The evolution of information storage and heredity (original) (raw)

Rethinking the Meaning of Biological Information

Biological Theory

Throughout the history of molecular biology, the primary meaning of biological information has been taken from the image of a word-based linguistic code. I want to argue that the metaphor of such a code does not begin to capture either the variety or the richness of the processes by which nucleotide sequences inform biological processes. Current research demonstrates that nucleotide sequences inform not only development but also heredity and evolution, and they do so in all sorts of ways. Even though they do not exhaust the varieties of biological information employed in these processes, I claim that the power of DNA sequences to inform these processes is richer and perhaps far greater than the conventional understanding of genetic information permits, indeed richer than what any of our images of simple linguistic codes or of senders and receivers permits. Rather than a tape in a Turing machine or a message or signal sent through the generations, DNA is first and foremost a physicoc...

The physical basis of coding and reliability in biological evolution

I hope that in the MS you are preparing for us you will not mind throwing in a few quite elementary paragraphs for the benefit of the inadequately educated biologist. For instance, I am still not a bit clear about the meaning of 'a non-holonomic constraint: I think also that you will have to make a more definite bridge between the quantum versus classical thinking in physics and the simple-minded empirical biological approach. For instance, you argue that the simplest classical machines which exhibit an abstractly defined heredity actually perform more like catalysts than like templates; from which you go on to attribute the specificity of base-pairing in DNA replication to the polymerases -but the biologist will be thinking that a gene mutation which is heritable is not, primarily, a change in a polymerase but in a base sequence. I want you to go further into the distinction between 'enzymes as realizers: i.e. which make it possible for adenine to get coupled up with thymine, and 'enzymes as determinants of specificity: i. e. deciding whether adenine gets coupled with thymine or with guanine.

Giving substance to biological information (subm.)

The idea that biological information is created by evolution, passed on in heredity, and expressed during development is an attractive gloss on what has been revealed by the last century of advances in biology. But on closer examination it is hard to see what scientific substance corresponds to this vision. Several biologists and philosophers of biology have suggested that `biological information' is no more than a collection of loose metaphors. Others have offered their own theories of biological information, but most of these have been oddly unrelated to actual biological practice. Here we argue that the conception of information used by Francis Crick in his `sequence hypothesis' and `central dogma', a conception closely related to the older idea of `biological specificity', is adequate to state a substantial, general theory of biological information. There are two aspects to this account, corresponding to a fundamental duality in information theory between Shannon and Kolmogorov measures.

Epistemic, Evolutionary, and Physical Conditions for Biological Information

Biosemiotics 6(1) 9-32, 2013, 2013

Abstract The necessary but not sufficient conditions for biological informational concepts like signs, symbols, memories, instructions, and messages are (1) an object or referent that the information is about, (2) a physical embodiment or vehicle that stands for what the information is about (the object), and (3) an interpreter or agent that separates the referent information from the vehicle’s material structure, and that establishes the stands-for relation. This separation is named the epistemic cut, and explaining clearly how the stands-for relation is realized is named the symbol-matter problem. (4) A necessary physical condition is that all informational vehicles are material boundary conditions or constraints acting on the lawful dynamics of local systems. It is useful to define a dependency hierarchy of information types: (1) syntactic information (i.e., communication theory), (2) heritable information acquired by variation and natural selection, (3) non-heritable learned or creative information, and (4) measured physical information in the context of natural laws. High information storage capacity is most reliably implemented by discrete linear sequences of non-dynamic vehicles, while the execution of information for control and construction is a non-holonomic dynamic process. The first epistemic cut occurs in self-replication. The first interpretation of base sequence information is by protein folding; the last interpretation of base sequence information is by natural selection. Evolution has evolved senses and nervous systems that acquire non-heritable information, and only very recently after billions of years, the competence for human language. Genetic and human languages are the only known complete general purpose languages. They have fundamental properties in common, but are entirely different in their acquisition, storage and interpretation.

The information continuum model of evolution

Biosystems, 2021

Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do-and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.

The notion of information in biology, an appraisal

BIO Web of Conferences, 2015

Developed during the first half of the 20th century, in three different fields, theoretical physics, statistics applied to agronomy and telecommunication engineering, the notion of information has become a scientific concept in the context of the Second War World. It is in this highly interdisciplinary environment that "information theory" emerged, combining the mathematical theory of communication and cybernetics. This theory has grown exponentially in many disciplines, including biology. The discovery of the genetic "code" has benefited from the development of a common language based on information theory and has fostered a almost imperialist development of molecular genetics, which culminated in the Human Genome Project. This project however could not fill all the raised expectations and epigenetics have shown the limits of this approach. Still, the theory of information continues to be applied in the current research, whether the application of the self-correcting coding theory to explain the conservation of genomes on a geological scale or aspects the theory of evolution. In a comment published in October 2014 in the well-known journal Nature, specialists of evolutionary theory discussed with "point" and "counterpoint" whether their field needed a complete rethink or not [1]. The advocates of a theoretical change stated: "We hold that organisms are constructed in development, not simply "programmed" to develop by genes. Living things do not evolve to fit into preexisting environments, but co-construct and coevolve with their environments, in the process changing the structure of ecosystems." On the online version of the paper, David Tyler from the Cell Biology Department of the University of Valencia made this insightful remark: "It seems to me that the key issues relate to biological information and the word 'evolution' needs to be defined in a way that does justice to the origin (or loss) of information." In the same vein, a geneticist like Antoine Danchin worked on the links between the reproduction of cells and the replication of genomes, in relation to ageing [2]. He came to the conclusion that "making young structures from aged ones implies creating information" and added "I revisit Information Theory, showing that the laws of physics permit de novo creation of information, provided an energy-dependent process preserving functional entities makes room for entities accumulating information." Information seems to appear a central notion, next to matter, energy, time and mass. In the last couple of years scientists like Vedral or Battail respectively tried to reinterpret physics or biology putting the notion of information at the core or their approach [3, 4]. What can be the place of historians in such a contemporary scientific discussion? The lack of hindsight make it from the beginning a very difficult task to undertake. Most of those who recognized themselves as historians will officially consider that assessing the value of current scientific research does definitively not belong to their goals. Marc Bloch, the father of the famous Annales school, This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The evolution of information in the major transitions

Journal of Theoretical Biology, 2006

Maynard Smith and Szathma´ry's analysis of the major transitions in evolution was based on changes in the way information is stored, transmitted and interpreted. With the exception of the transition to human linguistic societies, their discussion centred on changes in DNA and the genetic system. We argue that information transmitted by non-genetic means has played a key role in the major transitions, and that new and modified ways of transmitting non-DNA information resulted from them. We compare and attempt to categorise the major transitions, and suggest that the transition from RNA as both gene and enzyme to DNA as genetic material and proteins as enzymes may have been a double one. Unlike Maynard Smith and Szathma´ry, we regard the emergence of the nervous system as a major transition. The evolution of a nervous system not only changed the way that information was transmitted between cells and profoundly altered the nature of the individuals in which it was present, it also led to a new type of heredity-social and cultural heredity-based on the transmission of behaviourally acquired information. r