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syzygy42
2012-May-14, 09:44 PM
In trying to gain a better understanding of abiogenesis, we a faced with numerous challenges, the primary one being that the only representative we have is that of Earth. Our origins are obscured by billions of years of geological and evolutionary history. We only have a handful of rocks dating to the era when life is thought to emerge, and the validity of life's signatures from these rocks, especially the early ones, is hotly debated. As important as when life emerged is the question of where life emerged. Reconstructing plausible chemical scenarios necessarily assumes a particular environment, a place.

Given our incomplete understanding of the habitats present on the early Earth, are there other methods that we can use to constrain the conditions from which life arose? One method is the use of phylogenetic analysis to infer the genetic makeup and phenotypic properties of the oldest common ancestors to extant organisms. In addition to the sequence of 16S ribosomal RNA, a core set of genes encoding proteins that are found in (nearly) all extant organisms whose full genome sequences have been determined. Not surprisingly, these proteins most function in DNA replication, RNA transcription, and translation -- with a smattering of other physiological functions. Unfortunately, analysis of these genes and other less ubiquitous genes leads us only back so far: to a time well after the emergence of independently living organisms. Lifestyles of these early organisms is a continuing subject of debate.

Nevertheless, a recent paper by Mulkidjanian et al. in PNAS have used the inorganic requirements of this set of ubiquitous genes as well as the conserved nature of the intracellular environment to propose that the first cells arose in vapor dominated zones of inland geothermal systems.

Their reasoning is straight forward. During the evolution of the earliest cells, their primitive membranes would have been fairly permeable with the external and internal environments close to equilibrium. It was under these conditions that the evolution of the core macromolecular machinery evolved. Escape from this environment could only occur after a more sophisticated membrane had evolved to maintain an internal environment favorable to the key processes in the face of a changing external environment. Once this was accomplished, the internal environment would have been frozen since to change the internal environment would have required adaptation of many different catalysts involved in different processes rather than evolution of a new function to deal with the new environment.

Indeed, all extant organisms have a reducing internal environment, reflecting the development of processes in an anoxic environment. This has been known for quite some time, but the authors extend this analysis to the inorganic ions involved in ubiquitous protein function and to the consistent intracellular ion concentrations found in extant cells. Comparing ion concentrations found in the present day and primordial oceans to those found in today's cells, several differences stand out. The largest and most significant is that the internal environment favored potassium (K) over sodium (Na). Whereas the Na concentration in modern and primordial seawater is ~400 mM and the K concentration ~10 mM, cell cytoplasm have ~10 mM Na and 100 mM K. The other two significant ions are zinc (Zn) and phosphate (PO4). The latter is important for energy metabolism as well as being an integral component of DNA, RNA and membranes.

When one looks at the cation requirements of the ubiquitous protein set, K, Zn and Mn (manganese) are required for function with Na occasionally inhibiting activity. They then ask where such concentrations could be found. They argue that underwater thermal systems would have a high concentration of Na, essentially equal to that of the primordial oceans. Thus, these systems are unlikely to be the location from which life emerged. Looking elsewhere, they have identified continental geothermal fields as the more likely location, specifically the vapor dominated zone. To back this up, they have sampled several several thermal springs and find that in a few, there are high concentrations of Zn and phosphate and K/Na ratios greater than one. These locations had not garnered much attention previously since the current sites are highly acidic. They note that vapors at these sites include a high concentration of hydrogen sulfide which is now oxidized to sulfuric acid, a process absent in the anoxic past.

Their basic model is that primordial life evolved in these hatcheries and escaped only after a sophisticated membrane had evolved to regulate the internal environment under different external conditions. As with any scenario, this is certainly not the last word on the subject. Rather, it's importance lies with setting up laboratory conditions to study early steps in abiogenesis.

http://www.pnas.org/content/early/2012/02/08/1117774109.short

Open access

Trakar
2012-May-16, 08:04 PM
In trying to gain a better understanding of abiogenesis, we a faced with numerous challenges, the primary one being that the only representative we have is that of Earth. Our origins are obscured by billions of years of geological and evolutionary history. We only have a handful of rocks dating to the era when life is thought to emerge, and the validity of life's signatures from these rocks, especially the early ones, is hotly debated. As important as when life emerged is the question of where life emerged. Reconstructing plausible chemical scenarios necessarily assumes a particular environment, a place.

Given our incomplete understanding of the habitats present on the early Earth, are there other methods that we can use to constrain the conditions from which life arose? One method is the use of phylogenetic analysis to infer the genetic makeup and phenotypic properties of the oldest common ancestors to extant organisms. In addition to the sequence of 16S ribosomal RNA, a core set of genes encoding proteins that are found in (nearly) all extant organisms whose full genome sequences have been determined. Not surprisingly, these proteins most function in DNA replication, RNA transcription, and translation -- with a smattering of other physiological functions. Unfortunately, analysis of these genes and other less ubiquitous genes leads us only back so far: to a time well after the emergence of independently living organisms. Lifestyles of these early organisms is a continuing subject of debate.

