Macromolecules

@article{fox1959biological,
    author = "Fox, Sidney W.",
    title = "Biological replication of macromolecules",
    year = "1959",
    journal = "Journal of Chemical Education",
    url = "https://doi.org/10.1021/ed036pa706",
    doi = "10.1021/ed036pa706",
    number = "11",
    openalex = "W1964669553",
    pages = "A706",
    volume = "36"
}

@article{fox1959review1,
    author = "Fox, S. W",
    title = "Review of the book The Biological Replication of Macromolecules",
    year = "1959",
    journal = "Journal of Chemical Education, v. 36, p. 706A",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1959, Review of the book The Biological Replication of Macromolecules: Journal of Chemical Education, v. 36, p. 706A.}"
}

@article{sadron1959the,
    author = "Sadron, Charles",
    title = "The biological replication of macromolecules",
    year = "1959",
    journal = "Archives of Biochemistry and Biophysics",
    url = "https://doi.org/10.1016/0003-9861(59)90073-6",
    doi = "10.1016/0003-9861(59)90073-6",
    number = "2",
    openalex = "W269866933",
    pages = "573",
    volume = "83"
}

Possible relaxation mechanisms are considered that may account for the observed interactions of low-amplitude ultrasound with macromolecules in dilute aqueous solution and also in high concentration. Such studies are relevant to the kinetics of association and dissociation of hydrated macromolecules in the former case and of ordered liquid structures, such as membrances, in the latter case. [Work supported by grants from the National Institute of General Medical Sciences, National Institutes of Health, Public Health Service, U. S. Department of Health, Education, and Welfare, and the National Science Foundation.]

@article{edmonds1966ultrasonic,
    author = "Edmonds, Peter D.",
    title = "Ultrasonic Relaxational Behavior of Biological Macromolecules",
    year = "1966",
    journal = "The Journal of the Acoustical Society of America",
    abstract = "Possible relaxation mechanisms are considered that may account for the observed interactions of low-amplitude ultrasound with macromolecules in dilute aqueous solution and also in high concentration. Such studies are relevant to the kinetics of association and dissociation of hydrated macromolecules in the former case and of ordered liquid structures, such as membrances, in the latter case. [Work supported by grants from the National Institute of General Medical Sciences, National Institutes of Health, Public Health Service, U. S. Department of Health, Education, and Welfare, and the National Science Foundation.]",
    url = "https://doi.org/10.1121/1.1942814",
    doi = "10.1121/1.1942814",
    number = "6\_Supplement",
    openalex = "W2053129287",
    pages = "1243-1243",
    volume = "39"
}

@article{doi101007bf01659185,
    author = "Fox, Sidney W.",
    title = "Origins of biological information and the genetic code",
    year = "1974",
    journal = "Molecular and Cellular Biochemistry",
    url = "https://doi.org/10.1007/bf01659185",
    doi = "10.1007/bf01659185",
    openalex = "W2036713118",
    references = "doi101351pac197334030641"
}

@inproceedings{minakata1974dielectric,
    author = "Minakata, Akira and Takashima, Shiro",
    title = "Dielectric behavior of biological macromolecules",
    year = "1974",
    booktitle = "Digest of Literature on Dielectrics Volume 38 1974",
    url = "https://doi.org/10.1109/dld.1974.7739039",
    doi = "10.1109/dld.1974.7739039",
    openalex = "W2556659871",
    pages = "661-674",
    references = "doi101002bip1970360090606, doi101002bip1974360130702, doi101007978940102185217, doi101007bf01381691, doi1010160006291x75903332, doi1010160301462274800475, doi1010160301462274800487, doi101016s0006349575857973, doi10108000222739197211688843, doi101109tbme1974324293"
}

@article{fox1980the,
    author = "Fox, Sidney W.",
    title = "The origins of behavior in macromolecules and protocells",
    year = "1980",
    journal = "Comparative Biochemistry and Physiology Part B: Comparative Biochemistry",
    url = "https://doi.org/10.1016/0305-0491(80)90330-2",
    doi = "10.1016/0305-0491(80)90330-2",
    number = "3",
    pages = "423-436",
    volume = "67"
}

