Abiogenesis discussion

[Paul Wally]

Finding life's building-block molecules in meteorites is one thing. How they are combined into a replicating life or pre-life form is quite another.

Stuart Kauffman studied this for about 20 years. He modeled generic molecules, making reasonable assumptions consistent with known chemical properties... and let them react, as molecules will do. I cannot do justice to his findings in a few sentences or paragraphs. But IIRC, if you get a large enough number of different molecules together, all reacting with each other differently, at some point you get emergent order. He essentially quantified it.

There are these complex possibilities inherent in the kind of chemistry that we can study in a laboratory and then there is also the kind of chemistry occurring over geological timescales. I think both are important in understanding the emergence of life. As far as geological timescale chemistry is concerned, I want to hypothesize that there will also be some very unlikely reactions, the kinds of reactions that we would not readily observe in a standard chemical reaction experiment. For example if
we have a mixture of different chemicals it will be interesting to know whether there are certain kinds of reactions or chemical bonding within that mixture which have a very low probability of occurring within 1 minute but a much higher probability of occurring within say one year. We see almost analogous kinds of experiments in physics e.g. with neutrino detection where they wait for improbable events to happen. I don't know whether there are analogous kinds of experiments in chemistry or whether chemical bonding can have a probability attached to it, but it would be interesting if there are.

[transreality]

Here are some links to interesting abiogenesis and early evolution studies just published, taken from this review.

A plausible scenario for the origin of life; the evolution of RNA precursors

Oldest Fossils on Earth: bacteria from 3.4 billion years ago

Early Oxygen in the Oceans: 300myr before the 'oxygen crisis'

from intracellular cooperation to multicellularity: clumping yeast out compete singular yeast

[transreality]

The Never-Ending Story—The Origin and Diversification
of Life


This article reviews abiogenesis and early evolution theories, in an easy to read narrative, intended for education purposes.


"So which theory is correct? Well, if solely taken on the merits of their initial laurels, neither: Ribonucleotides have
yet to be produced under any prebiotic conditions deemed universally reasonable, and, at up to 400°C, black smokers
might be too chemically extreme to serve as the biosynthetic cradle of life. Though hardly worth mentioning, a
third kitchen, “panspermia,” merely proposes to shift the primordial diner to another part of the galaxy where life
would still have to overcome the same initial start-up problems before being sent out as samplers even became an
option. Nevertheless, it would be as inaccurate to portray these theories as competing, mutually exclusive ideas as it
is to set them up as straw men to parody. In science, theories are constantly under scrutiny, re-evaluation, and
synthesis, leading to modification over time (or at least they should be). No reputable scientist believes that a pool of
organic chemicals spontaneously became a microbe with all the parts of a contemporary bacterium through a simple
stirring of the pot."

[Cougar]

I want to hypothesize that there will also be some very unlikely reactions....

A big step in Kauffman's research into abiogenesis was autocatalysis.

[Selfsim]

An interesting development … chemical pathway for formation of PAHs at interstellar temperatures demonstrated for the first time:

Researchers discover novel chemical route to form organic molecules

“These findings challenge conventional wisdom that PAH-formation only occurs at high temperatures such as in combustion systems and implies that low temperature chemistry can initiate the synthesis of the very first PAH in the interstellar medium,” said co-author Tielens.

In the future, the team plans to expand these studies to unravel the formation routes to more complex PAHs like phenanthrene and anthracene, and also to nitrogen-substituted PAHs such as indole and quinoline. This concept can be also expanded to functionalized PAHs with organic side chains thus bringing researchers closer to solving the decade old puzzle of how complex PAHs and their derivatives can be synthesized in combustion flames and in cold interstellar space.

Regards

[Selfsim]

Just thought I'd follow up on Tensor's recent arXiv papers post, (thanks Tensor), wherein he reported on a new study:

A Search for Hydroxylamine (NH₂OH) toward Select Astronomical Sources:

So, the question posed in this study, is how do complex amino acid molecules, like glycine, (recently found in Stardust's cometary return sample), form extraterrestrially ?

