A Field Trip to the Archaean in Search of Darwin’s Warm Little Pond
First Round of Evaluation
Round 1: Reviewer 1 Report and Author Response
Major comment:
1. The novelty of the suggested model - as compared to other published models - should be specified more precisely.
In the abstract the author writes: "Combining the field observations with the laboratory results we describe the terrestrial origin of life hypothesis which provides a novel and testable evolutionary model in which life begins as protocells assembling in fresh water hydrothermal pools".
The terrestrial origin of life hypothesis in which life begins in a fresh water pool is not quite novel. It was first suggested by Charles Darwin, the respective quote is given in the manuscript. This hypothesis was then specified - via invoking hydrothermal pools - by a lot of people, including the quoted Deamer (2006), Mulkidjanian et al (2012), Damer and Deamer (2015) and not quoted Ricardo and Szostak (2009), Maruyama et al. (2013) and some others.
Author Response: Abstract has been rewritten accordingly. I located Ricardo and Szostak (2009). In scientific American:
http://www.nature.com/scientificamerican/journal/v301/n3/full/scientificamerican0909-54.html
But cannot find this reference.
Maruyama et al. (2013)
The Szostak Lab’s protocell work has been cited elsewhere in the essay. Recent work encapsulating
ribozymes in liposomes will be cited in a more detailed treatment of this hypothesis.
From the opinion of this reviewer, certain novelty of the suggested model, as compared, e.g. to the model of Damer and Deamer (2015) could be attributed to a (hypothetical) three-state - and not a two-state - scheme where the primordial ecosystem cycles between dry, gel and hydrated states respectively and not just between the dry and hydrated states. It seems, that only this feature can be claimed as novel.
Author Response: I have included a new section listing the novel features of the model beyond the initial ideas in (Damer & Deamer, 2015), which also carry testable predictions. Like Darwin’s trip on The Beagle, it was only with a journey to the field, in this case the Pilbara that the final key pieces fell into place. Thus, by placing the coupled phases scenario within the natural context, it became a full terrestrial origin of life hypothesis. For your convenience the features summary is included here:
Summary of novel features and testable predictions of the model
The novel features of the model, each embodying a series of testable predictions offered to experimentalists, are
summarized here:
I. A kinetic trap cycling polymers through coupled phases of hydration and dehydration will produce large numbers of random molecular systems synthesized between dehydrated lipid lamellae (Figure 9, top left) which become encapsulated within large numbers of lipid compartments (protocells).
II. Combinatorial selection of encapsulated functional polymers will be observed within this kinetic trap. The initial selection criterion will be the stability of membranous compartments encapsulating polymers which will be tested in the hydrous phase (Figure 9, top right).
III. During dehydration events, stable protocells will crowd together with concentrated nutrients forming a gel phase (Figure 9, center) which provides a protected environment supporting interaction of the system of protocells, early forms of metabolism, and sharing of functions and products.
IV. These three phases will subject molecular systems to a variety of selective pressures, driving the system to surmount hurdles to achieve stepwise molecular evolution of new functions.
V. Pure self assembly and random synthesis will enable the initial stages of the model, but in later cycles, active functions expressed by sets of robust heritable instructions will enable Darwinian evolution to take hold.
VI. Degradation rates of synthesized polymers will set upper bounds on the dwell time within each phase. Products of degradation and other non-functional byproducts must be periodically recycled or selectively expelled and functional systems re-synthesized through heritable instructions and a continuous source of incoming solutes (Figure 9, top right).
VII. A protocell gel progenote capable of growth and adaptation enabled by functions expressed through shared genetic representations will emerge and become robust to distribution to a variety of watery venues in a plausible Archaean volcanic landscape. This progenote will be suggestive of a pathway to the first microbial communities and viable free-living cells.
Therefore, upon revision, the evolution of the concept of the terrestrial origin of life should be considered in a more detail with previous works properly quoted. The novel feature of the three-stage cycling should also be discussed in some more detail and related to the earlier literature. Specifically. John Bernal (1949) should be quoted as the author of the two-state dry-wetting scenario. The previous works on importance of the gel state for the origin of life should be also quoted and discussed (see e.g. Trevors, J.T.; Pollack, G.H. Hypothesis: The origin of life in a hydrogel environment. Prog. Biophys. Mol. Biol. 2005, 89, 1-8, and papers of R. Egel in "Life").
Author Response: I have referenced Trevors & Pollack. Thank you for bringing their work to my attention. See Bernal reference below.
