scholarly journals Genetic, epigenetic and exogenetic information in development and evolution

2017 ◽  
Vol 7 (5) ◽  
pp. 20160152 ◽  
Author(s):  
Paul E. Griffiths
Keyword(s):  
Precise Determination ◽  
Biological Information ◽  
Epigenetic Marks ◽  
Information Theoretic ◽  
Coding Regions ◽  
Francis Crick ◽  
Natural Extensions ◽  
Causal Specificity ◽  
Development And Evolution ◽  
Do So

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development.

scholarly journals The Past, Present, and Future of Demand-Driven Acquisitions in Academic Libraries

2015 ◽  
Vol 76 (2) ◽  
pp. 205-221 ◽  
Author(s):  
Edward A. Goedeken ◽  
Karen Lawson
Keyword(s):  
Academic Libraries ◽  
Academic Library ◽  
User Involvement ◽  
State University ◽  
Iowa State University ◽  
The Past ◽  
Constant State ◽  
Call Number ◽  
Development And Evolution ◽  
Do So

Demand-driven acquisitions (DDA) programs have become a well-established approach toward integrating user involvement in the process of building academic library collections. However, these programs are in a constant state of evolution. A recent iteration in this evolution of ebook availability is the advent of large ebook collections whose contents libraries can lease, but not own only if they choose to do so. This study includes an investigation of patron usage and librarian ebook selection by comparing call number data generated by usage of three entities: (1) an ebrary PDA; (2) Academic Complete, which is a leased collection of ebooks; and (3) subject librarian selections based on the YPB approval plan at Iowa State University. The context is provided through a description of the development and evolution of demand driven acquisitions programs with an analysis of where libraries have been and where they are going with enhancing the collection development in academic libraries.

scholarly journals The epigenome and top-down causation

2011 ◽  
Vol 2 (1) ◽  
pp. 42-48 ◽  
Author(s):  
P. C. W. Davies
Keyword(s):  
Systems Theory ◽  
Physical Object ◽  
Biological Information ◽  
Top Down ◽  
Molecular Sequences ◽  
Information Theoretic ◽  
Time Operation ◽  
Real Time Operation ◽  
Physical And Chemical ◽  
Self Organizing

Genes store heritable information, but actual gene expression often depends on many so-called epigenetic factors, both physical and chemical, external to DNA. Epigenetic changes can be both reversible and heritable. The genome is associated with a physical object (DNA) with a specific location, whereas the epigenome is a global, systemic, entity. Furthermore, genomic information is tied to specific coded molecular sequences stored in DNA. Although epigenomic information can be associated with certain non-DNA molecular sequences, it is mostly not. Therefore, there does not seem to be a stored ‘epigenetic programme’ in the information-theoretic sense. Instead, epigenomic control is—to a large extent—an emergent self-organizing phenomenon, and the real-time operation of the epigenetic ‘project’ lies in the realm of nonlinear bifurcations, interlocking feedback loops, distributed networks, top-down causation and other concepts familiar from the complex systems theory. Lying at the heart of vital eukaryotic processes are chromatin structure, organization and dynamics. Epigenetics provides striking examples of how bottom-up genetic and top-down epigenetic causation intermingle. The fundamental question then arises of how causal efficacy should be attributed to biological information. A proposal is made to implement explicit downward causation by coupling information directly to the dynamics of chromatin, thus permitting the coevolution of dynamical laws and states, and opening up a new sector of dynamical systems theory that promises to display rich self-organizing and self-complexifying behaviour.

scholarly journals Seeds integrate biological information about conspecific and allospecific neighbours

2017 ◽  
Vol 284 (1857) ◽  
pp. 20170800 ◽  
Author(s):  
Akira Yamawo ◽  
Hiromi Mukai
Keyword(s):  
Trifolium Repens ◽  
Developmental Stages ◽  
Interspecific Interactions ◽  
Water Soluble ◽  
Biological Information ◽  
Environmental Cues ◽  
Multiple Sources ◽  
Plantago Asiatica ◽  
Adaptive Behaviours ◽  
Do So

Numerous organisms integrate information from multiple sources and express adaptive behaviours, but how they do so at different developmental stages remains to be identified. Seeds, which are the embryonic stage of plants, need to make decisions about the timing of emergence in response to environmental cues related to survival. We investigated the timing of emergence of Plantago asiatica (Plantaginaceae) seed while manipulating the presence of Trifolium repens seed and the relatedness of neighbouring P. asiatica seed. The relatedness of neighbouring P. asiatica seed and the presence of seeds of T. repens did not on their own influence the timing of P. asiatica emergence. However, when encountering a T. repens seed, a P. asiatica seed emerged faster in the presence of a sibling seed than in the presence of a non-sibling seed. Water extracts of seeds gave the same result. We show that P. asiatica seeds integrate information about the relatedness of neighbouring P. asiatica seeds and the presence of seeds of a different species via water-soluble chemicals and adjust their emergence behaviour in response. These findings suggest the presence of kin-dependent interspecific interactions.

