scholarly journals How Molecules Became Signs

Biosemiotics ◽  
2021 ◽  
Author(s):  
Terrence W. Deacon

AbstractTo explore how molecules became signs I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” This requires focusing on the interpreting system and its interpretive competence. To avoid assuming any properties that need to be explained I develop what I consider to be a simplest possible molecular model system which only assumes known physics and chemistry but nevertheless exemplifies the interpretive properties of interest. Three progressively more complex variants of this model of interpretive competence are developed that roughly parallel an icon-index-symbol hierarchic scaffolding logic. The implication of this analysis is a reversal of the current dogma of molecular and evolutionary biology which treats molecules like DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances that the interpretive dynamics of viruses and cells have taken advantage of. These molecules are not the source of biological information but are instead semiotic artifacts onto which dynamical functional constraints have been progressively offloaded during the course of evolution.

2015 ◽  
Vol 61 ◽  
pp. 5-22
Author(s):  
Sir Dai Rees

Struther Arnott worked tirelessly as a researcher, teacher, leader and maker and implementer of policy in universities in Britain and the USA, always carrying his colleagues along with him through his infectious energy and breadth of academic enthusiasms and values. His outlook was shaped by the stimulus of a broad Scottish education that launched wide interests inside and outside science, including the history and literature of classical civilizations. His early research, with John Monteath Robertson FRS, was into structure determination by X-ray diffraction methods for single crystals, at a time when the full power of computers was just becoming realized for solution of the phase problem. With tenacity and originality, he then extended these approaches to materials that were to a greater or lesser extent disordered and even more difficult to solve because their diffraction patterns were poorer in information content. He brought many problems to definitive and detailed conclusion in a field that had been notable for solutions that were partial or vague, especially with oriented fibres of DNA and RNA but also various polysaccharides and synthetic polymers. His first approach was to use molecular model building in combination with difference Fourier analysis. This was followed later, and to even greater effect, by a computer refinement method that he developed himself and called linkedatom least-squares refinement. This has now been adopted as the standard approach by most serious centres of fibre diffraction analysis throughout the world. After the 10 years in which he consolidated his initial reputation at the Medical Research Council Biophysics Unit at King's College, London, in association with Maurice Wilkins FRS, he moved to Purdue University in the USA, first as Professor of Biology then becoming successively Head of the Department of Biological Sciences and Vice-President for Research and Dean of the Graduate School. As well as continuing his research, he contributed to the transformation of biological sciences at that university and to the development of the university's general management. He finally returned to his roots in Scotland as Principal and Vice-Chancellor of the University of St Andrews, to draw on his now formidable experience of international scholarship and institutional management, to reshape the patterns of academic life and mission to sit more happily and successfully within an environment that had become beset with conflict and change. He achieved this without disturbance to the harmony and wisdom embodied in the venerable traditions of that ancient Scottish yet cosmopolitan university.


Genetics ◽  
1998 ◽  
Vol 150 (3) ◽  
pp. 977-986 ◽  
Author(s):  
Yangsuk Park ◽  
John Hanish ◽  
Arthur J Lustig

Abstract Previous studies from our laboratory have demonstrated that tethering of Sir3p at the subtelomeric/telomeric junction restores silencing in strains containing Rap1-17p, a mutant protein unable to recruit Sir3p. This tethered silencing assay serves as a model system for the early events that follow recruitment of silencing factors, a process we term initiation. A series of LexA fusion proteins in-frame with various Sir3p fragments were constructed and tested for their ability to support tethered silencing. Interestingly, a region comprising only the C-terminal 144 amino acids, termed the C-terminal domain (CTD), is both necessary and sufficient for restoration of silencing. Curiously, the LexA-Sir3N205 mutant protein overcomes the requirement for the CTD, possibly by unmasking a cryptic initiation site. A second domain spanning amino acids 481-835, termed the nonessential for initiation domain (NID), is dispensable for the Sir3p function in initiation, but is required for the recruitment of the Sir4p C terminus. In addition, in the absence of the N-terminal 481 amino acids, the NID negatively influences CTD activity. This suggests the presence of a third region, consisting of the N-terminal half (1-481) of Sir3p, termed the positive regulatory domain (PRD), which is required to initiate silencing in the presence of the NID. These data suggest that the CTD “active” site is under both positive and negative control mediated by multiple Sir3p domains.