@misc{fox1980the2,
    author = "Fox, S. W",
    title = "The origins of behavior in macromolecules and protocells",
    year = "1980",
    howpublished = "Comparative Biochemistry and Physiology, v. 67B, p. 423-436",
    note = "talkorigins\_source = {true}; raw\_reference = {Fox, S. W., 1980, The origins of behavior in macromolecules and protocells: Comparative Biochemistry and Physiology, v. 67B, p. 423-436.}"
}

The evolution of parasite virulence and the origin of cooperative genomes in primitive cells are both problems that balance cooperative and competitive interactions among symbionts. I analyse the trade-off among three correlated traits: competitiveness against other genotypes for resources within hosts (protocells), damage to the host (virulence), and rate of horizontal transmission from one host to another. All three life-history components are strongly influenced by kin selection. For example, when genetic relatedness within hosts is high, each genotype is competing for resources with closely related genotypes. This competition among relatives favours increased horizontal transmission to colonize new hosts and compete against non-relatives. My analysis shows that many aspects of parasite and protocell evolution must be studied with the theoretical tools of social evolution. I discuss extensions that are required for a general theory of symbiosis.

@article{doi101098rspb19940156,
    author = "Frank, Steven A.",
    title = "Kin selection and virulence in the evolution of protocells and parasites",
    year = "1994",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "The evolution of parasite virulence and the origin of cooperative genomes in primitive cells are both problems that balance cooperative and competitive interactions among symbionts. I analyse the trade-off among three correlated traits: competitiveness against other genotypes for resources within hosts (protocells), damage to the host (virulence), and rate of horizontal transmission from one host to another. All three life-history components are strongly influenced by kin selection. For example, when genetic relatedness within hosts is high, each genotype is competing for resources with closely related genotypes. This competition among relatives favours increased horizontal transmission to colonize new hosts and compete against non-relatives. My analysis shows that many aspects of parasite and protocell evolution must be studied with the theoretical tools of social evolution. I discuss extensions that are required for a general theory of symbiosis.",
    url = "https://doi.org/10.1098/rspb.1994.0156",
    doi = "10.1098/rspb.1994.0156",
    openalex = "W1990689735"
}

@article{doi101007bf00700418,
    author = "Fox, Sidney W. and Bahn, Peter and Dose, Klaus and Harada, Kaoru and Hsu, Laura and Ishima, Yoshio and Jungck, John R. and Kendrick, Jean and Krampitz, Gottfried and Lacey, James C. and Matsuno, Koichiro and Melius, Paul and Middlebrook, Mavis and Nakashima, Tadayoshi and Pappelis, A. J. and Pol, Alexander and Rohlfing, Duane L. and Vegotsky, Allen and Waehneldt, Thomas V. and Wax, Harry and Yu, Bi",
    title = "Experimental retracement of the origins of a protocell",
    year = "1995",
    journal = "Journal of Biological Physics",
    url = "https://doi.org/10.1007/bf00700418",
    doi = "10.1007/bf00700418",
    openalex = "W3003518638",
    references = "doi101007978364277211512, doi1010160303264781900046"
}

Self-assembled vesicles are essential components of primitive cells. We review the importance of vesicles during the origins of life, fundamental thermodynamics and kinetics of self-assembly, and experimental models of simple vesicles, focusing on prebiotically plausible fatty acids and their derivatives. We review recent work on interactions of simple vesicles with RNA and other studies of the transition from vesicles to protocells. Finally we discuss current challenges in understanding the biophysics of protocells, as well as conceptual questions in information transmission and self-replication.

@article{doi101101cshperspecta002170,
    author = "Chen, Irene A. and Walde, Peter",
    title = "From Self-Assembled Vesicles to Protocells",
    year = "2010",
    journal = "Cold Spring Harbor Perspectives in Biology",
    abstract = "Self-assembled vesicles are essential components of primitive cells. We review the importance of vesicles during the origins of life, fundamental thermodynamics and kinetics of self-assembly, and experimental models of simple vesicles, focusing on prebiotically plausible fatty acids and their derivatives. We review recent work on interactions of simple vesicles with RNA and other studies of the transition from vesicles to protocells. Finally we discuss current challenges in understanding the biophysics of protocells, as well as conceptual questions in information transmission and self-replication.",
    url = "https://doi.org/10.1101/cshperspect.a002170",
    doi = "10.1101/cshperspect.a002170",
    openalex = "W2134171083",
    references = "doi101002adma200300010, doi101007bf00623322, doi101021cr60130a002, doi101039f29767201525, doi101093oso97801985029440010001, doi101111j155856461995tb04464x, openalexw1506850331, openalexw2065318865"
}

