Foundations of Biology

Round 1

Reviewer 1 Report

This brief essay discusses, on the deepest level, the philosophical foundations of biology.  Most of us are busy all the time doing our specific research and reporting the results in technical papers, and we rarely think, much less write, about general foundational principles.  We should all feel indebted to the authors who had courage to stop exploring the local landscape under their feet and at least attempt to take a bird's eye view.  In the terminology of Freeman Dyson, most of us are frogs, and the authors remind us that only combined with birds can frogs achieve anything.

Authors present their bird's eye view of biology in terms of four fundamental biological theories.  While evolution theory and cell theory are rather common, information theory and physico-chemical one are formulated in a refreshing novel way.  The latter one is very closely related, in my view at least, with the rather famous quotation from Feynman Lectures on Physics where he says "The most important hypothesis in all of biology, for example, is that everything that animals do, atoms do. In other words, there is nothing that living things do that cannot be understood from the point of view that they are made of atoms acting according to the laws of physics".     But in Feynman's book, this is perceived as a physicist's manifesto, while authors show how this indeed penetrates the logical foundations of biology.

As far as evolution is concerned, it is also quite comment to consider many (if not most) things in biology as the consequence of choices made earlier, as a result of "memorization" of more or less random choice.  Authors follow the line of their previous work on deriving from logic the requirements for the possible information carrier in biology, and they show that the role of random choices is frequently overstated.  

My favorite passages in the work are about the role of inductive and deductive reasoning in biology -- the subject I have rarely seen discussed (perhaps under the tacit -- and clearly wrong -- assumption that all of biology is purely inductive).

The only critical remark I can make about this very well written, well thought through, and extremely thought provoking paper is the nature of its bibliography list.  As an example, authors mention the work of von Neumann on self-replicating automata, but reference to the corresponding work is some distance away.  I am not necessarily advocating here the inclusion of a more direct reference to the work by von Neumann (or, for that matter, Darwin, Mendel etc).  Rather, I would find it useful to have references to more recent and maybe simplified discussions of relevant concepts.  I encourage authors to think what kind of references do their readers need?  Do they really need the reference to the "Origins of Species"?  I doubt that there is anybody among the readers who have not heard of this book, but they still may benefit from a note by knowledgeable authors suggesting them some useful important comments in current literature.

Otherwise, I think the work is so much thought provoking that it must be published as a matter of course. 

 

 

Author Response

Response Reviewer 1

The only critical remark made by the reviewer concerns the nature of the bibliography. This is an important issue:

• We have tried, throughout the paper, to cite the primary sources rather than the secondary literature, thus “standing on the shoulders of giants”. This is a very difficult task, and we realise that our list of references is imperfect, being neither exhaustive (for instance the description of the theory of Brownian motion could include the works of Einstein, Langevin , Ornstein-Uhlenbeck etc) nor up-to-date. We have cited Darwin, Mendel, von Neumann and others for the essential reason that they remain today great sources for inspiration. In addition, the knowledge of primary sources contributes to simplify the search for subsequent relevant literature through citation analysis. This can be illustrated with the work of von Neumann on self-reproducing automata, where a citation search easily identifies the subsequent works of Robert Rosen, Pattee, Burks, JH Holland, GJ Chaitin, Langton, Wolfram, S. Brenner and Libchaber among others. Freeman Dyson is in fact one these knowledgeable authors who examine von Neumann’ work in Disturbing the Universe (1979).  Dyson describes first the work done by von Neumann in 1948, concluding that “Von Neumann’s analysis showed that a structure of this kind was logically necessary and sufficient for a self-reproducing automaton, and he conjectured that it must also exist in living cells”, then states “Five years later Crick and Watson discovered the structure of DNA, and know every child learns in high school the biological identification of von Neumann’s four components.” These comments are still thought provoking today.
• The comments of the Reviewer have helped us better understand the relationship between von Neumann’s approach and our construction of the genetic material. We plan to discuss its current significance in this companion work.
• We have revised the paper, in the section discussing the automaton and at the end of the conclusion in order to answer to the Reviewer.

 We thank the Reviewer for this critical comment.

Author Response File: Author Response.docx

Reviewer 2 Report

The authors present a refreshingly singular view of the biological sciences by teasing apart and analyzing the very foundations that this discipline rests upon.

This view would be greatly strengthened by the significant inclusion of examples drawn from the current language of biology which is based on the genomic sciences. Here, large scale measurements of biological entities and systems enables comprehensive, and statistically meaningful understandings of populations of individuals, cells, sub-cellular components, etc. at the molecular level. And when complemented by cogent physical thinking and computer simulations, such contemporary investigations are ushering in a "new biology."  More specifically, such examples might draw upon our recent leap in nucleic acid sequencing technologies and associated computational approaches that are increasingly being embraced and advanced by biophysicists.

Author Response

Response to Reviewer 2

The Reviewer suggests that our work would be improved by a significant inclusion of examples drawn from current biology, in particular from genomic sciences. We thank the referee for this comment, and for the valuable list of potential issues that we could address. We plan to take them into account in our companion work where we construct informational biopolymers (nucleic acids and proteins): this is a more appropriate place for such a discussion. Our paper being an investigation of the foundations of biology, has been by necessity largely concerned with the history of this discipline, and major current issues have been left out. We have made this statement at the end the conclusions as an answer to the Reviewer.

Author Response File: Author Response.docx