Biosystems最新文献

{"title":"An irreversible thermodynamic model of pre-biological small circular molecular dissipative structures inside vacuoles on the Archean Ocean surface.","authors":"Jorge A Montemayor-Aldrete, José Manuel Nieto-Villar, Carlos J Villagómez, Rafael F Márquez-Caballé","doi":"10.1016/j.biosystems.2024.105379","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105379","url":null,"abstract":"<p><p>A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms [1-3], is developed to describe the maximum possible concentration of solar power to be dissipated on topological circular molecules structures encapsulated in lipid-walled vacuoles, which floated in the Archean oceans. By considering previously, the analysis of 71 species examined by covering 18 orders of mass magnitude from the Megapteranovaeangliae to Saccharomyces cerevisiae[2], suggest that in molecular structures of smaller masses than any living being known nowadays, the power dissipation must be directly proportional to the power of the photons of solar origin that impinge them to give rise to the formation of more complex self-assembled molecular structures at the prebiotic stage by a quantum mechanics model of resonant photon wavelength excitation. The analysis of 12 circular molecules (encapsulated in lipid-walled vacuoles) relevant to the evolution of life on planet Earth such as the five nucleobases, and some aromatic molecules as pyrimidine, porphyrin, chlorin, coumarin, xanthine, etc., were carried out. Considering one vacuole of each type of molecule per square meter of the ocean's surface of planet Earth ( vacuoles), their dissipative operation would require only times the matter used by the biomass currently existing on Earth. Relevant numbers for the annual dissipative cycles corresponding to high energy photo chemical events, which in principle allow the assembling of more complex polymers, were obtained. The previous figures are compatible with some results obtained by followers (Miller and Lazcano) of the primordial soup theory [4-5], when they, under certain suppositions about the Archean chemical kinetical changes on the precursors of RNA and DNA try to justify the formation rate of RNA and DNA components and the emergence of life within a 10-million-year window, 3.5 billion years ago. The physical foundation perspective and the simplicity of the proposed approach suggests that it can serve as a possible template for both, the development of new kind of experiments, and for prebiotic theories that address self-organization occurring inside such vacuoles. Our model provides a new way to conceptualize the self-production of simple cyclic dissipative molecular structures in the Archean period of planet Earth. © 2017 ElsevierInc.Allrightsreserved.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105379"},"PeriodicalIF":2.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"\"Assembly Theory\" in Life Origin Models: A Critical Review.","authors":"David Lynn Abel","doi":"10.1016/j.biosystems.2024.105378","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105378","url":null,"abstract":"<p><p>Any homeostatic protometabolism would have required orchestration of disparate biochemical pathways into integrated circuits. Extraordinarily specific molecular assemblies were also required at the right time and place. Assembly Theory conflated with its cousins-Complexity Theory, Chaos theory, Quantum Mechanics, Irreversible Nonequilibrium Thermodynamics and Molecular Evolution theory- collectively have great naturalistic appeal in hopes of their providing the needed exquisite steering and controls. They collectively offer the best hope of circumventing the need for active selection required to formally orchestrate bona fide formal organization (as opposed to the mere self-ordering of chaos theory) (Abel and Trevors, 2006b). This paper focuses specifically on AT's contribution to naturalistic life-origin models.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105378"},"PeriodicalIF":2.0,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genetic code is not universal.","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2024.105382","DOIUrl":"10.1016/j.biosystems.2024.105382","url":null,"abstract":"<p><p>Recently, a new genetic code with 62 sense codons, coding for 21 amino acids, and only 2 termination codons has been identified in archaea. The authors argue that the appearance of this variant of the genetic code is due to the relatively recent and complete recoding of all UAG stop codons to codons encoding for pyrrolysine. I re-evaluate this discovery by presenting arguments that favour the early, i.e. ancestral, appearance of this variant of the genetic code during the origin of the genetic code itself. These arguments are capable of supporting that during the origin of the organization of the genetic code, at least two versions of the genetic code evolved in the domain of the Archaea. Thus, the genetic code would not be absolutely universal.