Accordingly, the abstract should be completely re-written (see also comment 2 below)
Author Response: The abstract has been rewritten and the title of the essay changed to incorporate the reviewer’s comments.
Related minor comments:
2. The author writes in the abstract: "It has generally been assumed that life began in a marine environment such as deep ocean hydrothermal vents".
Author Response: The abstract and title of the essay have been rewritten accordingly.
This statement is misleading. As noted in the manuscript proper, the science of abiogenesis started from Charles Darwin who insightfully conceived a "warm little pond" and not deep sea vents.
Oparin and Haldane considered non-specified marine environments with explicit consideration of the UV light as a beneficial factor, which rules out deep sea vents.
John Bernal was first to realize that all large biomolecules are formed - from monomers - by condensation, with release of water, which implies that they could emerge spontaneously only under dry condition. He suggested tidal zones as cradles of life, so that the mainstream community of origin of life researches (e.g. S. Miller, A. Lazcano, N. Lahav) has considered the fluctuating tidal zones as most probable places where life may have emerged - until Deamer and others suggested that continental geothermal systems also would provide fluctuating conditions.
Author Response: After an exhaustive search I have found only one indirect reference to: Bernal, J. (1959) The Origin of Life on Earth, pp. 38-53, Pergamon Press, New York referring to Bernal’s proposal for polymerization through adsorption to clay surfaces enabled by dehydration condensation. I have not been able to find this book for the exact text. As I am focused on dehydration energy as applied to condensation reactions between lipid lamellae, isolated away from mineral surfaces, I would rather not deal with alternative hypothesis (clay, proteinoids, etc) that do not involve the presence of lipid. Other articles have done a good job reviewing these alternatives and I will do so in a longer piece in the future.
As pointed out in the essay, any saline environment, such as tidal pools, also present barriers to the formation of stable membraneous structures, hence the focus on fresh water (inland) settings.
The deep-sea hydrothermal vents came into play only in 1981, when Corliss suggested them as cradles of life (after discovering them just a few years before that). These environments are favored by some geologists who somehow ignore the Bernal's constrain on requirement of periodically dry conditions for primordial syntheses. However, the deep-sea vent hypothesis never was a general viewpoint within scientific community.
Author Response: I have included a reference to Corliss et al. (1981). Even though the deep-sea vent hypothesis was never a general viewpoint, a great deal of research effort (and dollars) have been focused on this area for decades. See comment re: Bernal above.
3. The description of the hydration step is vague. Generally, as mentioned in the manuscript, the hydration could result from a rainfall. However, in a hydrothermal system, where the delivery of water is continuous, the periodic hydration might be due to fluctuations in the hydrothermal water supply and/or day/night fluctuations. All these possibilities should be discussed.
Author Response: Sources for hydration events have been made more specific with the following addition:
Short term dehydration and rehydration of the pool through periodic fluctuations in hydrothermal water supply, rainfall events, and dew from day-night cycles or through changing humidity cause the outer layers of the dried lamellae to disperse large numbers of protocells into the bulk solution.
4. There is a huge literature on reconstructing the progenote (the Last Universal Common Ancestor?) from genome data. This literature should be checked and discussed. For example, it is unlikely that LUCA, not to mention the preceding life forms, contained DNA. Most likely, they were RNA based organisms (cf with Fig. 7 of the manuscript).
Author Response: You are correct that any progenote is unlikely to have used DNA (unless experimental evidence suggests otherwise). So the progenote cannot be reconstructed from genome data. I believe that any progenote, being long before LUCA, lies outside our ability to use such tools and techniques. I added the following clarifying language to differentiate our progenote from LUCA:
A predecessor would therefore possess a subset of these adaptations. The microbial mats observed at Gallery Hill (Figure 8, center) are suggestive of intermediate form between an earlier ancestor and a marine stromatolite. However, microbial communities as represented by living examples today and in the earliest fossil record arose long after LUCA, the last universal common ancestor. It should be noted that the path from a putative progenote to autonomous cellular structures defined as LUCA is not expected to be tree-like, but more likely will resemble the shrub metaphor of Doolittle (2000).
Also I earlier clarified the definition of our progenote through Woese’s definition and some suggestion of the
pathway of evolution of the progenote, toward LUCA:
I propose that the gel phase is an example of a progenote as described by Woese and Fox, (1977) and Woese, (2002) in which member protocells are engaged in the collective process of evolving the relationship between genotype and phenotype. As individual protocells gradually accumulate and internalize genomic function, they will develop more autonomous phenotypic expression. A new phase of the progenote will arise when member protocells can individually replicate encapsulated genomic and functional polymers and pass them on to daughter cells without depending on dehydration synthesis. The resulting speciation and specialization of increasingly independent protocells will lead to communities becoming robust to steeper gradients of environmental pressures.
