Modeling complex biological systems: Tackling the parameter curse through evolution

Mapping Intimacies ◽

10.32942/osf.io/safm4 ◽

2021 ◽

Author(s):

paulien Hogeweg

Keyword(s):

Biological Systems ◽

Evolutionary Model ◽

Lac Operon ◽

Evolutionary Methods

In this perspective paper we review a previously published evolutionary model of the lac-operon to argue and demonstrate the importance of using evolutionary methods to derive relevant parameters. We show that by doing so we can debug experimental and modeling artifacts.

Download Full-text

Phylogenetic aspects of the concept of intelligent life design

Bio-Algorithms and Med-Systems ◽

10.1515/bams-2015-0018 ◽

2015 ◽

Vol 11 (3) ◽

Author(s):

Zbigniew Krajewski

Keyword(s):

Real World ◽

Biological Systems ◽

Evolutionary Model ◽

Likelihood Method ◽

Design System ◽

The Real ◽

Accommodation Process ◽

New Treatment ◽

Life Design ◽

Intelligent Life

AbstractThis paper presents a new treatment of molecular evolutionary model as a product of intelligent changes. The aim of this paper is to obtain a life design system, drawing on processes occurring in nature regardless of explanations of the origins of life. The idea of intelligent design and molecular relationship is considered as a basic concept of the intelligent life design system, using some analogies taken from molecular evolutionary models. Three steps of life design system are outlined; however, the main subject is an attempt to find certain similar effects of the design system processes and the processes simulated with basic evolutionary substitution models: Jukes-Cantor; Felsenstein; and Hasegawa, Kishino, and Yano (HKY). An idea of gene reduction has been applied, from more complex (taking into account information density) biological systems to less complex, specialised biological systems. Two steps have been taken into consideration: a test stage in the virtual world and an adaptation finishing process after running the systems in the real world. Two algorithms have been applied. The first one has applied similarity related to an accommodation process to required conditions in the virtual and the real world. The second algorithm has applied accommodation to required conditions separately (expressed as amino acid substitution) in the first step, using a convenient criterion, and further (similar to observable) accommodation in the real world. A phylogenetic tree, similar to a real one, has been calculated using the above method for mammals, for mtDNA, with the maximum likelihood method, and with the aid of PhyML for the HKY model. This paper is an introduction showing an aspect of the life design system, related to phylogenetic relationships.

Download Full-text

Modelling Biological Systems: A New Algorithm for the Inference of Boolean Networks

Mathematics ◽

10.3390/math9040373 ◽

2021 ◽

Vol 9 (4) ◽

pp. 373

Author(s):

Mario Rubio-Chavarría ◽

Cristina Santamaría ◽

Belén García-Mora ◽

Gregorio Rubio

Keyword(s):

Traffic Management ◽

Epithelial Mesenchymal Transition ◽

Directed Graphs ◽

Biological Systems ◽

Computational Cost ◽

Computation Time ◽

Boolean Networks ◽

Model Systems ◽

Lac Operon ◽

Mesenchymal Transition

Biological systems are commonly constituted by a high number of interacting agents. This great dimensionality hinders biological modelling due to the high computational cost. Therefore, new modelling methods are needed to reduce computation time while preserving the properties of the depicted systems. At this point, Boolean Networks have been revealed as a modelling tool with high expressiveness and reduced computing times. The aim of this work has been to introduce an automatic and coherent procedure to model systems through Boolean Networks. A synergy that harnesses the strengths of both approaches is obtained by combining an existing approach to managing information from biological pathways with the so-called Nested Canalising Boolean Functions (NCBF). In order to show the power of the developed method, two examples of an application with systems studied in the bibliography are provided: The epithelial-mesenchymal transition and the lac operon. Due to the fact that this method relies on directed graphs as a primary representation of the systems, its applications exceed life sciences into areas such as traffic management or machine learning, in which these graphs are the main expression of the systems handled.

Download Full-text

Why do people believe in a zero-sum economy?

Behavioral and Brain Sciences ◽

10.1017/s0140525x18000389 ◽

2018 ◽

Vol 41 ◽

Cited By ~ 1

Author(s):

Samuel G. B. Johnson

Keyword(s):

Perspective Taking ◽

Evolutionary Model ◽

Everyday Experience ◽

Coalitional Psychology ◽

The Face ◽

Zero Sum

AbstractZero-sum thinking and aversion to trade pervade our society, yet fly in the face of everyday experience and the consensus of economists. Boyer & Petersen's (B&P's) evolutionary model invokes coalitional psychology to explain these puzzling intuitions. I raise several empirical challenges to this explanation, proposing two alternative mechanisms – intuitive mercantilism (assigning value to money rather than goods) and errors in perspective-taking.

Download Full-text

Transmission Electron Microscopy of Protein Macromolecules

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100066176 ◽

1971 ◽

Vol 29 ◽

pp. 424-425

Author(s):

Henry S. Slayter

Keyword(s):

Biological Systems ◽

Metal Vapor ◽

Resolving Power ◽

Electron Microscopic ◽

Chemical Methods ◽

Molecular Weights ◽

The Past ◽

Physical Chemical ◽

Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

Download Full-text

Freeze-fracture cytochemistry: A goal set by Russell Steere in 1957

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010014614x ◽

1993 ◽

Vol 51 ◽

pp. 60-61

Author(s):

Nicholas J Severs

Keyword(s):

Chemical Nature ◽

Biological Systems ◽

Freeze Fracture ◽

Structural Components ◽

Major Goal ◽

Membrane Biology ◽

Routine Application ◽

The Future ◽

Freeze Etching

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.

Download Full-text

Seeking to uncover biology's chemical roots

Emerging Topics in Life Sciences ◽

10.1042/etls20190012 ◽

2019 ◽

Vol 3 (5) ◽

pp. 435-443 ◽

Cited By ~ 3

Author(s):

Addy Pross

Keyword(s):

Environmental Changes ◽

Biological Systems ◽

Significant Development ◽

The Road ◽

Physical Chemical ◽

Systems Chemistry ◽

Biological World ◽

Inanimate Matter ◽

The Origin Of Life ◽

Opening Up

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.

Download Full-text