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105382"},"PeriodicalIF":2.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The problem of evolutionary directionality 50 years following the works of Sergei Meyen.","authors":"A V Melkikh","doi":"10.1016/j.biosystems.2024.105383","DOIUrl":"https://doi.org/10.1016/j.biosystems.2024.105383","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105383"},"PeriodicalIF":2.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cancer memory as a mechanism to establish malignancy.","authors":"Thomas Lissek","doi":"10.1016/j.biosystems.2024.105381","DOIUrl":"10.1016/j.biosystems.2024.105381","url":null,"abstract":"<p><p>Cancers during oncogenic progression hold information in epigenetic memory which allows flexible encoding of malignant phenotypes and more rapid reaction to the environment when compared to purely mutation-based clonal evolution mechanisms. Cancer memory describes a proposed mechanism by which complex information such as metastasis phenotypes, therapy resistance and interaction patterns with the tumor environment might be encoded at multiple levels via mechanisms used in memory formation in the brain and immune system (e.g. single-cell epigenetic changes and distributed state modifications in cellular ensembles). Carcinogenesis might hence be the result of physiological multi-level learning mechanisms unleashed by defined heritable oncogenic changes which lead to tumor-specific loss of goal state integration into the whole organism. The formation of cancer memories would create and bind new levels of individuality within the host organism into the entity we call cancer. Translational implications of cancer memory are that cancers could be engaged at higher organizational levels (e.g. be \"trained\" for memory extinction) and that compounds that are known to interfere with memory processes could be investigated for their potential to block cancer memory formation or recall. It also suggests that diagnostic measures should extend beyond sequencing approaches to functional diagnosis of cancer physiology.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105381"},"PeriodicalIF":2.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological drivers for the absence of task shifting in termite-tunneling activity: A simulation study.","authors":"Sang-Hee Lee, Cheol-Min Park","doi":"10.1016/j.biosystems.2024.105380","DOIUrl":"10.1016/j.biosystems.2024.105380","url":null,"abstract":"<p><p>Subterranean termites build complex underground tunnel networks to efficiently gather food. Empirical observations indicate specific individuals are dedicated to tunneling, rarely interchanging tasks. However, considering the limited tunneling energy of termite populations, it is reasonable to expect regular task shifts between fatigued and rested individuals to maintain continuous tunneling and optimize foraging. To explore this disparity, we developed a sophisticated individual-based model simulating the termite tunneling process in two scenarios: one with task shifting and one without. In the task shift scenario, the initial group of termites excavates the tunnel, expends all their energy, and returns to the nest. A new group is then deployed to the tunnel tip to continue the excavation, collectively creating the final tunnel pattern. In the no task shift scenario, the initial group completes the tunneling without transitioning to subsequent groups. We compared the tunnel patterns of these two scenarios, focusing on tunnel directionality and size. The comparison revealed statistically no significant difference in tunnel directionality between the scenarios. However, the tunnel size was notably larger in the absence of task shift, suggesting that continuous tunneling without task shift may enhance food searching efficiency. In the discussion section, we briefly address the limitations of the model arising from differences between the simulations and actual termite systems. Additionally, we touch on the idea to explain the fact that only a fixed proportion of workers in a termite colony participate in tunneling activities.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105380"},"PeriodicalIF":2.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling the origin, evolution, and functioning of the genetic code.","authors":"Branko Dragovich, Elena Fimmel, Andrei Khrennikov, Nataša Ž Mišić","doi":"10.1016/j.biosystems.2024.105373","DOIUrl":"10.1016/j.biosystems.2024.105373","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105373"},"PeriodicalIF":2.