Do these complex molecules first form in the gaseous phases before accretion, or are they formed in reactions of smaller precursors, after their incorporation into cometary bodies ?

It appears that glycine, α-and β-alanine amino acids have been shown to have formed in the lab through the reaction of ionised hydroxylamine, (in the gas phase), with acetic and propanoic acids. Acetic acid has been detected in other 'environments' (not sure yet exactly where/what these are, at the moment), so the hunt is on to find hydroxylamine in space, as the possible precursor. They report they conducted a spectral analysis of seven different astronomical sources, and did not detect any. The hunt goes on.

Interesting ...
I think the detection of glycine, in Stardust's return sample, is about the best direct evidence we have of extraterrestrial amino acids, at the moment (?)

There are clearly a lot more big steps before one can get a DNA molecule, (putting it mildly), but the clues are beginning to stack up.
What we need is to find some complex longer-chain amino acids on a local rocky planet/moon, comet or asteroid - which seems to me, not too far beyond belief.

Regards

[transreality]

I just wonder how the production of 'complex' organic molecules in space is relevant to abiogenesis on earth. These may represent parallel but unconnected pathways. The processes that develop these organic molecules are also going to be present on an early earth. They may well form in the gaseous envelope of a star, or in when liquid water is present in a primitive comet, but those same chemical processes are going to be present in a volcanic eruption, or in an early sea.

Ammonium nitrate naturally forms in the air, and reduction by sulpuric acid and sulphur dioxide would seem to be the main route of synthesis of hydroxyalamine, these are not uncommon in volcanic environments. Glycine has been documented from volcanic sources, in this study at least:

Volcanic processes and the synthesis of simple organic compounds on primitive earth.

This study makes a rough estimate that a typical hydrothermal system generates around 10^7Kg of organic compounds during its lifetime. At the same time the products of a underwater volcano, or system of hydrothermal vents will have far less exposure to UV dissociation, for example, than compounds produced in the envelope of a young star, or released from the outgassing of a comet. I can't see the justification for the typical statement that the precursor molecules of life arrived from space.

[tnjrp]

I can't see the justification for the typical statement that the precursor molecules of life arrived from space.

I'm not sure if it's such a typical statement in that specific form, tho it is one that tends to get more headlines than your average abiogen hypothesis. Mostly I see it used to stress that complex oraganic molecules are formed under surprsingly variable conditions, which does seem to be the case.

[Selfsim]

I just wonder how the production of 'complex' organic molecules in space is relevant to abiogenesis on earth. These may represent parallel but unconnected pathways. The processes that develop these organic molecules are also going to be present on an early earth. They may well form in the gaseous envelope of a star, or in when liquid water is present in a primitive comet, but those same chemical processes are going to be present in a volcanic eruption, or in an early sea.

Ammonium nitrate naturally forms in the air, and reduction by sulpuric acid and sulphur dioxide would seem to be the main route of synthesis of hydroxyalamine, these are not uncommon in volcanic environments. Glycine has been documented from volcanic sources, in this study at least:

Volcanic processes and the synthesis of simple organic compounds on primitive earth.

This study makes a rough estimate that a typical hydrothermal system generates around 10^7Kg of organic compounds during its lifetime. At the same time the products of a underwater volcano, or system of hydrothermal vents will have far less exposure to UV dissociation, for example, than compounds produced in the envelope of a young star, or released from the outgassing of a comet. I can't see the justification for the typical statement that the precursor molecules of life arrived from space.