Compartmentalization of primitive biochemical reactions within membrane-bound water micro-droplets is considered an essential step in the origin of life. In the absence of complex biochemical machinery, the hypothetical precursors to the first biological cells (protocells) would be dependent on the self-organization of their components and physicochemical conditions of the environment to attain a basic level of autonomy and evolutionary viability. Many researchers consider the self-organization of lipid and fatty acid molecules into bilayer vesicles as a simple form of membrane-based compartmentalization that can be developed for the experimental design and construction of plausible protocell models. In this tutorial review, we highlight some of the recent advances and issues concerning the construction of simple cell-like systems in the laboratory. Overcoming many of the current scientific challenges should lead to new types of chemical bio-reactors and artificial cell-like entities, and bring new insights concerning the possible pathways responsible for the origin of life.

@article{doi101039c1cs15211d,
    author = "Dzieciol, Alicja J. and Mann, Stephen",
    title = "Designs for life: protocell models in the laboratory",
    year = "2011",
    journal = "Chemical Society Reviews",
    abstract = "Compartmentalization of primitive biochemical reactions within membrane-bound water micro-droplets is considered an essential step in the origin of life. In the absence of complex biochemical machinery, the hypothetical precursors to the first biological cells (protocells) would be dependent on the self-organization of their components and physicochemical conditions of the environment to attain a basic level of autonomy and evolutionary viability. Many researchers consider the self-organization of lipid and fatty acid molecules into bilayer vesicles as a simple form of membrane-based compartmentalization that can be developed for the experimental design and construction of plausible protocell models. In this tutorial review, we highlight some of the recent advances and issues concerning the construction of simple cell-like systems in the laboratory. Overcoming many of the current scientific challenges should lead to new types of chemical bio-reactors and artificial cell-like entities, and bring new insights concerning the possible pathways responsible for the origin of life.",
    url = "https://doi.org/10.1039/c1cs15211d",
    doi = "10.1039/c1cs15211d",
    openalex = "W2132859930",
    references = "doi101002jcp1040730108, doi1010160005273677900992, doi101038319618a0, doi10103835053176, doi101038nature07018, doi101073pnas0408236101, doi101101cshperspecta002170, doi101126science1089904, doi101126science2705235397, doi1012019780203833445, doi105860choice421295"
}

@article{doi101007s1108401292914,
    author = "Melkikh, Alexey V. and Chesnokova, Oksana I.",
    title = "Origin of the Directed Movement of Protocells in the Early Stages of the Evolution of Life",
    year = "2012",
    journal = "Origins of Life and Evolution of Biospheres",
    url = "https://doi.org/10.1007/s11084-012-9291-4",
    doi = "10.1007/s11084-012-9291-4",
    openalex = "W2024995725",
    references = "doi101007s1108400891390"
}

