Proto-Neurons from Abiotic Polypeptides

Round 1

Reviewer 1 Report

Comments to the Author
The current Review ID: encyclopedia-2834682, describes the proto–neurons from abiotic polypeptides. The topic of the manuscript is appropriately suited for publication in Encyclopedia-MDPI. The manuscript is in general well written and organized. It provides a large amount of experimental data, and the work seems to be carefully executed. The authors used appropriate methods to address the aims and objectives of the study. The results obtained are also interesting and relevant. Overall, the study is technically solid and includes appropriate methods as well as pertinent results. However, and for the sake of full impact only, the authors are invited to consider the following list of suggestions and recommendations.
The reviewer has some specific comments/suggestions provided below:
1- In the introduction section and elsewhere: Please remove or change the personal words “we” and “our” by other expressions.
2- Since proteinoid microspheres as protoneural networks have been described also in the patent literature it would have been worth to look at such literature as well and not only into the scientific literature.
3- There are some mistakes in the reference section. Please re-check and consult the updated guides to authors, which is available on this journal’s web site, to make them fully comply with the requested style and format of the journal. Additionally, please provide a details bibliography for ref nos: 3 and 4.
4- Are all the references (206) being necessary since many of them are old!

Author Response

Reviewer 1

The current Review ID: encyclopedia-2834682, describes the proto–neurons from abiotic polypeptides. The topic of the manuscript is appropriately suited for publication in Encyclopedia-MDPI. The manuscript is in general well written and organized. It provides a large amount of experimental data, and the work seems to be carefully executed. The authors used appropriate methods to address the aims and objectives of the study. The results obtained are also interesting and relevant. Overall, the study is technically solid and includes appropriate methods as well as pertinent results. However, and for the sake of full impact only, the authors are invited to consider the following list of suggestions and recommendations.
The reviewer has some specific comments/suggestions provided below:

1- In the introduction section and elsewhere: Please remove or change the personal words “we” and “our” by other expressions.

Authors Response:

Thank you for the feedback regarding use of personal pronouns in the paper.In response to your guidance, we have removed all instances where "we" or "our" was used to present ideas or results. For example:

In this review article, the aim is to offer a thorough summary of the existing research on proteinoids, while also sharing significant experimental advances from the laboratory that contribute to the current knowledge.

The article will explore the history of prebiotic chemistry experiments on abiotic polypeptide formation and self--assembly, investigate proposed evolutionary mechanisms, and analyze the structure and function of these proto--biopolymers.

Proteinoids could form under suitable environmental conditions over an extended period of time.

Key mathematical variables are defined to represent various components of the analysis of neural spiking.

2- Since proteinoid microspheres as protoneural networks have been described also in the patent literature it would have been worth to look at such literature as well and not only into the scientific literature.

As you have advised, we have added discussion in the Background section referencing key patents on proteinoids technology:

\bibitem[Kraft et al.(2022)]{kraft2022methods}

Kraft, et al.

\newblock Methods for the Synthesis of Activated Ethylfumarates and Their Use as Intermediates.

\newblock {\em United States Patent}, Number: US 11,479,535 B2, October 25, 2022.

3- There are some mistakes in the reference section. Please re-check and consult the updated guides to authors, which is available on this journal’s web site, to make them fully comply with the requested style and format of the journal. Additionally, please provide a details bibliography for ref nos: 3 and 4.

As per your guidance, we have systematically checked the LaTeX bibliography list against the compiled PDF citations to fix these linker errors.

For example ref no3

\bibitem[Liang et~al.()Liang, De~Los~Rios, and Busiello]{liangnon}

Liang, S.; De~Los~Rios, P.; Busiello, D.M.

\newblock Non-Equilibrium Chemical Reactions Under Non-Isothermal Conditions: Kinetic Stabilization, Selection and Thermophoresis. Master Project, Section of Physics, École Polytechnique Fédérale de Lausanne, 2020.

4- Are all the references (206) being necessary since many of them are old!

Thanks for your thoughtful comment. In fact, study on proteinoids has been going on since the 1960s. Because of this, some older references have been included to show the field's historical background.

Reviewer 2 Report

This review article was organized very well. It introduced research progresses and structure-function features of abiogenic proteinoids and in a comprehensive manner. In addition, it highlighted their great potential in bridging the gap between non-living and living matters to mimicking cell-like activities. Especially, molecular assemblies of short peptides and applications were emphasized. Also, they discussed the interactions with environmental conditions. Basically, I think it can be accepted by this journal after considering the following points.