The glycine retrieved from Wild 2 by Stardust, was measured for its relative abundance of its carbon isotopes. It contained more C-13 than glycine which forms on Earth, proving that Stardust's glycine originated in space.
The study focuses more on explaining how it originated in space. I don't seem to be able to find any words attempting to correlate it with abiogenesis on Earth (??)
The fact that there is a difference in isotope proportions, shows there are different pathways and environments where it can form.
The diversity of environments where it can form, highlights the imprecision of using remotely sensed amino-acids over light-year distances, as an exo-biology indicator.
Regards

[syzygy42]

So the question is basically: How does self-replicating and evolving complex molecules emerge naturally in chemical processes. This is a discussion of possibilities implicit in chemistry, physics and planetary sciences. So it's very much a theoretical issue but it's also an issue of experimental methodology. What is the most effective methods for investigating the phenomenon empirically and quasi-empirically; experimental, computational or observational?

I'm looking forward to an interesting and creative discussion on this topic.

All of the above, and more. The interplay between theory and experiment is critical to the development of any scientific endeavor, and the two approaches are complementary. We need a theoretical framework to interpret our experimental observations and to design experiments that ask Nature, "Are we on the right track?" Moreover, we interpret our observations through our existing theoretical concepts, and we understand more about Nature as our theories evolve. Experiment works here as a natural selective force pruning back our misconceptions.

To illustrate the importance of theory let me retell a story about Darwin from a recent lecture by Paul Nurse. Everybody who has taken high school biology has encountered Mendel and his peas with the associated concepts of independent assortment and dominance. The basis for 3:1 ratio of the dominant:recessive phenotype seems so obvious today that we hardly give it a second thought. Yet, it turns out that Darwin also observed this exact same ratio with crosses with some of his flowers. He duly noted the ratio and never asked the question of how it comes about. Why did Mendel pick up on this and not Darwin? Nurse proposes that it was a difference in their backgrounds: whereas Mendel was trained as a physicist, Darwin was trained as a naturalist. Mendel, with his physics background, was able to make the intellectual leap from ratios to particles; Darwin simply observed the ratio. This is not particularly surprising since the theoretical and atomistic/molecular nature of matter was just beginning to mature.

In trying to understand abiogenesis, we are challenged in many ways. Our theoretical understanding of physics, chemistry and biology, which has served us so well over the last century, may be at best insufficient to explain the transition from non-living to living. At worst, our more successful theories will prevent us from developing a new perspective. Yet, any new concept has to agree with what we already know to be well established. As Peter Mitchell (chemiosmotic theory) remarked, "The trouble with most scientists is not that they don't have good memories, but that they don't have good forgeteries."

We are also challenged by the multifarious disciplines required to arrive at a deeper understanding of the process: from geology, chemistry, biophysics, genetics, metabolism, and physiology to solar dynamics, planet formation, and atmospheric physics. Even if it takes another century or two to arrive at another theory, just posing the question has, and will, expand our understanding of the world we live in.

I want to thank you Paul for beginning this discussion -- it brought me out of the lurker category. The responses have been quite well reasoned. I'll be posting in the future addressing specific issues and interesting results. I look forward to future discussions.

Paul Nurse's talk: http://www.youtube.com/watch?v=8-cTlKVsvvM

[Paul Wally]

To illustrate the importance of theory let me retell a story about Darwin from a recent lecture by Paul Nurse. Everybody who has taken high school biology has encountered Mendel and his peas with the associated concepts of independent assortment and dominance. The basis for 3:1 ratio of the dominant:recessive phenotype seems so obvious today that we hardly give it a second thought. Yet, it turns out that Darwin also observed this exact same ratio with crosses with some of his flowers. He duly noted the ratio and never asked the question of how it comes about. Why did Mendel pick up on this and not Darwin? Nurse proposes that it was a difference in their backgrounds: whereas Mendel was trained as a physicist, Darwin was trained as a naturalist. Mendel, with his physics background, was able to make the intellectual leap from ratios to particles; Darwin simply observed the ratio. This is not particularly surprising since the theoretical and atomistic/molecular nature of matter was just beginning to mature.