Cognition On Tap

2018 ◽  
Vol 4 (2) ◽  
pp. 89-104
Author(s):  
James Steinhoff
Keyword(s):  
Machine Learning ◽  
Social Context ◽  
Social Factors ◽  
Social Consequences ◽  
Popular Media ◽  
The Social ◽  
Technical Details ◽  
Algorithmic Bias ◽  
Development And Evolution ◽  
Do So

Abstract The thriving contemporary form of artificial intelligence (AI) called machine learning is often represented sensationally in popular media as a semi-mystical technology. Machine learning systems are frequently ascribed anthropomorphic capacities for learning, emoting and reasoning which, it is suggested, might lead to the alleviation of humanity’s woes. One critical reaction to such sensational proclamations has been to focus on the mundane reality of contemporary machine learning as mere inductive prediction based on statistical generalizations, albeit with surprisingly powerful abilities (Pasquinelli 2017). While the deflationist reaction is a necessary reply to sensationalist agitation, adequate comprehension of modern AI cannot be achieved while neglecting its material and social context. One does not have to subscribe wholeheartedly to the social construction of technology thesis1 to allow that the development and evolution of technologies are influenced by social factors. For AI, the most important aspect of the current social context is arguably capital, which increasingly dominates AI research and production. One former computer science professor describes a “giant sucking sound of [AI] academics going into industry” (Metz 2017). This paper introduces capital’s theory of AI as utility and initiates a discussion on its social consequences. First, I discuss utilities and their infrastructures and introduce a few critical thoughts on the topic. Second, I situate modern AI by way of a brief history. Third, I detail capital’s view of AI as a utility and the technical details underpinning it. Fourth, I sketch how AI as a utility frames a social problematic beyond the important issues of algorithmic bias and the automation of work. I do so by extrapolating from one consequence of AI as a utility which multiple capitalist firms predict: the curation of human subjectivities.

scholarly journals DTM at 25: Essays on Themes and Future Directions

2013 ◽  
Author(s):  
Dan Braha ◽  
David C. Brown ◽  
Amaresh Chakrabarti ◽  
Andy Dong ◽  
Georges Fadel ◽  
...  
Keyword(s):  
Design Theory ◽  
Design Knowledge ◽  
Paper Award ◽  
Future Directions ◽  
Research Themes ◽  
History Of ◽  
Design Theory And Methodology ◽  
Systems View ◽  
Development And Evolution ◽  
Do So

This paper describes the development and evolution of research themes in the Design Theory and Methodology (DTM) conference. Essays containing reflections on the history of DTM, supported by an analysis of session titles and papers winning the “best paper award”, describe the development of the research themes. A second set of essays describes the evolution of several key research themes. Two broad trends in research themes are evident, with a third one emerging. The topics of the papers in the first decade or so reflect an underlying aim to apply artificial intelligence toward developing systems that could ‘design’. To do so required understanding how human designers behave, formalizing design processes so that they could be computed, and formalizing representations of design knowledge. The themes in the first DTM conference and the recollections of the DTM founders reflect this underlying aim. The second decade of DTM saw the emergence of product development as an underlying concern and included a growth in a systems view of design. More recently, there appears to be a trend toward design-led innovation, which entails both executing the design process more efficiently and understanding the characteristics of market-leading designs so as to produce engineered products and systems of exceptional levels of quality and customer satisfaction.

scholarly journals Structure Optimization for Large Gene Networks Based on Greedy Strategy

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Francisco Gómez-Vela ◽  
Domingo S. Rodriguez-Baena ◽  
José Luis Vázquez-Noguera
Keyword(s):  
Gene Networks ◽  
Gene Network ◽  
Structure Optimization ◽  
Biological Indicators ◽  
Biological Information ◽  
Greedy Heuristic ◽  
Biological Processes ◽  
Information Ratio ◽  
Large Gene ◽  
Do So