Nevertheless, a recent paper by Mulkidjanian et al. in PNAS have used the inorganic requirements of this set of ubiquitous genes as well as the conserved nature of the intracellular environment to propose that the first cells arose in vapor dominated zones of inland geothermal systems.

Their reasoning is straight forward. During the evolution of the earliest cells, their primitive membranes would have been fairly permeable with the external and internal environments close to equilibrium. It was under these conditions that the evolution of the core macromolecular machinery evolved. Escape from this environment could only occur after a more sophisticated membrane had evolved to maintain an internal environment favorable to the key processes in the face of a changing external environment. Once this was accomplished, the internal environment would have been frozen since to change the internal environment would have required adaptation of many different catalysts involved in different processes rather than evolution of a new function to deal with the new environment.

Indeed, all extant organisms have a reducing internal environment, reflecting the development of processes in an anoxic environment. This has been known for quite some time, but the authors extend this analysis to the inorganic ions involved in ubiquitous protein function and to the consistent intracellular ion concentrations found in extant cells. Comparing ion concentrations found in the present day and primordial oceans to those found in today's cells, several differences stand out. The largest and most significant is that the internal environment favored potassium (K) over sodium (Na). Whereas the Na concentration in modern and primordial seawater is ~400 mM and the K concentration ~10 mM, cell cytoplasm have ~10 mM Na and 100 mM K. The other two significant ions are zinc (Zn) and phosphate (PO4). The latter is important for energy metabolism as well as being an integral component of DNA, RNA and membranes.

When one looks at the cation requirements of the ubiquitous protein set, K, Zn and Mn (manganese) are required for function with Na occasionally inhibiting activity. They then ask where such concentrations could be found. They argue that underwater thermal systems would have a high concentration of Na, essentially equal to that of the primordial oceans. Thus, these systems are unlikely to be the location from which life emerged. Looking elsewhere, they have identified continental geothermal fields as the more likely location, specifically the vapor dominated zone. To back this up, they have sampled several several thermal springs and find that in a few, there are high concentrations of Zn and phosphate and K/Na ratios greater than one. These locations had not garnered much attention previously since the current sites are highly acidic. They note that vapors at these sites include a high concentration of hydrogen sulfide which is now oxidized to sulfuric acid, a process absent in the anoxic past.

Their basic model is that primordial life evolved in these hatcheries and escaped only after a sophisticated membrane had evolved to regulate the internal environment under different external conditions. As with any scenario, this is certainly not the last word on the subject. Rather, it's importance lies with setting up laboratory conditions to study early steps in abiogenesis.

http://www.pnas.org/content/early/2012/02/08/1117774109.short

Open access

Most interestig considerations and premise, have the researchers spoken out about follow-up directions they would like to pursue?

syzygy42
2012-May-17, 12:10 AM
Most interestig considerations and premise, have the researchers spoken out about follow-up directions they would like to pursue?

I don't know, but I can speculate. The part of the paper that I did not summarize involved a more speculative scenario involving RNA precursors and RNA synthesis with the involvement of UV light. I think that this is experimentally testable and they will be pursuing this line of experiments. I would also not be surprised if other labs incorporate some of their finding in their experiments. One of the authors, Eugene Koonin, works only on a computer -- he has no lab -- and I suspect that he will continue to work his magic in fleshing out the history of biological sequences, structures and functions.

Trakar
2012-May-17, 09:09 PM
I don't know, but I can speculate. The part of the paper that I did not summarize involved a more speculative scenario involving RNA precursors and RNA synthesis with the involvement of UV light. I think that this is experimentally testable and they will be pursuing this line of experiments. I would also not be surprised if other labs incorporate some of their finding in their experiments. One of the authors, Eugene Koonin, works only on a computer -- he has no lab -- and I suspect that he will continue to work his magic in fleshing out the history of biological sequences, structures and functions.

I tend to be wary of science which depends upon magical evidences.

syzygy42
2012-May-17, 11:45 PM
Oops.

syzygy42
2012-May-17, 11:47 PM
I tend to be wary of science which depends upon magical evidences.

Perhaps my choice of words was a bit confusing. By "magic", I meant it in the Arthur C. Clarke tradition: "Any sufficiently advanced technology is indistinguishable from magic." The tools available do seem a bit magical when you can input a protein and search the entire database of all sequenced proteins within a matter of minutes. The databases and analysis software are free and open to the public and can be run online at NCBI (http://www.ncbi.nlm.nih.gov/guide/sequence-analysis/). Of course it isn't magical and much hard work has been done to verify predictions from computer analysis with results from wet labs. Koonin has been at the forefront of sequence and structure analysis and the application of these tools to evolutionary biology from the late 1980s when significant sequence databases were first assembled. He heads a very innovative and productive group at NCBI whose major interest is genomic evolution. Just type his name into Google Scholar to see the breadth and depth of his work.