I quite agree with what you say about the importance of theory. Instead of just inductively generalizing an empirical law from the data, we should attempt to explain the empirical law from deeper and more fundamental mathematical principles. From such a more general theory other instances can be derived and tested against new evidence. For instance, the concept of "self-replicating and evolving molecules" is something that could be investigated purely mathematically. Here I'm thinking of work done in fields like artificial life, cellular automata, nonlinear dynamics etc. The principles learned in such mathematical studies could then be applied and tested with actual observations and laboratory chemical experiments. So there would be mutual interactions between theory, experiment and observation.

[A.DIM]

Here's an interesting take: Bit by Bit: The Darwinian Basis of Life.
With Joyce's bit calculations in mind I find it ever more difficult to believe abiogenesis occurred on Earth. A plethora of hypotheses have been proposed over the last half century yet we seem no closer to answers. The hardware / software problem looms large as ever.

[publiusr]

Abiogenesis in eutectic ice in comets---how might that work? We have plumes here, smokers at one g. So I wonder about the mechanics of plumes in microgravity--the attraction of vapors, particles to one another in space...I'm starting to think that folks who study vapors in combustion engines might even have a say. We take organics vaporize them and use them for thrust in making exhaust plumes. Now for a little reverse thinking?

[syzygy42]

A.DIM,
A plethora of hypotheses have been proposed over the last half century yet we seem no closer to answers.

While I agree with you that there have been more proposals than answers, I think that we are beginning to ask the right questions. Paul concluded above that there is a need for "mutual interactions between theory, experiment and observation." Unfortunately, the experiment and observation sides of the exploration have, until recently, been lacking. This is not due to a lack of interest. Rather, there have not been any agencies willing to fund projects whose primary objective is origin of life studies. I think that NASA's Astrobiology Institute is a step in the right direction, modest as it is.

I should also say that there has been significant indirect progress in widening our perspective. Starting with Woese's identification of the Archaea, the availability of sequence data has allowed us to look further back in time beyond the fossil record to reconstruct a phylogenetic history of life. Additionally, we have found thriving bacterial communities in places formerly thought to be uninhabitable, revealing surprising ways that organisms can extract food and energy from their environment.

This change in perspective is best illustrated by looking at the TCA cycle (Kreb's cycle), the bane of high school and college biology students the world over. With few exceptions, the way that it is taught is that it is a cycle that runs clockwise, extracting electrons and CO₂ as it goes. Yet, it is rarely taught that it can equally run in the opposite direction by using available electrons to incorporate CO₂. It is just this sort of observation that has led to some interesting and surprising chemistry, leading to a better understanding of what is possible in a prebiotic environment.

[Paul Wally]

Here's an interesting take: Bit by Bit: The Darwinian Basis of Life.
With Joyce's bit calculations in mind I find it ever more difficult to believe abiogenesis occurred on Earth. A plethora of hypotheses have been proposed over the last half century yet we seem no closer to answers. The hardware / software problem looms large as ever.

Thanks for that link. I would like to highlight some of the concepts in there that caught my interest.

Following an era of prebiotic chemistry, perhaps reaching a high level of chemical complexity,
molecular memory arises. Molecules of variable composition begin to replicate, mutate, and evolve in a Darwinian
manner.

(My underline)

I think the concept of molecular memory is important, but what is it really? We don't say oxygen or water molecules have memory simply because of their greater universality i.e. their ability to exist in large variety of possible environments. But suppose carbon coal is subjected to very high pressure it becomes diamond and when it returns to it's original environment it stays diamond; a hysteresis phenomenon. So somehow the diamond state is an implicit memory of a past environment.
I suppose that a molecule has memory when it depends on some very specific conditions for it's formation, which would make it less universal and more particular than say water or oxygen molecules.

What is the minimum number of bits it takes to
provide a replicating, evolving system that has the ongoing capacity to accrue more bits?

A more general question is: Are there mathematical or computer models (e.g. cellular automatons) wherein the system reaches a critical transition from consisting of non-self-replicating to self-replicating units, with perhaps the additional capacity to evolve (as a bonus)? This is now very general and abstract and may not involve any actual chemistry.

[tnjrp]

A plethora of hypotheses have been proposed over the last half century yet we seem no closer to answers. The hardware / software problem looms large as ever.