In the last few years, gene networks have become one of most important tools to model biological processes. Among other utilities, these networks visually show biological relationships between genes. However, due to the large amount of the currently generated genetic data, their size has grown to the point of being unmanageable. To solve this problem, it is possible to use computational approaches, such as heuristics-based methods, to analyze and optimize gene network’s structure by pruning irrelevant relationships. In this paper we present a new method, called GeSOp, to optimize large gene network structures. The method is able to perform a considerably prune of the irrelevant relationships comprising the input network. To do so, the method is based on a greedy heuristic to obtain the most relevant subnetwork. The performance of our method was tested by means of two experiments on gene networks obtained from different organisms. The first experiment shows how GeSOp is able not only to carry out a significant reduction in the size of the network, but also to maintain the biological information ratio. In the second experiment, the ability to improve the biological indicators of the network is checked. Hence, the results presented show that GeSOp is a reliable method to optimize and improve the structure of large gene networks.

STATISTICAL AND LINGUISTIC FEATURES OF DNA SEQUENCES

Fractals ◽  
1995 ◽  
Vol 03 (02) ◽  
pp. 269-284 ◽  
Author(s):  
S. HAVLIN ◽  
S.V. BULDYREV ◽  
A.L. GOLDBERGER ◽  
R.N. MANTEGNA ◽  
C.-K. PENG ◽  
...  
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Biological Information ◽  
Fluctuation Analysis ◽  
Linguistic Features ◽  
Base Pairs ◽  
Natural Languages ◽  
Noncoding Regions ◽  
Coding Regions ◽  
Eukaryotic Dna

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range—indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the “non-stationarity” feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Lévy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the “redundancy” of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Cellular Adaptations to Cytoplasmic Mg2+ Limitation

2021 ◽  
Vol 75 (1) ◽  
pp. 649-672
Author(s):  
Eduardo A. Groisman ◽  
Carissa Chan
Keyword(s):  
Protein Synthesis ◽  
Bacterial Species ◽  
Transcriptional Regulator ◽  
Living Cells ◽  
Open Reading Frames ◽  
Enzymatic Reactions ◽  
Leader Region ◽  
Coding Regions ◽  
Reading Frames ◽  
Do So

Mg2+ is the most abundant divalent cation in living cells. It is essential for charge neutralization, macromolecule stabilization, and the assembly and activity of ribosomes and as a cofactor for enzymatic reactions. When experiencing low cytoplasmic Mg2+, bacteria adopt two main strategies: They increase the abundance and activity of Mg2+ importers and decrease the abundance of Mg2+-chelating ATP and rRNA. These changes reduce regulated proteolysis by ATP-dependent proteases and protein synthesis in a systemic fashion. In many bacterial species, the transcriptional regulator PhoP controls expression of proteins mediating these changes. The 5′ leader region of some mRNAs responds to low cytoplasmic Mg2+ or to disruptions in translation of open reading frames in the leader regions by furthering expression of the associated coding regions, which specify proteins mediating survival when the cytoplasmic Mg2+ concentration is low. Microbial species often utilize similar adaptation strategies to cope with low cytoplasmic Mg2+ despite relying on different genes to do so.

scholarly journals Nothing in Cognitive Neuroscience Makes Sense Except in the Light of Evolution

NeuroSci ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 177-192
Author(s):  
Oscar Vilarroya
Keyword(s):  
Evolutionary Theory ◽  
Cognitive Neuroscience ◽  
Bottom Line ◽  
Adaptive Solution ◽  
The Brain ◽  
Development And Evolution ◽  
Do So

Evolutionary theory should be a fundamental guide for neuroscientists. This would seem a trivial statement, but I believe that taking it seriously is more complicated than it appears to be, as I argue in this article. Elsewhere, I proposed the notion of “bounded functionality” As a way to describe the constraints that should be considered when trying to understand the evolution of the brain. There are two bounded-functionality constraints that are essential to any evolution-minded approach to cognitive neuroscience. The first constraint, the bricoleur constraint, describes the evolutionary pressure for any adaptive solution to re-use any relevant resources available to the system before the selection situation appeared. The second constraint, the satisficing constraint, describes the fact that a trait only needs to behave more advantageously than its competitors in order to be selected. In this paper I describe how bounded-functionality can inform an evolutionary-minded approach to cognitive neuroscience. In order to do so, I resort to Nikolaas Tinbergen’s four questions about how to understand behavior, namely: function, causation, development and evolution. The bottom line of assuming Tinbergen’s questions is that any approach to cognitive neuroscience is intrinsically tentative, slow, and messy.

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