2019 ◽  
Vol 36 (8) ◽  
pp. 1686-1700 ◽  
Author(s):  
Covadonga Vara ◽  
Laia Capilla ◽  
Luca Ferretti ◽  
Alice Ledda ◽  
Rosa A Sánchez-Guillén ◽  
...  

Abstract One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein–DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.


2019 ◽  
Vol 374 (1774) ◽  
pp. 20180369 ◽  
Author(s):  
Santosh Manicka ◽  
Michael Levin

Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens—a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence. This article is part of the theme issue ‘Liquid brains, solid brains: How distributed cognitive architectures process information’.


2003 ◽  
Vol 2 (3) ◽  
pp. 185-193 ◽  
Author(s):  
James J. Elser

Astrobiology is an extremely wide-ranging field and thus is in special need of conceptual and theoretical frameworks that can integrate its various arenas of study. In this paper I review recent work associated with a conceptual framework known as ‘ecological stoichiometry’ and even more recent extensions in the development of ‘biological stoichiometry’. Ecological stoichiometry is the study of the balance of energy and multiple chemical elements in ecological interactions and has developed rapidly in the study of nutrient cycling and energy flow in aquatic food webs. It identifies the elemental composition of interacting biota as central in understanding the nature of their interactions and dynamics, including key feedbacks via nutrient recycling. Biological stoichiometry extends this mode of thinking to all types of biological systems. It especially seeks to better understand, at the biochemical and genetic levels, the factors influencing the elemental composition of living things and the evolutionary forces that drive and constrain that elemental composition. By connecting key concepts of ecosystem ecology, evolutionary biology and biochemistry, stoichiometric theory integrates biological information into a more coherent whole that holds considerable promise for application in astrobiology. Several examples of potential astrobiological applications of stoichiometric analysis are offered, including ones related to pre-biotic evolution, the Cambrian explosion, biosignatures and biological feedbacks on planetary carbon cycling.


1981 ◽  
Vol 29 (8) ◽  
pp. 929-936 ◽  
Author(s):  
J Tas ◽  
G Westerneng

Qualitative and quantitative aspects of the fluorescent propidium diiodide (PI) staining method have been investigated with model films of polyacrylamide gel incorporated with DNA, RNA, and other macromolecular compounds. PI was found to bind specifically to DNA and RNA, most probably by intercalation into double-stranded regions. Proteins, glycogen, and glycosaminoglycans did not show fluorescence after PI staining. Optimal conditions for dye binding and differentiation have been defined. The stability of nucleic acid-PI complexes, as present in model films, was shown to be very high in distilled water, while dissociation rapidly occurred in ionic media. Linear relationships were found between the fluorescence intensity of bound PI and both the thickness of the model films and the amount of DNA or RNA incorporated. The presence of histone protein bound ionically to DNA did not influence the fluorescent PI binding ability in any appreciable amount.


2020 ◽  
Vol 287 (1940) ◽  
pp. 20202538
Author(s):  
Rowan A. Lymbery ◽  
Jacob D. Berson ◽  
Jonathan P. Evans

The capacity for parents to influence offspring phenotypes via nongenetic inheritance is currently a major area of focus in evolutionary biology. Intriguing recent evidence suggests that sexual interactions among males and females, both before and during mating, are important mediators of such effects. Sexual interactions typically extend beyond gamete release, involving both sperm and eggs, and their associated fluids. However, the potential for gamete-level interactions to induce nongenetic parental effects remains under-investigated. Here, we test for such effects using an emerging model system for studying gamete interactions, the external fertilizer Mytilus galloprovincialis . We employed a split-ejaculate design to test whether exposing sperm to egg-derived chemicals (ECs) from a female would affect fertilization rate and offspring viability when those sperm were used to fertilize a different female's eggs. We found separate, significant effects of ECs from non-fertilizing females on both fertilization rate and offspring viability. The offspring viability effect indicates that EC-driven interactions can have nongenetic implications for offspring fitness independent of the genotypes inherited by those offspring. These findings provide a rare test of indirect parental effects driven exclusively by gamete-level interactions, and to our knowledge the first evidence that such effects occur via the gametic fluids of females.


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