Not sure about the problem you refer to, but I disagree on seeming to be no closer to the answer. OTOH if you are refering to an answer that everybody is going to accept then you are correct with an attendum that we will never get one.

[syzygy42]

Here's an interesting take: Bit by Bit: The Darwinian Basis of Life.

Thanks for the link.

[Colin Robinson]

I disagree on seeming to be no closer to the answer. OTOH if you are refering to an answer that everybody is going to accept then you are correct with an attendum that we will never get one.

I think that exploring the moons of the outer solar system may well provide clues about abiogenesis. Even if it turns out that there are no living things there. Not that I'm predicting absence of living things -- they may be there, they may not be there. But we know, at least, that there are carbon compounds, energy sources, liquid solvents, and presumably they have been interacting together over geological time. Even if life (as such) has not emerged, what has emerged? What sorts of complexities, what sorts of systems? The answers to these questions may be scientifically productive and exciting.

[glappkaeft]

Even if life (as such) has not emerged, what has emerged? What sorts of complexities, what sorts of systems? The answers to these questions may be scientifically productive and exciting.

It could very well be more interesting if life has not emerged yet. Precursors to life in the presence of existing life would probably quickly result in life saying "Oh look, yummy, yummy, nom, nom".

[A.DIM]

Abiogenesis in eutectic ice in comets---how might that work? We have plumes here, smokers at one g. So I wonder about the mechanics of plumes in microgravity--the attraction of vapors, particles to one another in space...I'm starting to think that folks who study vapors in combustion engines might even have a say. We take organics vaporize them and use them for thrust in making exhaust plumes. Now for a little reverse thinking?

Indeed, and why not go against the flow, as it were?
Personally I'm beginning to think those who study fluid dynamics should have a say.

[A.DIM]

Not sure about the problem you refer to, but I disagree on seeming to be no closer to the answer.

You know, the "chicken or egg" question what regards abiogenesis hypotheses: What came first, the genetic programs for making the machinery, or the assembly of the machinery before the programs?

OTOH if you are refering to an answer that everybody is going to accept then you are correct with an attendum that we will never get one.

Indeed, as of late we learn Study of ribosome evolution challenges RNA world hypothesis.

Proponents of the RNA world hypothesis make basic assumptions about the evolutionary origins of the ribosome without proper scientific support, Caetano-Anollés said. The most fundamental of these assumptions is that the part of the ribosome that is responsible for protein synthesis, the peptidyl transferase center (PTC) active site, is the most ancient.

In the new analysis, Caetano-Anollés and graduate student Ajith Harish (now a postdoctoral researcher at Lund University in Sweden) subjected the universal protein and RNA components of the ribosome to rigorous molecular analyses – mining them for evolutionary information embedded in their structures. (They also analyzed the thermodynamic properties of the ribosomal RNAs.)

They used this information to generate timelines of the evolutionary history of the ribosomal RNAs and proteins.
...

The timelines suggest that the PTC appeared well after other regions of the protein-RNA complex, Caetano-Anollés said. This strongly suggests, first, that proteins were around before ribosomal RNAs were recruited to help build them, and second, that the ribosomal RNAs were engaged in some other task before they picked up the role of aiding in protein synthesis, he said.

“This is the crucial piece of the puzzle,” Caetano-Anollés said. “If the evolutionary buildup of ribosomal proteins and RNA and the interactions between them occurred gradually, step-by-step, the origin of the ribosome cannot be the product of an RNA world. Instead, it must be the product of a ribonucleoprotein world, an ancient world that resembles our own. It appears the basic building blocks of the machinery of the cell have always been the same from the beginning of life to the present: evolving and interacting proteins and RNA molecules.”

I note "it must be the product of ... an ancient world that resembles our own."

[A.DIM]

Thanks for the link.

Certainly, and welcome to BAUT!

