To What Inanimate Matter Are We Most Closely Related and Does the Origin of Life Harbor Meaning?

Round 1

Reviewer 1 Report

The authors present an engaging historical and philosophical study of the question of origins in relation to location, opening and closing by addressing something we could call "geological relatedness": which type of geological matter living beings are most likely to be related to, not just chemically but, in fact, phylogenetically.

They give a critical appraisal of the traditional RNA-world and warm-little-pond (primordial-soup) views, and take a briefer look at other possible scenarios and ideas. At times the tone may strike some readers as a little belligerent, which is unfortunately too common in the field -- and, may I respectfully add, not helpful. I leave it to the authors to revise the instances that I have mentioned below, in case they agree that this would help their narrative.
The article remains mostly neutral throughout, critically but objectively observing ideas and their evidence or lack thereof. Towards the end the manuscript clearly sides with the alkaline hydrothermal vent theory (AHVT), which is of course to be expected given the fundamental role that the senior author has played in the development of that theory. This will not surprise anyone from the field, but the article should still have plenty to offer to the broader origins discussion, even for those that do not abide by the AHVT.

This being a philosophy article, the authors cannot be faulted for emitting their opinions. I generally find the tone balanced, except in the instances that I mention below.

In the next lines I give some suggestions that the authors may want to consider.

16: The authors cite Dobzhansky's famed 1973 article "Nothing in biology makes sense except in the light of evolution". This is an oft-quoted phrase from a more complex article than its title alone would suggest, in which Dobzhansky strongly defends creationism as not opposed to evolution. For example, on page 127, he writes:
"It is wrong to hold creation and evolution as mutually exclusive alternatives. I am a creationist *and* an evolutionist. Evolution is God's, or Nature's, method of Creation."
Whether or not one agrees with Dobzhansky, given the nature and inferred purpose of the authors own manuscript, I believe a fuller look at the 1973 article and its perennially out-of-context title could be a welcome addition.

49: Maynard Smith & Szathmáry's Major Transitions would seem a notable exception worth citing here.

84: On the topic of Priestly and Oxygen, the authors may want to consider mentioning that Lavoisier called nitrogen "azote" -- meaning "no life" -- because it was not possible to live from breathing air that contained only it and not oxygen. This name "azote", incidentally from the enlightenment times, still remains in several European languages. Also interestingly, I understand that during his oxygen isolation studies, Priestly visited Lavoisier in Paris, where the pair discussed their respective gas experiments and influenced each other's progress separating and identifying the components of air and other gases.

97-98: Regarding "in order to grow", given the topic and purpose of this article, keeping teleology to a minimum -- as the authors have otherwise done throughout the manuscript -- seems appropriate.

145: The authors may want to cite Darwin's other relevant Letter to Hooker, from 29 March 1863: "It is mere rubbish thinking, at present, of origin of life; one might as well think of origin of matter." Interestingly, this is preceded by a self criticism regarding his own wording in the Origin: "I have long regretted that I truckled to public opinion & used Pentateuchal term of creation, by which I really meant 'appeared' by some wholly unknown process."

153: This would seem natural: If all (modern & known) life has a common origin, then this origin was in one and only one place. Is this reasoning flawed somehow? The text could suggest it.

157: Perhaps I misunderstand, but I would not say that cells work as a chemical reaction -- in fact, quite the opposite: Chemical reactions go to equilibrium given a chance, whereas cells systematically avoid equilibrium, through a complex combination of chemical reactions and physical states. Maybe "how they work through chemical reactions" or "how their chemical reactions work" could be suitable alternatives.

203: Given how hostile the origins field is already, I am not sure the "somehow" is necessary. This is certainly subjective, so I leave it to the authors. There is much stronger language later in any case.

219: The past tense in "gave rise" makes it seem, to me at least, as though the RNA World in ponds is now finished, as others have conclusively claimed in recent years about hydrothermal vents. I would suggest "has given rise" could be a fairer use of grammar, whether or not one agrees with the (traditional view of the) RNA world.

239: Even if the late heavy bombardment never occurred or at least was not as "heavy" as originally thought, sufficient organics may still have been delivered in the form of carbonaceous chondrites and other carbon-containing meteorites to support (semi)heterotrophic views of the origin of life. Whether this was enough or adequate to support the actual origin of life, that's a different matter, but this is a discussion over theories and scenarios, not over the actual history -- which the authors note is itself unreachable.

255: Relatedly, do the compounds necessarily have to be inorganic? Have we unequivocally disproven heterotrophic origins theories?

258-267: I don't suppose this will go down very well with many in the origins community. It certainly does not have to, but I would suggest considering whether the tone may be a little too much on the aggressive side of passive-aggressive. Ultimately it is the authors' prerogative to make this point in these terms if they wish to. 

