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Measuring Active Information in Biological Systems 测量生物系统中的活性信息
BIO-complexity Pub Date : 2020-03-19 DOI: 10.5048/bio-c.2020.2
Jonathan Bartlett
{"title":"Measuring Active Information in Biological Systems","authors":"Jonathan Bartlett","doi":"10.5048/bio-c.2020.2","DOIUrl":"https://doi.org/10.5048/bio-c.2020.2","url":null,"abstract":"In computer search optimization theory, active information is a measurement of a search algorithm’s internal information as it relates to its problem space. While it has been previously applied to evolutionary search algorithms on computers, it has not been applied yet to biological systems. Active information can be very useful in differentiating between mutational adaptations which are based on internally-coded information and those which are the results of happenstance. However, biological systems present many practical problems regarding measuring active information which are not present in digital systems. This paper describes active information, how it can be used in biology, and how some of these problems can be overcome in specific cases.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2020 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41695531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Expected Algorithmic Specified Complexity 期望算法指定复杂度
BIO-complexity Pub Date : 2019-10-25 DOI: 10.5048/bio-c.2019.2
David Nemati, Eric M. Holloway
{"title":"Expected Algorithmic Specified Complexity","authors":"David Nemati, Eric M. Holloway","doi":"10.5048/bio-c.2019.2","DOIUrl":"https://doi.org/10.5048/bio-c.2019.2","url":null,"abstract":"Algorithmic specified complexity (ASC) is an information metric that measures meaning in an event, based on a chance hypothesis and a context. We prove expectation of ASC with regard to the chance hypothesis is always negative, and empirically apply our finding. We then use this result to prove expected ASC is conserved under stochastic processing, and that complexity for individual events is conserved under deterministic and stochastic processing.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48384526","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
The Cerebral Windkessel as a Dynamic Pulsation Absorber 脑风管作为动态脉冲吸收器
BIO-complexity Pub Date : 2019-10-21 DOI: 10.5048/bio-c.2019.3
M. Egnor
{"title":"The Cerebral Windkessel as a Dynamic Pulsation Absorber","authors":"M. Egnor","doi":"10.5048/bio-c.2019.3","DOIUrl":"https://doi.org/10.5048/bio-c.2019.3","url":null,"abstract":"Nearly all cerebrospinal fluid (CSF) flow and cerebral arterial and venous blood flow is pulsatile [1-4]. Capillary blood flow is nearly smooth [5,6,7]. The pulsatility of the CSF closely resembles the pulsatility of the intracranial veins [8,9], both of which have some characteristics of an arterial pulse, including, under some circumstances, a dicrotic notch [10]. Many aspects of the pulsatility of intracranial blood and CSF are difficult to understand, particularly because the pulsatile flow occurs in a rigid cranium which places obvious constraints on pulsatile dynamics. How is it that capillary blood flow is smooth, whereas the blood flow in the intracranial arteries and veins—sometimes only millimeters away from the capillaries— is quite pulsatile [3]? Why does the pulsatility of the veins resemble the pulsatility of the CSF [9]? Why do the CSF and venous pressure pulse waveforms have some characteristics of an arterial pulse [10]? Why does the intracranial pressure (ICP) pulse normally precede the arterial blood pressure (ABP) pulse, but lag with intracranial hypertension [1,6,11-14] (fig 1)? I propose that a useful approach to understanding these counterintuitive aspects of intracranial pulsatility is to consider the dynamics of the cerebral windkessel as that of a designed system. Such a system manifests design principles that accomplish specified goals, which for the cerebral windkessel is the buffering of arterial pulsatility—an unwanted ‘vibration’—in cerebral blood flow, while at the same time maintaining optimal cerebral blood flow and minimizing energy dissipation. This approach to exploring intracranial pulsatility entails reverse engineering of the cerebral windkessel, in accordance with established engineering principles of vibration control. Abstract","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46222568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Single-Couple Human Origin is Possible 人类起源的单一夫妇是可能的
BIO-complexity Pub Date : 2019-10-21 DOI: 10.5048/bio-c.2019.1
O. Hössjer, A. Gauger