[Colin Robinson]

“This is the crucial piece of the puzzle,” Caetano-Anollés said. “If the evolutionary buildup of ribosomal proteins and RNA and the interactions between them occurred gradually, step-by-step, the origin of the ribosome cannot be the product of an RNA world. Instead, it must be the product of a ribonucleoprotein world, an ancient world that resembles our own. It appears the basic building blocks of the machinery of the cell have always been the same from the beginning of life to the present: evolving and interacting proteins and RNA molecules.”

I note "it must be the product of ... an ancient world that resembles our own."

If I understand the passage correctly, they are saying "resembles our own" in the sense that there were both proteins and RNA molecules in the picture. That does not rule out one key aspect of the RNA world hypothesis -- the idea of an ancient biosphere with no DNA.

[syzygy42]

Certainly, and welcome to BAUT!

Thanks for the welcome.

With regard to your previous post, I watched one of his talks and breezed through the paper linked at the bottom of the the press release. (Note to press release writers: link the article mentioned within the text of the press release -- the earlier the better.) It is a very interesting paper but aligns with my personal bias. The caveat here is that there are several assumptions that went into this analysis, though they generally agree with different analyses using different methods.

As with any early scientific study, when hypotheses are numerous and experiments are few, there is usually a division into two vocal camps that seem to self-segregate along rather purist lines. A cosmology example is that of the value of the Hubble Constant: there were those that claimed that it was 50 and those that said it was 100. When the data finally came in, it turned out to be ~75. With the RNA World hypothesis, Wally Gilbert proposed it at the time when many preconceptions about what was possible in molecular biology were falling. In particular, the thought that catalysis was the sole property of proteins was overturned by the finding that RNA also had catalytic capabilities. Chicken and egg problem solved? What could be better than a molecule that could in principle replicate itself? The high point of this hypothesis was the demonstration that the catalytic site of the ribosome was comprised of RNA. A lot of effort has been devoted to finding a replicator with limited success, though the mechanism of protein synthesis has certainly progressed and is pretty amazing.

One nagging nagging question with a "pure" RNA World was where did the nucleotide substrates come from? Enter the metabolism first crowd who argued that the development of a stable catalytic network necessarily preceded the RNA world and supplied the raw materials for protein and RNA synthesis. Indeed, synthesizing significant amounts of sugars, fatty acids, and some amino acids is rather common in a variety of experiments that mimic different environmental conditions, whereas synthesis of RNA bases, nucleosides and nucleotides is rare. The structure and reactions of a prebiotic metabolic metabolic network are pretty much unknown. There are some plausible steps that have been experimentally demonstrated but there remain many gaps to fill.

So for me, coevolution from the basic to the complex seems to be the a decent stance to take, and don't rule anything out yet. My motto has been "Nature is always more interesting than you can imagine."

[Paul Wally]

For those interested in the simulation approach to the problem of abiogenesis, here's a paper Evolvable Self-Replicating Molecules in an Artificial Chemistry.

Here's a tantalizing extract:

In the context of early evolution, Szathm´ary stated [34]: “The potential now lies
in modelling chemical organization and evolution in abstracto.” Dittrich et al. [9]
also argued that ACs are “the right stuff” for simulating prebiotic and biochemical
evolution.However, until now the minimal requirement for evolution (the evolvable
self-replicator) has not been shown in an AC.

Perhaps it has been shown by now. The paper is dated 2002.

[syzygy42]

For those interested in the simulation approach to the problem of abiogenesis, here's a paper Evolvable Self-Replicating Molecules in an Artificial Chemistry.

Here's a tantalizing extract:


Perhaps it has been shown by now. The paper is dated 2002.

It's a difficult subject, both intellectually and computationally. Intellectually, you have to start to come to grips with graph theory and dynamics superimposed upon a graph (by graph I mean this.) Computationally, it can be a demanding problem, even if the initial code is fairly simple. We have to crawl before we can walk, and understanding simple toy models can lead to a deeper understanding and development of richer models.