We propose a hypothesis of a mathematical algorithm for coherent quantum frequencies that create stability of biological order. The concept is based on an extensive literature survey, comprising 175 articles from 1950 to 2015, dealing with effects of electromagnetic radiation on in vitro and in vivo life systems, indicating that typical discrete coherent frequencies of electromagnetic waves are able to stabilize cells, whereas others cause a clear destabilization. We find support for the hypothesis of H. FrA¶hlich, that a driven set of oscillators condenses in a broad energy range, may activate a vibrational mode in life organisms at room temperature. Taking into account the life sustaining frequencies, as extracted from literature, an algorithm of coherent frequencies of standing waves for the stability of biological order was inferred. Interestingly, we found that the origin of the particular biological algorithm can be mathematically approached by a selected ‘tempered Pythagorean scale’. The algorithm expresses one-dimensional wave equations known for vibrating strings and provides an answer to the question of SchrA¶dinger: how to solve the 'problem of small numbers': the notion that life systems contain insufficient internal information to explain their integral life complexity. This particular algorithm has been verified with regard to various frequencies of electromagnetic waves, as applied in the above-mentioned independent biological studies, in addition to the registration of a range of 23 different measured quantum resonances emitted by a selected inorganic silicate mineral, that is able to catalyze oligomerization of RNA. The origin of the biological algorithm has been condensed in a mathematical expression, in which all frequencies approach only ratios of 1:2 and 2:3. Electromagnetic waves with discrete frequencies, described by this algorithm are able to stabilize and even improve the life quality of cells, whereas frequencies, exactly in between distinct frequencies of the algorithm, are able to destabilize or even disrupt cells. A selected silicate, known as a candidate catalyst for the promotion of RNA synthesis and as quantum replicator, fully complies with this algorithm. Silicate quantum replicators, potentially, may have been instrumental in the initiation of first life at the edge of pre-biotic biological evolution. Our model shows that, at the quantum scale, an underlying order may have been present, that was a prerequisite for the initiation of first life. Far infrared dynamics, reminiscent of coherent non-relativistic super fluids in 3+1-dimensions, might have played a role. Finally, we address the question how the identified electromagnetic fields can influence neural systems in general and human (self) consciousness in particular.

@article{doi1014704nq2016141911,
    author = "Geesink, Hans J. H. and Meijer, Dirk K. F.",
    title = "Quantum Wave Information of Life Revealed: An Algorithm for Electromagnetic Frequencies that Create Stability of Biological Order, With Implications for Brain Function and Consciousness",
    year = "2016",
    journal = "NeuroQuantology",
    abstract = "We propose a hypothesis of a mathematical algorithm for coherent quantum frequencies that create stability of biological order. The concept is based on an extensive literature survey, comprising 175 articles from 1950 to 2015, dealing with effects of electromagnetic radiation on in vitro and in vivo life systems, indicating that typical discrete coherent frequencies of electromagnetic waves are able to stabilize cells, whereas others cause a clear destabilization. We find support for the hypothesis of H. FrA¶hlich, that a driven set of oscillators condenses in a broad energy range, may activate a vibrational mode in life organisms at room temperature. Taking into account the life sustaining frequencies, as extracted from literature, an algorithm of coherent frequencies of standing waves for the stability of biological order was inferred. Interestingly, we found that the origin of the particular biological algorithm can be mathematically approached by a selected ‘tempered Pythagorean scale’. The algorithm expresses one-dimensional wave equations known for vibrating strings and provides an answer to the question of SchrA¶dinger: how to solve the 'problem of small numbers': the notion that life systems contain insufficient internal information to explain their integral life complexity. This particular algorithm has been verified with regard to various frequencies of electromagnetic waves, as applied in the above-mentioned independent biological studies, in addition to the registration of a range of 23 different measured quantum resonances emitted by a selected inorganic silicate mineral, that is able to catalyze oligomerization of RNA. The origin of the biological algorithm has been condensed in a mathematical expression, in which all frequencies approach only ratios of 1:2 and 2:3. Electromagnetic waves with discrete frequencies, described by this algorithm are able to stabilize and even improve the life quality of cells, whereas frequencies, exactly in between distinct frequencies of the algorithm, are able to destabilize or even disrupt cells. A selected silicate, known as a candidate catalyst for the promotion of RNA synthesis and as quantum replicator, fully complies with this algorithm. Silicate quantum replicators, potentially, may have been instrumental in the initiation of first life at the edge of pre-biotic biological evolution. Our model shows that, at the quantum scale, an underlying order may have been present, that was a prerequisite for the initiation of first life. Far infrared dynamics, reminiscent of coherent non-relativistic super fluids in 3+1-dimensions, might have played a role. Finally, we address the question how the identified electromagnetic fields can influence neural systems in general and human (self) consciousness in particular.",
    url = "https://doi.org/10.14704/nq.2016.14.1.911",
    doi = "10.14704/nq.2016.14.1.911",
    openalex = "W2308635093",
    references = "doi101016jbiosystems201310005"
}

The general notion of an "RNA world" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated nucleotides that condensed to form RNA polymers, setting the stage for the chemical replication of polynucleotides through RNA-templated RNA polymerization. If a sufficient diversity of RNAs could be copied with reasonable rate and fidelity, then Darwinian evolution would begin with RNAs that facilitated their own reproduction enjoying a selective advantage. The concept of a "protocell" refers to a compartment where replication of the primitive genetic material took place and where primitive catalysts gave rise to products that accumulated locally for the benefit of the replicating cellular entity. Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.

