earth.

So to me, even if we make discoveries in the future and have found a way to make abiogenesis happen again, it still doesn't prove that this is how it started for life on earth.

I'm not saying we should not explore the science of abiogenesis. But for all intents and purposes all we've discovered is another form of abiogenesis.

 

[marplots]

What I'm saying is that even if we can replicate everything. Or even if we found a planet that just started developing life on the planet in the very beginning stages, we have no way of knowing if that is the same condition in which abiogenesis occurred for life on Earth.

So to me, even if we make discoveries in the future and have found a way to make abiogenesis happen again, it still doesn't prove that this is how it started for life on earth.

I'm not saying we should not explore the science of abiogenesis. But for all intents and purposes all we've discovered is another form of abiogenesis.

I agree, but I think this rather misses the point. The gap we want to close isn't an historical one, but a gap in understanding. History often erases evidence for particulars, but we think principles endure across time.

An example I read recently was about Exodus and whether or not the story could have happened as it is relayed to us in the Bible. Supposing that a trusted historical record is unavailable to either side of the issue, progress can still be made by arguing that Egypt at the time couldn't have supported the number of Jews mentioned - that's a principle argument based on ideas about populations and resources. In the same fashion, any instance of abiogenesis is going to give us some more general ideas about the emergence of life, regardless of whether that instance actually happened or not.

It can be wrong for earth but still right.

 

[truethat]

I agree, but I think this rather misses the point. The gap we want to close isn't an historical one, but a gap in understanding. History often erases evidence for particulars, but we think principles endure across time.

An example I read recently was about Exodus and whether or not the story could have happened as it is relayed to us in the Bible. Supposing that a trusted historical record is unavailable to either side of the issue, progress can still be made by arguing that Egypt at the time couldn't have supported the number of Jews mentioned - that's a principle argument based on ideas about populations and resources. In the same fashion, any instance of abiogenesis is going to give us some more general ideas about the emergence of life, regardless of whether that instance actually happened or not.

It can be wrong for earth but still right.

Ok I can go with that. Maybe I misunderstood what people were intending. Like I said we can certainly study abiogenesis when it comes to understanding how abiogenesis in and of itself works.

But as far as knowing how life first started on the planet, we cannot. There's only one answer to THAT question, we don't know.

Thanks for pointing out that distinction. It made it more clear.

 

[Belz...]

What I'm saying is that even if we can replicate everything. Or even if we found a planet that just started developing life on the planet in the very beginning stages, we have no way of knowing if that is the same condition in which abiogenesis occurred for life on Earth.

Exactly! When I see a bird take flight, I have no idea if birds that previously took flight have done so in the same way. No way to tell!

 

[marplots]

Exactly! When I see a bird take flight, I have no idea if birds that previously took flight have done so in the same way. No way to tell!

You mean those birds that look like bumble bees?