[Selfsim]

One nagging nagging question with a "pure" RNA World was where did the nucleotide substrates come from? Enter the metabolism first crowd who argued that the development of a stable catalytic network necessarily preceded the RNA world and supplied the raw materials for protein and RNA synthesis. Indeed, synthesizing significant amounts of sugars, fatty acids, and some amino acids is rather common in a variety of experiments that mimic different environmental conditions, whereas synthesis of RNA bases, nucleosides and nucleotides is rare. The structure and reactions of a prebiotic metabolic metabolic network are pretty much unknown. There are some plausible steps that have been experimentally demonstrated but there remain many gaps to fill.

Greetings syzygy42 !

The Nucleotide bases of RNA, (ie: A, U C and G), are naturally occurring - there's about ~100 which presently occur in nature. More have been synthesised.

Where they originally came from, may be what you are referring to here (??) .. if so, I'd agree that the origin of them, is a different discussion from one about modern nucleotides.

It seems the ribosome has become the focus of much of RNA research, as it seems to point to many clues stemming from the basic functions needed to build the first eukaroytic cell, and clues about how the genetic code evolved. The investigation (at the moment) seems to have been traced back to a question of how did the small RNA and small peptides manage to compile themselves into a ribosome. (?)

Interesting.

Regards

[tnjrp]

You know, the "chicken or egg" question what regards abiogenesis hypotheses: What came first, the genetic programs for making the machinery, or the assembly of the machinery before the programs?

I would think neither came clearly first, just like the chicken and egg problem is a fake one.

Indeed, as of late we learn Study of ribosome evolution challenges RNA world hypothesis.

Proponents of the RNA world hypothesis make basic assumptions about the evolutionary origins of the ribosome without proper scientific support, Caetano-Anollés said. The most fundamental of these assumptions is that the part of the ribosome that is responsible for protein synthesis, the peptidyl transferase center (PTC) active site, is the most ancient.

Caetano-Anollés talks fighting talk there, I see. I'd await the response from the RNA world proponents before jumping to conclusions that this challenge is as serious as he makes it out to be.

I note "it must be the product of ... an ancient world that resembles our own."

Yes, I can see why that paper appeals to you in particular.

RNA world is still not a theory of course and even theories should be criticized. Still, even if it turns out to be wrong we still aren't just treading water with abiogenesis research as a number of papers I've linked to earlier clearly attests.

[syzygy42]

Greetings syzygy42 !

Thanks

The Nucleotide bases of RNA, (ie: A, U C and G), are naturally occurring - there's about ~100 which presently occur in nature. More have been synthesised.

Where they originally came from, may be what you are referring to here (??) .. if so, I'd agree that the origin of them, is a different discussion from one about modern nucleotides.

Where the constituents came from is a very important question. Abiotic syntheses under various conditions produce a slew of compounds. The Murchison meteorite is a prime example of a natural experiment. It contains amino acids, purines and pyrimidines, though the relative abundance of amino acids over purines and pyrimidines was more than ~20 to one. Even this analysis is a little biased, since examination of the diversity of organic compounds provides an estimate of about 50,000 different compounds. If one is looking for amino acids/nucleobases you will find them. For amino acids, about 50 different ones have been detected with only 8 of the 20 protein found. Interestingly, these same 8 appear again and again in other abiotic simulation experiments. I haven't found any information on the diversity of aromatic nitrogenous bases, but I would suspect that they are equally diverse.

Making interesting organic compounds is really not a problem, assembling them into anything resembling a stable dynamic system is. The problem is basically a kinetic one. To accumulate, a compound has to be synthesized faster than it is degraded, modified or diluted. To be synthesized at an appreciable rate, its precursors must also be made at least at that rate. As anyone who has taken an organic chemistry lab knows, its the side reactions that kill your yield (and grade). For a stable dynamic system to self-assemble from a continuous supply of raw materials, there is a requirement that the compounds themselves contribute either directly or indirectly in their own synthesis. That is some of them must be catalysts that can selectively channel the precursors to regenerate the whole system. Freeman Dyson and Stuart Kauffman introduced the concept of an autocatalytic network as a possible mechanism to bootstrap from a random collection of catalysts and compounds to one that is at least self sustaining in a particular circumstance. This is not life per se, but it is getting there.