{"title":"A Single-Couple Human Origin is Possible","authors":"O. Hössjer, A. Gauger","doi":"10.5048/bio-c.2019.1","DOIUrl":"https://doi.org/10.5048/bio-c.2019.1","url":null,"abstract":"The problem of inferring history from genetic data is complex and underdetermined; there are many possible scenarios that would explain the same data. It can be made more tractable by making reasonable simplifications to the model, but it is continually important to remember what has been demonstrated and what is merely a parsimonious working assumption. In this paper we have chosen to model the demographic ancestry of humanity using the simplest of assumptions, with a homogeneous population whose size can vary over time. All other assumptions such as the mutation rates were standard, and no natural selection was in operation. Using a previously published backwards simulation method and some newly developed and faster algorithms, we run our single-couple origin model of humanity and compare the results to allele frequency spectra and linkage disequilibrium statistics from current genetic data. We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45218614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
A Unified Model of Complex Specified Information 复杂指定信息的统一模型
BIO-complexity Pub Date : 2018-12-14 DOI: 10.5048/BIO-C.2018.4
George D. Montañez
{"title":"A Unified Model of Complex Specified Information","authors":"George D. Montañez","doi":"10.5048/BIO-C.2018.4","DOIUrl":"https://doi.org/10.5048/BIO-C.2018.4","url":null,"abstract":"A mathematical theory of complex specified information is introduced which unifies several prior methods of computing specified complexity. Similar to how the exponential family of probability distributions have dissimilar surface forms yet share a common underlying mathematical identity, we define a model that allows us to cast Dembski’s semiotic specified complexity, Ewert et al.’s algorithmic specified complexity, Hazen et al.’s functional information, and Behe’s irreducible complexity into a common mathematical form. Adding additional constraints, we introduce canonical specified complexity models, for which one-sided conservation bounds are given, showing that large specified complexity values are unlikely under any given continuous or discrete distribution and that canonical models can be used to form statistical hypothesis tests, by bounding tail probabilities for arbitrary distributions.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42529812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Evolution's Waiting-Time Problem and Suggested Ways to Overcome It--A Critical Survey 进化论的等待时间问题及其克服方法——一项批判性调查
BIO-complexity Pub Date : 2018-07-17 DOI: 10.5048/BIO-C.2018.2
J. LeMaster
{"title":"Evolution's Waiting-Time Problem and Suggested Ways to Overcome It--A Critical Survey","authors":"J. LeMaster","doi":"10.5048/BIO-C.2018.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2018.2","url":null,"abstract":"In recent decades, severe waiting-time challenges have emerged for explanations of complex biological change within the Modern Evolutionary Synthesis. Theorists continue to propose natural mechanisms which purportedly shorten these waiting times, but do the arguments for these improvements take account of all relevant factors? Here we consider four proposed mechanisms for rapid evolution: symbiogenesis, the action of transposable elements, horizontal gene transfer, and the use of alternative evolutionary pathways. In all four cases we find that the claimed evolutionary benefit fails to take all aspects of the proposal into consideration. On the other hand, when laboratory processes analogous to evolution benefit from the teleological insights of the experimenters, we find that time no longer poses an insurmountable obstacle. By extension, it seems reasonable to propose teleology as the solution to biology’s waiting-time problem.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44858649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
The Dependency Graph of Life 生命的依赖图
BIO-complexity Pub Date : 2018-07-17 DOI: 10.5048/BIO-C.2018.3
W. Ewert
{"title":"The Dependency Graph of Life","authors":"W. Ewert","doi":"10.5048/BIO-C.2018.3","DOIUrl":"https://doi.org/10.5048/BIO-C.2018.3","url":null,"abstract":"The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency graph. We evaluate several predictions made by this model about both biological and synthetic data, finding them to be fulfilled.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46057434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Chrismooreia michaelbehei gen. et sp. nov. (Insecta: Odonata: Asiopteridae), a new fossil damsel-dragonfly from the Early Jurassic of England Chrismooreia michaelbehei gen. et sp. 11 .(昆虫纲:齿目目:亚洲翅目)，英国早侏罗世少女蜻蜓新化石
BIO-complexity Pub Date : 2018-04-27 DOI: 10.5048/BIO-C.2018.1
Guenter Bechly
