Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105387
William B. Miller Jr. , František Baluška , Arthur S. Reber , Predrag Slijepčević
The presumption that experiential consciousness requires a nervous system and brain has been central to the debate on the possibility of developing a conscious form of artificial intelligence (AI). The likelihood of future AI consciousness or devising tools to assess its presence has focused on how AI might mimic brain-centered activities. Currently, dual general assumptions prevail: AI consciousness is primarily an issue of functional information density and integration, and no substantive technical barriers exist to prevent its achievement. When the cognitive process that underpins consciousness is stipulated as a cellular attribute, these premises are directly contradicted. The innate characteristics of biological information and how that information is managed by individual cells have no parallels within machine-based AI systems. Any assertion of computer-based AI consciousness represents a fundamental misapprehension of these crucial differences.
{"title":"Biological mechanisms contradict AI consciousness: The spaces between the notes","authors":"William B. Miller Jr. , František Baluška , Arthur S. Reber , Predrag Slijepčević","doi":"10.1016/j.biosystems.2024.105387","DOIUrl":"10.1016/j.biosystems.2024.105387","url":null,"abstract":"<div><div>The presumption that experiential consciousness requires a nervous system and brain has been central to the debate on the possibility of developing a conscious form of artificial intelligence (AI). The likelihood of future AI consciousness or devising tools to assess its presence has focused on how AI might mimic brain-centered activities. Currently, dual general assumptions prevail: AI consciousness is primarily an issue of functional information density and integration, and no substantive technical barriers exist to prevent its achievement. When the cognitive process that underpins consciousness is stipulated as a cellular attribute, these premises are directly contradicted. The innate characteristics of biological information and how that information is managed by individual cells have no parallels within machine-based AI systems. Any assertion of computer-based AI consciousness represents a fundamental misapprehension of these crucial differences.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105387"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907907","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105373
Branko Dragovich, Elena Fimmel, Andrei Khrennikov, Nataša Ž. Mišić
{"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":"247 ","pages":"Article 105373"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105379
Jorge A. Montemayor-Aldrete , José Manuel Nieto-Villar , Carlos J. Villagómez , Rafael F. Márquez-Caballé
A prebiotic model, based in the framework of thermodynamic efficiency loss from small dissipative eukaryote organisms 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 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 of the primordial soup theory where 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.
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105384
Marko Vitas , Andrej Dobovišek
Explaining the emergence of life is perhaps the central and most challenging question in modern science. We are proposing a new hypothesis concerning the origins of life. The new hypothesis is based on the assumption that during the emergence of life, evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity. Additionally, the key abiotic and early biotic molecules required in the formation of early life, like cofactors, coenzymes, nucleic bases, prosthetic groups, polycyclic aromatic hydrocarbons (PAHs), some pigments, etc. are poorly soluble in aqueous media. To avoid the latter concentration problem, the new hypothesis assumes that life could have emerged in the nonpolar environments or low water systems, or at the interphase of the nonpolar and polar water phase, from where it was subsequently transferred to the aqueous environment. To support our hypothesis, we assume that hydrocarbons and oil on the Earth have abiotic origins.
{"title":"A possible origin of life in nonpolar environments","authors":"Marko Vitas , Andrej Dobovišek","doi":"10.1016/j.biosystems.2024.105384","DOIUrl":"10.1016/j.biosystems.2024.105384","url":null,"abstract":"<div><div>Explaining the emergence of life is perhaps the central and most challenging question in modern science. We are proposing a new hypothesis concerning the origins of life. The new hypothesis is based on the assumption that during the emergence of life, evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity. Additionally, the key abiotic and early biotic molecules required in the formation of early life, like cofactors, coenzymes, nucleic bases, prosthetic groups, polycyclic aromatic hydrocarbons (PAHs), some pigments, etc. are poorly soluble in aqueous media. To avoid the latter concentration problem, the new hypothesis assumes that life could have emerged in the nonpolar environments or low water systems, or at the interphase of the nonpolar and polar water phase, from where it was subsequently transferred to the aqueous environment. To support our hypothesis, we assume that hydrocarbons and oil on the Earth have abiotic origins.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105384"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900076","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105380
Sang-Hee Lee, Cheol-Min Park
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.
{"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":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105380"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105382
Massimo Di Giulio
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.
{"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":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105382"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105383
A.V. Melkikh
{"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":"10.1016/j.biosystems.2024.105383","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105383"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105378
David Lynn Abel
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.
{"title":"“Assembly Theory” in life-origin models: A critical review","authors":"David Lynn Abel","doi":"10.1016/j.biosystems.2024.105378","DOIUrl":"10.1016/j.biosystems.2024.105378","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105378"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.biosystems.2024.105381
Thomas Lissek
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.
{"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":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105381"},"PeriodicalIF":2.0,"publicationDate":"2025-01-01","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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