It is within this context that hydrothermal vents and ponds that have captured the attention of many researchers, given that they are natural incubators of organic compounds from simple, abundant precursors, and afford the possibility of retaining the members of an autocatalytic set. It is only when such a system can produce significant quantities of precursors that functional polymers can arise. Again, the ones that accumulate will be those that can contribute to the catalysis of their precursors. It may seem trivial to point out that each member of the network is required for the synthesis of itself, but when one considers all of the molecules within a cell, be they metabolite or DNA, they are required for their own synthesis. I have come to view all of the components of the cell as metabolites, whether they are intermediates in glycolysis, proteins or nucleic acids.

Obviously, there is much more work to be done in the development of a coherent theory of life and its origins. With the knowledge that we have gained in the past 50 years or so, I think real progress can be made and is being made.

It seems the ribosome has become the focus of much of RNA research, as it seems to point to many clues stemming from the basic functions needed to build the first eukaroytic cell, and clues about how the genetic code evolved. The investigation (at the moment) seems to have been traced back to a question of how did the small RNA and small peptides manage to compile themselves into a ribosome. (?)

While people focus on DNA, it's the amazing catalytic dance performed by the ribosome and its attendants that amazes me and that is the foundation upon which life was built. The dance list is growing: even Steve Chu has devoted a significant amount of research time to its study.

[Selfsim]

Where the constituents came from is a very important question. Abiotic syntheses under various conditions produce a slew of compounds. The Murchison meteorite is a prime example of a natural experiment. It contains amino acids, purines and pyrimidines, though the relative abundance of amino acids over purines and pyrimidines was more than ~20 to one. Even this analysis is a little biased, since examination of the diversity of organic compounds provides an estimate of about 50,000 different compounds. If one is looking for amino acids/nucleobases you will find them. For amino acids, about 50 different ones have been detected with only 8 of the 20 protein found. Interestingly, these same 8 appear again and again in other abiotic simulation experiments. I haven't found any information on the diversity of aromatic nitrogenous bases, but I would suspect that they are equally diverse.

Hmm .. not that it matters so much for this chit-chat, I believe there are 500 or so, naturally occuring amino acids. Of these, ~240 occur 'freely' in nature, (unbounded by proteins, where proteins are themselves, the end products of biosynthetic pathways). 20 are coded for by the Standard Genetic Code (with extra 2 'oddballs', as well).

Also interestingly, over the last ~80 years or so, about 170 molecules in all have been detected in the Interstellar Medium using mm wavelength spectroscopy.
Of these, ~34% are complex (arbitrarily >6 atoms per molecule), and 100% of these 'complex' molecules, are organic.
(Reference A. Belloche, Max Planck Institute, 'Complex Organic Molecules in the Interstellar Medium').

I have come to view all of the components of the cell as metabolites, whether they are intermediates in glycolysis, proteins or nucleic acids.

Hmm .. well, clearly metabolism is essential. Heritability and replication are also essential. Whilst these latter two, clearly require metabolism, they are separable functions which also make use of the same cell componentry.

Obviously, there is much more work to be done in the development of a coherent theory of life and its origins. With the knowledge that we have gained in the past 50 years or so, I think real progress can be made and is being made.

Sure .. Its great to see the developments taking place in this area ... its part of all what I've referred to elsewhere, as 'local exploration'.

While people focus on DNA, it's the amazing catalytic dance performed by the ribosome and its attendants that amazes me and that is the foundation upon which life was built. The dance list is growing: even Steve Chu has devoted a significant amount of research time to its study.

... and they've managed to sythesise ribosomes from scratch ! (Well, technically speaking its called 'bio-engineering' which capitalises on the flow-on benefits of DNA sequencing research, and a whole bunch of clever equipment).

Regards