@article{doi101101cshperspecta034801,
    author = "Joyce, Gerald F. and Szostak, Jack W.",
    title = "Protocells and RNA Self-Replication",
    year = "2018",
    journal = "Cold Spring Harbor Perspectives in Biology",
    abstract = {The general notion of an "RNA world" is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA, and RNA molecules were the chief agents of catalytic function. Assuming that all of the components of RNA were available in some prebiotic locale, these components could have assembled into activated nucleotides that condensed to form RNA polymers, setting the stage for the chemical replication of polynucleotides through RNA-templated RNA polymerization. If a sufficient diversity of RNAs could be copied with reasonable rate and fidelity, then Darwinian evolution would begin with RNAs that facilitated their own reproduction enjoying a selective advantage. The concept of a "protocell" refers to a compartment where replication of the primitive genetic material took place and where primitive catalysts gave rise to products that accumulated locally for the benefit of the replicating cellular entity. Replication of both the protocell and its encapsulated genetic material would have enabled natural selection to operate based on the differential fitness of competing cellular entities, ultimately giving rise to modern cellular life.},
    url = "https://doi.org/10.1101/cshperspect.a034801",
    doi = "10.1101/cshperspect.a034801",
    openalex = "W2892140782",
    references = "doi101007bf00623322, doi101021acschemrev6b00825, doi10103835053176, doi101038378767a0, doi101038418214a, doi101038nature02307, doi101038nature08013, doi101038nnano2011187, doi10108010409230490460765, doi101126science1059493"
}

Progress in development of biophysical analytic approaches has recently crossed paths with macromolecule condensates in cells. These cell condensates, typically termed liquid-like droplets, are formed by liquid-liquid phase separation (LLPS). More and more cell biologists now recognize that many of the membrane-less organelles observed in cells are formed by LLPS caused by interactions between proteins and nucleic acids. However, the detailed biophysical processes within the cell that lead to these assemblies remain largely unexplored. In this review, we evaluate recent discoveries related to biological phase separation including stress granule formation, chromatin regulation, and processes in the origin and evolution of life. We also discuss the potential issues and technical advancements required to properly study biological phase separation.

@article{doi101007s1255102000680x,
    author = "Yoshizawa, Takuya and Nozawa, Ryu‐Suke and Jia, Tony Z. and Saio, Tomohide and Mori, Eiichiro",
    title = "Biological phase separation: cell biology meets biophysics",
    year = "2020",
    journal = "Biophysical Reviews",
    abstract = "Progress in development of biophysical analytic approaches has recently crossed paths with macromolecule condensates in cells. These cell condensates, typically termed liquid-like droplets, are formed by liquid-liquid phase separation (LLPS). More and more cell biologists now recognize that many of the membrane-less organelles observed in cells are formed by LLPS caused by interactions between proteins and nucleic acids. However, the detailed biophysical processes within the cell that lead to these assemblies remain largely unexplored. In this review, we evaluate recent discoveries related to biological phase separation including stress granule formation, chromatin regulation, and processes in the origin and evolution of life. We also discuss the potential issues and technical advancements required to properly study biological phase separation.",
    url = "https://doi.org/10.1007/s12551-020-00680-x",
    doi = "10.1007/s12551-020-00680-x",
    openalex = "W3010929769",
    references = "doi101016jcell201204017, doi101016jcell201507047, doi101016jcell201812035, doi101016jtcb201802004, doi101017cbo9781316348772, doi10103835065132, doi101038nature10879, doi101038nrm20177, doi101101cshperspecta002170, doi101126science1181369, doi101126scienceaaf4382, doi101126scienceaar3958, doi101126scienceaax2747"
}

@misc{crossref2022biological,
    title = "Biological Macromolecules",
    year = "2022",
    url = "https://doi.org/10.1016/c2020-0-02562-4",
    doi = "10.1016/c2020-0-02562-4",
    openalex = "W4200582736"
}