Selection for Molecularly Complementary Modules (MCMs) Drives the Origins and Evolution of Pleiofunctional, Epistatic Interactomes (PEIs)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The main question addressed by the research is, how biological complexity can arise. The model presented gives a coherent and NEW explanation.

The explanatory model presented in this article is original and highly relevant to the field because no other model integrates all the available empirical data.

It adds the crucial role of complementarity of different modules, which is not part of competing models in this field.

The methodology is coherent and well proven by empirical data.

Conclusions are consistent with empirical data and adresses the main question very well. To make the section "Conclusions" more understandable it could be adapted to "Conclusions: Context makes the Difference"

References are appropriate.

Author Response

REVIEWER 1

Open Review

(x) I would not like to sign my review report
( ) I would like to sign my review report

Quality of English Language

( ) The English could be improved to more clearly express the research.
(x) The English is fine and does not require any improvement.

Is the work a significant contribution to the field?
Is the work well organized and comprehensively described?
Is the work scientifically sound and not misleading?
Are there appropriate and adequate references to related and previous work?

Comments and Suggestions for Authors

The main question addressed by the research is, how biological complexity can arise. The model presented gives a coherent and NEW explanation.

The explanatory model presented in this article is original and highly relevant to the field because no other model integrates all the available empirical data.

It adds the crucial role of complementarity of different modules, which is not part of competing models in this field.

The methodology is coherent and well proven by empirical data.

Conclusions are consistent with empirical data and adresses the main question very well. To make the section "Conclusions" more understandable it could be adapted to "Conclusions: Context makes the Difference"

References are appropriate.

 

Submission Date

05 December 2025

Date of this review

12 Dec 2025 11:56:46

 

I thank the reviewer for this positive review.

 

 

Reviewer 2 Report

Comments and Suggestions for Authors

Building on Molecularly Complementary Modules, the author is suggesting that "selection for molecularly complementary modules counter-acts and seriously constrains the diversification introduced by random variations giving rise to living systems characterized by highly conserved, pleiofunctional, epistatic interactomes."
More specifically, "This paper develops ideas that suggest prebiotic and early biotic selection for molecularly complementarity modules  (MCM) may have played a significant role in providing" mechanism for pleiofunctional, epistatic interactome.
It is unclear if this manuscript is a review (as it is labeled) or a research/synthesis one. If it is a review then the focus on extending MCM is misplaced. If it is research/synthesis then it would require more work on addressing whether or not this is a general phenomenon. For the latter, it is even more confusing as the author is saying that the idea is more than 20 years old (line 121). The author then sets to prove this idea, but only discusses two example (ascorbic acid and aminergic receptors, and coevolution of proteins and RNA), where a more rigorous analysis is warranted.
Furthermore, in the introduction the author is claiming the evolutionary history of genetic circuits does not exist. While this claim might not be technically incorrect, there has certainly been work done on the evolutionary of, for example, gene regulatory networks (https://doi.org/10.1093/icb/icaa116, https://doi.org/10.1038/nrg2499) and interactome (https://doi.org/10.1016/j.sbi.2017.10.012).
Finally, it would have been nice to further on how some of the claims were based, such as that in line 112-113 that gives no information on how this was 'determined'.
It is also advised to avoid being superfluous ("the most interesting", "clever", "startling", etc).
Among the many Root-Bernstein paper referenced, I could not find (Root-Bernstein & Root-Bernstein, 2015).

Author Response

REVIEWER 2

Open Review

(x) I would not like to sign my review report
( ) I would like to sign my review report

Quality of English Language

( ) The English could be improved to more clearly express the research.
(x) The English is fine and does not require any improvement.

Is the work a significant contribution to the field?
Is the work well organized and comprehensively described?
Is the work scientifically sound and not misleading?
Are there appropriate and adequate references to related and previous work?

Comments and Suggestions for Authors

Building on Molecularly Complementary Modules, the author is suggesting that "selection for molecularly complementary modules counter-acts and seriously constrains the diversification introduced by random variations giving rise to living systems characterized by highly conserved, pleiofunctional, epistatic interactomes."
More specifically, "This paper develops ideas that suggest prebiotic and early biotic selection for molecularly complementarity modules  (MCM) may have played a significant role in providing" mechanism for pleiofunctional, epistatic interactome.
It is unclear if this manuscript is a review (as it is labeled) or a research/synthesis one. If it is a review then the focus on extending MCM is misplaced. If it is research/synthesis then it would require more work on addressing whether or not this is a general phenomenon.

