What Is life? Rethinking Biology in Light of Fundamental Parameters

Abstract

Defining life is an arduous task that has puzzled philosophers and scientists for centuries. Yet biology suffers from a lack of clear definition, putting biologists in a paradoxical situation where one can describe at the atomic level complex objects that remain globally poorly defined. One could assume that such descriptions make it possible to perfectly characterize living systems. However, many cases of misinterpretation put this assumption into perspective. In this article, we focus on critical parameters such as time, water, entropy, space, quantum properties, and electrostatic potential to redefine the nature of living matter, with special emphasis on biological coding. Where does the DNA double helix come from, why cannot the reproduction of living organisms occur without mutations, what are the limitations of the genetic code, and why do not all proteins have a stable three-dimensional structure? There are so many questions that cannot be resolved without considering the aforementioned parameters. Indeed, (i) time and space constrain many biological mechanisms and impose drastic solutions on living beings (enzymes, transporters); (ii) water controls the fidelity of DNA replication and the structure/disorder balance of proteins; (iii) entropy is the driving force of many enzymatic reactions and molecular interactions; (iv) quantum mechanisms explain why a molecule as simple as hydrocyanic acid (HCN) foreshadows the helical structure of DNA, how DNA is stabilized, why mutations occur, and how the Earth magnetic field can influence the migration of birds; (v) electrostatic potential controls epigenetic mechanisms, lipid raft functions, and virus infections. We consider that raising awareness of these basic parameters is critical for better understanding what life is, and how it handles order and chaos through a combination of genetic and epigenetic mechanisms. Thus, we propose to incorporate these parameters into the definition of life.

Keywords: biology; electrostatic potential; origin of life; quantum biology; time; water.

Figure 1

To form the hexokinase/glucose complex, the two molecules must first dehydrate. The departure of water molecules from hexokinase induces a conformational change in the enzyme, which unmasks the active site of the enzyme. The driving force behind this mechanism is the increase in entropy caused by the departure of water molecules during the dehydration step. If we represent the formation of the glucose-hexokinase complex without taking water molecules into account (A), we reduce this mechanism to two partners, while water plays a major role (B). This picture is a free interpretation of the data published by Reid and Rand [29].

Figure 2

Electron transfers inside the CRY4 protein (orange arrows). The orange arrows indicate the four sequential electron transfers. Only the isoalloxazine part of the FAD is shown. From Wong et al. [49] (published by the Royal Society under the terms of the Creative Commons Attribution License, http://creativecommons.org/licenses/by/4.0/ (accessed on 31 January 2024), which permits unrestricted use, provided the original author and source are credited).

Figure 3

From hydrocyanic acid (H-C≡N) to adenine. Carbon atoms are colored black, nitrogen in blue, and hydrogen in grey. The aromatic base atoms are numbered 1 through 9. An excellent exercise given to students is to highlight the traces of hydrocyanic acid in the adenine molecule (C-N units identified by an asterisk) to understand the prebiotic origin of the base and where its nitrogen atoms come from. For clarity, some C-N units are highlighted in orange, the others in green.

Figure 4

From adenine to DNA. (A) self-aggregation of adenine molecules in water. The aromatic cycles stack at 3.4 Å whereas the polar amino group induces a shift between each vicinal adenine molecule (B). Note the regular alignment of the aromatic 6-atom ring (asterisk) and the successive shifts of the NH₂ groups (arrows). (C) This typical attraction/repulsion organization is also found in DNA, with the same 3.4 Å space between two adenine units. (D) It is remarkable that this very simple mechanism is the basis of the sophisticated regular structure of the DNA double helix (represented in atomic sticks and in surface electrostatic potential, the red color indicating the electronegative zones due to the anionic peripheral phosphate groups).

Figure 5

How the DNA double helix is stabilized. This simplified model of the double helix highlights the intra- and inter-strand stacking forces (red arrows), which mainly contribute to the stability of the DNA double helix. The base size dissymmetry (large size for purine bases, small size for pyrimidine bases) and the Pur-Pyr pairing mode (large-small) explain why the stacking forces apply between the two strands.

Figure 6

What a lipid raft looks like from a molecular and an electrostatic point of view. Gangliosides are colored in grey (left panel), oxygen atoms in red, phosphorus in yellow, and hydrocarbon chains in two-tone grey. A cholesterol molecule (chol) is visible on the left edge of the membrane. The electrostatic surface potential is represented on the right panel. surface Electronegative areas are colored red, electropositive areas are blue, and neutral areas are white/pale pink. Note that the raft emerges from the plasma membrane bilayer higher than bulk lipids (zwitterionic phosphatidylcholine displays both blue and red zones). PC, phosphatidylcholine. The gangliosides protrude at the membrane interface, giving lipid rafts an optimal situation that facilitates the attraction of biomolecules and pathogens. From Matveeva et al. [34] (published by MDPI under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/ (accessed on 31 January 2024), which permits unrestricted use, provided the original author and source are credited).

Figure 7

Highlighting the roots of biology. The fundamental parameters are represented as root networks that feed the tree with universal rules. The combined action of these parameters allowed the emergence of life on our planet, and potentially elsewhere in the universe.