A new view of biology

In a nutshell

Since the 1920s the underlying basis for biology has increasingly grown to be genetics: that at least is how the media see it. The physicist Max Delbrück defined genetics in 1935 as a closed logical science without a measurement system. In other words, it is not based on physics but rather on statistics. Genetics tells us nothing about how cells work. This contrasts with chemistry, for example, that is grounded in atomic theory. Genetics is, in fact, a methodology without a foundation in science. There is no reason why we cannot base the functioning of the cell, the basic unit in biology, on physics and that is exactly what this new view of biology seeks to do.

The “founders” underpinning the new view are not Mendel and Darwin but two scientists, one from the 18th and one 19th, centuries. The first is the French polymath Pierre Louie Moreau de Maupertuis. In about 1740 he produced the principle of least action. This is an amazingly powerful principle, not least because it is synonymous with the 2nd law of thermodynamics. This was first articulated by Clausius 100 years later. Maupertuis was one of the greatest scientists of his century. The second of these scientists is Edward Blyth. Blyth was a British naturalist and selective breeder of cattle and a contemporary of Darwin. Darwin certainly knew him and must surely have read an article in the Magazine of Natural History in 1935 where Blyth points out the importance of the ability of an organism to secure nutrient for growth and the transmission of features to the next generation. Darwin frequently cited Blyth’s work and spoke of him as one "whose opinion, from his large and varied stores of knowledge, I should value more than that of almost anyone”.

Let us first look at Blyth’s insight, because that is the more logical order. This is what he writes:

“[A]mong animals which procure their food by means of their agility, strength, or delicacy of sense, the one best organized must always obtain the greatest quantity; and must, therefore, become physically the strongest, and be thus enabled, by routing its opponents, to transmit its superior qualities to a greater number of offspring.”

Blyth is drawing attention to the importance of metabolism to the growth of an organism and the importance of that growth to the qualities that will be inherited by the next generation. The statement has an element of Darwin’s struggle for existence in it, but the most important point is that it stresses the importance of being organised to secure nutrient. What is self-evident from this statement is that growth is the fundamental aim of life and that includes replication as part of that same process. The new view, therefore, is based on metabolism, that is, in terms of physics, the dissipation of free energy in a thermodynamically open system at the biologically most fundamental level, the cell. Growth of organisms occurs by replicating cells and populations of organisms grow by replicating themselves.

Out of the many contributions to science Maupertuis made, including in genetics, the new view concentrate on his mathematics and his principle of least action. In terms of physics we can imagine an action as being the route between two states. What the principle says is that Nature, when confronted with that situation, takes the shortest available route. Light travels in the straightest line, an apple falls directly down from the branch. In very personal terms we can experience this principle by going out of doors on a very cold day without a coat. The two states in this example are our warm body and a cold environment. We will quickly get cold, much more quickly than if we put on an overcoat. In both cases we will cool down as quickly as possible under the prevailing conditions, the least action.

Maupertuis said that his principle applies to Nature in all its aspects. A thriving organism will, in terms of nutrient, be at a free energy minimum in an environment that is energy rich, meaning it contains available nutrient. The principal of least action says that the thriving organisms will consume that nutrient as efficiently as possible to grow, including through replication. If the energy balance is reversed and there is insufficient nutrient in the environment to feed the organisms, they will die. We will concentrate first on the cell as an open thermodynamic complex dissipative system at an energy-minima compared to its environment. The process of metabolism is the dissipation of free energy and according to the second law of thermodynamics the production of entropy. Entropy in this context is growth: the production of substance, in this case the material of cells and the cells that are the product of cell replication. This simple scenario based on the second law of thermodynamics is the basis for the new view of biology and how life originated and has evolved over the past ~3.5 billion years.

Summary of primary features of new view:

The cellular phenotype is quasi-stable attractor state of the complex dissipative system that emerges from gene product interactions in the cytoplasm of the cell.

The cellular phenotype is the epigenetic regulator of the cell and itself: it acts downwards on other cellular components, including the genome and its DNA.

The cellular phenotype is a process (of mainly protein chemistry) and not a thing, although the boundary of attraction of the attractor state gives the phenotype particle-like properties.

The cell nucleus is an organelle producing gene products, mainly peptides that are deployed (e.g., folded to proteins) by the phenotype and, from which the phenotypic properties emerge.

The attractor state is governed by rules of engagement which stipulate the identities of the active gene products participating in the attractor state.

The rules of engagement are nonholonomic, meaning that they are contingent in their history: they extend back to the origin of their species.

The genomic DNA is a data base, or library, for inactive versions of gene products, mainly peptides. DNA plays no active role itself in producing phenotype: it is passive.

At cell division the milieu of interacting activated gene products from a single cell is divided between two cells.

The unit of inheritance is the cellular phenotype.

The cellular phenotype of even the most primitive organism has something described as consciousness: an awareness of its environment and the ability to take purposeful actions.

The consciousness of the phenotype gives the cell agency in the process of development and in its evolution.

The attractor state/phenotype of a cell in a stably replicating organism is called the home attractor and has been subject to evolutionary conditioning to improve its robustness to perturbations.

The home attractor state can be perturbed and irreversibly lost due to stress on the cell leading to so called genomic instability and the adoption of a variant attractor state/phenotype.

Genomic instability is a misnomer: it is phenotypic instability and means that under perturbation, the phenotype can switch to a variant phenotype independently of the DNA sequence.

Variant attractor states have reduced robustness and are therefore more prone to further attractor transitions under stress. This property is the origin of what has been termed genomic instability.

Summary of the implications of the new view

For human health: DNA sequence sheds no light on phenotypic properties except in the comparatively rare circumstance (rare diseases accounting for about 15% of the disease burden) where the gene product of a single gene acts alone to cause a rare disease trait. Genomic instability, stimulated by environmental stress, is the likely cause of common diseases, specifically cancer but also circulatory disease.

For evolution: evolution is driven primarily by the principle of least action, not genetic variance. Organisms are agents with the aim of improving, through trial and error, their adaptiveness to their environment particularly in respect of the source of nutrient. Selection depends upon their ability to secure nutrient as efficiently as local conditions allow i.e., according to the principle of least action. That phenotypes can modify the environment and the environment modify the phenotype (via phenotypic instability) is the reason for the large diversity in species: environments, the ecosystems, differ in the challenges they offer a given species to secure nutrient and when isolated lead to variant species influenced by their agency, combined with phenotypic instability.