Yes, this is a hybrid paper, both synthesis and review, but certainly not new research. Some papers simply don’t fit standard formats, sorry.

For the latter, it is even more confusing as the author is saying that the idea is more than 20 years old (line 121). The author then sets to prove this idea, but only discusses two example (ascorbic acid and aminergic receptors, and coevolution of proteins and RNA), where a more rigorous analysis is warranted.

I have tried to address the issue of further testing the hypothesis presented here. It has taken 20 years to piece together the case studies that I have presented, each requiring (as the references show) a great deal of novel research resulting in novel findings, each of which required independent publication before it was possible to piece together the “big picture” that I am presenting here. I agree that many more such case studies are needed and I have made (and reiterated) that point at several places in the revised manuscript. I have additionally added suggestions for two additional test cases in the conclusion that may help to support or disprove the hypothesis.

Furthermore, in the introduction the author is claiming the evolutionary history of genetic circuits does not exist. While this claim might not be technically incorrect, there has certainly been work done on the evolutionary of, for example, gene regulatory networks (https://doi.org/10.1093/icb/icaa116, https://doi.org/10.1038/nrg2499) and interactome (https://doi.org/10.1016/j.sbi.2017.10.012).

I have rewritten the relevant section to better distinguish between “origins” of genetic circuits and their subsequent evolution (adaptation). I am interested here in origins, not modifications on existing circuits. I have, however, cited the references provided by the Reviewer as well as several others that investigate the adaptations of other genetic systems (see list provided at the end of this response).

Finally, it would have been nice to further on how some of the claims were based, such as that in line 112-113 that gives no information on how this was 'determined'.

I have added an explanation, though I doubt that it will satisfy the Reviewer. The claim that every molecule in a living system interacts with others in an interactome is not something that can be proven: it can only be disproven by counter-examples. Based on my experience and the sources I now cite in the text, I know of no counter-examples, but my experience is not all-knowing, and I have indicated the limitations of that knowledge. The statement should be taken as a challenge to the biological research community to disprove it or, failing that, to wonder why no counter-examples exist.

It is also advised to avoid being superfluous ("the most interesting", "clever", "startling", etc).

I have taken out as many of these superfluous terms as I came across. If there remain others, I apologize.
Among the many Root-Bernstein paper referenced, I could not find (Root-Bernstein & Root-Bernstein, 2015).

This journal was online only and went out of business. The paper is available on my ResearchGate website and I have provided a copy with this response.

 

Submission Date

05 December 2025

Date of this review

10 Dec 2025 19:19:22

 

 

Seelig B, Chen IA. Intellectual frameworks to understand complex biochemical systems at the origin of life. Nat Chem. 2025 Jan;17(1):11-19. doi: 10.1038/s41557-024-01698-4

 

Sadier A, Santana SE, Sears KE. The role of core and variable Gene Regulatory Network modules in tooth development and evolution. Integr Comp Biol. 2020 Aug 6:icaa116. doi: 10.1093/icb/icaa116

Erwin, D., Davidson, E. The evolution of hierarchical gene regulatory networks. Nat Rev Genet 10, 141–148 (2009). https://doi.org/10.1038/nrg2499

Ghadie MA, Coulombe-Huntington J, Xia Y. Interactome evolution: insights from genome-wide analyses of protein-protein interactions. Curr Opin Struct Biol. 2018 Jun;50:42-48. doi: 10.1016/j.sbi.2017.10.012. Epub 2017 Nov 5. PMID: 29112911

Brown, K. R., & Jurisica, I. (2007). Unequal evolutionary conservation of human protein interactions in interologous networks. Genome biology, 8(5), R95. https://doi.org/10.1186/gb-2007-8-5-r95

Yehorova, D., Crean, R. M., Kasson, P. M., & Kamerlin, S. C. L. (2024). Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families. Protein science : a publication of the Protein Society, 33(3), e4911. https://doi.org/10.1002/pro.4911

Mosca, R., Pache, R. A., & Aloy, P. (2012). The role of structural disorder in the rewiring of protein interactions through evolution. Molecular & cellular proteomics : MCP, 11(7), M111.014969. https://doi.org/10.1074/mcp.M111.014969

Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., & Ideker, T. (2005). Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America, 102(6), 1974–1979. https://doi.org/10.1073/pnas.0409522102

 

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The review “Selection for Molecularly Complementary Modules (MCM) Drives the Origins and Evolution of Pleiofunctional, Epistatic  Interactomes (PEI)” by Robert Root-Bernstein have presented a view at the possible reasons for stability and functionality of interactomes. Root-Bernstein based on two examples hypothesized the MCM mechanism of PEI evolution. The first example of the influence of MCM on PRI  presented as integrating of ascorbate-glutathione system into the glucose-insulin-insulin receptor system. The other example is a ribosome. Previously in manuscripts by Robert Root-Bernstein and Meredith Root-Bernstein was presented “ribosome-first” theory of cellular evolution. It was suggested that rRNA contain information encoding ribosome-self replication. This review notes that the MCM can be traced from the precursors of tRNAs through rRNA to the its genome. Сomplementarity of protein modules and RNAs could be selected for the integral interactome.

The review is very interesting undoubtedly, but the presented hypothesis requires further experimental genetic and biochemical confirmation.

Minor revisions:

1. In my opinion, models on figures 1 and 4 should be added structural formulas of chemical and organic compounds.
2. Since the author is considering the RNA world hypothesis, it is probably worth mentioning the work by A.S.Spirin “When, Where, and in What Environment Could the RNA World Appear and Evolve?” Paleontological Journal, 2007, Vol. 41, No. 5, pp. 481–488.

The manuscript can be published after minor revisions.

 

Author Response

REVIEWER 3

Open Review

(x) I would not like to sign my review report
( ) I would like to sign my review report

Quality of English Language

( ) The English could be improved to more clearly express the research.
(x) The English is fine and does not require any improvement.

Is the work a significant contribution to the field?
Is the work well organized and comprehensively described?
Is the work scientifically sound and not misleading?
Are there appropriate and adequate references to related and previous work?

Comments and Suggestions for Authors

The review “Selection for Molecularly Complementary Modules (MCM) Drives the Origins and Evolution of Pleiofunctional, Epistatic  Interactomes (PEI)” by Robert Root-Bernstein have presented a view at the possible reasons for stability and functionality of interactomes. Root-Bernstein based on two examples hypothesized the MCM mechanism of PEI evolution. The first example of the influence of MCM on PRI  presented as integrating of ascorbate-glutathione system into the glucose-insulin-insulin receptor system. The other example is a ribosome. Previously in manuscripts by Robert Root-Bernstein and Meredith Root-Bernstein was presented “ribosome-first” theory of cellular evolution. It was suggested that rRNA contain information encoding ribosome-self replication. This review notes that the MCM can be traced from the precursors of tRNAs through rRNA to the its genome. Сomplementarity of protein modules and RNAs could be selected for the integral interactome.

The review is very interesting undoubtedly, but the presented hypothesis requires further experimental genetic and biochemical confirmation.

As noted in my response to Reviewer 2, I have now added, in several places, statements that I am proposing a hypothesis based on limited case studies that clearly needs further testing. I have added a brief discussion of two additional possible cases that may provide such additional tests in the Conclusion, though obviously many more will be needed. Obviously, a book-length work will be required to do the idea justice!

Minor revisions:

1. In my opinion, models on figures 1 and 4 should be added structural formulas of chemical and organic compounds.

DONE!

1. Since the author is considering the RNA world hypothesis, it is probably worth mentioning the work by A.S.Spirin “When, Where, and in What Environment Could the RNA World Appear and Evolve?” Paleontological Journal, 2007, Vol. 41, No. 5, pp. 481–488.

Well, I have cited the Spirin article, but the Reviewer should be aware that his arguments are out-of-date and have been superseded by research by several groups showing that nucleoside synthesis is possible in aqueous solutions. Moreover, my group has, we believe, recently demonstrated a “one-pot synthesis” of amino acids, peptides, sugars, nucleosides and ATP. A full discussion of this issue has now been added along with the relevant references. It actually permits me to better discuss some of the assumptions underlying the ribosome evolution work, so thank you.

The manuscript can be published after minor revisions

 I appreciate the useful comments and suggestion!

 

Submission Date

05 December 2025

Date of this review

22 Dec 2025 11:15:43