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Cosmos, mind, matter: Is mind in spacetime?” [Biosyst. (2024) 105262]","authors":"Stuart Kauffman ,&nbsp;Sudip Patra","doi":"10.1016/j.biosystems.2024.105333","DOIUrl":"10.1016/j.biosystems.2024.105333","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105333"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142747041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cosmos, mind, matter: Is mind in spacetime?","authors":"Stuart Kauffman ,&nbsp;Sudip Patra","doi":"10.1016/j.biosystems.2024.105332","DOIUrl":"10.1016/j.biosystems.2024.105332","url":null,"abstract":"<div><div>We attempt in this article to formulate a conceptual and testable framework weaving Cosmos, Mind and Matter into a whole. We build on three recent discoveries, each requiring more evidence: i. The particles of the Standard Model, SU(3) × SU(2) × U(1), are formally capable of collective autocatalysis. This leads us to ask what roles such autocatalysis may have played in Cosmogenesis, and in trying to answer, Why our Laws? Why our Constants? A capacity of the particles of SU(3) × SU(2) × U(1) for collective autocatalysis may be open to experimental test, stunning if confirmed. ii. Reasonable evidence now suggests that matter can expand spacetime. The first issue is to establish this claim at or beyond 5 sigma if that can be done. If true, this process may elucidate Dark Matter, Dark Energy and Inflation and require alteration of Einstein's Field Equations. Cosmology would be transformed. iii. Evidence at 6.49 Sigma suggests that mind can alter the outcome of the two-slit experiment. If widely and independently verified, the foundations of quantum mechanics must be altered. Mind plays a role in the universe. That role may include Cosmic Mind.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105332"},"PeriodicalIF":2.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding cancer from a biophysical, developmental and systems biology perspective using the landscapes-attractor model","authors":"Thomas W. Grunt","doi":"10.1016/j.biosystems.2024.105376","DOIUrl":"10.1016/j.biosystems.2024.105376","url":null,"abstract":"<div><div>Biophysical, developmental and systems-biology considerations enable deeper understanding why cancer is life threatening despite intensive research. Here we use two metaphors. Both conceive the cell genome and the encoded molecular system as an interacting gene regulatory network (GRN). According to Waddington's epigenetic (quasi-potential)-landscape, an instrumental tool in ontogenetics, individual interaction patterns ( = expression profiles) within this GRN represent possible cell states with different stabilities. Network interactions with low stability are represented on peaks. Unstable interactions strive towards regions with higher stability located at lower altitude in valleys termed attractors that correspond to stable cell phenotypes. Cancer cells are seen as GRNs adopting aberrant semi-stable attractor states (cancer attractor). In the second metaphor, Wright's phylogenetic fitness (adaptive) landscape, each genome ( = GRN) is assigned a specific position in the landscape according to its structure and reproductive fitness in the specific environment. High elevation signifies high fitness and low altitude low fitness. Selection ensures that mutant GRNs evolve and move from valleys to peaks. The genetic flexibility is highlighted in the fitness landscape, while non-genetic flexibility is captured in the quasi-potential landscape. These models resolve several inconsistencies that have puzzled cancer researchers, such as the fact that phenotypes generated by non-genetic mechanisms coexist in a single tumor with phenotypes caused by mutations and they mitigate conflicts between cancer theories that claim cancer is caused by mutation (somatic mutation theory) or by disruption of tissue architecture (tissue organization field theory). Nevertheless, spontaneous mutations play key roles in cancer. Remarkable, fundamental natural laws such as the second law of thermodynamics and quantum mechanics state that mutations are inevitable events. The good side of this is that without mutational variability in DNA, evolutionary development would not have occurred, but its bad side is that the occurrence of cancer is essentially inevitable. In summary, both landscapes together fully describe the behavior of cancer under normal and stressful conditions such as chemotherapy. Thus, the landscapes-attractor model fully describes cancer cell behavior and offers new perspectives for future treatment.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105376"},"PeriodicalIF":2.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}