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Disclaimer: I am not asking whether or not the events that occur in Anathem are possible. I understand that this book is a work of speculative science fiction and this site has no interest in it as such. I'm asking about the physics of a particular plot device.

In Anathem, Neal Stephenson states that the configuration of hadrons within atomic nuclei created during (stellar) nucleosynthesis is dependent on the fundamental constants of the universe (non derivable constants such as the speed of light and the cosmological constant), and that this configuration affects the electrical properties of the elements, and thus their chemistry.

In the book, physicists have created machines that can generate energy densities on the order of the big bang (or so). The idea is, in the beginning of the universe, the fundamental constants were unfixed and ambiguous. As the universe cooled down, the constants became fixed, the forces separated, and the universe was born. By creating high energy densities, the values of the constants can be fudged, allowing nucleosynthesis that generates nuclei with hadronic configuration different from ordinary matter. With that different configuration comes different electrical properties and thus different chemistry. This last feature prevents (or interferes with) 'newmatter' or matter from parallel universes with different constants from interacting chemically with matter of the universe the book is set in. These physicists tweaked the constants until they generated 'newmatter' with desirable chemical properties.

I have two questions. First, do the constants of nature affect nucleosynthesis in any way that measurably changes the electrical properties of the orbitals? Second, is there any veracity to the claim that the fundamental physical constants were 'unfixed' during the first instants of the big bang and that they can be locally unfixed by high enough energy densities?

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The answer to your first question is definitely "yes". The fundamental constants tell you how strong all of the interactions in the universe are. Change them, you change the interactions and their relative strengths. No one knows the answer to your second question. –  Jerry Schirmer Jun 30 '13 at 18:03
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