1.     Figure 1 should be modified with higher quality.

2.     The Part 4 should be reorganized because it was a Review article.

3.     There were some repetitive contents in the present version. For instance, “3.1. Protocells from Proteinoids”. Please make them more concisely.

4.     If possible, the authors add some Figures to demonstrate more clearly.

Author Response

Reviewer 2

This review article was organized very well. It introduced research progresses and structure-function features of abiogenic proteinoids and in a comprehensive manner. In addition, it highlighted their great potential in bridging the gap between non-living and living matters to mimicking cell-like activities. Especially, molecular assemblies of short peptides and applications were emphasized. Also, they discussed the interactions with environmental conditions. Basically, I think it can be accepted by this journal after considering the following points.

1. Figure 1 should be modified with higher quality.

We appreciate the valuable feedback from reviewer 1, specifically regarding the suggestion to improve the quality of Figure 1. However, we would like to acknowledge the recommendation made by reviewer 2 to remove the materials and methods section. Following reviewer 2's suggestion, we have decided to remove Figure 1 as well.

2. The Part 4 should be reorganized because it was a Review article.

Reviewer 3 reported removing materials and methods section.

3. There were some repetitive contents in the present version. For instance, “3.1. Protocells from Proteinoids”. Please make them more concisely.

We appreciate the reviewer pointing out examples of repetitive content between sections. Per the feedback and to enhance conciseness, we have revised the subsection title “3.1. Protocells from Proteinoids” to the following:

From Amino Acids to Protocells: Self-Organization of Proteinoids into Models of Primordial Life.

4. If possible, the authors add some Figures to demonstrate more clearly.

We thank the reviewer for the recommendation to incorporate visual figures demonstrating proteinoids architecture. Per the request for enhanced clarity through graphical depictions, we have added the following molecular visualization figure in the revised manuscript:

Figure 1

Molecular model of an 11--residue thermal proteinoids peptide chain containing alternating glutamic acid and arginine units. Each glutamic acid (L--Glu) aspartic acid (L--Asp) and phenylalanine (L--Phe) monomer is depicted in ball--and--stick representation with nitrogen atoms colored blue, oxygen red, carbon dark grey, and hydrogen light grey. The polypeptide backbone illustrates structure formed through thermal condensation polymerization which can further self--assemble into higher--order proteinoid microspheres. The proteinoid structure was generated using ChimeraX molecular visualization software.

Reviewer 3 Report

In this manuscript, Mougkogiannis comprehensively summarized the existing research on proteinoids and shared their own experimental advances complementary to present knowledge.

Some additional clarifications and revisions are required. Here are some of my concerns.

1.     Abbreviations should be defined before use, such as, CMOS, HAP, and so on. 

2.     In Figure 10, even looking into the main text and its corresponding caption, I still could not figure out which one represents PSI and PPI. In addition, additional letter “s” was found below Figure 10;

3.     Some typo errors should be fixed, 

a.     letter “s” of section 1.1 and 2.2 (Life’s Origins and Fox’s Proteinoids) should be lower case; 

b.     some references are missing or labelled tautologically, such as, paragraph 1 and 2 of page 3; section 6.3 paragraph 3; section 7.4 paragraph 1; 

c.     line 833 of page 21, here accumulation rate should not be ΔhB, since line 816 of page 20 has claimed that h_B^acc represents accumulation rate; 

d.   line 837 of page 21, I do not understand why the author defines term and  but related terms cannot be found in contextual equations;

e.     line 476 of page 11: “to” should be removed;

f.      Figure 3: last c) caption should be corrected to caption d);

4.     It is weird that only one sentence forms a single paragraph in line 795 of page 18;

5.     Although authors state that they shared significant experimental advances from their laboratory in this literature review, it is still strange to observe a single section named “material and methods” bridging section proteinoids and cellular emergence and section proteinoids as molecular assemblies. I highly suggest removing this section from this literature review;

6.     In section 3.3.1, although the subtitle is named ion gradients, the context within this subsection is little related to ion gradients. It is better to rephrase its title or its content. Same issue is for section 5.2.1, from line 491 to 511 of page 11, these content are not related to mineral templating at all;

7.   The statement “This study offers a comprehensive understanding of the underlying physical mechanism responsible for the emergence of excitability” is confused. What does this study refer to? Does this study mean this literature review or just the cited reference?

Minor editing of English language required

Author Response

Reviewer 3

In this manuscript, Mougkogiannis comprehensively summarized the existing research on proteinoids and shared their own experimental advances complementary to present knowledge.

Some additional clarifications and revisions are required. Here are some of my concerns.