{"title":"Chrismooreia michaelbehei gen. et sp. nov. (Insecta: Odonata: Asiopteridae), a new fossil damsel-dragonfly from the Early Jurassic of England","authors":"Guenter Bechly","doi":"10.5048/BIO-C.2018.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2018.1","url":null,"abstract":"A new fossil damsel-dragonfly Chrismooreia michaelbehei gen. et sp. nov. (Insecta: Odonata: Asiopteridae) is described from the Early Jurassic of Charmouth in England. This fossil is the best preserved and first complete specimen of the Mesozoic family Asiopteridae, which was previously only known from isolated wings, and actually represents one of the most complete Liassic odonates known. Body characters are described for the first time and include compound eyes that meet dorsally, robust thorax, legs with short spines, and very long leaf-like cerci. The forewing venation features a short fusion of AA+Cu with MP near the tip of the discoidal cell, which is an absolutely unique character state within the order Odonata, here described for the first time. The wing venation shows a mixture of sphenophlebiid and asiopterid characters, with the latter characters dominating. The classification of Sphenophlebiidae is discussed and its synonymy with Asiopteridae is tentatively rejected, but not ruled out. As further addition to the Liassic odonate fauna from the Charmouth fossil locality, a specimen of Protomyrmeleon cf. brunonis is featured but not formally described as first record of the suborder Archizygoptera and the family Protomyrmeleontidae.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2018 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41913665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Evolutionary Teleonomy as a Unifying Principle for the Extended Evolutionary Synthesis 进化远视学作为广义进化综合的统一原理
BIO-complexity Pub Date : 2017-11-27 DOI: 10.5048/BIO-C.2017.2
Jonathan Bartlett
{"title":"Evolutionary Teleonomy as a Unifying Principle for the Extended Evolutionary Synthesis","authors":"Jonathan Bartlett","doi":"10.5048/BIO-C.2017.2","DOIUrl":"https://doi.org/10.5048/BIO-C.2017.2","url":null,"abstract":"Many people underestimate the effect that unifying principles have on the study of biology. Unifying principles are used to provide simplifying assumptions to complex problems which allow them to be effectively tackled by the tools at hand. However, erroneous unifying principles will generate simplifying assumptions that lead towards mischaracterizations of problems which inevitably lead to invalid conclusions. The unifying principles of the current Modern Synthesis of evolution are presently being challenged by the Extended Evolutionary Synthesis. However, the Extended Evolutionary Synthesis has so far failed to provide unifying principles of their own, which has caused many to question whether or not the Extended Evolutionary Synthesis is indeed a unique synthesis of evolutionary biology. Here, the concept of evolutionary teleonomy (Ernst Mayr’s concept of teleonomy applied to evolutionary processes themselves) is identified as a unifying principle of the Extended Evolutionary Synthesis. Additionally, specific examples are provided where modern research has been led astray by the unifying principles of the Modern Synthesis which would have been corrected by applying the Extended Evolutionary Synthesis with the unifying principle of evolutionary teleonomy.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47917875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Conservation of Information in Coevolutionary Searches 协同进化搜索中的信息守恒
BIO-complexity Pub Date : 2017-08-08 DOI: 10.5048/BIO-C.2017.1
W. Ewert, R. Marks
{"title":"Conservation of Information in Coevolutionary Searches","authors":"W. Ewert, R. Marks","doi":"10.5048/BIO-C.2017.1","DOIUrl":"https://doi.org/10.5048/BIO-C.2017.1","url":null,"abstract":"A number of papers show that the No Free Lunch theorem does not apply to coevolutionary search. This has been interpreted as meaning that, unlike classical full query searches, coevolutionary searches do not require extensive a priori knowledge about the domain. Alternately, coevolutionary searches can be viewed as providing incomplete information about fitness and differ from standard evolutionary searches where queries provide full fitness information. Knowing the full value of a fitness is better than knowing partial subjacent fitness information. Consequently, coevolution can be viewed as a degradation of search performance in this sense. We demonstrate this in a number of examples drawn from free lunch proofs in the literature. This observation does not diminish the power or utility of the coevolutionary search. Coevolutionary subjacent queries are often required due to the unavailability or expense of a full query. Nevertheless, coevolution does not allow an escape from the necessity of exploiting prior information in search processes and remains bounded by conservation of information in general and the No Free Lunch theorem in particular.","PeriodicalId":89660,"journal":{"name":"BIO-complexity","volume":"2017 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44715306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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