302-412: I find the discussion on Nei engaging and informative, but I am not presently persuaded that, in its present state, it fits the main narrative of the article. I may have missed the authors' intent, but they may want to revise this section somewhat (or even consider leaving it for a separate manuscript). Most surprisingly (to me), the authors seem to leave the concept of biological function entirely out of this section, and especially the novel development of function from non-functioning matter at the origin of life. It may well be that evolution is mutation driven, but in that case a discussion of function will be necessary, especially in the context of the origin of those first "functions", and more so within the article's discussion on teleology. Similarly, the closing "Possibly" is too ambiguous to be helpful to this particular reader in this particular context; line 442 suggests that the authors agree with Nei, and if that is the case it would be helpful to state it clearly in 412.

342: Whether or not one abides by Nei's mutation-driven theory, this would likely depend on factors such as the size of the population and the strength of neutral vs selective processes therein, both on individual organisms and on specific traits. If evolution of a given trait is occurring chiefly by drift and other neutral mechanisms, as seems to be unequivocally the case for many traits (most, Nei would probably argue), then mutation could indeed be seen as the primary driver (other than the neutral mechanism itself). Of course, this does not explain biological function, and it certainly does not explain origins, but the caveat seems worth mentioning.

538-539: True, but the point being made was about physical and chemical reactions, not cells.

697-701: I am not sure the not-so-veiled suggestion of religious bias in non-vent views is fair, justified, or helpful. Perhaps I misunderstood what the authors meant.

MINOR SUGGESTIONS    
37: comma before "such" might work better as a semicolon or full stop.

54: "a nucleic acid WITH three simple components"

82: Perhaps a comma before "let alone".

96: Did the authors mean to repeat "reactions"? If not, perhaps the second "reactions" could be changed to "(biochemical) processes".

235: "Moon-forming"

277: "that THAT of"?

303: Perhaps the authors would agree that brief (~one-line) definitions of epistemology and teleology could be useful to the uninitiated, especially students.

331: "phenomenON in nature is" (plural noun vs. singular verb).

331: "mutation-driven".

333: "process driving THE vectors" or "process-driving vectors"?

340: This is a philosophy paper, so the personal note is certainly admisible, but it doesn't strike me as helpful.

351: "cannot"

353: "as to" sounds teleological to me. Best to avoid given the topic in discussion.

505: "cell-like"

515: "organic"

516: remove -

517: remove comma after "advantages"

534: "life or its basic molecules"?

595: "early-Earth"

596: "atmosphere-derived"

616: "H2-producing"

716: "cannot"

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Philosophies manuscript – Vieira, Nagies and Martin

There is much to discuss in this paper and I am sure those who read this paper will be stimulated with much thought and interpretations of the ideas the authors present. I regard this manuscript as an existential expression of the authors and don’t have a reason to recommend changes. As a scientist, I am use to reviewing papers in which I look over the data, methods and interpretation of the data. In contrast, my comments to this manuscript are more a reflection of some of my reactions to the manuscript in which I regard as more important to me since they point out how influential a philosophical topic can be discussed by scientists rather than many of the papers I have read by philosophers discussing origin of life. I also fully understand the authors unwillingness to get involved in some of the thorny philosophical issues and particularly the definition of life and whether or not it has meaning. However, I would like to pose the question: is a characterization of life and particularly “minimal life” important in origin of life studies? This is not defining life, which I think is unnecessary, but knowing what to look for other than the evolved prokaryotic cells that currently exist and have existed for perhaps billions of years, including methanogens, for example. This is discussed a bit in section 1.6 of this manuscript where seven phases in the origin of life are listed. A couple of ideas I have about this that include essential inorganic elements for life (approximately 30 elements used by life and approximately 20 come from hydrothermal vents) and the role that key minerals might have played in the early stages of life’s origin.

Thinking about the topic of characterizations of life is also of foremost importance in our search for life off the Earth on other planetary bodies. A related topic is getting to the “unity of biochemistry” and eventually a common ancestor. Does this selection have some broad meaning and it has been discussed by others as more of a teleological argument that is discussed a bit in this manuscript? An interesting aside on philosophy and the origin of life is thinking of the discussion of the early origins work by Oparin and Haldane in this manuscript. Both were Marxist’s and had as a goal to remove creationism as an option for life’s origin.

Just a suggestion: I think that it might be useful for a broad audience who are likely to read this paper to include some references dealing with the problem of trying to define life including those by the philosopher Carol Cleland. She makes a strong argument why we can’t define life.

(Cleland, C. E. (2007) Epistemological issues in the study of microbial life: Alternative terrain biospheres? Studies in History and Philosophy of Biological and Biomedical Sciences 38(4), 847– 861.
Cleland, C. E. (2012) Life without definitions. Synthese 185, 125–144.

Cleland, C. E. and Chyba, C. F. (2007) Does “life” have a definition? In: Planets and Life: The Emerging Science of Astrobiology. W. T. Sullivan and J. A. Baross (eds.), Cambridge University Press, Cambridge, UK: 119–131)

The question of the meaning of life also conjures a wide range of options for discussions and again I agree with the authors take on this. However, I just read a paper in PNAS indicating that

the “structure of life emerged from randomness” and Darwinian evolution resulted in the RNA world.