Some individual protocells will eventually become robust enough to survive and reproduce independent of their source community, passing an important milestone on the continuum to life. Wider distribution and direct competition between free-living cells will drive this early life along the long winding road to LUCA.
5. The suggested three-stage model would gain in plausibility if merged with the RNA world concept (the works from the Szostak's group on behavior of RNA-containing lipid vesicles could be checked for experimental data on the subject).
Author Response: A substantial section was added to merge the model with the RNA World concept as follows:
The RNA World hypothesis (Gilbert, 1986; Joyce, 2002) suggests that transfer of proto-genetic sequence information could be first expressed by simple oligonucleotide templating (Olasagasti et al. 2011) then later through the combinatorial selection of a pool of functional ribozymes (Bartel and Szostak, 1993) some of which are capable of RNA-catalyzed template-driven synthesis of other RNA sequences by active ribozymes (Wochner et al., 2011; Lincoln and Joyce, 2009). These laboratory tests of RNA World concepts require cycling, interaction and combinatorial selection of large numbers of polymers encapsulated in glassware. A natural kinetic trap of the kind described above may have supported some version of these powerful laboratory demonstrations of molecular evolution and brought an RNA World, or more likely an RNA-Protein World, into being.
Round 1: Reviewer 2 Report and Author Response
This manuscript is written as essay. As an essay, this manuscript is quite fun to read and deals with interesting subjects. This manuscript also concisely summarizes the controversial ideas and concepts where the life originated in the early earth.
Author Response: Thank you for your constructive review and positive comments about the essay.
Round 1: Reviewer 3 Report and Author Response
Very interesting paper with an innovative approach to the old problem of origin of life. The manuscript itself is not a traditional one in the academic point of view, but it includes innovative ideas and approaches to the origin of life, providing a very interesting model for the origin and evolution of protocells in fresh water hydrothermal pools. It was written as a field trip letter without the traditional division in methods, results and discussion. It contains enough information which alloows the reader to understand and support the methodology, the results and the discussion of this new model. For me, as a reviwer, I believe it is enough adequate to be included in a scientific journal, eventually as a letter to the editor. However, this way of looking at the emergence of life goes beyond the proposals of Woese and Doolittle regarding the initial evolution of life, and supports the notion of multiple origins in straight correlation with the geochemical contexts, natural constraints, and environmental conditions. The kind of progenote proposed did not consist of one single type of organism, but of an open community of very diverse primitive cellular entities with intense symbiotic associations, antagonisms, and competition, and with a rapid and reticulate pattern of evolution. Other evidence for the widespread of these initial and universal synergistic and cooperative interactions is that, through symbiogenic mechanisms, microbial mats and stromatolites could form. These are the later of the first examples of a community ecological strategy based on cooperative and synergistic mechanisms to survive in the primitive Earth extreme environmental conditions.
I would like to see in the manuscript a relation between this approach and the inclusion of symbiogenic principles in the comprehension of life emergence, Please consider to include in the biblio the following reference:
• PEREIRA, L., RODRIGUES, T. & CARRAPIÇO, F., 2012. “A symbiogenic way in the origin of life”. In Genesis - in the Beginning. Precursors of Life, Chemical Models and Early. Biological Evolution, Cellular Origin, Life in Extreme Habitats and Astrobiology 22, 723–742. Seckbach, J. (ed.). Springer Science+Business Media Dordrecht 2012. DOI 10.1007/978-94-007-2941-4_36..
(http://azolla.fc.ulNaN/documents/SymbOrigLife2012.pdf)
• Villarreal LP, Witzany G (2010) Viruses are essential agents within the roots and stem of the tree of life. J Theor Biol 262:698–710
• Villarreal LP (2005) Viruses and the Evolution of Life, ASM Press.
• Corning PA (2005) Holistic darwinism. Synergy, cybernetics, and the bioeconomics of evolution. The University of Chicago Press, Chicago
Author Response: I will take the reviewer’s advice and include a more detailed treatment of cooperative and synergistic mechanisms of the putative progenote in a future article. For now I have included his recommended reference as well as some of key historical context as follows:
The gel aggregate also represents the first example of niche construction (Odling-Smee et al., 2003) in which a micro-environment is modified for the benefit of its members in a primordial example of endosymbiosis (Mereschkowsky 1910; Margulis 2011; Pereira et al., 2012).