1. Abbreviations should be defined before use, such as, CMOS, HAP, and so on. 

We thank the reviewer for the recommendation to spell out abbreviations prior to usage to optimize clarity. In the revised manuscript, the first instance of each abbreviation is now explicitly defined upon introducing the term, including:

CMOS → Complementary Metal-Oxide Semiconductor

HAP → Hydroxyapatite

2. In Figure 10, even looking into the main text and its corresponding caption, I still could not figure out which one represents PSI and PPI. In addition, additional letter “s” was found below Figure 10;

We thank the reviewer for the valuable feedback on improving clarity of Figure 10. As recommended, we have added labels within the figure. Additionally, the errant extra "s" underneath Figure 10 has been deleted.

3. Some typo errors should be fixed, 

a. letter “s” of section 1.1 and 2.2 (Life’s Origins and Fox’s Proteinoids) should be lower case; 

Thanks. We've corrected the mistakes.

b. some references are missing or labelled tautologically, such as, paragraph 1 and 2 of page 3; section 6.3 paragraph 3; section 7.4 paragraph 1;

We have revised the paper to include the missing references in paragraph 1 and 2 of page 3, section 6.3 paragraph 3, and section 7.4 paragraph 1. We ensured that each reference is relevant, accurate, and properly labelled.

c. line 833 of page 21, here accumulation rate should not be ΔhB, since line 816 of page 20 has claimed that h_B^accrepresents accumulation rate;

Thank you for your comment on line 833 of page 21. We appreciate your keen observation.

After carefully reconsidering this issue, we have made the following revisions:

Changed the term "ΔhB" to "h_B^acc" on line 833 to accurately represent the accumulation rate, in line with the claim made on line 816 of page 20.

Removed the unused "$k_1^$" and "$k_2^$" terms as per your suggestion.

Fixed any derivative notation issues that may have occurred.

d.   line 837 of page 21, I do not understand why the author defines term and but related terms cannot be found in contextual equations;

Thank you for your comment regarding line 837 of page 21. We apologize for the confusion caused by the  definitions of certain terms in our manuscript.

e. line 476 of page 11: “to” should be removed;

'to' has been removed.

f. Figure 3: last c) caption should be corrected to caption d);

corrected

4. It is weird that only one sentence forms a single paragraph in line 795 of page 18;

The sentence has been moved to the right place.

5. Although authors state that they shared significant experimental advances from their laboratory in this literature review, it is still strange to observe a single section named “material and methods” bridging section proteinoids and cellular emergence and section proteinoids as molecular assemblies. I highly suggest removing this section from this literature review;

We thank the reviewer for the valuable feedback on the positioning of the "Materials and Methods" section in this literature review. We agree including experimental details in this format is unconventional and likely confusing for readers. As recommended, we have removed the "Materials and Methods" section bridging the discussion between proteinoids and cellular emergence as well as molecular assemblies.

6.  In section 3.3.1, although the subtitle is named ion gradients, the context within this subsection is little related to ion gradients. It is better to rephrase its title or its content. Same issue is for section 5.2.1, from line 491 to 511 of page 11, these content are not related to mineral templating at all;

We appreciate the reviewer noting that the original subtitle “3.3.1 Ion Gradients” did not directly match the content covered within the subsection. Per the constructive feedback on improving consistency and precision, we have updated the subtitle to the following:

• 3.3.1. Structural Heterogeneity in Proteinoids

We appreciate the reviewer highlighting that the content from lines 491-511 on emergent cognitive properties exhibited by proteinoids is not well matched to the subsection titled “5.2.1 Mineral Templating”. Per the helpful critique, we have moved this discussion to a newly created section entitled:

• 4.1 Emergent Cognitive Properties in Proteinoids

7. The statement “This study offers a comprehensive understanding of the underlying physical mechanism responsible for the emergence of excitability” is confused. What does this study refer to? Does this study mean this literature review or just the cited reference?

We thank the reviewer for the feedback on improving clarity of the objectives statement. As suggested, we have revised the original sentence:

"This review examines characteristics exhibited by thermal proteinoids, including electrical activity and self--assembly properties, exploring possible roles of such polypeptides under prebiotic conditions in the emergence of early biomolecular complexity.''

Round 2

Reviewer 1 Report

I have carefully checked the revised review (MS. Ref. No.: ID: encyclopedia-2834682.R1). The authors have sincerely clarified all the issues that need to be addressed and satisfactorily revised the manuscript according to all the queries and comments raised by the reviewers, including my suggestions. The language and the communication of the relevant results, as well as the organization of the manuscript are checked and improved.

Reviewer 2 Report

The authors have addressed my concerning points well.

Reviewer 3 Report

All issue have been well addressed. It can be accept in present version.