Kudella, P. W. et al., 2021. Structural sequences emerge from random pool when replicated by templated ligation. PNAS 118 No. 8 e2018030118

This manuscript (Vieira et al) ends with the mention of water/rock reactions and the emergence of life and whether there is meaning in this. Is going from random chemical reactions to a form of metabolism and catabolism and eventually to complex structures capable of replication and evolution an inevitable consequence? This also got me thinking about Prigogine’s classic work on dissipative structures and that in spite of the second law of thermodynamics and the transition from order to disorder, “dissipative structures” can emerge with greater order and complexity. Is there meaning to be gleaned from this? You see what you have done to me with this manuscript.

I like that the authors have put emphasis on the possible settings where life originated and the rationale by the authors of this manuscript in discussing some of the diverse range of environments that have been hypothesized as primal origin of life settings. I do think that what is missing is a discussion of what the earth looked like at the period when we think that life originated based on isotopic and possible fossil records. Discussing earth during its first billion years would present serious caveats to some of the other hypothesized settings while providing support for the environment favored by the authors of this paper What do we think we know? There is evidence, based on rare Earth metals, for a strong hydrothermal imprint at the time of life’s origin. There is also evidence that during the first billion years of Earth’s history, there was too much heat from the mantle for plate tectonics to occur and the heat was primarily lost through plume volcanism. As a result, the crust would have been more mafic, allowing for a high incidence of serpentinization (see references below).

Dhuime B., Wuestefeld A., and Hawkesworth C. J. (2015) Emergence of modern continental crust about 3 billion years ago. Nature Geosci., 8(7), 552–555.

Tang M., Chen K., and Rudnick R. L. (2016) Archean upper crust transition from mafic to felsic marks the onset of plate tectonics. Science, 351(6271), 372–375.

How does this early earth geophysical/geological/geochemical characteristics fit in with the settings where signs of early evidence for life have been reported? Or, is there any relationship between the settings for present-day discoveries of evidence for life and the environmental setting for the origin of life or for that matter, the emergence of the “unity of biochemistry” and LUCA?

(Oldest microfossils at 3.4 Ga (giga annum) from the Pilbara Super group, Western Australia (Wacey et al., 2011),
Oldest stromatolite (layered mounds, columns, and sheet-like sedimentary rocks) at 3.7 Ga from the Isua Supra crustal belt, SW Greenland (Nutman et al., 2016)

Putative microfossils from hydrothermal environment at 3.77 Ga (Dodd et al., 2017)
Carbon isotope data (ratio of 12C/13C) from sedimentary rocks indicating CO2 fixation at 3.95 Ga (Tashiro et al., 2017)
Carbon isotope data (ratio of 12C/13C from graphite embedded in a Jack Hill (Australia) Zircon at 4.1 Ga (Bell et al., 2015))

The RNA world hypothesis has many interesting facets that have been brought forward as support including the use of ribose instead of deoxyribose, the later thought to be synthesized only by enzymes and not chemical synthesis, and the early Spiegelman experiments Spiegelman’s monster) with phage QB showing that when RNA is provided with all components including enzymes it retains only the replicating gene. What drives greater complexity? Also, is the abiotic synthesis of self-replicating RNA a sign of life? The concept of minimal life makes me think of the Koonin model for the origin of viruses in which “selfish replicators” preceded cells. Could self-replicating nucleic acids have preceded cells and were they the source of early cellular genomes?

Krupovic, M., V. V. Dolja and E. V. Koonin. 2019. Origin of viruses: primordial replicators recruiting capsids from hosts. Nature Rev. Microbiol. 17:449-458.

Wolf, Y. I., D. Kazlauskas, J. Iranzo, A. Lucia-Sanz, J. H. Kuhn, M. Krupovic, V. V. Dolja and E. F. Koonin. 2018. Origins and evolution of the global RNA virome. mBio, Vol. 9 Issue 6 e02329 Page 1-31.

On page 2 of this manuscript, the authors pose the question “Should we then just give up on studying origins?” I mentioned astrobiology earlier and the discussion of multiple origins and multiple life forms even though we don’t have a definition of life, but we can think about essential characteristics of life, at least I think we can. Anyway, we have no choice but to continue our search – it is human nature. In T. S. Elliot’s poem “The Little Gidding” from his Four Quartets: “We shall not cease from exploration and the end of all our exploring will be to arrive where we started and know the place for the first time” – the rest of the poem is also cool.

As a final aside, this manuscript made me think about Alfred North Whitehead and Process Philosophy and how many aspects of the origin of life may fit this philosophy. The simple way I think about Process Philosophy is that actuality is not just individual components but involves interwoven processes. This implies that a characteristic of this system is emergent and results in something greater than the sum of the parts. I guess Whitehead would regard this as process metaphysics. Hmmm – I am still thinking about this.

.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf